From 5ba8e431e37f0b86d0d9d243c8be0953447b047e Mon Sep 17 00:00:00 2001 From: OpenStudyBuilder Date: Tue, 28 Apr 2026 13:15:10 +0000 Subject: [PATCH] v2.9.0 --- CHANGE-LOG.md | 43 + clinical-mdr-api/.azuredevops/dependabot.yml | 23 + .../.claude/rules/code-standards.md | 1 + clinical-mdr-api/.claude/rules/testing.md | 7 + clinical-mdr-api/Pipfile | 6 +- clinical-mdr-api/Pipfile.lock | 1340 +- clinical-mdr-api/apiVersion | 2 +- .../activity_instance_repository.py | 61 +- .../concepts/concept_generic_repository.py | 15 + .../ct_codelist_aggregated_repository.py | 6 +- .../ct_codelist_generic_repository.py | 109 +- .../feature_flag_repository.py | 45 +- .../models/feature_flag.py | 2 + .../models/study_selections.py | 42 + .../models/study_template.py | 32 + ...onsor_model_dataset_variable_repository.py | 12 +- .../studies/study_template_repository.py | 126 + .../study_definition_repository.py | 314 +- .../study_definition_repository_impl.py | 56 +- .../study_selections/base.py | 39 +- .../study_activity_base_repository.py | 25 +- .../study_activity_group_repository.py | 67 +- .../study_activity_instance_repository.py | 190 +- .../study_activity_instruction_repository.py | 2 +- .../study_activity_repository.py | 114 +- .../study_activity_schedule_repository.py | 122 +- .../study_activity_subgroup_repository.py | 75 +- .../study_definition_document_repository.py | 23 + .../study_visit_repository.py | 20 +- .../ct_codelist_attributes.py | 4 +- .../study_template.py | 124 + .../domains/study_selections/study_visit.py | 2 +- .../activity_item_class.py | 3 +- .../models/complexity_score.py | 17 + .../models/concepts/activities/activity.py | 7 +- .../concepts/activities/activity_instance.py | 12 + .../controlled_terminologies/ct_codelist.py | 45 +- .../clinical_mdr_api/models/feature_flag.py | 10 +- .../models/study_selections/study.py | 144 +- .../study_selections/study_selection.py | 16 +- .../repositories/ct_catalogues.py | 145 +- .../clinical_mdr_api/routers/admin.py | 8 + .../concepts/activities/activity_instances.py | 134 +- .../controlled_terminologies/ct_codelists.py | 36 + .../routers/ddf/study_definitions.py | 9 + .../routers/studies/studies.py | 189 +- .../studies/study_disease_milestones.py | 12 +- .../services/_meta_repository.py | 9 + .../activity_item_class.py | 4 +- .../activities/activity_instance_service.py | 102 +- .../concepts/activities/activity_service.py | 21 +- .../controlled_terminologies/ct_codelist.py | 101 +- .../services/feature_flags.py | 4 +- .../services/studies/complexity_score.py | 125 +- .../services/studies/study.py | 336 +- .../study_activity_instance_selection.py | 37 + .../studies/study_activity_selection.py | 1138 +- .../studies/study_activity_selection_base.py | 276 +- .../studies/study_disease_milestone.py | 12 +- .../services/studies/study_selection_base.py | 14 + .../study_standard_version_selection.py | 19 + .../services/studies/study_visit.py | 3 +- .../tests/auth/integration/routes.py | 26 +- .../biomedical_concepts/test_activities.py | 108 +- .../test_activity_group_status_validation.py | 88 +- .../test_activity_instances.py | 29 +- .../test_paired_codelists.py | 114 +- .../integration/api/old/test_ct_stats.py | 9 +- .../api/study/test_study_soa_split.py | 58 +- .../test_adam_listings_mdvisit.py | 4 +- .../study_selections/test_study_activities.py | 89 +- .../test_study_activity_groups.py | 1 + .../test_study_activity_instances.py | 50 +- .../test_study_activity_subgroups.py | 1 + .../test_study_design_cells.py | 69 + .../api/study_selections/test_study_epochs.py | 98 + .../study_selections/test_study_flowchart.py | 2 +- .../test_study_soa_footnotes.py | 36 +- .../study_selections/test_study_versions.py | 21 +- .../api/study_selections/test_study_visits.py | 2 +- .../integration/api/test_feature_flags.py | 135 +- .../tests/integration/api/test_studies.py | 656 +- .../services/test_study_disease_milestone.py | 21 +- .../integration/services/test_study_visits.py | 29 +- .../tests/integration/utils/utils.py | 12 +- .../test_activity_instance.py | 3 + .../test_study_definition_repository_base.py | 8 +- .../tests/unit/services/soa_test_data.py | 4 +- .../unit/services/test_study_objectives.py | 11 +- .../tests/unit/utils/test_utils.py | 6 +- .../clinical_mdr_api/tests/utils/checks.py | 13 +- .../utils/db_integrity_checks.py | 2 +- ...inal_TechnicalSpecification_2025_1119.json | 8055 + .../m11-templates/m11-template.html | 5002 +- clinical-mdr-api/openapi.json | 2112 +- clinical-mdr-api/pyproject.toml | 8 +- clinical-mdr-api/sbom.md | 30 +- db-schema-migration/Pipfile | 12 +- .../remove_veeva_codelists.correction.json | 587643 +++++++++++++++ .../data_corrections/correction_020.py | 270 + ...verview.md => corrections_overview_019.md} | 1 - .../corrections_overview_020.md | 44 + .../migrations/migration_023.py | 58 + .../migrations/migration_overview_023.md | 33 + .../tests/test_correction_020.py | 359 + .../tests/test_migration_023.py | 85 + .../correction_verification_020.py | 136 + .../verifications/verification_023.py | 30 + documentation-portal/docs/.vuepress/config.js | 3 +- .../docs/guides/cdisc/test-cases.md | 2 +- .../datamodel/physical/control-terminology.md | 2 +- .../userguide/library/activity_concepts.md | 272 + .../userguide/studies/userguide_activities.md | 2 +- ... => guide_activities_study_activities.png} | Bin .../cdisc_data_models/FBDE/9-0/variable.csv | 2 +- .../FBDE/9-0/variable_class.csv | 2 +- .../old/ct_mt_proposal.graphml | 2 +- .../logical-model-compound-bc-sample.graphml | 2 +- .../physical_data_model/neo4j-model.graphml | 2 +- .../activity_instance_export.cypher | 74 + .../activity_instance_export.json | 187 +- .../activity_library_content_dashboard.json | 762 +- .../activity_metadata_check.json | 56 +- .../data_exchange_data_models.json | 2 +- ...hema_update_activity_intance_grouping.json | 243 + .../laboratory_data_specification.json | 2 +- .../neodash/neodash_reports/pre_define.json | 342 +- .../study_metadata_compare.json | 153 +- .../project_documentation/odm_csv_metadata.md | 2 +- .../datafiles/configuration/feature_flags.csv | 3 +- .../configuration/feature_flags.csv | 3 +- .../importers/run_import_activities.py | 44 +- .../importers/run_import_mockdatajson.py | 22 +- studybuilder/config/config.json | 10 +- studybuilder/package.json | 21 +- studybuilder/public/config.json | 10 +- studybuilder/public/sbom-clinical-mdr-api.md | 30 +- studybuilder/public/sbom-studybuilder.md | 1461 +- studybuilder/sbom.md | 1461 +- .../controlledTerminology/pairedCodelists.js | 3 + studybuilder/src/api/study.js | 3 + studybuilder/src/api/studyTemplate.js | 15 + studybuilder/src/components/layout/TopBar.vue | 1 + .../components/library/ActivitiesTable.vue | 76 +- .../library/ActivityGroupingsSummary.vue | 9 +- .../library/ActivityInstanceForm.vue | 87 +- .../library/ActivityInstanceOverview.vue | 122 +- .../library/ActivityInstanceSummary.vue | 170 + .../components/library/ActivitySummary.vue | 2 +- .../library/BaseActivityOverview.vue | 19 +- .../library/CodelistCreationForm.vue | 194 +- .../src/components/library/CodelistTable.vue | 4 + .../components/library/FormulationField.vue | 2 +- .../library/MedicinalProductForm.vue | 2 +- .../components/library/TemplateStudyTable.vue | 241 + .../crfs/CrfActivityInstanceManagement.vue | 14 + .../library/crfs/CrfAliasSelection.vue | 2 + .../library/crfs/CrfExtensionsEditForm.vue | 4 + .../crfs/CrfExtensionsManagementTable.vue | 6 + .../library/crfs/CrfExtensionsTable.vue | 1 + .../components/library/crfs/CrfItemForm.vue | 6 + .../crfs/CrfTranslatedTextSelection.vue | 8 + .../library/crfs/OdmBuildingViewer.vue | 13 + .../crfs/crfTreeComponents/CrfTreeForms.vue | 1 - .../crfTreeComponents/CrfTreeItemGroups.vue | 1 - .../crfs/crfTreeComponents/CrfTreeItems.vue | 4 +- .../crfs/crfTreeComponents/CrfTreeMain.vue | 1 - .../components/studies/ProtocolFlowchart.vue | 5 +- .../ScheduleOfActivities.vue | 33 + .../components/studies/StudyActivityForm.vue | 6 +- .../studies/StudyComplexityScoreDetails.vue | 200 + .../components/studies/StudyCreationForm.vue | 97 +- .../studies/StudyDraftedActivityEditForm.vue | 2 +- .../components/studies/StudyStatusTable.vue | 4 +- .../studies/StudyStructureCopyForm.vue | 35 + .../components/studies/StudySubpartsTable.vue | 17 +- .../tools/ExpandableHeaderContent.vue | 27 +- .../components/tools/FilterAutocomplete.vue | 4 +- .../tools/HorizontalStepperForm.vue | 3 + .../src/components/tools/MultipleSelect.vue | 5 +- .../tools/ParameterValueSelector.vue | 2 +- studybuilder/src/locales/en/api.json | 47 +- studybuilder/src/locales/en/app.json | 122 +- studybuilder/src/plugins/vuetify.js | 1 + studybuilder/src/router/index.js | 8 + studybuilder/src/stores/app.js | 128 +- .../administration/ComplexityBurdens.vue | 38 +- .../src/views/administration/FeatureFlags.vue | 79 +- .../src/views/library/ActivitiesPage.vue | 4 +- .../src/views/library/TemplateStudyPage.vue | 12 + studybuilder/yarn.lock | 1316 +- .../administration_feature_flags.feature | 12 +- .../data_completness_tags.feature | 2 +- .../about_library/about-library.feature | 2 +- .../library/code_lists/sponsor.feature | 10 +- .../activities/activity-groups.feature | 1 + .../activities/requested-activities.feature | 31 + ...ty-instances-wizard-stepper-events.feature | 104 + ...nces-wizard-stepper-extended-scope.feature | 3 +- ...s-wizard-stepper-fields-validation.feature | 3 +- ...es-wizard-stepper-numeric-findings.feature | 3 +- ...es-wizard-stepper-textual-findings.feature | 5 +- .../activity-instances.feature | 24 +- .../overview-page-activity-instance.feature | 21 +- .../crf-item-activity-instance-links.feature | 73 +- ...-tree-item-activity-instance-links.feature | 23 +- .../study-activities-exchange.feature | 3 +- .../study-activities-placeholder.feature | 3 +- ...tudy-activities-shared-placeholder.feature | 3 +- .../study_activities/study-activities.feature | 3 +- .../study-detailed-soa.feature | 11 +- .../suty-soa-protocol-lab-table.feature | 58 + .../study-activity-instances-edition.feature | 5 +- .../study-activity-instances.feature | 3 +- .../study-operational-soa.feature | 3 +- .../study_compounds.feature | 138 +- .../study_compounds_dosings.feature | 125 +- .../study_data_supplier.feature | 6 +- ...st-copy-study-activities-schedules.feature | 60 + ...inistration_data_completness_tags_steps.js | 104 +- .../administration_feature_flags_steps.js | 43 +- .../global_functions_steps.js | 6 + .../global_table_specific_steps.js | 10 +- ...tivities_instances_wizard_stepper_steps.js | 6 + .../library_activities_steps.js | 2 + .../library_activity_overview_page_common.js | 24 +- .../library_code_lists_steps.js | 1 + ..._crf_item_activity_instance_links_steps.js | 300 + ...tree-item_activity_instance_links_steps.js | 97 + .../library_crf_viewer_steps.js | 11 +- .../study_activities_steps.js | 20 + .../study_compound_dosings.js | 78 +- .../step_definitions/study_compounds_steps.js | 126 +- .../e2e/step_definitions/study_list_steps.js | 48 +- .../e2e/step_definitions/study_soa_steps.js | 4 + .../api_requests/library_activities.js | 8 +- .../api_requests/study_activities_requests.js | 21 +- .../api_requests/study_arm_requests.js | 15 +- .../api_requests/study_compounds_request.js | 87 + system-tests/ui-tests/cypress/support/e2e.js | 1 + system-tests/ui-tests/package.json | 2 + 241 files changed, 613213 insertions(+), 8544 deletions(-) create mode 100644 clinical-mdr-api/.azuredevops/dependabot.yml create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_template.py create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/studies/study_template_repository.py create mode 100644 clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_template.py create mode 100644 clinical-mdr-api/m11-templates/ICH_Step4_M11_Final_TechnicalSpecification_2025_1119.json create mode 100644 db-schema-migration/data_corrections/change_logs/remove_veeva_codelists.correction.json create mode 100644 db-schema-migration/data_corrections/correction_020.py rename db-schema-migration/data_corrections/{correction_019_overview.md => corrections_overview_019.md} (99%) create mode 100644 db-schema-migration/data_corrections/corrections_overview_020.md create mode 100644 db-schema-migration/migrations/migration_023.py create mode 100644 db-schema-migration/migrations/migration_overview_023.md create mode 100644 db-schema-migration/tests/test_correction_020.py create mode 100644 db-schema-migration/tests/test_migration_023.py create mode 100644 db-schema-migration/verifications/correction_verification_020.py create mode 100644 db-schema-migration/verifications/verification_023.py create mode 100644 documentation-portal/docs/guides/userguide/library/activity_concepts.md rename documentation-portal/docs/images/user_guides/{guide_activities_study activities.png => guide_activities_study_activities.png} (100%) create mode 100644 neo4j-mdr-db/neodash/neo4j_custom_procedures/background_queries/activity_instance_export.cypher create mode 100644 neo4j-mdr-db/neodash/neodash_reports/draft_reports/schema_update_activity_intance_grouping.json create mode 100644 studybuilder/src/api/studyTemplate.js create mode 100644 studybuilder/src/components/library/ActivityInstanceSummary.vue create mode 100644 studybuilder/src/components/library/TemplateStudyTable.vue create mode 100644 studybuilder/src/components/studies/StudyComplexityScoreDetails.vue create mode 100644 studybuilder/src/views/library/TemplateStudyPage.vue create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-events.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/suty-soa-protocol-lab-table.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/studies/study_list/study-list-copy-study-activities-schedules.feature create mode 100644 system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_item_activity_instance_links_steps.js create mode 100644 system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_tree-item_activity_instance_links_steps.js create mode 100644 system-tests/ui-tests/cypress/support/api_requests/study_compounds_request.js diff --git a/CHANGE-LOG.md b/CHANGE-LOG.md index 0335c5bc..34adf325 100644 --- a/CHANGE-LOG.md +++ b/CHANGE-LOG.md @@ -1,5 +1,48 @@ # OpenStudyBuilder (OSB) Commits changelog +## V 2.9 + +New Features and Enhancements +============ + +### Fixes and Enhancements + +- Many fixes in the Standard data model endpoints (SDTM). Non-exhaustive list : unstable or wrong ordering of elements, missing domains, duplicates in the results,... +Libraries are now managed in a way that truly enables having multiple sponsor libraries +- The ICH M11 preview under Studies, View Specifications is updated to the final M11 19 November 2025 version, with some improved display options. + +### New Feature + +- Added a display page for Sponsor Models. API to retrieve information are now in a first working state +- When adding a new study, you can now choose “Create a study with default settings.” This option copies study visits, epochs, and activities from a template study. This option is available only if a template study has been defined previously in Library, Admin Definitions, Template Study. Please note, that the studies that can be used as templates and are listed in the Template Study list are locked. +- E2E tests for "archived" library implemented. + +### Performance Improvements +- Faster batch creation of study activities when selecting 'Select from Library' path. +- Faster editing of a single study activity. +- Faster batch editing of study activities in SoA, e.g. moving a couple of study activities to different SoA Group and assigning a few schedules to each study activity. + +### End-to-End Automated test enhancements +- Various code improvements to ensure easier maintenance and overall tests stability. +- Administration > Feature Flags: Adjusted tests to the changes in the Feature Flags page. +- Library > Concepts > Activities > Activity Instances: Implemented tests for Events Activity Instance Class. +- Library > Concepts > Activities > Activity Instances: Adjusted tests to the changes in the Overview Page. +- Library > Concepts > Activities > Activity: Implemented tests for checking Study Linkage on the Activity Placeholder Overview Page. +- Library > Data Collection Standards > CRF Builder > CRF Items: Improved and implemented tests for Activity Instance linkage. +- Library > Data Collection Standards > CRF Builder > CRF Tree: Improved and implemented tests for Activity Instance linkage. +- Studies > Define Study > Study Activities > Schedule of Activities > Protocol - Lab Table: Defined and Implemented tests. +- Studies > Define Study > Study Interventions: Refactorization of Study Compounds and Study Compounds Dosings tests to use API calls for data creation. + +Solved Bugs +============ + +### Studies + + **> Define Studies > Activity Instances** + +- Fix StudyActivityInstance creation when ActivityPlaceholder is exchanged for multiple StudyActivities + + ## V 2.8 New Features and Enhancements diff --git a/clinical-mdr-api/.azuredevops/dependabot.yml b/clinical-mdr-api/.azuredevops/dependabot.yml new file mode 100644 index 00000000..b5618ba0 --- /dev/null +++ b/clinical-mdr-api/.azuredevops/dependabot.yml @@ -0,0 +1,23 @@ +version: 2 +updates: + - package-ecosystem: "pip" + directory: "/" + schedule: + interval: "daily" + time: "09:00" + timezone: "Europe/Paris" + open-pull-requests-limit: 10 + labels: + - "dependencies" + - "python" + groups: + dev-dependencies: + dependency-type: "development" + update-types: + - "minor" + - "patch" + prod-dependencies: + dependency-type: "production" + update-types: + - "minor" + - "patch" diff --git a/clinical-mdr-api/.claude/rules/code-standards.md b/clinical-mdr-api/.claude/rules/code-standards.md index ecf1ae0e..55ce1fdd 100644 --- a/clinical-mdr-api/.claude/rules/code-standards.md +++ b/clinical-mdr-api/.claude/rules/code-standards.md @@ -8,6 +8,7 @@ - **Naming**: Follow PEP 8, public API = no leading underscore - **Disabled Pylint Checks**: Missing docstrings, fixme, too-few-public-methods, too-many-ancestors, cyclic-import, etc. (see `pyproject.toml`) - **Descriptive variable names over clever abbreviations** +- **Imports always at the top of the file** - never use inline/local imports inside functions or test methods ## FastAPI Best Practices diff --git a/clinical-mdr-api/.claude/rules/testing.md b/clinical-mdr-api/.claude/rules/testing.md index 86be59e5..0a808afb 100644 --- a/clinical-mdr-api/.claude/rules/testing.md +++ b/clinical-mdr-api/.claude/rules/testing.md @@ -21,4 +21,11 @@ paths: - Shared utilities in `clinical_mdr_api/tests/utils/` - Integration tests run in parallel with `-n 4` flag +## Writing Tests + +- **Use real workflows, not shortcuts** - tests should trigger the actual code paths users hit, not manually arrange the end state +- **Use `TestUtils`** - check `clinical_mdr_api/tests/integration/utils/utils.py` before writing test setup from scratch +- **Verify the test fails without the fix** - before committing a bug fix test, confirm it actually fails on the old code +- **Search for existing test patterns** - look at similar test files in the same directory before writing a new test + diff --git a/clinical-mdr-api/Pipfile b/clinical-mdr-api/Pipfile index d5917cc0..74d70744 100644 --- a/clinical-mdr-api/Pipfile +++ b/clinical-mdr-api/Pipfile @@ -18,7 +18,7 @@ python-docx = "~=1.1.2" colour = "~=0.1.5" authlib = "~=1.6.5" pyjwt = "~=2.12.0" -cryptography = "~=46.0.5" +cryptography = "~=46.0" httpx = "~=0.27.2" starlette-context = "==0.4.0" python-multipart = "~=0.0.12" @@ -44,7 +44,7 @@ pyasn1 = "~=0.6.3" pytest = "~=8.4.1" pytest-bdd = "~=7.3.0" pytest-cov = "~=6.0.0" -pylint = "~=3.3.1" +pylint = "~=4.0.5" rich = "~=14.0.0" flake8 = "~=7.1.1" pep8 = "~=1.7.1" @@ -91,7 +91,7 @@ format = """sh -c " && python -m black clinical_mdr_api consumer_api common extensions \ " """ -audit = "python -m pip_audit --ignore-vuln CVE-2026-4539" +audit = "python -m pip_audit --ignore-vuln CVE-2026-4539 --ignore-vuln GHSA-jj8c-mmj3-mmgv --ignore-vuln CVE-2025-71176 --ignore-vuln CVE-2026-40347" openapi = "python generate_openapi_json.py" schemathesis = """ schemathesis diff --git a/clinical-mdr-api/Pipfile.lock b/clinical-mdr-api/Pipfile.lock index 6ab72d58..79b44291 100644 --- a/clinical-mdr-api/Pipfile.lock +++ b/clinical-mdr-api/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "4695f36491a01fd3b75aa5cf4050ce72043a343738c3156f07853956df03a013" + "sha256": "b2051a7730892c800fd66b79ed2c1360d6d739b34dbb6e446f1e771cafa6e901" }, "pipfile-spec": 6, "requires": { @@ -307,146 +307,146 @@ }, "charset-normalizer": { "hashes": [ - "sha256:06a7e86163334edfc5d20fe104db92fcd666e5a5df0977cb5680a506fe26cc8e", - "sha256:0c173ce3a681f309f31b87125fecec7a5d1347261ea11ebbb856fa6006b23c8c", - "sha256:0e28d62a8fc7a1fa411c43bd65e346f3bce9716dc51b897fbe930c5987b402d5", - "sha256:0e901eb1049fdb80f5bd11ed5ea1e498ec423102f7a9b9e4645d5b8204ff2815", - "sha256:11afb56037cbc4b1555a34dd69151e8e069bee82e613a73bef6e714ce733585f", - "sha256:150b8ce8e830eb7ccb029ec9ca36022f756986aaaa7956aad6d9ec90089338c0", - 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"sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b" + "sha256:6757cd03768053ff99f3039c1a36d6c0aa0b263438fcab17520b30a303a82b5f", + "sha256:81a9e26dd42fd28a23a2d169d86d7ac03b46e2f8b59ed4698fb4785f946d0176" ], - "markers": "python_version >= '3.8'", - "version": "==2.19.2" + "markers": "python_version >= '3.9'", + "version": "==2.20.0" }, "pylint": { "hashes": [ - "sha256:01f9b0462c7730f94786c283f3e52a1fbdf0494bbe0971a78d7277ef46a751e7", - "sha256:d312737d7b25ccf6b01cc4ac629b5dcd14a0fcf3ec392735ac70f137a9d5f83a" + "sha256:00f51c9b14a3b3ae08cff6b2cdd43f28165c78b165b628692e428fb1f8dc2cf2", + "sha256:8cd6a618df75deb013bd7eb98327a95f02a6fb839205a6bbf5456ef96afb317c" ], "index": "pypi", - "markers": "python_full_version >= '3.9.0'", - "version": "==3.3.9" + "markers": "python_full_version >= '3.10.0'", + "version": "==4.0.5" }, "pyparsing": { "hashes": [ @@ -3525,11 +3521,11 @@ }, "python-discovery": { "hashes": [ - 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"sha256:4b314d81163a3e1a169b6a0be2a000a0e204e8873c5de6586f453c55688d422f", - "sha256:fb8c01fe6ab13b9b7cdb46892b99b1d66754e1d7ab8e542e865ec13f526b5351" + "sha256:63a77fb8892bf28ebc3178683445222aa500e48ebad5ec77b0ad80f8726b1f50", + "sha256:9bad61a4268dac112f1c5cd4630a56ede601b6ed420300677a869083d70a4c44" ], "markers": "python_version >= '3.9'", - "version": "==3.1.7" + "version": "==3.1.8" }, "yarl": { "hashes": [ diff --git a/clinical-mdr-api/apiVersion b/clinical-mdr-api/apiVersion index bd5605d8..1116fe8f 100644 --- a/clinical-mdr-api/apiVersion +++ b/clinical-mdr-api/apiVersion @@ -1 +1 @@ -3.0.642 +3.0.657 diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_instance_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_instance_repository.py index 5db99260..b3fd69c4 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_instance_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_instance_repository.py @@ -1,7 +1,7 @@ import datetime from typing import Any -from neomodel import NodeClassNotDefined, db +from neomodel import DoesNotExist, NodeClassNotDefined, db from clinical_mdr_api.domain_repositories.concepts.concept_generic_repository import ( ConceptGenericRepository, @@ -428,13 +428,20 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( # ActivityInstance can only link to a single Activity node then it's safe to take a activity_name # from the random ActivityValue node related to any ActivityGroupings node linked to ActivityInstance activity_name = activity_value_node.name + # Prefer the Final version of each linked entity. If no Final version exists, fall back to the highest version. + # The sort key (is_final, version_tuple) ensures Final always ranks above Draft/Retired, + # and within the same status the highest version number wins. # Activity activity_root = activity_value_node.has_version.single() all_activity_rels = activity_value_node.has_version.all_relationships( activity_root ) latest_activity = max( - all_activity_rels, key=lambda r: version_string_to_tuple(r.version) + all_activity_rels, + key=lambda r: ( + r.status == LibraryItemStatus.FINAL.value, + version_string_to_tuple(r.version), + ), ) # ActivityGroup activity_group_value = activity_grouping.has_selected_group.get() @@ -443,7 +450,11 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( activity_group_root ) latest_group = max( - all_group_rels, key=lambda r: version_string_to_tuple(r.version) + all_group_rels, + key=lambda r: ( + r.status == LibraryItemStatus.FINAL.value, + version_string_to_tuple(r.version), + ), ) # ActivitySubGroup activity_subgroup_value = activity_grouping.has_selected_subgroup.get() @@ -452,7 +463,11 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( activity_subgroup_root ) latest_subgroup = max( - all_subgroup_rels, key=lambda r: version_string_to_tuple(r.version) + all_subgroup_rels, + key=lambda r: ( + r.status == LibraryItemStatus.FINAL.value, + version_string_to_tuple(r.version), + ), ) activity_groupings.append( @@ -968,14 +983,14 @@ def get_all_activity_instances_for_activity_grouping( filter_by_boolean_flags: bool = False, ) -> list[tuple[ActivityInstanceRoot, ActivityInstanceValue]]: query = """ - MATCH (activity_instance_root:ActivityInstanceRoot)-[:LATEST]->(activity_instance_value:ActivityInstanceValue) + MATCH (:ActivityRoot {uid:$activity_uid})-[:LATEST_FINAL]->(:ActivityValue)-[:HAS_GROUPING]->(activity_grouping:ActivityGrouping) + MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(:ActivitySubGroupValue)<-[:HAS_VERSION]-(:ActivitySubGroupRoot {uid:$activity_subgroup_uid}) + MATCH (activity_grouping)-[:HAS_SELECTED_GROUP]->(:ActivityGroupValue)<-[:HAS_VERSION]-(:ActivityGroupRoot {uid:$activity_group_uid}) + MATCH (activity_grouping)<-[:HAS_ACTIVITY]-(activity_instance_groupings_value:ActivityInstanceGroupingValue)<-[:LATEST_FINAL]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot) + MATCH (activity_instance_groupings_root)<-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot)-[:LATEST]->(activity_instance_value:ActivityInstanceValue) MATCH (activity_instance_root)-[:LATEST_FINAL]->(activity_instance_value) OPTIONAL MATCH (activity_instance_root)-[retired:HAS_VERSION {status: "Retired"}]->(activity_instance_value) WHERE retired.end_date IS NULL WITH activity_instance_root, activity_instance_value WHERE retired IS NULL - MATCH (activity_instance_root)-[:HAS_GROUPING_ROOT]->(activity_instance_groupings_root:ActivityInstanceGroupingRoot)-[:LATEST_FINAL]->(activity_instance_groupings_value:ActivityInstanceGroupingValue) - MATCH (activity_instance_groupings_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(:ActivityValue)<-[:HAS_VERSION]-(:ActivityRoot {uid:$activity_uid}) - MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(:ActivitySubGroupValue)<-[:HAS_VERSION]-(:ActivitySubGroupRoot {uid:$activity_subgroup_uid}) - MATCH (activity_grouping)-[:HAS_SELECTED_GROUP]->(:ActivityGroupValue)<-[:HAS_VERSION]-(:ActivityGroupRoot {uid:$activity_group_uid}) WITH DISTINCT activity_instance_root, activity_instance_value ORDER BY activity_instance_value.is_required_for_activity DESC, activity_instance_value.is_defaulted_for_activity DESC RETURN activity_instance_root as root, activity_instance_value as value @@ -1840,8 +1855,13 @@ def _get_root_and_library( self, uid: str ) -> tuple[VersionRoot | None, Library | None]: try: - parent_root = self.parent_root_class.nodes.get_or_none(uid=uid) + parent_root = self.parent_root_class.nodes.get(uid=uid) root: VersionRoot | None = parent_root.has_grouping_root.get() + except DoesNotExist as exc: + raise NotFoundException( + "ActivityInstance", + uid, + ) from exc except NodeClassNotDefined as exc: raise NotFoundException( msg="Resource doesn't exist - it was likely deleted in a concurrent transaction." @@ -2030,13 +2050,20 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( # ActivityInstance can only link to a single Activity node then it's safe to take a activity_name # from the random ActivityValue node related to any ActivityGroupings node linked to ActivityInstance activity_name = activity_value_node.name + # Prefer the Final version of each linked entity. If no Final version exists, fall back to the highest version. + # The sort key (is_final, version_tuple) ensures Final always ranks above Draft/Retired, + # and within the same status the highest version number wins. # Activity activity_root = activity_value_node.has_version.single() all_activity_rels = activity_value_node.has_version.all_relationships( activity_root ) latest_activity = max( - all_activity_rels, key=lambda r: version_string_to_tuple(r.version) + all_activity_rels, + key=lambda r: ( + r.status == LibraryItemStatus.FINAL.value, + version_string_to_tuple(r.version), + ), ) # ActivityGroup activity_group_value = activity_grouping.has_selected_group.get() @@ -2045,7 +2072,11 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( activity_group_root ) latest_group = max( - all_group_rels, key=lambda r: version_string_to_tuple(r.version) + all_group_rels, + key=lambda r: ( + r.status == LibraryItemStatus.FINAL.value, + version_string_to_tuple(r.version), + ), ) # ActivitySubGroup activity_subgroup_value = activity_grouping.has_selected_subgroup.get() @@ -2054,7 +2085,11 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( activity_subgroup_root ) latest_subgroup = max( - all_subgroup_rels, key=lambda r: version_string_to_tuple(r.version) + all_subgroup_rels, + key=lambda r: ( + r.status == LibraryItemStatus.FINAL.value, + version_string_to_tuple(r.version), + ), ) activity_groupings.append( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/concept_generic_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/concept_generic_repository.py index f6f7f10b..458412ea 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/concept_generic_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/concept_generic_repository.py @@ -319,6 +319,21 @@ def format_filter_sort_keys_for_headers_lite(cls, key: str): """ return key.replace(".", "_") + def find_by_uid( + self, + uid: str, + *, + version: str | None = None, + ) -> _AggregateRootType | None: + """Single-query read-only lookup by UID. + + Uses the Cypher-based find_all path (one DB round-trip) instead of + the neomodel ORM find_by_uid_2 path which issues many separate queries. + Not suitable for write operations — use find_by_uid_2(for_update=True) for those. + """ + results, _ = self.find_all(uids=[uid], version=version) + return results[0] if results else None + def find_all( self, library: str | None = None, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_aggregated_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_aggregated_repository.py index 7eef78e6..78587e27 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_aggregated_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_aggregated_repository.py @@ -86,7 +86,9 @@ class CTCodelistAggregatedRepository: author_username: coalesce(name_author.username, rel_data_name.author_id) } AS rel_data_name, head([(codelist_root)-[:PAIRED_CODE_CODELIST]->(paired_codes_cl_root:CTCodelistRoot) | paired_codes_cl_root.uid]) AS paired_codes_codelist_uid, - head([(codelist_root)<-[:PAIRED_CODE_CODELIST]-(paired_names_cl_root:CTCodelistRoot) | paired_names_cl_root.uid]) AS paired_names_codelist_uid + head([(codelist_root)<-[:PAIRED_CODE_CODELIST]-(paired_names_cl_root:CTCodelistRoot) | paired_names_cl_root.uid]) AS paired_names_codelist_uid, + head([(codelist_root)-[:PAIRED_CODE_CODELIST]->(pcr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)-[:LATEST]->(pcv:CTCodelistAttributesValue) | pcv.name]) AS paired_codes_codelist_name, + head([(codelist_root)<-[:PAIRED_CODE_CODELIST]-(pnr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)-[:LATEST]->(pnv:CTCodelistAttributesValue) | pnv.name]) AS paired_names_codelist_name """ generic_alias_clause = f""" DISTINCT codelist_root, codelist_name_root, codelist_name_value, codelist_attributes_root, codelist_attributes_value @@ -151,6 +153,8 @@ def _create_codelist_aggregate_instances_from_cypher_result( paired_codelists = CTPairedCodelists( paired_names_codelist_uid=codelist_dict.get("paired_names_codelist_uid"), paired_codes_codelist_uid=codelist_dict.get("paired_codes_codelist_uid"), + paired_names_codelist_name=codelist_dict.get("paired_names_codelist_name"), + paired_codes_codelist_name=codelist_dict.get("paired_codes_codelist_name"), ) return codelist_name_ar, codelist_attributes_ar, paired_codelists diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_generic_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_generic_repository.py index 0c66e578..688faf5f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_generic_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/ct_codelist_generic_repository.py @@ -467,36 +467,47 @@ def add_term( exceptions.ValidationException.raise_if( ct_term_node is None, msg=f"Term with UID '{term_uid}' doesn't exist." ) - new_term_name_node = ( - ct_term_node.has_name_root.single().has_latest_value.single() - ) - - for ct_codelist_term_node in ct_codelist_node.has_term.all(): - # Check if the has_term relationship has an end date. - # If so, it means the term was removed rom this codelist and we can skip the following checks. - has_term_rel = ct_codelist_node.has_term.relationship(ct_codelist_term_node) - if has_term_rel.end_date is not None: - continue - # Check if the same term is already added to the codelist - ct_term_end_node = ct_codelist_term_node.has_term_root.single() - exceptions.AlreadyExistsException.raise_if( - ct_term_end_node.uid == term_uid, - msg=f"Codelist with UID '{codelist_uid}' already has a Term with UID '{term_uid}'.", - ) - # Check if a term with the same submission value is already added to the codelist - if ct_codelist_term_node.submission_value == submission_value: + # Single Cypher query to check all duplicate conditions at once, + # replacing the N+1 loop that made 3 DB calls per existing term. + duplicate_check_query = """ + MATCH (new_term:CTTermRoot {uid: $term_uid})-[:HAS_NAME_ROOT]->()-[:LATEST]->(new_name_val) + WITH new_term, new_name_val + MATCH (codelist:CTCodelistRoot {uid: $codelist_uid})-[ht:HAS_TERM]->(clt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(existing_term:CTTermRoot) + WHERE ht.end_date IS NULL + MATCH (existing_term)-[:HAS_NAME_ROOT]->()-[:LATEST]->(existing_name_val) + WITH new_term, new_name_val, clt, existing_term, existing_name_val, + CASE WHEN existing_term.uid = $term_uid THEN 'uid' ELSE NULL END AS uid_match, + CASE WHEN clt.submission_value = $submission_value THEN 'submission_value' ELSE NULL END AS sv_match, + CASE WHEN existing_name_val.name = new_name_val.name THEN 'name' ELSE NULL END AS name_match + WHERE uid_match IS NOT NULL OR sv_match IS NOT NULL OR name_match IS NOT NULL + RETURN + coalesce(uid_match, sv_match, name_match) AS match_type, + clt.submission_value AS existing_submission_value, + existing_name_val.name AS existing_name + LIMIT 1 + """ + results, _ = db.cypher_query( + duplicate_check_query, + { + "codelist_uid": codelist_uid, + "term_uid": term_uid, + "submission_value": submission_value, + }, + ) + if results: + match_type, existing_sv, existing_name = results[0] + if match_type == "uid": raise exceptions.AlreadyExistsException( - msg=f"Codelist with UID '{codelist_uid}' already has a Term with submission value '{submission_value}'." + msg=f"Codelist with UID '{codelist_uid}' already has a Term with UID '{term_uid}'.", ) - - # Check if a term with the same name is already added to the codelist - existing_ct_term_name_node = ( - ct_term_end_node.has_name_root.single().has_latest_value.single() - ) - if new_term_name_node.name == existing_ct_term_name_node.name: + if match_type == "submission_value": + raise exceptions.AlreadyExistsException( + msg=f"Codelist with UID '{codelist_uid}' already has a Term with submission value '{existing_sv}'.", + ) + if match_type == "name": raise exceptions.AlreadyExistsException( - msg=f"Codelist with UID '{codelist_uid}' already has a Term with name '{new_term_name_node.name}'." + msg=f"Codelist with UID '{codelist_uid}' already has a Term with name '{existing_name}'.", ) ct_codelist_term_node = ct_term_node.has_term_root.get_or_none( @@ -812,20 +823,15 @@ def get_paired_codelist_uid(self, codelist_uid: str) -> str | None: :param codelist_uid: The UID of the codelist :return: Paired codelist UID or None """ - codelist_root = CTCodelistRoot.nodes.get_or_none(uid=codelist_uid) - if not codelist_root: - return None - - # Check if this codelist has a paired code codelist (outgoing relationship) - paired_code = codelist_root.has_paired_code_codelist.get_or_none() - if paired_code: - return paired_code.uid - - # Check if this codelist has a paired name codelist (incoming relationship) - paired_name = codelist_root.has_paired_name_codelist.get_or_none() - if paired_name: - return paired_name.uid - + query = """ + MATCH (codelist:CTCodelistRoot {uid: $codelist_uid}) + OPTIONAL MATCH (codelist)-[:PAIRED_CODE_CODELIST]->(paired_code:CTCodelistRoot) + OPTIONAL MATCH (codelist)<-[:PAIRED_CODE_CODELIST]-(paired_name:CTCodelistRoot) + RETURN coalesce(paired_code.uid, paired_name.uid) AS paired_uid + """ + results, _ = db.cypher_query(query, {"codelist_uid": codelist_uid}) + if results and results[0][0] is not None: + return results[0][0] return None def is_term_in_codelist(self, term_uid: str, codelist_uid: str) -> bool: @@ -835,23 +841,12 @@ def is_term_in_codelist(self, term_uid: str, codelist_uid: str) -> bool: :param codelist_uid: The UID of the codelist :return: True if the term is in the codelist, False otherwise """ - codelist_root = CTCodelistRoot.nodes.get_or_none(uid=codelist_uid) - if not codelist_root: - return False - - term_root = CTTermRoot.nodes.get_or_none(uid=term_uid) - if not term_root: - return False - - # Check if there's an active HAS_TERM relationship - for codelist_term in codelist_root.has_term.all(): - term_from_codelist = codelist_term.has_term_root.get_or_none() - if term_from_codelist and term_from_codelist.uid == term_uid: - has_term_rel = codelist_root.has_term.relationship(codelist_term) - if has_term_rel.end_date is None: - return True - - return False + results = CTCodelistRoot.nodes.filter( + uid=codelist_uid, + has_term__has_term_root__uid=term_uid, + **{"has_term|end_date__isnull": True}, + )[:1] + return len(results) > 0 def get_or_create_selected_term( self, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/feature_flag_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/feature_flag_repository.py index 56ef447f..45b83dda 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/feature_flag_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/feature_flag_repository.py @@ -12,6 +12,8 @@ class FeatureFlagRepository: def _transform_to_model(self, item: FeatureFlagNode) -> FeatureFlag: return FeatureFlag( sn=item.sn, + section=item.section, + feature=item.feature, name=item.name, enabled=item.enabled, description=item.description, @@ -64,6 +66,8 @@ def retrieve_feature_flag(self, sn: int) -> FeatureFlag: def create_feature_flag( self, + section: str, + feature: str, name: str, enabled: bool, description: str | None, @@ -82,6 +86,8 @@ def create_feature_flag( CREATE (n:FeatureFlag) SET n.sn = $sn, + n.section = $section, + n.feature = $feature, n.name = $name, n.enabled = $enabled, n.description = $description @@ -89,6 +95,8 @@ def create_feature_flag( """, params={ "sn": sn, + "section": section, + "feature": feature, "name": name, "enabled": enabled, "description": description, @@ -98,14 +106,37 @@ def create_feature_flag( return self._transform_to_model(rs[0][0][0]) - def update_feature_flag(self, sn: int, enabled: bool) -> FeatureFlag: - rs = db.cypher_query( - """ - MATCH (n:FeatureFlag {sn: $sn}) - SET n.enabled = $enabled + def update_feature_flag(self, sn: int, **updates) -> FeatureFlag: + """ + Update a feature flag with only the provided fields. + + Args: + sn: Serial number of the feature flag + **updates: Fields to update (section, feature, enabled) + + Returns: + Updated FeatureFlag + """ + if not updates: + # If no updates provided, just retrieve and return the existing flag + return self.retrieve_feature_flag(sn) + + # Build SET clause dynamically for only the provided fields + set_clauses = [f"n.{key} = ${key}" for key in updates] + set_clause = ", ".join(set_clauses) + + query = f""" + MATCH (n:FeatureFlag {{sn: $sn}}) + SET + {set_clause} RETURN n - """, - params={"sn": sn, "enabled": enabled}, + """ + + params = {"sn": sn, **updates} + + rs = db.cypher_query( + query, + params=params, resolve_objects=True, ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py index 4ab6ef38..ad223dfe 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py @@ -4,6 +4,8 @@ class FeatureFlag(ClinicalMdrNode): sn = IntegerProperty(unique_index=True) + section = StringProperty() + feature = StringProperty() name = StringProperty() enabled = BooleanProperty() description = StringProperty() diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py index fa879968..48ab5bd8 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py @@ -829,3 +829,45 @@ class StudyDefinitionDocument(StudySelection): study_value = RelationshipFrom( STUDY_VALUE_CLASS_NAME, "HAS_STUDY_DEFINITION_DOCUMENT", model=ClinicalMdrRel ) + + +# All domain classes that inherit StudySelection (excluding the abstract base). +STUDY_SELECTION_CONCRETE_LABELS: frozenset[str] = frozenset( + { + "StudyDataSupplier", + "StudyObjective", + "StudyEndpoint", + "StudyCompound", + "StudyCriteria", + "StudySoAGroup", + "StudyActivitySubGroup", + "StudyActivityGroup", + "StudyActivity", + "StudyActivityInstance", + "StudyActivitySchedule", + "StudyDesignCell", + "StudyArm", + "StudyElement", + "StudyActivityInstruction", + "StudyBranchArm", + "StudyCohort", + "StudyCompoundDosing", + "StudySoAFootnote", + "StudyDesignClass", + "StudySourceVariable", + "StudyVersion", + "StudyDefinitionDocument", + "StudyEpoch", + "StudyVisit", + "StudyDiseaseMilestone", + "StudyStandardVersion", + } +) + +# Omitted from clone/source-vs-target containment checks: footnote rows depend on +# which selection subgraph was copied, so counts are not comparable to the source. +STUDY_SELECTION_LABELS_EXCLUDED_FROM_CONTAINMENT: frozenset[str] = frozenset( + { + "StudySoAFootnote", + } +) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_template.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_template.py new file mode 100644 index 00000000..9c54dc42 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_template.py @@ -0,0 +1,32 @@ +from neomodel import RelationshipTo + +from clinical_mdr_api.domain_repositories.models.generic import ( + ClinicalMdrRel, + VersionRelationship, + VersionRoot, + VersionValue, +) +from common.neomodel import StringProperty + + +class StudyTemplateValue(VersionValue): + study_uid = StringProperty() + study_value_version = StringProperty() + + +class StudyTemplateRoot(VersionRoot): + has_version = RelationshipTo( + StudyTemplateValue, "HAS_VERSION", model=VersionRelationship + ) + has_latest_value = RelationshipTo( + StudyTemplateValue, "LATEST", model=ClinicalMdrRel + ) + latest_draft = RelationshipTo( + StudyTemplateValue, "LATEST_DRAFT", model=ClinicalMdrRel + ) + latest_final = RelationshipTo( + StudyTemplateValue, "LATEST_FINAL", model=ClinicalMdrRel + ) + latest_retired = RelationshipTo( + StudyTemplateValue, "LATEST_RETIRED", model=ClinicalMdrRel + ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py index ef642c52..15ca6403 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py @@ -326,22 +326,24 @@ def _get_or_create_instance( self._db_save_node(new_instance) # Connect with Codelists & Terms - for codelist_uid in ar.sponsor_model_dataset_variable_vo.references_codelists: + for codelist_uid in ( + ar.sponsor_model_dataset_variable_vo.references_codelists or [] + ): codelist_node = CTCodelistRoot.nodes.get_or_none(uid=codelist_uid) BusinessLogicException.raise_if_not( codelist_node, msg=f"Could not find codelist with uid '{codelist_uid}'.", ) new_instance.references_codelist.connect(codelist_node) - for term_uid in ar.sponsor_model_dataset_variable_vo.references_terms: + for term_uid in ar.sponsor_model_dataset_variable_vo.references_terms or []: term_node = CTTermRoot.nodes.get_or_none(uid=term_uid) BusinessLogicException.raise_if_not( term_node, msg=f"Could not find term with uid '{term_uid}'.", ) - for ( - codelist_uid - ) in ar.sponsor_model_dataset_variable_vo.references_codelists: + for codelist_uid in ( + ar.sponsor_model_dataset_variable_vo.references_codelists or [] + ): codelist_node = CTCodelistRoot.nodes.get_or_none(uid=codelist_uid) term_context = CTTermContext() self._db_save_node(term_context) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/studies/study_template_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/studies/study_template_repository.py new file mode 100644 index 00000000..217bd937 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/studies/study_template_repository.py @@ -0,0 +1,126 @@ +from typing import Any, cast + +from clinical_mdr_api.domain_repositories.library_item_repository import ( + LibraryItemRepositoryImplBase, +) +from clinical_mdr_api.domain_repositories.models.generic import ( + Library, + VersionRelationship, + VersionRoot, + VersionValue, +) +from clinical_mdr_api.domain_repositories.models.study_template import ( + StudyTemplateRoot, + StudyTemplateValue, +) +from clinical_mdr_api.domains.enums import LibraryItemStatus +from clinical_mdr_api.domains.study_definition_aggregates.study_template import ( + StudyTemplateAR, + StudyTemplateValueVO, +) +from clinical_mdr_api.domains.versioned_object_aggregate import LibraryItemMetadataVO + + +class StudyTemplateRepository(LibraryItemRepositoryImplBase): + root_class = StudyTemplateRoot + value_class = StudyTemplateValue + user: str + has_library = False + + def generate_uid(self) -> str: + return self.root_class.get_next_free_uid_and_increment_counter() + + def _create_aggregate_root_instance_from_version_root_relationship_and_value( + self, + root: VersionRoot, + library: Library, + relationship: VersionRelationship, + value: VersionValue, + **_kwargs, + ) -> StudyTemplateAR: + ar_root = cast(StudyTemplateRoot, root) + ar_value = cast(StudyTemplateValue, value) + return StudyTemplateAR.from_repository_values( + uid=ar_root.uid, + item_metadata=self._library_item_metadata_vo_from_relation(relationship), + study_template_value=StudyTemplateValueVO.from_repository_values( + study_uid=ar_value.study_uid, + study_value_version=ar_value.study_value_version, + ), + ) + + def _are_changes_possible( + self, + versioned_object: Any, + previous_versioned_object: Any, + ) -> bool: + """ + Allow persisting PATCHed template target during FINAL/RETIRED states. + + The base `LibraryItemRepositoryImplBase` only allows value-node changes for + DRAFT->DRAFT transitions. For Study templates, PATCH creates a new version + and then approves back to FINAL, while the template item's status ends up + FINAL->FINAL. We must allow a new value node when the target study reference + (uid/version) changes. + """ + + new_status = versioned_object.item_metadata.status + prev_status = previous_versioned_object.item_metadata.status + + if ( + prev_status == LibraryItemStatus.DRAFT + and new_status == LibraryItemStatus.DRAFT + ): + return True + + if new_status == LibraryItemStatus.FINAL and prev_status in [ + LibraryItemStatus.FINAL, + LibraryItemStatus.RETIRED, + ]: + prev_value = cast(StudyTemplateAR, previous_versioned_object).value + new_value = cast(StudyTemplateAR, versioned_object).value + return ( + prev_value.study_uid != new_value.study_uid + or prev_value.study_value_version != new_value.study_value_version + ) + + return False + + def _maintain_parameters( + self, + versioned_object: Any, + root: VersionRoot, + value: VersionValue, + ) -> None: + pass + + def _get_or_create_value( + self, root: VersionRoot, ar: StudyTemplateAR, force_new_value_node: bool = False + ) -> VersionValue: + value = StudyTemplateValue( + study_uid=ar.value.study_uid, + study_value_version=ar.value.study_value_version, + ) + self._db_save_node(node=value) + return value + + def _is_new_version_necessary( + self, ar: StudyTemplateAR, value: VersionValue + ) -> bool: + template_value = cast(StudyTemplateValue, value) + return ( + template_value.study_uid != ar.value.study_uid + or template_value.study_value_version != ar.value.study_value_version + ) + + def _create(self, item: StudyTemplateAR) -> StudyTemplateAR: + relation_data: LibraryItemMetadataVO = item.item_metadata + root = self.root_class(uid=item.uid) + self._db_save_node(root) + + value = self._get_or_create_value(root=root, ar=item) + root, value, _, _, _ = self._db_create_and_link_nodes( + root, value, self._library_item_metadata_vo_to_datadict(relation_data) + ) + self._maintain_parameters(item, root, value) + return item diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository.py index 1515cb49..ec62fac7 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository.py @@ -4,7 +4,6 @@ from typing import Any, Sequence from neomodel import db -from neomodel.sync_.match import Collect, NodeNameResolver, Path, Size from neomodel.sync_.node import NodeMeta from clinical_mdr_api.domain_repositories.generic_repository import ( @@ -18,6 +17,10 @@ StudyArrayField, StudyBooleanField, ) +from clinical_mdr_api.domain_repositories.models.study_selections import ( + STUDY_SELECTION_CONCRETE_LABELS, + STUDY_SELECTION_LABELS_EXCLUDED_FROM_CONTAINMENT, +) from clinical_mdr_api.domains.study_definition_aggregates.root import ( StudyDefinitionAR, StudyDefinitionSnapshot, @@ -262,103 +265,154 @@ def get_study_structure_overview_headers( ) def get_study_structure_statistics(self, uid: str) -> dict[str, int] | None: - result = ( - StudyValue.nodes.filter(latest_value__uid=uid) - .traverse( - Path( - value="has_study_arm", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_branch_arm", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_element", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_cohort", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_epoch", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_footnote__references_study_epoch", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_visit", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - Path( - value="has_study_footnote__references_study_visit", - optional=True, - include_nodes_in_return=False, - include_rels_in_return=False, - ), - ) - .annotate( - arm_count=Size( - Collect(NodeNameResolver("has_study_arm"), distinct=True) - ), - branch_count=Size( - Collect(NodeNameResolver("has_study_branch_arm"), distinct=True) - ), - element_count=Size( - Collect(NodeNameResolver("has_study_element"), distinct=True) - ), - cohort_count=Size( - Collect(NodeNameResolver("has_study_cohort"), distinct=True) - ), - epoch_count=Size( - Collect(NodeNameResolver("has_study_epoch"), distinct=True) - ), - epoch_footnote_count=Size( - Collect( - NodeNameResolver("has_study_footnote__references_study_epoch"), - distinct=True, - ) - ), - visit_count=Size( - Collect(NodeNameResolver("has_study_visit"), distinct=True) - ), - visit_footnote_count=Size( - Collect( - NodeNameResolver("has_study_footnote__references_study_visit"), - distinct=True, - ) - ), - ) - .all() - ) + query = """ +MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) +RETURN + SIZE([(sv)-[:HAS_STUDY_ARM]->(:StudyArm) | 1]) AS arm_count, + SIZE([(sv)-[:HAS_STUDY_BRANCH_ARM]->(:StudyBranchArm) | 1]) AS branch_count, + SIZE([(sv)-[:HAS_STUDY_ELEMENT]->(:StudyElement) | 1]) AS element_count, + SIZE([(sv)-[:HAS_STUDY_COHORT]->(:StudyCohort) | 1]) AS cohort_count, + SIZE([(sv)-[:HAS_STUDY_EPOCH]->(:StudyEpoch) | 1]) AS epoch_count, + SIZE([(sv)-[:HAS_STUDY_FOOTNOTE]->(:StudyFootnote)-[:REFERENCES_STUDY_EPOCH]->(:StudyEpoch) | 1]) AS epoch_footnote_count, + SIZE([(sv)-[:HAS_STUDY_VISIT]->(:StudyVisit) | 1]) AS visit_count, + SIZE([(sv)-[:HAS_STUDY_FOOTNOTE]->(:StudyFootnote)-[:REFERENCES_STUDY_VISIT]->(:StudyVisit) | 1]) AS visit_footnote_count, + SIZE([(sv)-[:HAS_STUDY_ACTIVITY]->(:StudyActivity) | 1]) AS study_activity_count, + SIZE([(sv)-[:HAS_STUDY_ACTIVITY_SCHEDULE]->(:StudyActivitySchedule) | 1]) AS study_activity_schedule_count +""" + result, _ = db.cypher_query(query=query, params={"uid": uid}) + if not result: return None + + counts = result[0] + return { + "arm_count": counts[0], + "branch_count": counts[1], + "element_count": counts[2], + "cohort_count": counts[3], + "epoch_count": counts[4], + "epoch_footnote_count": counts[5], + "visit_count": counts[6], + "visit_footnote_count": counts[7], + "study_activity_count": counts[8], + "study_activity_schedule_count": counts[9], + } + + def get_study_selection_labels_for_study(self, study_uid: str) -> list[str]: + """ + Distinct concrete study-selection labels present on the study's latest value + (only labels in :data:`STUDY_SELECTION_CONCRETE_LABELS`). + """ + query = """ + MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)-[rel]->(ss:StudySelection) + WHERE type(rel) <> 'HAS_PROTOCOL_SOA_CELL' AND type(rel) <> 'HAS_PROTOCOL_SOA_FOOTNOTE' + UNWIND labels(ss) AS lb + WITH lb + WHERE lb IN $known_labels + RETURN DISTINCT lb AS label + ORDER BY label + """ + rows, _ = db.cypher_query( + query, + { + "study_uid": study_uid, + "known_labels": list(STUDY_SELECTION_CONCRETE_LABELS), + }, + ) + return [str(r[0]) for r in rows] + + def get_study_selection_statistics_for_labels( + self, study_uid: str, labels: list[str] + ) -> dict[str, dict[str, int]]: + """ + Per-label selection counts and distinct CT term root counts (via CTTermContext) + for the given labels on the study's latest value. + """ + if not labels: + return {} + query = """ + UNWIND $labels AS want + OPTIONAL MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)-[rel]->(ss:StudySelection) + WHERE type(rel) <> 'HAS_PROTOCOL_SOA_CELL' AND type(rel) <> 'HAS_PROTOCOL_SOA_FOOTNOTE' + AND want IN labels(ss) + OPTIONAL MATCH (ss)-[]->(ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(tr:CTTermRoot) + RETURN want, + count(DISTINCT ss) AS selection_count, + count(DISTINCT tr) AS distinct_ct_term_root_count + ORDER BY want + """ + rows, _ = db.cypher_query(query, {"study_uid": study_uid, "labels": labels}) + out: dict[str, dict[str, int]] = {} + for row in rows: + want, sel_count, term_count = row[0], int(row[1]), int(row[2]) + out[str(want)] = { + "selection_count": sel_count, + "distinct_ct_term_root_count": term_count, + } + return out + + def get_study_selection_containment( + self, source_study_uid: str, target_study_uid: str + ) -> dict[str, Any]: + """ + Whether **target** selection statistics (counts only for labels that appear on + **target**) are numerically contained in **source**: + for each such label, target counts must be <= source counts. + + Used to compare a clone (target) against its source study when only a subset + of labels may have been copied, or to verify full clone equality (then counts + match and containment holds). + + ``StudySoAFootnote`` is excluded: clone copies footnotes conditionally, so + footnote counts are not compared on source or target. + """ + labels = [ + lb + for lb in self.get_study_selection_labels_for_study(target_study_uid) + if lb not in STUDY_SELECTION_LABELS_EXCLUDED_FROM_CONTAINMENT + ] + if not labels: + return { + "target_contained_in_source": True, + "labels_from_target": [], + "per_label": [], + } + src_stats = self.get_study_selection_statistics_for_labels( + source_study_uid, labels + ) + tgt_stats = self.get_study_selection_statistics_for_labels( + target_study_uid, labels + ) + per_label: list[dict[str, Any]] = [] + all_contained = True + for lb in labels: + s = src_stats.get( + lb, + {"selection_count": 0, "distinct_ct_term_root_count": 0}, + ) + t = tgt_stats.get( + lb, + {"selection_count": 0, "distinct_ct_term_root_count": 0}, + ) + sc, stc = s["selection_count"], s["distinct_ct_term_root_count"] + tc, ttc = t["selection_count"], t["distinct_ct_term_root_count"] + label_ok = tc <= sc and ttc <= stc + if not label_ok: + all_contained = False + per_label.append( + { + "label": lb, + "target_selection_count": tc, + "source_selection_count": sc, + "target_distinct_ct_term_root_count": ttc, + "source_distinct_ct_term_root_count": stc, + "label_contained": label_ok, + } + ) return { - "arm_count": result[0][3], - "branch_count": result[0][4], - "element_count": result[0][5], - "cohort_count": result[0][6], - "epoch_count": result[0][7], - "epoch_footnote_count": result[0][8], - "visit_count": result[0][9], - "visit_footnote_count": result[0][10], + "target_contained_in_source": all_contained, + "labels_from_target": labels, + "per_label": per_label, } def copy_study_items( @@ -369,27 +423,22 @@ def copy_study_items( author_id: str, ) -> dict[str, int] | None: parameters: dict[str, str | list[str] | datetime.datetime] = {} - exclusions = """ - NOT EXISTS((selection_src)--(:StudyActivity)) - AND NOT EXISTS((selection_src)--(:StudyActivitySubGroup)) - AND NOT EXISTS((selection_src)--(:StudyActivityGroup)) - AND NOT EXISTS((selection_src:StudySoAFootnote)--(:StudyActivitySchedule)) - AND NOT EXISTS((selection_src)--(:StudyActivityInstance)) - AND NOT EXISTS((selection_src)--(:StudySoAGroup)) - """ - if ( - "StudySoAFootnote" in list_of_items_to_copy - and "StudyVisit" not in list_of_items_to_copy - ): - exclusions += """ - AND NOT ((selection_src:StudySoAFootnote)--(:StudyVisit) AND NOT (selection_src:StudySoAFootnote)--(:StudyVisit)--(:Delete)) - """ - if ( - "StudySoAFootnote" in list_of_items_to_copy - and "StudyEpoch" not in list_of_items_to_copy + exclusions = "TRUE" + for label in ( + "StudyVisit", + "StudyEpoch", + "StudyActivity", + "StudyActivitySubGroup", + "StudyActivityGroup", + "StudySoAGroup", + "StudyActivitySchedule", ): - exclusions += """ - AND NOT ((selection_src:StudySoAFootnote)--(:StudyEpoch) AND NOT (selection_src:StudySoAFootnote)--(:StudyEpoch)--(:Delete)) + if ( + "StudySoAFootnote" in list_of_items_to_copy + and label not in list_of_items_to_copy + ): + exclusions += f""" + AND NOT ((selection_src:StudySoAFootnote)--(:{label})) """ # COPY NODES AND OUTBOUND RELATIONSHIPS @@ -872,7 +921,8 @@ def where_stmt(): COALESCE(author.username, current_version.author_id) as author, latest_locked_version, latest_released_version, - [(sr)-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) | t.name] as data_completeness_tags + [(sr)-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) | t.name] as data_completeness_tags, + sv.description ORDER BY uid """ rs = db.cypher_query(query) @@ -897,6 +947,7 @@ def where_stmt(): "latest_locked_version": row[16], "latest_released_version": row[17], "data_completeness_tags": row[18], + "description": row[19], } for row in rs[0] ] @@ -1204,22 +1255,39 @@ def get_audit_trail_by_uid( @abstractmethod def _retrieve_study_subpart_with_history( - self, uid: str, is_subpart: bool = False, study_value_version: str | None = None - ): + self, + uid: str, + is_subpart: bool = False, + study_value_version: str | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, + ) -> GenericFilteringReturn: """ Private method to retrieve an audit trail for a study's subparts by UID. - :return: A list of Study subpart audit trail objects. + :return: A GenericFilteringReturn containing Study subpart audit trail objects. """ def get_subpart_audit_trail_by_uid( - self, uid: str, is_subpart: bool = False, study_value_version: str | None = None - ) -> list[Any]: + self, + uid: str, + is_subpart: bool = False, + study_value_version: str | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, + ) -> GenericFilteringReturn: """ Public method which is to retrieve the audit trail for a given study identified by UID. - :return: A list of retrieved data in a form StudyAuditTrailAR instances. + :return: A GenericFilteringReturn containing StudySubpartAuditTrail instances. """ return self._retrieve_study_subpart_with_history( - uid, is_subpart, study_value_version=study_value_version + uid, + is_subpart, + study_value_version=study_value_version, + page_number=page_number, + page_size=page_size, + total_count=total_count, ) @abstractmethod diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository_impl.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository_impl.py index f514ddeb..e4a67fab 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository_impl.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_definitions/study_definition_repository_impl.py @@ -86,7 +86,7 @@ from common import exceptions from common.config import settings from common.telemetry import trace_calls -from common.utils import convert_to_datetime +from common.utils import convert_to_datetime, validate_max_skip_clause MAINTAIN_RELATIONSHIPS_FOR_NEW_STUDY_VALUE = { "belongs_to_study_parent_part", @@ -2922,12 +2922,18 @@ def get_latest_released_version_from_specific_datetime( return latest_version_relationship[2].version def _retrieve_study_subpart_with_history( - self, uid: str, is_subpart: bool = False, study_value_version: str | None = None - ) -> list[Any]: + self, + uid: str, + is_subpart: bool = False, + study_value_version: str | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, + ) -> GenericFilteringReturn: """ returns the audit trail for all study subparts of the study """ - params: dict[str, str | list[str]] = {} + params: dict[str, str | list[str] | int] = {} if not is_subpart: params = {"study_uid": uid} if study_value_version: @@ -2960,14 +2966,27 @@ def _retrieve_study_subpart_with_history( else: parent_in_version = "" - rs = db.cypher_query( - f""" + base_query = f""" MATCH (ssr:StudyRoot)-[h_rel:HAS_VERSION]->(ssv:StudyValue) {parent_in_version} WHERE ssr.uid IN $subpart_uids OPTIONAL MATCH (ssv)<-[:AFTER]-(asa:StudyAction) OPTIONAL MATCH (ssv)<-[:BEFORE]-(bsa:StudyAction) OPTIONAL MATCH (ssv)<-[:HAS_STUDY_SUBPART]-(psv:StudyValue)<-[p_h_rel:HAS_VERSION]-(psr:StudyRoot) + """ + + if page_size > 0: + validate_max_skip_clause(page_number=page_number, page_size=page_size) + skip = (page_number - 1) * page_size + params["skip"] = skip + params["limit"] = page_size + pagination_clause = "SKIP $skip LIMIT $limit" + else: + pagination_clause = "" + + rs = db.cypher_query( + f""" + {base_query} RETURN DISTINCT psr.uid AS parent_uid, ssr.uid AS subpart_uid, @@ -2979,12 +2998,34 @@ def _retrieve_study_subpart_with_history( h_rel.end_date AS end_date, labels(asa) AS change_type ORDER BY start_date DESC + {pagination_clause} """, params=params, ) rs = utils.db_result_to_list(rs) rs.reverse() + total = -1 + if total_count: + count_result = db.cypher_query( + f""" + {base_query} + WITH DISTINCT + psr.uid AS parent_uid, + ssr.uid AS subpart_uid, + ssv.subpart_id AS subpart_id, + ssv.study_acronym AS study_acronym, + ssv.study_subpart_acronym AS study_subpart_acronym, + h_rel.author_id AS author_id, + h_rel.start_date AS start_date, + h_rel.end_date AS end_date, + labels(asa) AS change_type + RETURN count(*) AS total + """, + params=params, + ) + total = count_result[0][0][0] + result = [] if not is_subpart: subpart_status = set() @@ -3060,7 +3101,8 @@ def _retrieve_study_subpart_with_history( result.reverse() - return calculate_diffs(result, StudySubpartAuditTrail) + items = calculate_diffs(result, StudySubpartAuditTrail) + return GenericFilteringReturn(items=items, total=total) @staticmethod def get_soa_preferences( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/base.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/base.py index f73117db..34e21964 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/base.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/base.py @@ -1,10 +1,12 @@ import datetime from dataclasses import dataclass +from neomodel import db + from clinical_mdr_api.domain_repositories.generic_repository import ( _manage_versioning_with_relations, ) -from clinical_mdr_api.domain_repositories.models.study import StudyRoot, StudyValue +from clinical_mdr_api.domain_repositories.models.study import StudyValue from clinical_mdr_api.domain_repositories.models.study_audit_trail import ( Create, Delete, @@ -33,7 +35,7 @@ class StudySelectionRepository: We handle common operations here. """ - def _from_repository_values(self, study_uid: str, selection): + def _from_repository_values(self, study_uid: str, selection, selection_vo=None): """Must be defined by subclasses.""" raise NotImplementedError @@ -51,13 +53,15 @@ def perform_save( raise NotImplementedError def save(self, selection_vo, author_id: str): - study_root_node = StudyRoot.nodes.get_or_none(uid=selection_vo.study_uid) - - NotFoundException.raise_if( - study_root_node is None, "Study", selection_vo.study_uid + # Single Cypher to fetch StudyRoot + latest StudyValue (replaces 2 neomodel lookups) + results, _ = db.cypher_query( + "MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) RETURN sr, sv", + {"uid": selection_vo.study_uid}, + resolve_objects=True, ) + NotFoundException.raise_if(not results, "Study", selection_vo.study_uid) + study_root_node, latest_study_value_node = results[0] - latest_study_value_node = study_root_node.latest_value.single() new_selection = self.perform_save( latest_study_value_node, selection_vo, author_id ) @@ -83,7 +87,9 @@ def save(self, selection_vo, author_id: str): author_id=author_id, ) - return self._from_repository_values(selection_vo.study_uid, new_selection) + return self._from_repository_values( + selection_vo.study_uid, new_selection, selection_vo=selection_vo + ) def get_study_selection(self, study_value_node: StudyValue, selection_uid: str): """Must be defined by subclasses.""" @@ -91,17 +97,22 @@ def get_study_selection(self, study_value_node: StudyValue, selection_uid: str): @trace_calls(args=[1, 2], kwargs=["study_uid", "selection_uid"]) def delete(self, study_uid: str, selection_uid: str, author_id: str) -> None: - study_root_node = StudyRoot.nodes.get_or_none(uid=study_uid) - - NotFoundException.raise_if(study_root_node is None, "Study", study_uid) + # Single Cypher to fetch StudyRoot + latest StudyValue (replaces 2 neomodel lookups) + results, _ = db.cypher_query( + "MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) RETURN sr, sv", + {"uid": study_uid}, + resolve_objects=True, + ) + NotFoundException.raise_if(not results, "Study", study_uid) + study_root_node, latest_study_value_node = results[0] - latest_study_value_node = study_root_node.latest_value.single() selection = self.get_study_selection(latest_study_value_node, selection_uid) selection_vo = self._from_repository_values(study_uid, selection) new_selection = self.perform_save( latest_study_value_node, selection_vo, author_id ) - # Audit trail + # Audit trail — _manage_versioning_with_relations also disconnects `selection` + # from the StudyValue, so we only need to disconnect `new_selection` here. _manage_versioning_with_relations( study_root=study_root_node, action_type=Delete, @@ -111,8 +122,6 @@ def delete(self, study_uid: str, selection_uid: str, author_id: str) -> None: author_id=author_id, ) new_selection.study_value.disconnect(latest_study_value_node) - # Delete relation - selection.study_value.disconnect(latest_study_value_node) def _get_selection_with_history( self, study_uid: str, selection_uid: str | None = None diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_base_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_base_repository.py index 7f719235..6d8662f5 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_base_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_base_repository.py @@ -1,5 +1,6 @@ import abc import datetime +from dataclasses import replace from typing import Any, Generic, TypeVar from neomodel import db @@ -277,9 +278,13 @@ def save( closure_data = study_selection.repository_closure_data closure_data_length = len(closure_data) - # getting the latest study value node - study_root_node: StudyRoot = StudyRoot.nodes.get(uid=study_selection.study_uid) - latest_study_value_node: StudyValue = study_root_node.latest_value.get_or_none() + # Single Cypher to fetch StudyRoot + latest StudyValue (replaces 2 neomodel lookups) + results, _ = db.cypher_query( + "MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) RETURN sr, sv", + {"uid": study_selection.study_uid}, + resolve_objects=True, + ) + study_root_node, latest_study_value_node = results[0] # process new/changed/deleted elements for each activity selections_to_remove = [] @@ -362,6 +367,7 @@ def save( ) # loop through and add selections + order_by_uid: dict[str, int] = {} for order, selection in selections_to_add: last_study_selection_node = None if selection.study_selection_uid in audit_trail_nodes: @@ -392,6 +398,19 @@ def save( last_study_selection_node, False, ) + order_by_uid[selection.study_selection_uid] = order + + # Write the DB-assigned order back into the frozen VOs so callers can read the + # correct order directly from the aggregate without a second find_by_study round-trip. + if order_by_uid and self.is_repository_based_on_ordered_selection(): + study_selection.study_objects_selection = [ + ( + replace(sel, order=order_by_uid[sel.study_selection_uid]) + if sel.study_selection_uid in order_by_uid + else sel + ) + for sel in study_selection.study_objects_selection + ] @trace_calls def _get_selection_with_history( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_group_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_group_repository.py index b137dc42..593fb7bb 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_group_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_group_repository.py @@ -24,7 +24,6 @@ StudySelectionActivityGroupAR, StudySelectionActivityGroupVO, ) -from clinical_mdr_api.utils import unpack_list_of_lists from common.telemetry import trace_calls from common.utils import convert_to_datetime @@ -306,22 +305,26 @@ def get_all_study_activity_groups_for_study_activity( return study_activity_groups[0] return [] - def find_study_activity_group_with_same_groupings( + @trace_calls + def find_study_activity_group_vo_with_same_groupings( self, study_uid: str, activity_group_uid: str, soa_group_term_uid: str, sync_latest_version: bool = False, - ) -> StudyActivityGroup | None: + ) -> StudySelectionActivityGroupVO | None: + """Returns a fully-populated VO for the existing StudyActivityGroup matching the given + groupings, or None if not found. Avoids a full AR load.""" query = """ MATCH (activity_group_root:ActivityGroupRoot)-[:HAS_VERSION]->(activity_group_value:ActivityGroupValue) - <-[:HAS_SELECTED_ACTIVITY_GROUP]-(study_activity_group:StudyActivityGroup)<-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP] + <-[:HAS_SELECTED_ACTIVITY_GROUP]-(sag:StudyActivityGroup)<-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP] -(study_activity:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(:StudyValue)<-[:LATEST]-(:StudyRoot {uid:$study_uid}) - MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_SOA_GROUP]->(:StudySoAGroup)-[:HAS_FLOWCHART_GROUP]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(flowchart_group_term:CTTermRoot) - WHERE NOT (study_activity_group)<-[:BEFORE]-() AND NOT (study_activity_group)<-[]-(:Delete) + MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_SOA_GROUP]->(soag:StudySoAGroup) + -[:HAS_FLOWCHART_GROUP]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(flowchart_group_term:CTTermRoot) + WHERE NOT (sag)<-[:BEFORE]-() AND NOT (sag)<-[]-(:Delete) AND activity_group_root.uid=$activity_group_uid AND flowchart_group_term.uid=$soa_group_term_uid - WITH DISTINCT study_activity_group, activity_group_root, activity_group_value, $sync_latest_version AS sync_latest_version + WITH DISTINCT sag, activity_group_root, activity_group_value, soag, $sync_latest_version AS sync_latest_version CALL apoc.do.case([ sync_latest_version=true, 'WHERE (activity_group_root)-[:LATEST]->(activity_group_value) RETURN *' @@ -333,9 +336,33 @@ def find_study_activity_group_with_same_groupings( sync_latest_version: sync_latest_version }) YIELD value - RETURN DISTINCT study_activity_group, activity_group_value + WITH DISTINCT sag, activity_group_root, activity_group_value, soag + CALL { + WITH activity_group_root, activity_group_value + MATCH (activity_group_root)-[ver:HAS_VERSION]-(activity_group_value) + WHERE ver.status IN ['Final', 'Retired'] + WITH ver + ORDER BY [i IN split(ver.version, '.') | toInteger(i)] DESC, + ver.end_date DESC, ver.start_date DESC + LIMIT 1 + RETURN ver.version AS activity_group_version + } + MATCH (sag)<-[:AFTER]-(after_action:StudyAction) + RETURN DISTINCT + sag.uid AS study_selection_uid, + coalesce(sag.show_activity_group_in_protocol_flowchart, false) AS show_activity_group_in_protocol_flowchart, + sag.order AS order, + coalesce(sag.accepted_version, false) AS accepted_version, + activity_group_root.uid AS activity_group_uid, + activity_group_value.name AS activity_group_name, + activity_group_version, + soag.uid AS study_soa_group_uid, + after_action.date AS start_date, + after_action.author_id AS author_id + ORDER BY after_action.date DESC + LIMIT 1 """ - study_activity_groups, _ = db.cypher_query( + results, keys = db.cypher_query( query, params={ "study_uid": study_uid, @@ -343,8 +370,22 @@ def find_study_activity_group_with_same_groupings( "soa_group_term_uid": soa_group_term_uid, "sync_latest_version": sync_latest_version, }, - resolve_objects=True, ) - if len(study_activity_groups) > 0: - return unpack_list_of_lists(study_activity_groups)[0] - return None + if not results: + return None + row = dict(zip(keys, results[0])) + return StudySelectionActivityGroupVO.from_input_values( + study_uid=study_uid, + study_selection_uid=row["study_selection_uid"], + activity_group_uid=row["activity_group_uid"], + activity_group_name=row["activity_group_name"], + activity_group_version=row["activity_group_version"], + show_activity_group_in_protocol_flowchart=row[ + "show_activity_group_in_protocol_flowchart" + ], + order=row["order"], + study_soa_group_uid=row["study_soa_group_uid"], + start_date=convert_to_datetime(value=row["start_date"]), + author_id=row["author_id"], + accepted_version=row["accepted_version"], + ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instance_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instance_repository.py index fb702764..898b2c62 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instance_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instance_repository.py @@ -724,95 +724,80 @@ def _add_new_selection( last_study_selection_node: StudyActivityInstance, for_deletion: bool = False, ): - # Fetch nodes referenced by uids - query = [ + # Build a single Cypher statement that MATCHes all dependency nodes, CREATEs the + # StudyActivityInstance node, and CREATEs all its core relationships in one round-trip. + # Optional relationships (baseline visits, supplier, origin_type/source) are handled + # below via separate queries because they require conditional validation logic. + match_lines = [ "MATCH (study_activity:StudyActivity {uid:$study_activity_uid}) WHERE NOT (study_activity)-[:BEFORE]-()", + "MATCH (study_value:StudyValue) WHERE elementId(study_value) = $study_value_eid", ] - params = { + params: dict[str, Any] = { "study_activity_uid": selection.study_activity_uid, + "study_value_eid": latest_study_value_node.element_id, + "sai_uid": selection.study_selection_uid, + "sai_show": selection.show_activity_instance_in_protocol_flowchart, + "sai_keep_old": selection.keep_old_version, + "sai_keep_old_date": selection.keep_old_version_date, + "sai_is_reviewed": selection.is_reviewed, + "sai_is_important": selection.is_important, + "sai_accepted": selection.accepted_version, } - returns = ["study_activity"] + + optional_matches: list[str] = [] + create_instance_rels: list[str] = [] + if selection.activity_instance_uid: if selection.activity_instance_version: - query.append( - """MATCH (instance_root:ActivityInstanceRoot {uid: $activity_instance_uid}) - -[:HAS_VERSION {version: $activity_instance_version}]->(latest_activity_instance_value:ActivityInstanceValue) WITH * LIMIT 1""" + optional_matches.append( + "MATCH (instance_root:ActivityInstanceRoot {uid: $activity_instance_uid})" + "-[:HAS_VERSION {version: $activity_instance_version}]->(latest_activity_instance_value:ActivityInstanceValue)" + " WITH * LIMIT 1" ) params["activity_instance_version"] = ( selection.activity_instance_version ) else: - query.append( + optional_matches.append( "MATCH (instance_root:ActivityInstanceRoot {uid: $activity_instance_uid})-[:LATEST]->(latest_activity_instance_value:ActivityInstanceValue)" ) params["activity_instance_uid"] = selection.activity_instance_uid - returns.append("latest_activity_instance_value") - if selection.study_data_supplier_uid: - query.append( - "MATCH (study_data_supplier:StudyDataSupplier {uid: $study_data_supplier_uid}) WHERE NOT (study_data_supplier)-[:BEFORE]-()" - ) - params["study_data_supplier_uid"] = selection.study_data_supplier_uid - returns.append("study_data_supplier") - if selection.origin_type_uid: - query.append( - "OPTIONAL MATCH (origin_type_root:CTTermRoot {uid: $origin_type_uid})" - ) - params["origin_type_uid"] = selection.origin_type_uid - returns.append("origin_type_root") - if selection.origin_source_uid: - query.append( - "OPTIONAL MATCH (origin_source_root:CTTermRoot {uid: $origin_source_uid})" + create_instance_rels.append( + "CREATE (sai)-[:HAS_SELECTED_ACTIVITY_INSTANCE]->(latest_activity_instance_value)" ) - params["origin_source_uid"] = selection.origin_source_uid - returns.append("origin_source_root") - query.append(f"RETURN {', '.join(returns)}") - query_str = "\n".join(query) - results, keys = db.cypher_query(query_str, params, resolve_objects=True) - if len(results) != 1: - raise exceptions.BusinessLogicException( - msg=f"There should be one row returned with dependencies for StudyActivityInstance '{selection.study_selection_uid}'." - ) - - nodes = dict(zip(keys, results[0])) - latest_activity_instance_value_node: ActivityInstanceValue | None = nodes.get( - "latest_activity_instance_value" + create_node = ( + "CREATE (sai:StudyActivityInstance:StudySelection" + " {uid: $sai_uid," + " show_activity_instance_in_protocol_flowchart: $sai_show," + " keep_old_version: $sai_keep_old, keep_old_version_date: $sai_keep_old_date," + " is_reviewed: $sai_is_reviewed, is_important: $sai_is_important," + " accepted_version: $sai_accepted})" ) - study_activity_node: StudyActivity = nodes["study_activity"] - study_data_supplier_node: StudyDataSupplier | None = nodes.get( - "study_data_supplier" - ) - origin_type_root: CTTermRoot | None = nodes.get("origin_type_root") - origin_source_root: CTTermRoot | None = nodes.get("origin_source_root") - - # Create new activity selection - study_activity_instance_selection_node = StudyActivityInstance( - uid=selection.study_selection_uid, - show_activity_instance_in_protocol_flowchart=selection.show_activity_instance_in_protocol_flowchart, - keep_old_version=selection.keep_old_version, - keep_old_version_date=selection.keep_old_version_date, - is_reviewed=selection.is_reviewed, - is_important=selection.is_important, - accepted_version=selection.accepted_version, - ).save() + create_core_rels = [ + "CREATE (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_INSTANCE]->(sai)", + ] if not for_deletion: - # Connect new node with study value - latest_study_value_node.has_study_activity_instance.connect( - study_activity_instance_selection_node + create_core_rels.append( + "CREATE (study_value)-[:HAS_STUDY_ACTIVITY_INSTANCE]->(sai)" ) - if selection.activity_instance_uid and latest_activity_instance_value_node: - # Connect new node with Activity value - study_activity_instance_selection_node.has_selected_activity_instance.connect( - latest_activity_instance_value_node - ) - - # Connect StudyActivityInstance with StudyActivity node - study_activity_instance_selection_node.study_activity_has_study_activity_instance.connect( - study_activity_node + all_lines = ( + match_lines + + optional_matches + + [create_node] + + create_core_rels + + create_instance_rels + + ["RETURN sai"] ) + results, _ = db.cypher_query("\n".join(all_lines), params, resolve_objects=True) + if not results or not results[0]: + raise exceptions.BusinessLogicException( + msg=f"Failed to create StudyActivityInstance node for '{selection.study_selection_uid}'." + ) + study_activity_instance_selection_node: StudyActivityInstance = results[0][0] - # Handle baseline visit relationships + # Handle baseline visit relationships (require per-visit validation) for baseline_visit in selection.study_activity_instance_baseline_visits or []: baseline_visit_uid = baseline_visit["uid"] baseline_visit_node = latest_study_value_node.has_study_visit.get_or_none( @@ -845,13 +830,27 @@ def _add_new_selection( ) # Connect StudyDataSupplier if provided - if selection.study_data_supplier_uid and study_data_supplier_node: - study_activity_instance_selection_node.has_study_data_supplier.connect( - study_data_supplier_node + if selection.study_data_supplier_uid: + supplier_results, _ = db.cypher_query( + "MATCH (study_data_supplier:StudyDataSupplier {uid: $uid}) WHERE NOT (study_data_supplier)-[:BEFORE]-() RETURN study_data_supplier", + {"uid": selection.study_data_supplier_uid}, + resolve_objects=True, ) + if supplier_results: + study_activity_instance_selection_node.has_study_data_supplier.connect( + supplier_results[0][0] + ) # Connect Origin Type CT term if provided if selection.origin_type_uid: + origin_type_results, _ = db.cypher_query( + "OPTIONAL MATCH (origin_type_root:CTTermRoot {uid: $uid}) RETURN origin_type_root", + {"uid": selection.origin_type_uid}, + resolve_objects=True, + ) + origin_type_root: CTTermRoot | None = None + if origin_type_results and origin_type_results[0][0]: + origin_type_root = origin_type_results[0][0] ValidationException.raise_if( origin_type_root is None, msg=f"Origin Type Term with UID '{selection.origin_type_uid}' doesn't exist.", @@ -868,6 +867,14 @@ def _add_new_selection( # Connect Origin Source CT term if provided if selection.origin_source_uid: + origin_source_results, _ = db.cypher_query( + "OPTIONAL MATCH (origin_source_root:CTTermRoot {uid: $uid}) RETURN origin_source_root", + {"uid": selection.origin_source_uid}, + resolve_objects=True, + ) + origin_source_root: CTTermRoot | None = None + if origin_source_results and origin_source_results[0][0]: + origin_source_root = origin_source_results[0][0] ValidationException.raise_if( origin_source_root is None, msg=f"Origin Source Term with UID '{selection.origin_source_uid}' doesn't exist.", @@ -917,6 +924,49 @@ def get_all_study_activity_instances_for_study_activity( ).distinct() return study_activity_instances + def find_selection_vo_by_uid( + self, + study_uid: str, + study_selection_uid: str, + ) -> StudySelectionActivityInstanceVO | None: + """Fetch a single fully-populated VO by its study_selection_uid. + + Uses the same MATCH/CALL blocks as the listing query but filtered to + one StudyActivityInstance node, avoiding a full aggregate load. + """ + additional_match = self._additional_match() + # Inject the UID filter into the existing WHERE clause that follows + # "WITH sr, sv, sa, study_activity WHERE sa IS NOT NULL" + additional_match = additional_match.replace( + "WHERE sa IS NOT NULL", + "WHERE sa IS NOT NULL AND sa.uid = $study_selection_uid", + 1, + ) + query = ( + "MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)" + + additional_match + + self._order_by_query() + + self._return_clause() + ) + results = db.cypher_query( + query, + { + "study_uid": study_uid, + "study_selection_uid": study_selection_uid, + "uids": study_uid, + }, + ) + from clinical_mdr_api import ( + utils as _utils, # local to avoid circular at module level + ) + + rows = _utils.db_result_to_list(results) + if not rows: + return None + selection = rows[0] + acv = selection.get("accepted_version", False) or False + return self._create_value_object_from_repository(selection=selection, acv=acv) + def get_all_study_activity_instances_impacted_by_schedule_deletion( self, study_uid: str, schedule_uid: str ) -> list[StudyActivityInstance]: diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instruction_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instruction_repository.py index f6a8604a..731df836 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instruction_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_instruction_repository.py @@ -17,7 +17,7 @@ class StudyActivityInstructionRepository(base.StudySelectionRepository): def _from_repository_values( - self, study_uid: str, selection: StudyActivityInstruction + self, study_uid: str, selection: StudyActivityInstruction, selection_vo=None ) -> StudyActivityInstructionVO: study_action = selection.has_after.all()[0] study_activity = selection.study_activity.single() diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py index 998a883e..49931f3a 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py @@ -382,86 +382,80 @@ def _add_new_selection( last_study_selection_node: StudyActivity, for_deletion: bool = False, ): - # Fetch nodes referenced by uids - query = [ - "MATCH (activity_root:ActivityRoot {uid: $activity_uid})-[:HAS_VERSION {version: $activity_version}]->(latest_activity_value:ActivityValue) WITH * LIMIT 1", + # Build a single Cypher statement that MATCHes all dependency nodes, CREATEs the + # StudyActivity node, and CREATEs all its relationships in one round-trip. + match_lines = [ + "MATCH (activity_root:ActivityRoot {uid: $activity_uid})" + "-[:HAS_VERSION {version: $activity_version}]->(latest_activity_value:ActivityValue)" + " WITH * LIMIT 1", + "MATCH (study_value:StudyValue) WHERE elementId(study_value) = $study_value_eid", "MATCH (study_soa_group:StudySoAGroup {uid:$study_soa_group_uid}) WHERE NOT (study_soa_group)-[:BEFORE]-()", ] - params = { - "study_uid": selection.study_uid, + params: dict[str, Any] = { + "sa_uid": selection.study_selection_uid, + "sa_order": order, + "sa_show_activity": selection.show_activity_in_protocol_flowchart, + "sa_keep_old": selection.keep_old_version, + "sa_keep_old_date": selection.keep_old_version_date, + "sa_accepted": selection.accepted_version, "activity_uid": selection.activity_uid, "activity_version": selection.activity_version, "study_soa_group_uid": selection.study_soa_group_uid, + "study_value_eid": latest_study_value_node.element_id, } - returns = ["latest_activity_value", "study_soa_group"] + + optional_matches: list[str] = [] + create_rels: list[str] = [] + if selection.study_activity_subgroup_uid: - query.append( - "MATCH (study_activity_subgroup:StudyActivitySubGroup {uid: $study_activity_subgroup_uid}) WHERE NOT (study_activity_subgroup)-[:BEFORE]-()" + optional_matches.append( + "MATCH (study_activity_subgroup:StudyActivitySubGroup {uid: $study_activity_subgroup_uid})" + " WHERE NOT (study_activity_subgroup)-[:BEFORE]-()" ) params["study_activity_subgroup_uid"] = ( selection.study_activity_subgroup_uid ) - returns.append("study_activity_subgroup") + create_rels.append( + "CREATE (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_SUBGROUP]->(study_activity_subgroup)" + ) + if selection.study_activity_group_uid: - query.append( - "MATCH (study_activity_group:StudyActivityGroup {uid: $study_activity_group_uid}) WHERE NOT (study_activity_group)-[:BEFORE]-()" + optional_matches.append( + "MATCH (study_activity_group:StudyActivityGroup {uid: $study_activity_group_uid})" + " WHERE NOT (study_activity_group)-[:BEFORE]-()" ) params["study_activity_group_uid"] = selection.study_activity_group_uid - returns.append("study_activity_group") - - query.append(f"RETURN {', '.join(returns)}") - query_str = "\n".join(query) - results, keys = db.cypher_query(query_str, params, resolve_objects=True) - if len(results) != 1: - raise exceptions.BusinessLogicException( - msg=f"There should be one row returned with dependencies for StudyActivity '{selection.study_selection_uid}'." + create_rels.append( + "CREATE (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP]->(study_activity_group)" ) - nodes = dict(zip(keys, results[0])) - latest_activity_value_node: ActivityValue = nodes["latest_activity_value"] - study_soa_group_node: StudySoAGroup = nodes["study_soa_group"] - study_activity_subgroup_node: StudyActivitySubGroup | None = nodes.get( - "study_activity_subgroup" - ) - study_activity_group_node: StudyActivityGroup | None = nodes.get( - "study_activity_group" + create_node = ( + "CREATE (sa:StudyActivity:StudySelection {uid: $sa_uid, order: $sa_order," + " show_activity_in_protocol_flowchart: $sa_show_activity," + " keep_old_version: $sa_keep_old, keep_old_version_date: $sa_keep_old_date," + " accepted_version: $sa_accepted})" ) - - # Create new activity selection - study_activity_selection_node = StudyActivity( - uid=selection.study_selection_uid, - order=order, - show_activity_in_protocol_flowchart=selection.show_activity_in_protocol_flowchart, - keep_old_version=selection.keep_old_version, - keep_old_version_date=selection.keep_old_version_date, - accepted_version=selection.accepted_version, - ).save() + create_core_rels = [ + "CREATE (sa)-[:HAS_SELECTED_ACTIVITY]->(latest_activity_value)", + "CREATE (sa)-[:STUDY_ACTIVITY_HAS_STUDY_SOA_GROUP]->(study_soa_group)", + ] if not for_deletion: - # Connect new node with study value - latest_study_value_node.has_study_activity.connect( - study_activity_selection_node - ) - - # Connect new node with Activity value - study_activity_selection_node.has_selected_activity.connect( - latest_activity_value_node - ) - # Connect StudyActivity with StudySoAGroup node - study_activity_selection_node.has_soa_group_selection.connect( - study_soa_group_node + create_core_rels.append("CREATE (study_value)-[:HAS_STUDY_ACTIVITY]->(sa)") + + all_lines = ( + match_lines + + optional_matches + + [create_node] + + create_core_rels + + create_rels + + ["RETURN sa"] ) - - if selection.study_activity_subgroup_uid: - # Connect StudyActivity with StudyActivitySubGroup node - study_activity_selection_node.study_activity_has_study_activity_subgroup.connect( - study_activity_subgroup_node - ) - - if selection.study_activity_group_uid: - # Connect StudyActivity with StudyActivityGroup node - study_activity_selection_node.study_activity_has_study_activity_group.connect( - study_activity_group_node + results, _ = db.cypher_query("\n".join(all_lines), params, resolve_objects=True) + if not results or not results[0]: + raise exceptions.BusinessLogicException( + msg=f"Failed to create StudyActivity node for '{selection.study_selection_uid}'." ) + study_activity_selection_node: StudyActivity = results[0][0] _manage_versioning_with_relations( study_root=study_root, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py index 881c316b..d8094f94 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py @@ -4,8 +4,14 @@ from neomodel import RelationshipDefinition, StructuredNode, db from clinical_mdr_api import utils +from clinical_mdr_api.domain_repositories.generic_repository import ( + _manage_versioning_with_relations, +) from clinical_mdr_api.domain_repositories.models._utils import ListDistinct from clinical_mdr_api.domain_repositories.models.study import StudyValue +from clinical_mdr_api.domain_repositories.models.study_audit_trail import ( + Delete as DeleteAction, +) from clinical_mdr_api.domain_repositories.models.study_selections import ( StudyActivity, StudyActivitySchedule, @@ -33,8 +39,18 @@ class SelectionHistory(base.SelectionHistory): class StudyActivityScheduleRepository(base.StudySelectionRepository): def _from_repository_values( - self, study_uid: str, selection: StudyActivitySchedule + self, study_uid: str, selection: StudyActivitySchedule, selection_vo=None ) -> StudyActivityScheduleVO: + # When selection_vo is provided (from save/delete), use its fields directly + # instead of doing 3 separate .single() neomodel lookups. + if selection_vo is not None: + return StudyActivityScheduleVO( + uid=selection.uid, + study_uid=study_uid, + study_activity_uid=selection_vo.study_activity_uid, + study_activity_instance_uid=selection_vo.study_activity_instance_uid, + study_visit_uid=selection_vo.study_visit_uid, + ) study_activity = selection.study_activity.single() study_visit = selection.study_visit.single() @@ -61,7 +77,7 @@ def perform_save( study_value_node: StudyValue, selection_vo: StudyActivityScheduleVO, author_id: str, - ) -> StudyActivityScheduleVO: + ) -> StudyActivitySchedule: # Detach previous node from study if selection_vo.uid is not None: self._remove_old_selection_if_exists(selection_vo.study_uid, selection_vo) @@ -76,34 +92,36 @@ def perform_save( msg=f"There already exist a schedule for the same Activity and Visit in the Study with UID '{selection_vo.study_uid}'", ) - # Create new node - schedule = StudyActivitySchedule(uid=selection_vo.uid).save() - - study_activity_node = study_value_node.has_study_activity.get_or_none( - uid=selection_vo.study_activity_uid - ) - - NotFoundException.raise_if( - study_activity_node is None, - "Study Activity", - selection_vo.study_activity_uid, - ) - - schedule.study_activity.connect(study_activity_node) - - study_visit_node = study_value_node.has_study_visit.get_or_none( - uid=selection_vo.study_visit_uid + # Pre-generate UID so we can CREATE node + all relationships in one round-trip. + uid = ( + selection_vo.uid + or StudyActivitySchedule.get_next_free_uid_and_increment_counter() ) - - NotFoundException.raise_if( - study_visit_node is None, "Study Visit", selection_vo.study_visit_uid + results, _ = db.cypher_query( + """ + MATCH (study_value:StudyValue) WHERE elementId(study_value) = $study_value_eid + MATCH (study_value)-[:HAS_STUDY_ACTIVITY]->(study_activity:StudyActivity {uid: $study_activity_uid}) + MATCH (study_value)-[:HAS_STUDY_VISIT]->(study_visit:StudyVisit {uid: $study_visit_uid}) + CREATE (schedule:StudyActivitySchedule:StudySelection {uid: $uid}) + CREATE (study_value)-[:HAS_STUDY_ACTIVITY_SCHEDULE]->(schedule) + CREATE (study_activity)-[:STUDY_ACTIVITY_HAS_SCHEDULE]->(schedule) + CREATE (study_visit)-[:STUDY_VISIT_HAS_SCHEDULE]->(schedule) + RETURN schedule + """, + { + "study_value_eid": study_value_node.element_id, + "study_activity_uid": selection_vo.study_activity_uid, + "study_visit_uid": selection_vo.study_visit_uid, + "uid": uid, + }, + resolve_objects=True, ) - - # Create relations - schedule.study_visit.connect(study_visit_node) - study_value_node.has_study_activity_schedule.connect(schedule) - - return schedule + if not results or not results[0]: + raise BusinessLogicException( + msg=f"Failed to create StudyActivitySchedule for activity '{selection_vo.study_activity_uid}' " + f"and visit '{selection_vo.study_visit_uid}'." + ) + return results[0][0] def find_schedule_for_study_visit_and_study_activity( self, study_uid: str, study_activity_uid: str, study_visit_uid: str @@ -150,6 +168,54 @@ def get_study_selection( def generate_uid(self) -> str: return StudyActivity.get_next_free_uid_and_increment_counter() + @trace_calls(args=[1, 2], kwargs=["study_uid", "selection_uid"]) + def delete(self, study_uid: str, selection_uid: str, author_id: str) -> None: + # Single Cypher to fetch StudyRoot + latest StudyValue + results, _ = db.cypher_query( + "MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) RETURN sr, sv", + {"uid": study_uid}, + resolve_objects=True, + ) + NotFoundException.raise_if(not results, "Study", study_uid) + study_root_node, latest_study_value_node = results[0] + + selection = self.get_study_selection(latest_study_value_node, selection_uid) + + # Single Cypher to fetch related UIDs (replaces 3 .single() calls) + uid_results, _ = db.cypher_query( + """ + MATCH (sas:StudyActivitySchedule) WHERE elementId(sas) = $eid + MATCH (sas)<-[:STUDY_ACTIVITY_HAS_SCHEDULE]-(sa:StudyActivity) + MATCH (sas)<-[:STUDY_VISIT_HAS_SCHEDULE]-(sv:StudyVisit) + OPTIONAL MATCH (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_INSTANCE]->(sai:StudyActivityInstance) + RETURN sa.uid AS sa_uid, sv.uid AS sv_uid, sai.uid AS sai_uid + """, + {"eid": selection.element_id}, + ) + sa_uid, sv_uid, sai_uid = uid_results[0] if uid_results else (None, None, None) + assert isinstance(sa_uid, str) + selection_vo = StudyActivityScheduleVO( + uid=selection.uid, + study_uid=study_uid, + study_activity_uid=sa_uid, + study_activity_instance_uid=sai_uid, + study_visit_uid=sv_uid, + ) + + new_selection = self.perform_save( + latest_study_value_node, selection_vo, author_id + ) + # Audit trail — _manage_versioning_with_relations also disconnects `selection` + _manage_versioning_with_relations( + study_root=study_root_node, + action_type=DeleteAction, + before=selection, + after=new_selection, + exclude_relationships=self.exclude_relationships(), + author_id=author_id, + ) + new_selection.study_value.disconnect(latest_study_value_node) + def _get_selection_with_history( self, study_uid: str, selection_uid: str | None = None ): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_subgroup_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_subgroup_repository.py index 94c21ca7..10046152 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_subgroup_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_subgroup_repository.py @@ -23,7 +23,6 @@ StudySelectionActivitySubGroupAR, StudySelectionActivitySubGroupVO, ) -from clinical_mdr_api.utils import unpack_list_of_lists from common.telemetry import trace_calls from common.utils import convert_to_datetime @@ -300,40 +299,68 @@ def get_all_study_activity_subgroups_for_study_activity( return study_activity_subgroups[0] return [] - def find_study_activity_subgroup_with_same_groupings( + @trace_calls + def find_study_activity_subgroup_vo_with_same_groupings( self, study_uid: str, activity_subgroup_uid: str, activity_group_uid: str, soa_group_term_uid: str, sync_latest_version: bool = False, - ) -> StudyActivitySubGroup | None: + ) -> StudySelectionActivitySubGroupVO | None: + """Returns a fully-populated VO for the existing StudyActivitySubGroup matching the given + groupings, or None if not found. Avoids a full AR load.""" query = """ - MATCH (activity_subgroup_root:ActivitySubGroupRoot)-[:HAS_VERSION]->(activity_sub_group_value:ActivitySubGroupValue) - <-[:HAS_SELECTED_ACTIVITY_SUBGROUP]-(study_activity_subgroup:StudyActivitySubGroup)<-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_SUBGROUP] + MATCH (activity_subgroup_root:ActivitySubGroupRoot)-[:HAS_VERSION]->(activity_subgroup_value:ActivitySubGroupValue) + <-[:HAS_SELECTED_ACTIVITY_SUBGROUP]-(sasg:StudyActivitySubGroup)<-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_SUBGROUP] -(study_activity:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(:StudyValue)<-[:LATEST]-(:StudyRoot {uid:$study_uid}) - MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP]->(:StudyActivityGroup) + MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP]->(sag:StudyActivityGroup) -[:HAS_SELECTED_ACTIVITY_GROUP]->(:ActivityGroupValue)<-[:HAS_VERSION]-(activity_group_root:ActivityGroupRoot) - MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_SOA_GROUP]->(:StudySoAGroup)-[:HAS_FLOWCHART_GROUP]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(flowchart_group_term:CTTermRoot) - WHERE NOT (study_activity_subgroup)<-[:BEFORE]-() AND NOT (study_activity_subgroup)<-[]-(:Delete) + MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_SOA_GROUP]->(:StudySoAGroup) + -[:HAS_FLOWCHART_GROUP]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(flowchart_group_term:CTTermRoot) + WHERE NOT (sasg)<-[:BEFORE]-() AND NOT (sasg)<-[]-(:Delete) AND activity_subgroup_root.uid=$activity_subgroup_uid AND activity_group_root.uid=$activity_group_uid AND flowchart_group_term.uid=$soa_group_term_uid - WITH DISTINCT study_activity_subgroup, activity_subgroup_root, activity_sub_group_value, $sync_latest_version AS sync_latest_version + WITH DISTINCT sasg, activity_subgroup_root, activity_subgroup_value, sag, $sync_latest_version AS sync_latest_version CALL apoc.do.case([ sync_latest_version=true, - 'WHERE (activity_subgroup_root)-[:LATEST]->(activity_sub_group_value) RETURN *' + 'WHERE (activity_subgroup_root)-[:LATEST]->(activity_subgroup_value) RETURN *' ], '', { activity_subgroup_root: activity_subgroup_root, - activity_sub_group_value: activity_sub_group_value, + activity_subgroup_value: activity_subgroup_value, sync_latest_version: sync_latest_version }) YIELD value - RETURN DISTINCT study_activity_subgroup, activity_sub_group_value + WITH DISTINCT sasg, activity_subgroup_root, activity_subgroup_value, sag + CALL { + WITH activity_subgroup_root, activity_subgroup_value + MATCH (activity_subgroup_root)-[ver:HAS_VERSION]-(activity_subgroup_value) + WHERE ver.status IN ['Final', 'Retired'] + WITH ver + ORDER BY [i IN split(ver.version, '.') | toInteger(i)] DESC, + ver.end_date DESC, ver.start_date DESC + LIMIT 1 + RETURN ver.version AS activity_subgroup_version + } + MATCH (sasg)<-[:AFTER]-(after_action:StudyAction) + RETURN DISTINCT + sasg.uid AS study_selection_uid, + COALESCE(sasg.show_activity_subgroup_in_protocol_flowchart, false) AS show_activity_subgroup_in_protocol_flowchart, + sasg.order AS order, + coalesce(sasg.accepted_version, false) AS accepted_version, + activity_subgroup_root.uid AS activity_subgroup_uid, + activity_subgroup_value.name AS activity_subgroup_name, + activity_subgroup_version, + sag.uid AS study_activity_group_uid, + after_action.date AS start_date, + after_action.author_id AS author_id + ORDER BY after_action.date DESC + LIMIT 1 """ - study_activity_subgroups, _ = db.cypher_query( + results, keys = db.cypher_query( query, params={ "study_uid": study_uid, @@ -342,8 +369,22 @@ def find_study_activity_subgroup_with_same_groupings( "soa_group_term_uid": soa_group_term_uid, "sync_latest_version": sync_latest_version, }, - resolve_objects=True, ) - if len(study_activity_subgroups) > 0: - return unpack_list_of_lists(study_activity_subgroups)[0] - return None + if not results: + return None + row = dict(zip(keys, results[0])) + return StudySelectionActivitySubGroupVO.from_input_values( + study_uid=study_uid, + study_selection_uid=row["study_selection_uid"], + activity_subgroup_uid=row["activity_subgroup_uid"], + activity_subgroup_name=row["activity_subgroup_name"], + activity_subgroup_version=row["activity_subgroup_version"], + show_activity_subgroup_in_protocol_flowchart=row[ + "show_activity_subgroup_in_protocol_flowchart" + ], + order=row["order"], + study_activity_group_uid=row["study_activity_group_uid"], + start_date=convert_to_datetime(value=row["start_date"]), + author_id=row["author_id"], + accepted_version=row["accepted_version"], + ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_definition_document_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_definition_document_repository.py index 4b2cc0dd..9e658bb6 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_definition_document_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_definition_document_repository.py @@ -15,6 +15,7 @@ ) from clinical_mdr_api.services._utils import ensure_transaction from common.auth.user import user +from common.config import settings class StudyDefinitionDocumentRepository: @@ -69,6 +70,28 @@ def get_latest_protocol_header_version( study_definition_document = result[0][0] return f"{study_definition_document.protocol_header_major_version}.{study_definition_document.protocol_header_minor_version}" + def has_final_protocol_locked_version( + self, study_uid: str, study_value_version: str | None = None + ) -> bool: + params: dict[str, str | int | None] = { + "study_uid": study_uid, + "final_protocol_submval": settings.final_protocol_term_submval, + } + if study_value_version: + params["version"] = study_value_version + query = "MATCH (:StudyRoot {uid: $study_uid})-[:HAS_VERSION{status:'LOCKED',version:$version}]->(:StudyValue)" + else: + query = "MATCH (:StudyRoot {uid: $study_uid})-[:HAS_VERSION{status:'LOCKED'}]->(:StudyValue)" + query += """ + -[:HAS_STUDY_VERSION]->(sv:StudyVersion) + -[:HAS_REASON_FOR_LOCK]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(term_root:CTTermRoot) + <-[:HAS_TERM_ROOT]-(codelist_term:CTCodelistTerm) + WHERE codelist_term.submission_value = $final_protocol_submval + RETURN count(sv) > 0 AS has_final_protocol + """ + result, _ = db.cypher_query(query, params=params) + return bool(result and result[0] and result[0][0]) + @ensure_transaction(db) def create_or_update_study_definition_document( self, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py index 71fe7ea9..cb3ba5bf 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py @@ -728,10 +728,24 @@ def list_all_visits_query( query.append(dedent(""" RETURN - study_visit { .*, + { + uid: study_visit.uid, + show_visit: coalesce(study_visit.show_visit, false), + is_global_anchor_visit: coalesce(study_visit.is_global_anchor_visit, false), + is_soa_milestone: coalesce(study_visit.is_soa_milestone, false), + visit_number: study_visit.visit_number, + unique_visit_number: toInteger(study_visit.unique_visit_number), + visit_class: study_visit.visit_class, + visit_subclass: study_visit.visit_subclass, + short_visit_label: study_visit.short_visit_label, + visit_name_label: study_visit.visit_name_label, + description: study_visit.description, + start_rule: study_visit.start_rule, + end_rule: study_visit.end_rule, + status: study_visit.status, consecutive_visit_group: CASE group.visit_group.group_format - WHEN "range" THEN head(group.consecutive_visits).vis.short_visit_label + "-" + last(group.consecutive_visits).vis.short_visit_label - WHEN "list" THEN apoc.text.join([visit in group.consecutive_visits | visit.vis.short_visit_label], ',') + WHEN "range" THEN head(group.consecutive_visits).vis.short_visit_label + "-" + last(group.consecutive_visits).vis.short_visit_label + WHEN "list" THEN apoc.text.join([visit in group.consecutive_visits | visit.vis.short_visit_label], ',') ELSE null END, consecutive_visit_group_uid: group.visit_group.uid, visit_short_name: study_visit.short_visit_label, diff --git a/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_attributes.py b/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_attributes.py index 3a3e6ece..2a5f4b11 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_attributes.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_attributes.py @@ -21,11 +21,13 @@ @dataclass(frozen=True) class CTPairedCodelists: """ - Small class to hold the paired codelists UIDs + Small class to hold the paired codelists UIDs and names """ paired_names_codelist_uid: str | None paired_codes_codelist_uid: str | None + paired_names_codelist_name: str | None = None + paired_codes_codelist_name: str | None = None @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_template.py b/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_template.py new file mode 100644 index 00000000..aa9bc81f --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_template.py @@ -0,0 +1,124 @@ +from dataclasses import dataclass, field +from typing import Any, Self + +from clinical_mdr_api.domains.versioned_object_aggregate import ( + LibraryItemMetadataVO, + ObjectAction, + VersioningActionMixin, +) +from common.exceptions import BusinessLogicException + + +@dataclass(frozen=True) +class StudyTemplateValueVO: + study_uid: str + study_value_version: str + + @classmethod + def from_input_values( + cls, + *, + study_uid: str, + study_value_version: str, + ) -> Self: + return cls.from_repository_values( + study_uid=study_uid, + study_value_version=study_value_version, + ) + + @classmethod + def from_repository_values( + cls, + *, + study_uid: str, + study_value_version: str, + ) -> Self: + return cls( + study_uid=study_uid, + study_value_version=study_value_version, + ) + + +@dataclass +class StudyTemplateAR(VersioningActionMixin): + _value: StudyTemplateValueVO + _item_metadata: LibraryItemMetadataVO + _uid: str | None = None + _is_deleted: bool = field(init=False, default=False) + repository_closure_data: Any = field( + init=False, compare=False, repr=True, default=None + ) + + def get_possible_actions(self) -> set[ObjectAction]: + raise NotImplementedError("Possible actions retrieval not implemented.") + + @property + def item_metadata(self) -> LibraryItemMetadataVO: + return self._item_metadata + + @property + def value(self) -> StudyTemplateValueVO: + return self._value + + @property + def uid(self) -> str | None: + return self._uid + + @property + def is_deleted(self) -> bool: + return self._is_deleted + + def create_new_version(self, author_id: str): + super()._create_new_version(author_id) + + def edit_draft( + self, + *, + author_id: str, + change_description: str, + new_study_template_value: StudyTemplateValueVO, + ) -> None: + if self._value != new_study_template_value: + super()._edit_draft( + author_id=author_id, + change_description=change_description, + ) + self._value = new_study_template_value + + @classmethod + def from_input_values( + cls, + *, + author_id: str, + study_template_value: StudyTemplateValueVO, + generate_uid_callback=lambda: None, + ) -> Self: + return cls( + _uid=generate_uid_callback(), + _value=study_template_value, + _item_metadata=LibraryItemMetadataVO.get_initial_item_metadata( + author_id=author_id + ), + ) + + @classmethod + def from_repository_values( + cls, + *, + uid: str, + item_metadata: LibraryItemMetadataVO, + study_template_value: StudyTemplateValueVO, + ) -> Self: + return cls( + _uid=uid, + _item_metadata=item_metadata, + _value=study_template_value, + ) + + def _is_edit_allowed_in_non_editable_library(self): + return True + + def soft_delete(self): + raise BusinessLogicException( + msg="Deleting the Study Template configuration is not supported." + ) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/study_selections/study_visit.py b/clinical-mdr-api/clinical_mdr_api/domains/study_selections/study_visit.py index d68168b8..7db0ac54 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/study_selections/study_visit.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/study_selections/study_visit.py @@ -200,7 +200,7 @@ def visit_short_name(self): ] return visit_short_name + chosen_letter if self.visit_class in [VisitClass.UNSCHEDULED_VISIT, VisitClass.NON_VISIT]: - return visit_number + return f"V{visit_number}" return visit_short_name return self.vis_short_name diff --git a/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_item_class.py b/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_item_class.py index 25dcc524..b748132a 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_item_class.py +++ b/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_item_class.py @@ -463,8 +463,7 @@ def from_codelist_and_terms( library_name=cl_name_and_attrs.library_name, name=cl_name_and_attrs.name, attributes=cl_name_and_attrs.attributes, - paired_codes_codelist_uid=cl_name_and_attrs.paired_codes_codelist_uid, - paired_names_codelist_uid=cl_name_and_attrs.paired_names_codelist_uid, + paired_codelist=cl_name_and_attrs.paired_codelist, term_uids=term_uids, ) diff --git a/clinical-mdr-api/clinical_mdr_api/models/complexity_score.py b/clinical-mdr-api/clinical_mdr_api/models/complexity_score.py index f8e084c1..8dc3d65b 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/complexity_score.py +++ b/clinical-mdr-api/clinical_mdr_api/models/complexity_score.py @@ -37,6 +37,23 @@ def from_dict(cls, data: Any) -> Self: ) +class ComplexityScoreVisit(BaseModel): + type: Annotated[str, Field()] + count: Annotated[int, Field()] + burden: Annotated[float, Field()] + + +class ComplexityScoreAssessment(BaseModel): + type: Annotated[str, Field()] + count: Annotated[int, Field()] + burden: Annotated[float, Field()] + + +class ComplexityScoreDetails(BaseModel): + visits: Annotated[list[ComplexityScoreVisit], Field()] + assessments: Annotated[list[ComplexityScoreAssessment], Field()] + + class BurdenInput(PostInputModel): burden_id: Annotated[str, Field()] name: Annotated[str, Field()] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity.py b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity.py index db854f5b..e761aee9 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity.py +++ b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity.py @@ -62,9 +62,12 @@ def from_activity_uid( if uid is not None: activity = find_activity_by_uid(uid, version=version) if activity is not None: - simple_activity_model = cls(uid=uid, name=activity.concept_vo.name) + resolved_version = version or activity.item_metadata.version + simple_activity_model = cls( + uid=uid, name=activity.concept_vo.name, version=resolved_version + ) else: - simple_activity_model = cls(uid=uid, name=None) + simple_activity_model = cls(uid=uid, name=None, version=version) return simple_activity_model @classmethod diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_instance.py b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_instance.py index ba80c8d5..1420bb34 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_instance.py +++ b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_instance.py @@ -316,14 +316,17 @@ def from_activity_ar( activity_group=ActivityHierarchySimpleModel( uid=activity_grouping.activity_group_uid, name=activity_grouping.activity_group_name, + version=activity_grouping.activity_group_version, ), activity_subgroup=ActivityHierarchySimpleModel( uid=activity_grouping.activity_subgroup_uid, name=activity_grouping.activity_subgroup_name, + version=activity_grouping.activity_subgroup_version, ), activity=ActivityHierarchySimpleModel( uid=activity_grouping.activity_uid or "", name=activity_grouping.activity_name, + version=activity_grouping.activity_version, ), ) else: @@ -370,14 +373,17 @@ def from_activity_instance_ar_objects( activity_group=ActivityHierarchySimpleModel( uid=activity_instance_grouping_vo.activity_group_uid, name=activity_instance_grouping_vo.activity_group_name, + version=activity_instance_grouping_vo.activity_group_version, ), activity_subgroup=ActivityHierarchySimpleModel( uid=activity_instance_grouping_vo.activity_subgroup_uid, name=activity_instance_grouping_vo.activity_subgroup_name, + version=activity_instance_grouping_vo.activity_subgroup_version, ), activity=ActivityHierarchySimpleModel( uid=activity_instance_grouping_vo.activity_uid or "", name=activity_instance_grouping_vo.activity_name, + version=activity_instance_grouping_vo.activity_version, ), ) for activity_instance_grouping_vo in activity_instance_ar.concept_vo.activity_groupings @@ -568,14 +574,17 @@ def from_activity_ar( activity_group=ActivityHierarchySimpleModel( uid=activity_grouping.activity_group_uid, name=activity_grouping.activity_group_name, + version=activity_grouping.activity_group_version, ), activity_subgroup=ActivityHierarchySimpleModel( uid=activity_grouping.activity_subgroup_uid, name=activity_grouping.activity_subgroup_name, + version=activity_grouping.activity_subgroup_version, ), activity=ActivityHierarchySimpleModel( uid=activity_grouping.activity_uid or "", name=activity_grouping.activity_name, + version=activity_grouping.activity_version, ), ) else: @@ -690,14 +699,17 @@ def from_activity_instance_ar_objects( activity_group=ActivityHierarchySimpleModel( uid=activity_instance_grouping_vo.activity_group_uid, name=activity_instance_grouping_vo.activity_group_name, + version=activity_instance_grouping_vo.activity_group_version, ), activity_subgroup=ActivityHierarchySimpleModel( uid=activity_instance_grouping_vo.activity_subgroup_uid, name=activity_instance_grouping_vo.activity_subgroup_name, + version=activity_instance_grouping_vo.activity_subgroup_version, ), activity=ActivityHierarchySimpleModel( uid=activity_instance_grouping_vo.activity_uid or "", name=activity_instance_grouping_vo.activity_name, + version=activity_instance_grouping_vo.activity_version, ), ) for activity_instance_grouping_vo in activity_instance_ar.concept_vo.activity_groupings diff --git a/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_codelist.py b/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_codelist.py index 80c18aba..b2fe7bf4 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_codelist.py +++ b/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_codelist.py @@ -140,14 +140,38 @@ class CTCodelistCreateInput(PostInputModel): library_name: Annotated[str, Field(min_length=1)] +class CTCodelistCodelistInformation(PostInputModel): + name: Annotated[str, Field(min_length=1)] + submission_value: Annotated[str, Field(min_length=1)] + nci_preferred_name: Annotated[str | None, Field(min_length=1)] = None + definition: Annotated[str, Field(min_length=1)] + sponsor_preferred_name: Annotated[str, Field(min_length=1)] + + +class CTPairedCodelistCreateInput(PostInputModel): + catalogue_names: Annotated[list[str], Field()] + name_information: Annotated[CTCodelistCodelistInformation, Field()] + code_information: Annotated[CTCodelistCodelistInformation, Field()] + extensible: Annotated[bool, Field()] + is_ordinal: Annotated[bool, Field()] + codelist_type: Annotated[str, Field()] = DEFAULT_CODELIST_TYPE + template_parameter: Annotated[bool, Field()] + parent_codelist_uid: Annotated[str | None, Field(min_length=1)] = None + library_name: Annotated[str, Field(min_length=1)] + + +class CTPairedCodelistInfo(BaseModel): + uid: Annotated[str, Field()] + name: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None + + class CTCodelistNameAndAttributes(BaseModel): @classmethod def from_ct_codelist_ar( cls, ct_codelist_name_ar: CTCodelistNameAR, ct_codelist_attributes_ar: CTCodelistAttributesAR, - paired_codes_codelist_uid: str | None = None, - paired_names_codelist_uid: str | None = None, + paired_codelist: CTPairedCodelistInfo | None = None, ) -> Self: codelist_name_and_attributes = cls( catalogue_names=ct_codelist_attributes_ar.ct_codelist_vo.catalogue_names, @@ -163,8 +187,7 @@ def from_ct_codelist_ar( attributes=CTCodelistAttributes.from_ct_codelist_ar_without_common_codelist_fields( ct_codelist_attributes_ar ), - paired_codes_codelist_uid=paired_codes_codelist_uid, - paired_names_codelist_uid=paired_names_codelist_uid, + paired_codelist=paired_codelist, ) return codelist_name_and_attributes @@ -174,8 +197,7 @@ def from_name_and_attributes( cls, ct_codelist_name: CTCodelistName, ct_codelist_attributes: CTCodelistAttributes, - paired_codes_codelist_uid: str | None = None, - paired_names_codelist_uid: str | None = None, + paired_codelist: CTPairedCodelistInfo | None = None, ) -> Self: codelist_name_and_attributes = cls( catalogue_names=ct_codelist_attributes.catalogue_names, @@ -185,8 +207,7 @@ def from_name_and_attributes( library_name=ct_codelist_attributes.library_name, name=ct_codelist_name, attributes=ct_codelist_attributes, - paired_codes_codelist_uid=paired_codes_codelist_uid, - paired_names_codelist_uid=paired_names_codelist_uid, + paired_codelist=paired_codelist, ) return codelist_name_and_attributes @@ -211,12 +232,8 @@ def from_name_and_attributes( attributes: Annotated[CTCodelistAttributes, Field()] - paired_codes_codelist_uid: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None - - paired_names_codelist_uid: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) + paired_codelist: Annotated[ + CTPairedCodelistInfo | None, Field(json_schema_extra={"nullable": True}) ] = None diff --git a/clinical-mdr-api/clinical_mdr_api/models/feature_flag.py b/clinical-mdr-api/clinical_mdr_api/models/feature_flag.py index 81a2c02b..37839f30 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/feature_flag.py +++ b/clinical-mdr-api/clinical_mdr_api/models/feature_flag.py @@ -1,4 +1,4 @@ -from typing import Annotated +from typing import Annotated, Literal from pydantic import Field @@ -7,6 +7,8 @@ class FeatureFlag(BaseModel): sn: Annotated[int, Field()] + section: Annotated[str, Field()] + feature: Annotated[str, Field()] name: Annotated[str, Field()] enabled: Annotated[bool, Field()] description: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( @@ -15,10 +17,14 @@ class FeatureFlag(BaseModel): class FeatureFlagInput(PostInputModel): + section: Annotated[Literal["admin", "library", "studies"], Field()] + feature: Annotated[str, Field(min_length=1)] name: Annotated[str, Field(min_length=1)] enabled: Annotated[bool, Field()] description: Annotated[str | None, Field(min_length=1)] = None class FeatureFlagPatchInput(PatchInputModel): - enabled: Annotated[bool, Field()] = False + section: Annotated[Literal["admin", "library", "studies"] | None, Field()] = None + feature: Annotated[str | None, Field(min_length=1)] = None + enabled: Annotated[bool | None, Field()] = None diff --git a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study.py b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study.py index 14771098..1f15ddf0 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study.py +++ b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study.py @@ -4,7 +4,7 @@ from decimal import Decimal from typing import Annotated, Any, Callable, Collection, Self, overload -from pydantic import ConfigDict, Field +from pydantic import ConfigDict, Field, model_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC from clinical_mdr_api.domain_repositories.controlled_terminologies import ( @@ -18,7 +18,7 @@ ) from clinical_mdr_api.domains.controlled_terminologies.ct_term_name import CTTermNameAR from clinical_mdr_api.domains.dictionaries.dictionary_term import DictionaryTermAR -from clinical_mdr_api.domains.enums import ValidationMode +from clinical_mdr_api.domains.enums import LibraryItemStatus, ValidationMode from clinical_mdr_api.domains.projects.project import ProjectAR from clinical_mdr_api.domains.study_definition_aggregates.registry_identifiers import ( RegistryIdentifiersVO, @@ -40,7 +40,12 @@ SimpleTermModel, ) from clinical_mdr_api.models.study_selections.duration import DurationJsonModel -from clinical_mdr_api.models.utils import BaseModel, PatchInputModel, PostInputModel +from clinical_mdr_api.models.utils import ( + BaseModel, + EditInputModel, + PatchInputModel, + PostInputModel, +) from common.config import settings from common.exceptions import ( BusinessLogicException, @@ -137,6 +142,49 @@ class StudySoaSplit(StudySoaSplitInput): study_uid: Annotated[str, Field(description="Uid of study")] +class StudyTemplateInput(PostInputModel): + study_uid: Annotated[str, Field(min_length=1, description="Uid of template study")] + study_value_version: Annotated[ + str, + Field( + min_length=1, + description="Study value version of template study, e.g. '1.0'", + ), + ] + + +class StudyTemplatePatchInput(EditInputModel): + study_uid: Annotated[ + str, + Field( + description="Uid of template study; empty string clears the configured target", + ), + ] + study_value_version: Annotated[ + str, + Field( + description="Released study value version; required when study_uid is non-empty", + ), + ] + + @model_validator(mode="after") + def _study_version_required_when_study_uid_set(self) -> Self: + if self.study_uid.strip() and not self.study_value_version.strip(): + raise ValueError( + "study_value_version is required when study_uid is non-empty" + ) + return self + + +class StudyTemplate(BaseModel): + uid: Annotated[str, Field(description="Uid of study template root")] + study_uid: Annotated[str, Field(description="Uid of template study")] + study_value_version: Annotated[str, Field(description="Study value version")] + status: Annotated[LibraryItemStatus, Field(description="Template item status")] + version: Annotated[str, Field(description="Template item version")] + change_description: Annotated[str, Field(description="Version change description")] + + class RegistryIdentifiersJsonModel(BaseModel): ct_gov_id: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None @@ -1771,6 +1819,9 @@ class VersionInfo(BaseModel): ] = None number: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None title: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None + description: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( + None + ) subpart_id: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( None ) @@ -1810,6 +1861,7 @@ def from_input( id=val["id"], main_id=val["main_id"], title=val.get("title"), + description=val.get("description"), subpart_id=val.get("subpart_id"), subpart_acronym=val.get("subpart_acronym"), clinical_programme_name=val["clinical_programme_name"], @@ -1936,6 +1988,70 @@ class StudyStructureStatistics(BaseModel): visit_footnote_count: Annotated[ int, Field(description="Number of connected footnotes (visit level)") ] + study_activity_count: Annotated[ + int, Field(description="Number of connected study activities") + ] + study_activity_schedule_count: Annotated[ + int, Field(description="Number of connected study activity schedules") + ] + + +class StudySelectionContainmentLabelRow(BaseModel): + """Per-label comparison when checking if target is contained in source.""" + + label: Annotated[str, Field(description="Concrete study selection label")] + target_selection_count: Annotated[int, Field(description="Selections on target")] + source_selection_count: Annotated[int, Field(description="Selections on source")] + target_distinct_ct_term_root_count: Annotated[ + int, + Field( + description="Distinct CT term roots on target (via CTTermContext on selections)" + ), + ] + source_distinct_ct_term_root_count: Annotated[ + int, + Field( + description="Distinct CT term roots on source (via CTTermContext on selections)" + ), + ] + label_contained: Annotated[ + bool, + Field( + description="True if target selection and term counts are <= source for this label" + ), + ] + + +class StudySelectionContainmentResult(BaseModel): + """ + Whether the **target** study's selection statistics are contained in the **source**. + + Only labels that appear on the **target** study are considered (except + ``StudySoAFootnote``, which is skipped because SoA footnotes are copied + conditionally). Containment means for each such label, target counts are less + than or equal to source counts (selection nodes and distinct CT term roots via + CTTermContext). + """ + + target_contained_in_source: Annotated[ + bool, + Field( + description="True if containment holds for every compared label present on target" + ), + ] + labels_from_target: Annotated[ + list[str], + Field( + description=( + "Concrete selection labels on the target used in the comparison " + "(excludes StudySoAFootnote)" + ) + ), + ] + per_label: Annotated[ + list[StudySelectionContainmentLabelRow], + Field(description="Breakdown per label"), + ] class StudyCreateInput(PostInputModel): @@ -1958,6 +2074,12 @@ class StudyCloneInput(StudyCreateInput): copy_study_epoch: Annotated[bool, Field()] = False copy_study_epochs_study_footnote: Annotated[bool, Field()] = False copy_study_design_matrix: Annotated[bool, Field()] = False + copy_study_soa_group: Annotated[bool, Field()] = False + copy_study_activity: Annotated[bool, Field()] = False + copy_study_activity_instance: Annotated[bool, Field()] = False + copy_study_activity_group: Annotated[bool, Field()] = False + copy_study_activity_subgroup: Annotated[bool, Field()] = False + copy_study_activity_schedule: Annotated[bool, Field()] = False validation_mode: Annotated[ValidationMode, Field()] = ValidationMode.STRICT @@ -2077,6 +2199,22 @@ def from_study_field_audit_trail_vo( ) +class StudyProtocolHeaderVersion(BaseModel): + protocol_header_version: Annotated[ + str | None, + Field( + description="The latest available protocol header version.", + json_schema_extra={"nullable": True}, + ), + ] = None + has_final_protocol_locked_version: Annotated[ + bool, + Field( + description="Indicates whether the study contains a locked version with 'Final Protocol' as the reason for lock.", + ), + ] = False + + class StudyProtocolTitle(BaseModel): study_uid: Annotated[ str | None, diff --git a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_selection.py b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_selection.py index e5400649..64f64fc8 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_selection.py +++ b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_selection.py @@ -2718,7 +2718,11 @@ def activity_instance_from_study_activity_instance_vo( test_name_code=study_activity_instance_vo.activity_instance_test_name_code, standard_unit=study_activity_instance_vo.activity_instance_standard_unit, version=study_activity_instance_vo.activity_instance_version, - status=study_activity_instance_vo.activity_instance_status.value, + status=( + study_activity_instance_vo.activity_instance_status.value + if study_activity_instance_vo.activity_instance_status + else None + ), is_default_selected_for_activity=study_activity_instance_vo.activity_instance_is_default_selected_for_activity, is_required_for_activity=study_activity_instance_vo.activity_instance_is_required_for_activity, ) @@ -2736,7 +2740,11 @@ def latest_activity_instance_from_study_activity_instance_vo( name=study_activity_instance_vo.latest_activity_instance_class_name, ), version=study_activity_instance_vo.latest_activity_instance_version, - status=study_activity_instance_vo.latest_activity_instance_status.value, + status=( + study_activity_instance_vo.latest_activity_instance_status.value + if study_activity_instance_vo.latest_activity_instance_status + else None + ), ) @@ -3088,8 +3096,8 @@ def from_study_selection_activity_instance_vo_and_order( [ SimpleStudyVisit( uid=baseline_visit["uid"], - visit_name=baseline_visit["visit_name"], - visit_type_name=baseline_visit["visit_type_name"], + visit_name=baseline_visit.get("visit_name") or "", + visit_type_name=baseline_visit.get("visit_type_name") or "", ) for baseline_visit in ( study_selection.study_activity_instance_baseline_visits or [] diff --git a/clinical-mdr-api/clinical_mdr_api/repositories/ct_catalogues.py b/clinical-mdr-api/clinical_mdr_api/repositories/ct_catalogues.py index 532f0646..c4fb7152 100644 --- a/clinical-mdr-api/clinical_mdr_api/repositories/ct_catalogues.py +++ b/clinical-mdr-api/clinical_mdr_api/repositories/ct_catalogues.py @@ -13,9 +13,7 @@ class CatalogueComparisonType(Enum): - """ - Enum for Type of the catalogue comparison - """ + """Catalogue comparison type.""" ATTRIBUTES_COMPARISON = "attributes" SPONSOR_COMPARISON = "sponsor" @@ -27,19 +25,19 @@ def get_ct_catalogues_changes( catalogue_name: str | None, comparison_type: CatalogueComparisonType, start_datetime: datetime, - end_datetime=datetime, + end_datetime: datetime, ) -> dict[str, Any]: filter_parameters = [] if library_name is not None: filter_by_library_name = """ - $library_name=head([(library:Library)-[:{LIBRARY_CT_REL}]->({CT_OBJECT}) | library.name])""" + EXISTS {{ MATCH (:Library {{name: $library_name}})-[:{LIBRARY_CT_REL}]->({CT_OBJECT}) }}""" filter_parameters.append(filter_by_library_name) if catalogue_name is not None: filter_by_catalogue_name = """ - $catalogue_name IN [(catalogue:CTCatalogue)-[:HAS_CODELIST]->(codelist_root) | catalogue.name]""" + EXISTS {{ MATCH (:CTCatalogue {{name: $catalogue_name}})-[:HAS_CODELIST]->(codelist_root) }}""" filter_parameters.append(filter_by_catalogue_name) filter_statements = ( - "AND " + " AND ".join(filter_parameters) if len(filter_parameters) > 0 else "" + "AND " + " AND ".join(filter_parameters) if filter_parameters else "" ) codelist_filter_statements = filter_statements.format( LIBRARY_CT_REL="CONTAINS_CODELIST", CT_OBJECT="codelist_root" @@ -53,79 +51,52 @@ def get_ct_catalogues_changes( else: relationship_type = "HAS_NAME_ROOT" + # Single-pass: match versions < end_datetime once, split old/new via collected lists. codelist_data_retrieval = f""" MATCH (codelist_root:CTCodelistRoot)-[:{relationship_type}]-> - (old_codelist_ver_root)-[old_versions]->(old_codelist_ver_value) - WHERE old_versions.start_date < datetime($start_datetime) - {codelist_filter_statements} - WITH codelist_root, old_versions, old_codelist_ver_value - ORDER BY old_versions.start_date DESC - WITH codelist_root, - collect(old_codelist_ver_value)[0] AS old_codelist_ver_value, - collect(old_versions.start_date)[0] AS latest_date, - collect(old_versions) AS old_versions_collection - WITH codelist_root, - old_codelist_ver_value, - latest_date, - head([x IN old_versions_collection WHERE x.start_date = latest_date | x ]) AS latest_version - WITH collect(apoc.map.fromValues([codelist_root.uid, {{value_node:old_codelist_ver_value, change_date: latest_date}}])) AS old_items - - MATCH (codelist_root:CTCodelistRoot)-[:{relationship_type}]-> - (new_codelist_ver_root)-[new_versions]->(new_codelist_ver_value) - WHERE new_versions.start_date < datetime($end_datetime) + (ver_root)-[ver]->(ver_value) + WHERE ver.start_date < datetime($end_datetime) {codelist_filter_statements} - WITH old_items, codelist_root, new_versions, new_codelist_ver_value - ORDER BY new_versions.start_date DESC - WITH old_items, - codelist_root, - collect(new_codelist_ver_value)[0] AS new_codelist_ver_value, - collect(new_versions.start_date)[0] AS latest_date, - collect(new_versions) AS new_versions_collection - WITH old_items, - codelist_root, - new_codelist_ver_value, - latest_date, head([x IN new_versions_collection WHERE x.start_date = latest_date | x ]) AS latest_version - WITH old_items, - collect(apoc.map.fromValues([codelist_root.uid, {{value_node:new_codelist_ver_value, change_date: latest_date}}])) AS new_items + WITH codelist_root, ver_value, ver.start_date AS ver_date + ORDER BY ver_date DESC + WITH codelist_root, + collect(ver_value) AS vals, + collect(ver_date) AS dates + WITH codelist_root, vals, dates, + vals[0] AS new_val, dates[0] AS new_date, + head([i IN range(0, size(dates)-1) WHERE dates[i] < datetime($start_datetime)]) AS old_idx + WITH + [x IN collect(CASE WHEN old_idx IS NOT NULL THEN + apoc.map.fromValues([codelist_root.uid, {{value_node: vals[old_idx], change_date: dates[old_idx]}}]) + END) WHERE x IS NOT NULL] AS old_items, + collect( + apoc.map.fromValues([codelist_root.uid, {{value_node: new_val, change_date: new_date}}]) + ) AS new_items """ + # Single-pass term query: same strategy as codelist query. term_data_retrieval = f""" MATCH (codelist_root:CTCodelistRoot)-[:HAS_TERM]->(:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root)-[:{relationship_type}]-> - (old_term_ver_root)-[old_versions]->(old_term_ver_value) - WHERE old_versions.start_date < datetime($start_datetime) + (ver_root)-[ver]->(ver_value) + WHERE ver.start_date < datetime($end_datetime) {term_filter_statements} - WITH term_root, old_versions, old_term_ver_value - ORDER BY old_versions.start_date DESC - WITH term_root, - collect(old_term_ver_value)[0] AS old_term_ver_value, - collect(old_versions.start_date)[0] AS latest_date, - collect(old_versions) AS old_versions_collection - WITH term_root, - old_term_ver_value, - latest_date, - head([x IN old_versions_collection WHERE x.start_date = latest_date | x ]) AS latest_version - WITH collect(apoc.map.fromValues([term_root.uid, {{value_node:old_term_ver_value, codelists:[ - (term_root)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)<-[:HAS_TERM]-(codelist_root) | codelist_root.uid], change_date: latest_date}}])) AS old_items - - MATCH (codelist_root:CTCodelistRoot)-[:HAS_TERM]->(:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root)-[:{relationship_type}]-> - (new_term_ver_root)-[new_versions]->(new_term_ver_value) - WHERE new_versions.start_date < datetime($end_datetime) - {term_filter_statements} - WITH old_items, term_root, new_versions, new_term_ver_value - ORDER BY new_versions.start_date DESC - WITH old_items, - term_root, - collect(new_term_ver_value)[0] AS new_term_ver_value, - collect(new_versions.start_date)[0] AS latest_date, - collect(new_versions) AS new_versions_collection - WITH old_items, - term_root, - new_term_ver_value, - latest_date, - head([x IN new_versions_collection WHERE x.start_date = latest_date | x ]) AS latest_version - WITH old_items, - collect(apoc.map.fromValues([term_root.uid, {{value_node:new_term_ver_value, codelists:[ - (term_root)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)<-[:HAS_TERM]-(codelist_root) | codelist_root.uid], change_date: latest_date}}])) AS new_items + WITH term_root, ver_value, ver.start_date AS ver_date + ORDER BY ver_date DESC + WITH term_root, + collect(ver_value) AS vals, + collect(ver_date) AS dates + WITH term_root, vals, dates, + vals[0] AS new_val, dates[0] AS new_date, + head([i IN range(0, size(dates)-1) WHERE dates[i] < datetime($start_datetime)]) AS old_idx + WITH + [x IN collect(CASE WHEN old_idx IS NOT NULL THEN + apoc.map.fromValues([term_root.uid, {{value_node: vals[old_idx], codelists:[ + (term_root)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)<-[:HAS_TERM]-(cl) | cl.uid], change_date: dates[old_idx]}}]) + END) WHERE x IS NOT NULL] AS old_items, + collect( + apoc.map.fromValues([term_root.uid, {{value_node: new_val, codelists:[ + (term_root)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)<-[:HAS_TERM]-(cl) | cl.uid], change_date: new_date}}]) + ) AS new_items """ term_return_clause = """ @@ -153,16 +124,16 @@ def get_ct_catalogues_changes( codelist_ret, _ = db.cypher_query(complete_codelist_query, query_params) output["new_codelists"] = ( sorted(codelist_ret[0][0], key=lambda ct_codelist: ct_codelist["change_date"]) - if len(codelist_ret) > 0 + if codelist_ret else [] ) output["deleted_codelists"] = ( sorted(codelist_ret[0][1], key=lambda ct_codelist: ct_codelist["change_date"]) - if len(codelist_ret) > 0 + if codelist_ret else [] ) - output["updated_codelists"] = codelist_ret[0][2] if len(codelist_ret) > 0 else [] - all_codelists_in_package = codelist_ret[0][3] if len(codelist_ret) > 0 else {} + output["updated_codelists"] = codelist_ret[0][2] if codelist_ret else [] + all_codelists_in_package = codelist_ret[0][3] if codelist_ret else {} # terms query complete_term_query = " ".join( @@ -171,28 +142,24 @@ def get_ct_catalogues_changes( terms_ret, _ = db.cypher_query(complete_term_query, query_params) output["new_terms"] = ( sorted(terms_ret[0][0], key=lambda ct_term: ct_term["change_date"]) - if len(terms_ret) > 0 + if terms_ret else [] ) output["deleted_terms"] = ( sorted(terms_ret[0][1], key=lambda ct_term: ct_term["change_date"]) - if len(terms_ret) > 0 + if terms_ret else [] ) output["updated_terms"] = ( sorted(terms_ret[0][2], key=lambda ct_term: ct_term["change_date"]) - if len(terms_ret) > 0 + if terms_ret else [] ) - # The following section adds codelists that contains some terms from the - # * new_terms - # * deleted_terms - # * updated_terms - # columns to the 'updated_codelists' column to mark given codelist as updated. - updated_codelist_uids = [ + # Add codelists containing changed terms to 'updated_codelists'. + updated_codelist_uids: set[str] = { codelist["uid"] for codelist in output["updated_codelists"] - ] + } for terms in [ output["new_terms"], output["deleted_terms"], @@ -200,15 +167,11 @@ def get_ct_catalogues_changes( ]: for term in terms: for codelist in term["codelists"]: - # we only want to add a codelist to the 'updated_codelists' column if given codelist - # is not already there and this codelist is from the package that we are currently comparing if ( codelist not in updated_codelist_uids and codelist in all_codelists_in_package ): - # updated_codelists_uids is a helper list to track all uids - # of codelists in the package that is being compared - updated_codelist_uids.append(codelist) + updated_codelist_uids.add(codelist) output["updated_codelists"].append( { "uid": codelist, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/admin.py b/clinical-mdr-api/clinical_mdr_api/routers/admin.py index 4de4196d..641d7b11 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/admin.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/admin.py @@ -69,6 +69,14 @@ def clear_caches() -> list[dict[Any, Any]]: if cache_store is not None: cache_store.clear() + # Clear shared service-level caches + from clinical_mdr_api.services.studies.study_activity_selection_base import ( + StudyActivitySelectionBaseService, + ) + + with StudyActivitySelectionBaseService._shared_terms_date_cache_lock: + StudyActivitySelectionBaseService._shared_terms_date_cache.clear() + return get_caches() diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/activities/activity_instances.py b/clinical-mdr-api/clinical_mdr_api/routers/concepts/activities/activity_instances.py index 6ae289a9..f7deb113 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/activities/activity_instances.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/concepts/activities/activity_instances.py @@ -873,25 +873,25 @@ def approve( @router.delete( - "/{activity_instance_uid}/attributes/activations", + "/{activity_instance_uid}/activations", dependencies=[security, rbac.LIBRARY_WRITE], - summary=" Inactivate final version of an activity instance attributes", + summary="Inactivate final version of an activity instance (attributes and groupings)", description=""" State before: - - uid must exist and activity instance must be in status Final. - + - uid must exist and both the activity instance attributes and groupings must be in status Final. + Business logic: - - The latest 'Final' version will remain the same as before. - - The status will be automatically set to 'Retired'. + - The latest 'Final' version will remain the same as before (for both attributes and groupings). + - The status will be automatically set to 'Retired' for both attributes and groupings. - The 'change_description' property will be set automatically. - The 'version' property will remain the same as before. - + State after: - - Activity instance changed status to Retired. - - Audit trail entry must be made with action of inactivating to retired version. - + - Activity instance attributes and groupings changed status to Retired. + - Audit trail entries must be made with action of inactivating to retired version. + Possible errors: - - Invalid uid or status not Final. + - Invalid uid, or attributes/groupings status not Final. """, status_code=200, responses={ @@ -900,7 +900,8 @@ def approve( 400: { "model": ErrorResponse, "description": "Forbidden - Reasons include e.g.: \n" - "- The activity instance is not in final status.", + "- The activity instance attributes are not in final status.\n" + "- The activity instance groupings are not in final status.", }, 404: { "model": ErrorResponse, @@ -916,25 +917,25 @@ def inactivate( @router.post( - "/{activity_instance_uid}/attributes/activations", + "/{activity_instance_uid}/activations", dependencies=[security, rbac.LIBRARY_WRITE], - summary="Reactivate retired version of an activity instance attributes", + summary="Reactivate retired version of an activity instance (attributes and groupings)", description=""" State before: - - uid must exist and activity instance must be in status Retired. - + - uid must exist and both the activity instance attributes and groupings must be in status Retired. + Business logic: - - The latest 'Retired' version will remain the same as before. - - The status will be automatically set to 'Final'. + - The latest 'Retired' version will remain the same as before (for both attributes and groupings). + - The status will be automatically set to 'Final' for both attributes and groupings. - The 'change_description' property will be set automatically. - The 'version' property will remain the same as before. State after: - - Activity instance changed status to Final. - - An audit trail entry must be made with action of reactivating to final version. - + - Activity instance attributes and groupings changed status to Final. + - Audit trail entries must be made with action of reactivating to final version. + Possible errors: - - Invalid uid or status not Retired. + - Invalid uid, or attributes/groupings status not Retired. """, status_code=200, responses={ @@ -943,7 +944,8 @@ def inactivate( 400: { "model": ErrorResponse, "description": "Forbidden - Reasons include e.g.: \n" - "- The activity instance is not in retired status.", + "- The activity instance attributes are not in retired status.\n" + "- The activity instance groupings are not in retired status.", }, 404: { "model": ErrorResponse, @@ -1128,92 +1130,6 @@ def approve_groupings( return activity_instance_service.approve(uid=activity_instance_uid) -@router.delete( - "/{activity_instance_uid}/groupings/activations", - dependencies=[security, rbac.LIBRARY_WRITE], - summary=" Inactivate final version of an activity instance groupings", - description=""" -State before: - - uid must exist and activity instance must be in status Final. - -Business logic: - - The latest 'Final' version will remain the same as before. - - The status will be automatically set to 'Retired'. - - The 'change_description' property will be set automatically. - - The 'version' property will remain the same as before. - -State after: - - Activity instance changed status to Retired. - - Audit trail entry must be made with action of inactivating to retired version. - -Possible errors: - - Invalid uid or status not Final. - """, - status_code=200, - responses={ - 403: _generic_descriptions.ERROR_403, - 200: {"description": "OK."}, - 400: { - "model": ErrorResponse, - "description": "Forbidden - Reasons include e.g.: \n" - "- The activity instance is not in final status.", - }, - 404: { - "model": ErrorResponse, - "description": "Not Found - The activity instance with the specified 'activity_instance_uid' could not be found.", - }, - }, -) -def inactivate_groupings( - activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> ActivityInstanceGroupings: - activity_instance_service = ActivityInstanceGroupingsService() - return activity_instance_service.inactivate_final(uid=activity_instance_uid) - - -@router.post( - "/{activity_instance_uid}/groupings/activations", - dependencies=[security, rbac.LIBRARY_WRITE], - summary="Reactivate retired version of an activity instance groupings", - description=""" -State before: - - uid must exist and activity instance must be in status Retired. - -Business logic: - - The latest 'Retired' version will remain the same as before. - - The status will be automatically set to 'Final'. - - The 'change_description' property will be set automatically. - - The 'version' property will remain the same as before. - -State after: - - Activity instance changed status to Final. - - An audit trail entry must be made with action of reactivating to final version. - -Possible errors: - - Invalid uid or status not Retired. - """, - status_code=200, - responses={ - 403: _generic_descriptions.ERROR_403, - 200: {"description": "OK."}, - 400: { - "model": ErrorResponse, - "description": "Forbidden - Reasons include e.g.: \n" - "- The activity instance is not in retired status.", - }, - 404: { - "model": ErrorResponse, - "description": "Not Found - The activity instance with the specified 'activity_instance_uid' could not be found.", - }, - }, -) -def reactivate_groupings( - activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> ActivityInstanceGroupings: - activity_instance_service = ActivityInstanceGroupingsService() - return activity_instance_service.reactivate_retired(uid=activity_instance_uid) - - @router.delete( "/{activity_instance_uid}", dependencies=[security, rbac.LIBRARY_WRITE], diff --git a/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/ct_codelists.py b/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/ct_codelists.py index f9698091..bacfc09b 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/ct_codelists.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/ct_codelists.py @@ -16,6 +16,7 @@ CTCodelistPairedInput, CTCodelistTerm, CTCodelistTermInput, + CTPairedCodelistCreateInput, CTPairedCodelistTerm, ) from clinical_mdr_api.models.utils import CustomPage @@ -384,6 +385,41 @@ def update_paired_codelist( return results +@router.post( + "/paired-codelists", + dependencies=[security, rbac.LIBRARY_WRITE], + summary="Creates a new set of paired codelists.", + description="""Creates two codelists (one for names, one for codes) and links them as paired codelists. +Each codelist gets its own name, submission_value, nci_preferred_name, definition, and sponsor_preferred_name +via the name_information and code_information fields respectively. +""", + status_code=201, + responses={ + 403: _generic_descriptions.ERROR_403, + 201: { + "description": "Created - The paired codelists were successfully created." + }, + 400: { + "model": ErrorResponse, + "description": "Forbidden - Reasons include e.g.: \n" + "- The catalogue doesn't exist.\n" + "- The library doesn't exist.\n" + "- The library doesn't allow to add new items.\n", + }, + }, +) +def create_paired_codelists( + paired_codelist_input: Annotated[ + CTPairedCodelistCreateInput, + Body( + description="Properties to create a set of paired codelists (names and codes).", + ), + ], +) -> CTCodelistPaired: + ct_codelist_service = CTCodelistService() + return ct_codelist_service.create_paired_codelists(paired_codelist_input) + + @router.get( "/paired-codelists/{codelist_uid}/terms", dependencies=[security, rbac.LIBRARY_READ], diff --git a/clinical-mdr-api/clinical_mdr_api/routers/ddf/study_definitions.py b/clinical-mdr-api/clinical_mdr_api/routers/ddf/study_definitions.py index d0a571cb..3733387c 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/ddf/study_definitions.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/ddf/study_definitions.py @@ -101,8 +101,17 @@ def get_study_m11_protocol( study_uid, study_value_version=None ) + with open( + str(M11_TEMPLATES_DIR_PATH) + + "/ICH_Step4_M11_Final_TechnicalSpecification_2025_1119.json", + "r", + encoding="utf-8", + ) as f: + specification = f.read() + with trace_block("context_creation", "Creating context for M11 template rendering"): context = { + "specification_20251119": specification, "study_id": study_uid, "study_indications": ddf_study.versions[0].studyDesigns[0].indications, "study_interventions": ddf_study.versions[0].studyInterventions[0], diff --git a/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py b/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py index 78eba137..8f1e2377 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py @@ -12,6 +12,7 @@ StudyCopyComponentEnum, StudyStatus, ) +from clinical_mdr_api.models.complexity_score import ComplexityScoreDetails from clinical_mdr_api.models.study_selections.study import ( CompactStudy, LockReleaseInput, @@ -24,7 +25,9 @@ StudyPatchRequestJsonModel, StudyPreferredTimeUnit, StudyPreferredTimeUnitInput, + StudyProtocolHeaderVersion, StudyProtocolTitle, + StudySelectionContainmentResult, StudySimple, StudySoaPreferences, StudySoaPreferencesInput, @@ -35,11 +38,14 @@ StudySubpartAuditTrail, StudySubpartCreateInput, StudySubpartReorderingInput, + StudyTemplate, + StudyTemplateInput, + StudyTemplatePatchInput, StudyVersionHistory, UnlockInput, ) from clinical_mdr_api.models.study_selections.study_pharma_cm import StudyPharmaCM -from clinical_mdr_api.models.utils import CustomPage +from clinical_mdr_api.models.utils import CustomPage, EditInputModel from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions, decorators from clinical_mdr_api.routers._generic_descriptions import ( @@ -62,6 +68,10 @@ router = APIRouter() StudyUID = Path(description="The unique id of the study.") +TargetStudyUID = Path( + description="The unique id of the target study (e.g. a clone). " + "Only selection labels that appear on this study are included in the comparison." +) @router.get( @@ -227,6 +237,7 @@ def get_all( "acronym", "number", "title", + "description", "subpart_id", "subpart_acronym", "clinical_programme=clinical_programme_name", @@ -318,6 +329,92 @@ def get_studies_list( ) +@router.get( + "/template", + dependencies=[security, rbac.STUDY_READ], + summary="Returns the active study template, if any.", + status_code=200, + responses={403: _generic_descriptions.ERROR_403}, +) +def get_study_template() -> StudyTemplate | None: + return StudyService().get_study_template() + + +@router.post( + "/template", + dependencies=[security, rbac.STUDY_WRITE], + summary="Creates the study template configuration.", + status_code=201, + responses={ + 403: _generic_descriptions.ERROR_403, + 400: _generic_descriptions.ERROR_400, + }, +) +def create_study_template( + study_template_input: Annotated[ + StudyTemplateInput, Body(description="Study template target study reference.") + ], +) -> StudyTemplate: + return StudyService().create_study_template(study_template_input) + + +@router.patch( + "/template", + dependencies=[security, rbac.STUDY_WRITE], + summary="Updates the study template with a new version.", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 400: _generic_descriptions.ERROR_400, + 404: _generic_descriptions.ERROR_404, + }, +) +def patch_study_template( + patch_input: Annotated[ + StudyTemplatePatchInput, Body(description="Updated study template target.") + ], +) -> StudyTemplate: + return StudyService().patch_study_template(patch_input) + + +@router.delete( + "/template/activations", + dependencies=[security, rbac.STUDY_WRITE], + summary="Retires the current study template.", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def retire_study_template( + _: Annotated[ + EditInputModel | None, + Body(description="Optional change description payload.", embed=False), + ] = None, +) -> StudyTemplate: + return StudyService().retire_study_template() + + +@router.post( + "/template/activations", + dependencies=[security, rbac.STUDY_WRITE], + summary="Reactivates a retired study template.", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def reactivate_study_template( + _: Annotated[ + EditInputModel | None, + Body(description="Optional change description payload.", embed=False), + ] = None, +) -> StudyTemplate: + return StudyService().reactivate_study_template() + + @router.get( "/structure-overview", dependencies=[security, rbac.STUDY_READ], @@ -690,6 +787,40 @@ def get_structure_statistics( return study_service.get_study_structure_statistics(study_uid) +@router.get( + "/{study_uid}/study-selection-containment/{target_study_uid}", + dependencies=[security, rbac.STUDY_READ], + summary=( + "Whether target study selection statistics are contained in the source study." + ), + description=( + "Compares selection counts (and distinct CT term roots) for each concrete " + "selection label that appears on **target_study_uid** against **study_uid** " + "(source). Returns whether target counts are <= source for every such label, " + "plus per-label figures. **StudySoAFootnote** is excluded (conditional clone " + "rules make footnote counts incomparable)." + ), + response_model_exclude_unset=True, + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: { + "model": ErrorResponse, + "description": "Not Found - source or target study uid.", + }, + }, +) +def get_study_selection_containment( + study_uid: Annotated[str, StudyUID], + target_study_uid: Annotated[str, TargetStudyUID], +) -> StudySelectionContainmentResult: + study_service = StudyService() + return study_service.get_study_selection_containment( + source_study_uid=study_uid, + target_study_uid=target_study_uid, + ) + + @router.get( "/{study_uid}/pharma-cm", dependencies=[security, rbac.STUDY_READ], @@ -869,7 +1000,7 @@ def get_snapshot_history( @router.get( "/{study_uid}/protocol-header-versions", dependencies=[security, rbac.STUDY_READ], - summary="Returns the latest available protocol header version or the one associated with specified study value version.", + summary="Returns the latest available protocol header version and whether the study contains a 'Final Protocol' locked version.", response_model_exclude_unset=True, status_code=200, responses={ @@ -881,7 +1012,7 @@ def get_snapshot_history( ) def get_protocol_header_version( study_uid: Annotated[str, StudyUID], -) -> str | None: +) -> StudyProtocolHeaderVersion: return StudyService().get_protocol_header_version(study_uid=study_uid) @@ -942,10 +1073,24 @@ def get_study_subpart_audit_trail( study_value_version: Annotated[ str | None, _generic_descriptions.STUDY_VALUE_VERSION_QUERY ] = None, -) -> list[StudySubpartAuditTrail]: + page_number: _generic_descriptions.PAGE_NUMBER_QUERY = settings.default_page_number, + page_size: _generic_descriptions.PAGE_SIZE_QUERY = settings.default_page_size, + total_count: _generic_descriptions.TOTAL_COUNT_QUERY = False, +) -> CustomPage[StudySubpartAuditTrail]: study_service = StudyService() - return study_service.get_subpart_audit_trail_by_uid( - uid=study_uid, is_subpart=is_subpart, study_value_version=study_value_version + result = study_service.get_subpart_audit_trail_by_uid( + uid=study_uid, + is_subpart=is_subpart, + study_value_version=study_value_version, + page_number=page_number, + page_size=page_size, + total_count=total_count, + ) + return CustomPage.create( + items=result.items, + total=result.total, + page=page_number, + size=page_size, ) @@ -1387,3 +1532,35 @@ def get_complexity_score( study_uid=study_uid, study_version_number=study_version_number, ) + + +@router.get( + "/{study_uid}/complexity-score-details", + dependencies=[security, rbac.STUDY_READ], + summary="Get detailed study complexity score breakdown", + response_model=ComplexityScoreDetails, + response_model_by_alias=False, + status_code=200, + responses={ + 404: { + "model": ErrorResponse, + "description": "Not Found - study with the specified 'study_uid' doesn't exist", + }, + }, +) +def get_complexity_score_details( + study_uid: Annotated[str, StudyUID], + study_version_number: Annotated[ + str | None, + Query( + description="Study Version Number", + openapi_examples={"2.1": {"value": "2.1"}}, + alias="study_value_version", + ), + ] = None, +) -> ComplexityScoreDetails: + service = ComplexityScoreService() + return service.get_complexity_score_details( + study_uid=study_uid, + study_version_number=study_version_number, + ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/studies/study_disease_milestones.py b/clinical-mdr-api/clinical_mdr_api/routers/studies/study_disease_milestones.py index 11f7c8c1..3c388883 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/studies/study_disease_milestones.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/studies/study_disease_milestones.py @@ -345,16 +345,17 @@ def post_new_disease_milestone_create( }, ) @decorators.validate_if_study_is_not_locked("study_uid") -# pylint: disable=unused-argument def delete_study_disease_milestone( - study_uid: Annotated[str, studyUID], # TODO: Use this argument! + study_uid: Annotated[str, studyUID], study_disease_milestone_uid: Annotated[ str, study_disease_milestone_uid_description ], ): service = StudyDiseaseMilestoneService() - service.delete(study_disease_milestone_uid=study_disease_milestone_uid) + service.delete( + study_uid=study_uid, study_disease_milestone_uid=study_disease_milestone_uid + ) @router.patch( @@ -398,9 +399,8 @@ def delete_study_disease_milestone( }, ) @decorators.validate_if_study_is_not_locked("study_uid") -# pylint: disable=unused-argument def patch_reorder( - study_uid: Annotated[str, studyUID], # TODO: Use this argument! + study_uid: Annotated[str, studyUID], study_disease_milestone_uid: Annotated[ str, study_disease_milestone_uid_description ], @@ -411,6 +411,7 @@ def patch_reorder( ) -> study_disease_milestone.StudyDiseaseMilestone: service = StudyDiseaseMilestoneService() return service.reorder( + study_uid=study_uid, study_disease_milestone_uid=study_disease_milestone_uid, new_order=new_order_input.new_order, ) @@ -461,6 +462,7 @@ def patch_update_disease_milestone( ) -> study_disease_milestone.StudyDiseaseMilestone: service = StudyDiseaseMilestoneService() return service.edit( + study_uid=study_uid, study_disease_milestone_uid=study_disease_milestone_uid, study_disease_milestone_input=selection, ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py b/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py index 77c03725..bd711ff0 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py @@ -156,6 +156,9 @@ from clinical_mdr_api.domain_repositories.standard_data_models.dataset_variable_repository import ( DatasetVariableRepository, ) +from clinical_mdr_api.domain_repositories.studies.study_template_repository import ( + StudyTemplateRepository, +) from clinical_mdr_api.domain_repositories.study_definitions.study_definition_repository import ( StudyDefinitionRepository, ) @@ -819,6 +822,12 @@ def study_design_class_repository(self) -> StudyDesignClassRepository: def study_source_variable_repository(self) -> StudySourceVariableRepository: return self.get_repository_instance(StudySourceVariableRepository) + @property + def study_template_repository(self) -> StudyTemplateRepository: + return self.get_repository_instance( + StudyTemplateRepository, user=self._author_id + ) + @property def user_repository(self) -> UserRepository: return self.get_repository_instance(UserRepository) diff --git a/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_item_class.py b/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_item_class.py index 720d27a5..a968e2a6 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_item_class.py +++ b/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_item_class.py @@ -37,6 +37,7 @@ ) from clinical_mdr_api.services.controlled_terminologies.ct_codelist import ( CTCodelistService, + _paired_codelist_info_from, ) from common.exceptions import NotFoundException from common.utils import version_string_to_tuple @@ -265,8 +266,7 @@ def get_codelists_of_activity_item_class( CTCodelistNameAndAttributes.from_ct_codelist_ar( name, attrs, - paired_codes_codelist_uid=paired.paired_codes_codelist_uid, - paired_names_codelist_uid=paired.paired_names_codelist_uid, + paired_codelist=_paired_codelist_info_from(paired), ), codelists_and_terms[attrs.uid], ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_instance_service.py b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_instance_service.py index 146d967c..4bcf17c6 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_instance_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_instance_service.py @@ -1,6 +1,8 @@ import datetime from typing import Any +from neomodel import db + from clinical_mdr_api.domain_repositories.concepts.activities.activity_instance_repository import ( ActivityInstanceAttributesRepository, ActivityInstanceGroupingsRepository, @@ -20,7 +22,10 @@ CTCodelistItem, CTTermItem, ) -from clinical_mdr_api.domains.versioned_object_aggregate import LibraryVO +from clinical_mdr_api.domains.versioned_object_aggregate import ( + LibraryItemStatus, + LibraryVO, +) from clinical_mdr_api.models.concepts.activities.activity_instance import ( ActivityInstance, ActivityInstanceAttributes, @@ -38,6 +43,7 @@ CompactUnitDefinition, ) from clinical_mdr_api.models.utils import BaseModel +from clinical_mdr_api.services._utils import ensure_transaction from clinical_mdr_api.services.concepts import constants from clinical_mdr_api.services.concepts.concept_generic_service import ( ConceptGenericService, @@ -543,6 +549,100 @@ def _edit_aggregate( ) return item + @ensure_transaction(db) + def inactivate_final( + self, + uid: str, + cascade_inactivate: bool = False, + force_new_value_node: bool = False, + ) -> BaseModel: + """ + Inactivates both the attributes and the groupings tracks of an + activity instance. Both tracks must currently be in Final status. + """ + attributes_item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + + groupings_repository = self._repos.activity_instance_groupings_repository + groupings_item = groupings_repository.find_by_uid_2(uid=uid, for_update=True) + NotFoundException.raise_if( + groupings_item is None, + msg=(f"Activity Instance Groupings with UID '{uid}' doesn't exist."), + ) + + BusinessLogicException.raise_if( + attributes_item.item_metadata.status != LibraryItemStatus.FINAL, + msg=( + "Cannot inactivate: activity instance attributes are not in" + " Final status." + ), + ) + BusinessLogicException.raise_if( + groupings_item.item_metadata.status != LibraryItemStatus.FINAL, + msg=( + "Cannot inactivate: activity instance groupings are not in" + " Final status." + ), + ) + + attributes_item.inactivate( + author_id=self.author_id, force_new_value_node=force_new_value_node + ) + groupings_item.inactivate( + author_id=self.author_id, force_new_value_node=force_new_value_node + ) + self.repository.save(attributes_item, force_new_value_node=force_new_value_node) + groupings_repository.save( + groupings_item, force_new_value_node=force_new_value_node + ) + return self._transform_aggregate_root_to_pydantic_model(attributes_item) + + @ensure_transaction(db) + def reactivate_retired( + self, + uid: str, + cascade_reactivate: bool = False, + force_new_value_node: bool = False, + ) -> BaseModel: + """ + Reactivates both the attributes and the groupings tracks of an + activity instance. Both tracks must currently be in Retired status. + """ + attributes_item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + + groupings_repository = self._repos.activity_instance_groupings_repository + groupings_item = groupings_repository.find_by_uid_2(uid=uid, for_update=True) + NotFoundException.raise_if( + groupings_item is None, + msg=(f"Activity Instance Groupings with UID '{uid}' doesn't exist."), + ) + + BusinessLogicException.raise_if( + attributes_item.item_metadata.status != LibraryItemStatus.RETIRED, + msg=( + "Cannot reactivate: activity instance attributes are not in" + " Retired status." + ), + ) + BusinessLogicException.raise_if( + groupings_item.item_metadata.status != LibraryItemStatus.RETIRED, + msg=( + "Cannot reactivate: activity instance groupings are not in" + " Retired status." + ), + ) + + attributes_item.reactivate( + author_id=self.author_id, force_new_value_node=force_new_value_node + ) + groupings_item.reactivate( + author_id=self.author_id, force_new_value_node=force_new_value_node + ) + self.repository.save(attributes_item, force_new_value_node=force_new_value_node) + groupings_repository.save( + groupings_item, force_new_value_node=force_new_value_node + ) + return self._transform_aggregate_root_to_pydantic_model(attributes_item) + class ActivityInstanceGroupingsService( ConceptGenericService[ActivityInstanceGroupingsAR] diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_service.py b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_service.py index f636a438..7c292197 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_service.py @@ -111,6 +111,7 @@ def _to_activity_grouping_vo( def _to_activity_grouping_vos( self, activity_groupings: Iterable[ActivityGrouping | ActivityGroupingVO], + existing_groupings: list[ActivityGroupingVO] | None = None, ) -> list[ActivityGroupingVO]: acg_and_acsg_by_uid: tuple[Any, ...] = ( self._get_activity_groups_and_subgroups_from_activity_groupings( @@ -120,8 +121,23 @@ def _to_activity_grouping_vos( activity_groups_by_uid: dict[Any, Any] = acg_and_acsg_by_uid[0] activity_subgroups_by_uid: dict[Any, Any] = acg_and_acsg_by_uid[1] + # Build set of existing (group, subgroup) pairs to skip validation for carried-over groupings + existing_pairs: set[tuple[str, str]] = set() + if existing_groupings: + existing_pairs = { + (g.activity_group_uid, g.activity_subgroup_uid) + for g in existing_groupings + } + # Validate that all activity groups and subgroups are in Final status for activity_grouping in activity_groupings: + # Skip validation for groupings carried over from the previous version + if ( + activity_grouping.activity_group_uid, + activity_grouping.activity_subgroup_uid, + ) in existing_pairs: + continue + # Check activity group status if activity_grouping.activity_group_uid in activity_groups_by_uid: activity_group = activity_groups_by_uid[ @@ -212,7 +228,10 @@ def _edit_aggregate( if "activity_groupings" in concept_edit_input.model_fields_set: # Use _to_activity_grouping_vos which includes validation activity_groupings = ( - self._to_activity_grouping_vos(concept_edit_input.activity_groupings) + self._to_activity_grouping_vos( + concept_edit_input.activity_groupings, + existing_groupings=item.concept_vo.activity_groupings, + ) if concept_edit_input.activity_groupings else [] ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/controlled_terminologies/ct_codelist.py b/clinical-mdr-api/clinical_mdr_api/services/controlled_terminologies/ct_codelist.py index a253ea0c..814833a0 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/controlled_terminologies/ct_codelist.py +++ b/clinical-mdr-api/clinical_mdr_api/services/controlled_terminologies/ct_codelist.py @@ -9,6 +9,7 @@ from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_attributes import ( CTCodelistAttributesAR, CTCodelistAttributesVO, + CTPairedCodelists, ) from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_name import ( CTCodelistNameAR, @@ -23,6 +24,8 @@ CTCodelistPaired, CTCodelistPairedInput, CTCodelistTerm, + CTPairedCodelistCreateInput, + CTPairedCodelistInfo, CTPairedCodelistTerm, ) from clinical_mdr_api.models.utils import GenericFilteringReturn @@ -46,6 +49,20 @@ _AggregateRootType = TypeVar("_AggregateRootType") +def _paired_codelist_info_from( + paired: CTPairedCodelists, +) -> CTPairedCodelistInfo | None: + if paired.paired_codes_codelist_uid: + return CTPairedCodelistInfo( + uid=paired.paired_codes_codelist_uid, name=paired.paired_codes_codelist_name + ) + if paired.paired_names_codelist_uid: + return CTPairedCodelistInfo( + uid=paired.paired_names_codelist_uid, name=paired.paired_names_codelist_name + ) + return None + + class CTCodelistService: _repos: MetaRepository author_id: str @@ -221,6 +238,67 @@ def create( paired_names_codelist_uid=codelist_input.paired_names_codelist_uid, ) + def create_paired_codelists( + self, + paired_codelist_input: CTPairedCodelistCreateInput, + ) -> CTCodelistPaired: + names_codelist_input = CTCodelistCreateInput( + catalogue_names=paired_codelist_input.catalogue_names, + name=paired_codelist_input.name_information.name, + submission_value=paired_codelist_input.name_information.submission_value, + nci_preferred_name=paired_codelist_input.name_information.nci_preferred_name, + definition=paired_codelist_input.name_information.definition, + extensible=paired_codelist_input.extensible, + is_ordinal=paired_codelist_input.is_ordinal, + codelist_type=paired_codelist_input.codelist_type, + sponsor_preferred_name=paired_codelist_input.name_information.sponsor_preferred_name, + template_parameter=paired_codelist_input.template_parameter, + parent_codelist_uid=paired_codelist_input.parent_codelist_uid, + terms=[], + library_name=paired_codelist_input.library_name, + ) + codes_codelist_input = CTCodelistCreateInput( + catalogue_names=paired_codelist_input.catalogue_names, + name=paired_codelist_input.code_information.name, + submission_value=paired_codelist_input.code_information.submission_value, + nci_preferred_name=paired_codelist_input.code_information.nci_preferred_name, + definition=paired_codelist_input.code_information.definition, + extensible=paired_codelist_input.extensible, + is_ordinal=paired_codelist_input.is_ordinal, + codelist_type=paired_codelist_input.codelist_type, + sponsor_preferred_name=paired_codelist_input.code_information.sponsor_preferred_name, + template_parameter=paired_codelist_input.template_parameter, + parent_codelist_uid=paired_codelist_input.parent_codelist_uid, + terms=[], + library_name=paired_codelist_input.library_name, + ) + + names_codelist = self.create(names_codelist_input) + codes_codelist = self.create(codes_codelist_input) + + self._repos.ct_codelist_aggregated_repository.merge_link_to_codes_codelist( + names_codelist.codelist_uid, + codes_codelist.codelist_uid, + ) + + attributes_service = CTCodelistAttributesService() + names_service = CTCodelistNameService() + + return CTCodelistPaired.from_ct_codelists( + paired_names_codelist_name=names_service.get_by_uid( + names_codelist.codelist_uid + ), + paired_names_codelist_attrs=attributes_service.get_by_uid( + names_codelist.codelist_uid + ), + paired_codes_codelist_name=names_service.get_by_uid( + codes_codelist.codelist_uid + ), + paired_codes_codelist_attrs=attributes_service.get_by_uid( + codes_codelist.codelist_uid + ), + ) + def get_all_codelists( self, catalogue_name: str | None = None, @@ -257,8 +335,7 @@ def get_all_codelists( CTCodelistNameAndAttributes.from_ct_codelist_ar( ct_codelist_name_ar, ct_codelist_attributes_ar, - paired_codes_codelist_uid=paired.paired_codes_codelist_uid, - paired_names_codelist_uid=paired.paired_names_codelist_uid, + paired_codelist=_paired_codelist_info_from(paired), ) for ct_codelist_name_ar, ct_codelist_attributes_ar, paired in all_aggregated_codelists ] @@ -378,8 +455,7 @@ def get_sub_codelists_that_have_given_terms( CTCodelistNameAndAttributes.from_ct_codelist_ar( ct_codelist_name_ar, ct_codelist_attributes_ar, - paired_codes_codelist_uid=paired.paired_codes_codelist_uid, - paired_names_codelist_uid=paired.paired_names_codelist_uid, + paired_codelist=_paired_codelist_info_from(paired), ) for ct_codelist_name_ar, ct_codelist_attributes_ar, paired in all_aggregated_sub_codelists if ct_codelist_attributes_ar.uid in uid_of_sub_codelist_with_terms @@ -456,20 +532,9 @@ def add_term( ) BusinessLogicException.raise_if( parent_codelist_uid - and len( - self._repos.ct_term_aggregated_repository.find_all_aggregated_result( - filter_by={ - "codelists.codelist_uid": { - "v": [parent_codelist_uid], - "op": "eq", - }, - "term_uid": {"v": [term_uid], "op": "eq"}, - } - )[ - 0 - ] - ) - <= 0, + and not self._repos.ct_codelist_attribute_repository.is_term_in_codelist( + term_uid=term_uid, codelist_uid=parent_codelist_uid + ), msg=f"Term with UID '{term_uid}' isn't in use by Parent Codelist with UID '{parent_codelist_uid}'.", ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/feature_flags.py b/clinical-mdr-api/clinical_mdr_api/services/feature_flags.py index 5c87634e..d79114a7 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/feature_flags.py +++ b/clinical-mdr-api/clinical_mdr_api/services/feature_flags.py @@ -37,6 +37,8 @@ def create_feature_flag( ) return self.repo.create_feature_flag( + section=feature_flag_input.section, + feature=feature_flag_input.feature, name=feature_flag_input.name, enabled=feature_flag_input.enabled, description=feature_flag_input.description, @@ -49,7 +51,7 @@ def update_feature_flag( feature_flag_patch_input: FeatureFlagPatchInput, ) -> FeatureFlag: return self.repo.update_feature_flag( - sn=sn, enabled=feature_flag_patch_input.enabled + sn=sn, **feature_flag_patch_input.model_dump(exclude_unset=True) ) @db.transaction diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py b/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py index b90b1c89..31049f07 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py @@ -7,6 +7,9 @@ Burden, BurdenIdInput, BurdenInput, + ComplexityScoreAssessment, + ComplexityScoreDetails, + ComplexityScoreVisit, ) from common import exceptions from common.utils import get_db_result_as_dict @@ -43,6 +46,15 @@ class VisitsSummary: non_physical_visits: int +@dataclass +class VisitTypeBurdens: + any: float + physical: float + virtual: float + initial: float + follow_up: float + + class ComplexityScoreService: @classmethod @@ -246,15 +258,95 @@ def calculate_site_complexity_score( total_score = ( initial_visit_burden + follow_up_visit_burden - + self.get_visits_site_burden(visits_summary, activity_burden_dict) - + self.get_activities_site_burden(soa, activity_burden_dict) + + self.get_total_visits_site_burden(visits_summary, activity_burden_dict) + + self.get_total_activities_site_burden(soa, activity_burden_dict) ) # Round total score to 3 decimal places return round(total_score, 3) + def get_complexity_score_details( + self, study_uid: str, study_version_number: str | None + ) -> ComplexityScoreDetails: + visits_summary = self.get_visits_summary(study_uid, study_version_number) + soa = self.get_soa(study_uid, study_version_number) + activity_burdens = self.get_activity_burdens() + activity_burden_dict = {ab.activity_subgroup_uid: ab for ab in activity_burdens} + + burdens = self.get_visit_types_site_burdens(activity_burden_dict) + + visits = [ + ComplexityScoreVisit( + type="initial", + count=1, + burden=burdens.initial, + ), + ComplexityScoreVisit( + type="follow_up", + count=1, + burden=burdens.follow_up, + ), + ComplexityScoreVisit( + type="physical", + count=visits_summary.physical_visits, + burden=round(burdens.any + burdens.physical, 3), + ), + ComplexityScoreVisit( + type="virtual", + count=visits_summary.non_physical_visits, + burden=round(burdens.any + burdens.virtual, 3), + ), + ] + + assessments = [] + for row in soa: + if not row.activity_subgroup_name: + continue + activity_burden = activity_burden_dict.get(row.activity_subgroup_uid) + visit_count = len(row.visits) + burden = round(activity_burden.site_burden, 3) if activity_burden else 0.0 + assessments.append( + ComplexityScoreAssessment( + type=row.activity_subgroup_name, + count=visit_count, + burden=burden, + ) + ) + + return ComplexityScoreDetails(visits=visits, assessments=assessments) + @classmethod - def get_visits_site_burden( + def get_visit_types_site_burdens(cls, activity_burden_dict) -> VisitTypeBurdens: + return VisitTypeBurdens( + any=( + activity_burden_dict.get(ANY_VISIT_BURDEN_ID).site_burden + if ANY_VISIT_BURDEN_ID in activity_burden_dict + else ANY_VISIT_BURDEN_DEFAULT_VAL + ), + virtual=( + activity_burden_dict.get(NON_PHYSICAL_VISIT_BURDEN_ID).site_burden + if NON_PHYSICAL_VISIT_BURDEN_ID in activity_burden_dict + else NON_PHYSICAL_VISIT_BURDEN_DEFAULT_VAL + ), + physical=( + activity_burden_dict.get(PHYSICAL_VISIT_BURDEN_ID).site_burden + if PHYSICAL_VISIT_BURDEN_ID in activity_burden_dict + else PHYSICAL_VISIT_BURDEN_DEFAULT_VAL + ), + initial=( + activity_burden_dict.get(ROUTINE_INITIAL_VISIT_BURDEN_ID).site_burden + if ROUTINE_INITIAL_VISIT_BURDEN_ID in activity_burden_dict + else ROUTINE_INITIAL_VISIT_BURDEN_DEFAULT_VAL + ), + follow_up=( + activity_burden_dict.get(ROUTINE_FOLLOW_UP_VISIT_BURDEN_ID).site_burden + if ROUTINE_FOLLOW_UP_VISIT_BURDEN_ID in activity_burden_dict + else ROUTINE_FOLLOW_UP_VISIT_BURDEN_DEFAULT_VAL + ), + ) + + @classmethod + def get_total_visits_site_burden( cls, visits_summary: VisitsSummary, activity_burden_dict ) -> float: # Total = @@ -262,33 +354,18 @@ def get_visits_site_burden( # + non_physical_visits * "simple or brief tel. visit [NC008]" burden = x * 0.60 # + physical_visits * "brief visit with vital signs [99211]" burden = x * 0.18 - burden_any_visit = ( - activity_burden_dict.get(ANY_VISIT_BURDEN_ID).site_burden - if ANY_VISIT_BURDEN_ID in activity_burden_dict - else ANY_VISIT_BURDEN_DEFAULT_VAL - ) - burden_non_physical = ( - activity_burden_dict.get(NON_PHYSICAL_VISIT_BURDEN_ID).site_burden - if NON_PHYSICAL_VISIT_BURDEN_ID in activity_burden_dict - else NON_PHYSICAL_VISIT_BURDEN_DEFAULT_VAL - ) - burden_physical = ( - activity_burden_dict.get(PHYSICAL_VISIT_BURDEN_ID).site_burden - if PHYSICAL_VISIT_BURDEN_ID in activity_burden_dict - else PHYSICAL_VISIT_BURDEN_DEFAULT_VAL - ) + burdens = cls.get_visit_types_site_burdens(activity_burden_dict) total_score = 0.0 - total_score += ( - visits_summary.non_physical_visits + visits_summary.physical_visits - ) * burden_any_visit - total_score += visits_summary.non_physical_visits * burden_non_physical - total_score += visits_summary.physical_visits * burden_physical + total_score += visits_summary.non_physical_visits * ( + burdens.any + burdens.virtual + ) + total_score += visits_summary.physical_visits * (burdens.any + burdens.physical) return total_score @classmethod - def get_activities_site_burden(cls, soa, activity_burden_dict) -> float: + def get_total_activities_site_burden(cls, soa, activity_burden_dict) -> float: # Activity burdens summed up over all visits # - all activities under the same activity subgroup will be added once per visit diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study.py index 379ada73..b87967b8 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study.py @@ -26,7 +26,7 @@ ) from clinical_mdr_api.domains.controlled_terminologies.ct_term_name import CTTermNameAR from clinical_mdr_api.domains.dictionaries.dictionary_term import DictionaryTermAR -from clinical_mdr_api.domains.enums import ValidationMode +from clinical_mdr_api.domains.enums import LibraryItemStatus, ValidationMode from clinical_mdr_api.domains.projects.project import ProjectAR from clinical_mdr_api.domains.study_definition_aggregates.registry_identifiers import ( RegistryIdentifiersVO, @@ -48,6 +48,10 @@ StudyPopulationVO, StudyStatus, ) +from clinical_mdr_api.domains.study_definition_aggregates.study_template import ( + StudyTemplateAR, + StudyTemplateValueVO, +) from clinical_mdr_api.domains.study_selections.study_selection_standard_version import ( StudyStandardVersionVO, ) @@ -69,7 +73,9 @@ StudyPatchRequestJsonModel, StudyPopulationJsonModel, StudyPreferredTimeUnit, + StudyProtocolHeaderVersion, StudyProtocolTitle, + StudySelectionContainmentResult, StudySimple, StudySoaPreferences, StudySoaPreferencesInput, @@ -77,9 +83,11 @@ StudySoaSplitInput, StudyStructureOverview, StudyStructureStatistics, - StudySubpartAuditTrail, StudySubpartCreateInput, StudySubpartReorderingInput, + StudyTemplate, + StudyTemplateInput, + StudyTemplatePatchInput, StudyVersionHistory, ) from clinical_mdr_api.models.utils import GenericFilteringReturn @@ -111,6 +119,8 @@ from common.telemetry import trace_calls from common.utils import booltostr +log = logging.getLogger(__name__) + def validate_if_study_is_not_locked( study_uid_arg_name: str, study_uid_arg_index: int = 0 @@ -417,6 +427,34 @@ def get_study_structure_statistics(self, uid: str) -> StudyStructureStatistics: return StudyStructureStatistics(**counters) + @ensure_transaction(db) + def get_study_selection_containment( + self, source_study_uid: str, target_study_uid: str + ) -> StudySelectionContainmentResult: + """ + Check whether **target** study selection statistics (labels taken from target) + are numerically contained in **source** (target counts <= source per label). + + ``StudySoAFootnote`` is excluded from the comparison (clone-dependent). + + Validates that both studies exist. + """ + if ( + self._repos.study_definition_repository.find_by_uid(source_study_uid) + is None + ): + raise NotFoundException("Study Definition", source_study_uid) + if ( + self._repos.study_definition_repository.find_by_uid(target_study_uid) + is None + ): + raise NotFoundException("Study Definition", target_study_uid) + raw = self._repos.study_definition_repository.get_study_selection_containment( + source_study_uid=source_study_uid, + target_study_uid=target_study_uid, + ) + return StudySelectionContainmentResult(**raw) + def _group_study_structure_overview_by_data(self, items): parsed_items: dict[tuple[Any, ...], StudyStructureOverview] = {} @@ -985,12 +1023,23 @@ def get_fields_audit_trail_by_uid( @db.transaction def get_subpart_audit_trail_by_uid( - self, uid: str, is_subpart: bool = False, study_value_version: str | None = None - ) -> list[StudySubpartAuditTrail]: + self, + uid: str, + is_subpart: bool = False, + study_value_version: str | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, + ) -> GenericFilteringReturn: try: return ( self._repos.study_definition_repository.get_subpart_audit_trail_by_uid( - uid, is_subpart, study_value_version=study_value_version + uid, + is_subpart, + study_value_version=study_value_version, + page_number=page_number, + page_size=page_size, + total_count=total_count, ) ) finally: @@ -1127,10 +1176,18 @@ def get_protocol_header_version( self, study_uid: str, study_value_version: str | None = None, - ) -> str | None: - return self._repos.study_definition_document_repository.get_latest_protocol_header_version( + ) -> StudyProtocolHeaderVersion: + protocol_header_version = self._repos.study_definition_document_repository.get_latest_protocol_header_version( study_uid=study_uid, study_value_version=study_value_version ) + has_final_protocol = self._repos.study_definition_document_repository.has_final_protocol_locked_version( + study_uid=study_uid, + study_value_version=study_value_version, + ) + return StudyProtocolHeaderVersion( + protocol_header_version=protocol_header_version, + has_final_protocol_locked_version=has_final_protocol, + ) def get_distinct_values_for_header( self, @@ -1309,6 +1366,42 @@ def clone_study( msg="Study Element should be also included", ) list_of_items_to_copy.append("StudyDesignCell") + if study_clone_input.copy_study_soa_group: + list_of_items_to_copy.append("StudySoAGroup") + if study_clone_input.copy_study_activity_group: + list_of_items_to_copy.append("StudyActivityGroup") + if study_clone_input.copy_study_activity_subgroup: + BusinessLogicException.raise_if( + study_clone_input.copy_study_activity_group is False, + msg="Study Activity Group should be also included", + ) + list_of_items_to_copy.append("StudyActivitySubGroup") + if study_clone_input.copy_study_activity: + BusinessLogicException.raise_if( + study_clone_input.copy_study_activity_group is False, + msg="Study Activity Group should be also included", + ) + BusinessLogicException.raise_if( + study_clone_input.copy_study_activity_subgroup is False, + msg="Study Activity Subgroup should be also included", + ) + list_of_items_to_copy.append("StudyActivity") + if study_clone_input.copy_study_activity_instance: + BusinessLogicException.raise_if( + study_clone_input.copy_study_activity is False, + msg="Study Activity should be also included", + ) + list_of_items_to_copy.append("StudyActivityInstance") + if study_clone_input.copy_study_activity_schedule: + BusinessLogicException.raise_if( + study_clone_input.copy_study_visit is False, + msg="Study Visit should be also included", + ) + BusinessLogicException.raise_if( + study_clone_input.copy_study_activity is False, + msg="Study Activity should be also included", + ) + list_of_items_to_copy.append("StudyActivitySchedule") BusinessLogicException.raise_if_not( study_clone_input.copy_study_arm or study_clone_input.copy_study_branch_arm @@ -1318,20 +1411,26 @@ def clone_study( or study_clone_input.copy_study_visit or study_clone_input.copy_study_visits_study_footnote or study_clone_input.copy_study_epochs_study_footnote - or study_clone_input.copy_study_design_matrix, + or study_clone_input.copy_study_design_matrix + or study_clone_input.copy_study_soa_group + or study_clone_input.copy_study_activity_group + or study_clone_input.copy_study_activity_subgroup + or study_clone_input.copy_study_activity + or study_clone_input.copy_study_activity_instance + or study_clone_input.copy_study_activity_schedule, msg="At least one item should be selected", ) # Validate source study integrity before cloning validation_mode = study_clone_input.validation_mode - logging.info( + log.info( "Running integrity checks for source study %s (mode: %s)", study_src_uid, validation_mode, ) execute_all_checks_for_study(study_src_uid, mode=validation_mode) - logging.info("Integrity checks passed for source study %s", study_src_uid) + log.info("Integrity checks passed for source study %s", study_src_uid) self._repos.study_definition_repository.copy_study_items( study_src_uid=study_src_uid, @@ -1340,14 +1439,60 @@ def clone_study( author_id=self.author_id, ) + containment = self.get_study_selection_containment( + source_study_uid=study_src_uid, + target_study_uid=study_created.uid, + ) + if not containment.target_contained_in_source: + failed_detail = "; ".join( + ( + f"{row.label} (target selections={row.target_selection_count}, " + f"source={row.source_selection_count}; " + f"target distinct CT term roots={row.target_distinct_ct_term_root_count}, " + f"source={row.source_distinct_ct_term_root_count})" + ) + for row in containment.per_label + if not row.label_contained + ) + containment_msg = ( + "Cloned study selection counts are not contained in the source study " + "for one or more labels (StudySoAFootnote excluded). " + f"{failed_detail}" + ) + if validation_mode == ValidationMode.STRICT: + log.error( + "Study selection containment failed after clone (strict): " + "source=%s target=%s. %s", + study_src_uid, + study_created.uid, + failed_detail, + ) + raise BusinessLogicException(msg=containment_msg) + log.warning( + "Study selection containment check did not pass after clone " + "(warning mode; continuing): source=%s target=%s. %s", + study_src_uid, + study_created.uid, + containment_msg, + ) + else: + log.info( + "Study selection containment passed for clone (mode=%s): source=%s " + "target=%s (%d label(s) compared)", + validation_mode.value, + study_src_uid, + study_created.uid, + len(containment.labels_from_target), + ) + # Validate cloned study integrity after cloning - logging.info( + log.info( "Running integrity checks for cloned study %s (mode: %s)", study_created.uid, validation_mode, ) execute_all_checks_for_study(study_created.uid, mode=validation_mode) - logging.info("Integrity checks passed for cloned study %s", study_created.uid) + log.info("Integrity checks passed for cloned study %s", study_created.uid) return study_created @@ -2782,7 +2927,7 @@ def run_integrity_checks(self, study_uids: list[str] | None = None) -> tuple[ ValueError, AttributeError, ) as normalize_error: - logging.warning( + log.warning( "Error normalizing noncompliant_node_ids for check %s: %s. Raw data: %s", check_result.check_id, normalize_error, @@ -2804,7 +2949,7 @@ def run_integrity_checks(self, study_uids: list[str] | None = None) -> tuple[ ) except (ValueError, TypeError) as validation_error: # If validation fails, create a simplified result with error - logging.warning( + log.warning( "Error creating IntegrityCheckResult for check %s: %s", check_result.check_id, validation_error, @@ -2903,3 +3048,166 @@ def run_integrity_check_for_study( raise NotFoundException(f"Study with uid {study_uid} was not found.") return study_results[0] + + def ensure_study_integrity_after_mutation( + self, study_uid: str, *, context: str + ) -> None: + """ + Run study integrity checks after a mutation and log warning on failures. + + Args: + study_uid: UID of the mutated study. + context: Human-readable mutation context for log attribution. + """ + integrity = self.run_integrity_check_for_study(study_uid) + if not integrity.all_passed or integrity.error: + failed_check_ids = [c.check_id for c in integrity.checks if not c.passed] + log.warning( + "Study integrity check failed after %s: study_uid=%s " + "integrity_error=%s failed_check_ids=%s", + context, + study_uid, + integrity.error, + failed_check_ids, + ) + + @staticmethod + def _to_study_template_model(study_template_ar: StudyTemplateAR) -> StudyTemplate: + return StudyTemplate( + uid=study_template_ar.uid or "", + study_uid=study_template_ar.value.study_uid, + study_value_version=study_template_ar.value.study_value_version, + status=study_template_ar.item_metadata.status, + version=study_template_ar.item_metadata.version, + change_description=study_template_ar.item_metadata.change_description, + ) + + def _validate_study_template_target( + self, study_uid: str, study_value_version: str + ) -> None: + self.check_if_study_uid_and_version_exists( + study_uid=study_uid, study_value_version=study_value_version + ) + + def _get_single_study_template( + self, status: LibraryItemStatus | None = None + ) -> StudyTemplateAR | None: + items = list(self._repos.study_template_repository.find_all(status=status)) + BusinessLogicException.raise_if( + len(items) > 1, + msg="Only one Study Template configuration is allowed.", + ) + return items[0] if items else None + + @db.transaction + def get_study_template(self) -> StudyTemplate | None: + item = self._get_single_study_template() + if item is None or ( + item.item_metadata.status + not in [LibraryItemStatus.FINAL, LibraryItemStatus.RETIRED] + ): + return None + return self._to_study_template_model(item) + + @db.transaction + def create_study_template( + self, study_template_input: StudyTemplateInput + ) -> StudyTemplate: + self._validate_study_template_target( + study_uid=study_template_input.study_uid, + study_value_version=study_template_input.study_value_version, + ) + existing = self._get_single_study_template() + BusinessLogicException.raise_if( + existing is not None, + msg="Study Template configuration already exists. Use PATCH to update it.", + ) + + study_template_ar = StudyTemplateAR.from_input_values( + author_id=self.author_id, + generate_uid_callback=self._repos.study_template_repository.generate_uid_callback, + study_template_value=StudyTemplateValueVO.from_input_values( + study_uid=study_template_input.study_uid, + study_value_version=study_template_input.study_value_version, + ), + ) + study_template_ar.approve(self.author_id) + self._repos.study_template_repository.save(study_template_ar) + return self._to_study_template_model(study_template_ar) + + @db.transaction + def patch_study_template( + self, patch_input: StudyTemplatePatchInput + ) -> StudyTemplate: + study_uid_value = patch_input.study_uid.strip() + if not study_uid_value: + study_uid_value = "" + study_value_version_value = "" + else: + study_value_version_value = patch_input.study_value_version.strip() + + if study_uid_value: + self._validate_study_template_target( + study_uid=study_uid_value, + study_value_version=study_value_version_value, + ) + study_template_ar = self._get_single_study_template() + NotFoundException.raise_if( + study_template_ar is None, "Study Template configuration", "latest" + ) + study_template_ar = self._repos.study_template_repository.find_by_uid_2( + study_template_ar.uid, for_update=True + ) + NotFoundException.raise_if( + study_template_ar is None, "Study Template configuration", "latest" + ) + + if study_template_ar.item_metadata.status in [ + LibraryItemStatus.FINAL, + LibraryItemStatus.RETIRED, + ]: + study_template_ar.create_new_version(self.author_id) + + study_template_ar.edit_draft( + author_id=self.author_id, + change_description=patch_input.change_description, + new_study_template_value=StudyTemplateValueVO.from_input_values( + study_uid=study_uid_value, + study_value_version=study_value_version_value, + ), + ) + study_template_ar.approve(self.author_id) + self._repos.study_template_repository.save(study_template_ar) + return self._to_study_template_model(study_template_ar) + + @db.transaction + def retire_study_template(self) -> StudyTemplate: + study_template_ar = self._get_single_study_template() + NotFoundException.raise_if( + study_template_ar is None, "Study Template configuration", "latest" + ) + study_template_ar = self._repos.study_template_repository.find_by_uid_2( + study_template_ar.uid, for_update=True + ) + NotFoundException.raise_if( + study_template_ar is None, "Study Template configuration", "latest" + ) + study_template_ar.inactivate(self.author_id) + self._repos.study_template_repository.save(study_template_ar) + return self._to_study_template_model(study_template_ar) + + @db.transaction + def reactivate_study_template(self) -> StudyTemplate: + study_template_ar = self._get_single_study_template() + NotFoundException.raise_if( + study_template_ar is None, "Study Template configuration", "latest" + ) + study_template_ar = self._repos.study_template_repository.find_by_uid_2( + study_template_ar.uid, for_update=True + ) + NotFoundException.raise_if( + study_template_ar is None, "Study Template configuration", "latest" + ) + study_template_ar.reactivate(self.author_id) + self._repos.study_template_repository.save(study_template_ar) + return self._to_study_template_model(study_template_ar) diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instance_selection.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instance_selection.py index 422d21f1..80028227 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instance_selection.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instance_selection.py @@ -444,6 +444,43 @@ def _patch_prepare_new_value_object( origin_source_uid=request_object.origin_source_uid, ) + @ensure_transaction(db) + def patch_selection( + self, + study_uid: str, + study_selection_uid: str, + selection_update_input: StudySelectionActivityInstanceEditInput, + ): + super().patch_selection( + study_uid=study_uid, + study_selection_uid=study_selection_uid, + selection_update_input=selection_update_input, + ) + # Fetch the single updated VO directly (avoids loading the full aggregate). + return self._get_specific_selection_vo_as_response( + study_uid=study_uid, + study_selection_uid=study_selection_uid, + ) + + def _get_specific_selection_vo_as_response( + self, + study_uid: str, + study_selection_uid: str, + ) -> StudySelectionActivityInstance: + """Fetch a single fully-resolved VO and convert to response model.""" + vo = self._repos.study_activity_instance_repository.find_selection_vo_by_uid( + study_uid=study_uid, + study_selection_uid=study_selection_uid, + ) + if vo is None: + raise exceptions.NotFoundException( + msg=f"Study activity instance selection with UID '{study_selection_uid}' not found." + ) + return self._transform_from_vo_to_response_model( + study_uid=study_uid, + specific_selection=vo, + ) + def get_specific_selection( self, study_uid: str, diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py index 084bb13c..12f8e407 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py @@ -268,13 +268,22 @@ def _validate_no_study_wide_duplicate( def _update_aggregate( self, selection_aggregate: StudySelectionActivityAR, - previous_selection: StudySelectionActivityVO, updated_selection: StudySelectionActivityVO, - ): - self._validate_no_study_wide_duplicate( - study_uid=selection_aggregate.study_uid, - updated_selection=updated_selection, - ) + previous_selection: StudySelectionActivityVO | None = None, + ) -> StudySelectionActivityVO: + updated_vo: StudySelectionActivityVO | None = None + # Only re-validate uniqueness when fields that affect duplicate detection have actually changed + if ( + previous_selection.activity_name != updated_selection.activity_name + or previous_selection.activity_subgroup_uid + != updated_selection.activity_subgroup_uid + or previous_selection.activity_group_uid + != updated_selection.activity_group_uid + ): + self._validate_no_study_wide_duplicate( + study_uid=selection_aggregate.study_uid, + updated_selection=updated_selection, + ) if ( previous_selection.study_activity_subgroup_uid != updated_selection.study_activity_subgroup_uid @@ -284,14 +293,28 @@ def _update_aggregate( and previous_selection.study_soa_group_uid != updated_selection.study_soa_group_uid ): - new_selection_aggregate = self.repository.find_by_study( - study_uid=selection_aggregate.study_uid, - for_update=True, - study_activity_subgroup_uid=updated_selection.study_activity_subgroup_uid, - study_soa_group_uid=updated_selection.study_soa_group_uid, - find_requested_study_activities=updated_selection.activity_library_name - == settings.requested_library_name, - ) + find_requested = ( + updated_selection.activity_library_name + == settings.requested_library_name + ) + activity_ar_cache_key = ( + updated_selection.study_activity_subgroup_uid, + updated_selection.study_soa_group_uid, + find_requested, + ) + ar_cache_key = self._get_batch_ar_cache_key(*activity_ar_cache_key) + if self._batch_cache is not None and ar_cache_key in self._batch_cache: + new_selection_aggregate = self._batch_cache[ar_cache_key] + else: + new_selection_aggregate = self.repository.find_by_study( + study_uid=selection_aggregate.study_uid, + for_update=True, + study_activity_subgroup_uid=updated_selection.study_activity_subgroup_uid, + study_soa_group_uid=updated_selection.study_soa_group_uid, + find_requested_study_activities=find_requested, + ) + if self._batch_cache is not None: + self._batch_cache[ar_cache_key] = new_selection_aggregate new_selection_aggregate.add_object_selection( updated_selection, object_exist_callback=self._get_selected_object_exist_check(), @@ -302,6 +325,22 @@ def _update_aggregate( ) new_selection_aggregate.validate() self.repository.save(new_selection_aggregate, author_id=self.author) + # Invalidate Activity cache only when activity_uid changed (used_by_studies affected) + if previous_selection.activity_uid != updated_selection.activity_uid: + with self._repos.activity_repository.lock_store_item_by_uid: + self._repos.activity_repository.cache_store_item_by_uid.clear() + # Grab the VO with the correct order written back by save() + updated_vo = new_selection_aggregate.get_specific_object_selection( + updated_selection.study_selection_uid + )[ + 0 + ] # type: ignore[assignment] + # Keep closure current so the next batch-mode PATCH with the same destination scope + # sees the already-saved state and only diffs its own new selection. + if self._batch_cache is not None: + new_selection_aggregate.repository_closure_data = ( + new_selection_aggregate.study_objects_selection + ) selection_aggregate.remove_object_selection( updated_selection.study_selection_uid @@ -309,39 +348,60 @@ def _update_aggregate( selection_aggregate.add_selection_to_closure_from_other_ar( updated_selection ) - # The SoAGroup of previous StudyActivity should be updated if currently there is none StudyActivities in that SoAGroup - study_soa_group_aggregate = ( - self._repos.study_soa_group_repository.find_by_study( - study_uid=previous_selection.study_uid, - for_update=True, - ) - ) - - is_soa_group_update_needed = False - for new_order, study_soa_group_selection in enumerate( - study_soa_group_aggregate.study_objects_selection, start=1 - ): - reordered_study_soa_group_selection = dataclasses.replace( - study_soa_group_selection, order=new_order + # Evict the old-scope AR from the activity cache. The moved activity is no longer in + # that scope on DB, but the cached AR's repository_closure_data still contains it. + # A subsequent batch POST to the old scope would reuse the stale AR and the save diff + # would try to issue a redundant Delete audit node for the already-moved activity. + if self._batch_cache is not None: + old_find_requested = ( + previous_selection.activity_library_name + == settings.requested_library_name ) - if study_soa_group_selection.order != new_order: - is_soa_group_update_needed = True - study_soa_group_aggregate.update_selection( - updated_study_object_selection=reordered_study_soa_group_selection, - object_exist_callback=self._repos.activity_subgroup_repository.final_concept_exists, - ct_term_level_exist_callback=self._repos.ct_term_name_repository.term_specific_exists_by_uid, + old_scope_key = ( + previous_selection.study_activity_subgroup_uid, + previous_selection.study_soa_group_uid, + old_find_requested, ) - # if some StudySoAGroup order was changed - if is_soa_group_update_needed: - study_soa_group_aggregate.validate() - # sync with DB and save the update - self._repos.study_soa_group_repository.save( - study_soa_group_aggregate, self.author + old_cache_key = self._get_batch_ar_cache_key(*old_scope_key) + self._batch_cache.pop(old_cache_key, None) + # Recompact SoAGroup / ActivitySubGroup / ActivityGroup orders under the *old* parent + # in case this SA was the last one there and the hierarchy node becomes invisible. + # In batch mode, each unique old-parent scope is reordered at most once. + soa_reorder_key = self._get_batch_reordered_key("soa") + if self._batch_cache is None or soa_reorder_key not in self._batch_cache: + study_soa_group_aggregate = ( + self._repos.study_soa_group_repository.find_by_study( + study_uid=previous_selection.study_uid, + for_update=True, + ) ) + is_soa_group_update_needed = False + for new_order, study_soa_group_selection in enumerate( + study_soa_group_aggregate.study_objects_selection, start=1 + ): + if study_soa_group_selection.order != new_order: + is_soa_group_update_needed = True + reordered_study_soa_group_selection = dataclasses.replace( + study_soa_group_selection, order=new_order + ) + study_soa_group_aggregate.update_selection( + updated_study_object_selection=reordered_study_soa_group_selection, + ) + if is_soa_group_update_needed: + study_soa_group_aggregate.validate() + self._repos.study_soa_group_repository.save( + study_soa_group_aggregate, self.author + ) + if self._batch_cache is not None: + self._batch_cache[soa_reorder_key] = True - # If previous StudyActivity was assigned with some StudyActivitySubGroup - # The past StudyActivitySubGroup orders should be updated - if previous_selection.study_activity_subgroup_uid: + subgroup_reorder_key = self._get_batch_reordered_key( + "subgroup", previous_selection.study_activity_group_uid + ) + if previous_selection.study_activity_subgroup_uid and ( + self._batch_cache is None + or subgroup_reorder_key not in self._batch_cache + ): study_activity_subgroup_aggregate = self._repos.study_activity_subgroup_repository.find_by_study( study_uid=previous_selection.study_uid, for_update=True, @@ -351,27 +411,30 @@ def _update_aggregate( for new_order, study_activity_subgroup_selection in enumerate( study_activity_subgroup_aggregate.study_objects_selection, start=1 ): - reordered_study_activity_subgroup_selection = dataclasses.replace( - study_activity_subgroup_selection, order=new_order - ) - study_activity_subgroup_aggregate.update_selection( - updated_study_object_selection=reordered_study_activity_subgroup_selection, - object_exist_callback=self._repos.activity_subgroup_repository.final_concept_exists, - ct_term_level_exist_callback=self._repos.ct_term_name_repository.term_specific_exists_by_uid, - ) if study_activity_subgroup_selection.order != new_order: is_study_activity_subgroup_update_needed = True - # if some StudyActivitySubGroup order was changed + reordered_study_activity_subgroup_selection = ( + dataclasses.replace( + study_activity_subgroup_selection, order=new_order + ) + ) + study_activity_subgroup_aggregate.update_selection( + updated_study_object_selection=reordered_study_activity_subgroup_selection, + ) if is_study_activity_subgroup_update_needed: study_activity_subgroup_aggregate.validate() - # sync with DB and save the update self._repos.study_activity_subgroup_repository.save( study_activity_subgroup_aggregate, self.author ) + if self._batch_cache is not None: + self._batch_cache[subgroup_reorder_key] = True - # If previous StudyActivitySelection was assigned with some StudyActivityGroup - # The past StudyActivityGroup orders should be updated - if previous_selection.study_activity_group_uid: + group_reorder_key = self._get_batch_reordered_key( + "group", previous_selection.study_soa_group_uid + ) + if previous_selection.study_activity_group_uid and ( + self._batch_cache is None or group_reorder_key not in self._batch_cache + ): study_activity_group_aggregate = ( self._repos.study_activity_group_repository.find_by_study( study_uid=previous_selection.study_uid, @@ -383,23 +446,21 @@ def _update_aggregate( for new_order, study_activity_group_selection in enumerate( study_activity_group_aggregate.study_objects_selection, start=1 ): - reordered_study_activity_group_selection = dataclasses.replace( - study_activity_group_selection, order=new_order - ) - study_activity_group_aggregate.update_selection( - updated_study_object_selection=reordered_study_activity_group_selection, - object_exist_callback=self._repos.activity_group_repository.final_concept_exists, - ct_term_level_exist_callback=self._repos.ct_term_name_repository.term_specific_exists_by_uid, - ) if study_activity_group_selection.order != new_order: is_study_activity_group_update_needed = True - # if some StudyActivityGroup order was changed + reordered_study_activity_group_selection = dataclasses.replace( + study_activity_group_selection, order=new_order + ) + study_activity_group_aggregate.update_selection( + updated_study_object_selection=reordered_study_activity_group_selection, + ) if is_study_activity_group_update_needed: study_activity_group_aggregate.validate() - # sync with DB and save the update self._repos.study_activity_group_repository.save( study_activity_group_aggregate, self.author ) + if self._batch_cache is not None: + self._batch_cache[group_reorder_key] = True else: # let the aggregate update the value object selection_aggregate.update_selection( @@ -409,6 +470,22 @@ def _update_aggregate( ) selection_aggregate.validate() self.repository.save(selection_aggregate, self.author) + # Invalidate Activity cache only when activity_uid changed (used_by_studies affected). + if ( + previous_selection is not None + and previous_selection.activity_uid != updated_selection.activity_uid + ): + with self._repos.activity_repository.lock_store_item_by_uid: + self._repos.activity_repository.cache_store_item_by_uid.clear() + # In the no-parent-change case the activity stayed in selection_aggregate; + # grab the VO with the correct order written back by save(). + if updated_vo is None: + updated_vo = selection_aggregate.get_specific_object_selection( + updated_selection.study_selection_uid + )[ + 0 + ] # type: ignore[assignment] + return updated_vo def update_dependent_objects( self, @@ -472,8 +549,7 @@ def replace_study_activity_with_multiple_activities( - First item in the list replaces the original StudyActivity - Remaining items create new StudyActivities - Schedules are preserved for the replaced StudyActivity and replicated to all new ones - - StudyActivityInstances are recreated for the replaced StudyActivity only (existing behavior) - - StudyActivityInstances are NOT created for newly created StudyActivities + - StudyActivityInstances are recreated for the replaced StudyActivity and newly created StudyActivities """ if not replacements: raise ValidationException( @@ -523,8 +599,8 @@ def replace_study_activity_with_multiple_activities( # Process remaining items: Create new StudyActivities for replacement in replacements[1:]: # Validate activity groupings using the same validation as patch_selection - activity_ar = self._repos.activity_repository.find_by_uid_2( - replacement.activity_uid, for_update=True + activity_ar = self._repos.activity_repository.find_by_uid( + replacement.activity_uid ) NotFoundException.raise_if_not( activity_ar, "Activity", replacement.activity_uid @@ -566,29 +642,6 @@ def replace_study_activity_with_multiple_activities( study_uid=study_uid, selection_create_input=create_input ) - # Remove StudyActivityInstances that were automatically created by make_selection - # We don't want instances for newly created StudyActivities, only for the replaced one - study_activity_instances = self._repos.study_activity_instance_repository.get_all_study_activity_instances_for_study_activity( - study_uid=study_uid, - study_activity_uid=new_study_activity.study_activity_uid, - ) - for study_activity_instance in study_activity_instances: - ( - study_activity_instance_ar, - _, - _, - ) = self._get_specific_activity_instance_selection_by_uids( - study_uid=study_uid, - study_selection_uid=study_activity_instance.uid, - for_update=True, - ) - study_activity_instance_ar.remove_object_selection( - study_activity_instance.uid - ) - self._repos.study_activity_instance_repository.save( - study_activity_instance_ar, self.author - ) - # Replicate schedules to the new StudyActivity # Use the schedules we fetched before replacement (they're still valid) assert ( @@ -605,8 +658,8 @@ def replace_study_activity_with_multiple_activities( return results def _validate_activity(self, activity_uid: str) -> ActivityAR: - activity_ar: ActivityAR = self._repos.activity_repository.find_by_uid_2( - activity_uid, for_update=True + activity_ar: ActivityAR | None = self._repos.activity_repository.find_by_uid( + activity_uid ) NotFoundException.raise_if_not(activity_ar, "Activity", activity_uid) @@ -630,12 +683,26 @@ def _create_value_object( ): # activity_ar: ActivityAR = kwargs.get("activity_ar") study_soa_group_selection_uid = kwargs["study_soa_group_selection_uid"] + study_soa_group_order = kwargs.get("study_soa_group_order") study_activity_subgroup_selection_uid = kwargs.get( "study_activity_subgroup_selection_uid" ) + study_activity_subgroup_order = kwargs.get("study_activity_subgroup_order") study_activity_group_selection_uid = kwargs.get( "study_activity_group_selection_uid" ) + study_activity_group_order = kwargs.get("study_activity_group_order") + activity_group_name = kwargs.get("activity_group_name") + activity_subgroup_name = kwargs.get("activity_subgroup_name") + show_soa_group_in_protocol_flowchart = kwargs.get( + "show_soa_group_in_protocol_flowchart", False + ) + show_activity_group_in_protocol_flowchart = kwargs.get( + "show_activity_group_in_protocol_flowchart", True + ) + show_activity_subgroup_in_protocol_flowchart = kwargs.get( + "show_activity_subgroup_in_protocol_flowchart", True + ) BusinessLogicException.raise_if( activity_ar.library.name != settings.requested_library_name @@ -673,8 +740,16 @@ def _create_value_object( activity_library_name=activity_ar.library.name, soa_group_term_uid=selection_create_input.soa_group_term_uid, study_soa_group_uid=study_soa_group_selection_uid, + study_soa_group_order=study_soa_group_order, study_activity_subgroup_uid=study_activity_subgroup_selection_uid, + study_activity_subgroup_order=study_activity_subgroup_order, study_activity_group_uid=study_activity_group_selection_uid, + study_activity_group_order=study_activity_group_order, + activity_group_name=activity_group_name, + activity_subgroup_name=activity_subgroup_name, + show_soa_group_in_protocol_flowchart=show_soa_group_in_protocol_flowchart, + show_activity_group_in_protocol_flowchart=show_activity_group_in_protocol_flowchart, + show_activity_subgroup_in_protocol_flowchart=show_activity_subgroup_in_protocol_flowchart, order=None, generate_uid_callback=self.repository.generate_uid, activity_subgroup_uid=selection_create_input.activity_subgroup_uid, @@ -829,12 +904,12 @@ def _create_activity_subgroup_selection_value_object( @classmethod def _validate_activity_subgroup( cls, - activity_subgroup_uid: str | None, + activity_subgroup_uid: str, perform_subgroup_validation: bool = True, activity_subgroup_version: str | None = None, ) -> ActivitySubGroupAR: activity_subgroup_service = ActivitySubGroupService() - activity_subgroup_ar = activity_subgroup_service.repository.find_by_uid_2( + activity_subgroup_ar = activity_subgroup_service.repository.find_by_uid( activity_subgroup_uid, version=activity_subgroup_version ) NotFoundException.raise_if_not( @@ -857,12 +932,12 @@ def _validate_activity_subgroup( @classmethod def _validate_activity_group( cls, - activity_group_uid: str | None, + activity_group_uid: str, perform_group_validation: bool = True, activity_group_version: str | None = None, ) -> ActivityGroupAR: activity_group_service = ActivityGroupService() - activity_group_ar = activity_group_service.repository.find_by_uid_2( + activity_group_ar = activity_group_service.repository.find_by_uid( activity_group_uid, version=activity_group_version ) @@ -1015,36 +1090,35 @@ def _patch_soa_group_selection_value_object( is_soa_group_changed: bool, ): soa_group_term_uid = str(selection_create_input.soa_group_term_uid) - selection_aggregate = self._repos.study_soa_group_repository.find_by_study( - study_uid=study_uid - ) - assert selection_aggregate is not None - new_selection, _ = selection_aggregate.get_specific_object_selection( - study_selection_uid=current_study_activity.study_soa_group_uid - ) - if is_soa_group_changed: - ct_term_ar = self._repos.ct_term_name_repository.find_by_uid( - soa_group_term_uid + if not is_soa_group_changed: + # SoA group unchanged — build a lightweight VO from known values; avoids find_by_study round-trip + return StudySoAGroupVO.from_input_values( + study_uid=study_uid, + author_id=self.author, + soa_group_term_uid=current_study_activity.soa_group_term_uid, + study_selection_uid=current_study_activity.study_soa_group_uid, + order=current_study_activity.study_soa_group_order, + show_soa_group_in_protocol_flowchart=current_study_activity.show_soa_group_in_protocol_flowchart, ) - NotFoundException.raise_if_not( - ct_term_ar, "SoA Group CT Term", soa_group_term_uid - ) + ct_term_ar = self._repos.ct_term_name_repository.find_by_uid(soa_group_term_uid) - NotFoundException.raise_if( - ct_term_ar.item_metadata.status - in [ - LibraryItemStatus.DRAFT, - LibraryItemStatus.RETIRED, - ], - msg=f"There is no approved SoAGroup CTTerm with UID '{soa_group_term_uid}'.", - ) - # get VO if possible or create it - new_selection = self._get_or_create_study_soa_group( - study_uid=study_uid, soa_group_term_uid=soa_group_term_uid - ) + NotFoundException.raise_if_not( + ct_term_ar, "SoA Group CT Term", soa_group_term_uid + ) - return new_selection + NotFoundException.raise_if( + ct_term_ar.item_metadata.status + in [ + LibraryItemStatus.DRAFT, + LibraryItemStatus.RETIRED, + ], + msg=f"There is no approved SoAGroup CTTerm with UID '{soa_group_term_uid}'.", + ) + # get VO if possible or create it + return self._get_or_create_study_soa_group( + study_uid=study_uid, soa_group_term_uid=soa_group_term_uid + ) def _create_soa_group_selection_value_object( self, study_uid: str, soa_group_term_uid: str @@ -1076,6 +1150,10 @@ def _create_soa_group_selection_value_object( def _get_or_create_study_soa_group( self, study_uid: str, soa_group_term_uid: str ) -> StudySoAGroupVO: + cache_key = self._get_batch_vo_cache_key("soa", study_uid, soa_group_term_uid) + if self._batch_cache is not None and cache_key in self._batch_cache: + return self._batch_cache[cache_key] + study_soa_group_node = ( self._repos.study_soa_group_repository.find_study_soa_group_in_a_study( study_uid=study_uid, @@ -1083,12 +1161,15 @@ def _get_or_create_study_soa_group( ) ) if study_soa_group_node: - ( - _, - study_soa_group_selection, - _, - ) = self._get_specific_soa_group_selection_by_uids( - study_uid=study_uid, study_selection_uid=study_soa_group_node.uid + # Node already found — construct a lightweight VO directly; avoids a second find_by_study. + # Pass the node's order and show_* flag so the VO carries them without a reload. + study_soa_group_selection = StudySoAGroupVO.from_input_values( + study_uid=study_uid, + author_id=self.author, + soa_group_term_uid=soa_group_term_uid, + study_selection_uid=study_soa_group_node.uid, + order=study_soa_group_node.order, + show_soa_group_in_protocol_flowchart=study_soa_group_node.show_soa_group_in_protocol_flowchart, ) else: study_soa_group_selection = self._create_soa_group_selection_value_object( @@ -1109,6 +1190,14 @@ def _get_or_create_study_soa_group( self._repos.study_soa_group_repository.save( study_soa_group_aggregate, self.author ) + # save() writes the DB-assigned order back into the aggregate; read the updated VO. + study_soa_group_selection, _ = ( + study_soa_group_aggregate.get_specific_object_selection( + study_soa_group_selection.study_selection_uid + ) + ) + if self._batch_cache is not None: + self._batch_cache[cache_key] = study_soa_group_selection return study_soa_group_selection def _get_or_create_study_activity_subgroup( @@ -1128,23 +1217,25 @@ def _get_or_create_study_activity_subgroup( ) if activity_subgroup_uid and activity_group_uid and soa_group_term_uid: - study_activity_subgroup_node = self._repos.study_activity_subgroup_repository.find_study_activity_subgroup_with_same_groupings( + cache_key = self._get_batch_vo_cache_key( + "subgroup", + study_uid, + activity_subgroup_uid, + activity_group_uid, + soa_group_term_uid, + sync_latest_version, + ) + if self._batch_cache is not None and cache_key in self._batch_cache: + return self._batch_cache[cache_key] + + study_activity_subgroup_selection = self._repos.study_activity_subgroup_repository.find_study_activity_subgroup_vo_with_same_groupings( study_uid=study_uid, activity_subgroup_uid=activity_subgroup_uid, activity_group_uid=activity_group_uid, soa_group_term_uid=soa_group_term_uid, sync_latest_version=sync_latest_version, ) - if study_activity_subgroup_node: - ( - _, - study_activity_subgroup_selection, - _, - ) = self._get_specific_activity_subgroup_selection_by_uids( - study_uid=study_uid, - study_selection_uid=study_activity_subgroup_node.uid, - ) - else: + if study_activity_subgroup_selection is None: # create new VO to add study_activity_subgroup_selection = ( self._create_activity_subgroup_selection_value_object( @@ -1172,6 +1263,14 @@ def _get_or_create_study_activity_subgroup( self._repos.study_activity_subgroup_repository.save( study_activity_subgroup_aggregate, self.author ) + # save() writes the DB-assigned order back into the aggregate; read the updated VO. + study_activity_subgroup_selection, _ = ( + study_activity_subgroup_aggregate.get_specific_object_selection( + study_activity_subgroup_selection.study_selection_uid + ) + ) + if self._batch_cache is not None: + self._batch_cache[cache_key] = study_activity_subgroup_selection return study_activity_subgroup_selection def _get_or_create_study_activity_group( @@ -1193,22 +1292,23 @@ def _get_or_create_study_activity_group( and soa_group_term_uid and study_soa_group_uid ): - study_activity_group_node = self._repos.study_activity_group_repository.find_study_activity_group_with_same_groupings( + cache_key = self._get_batch_vo_cache_key( + "group", + study_uid, + activity_group_uid, + soa_group_term_uid, + sync_latest_version, + ) + if self._batch_cache is not None and cache_key in self._batch_cache: + return self._batch_cache[cache_key] + + study_activity_group_selection = self._repos.study_activity_group_repository.find_study_activity_group_vo_with_same_groupings( study_uid=study_uid, activity_group_uid=activity_group_uid, soa_group_term_uid=soa_group_term_uid, sync_latest_version=sync_latest_version, ) - if study_activity_group_node: - ( - _, - study_activity_group_selection, - _, - ) = self._get_specific_activity_group_selection_by_uids( - study_uid=study_uid, - study_selection_uid=study_activity_group_node.uid, - ) - else: + if study_activity_group_selection is None: # create new VO to add study_activity_group_selection = ( self._create_activity_group_selection_value_object( @@ -1236,6 +1336,14 @@ def _get_or_create_study_activity_group( self._repos.study_activity_group_repository.save( study_activity_group_aggregate, self.author ) + # save() writes the DB-assigned order back into the aggregate; read the updated VO. + study_activity_group_selection, _ = ( + study_activity_group_aggregate.get_specific_object_selection( + study_activity_group_selection.study_selection_uid + ) + ) + if self._batch_cache is not None: + self._batch_cache[cache_key] = study_activity_group_selection return study_activity_group_selection def _create_study_activity_instances( @@ -1266,6 +1374,20 @@ def _create_study_activity_instances( if len(linked_activity_instances) == 0: linked_activity_instances[None] = False + # In batch mode reuse the cached AR so all POSTs share one find_by_study + one save; + # in non-batch mode load fresh and save immediately as before. + if self._batch_instance_ar is not None: + study_activity_instance_aggregate = self._batch_instance_ar + else: + study_activity_instance_aggregate = ( + self._repos.study_activity_instance_repository.find_by_study( + study_uid=study_uid, for_update=True + ) + ) + assert study_activity_instance_aggregate is not None + if self._batch_cache is not None: + # Batch mode — cache for reuse by subsequent POST operations + self._batch_instance_ar = study_activity_instance_aggregate for ( activity_instance_uid, is_required_for_activity, @@ -1281,45 +1403,43 @@ def _create_study_activity_instances( generate_uid_callback=self._repos.study_activity_instance_repository.generate_uid, is_reviewed=is_required_for_activity, ) # add VO to aggregate - - study_activity_instance_aggregate = ( - self._repos.study_activity_instance_repository.find_by_study( - study_uid=study_uid, for_update=True - ) - ) - assert study_activity_instance_aggregate is not None study_activity_instance_aggregate.add_object_selection( activity_instance_selection, self._repos.activity_instance_repository.check_exists_final_version, ) - study_activity_instance_aggregate.validate() - # sync with DB and save the update + study_activity_instance_aggregate.validate() + if self._batch_instance_ar is None: + # Non-batch mode — save immediately self._repos.study_activity_instance_repository.save( study_activity_instance_aggregate, self.author ) + # Batch mode: AR is already cached; the batch finally block flushes once at the end def _recreate_study_activity_instances_after_activity_replacement( self, study_uid: str, study_activity_selection: StudySelectionActivityVO ): - # Remove related Study activity instances + # Flush any deferred batch-mode instance saves so the DB query below sees current state + if self._batch_instance_ar is not None: + self._repos.study_activity_instance_repository.save( + self._batch_instance_ar, self.author + ) + self._batch_instance_ar = None + # Remove related Study activity instances — load aggregate once, remove all, save once study_activity_instances = self._repos.study_activity_instance_repository.get_all_study_activity_instances_for_study_activity( study_uid=study_uid, study_activity_uid=study_activity_selection.study_selection_uid, ) - for study_activity_instance in study_activity_instances: - # delete study activity instance - ( - study_activity_instance_ar, - _, - _, - ) = self._get_specific_activity_instance_selection_by_uids( - study_uid=study_uid, - study_selection_uid=study_activity_instance.uid, - for_update=True, - ) - study_activity_instance_ar.remove_object_selection( - study_activity_instance.uid + if study_activity_instances: + study_activity_instance_ar = ( + self._repos.study_activity_instance_repository.find_by_study( + study_uid, for_update=True + ) ) + assert study_activity_instance_ar is not None + for study_activity_instance in study_activity_instances: + study_activity_instance_ar.remove_object_selection( + study_activity_instance.uid + ) self._repos.study_activity_instance_repository.save( study_activity_instance_ar, self.author ) @@ -1350,10 +1470,13 @@ def make_selection( ) -> StudySelectionActivity: repos = self._repos try: - study_soa_group_selection_uid = self._get_or_create_study_soa_group( + study_soa_group_selection = self._get_or_create_study_soa_group( study_uid=study_uid, soa_group_term_uid=selection_create_input.soa_group_term_uid, - ).study_selection_uid + ) + study_soa_group_selection_uid = ( + study_soa_group_selection.study_selection_uid + ) activity_ar = self._validate_activity(selection_create_input.activity_uid) @@ -1402,18 +1525,67 @@ def make_selection( selection_create_input=selection_create_input, activity_ar=activity_ar, study_soa_group_selection_uid=study_soa_group_selection_uid, + study_soa_group_order=study_soa_group_selection.order, study_activity_subgroup_selection_uid=study_activity_subgroup_selection_uid, + study_activity_subgroup_order=( + study_activity_subgroup_selection.order + if study_activity_subgroup_selection + else None + ), study_activity_group_selection_uid=study_activity_group_selection_uid, + study_activity_group_order=( + study_activity_group_selection.order + if study_activity_group_selection + else None + ), + activity_group_name=( + study_activity_group_selection.activity_group_name + if study_activity_group_selection + else None + ), + activity_subgroup_name=( + study_activity_subgroup_selection.activity_subgroup_name + if study_activity_subgroup_selection + else None + ), + show_soa_group_in_protocol_flowchart=study_soa_group_selection.show_soa_group_in_protocol_flowchart, + show_activity_group_in_protocol_flowchart=( + study_activity_group_selection.show_activity_group_in_protocol_flowchart + if study_activity_group_selection + else True + ), + show_activity_subgroup_in_protocol_flowchart=( + study_activity_subgroup_selection.show_activity_subgroup_in_protocol_flowchart + if study_activity_subgroup_selection + else True + ), ) # add VO to aggregate - study_activity_aggregate = self.repository.find_by_study( - study_uid=study_uid, - for_update=True, - study_activity_subgroup_uid=study_activity_subgroup_selection_uid, - study_soa_group_uid=study_soa_group_selection_uid, - find_requested_study_activities=study_activity_selection.activity_library_name - == settings.requested_library_name, + # In batch mode reuse the cached AR so all POSTs with the same (subgroup, soa) grouping + # share one find_by_study(for_update) + acquire._write_lock; the AR is saved per-POST + # but closure_data is updated after each save so the diff stays correct. + find_requested = ( + study_activity_selection.activity_library_name + == settings.requested_library_name ) + activity_ar_cache_key = ( + study_activity_subgroup_selection_uid, + study_soa_group_selection_uid, + find_requested, + ) + ar_cache_key = self._get_batch_ar_cache_key(*activity_ar_cache_key) + if self._batch_cache is not None and ar_cache_key in self._batch_cache: + study_activity_aggregate = self._batch_cache[ar_cache_key] + else: + study_activity_aggregate = self.repository.find_by_study( + study_uid=study_uid, + for_update=True, + study_activity_subgroup_uid=study_activity_subgroup_selection_uid, + study_soa_group_uid=study_soa_group_selection_uid, + find_requested_study_activities=find_requested, + ) + if self._batch_cache is not None: + self._batch_cache[ar_cache_key] = study_activity_aggregate assert study_activity_aggregate is not None study_activity_aggregate.add_object_selection( study_activity_selection, @@ -1425,8 +1597,16 @@ def make_selection( updated_selection=study_activity_selection, ) study_activity_aggregate.validate() - # sync with DB and save the update self.repository.save(study_activity_aggregate, self.author) + # Invalidate Activity cache so GET /concepts/activities/... will recalculate used_by_studies + with repos.activity_repository.lock_store_item_by_uid: + repos.activity_repository.cache_store_item_by_uid.clear() + # Update closure so the cached AR reflects the just-saved state; the next POST + # in the same batch will then only diff its own new selection. + if self._batch_cache is not None: + study_activity_aggregate.repository_closure_data = ( + study_activity_aggregate.study_objects_selection + ) # create StudyActivityInstance selection if ( @@ -1439,23 +1619,24 @@ def make_selection( study_activity_selection=study_activity_selection, ) - study_activity_aggregate = self.repository.find_by_study( - study_uid=study_uid, - ) - # Fetch the new selection which was just added - ( - new_selection, - _, - ) = study_activity_aggregate.get_specific_object_selection( + # save() writes the computed order back into the in-memory aggregate, + # so we can read the fully-populated VO directly without a DB round-trip. + new_selection, _ = study_activity_aggregate.get_specific_object_selection( study_activity_selection.study_selection_uid ) + + # In batch mode, update the patch AR selections cache with the new VO + # so subsequent PATCHes see the newly created entity without a DB reload. + if self._batch_cache is not None: + self._append_to_patch_ar_selections_cache(new_selection) + terms_at_specific_datetime = self._extract_study_standards_effective_date( study_uid=study_uid ) # add the activity and return return self._transform_from_vo_to_response_model( study_uid=study_activity_aggregate.study_uid, - specific_selection=new_selection, + specific_selection=new_selection, # type: ignore[arg-type] terms_at_specific_datetime=terms_at_specific_datetime, ) finally: @@ -1472,8 +1653,8 @@ def delete_selection(self, study_uid: str, study_selection_uid: str): repos = self._repos try: - # Load aggregate - selection_aggregate, _ = self._find_ar_to_patch( + # Load aggregate and capture the VO being deleted (needed for cache updates) + selection_aggregate, deleted_vo = self._find_ar_to_patch( study_uid=study_uid, study_selection_uid=study_selection_uid ) @@ -1562,26 +1743,29 @@ def delete_selection(self, study_uid: str, study_selection_uid: str): # Remove related Study activity instances with trace_block("Removing related study activity instances"): + # Flush any deferred batch-mode instance saves so the DB query below sees current state + if self._batch_instance_ar is not None: + repos.study_activity_instance_repository.save( + self._batch_instance_ar, self.author + ) + self._batch_instance_ar = None study_activity_instances = repos.study_activity_instance_repository.get_all_study_activity_instances_for_study_activity( study_uid=study_uid, study_activity_uid=study_selection_uid ) - for study_activity_instance in study_activity_instances: - # Skip placeholders (they don't have a database node to delete) - if study_activity_instance.uid is None: - continue - # delete study activity instance - ( - study_activity_instance_ar, - _, - _, - ) = self._get_specific_activity_instance_selection_by_uids( - study_uid=study_uid, - study_selection_uid=study_activity_instance.uid, - for_update=True, - ) - study_activity_instance_ar.remove_object_selection( - study_activity_instance.uid + non_placeholder_instances = [ + inst for inst in study_activity_instances if inst.uid is not None + ] + if non_placeholder_instances: + study_activity_instance_ar = ( + repos.study_activity_instance_repository.find_by_study( + study_uid, for_update=True + ) ) + assert study_activity_instance_ar is not None + for study_activity_instance in non_placeholder_instances: + study_activity_instance_ar.remove_object_selection( + study_activity_instance.uid + ) repos.study_activity_instance_repository.save( study_activity_instance_ar, self.author ) @@ -1593,7 +1777,17 @@ def delete_selection(self, study_uid: str, study_selection_uid: str): # sync with DB and save the update repos.study_activity_repository.save(selection_aggregate, self.author) # Invalidate Activity cache so GET /concepts/activities/... will recalculate used_by_studies - repos.activity_repository.cache_store_item_by_uid.clear() + with repos.activity_repository.lock_store_item_by_uid: + repos.activity_repository.cache_store_item_by_uid.clear() + + # In batch mode, update caches with targeted eviction instead of blanket invalidation. + if self._batch_cache is not None: + self._remove_from_patch_ar_selections_cache(study_selection_uid) + self._evict_ar_cache_for_scope( + study_activity_subgroup_uid=deleted_vo.study_activity_subgroup_uid, + study_soa_group_uid=deleted_vo.study_soa_group_uid, + activity_library_name=deleted_vo.activity_library_name, + ) finally: repos.close() @@ -1607,6 +1801,7 @@ def _update_underlying_activity_if_needed( | UpdateActivityPlaceholderToSponsorActivity ), ): + activity_ar: ActivityAR | None # update underlying Activity if isinstance(request_object, StudySelectionActivityRequestEditInput): activity_ar = self._patch_selected_activity( @@ -1623,7 +1818,7 @@ def _update_underlying_activity_if_needed( ) and request_object.activity_uid ): - activity_ar = self._repos.activity_repository.find_by_uid_2( + activity_ar = self._repos.activity_repository.find_by_uid( request_object.activity_uid ) ValidationException.raise_if_not( @@ -1631,7 +1826,14 @@ def _update_underlying_activity_if_needed( msg=f"The Activity with UID '{current_object.activity_uid}' doesn't exist.", ) else: - activity_ar = self._repos.activity_repository.find_by_uid_2( + # Skip fetching activity AR when no grouping-related fields are changing; + # _patch_prepare_new_value_object falls back to current_object values in that case + if ( + request_object.activity_group_uid is None + and request_object.activity_subgroup_uid is None + ): + return None + activity_ar = self._repos.activity_repository.find_by_uid( current_object.activity_uid, version=current_object.activity_version, ) @@ -1645,9 +1847,11 @@ def _validate_new_activity_groupings( | StudySelectionActivityRequestEditInput | UpdateActivityPlaceholderToSponsorActivity ), - activity_ar: ActivityAR, + activity_ar: ActivityAR | None, current_object: StudySelectionActivityVO, ): + if activity_ar is None: + return ValidationException.raise_if( request_object.activity_group_uid is None and request_object.activity_subgroup_uid is not None @@ -1706,10 +1910,7 @@ def _patch_or_get_study_activity_group( is_soa_group_changed: bool, study_soa_group_uid: str, sync_latest_version: bool = False, - ): - activity_group_uid = current_object.activity_group_uid - activity_group_name = current_object.activity_group_name - study_activity_group_uid = current_object.study_activity_group_uid + ) -> StudySelectionActivityGroupVO: soa_group_term_uid = ( request_object.soa_group_term_uid if not isinstance(request_object, StudyActivitySyncLatestVersionInput) @@ -1719,8 +1920,7 @@ def _patch_or_get_study_activity_group( request_object.activity_group_uid and current_object.activity_group_uid != request_object.activity_group_uid ) or sync_latest_version: - activity_group_uid = request_object.activity_group_uid - study_activity_group = self._get_or_create_study_activity_group( + return self._get_or_create_study_activity_group( study_uid=current_object.study_uid, activity_subgroup_uid=request_object.activity_subgroup_uid, activity_group_uid=request_object.activity_group_uid, @@ -1729,30 +1929,29 @@ def _patch_or_get_study_activity_group( sync_latest_version=sync_latest_version, current_object=current_object, ) - study_activity_group_uid = study_activity_group.study_selection_uid - activity_group_name = study_activity_group.activity_group_name # When SoAGroup is changed we need to update StudyActivityGroup for other shared nodes if given StudyActivity contains StudyActivityGroup - elif is_soa_group_changed and activity_group_uid: - activity_group_selection = self._get_or_create_study_activity_group( + if is_soa_group_changed and current_object.activity_group_uid: + return self._get_or_create_study_activity_group( study_uid=current_object.study_uid, activity_subgroup_uid=current_object.activity_subgroup_uid, - activity_group_uid=activity_group_uid, + activity_group_uid=current_object.activity_group_uid, soa_group_term_uid=soa_group_term_uid, study_soa_group_uid=study_soa_group_uid, perform_group_validation=False, sync_latest_version=sync_latest_version, current_object=current_object, ) - ( - activity_group_uid, - activity_group_name, - study_activity_group_uid, - ) = ( - activity_group_selection.activity_group_uid, - None, - activity_group_selection.study_selection_uid, - ) - return activity_group_uid, activity_group_name, study_activity_group_uid + # Unchanged — build lightweight VO from current_object + return StudySelectionActivityGroupVO.from_input_values( + study_uid=current_object.study_uid, + author_id=self.author, + activity_group_uid=current_object.activity_group_uid, # type: ignore[arg-type] + activity_group_name=current_object.activity_group_name, + activity_group_version=None, + study_selection_uid=current_object.study_activity_group_uid, + order=current_object.study_activity_group_order, + show_activity_group_in_protocol_flowchart=current_object.show_activity_group_in_protocol_flowchart, + ) def _patch_or_get_study_activity_subgroup( self, @@ -1768,10 +1967,7 @@ def _patch_or_get_study_activity_subgroup( is_study_activity_group_changed: bool, study_activity_group_uid: str | None, sync_latest_version: bool = False, - ): - activity_subgroup_uid = current_object.activity_subgroup_uid - activity_subgroup_name = current_object.activity_subgroup_name - study_activity_subgroup_uid = current_object.study_activity_subgroup_uid + ) -> StudySelectionActivitySubGroupVO: soa_group_term_uid = ( request_object.soa_group_term_uid if not isinstance(request_object, StudyActivitySyncLatestVersionInput) @@ -1782,9 +1978,7 @@ def _patch_or_get_study_activity_subgroup( and current_object.activity_subgroup_uid != request_object.activity_subgroup_uid ) or sync_latest_version: - activity_subgroup_uid = request_object.activity_subgroup_uid - - study_activity_subgroup = self._get_or_create_study_activity_subgroup( + return self._get_or_create_study_activity_subgroup( study_uid=current_object.study_uid, activity_subgroup_uid=request_object.activity_subgroup_uid, activity_group_uid=request_object.activity_group_uid @@ -1794,15 +1988,13 @@ def _patch_or_get_study_activity_subgroup( sync_latest_version=sync_latest_version, current_object=current_object, ) - study_activity_subgroup_uid = study_activity_subgroup.study_selection_uid - activity_subgroup_name = study_activity_subgroup.activity_subgroup_name # When SoAGroup or StudyActivityGroup is changed we need to update StudyActivitySubGroup for other shared nodes if given StudyActivity contains StudyActivitySubGroup - elif ( + if ( is_soa_group_changed or is_study_activity_group_changed - ) and activity_subgroup_uid: - activity_subgroup_selection = self._get_or_create_study_activity_subgroup( + ) and current_object.activity_subgroup_uid: + return self._get_or_create_study_activity_subgroup( study_uid=current_object.study_uid, - activity_subgroup_uid=activity_subgroup_uid, + activity_subgroup_uid=current_object.activity_subgroup_uid, activity_group_uid=current_object.activity_group_uid, soa_group_term_uid=soa_group_term_uid, perform_subgroup_validation=False, @@ -1810,20 +2002,16 @@ def _patch_or_get_study_activity_subgroup( sync_latest_version=sync_latest_version, current_object=current_object, ) - ( - activity_subgroup_uid, - activity_subgroup_name, - study_activity_subgroup_uid, - ) = ( - activity_subgroup_selection.activity_subgroup_uid, - None, - activity_subgroup_selection.study_selection_uid, - ) - - return ( - activity_subgroup_uid, - activity_subgroup_name, - study_activity_subgroup_uid, + # Unchanged — build lightweight VO from current_object + return StudySelectionActivitySubGroupVO.from_input_values( + study_uid=current_object.study_uid, + author_id=self.author, + activity_subgroup_uid=current_object.activity_subgroup_uid, # type: ignore[arg-type] + activity_subgroup_name=current_object.activity_subgroup_name, + activity_subgroup_version=None, + study_selection_uid=current_object.study_activity_subgroup_uid, + order=current_object.study_activity_subgroup_order, + show_activity_subgroup_in_protocol_flowchart=current_object.show_activity_subgroup_in_protocol_flowchart, ) def _patch_prepare_new_value_object( @@ -1877,11 +2065,7 @@ def _patch_prepare_new_value_object( ) # update StudyActivityGroup - ( - activity_group_uid, - activity_group_name, - study_activity_group_uid, - ) = self._patch_or_get_study_activity_group( + updated_group = self._patch_or_get_study_activity_group( request_object=request_object, current_object=current_object, is_soa_group_changed=is_soa_group_changed, @@ -1889,34 +2073,44 @@ def _patch_prepare_new_value_object( ) is_study_activity_group_changed = ( - study_activity_group_uid != current_object.study_activity_group_uid + updated_group.study_selection_uid != current_object.study_activity_group_uid ) # update StudyActivitySubGroup - ( - activity_subgroup_uid, - activity_subgroup_name, - study_activity_subgroup_uid, - ) = self._patch_or_get_study_activity_subgroup( + updated_subgroup = self._patch_or_get_study_activity_subgroup( request_object=request_object, current_object=current_object, is_soa_group_changed=is_soa_group_changed, is_study_activity_group_changed=is_study_activity_group_changed, - study_activity_group_uid=study_activity_group_uid, + study_activity_group_uid=updated_group.study_selection_uid, ) updated_study_activity_vo = StudySelectionActivityVO.from_input_values( study_uid=current_object.study_uid, - activity_uid=activity_ar.uid, - activity_version=activity_ar.item_metadata.version, - activity_name=activity_ar.name, + activity_uid=( + activity_ar.uid if activity_ar else current_object.activity_uid + ), + activity_version=( + activity_ar.item_metadata.version + if activity_ar + else current_object.activity_version # type: ignore[arg-type] + ), + activity_name=( + activity_ar.name if activity_ar else current_object.activity_name + ), soa_group_term_uid=updated_soa_selection.soa_group_term_uid, study_soa_group_uid=updated_soa_selection.study_selection_uid, + study_soa_group_order=updated_soa_selection.order, study_selection_uid=current_object.study_selection_uid, - study_activity_subgroup_uid=study_activity_subgroup_uid, - activity_subgroup_uid=activity_subgroup_uid, - activity_subgroup_name=activity_subgroup_name, - study_activity_group_uid=study_activity_group_uid, - activity_group_uid=activity_group_uid, - activity_group_name=activity_group_name, + study_activity_subgroup_uid=updated_subgroup.study_selection_uid, + study_activity_subgroup_order=updated_subgroup.order, + activity_subgroup_uid=updated_subgroup.activity_subgroup_uid, + activity_subgroup_name=updated_subgroup.activity_subgroup_name, + study_activity_group_uid=updated_group.study_selection_uid, + study_activity_group_order=updated_group.order, + activity_group_uid=updated_group.activity_group_uid, + activity_group_name=updated_group.activity_group_name, + show_soa_group_in_protocol_flowchart=updated_soa_selection.show_soa_group_in_protocol_flowchart, + show_activity_group_in_protocol_flowchart=updated_group.show_activity_group_in_protocol_flowchart, + show_activity_subgroup_in_protocol_flowchart=updated_subgroup.show_activity_subgroup_in_protocol_flowchart, show_activity_in_protocol_flowchart=request_object.show_activity_in_protocol_flowchart, keep_old_version=request_object.keep_old_version, keep_old_version_date=keep_old_version_date, @@ -1933,46 +2127,87 @@ def handle_batch_operations( study_uid: str, operations: list[StudySelectionActivityBatchInput], ) -> list[StudySelectionActivityBatchOutput]: + """Handle a batch of study activity selection operations with proper cache management. + + This method processes POST, PATCH, and DELETE operations in sequence while + maintaining cache consistency. Each operation may invalidate caches that + affect subsequent operations in the batch. + + Cache Lifecycle: + 1. Initialize all caches at batch start + 2. Each operation may invalidate related cache entries + 3. Cache state is preserved between operations for performance + 4. All caches are cleared in finally block + + Args: + study_uid: Study identifier for all operations + operations: List of batch operations to execute + + Returns: + List of batch operation results with status codes and content + """ results = [] - for operation in operations: - item = None - try: - if operation.method == "PATCH": - item = self.patch_selection( - study_uid, - operation.content.study_activity_uid, - operation.content.content, - ) - response_code = status.HTTP_200_OK - elif operation.method == "DELETE": - self.delete_selection( - study_uid, operation.content.study_activity_uid - ) - response_code = status.HTTP_204_NO_CONTENT - elif operation.method == "POST": - if isinstance(operation.content, StudySelectionActivityCreateInput): - item = self.make_selection(study_uid, operation.content) - response_code = status.HTTP_201_CREATED + + # Initialize all batch caches and tracking + self._initialize_batch_caches() + + try: + for operation in operations: + item = None + try: + if operation.method == "PATCH": + item = self.patch_selection( + study_uid, + operation.content.study_activity_uid, + operation.content.content, + ) + response_code = status.HTTP_200_OK + + elif operation.method == "DELETE": + self.delete_selection( + study_uid, operation.content.study_activity_uid + ) + response_code = status.HTTP_204_NO_CONTENT + + elif operation.method == "POST": + if isinstance( + operation.content, StudySelectionActivityCreateInput + ): + item = self.make_selection(study_uid, operation.content) + response_code = status.HTTP_201_CREATED + else: + raise ValidationException( + msg="POST operation requires StudySelectionActivityCreateInput as request payload." + ) else: - raise ValidationException( - msg="POST operation requires StudySelectionActivityCreateInput as request payload." + raise MethodNotAllowedException(method=operation.method) + + results.append( + StudySelectionActivityBatchOutput.model_construct( + response_code=response_code, + content=item, ) - else: - raise MethodNotAllowedException(method=operation.method) - results.append( - StudySelectionActivityBatchOutput( - response_code=response_code, - content=item, ) - ) - except MDRApiBaseException as error: - results.append( - StudySelectionActivityBatchOutput.model_construct( - response_code=error.status_code, - content=BatchErrorResponse(message=str(error)), + + except MDRApiBaseException as error: + results.append( + StudySelectionActivityBatchOutput.model_construct( + response_code=error.status_code, + content=BatchErrorResponse(message=str(error)), + ) ) + raise error + + finally: + # Save any pending batch instance AR before clearing caches + if self._batch_instance_ar is not None: + self._repos.study_activity_instance_repository.save( + self._batch_instance_ar, self.author ) - raise error + + # Clear all caches and tracking state + self._clear_all_batch_caches() + return results @ensure_transaction(db) @@ -1981,42 +2216,63 @@ def handle_review_changes( study_uid: str, operations: list[StudySelectionActivityReviewBatchInput], ) -> list[StudySelectionActivityBatchOutput]: + """Handle a batch of review changes with proper cache management. + + Review operations are simpler than full batch operations but still + require cache management for consistency between operations. + """ results = [] - for operation in operations: - item = None - try: - if operation.action == StudySelectionReviewAction.ACCEPT: - item = self.update_selection_to_latest_version( - study_uid=study_uid, - study_selection_uid=operation.uid, - sync_latest_version_input=StudyActivitySyncLatestVersionInput( - activity_group_uid=operation.content.activity_group_uid, - activity_subgroup_uid=operation.content.activity_subgroup_uid, - ), - ) - response_code = status.HTTP_200_OK - elif operation.action == StudySelectionReviewAction.DECLINE: - self.patch_selection( - study_uid=study_uid, - study_selection_uid=operation.uid, - selection_update_input=operation.content, - ) - response_code = status.HTTP_204_NO_CONTENT - else: - raise MethodNotAllowedException(method=operation.action) - results.append( - StudySelectionActivityBatchOutput( - response_code=response_code, - content=item, + + # Initialize all batch caches for review operations + self._initialize_batch_caches() + + try: + for operation in operations: + item = None + try: + if operation.action == StudySelectionReviewAction.ACCEPT: + item = self.update_selection_to_latest_version( + study_uid=study_uid, + study_selection_uid=operation.uid, + sync_latest_version_input=StudyActivitySyncLatestVersionInput( + activity_group_uid=operation.content.activity_group_uid, + activity_subgroup_uid=operation.content.activity_subgroup_uid, + ), + ) + response_code = status.HTTP_200_OK + elif operation.action == StudySelectionReviewAction.DECLINE: + self.patch_selection( + study_uid=study_uid, + study_selection_uid=operation.uid, + selection_update_input=operation.content, + ) + response_code = status.HTTP_204_NO_CONTENT + else: + raise MethodNotAllowedException(method=operation.action) + results.append( + StudySelectionActivityBatchOutput( + response_code=response_code, + content=item, + ) ) - ) - except MDRApiBaseException as error: - results.append( - StudySelectionActivityBatchOutput.model_construct( - response_code=error.status_code, - content=BatchErrorResponse(message=str(error)), + except MDRApiBaseException as error: + results.append( + StudySelectionActivityBatchOutput.model_construct( + response_code=error.status_code, + content=BatchErrorResponse(message=str(error)), + ) ) + raise error + finally: + # Save any pending batch instance AR before clearing caches + if self._batch_instance_ar is not None: + self._repos.study_activity_instance_repository.save( + self._batch_instance_ar, self.author ) + + # Clear all caches and tracking state + self._clear_all_batch_caches() + return results @ensure_transaction(db) @@ -2025,66 +2281,93 @@ def handle_soa_edit_batch_operations( study_uid: str, operations: list[StudySoAEditBatchInput], ) -> list[StudySoAEditBatchOutput]: + """Handle a batch of SoA edit operations with proper cache management. + + SoA edit operations can modify study activities and schedules, requiring + comprehensive cache invalidation to maintain consistency. + """ study_activity_schedules_service = StudyActivityScheduleService() results = [] - for operation in operations: - item = None - try: - if ( - operation.method == "PATCH" - and operation.object == SoAItemType.STUDY_ACTIVITY.value - ): - item = self.patch_selection( - study_uid, - operation.content.study_activity_uid, - operation.content.content, - ) - response_code = status.HTTP_200_OK - elif operation.method == "POST": - if operation.object == SoAItemType.STUDY_ACTIVITY.value: - if isinstance( - operation.content, StudySelectionActivityCreateInput + + # Initialize all batch caches and tracking + self._initialize_batch_caches() + try: + for operation in operations: + item = None + try: + if ( + operation.method == "PATCH" + and operation.object == SoAItemType.STUDY_ACTIVITY.value + ): + item = self.patch_selection( + study_uid, + operation.content.study_activity_uid, + operation.content.content, + ) + response_code = status.HTTP_200_OK + elif operation.method == "POST": + if operation.object == SoAItemType.STUDY_ACTIVITY.value: + if isinstance( + operation.content, StudySelectionActivityCreateInput + ): + item = self.make_selection(study_uid, operation.content) + else: + raise ValidationException( + msg="POST operation requires StudySelectionActivityCreateInput as request payload." + ) + elif ( + operation.object + == SoAItemType.STUDY_ACTIVITY_SCHEDULE.value ): - item = self.make_selection(study_uid, operation.content) - else: - raise ValidationException( - msg="POST operation requires StudySelectionActivityCreateInput as request payload." + if isinstance( + operation.content, StudyActivityScheduleCreateInput + ): + item = study_activity_schedules_service.create( + study_uid, operation.content + ) + else: + raise ValidationException( + msg="POST operation requires StudyActivityScheduleCreateInput as request payload." + ) + + response_code = status.HTTP_201_CREATED + elif operation.method == "DELETE": + if operation.object == SoAItemType.STUDY_ACTIVITY.value: + self.delete_selection( + study_uid, operation.content.study_activity_uid ) - elif operation.object == SoAItemType.STUDY_ACTIVITY_SCHEDULE.value: - if isinstance( - operation.content, StudyActivityScheduleCreateInput + elif ( + operation.object + == SoAItemType.STUDY_ACTIVITY_SCHEDULE.value ): - item = study_activity_schedules_service.create( - study_uid, operation.content + item = study_activity_schedules_service.delete( + study_uid, operation.content.uid ) - else: - raise ValidationException( - msg="POST operation requires StudyActivityScheduleCreateInput as request payload." - ) - - response_code = status.HTTP_201_CREATED - elif operation.method == "DELETE": - if operation.object == SoAItemType.STUDY_ACTIVITY.value: - self.delete_selection( - study_uid, operation.content.study_activity_uid + response_code = status.HTTP_204_NO_CONTENT + else: + raise MethodNotAllowedException(method=operation.method) + results.append( + StudySoAEditBatchOutput( + response_code=response_code, content=item ) - elif operation.object == SoAItemType.STUDY_ACTIVITY_SCHEDULE.value: - item = study_activity_schedules_service.delete( - study_uid, operation.content.uid + ) + except MDRApiBaseException as error: + results.append( + StudySoAEditBatchOutput.model_construct( + response_code=error.status_code, + content=BatchErrorResponse(message=str(error)), ) - response_code = status.HTTP_204_NO_CONTENT - else: - raise MethodNotAllowedException(method=operation.method) - results.append( - StudySoAEditBatchOutput(response_code=response_code, content=item) - ) - except MDRApiBaseException as error: - results.append( - StudySoAEditBatchOutput.model_construct( - response_code=error.status_code, - content=BatchErrorResponse(message=str(error)), ) + finally: + # Save any pending batch instance AR before clearing caches + if self._batch_instance_ar is not None: + self._repos.study_activity_instance_repository.save( + self._batch_instance_ar, self.author ) + + # Clear all caches and tracking state + self._clear_all_batch_caches() + return results @ensure_transaction(db) @@ -2100,11 +2383,17 @@ def update_activity_request_with_sponsor_activity( assert selection_aggregate is not None # Load the current VO for updates - activity_ar = self._repos.activity_repository.find_by_uid_2( + activity_ar = self._repos.activity_repository.find_by_uid( current_vo.activity_uid ) - replaced_activity_ar = self._repos.activity_repository.find_by_uid_2( - activity_ar.concept_vo.replaced_by_activity + NotFoundException.raise_if_not(activity_ar, "Activity", current_vo.activity_uid) + replaced_activity_ar = self._repos.activity_repository.find_by_uid( + activity_ar.concept_vo.replaced_by_activity # type: ignore[arg-type] + ) + NotFoundException.raise_if_not( + replaced_activity_ar, + "Activity", + activity_ar.concept_vo.replaced_by_activity, ) updated_study_activity = self.patch_selection( study_uid=study_uid, @@ -2208,7 +2497,6 @@ def update_selection_to_latest_version( ) # update StudyActivityGroup - study_activity_group_uid = selection.study_activity_group_uid is_study_activity_group_changed: bool = False sync_activity_group_version: bool = False if sync_latest_version_input and sync_latest_version_input.activity_group_uid: @@ -2220,11 +2508,7 @@ def update_selection_to_latest_version( if latest_activity_group_name != current_selection.activity_group_name: sync_activity_group_version = True if sync_latest_version_input and sync_latest_version_input.activity_group_uid: - ( - activity_group_uid, - _, - study_activity_group_uid, - ) = self._patch_or_get_study_activity_group( + updated_group = self._patch_or_get_study_activity_group( request_object=sync_latest_version_input, current_object=selection, is_soa_group_changed=False, @@ -2232,17 +2516,17 @@ def update_selection_to_latest_version( sync_latest_version=sync_activity_group_version, ) is_study_activity_group_changed = ( - selection.study_activity_group_uid != study_activity_group_uid + selection.study_activity_group_uid != updated_group.study_selection_uid ) - if study_activity_group_uid is None: + if not updated_group.study_selection_uid: raise BusinessLogicException( msg="Study Activity Group UID cannot be None when syncing to latest version." ) selection = selection.update_activity_group( - activity_group_uid=activity_group_uid, - study_activity_group_uid=study_activity_group_uid, + activity_group_uid=updated_group.activity_group_uid, + study_activity_group_uid=updated_group.study_selection_uid, ) sync_activity_subgroup_version: bool = False @@ -2269,22 +2553,18 @@ def update_selection_to_latest_version( raise ValidationException( msg="Sync latest version input can't be None at this point" ) - ( - activity_subgroup_uid, - _, - study_activity_subgroup_uid, - ) = self._patch_or_get_study_activity_subgroup( + updated_subgroup = self._patch_or_get_study_activity_subgroup( request_object=sync_latest_version_input, current_object=selection, is_soa_group_changed=False, is_study_activity_group_changed=is_study_activity_group_changed, - study_activity_group_uid=study_activity_group_uid, + study_activity_group_uid=updated_group.study_selection_uid, sync_latest_version=sync_activity_subgroup_version or is_study_activity_group_changed, ) selection = selection.update_activity_subgroup( - activity_subgroup_uid=activity_subgroup_uid, - study_activity_subgroup_uid=study_activity_subgroup_uid, + activity_subgroup_uid=updated_subgroup.activity_subgroup_uid, + study_activity_subgroup_uid=updated_subgroup.study_selection_uid, ) self._update_aggregate( selection_aggregate=selection_ar, @@ -2297,12 +2577,22 @@ def update_selection_to_latest_version( selection_aggregate = self.repository.find_by_study( study_uid=study_uid, ) - # Fetch the new selection which was just added + # Fetch the new selection which was just updated ( new_selection, _, ) = selection_aggregate.get_specific_object_selection(study_selection_uid) + # Keep _batch_patch_ar_selections current for subsequent operations in the same batch. + # patch_selection does this in the base class; update_selection_to_latest_version + # calls _update_aggregate directly so we mirror the same update here using the + # fully-populated VO from the reload above. Uses immutable update to prevent cache coherence issues. + if self._batch_patch_ar_selections is not None: + self._batch_patch_ar_selections = [ + new_selection if vo.study_selection_uid == study_selection_uid else vo + for vo in self._batch_patch_ar_selections + ] + return self._transform_from_vo_to_response_model( study_uid=study_uid, specific_selection=new_selection, diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection_base.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection_base.py index 6c5c8ddd..e5e26f7a 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection_base.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection_base.py @@ -1,8 +1,10 @@ import abc +import threading from collections import defaultdict from datetime import datetime from typing import Any, Callable, Generic, Iterable, TypeVar +from cachetools import TTLCache from neomodel import db from clinical_mdr_api.domain_repositories.study_selections.study_activity_base_repository import ( @@ -29,6 +31,7 @@ from clinical_mdr_api.services.studies.study_selection_base import StudySelectionMixin from common import exceptions from common.auth.user import user +from common.config import settings from common.telemetry import trace_calls _AggregateRootType = TypeVar("_AggregateRootType", bound=StudySelectionBaseAR) @@ -45,9 +48,34 @@ class StudyActivitySelectionBaseService( _vo_to_ar_filter_map: dict[Any, Any] = {} + # Shared class-level cache for study standards effective dates across all service instances + # Uses config values for consistent cache behavior across the application + _shared_terms_date_cache: TTLCache = TTLCache( + maxsize=settings.cache_max_size, ttl=settings.cache_ttl + ) + # Thread lock for safe concurrent access to the shared cache + _shared_terms_date_cache_lock: threading.RLock = threading.RLock() + def __init__(self): self._repos = MetaRepository() + # Unified batch cache - single TTLCache with namespaced keys for all batch operations. + # Uses dedicated batch_cache_* settings (NOT the cross-request cache_ttl which may be 0). + # Batch caches are instance-scoped and explicitly cleared in _clear_all_batch_caches. + self._batch_cache: TTLCache | None = None + + # Single cached instance AR to avoid repeated find_by_study/save per POST + # Flushed to DB in the batch finally block (or on first PATCH/DELETE that needs DB state) + self._batch_instance_ar: Any | None = ( + None # Keep as single value - no TTL needed + ) + + # Cached selection list for _find_ar_to_patch operations + # Avoids repeated find_by_study(for_update=True) calls during batch PATCH + self._batch_patch_ar_selections: list | None = ( + None # Keep as list - single value per batch + ) + @property def author(self): return user().id() @@ -69,6 +97,136 @@ def _get_selected_object_exist_check( ) -> Callable[[str], bool]: return self.selected_object_repository.final_concept_exists + def _initialize_batch_caches(self) -> None: + """Initialize all batch-related caches and tracking sets for a new batch operation. + + Cache Lifecycle Management: + - Called at the start of handle_batch_operations + - Caches persist throughout the entire batch for performance + - Individual operations may invalidate specific cache entries + - All caches are cleared in the finally block + """ + + self._batch_cache = TTLCache( + maxsize=settings.cache_max_size, ttl=settings.cache_ttl + ) + self._batch_patch_ar_selections = [] # Keep as list - single value per batch + + def _clear_all_batch_caches(self) -> None: + """Clear all batch-related caches and reset tracking state. + + This method ensures a clean state after batch processing and prevents + memory leaks from retained cache references. + """ + if self._batch_cache is not None: + try: + # Explicitly clear all entries to trigger internal cleanup + self._batch_cache.clear() + # Force garbage collection of expired entries + # TTLCache may have internal timers that need explicit cleanup + if hasattr(self._batch_cache, "expire"): + self._batch_cache.expire() + except Exception as e: # pylint: disable=broad-exception-caught + # Log but don't fail - cleanup is best-effort + import logging + + logging.warning("Error during batch cache cleanup: %s", e) + finally: + self._batch_cache = None + + self._batch_instance_ar = None + self._batch_patch_ar_selections = None + + # Unified Cache Access Helpers + def _get_batch_vo_cache_key(self, *args) -> tuple[str, ...]: + """Generate namespaced key for VO cache entries.""" + return ("vo", *args) + + def _get_batch_ar_cache_key(self, *args) -> tuple[str, ...]: + """Generate namespaced key for AR cache entries.""" + return ("ar", *args) + + def _get_batch_reordered_key(self, *args) -> tuple[str, ...]: + """Generate namespaced key for reordered parent tracking.""" + return ("reordered", *args) + + def _append_to_patch_ar_selections_cache(self, new_vo: _VOType) -> None: + """Append a newly created VO to the patch AR selections cache. + + Called after POST so subsequent PATCHes see the new entity without + a DB reload. Uses immutable update to prevent cache coherence issues. + """ + if self._batch_patch_ar_selections is None: + return + self._batch_patch_ar_selections = [*self._batch_patch_ar_selections, new_vo] + + def _remove_from_patch_ar_selections_cache(self, study_selection_uid: str) -> None: + """Remove a deleted VO from the patch AR selections cache. + + Called after DELETE so subsequent PATCHes no longer see the removed entity + without a DB reload. + """ + if self._batch_patch_ar_selections is None: + return + self._batch_patch_ar_selections = [ + vo + for vo in self._batch_patch_ar_selections + if vo.study_selection_uid != study_selection_uid + ] + + def _clear_batch_caches(self) -> None: + """Clear unified batch cache for data consistency.""" + if self._batch_cache is not None: + self._batch_cache.clear() + + @classmethod + def clear_study_standards_cache_for_study(cls, study_uid: str) -> None: + """Clear cached study standards effective dates for a specific study. + + Call this when study standards are modified (create/edit/delete operations) + to ensure subsequent queries see updated effective dates. + + Args: + study_uid: The study whose standards cache entries should be cleared + """ + with cls._shared_terms_date_cache_lock: + if not cls._shared_terms_date_cache: + return + + # Remove all cache entries for this study (across all versions) + keys_to_remove = [ + key + for key in cls._shared_terms_date_cache.keys() + if key[0] + == study_uid # Cache key format: (study_uid, study_value_version) + ] + for key in keys_to_remove: + del cls._shared_terms_date_cache[key] + + def _evict_ar_cache_for_scope( + self, + study_activity_subgroup_uid: str | None, + study_soa_group_uid: str, + activity_library_name: str, + ) -> None: + """Evict the specific scope's AR cache entry after DELETE. + + Only the deleted entity's scope becomes stale. Other scopes remain valid. + Also clears reordered-parent tracking since the hierarchy may need re-compaction. + """ + if self._batch_cache is None: + return + find_requested = activity_library_name == settings.requested_library_name + scope_key = self._get_batch_ar_cache_key( + study_activity_subgroup_uid, study_soa_group_uid, find_requested + ) + self._batch_cache.pop(scope_key, None) + + # Parent hierarchy may need re-compaction after deletion + reordered_keys = [k for k in self._batch_cache.keys() if k[0] == "reordered"] + for key in reordered_keys: + del self._batch_cache[key] + @abc.abstractmethod def _transform_all_to_response_model( self, @@ -327,12 +485,49 @@ def get_specific_selection( @trace_calls(args=[1, 2], kwargs=["study_uid", "study_selection_uid"]) def _find_ar_to_patch( - self, study_uid: str, study_selection_uid: str + self, study_uid: str, study_selection_uid: str, for_update: bool = True ) -> tuple[_AggregateRootType, _VOType]: - # Load aggregate - selection_aggregate = self.repository.find_by_study( - study_uid=study_uid, for_update=True - ) + """Find aggregate root and value object for patching operations. + + In batch mode, this method uses cached selection lists to avoid repeated + database queries. The cache is automatically invalidated when POST/DELETE + operations modify the entity set that PATCH operations need to see. + + Args: + study_uid: Study identifier + study_selection_uid: Selection identifier to patch + for_update: Whether to acquire update locks + + Returns: + Tuple of (selection_aggregate, current_vo) for the patch operation + """ + # In batch mode, use cached selections if available and not invalidated. + # Three states for _batch_patch_ar_selections: + # non-empty list → cache populated, use it + # [] → batch initialised but not yet seeded → load from DB and store + # None → non-batch mode or cache was invalidated → load from DB without storing + if for_update and self._batch_patch_ar_selections: + # Build AR from cached selections — avoids DB round-trip + selections = self._batch_patch_ar_selections + selection_aggregate = ( + self.repository._aggregate_root_type.from_repository_values( + study_uid=study_uid, study_objects_selection=selections + ) + ) + selection_aggregate.repository_closure_data = selections + elif for_update and self._batch_patch_ar_selections is not None: + # Empty list [] — batch mode started, seed the cache from DB + selection_aggregate = self.repository.find_by_study( + study_uid=study_uid, for_update=for_update + ) + self._batch_patch_ar_selections = list( + selection_aggregate.study_objects_selection + ) + else: + # None — non-batch mode or cache was invalidated — load from database + selection_aggregate = self.repository.find_by_study( + study_uid=study_uid, for_update=for_update + ) assert selection_aggregate is not None @@ -341,17 +536,17 @@ def _find_ar_to_patch( study_selection_uid=study_selection_uid ) selection_aggregate = self._filter_ars_from_same_parent( - selection_aggregate=selection_aggregate, selection_vo=current_vo + selection_aggregate=selection_aggregate, selection_vo=current_vo # type: ignore[arg-type] ) return selection_aggregate, current_vo def _update_aggregate( self, selection_aggregate: _AggregateRootType, - # pylint: disable=unused-argument - previous_selection: _VOType, updated_selection: _VOType, - ): + # pylint: disable=unused-argument + previous_selection: _VOType | None = None, + ) -> _VOType: # let the aggregate update the value object selection_aggregate.update_selection( updated_study_object_selection=updated_selection, @@ -362,6 +557,11 @@ def _update_aggregate( # sync with DB and save the update self.repository.save(selection_aggregate, self.author) + # After save(), the repository writeback has updated the in-memory VO with the correct order. + updated_vo, _ = selection_aggregate.get_specific_object_selection( + updated_selection.study_selection_uid + ) + return updated_vo @ensure_transaction(db) def patch_selection( @@ -383,10 +583,10 @@ def patch_selection( current_object=current_vo, ) - self._update_aggregate( + updated_selection = self._update_aggregate( selection_aggregate=selection_aggregate, - previous_selection=current_vo, updated_selection=updated_selection, + previous_selection=current_vo, ) # # sync related nodes @@ -394,16 +594,26 @@ def patch_selection( study_selection=updated_selection, previous_study_selection=current_vo ) - selection_aggregate, updated_selection = self._find_ar_to_patch( - study_uid=study_uid, study_selection_uid=study_selection_uid - ) + # Keep the batch AR-selection cache current after each PATCH save. + # This ensures subsequent PATCH operations in the same batch see the updated state. + # Uses immutable update to prevent cache coherence issues. + if self._batch_patch_ar_selections is not None: + self._batch_patch_ar_selections = [ + ( + updated_selection + if vo.study_selection_uid == study_selection_uid + else vo + ) + for vo in self._batch_patch_ar_selections + ] + terms_at_specific_datetime = self._extract_study_standards_effective_date( study_uid=study_uid ) # add the activity and return return self._transform_from_vo_to_response_model( - study_uid=selection_aggregate.study_uid, + study_uid=study_uid, specific_selection=updated_selection, terms_at_specific_datetime=terms_at_specific_datetime, ) @@ -494,19 +704,41 @@ def _get_linked_activities( selection_vos: Iterable[StudySelectionBaseVO], filter_out_retired_groupings: bool = False, ) -> list[ActivityAR]: - version_specific_uids = defaultdict(set) + version_specific_uids: dict[str, set[str]] = defaultdict(set) + latest_uids: dict[str, set[str]] = defaultdict(set) for selection_vo in selection_vos: version_specific_uids[selection_vo.activity_uid].add( selection_vo.activity_version ) - version_specific_uids[selection_vo.activity_uid].add("LATEST") + latest_uids[selection_vo.activity_uid].add("LATEST") if not version_specific_uids: return [] - return self._repos.activity_repository.get_all_optimized( - version_specific_uids=version_specific_uids, - include_retired_versions=True, - filter_out_retired_groupings=filter_out_retired_groupings, - )[0] + if not filter_out_retired_groupings: + for uid, versions in latest_uids.items(): + version_specific_uids[uid].update(versions) + return self._repos.activity_repository.get_all_optimized( + version_specific_uids=version_specific_uids, + include_retired_versions=True, + )[0] + + # When filtering retired groupings, fetch pinned versions unfiltered (so the study's + # pinned `activity` always shows all its original groupings) and fetch the LATEST + # versions with the filter applied (so `latest_activity` only shows active groupings). + # Combining both allows _find_versions to resolve each field independently. + pinned_results: list[ActivityAR] = ( + self._repos.activity_repository.get_all_optimized( + version_specific_uids=version_specific_uids, + include_retired_versions=True, + )[0] + ) + latest_results: list[ActivityAR] = ( + self._repos.activity_repository.get_all_optimized( + version_specific_uids=latest_uids, + include_retired_versions=True, + filter_out_retired_groupings=True, + )[0] + ) + return pinned_results + latest_results diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_disease_milestone.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_disease_milestone.py index 8a30764f..2a3644db 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_disease_milestone.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_disease_milestone.py @@ -3,6 +3,9 @@ from neomodel import db +from clinical_mdr_api.domain_repositories._utils.helpers import ( + acquire_write_lock_study_value, +) from clinical_mdr_api.domains.study_definition_aggregates.study_metadata import ( StudyStatus, ) @@ -262,6 +265,7 @@ def create( study_uid: str, study_disease_milestone_input: StudyDiseaseMilestoneCreateInput, ): + acquire_write_lock_study_value(uid=study_uid) all_disease_milestones = self.repo.find_all_disease_milestones_by_study( study_uid ) @@ -295,9 +299,11 @@ def create( @db.transaction def edit( self, + study_uid: str, study_disease_milestone_uid: str, study_disease_milestone_input: StudyDiseaseMilestoneEditInput, ): + acquire_write_lock_study_value(uid=study_uid) study_disease_milestone = self.repo.find_by_uid(study_disease_milestone_uid) self._validate_update(study_disease_milestone_input, study_disease_milestone) fill_missing_values_in_base_model_from_reference_base_model( @@ -316,7 +322,8 @@ def edit( return self._transform_all_to_response_model(updated_item) @db.transaction - def reorder(self, study_disease_milestone_uid: str, new_order: int): + def reorder(self, study_uid: str, study_disease_milestone_uid: str, new_order: int): + acquire_write_lock_study_value(uid=study_uid) new_order -= 1 disease_milestone = self.repo.find_by_uid(study_disease_milestone_uid) study_disease_milestones = self.repo.find_all_disease_milestones_by_study( @@ -353,7 +360,8 @@ def reorder(self, study_disease_milestone_uid: str, new_order: int): return self._transform_all_to_response_model(disease_milestone) @db.transaction - def delete(self, study_disease_milestone_uid: str): + def delete(self, study_uid: str, study_disease_milestone_uid: str): + acquire_write_lock_study_value(uid=study_uid) study_disease_milestone = self.repo.find_by_uid(study_disease_milestone_uid) self.repo.save(study_disease_milestone, delete_flag=True) diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_selection_base.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_selection_base.py index 21c5aca5..676cc5b3 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_selection_base.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_selection_base.py @@ -783,6 +783,17 @@ def _get_specific_activity_instance_selection_by_uids( def _extract_study_standards_effective_date( self, study_uid, study_value_version: str | None = None ) -> datetime | None: + cache_key = (study_uid, study_value_version) + # Use shared class-level cache for study standards effective dates + from clinical_mdr_api.services.studies.study_activity_selection_base import ( + StudyActivitySelectionBaseService, + ) + + cache = StudyActivitySelectionBaseService._shared_terms_date_cache + with StudyActivitySelectionBaseService._shared_terms_date_cache_lock: + if cache_key in cache: + return cache[cache_key] + repos = self._repos study_standard_versions = ( repos.study_standard_version_repository.find_standard_versions_in_study( @@ -811,6 +822,9 @@ def _extract_study_standards_effective_date( 59, 999999, ) + # Save to shared class-level cache + with StudyActivitySelectionBaseService._shared_terms_date_cache_lock: + cache[cache_key] = terms_at_specific_datetime return terms_at_specific_datetime @trace_calls diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_standard_version_selection.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_standard_version_selection.py index ddeafab9..f4037d6b 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_standard_version_selection.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_standard_version_selection.py @@ -24,6 +24,9 @@ calculate_diffs_history, fill_missing_values_in_base_model_from_reference_base_model, ) +from clinical_mdr_api.services.studies.study_activity_selection_base import ( + StudyActivitySelectionBaseService, +) from common import exceptions from common.auth.user import user @@ -188,6 +191,12 @@ def create( ) updated_item = self.repo.save(created_study_standard_version) + + # Clear study standards caches across all study activity services + StudyActivitySelectionBaseService.clear_study_standards_cache_for_study( + study_uid + ) + return self._transform_all_to_response_model(updated_item) @db.transaction @@ -248,6 +257,11 @@ def edit( updated_item = self.repo.save(study_standard_version) + # Clear study standards caches across all study activity services + StudyActivitySelectionBaseService.clear_study_standards_cache_for_study( + study_uid + ) + return self._transform_all_to_response_model(updated_item) raise exceptions.BusinessLogicException(msg="There's nothing to change") @@ -258,6 +272,11 @@ def delete(self, study_uid: str, study_standard_version_uid: str): ) self.repo.save(study_standard_version, delete_flag=True) + # Clear study standards caches across all study activity services + StudyActivitySelectionBaseService.clear_study_standards_cache_for_study( + study_uid + ) + @db.transaction def audit_trail( self, diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_visit.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_visit.py index eefe11a9..87be863a 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_visit.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_visit.py @@ -1044,7 +1044,7 @@ def _from_input_values( time_unit_object=time_unit_object, description=create_input.description, start_rule=( - settings.unscheduled_visit_start_rule + create_input.start_rule or settings.unscheduled_visit_start_rule if create_input.visit_class == VisitClass.UNSCHEDULED_VISIT else create_input.start_rule ), @@ -1425,6 +1425,7 @@ def edit( @ensure_transaction(db) def delete(self, study_uid: str, study_visit_uid: str): + acquire_write_lock_study_value(uid=study_uid) study_visits = self.repo.find_all_visits_by_study_uid(study_uid) timeline = TimelineAR(study_uid=study_uid, _visits=study_visits) ordered_visits = timeline.ordered_study_visits diff --git a/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/routes.py b/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/routes.py index 43dff0da..d1ed2476 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/routes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/routes.py @@ -992,6 +992,7 @@ ("/ct/codelists/{codelist_uid}/names/approvals", "POST", {"Library.Write"}), ("/ct/codelists/{codelist_uid}/paired", "GET", {"Library.Read"}), ("/ct/codelists/{codelist_uid}/paired", "PATCH", {"Library.Write"}), + ("/ct/paired-codelists", "POST", {"Library.Write"}), ("/ct/paired-codelists/{codelist_uid}/terms", "GET", {"Library.Read"}), ("/ct/terms", "POST", {"Library.Write"}), ("/ct/terms", "GET", {"Library.Read"}), @@ -1143,12 +1144,12 @@ {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/activations", + "/concepts/activities/activity-instances/{activity_instance_uid}/activations", "POST", {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/activations", + "/concepts/activities/activity-instances/{activity_instance_uid}/activations", "DELETE", {"Library.Write"}, ), @@ -1182,16 +1183,6 @@ "POST", {"Library.Write"}, ), - ( - "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations", - "POST", - {"Library.Write"}, - ), - ( - "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations", - "DELETE", - {"Library.Write"}, - ), ("/activity-instance-classes", "GET", {"Library.Read"}), ("/activity-instance-classes/versions", "GET", {"Library.Read"}), ("/activity-instance-classes/headers", "GET", {"Library.Read"}), @@ -1743,11 +1734,21 @@ ("/studies/list", "GET", {"Study.Read"}), ("/studies/structure-overview", "GET", {"Study.Read"}), ("/studies/structure-overview/headers", "GET", {"Study.Read"}), + ("/studies/template", "GET", {"Study.Read"}), + ("/studies/template", "POST", {"Study.Write"}), + ("/studies/template", "PATCH", {"Study.Write"}), + ("/studies/template/activations", "DELETE", {"Study.Write"}), + ("/studies/template/activations", "POST", {"Study.Write"}), ("/studies/{study_uid}/locks", "POST", {"Study.Write"}), ("/studies/{study_uid}/unlocks", "POST", {"Study.Write"}), ("/studies/{study_uid}/release", "POST", {"Study.Write"}), ("/studies/{study_uid}/order", "PATCH", {"Study.Write"}), ("/studies/{study_uid}/structure-statistics", "GET", {"Study.Read"}), + ( + "/studies/{study_uid}/study-selection-containment/{target_study_uid}", + "GET", + {"Study.Read"}, + ), ("/studies/{study_uid}", "DELETE", {"Study.Write"}), ("/studies/{study_uid}", "PATCH", {"Study.Write"}), ("/studies/{study_uid}", "GET", {"Study.Read"}), @@ -2436,6 +2437,7 @@ ("/studies/{study_uid}/soa-splits", "DELETE", {"Study.Write"}), ("/studies/{study_uid}/soa-splits/{study_visit_uid}", "DELETE", {"Study.Write"}), ("/studies/{study_uid}/complexity-score", "GET", {"Study.Read"}), + ("/studies/{study_uid}/complexity-score-details", "GET", {"Study.Read"}), ("/concepts/unit-definitions", "GET", {"Library.Read"}), ("/concepts/unit-definitions/headers", "GET", {"Library.Read"}), ("/concepts/unit-definitions/{unit_definition_uid}", "GET", {"Library.Read"}), diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activities.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activities.py index 8751c2d3..b4bccfee 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activities.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activities.py @@ -459,9 +459,7 @@ def test_get_activity(api_client): response = api_client.get( f"/concepts/activities/activities/{activities_all[0].uid}" ) - res = response.json() - - assert_response_status_code(response, 200) + res = parse_json_response(response, assert_status=200) # Check fields included in the response assert set(res.keys()) == set(ACTIVITY_FIELDS_ALL) @@ -508,7 +506,7 @@ def test_get_activity_pagination(api_client): sort_by = '{"name": true}' for page_number in range(1, 4): url = f"/concepts/activities/activities?page_number={page_number}&page_size=3&sort_by={sort_by}" - res = parse_json_response(api_client.get(url)) + res = parse_json_response(api_client.get(url), assert_status=200) res_names = [item["name"] for item in res["items"]] results_paginated[page_number] = res_names log.info("Page %s: %s", page_number, res_names) @@ -524,7 +522,8 @@ def test_get_activity_pagination(api_client): res_all = parse_json_response( api_client.get( f"/concepts/activities/activities?page_number=1&page_size=100&sort_by={sort_by}" - ) + ), + assert_status=200, ) results_all_in_one_page = list(map(lambda x: x["name"], res_all["items"])) log.info("All rows in one page: %s", results_all_in_one_page) @@ -537,7 +536,8 @@ def test_get_activity_pagination(api_client): res_all = parse_json_response( api_client.get( f"/concepts/activities/activities?page_number=1&page_size=100&sort_by={sort_by}" - ) + ), + assert_status=200, ) all_results = list( map( @@ -557,7 +557,8 @@ def test_get_activity_pagination(api_client): res_all = parse_json_response( api_client.get( f"/concepts/activities/activities?page_number=1&page_size=100&sort_by={sort_by}" - ) + ), + assert_status=200, ) all_results = list( map( @@ -577,7 +578,8 @@ def test_get_activity_pagination(api_client): res_all = parse_json_response( api_client.get( f"/concepts/activities/activities?page_number=1&page_size=100&sort_by={sort_by}" - ) + ), + assert_status=200, ) all_results = list( map( @@ -597,7 +599,8 @@ def test_get_activity_pagination(api_client): res_all = parse_json_response( api_client.get( f"/concepts/activities/activities?page_number=1&page_size=100&sort_by={sort_by}" - ) + ), + assert_status=200, ) all_results = list( map( @@ -622,9 +625,7 @@ def test_get_activity_versions(api_client): # Get all versions of all activities response = api_client.get("/concepts/activities/activities/versions?page_size=100") - res = response.json() - - assert_response_status_code(response, 200) + res = parse_json_response(response, assert_status=200) # Check fields included in the response assert set(res.keys()) == set(["items", "total", "page", "size"]) @@ -655,9 +656,8 @@ def test_filtering_versions_wildcard( ): url = f"/concepts/activities/activities/versions?filters={filter_by}" response = api_client.get(url) - res = response.json() + res = parse_json_response(response, assert_status=200) - assert_response_status_code(response, 200) if expected_result_prefix: assert len(res["items"]) > 0 nested_path = None @@ -708,9 +708,8 @@ def test_filtering_versions_exact( ): url = f"/concepts/activities/activities/versions?filters={filter_by}" response = api_client.get(url) - res = response.json() + res = parse_json_response(response, assert_status=200) - assert_response_status_code(response, 200) if expected_result: assert len(res["items"]) > 0 @@ -748,8 +747,7 @@ def test_explicit_filtering_by_activity_subgroup_and_group_uid(api_client): "activity_group_uid": activity_group.uid, }, ) - assert_response_status_code(response, 200) - res = response.json()["items"] + res = parse_json_response(response, assert_status=200)["items"] assert len(res) == 0 response = api_client.get( @@ -759,8 +757,7 @@ def test_explicit_filtering_by_activity_subgroup_and_group_uid(api_client): "activity_group_uid": different_activity_group.uid, }, ) - assert_response_status_code(response, 200) - res = response.json()["items"] + res = parse_json_response(response, assert_status=200)["items"] assert len(res) == 6 assert res[0]["uid"] == activity_with_multiple_groupings.uid @@ -785,8 +782,7 @@ def test_explicit_filtering_by_activity_subgroup_and_group_uid(api_client): "activity_group_uid": different_activity_group.uid, }, ) - assert_response_status_code(response, 200) - res = response.json()["items"] + res = parse_json_response(response, assert_status=200)["items"] assert len(res) == 0 @@ -803,24 +799,24 @@ def test_grouped_groupings_payload_flag(api_client): "page_size": 0, }, ) - assert_response_status_code(response, 200) - res = response.json()["items"] + items = parse_json_response(response, assert_status=200)["items"] + assert any( - len(activity["activity_groupings"]) > 1 for activity in res + len(activity["activity_groupings"]) > 1 for activity in items ), "Test precondition failed: At least one activity should have multiple groupings" assert any( - len(activity["activity_instances"]) > 1 for activity in res + len(activity["activity_instances"]) > 1 for activity in items ), "Test precondition failed: At least one activity should have multiple instances" # Check that the activity with multiple groupings is present and has two instances linked to it assert any( - activity["uid"] == activity_with_multiple_groupings.uid for activity in res + activity["uid"] == activity_with_multiple_groupings.uid for activity in items ), "Test precondition failed: The activity with multiple groupings is not present in the response" # Collect groupings and number of instances for later comparison grouped_groupings = set() nbr_instances_grouped = 0 - for activity in res: + for activity in items: if activity["uid"] == activity_with_multiple_groupings.uid: assert ( len(activity["activity_instances"]) == 2 @@ -847,12 +843,11 @@ def test_grouped_groupings_payload_flag(api_client): "page_size": 0, }, ) - assert_response_status_code(response, 200) - res = response.json()["items"] + items = parse_json_response(response, assert_status=200)["items"] ungrouped_groupings = set() nbr_instances_ungrouped = 0 - for activity in res: + for activity in items: nbr_instances_ungrouped += len(activity["activity_instances"]) if activity["uid"] == activity_with_multiple_groupings.uid: assert ( @@ -927,11 +922,8 @@ def test_create_activity_unique_name_validation(api_client): "library_name": archived_library["name"], }, ) - assert_response_status_code(response, 409) - assert ( - response.json()["message"] - == f"Activity with Name '{activity_name}' already exists." - ) + res = parse_json_response(response, assert_status=409) + assert res["message"] == f"Activity with Name '{activity_name}' already exists." # Create activity with the same name as the first one but in different Library response = api_client.post( @@ -948,8 +940,7 @@ def test_create_activity_unique_name_validation(api_client): "library_name": "Sponsor", }, ) - assert_response_status_code(response, 201) - res = response.json() + res = parse_json_response(response, assert_status=201) assert res["name"] == activity_name assert res["library_name"] == "Sponsor" @@ -968,11 +959,8 @@ def test_create_activity_unique_name_validation(api_client): "library_name": archived_library["name"], }, ) - assert_response_status_code(response, 409) - assert ( - response.json()["message"] - == f"Activity with Name '{activity_name2}' already exists." - ) + res = parse_json_response(response, assert_status=409) + assert res["message"] == f"Activity with Name '{activity_name2}' already exists." def test_update_activity_to_new_grouping(api_client): @@ -1022,8 +1010,7 @@ def test_update_activity_to_new_grouping(api_client): f"/concepts/activities/activity-sub-groups/{subgroup.uid}" ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert res["name"] == edited_subgroup_name @@ -1062,8 +1049,7 @@ def test_update_activity_to_new_grouping(api_client): # Get the activity by uid and assert that it was updated to the new subgroup version response = api_client.get(f"/concepts/activities/activities/{activity.uid}") - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert res["version"] == "2.0" assert res["status"] == "Final" @@ -1103,8 +1089,7 @@ def test_update_activity(api_client): "change_description": "Updated synonyms and groupings", }, ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert res["uid"] == activity.uid assert res["name"] == "name-CCC" @@ -1157,7 +1142,7 @@ def test_cannot_create_activity_with_non_unique_synonyms(api_client): }, ) assert_response_status_code(response, 409) - res = response.json() + res = parse_json_response(response, assert_status=409) assert res["type"] == "AlreadyExistsException" assert ( @@ -1191,7 +1176,7 @@ def test_cannot_update_activity_with_non_unique_synonyms(api_client): }, ) assert_response_status_code(response, 409) - res = response.json() + res = parse_json_response(response, assert_status=409) assert res["type"] == "AlreadyExistsException" assert ( @@ -1259,8 +1244,7 @@ def test_cascade_edit_activities(api_client): f"/concepts/activities/activity-instances/{activity_instance.uid}" ) - res = response.json() - assert_response_status_code(response, 200) + res = parse_json_response(response, assert_status=200) assert res["name"] == "Cascade Activity Instance" assert len(res["activity_groupings"]) == 1 assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid @@ -1326,8 +1310,7 @@ def test_cascade_edit_activities(api_client): response = api_client.get( f"/concepts/activities/activity-instances/{activity_instance.uid}" ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert len(res["activity_groupings"]) == 1 # Update the activity by adding new activity groupings @@ -1373,8 +1356,7 @@ def test_cascade_edit_activities(api_client): response = api_client.get( f"/concepts/activities/activity-instances/{activity_instance.uid}" ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert len(res["activity_groupings"]) == 1 assert res["groupings_version"] == "3.0" assert res["groupings_status"] == "Final" @@ -1414,8 +1396,7 @@ def test_cascade_edit_activities(api_client): response = api_client.get( f"/concepts/activities/activity-instances/{activity_instance.uid}" ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert len(res["activity_groupings"]) == 1 assert res["groupings_version"] == "3.0" assert res["groupings_status"] == "Final" @@ -1425,8 +1406,7 @@ def test_cascade_edit_activities(api_client): response = api_client.get( f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions" ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) unchanged_draft = TestUtils._get_version_from_list(res, "1.1") updated_draft = TestUtils._get_version_from_list(res, "1.2") new_final = TestUtils._get_version_from_list(res, "2.0") @@ -1475,8 +1455,7 @@ def test_cascade_edit_activities(api_client): response = api_client.get( f"/concepts/activities/activity-instances/{activity_instance.uid}" ) - assert_response_status_code(response, 200) - res = response.json() + res = parse_json_response(response, assert_status=200) assert res["groupings_version"] == "3.0" assert res["groupings_status"] == "Final" @@ -1798,8 +1777,7 @@ def test_create_activity_without_groupings_not_allowed(api_client): "activity_groupings": [], }, ) - assert_response_status_code(response, 400) - res = response.json() + res = parse_json_response(response, assert_status=400) assert res["type"] == "BusinessLogicException" assert res["message"] == "Sponsor activities must have at least one grouping." diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_group_status_validation.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_group_status_validation.py index ac0d7f60..c02f4815 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_group_status_validation.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_group_status_validation.py @@ -4,6 +4,7 @@ from fastapi.testclient import TestClient from clinical_mdr_api.main import app +from clinical_mdr_api.models.concepts.activities.activity import ActivityEditInput from clinical_mdr_api.services.concepts.activities.activity_group_service import ( ActivityGroupService, ) @@ -23,6 +24,7 @@ # pylint: disable=unused-argument # pylint: disable=redefined-outer-name # pylint: disable=too-many-arguments +# pylint: disable=unsubscriptable-object # pytest fixture functions have other fixture functions as arguments, # which pylint interprets as unused arguments @@ -185,10 +187,6 @@ def test_edit_activity_with_retired_activity_group_fails(): activity_service = ActivityService() with pytest.raises(BusinessLogicException) as exc_info: - from clinical_mdr_api.models.concepts.activities.activity import ( - ActivityEditInput, - ) - edit_input = ActivityEditInput( name=activity.name, name_sentence_case=activity.name_sentence_case, @@ -213,6 +211,87 @@ def test_edit_activity_with_retired_activity_group_fails(): ) +def test_edit_activity_to_remove_retired_subgroup_grouping_succeeds(): + """Test that editing an activity to remove a grouping with a retired sub-group + succeeds when the remaining groupings are carried over from the previous version. + + This reproduces the real-world circular dependency reported in the bug: + 1. Activity group and two sub-groups are Final, activity is Final + 2. One sub-group is retired + 3. A new version of the group is created and approved with cascade, + which cascade-edits the activity to a new Final version + 4. Another new version of the group is created (now Draft again) + 5. User creates a draft of the activity and tries to remove the retired + sub-group grouping, but the carried-over grouping referencing the + Draft group blocks the edit + """ + activity_group_service = ActivityGroupService() + activity_service = ActivityService() + + # Create and approve an activity group and two sub-groups + activity_group = TestUtils.create_activity_group( + name=TestUtils.random_str(20, "ActivityGroup-"), + approve=True, + ) + subgroup_to_keep = TestUtils.create_activity_subgroup( + name=TestUtils.random_str(20, "SubgroupKeep-"), + approve=True, + ) + subgroup_to_retire = TestUtils.create_activity_subgroup( + name=TestUtils.random_str(20, "SubgroupRetire-"), + approve=True, + ) + + # Create activity with two groupings, then approve it (Final v1.0) + activity = TestUtils.create_activity( + name=TestUtils.random_str(20, "Activity-"), + activity_subgroups=[subgroup_to_keep.uid, subgroup_to_retire.uid], + activity_groups=[activity_group.uid, activity_group.uid], + approve=True, + ) + + # Retire one sub-group + ActivitySubGroupService().inactivate_final(uid=subgroup_to_retire.uid) + + # Create new version of the group (Draft v2.0) and approve it with cascade. + # The cascade automatically creates a new version of the activity and approves it. + activity_group_service.create_new_version(uid=activity_group.uid) + activity_group_service.approve( + uid=activity_group.uid, cascade_edit_and_approve=True + ) + + # Create yet another new version of the group (now Draft v3.0). + # The activity's carried-over grouping now references a Draft group. + activity_group_service.create_new_version(uid=activity_group.uid) + + # Create new draft version of the activity (so we can edit it) + activity_service.create_new_version(uid=activity.uid) + + # Edit the activity to remove the retired sub-group grouping, + # keeping only the (draft-group, final-subgroup) pair. + # This should succeed because we're only carrying over an existing grouping, + # not adding a new one. + edit_input = ActivityEditInput( + name=activity.name, + name_sentence_case=activity.name_sentence_case, + change_description="Remove retired sub-group grouping", + activity_groupings=[ + { + "activity_group_uid": activity_group.uid, + "activity_subgroup_uid": subgroup_to_keep.uid, + } + ], + ) + result = activity_service.edit_draft( + uid=activity.uid, concept_edit_input=edit_input, patch_mode=False + ) + + assert result is not None + assert len(result.activity_groupings) == 1 + assert result.activity_groupings[0].activity_group_uid == activity_group.uid + assert result.activity_groupings[0].activity_subgroup_uid == subgroup_to_keep.uid + + def test_create_activity_with_final_groups_succeeds(): """Test that creating an activity with final (approved) groups succeeds.""" # Create and approve activity group and subgroup @@ -238,6 +317,5 @@ def test_create_activity_with_final_groups_succeeds(): assert activity.uid is not None assert activity.activity_groupings is not None assert len(activity.activity_groupings) == 1 - # pylint: disable=unsubscriptable-object assert activity.activity_groupings[0].activity_group_uid == activity_group.uid assert activity.activity_groupings[0].activity_subgroup_uid == activity_subgroup.uid diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instances.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instances.py index 2504fd99..97c0c899 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instances.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instances.py @@ -1184,6 +1184,11 @@ def test_get_activity_instance_groupings_versions(api_client): assert item["start_date"] is not None assert item["status"] is not None assert item["version"] is not None + # check that activity_groupings contain version info for linked entities + for grouping in item["activity_groupings"]: + assert grouping["activity"]["version"] is not None + assert grouping["activity_subgroup"]["version"] is not None + assert grouping["activity_group"]["version"] is not None # Check that the items are sorted by start_date descending sorted_items = sorted(res, key=itemgetter("start_date"), reverse=True) @@ -1233,6 +1238,7 @@ def test_edit_activity_instance_groupings(api_client): assert len(res["activity_groupings"]) == 1 assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid assert res["activity_groupings"][0]["activity"]["name"] == activity.name + assert res["activity_groupings"][0]["activity"]["version"] is not None assert ( res["activity_groupings"][0]["activity_subgroup"]["uid"] == activity_subgroup.uid @@ -1241,8 +1247,10 @@ def test_edit_activity_instance_groupings(api_client): res["activity_groupings"][0]["activity_subgroup"]["name"] == activity_subgroup.name ) + assert res["activity_groupings"][0]["activity_subgroup"]["version"] is not None assert res["activity_groupings"][0]["activity_group"]["uid"] == activity_group.uid assert res["activity_groupings"][0]["activity_group"]["name"] == activity_group.name + assert res["activity_groupings"][0]["activity_group"]["version"] is not None assert res["version"] == "0.1" assert res["status"] == "Draft" @@ -1267,6 +1275,7 @@ def test_edit_activity_instance_groupings(api_client): assert len(res["activity_groupings"]) == 1 assert res["activity_groupings"][0]["activity"]["uid"] == activity2.uid assert res["activity_groupings"][0]["activity"]["name"] == activity2.name + assert res["activity_groupings"][0]["activity"]["version"] is not None assert ( res["activity_groupings"][0]["activity_subgroup"]["uid"] == activity_subgroup.uid @@ -1275,8 +1284,10 @@ def test_edit_activity_instance_groupings(api_client): res["activity_groupings"][0]["activity_subgroup"]["name"] == activity_subgroup.name ) + assert res["activity_groupings"][0]["activity_subgroup"]["version"] is not None assert res["activity_groupings"][0]["activity_group"]["uid"] == activity_group.uid assert res["activity_groupings"][0]["activity_group"]["name"] == activity_group.name + assert res["activity_groupings"][0]["activity_group"]["version"] is not None assert res["version"] == "0.2" assert res["status"] == "Draft" @@ -1292,6 +1303,7 @@ def test_edit_activity_instance_groupings(api_client): assert res["version"] == "0.1" assert len(res["activity_groupings"]) == 1 assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid + assert res["activity_groupings"][0]["activity"]["version"] is not None # Get version 0.2 response = api_client.get( @@ -1783,18 +1795,27 @@ def test_activity_instance_attributes_versioning(api_client): assert res["message"] == "The object isn't in draft status." response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations" + f"/concepts/activities/activity-instances/{activity_instance_uid}/activations" ) assert_response_status_code(response, 400) res = response.json() - assert res["message"] == "Only RETIRED version can be reactivated." + assert res["message"] == ( + "Cannot reactivate: activity instance attributes are not in Retired status." + ) + + # Groupings must also be Final before the merged inactivate endpoint is allowed + response = api_client.post( + f"/concepts/activities/activity-instances/{activity_instance_uid}/groupings/approvals" + ) + assert_response_status_code(response, 201) + response = api_client.delete( - f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations" + f"/concepts/activities/activity-instances/{activity_instance_uid}/activations" ) assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations" + f"/concepts/activities/activity-instances/{activity_instance_uid}/activations" ) assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelists.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelists.py index 212636aa..fc83959f 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelists.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelists.py @@ -29,6 +29,7 @@ catalogue: str URL = "/ct/codelists" +PAIRED_URL = "/ct/paired-codelists" @pytest.fixture(scope="module") @@ -84,10 +85,8 @@ def test_get_paired_codelist(api_client): response_json = response.json() print(response_json) assert len(response_json["items"]) == 1 - assert response_json["items"][0]["paired_names_codelist_uid"] is None - assert ( - response_json["items"][0]["paired_codes_codelist_uid"] == codes_cl.codelist_uid - ) + assert response_json["items"][0]["paired_codelist"]["uid"] == codes_cl.codelist_uid + assert response_json["items"][0]["paired_codelist"]["name"] is not None # Check the codelist with codes response = api_client.get(f"{URL}/{codes_cl.codelist_uid}/paired") @@ -108,10 +107,8 @@ def test_get_paired_codelist(api_client): response_json = response.json() print(response_json) assert len(response_json["items"]) == 1 - assert ( - response_json["items"][0]["paired_names_codelist_uid"] == names_cl.codelist_uid - ) - assert response_json["items"][0]["paired_codes_codelist_uid"] is None + assert response_json["items"][0]["paired_codelist"]["uid"] == names_cl.codelist_uid + assert response_json["items"][0]["paired_codelist"]["name"] is not None def test_post_paired_codelist(api_client): @@ -211,3 +208,104 @@ def test_unlink_paired_codelists(api_client): response_json = response.json() assert response_json["codes"] is None assert response_json["names"] is None + + +def test_create_paired_codelists(api_client): + response = api_client.post( + PAIRED_URL, + json={ + "catalogue_names": [catalogue], + "name_information": { + "name": "paired names codelist", + "submission_value": "PAIRED_NAMES_SV", + "nci_preferred_name": "Names NCI Preferred", + "definition": "Names codelist definition", + "sponsor_preferred_name": "Names Sponsor Preferred", + }, + "code_information": { + "name": "paired codes codelist", + "submission_value": "PAIRED_CODES_SV", + "nci_preferred_name": "Codes NCI Preferred", + "definition": "Codes codelist definition", + "sponsor_preferred_name": "Codes Sponsor Preferred", + }, + "extensible": True, + "is_ordinal": False, + "template_parameter": False, + "library_name": "Sponsor", + }, + ) + assert_response_status_code(response, 201) + res = response.json() + + # Response should have both names and codes codelists + assert res["names"] is not None + assert res["codes"] is not None + + names_uid = res["names"]["codelist_uid"] + codes_uid = res["codes"]["codelist_uid"] + assert names_uid != codes_uid + + # Verify names codelist attributes + names_attrs = res["names"]["attributes"] + assert names_attrs["name"] == "paired names codelist" + assert names_attrs["submission_value"] == "PAIRED_NAMES_SV" + assert names_attrs["nci_preferred_name"] == "Names NCI Preferred" + assert names_attrs["definition"] == "Names codelist definition" + names_name = res["names"]["name"] + assert names_name["name"] == "Names Sponsor Preferred" + + # Verify codes codelist attributes + codes_attrs = res["codes"]["attributes"] + assert codes_attrs["name"] == "paired codes codelist" + assert codes_attrs["submission_value"] == "PAIRED_CODES_SV" + assert codes_attrs["nci_preferred_name"] == "Codes NCI Preferred" + assert codes_attrs["definition"] == "Codes codelist definition" + codes_name = res["codes"]["name"] + assert codes_name["name"] == "Codes Sponsor Preferred" + + # Verify pairing from the names codelist side + response = api_client.get(f"{URL}/{names_uid}/paired") + assert_response_status_code(response, 200) + paired = response.json() + assert paired["codes"]["codelist_uid"] == codes_uid + assert paired["names"] is None + + # Verify pairing from the codes codelist side + response = api_client.get(f"{URL}/{codes_uid}/paired") + assert_response_status_code(response, 200) + paired = response.json() + assert paired["names"]["codelist_uid"] == names_uid + assert paired["codes"] is None + + +def test_create_paired_codelists_minimal(api_client): + """Test creating paired codelists with minimal optional fields.""" + response = api_client.post( + PAIRED_URL, + json={ + "catalogue_names": [catalogue], + "name_information": { + "name": "minimal names codelist", + "submission_value": "MIN_NAMES_SV", + "definition": "Minimal names definition", + "sponsor_preferred_name": "Min Names Sponsor", + }, + "code_information": { + "name": "minimal codes codelist", + "submission_value": "MIN_CODES_SV", + "definition": "Minimal codes definition", + "sponsor_preferred_name": "Min Codes Sponsor", + }, + "extensible": False, + "is_ordinal": False, + "template_parameter": False, + "library_name": "Sponsor", + }, + ) + assert_response_status_code(response, 201) + res = response.json() + assert res["names"] is not None + assert res["codes"] is not None + assert res["names"]["attributes"]["nci_preferred_name"] is None + assert res["codes"]["attributes"]["nci_preferred_name"] is None diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_ct_stats.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_ct_stats.py index 047442c5..05f14aac 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_ct_stats.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_ct_stats.py @@ -66,8 +66,7 @@ def test_ct_stats(api_client): "library_name": "Sponsor", "parent_codelist_uid": None, "child_codelist_uids": [], - "paired_codes_codelist_uid": None, - "paired_names_codelist_uid": None, + "paired_codelist": None, "name": { "catalogue_names": [], "codelist_uid": None, @@ -110,8 +109,7 @@ def test_ct_stats(api_client): "library_name": "CDISC", "parent_codelist_uid": None, "child_codelist_uids": [], - "paired_codes_codelist_uid": None, - "paired_names_codelist_uid": None, + "paired_codelist": None, "name": { "catalogue_names": [], "codelist_uid": None, @@ -154,8 +152,7 @@ def test_ct_stats(api_client): "library_name": "Sponsor", "parent_codelist_uid": None, "child_codelist_uids": [], - "paired_codes_codelist_uid": None, - "paired_names_codelist_uid": None, + "paired_codelist": None, "name": { "catalogue_names": [], "codelist_uid": None, diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py index 37705653..76d9483a 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py @@ -79,7 +79,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): # Initially no SOA splits, returns an empty list response = api_client.get(f"/studies/{test_data.study.uid}/soa-splits") - returned = parse_json_response(response, status=200) + returned = parse_json_response(response, assert_status=200) assert returned == [] # Add a uid to SoA splits @@ -87,7 +87,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", json={"uid": test_data.visits[5].uid}, ) - returned = parse_json_response(response) + returned = parse_json_response(response, assert_status=200) expected = [{"uid": test_data.visits[5].uid, "study_uid": test_data.study.uid}] assert returned == expected @@ -95,7 +95,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = parse_json_response(response) + returned = parse_json_response(response, assert_status=200) assert returned == expected # Add another uid to SoA splits @@ -103,7 +103,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", json={"uid": test_data.visits[3].uid}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [ {"uid": test_data.visits[3].uid, "study_uid": test_data.study.uid}, {"uid": test_data.visits[5].uid, "study_uid": test_data.study.uid}, @@ -122,7 +122,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", json={"uid": test_data.visits[1].uid}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [ {"uid": test_data.visits[1].uid, "study_uid": test_data.study.uid}, {"uid": test_data.visits[3].uid, "study_uid": test_data.study.uid}, @@ -141,14 +141,14 @@ def test_study_soa_splits(api_client: TestClient, test_database): response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == expected # Delete an uid from SoA splits response = api_client.delete( f"/studies/{test_data.study.uid}/soa-splits/{test_data.visits[3].uid}", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [ {"uid": test_data.visits[1].uid, "study_uid": test_data.study.uid}, {"uid": test_data.visits[5].uid, "study_uid": test_data.study.uid}, @@ -159,7 +159,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == expected # Lock the study @@ -173,14 +173,14 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v1_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Get SoA splits for latest version response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Try to add another uid to SoA splits to locked study - should fail @@ -206,21 +206,21 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v1_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Get SoA splits for latest version response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Delete an uid from SoA splits response = api_client.delete( f"/studies/{test_data.study.uid}/soa-splits/{test_data.visits[1].uid}", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [{"uid": test_data.visits[5].uid, "study_uid": test_data.study.uid}] assert returned == expected @@ -229,7 +229,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v1_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Lock and unlock the study again @@ -245,14 +245,14 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v1_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Get SoA splits for latest version response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == expected # Get SoA splits for v2 version @@ -260,7 +260,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v2_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v2_expected # Add another uid to SoA splits @@ -268,7 +268,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", json={"uid": test_data.visits[4].uid}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [ {"uid": test_data.visits[4].uid, "study_uid": test_data.study.uid}, {"uid": test_data.visits[5].uid, "study_uid": test_data.study.uid}, @@ -280,14 +280,14 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v1_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected # Get SoA splits for latest version response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == expected # Get SoA splits for v2 version @@ -295,14 +295,14 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v2_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v2_expected # Delete all SoA splits response = api_client.delete( f"/studies/{test_data.study.uid}/soa-splits/{test_data.visits[5].uid}", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [{"uid": test_data.visits[4].uid, "study_uid": test_data.study.uid}] assert returned == expected response = api_client.delete( @@ -314,7 +314,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = parse_json_response(response) + returned = parse_json_response(response, assert_status=200) assert returned == [] # Get SoA splits for v2 version @@ -322,7 +322,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v2_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v2_expected # Get SoA splits for v1 version @@ -330,7 +330,7 @@ def test_study_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", params={"study_value_version": v1_version}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == v1_expected @@ -341,7 +341,7 @@ def test_study_locked_with_no_soa_splits(api_client: TestClient, test_database): # Initially no SOA splits response = api_client.get(f"/studies/{test_data.study.uid}/soa-splits") - returned = parse_json_response(response, status=200) + returned = parse_json_response(response, assert_status=200) assert returned == [] # Try to delete an uid from non-existing SoA splits @@ -362,7 +362,7 @@ def test_study_locked_with_no_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", json={"uid": test_data.visits[4].uid}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [{"uid": test_data.visits[4].uid, "study_uid": test_data.study.uid}] assert returned == expected @@ -371,7 +371,7 @@ def test_study_locked_with_no_soa_splits(api_client: TestClient, test_database): f"/studies/{test_data.study.uid}/soa-splits", json={"uid": test_data.visits[6].uid}, ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) expected = [ {"uid": test_data.visits[4].uid, "study_uid": test_data.study.uid}, {"uid": test_data.visits[6].uid, "study_uid": test_data.study.uid}, @@ -390,7 +390,7 @@ def test_study_locked_with_no_soa_splits(api_client: TestClient, test_database): response = api_client.get( f"/studies/{test_data.study.uid}/soa-splits", ) - returned = _sort_by_uid(parse_json_response(response)) + returned = _sort_by_uid(parse_json_response(response, assert_status=200)) assert returned == expected diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_adam_listings_mdvisit.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_adam_listings_mdvisit.py index 8a36ffda..1cf3ac92 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_adam_listings_mdvisit.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_adam_listings_mdvisit.py @@ -238,7 +238,7 @@ def test_adam_with_protocol_soa_html_with_time_units(api_client): AVISIT2="Week 11", AVISIT2N="11", ) - expected_output.STUDYID = mock.ANY + expected_output.STUDYID = mock.ANY # pylint: disable=invalid-name assert res[0] == expected_output.model_dump() day_uid = get_unit_uid_by_name("day") response = api_client.patch( @@ -266,5 +266,5 @@ def test_adam_with_protocol_soa_html_with_time_units(api_client): AVISIT2="Week 11", AVISIT2N="11", ) - expected_output.STUDYID = mock.ANY + expected_output.STUDYID = mock.ANY # pylint: disable=invalid-name assert res[0] == expected_output.model_dump() diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activities.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activities.py index e932e310..cfc19673 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activities.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activities.py @@ -558,7 +558,6 @@ def test_update_library_items_of_relationship_to_value_nodes(api_client): response = api_client.post( f"/concepts/activities/activities/{library_activity_uid}/versions", ) - res = response.json() assert_response_status_code(response, 201) response = api_client.put( @@ -571,13 +570,11 @@ def test_update_library_items_of_relationship_to_value_nodes(api_client): "activity_groupings": initial_activity_groupings, }, ) - res = response.json() assert_response_status_code(response, 200) response = api_client.post( f"/concepts/activities/activity-sub-groups/{library_activity_grouping_subgroup_uid}/versions", ) - res = response.json() assert_response_status_code(response, 201) response = api_client.put( @@ -591,18 +588,15 @@ def test_update_library_items_of_relationship_to_value_nodes(api_client): "activity_groups": [library_activity_grouping_group_uid], }, ) - res = response.json() assert_response_status_code(response, 200) response = api_client.post( f"/concepts/activities/activities/{library_activity_uid}/approvals" ) - res = response.json() assert_response_status_code(response, 201) response = api_client.post( f"/concepts/activities/activity-sub-groups/{library_activity_grouping_subgroup_uid}/approvals" ) - res = response.json() assert_response_status_code(response, 201) # check that the Library item has been changed @@ -636,7 +630,6 @@ def test_update_library_items_of_relationship_to_value_nodes(api_client): response = api_client.post( f"/concepts/activities/activities/{library_activity_uid}/versions", ) - res = response.json() assert_response_status_code(response, 201) response = api_client.put( f"/concepts/activities/activities/{library_activity_uid}", @@ -648,19 +641,16 @@ def test_update_library_items_of_relationship_to_value_nodes(api_client): "activity_groupings": initial_activity_groupings, }, ) - res = response.json() assert_response_status_code(response, 200) response = api_client.post( f"/concepts/activities/activities/{library_activity_uid}/approvals" ) - res = response.json() assert_response_status_code(response, 201) # change activity name and approve the version response = api_client.post( f"/concepts/activities/activity-sub-groups/{library_activity_grouping_subgroup_uid}/versions", ) - res = response.json() assert_response_status_code(response, 201) response = api_client.put( f"/concepts/activities/activity-sub-groups/{library_activity_grouping_subgroup_uid}", @@ -673,12 +663,10 @@ def test_update_library_items_of_relationship_to_value_nodes(api_client): "activity_groups": [library_activity_grouping_group_uid], }, ) - res = response.json() assert_response_status_code(response, 200) response = api_client.post( f"/concepts/activities/activity-sub-groups/{library_activity_grouping_subgroup_uid}/approvals" ) - res = response.json() assert_response_status_code(response, 201) @@ -963,6 +951,19 @@ def test_maintain_outbound_rels(api_client): assert len(res) == 0 +def _normalize_versioned_study_data( + outer_list: list[dict[str, Any]], + visits_items: list[dict[str, Any]], + set_study_version: bool = True, +) -> None: + for i, item in enumerate(outer_list): + if set_study_version: + item["study_version"] = mock.ANY + for j in visits_items[i]: + if isinstance(visits_items[i][j], dict): + visits_items[i][j]["queried_effective_date"] = mock.ANY + + def test_versioning_on_activity_activity_instruction_activity_schedule_as_group( api_client, ): @@ -1160,44 +1161,32 @@ def test_versioning_on_activity_activity_instruction_activity_schedule_as_group( assert len(res) == 0 # CHECK if data of locked study version was not changed + visits_items = expected_visits["items"] # compare study visits of locked study version - for i, _ in enumerate(expected_visits["items"]): - expected_visits["items"][i]["study_version"] = mock.ANY - for j in expected_visits["items"][i]: - if isinstance(expected_visits["items"][i][j], dict): - expected_visits["items"][i][j]["queried_effective_date"] = mock.ANY + _normalize_versioned_study_data(expected_visits["items"], visits_items) current_visits = api_client.get( f"/studies/{study_for_versioning.uid}/study-visits?study_value_version=1" ).json() assert current_visits == expected_visits # compare study activities of locked study version - for i, _ in enumerate(expected_activities["items"]): - expected_activities["items"][i]["study_version"] = mock.ANY - for j in expected_visits["items"][i]: - if isinstance(expected_visits["items"][i][j], dict): - expected_visits["items"][i][j]["queried_effective_date"] = mock.ANY + _normalize_versioned_study_data(expected_activities["items"], visits_items) current_activities = api_client.get( f"/studies/{study_for_versioning.uid}/study-activities?study_value_version=1" ).json() assert current_activities == expected_activities # compare study activity schedules of locked study version - for i, _ in enumerate(expected_activity_schedules): - for j in expected_visits["items"][i]: - if isinstance(expected_visits["items"][i][j], dict): - expected_visits["items"][i][j]["queried_effective_date"] = mock.ANY + _normalize_versioned_study_data( + expected_activity_schedules, visits_items, set_study_version=False + ) current_activity_schedules = api_client.get( f"/studies/{study_for_versioning.uid}/study-activity-schedules?study_value_version=1" ).json() assert current_activity_schedules == expected_activity_schedules # compare study activity instructions of locked study version - for i, _ in enumerate(expected_activity_instructions): - expected_activity_instructions[i]["study_version"] = mock.ANY - for j in expected_visits["items"][i]: - if isinstance(expected_visits["items"][i][j], dict): - expected_visits["items"][i][j]["queried_effective_date"] = mock.ANY + _normalize_versioned_study_data(expected_activity_instructions, visits_items) current_activity_instructions = api_client.get( f"/studies/{study_for_versioning.uid}/study-activity-instructions?study_value_version=1" ).json() @@ -2379,6 +2368,7 @@ def test_study_activity_version_selecting_ct_package(api_client): "change_description": "string", }, ) + assert_response_status_code(response, 200) response = api_client.post(f"/ct/terms/{ctterm_uid}/names/approvals") assert_response_status_code(response, 201) @@ -4191,6 +4181,37 @@ def test_cross_soa_group_duplicate_study_activity_blocked_on_create(api_client): ) +def test_clone_big_study_with_study_activity_flags_enabled(api_client): + response = api_client.post( + "/studies/Study_000001/clone", + json={ + "study_number": "9001", + "study_acronym": "9001", + "project_number": project.project_number, + "description": "Clone with study activity flags enabled", + "copy_study_arm": True, + "copy_study_branch_arm": True, + "copy_study_cohort": True, + "copy_study_element": True, + "copy_study_visit": True, + "copy_study_epoch": True, + "copy_study_visits_study_footnote": True, + "copy_study_epochs_study_footnote": True, + "copy_study_design_matrix": True, + "copy_study_soa_group": True, + "copy_study_activity_group": True, + "copy_study_activity_subgroup": True, + "copy_study_activity": True, + "copy_study_activity_instance": True, + "copy_study_activity_schedule": True, + "validation_mode": ValidationMode.WARNING.value, + }, + ) + assert_response_status_code(response, 201) + study_cloned = response.json() + assert study_cloned["uid"] != "Study_000001" + + def test_cross_soa_group_duplicate_study_activity_blocked_on_patch(api_client): test_study = TestUtils.create_study(project_number=project.project_number) @@ -4821,9 +4842,9 @@ def test_study_activity_invalidate_keep_old_version(api_client): ) assert_response_status_code(response, 200) - # TODO fix study-activities get by uid as it returns same activity for latest_activity and activity if activity is retired - # it should return Retired one as latest_activity and Final one as activity - # as temporary fix calling get all that works fine as for now. + # Known limitation: get by uid returns same activity for latest_activity and activity when activity is retired. + # It should return Retired one as latest_activity and Final one as activity. + # As temporary fix calling get all that works fine as for now. response = api_client.get(f"/studies/{test_study.uid}/study-activities") assert_response_status_code(response, 200) res = response.json()["items"] diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_groups.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_groups.py index 2b1c6e26..099b59f8 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_groups.py @@ -366,6 +366,7 @@ def test_modify_visibility_flag_in_protocol_flowchart( assert_response_status_code(response, 201) locked_results = res locked_results["study_version"] = ANY + locked_results["start_date"] = ANY response = api_client.patch( f"/studies/{study.uid}/study-activities/{study_activity_uid}", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_instances.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_instances.py index 851b39b4..0c398dc3 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_instances.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_instances.py @@ -15,6 +15,7 @@ from fastapi.testclient import TestClient from neomodel import db +from clinical_mdr_api.domains.enums import ValidationMode from clinical_mdr_api.domains.study_selections.study_selection_activity_instance import ( StudyActivityInstanceState, ) @@ -690,6 +691,7 @@ def test_create_study_activity_instance(api_client): "study_visit_uid": study_visit_1.uid, }, ) + assert_response_status_code(response, 201) response = api_client.post( f"/studies/{test_study.uid}/study-activity-instances", @@ -816,6 +818,7 @@ def test_edit_study_activity_instance(api_client): "study_visit_uid": study_visit_2.uid, }, ) + assert_response_status_code(response, 201) # Test is_important & baseline visits # Test is_important field - initially should be False @@ -1102,12 +1105,12 @@ def test_study_activity_instance_header_endpoint(api_client): "flowchart_group": {"term_uid": term_efficacy_uid}, }, ) - res = parse_json_response(response, status=201) + res = parse_json_response(response, assert_status=201) response = api_client.post( f"/concepts/activities/activities/{res['uid']}/approvals" ) - res = parse_json_response(response, status=201) + res = parse_json_response(response, assert_status=201) hello_activity = Activity(**res) response = api_client.post( @@ -1123,7 +1126,7 @@ def test_study_activity_instance_header_endpoint(api_client): response = api_client.get( f"/studies/{test_study.uid}/study-activity-instances/headers?field_name=activity.name", ) - res = parse_json_response(response, status=200) + res = parse_json_response(response, assert_status=200) assert res == [ randomized_activity.name, body_mes_activity.name, @@ -1135,7 +1138,7 @@ def test_study_activity_instance_header_endpoint(api_client): response = api_client.get( f"/studies/{test_study.uid}/study-activity-instances/headers?field_name=activity.library_name", ) - res = parse_json_response(response, status=200) + res = parse_json_response(response, assert_status=200) assert set(res) == {randomized_activity.library_name, hello_activity.library_name} # delete Test Study @@ -1975,7 +1978,7 @@ def test_study_activity_instances_review_changes_batch(api_client): ) response = api_client.delete( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/activations" ) assert_response_status_code(response, 200) @@ -2021,7 +2024,7 @@ def test_study_activity_instances_review_changes_batch(api_client): assert res["state"] == StudyActivityInstanceState.REVIEW_NOT_NEEDED.value response = api_client.post( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/activations" ) assert_response_status_code(response, 200) @@ -2144,7 +2147,7 @@ def test_study_activity_instances_invalidate_keep_old_version(api_client): assert study_activity_instances[0]["activity_instance"]["status"] == "Final" response = api_client.delete( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/activations" ) assert_response_status_code(response, 200) @@ -2177,7 +2180,7 @@ def test_study_activity_instances_invalidate_keep_old_version(api_client): assert res["latest_activity_instance"]["status"] == "Retired" response = api_client.post( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/activations" ) assert_response_status_code(response, 200) @@ -3087,3 +3090,34 @@ def test_state_remove_instance_when_too_many_instances(api_client): assert item["state"] == StudyActivityInstanceState.REMOVE_INSTANCE.value TestUtils.delete_study(test_study.uid) + + +def test_clone_big_study_with_study_activity_flags_enabled(api_client): + response = api_client.post( + "/studies/Study_000001/clone", + json={ + "study_number": "9002", + "study_acronym": "9002", + "project_number": project.project_number, + "description": "Clone with study activity flags enabled", + "copy_study_arm": True, + "copy_study_branch_arm": True, + "copy_study_cohort": True, + "copy_study_element": True, + "copy_study_visit": True, + "copy_study_epoch": True, + "copy_study_visits_study_footnote": True, + "copy_study_epochs_study_footnote": True, + "copy_study_design_matrix": True, + "copy_study_soa_group": True, + "copy_study_activity_group": True, + "copy_study_activity_subgroup": True, + "copy_study_activity": True, + "copy_study_activity_instance": True, + "copy_study_activity_schedule": True, + "validation_mode": ValidationMode.WARNING.value, + }, + ) + assert_response_status_code(response, 201) + study_cloned = response.json() + assert study_cloned["uid"] != "Study_000001" diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_subgroups.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_subgroups.py index 28c86062..2a8fb7ef 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_subgroups.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_activity_subgroups.py @@ -345,6 +345,7 @@ def test_modify_visibility_flag_in_protocol_flowchart( assert_response_status_code(response, 201) locked_data = res locked_data["study_version"] = ANY + locked_data["start_date"] = ANY response = api_client.patch( f"/studies/{study.uid}/study-activities/{study_activity_uid}", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_design_cells.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_design_cells.py index 71c75696..93908bab 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_design_cells.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_design_cells.py @@ -550,6 +550,12 @@ def test_study_design_cell_with_study_epoch_relationship(api_client): "copy_study_visits_study_footnote": True, "copy_study_epochs_study_footnote": True, "copy_study_design_matrix": True, + "copy_study_soa_group": True, + "copy_study_activity_group": True, + "copy_study_activity_subgroup": True, + "copy_study_activity": True, + "copy_study_activity_instance": True, + "copy_study_activity_schedule": True, "validation_mode": ValidationMode.STRICT.value, }, ) @@ -634,6 +640,20 @@ def test_study_design_cell_with_study_epoch_relationship(api_client): final_design_cell_by_branch_arm[i]["start_date"] = mock.ANY assert cloned_design_cell_by_branch_arm_any == final_design_cell_by_branch_arm + containment_response = api_client.get( + f"/studies/{study.uid}/study-selection-containment/{study_cloned['uid']}" + ) + assert_response_status_code(containment_response, 200) + containment = containment_response.json() + assert containment["target_contained_in_source"] + for row in containment["per_label"]: + assert row["label_contained"] + assert row["target_selection_count"] == row["source_selection_count"] + assert ( + row["target_distinct_ct_term_root_count"] + == row["source_distinct_ct_term_root_count"] + ) + response = api_client.post( f"/studies/{study.uid}/clone", json={ @@ -650,6 +670,12 @@ def test_study_design_cell_with_study_epoch_relationship(api_client): "copy_study_visits_study_footnote": False, "copy_study_epochs_study_footnote": False, "copy_study_design_matrix": False, + "copy_study_soa_group": False, + "copy_study_activity_group": False, + "copy_study_activity_subgroup": False, + "copy_study_activity": False, + "copy_study_activity_instance": False, + "copy_study_activity_schedule": False, "validation_mode": ValidationMode.STRICT.value, }, ) @@ -673,9 +699,52 @@ def test_study_design_cell_with_study_epoch_relationship(api_client): "copy_study_visits_study_footnote": False, "copy_study_epochs_study_footnote": False, "copy_study_design_matrix": False, + "copy_study_soa_group": False, + "copy_study_activity_group": False, + "copy_study_activity_subgroup": False, + "copy_study_activity": False, + "copy_study_activity_instance": False, + "copy_study_activity_schedule": False, "validation_mode": ValidationMode.STRICT.value, }, ) assert_response_status_code(response, 400) res = response.json() assert res["message"] == "Study Branch should be also included" + + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)-[rel]->(ss:StudyBranchArm) + WHERE type(rel) <> 'HAS_PROTOCOL_SOA_CELL' AND type(rel) <> 'HAS_PROTOCOL_SOA_FOOTNOTE' + WITH ss LIMIT 1 + REMOVE ss:StudyBranchArm + SET ss:StudyBranchArm_THIS_IS_A_TEST + """, + {"study_uid": study_cloned["uid"]}, + ) + containment_after_partial = api_client.get( + f"/studies/{study.uid}/study-selection-containment/{study_cloned['uid']}" + ) + assert_response_status_code(containment_after_partial, 200) + partial = containment_after_partial.json() + assert partial["target_contained_in_source"] + branch_rows = [r for r in partial["per_label"] if r["label"] == "StudyBranchArm"] + if branch_rows: + assert ( + branch_rows[0]["target_selection_count"] + < branch_rows[0]["source_selection_count"] + ) + assert branch_rows[0]["label_contained"] + else: + assert "StudyBranchArm" not in partial["labels_from_target"] + + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)-[rel]->(ss:StudyBranchArm_THIS_IS_A_TEST) + WHERE type(rel) <> 'HAS_PROTOCOL_SOA_CELL' AND type(rel) <> 'HAS_PROTOCOL_SOA_FOOTNOTE' + WITH ss LIMIT 1 + REMOVE ss:StudyBranchArm_THIS_IS_A_TEST + SET ss:StudyBranchArm + """, + {"study_uid": study_cloned["uid"]}, + ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_epochs.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_epochs.py index 51274042..401d727f 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_epochs.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_epochs.py @@ -663,3 +663,101 @@ def test_get_all_epochs_invalid_study_uid_or_version( response = api_client.get(f"/studies/{study_uid}/study-epochs", params=params) assert_response_status_code(response, 404) + + +def test_preview_epoch_does_not_create_duplicate_terms_in_epoch_codelist(api_client): + """Preview a study epoch with Screening subtype (C101526) and verify + that the number of terms in the Epoch codelist (C99079) does not change.""" + catalogue_name, library_name = get_catalogue_name_library_name(use_test_utils=True) + + # Create a Screening epoch subtype and link it to an existing epoch type + screening_subtype = TestUtils.create_ct_term( + codelist_uid="CTCodelist_00003", + term_uid="C101526", + submission_value="SCREENING", + sponsor_preferred_name="Screening", + order=10, + catalogue_name=catalogue_name, + library_name=library_name, + approve=True, + ) + TestUtils.add_ct_term_parent( + term=screening_subtype, + parent_uid="EpochType_0001", + relationship_type="type", + ) + + # Create a dedicated study for this test + preview_study = TestUtils.create_study() + + # Count terms in the Epoch codelist before preview + response = api_client.get( + "/ct/terms", + params={"codelist_uid": "C99079", "total_count": True, "page_size": 0}, + ) + assert_response_status_code(response, 200) + terms_before = response.json()["total"] + + # Call the preview endpoint + response = api_client.post( + f"/studies/{preview_study.uid}/study-epochs/preview", + json={ + "study_uid": preview_study.uid, + "epoch_subtype": screening_subtype.term_uid, + }, + ) + assert_response_status_code(response, 200) + preview_result = response.json() + + assert ( + preview_result["epoch_subtype_ctterm"]["term_uid"] == screening_subtype.term_uid + ) + assert ( + preview_result["epoch_subtype_ctterm"]["sponsor_preferred_name"] == "Screening" + ) + + # Count terms in the Epoch codelist after preview — should be unchanged + response = api_client.get( + "/ct/terms", + params={"codelist_uid": "C99079", "total_count": True, "page_size": 0}, + ) + assert_response_status_code(response, 200) + terms_after = response.json()["total"] + + assert terms_after == terms_before + 1, ( + f"Preview should create new terms in the Epoch codelist (C99079). " + f"Terms before: {terms_before}, terms after: {terms_after}" + ) + + terms_before = terms_after + + # Call the preview endpoint + response = api_client.post( + f"/studies/{preview_study.uid}/study-epochs/preview", + json={ + "study_uid": preview_study.uid, + "epoch_subtype": screening_subtype.term_uid, + }, + ) + assert_response_status_code(response, 200) + preview_result = response.json() + + assert ( + preview_result["epoch_subtype_ctterm"]["term_uid"] == screening_subtype.term_uid + ) + assert ( + preview_result["epoch_subtype_ctterm"]["sponsor_preferred_name"] == "Screening" + ) + + # Count terms in the Epoch codelist after preview — should be unchanged + response = api_client.get( + "/ct/terms", + params={"codelist_uid": "C99079", "total_count": True, "page_size": 0}, + ) + assert_response_status_code(response, 200) + terms_after = response.json()["total"] + + assert terms_after == terms_before, ( + f"Preview should create new terms in the Epoch codelist (C99079). " + f"Terms before: {terms_before}, terms after: {terms_after}" + ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_flowchart.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_flowchart.py index 320500fb..c9d3280f 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_flowchart.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_flowchart.py @@ -1204,7 +1204,7 @@ def test_get_study_flowchart_versioned(api_client, temp_database_populated): "study_value_version": released_study_version, }, ) - released_soa = parse_json_response(response, status=200) + released_soa = parse_json_response(response, assert_status=200) # THEN: SoA of the released study version is the same as the previous draft SoA assert released_soa == r1_soa diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_soa_footnotes.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_soa_footnotes.py index bf880ad8..044fbfe4 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_soa_footnotes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_soa_footnotes.py @@ -1578,6 +1578,12 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client "copy_study_visits_study_footnote": False, "copy_study_epochs_study_footnote": True, "copy_study_design_matrix": True, + "copy_study_soa_group": True, + "copy_study_activity_group": False, + "copy_study_activity_subgroup": False, + "copy_study_activity": False, + "copy_study_activity_instance": False, + "copy_study_activity_schedule": False, "validation_mode": ValidationMode.WARNING.value, # TODO: FIX DELETION, FAILING ON INTEGRITY CHECK }, ).json() @@ -1657,6 +1663,12 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client "copy_study_visits_study_footnote": False, "copy_study_epochs_study_footnote": False, "copy_study_design_matrix": False, + "copy_study_soa_group": False, + "copy_study_activity_group": False, + "copy_study_activity_subgroup": False, + "copy_study_activity": False, + "copy_study_activity_instance": False, + "copy_study_activity_schedule": False, "validation_mode": ValidationMode.WARNING.value, # TODO: FIX DELETION, FAILING ON INTEGRITY CHECK }, ).json() @@ -1682,6 +1694,12 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client "copy_study_visits_study_footnote": True, "copy_study_epochs_study_footnote": True, "copy_study_design_matrix": True, + "copy_study_soa_group": True, + "copy_study_activity_group": True, + "copy_study_activity_subgroup": True, + "copy_study_activity": True, + "copy_study_activity_instance": True, + "copy_study_activity_schedule": True, "validation_mode": ValidationMode.WARNING.value, # TODO: FIX DELETION, FAILING ON INTEGRITY CHECK }, ).json() @@ -1689,6 +1707,13 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client cloned_footnotes = api_client.get( f"/studies/{study_cloned['uid']}/study-soa-footnotes" ).json() + _activity_ref_types = { + "StudyActivityGroup", + "StudyActivitySubGroup", + "StudyActivity", + "StudyActivityInstance", + "StudyActivitySchedule", + } cloned_footnotes_any = copy.deepcopy(cloned_footnotes) for i, _ in enumerate(cloned_footnotes_any["items"]): cloned_footnotes_any["items"][i]["study_version"] = mock.ANY @@ -1696,10 +1721,16 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client cloned_footnotes_any["items"][i]["modified"] = mock.ANY cloned_footnotes_any["items"][i]["uid"] = mock.ANY cloned_footnotes_any["items"][i]["order"] = mock.ANY + cloned_footnotes_any["items"][i]["template"] = mock.ANY for j, __ in enumerate(cloned_footnotes_any["items"][i]["referenced_items"]): cloned_footnotes_any["items"][i]["referenced_items"][j][ "item_uid" ] = mock.ANY + cloned_footnotes_any["items"][i]["referenced_items"] = [ + {**item, "item_uid": mock.ANY, "visible_in_protocol_soa": mock.ANY} + for item in cloned_footnotes_any["items"][i]["referenced_items"] + if item["item_type"] not in _activity_ref_types + ] # Fetch footnotes for the original study final_footnotes = api_client.get(f"/studies/{study.uid}/study-soa-footnotes").json() @@ -1711,7 +1742,7 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client if [ True for item in footnote["referenced_items"] - if item["item_type"] in {"StudyActivityGroup"} + if item["item_type"] in _activity_ref_types ]: continue footnote.update( @@ -1721,13 +1752,14 @@ def test_update_footnote_library_items_of_relationship_to_value_nodes(api_client "modified": mock.ANY, "uid": mock.ANY, "order": mock.ANY, + "template": mock.ANY, } ) footnote["referenced_items"] = [ {**item, "item_uid": mock.ANY, "visible_in_protocol_soa": mock.ANY} for item in footnote["referenced_items"] - if item["item_type"] not in {"StudyActivityGroup"} + if item["item_type"] not in _activity_ref_types ] normalized_footnotes.append(footnote) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py index 1285f4b5..09d58ca9 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py @@ -66,7 +66,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res is None + assert res["protocol_header_version"] is None + assert res["has_final_protocol_locked_version"] is False # snapshot history before lock response = api_client.get( @@ -170,7 +171,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res is None + assert res["protocol_header_version"] is None + assert res["has_final_protocol_locked_version"] is False # get all standard versions response = api_client.get( @@ -240,7 +242,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res is None + assert res["protocol_header_version"] is None + assert res["has_final_protocol_locked_version"] is False # get all standard versions response = api_client.get( @@ -307,7 +310,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res == "0.1" + assert res["protocol_header_version"] == "0.1" + assert res["has_final_protocol_locked_version"] is False # snapshot history after release response = api_client.get( @@ -371,7 +375,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res == "0.2" + assert res["protocol_header_version"] == "0.2" + assert res["has_final_protocol_locked_version"] is False # snapshot history after second release response = api_client.get( f"/studies/{study_with_history.uid}/snapshot-history", @@ -444,7 +449,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res == "1.0" + assert res["protocol_header_version"] == "1.0" + assert res["has_final_protocol_locked_version"] is True # snapshot history after lock response = api_client.get( @@ -593,7 +599,8 @@ def test_get_snapshot_history(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res == "2.0" + assert res["protocol_header_version"] == "2.0" + assert res["has_final_protocol_locked_version"] is True # snapshot history excluding versions without protocol header version response = api_client.get( diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py index 3dec7d46..a080a0e8 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py @@ -2696,6 +2696,6 @@ def assert_get_all_visits_lite_compares( if study_value_version: params["study_value_version"] = study_value_version response = api_client.get(f"/studies/{study_uid}/study-visits", params=params) - results = parse_json_response(response, status=200) + results = parse_json_response(response, assert_status=200) visits = [StudyVisitLite(**item) for item in results["items"]] assert visits == expected_visits diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_feature_flags.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_feature_flags.py index 1d8015f5..a8954aa1 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_feature_flags.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_feature_flags.py @@ -91,7 +91,13 @@ def test_get_feature_flag(api_client): def test_create_feature_flag(api_client): - data = {"name": "Name", "enabled": False, "description": "Description"} + data = { + "section": "admin", + "feature": "Feature", + "name": "Name", + "enabled": False, + "description": "Description", + } response = api_client.post("/feature-flags", json=data) assert_response_status_code(response, 201) @@ -103,13 +109,128 @@ def test_create_feature_flag(api_client): def test_update_feature_flag(api_client): - data = {"enabled": True} + data = {"section": "studies", "feature": "Feature XX", "enabled": True} response = api_client.patch("/feature-flags/11", json=data) assert_response_status_code(response, 200) res = response.json() assert res["sn"] == 11 - assert res["enabled"] == data["enabled"] + for field, value in data.items(): + assert res[field] == value + + +def test_patch_feature_flag_only_section(api_client): + """Test that PATCH updates only the section field, leaving others unchanged""" + # Get the original feature flag + original = api_client.get(f"/feature-flags/{feature_flags[1].sn}").json() + + # Update only the section + data = {"section": "library"} + response = api_client.patch(f"/feature-flags/{feature_flags[1].sn}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + assert res["sn"] == feature_flags[1].sn + assert res["section"] == "library" # Updated field + # Verify other fields remain unchanged + assert res["feature"] == original["feature"] + assert res["name"] == original["name"] + assert res["enabled"] == original["enabled"] + assert res["description"] == original["description"] + + +def test_patch_feature_flag_only_feature(api_client): + """Test that PATCH updates only the feature field, leaving others unchanged""" + # Get the original feature flag + original = api_client.get(f"/feature-flags/{feature_flags[2].sn}").json() + + # Update only the feature + data = {"feature": "Updated Feature Name"} + response = api_client.patch(f"/feature-flags/{feature_flags[2].sn}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + assert res["sn"] == feature_flags[2].sn + assert res["feature"] == "Updated Feature Name" # Updated field + # Verify other fields remain unchanged + assert res["section"] == original["section"] + assert res["name"] == original["name"] + assert res["enabled"] == original["enabled"] + assert res["description"] == original["description"] + + +def test_patch_feature_flag_only_enabled(api_client): + """Test that PATCH updates only the enabled field, leaving others unchanged""" + # Get the original feature flag + original = api_client.get(f"/feature-flags/{feature_flags[3].sn}").json() + original_enabled_state = original["enabled"] + + # Toggle the enabled state + data = {"enabled": not original_enabled_state} + response = api_client.patch(f"/feature-flags/{feature_flags[3].sn}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + assert res["sn"] == feature_flags[3].sn + assert res["enabled"] == (not original_enabled_state) # Updated field + # Verify other fields remain unchanged + assert res["section"] == original["section"] + assert res["feature"] == original["feature"] + assert res["name"] == original["name"] + assert res["description"] == original["description"] + + +def test_patch_feature_flag_multiple_fields(api_client): + """Test that PATCH can update multiple fields at once""" + # Get the original feature flag + original = api_client.get(f"/feature-flags/{feature_flags[4].sn}").json() + + # Update multiple fields + data = {"section": "studies", "enabled": True} + response = api_client.patch(f"/feature-flags/{feature_flags[4].sn}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + assert res["sn"] == feature_flags[4].sn + assert res["section"] == "studies" # Updated + assert res["enabled"] is True # Updated + # Verify other fields remain unchanged + assert res["feature"] == original["feature"] + assert res["name"] == original["name"] + assert res["description"] == original["description"] + + +def test_patch_feature_flag_empty_body(api_client): + """Test that PATCH with empty body returns the feature flag unchanged""" + # Get the original feature flag + original = api_client.get(f"/feature-flags/{feature_flags[5].sn}").json() + + # Send empty patch + data = {} + response = api_client.patch(f"/feature-flags/{feature_flags[5].sn}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + # Verify all fields remain unchanged + assert res == original + + +def test_patch_feature_flag_enabled_false(api_client): + """Test that PATCH can explicitly set enabled to False""" + # First set enabled to True + api_client.patch(f"/feature-flags/{feature_flags[6].sn}", json={"enabled": True}) + + # Verify it's True + current = api_client.get(f"/feature-flags/{feature_flags[6].sn}").json() + assert current["enabled"] is True + + # Now set it to False + data = {"enabled": False} + response = api_client.patch(f"/feature-flags/{feature_flags[6].sn}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + assert res["enabled"] is False # Should be explicitly False, not default def test_delete_feature_flag(api_client): @@ -129,7 +250,13 @@ def test_delete_feature_flag(api_client): def test_cannot_create_feature_flag_with_existing_name(api_client): response = api_client.post( "/feature-flags", - json={"name": "Name", "enabled": False, "description": "Description"}, + json={ + "section": "admin", + "feature": "Feature", + "name": "Name", + "enabled": False, + "description": "Description", + }, ) assert_response_status_code(response, 409) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_studies.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_studies.py index a0fe33dd..34a3d4a4 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_studies.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_studies.py @@ -23,6 +23,9 @@ from fastapi.testclient import TestClient from neomodel import db +from clinical_mdr_api.domains.study_definition_aggregates.study_metadata import ( + StudyStatus, +) from clinical_mdr_api.main import app from clinical_mdr_api.models.concepts.unit_definitions.unit_definition import ( UnitDefinitionModel, @@ -1741,9 +1744,12 @@ def test_remove_study_subpart_from_parent_part(api_client): # pylint: disable=too-many-statements def test_get_audit_trail_of_all_study_subparts_of_study(api_client): - response = api_client.get(f"/studies/{study_with_subparts.uid}/audit-trail") + response = api_client.get( + f"/studies/{study_with_subparts.uid}/audit-trail?page_size=0" + ) assert_response_status_code(response, 200) res = response.json() + items = res["items"] for i in [ "subpart_uid", "subpart_id", @@ -1754,82 +1760,82 @@ def test_get_audit_trail_of_all_study_subparts_of_study(api_client): "change_type", "changes", ]: - assert i in res[0] - - assert len(res) == 36 - - assert res[0]["subpart_id"] == "i" - assert res[0]["subpart_uid"] == "Study_000034" - assert res[1]["subpart_id"] == "h" - assert res[1]["subpart_uid"] == "Study_000033" - assert res[2]["subpart_id"] == "g" - assert res[2]["subpart_uid"] == "Study_000032" - assert res[3]["subpart_id"] == "f" - assert res[3]["subpart_uid"] == "Study_000030" - assert res[4]["subpart_id"] == "e" - assert res[4]["subpart_uid"] == "Study_000029" - assert res[5]["subpart_id"] == "d" - assert res[5]["subpart_uid"] == "Study_000031" - assert res[6]["subpart_id"] == "c" - assert res[6]["subpart_uid"] == "Study_000027" - assert res[7]["subpart_id"] == "b" - assert res[7]["subpart_uid"] == "Study_000026" - assert res[8]["subpart_id"] == "a" - assert res[8]["subpart_uid"] == "Study_000028" - assert res[9]["subpart_id"] == "j" - assert res[9]["subpart_uid"] == "Study_000035" - assert res[10]["subpart_id"] == "a" - assert res[10]["subpart_uid"] == "Study_000035" - assert res[11]["subpart_id"] == "j" - assert res[11]["subpart_uid"] == "Study_000034" - assert res[12]["subpart_id"] == "i" - assert res[12]["subpart_uid"] == "Study_000033" - assert res[13]["subpart_id"] == "h" - assert res[13]["subpart_uid"] == "Study_000032" - assert res[14]["subpart_id"] == "g" - assert res[14]["subpart_uid"] == "Study_000030" - assert res[15]["subpart_id"] == "f" - assert res[15]["subpart_uid"] == "Study_000029" - assert res[16]["subpart_id"] == "e" - assert res[16]["subpart_uid"] == "Study_000031" - assert res[17]["subpart_id"] == "d" - assert res[17]["subpart_uid"] == "Study_000027" - assert res[18]["subpart_id"] == "c" - assert res[18]["subpart_uid"] == "Study_000026" - assert res[19]["subpart_id"] == "b" - assert res[19]["subpart_uid"] == "Study_000028" - assert res[20]["subpart_id"] == "d" - assert res[20]["subpart_uid"] == "Study_000031" - assert res[21]["subpart_id"] == "f" - assert res[21]["subpart_uid"] == "Study_000030" - assert res[22]["subpart_id"] == "e" - assert res[22]["subpart_uid"] == "Study_000029" - assert res[23]["subpart_id"] == "a" - assert res[23]["subpart_uid"] == "Study_000028" - assert res[24]["subpart_id"] == "c" - assert res[24]["subpart_uid"] == "Study_000027" - assert res[25]["subpart_id"] == "b" - assert res[25]["subpart_uid"] == "Study_000026" - assert res[26]["subpart_id"] == "j" - assert res[26]["subpart_uid"] == "Study_000035" - assert res[27]["subpart_id"] == "i" - assert res[27]["subpart_uid"] == "Study_000034" - assert res[28]["subpart_id"] == "h" - assert res[28]["subpart_uid"] == "Study_000033" - assert res[29]["subpart_id"] == "g" - assert res[29]["subpart_uid"] == "Study_000032" - assert res[30]["subpart_id"] == "f" - assert res[30]["subpart_uid"] == "Study_000031" - assert res[31]["subpart_id"] == "e" - assert res[31]["subpart_uid"] == "Study_000030" - assert res[32]["subpart_id"] == "d" - assert res[32]["subpart_uid"] == "Study_000029" - assert res[33]["subpart_id"] == "c" - assert res[33]["subpart_uid"] == "Study_000028" - assert res[34]["subpart_id"] == "b" - assert res[34]["subpart_uid"] == "Study_000027" - assert res[35]["subpart_id"] == "a" - assert res[35]["subpart_uid"] == "Study_000026" + assert i in items[0] + + assert len(items) == 36 + + assert items[0]["subpart_id"] == "i" + assert items[0]["subpart_uid"] == "Study_000034" + assert items[1]["subpart_id"] == "h" + assert items[1]["subpart_uid"] == "Study_000033" + assert items[2]["subpart_id"] == "g" + assert items[2]["subpart_uid"] == "Study_000032" + assert items[3]["subpart_id"] == "f" + assert items[3]["subpart_uid"] == "Study_000030" + assert items[4]["subpart_id"] == "e" + assert items[4]["subpart_uid"] == "Study_000029" + assert items[5]["subpart_id"] == "d" + assert items[5]["subpart_uid"] == "Study_000031" + assert items[6]["subpart_id"] == "c" + assert items[6]["subpart_uid"] == "Study_000027" + assert items[7]["subpart_id"] == "b" + assert items[7]["subpart_uid"] == "Study_000026" + assert items[8]["subpart_id"] == "a" + assert items[8]["subpart_uid"] == "Study_000028" + assert items[9]["subpart_id"] == "j" + assert items[9]["subpart_uid"] == "Study_000035" + assert items[10]["subpart_id"] == "a" + assert items[10]["subpart_uid"] == "Study_000035" + assert items[11]["subpart_id"] == "j" + assert items[11]["subpart_uid"] == "Study_000034" + assert items[12]["subpart_id"] == "i" + assert items[12]["subpart_uid"] == "Study_000033" + assert items[13]["subpart_id"] == "h" + assert items[13]["subpart_uid"] == "Study_000032" + assert items[14]["subpart_id"] == "g" + assert items[14]["subpart_uid"] == "Study_000030" + assert items[15]["subpart_id"] == "f" + assert items[15]["subpart_uid"] == "Study_000029" + assert items[16]["subpart_id"] == "e" + assert items[16]["subpart_uid"] == "Study_000031" + assert items[17]["subpart_id"] == "d" + assert items[17]["subpart_uid"] == "Study_000027" + assert items[18]["subpart_id"] == "c" + assert items[18]["subpart_uid"] == "Study_000026" + assert items[19]["subpart_id"] == "b" + assert items[19]["subpart_uid"] == "Study_000028" + assert items[20]["subpart_id"] == "d" + assert items[20]["subpart_uid"] == "Study_000031" + assert items[21]["subpart_id"] == "f" + assert items[21]["subpart_uid"] == "Study_000030" + assert items[22]["subpart_id"] == "e" + assert items[22]["subpart_uid"] == "Study_000029" + assert items[23]["subpart_id"] == "a" + assert items[23]["subpart_uid"] == "Study_000028" + assert items[24]["subpart_id"] == "c" + assert items[24]["subpart_uid"] == "Study_000027" + assert items[25]["subpart_id"] == "b" + assert items[25]["subpart_uid"] == "Study_000026" + assert items[26]["subpart_id"] == "j" + assert items[26]["subpart_uid"] == "Study_000035" + assert items[27]["subpart_id"] == "i" + assert items[27]["subpart_uid"] == "Study_000034" + assert items[28]["subpart_id"] == "h" + assert items[28]["subpart_uid"] == "Study_000033" + assert items[29]["subpart_id"] == "g" + assert items[29]["subpart_uid"] == "Study_000032" + assert items[30]["subpart_id"] == "f" + assert items[30]["subpart_uid"] == "Study_000031" + assert items[31]["subpart_id"] == "e" + assert items[31]["subpart_uid"] == "Study_000030" + assert items[32]["subpart_id"] == "d" + assert items[32]["subpart_uid"] == "Study_000029" + assert items[33]["subpart_id"] == "c" + assert items[33]["subpart_uid"] == "Study_000028" + assert items[34]["subpart_id"] == "b" + assert items[34]["subpart_uid"] == "Study_000027" + assert items[35]["subpart_id"] == "a" + assert items[35]["subpart_uid"] == "Study_000026" # update study title to be able to lock it response = api_client.patch( @@ -1902,17 +1908,22 @@ def test_get_audit_trail_of_all_study_subparts_of_study(api_client): assert_response_status_code(response, 201) response = api_client.get( - f"/studies/{study_with_subparts.uid}/audit-trail?study_value_version=1" + f"/studies/{study_with_subparts.uid}/audit-trail?study_value_version=1&page_size=0" ) assert_response_status_code(response, 200) res = response.json() - assert all(i["end_date"] for i in res if i["subpart_uid"] == "Study_000026") + assert all( + i["end_date"] for i in res["items"] if i["subpart_uid"] == "Study_000026" + ) def test_get_audit_trail_of_study_subpart(api_client): - response = api_client.get("/studies/Study_000030/audit-trail?is_subpart=true") + response = api_client.get( + "/studies/Study_000030/audit-trail?is_subpart=true&page_size=0" + ) assert_response_status_code(response, 200) res = response.json() + items = res["items"] for i in [ "subpart_uid", "subpart_id", @@ -1923,32 +1934,32 @@ def test_get_audit_trail_of_study_subpart(api_client): "change_type", "changes", ]: - assert i in res[0] - - assert len(res) == 11 - - assert res[0]["subpart_id"] == "e" - assert res[0]["subpart_uid"] == "Study_000030" - assert res[1]["subpart_id"] == "e" - assert res[1]["subpart_uid"] == "Study_000030" - assert res[2]["subpart_id"] == "e" - assert res[2]["subpart_uid"] == "Study_000030" - assert res[3]["subpart_id"] == "e" - assert res[3]["subpart_uid"] == "Study_000030" - assert res[4]["subpart_id"] == "f" - assert res[4]["subpart_uid"] == "Study_000030" - assert res[5]["subpart_id"] == "f" - assert res[5]["subpart_uid"] == "Study_000030" - assert res[6]["subpart_id"] == "f" - assert res[6]["subpart_uid"] == "Study_000030" - assert res[7]["subpart_id"] == "f" - assert res[7]["subpart_uid"] == "Study_000030" - assert res[8]["subpart_id"] == "g" - assert res[8]["subpart_uid"] == "Study_000030" - assert res[9]["subpart_id"] == "f" - assert res[9]["subpart_uid"] == "Study_000030" - assert res[10]["subpart_id"] == "e" - assert res[10]["subpart_uid"] == "Study_000030" + assert i in items[0] + + assert len(items) == 11 + + assert items[0]["subpart_id"] == "e" + assert items[0]["subpart_uid"] == "Study_000030" + assert items[1]["subpart_id"] == "e" + assert items[1]["subpart_uid"] == "Study_000030" + assert items[2]["subpart_id"] == "e" + assert items[2]["subpart_uid"] == "Study_000030" + assert items[3]["subpart_id"] == "e" + assert items[3]["subpart_uid"] == "Study_000030" + assert items[4]["subpart_id"] == "f" + assert items[4]["subpart_uid"] == "Study_000030" + assert items[5]["subpart_id"] == "f" + assert items[5]["subpart_uid"] == "Study_000030" + assert items[6]["subpart_id"] == "f" + assert items[6]["subpart_uid"] == "Study_000030" + assert items[7]["subpart_id"] == "f" + assert items[7]["subpart_uid"] == "Study_000030" + assert items[8]["subpart_id"] == "g" + assert items[8]["subpart_uid"] == "Study_000030" + assert items[9]["subpart_id"] == "f" + assert items[9]["subpart_uid"] == "Study_000030" + assert items[10]["subpart_id"] == "e" + assert items[10]["subpart_uid"] == "Study_000030" def test_cannot_use_a_study_parent_part_as_study_subpart(api_client): @@ -2998,6 +3009,33 @@ def test_study_structure_statistics( assert content["branch_count"] == 0 assert content["epoch_footnote_count"] == 0 assert content["visit_footnote_count"] == 0 + assert content["study_activity_count"] == 0 + assert content["study_activity_schedule_count"] == 0 + + +def test_study_selection_containment(api_client, tst_study): + """Source/target existence and self-comparison (full equality per label).""" + response = api_client.get( + f"studies/123000/study-selection-containment/{tst_study.uid}" + ) + assert_response_status_code(response, 404) + response = api_client.get( + f"studies/{tst_study.uid}/study-selection-containment/123000" + ) + assert_response_status_code(response, 404) + response = api_client.get( + f"studies/{tst_study.uid}/study-selection-containment/{tst_study.uid}" + ) + assert_response_status_code(response, 200) + data = response.json() + assert data["target_contained_in_source"] + for row in data["per_label"]: + assert row["label_contained"] + assert row["target_selection_count"] == row["source_selection_count"] + assert ( + row["target_distinct_ct_term_root_count"] + == row["source_distinct_ct_term_root_count"] + ) # pylint: disable=invalid-name @@ -3018,6 +3056,7 @@ def test_get_studies_list(api_client): "acronym", "number", "title", + "description", "subpart_id", "subpart_acronym", "clinical_programme_name", @@ -3080,6 +3119,44 @@ def test_get_study_complexity_score(api_client): assert res_version_1 >= 0 +@pytest.mark.parametrize( + "study_value_version", + [ + pytest.param(None), + pytest.param("1"), + ], +) +def test_get_study_complexity_score_details(api_client, study_value_version): + params = {"study_value_version": study_value_version} if study_value_version else {} + + # Verify that the `details` endpoint return the same version of the complexity score as the total complexity score endpoint, + # and that the total complexity score is the sum of the individual components returned in the details endpoint. + res_total = api_client.get(f"/studies/{study.uid}/complexity-score", params=params) + res_details = api_client.get( + f"/studies/{study.uid}/complexity-score-details", params=params + ) + assert_response_status_code(res_total, 200) + assert_response_status_code(res_details, 200) + + cs_details = res_details.json() + assert isinstance(cs_details, dict) + for component in ["visits", "assessments"]: + assert component in cs_details + assert isinstance(cs_details[component], list) + for item in cs_details[component]: + assert isinstance(item["type"], str) + assert isinstance(item["burden"], (int, float)) + assert isinstance(item["count"], (int, float)) + assert item["burden"] >= 0 + assert item["count"] >= 0 + + # Assert that the total complexity score is the sum of count * burden for each visit and each assessment + total_calculated = sum( + v["count"] * v["burden"] for v in cs_details["visits"] + ) + sum(a["count"] * a["burden"] for a in cs_details["assessments"]) + assert total_calculated == pytest.approx(res_total.json()) + + def test_get_integrity_check_for_study(api_client): """Test integrity check endpoint for a specific study""" study_int = TestUtils.create_study() @@ -3252,3 +3329,370 @@ def test_cannot_update_study_to_an_already_existing_study_acronym(api_client): res = response.json() assert res["type"] == "AlreadyExistsException" assert res["message"] == "Study with Study Acronym 'study_root' already exists." + + +def test_study_template_create_patch_retire_reactivate(api_client): + def _term_uid(value): + if isinstance(value, dict): + return value["term_uid"] + if hasattr(value, "term_uid"): + return value.term_uid + return value + + lock_reason_uid = _term_uid(test_data_dict["reason_for_lock_terms"][0]) + release_reason_uid = _term_uid(test_data_dict["reason_for_lock_terms"][0]) + unlock_reason_uid = _term_uid(test_data_dict["reason_for_unlock_terms"][0]) + + template_study = TestUtils.create_study() + template_study_title = "Template study title" + TestUtils.set_study_title(template_study.uid, study_title=template_study_title) + lock_response = api_client.post( + f"/studies/{template_study.uid}/locks", + json={ + "change_description": "lock template study", + "reason_for_change_uid": lock_reason_uid, + }, + ) + assert_response_status_code(lock_response, 201) + template_version = lock_response.json()["current_metadata"]["version_metadata"][ + "version_number" + ] + + response = api_client.post( + "/studies/template", + json={ + "study_uid": template_study.uid, + "study_value_version": template_version, + }, + ) + assert_response_status_code(response, 201) + created = response.json() + assert created["study_uid"] == template_study.uid + assert created["study_value_version"] == template_version + assert created["status"] == "Final" + + released_study = TestUtils.create_study() + study_b_title = "Study B title" + TestUtils.set_study_title(released_study.uid, study_title=study_b_title) + lock_response = api_client.post( + f"/studies/{released_study.uid}/locks", + json={ + "change_description": "lock released study", + "reason_for_change_uid": lock_reason_uid, + }, + ) + assert_response_status_code(lock_response, 201) + response = api_client.post( + f"/studies/{released_study.uid}/unlocks", + json={ + "change_description": "Unlock Study B for initial release", + "reason_for_change_uid": unlock_reason_uid, + }, + ) + assert_response_status_code(response, 201) + release_response = api_client.post( + f"/studies/{released_study.uid}/release", + json={ + "change_description": "release study", + "reason_for_change_uid": release_reason_uid, + }, + ) + assert_response_status_code(release_response, 201) + # `release` keeps the Study in DRAFT state, so `current_metadata.version_number` + # in the response can be `None`. Instead, resolve the latest RELEASED snapshot version. + study_history = ( + StudyService().get_study_snapshot_history(study_uid=released_study.uid).items + ) + release_history = sorted( + (item for item in study_history if StudyStatus.RELEASED in item.study_status), + key=lambda item: item.modified_date, + reverse=True, + ) + assert release_history + released_version = release_history[0].metadata_version + assert released_version is not None + + response = api_client.patch( + "/studies/template", + json={ + "study_uid": released_study.uid, + "study_value_version": released_version, + "change_description": "Switch template study", + }, + ) + assert_response_status_code(response, 200) + patched = response.json() + assert patched["study_uid"] == released_study.uid + assert patched["study_value_version"] == released_version + assert patched["status"] == "Final" + + response = api_client.get("/studies/template") + assert_response_status_code(response, 200) + active_template_v1 = response.json() + assert active_template_v1["study_uid"] == released_study.uid + assert active_template_v1["study_value_version"] == released_version + + # Add a second FINAL version for the same StudyB (unlock if needed -> patch short title -> release) + current_status_response = api_client.get(f"/studies/{released_study.uid}") + assert_response_status_code(current_status_response, 200) + current_status = current_status_response.json()["current_metadata"][ + "version_metadata" + ]["study_status"] + if current_status == "LOCKED": + response = api_client.post( + f"/studies/{released_study.uid}/unlocks", + json={ + "change_description": "Unlock Study B for v2", + "reason_for_change_uid": unlock_reason_uid, + }, + ) + assert_response_status_code(response, 201) + + study_short_title_v2 = TestUtils.random_str(8, prefix="study-short-v2-") + response = api_client.patch( + f"/studies/{released_study.uid}", + json={ + "current_metadata": { + "study_description": { + "study_title": study_b_title, + "study_short_title": study_short_title_v2, + } + } + }, + ) + assert_response_status_code(response, 200) + + # Release requires DRAFT; by now the study is expected to be editable. + release_response_v2 = api_client.post( + f"/studies/{released_study.uid}/release", + json={ + "change_description": "Release Study B v2", + "reason_for_change_uid": release_reason_uid, + }, + ) + assert_response_status_code(release_response_v2, 201) + + # `release` keeps the Study in DRAFT state, so `current_metadata.version_number` + # in the response can be `None`. Instead, resolve the latest RELEASED snapshot version. + study_history = ( + StudyService().get_study_snapshot_history(study_uid=released_study.uid).items + ) + release_history = sorted( + (item for item in study_history if StudyStatus.RELEASED in item.study_status), + key=lambda item: item.modified_date, + reverse=True, + ) + assert release_history + released_version_v2 = release_history[0].metadata_version + assert released_version_v2 is not None + + # PATCH the template to point to StudyB v2, then GET immediately to verify persistence + response = api_client.patch( + "/studies/template", + json={ + "study_uid": released_study.uid, + "study_value_version": released_version_v2, + "change_description": "Switch template study to v2", + }, + ) + assert_response_status_code(response, 200) + patched_v2 = response.json() + assert patched_v2["study_uid"] == released_study.uid + assert patched_v2["study_value_version"] == released_version_v2 + assert patched_v2["status"] == "Final" + + response = api_client.get("/studies/template") + assert_response_status_code(response, 200) + active_template_v2 = response.json() + assert active_template_v2["study_uid"] == released_study.uid + assert active_template_v2["study_value_version"] == released_version_v2 + + response = api_client.delete("/studies/template/activations") + assert_response_status_code(response, 200) + retired = response.json() + assert retired["status"] == "Retired" + + response = api_client.get("/studies/template") + assert_response_status_code(response, 200) + retired_template = response.json() + assert retired_template is not None + assert retired_template["status"] == "Retired" + assert retired_template["uid"] == retired["uid"] + assert retired_template["study_uid"] == released_study.uid + assert retired_template["study_value_version"] == released_version_v2 + + response = api_client.post("/studies/template/activations") + assert_response_status_code(response, 200) + reactivated = response.json() + assert reactivated["status"] == "Final" + assert reactivated["study_uid"] == released_study.uid + assert reactivated["study_value_version"] == released_version_v2 + + response = api_client.get("/studies/template") + assert_response_status_code(response, 200) + active_template = response.json() + assert active_template["study_uid"] == released_study.uid + assert active_template["study_value_version"] == released_version_v2 + + +def test_study_template_rejects_draft_study_version(api_client): + def _term_uid(value): + if isinstance(value, dict): + return value["term_uid"] + if hasattr(value, "term_uid"): + return value.term_uid + return value + + draft_study = TestUtils.create_study() + TestUtils.set_study_title(draft_study.uid) + lock_reason_uid = _term_uid(test_data_dict["reason_for_lock_terms"][0]) + unlock_reason_uid = _term_uid(test_data_dict["reason_for_unlock_terms"][0]) + lock_response = api_client.post( + f"/studies/{draft_study.uid}/locks", + json={ + "change_description": "lock to create draft later", + "reason_for_change_uid": lock_reason_uid, + }, + ) + assert_response_status_code(lock_response, 201) + unlock_response = api_client.post( + f"/studies/{draft_study.uid}/unlocks", + json={"reason_for_change_uid": unlock_reason_uid}, + ) + assert_response_status_code(unlock_response, 201) + + response = api_client.patch( + "/studies/template", + json={ + "study_uid": draft_study.uid, + "study_value_version": "1.1", + "change_description": "Try draft version", + }, + ) + assert_response_status_code(response, 404) + assert "version" in response.json()["message"] + + +def test_study_template_rejects_empty_target_fields(api_client): + response = api_client.post( + "/studies/template", + json={"study_uid": "", "study_value_version": ""}, + ) + + assert_response_status_code(response, 400) + assert response.json()["details"] == [ + { + "error_code": "string_too_short", + "field": ["body", "study_uid"], + "msg": "String should have at least 1 character", + "ctx": {"min_length": 1}, + }, + { + "error_code": "string_too_short", + "field": ["body", "study_value_version"], + "msg": "String should have at least 1 character", + "ctx": {"min_length": 1}, + }, + ] + + +def _post_or_patch_study_template( + api_client, + study_uid: str, + study_value_version: str, + *, + change_description: str, +): + response = api_client.post( + "/studies/template", + json={"study_uid": study_uid, "study_value_version": study_value_version}, + ) + if response.status_code == 400: + body = response.json() + if body.get("type") == "BusinessLogicException" and "already exists" in ( + body.get("message") or "" + ): + response = api_client.patch( + "/studies/template", + json={ + "study_uid": study_uid, + "study_value_version": study_value_version, + "change_description": change_description, + }, + ) + return response + + +def test_study_template_patch_clears_target_with_empty_study_uid(api_client): + def _term_uid(value): + if isinstance(value, dict): + return value["term_uid"] + if hasattr(value, "term_uid"): + return value.term_uid + return value + + lock_reason_uid = _term_uid(test_data_dict["reason_for_lock_terms"][0]) + template_study = TestUtils.create_study() + TestUtils.set_study_title(template_study.uid) + lock_response = api_client.post( + f"/studies/{template_study.uid}/locks", + json={ + "change_description": "lock template study", + "reason_for_change_uid": lock_reason_uid, + }, + ) + assert_response_status_code(lock_response, 201) + template_version = lock_response.json()["current_metadata"]["version_metadata"][ + "version_number" + ] + + response = _post_or_patch_study_template( + api_client, + template_study.uid, + template_version, + change_description="Seed template for clear-target test", + ) + assert_response_status_code(response, [200, 201]) + + response = api_client.patch( + "/studies/template", + json={ + "study_uid": "", + "study_value_version": "", + "change_description": "Clear template target", + }, + ) + assert_response_status_code(response, 200) + cleared = response.json() + assert cleared["study_uid"] == "" + assert cleared["study_value_version"] == "" + + response = api_client.get("/studies/template") + assert_response_status_code(response, 200) + persisted = response.json() + assert persisted["study_uid"] == "" + assert persisted["study_value_version"] == "" + + response = api_client.patch( + "/studies/template", + json={ + "study_uid": "", + "study_value_version": "ignored-version", + "change_description": "Clear template target (version ignored)", + }, + ) + assert_response_status_code(response, 200) + assert response.json()["study_value_version"] == "" + + +def test_study_template_patch_requires_version_when_study_uid_set(api_client): + study = TestUtils.create_study() + response = api_client.patch( + "/studies/template", + json={ + "study_uid": study.uid, + "study_value_version": "", + "change_description": "missing version", + }, + ) + assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_disease_milestone.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_disease_milestone.py index 04d2533a..8e3d860f 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_disease_milestone.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_disease_milestone.py @@ -102,12 +102,12 @@ def test__reorder_disease_milestones(self): self.assertEqual(dm3.order, 3) with self.assertRaises(exceptions.BusinessLogicException): - disease_milestone_service.reorder(dm3.uid, 0) + disease_milestone_service.reorder(dm3.study_uid, dm3.uid, 0) with self.assertRaises(exceptions.BusinessLogicException): - disease_milestone_service.reorder(dm3.uid, 4) + disease_milestone_service.reorder(dm3.study_uid, dm3.uid, 4) - disease_milestone_service.reorder(dm3.uid, 1) + disease_milestone_service.reorder(dm3.study_uid, dm3.uid, 1) dm_after1 = disease_milestone_service.find_by_uid(dm1.uid) dm_after2 = disease_milestone_service.find_by_uid(dm2.uid) @@ -117,7 +117,7 @@ def test__reorder_disease_milestones(self): self.assertEqual(dm_after2.order, 3) self.assertEqual(dm_after3.order, 1) - disease_milestone_service.reorder(dm1.uid, 3) + disease_milestone_service.reorder(dm1.study_uid, dm1.uid, 3) dm_after1 = disease_milestone_service.find_by_uid(dm1.uid) dm_after2 = disease_milestone_service.find_by_uid(dm2.uid) @@ -137,7 +137,7 @@ def test__reorder_disease_milestones(self): self.assertEqual(dm4.order, 4) dm5 = disease_milestone_service.find_by_uid(disease_milestone_subtype_3.uid) self.assertEqual(dm5.order, 5) - disease_milestone_service.reorder(dm5.uid, 4) + disease_milestone_service.reorder(dm5.study_uid, dm5.uid, 4) dm4 = disease_milestone_service.find_by_uid(disease_milestone_subtype_2.uid) self.assertEqual(dm4.order, 5) dm5 = disease_milestone_service.find_by_uid(disease_milestone_subtype_3.uid) @@ -212,6 +212,7 @@ def test__edit_disease_milestone(self): reason_for_unlock_term_uid=self.reason_for_unlock_term_uid, ) edited_disease_milestone = disease_milestone_service.edit( + study_uid=disease_milestone.study_uid, study_disease_milestone_uid=disease_milestone.uid, study_disease_milestone_input=edit_input, ) @@ -244,6 +245,7 @@ def test__get_versions(self): disease_milestone_type="Disease_Milestone_Type_0002", ) disease_milestone_service.edit( + study_uid=disease_milestone.study_uid, study_disease_milestone_uid=disease_milestone.uid, study_disease_milestone_input=edit_input, ) @@ -265,6 +267,7 @@ def test__get_versions(self): change_description="rules change", ) disease_milestone_service.edit( + study_uid=disease_milestone.study_uid, study_disease_milestone_uid=disease_milestone.uid, study_disease_milestone_input=edit_input, ) @@ -316,7 +319,9 @@ def test__delete_study_disease_milestone(self): reason_for_unlock_term_uid=self.reason_for_unlock_term_uid, ) - disease_milestone_service.delete(study_disease_milestone_uid=dm1.uid) + disease_milestone_service.delete( + study_uid=dm1.study_uid, study_disease_milestone_uid=dm1.uid + ) dm1 = disease_milestone_service.find_by_uid(disease_milestone2.uid) dm2 = disease_milestone_service.find_by_uid(disease_milestone3.uid) @@ -324,7 +329,9 @@ def test__delete_study_disease_milestone(self): self.assertEqual(dm1.order, 2) self.assertEqual(dm2.order, 3) - disease_milestone_service.delete(study_disease_milestone_uid=dm1.uid) + disease_milestone_service.delete( + study_uid=dm1.study_uid, study_disease_milestone_uid=dm1.uid + ) dm1 = disease_milestone_service.find_by_uid(dm2.uid) self.assertEqual(dm1.order, 2) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py index f108eafa..b9838139 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py @@ -1234,6 +1234,9 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): self.assertEqual(all_visits[2].time_reference, None) self.assertEqual(all_visits[2].time_reference, None) self.assertEqual(all_visits[2].visit_number, settings.non_visit_number) + self.assertEqual( + all_visits[2].visit_short_name, f"V{settings.non_visit_number}" + ) self.assertEqual(all_visits[2].min_visit_window_value, -9999) self.assertEqual(all_visits[2].max_visit_window_value, 9999) @@ -1245,7 +1248,6 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): "consecutive_visit_group": None, "show_visit": True, "description": "description", - "start_rule": "start_rule", "end_rule": "end_rule", "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, "visit_type": {"term_uid": "VisitType_0003"}, @@ -1256,6 +1258,11 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): unscheduled_visit = visit_service.create( study_uid=self.study.uid, study_visit_input=visit_input ) + # When no start_rule is provided, it should default to settings value + self.assertEqual( + unscheduled_visit.start_rule, + settings.unscheduled_visit_start_rule, + ) with self.assertRaises(ValidationException) as message: non_visit_input.update({"uid": unscheduled_visit.uid}) edit_input = StudyVisitEditInput(**non_visit_input) @@ -1269,9 +1276,14 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): message.exception.msg, ) + custom_start_rule = "Custom unscheduled start rule" updated_description = "Updated description" unscheduled_visit_input.update( - {"uid": unscheduled_visit.uid, "description": updated_description} + { + "uid": unscheduled_visit.uid, + "description": updated_description, + "start_rule": custom_start_rule, + } ) edited_unscheduled_visit = visit_service.edit( study_uid=self.study.uid, @@ -1279,6 +1291,19 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): study_visit_input=StudyVisitEditInput(**unscheduled_visit_input), ) assert edited_unscheduled_visit.description == updated_description + # When start_rule is provided, it should use the provided value + self.assertEqual( + edited_unscheduled_visit.start_rule, + custom_start_rule, + ) + + all_visits = visit_service.get_all_visits(study_uid=self.study.uid).items + unscheduled = [ + v for v in all_visits if v.visit_class == VisitClass.UNSCHEDULED_VISIT + ][0] + self.assertEqual( + unscheduled.visit_short_name, f"V{settings.unscheduled_visit_number}" + ) def test__create_special_visit(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/utils.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/utils.py index c30b52cb..2247da59 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/utils.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/utils.py @@ -7,7 +7,7 @@ import logging from datetime import date, datetime, timedelta, timezone from random import randint -from typing import Any +from typing import Any, Literal from xml.etree import ElementTree import openpyxl @@ -836,12 +836,20 @@ def update_entity_status( @classmethod def create_feature_flag( cls, + section: Literal["admin", "library", "studies"] = "library", + feature: str = "Feature name", name: str = "Feature Flag Name", enabled: bool = False, description: str | None = "Feature Flag Description", ) -> FeatureFlag: service: FeatureFlagService = FeatureFlagService() - payload = FeatureFlagInput(name=name, enabled=enabled, description=description) + payload = FeatureFlagInput( + section=section, + feature=feature, + name=name, + enabled=enabled, + description=description, + ) return service.create_feature_flag(payload) @classmethod diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity_instance.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity_instance.py index ff69e934..312ddc9e 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity_instance.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity_instance.py @@ -38,8 +38,11 @@ def create_random_activity_instance_grouping_vo() -> ActivityInstanceGroupingVO: random_activity_instance_grouping_vo = ActivityInstanceGroupingVO( activity_group_uid=random_str(), + activity_group_version=random_str(), activity_subgroup_uid=random_str(), + activity_subgroup_version=random_str(), activity_uid=random_str(), + activity_version=random_str(), ) return random_activity_instance_grouping_vo diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py index b34ad8cd..11a45cc0 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py @@ -245,7 +245,13 @@ def _retrieve_fields_audit_trail( raise NotImplementedError("Study fields audit trail is not yet mocked.") def _retrieve_study_subpart_with_history( - self, uid: str, is_subpart: bool = False, study_value_version: str | None = None + self, + uid: str, + is_subpart: bool = False, + study_value_version: str | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, ): raise NotImplementedError("Study Subpart audit trail is not yet mocked.") diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py index db07355e..3f49d6e7 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py @@ -385,7 +385,7 @@ study_duration_weeks=None, visit_number=settings.unscheduled_visit_number, unique_visit_number=settings.unscheduled_visit_number, - visit_short_name=str(settings.unscheduled_visit_number), + visit_short_name=f"V{settings.unscheduled_visit_number}", visit_window_unit_name="days", visit_class=VisitClass.UNSCHEDULED_VISIT, visit_subclass=VisitSubclass.SINGLE_VISIT, @@ -415,7 +415,7 @@ study_duration_weeks=None, visit_number=settings.non_visit_number, unique_visit_number=settings.non_visit_number, - visit_short_name=str(settings.non_visit_number), + visit_short_name=f"V{settings.non_visit_number}", visit_window_unit_name="days", visit_class=VisitClass.NON_VISIT, visit_subclass=VisitSubclass.SINGLE_VISIT, diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_objectives.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_objectives.py index e08b97f0..a17803e5 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_objectives.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_objectives.py @@ -7,7 +7,6 @@ EndpointUnits, ) from clinical_mdr_api.models.controlled_terminologies.ct_term import ( - CTTermName, SimpleCodelistTermModel, ) from clinical_mdr_api.models.study_selections.study_selection import ( @@ -36,12 +35,6 @@ submission_value="OBJPRIM", order=1, ) -TERM_PRI_END = CTTermName( - term_uid="C98772_OUTMSPRI", - sponsor_preferred_name="Primary Endpoint", - sponsor_preferred_name_sentence_case="primary endpoint", - queried_effective_date=None, -) TERM_PRI_END = SimpleCodelistTermModel( term_uid="C98772", term_name="Primary Endpoint", @@ -83,8 +76,8 @@ ENDPOINT_4 = Endpoint( uid="Endpoint_000004", - name="

Disease control rate of Actrapid + Empagliflozin cohort

", - name_plain="Disease control rate of Actrapid + Empagliflozin cohort", + name="

Disease control rate of Drug A

", + name_plain="Disease control rate of Drug A", ) ENDPOINT_3 = Endpoint( uid="Endpoint_000003", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_utils.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_utils.py index d88300a7..0210dba0 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_utils.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_utils.py @@ -138,12 +138,12 @@ def test_camel_case_data(self, input_data, expected): assert utils.camel_case_data(input_data) == expected def test_is_attribute_in_model(self): - class _model(BaseModel): + class _SampleModel(BaseModel): z: str = "something" x: int = 123 - assert utils.is_attribute_in_model("x", _model) - assert not utils.is_attribute_in_model("y", _model) + assert utils.is_attribute_in_model("x", _SampleModel) + assert not utils.is_attribute_in_model("y", _SampleModel) @parameterized.expand( [ diff --git a/clinical-mdr-api/clinical_mdr_api/tests/utils/checks.py b/clinical-mdr-api/clinical_mdr_api/tests/utils/checks.py index 3fcd855b..f17071ed 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/utils/checks.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/utils/checks.py @@ -47,9 +47,16 @@ def assert_json_response(response: httpx.Response): def parse_json_response( - response: httpx.Response, status: int | Iterable[int] = 200 + response: httpx.Response, *, assert_status: int | Iterable[int] | None = None ) -> Any: - """Shorthand of checking status code and Content-Type header and returning parsed JSON response""" - assert_response_status_code(response, status) + """ + Decode response body as JSON, checking Content-Type header, and optionally checking HTTP status code + + :param response: httpx.Response to parse + :param assert_status: Optional HTTP status code or iterable of codes to assert before parsing + :return: Decoded JSON content of the response + """ + if assert_status is not None: + assert_response_status_code(response, assert_status) assert_json_response(response) return response.json() diff --git a/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py b/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py index 0726c0ee..19f7a525 100644 --- a/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py +++ b/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py @@ -209,7 +209,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): "All HAS_VERSION relationships with status LOCKED have a matching HAS_VERSION with status RELEASED", """ MATCH (root:StudyRoot {uid: $study_uid})-[hvl:HAS_VERSION {status: "LOCKED"}]->(value) - WHERE NOT (root)-[:HAS_VERSION {change_description: hvl.change_description, status: "RELEASED"}]->(value) + WHERE NOT (root)-[:HAS_VERSION {status: "RELEASED"}]->(value) """ + build_root_summary_return_statement("root"), ), ( diff --git a/clinical-mdr-api/m11-templates/ICH_Step4_M11_Final_TechnicalSpecification_2025_1119.json b/clinical-mdr-api/m11-templates/ICH_Step4_M11_Final_TechnicalSpecification_2025_1119.json new file mode 100644 index 00000000..616036bf --- /dev/null +++ b/clinical-mdr-api/m11-templates/ICH_Step4_M11_Final_TechnicalSpecification_2025_1119.json @@ -0,0 +1,8055 @@ +[ + { + "page": 4, + "term": "Sponsor Confidentiality Statement:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Sponsor Confidentiality Statement:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 5, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C181236", + "user_guidance": "Insert the sponsor’s confidentiality statement, if applicable; otherwise delete.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading\nConcept: C181236 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 5, + "term": "Full Title:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Full Title:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 5, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C132346", + "user_guidance": "The protocol should have a descriptive title that identifies the scientific aspects of the trial sufficiently to ensure it is immediately evident what the trial is investigating and on whom, and to allow retrieval from literature or internet searches.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C132346 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 6, + "term": "Trial Acronym:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Trial Acronym:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 6, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C94108", + "user_guidance": "Acronym or abbreviation used publicly to identify the clinical trial. Delete this line from the table if not applicable.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Protocol Identifier\nConcept: C94108 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 6, + "term": "Sponsor Protocol Identifier:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Sponsor Protocol Identifier", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 7, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C132351", + "user_guidance": "A unique alphanumeric identifier for the trial, designated by the sponsor.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading\nConcept: C132351 ICH OID 2.16.840.1.113883.3.989.2.3.3.16\nNote: Must have at least One Character, may not be space (null)", + "repeating_reuse_rules": "No" + }, + { + "page": 7, + "term": "Original Protocol:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Original Protocol:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 7, + "term": "[Original Protocol]", + "_comment": "Used to be [Original Protocol Indicator]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218672", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title page", + "value": "Code List C217046: ICH OID 2.16.840.1.113883.3.989.2.3.1.11\nYes (C49488), No (C49487)", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218672 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 8, + "term": "Version Number:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Version Number:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 8, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C181232", + "user_guidance": "For use by the sponsor at their discretion.", + "conformance": "Optional", + "cardinality": "One to one, Protocol Identifier", + "relationship": "Title Page", + "value": "Number", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C181232 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 8, + "term": "Version Date:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one; One to Version Number", + "relationship": "Title Page", + "value": "Version Date:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 9, + "term": "", + "data_type": "Date", + "dvh": "D", + "definition": "C93813", + "user_guidance": "For use by the sponsor at their discretion.", + "conformance": "Optional", + "cardinality": "One to one; one to Version Number", + "relationship": "Title page", + "value": "Date Format", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Version Number; Sponsor Protocol Identifier\nConcept: C93813 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 9, + "term": "{Amendment Identifier:}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is an amendment", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title page", + "value": "Amendment Identifier:", + "business_rules": "Value Allowed: No\nRelationship: Table Row Heading, Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "Yes, reuse to/from table for document history" + }, + { + "page": 9, + "term": "{Amendment Identifier}", + "data_type": "Text", + "dvh": "D", + "definition": "C218477", + "user_guidance": "Enter the amendment identifier (e.g., amendment number). If this is the original\ninstance of the protocol, delete this row or enter \"Not applicable\"", + "conformance": "Conditional: when there is an amendment", + "cardinality": "One to one; One to Protocol Identifier if not original", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes if Original Protocol = No; blank if Original Protocol = Yes\nRelationship: Heading, Sponsor Protocol Identifier\nConcept: C218477 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for Table for Document History" + }, + { + "page": 10, + "term": "{Amendment Scope:}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Amendment Scope:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 10, + "term": "{[Amendment Scope]}", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218673", + "user_guidance": "If this is the original instance of the protocol, delete this row or enter \"Not applicable\". For an amendment that applies to all sites in the trial, enter “Global” and delete the Country, Region and Site Identifier fields. If amending a single-country trial, enter “Global”.", + "conformance": "Conditional: when there is an amendment", + "cardinality": "One to one, One to Amendment Identifier", + "relationship": "Title page", + "value": "Code List C217047: ICH OID 2.16.840.1.113883.3.989.2.3.1.3\nBlank; Global (C68846),\nNot Global (C217026)", + "business_rules": "Value Allowed: Yes; if Original Protocol = No; blank if Original Protocol = Yes\nRelationship: Heading, Amendment Identifier, Sponsor Protocol Identifier\nConcept: C218673 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 11, + "term": "{[Country Identifier] or [Region Identifier] or }", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C20108\nC218674\nC83081", + "user_guidance": "For an amendment that does not apply to all sites in the trial, select “Not Global” and utilise one of the identifiers based on amendment scope.", + "conformance": "Conditional: when Amendment scope is not global", + "cardinality": "One to one; Many to Amendment Scope; One to Amendment Identifier; One to\nSponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Country specific: [Country Identifier] (ISO 3166 Country Codes, Alpha 3; ISO\n3166 Country Codes, Alpha 2; GENC)\nor\nRegion Specific: [Region Identifier] (ISO 3166 Region Codes, Alpha 3; ISO\n3166 Region Codes, Alpha 2; GENC)\nor\nSite specific: [Site Identifier] (Text)\nSite Identifier Text\nConditional Blank for Original Protocol Indicator = yes", + "business_rules": "Value Allowed: Yes\nRelationship: Heading, Amendment Scope, Amendment Identifier, Sponsor\nProtocol Identifier\nConcept: C20108 ICH OID 2.16.840.1.113883.3.989.2.3.3.16; C218674 ICH\nOID 2.16.840.1.113883.3.989.2.3.3.16; C83081 ICH OID\n2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable in 12.2 Country/Region-Specific Differences" + }, + { + "page": 11, + "term": "Sponsor’s Investigational Product Code(s):", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Sponsor’s Investigational Product Code(s):", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each Investigational compound" + }, + { + "page": 12, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218675", + "user_guidance": "Enter the sponsor’s unique identifier for investigational product(s) in the trial. Add fields as needed.", + "conformance": "Optional: if there is Sponsor Investigational Product Code", + "cardinality": "One to one, Many to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218675 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for each Investigational compound\nYes, repeatable in 1.1.2 under Intervention" + }, + { + "page": 12, + "term": "Investigational Product Name(s):", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one; Many to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Investigational Product Name(s):", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 12, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C97054", + "user_guidance": "Omit nonproprietary name field if a nonproprietary name has not yet been assigned.", + "conformance": "Optional", + "cardinality": "One to many; Many to Sponsor Investigational Product Code(s); Many to\nSponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text Use for example WHO INN, USAN, JAN, XEVMPD", + "business_rules": "Value Allowed: Yes\nRelationship: Heading, Sponsor Protocol Identifier\nConcept: C97054 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for each nonproprietary name\nYes, repeatable in 1.1.2 under intervention" + }, + { + "page": 13, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C71898", + "user_guidance": "Omit proprietary name field if not yet established.", + "conformance": "Optional; Blank", + "cardinality": "One to many; Many to Sponsor Investigational Product Code(s); Many to\nSponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Protocol Identifier; Compound Code\nConcept: C71898 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for each proprietary name" + }, + { + "page": 13, + "term": "Trial Phase:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Trial Phase:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading; Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 13, + "term": "[Trial Phase]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C48281", + "user_guidance": "For trials combining investigational drugs or vaccines with devices, classify according to the phase of drug development.", + "conformance": "Required", + "cardinality": "One to one; Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Code List C217045: ICH OID 2.16.840.1.113883.3.989.2.3.1.18\nEarly Phase 1 (C54721); Phase 1 (C15600); Phase 1/Phase 2 (C15693); Phase\n1/Phase 2/Phase 3 (C198366); Phase 1/Phase 3 (C198367); Phase 2 (C15601);\nPhase 2/Phase 3 (C15694); Phase 2/Phase 3/Phase 4 (C217024); Phase 3\n(C15602); Phase 3/Phase 4 (C217025); Phase 4 (C15603)", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C48281 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 14, + "term": "Short Title:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Short Title:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 14, + "term": "", + "_comment": "Use to be ", + "data_type": "Text", + "dvh": "D", + "definition": "C94105", + "user_guidance": "Short title should convey in plain language what the trial is about and should be suitable for use as “Brief Title” or “Title in Plain Language” in global clinical trial registries. It can also be suitable for use with informed consent forms (ICF) and ethics committee submissions.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C94105 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 14, + "term": "Sponsor Name and Address:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Sponsor Name and Address:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 15, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C222495", + "user_guidance": "Provide the legal name and address of the individual or pharmaceutical or medical device company, governmental agency, academic institution, private organisation, or other organisation who takes primary responsibility for and initiates a clinical investigation. If more than one sponsor, list the primary sponsor in the Sponsor Name and Sponsor Legal Address fields. If co-sponsor is applicable, enter co-sponsor name and legal address. Add additional fields if more than one co-sponsor is applicable.", + "conformance": "Required", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C222495 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 15, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C222495", + "user_guidance": "Provide the legal name and address of the individual or pharmaceutical or medical device company, governmental agency, academic institution, private organisation, or other organisation who takes primary responsibility for and initiates a clinical investigation. If more than one sponsor, list the primary sponsor in the Sponsor Name and Sponsor Legal Address fields. If co-sponsor is applicable, enter co-sponsor name and legal address. Add additional fields if more than one co-sponsor is applicable.", + "conformance": "Required", + "cardinality": "One to one; One to Sponsor Name", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Name\nConcept: C222495 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 16, + "term": "Co-Sponsor Name and Address:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Name; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Co-Sponsor Name and Address:", + "business_rules": "Value Allowed: No\nRelationship: Heading; Sponsor Name; Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 16, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218678", + "user_guidance": "provide the legal name and address of the individual or pharmaceutical or medical device company, governmental agency, academic institution, private organisation, or other organisation who takes primary responsibility for and initiates a clinical investigation. if more than one sponsor, list the primary sponsor in the sponsor name and sponsor legal address fields. if co-sponsor is applicable, enter co-sponsor name and legal address. add additional fields if more than one co-sponsor is applicable.", + "conformance": "Optional", + "cardinality": "One to one; One to Co-Sponsor Name; One to Sponsor Name; One to Sponsor\nProtocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Co-Sponsor Name; Sponsor Name; Protocol Identifier\nConcept: C218678 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes.\nRepeat for each Co-Sponsor Name" + }, + { + "page": 17, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218679", + "user_guidance": "Provide the legal name and address of the individual or pharmaceutical or medical device company, governmental agency, academic institution, private organisation, or other organisation who takes primary responsibility for and initiates a clinical investigation. If more than one sponsor, list the primary sponsor in the Sponsor Name and Sponsor Legal Address fields. If co-sponsor is applicable, enter co-sponsor name and legal address. Add additional fields if more than one co-sponsor is applicable.", + "conformance": "Optional", + "cardinality": "One to one; One to Heading; One to Co-Sponsor Name", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Co-Sponsor Name\nConcept: C218679 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes\nRepeat for each associated Co-Sponsor Legal Address. There is only one Co-\nSponsor Legal Address for each Co-Sponsor Name." + }, + { + "page": 17, + "term": "Local Sponsor Name and Address:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Name and Address; One to Protocol Sponsor\nIdentifier", + "relationship": "Title Page", + "value": "Local Sponsor Name and Address:", + "business_rules": "Value Allowed: No\nRelationship: Heading Sponsor Name and Address\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 17, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218680", + "user_guidance": "In some countries, the clinical trial Sponsor may be the local affiliate company (or designee). In such cases, indicate this in the Local Sponsor Name and Address Field.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Name and Address; Many to Sponsor Name", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Name and Address; Sponsor Name; Country\nConcept: C218680 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for each Local Sponsor Name" + }, + { + "page": 18, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218681", + "user_guidance": "In some countries, the clinical trial sponsor may be the local affiliate company (or designee). In such cases, indicate this in the Local Sponsor Name and Local Sponsor Legal Address Fields.", + "conformance": "Optional", + "cardinality": "One to one; One to Local Sponsor; One to Country", + "relationship": "Title page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Local Sponsor; Country\nConcept: C218681 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes\nRepeat for each associated Local Sponsor Name. There is only one Address for\neach Local Sponsor Name" + }, + { + "page": 18, + "term": "Device Manufacturer Name and Address:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Device Manufacturer Name and Address:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "N o" + }, + { + "page": 19, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218682", + "user_guidance": "Manufacturer name and address information is required only for drug/device combination protocols that include investigational device(s) and should not be included for other protocols. Include the manufacturer address only if the manufacturer is different than the sponsor listed above. Add additional fields as needed if multiple investigational devices will be used in the trial or if there are multiple manufacturers for a single device. Delete this line if not applicable.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier; One to Sponsor Name", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier; Sponsor Name\nConcept: C218682 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for each Device Manufacturers" + }, + { + "page": 19, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218683", + "user_guidance": "Manufacturer name and address information is required only for drug/device combination protocols that include investigational device(s) and should not be included for other protocols. Include the manufacturer address only if the manufacturer is different than the sponsor listed above. Add additional fields as needed if multiple investigational devices will be used in the trial or if there are multiple manufacturers for a single device. Delete this line if not applicable.", + "conformance": "Optional", + "cardinality": "One to one; One to Device Manufacturer Name", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Device Manufacturing Name\nConcept: C218683 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes. Repeatable for each associated Device Manufacturer Name. There is only\none Device Manufacturer Address for each associated Device Manufacturer\nName" + }, + { + "page": 19, + "term": "Regulatory or Clinical Trial Identifier(s):", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Regulatory or Clinical Trial Identifier(s):", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 20, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218684", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes; EU CT number: yyyy-5xxxxx-xx with YYYY\ncorresponding to a year i.e. 2024 and x being an integer\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218684 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 20, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218685", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Protocol Identifier\nConcept: C218685 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 21, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218686", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Protocol Identifier\nConcept: C218686 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 21, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218687", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Protocol Identifier\nConcept: C218687 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 21, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C172240", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C172240 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 22, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218688", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218688 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 22, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218689", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "UTN/WHO: Uxxxx-xxxx-xxxx with X being an integer", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218689 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 23, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218690", + "user_guidance": "Include all identifiers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.", + "conformance": "Optional", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "Title Page", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218690 ICH OID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes, repeatable for each regulatory agency identifier" + }, + { + "page": 23, + "term": "Sponsor Approval:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Title page", + "value": "Sponsor Approval:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 23, + "term": "{ or }", + "data_type": "Date or Text", + "dvh": "V", + "definition": "C132352\nC218484", + "user_guidance": "All versions should be uniquely identifiable.", + "conformance": "Required", + "cardinality": "One to one; One to Protocol Identifier; One to Original Protocol One to\nAmendment Identifier", + "relationship": "Title Page", + "value": "Sponsor Approval Date is a date\nLocation where sponsor approval information can be found is text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Protocol Identifier; Protocol Amendment\nConcept: C132352 ICH OID 2.16.840.1.113883.3.989.2.3.3.16; C218484 ICH\nOID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "Yes,\nNot repeatable\nreuse to Sponsor Approval Date in Section 12.3" + }, + { + "page": 24, + "term": "Sponsor Signatory:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Sponsor Signatory:", + "business_rules": "Value Allowed: No\nRelationship: Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 24, + "term": "{ or }", + "data_type": "Image and/or Text", + "dvh": "D", + "definition": "C222014\nC222064", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Sponsor Signatory Text and/or Image\nOR\nLocation where Sponsor Signatory information can be found (Text)", + "business_rules": "Value Allowed: Yes\nRelationship: Heading\nConcept: C222014 ICH OID 2.16.840.1.113883.3.989.2.3.3.16; C222064 ICH\nOID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 25, + "term": "Medical Expert Contact:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Title Page", + "value": "Medical Expert Contact:", + "business_rules": "Value Allowed: No\nRelationship: Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 25, + "term": "{< Medical Expert contact information (as designated by sponsor)> or }", + "data_type": "Text", + "dvh": "D", + "definition": "C218693\nC222063", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one;", + "relationship": "Title Page", + "value": "Medical Expert contact information (Text)\nOR\nLocation where Medical Expert contact information can be found (Text)", + "business_rules": "Value Allowed: Yes\nRelationship: Medical Expert Contact Response\nConcept: C218693 ICH OID 2.16.840.1.113883.3.989.2.3.3.16, C222063 ICH\nOID 2.16.840.1.113883.3.989.2.3.3.16", + "repeating_reuse_rules": "No" + }, + { + "page": 25, + "term": "Amendment Details:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Amendment Details", + "business_rules": "Value Allowed: No\nRelationship: Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 26, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218694", + "user_guidance": "Choose the applicable statement below. For an original protocol that has not been amended, retain the first statement below and delete the remainder of this entire section. {This protocol has not been amended.} Or {This is the first protocol amendment.} Or include the below {This protocol has been amended previously. Details of prior amendments are presented in Section 12.3 Prior Protocol Amendment(s).}", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Code List C217274: ICH OID 2.16.840.1.113883.3.989.2.3.1.1\nThis protocol has not been amended. (C218485)\nOR\nThis is the first protocol amendment. (C218486)\nOR\nThis protocol has been amended previously. Details of prior amendments are\npresented in Section 12.3 Prior Protocol Amendment(s). (C218487)", + "business_rules": "Value Allowed: Yes\nRelationship: Heading\nConcept: C218694 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 26, + "term": "{Current Amendment}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If Protocol is Original = No", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Current Amendment", + "business_rules": "Value Allowed: No\nRelationship: Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 27, + "term": "{The table below describes the current amendment.}", + "data_type": "Text", + "dvh": "H", + "definition": "Universal text", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "The table below describes the current amendment.", + "business_rules": "Value Allowed: No\nRelationship: Current Amendment\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 27, + "term": "Approximate <#/%> Enrolled at Time of Sponsor Approval:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Approximate # enrolled at Time of Sponsor Approval:\nor\nApproximate % enrolled at Time of Sponsor Approval:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 27, + "term": "Approximately <#/%> enrolled", + "data_type": "Number", + "dvh": "D", + "definition": "C218478", + "user_guidance": "Enter the approximate number or percentage of participants enrolled as a percentage of the expected total. If the number of expected participants is changing as a result of the current amendment, use the updated number of expected participants to estimate the current percentage of enrollment. Estimates are adequate, as precise enrollment figures will likely be changing while an amendment is being prepared. • For a global or single-country amendment, provide the estimated total enrollment at the time the sponsor approved the amendment. • For global amendments providing (or consolidating) only country/region-specific requirements, list approximate local enrollment (total or percentage) at the time of the amendment and select “locally”. • If consolidating a series of local amendments, list the status of all the relevant locations. For a country/regional amendment, provide the estimated local or regional enrollment at the time the sponsor approved the amendment.", + "conformance": "Conditional if Original Protocol =No", + "cardinality": "One to Amendment Number", + "relationship": "Amendment Details", + "value": "Integer for Number or one decimal point for percent", + "business_rules": "Value Allowed: Yes\nRelationship: Table Row Heading; Statement\nConcept: C218478 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, reuse to section 12.3" + }, + { + "page": 28, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218695", + "user_guidance": "Enter the approximate number or percentage of participants enrolled as a percentage of the expected total. If the number of expected participants is changing as a result of the current amendment, use the updated number of expected participants to estimate the current percentage of enrollment. Estimates are adequate, as precise enrollment figures will likely be changing while an amendment is being prepared. • For a global or single-country amendment, provide the estimated total enrollment at the time the sponsor approved the amendment. • For global amendments providing (or consolidating) only country/region-specific requirements, list approximate local enrollment (total or percentage) at the time of the amendment and select “locally”. • If consolidating a series of local amendments, list the status of all the relevant locations. For a country/regional amendment, provide the estimated local or regional enrollment at the time the sponsor approved the amendment.", + "conformance": "Conditional if Original Protocol =No", + "cardinality": "One to Amendment Number", + "relationship": "Amendment Details", + "value": "Code List C217275: ICH OID 2.16.840.1.113883.3.989.2.3.1.2\nGlobally (C68846); Locally (C41065); By Cohort (C218489)", + "business_rules": "Value Allowed: Yes\nRelationship: Statement\nConcept: C218695 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, reuse to section 12.3" + }, + { + "page": 29, + "term": "{Reason(s) for Amendment:}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If Original Protocol = No", + "cardinality": "One to one; Amendment Number", + "relationship": "Amendment Details", + "value": "Reason(s) for Amendment:", + "business_rules": "Value Allowed: No\nRelationship: Table row heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 29, + "term": "Primary:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If Original Protocol = No", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Primary:", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 29, + "_comment": "Used to be [Primary Reason for Amendment]}", + "term": "Primary Reason for Amendment", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218696", + "user_guidance": "Choose from the available categories as the primary reason and secondary reason(s) for the amendment. Select the closest match among the choices. Changes to primary estimand, endpoints, or related measures should be listed as a change of strategy. If none of the choices apply, choose “other” and provide a description. If no secondary reason, indicate “not applicable” for the secondary reason.", + "conformance": "Conditional: if the protocol is = No", + "cardinality": "One to Amendment Details", + "relationship": "Amendment Details", + "value": "Code List C217276: ICH OID 2.16.840.1.113883.3.989.2.3.1.14\n• Regulatory Agency Request To Amend (C218490)\n• New Regulatory Guidance (C218491)\n• IRB/IEC Feedback (C218492)\n• New Safety Information Available (C218493)\n• Manufacturing Change (C218494)\n• IMP Addition (C218495)\n• Change In Strategy (C218496)\n• Change In Standard Of Care (C218497)\n• New Data Available (Other Than Safety Data) (C218498)\n• Investigator/Site Feedback (C218499)\n• Recruitment Difficulty (C218500)\n• Inconsistency And/Or Error In The Protocol (C218501)\n• Protocol Design Error (C218502)\n• Other (C17649)\n• Not Applicable (C48660)", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier; Protocol Amendment\nConcept: C218696 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, Multiple values can be selected except when it is Original Protocol" + }, + { + "page": 30, + "term": "Other", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Other", + "business_rules": "Value Allowed: No\nRelationship: Selection of Other\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 30, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C17649", + "user_guidance": "* Choose from the available categories the primary reason and secondary reason(s) for the amendment. Select the closest match among the choices. Changes to primary estimand, endpoints, or related measures should be listed as a change of strategy. If none of the choices apply, choose “other” and provide a description. If no secondary reason, indicate “Not applicable” for the secondary reason.", + "conformance": "Conditional if Other is selected as a Valid Value", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Primary reason; Sponsor Protocol Identifier; Protocol\nAmendment\nConcept: C17649 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 31, + "term": "Secondary:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Secondary:", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 31, + "term": "{[Secondary Reason for Amendment]}", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218697", + "user_guidance": "Choose from the available categories as the primary reason and secondary reason(s) for the amendment. Select the closest match among the choices. Changes to primary estimand, endpoints, or related measures should be listed as a change of strategy. If none of the choices apply, choose “other” and provide a description. If no secondary reason, indicate “not applicable” for the secondary reason.", + "conformance": "Conditional If Protocol Original = No", + "cardinality": "One to one; One to Protocol Identifier; One to Amendment Identifier", + "relationship": "Amendment Details", + "value": "Code List C217276: ICH OID 2.16.840.1.113883.3.989.2.3.1.14\n• Regulatory Agency Request To Amend (C218490)\n• New Regulatory Guidance (C218491)\n• IRB/IEC Feedback (C218492)\n• New Safety Information Available (C218493)\n• Manufacturing Change (C218494)\n• IMP Addition (C218495)\n• Change In Strategy (C218496)\n• Change In Standard Of Care (C218497)\n• New Data Available (Other Than Safety Data) (C218498)\n• Investigator/Site Feedback (C218499)\n• Recruitment Difficulty (C218500)\n• Inconsistency And/Or Error In The Protocol (C218501)\n• Protocol Design Error (C218502)\n• Other (C17649)\n• Not applicable (C48660)", + "business_rules": "Value Allowed: Yes\nRelationship: Heading, Sponsor Protocol Identifier, Protocol Amendment\nConcept: C218697 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, Multiple accepted except for the Original" + }, + { + "page": 32, + "term": "Other", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Other", + "business_rules": "Value Allowed: No\nRelationship: Selection of Other\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 32, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C17649", + "user_guidance": "* Choose from the available categories the primary reason and secondary reason(s) for the amendment. Select the closest match among the choices. Changes to primary estimand, endpoints, or related measures should be listed as a change of strategy. If none of the choices apply, choose “other” and provide a description. If no secondary reason, indicate “Not applicable” for the secondary reason.", + "conformance": "Conditional if Other is selected as a Valid Value", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Secondary Reason; Sponsor Protocol Identifier; Protocol\nAmendment\nConcept: C17649 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 33, + "term": "{Amendment Summary:}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if original protocol = No", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Amendment Summary:", + "business_rules": "Value Allowed: No\nRelationship: Amendment details, Amendment Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 33, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C42581", + "user_guidance": "Briefly describe key changes. Changes that are included in the amendment but unrelated to the key changes do not need to be described here.", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to Amendment identifier", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details; Amendment Identifier; Sponsor Protocol\nIdentifier\nConcept: C42581 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 34, + "term": "{Is this amendment likely to have a substantial impact on the safety or rights of the participants?}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to one amendment identifier", + "relationship": "Amendment Details", + "value": "Is this amendment likely to have a substantial impact on the safety or rights of\nthe participants?", + "business_rules": "Value Allowed: No\nRelationship: Amendment Details\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 34, + "term": "{[Yes/No]}", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218698", + "user_guidance": "N/A", + "conformance": "Conditional If there is an amendment", + "cardinality": "One to one; One to Amendment Identifier; One to Sponsor Protocol Identifier", + "relationship": "Amendment Details", + "value": "Code List C217046: ICH OID 2.16.840.1.113883.3.989.2.3.1.11\nYes (C49488); No (C49487)", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details; Amendment Identifier; Sponsor Protocol\nIdentifier\nConcept: C218698 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 34, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218699", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment and if \"Is this amendment likely to have a\nsubstantial impact on the safety or rights of the participants? \" is Yes", + "cardinality": "One to one Amendment Identifier,\nIs this amendment likely to have a substantial impact on the safety or rights of the\nparticipants? Response when Yes", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details, Amendment Identifier, Sponsor Protocol\nIdentifier\nWhen the value is yes there is a text response for explanation\nConcept: C218699 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 35, + "term": "{Is this amendment likely to have a substantial impact on the reliability and robustness of the data generated in the clinical trial?}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is an amendment", + "cardinality": "One to amendment details, One amendment identifier, Sponsor Protocol\nIdentifier", + "relationship": "Amendment Details", + "value": "Is this amendment likely to have a substantial impact on the reliability and\nrobustness of the data generated in the clinical trial?", + "business_rules": "Value Allowed: No\nRelationship: Amendment Details, Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 35, + "term": "{[Yes/No]}", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218700", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to one; One to Amendment Identifier; One to Sponsor Protocol Identifier", + "relationship": "Amendment Details", + "value": "Code List C217046: ICH OID 2.16.840.1.113883.3.989.2.3.1.11\nYes (C49488), No (C49487)", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details; Amendment Identifier; Sponsor Protocol\nIdentifier\nConcept: C218700 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 36, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218701", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment and if the answer to \"Is this amendment\nlikely to have a substantial impact on the reliability and robustness of the data\ngenerated in the clinical trial?\" is Yes", + "cardinality": "One to amendment identifier", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details; Amendment Identifier; Sponsor Protocol\nIdentifier\nWhen the value is yes there is a text response for explanation\nConcept: C218701 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "No" + }, + { + "page": 36, + "term": "{Overview of Changes in the Current Amendment}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Instructions for the Overview of Changes: • If an Overview of Changes already exists from a prior amendment, move it to Section 12.3 Prior Protocol Amendment(s), and populate a new Overview of Changes table for the current amendment. • List the changes that apply to the current amendment. Provide a brief description of the change(s) and a concise scientific rationale for specific changes (e.g., change to inclusion/exclusion criteria). • If the same change affects multiple parts of the protocol, it is acceptable to list multiple locations in the right column. • Table can be sorted in any order preferred by the sponsor. • Minor edits such as clarifications and corrections to typographical errors do not need to be itemised in this table. • The changes listed in the table do not need to be detailed in revision marks, as these can be provided in a separate supporting document. • Tabular presentation is common but not required. The page can be changed to landscape orientation if necessary. (Add rows as needed)", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Overview of Changes in the Current Amendment", + "business_rules": "Value Allowed: No\nRelationship: Amendment Details\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 37, + "term": "{Description of Change}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to many", + "relationship": "Amendment Details", + "value": "Description of Change", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading; Amendment Details\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 37, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218483", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to many", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Table Column Heading and Row; Amendment Details; Column\nHeading; Row Heading\nConcept: C218483 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, repeatable for each Description of Change in the amendment" + }, + { + "page": 37, + "term": "{Brief Rationale for Change}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to many", + "relationship": "Amendment Details", + "value": "Brief Rationale for Change", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 38, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C181233", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to many", + "relationship": "Amendment Details", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details; Table Column Heading Row; Description of\nchange; Section # and Name\nConcept: C181233 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, repeatable for each Description of Change in the amendment" + }, + { + "page": 38, + "term": "{Section # and Name}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to many", + "relationship": "Amendment Details", + "value": "Section # and Name", + "business_rules": "Value Allowed: No\nRelationship: Amendment Details; Description of Change; Brief Rationale for\nChange; Table Heading Row\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 39, + "term": "
", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218479", + "user_guidance": "N/A", + "conformance": "Conditional: if there is an amendment", + "cardinality": "One to many\nRow description of change\nDescription of Change, Rationale for Amendment Change", + "relationship": "Amendment Details", + "value": "Code List C217272: ICH OID 2.16.840.1.113883.3.989.2.3.13\nC217342 Section 1\nC217343 Section 2\nC217344 Section 3\nC217345 Section 4\nC217346 Section 5\nC217347 Section 6\nC217348 Section 7\nC217349 Section 8\nC217350 Section 9\nC217351 Section 10\nC217352 Section 11\nC217353 Section 12\nC217354 Section 13\nC217355 Section 14\nC217356 Section Title Page\nC217357 Section Amendment Details", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Details, Brief Rational; Change description; Table\nConcept: C218479 ICH OID 2.16.840.1.113883.3.989.2.3.3.15", + "repeating_reuse_rules": "Yes, repeatable for each Description of Change in the amendment" + }, + { + "page": 39, + "term": "Table of Contents", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "Table of Contents", + "value": "Table of Contents", + "business_rules": "Value Allowed: No\nRelationship: N/A\nConcept: N/A", + "repeating_reuse_rules": "No" + }, + { + "page": 40, + "term": "Table of Contents", + "data_type": "Table of contents generated by a Word processing software", + "dvh": "D", + "definition": "N/A", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "N/A", + "relationship": "Table of Contents", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: N/A\nConcept: N/A", + "repeating_reuse_rules": "No" + }, + { + "page": 40, + "term": "1 PROTOCOL SUMMARY", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1", + "value": "PROTOCOL SUMMARY", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 40, + "term": "1.1 Protocol Synopsis", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "The protocol synopsis is a short summary of the key points of the trial. In order to keep the synopsis brief, cross references to full details in the main body of the protocol are acceptable. No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1", + "value": "Protocol Synopsis", + "business_rules": "Value Allowed: No\nRelationship: 1 PROTOCOL SUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 41, + "term": "1.1.1 Primary and Secondary Objectives and Estimands", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.1", + "value": "Primary and Secondary Objectives and Estimands", + "business_rules": "Value Allowed: No\nRelationship: 1.1 Protocol Synopsis; 1 PROTOCOL SUMMARY; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 41, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218839", + "user_guidance": "Summarise the primary and secondary objectives and any associated estimands in natural, nontechnical (layperson) language. For trials intended to estimate a treatment effect or test a hypothesis related to a treatment effect, include the primary and secondary objectives and any associated estimands using a nontechnical summary describing the objective and treatment effect of interest (estimand). For other types of trials not intended to estimate a treatment effect or test a hypothesis related to a treatment effect, define trial objectives and describe additional information relevant to the clinical question(s) of interest (e.g., the endpoint(s) associated with each objective). For trials with numerous objectives in which the description of objectives will exceed half a page, consider including the most important objectives and estimands in the synopsis and refer to Section 3 Trial Objectives and Associated Estimands, which covers the objectives and estimands in technical detail. For considerations on estimands, refer to ICH E9(R1).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 1.1.1 Primary and Secondary Objectives and Estimands\nConcept: C218839 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, Reuse and for each Primary Objective\nfrom section 3.1, reuse for each\nSecondary Objective from section 3.2." + }, + { + "page": 42, + "term": "1.1.2 Overall Design", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Overall Design", + "business_rules": "Value Allowed: No\nRelationship: 1.1 Protocol Synopsis; 1 PROTOCOL SUMMARY; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 42, + "term": "Key aspects of the trial design are summarised below.", + "data_type": "Text", + "dvh": "H", + "definition": "Universal text", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Key aspects of the trial design are summarised below.", + "business_rules": "Value Allowed: No\nRelationship: 1.1.2 Overall Design; 1.1 Protocol Synopsis; 1 PROTOCOL\nSUMMARY; Table of Contents\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 42, + "term": "Intervention:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Intervention:", + "business_rules": "Value Allowed: No\nRelationship: Table Cell title\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 43, + "term": "[Sponsor’s Investigational Product Code(s)]", + "data_type": "Text", + "dvh": "D", + "definition": "C218675", + "user_guidance": "N/A", + "conformance": "Required Either Sponsor Investigational Product Code or Nonproprietary Name", + "cardinality": "One to one; One to Heading; One to Protocol Identifier", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row title; Sponsor’s Protocol Identifier\nConcept: C218675 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable from Title Page Sponsor Investigational Product Code(s)\nyes, reuse for each Investigational Product" + }, + { + "page": 43, + "term": "[NonProprietary Name(s)]", + "data_type": "Text", + "dvh": "D", + "definition": "C97054", + "user_guidance": "N/A", + "conformance": "Required Either Sponsor Investigational Product Code or Nonproprietary Name", + "cardinality": "One to one; One to Heading; One to Protocol Identifier", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row title; Sponsor’s Protocol Identifier\nConcept: C97054 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable from Title Page Nonproprietary Name(s)\nYes, reuse for each Investigational Product" + }, + { + "page": 44, + "term": "Intervention Model:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Intervention Model:", + "business_rules": "Value Allowed: No\nRelationship: Table Cell title\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 44, + "term": "[Intervention Model]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C98746", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; One to Heading; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Code List C217277: ICH OID 2.16.840.1.113883.3.989.2.3.1.6\nSingle Group (C82640); Parallel Group (C82639); Cross-over (C82637);\nFactorial (C82638); Sequential (C142568); Other (C17649)", + "business_rules": "Value Allowed: Yes\nRelationship: Row title; Sponsor Protocol Identifier\nConcept: C98746 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 44, + "term": "Population Type:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Population Type:", + "business_rules": "Value Allowed: No\nRelationship: Table Cell title\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 45, + "term": "[Population Type]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218703", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; One to Heading; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Code List C217278: ICH OID 2.16.840.1.113883.3.989.2.3.1.12\nWith Disease (C218503); Without Disease (C218504)", + "business_rules": "Value Allowed: Yes\nRelationship: Row Title; Sponsor Protocol Identifier\nConcept: C218703 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 45, + "term": "Control Type:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Control Type:", + "business_rules": "Value Allowed: No\nRelationship: Table Cell Title\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 45, + "term": "[Control Type]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C49647", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; One to Heading; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Code List C217279: ICH OID 2.16.840.1.113883.3.989.2.3.1.4\nPlacebo (C49648); Active Comparator (C49649); Dose Response (C120841);\nDifferent Dose or Regimen (C218505); External (C218506); Sham Procedure\n(C184727); No Control (C28280)", + "business_rules": "Value Allowed: Yes\nRelationship: Row Title; Sponsor Protocol Identifier\nConcept: C49647 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 46, + "term": "Population Diagnosis or Condition:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Population Diagnosis or Condition:", + "business_rules": "Value Allowed: No\nRelationship: Table cell title\nConcept: N/A", + "repeating_reuse_rules": "No" + }, + { + "page": 46, + "term": "[Population Diagnosis or Condition]", + "data_type": "Valid Value or Text", + "dvh": "V or D", + "definition": "C112038", + "user_guidance": "Population Diagnosis or Condition: MedDRA Preferred Term(s) or indicate “other” and describe.", + "conformance": "Required", + "cardinality": "One to one; One to Heading; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Use examples MedDRA PT or SNOMED\nCT: “acute lung injury,” or a specific biomarker profile); indicate “N/A –\nHealthy” for studies in healthy volunteers", + "business_rules": "Value Allowed: Yes\nRelationship: Row Title Heading; Sponsor Protocol Identifier\nConcept: C112038 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable for each population diagnosis or condition" + }, + { + "page": 46, + "term": "Control Description:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Control Description:", + "business_rules": "Value Allowed: No\nRelationship: Table Cell title; Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 47, + "term": "{[Nonproprietary Name] or [INN] or <“Not applicable”>}", + "data_type": "Text", + "dvh": "D", + "definition": "A narrative representation of the comparator against which the study intervention\nis evaluated.", + "user_guidance": "Further clarification:\n• Control Description: if active comparator or low dose, pick\nnonproprietary name or International Nonproprietary Name; indicate\n\"Not applicable\" if not applicable", + "conformance": "Conditional: if there is a nonproprietary name or INN or Not applicable", + "cardinality": "One to many", + "relationship": "1.1.2", + "value": "[Nonproprietary Name] or [INN] or <\"Not applicable\">", + "business_rules": "Value Allowed: Yes\nRelationship: Row title; Sponsor Protocol Identifier\nConcept: N/A", + "repeating_reuse_rules": "No" + }, + { + "page": 47, + "term": "[Nonproprietary Name]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C97054", + "user_guidance": "Further clarification:\n• Control Description: if active comparator or low dose, pick\nnonproprietary name or International Nonproprietary Name; indicate\n\"Not applicable\" if not applicable", + "conformance": "Conditional: if there is a Nonproprietary Name", + "cardinality": "One to many", + "relationship": "1.1.2", + "value": "Use for example WHO INN, USAN, JAN, XEVMPD", + "business_rules": "Value Allowed: Yes\nRelationship: Row title; Control Description; Sponsor Protocol Identifier\nConcept: C97054 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable for each Nonproprietary Name used as control" + }, + { + "page": 48, + "term": "or [INN] or", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C142585", + "user_guidance": "Further clarification:\n• Control Description: if active comparator or low dose, pick\nnonproprietary name or International Nonproprietary Name; indicate\n\"Not applicable\" if not applicable", + "conformance": "Conditional: if there is an INN", + "cardinality": "One to many", + "relationship": "1.1.2", + "value": "Use for example WHO INN, USAN, JAN, XEVMPD", + "business_rules": "Value Allowed: Yes\nRelationship: Row title; Control Description; Protocol Identifier\nConcept: C142585 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable for each INN used as control" + }, + { + "page": 48, + "term": "<“Not applicable”>", + "data_type": "Text", + "dvh": "V", + "definition": "Universal text", + "user_guidance": "Further clarification:\n• Control Description: if active comparator or low dose, pick\nnonproprietary name or International Nonproprietary Name; indicate\n\"Not applicable\" if not applicable", + "conformance": "Conditional: if there is no nonproprietary name and INN", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "N/A", + "business_rules": "Value Allowed: Yes, cannot have not applicable if Nonproprietary Name or INN\nare completed\nRelationship: Row title; Control Description; Protocol Identifier\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 48, + "term": "Population Age:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to two", + "relationship": "1.1.2", + "value": "Population Age:", + "business_rules": "Value Allowed: No\nRelationship: Row Table cell title\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 49, + "term": "Minimum:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to two; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Minimum:", + "business_rules": "Value Allowed: No\nRelationship: Population Age; Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 49, + "term": "", + "data_type": "Number", + "dvh": "D", + "definition": "C49693", + "user_guidance": "Population Age: for trials in which multiple age ranges may be eligible (e.g., a younger cohort and an older cohort), indicate the minimum and maximum ages for the trial overall, with an additional comment for any excluded age ranges.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Integer", + "business_rules": "Value Allowed: Yes\nRelationship: Population Age; Minimum; Unit of Age\nConcept: C49693 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 49, + "term": "[Units of Age]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C50400", + "user_guidance": "Population Age: For trials in which multiple age ranges may be eligible (e.g., a younger cohort and an older cohort), indicate the minimum and maximum ages for the trial overall, with an additional comment for any excluded age ranges.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Code List C217048: ICH OID 2.16.840.1.113883.3.989.2.3.1.23\nHours (C25529); Days (C25301); Weeks (C29844); Months (C29846); Years\n(C29848)", + "business_rules": "Value Allowed: Yes\nRelationship: Population age; Minimum, Numeric Minimum\nConcept: C50400 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 50, + "term": "Maximum:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to two; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Maximum:", + "business_rules": "Value Allowed: No\nRelationship: Population Age; Sponsor Protocol Identifier\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 50, + "term": "", + "data_type": "Number", + "dvh": "D", + "definition": "C49694", + "user_guidance": "Population Age: For trials in which multiple age ranges may be eligible (for example, a younger cohort and an older cohort), indicate the minimum and maximum ages for the trial overall, with an additional comment for any excluded age ranges.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Integer", + "business_rules": "Value Allowed: Yes\nRelationship: Population Age; Maximum Age; Unit of Age\nConcept: C49694 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 51, + "term": "[Units of Age]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C50400", + "user_guidance": "Population Age: For trials in which multiple age ranges may be eligible (for example, a younger cohort and an older cohort), indicate the minimum and maximum ages for the trial overall, with an additional comment for any excluded age ranges.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Code List C217048: ICH OID 2.16.840.1.113883.3.989.2.3.1.23\nHours (C25529); Days (C25301); Weeks (C29844); Months (C29846); Years\n(C29848)", + "business_rules": "Value Allowed: Yes\nRelationship: Population Age; Maximum, Numeric Maximum\nConcept: C50400 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 51, + "term": "Intervention Assignment Method:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Intervention Assignment Method:", + "business_rules": "Value Allowed: No\nRelationship: Row Table cell Title\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 51, + "term": "[Intervention Assignment Method]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218475", + "user_guidance": "Intervention Assignment Method: If applicable, describe the type of randomisation to be used (e.g., simple randomisation, block randomisation). If applicable, describe the other intervention assignment method", + "conformance": "Required", + "cardinality": "One to one; One to Sponsor Protocol Identifier", + "relationship": "1.1.2", + "value": "Code List C217280: ICH OID 2.16.840.1.113883.3.989.2.3.1.18\nRandomisation (C25196); No Intervention Assignment Method (C222801);\nOther (C17649)", + "business_rules": "Value Allowed: Yes\nRelationship: Row title identifier; Sponsor Protocol Identifiers\nConcept: C218475 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 52, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C223137", + "user_guidance": "Intervention Assignment Method: If applicable, describe the type of randomisation to be used (e.g., simple randomisation, block randomisation). If applicable, describe the other intervention assignment method", + "conformance": "Conditional if Randomisation is selected as Valid Value", + "cardinality": "One to one; One to Sponsor Protocol Identifier; One to Randomisation", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Intervention Assignment Row title identifier; Sponsor Protocol\nIdentifiers\nConcept: C223137 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 52, + "term": "{", + "data_type": "Number", + "dvh": "D", + "definition": "C49692", + "user_guidance": "State the expected number of participants to be assigned to trial intervention/enrolled. Indicate whether the number provided is the target or maximum number of individuals to be randomly assigned to trial intervention/enrolled.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Integer; participants will be", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifiers\nConcept: C49692 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 60, + "term": "[randomly assigned to trial intervention/enrolled]", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218711", + "user_guidance": "State the expected number of participants to be assigned to trial intervention/enrolled. Indicate whether the number provided is the target or maximum number of individuals to be randomly assigned to trial intervention/enrolled", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "randomly assigned to trial intervention/enrolled", + "business_rules": "Value Allowed: Yes\nRelationship: Heading; Sponsor Protocol Identifier\nConcept: C218711 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 60, + "term": "Duration", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Duration:", + "business_rules": "Value Allowed: No\nRelationship: 1.1.2 Overall Design, 1.1 Protocol Synopsis, 1 PROTOCOL\nSUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 61, + "term": "Total planned duration of trial intervention for each participant:", + "data_type": "Text", + "dvh": "H", + "definition": "Universal text", + "user_guidance": "Select one of the two options for total planned duration of trial intervention and trial participation for each participant. Note that the total duration of trial participation should include any washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Total planned duration of trial intervention for each participant:", + "business_rules": "Value Allowed: No\nRelationship: Duration\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 61, + "term": "{ [total planned duration of trial unit of time]}", + "data_type": "Integer, Valid value", + "dvh": "D, V", + "definition": "C218712\nC218713", + "user_guidance": "Select one of the two options for total planned duration of trial intervention and trial participation for each participant. Note that the total duration of trial participation should include any washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”).", + "conformance": "Conditional: when Planned Duration of trial Intervention Number and unit of\ntime", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Total planned duration of trial intervention: Integer\nTotal planned duration of trial intervention unit of time:\nCode List C217048: ICH OID 2.16.840.1.113883.3.989.2.3.1.23\nDays (C25301); Hours (C25529); Months (C29846); Weeks (C29844); Years\n(C29848)", + "business_rules": "Value Allowed: Yes\nRelationship: Total duration of trial intervention for each participant:\nConcept: C218712 ICH OID 2.16.840.1.113883.3.989.2.3.3.1; C218713 ICH\nOID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 62, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218714", + "user_guidance": "Select one of the two options for total planned duration of trial intervention and trial participation for each participant. Note that the total duration of trial participation should include any washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”). Or, if duration will vary", + "conformance": "Conditional: when an alternate description for planned duration of trial\nIntervention if the duration varies", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Total duration of trial intervention for each participant:\nConcept: C218714 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 62, + "term": "Total planned duration of trial participation for each participant:", + "data_type": "Text", + "dvh": "H", + "definition": "Universal text", + "user_guidance": "Select one of the two options for total planned duration of trial intervention and trial participation for each participant. Note that the total duration of trial participation should include any washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Total planned duration of trial participation for each participant:", + "business_rules": "Value Allowed: No\nRelationship: Duration\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 63, + "term": "{ [Total planned duration of trial participation unit of time]}", + "data_type": "Integer, Valid value", + "dvh": "D, V", + "definition": "C218715\nC218716", + "user_guidance": "Select one of the two options for total planned duration of trial intervention and trial participation for each participant. Note that the total duration of trial participation should include any washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”).", + "conformance": "Conditional: when planned duration of trial participation number and unit of time", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Total planned duration of trial participation: Integer\nTotal planned duration of trial participation unit of time:\nCode List C217048: ICH OID 2.16.840.1.113883.3.989.2.3.1.23\nDays (C25301); Hours (C25529); Months (C29846); Weeks (C29844); Years\n(C29848)", + "business_rules": "Value Allowed: Yes\nRelationship: Total duration of trial participation for each participant:\nConcept: C218715 ICH OID 2.16.840.1.113883.3.989.2.3.3.1; C218716 ICH\nOID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 63, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218717", + "user_guidance": "Select one of the two options for total planned duration of trial intervention and trial participation for each participant. Note that the total duration of trial participation should include any washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”). Or, if duration will vary", + "conformance": "Conditional: when an alternate description for planned duration of trial\nparticipation if duration will vary", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Total duration of planned duration of trial participation if duration\nwill vary:\nConcept: C218717 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 64, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218838", + "user_guidance": "If necessary, include any clarifications or cross-references to details in the main body of the protocol in the optional field below.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Duration\nConcept: C218838 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 64, + "term": "Committees:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Committees:", + "business_rules": "Value Allowed: No\nRelationship: 1.1.2 Overall Design; 1.1 Protocol Synopsis; 1 PROTOCOL\nSUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 64, + "term": "Independent Committees:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Independent Committees:", + "business_rules": "Value Allowed: No\nRelationship: Committees; 1.1.2 Overall Design; 1.1 Protocol Synopsis; 1\nPROTOCOL SUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 65, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218718", + "user_guidance": "Indicate whether any committee(s) will be reviewing data while the trial is ongoing, and the type of committee. Common examples include Data Monitoring Committee, Dose Escalation Committee, or Endpoint Adjudication Committee; describe others, if applicable. List independent committees in the space indicated. Other committees may be included in the separate space provided. Committees listed here should be fully described in Section 11.4 Committees.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "1.1.2", + "value": "Code List C217282: ICH OID 2.16.840.1.113883.3.989.2.3.1.5\nIndependent Data Monitoring Committee (C142578); Dose Escalation\nCommittee (C215671); Endpoint Adjudication Committee (C78726); Other\n(C17649); None (C41132)", + "business_rules": "Value Allowed: Yes, more than one committee can be selected\nRelationship: Independent Committees\nConcept: C218718 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 65, + "term": "Other Committees:", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Other Committees:", + "business_rules": "Value Allowed: No\nRelationship: Committees; 1.1.2 Overall Design; 1.1 Protocol Synopsis; 1\nPROTOCOL SUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 66, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218719", + "user_guidance": "Indicate whether any committee(s) will be reviewing data while the trial is ongoing, and the type of committee. Common examples include Data Monitoring Committee, Dose Escalation Committee, or Endpoint Adjudication Committee; describe others, if applicable. List independent committees in the space indicated. Other committees may be included in the separate space provided. Committees listed here should be fully described in Section 11.4 Committees. Delete “Other Committees” if not applicable.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "1.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Other Committees\nConcept: C218719 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "No" + }, + { + "page": 66, + "term": "1.2 Trial Schema", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "1.2", + "value": "Trial Schema", + "business_rules": "Value Allowed: No\nRelationship: 1 PROTOCOL SUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 66, + "term": "", + "data_type": "Image; Text", + "dvh": "D", + "definition": "C93682", + "user_guidance": "The purpose of this section is to provide a visual depiction of the trial design, orienting users of the protocol to the key features of the design. The schema depicts the trial arms, the flow of individual participant through the progression of trial period(s)/epochs (such as screening, washout/run-in, intervention, and key milestones [e.g., randomisation, cross-over, end of treatment, end of study, post-treatment follow-up]). For complex trials, additional schemas may be added to describe activities or trial periods in greater detail.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.2", + "value": "Image; Text", + "business_rules": "Value Allowed: Yes\nRelationship: 1.2 Trial Schema\nConcept: C93682 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable within Section" + }, + { + "page": 67, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218720", + "user_guidance": "The purpose of this section is to provide a visual depiction of the trial design, orienting users of the protocol to the key features of the design. The schema depicts the trial arms, the flow of individual participant through the progression of trial period(s)/epochs (such as screening, washout/run-in, intervention, and key milestones [e.g., randomisation, cross-over, end of treatment, end of study, post-treatment follow-up]). For complex trials, additional schemas may be added to describe activities or trial periods in greater detail.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 1.2 Trial Schema\nConcept: C218720 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable and aligned with appropriate schema" + }, + { + "page": 67, + "term": "1.3 Schedule of Activities", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.3", + "value": "Schedule of Activities", + "business_rules": "Value Allowed: No\nRelationship: 1 PROTOCOL SUMMARY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 68, + "term": "", + "data_type": "Table; Text; Image", + "dvh": "D", + "definition": "C132349", + "user_guidance": "The schedule of activities must capture the procedures that will be accomplished at each trial visit, and all contact with participants (e.g., telephone contacts). This includes any tests that are used for eligibility, participant randomisation or stratification, or decisions on trial intervention discontinuation. Allowable windows should be stated for all visits and procedures. A tabular format is recommended. When applicable for studies with extensive sampling (e.g., serial PK sampling), a separate table may be added.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "1.3", + "value": "Table; text; Image", + "business_rules": "Value Allowed: Yes\nRelationship: 1.3 Schedule of Activities\nConcept: C132349 ICH OID 2.16.840.1.113883.3.989.2.3.3.1", + "repeating_reuse_rules": "Yes, repeatable for each Schedule of Activity if needed" + }, + { + "page": 68, + "term": "2 INTRODUCTION", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "2", + "value": "INTRODUCTION", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 69, + "term": "2.1 Purpose of Trial", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "2.1", + "value": "Purpose of Trial", + "business_rules": "Value Allowed: No\nRelationship: 2 INTRODUCTION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 69, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C146997", + "user_guidance": "Explain why the trial is needed, and why the research questions being asked are important. Do not restate the objectives or estimands. Do not restate the IB; rather, cross reference to the IB as applicable to the description.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 2.1 Purpose of Trial\nConcept: C146997 ICH OID 2.16.840.1.113883.3.989.2.3.3.2", + "repeating_reuse_rules": "No" + }, + { + "page": 69, + "term": "2.2 Assessment of Risks and Benefits", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Include an assessment of known and potential risks and benefits, if any, as a result of participating in the trial from the perspective of an individual participant, including the basis of the risk (e.g., nonclinical trials or prior clinical trials). This section may be structured under one single heading 2.2 Assessment of Risks and Benefits, or if applicable under 3 subheadings as 2.2.1 Risk Summary and Mitigation Strategy, 2.2.2 Benefit Summary and 2.2.3 Overall Risk-Benefit Assessment.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "2.2", + "value": "Assessment of Risks and Benefits", + "business_rules": "Value Allowed: No\nRelationship: 2 INTRODUCTION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 70, + "term": "2.2.1 Risk Summary and Mitigation Strategy", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to many", + "relationship": "2.2.1", + "value": "Risk Summary and Mitigation Strategy", + "business_rules": "Value Allowed: No\nRelationship: 2.2 Assessment of Risks and Benefits; 2 INTRODUCTION; Table\nof Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 70, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218721", + "user_guidance": "Trial Intervention – Describe risks related to trial-specific treatments and interventions. For the protocol, focus on the relevant key risks for this trial. Provide a brief description of strategies to mitigate identified risks or provide a cross reference to the relevant protocol section.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "2.2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 2.2.1 Risk Summary and Mitigation Strategy\nConcept: C218721 ICH OID 2.16.840.1.113883.3.989.2.3.3.2", + "repeating_reuse_rules": "No" + }, + { + "page": 71, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218722", + "user_guidance": "Trial Procedures – Describe risks associated with the design (e.g., placebo arm) and procedures specific to this trial (e.g., biopsies), and any measures to control or mitigate the risks. Provide a brief description of strategies to mitigate identified risks or provide a cross-reference to the relevant protocol section. This is not intended to be an exhaustive list of all possible risks associated with trial procedures but should focus on the unique risks inherent in the design or less common or high-risk procedures.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "2.2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 2.2.1 Risk Summary and Mitigation Strategy\nConcept: C218722 ICH OID 2.16.840.1.113883.3.989.2.3.3.2", + "repeating_reuse_rules": "No" + }, + { + "page": 71, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218723", + "user_guidance": "Other – Consider risks associated with other items (e.g., challenge agents, imaging agents, medical devices). This could include discussion of risk mitigation for special populations, if not described elsewhere. Insert a line for each, as needed.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "2.2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 2.2.1 Risk Summary and Mitigation Strategy\nConcept: C218723 ICH OID 2.16.840.1.113883.3.989.2.3.3.2", + "repeating_reuse_rules": "No" + }, + { + "page": 72, + "term": "2.2.2 Benefit Summary", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "2.2.2", + "value": "Benefit Summary", + "business_rules": "Value Allowed: No\nRelationship: 2.2 Assessment of Risks and Benefits; 2 INTRODUCTION; Table\nof Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 72, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218724", + "user_guidance": "The benefit summary should describe any physical, psychological, social, or other potential benefits to individual participants as a result of participating in the trial, addressing immediate potential benefits and/or long-range potential benefits. Clearly state if no benefits to an individual participant can be anticipated, or if potential benefits are unknown. For early clinical trials such as Phase 1 or trials in healthy participants, benefits for an individual participant (other than those of altruism) are expected to be minimal. Benefits to society in general may also be included but should be described separately from the individual participant perspective.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "2.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 2.2.2 Benefit Summary\nConcept: C218724 ICH OID 2.16.840.1.113883.3.989.2.3.3.2", + "repeating_reuse_rules": "No" + }, + { + "page": 72, + "term": "2.2.3 Overall Risk-Benefit Assessment", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "2.2.3", + "value": "Overall Risk-Benefit Assessment", + "business_rules": "Value Allowed: No\nRelationship: 2.2 Assessment of Risks and Benefits; 2 INTRODUCTION; Table\nof Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 73, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218725", + "user_guidance": "Provide a succinct, concluding statement on the perceived balance between risks that have been identified from cumulative safety data, protocol procedures, and anticipated efficacy/benefits within the context of the proposed trial.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "2.2.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 2.2.3 Overall Risk-Benefit Assessment OR 2.2 Assessment of\nRisks and Benefits (when the Optional Level 3 subheading [2.2.3] is not used)\nIf the Optional Level 3 subheadings [2.2.1, 2.2.2, 2.2.3] are not used, the user\nguidance below Section 2.2 applies.\nConcept: C218725 ICH OID 2.16.840.1.113883.3.989.2.3.3.2", + "repeating_reuse_rules": "No" + }, + { + "page": 73, + "term": "3 TRIAL OBJECTIVES AND ASSOCIATED ESTIMANDS", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "In this section, precisely define each trial objective and refine each trial objective into a precise clinical question of interest by defining the associated estimand. For considerations on estimands, refer to ICH E9(R1). Ensure alignment with every other section of the protocol. Include additional level 3 headings (e.g., add a new level 3 heading for each secondary objective as needed). If there is more than one objective in a category (e.g., more than one secondary objective), number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "3", + "value": "TRIAL OBJECTIVES AND ASSOCIATED ESTIMANDS", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 74, + "term": "3.1 Primary Objective(s) and Associated Estimand(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only)", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "3.1", + "value": "Primary Objective(s) and Associated Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 3 TRIAL OBJECTIVES AND ASSOCIATED ESTIMANDS;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 74, + "term": "3.1.X Primary Objective <#>", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "For all trials, precisely state each primary trial objective by providing a meaningful and concise description of the treatment effect of interest using natural, nontechnical language for clear understanding by sponsors, investigators, clinical site personnel, trial participants, ethics committees, and regulators. For trials intended to estimate a treatment effect or test a hypothesis related to a treatment effect, use the table to precisely describe the associated estimand(s). This includes specification of the population targeted by the clinical question, the treatment condition(s), the endpoint (or variable), and the population-level summary. Precise specifications of treatment, population, and variable are likely to address many of the intercurrent events. Other intercurrent events not already addressed in the clinical question of interest by the aforementioned attributes should be described with their associated strategies. For other types of trials not intended to estimate a treatment effect or test a hypothesis related to a treatment effect, describe additional information relevant to the clinical question(s) of interest (at a minimum, present the endpoint(s) associated with each objective). No text is intended here (heading only)", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Primary Objective <#>: # is a unique number for each Primary Objective; if\nthere is only one Primary Objective, # is blank. If more than one Primary\nObjective, add sequential unique number for each objective", + "business_rules": "Value Allowed: No\nRelationship: 3.1 Primary Objective and Associated Estimand(s); 3. TRIAL\nOBJECTIVES AND ASSOCIATED ESTIMAND; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective.\nYes, reuse to the table in Section 1.1.1.for each Primary Objective" + }, + { + "page": 75, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C85826", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; One to Table of Contents Number 3.1.X; One to Estimand\nCharacteristics Table, Primary Objective <#>, Protocol Identifier", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text and unique integer which is same as Level 3 number for the section.", + "business_rules": "Value Allowed: Yes\nRelationship: 3.1.X Primary Objective <#>\nConcept: C85826 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective.\nYes, reuse to the table in Section 1.1.1.for each Primary Objective" + }, + { + "page": 75, + "term": "Estimand Characteristic", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "Enter information in table of estimand characteristics below including endpoint at a minimum.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Estimand Characteristic", + "business_rules": "Value Allowed: No\nRelationship: 3.1 Primary Objective(s) and associated Estimand(s); Table\ncolumn Heading; Description; Population; Treatment; Endpoint; Population-\nLevel Summary; Other Intercurrent Event\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective\nYes, reuse to the table in Section 1.1.1.for each Primary Objective" + }, + { + "page": 76, + "term": "Description", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "Enter information in table of estimand characteristics below including endpoint at a minimum.", + "conformance": "Required", + "cardinality": "One to many rows", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Description", + "business_rules": "Value Allowed: No\nRelationship: 3.1 Primary Objective(s) and associated Estimand(s); Table\ncolumn Heading; Estimand Characteristic; Population; Treatment; Endpoint;\nPopulation-Level; Other Intercurrent Event; Strategy\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective\nYes, reuse to the table in Section 1.1.1.for each Primary Objective" + }, + { + "page": 76, + "term": "{Population}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a population as estimand characteristic", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Population", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 77, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C70833", + "user_guidance": "List of key characteristics, such as demographic characteristics (e.g., age, sex) and clinical characteristics (e.g., prior therapies, symptoms, severity, biomarker status)", + "conformance": "Conditional: If there is a population as estimand characteristic", + "cardinality": "One to Row Heading; One to Primary Objective Table; Primary Objective <#>;\nProtocol Identifier", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description\nConcept: C70833 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 77, + "term": "{Treatment}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a treatment as estimand characteristic", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Treatment", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 77, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C49236", + "user_guidance": "List of key aspects of treatment regimens in each treatment group, including at least investigational agents, dosage, and administration route", + "conformance": "Conditional: If there is a treatment as estimand characteristic", + "cardinality": "One to Row Heading; One to Primary Objective Table; Project Identifier", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description\nConcept: C49236 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 78, + "term": "Endpoint", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Endpoint", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 78, + "term": "{< Endpoint >}", + "data_type": "Text", + "dvh": "D", + "definition": "C25212", + "user_guidance": "Definition of the endpoint", + "conformance": "Required", + "cardinality": "One to Row Heading; One to Primary Objective Table; Project Identifier", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description\nConcept: C25212 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 78, + "term": "{Population-level Summary}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a population -level summary as estimand characteristic", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Population-level Summary", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristics\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 79, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188853", + "user_guidance": "Description of the population-level summary (e.g., mean difference, relative risk)", + "conformance": "Conditional: If there is a population-level summary as estimand", + "cardinality": "One to Row Heading; One to Primary Objective Table; Project Identifier", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description\nConcept: C188853 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 79, + "term": "{Other Intercurrent Event}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is one or more other intercurrent events as estimand\ncharacteristic.", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Other Intercurrent Event", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristics\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 79, + "term": "{Strategy}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is one or more other intercurrent events as estimand\ncharacteristic.", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Strategy", + "business_rules": "Value Allowed: No\nRelationship: Table column Heading; Other Intercurrent Event; Description\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each numbered Primary Objective" + }, + { + "page": 80, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188856", + "user_guidance": "Description of the strategy to address the intercurrent event (e.g., a treatment policy strategy); cross reference the justification in Section 4 Trial Design. If there is >1 intercurrent event for an objective, add additional intercurrent event rows", + "conformance": "Conditional: If there is one or more other intercurrent events as estimand\ncharacteristic.", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Estimand Characteristics\nConcept: C188856 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each intercurrent event" + }, + { + "page": 80, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188857", + "user_guidance": "Description of the strategy to address the intercurrent event (e.g., a treatment policy strategy); cross reference the justification in Section 4 Trial Design. If there is >1 intercurrent event for an objective, add additional intercurrent event rows", + "conformance": "Conditional: If there is one or more other intercurrent events as estimand\ncharacteristic.", + "cardinality": "One to one", + "relationship": "3.1.X\nwhere X is a unique number for each Primary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Strategy; Description\nConcept: C188857 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each intercurrent event relationship" + }, + { + "page": 81, + "term": "3.2 Secondary Objective(s) and Associated Estimand(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "3.2", + "value": "Secondary Objective(s) and Associated Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 3 TRIAL OBJECTIVES AND ASSOCIATED ESTIMAND(S);\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 81, + "term": "{3.2.X Secondary Objective <#>}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Describe the secondary objective(s) and associated estimand(s) as outlined in Section 3.1 Primary Objective(s) and Associated Estimand(s). Use the same approach as above and include table for a precise estimand description. No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable”.", + "conformance": "Conditional: when there are secondary objective heading for each secondary\nrequirement", + "cardinality": "One to one", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Secondary Objective <#>: # is a unique number for each Secondary Objective; if\nthere is only one Secondary Objective, # is blank. If more than one Secondary\nObjective, add sequential unique number for each objective", + "business_rules": "Value Allowed: No\nRelationship: 3.2 Secondary Objective and Associated Endpoints; 3 TRIAL\nOBJECTIVES AND ASSOCIATED ESTIMAND(S); Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 81, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C85827", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one; Table of Contents Number 3.2.X; One to Estimand Characteristic\nTable, Secondary Objective <#>, Protocol Identifier", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text and unique integer which is same as Level 3 number for the section.", + "business_rules": "Value Allowed: Yes\nRelationship: 3.2.X Secondary Objective <#>; Estimand Characteristics table\nConcept: C85827 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 82, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "N/A", + "user_guidance": "If a Secondary Objective has been entered, enter information in table of estimand characteristics below including endpoint at a minimum}", + "conformance": "Conditional: either Enter Table of Estimand Characteristics or details of the\ncharacteristics relevant to objective", + "cardinality": "One to many rows", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Estimand Characteristics", + "business_rules": "Value Allowed: No\nRelationship: 3.3.2 Secondary Objective(s) and associated Estimand(s)\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 82, + "term": "{Estimand Characteristics}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a Secondary Objective", + "cardinality": "One to many rows", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Estimand Characteristics", + "business_rules": "Value Allowed: No\nRelationship: 3.2 Secondary Objective(s) and associated Estimand(s); Table\ncolumn Heading; Description, Population; Treatment; Endpoint; Population-\nLevel Summary; Intercurrent Event\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 83, + "term": "{Description}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional", + "cardinality": "One to many rows", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Description", + "business_rules": "Value Allowed: No\nRelationship: 3.3.2 Secondary Objective(s) and associated Estimand(s); Table\ncolumn Heading; Estimand Characteristics; Population; Treatment; Endpoint,\nPopulation-Level Summary; Other Intercurrent Event; Strategy\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 83, + "term": "{Population}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a population", + "cardinality": "One to one", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Population", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 83, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C70833", + "user_guidance": "List of key characteristics, such as demographic characteristics (e.g. age, sex) and clinical characteristics (e.g. prior therapies, symptoms, severity, biomarker status)", + "conformance": "Conditional: If there is a population for Secondary", + "cardinality": "One to Row Heading; One to Secondary Objective Table; Secondary Objective\n<#>; Protocol Identifier", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading, Description; Estimand Characteristic\nConcept: C70833 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 84, + "term": "{Treatment}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a population", + "cardinality": "One to one", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Treatment", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 84, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C49236", + "user_guidance": "List of key aspects of treatment regimens in each treatment group, including at least investigational agents, dosage, and administration route", + "conformance": "Conditional: If there is a population for Secondary", + "cardinality": "One to Row Heading, One to Secondary Objective Table, Project Identifier", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading, Description; Estimand Characteristics\nConcept: C49236 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 84, + "term": "{Endpoint}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a Secondary Objective", + "cardinality": "One to one", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Endpoint", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Description; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 85, + "term": "{< Endpoint >}", + "data_type": "Text", + "dvh": "D", + "definition": "C25212", + "user_guidance": "Definition of the endpoint", + "conformance": "Conditional: if there is a Secondary Objective", + "cardinality": "One to Row Heading, One to Secondary Objective Table, Project Identifier", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description; Table Estimand Characteristics;\nSecondary (1…n) Estimand\nConcept: C25212 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 85, + "term": "{Population-level Summary}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a Population-level Summary", + "cardinality": "One to", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Population-level Summary", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristics\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 85, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188853", + "user_guidance": "Description of the population-level summary (e.g., mean difference, relative risk)", + "conformance": "Conditional: If there is a population for Secondary", + "cardinality": "One to Row Heading; One to Secondary Objective Table; Project Identifier", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description; Table estimand Characteristics;\nSecondary (1…n) Estimand; Protocol Identifier\nConcept: C188853 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 86, + "term": "{Other Intercurrent Event}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is one or more other intercurrent events", + "cardinality": "One to one", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Other Intercurrent Event", + "business_rules": "Value Allowed: No\nRelationship: 3.3.2 Secondary Objective(s) and associated Estimand(s); Table\nColumn Heading\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 86, + "term": "{Strategy}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is one or more other intercurrent events", + "cardinality": "One to many rows", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Strategy", + "business_rules": "Value Allowed: No\nRelationship: Table column Heading; Other Intercurrent Event (1…n)\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Secondary Objective." + }, + { + "page": 87, + "term": "{Description of Intercurrent Event}", + "data_type": "Text", + "dvh": "H", + "definition": "C188856", + "user_guidance": "Enter Description of Intercurrent Event", + "conformance": "Conditional: If there is one or more other intercurrent events.", + "cardinality": "One to one or as many intercurrent event as available", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristics; Protocol Identifier\nConcept: C188856 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each intercurrent event" + }, + { + "page": 87, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188857", + "user_guidance": "Description of the strategy to address the intercurrent event (e.g. a treatment policy strategy); cross-reference the justification in Section 4. If there is >1 intercurrent event for an objective, add additional intercurrent event rows", + "conformance": "Conditional: If there is one or more other intercurrent events.", + "cardinality": "One to one", + "relationship": "3.2.X\nwhere X is a unique number for each Secondary Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description of Intercurrent Event\nConcept: C188857 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each intercurrent event relationship" + }, + { + "page": 87, + "term": "3.3 Exploratory Objective(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "State each exploratory objective. This should generally include documentation of associated exploratory endpoints. It may be helpful in some cases to describe precise estimands to provide clarity on what is being estimated. Use the same approach as above and include table for a precise estimand description. No text is intended here (heading only) unless there is no exploratory objective, in which case indicate “Not applicable”.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "3.3", + "value": "Exploratory Objective(s)", + "business_rules": "Value Allowed: No\nRelationship: TRIAL OBJECTIVES AND ENDPOINT; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 88, + "term": "{3.3.X Exploratory Objective <#>}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "State each exploratory objective. This should generally include documentation of associated exploratory endpoints. It may be helpful in some cases to describe precise estimands to provide clarity on what is being estimated. Use the same approach as above and include table for a precise estimand description. No text is intended here (heading only) unless there is no exploratory objective, in which case indicate “Not applicable”.", + "conformance": "Conditional: when there are exploratory objective heading for each exploratory\nrequirement", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Exploratory Objective <#>: # is a unique number for each Exploratory\nObjective; if there is only one Exploratory Objective, # is blank If more than one\nExploratory Objective, add sequential unique number for each objective", + "business_rules": "Value Allowed: No\nRelationship: 3.3 Exploratory Objective(s); 3 TRIAL OBJECTIVES AND\nASSOCIATED ESTIMANDS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 88, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C163559", + "user_guidance": "N/A", + "conformance": "Conditional: if an Exploratory Objective is part of the trial", + "cardinality": "One to Table of Contents Number 3.3.X; One to Estimand Characteristic Table,\nExploratory Objective <#>, Protocol Identifier", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes Relationship: 3.3.X Exploratory Objective\nConcept: C163559 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 89, + "term": "{
including Endpoint at a minimum}", + "data_type": "Text", + "dvh": "D", + "definition": "N/A", + "user_guidance": "If an Exploratory Objective has been entered, enter information in table of estimand characteristics below including endpoint at a minimum:", + "conformance": "Conditional: either Enter Table of Estimand Characteristics or details of the\ncharacteristics relevant to objective", + "cardinality": "One to many", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 3.3.3 Exploratory Objective(s) and associated Estimand(s); Table\ncolumn Heading; Description; Population; Treatment; Endpoint; Population-\nLevel; Intercurrent Event (1…n)\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 89, + "term": "{Estimand Characteristic}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is exploratory endpoint(s).", + "cardinality": "One to many rows", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Estimand Characteristics", + "business_rules": "Value Allowed: No\nRelationship: 3.3.X Exploratory Objective; Table Column Heading;\nDescription; Population; Treatment; Endpoint; Population-Level; Intercurrent\nEvent\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 89, + "term": "{Description}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is exploratory endpoint(s)", + "cardinality": "One to many rows", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Description", + "business_rules": "Value Allowed: No\nRelationship: 3.3.X Exploratory Objective Table Column Heading; Estimand\nCharacteristic; Population; Treatment; Endpoint; Population-Level; Intercurrent\nEvent (1…n); Strategy\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 90, + "term": "{Population}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a population as estimand", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Population", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 90, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C70833", + "user_guidance": "List of key characteristics, such as demographic characteristics (e.g. age, sex) and clinical characteristics (e.g. prior therapies, symptoms, severity, biomarker status)", + "conformance": "Conditional: If there is a population as estimand characteristic", + "cardinality": "One to Row Heading; One to Exploratory Objective Table, Exploratory\nObjective <#>, Protocol Identifier", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading, Description; Table Estimand Characteristics;\nExploratory (1…n) Estimand\nConcept: C70833 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 91, + "term": "{Treatment}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a treatment as estimand.", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Treatment", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 91, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C49236", + "user_guidance": "List of key aspects of treatment regimens in each treatment group, including at least investigational agents, dosage, and administration route", + "conformance": "Conditional: If there is a treatment as estimand", + "cardinality": "One to Row Heading; One to Exploratory Objective Table; Project Identifier", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading, Description; Table Estimand Characteristics;\nExploratory (1…n) Estimand; Protocol Identifier\nConcept: C49236 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 91, + "term": "{Endpoint}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is exploratory endpoint(s).", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Endpoint", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 92, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C25212", + "user_guidance": "Definition of the endpoint", + "conformance": "Conditional: if there is exploratory endpoint(s).", + "cardinality": "One to Row Heading; One to Exploratory Objective Table, Project Identifier", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description; Table Estimand Characteristics;\nExploratory (1…n) Estimand\nConcept: C25212 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 92, + "term": "{Population-level Summary}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is a population-level summary", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Population-level Summary", + "business_rules": "Value Allowed: No\nRelationship: Row Heading; Estimand Characteristics\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 92, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188853", + "user_guidance": "List of key characteristics, such as demographic characteristics (e.g. age, sex) and clinical characteristics (e.g. prior therapies, symptoms, severity, biomarker status)", + "conformance": "Conditional: If there is a population-level summary", + "cardinality": "One to Row Heading; One to Exploratory Objective Table, Project Identifier", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Description; Table Estimand Characteristics;\nExploratory (1…n) Estimand\nConcept: C188853 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 93, + "term": "{Other Intercurrent Event}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is one or more other intercurrent event as estimand\ncharacteristic.", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Other Intercurrent Event", + "business_rules": "Value Allowed: No\nRelationship: 3.3.3 Exploratory Objective(s) and associated Estimand(s); Table\ncolumn Heading; Estimand Characteristic\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 93, + "term": "{Strategy}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: If there is one or more other intercurrent event as estimand.", + "cardinality": "One to many rows", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Strategy", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading; Estimand Characteristics; Other\nIntercurrent Event\nConcept: Heading", + "repeating_reuse_rules": "Y es, repeatable for each numbered Exploratory Objective." + }, + { + "page": 93, + "term": "{Description of Intercurrent Event}", + "data_type": "Text", + "dvh": "D", + "definition": "C188856", + "user_guidance": "Enter Description of Intercurrent Event", + "conformance": "Conditional: If there is one or more other intercurrent events as estimand\ncharacteristic.", + "cardinality": "One to one or as many intercurrent event as available", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading, Estimand Characteristics\nConcept: C188856 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each intercurrent event" + }, + { + "page": 94, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C188857", + "user_guidance": "Description of the strategy to address the intercurrent event (e.g., a treatment policy strategy); cross reference the justification in Section 4 Trial Design. If there is >1 intercurrent event for an objective, add additional intercurrent event rows", + "conformance": "Conditional: If there is one or more other intercurrent events as estimand\ncharacteristic.", + "cardinality": "One to one", + "relationship": "3.3.X\nwhere X is a unique number for each Exploratory Objective", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Row Heading; Strategy; Description\nConcept: C188857 ICH OID 2.16.840.1.113883.3.989.2.3.3.3", + "repeating_reuse_rules": "Yes, repeatable for each intercurrent event relationship" + }, + { + "page": 94, + "term": "4 TRIAL DESIGN", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "In the subsections below, describe the trial design with specific mention, as applicable, of the components of an adequate and well-controlled trial and reflect the principles of Quality by Design. The description of the design should be concise and consistent with Section 1.1 Protocol Synopsis and Section 1.2 Trial Schema. The trial design should align with objectives/estimand(s) described in Section 3 Trial Objectives and Associated Estimands. This section is intended to provide a description for the important aspects of the trial design and rationale for its key attributes. Operational details needed to implement the trial design should be covered in more detail in subsequent sections. No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4", + "value": "TRIAL DESIGN", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 95, + "term": "4.1 Description of Trial Design", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "4.1", + "value": "Description of Trial Design", + "business_rules": "Value Allowed: No\nRelationship: 4 TRIAL DESIGN; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 95, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C147139", + "user_guidance": "Describe the overall trial design and intervention model (e.g., single group, parallel group, cross-over, factorial, sequential), the expected number of participants, and the control method (e.g., placebo, active comparator, low dose, external, standard of care, sham procedure, or none [uncontrolled]). If there are any key aspects of the investigational trial intervention that inform the selection of the intervention model, this should be described. If applicable, indicate other design characteristics (e.g., superiority, noninferiority, dose escalation, or equivalence). If the trial will have an adaptive or novel design (e.g., the trial will be conducted under a master protocol), provide a summary of these design aspects. If applicable, describe within-trial transition rules (e.g., transitions involving cohorts or trial parts). Dose escalation or dose-ranging details should also be described.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.1 Description of Trial Design\nConcept: C147139 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 96, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218726", + "user_guidance": "Describe the trial duration with reference to Section 1.2 Trial Schema. Explain what the overall duration for an individual participant is anticipated to be and why, including the sequence and duration of trial periods (e.g., screening, run-in, randomisation, treatment [fixed dose/titration], follow-up/washout periods). Where applicable, include discussion of sentinel dosing (or lack thereof), dose escalation, and cohort expansion. If dose modification decisions are dependent upon review by a committee, include details in Section 11.4 Committees.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.1 Description of Trial Design\nConcept: C218726 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 96, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C219658", + "user_guidance": "State the method of assignment to trial intervention and the level and method of blinding that will be used, with cross reference to Section 6.7 Investigational Trial Intervention Assignment, Randomisation and Blinding.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.1 Description of Trial Design\nConcept: C219658 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 97, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218727", + "user_guidance": "State the method of assignment to trial intervention and the level and method of blinding that will be used, with cross reference to Section 6.7 Investigational Trial Intervention Assignment, Randomisation and Blinding.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.1 Description of Trial Design\nConcept: C218727 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 97, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218728", + "user_guidance": "Describe any other important aspects of the design, e.g.: • geographic scope of trial (e.g., single-centre, multicentre, or multicentre and multinational) • use of decentralised elements in the trial • planned use of a Data Monitoring Committee, or similar review group and cross reference Section 11.4 Committees, for details • whether an interim analysis is planned; if so, refer to details in Section 10.9 Interim Analyses • any planned extension trial, long-term follow-up/registry, future use of samples or data, or post-trial sample analysis or other data-related activities", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.1 Description of Trial Design\nConcept: C218728 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 98, + "term": "4.1.1 Stakeholder Input into Design", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1.1", + "value": "Stakeholder Input into Design", + "business_rules": "Value Allowed: No\nRelationship: 4.1.1 Stakeholder Input into Design; 4.1 Description of Trial\nDesign; 4 TRIAL DESIGN; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 98, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218729", + "user_guidance": "If applicable, describe any stakeholder (e.g., patient, healthcare professional and patient advocacy groups) involvement in the design of the trial and any suggestions implemented.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "4.1.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.1.1 Stakeholder Input into Design\nConcept: C218729 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 98, + "term": "4.2 Rationale for Trial Design", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.2", + "value": "Rationale for Trial Design", + "business_rules": "Value Allowed: No\nRelationship: 4 TRIAL DESIGN; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 99, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C142705", + "user_guidance": "if not using below optional subheadings.", + "conformance": "Conditional: If Level 3 subheadings are not used", + "cardinality": "One to one", + "relationship": "4.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2 Rationale for Trial Design\nConcept: C142705 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 99, + "term": "4.2.1 Rationale for Estimand(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.1", + "value": "Rationale for Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design; 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 99, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218730", + "user_guidance": "When estimands are associated with the Primary and Secondary Objectives described in Section 3 Trial Objectives and Associated Estimands, provide a rationale for the estimand(s) not described elsewhere in the document. This should include a rationale that the selected endpoint(s) are clinically relevant and provide a reliable and valid measurement of the intended intervention effect(s). It should also include a rationale for the selected strategies for handling intercurrent events.", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.1 Rationale for Estimand(s)\nConcept: C218730 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 100, + "term": "4.2.2 Rationale for Intervention Model", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.2", + "value": "Rationale for Intervention Model", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design; 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 100, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C215629", + "user_guidance": "Provide a rationale for the trial intervention model described in Section 4.1 Description of Trial Design with a cross reference to Section 6.2 Rationale for Investigational Trial Intervention Dose and Regimen. Rationale for choice of comparator, if applicable, should be described separately in Section 4.2.3 Rationale for Control Type. A rationale for the choice of trial population should be described separately in Section 5.1 Description of Trial Population and Rationale.", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.2 Rationale for Intervention Model\nConcept: C215629 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 101, + "term": "4.2.3 Rationale for Control Type", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.3", + "value": "Rationale for Control Type", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design; 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 101, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218731", + "user_guidance": "If applicable, provide a rationale for the type and choice of control selected for the trial (e.g., placebo, active drug, combination, external). Describe any known or potential problems associated with the control group selected in light of the specific disease and intervention(s) being studied. If comparators will differ by region, describe. The rationale for dose and/or dose regimen is explained in Section 6.2 Rationale for Investigational Trial Intervention Dose and Regimen.", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.3 Rationale for Control Type\nConcept: C218731 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 101, + "term": "4.2.4 Rationale for Trial Duration", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.4", + "value": "Rationale for Trial Duration", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design, 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 102, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218732", + "user_guidance": "Provide a rationale that the trial duration is appropriate for a reliable and relevant evaluation of the trial intervention per the trial objective(s).", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.4 Rationale for Trial Duration\nConcept: C218732 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 102, + "term": "4.2.5 Rationale for Adaptive or Novel Trial Design", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.5", + "value": "Rationale for Adaptive or Novel Design", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design; 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 103, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218733", + "user_guidance": "If applicable, provide a rationale for the use of an adaptive or novel design.", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.5 Rationale for Adoptive or Novel Trial Design\nConcept: C218733 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 103, + "term": "4.2.6 Rationale for Interim Analysis", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.6", + "value": "Rationale for Interim Analysis", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design; 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 103, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218734", + "user_guidance": "If applicable, provide a rationale for any interim analysis planned with respect to its purpose (e.g., stopping the trial early for efficacy or futility) and timing.", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.6 Rationale for Interim Analysis\nConcept: C218734 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 104, + "term": "4.2.7 Rationale for Other Trial Design Aspects", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.7", + "value": "Rationale for Other Trial Design Aspects", + "business_rules": "Value Allowed: No\nRelationship: 4.2 Rationale for Trial Design, 4 TRIAL DESIGN; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 104, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218735", + "user_guidance": "Discuss rationale for any additional aspects of the design not addressed above.", + "conformance": "Conditional: when is not used", + "cardinality": "One to one", + "relationship": "4.2.7", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.2.7 Rationale for Other Trial Design Aspects\nConcept: C218735 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 104, + "term": "4.3 Trial Stopping Rules", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.3", + "value": "Trial Stopping Rules", + "business_rules": "Value Allowed: No\nRelationship: 4 TRIAL DESIGN; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 105, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C142698", + "user_guidance": "If applicable, describe any trial-specific stopping rules, including guidance on when the trial should be stopped for efficacy or safety reasons, when a cohort or dose escalation should be terminated, and/or when a given treatment arm should be terminated. If applicable, describe any rules that may result in a temporary pause of dosing and/or enrollment into the trial and criteria for restarting enrollment. Ensure that the trial-specific stopping rules are aligned with the specifications that are described in Section 10.9 Interim Analyses.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.3 Trial Stopping Rules\nConcept: C142698 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 105, + "term": "4.4 Start of Trial and End of Trial", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "4.4", + "value": "Start of Trial and End of Trial", + "business_rules": "Value Allowed: No\nRelationship: 4 TRIAL DESIGN; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 106, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218736", + "user_guidance": "Define key timepoints in the trial, including trial start and end definitions (e.g., a key timepoint definition for start of trial might be when the ICF is signed by the first participant, and a key timepoint definition for end of trial might be when participants are no longer being examined or the last participant’s last trial assessment has occurred). Consider local regulatory requirements for these and other definitions (e.g., the first act of recruitment). If appropriate, provide a cross reference to Section 11.11 Early Site Closure.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.4 Start of Trial and End of Trial\nConcept: C218736 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 106, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218737", + "user_guidance": "Define key timepoints in the trial, including trial start and end definitions (e.g., a key timepoint definition for start of trial might be when the informed consent is signed by the first participant, and a key timepoint definition for end of trial might be when participants are no longer being examined or the last participant’s last trial assessment has occurred). If applicable, consider local regulatory requirements for these and other definitions (e.g., the first act of recruitment). If appropriate, provide a cross reference to Section 11.11 Early Site Closure.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.4 Start of Trial\nConcept: C218737 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 107, + "term": "4.5 Access to Trial Intervention After End of Trial", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.5", + "value": "Access to Trial Intervention After End of Trial", + "business_rules": "Value Allowed: No\nRelationship: 4 TRIAL DESIGN; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 107, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218738", + "user_guidance": "If applicable, describe any possibilities for access to trial intervention, if any, beyond completion of the trial. Planned extension trials, if described in Section 4.1 Description of Trial Design, do not need to be repeated in this section.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "4.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 4.5 Access to Trial Intervention After End of Trial\nConcept: C218738 ICH OID 2.16.840.1.113883.3.989.2.3.3.4", + "repeating_reuse_rules": "No" + }, + { + "page": 107, + "term": "5 TRIAL POPULATION", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "In the subsections below, describe the trial population: inclusion and exclusion criteria, contraception requirements and lifestyle restrictions. The trial population should generally be aligned with the population attribute of the primary estimand that was defined in Section 3 Trial Objectives and Associated Estimands. Consider the following when developing participant eligibility criteria to be listed in Section 5.2 Inclusion Criteria and Section 5.3 Exclusion Criteria: • List the criteria necessary for participation in the trial. Ensure that each criterion can be easily assessed definitively and answered with yes/no responses. • Criteria should be written to avoid protocol waivers or exemptions. • If participants require screening, distinguish between screening vs enrolling participants. • Identify specific laboratory tests or clinical characteristics that will be used as criteria for inclusion or exclusion and any documentation needed to demonstrate the criterion is met (e.g., laboratory tests or imaging). If permitting existing medical diagnosis, imaging, genetic tests, or laboratory results, state any required window or acceptable test type. • If measures to enrich the trial population for pre-specified subgroups of interest are used, these should be described. No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5", + "value": "TRIAL POPULATION", + "business_rules": "Value Allowed: No\nRelationship: Table of contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 108, + "term": "5.1 Description of Trial Population and Rationale", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.1", + "value": "Description of Trial Population and Rationale", + "business_rules": "Value Allowed: No\nRelationship: 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 108, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218739", + "user_guidance": "Describe the population selected (e.g., healthy participants, adult participants, paediatric participants, pregnant participants, or breastfeeding participants) and how the enrollment criteria reflect the populations that are likely to use the drug if approved. Specify the population age range (e.g., ≤ 3 months, ≥ 18 to ≤ 80 years old) including the timepoint at which qualification for age criteria is determined (e.g., at time of screening vs randomisation for paediatric trials). Specify any key diagnostic criteria for the population (e.g., “acute lung injury”, or a specific biomarker profile). If applicable, describe similar conditions or diseases and their differential diagnosis. Provide a rationale for the trial population ensuring that the population selected is well defined and clinically recognisable. Describe how the selected population can meet the trial objectives and how the enrollment criteria reflect the population of interest. If a clinical question targets a subset of the entire trial population, such as one defined by a particular baseline characteristic (e.g., a specific biomarker), the rationale for selecting this subset should be provided in this section. Justify whether the trial intervention is to be evaluated in paediatric participants, in adults unable to consent for themselves, other vulnerable participant populations, or those that may respond to the trial intervention differently (e.g., elderly, hepatic or renally impaired, or immunocompromised participants).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.1 Description of Trial Population and Rationale\nConcept: C218739 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 109, + "term": "Prospective approval of protocol deviations to recruitment and enrollment criteria,also known as protocol waivers or exemptions, is not permitted.", + "data_type": "Text", + "dvh": "H", + "definition": "Universal Text", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.1", + "value": "Prospective approval of protocol deviations to recruitment and enrollment criteria,\nalso known as protocol waivers or exemptions, is not permitted.", + "business_rules": "Value Allowed: No\nRelationship: 5.1 Description of Trial Population and Rationale\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 110, + "term": "5.2 Inclusion Criteria", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Inclusion criteria are characteristics that define the trial population, i.e., those criteria that every potential participant must satisfy to qualify for trial enrollment.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "5.2", + "value": "5.2 Inclusion Criteria", + "business_rules": "Value Allowed: No\nRelationship: 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 110, + "term": "To be eligible to participate in this trial, an individual must meet all the following criteria:", + "data_type": "Text", + "dvh": "H", + "definition": "Universal text", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.2", + "value": "To be eligible to participate in this trial, an individual must meet all the following\ncriteria:", + "business_rules": "Value Allowed: No\nRelationship: 5.2 Inclusion Criteria\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 110, + "term": "<#>", + "data_type": "Number", + "dvh": "D", + "definition": "N/A", + "user_guidance": "Add criteria as needed. Consider numbering the criteria sequentially.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.2", + "value": "# is an integer unique number and not replaceable", + "business_rules": "Value Allowed: Yes\nRelationship: 5.2 Inclusion Criteria\nConcept: Sequential number", + "repeating_reuse_rules": "Yes, repeatable for each Inclusion Criterion" + }, + { + "page": 111, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C25532", + "user_guidance": "Add criteria as needed. Consider numbering the criteria sequentially.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: to Number #, 5.2 Inclusion Criteria\nConcept: C25532 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "Yes, number consecutively, repeatable for each Inclusion Criterion. If deleted for\nan amendment, do not replace and do not duplicate" + }, + { + "page": 111, + "term": "5.3 Exclusion Criteria", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Exclusion criteria are characteristics that make an individual ineligible for participation.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "5.3", + "value": "Exclusion Criteria", + "business_rules": "Value Allowed: No\nRelationship: 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 111, + "term": "An individual who meets any of the following criteria will be excluded from participation in this trial:", + "data_type": "Text", + "dvh": "H", + "definition": "Universal text", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.3", + "value": "An individual who meets any of the following criteria will be excluded from\nparticipation in this trial:", + "business_rules": "Value Allowed: No\nRelationship: 5.3 Exclusion Criteria; 5 TRIAL POPULATION; Table of Contents\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 112, + "term": "<#>", + "data_type": "Number", + "dvh": "D", + "definition": "N/A", + "user_guidance": "Add criteria as needed. Consider numbering the criteria sequentially.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.3", + "value": "# is an identifier unique number and not replaceable", + "business_rules": "Value Allowed: Yes\nRelationship: 5.3 Exclusion Criteria\nConcept: Sequential number", + "repeating_reuse_rules": "Yes. number consecutively, repeatable for each Exclusion Criterion. If deleted for\nan amendment, do not replace and do not duplicate" + }, + { + "page": 112, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C25370", + "user_guidance": "Add criteria as needed. Consider numbering the criteria sequentially.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: to Number #; 5.3 Exclusion Criteria\nConcept: C25370 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "Yes, repeatable for each Exclusion Criterion, if deleted do not replace, do not\nduplicate" + }, + { + "page": 113, + "term": "5.4 Contraception", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.4", + "value": "Contraception", + "business_rules": "Value Allowed: No\nRelationship: 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 113, + "term": "5.4.1 Definitions Related to Childbearing Potential", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.4.1", + "value": "Definitions Related to Childbearing Potential", + "business_rules": "Value Allowed: No\nRelationship: 5.4 Contraception; 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 113, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218740", + "user_guidance": "Specify the definitions of: • participant of childbearing potential • participant of nonchildbearing potential", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.4.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.4.1 Definitions Related to Childbearing Potential\nConcept: C218740 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 114, + "term": "5.4.2 Contraception Requirements", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.4", + "value": "Contraception Requirements", + "business_rules": "Value Allowed: No\nRelationship: 5.4 Contraception; 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 114, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218741", + "user_guidance": "Specify the: • contraceptive methods required • duration of use", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.4.2 Contraception Requirements\nConcept: C218741 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 114, + "term": "5.5 Lifestyle Restrictions", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.5", + "value": "Lifestyle Restrictions", + "business_rules": "Value Allowed: No\nRelationship: 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 115, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218742", + "user_guidance": "In the following subsections, describe any restrictions during the trial pertaining to lifestyle and/or diet, intake of caffeine, alcohol, or tobacco, or physical and other activities. If not applicable, include a statement that no restrictions are required.", + "conformance": "Conditional: If Level 3 subheadings are not used", + "cardinality": "One to one", + "relationship": "5.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.5 Lifestyle Restrictions\nConcept: C218742 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 115, + "term": "5.5.1 Meals and Dietary Restrictions", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.1", + "value": "Meals and Dietary Restrictions", + "business_rules": "Value Allowed: No\nRelationship: 5.5 Lifestyle Restrictions; 5 TRIAL POPULATION; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 116, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218743", + "user_guidance": "If applicable, describe any restrictions on diet (e.g., food and drink restrictions, timing of meals relative to dosing, etc.).", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.5.1 Meals and Dietary Restrictions\nConcept: C218743 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 116, + "term": "5.5.2 Caffeine, Alcohol, Tobacco, and Other Restrictions", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.2", + "value": "Caffeine, Alcohol, Tobacco, and Other Restrictions", + "business_rules": "Value Allowed: No\nRelationship: 5.5 Lifestyle Restrictions; 5 TRIAL POPULATION; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 116, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218744", + "user_guidance": "If applicable, describe any restrictions on the intake of caffeine, alcohol, tobacco, or other restrictions.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.5.2 Caffeine, Alcohol, Tobacco, and Other Restrictions\nConcept: C218744 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 117, + "term": "5.5.3 Physical Activity Restrictions", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.3", + "value": "Physical Activity Restrictions", + "business_rules": "Value Allowed: No\nRelationship: 5.5 Lifestyle Restrictions; 5 TRIAL POPULATION; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 117, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218745", + "user_guidance": "If applicable, describe any restrictions on physical activity (e.g., participants may be required to remain in bed for 4 to 6 hours after dosing).", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.5.3 Physical Activity Restrictions\nConcept: C218745 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 118, + "term": "5.5.4 Other Activity Restrictions", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.4", + "value": "Other Activity Restrictions", + "business_rules": "Value Allowed: No\nRelationship: 5.5 Lifestyle Restrictions; 5 TRIAL POPULATION; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 118, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218746", + "user_guidance": "If applicable, describe restrictions on any other activity (e.g., blood or tissue donation, driving, heavy machinery use, or sun exposure).", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "5.5.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.5.4 Other Activity Restrictions\nConcept: C218746 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 118, + "term": "5.6 Screen Failure and Rescreening", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "5.6", + "value": "Screen Failure and Rescreening", + "business_rules": "Value Allowed: No\nRelationship: 5 TRIAL POPULATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 119, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C49628", + "user_guidance": "Describe screen failure and indicate how screen failure will be handled in the trial, including conditions and criteria under which rescreening is acceptable. If applicable, indicate the circumstances and time window under which a repeat procedure is allowed for screen failure relating to specific inclusion/exclusion criteria for the trial.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.6 Screen Failure and Rescreening\nConcept: C49628 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 119, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C179373", + "user_guidance": "Describe screen failure and indicate how screen failure will be handled in the trial, including conditions and criteria under which rescreening is acceptable. If applicable, indicate the circumstances and time window under which a repeat procedure is allowed for screen failure relating to specific inclusion/exclusion criteria for the trial.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "5.6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 5.6 Screen Failure and Rescreening\nConcept: C179373 ICH OID 2.16.840.1.113883.3.989.2.3.3.5", + "repeating_reuse_rules": "No" + }, + { + "page": 120, + "term": "6 TRIAL INTERVENTION AND CONCOMITANT THERAPY", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6", + "value": "TRIAL INTERVENTION AND CONCOMITANT THERAPY", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 120, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218747", + "user_guidance": "Trial interventions are all pre-specified investigational and noninvestigational medicinal products, medical devices or other interventions intended for the participants during the trial. The investigational trial intervention is the product(s) used in the trial as part of trial objectives, including control(s) (e.g., active comparator, placebo). Description of the investigational trial intervention is provided in Section 6.1 Description of Investigational Trial Intervention. Other trial interventions that are not part of trial objectives or do not have an investigational role in this trial are described in Section 6.9 Description of Noninvestigational Trial Intervention. Any regional requirements should be noted in the appropriate subsections. Provide an overview of investigational and noninvestigational trial interventions. Designate the trial intervention as IMP or NIMP/AxMP based on trial design and regional requirements. Consider the optional table below.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY\nConcept: C218747 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 120, + "term": "Arm Name", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Arm Name", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 121, + "term": "Arm Type", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Arm Type", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 121, + "term": "Intervention Name", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Intervention Name", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 122, + "term": "Intervention Type", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Intervention Type", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 122, + "term": "Pharmaceutical Dose Form", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Pharmaceutical Dose Form", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 122, + "term": "Dosage Strength(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Dosage Strength(s)", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 123, + "term": "Dosage Level(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Dosage Level(s)", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 123, + "term": "Route of Administration", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Route of Administration", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 123, + "term": "Regimen/Treatment Period/Vaccination Regimen", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Regimen/Treatment Period/Vaccination Regimen", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 124, + "term": "Use", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Use", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 124, + "term": "IMP/NIMP", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "IMP/NIMP", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 124, + "term": "Sourcing", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Sourcing", + "business_rules": "Value Allowed: No\nRelationship: Optional Table Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 125, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C93729", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many; one to interventions for Arm Name", + "relationship": "6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name\nConcept: C93729 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Arm Name and Intervention Name and Use combination" + }, + { + "page": 125, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C172457", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Arm Name", + "relationship": "6", + "value": "Code List C217283: ICH OID 2.16.840.1.113883.3.989.2.3.1.15\nActive Comparator Arm (C174267), Control Arm (C174226), Experimental Arm\n(C174266), No Intervention Arm (C174270), Placebo Comparator Arm\n(C174268), Sham Comparator Arm (C174269).", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Arm Type\nConcept: C172457 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Arm Name" + }, + { + "page": 125, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C177930", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to Arm Name and Arm Type", + "relationship": "6", + "value": "Select Nonproprietary Name or Sponsor Investigational Product Code", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Intervention Name\nConcept: C177930 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Arm Name and Arm Type" + }, + { + "page": 126, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C98747", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Intervention Name", + "relationship": "6", + "value": "Code List C217284: ICH OID 2.16.840.1.113883.3.989.2.3.1.7\nDrug (C1909), Medical Device (C16830), Biologic (C307), Vaccine (C923), Non-\nSurgical Procedure (C218507), Surgery (C15329), Radiation (C15313),\nBehavioral (C15184), Genetic (C15238), Dietary Supplement (C1505),\nCombination Product (C54696), Diagnostic (C18020)", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name, Arm Type and Intervention Name\nConcept: C98747 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Arm Name and Arm Type combination" + }, + { + "page": 126, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C42636", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Arm Name, Arm Type and Intervention Name combination", + "relationship": "6", + "value": "Use IDMP (ISO 11239) or CDISC SDTM Terminology", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Pharmaceutical Dose Form\nConcept: C42636 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name and Pharmaceutical Dose Form" + }, + { + "page": 126, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C142517", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Pharmaceutical Dose Form", + "relationship": "6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Dosage Strength\nConcept: C142517 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name and Pharmaceutical Dose Form per\nArm Name and Arm Type" + }, + { + "page": 127, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C94394", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Intervention Name and Pharmaceutical Dose Form", + "relationship": "6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Dose Level\nConcept: C94394 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name, Pharmaceutical Dose Form, Dosage\nStrength and Dosage Level per Arm Name" + }, + { + "page": 127, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C38114", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Intervention Name and Pharmaceutical Dose Form", + "relationship": "6", + "value": "Use IDMP (ISO 11239) or CDISC SDTM Terminology", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Route of Administration\nConcept: C38114 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name, Pharmaceutical Dose Form, per Arm\nName" + }, + { + "page": 127, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C15697", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Intervention Name, Pharmaceutical Dose Form, Dosage Strength per\nArm Name", + "relationship": "6", + "value": "Describe Regimen/Treatment Period/Vaccination Regimen", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Regimen/Treatment Period/Vaccination Regimen\nConcept: C15697 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each arm name" + }, + { + "page": 128, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218748", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Intervention Name", + "relationship": "6", + "value": "Code List C217285: ICH OID 2.16.840.1.113883.3.989.2.3.1.8\nExperimental Intervention (C41161), Placebo (C753), Rescue Medicine\n(C165835), Background Treatment (C165822), Challenge Agent (C158128),\nDiagnostic (C18020), Additional Required Treatment (C207614)", + "business_rules": "Value Allowed: Yes\nRelationship: Arm Name and Use\nConcept: C218748 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name per Arm Name" + }, + { + "page": 128, + "term": "", + "data_type": "Valid value", + "dvh": "V", + "definition": "C218749", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to each Intervention Name", + "relationship": "6", + "value": "Code List C217286: ICH OID 2.16.840.1.113883.3.989.2.3.1.10\nIMP (C202579), NIMP (C156473)", + "business_rules": "Value Allowed: Yes\nRelationship: One per each Intervention Name\nConcept: C218749 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name per Arm Name" + }, + { + "page": 129, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218750", + "user_guidance": "N/A", + "conformance": "Optional: if the table used", + "cardinality": "One to many", + "relationship": "6", + "value": "Code List C217052: ICH OID 2.16.840.1.113883.3.989.2.3.1.9\nCentrally Sourced (C215659), Locally Sourced (C215660)", + "business_rules": "Value Allowed: Yes\nRelationship: One per each Intervention Name\nConcept: C218750 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "Yes, repeatable for each Intervention Name per Arm Name" + }, + { + "page": 129, + "term": "6.1 Description of Investigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.1", + "value": "Description of Investigational Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 129, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218751", + "user_guidance": "Describe the investigational trial intervention to be administered in each arm of the trial and for each period of the trial including route and mode of administration, dose, dosage regimen, duration of intervention, use, packaging and labelling. Refer to approved regional labelling, as appropriate. For investigational drug/device combination products, include details on the configuration and use of the device and device manufacturer. A device user manual may be referenced in this section.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.1 Description of Investigational Trial Intervention\nConcept: C218751 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 130, + "term": "6.2 Rationale for Investigational Trial Intervention Dose and Regimen", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.2", + "value": "Rationale for Investigational Trial Intervention Dose and Regimen", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 130, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218752", + "user_guidance": "Provide a rationale for the selection of the dose(s) or dose range, pharmaceutical dose form, route of administration, and dosing regimen of the investigational trial interventions, as applicable. This rationale should include relevant results from nonclinical studies and clinical trials that support selection of the dose and regimen. Discuss impact of differences in trial population characteristics (e.g., age, sex, race) that could lead to differences in pharmacokinetics and pharmacodynamics in this trial as compared to previous trials. If applicable, justify any differences in dose regimen or therapeutic use relative to approved labelling. Describe prior trials and other information that support the dose and/or dose regimen of the investigational trial intervention. Include a rationale for prospective dose adjustments incorporated in the trial, if any.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.2 Rationale for Investigational Trial Intervention Dose and\nRegimen\nConcept: C218752 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 131, + "term": "6.3 Investigational Trial Intervention Administration", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.3", + "value": "Investigational Trial Intervention Administration", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 131, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218753", + "user_guidance": "Describe the detailed procedures for administration of each participant’s dose of each investigational trial intervention. This may include the timing of dosing (e.g., time of day, interval), the duration (e.g., the length of time participants will be administered the investigational trial intervention), and the timing of dosing relative to meals. Include any specific instructions on who, when or how to prepare and take the dose(s) and how to handle any delayed or missed doses. Dose escalation or cohort expansion as part of the overall design should be covered in Section 4.1 Description of Trial Design.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.3 Investigational Trial Intervention Administration\nConcept: C218753 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 132, + "term": "6.4 Investigational Trial Intervention Dose Modification", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.4", + "value": "Investigational Trial Intervention Dose Modification", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 132, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218754", + "user_guidance": "For each participant, describe any dose modifications allowed, including conditions for such dose modifications, particularly regarding failure to respond or safety concerns. State any minimum period required before a participant’s dose might be raised to the next higher dose or dose range. Include whether it is permissible to start and stop treatment and how dose reductions (if permitted) are to be managed. Information on stopping investigational trial intervention for participants due to safety/other reasons should be described in Section 7 Participant Discontinuation of Trial Intervention and Discontinuation or Withdrawal from Trial.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.4 Investigational Trial Intervention Dose Modification\nConcept: C218754 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 133, + "term": "6.5 Management of Investigational Trial Intervention Overdose", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": null, + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.5", + "value": "Management of Investigational Trial Intervention Overdose", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 133, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218755", + "user_guidance": "Describe what is meant by investigational trial intervention overdose. Provide any available information on managing overdose and ensure it is consistent with the Investigator’s Brochure or product labelling. Cross reference these documents as applicable.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.5 Management of Investigational Trial Intervention Overdose\nConcept: C218755 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 134, + "term": "6.6 Preparation, Storage, Handling and Accountability of Investigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6", + "value": "Preparation, Storage, Handling and Accountability of Investigational Trial\nIntervention", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 134, + "term": "6.6.1 Preparation of Investigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6.1", + "value": "Preparation of Investigational Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6.6 Preparation, Storage, Handling and Accountability of\nInvestigational Trial Intervention; 6 TRIAL INTERVENTION AND\nCONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 134, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C176274", + "user_guidance": "Describe any preparation of the investigational trial intervention, and when necessary, who should prepare it. When applicable, describe the maximum hold time once thawed/mixed before administration. Include thawing, diluting, mixing, and reconstitution/preparation instructions. For drug/device combination products, include any relevant assembly or use instructions and reference the package insert that is provided separately. If the instructions are lengthy or complicated, it is acceptable to reference the package insert (if applicable) or include instructions in separate documents provided to the site (e.g., a pharmacy manual) and reference the separate documents.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.6.1 Preparation of Investigational Trial Intervention\nConcept: C176274 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 135, + "term": "6.6.2 Storage and Handling of Investigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6.2", + "value": "Storage and Handling of Investigational Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6.6 Preparation, Storage, Handling and Accountability of\nInvestigational Trial Intervention; 6 TRIAL INTERVENTION AND\nCONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 135, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C115525", + "user_guidance": "Describe storage and handling requirements (e.g., protection from light, temperature, humidity) for the investigational trial intervention(s). For trials in which multidose vials are utilised, provide additional information regarding stability and expiration time after initial use (e.g., if the seal is broken). Explain how the investigational trial intervention will be provided to the investigator. If applicable, include details about kits, packaging, or other material of the investigational trial intervention for blinding purposes. If the instructions are lengthy or complicated, it is acceptable to reference the package insert (if applicable) or include instructions in separate documents provided to the site (e.g., a pharmacy manual) and reference the separate documents.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.6.2 Storage and Handling of Investigational Trial Intervention\nConcept: C115525 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 136, + "term": "6.6.3 Accountability of Investigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6.3", + "value": "Accountability of Investigational Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6.6 Preparation, Storage, Handling and Accountability of\nInvestigational Trial Intervention; 6 TRIAL INTERVENTION AND\nCONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 136, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C176267", + "user_guidance": "Describe the accountability method, including: • how the investigational trial intervention will be distributed • who will distribute the investigational trial intervention • participation of a drug storage repository or pharmacy, if applicable • plans for disposal or return of unused product • plans for reconciliation of investigational trial intervention, if applicable", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.6.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.6.3 Accountability of Investigational Trial Intervention\nConcept: C176267 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 137, + "term": "6.7 Investigational Trial Intervention Assignment, Randomisation and Blinding", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.7", + "value": "Investigational Trial Intervention Assignment, Randomisation and Blinding", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 137, + "term": "6.7.1 Participant Assignment to Investigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.7.1", + "value": "Participant Assignment to Investigational Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6.7 Investigational Trial Intervention Assignment, Randomisation\nand Blinding; 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 138, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218756", + "user_guidance": "State that at enrollment, participant identification codes should be assigned. Describe the method of assigning participants to investigational trial intervention without being so specific that blinding or randomisation might be compromised. If assignment to investigational trial intervention is by randomisation, describe when randomisation will occur relative to screening. If permuted block randomisation is employed, do not state the block size in the protocol. If adaptive randomisation or other methods of covariate balancing/minimisation are employed, include a cross reference to the methods of analysis in Section 10 Statistical Considerations. As applicable, details regarding the implementation of procedures to minimise bias should be described.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.7.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.7.1 Participant Assignment to Investigational Trial Intervention\nConcept: C218756 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 138, + "term": "6.7.2 {Randomisation}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when randomised trial", + "cardinality": "One to one", + "relationship": "6.7.2", + "value": "Randomisation", + "business_rules": "Value Allowed: No\nRelationship: 6.7 Investigational Trial Intervention Assignment, Randomisation\nand Blinding; 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 138, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C25196", + "user_guidance": "Describe the randomisation procedures (e.g., central randomisation procedures), the method used to generate the randomisation schedule (e.g., computer generated), the source of the randomisation schedule (e.g., sponsor, investigator, or other), and whether IRT(s) will be used. To maintain the integrity of the blinding, do not include the block size.", + "conformance": "Conditional: when randomised trial", + "cardinality": "One to one", + "relationship": "6.7.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.7.2 Randomisation\nConcept: C25196 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 139, + "term": "6.7.3 {Measures to Maintain Blinding}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when blind trial", + "cardinality": "One to one", + "relationship": "6.7.3", + "value": "Measures to Maintain Blinding", + "business_rules": "Value Allowed: No\nRelationship: 6.7 Investigational Trial Intervention Assignment, Randomisation\nand Blinding; 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 139, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C189349", + "user_guidance": "Describe measures that will be used to maintain blinding: • The investigational trial interventions are as indistinguishable as possible • Plans for the maintenance of randomisation codes and appropriate blinding for the trial • Procedures for planned (e.g., interim analysis) and unintentional (e.g., breach of procedure) breaking of randomisation codes For unplanned but intentional actions (e.g., safety events), refer to Section 6.7.4 Emergency Unblinding at the Site. If the trial allows for some investigators or other designated staff to remain unblinded (e.g., to allow them to adjust investigational trial intervention), the means of maintaining the blinding for other investigators or staff should be explained. Measures to prevent unblinding by laboratory measurements or while performing study assessments, if used, should be described.", + "conformance": "Conditional: when blind trial", + "cardinality": "One to one", + "relationship": "6.7.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.7.3 Measures to Maintain Blinding\nConcept: C189349 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 140, + "term": "6.7.4 {Emergency Unblinding at the Site}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when blind trial", + "cardinality": "One to one", + "relationship": "6.7.4", + "value": "Emergency Unblinding at the Site", + "business_rules": "Value Allowed: No\nRelationship: 6.7 Investigational Trial Intervention Assignment, Randomisation\nand Blinding; 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 140, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218757", + "user_guidance": "Describe the criteria for breaking the trial blind or participant code. Describe the circumstances that would require breaking the blind, either for an individual participant or for all participants, and specify who will be responsible for this decision. Include the procedure for emergency unblinding as well as documentation of unblinding. Indicate to whom the intentional and unplanned unblinding should be reported.", + "conformance": "Conditional: when blind trial", + "cardinality": "One to one", + "relationship": "6.7.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.7.4 Emergency Unblinding at the Site\nConcept: C218757 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 141, + "term": "6.8 Investigational Trial Intervention Adherence", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.8", + "value": "Investigational Trial Intervention Adherence", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 141, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218758", + "user_guidance": "Describe the measures to monitor and document participants’ adherence to investigational trial intervention (e.g., trial intervention accountability records, paper or electronic diaries, or investigational trial intervention concentration measurements). List what documents are mandatory to complete (e.g., participant drug log) and identify which records will be used as the source records for documenting investigational trial intervention adherence.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.8", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.8 Investigational Trial Intervention Adherence\nConcept: C218758 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 142, + "term": "6.9 Description of Noninvestigational Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.9", + "value": "Description of Noninvestigational Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 142, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218759", + "user_guidance": "As stated in Section 6 Trial Intervention and Concomitant Therapy, noninvestigational interventions are pre-specified products used in the trial but are not part of trial objectives and hence, are not investigational trial interventions.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.9", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.9 Description of Noninvestigational Trial Intervention\nConcept: C218759 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 142, + "term": "6.9.1 {Background Trial Intervention}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when any background interventions are defined", + "cardinality": "One to one", + "relationship": "6.9.1", + "value": "Background Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6.9 Description of Noninvestigational Trial Intervention; 6 TRIAL\nINTERVENTION AND CONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 143, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C222329", + "user_guidance": "Describe any background intervention(s), including administration and any conditions for use.", + "conformance": "Conditional: when any background interventions are defined", + "cardinality": "One to one", + "relationship": "6.9.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.9.1 Background Trial Intervention\nConcept: C222329", + "repeating_reuse_rules": "No" + }, + { + "page": 143, + "term": "6.9.2 {Rescue Therapy}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when any rescue therapies are defined", + "cardinality": "One to one", + "relationship": "6.9.2", + "value": "Rescue Therapy", + "business_rules": "Value Allowed: No\nRelationship: 6.9 Description of Noninvestigational Trial Intervention; 6 TRIAL\nINTERVENTION AND CONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 144, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C222330", + "user_guidance": "List all permitted rescue medications, treatments, and/or procedures, including any relevant instructions on administration and any conditions of use. If administration of rescue therapy leads to the temporary or permanent discontinuation of trial intervention, refer to Section 7 Participant Discontinuation of Trial Intervention and Discontinuation or Withdrawal from Trial.", + "conformance": "Conditional: when any rescue therapies are defined", + "cardinality": "One to one", + "relationship": "6.9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.9.2 Rescue Therapy\nConcept: C222330 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 144, + "term": "6.9.3 {Other Noninvestigational Trial Intervention}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when any other noninvestigational trial interventions are defined", + "cardinality": "One to one", + "relationship": "6.9.3", + "value": "Other Noninvestigational Intervention", + "business_rules": "Value Allowed: No\nRelationship: 6.9 Description of Noninvestigational Trial Intervention; 6 TRIAL\nINTERVENTION AND CONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 144, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218761", + "user_guidance": "If applicable, describe the use of any other noninvestigational trial intervention (e.g., challenge agents or diagnostics).", + "conformance": "Conditional: when any other noninvestigational trial interventions are defined", + "cardinality": "One to one", + "relationship": "6.9.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.9.3 Other Noninvestigational Trial Intervention\nConcept: C218761 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 145, + "term": "6.10 Concomitant Therapy", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.10", + "value": "Concomitant Therapy", + "business_rules": "Value Allowed: No\nRelationship: 6 TRIAL INTERVENTION AND CONCOMITANT THERAPY;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 145, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C53630", + "user_guidance": "Specify the concomitant medications, supplements, complementary and alternative therapies, treatments, and/or procedures that are prohibited or permitted during the trial and include details about when the information will be collected (e.g., during screening, at each visit). When appropriate to separate the content, the below subheadings may be used.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "6.10", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.10 Concomitant Therapy\nConcept: C53630 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 146, + "term": "6.10.1 {Prohibited Concomitant Therapy}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when any prohibited concomitant therapies are defined", + "cardinality": "One to one", + "relationship": "6.10.1", + "value": "Prohibited Concomitant Therapy", + "business_rules": "Value Allowed: No\nRelationship: 6.10 Concomitant Therapy; 6 TRIAL INTERVENTION AND\nCONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 146, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218762", + "user_guidance": "If applicable, describe any prohibited concomitant therapy.", + "conformance": "Conditional: when any prohibited concomitant therapies are defined", + "cardinality": "One to one", + "relationship": "6.10.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.10.1 Prohibited Concomitant Therapy\nConcept: C218762 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 146, + "term": "6.10.2 {Permitted Concomitant Therapy}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when any permitted concomitant therapies are defined", + "cardinality": "One to one", + "relationship": "6.10.2", + "value": "Permitted Concomitant Therapy", + "business_rules": "Value Allowed: No\nRelationship: 6.10 Concomitant Therapy; 6 TRIAL INTERVENTION AND\nCONCOMITANT THERAPY; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 147, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218763", + "user_guidance": "If applicable, describe any permitted concomitant therapy.", + "conformance": "Conditional: when any permitted concomitant therapies are defined", + "cardinality": "One to one", + "relationship": "6.10.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 6.10.2 Permitted Concomitant Therapy\nConcept: C218763 ICH OID 2.16.840.1.113883.3.989.2.3.3.6", + "repeating_reuse_rules": "No" + }, + { + "page": 147, + "term": "7 PARTICIPANT DISCONTINUATION OF TRIAL INTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM TRIAL", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "This section must align with the intercurrent events and their handling strategies introduced in Section 3 Trial Objectives and Associated Estimands, and with the investigational trial intervention described in Section 6 Trial Intervention and Concomitant Therapy. No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7", + "value": "PARTICIPANT DISCONTINUATION OF TRIAL INTERVENTION AND\nDISCONTINUATION OR WITHDRAWAL FROM TRIAL", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 148, + "term": "7.1 Discontinuation of Trial Intervention for Individual Participants", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1", + "value": "Discontinuation of Trial Intervention for Individual Participants", + "business_rules": "Value Allowed: No\nRelationship: 7 PARTICIPANT DISCONTINUATION OF TRIAL\nINTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM\nTRIAL; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 148, + "term": "7.1.1 Permanent Discontinuation of Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1.1", + "value": "Permanent Discontinuation of Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 7.1 Discontinuation of Trial Intervention for Individual Participants,\n7 PARTICIPANT DISCONTINUATION OF TRIAL INTERVENTION AND\nDISCONTINUATION OR WITHDRAWAL FROM TRIAL; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 149, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218764", + "user_guidance": "Describe: • the criteria for discontinuation of a participant from any trial intervention, carefully evaluating which are appropriate for the trial population and therapy being studied • how participants who discontinue trial intervention will be followed after discontinuation. Depending on the chosen intercurrent event handling strategy, it will be important to continue to follow and ascertain outcomes in participants who discontinue trial intervention through the end of the trial to prevent missing data in important analyses. Refer to Section 1.3 Schedule of Activities for assessments to be performed at the time of and following discontinuation of trial intervention • the process for collecting and recording the detailed reasons for discontinuing trial intervention if not described elsewhere", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 7.1.1 Permanent Discontinuation of Trial Intervention\nConcept: C218764 ICH OID 2.16.840.1.113883.3.989.2.3.3.7", + "repeating_reuse_rules": "No" + }, + { + "page": 149, + "term": "7.1.2 Temporary Discontinuation of Trial Intervention", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1.2", + "value": "Temporary Discontinuation of Trial Intervention", + "business_rules": "Value Allowed: No\nRelationship: 7.1 Discontinuation of Trial Intervention for Individual\nParticipants; 7 PARTICIPANT DISCONTINUATION OF TRIAL\nINTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM\nTRIAL; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 150, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218765", + "user_guidance": "Describe: • the criteria for temporary discontinuation or interruption of trial intervention for an individual participant • what to do and which restrictions still apply if the participant has to temporarily discontinue or interrupt trial intervention • which assessments will be performed for the stated duration of the trial Details of any rechallenge or restart after temporary discontinuation of trial intervention due to a safety-related event should be included in Section 7.1.3 Rechallenge.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 7.1.2 Temporary Discontinuation of Trial Intervention\nConcept: C218765 ICH OID 2.16.840.1.113883.3.989.2.3.3.7", + "repeating_reuse_rules": "No" + }, + { + "page": 150, + "term": "7.1.3 Rechallenge", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1.3", + "value": "Rechallenge", + "business_rules": "Value Allowed: No\nRelationship: 7.1 Discontinuation of Trial Intervention for Individual\nParticipants; 7 PARTICIPANT DISCONTINUATION OF TRIAL\nINTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM\nTRIAL; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 150, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218766", + "user_guidance": "Describe the criteria for rechallenge/restarting trial intervention, how and when to perform rechallenge, the number of rechallenges allowed during the trial, and whether all, or specify which, assessments will be performed for the stated duration of the trial. If rechallenge is not allowed, state this.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.1.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 7.1.3 Rechallenge\nConcept: C218766 ICH OID 2.16.840.1.113883.3.989.2.3.3.7", + "repeating_reuse_rules": "No" + }, + { + "page": 151, + "term": "7.2 Participant Discontinuation or Withdrawal from the Trial", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.2", + "value": "Participant Discontinuation or Withdrawal from the Trial", + "business_rules": "Value Allowed: No\nRelationship: 7 PARTICIPANT DISCONTINUATION OF TRIAL\nINTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM\nTRIAL; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 151, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218767", + "user_guidance": "Describe the criteria for participant discontinuation or withdrawal from the trial. Describe the reason for withdrawal and the type of data to be collected for the final assessments with reference to the schedule of activities for the participant’s end of study visit unless provided in another section. In many cases, the only reason for a participant being considered withdrawn from the trial should be a participant’s withdrawal of consent to continue to participate in the trial. All other participants, including those who discontinue trial intervention, should remain in the trial and continue to be followed to prevent missing data in important analyses. Refer to Section 10 Statistical Considerations for the data that must be collected for the trial estimands.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 7.2 Participants Discontinuation or Withdrawal from the Trial\nConcept: C218767 ICH OID 2.16.840.1.113883.3.989.2.3.3.7", + "repeating_reuse_rules": "No" + }, + { + "page": 152, + "term": "7.3 Management of Loss to Follow-Up", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.3", + "value": "Management of Loss to Follow-Up", + "business_rules": "Value Allowed: No\nRelationship: 7 PARTICIPANT DISCONTINUATION OF TRIAL\nINTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM\nTRIAL; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 152, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218768", + "user_guidance": "Describe how the trial will define how participants are lost to follow-up. In general, participants should be considered lost to follow-up only if they cannot be reached despite multiple attempts to contact them. Also describe approaches that will be used to minimise loss to follow-up, such as multiple, diverse methods to remain in contact with participants (e.g., telephone calls, texts, and emails to the participant) and how contacts will be recorded.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "7.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 7.3 Management of Loss to Follow-up\nConcept: C218768 ICH OID 2.16.840.1.113883.3.989.2.3.3.7", + "repeating_reuse_rules": "No" + }, + { + "page": 153, + "term": "8 TRIAL ASSESSMENTS AND PROCEDURES", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "In this section: • Describe the assessments and procedures required during each phase of the trial that are relevant to the stated endpoints and related intercurrent events (e.g., surgery or use of rescue therapy). Provide details that are not already presented in the SoA, taking care not to duplicate information. • Ensure alignment with every other section of the protocol. In particular, this section must align with: o the intercurrent events and associated strategies for handling them described in Section 3 Trial Objectives and Associated Estimands o trial intervention and therapies outlined in Section 6 Trial Intervention and Concomitant Therapy o discontinuation and withdrawal procedures in Section 7 Participant Discontinuation of Trial Intervention and Discontinuation or Withdrawal From Trial o the statistical analysis that is defined in Section 10 Statistical Considerations • Reference the literature for the validation of scales/instruments/questionnaires/assays. • Instructions or protocols for specialised tests and scales/instruments/questionnaires/assays may be presented in an appendix or a separate document and cross referenced. • If the trial includes qualitative interviews, describe these evaluations. • Include minimums and limits for procedures (e.g., number of imaging procedures/biopsies, radiation exposure, etc.) if appropriate to the trial. 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Cross reference Section 8.7 Immunogenicity Assessments if immunogenicity assessments are used in efficacy determination.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.3 Efficacy Assessments and Procedures\nConcept: C218772 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 157, + "term": "8.4 Safety Assessments and Procedures", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.4", + "value": "Safety Assessments and Procedures", + "business_rules": "Value Allowed: No\nRelationship: 8 TRIAL ASSESSMENTS AND PROCEDURES; Table of\nContents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 157, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218773", + "user_guidance": "Describe safety assessments and procedures utilising the following subsections as applicable. Add level 3 headings as needed. • Identify any noninvestigator party involved in the evaluation of laboratory or other safety assessments (e.g., sponsor or external Independent Data Monitoring Committee; cross reference Section 11.4 Committees for details as applicable). • Include guidelines for the medical management of relevant laboratory or other safety assessment abnormalities.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.4 Safety Assessments and Procedures\nConcept: C218773 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 157, + "term": "8.4.1 {Physical Examination}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when Physical Examination is required", + "cardinality": "One to one", + "relationship": "8.4.1", + "value": "Physical Examination", + "business_rules": "Value Allowed: No\nRelationship: 8.4 Safety Assessment and Procedures; 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8 TRIAL ASSESSMENTS\nAND PROCEDURES; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 159, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C154628", + "user_guidance": "Include any specific instructions for the collection and interpretation of vital signs.", + "conformance": "Conditional: when Vital Signs are required", + "cardinality": "One to one", + "relationship": "8.4.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.4.2 Vital Signs\nConcept: C154628 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 159, + "term": "8.4.3{Electrocardiograms}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when Electrocardiograms are required", + "cardinality": "One to one", + "relationship": "8.4.3", + "value": "Electrocardiograms", + "business_rules": "Value Allowed: No\nRelationship: 8.4 Safety Assessments and Procedures; 8 TRIAL ASSESSMENTS\nAND PROCEDURES; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 159, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C168186", + "user_guidance": "Include any specific instructions for the collection, interpretation, and archiving of ECGs.", + "conformance": "Conditional: when Electrocardiograms are required", + "cardinality": "One to one", + "relationship": "8.4.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.4.3 Electrocardiograms\nConcept: C168186 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 160, + "term": "8.4.4 {Clinical Laboratory Assessments}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when Clinical Laboratory Assessments are required", + "cardinality": "One to one", + "relationship": "8.4.4", + "value": "Clinical Laboratory Assessments", + "business_rules": "Value Allowed: No\nRelationship: 8.4 Safety Assessments and Procedures; 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8 TRIAL ASSESSMENTS\nAND PROCEDURES; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 162, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218775", + "user_guidance": "If the trial meets any of the criteria requiring suicidal ideation and behaviour risk monitoring by the guidance/guideline in each region, include justification for the need for suicidal ideation and behaviour risk monitoring in the study and add any specific instructions for the collection and interpretation of the assessment. In case this is an AESI in the study, justification should also be provided in Section 9.2.4 Adverse Events of Special Interest.", + "conformance": "Conditional: when Suicidal Ideation and Behaviour Risk Monitoring are required", + "cardinality": "One to one", + "relationship": "8.4.6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.4.6 Suicidal Ideation and Behaviour Risk Monitoring\nConcept: C218775 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 162, + "term": "8.5 Pharmacokinetics", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.5", + "value": "Pharmacokinetics", + "business_rules": "Value Allowed: No\nRelationship: 8 TRIAL ASSESSMENTS AND PROCEDURES; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 163, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218776", + "user_guidance": "Include any specific instructions for the collection and assay of samples and interpretation of PK assessments. • Describe the biological samples collected, the handling of samples, and the assay method. o Specific sample collection and processing instructions can be described in an appendix or a separate document and cross referenced. • Describe the retention time for the samples (ensuring alignment with the ICF). • Indicate the types of analyses for each sample. • Define the PK parameters to be calculated and the calculation methods.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.5 Pharmacokinetics\nConcept: C218776 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 163, + "term": "8.6 Biomarkers", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Include any specific instructions for the collection of samples and interpretation of biomarkers in the subsections below as applicable. Safety biomarkers should be included in Section 8.4 Safety Assessments and Procedures, and immunogenicity biomarkers should be included in Section 8.7 Immunogenicity Assessments. No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.6", + "value": "Biomarkers", + "business_rules": "Value Allowed: No\nRelationship: 8 TRIAL ASSESSMENTS AND PROCEDURES; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 164, + "term": "8.6.1 Genetics, Genomics, Pharmacogenetics, and Pharmacogenomics", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.6.1", + "value": "Genetics and Pharmacogenomics", + "business_rules": "Value Allowed: No\nRelationship: 8.6 Biomarkers; 8 TRIAL ASSESSMENTS AND PROCEDURES;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 164, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218777", + "user_guidance": "Include any specific instructions for the collection and assay of samples for genetic, genomics, pharmacogenetics and/or pharmacogenomic analysis. • Describe the biological samples that will be collected (e.g., tissue, serum, plasma), handling of samples, and the assay method. o Specific sample collection and processing instructions can be described in an appendix or a separate document and cross referenced. • Describe the retention time for the samples (ensuring alignment with the ICF). • Indicate the types of analyses that may be studied for each sample.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.6.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.6.1 Genetics, Genomics, Pharmacogenetics, and\nPharmacogenomics\nConcept: C218777 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 165, + "term": "8.6.2 Pharmacodynamic Biomarkers", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.6.2", + "value": "Pharmacodynamic Biomarkers", + "business_rules": "Value Allowed: No\nRelationship: 8.6 Biomarkers, 8 TRIAL ASSESSMENTS AND PROCEDURES;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 165, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218778", + "user_guidance": "Include any specific instructions for the collection of samples and assessment of pharmacodynamic biomarkers. • Describe the biological samples that will be collected (e.g., tissue, serum, plasma). o Specific sample collection and processing instructions can be described in an appendix or a separate document and cross referenced. • Describe the retention time for the samples (ensuring alignment with the ICF). • Indicate the types of biomarkers that will be studied for each sample. • Specify whether each sample is optional or required. Required samples must be based on a protocol objective.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.6.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.6.2 Pharmacodynamic Biomarkers\nConcept: C218778 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 166, + "term": "8.6.3 {Other Biomarkers}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when Other Biomarkers are required", + "cardinality": "One to one", + "relationship": "8.6.3", + "value": "Other Biomarkers", + "business_rules": "Value Allowed: No\nRelationship: 8.6 Biomarkers; 8 TRIAL ASSESSMENTS AND PROCEDURES;\nTable of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 166, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218779", + "user_guidance": "Include any specific instructions for the collection of samples and assessment of other biomarkers. • Describe the biological samples that will be collected (e.g., tissue, serum, plasma). o Specific sample collection and processing instructions can be described in an appendix or a separate document and cross referenced. • Describe the retention time for the samples (ensuring alignment with the ICF). • Indicate the types of biomarkers that will be studied for each sample. • Specify whether each sample is optional or required. Required samples must be based on a protocol objective.", + "conformance": "Conditional: when Other Biomarkers are required", + "cardinality": "One to one", + "relationship": "8.6.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.6.3 Other Biomarkers\nConcept: C218779 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 167, + "term": "8.7 Immunogenicity Assessments", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.7", + "value": "Immunogenicity Assessments", + "business_rules": "Value Allowed: No\nRelationship: 8 TRIAL ASSESSMENTS AND PROCEDURES; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 167, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218780", + "user_guidance": "Include any specific instructions for the collection of samples and interpretation of immunogenicity. If immunogenicity assessments are included within Section 8.3 Efficacy Assessments and Procedures or Section 8.4 Safety Assessments and Procedures, cross reference that section. • Describe the biological samples that will be collected (e.g., tissue, serum, plasma). o Specific sample collection and processing instructions can be described in an appendix or a separate document and cross referenced. • Describe the retention time for the samples (ensuring alignment with the ICF). • Indicate the types of biomarkers that will be studied for each sample. • Specify whether each sample is optional or required. Required samples must be based on a protocol objective.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.7", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.7 Immunogenicity Assessments\nConcept: C218780 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 168, + "term": "8.8 Medical Resource Utilisation and Health Economics", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.8", + "value": "Medical Resource Utilisation and Health Economics", + "business_rules": "Value Allowed: No\nRelationship: 8 TRIAL ASSESSMENTS AND PROCEDURES; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 168, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C176849", + "user_guidance": "This section does not apply to COAs. Include this section only for any value evidence and outcomes assessments not included in either the efficacy or safety sections. Describe the health outcome measures, collection method (e.g., diary, physician interview), and participant burden.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "8.8", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 8.8 Medical Resource Utilisation and Health Economics\nConcept: C176849 ICH OID 2.16.840.1.113883.3.989.2.3.3.8", + "repeating_reuse_rules": "No" + }, + { + "page": 169, + "term": "9 ADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9", + "value": "ADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 169, + "term": "9.1 Definitions", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1", + "value": "Definitions", + "business_rules": "Value Allowed: No\nRelationship: 9 ADVERSE EVENTS, SERIOUS ADVERSE EVENTS,\nPRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 170, + "term": "9.1.1 Definitions of Adverse Events", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1.1", + "value": "Definitions of Adverse Events", + "business_rules": "Value Allowed: No\nRelationship: 9.1 Definitions; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 170, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218476", + "user_guidance": "Specify the AE definitions, including: • any relevant regional AE requirements • any events that meet and do not meet the AE definition • any trial-specific AE clarifications • if applicable, any clarifications on the AE and SAE definitions for efficacy trials (e.g., lack of efficacy or failure of pharmacological actions)", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.1.1 Definitions of Adverse Events\nConcept: C218476 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 170, + "term": "9.1.2 Definitions of Serious Adverse Events", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1.2", + "value": "Definitions of Serious Adverse Events", + "business_rules": "Value Allowed: No\nRelationship: 9.1 Definitions; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 171, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218781", + "user_guidance": "Specify the SAE definitions, including: • any relevant regional SAE requirements • any events that meet and do not meet the SAE definition • any trial-specific SAE clarifications", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.1.2 Definitions of Serious Adverse Events\nConcept: C218781 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 171, + "term": "9.1.3 Definitions of Product Complaints", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1.3", + "value": "Definitions of Product Complaints", + "business_rules": "Value Allowed: No\nRelationship: 9.1 Definitions; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 172, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218782", + "user_guidance": "S pecify the definitions of product complaints in the context of the trial.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.1.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.1.3 Definitions of Product Complaints\nConcept: C218782 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 172, + "term": "9.1.3.1 {Definitions of Medical Device Product Complaints}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Medical Device Product Complaints", + "cardinality": "One to one", + "relationship": "9.1.3.1", + "value": "Definitions of Medical Device Product Complaints", + "business_rules": "Value Allowed: No\nRelationship: 9.3.1 Definition of Product Complaints; 9.1 Definitions; 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 172, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218783", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Medical Device Product Complaints", + "cardinality": "One to one", + "relationship": "9.1.3.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.1.3.1 Definitions of Medical Device Product Complaints\nConcept: C218783 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 173, + "term": "9.2 Timing and Procedures for Collection and Reporting", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Timing and Procedures for Collection and Reporting", + "business_rules": "Value Allowed: No\nRelationship: 9 ADVERSE EVENTS, SERIOUS ADVERSE EVENTS,\nPRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 173, + "term": "This table describes the timing and procedures for collecting and reporting events.", + "data_type": "Text", + "dvh": "H", + "definition": "Optional text", + "user_guidance": "Specify timing and procedures for collection and reporting of AEs, SAEs, product complaints (including medical device product complaints if applicable) and pregnancy and postpartum information in the sections below. This information may be summarised in a tabular format as shown in the example table below.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "9.2", + "value": "This table describes the timing and procedures for collecting and reporting events.", + "business_rules": "Value Allowed: No\nRelationship: Timing and Procedures for Collection and Reporting\nConcept: Optional text", + "repeating_reuse_rules": "No" + }, + { + "page": 174, + "term": "Event Type", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional: If the table is used.", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Event Type", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 174, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218784", + "user_guidance": "N/A", + "conformance": "Optional if the table is used", + "cardinality": "One to many", + "relationship": "9.2", + "value": "Code List C217287: ICH OID 2.16.840.1.113883.3.989.2.3.1.22\nAdverse Event (C41331), Serious Adverse Event (C41335), Trial Intervention\nComplaint (C218508), Drug/Device Combination Product Complaint (C222331),\nPregnancy Event (C25742), Lactation Event (C218510), Post-Partum Event\n(C218511), Reportable Adverse Event of Special Interest (C218512), Not\nReportable Adverse Event of Special Interest (C218513), Other (C17649)", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type\nConcept: C218784 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Event Type" + }, + { + "page": 174, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C222263", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Other\nConcept: C222263 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 175, + "term": "Situational Scope", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Situational Scope", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 175, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218785", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type, Situational Scope\nConcept: C218785 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Event Type" + }, + { + "page": 175, + "term": "Reportable Period Start", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Reportable Period Start", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 176, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218786", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type; Situational Scope\nConcept: C218786 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Event Type and Situational Scope" + }, + { + "page": 176, + "term": "Reportable Period End", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Reportable Period End", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 176, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218787", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type; Situational Scope; Reportable Period Start\nConcept: C218787 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Reportable Period Start" + }, + { + "page": 177, + "term": "Timing for Reporting to Sponsor or Designee", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Timing for Reporting to Sponsor or Designee", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 177, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218788", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type, Situational Scope\nConcept: C218788 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Event Type, Situational Scope, and Reportable Period Start" + }, + { + "page": 177, + "term": "Method for Reporting", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional if table used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Method for Reporting", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 178, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218789", + "user_guidance": "N/A", + "conformance": "Optional if used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type, Situational Scope\nConcept: C218789 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Event Type, Situational Scope and Reportable Period Start" + }, + { + "page": 178, + "term": "Back-up Method for Reporting", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Optional if table is used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Back-up Method for Reporting", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 179, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218790", + "user_guidance": "N/A", + "conformance": "Optional if table is used", + "cardinality": "One to one", + "relationship": "9.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Event Type; Situational Scope\nConcept: C218790 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "Yes, repeatable for each Event Type, Situational Scope, and Reportable Period\nStart." + }, + { + "page": 179, + "term": "9.2.1 Timing", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.1", + "value": "Timing", + "business_rules": "Value Allowed: No\nRelationship: 9.2 Timing and Procedures for Collection and Reporting, 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 179, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218791", + "user_guidance": "Specify timing for collection and reporting, including: • start and end dates for collection and reporting • frequency of collection and reporting • cross reference to the Schedule of Assessments as appropriate", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.2.1 Timing\nConcept: C218791 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 180, + "term": "9.2.2 Collection Procedures", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Specify procedures for collection and recording of AEs, SAEs, product complaints (including medical device product complaints if applicable) and pregnancy and postpartum information in the sections below.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Collection Procedures", + "business_rules": "Value Allowed: No\nRelationship: 9.2 Timing and Procedures for Collection and Reporting; 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 180, + "term": "Identification", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Identification", + "business_rules": "Value Allowed: No\nRelationship: 9.2.2 Collection Procedures; 9.2 Timing and Procedures for\nCollection and Reporting; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 181, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218792", + "user_guidance": "Specify how information will be identified (e.g., self-reported, solicited questions).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Identification and 9.2.2 Collection Procedures\nConcept: C218792 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 181, + "term": "Severity", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Severity", + "business_rules": "Value Allowed: No\nRelationship: 9.2.2 Collection Procedures; 9.2 Timing and Procedures for\nCollection and Reporting; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 181, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C25676", + "user_guidance": "Specify the intensity rating categories/scale.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Severity; 9.2.2 Collection Procedures\nConcept: C25676 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 182, + "term": "Causality", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Causality", + "business_rules": "Value Allowed: No\nRelationship: 9.2.2 Collection Procedures; 9.2 Timing and Procedures for\nCollection and Reporting; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 182, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C82552", + "user_guidance": "Specify: • the causality categories/scale • procedures for assessing causality", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Causality; 9.2.2 Collection Procedures\nConcept: C82552 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 183, + "term": "Recording", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Recording", + "business_rules": "Value Allowed: No\nRelationship: 9.2.2 Collection Procedures; 9.2 Timing and Procedures for\nCollection and Reporting; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 183, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218793", + "user_guidance": "Specify procedures for recording.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Recording; 9.2.2 Collection Procedures\nConcept: C218793 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 183, + "term": "Follow-up", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Follow-up", + "business_rules": "Value Allowed: No\nRelationship: 9.2.2 Collection Procedures; 9.2 Timing and Procedures for\nCollection and Reporting; 9 ADVERSE EVENTS, SERIOUS ADVERSE\nEVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 184, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218794", + "user_guidance": "Specify the procedures for follow-up. Include the assessment tools that will be used to monitor the events and the duration of follow-up after appearance of the events.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Follow-up and 9.2.2 Collection Procedures\nConcept: C218794 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 184, + "term": "9.2.3 Reporting", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.3", + "value": "Reporting", + "business_rules": "Value Allowed: No\nRelationship: 9.2 Timing and Procedures for Collection and Reporting; 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 184, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218795", + "user_guidance": "Specify the reporting method (e.g., an electronic data collection tool or a paper CRF), backup reporting method, if applicable, and reporting timeline to the sponsor.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.2.3 Reporting\nConcept: C218795 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 185, + "term": "9.2.3.1 Regulatory Reporting Requirements", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.3.1", + "value": "Regulatory Reporting Requirements", + "business_rules": "Value Allowed: No\nRelationship: 9.2 Timing and Procedures for Collection and Reporting; 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents.\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 185, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218796", + "user_guidance": "Specify: • the investigator’s responsibilities for reporting to the sponsor (and to ethics committees, where required), specifying timing of reporting to allow the sponsor to meet their responsibilities • the sponsor’s legal/regulatory responsibilities for reporting to regulatory authorities, ethics committees, and investigators • suspected unexpected serious adverse reaction reporting", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.3.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.2.3.1 Regulatory Reporting Requirements\nConcept: C218796 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 186, + "term": "9.2.4 Adverse Events of Special Interest", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.4", + "value": "Adverse Events of Special Interest", + "business_rules": "Value Allowed: No\nRelationship: 9.2 Timing and Procedures for Collection and Reporting; 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 186, + "term": "{} Or {}", + "data_type": "Text", + "dvh": "D", + "definition": "C217358", + "user_guidance": "Specify any AESI, including: • any event (serious or nonserious) of scientific and medical concern relative to the trial intervention, for which ongoing monitoring and rapid communication by the investigator to the sponsor can be appropriate • other events that merit reporting to the sponsor, trial leadership, IRB, and regulatory agencies Include the following for each AESI: • the definition • the approach for ascertaining information • if applicable, any approach to confirm or adjudicate the event", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.4", + "value": "Text or state “Not applicable”", + "business_rules": "Value Allowed: Yes\nRelationship: 9.2.4 Adverse Events of Special Interest\nConcept: C217358 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 187, + "term": "9.2.5 Disease-related Events or Outcomes Not Qualifying as AEs or SAEs", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.5", + "value": "Disease-related Events or Outcomes Not Qualifying as AEs or SAEs", + "business_rules": "Value Allowed: No\nRelationship: 9.2 Timing and Procedures for Collection and Reporting; 9\nADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT\nCOMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND\nSPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 187, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218797", + "user_guidance": "Specify any DREs, DROs, or both that will not be reported as AEs or SAEs (e.g., seizures in anticonvulsant trials) or state “Not applicable.”", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.2.5", + "value": "Text", + "business_rules": "Value Allowed: Yes", + "repeating_reuse_rules": "No\nRelationship: 9.2.5 Disease-related Events or Outcomes Not Qualifying as AEs or\nSAEs\nConcept: C218797 ICH OID 2.16.840.1.113883.3.989.2.3.3.9 No" + }, + { + "page": 188, + "term": "9.3 Pregnancy and Postpartum Information", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Whenever possible, pregnancy (direct or via partner) should be documented and followed up to collect relevant pregnancy outcomes. Any negative or consequential outcome(s) in the pregnant participant/partner or foetus, neonate or infant should be reported as an AE or SAE. Refer to Section 9.2 Timing and Procedures for Collection and Reporting for AE and SAE related procedures as applicable. If the negative event meets the seriousness criteria, then this is considered an SAE (e.g., spontaneous abortion, foetal death, stillbirth, congenital anomalies, ectopic pregnancy, or pre-eclampsia) and reported per Section 9.2.3 Reporting. No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.3", + "value": "Pregnancy and Postpartum Information", + "business_rules": "Value Allowed: No\nRelationship: 9 ADVERSE EVENTS, SERIOUS ADVERSE EVENTS,\nPRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 188, + "term": "9.3.1 {Participants Who Become Pregnant During the Trial}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when collecting pregnancy data for a trial participant who becomes\npregnant during the trial.", + "cardinality": "One to one", + "relationship": "9.3.1", + "value": "Participants Who Become Pregnant During the Trial", + "business_rules": "Value Allowed: No\nRelationship: 9.3 Pregnancy and Postpartum Information; 9 ADVERSE\nEVENTS, SERIOUS ADVERSE EVENTS, PRODUCT COMPLAINTS,\nPREGNANCY AND POSTPARTUM INFORMATION, AND SPECIAL\nSAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 189, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218798", + "user_guidance": "Specify: • the assessments to be performed • type and duration of monitoring • whether participants who become pregnant during the trial may continue with trial intervention or must be discontinued from trial intervention (refer to Section 7 Participant Discontinuation of Trial Intervention and Discontinuation or Withdrawal from Trial as applicable) • any trial modifications that need to be made for participants who become pregnant • what information will be collected about a participant who becomes pregnant during the trial (e.g., recording and reporting to the sponsor, postpartum follow-up, trial intervention discontinuation or continuation, or trial withdrawal) For postpartum follow-up, include the time period (e.g., initial child development) with justification. If exposure to trial intervention during breastfeeding is applicable, specify: • the assessments to be performed • type and duration of monitoring • information to be collected for both the participant and child", + "conformance": "Conditional: when collecting pregnancy data for a trial participant who becomes\npregnant during the trial.", + "cardinality": "One to one", + "relationship": "9.3.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.3.1 Participants Who Become Pregnant During the Trial\nConcept: C218798 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 189, + "term": "9.3.2 {Participants Whose Partners Become Pregnant During the Trial}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when collecting pregnancy data for the partner of a trial participant\nwho becomes pregnant during the trial.", + "cardinality": "One to one", + "relationship": "9.3.2", + "value": "Participants Whose Partners Become Pregnant", + "business_rules": "Value Allowed: No\nRelationship: 9.3 Pregnancy and Postpartum Information; 9 ADVERSE\nEVENTS, SERIOUS ADVERSE EVENTS, PRODUCT COMPLAINTS,\nPREGNANCY AND POSTPARTUM INFORMATION, AND SPECIAL\nSAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 190, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218799", + "user_guidance": "Specify: • whether the investigator will attempt to collect pregnancy information about a participant’s partner who becomes pregnant during the specified period in the trial • whether the participant whose partner becomes pregnant should be discontinued from trial intervention (refer to Section 7 Participant Discontinuation of Trial Intervention and Discontinuation or Withdrawal from Trial as applicable) • the assessments to be performed, type and duration of monitoring, and the information to be collected", + "conformance": "Conditional: when collecting pregnancy data for the partner of a trial participant\nwho becomes pregnant during the trial.", + "cardinality": "One to one", + "relationship": "9.3.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.3.2 Participants Whose Partners Become Pregnant During the\nTrial\nConcept: C218799 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 191, + "term": "9.4 Special Safety Situations", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.4", + "value": "Special Safety Situations", + "business_rules": "Value Allowed: No\nRelationship: 9 ADVERSE EVENTS, SERIOUS ADVERSE EVENTS,\nPRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM\nINFORMATION, AND SPECIAL SAFETY SITUATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 191, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218800", + "user_guidance": "Specify special safety situations associated with the trial intervention(s) that do not qualify as an AE or SAE but require regulatory reporting. Examples include: • misuse or abuse • off-label use (if applicable) • medication error (prescription or dispensing error) • occupational exposure • use outside of what is foreseen in the protocol • unintended exposure of embryo, foetus, or child via maternal exposure (pregnancy or breastfeeding) or via paternal exposure (semen) • lack of therapeutic efficacy; this is not applicable for studies that measure efficacy as a study endpoint • suspected transmission of an infectious agent; this is only applicable for injected or biologic medicinal products • product complaint, including falsified or counterfeit products • suspected drug-food or drug-drug interaction", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "9.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 9.4 Special Safety Situations\nConcept: C218800 ICH OID 2.16.840.1.113883.3.989.2.3.3.9", + "repeating_reuse_rules": "No" + }, + { + "page": 192, + "term": "10 STATISTICAL CONSIDERATIONS", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Ensure that the planned data analysis complies with ICH E9 and ICH E9(R1) guidelines. In general, all relevant data collected in the trial should be considered in this section. No text is intended here (heading only)", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10", + "value": "STATISTICAL CONSIDERATIONS", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 192, + "term": "10.1 General Considerations", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.1", + "value": "General Considerations", + "business_rules": "Value Allowed: No\nRelationship:10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 192, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C164387", + "user_guidance": "Provide general statements related to statistical considerations, such as whether a separate statistical analysis plan exists, which summary statistics will be provided, and the timing of analyses (e.g., “The analysis will include all participant data at trial completion”).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.1 General Considerations; 10 STATISTICAL\nCONSIDERATIONS; Table of Contents\nConcept: C164387 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 193, + "term": "10.2 Analysis Sets", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.2", + "value": "Analysis Sets", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 193, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218801", + "user_guidance": "Describe analysis sets to be considered at the trial level, i.e., the set of participants whose data are to be included in the analyses, aligned with estimands. Clearly specify the analysis set to be used for each analysis described in Section 10 Statistical Considerations.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.2 Analysis Sets; 10 STATISTICAL CONSIDERATIONS; Table\nof Contents\nConcept: C218801 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 194, + "term": "10.3 Analyses of Demographics and Other Baseline Variables", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.3", + "value": "Analyses of Demographics and Other Baseline Variables", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 194, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218802", + "user_guidance": "Describe the summary statistics that will be used to characterise the distribution of demographic and other relevant variables at baseline. Specify when the variables will be measured (e.g., at trial inclusion, prior to randomisation, or at the time of randomisation). Relevant variables include but are not limited to: stratification variables specified in Section 6.7 Investigational Trial Intervention Assignment, Randomisation and Blinding, covariates for the statistical models specified in Section 10.4 Analyses Associated with the Primary Objective(s), other suspected predictive or prognostic variables, and variables used for planned subgroup analyses.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.3 Analyses of Demographics and Other Baseline Variables; 10\nSTATISTICAL CONSIDERATIONS; Table of Contents\nConcept: C218802 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 195, + "term": "10.4 Analyses Associated with the Primary Objective(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Include additional level 3 headings for each primary objective as needed. If there is more than one primary objective, number each objective consecutively as the level 3 heading (e.g., Primary Objective 1, Primary Objective 2, etc.). No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "10.4", + "value": "Analyses Associated with the Primary Objective(s)", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 195, + "term": "10.4.X Primary Objective <#>", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required: Collection for each Primary Objective (e.g., 10.4.1, 10.4.2, 10.4.3,\n10.4.4, 10.4.5).\nFor more than one Primary Objective repeat the collection as level 4 headings\nwhere X is = to the number of Primary Objectives", + "cardinality": "One to many", + "relationship": "10.4.X", + "value": "Primary Objective <#>: # is a unique number for each Primary Objective; if there\nis only one Primary Objective, # is blank. If more than one Primary Objective,\nadd sequential unique number for each objective.", + "business_rules": "Value Allowed: No\nRelationship: 3.1.X Primary Objective <#>; 10.4 Analyses Associated with the\nPrimary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective." + }, + { + "page": 196, + "term": "10.4.X.1 Statistical Analysis Method", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.4.X.1", + "value": "Statistical Analysis Method", + "business_rules": "Value Allowed: No\nRelationship: 10.4.X Primary Objective <#>; 10.4 Analyses Associated with the\nPrimary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 196, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218482", + "user_guidance": "Describe the statistical analysis methods that will be used to evaluate the primary objective(s) and associated estimand(s) in Section 3.1 Primary Objective(s) and Associated Estimand(s). Ensure that the statistical hypothesis/model/analysis (and corresponding assumptions) is aligned with the primary estimand(s). For each objective, when applicable, state the null and alternative hypotheses, including the pre-planned type 1 error rate, or alternative criteria for evaluating whether the objective has been met, and relevant operating characteristics if appropriate. Describe the statistical model used and the factors that will be included (e.g., covariates and interactions) and any rules for handling these factors (e.g., pooling of centres). If modelling and simulation methods are to be used, describe the model (inputs and outputs), the underlying assumptions, and the method of model fitting.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.4.X.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.4.X.1 Statistical Analysis Method\nConcept: C218482 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 197, + "term": "10.4.X.2 Handling of Data in Relation to Primary Estimand(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.4.X.2", + "value": "Handling of Data in Relation to Primary Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 10.4.X Primary Objective(s) <#>; 10.4 Analyses Associated with\nthe Primary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 197, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218803", + "user_guidance": "For each intercurrent event of the primary estimand(s) defined in Section 3.1 Primary Objective(s) and Associated Estimand(s), explain how data will be handled for the statistical analysis in line with the primary estimand. The handling of intercurrent events in the statistical analysis should be aligned with the specific estimand strategies being used. This section should describe in more detail the rationale and handling of the data rather than repeating information from the preceding sections.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.4.X.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.4.X.2 Handling of Data in Relation to Primary Estimand(s)\nConcept: C218803 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 197, + "term": "10.4.X.3 Handling of Missing Data in Relation to Primary Estimand(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.4.X.3", + "value": "Handling of Missing Data in Relation to Primary Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 10.4.X Primary Objective(s) <#>; 10.4 Analyses Associated with\nthe Primary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 198, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218804", + "user_guidance": "Describe how missing data will be addressed (e.g., imputation method and model), state the underlying assumptions, and provide a rationale for the approach.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.4.X.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.4.X.3 Handling of Missing Data\nConcept: C218804 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 198, + "term": "10.4.X.4 {Sensitivity Analysis}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Sensitivity Analysis for a Primary Objective", + "cardinality": "One to one", + "relationship": "10.4.X.4", + "value": "Sensitivity Analysis", + "business_rules": "Value Allowed: No\nRelationship: 10.4.X Primary Objective(s); 10.4 Analyses Associated with the\nPrimary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 199, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218480", + "user_guidance": "Describe any sensitivity analyses and how their assumptions changed from the assumptions of the main statistical analysis. Sensitivity analyses are a series of analyses conducted with the intent to explore the robustness of inferences from the main estimator to deviations from its underlying modelling assumptions and limitations in the data.", + "conformance": "Conditional: when there is Sensitivity Analysis for a Primary Objective", + "cardinality": "One to many", + "relationship": "10.4.X.4", + "value": "Text", + "business_rules": "Value Allowed Yes\nRelationship: 10.4.X.4 Sensitivity Analysis\nConcept: C218480 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 199, + "term": "10.4.X.5 {Supplementary Analysis}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Supplementary Analysis for a Primary Objective", + "cardinality": "One to one", + "relationship": "10.4.X.5", + "value": "Supplementary Analysis", + "business_rules": "Value Allowed: No\nRelationship: 10.4.X Primary Objective(s); 10.4 Analyses Associated with the\nPrimary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 199, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218481", + "user_guidance": "Describe any supplementary analysis, if applicable. Supplementary analyses are conducted in addition to the main and sensitivity analyses with the intent to provide additional insights into the understanding of the treatment effect.", + "conformance": "Conditional: when there is Supplementary Analysis for a Primary Objective", + "cardinality": "One to one", + "relationship": "10.4.X.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.4.X.5 Supplementary Analysis\nConcept: C218481 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.4.X.1,\n10.4.X.2, 10.4.X.3, 10.4.X.4, 10.4.X.5)." + }, + { + "page": 200, + "term": "10.5 Analyses Associated with the Secondary Objective(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Describe the statistical analysis methods that will be used to evaluate the secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable.”", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "10.5", + "value": "Analyses Associated with the Secondary Objective(s)", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 200, + "term": "10.5.X {Secondary Objective <#>}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Conditional: Collection for each Secondary Objective (e.g., 10.5.1, 10.5.2, 10.5.3,\n10.5.4, 10.5.5).\nFor more than one Secondary Objective repeat the collection as level 4 headings\nwhere X is = to the number of Secondary Objectives", + "cardinality": "One to many", + "relationship": "10.5.X", + "value": "Secondary Objective <#>. # is a unique number for each Secondary Objective; if\nthere is only one Secondary Objective, # is blank. If more than one Secondary\nObjective, add sequential unique number for each objective.", + "business_rules": "Value Allowed: No\nRelationship: 3.2.X Secondary Objective <#>; 10.5 Analyses Associated with\nthe Secondary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective." + }, + { + "page": 201, + "term": "10.5.X.1 {Statistical Analysis Method}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Secondary Objective", + "cardinality": "One to one", + "relationship": "10.5.X.1", + "value": "Statistical Analysis Method", + "business_rules": "Value Allowed: No\nRelationship: 10.5.X Secondary Objective <#>; 10.5 Analyses Associated with\nthe Secondary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of Level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 201, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218482", + "user_guidance": "Describe the statistical analysis methods that will be used to evaluate the secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable.” Clearly specify any secondary hypotheses that will be tested for confirmatory purposes.", + "conformance": "Conditional: when there is Secondary Objective", + "cardinality": "One to one", + "relationship": "10.5.X.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.5.X.1 Statistical Analysis Method\nConcept: C218482 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 202, + "term": "10.5.X.2 {Handling of Data in Relation to Secondary Estimand(s)}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Secondary Estimand", + "cardinality": "One to one", + "relationship": "10.5.X.2", + "value": "Handling of Data in Relation to Secondary Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 10.5.X Secondary Objective <#>; 10.5 Analyses Associated with\nthe Secondary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of Level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 202, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218805", + "user_guidance": "Describe the statistical analysis methods that will be used to evaluate the secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable.”", + "conformance": "Conditional: when there is Secondary Estimand", + "cardinality": "One to one", + "relationship": "10.5.X.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship:10.5.X.2 Handling of Data in Relation to Secondary Estimand(s)\nConcept: C218805 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 203, + "term": "10.5.1.3 {Handling of Missing Data in Relation to Secondary Estimand(s)}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Secondary Estimand", + "cardinality": "One to one", + "relationship": "10.5.X.3", + "value": "Handling of Missing Data in Relation to Secondary Estimand(s)", + "business_rules": "Value Allowed: No\nRelationship: 10.5.X Secondary Objective <#>; 10.5 Analysis Associated with\nthe Secondary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 203, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218806", + "user_guidance": "Describe the statistical analysis methods that will be used to evaluate the secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable.”", + "conformance": "Conditional: when there is Secondary Estimand", + "cardinality": "One to one", + "relationship": "10.5.X.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.5.X.3 Handling of Missing Data in Relation to Secondary\nEstimand(s)\nConcept: C218806 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 204, + "term": "10.5.X.4 {Sensitivity Analysis}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is Sensitivity Analysis for a Secondary Objective", + "cardinality": "One to one", + "relationship": "10.5.X.4", + "value": "Sensitivity Analysis", + "business_rules": "Value Allowed: No\nRelationship: 10.5.X Secondary Objective <#>; 10.5 Analysis Associated with\nthe Secondary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 204, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218480", + "user_guidance": "Describe the statistical analysis methods will be used to evaluate the secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable.”", + "conformance": "Conditional: when there is Secondary Objective and Sensitivity Analysis for a\nSecondary Objective", + "cardinality": "One to one", + "relationship": "10.5.X.4", + "value": "Text", + "business_rules": "Value Allowed Yes\nRelationship: 10.5.X.4 Sensitivity Analysis\nConcept: C218480 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 205, + "term": "10.5.X.5 {Supplementary Analysis}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional: when there is a Supplementary Analysis for a Secondary Objective", + "cardinality": "One to one", + "relationship": "10.5.X.5", + "value": "Supplementary Analysis", + "business_rules": "Value Allowed: No\nRelationship: 10.5.X Secondary Objective <#>; 10.5 Analysis Associated with\nthe Secondary Objective(s); 10 STATISTICAL CONSIDERATIONS; Table of\nContents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each objective." + }, + { + "page": 205, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218481", + "user_guidance": "Describe the statistical analysis methods that will be used to evaluate the secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.). No text is intended here (heading only) unless there is no secondary objective, in which case indicate “Not applicable.”", + "conformance": "Conditional: when there is Supplementary Analysis for a Secondary Objective", + "cardinality": "One to one", + "relationship": "10.5.X.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.5.X.5 Supplementary Analysis\nConcept: C218481 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each objective as a series of level 4 sections (10.5.X.1,\n10.5.X.2, 10.5.X.3, 10.5.X.4, 10.5.X.5)." + }, + { + "page": 206, + "term": "10.6 Analyses Associated with the Exploratory Objective(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.6", + "value": "Analyses Associated with the Exploratory Objective(s)", + "business_rules": "Value Allowed: No\nRelationship: 3.3.X Exploratory Objective <#>; 10 STATISTICAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 206, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218807", + "user_guidance": "Describe any exploratory analyses, if applicable. Additional subsections may be created to describe the analyses for each exploratory objective, as needed. If there is no exploratory objective, indicate “Not applicable”.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.6 Analysis Associated with the Exploratory Objective(s),\nConcept: C218807 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 207, + "term": "10.7 Safety Analyses", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.7", + "value": "Safety Analyses", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 207, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218808", + "user_guidance": "If safety is a primary and/or secondary objective, describe the corresponding safety analyses in the appropriate section above (Section 10.4 Analyses Associated with the Primary Objective[s] or Section 10.5 Analyses Associated with the Secondary Objective[s]). In this section, describe statistical methods that will be used to analyse relevant safety outcomes, including any AESI. This should typically include specification of a measure to estimate risk within treatment arms, a measure to compare risks across treatment arms, and a measure of statistical uncertainty around the comparison (e.g., a confidence interval).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.7", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.7 Safety Analyses\nConcept: C218808 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 208, + "term": "10.8 Other Analyses", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.8", + "value": "Other Analyses", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 208, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218809", + "user_guidance": "Describe other analyses not included in Sections 10.3-10.7, such as subgroup analyses.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.8", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.8 Other Analyses\nConcept: C218809 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 208, + "term": "10.9 Interim Analyses", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.9", + "value": "Interim Analyses", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 209, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C142582", + "user_guidance": "Describe any interim analyses and criteria for stopping or adapting the trial. Ensure alignment with Section 4.3 Trial Stopping Rules. The description should include, but is not limited to, the following. Under circumstances where interim analysis details could impede the integrity of the trial, some of the information can be added in other documents outside of the protocol. • any planned interim analysis, even if it is only to be performed at the request of an oversight body (for example, DMC) • the purpose of the interim analysis, including whether the interim analysis may be used for stopping and/or other trial adaptations (e.g., sample size re- estimation, alteration to the proportion of participants allocated to each trial group, or changes to eligibility criteria) • the applied statistical method (e.g., group sequential test) and spending function (e.g., O’Brien-Fleming), as applicable • the parties responsible for performing and reviewing the results of the analyses (e.g., DMC, independent statistician) • when the analyses will be conducted (timing and/or triggers) • the decision criteria—statistical or other—that will be adopted to judge the interim results as part of a guideline for early stopping or other adaptations • who will see the outcome data while the trial is ongoing • whether these individuals will remain blinded to trial groups • how the integrity of the trial will be protected (e.g., maintaining blinding) when decisions are made after interim analyses (e.g., a decision to continue the trial or implement a specific adaptation)", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.9", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.9 Interim Analyses\nConcept: C142582 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "Yes, repeatable for each interim analysis" + }, + { + "page": 210, + "term": "10.10 Multiplicity Adjustments", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.10", + "value": "Multiplicity Adjustments", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 210, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218810", + "user_guidance": "Multiple testing procedures may be needed to limit the probability of false positive findings in a trial. Reasons for carrying out multiple statistical tests include, but are not restricted to, multiple endpoints, multiple treatment groups, multiple hypotheses, subgroups, and multiple timepoints. Describe any approaches to multiplicity control for the trial. This description might go beyond the analysis of primary objectives. Specify the statistical approach to control the overall type I error rate as well as the (adjusted) significance levels to test specific hypotheses, as applicable. Clarify whether the tests/confidence intervals are one- or two-sided. State the circumstances under which a trial will be considered to have met its primary objective(s). For example, in a study with two primary efficacy endpoints, this section should state whether the study would be expected to provide statistical evidence on at least one or on both of the endpoints in order to confirm the efficacy of the treatment. For some statistical approaches it might be helpful to include a graphical depiction, as visualisation will be helpful for understanding, coupled with the clinical translation of the mathematical choices. Details regarding interim analyses should be provided in Section 10.9 Interim Analyses.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.10", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship:10.10 Multiplicity Adjustments\nConcept: C218810 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 211, + "term": "10.11 Sample Size Determination", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.11", + "value": "Sample Size Determination", + "business_rules": "Value Allowed: No\nRelationship: 10 STATISTICAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 211, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C115467", + "user_guidance": "This section should detail the methods used for the determination of the sample size. The sample size calculation should be aligned with the primary estimand(s) and the primary analysis; otherwise, a justification is needed. Details of sample size calculation should include all relevant information to enable reproduction of the sample size, e.g.: • references to any prior studies on which assumptions were based • significance level (including information on the choice of one- or two-sided level) • power • assumed treatment effect and variability • how dropout rate and intercurrent events have been incorporated into sample size calculation • precision of estimator/length of confidence interval Any assumptions made should be stated and justified. Further analysis of how deviations from the assumptions will affect the sample size should be included. If complex simulations were used to calculate the sample size, consider including details in a separate simulation report as an appendix to the protocol. If the planned sample size is not derived statistically, then this should be explicitly stated along with a rationale for the intended sample size (e.g., exploratory nature of pilot trials; pragmatic considerations for trials in rare diseases).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "10.11", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 10.11 Sample Size Determination\nConcept: C115467 ICH OID 2.16.840.1.113883.3.989.2.3.3.10", + "repeating_reuse_rules": "No" + }, + { + "page": 212, + "term": "11 TRIAL OVERSIGHT AND OTHER GENERAL CONSIDERATIONS", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11", + "value": "TRIAL OVERSIGHT AND OTHER GENERAL CONSIDERATIONS", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 212, + "term": "11.1 Regulatory and Ethical Considerations", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.1", + "value": "Regulatory and Ethical Considerations", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 212, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218811", + "user_guidance": "Provide a high-level statement on the prevailing ethical, legal, and regulatory guidelines that will be applied throughout the trial. This trial will be conducted in accordance with the protocol and with the following: • Ethical principles that have their origin in the Declaration of Helsinki for medical research involving human subjects • Consensus ethical principles derived from international guidelines including the Declaration of Helsinki and the Council for International Organisations of Medical Sciences (CIOMS) International Ethical Guidelines • ICH Good Clinical Practice (GCP) Guidelines • Applicable laws and regulations", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.1 Regulatory and Ethical Considerations\nConcept: C218811 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 213, + "term": "11.2 Trial Oversight", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.2", + "value": "Trial Oversight", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 213, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218812", + "user_guidance": "Concisely summarise the trial oversight, listing the investigator and sponsor responsibilities not covered in other sections of the protocol that are essential for trial conduct, specifying the ones related to quality assurance. if not using below optional subheadings.", + "conformance": "Conditional: if not using the optional subheadings Level 3 (11.2.1 and 11.2.2)", + "cardinality": "One to one", + "relationship": "11.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.2 Trial Oversight\nConcept: C218812 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 214, + "term": "11.2.1 Investigator Responsibilities", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "11.2.1", + "value": "Investigator Responsibilities", + "business_rules": "Value Allowed: No\nRelationship: 11.2 Trial Oversight; 11 TRIAL OVERSIGHT AND OTHER\nGENERAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 214, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218813", + "user_guidance": "Describe the investigator responsibilities, including the oversight of trial-related activities delegated to a third party that may impact the trial conduct at sites, if applicable and if not addressed elsewhere.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "11.2.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.2.1 Investigator Responsibilities\nConcept: C218813 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 215, + "term": "11.2.2 Sponsor Responsibilities", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "11.2.2", + "value": "Sponsor Responsibilities", + "business_rules": "Value Allowed: No\nRelationship: 11.2 Trial Oversight; 11 TRIAL OVERSIGHT AND OTHER\nGENERAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 215, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218814", + "user_guidance": "Describe the sponsor responsibilities, including activities to be transferred to a third party that may impact the investigator sites, if applicable.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "11.2.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.2.2 Sponsor Responsibilities\nConcept: C218814 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 215, + "term": "11.3 Informed Consent Process", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "11.3", + "value": "Informed Consent Process", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 216, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C184390", + "user_guidance": "Specify the key elements of the informed consent process, including any special needs and how these are addressed (e.g., assent, capacity, legally acceptable representative, adolescents who may reach age of majority during the trial, pregnant participants and pregnant partners of participants).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.3 Informed Consent Process\nConcept: C184390 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 216, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218815", + "user_guidance": "Specify the key elements of the informed consent process, including any special needs and how these are addressed (e.g., assent, capacity, legally acceptable representative, adolescents who may reach age of majority during the trial, pregnant participants and pregnant partners of participants).", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "11.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.3 Informed Consent Process\nConcept: C218815 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 217, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218816", + "user_guidance": "If enrollment in the trial may occur during an emergency in which the participant or their legally acceptable representative is not able or available to give consent, describe the consent process.", + "conformance": "Optional", + "cardinality": "One to one", + "relationship": "11.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.3 Informed Consent Process\nConcept: C218816 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 217, + "term": "11.3.1 {Informed Consent for Rescreening}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "11.3.1", + "value": "Informed Consent for Rescreening", + "business_rules": "Value Allowed: No\nRelationship: 11.3 Informed Consent Process; 11 TRIAL OVERSIGHT AND\nOTHER GENERAL CONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 217, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218817", + "user_guidance": "If participants can be rescreened as described in Section 5.6 Screen Failure and Rescreening, state whether the participant needs to complete a new ICF. Screen failure and rescreening should be clearly defined in the protocol, with a cross reference to those definitions.", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "11.3.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.3.1 Informed Consent for Rescreening\nConcept: C218817 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 218, + "term": "11.3.2 {Informed Consent for Use of Remaining Samples in Exploratory\nResearch}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "11.3.2", + "value": "Informed Consent for Use of Remaining Samples in Exploratory Research", + "business_rules": "Value Allowed: No\nRelationship: 11.3 Informed Consent Process; 11 TRIAL OVERSIGHT AND\nOTHER GENERAL CONSIDERATION; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 218, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C218818", + "user_guidance": "If participants will be asked to consent to optional exploratory research using the remainder of mandatory samples, describe the use of remaining samples for optional exploratory research. If any exploratory research is planned and additional written consent regarding the use of remaining samples for exploratory research will be obtained, describe the consent process.", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "11.3.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.3.2 Informed Consent for Use of Remaining Samples in\nExploratory Research\nConcept: C218818 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 219, + "term": "11.4 Committees", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.4", + "value": "Committees", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 219, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218819", + "user_guidance": "Briefly describe the administrative structure of committees that will be reviewing data while the trial is ongoing, and the type of committee (e.g., Dose Escalation Committee, Data Monitoring Committee or Data Safety Monitoring Board). Note that specific details may be required depending on local law or regulation. If applicable, committee charters may be cross referenced. If no committees are involved, state “Not applicable.”", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.4", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.4 Committees\nConcept: C218819 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 220, + "term": "11.5 Insurance and Indemnity", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.5", + "value": "Insurance and Indemnity", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 220, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218820", + "user_guidance": "Concisely summarise the arrangements for participant insurance and indemnity if not addressed in a separate agreement, if required by the applicable regulatory requirements.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.5", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.5 Insurance and Indemnity\nConcept: C218820 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 220, + "term": "11.6 Risk-Based Quality Management", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.6", + "value": "Risk-Based Quality Management", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 221, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218821", + "user_guidance": "Describe the identified critical to quality factors, associated risks and risk mitigation strategies for the trial or refer to the location where this is described and updated during the trial based on emerging data.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.6", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.6 Risk-Based Quality Management\nConcept: C218821 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 221, + "term": "11.7 Data Governance", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.7", + "value": "Data Governance", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 222, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218822", + "user_guidance": "Describe the key systems and processes for critical trial integrity, traceability and security including a summary of the approaches enabling accurate data collection, reporting, monitoring, transfer, retention, and access if not addressed in separate agreement(s).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.7", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.7 Data Governance\nConcept: C218822 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 222, + "term": "11.8 Data Protection", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.8", + "value": "Data Protection", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 222, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218823", + "user_guidance": "Describe the measures to protect the privacy and confidentiality of personal information of trial participants in accordance with applicable regulatory requirements on personal data protection and any measures that should be taken in case of a data security breach.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.8", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.8 Data Protection\nConcept: C218823 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 223, + "term": "11.9 Source Records", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "11.9", + "value": "Source Records", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 223, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218824", + "user_guidance": "State the importance of source records and expectation for traceability. Delineate expectations for investigators (e.g., maintain and ensure availability of essential records) and trial monitors (e.g., ensure participant protections, ensure that the trial is conducted according to GCP). Identify what constitutes source records and its origin or provide a reference to the location of this information, if contained in a separate document. Describe the provision for direct access to source records enabling clinical trial- related monitoring, audits and regulatory inspections, if not included in separate agreement(s).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.9", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.9 Source Records\nConcept: C218824 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 224, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218825", + "user_guidance": "State the importance of source records and expectation for traceability. Delineate expectations for investigators (e.g., maintain and ensure availability of essential records) and trial monitors (e.g., ensure participant protections, ensure that the trial is conducted according to GCP). Identify what constitutes source records and its origin or provide a reference to the location of this information, if contained in a separate document. Describe the provision for direct access to source records enabling clinical trial- related monitoring, audits and regulatory inspections, if not included in separate agreement(s).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.9", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.9 Source Records\nConcept: C218825 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 224, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218826", + "user_guidance": "State the importance of source records and expectation for traceability. Delineate expectations for investigators (e.g., maintain and ensure availability of essential records) and trial monitors (e.g., ensure participant protections, ensure that the trial is conducted according to GCP). Identify what constitutes source records and its origin or provide a reference to the location of this information, if contained in a separate document. Describe the provision for direct access to source records enabling clinical trial- related monitoring, audits and regulatory inspections, if not included in separate agreement(s).", + "conformance": null, + "cardinality": "One to one", + "relationship": "11.9", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.9 Source Records\nConcept: C218826 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 225, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C222675", + "user_guidance": "State the importance of source records and expectation for traceability. Delineate expectations for investigators (e.g., maintain and ensure availability of essential records) and trial monitors (e.g., ensure participant protections, ensure that the trial is conducted according to GCP). Identify what constitutes source records and its origin or provide a reference to the location of this information, if contained in a separate document. Describe the provision for direct access to source records enabling clinical trial- related monitoring, audits and regulatory inspections, if not included in separate agreement(s).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.9", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.9 Source Records\nConcept: C222675 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 225, + "term": "11.10 Protocol Deviations", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.10", + "value": "Protocol Deviations", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 226, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218827", + "user_guidance": "Describe plans for detecting, reviewing, and reporting any deviations from the protocol or include reference to a separate document.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.10", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.10 Protocol Deviations\nConcept: C218827 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 226, + "term": "11.11 Early Site Closure", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "11.11", + "value": "Early Site Closure", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 226, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218828", + "user_guidance": "List the sponsor’s rights to close a site early. Likewise, list the investigator’s rights to initiate early site closure.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.11", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.11 Early Site Closure\nConcept: C218828 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 227, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218829", + "user_guidance": "List the criteria for early closure of a site by the sponsor or investigator.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.11", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.11 Early Site Closure\nConcept: C218829 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 227, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218830", + "user_guidance": "List the responsibilities of the sponsor and investigator following early site closure (e.g., informing the ethics committee[s], and prompt notification of the participant and their transition to appropriate therapy and/or follow-up).", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.11", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.11 Early Site Closure\nConcept: C218830 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 227, + "term": "11.12 Data Dissemination", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.12", + "value": "Data Dissemination", + "business_rules": "Value Allowed: No\nRelationship: 11 TRIAL OVERSIGHT AND OTHER GENERAL\nCONSIDERATIONS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 228, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218831", + "user_guidance": "Describe whether the clinical trial will be registered in public databases, including reporting of results, if applicable.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "11.12", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 11.12 Data Dissemination\nConcept: C218831 ICH OID 2.16.840.1.113883.3.989.2.3.3.11", + "repeating_reuse_rules": "No" + }, + { + "page": 228, + "term": "12 APPENDIX: SUPPORTING DETAILS", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "No text is intended here (heading only). Additional supporting detail appendices may be added at the end of the existing level 2 headings as needed.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "12", + "value": "APPENDIX: SUPPORTING DETAILS", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 229, + "term": "12.1 Clinical Laboratory Tests", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "12.1", + "value": "Clinical Laboratory Tests", + "business_rules": "Value Allowed: No\nRelationship: 12 APPENDIX: SUPPORTING DETAILS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 229, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C25294", + "user_guidance": "Specify which laboratory parameters should be included in each clinical laboratory assessment panel (e.g., haematology, chemistry, urinalysis). A tabular presentation for such information is common. If applicable, include equations and references for locally calculated laboratory results. If not applicable, retain heading and enter “Not applicable.”", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "12.1", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 12.1 Clinical Laboratory Tests\nConcept: C25294 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "No" + }, + { + "page": 229, + "term": "12.2 Country/Region-Specific Differences", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "12.2", + "value": "Country/Region-Specific Differences", + "business_rules": "Value Allowed: No\nRelationship: 12 APPENDIX: SUPPORTING DETAILS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 230, + "term": "", + "data_type": "Optional Text", + "dvh": "D", + "definition": "N/A", + "user_guidance": "Although global clinical trial practices are increasingly harmonised, some country/ region-specific differences in requirements do exist (e.g., document retention periods, contraception requirements). Where differences in requirements cannot be reconciled, the sponsor should explain how country/region-specific differences will be documented and communicated (e.g., by country/region-specific amendments or addenda). An alternative to country/region-specific amendments is to list the specific differences by country or countries in this section, including a reference to the relevant section of the protocol where each differing requirement applies. If not applicable, retain the heading and enter “Not applicable.”", + "conformance": "Optional: if there are no Country/Region-Specific Differences", + "cardinality": "One to one", + "relationship": "12.2", + "value": "Not Applicable", + "business_rules": "Value Allowed: No\nRelationship: 12.2 Country/Region-Specific Differences\nConcept: Optional Text", + "repeating_reuse_rules": "No" + }, + { + "page": 230, + "term": "[Country/Region Identifier]", + "data_type": "Valid Value", + "dvh": "H", + "definition": "C218832", + "user_guidance": "Although global clinical trial practices are increasingly harmonised, some country/ region-specific differences in requirements do exist (e.g., document retention periods, contraception requirements). Where differences in requirements cannot be reconciled, the sponsor should explain how they will document and communicate country/region-specific differences (e.g., by country/region-specific amendments or addenda). An alternative to country/region-specific amendments is to list the specific differences by country or countries in this section, including a reference to the relevant section of the protocol where the differing requirement applies. If not applicable, retain the heading and enter “Not applicable.”", + "conformance": "Optional: if there is Country/Region-Specific Differences", + "cardinality": "One to many", + "relationship": "12.2", + "value": "Country Identifier (ISO 3166 Country Codes, Alpha 3; ISO 3166 Country Codes,\nAlpha 2; GENC)\nor\nRegion Identifier (ISO 3166 Region Codes, Alpha 3; ISO 3166 Region Codes,\nAlpha 2; GENC)", + "business_rules": "Value Allowed: Yes\nRelationship: 12.2 Country/Region-Specific Differences\nConcept: C218832 ICH OID 2.16.840.1.113883.3.989.2.3.3.12, Heading,\nIdentifier, ISO 3166 Country Codes, Alpha 2; ISO 3166 Region Codes, Alpha 2", + "repeating_reuse_rules": "Yes, repeatable for each Country/Region" + }, + { + "page": 231, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218833", + "user_guidance": "Although global clinical trial practices are increasingly harmonised, some country/ region-specific differences in requirements do exist (e.g., document retention periods, contraception requirements). Where differences in requirements cannot be reconciled, the sponsor should explain how they will document and communicate country/region-specific differences (e.g., by country/region-specific amendments or addenda). An alternative to country/region-specific amendments is to list the specific differences by country or countries in this section, including a reference to the relevant section of the protocol where the differing requirement applies.", + "conformance": "Optional if there is Country/Region-Specific Differences", + "cardinality": "One to many", + "relationship": "12.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 12.2 Country /Region Identifier; Country/Region-Specific\nDifferences\nConcept: C218833 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable for each Country/Region" + }, + { + "page": 232, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218834", + "user_guidance": "Although global clinical trial practices are increasingly harmonised, some country/region-specific differences in requirements do exist (e.g., document retention periods, contraception requirements). Where differences in requirements cannot be reconciled, the sponsor should explain how they will document and communicate country/region-specific differences (e.g., by country/region-specific amendments or addenda). An alternative to country/region-specific amendments is to list the specific differences by country or countries in this section, including a reference to the relevant section of the protocol where the differing requirement applies. If not applicable, retain the heading and enter “Not applicable.”", + "conformance": "Optional if there is Country/Region-Specific Differences", + "cardinality": "One to many", + "relationship": "12.2", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Country /Region Identifier; 12.2 Country/Region-Specific\nDifferences\nConcept: C218834 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable for each country/region" + }, + { + "page": 232, + "term": "12.3 Prior Protocol Amendment(s)", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "12.3", + "value": "Prior Protocol Amendment(s)", + "business_rules": "Value Allowed: No\nRelationship: 12 APPENDIX: SUPPORTING DETAILS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 232, + "term": "Prior Protocol Amendment(s)", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218835", + "user_guidance": "Choose the applicable statement below. For an original protocol that has not been amended, retain the first statement below and delete the remainder of this entire section. {This protocol has not been amended.} Or {This is the first protocol amendment.} Or include the below as applicable. {This protocol has been amended previously. The Protocol Amendment Summary of Changes for the current amendment is located directly before the Table of Contents. Prior amendment(s) to this protocol are listed in the table below, beginning with the most recent.}", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Code List C217274: ICH OID 2.16.840.1.113883.3.989.2.3.1.1\nThis protocol has not been amended. (C218485)\nOr\nThis is the first protocol amendment. (C218486)\nOr include the below as applicable.\nThis protocol has been amended previously. The Protocol Amendment Summary\nof Changes for the current amendment is located directly before the Table of\nContents. Prior amendment(s) to this protocol are listed in the table below,\nbeginning with the most recent. (C218488)", + "business_rules": "Value Allowed: Yes\nRelationship: 12.3 Prior Protocol Amendment(s)\nConcept: C218835 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "No" + }, + { + "page": 233, + "term": "Document", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "Previous amendments should appear in reverse chronological order with the most recent at the top (e.g., Amendment 3, 2, 1). Delete or add lines as needed. Inclusion of region-, country-, and site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable from global amendments. If including the column with enrollment numbers, follow the instructions below. • For global amendments to international clinical trials or amendments to a single-country trial, list the approximate global enrollment total or percentage at the time of the amendment and select “globally”. • For global amendments consolidating only country/region-specific requirements, list approximate local enrollment total or percentage at the time of the amendment and select “locally”. If consolidating a series of local amendments, list the status of all the relevant locations. • For country/region-specific amendments to international clinical trials, list the approximate local enrollment total or percentage at the time of the amendment and select “locally”. • For trials in which enrollment status by cohort is more meaningful, such as for single-site or early-phase studies, listing the approximate enrollment by cohort is an option. If multiple cohorts are ongoing at the time of the amendment, list the status of all the ongoing cohorts. • Enter the approximate number or percentage of participants enrolled as a percentage of the expected total.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "12.3", + "value": "Document", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading; 12.3 Prior Protocol Amendment(s)\nConcept: Table Column Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 234, + "term": "Sponsor Approval Date", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "Previous amendments should appear in reverse chronological order with the most recent at the top (e.g., Amendment 3, 2, 1). Delete or add lines as needed. Inclusion of region-, country-, and site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable from global amendments. If including the column with enrollment numbers, follow the instructions below. • For global amendments to international clinical trials or amendments to a single-country trial, list the approximate global enrollment total or percentage at the time of the amendment and select “globally”. • For global amendments consolidating only country/region-specific requirements, list approximate local enrollment total or percentage at the time of the amendment and select “locally”. If consolidating a series of local amendments, list the status of all the relevant locations. • For country/region-specific amendments to international clinical trials, list the approximate local enrollment total or percentage at the time of the amendment and select “locally”. • For trials in which enrollment status by cohort is more meaningful, such as for single-site or early-phase studies, listing the approximate enrollment by cohort is an option. If multiple cohorts are ongoing at the time of the amendment, list the status of all the ongoing cohorts. • Enter the approximate number or percentage of participants enrolled as a percentage of the expected total.", + "conformance": "Required", + "cardinality": "One to many", + "relationship": "12.3", + "value": "Sponsor Approval Date", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading; 12.3 Prior Protocol Amendment(s)\nConcept: Table Column Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 235, + "term": "Approximate Enrollment when Sponsor Approved Amendment", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "Previous amendments should appear in reverse chronological order with the most recent at the top (e.g., Amendment 3, 2, 1). Delete or add lines as needed. Inclusion of region-, country-, and site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable from global amendments. If including the column with enrollment numbers, follow the instructions below. • For global amendments to international clinical trials or amendments to a single-country trial, list the approximate global enrollment total or percentage at the time of the amendment and select “globally”. • For global amendments consolidating only country/region-specific requirements, list approximate local enrollment total or percentage at the time of the amendment and select “locally”. If consolidating a series of local amendments, list the status of all the relevant locations. • For country/region-specific amendments to international clinical trials, list the approximate local enrollment total or percentage at the time of the amendment and select “locally”. • For trials in which enrollment status by cohort is more meaningful, such as for single-site or early-phase studies, listing the approximate enrollment by cohort is an option. If multiple cohorts are ongoing at the time of the amendment, list the status of all the ongoing cohorts. • Enter the approximate number or percentage of participants enrolled as a percentage of the expected total.", + "conformance": "Optional if there is an amendment and sponsor chooses to use", + "cardinality": "One to many", + "relationship": "12.3", + "value": "Approximate Enrollment when Sponsor Approved Amendment", + "business_rules": "Value Allowed: No\nRelationship: Table Column Heading; 12.3 Prior Protocol Amendment(s)\nConcept: Table Column Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 236, + "term": "", + "data_type": "Text or Universal Text “Original Protocol”", + "dvh": "D", + "definition": "C218477", + "user_guidance": "Previous amendments should appear in reverse chronological order with the most recent at the top (e.g., Amendment 3, 2, 1). Delete or add lines as needed. Inclusion of region-, country-, and site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable from global amendments. If including the column with enrollment numbers, follow the instructions below. • For global amendments to international clinical trials or amendments to a single-country trial, list the approximate global enrollment total or percentage at the time of the amendment and select “globally”. • For global amendments consolidating only country/region-specific requirements, list approximate local enrollment total or percentage at the time of the amendment and select “locally”. If consolidating a series of local amendments, list the status of all the relevant locations. • For country/region-specific amendments to international clinical trials, list the approximate local enrollment total or percentage at the time of the amendment and select “locally”. • For trials in which enrollment status by cohort is more meaningful, such as for single-site or early-phase studies, listing the approximate enrollment by cohort is an option. If multiple cohorts are ongoing at the time of the amendment, list the status of all the ongoing cohorts. • Enter the approximate number or percentage of participants enrolled as a percentage of the expected total.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Text or Universal Text “Original Protocol”", + "business_rules": "Value Allowed: Yes\nRelationship: Table Column Heading “Document”\nConcept: C218477 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, reuse from the title page or other previous amendment" + }, + { + "page": 236, + "term": "", + "data_type": "Date", + "dvh": "D", + "definition": "C132352", + "user_guidance": "Previous amendments should appear in reverse chronological order with the most recent at the top (e.g., Amendment 3, 2, 1). Delete or add lines as needed. Inclusion of region-, country-, and site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable from global amendments. If including the column with enrollment numbers, follow the instructions below. • For global amendments to international clinical trials or amendments to a single-country trial, list the approximate global enrollment total or percentage at the time of the amendment and select “globally”. • For global amendments consolidating only country/region-specific requirements, list approximate local enrollment total or percentage at the time of the amendment and select “locally”. If consolidating a series of local amendments, list the status of all the relevant locations. • For country/region-specific amendments to international clinical trials, list the approximate local enrollment total or percentage at the time of the amendment and select “locally”. • For trials in which enrollment status by cohort is more meaningful, such as for single-site or early-phase studies, listing the approximate enrollment by cohort is an option. If multiple cohorts are ongoing at the time of the amendment, list the status of all the ongoing cohorts. • Enter the approximate number or percentage of participants enrolled as a percentage of the expected total.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Date", + "business_rules": "Value Allowed: Yes\nRelationship: Table Column Heading “Amendment Identifier “Sponsor\nApproval Date”\nConcept: C132352 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, reuse from the title page or other previous amendment" + }, + { + "page": 237, + "term": "Approximately <#/%> enrolled", + "data_type": "Text", + "dvh": "D", + "definition": "C218478", + "user_guidance": "N/A", + "conformance": "Optional: if Original Protocol =No", + "cardinality": "One to one", + "relationship": "Amendment Details", + "value": "Integer for Number or one decimal point for percent", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Identifier; Sponsor Approval Date\nConcept: C218478 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, reuse from the title page or other previous amendment" + }, + { + "page": 238, + "term": "", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218695", + "user_guidance": "Enter the approximate number or percentage of participants enrolled as a percentage of the expected total. If the number of expected participants is changing as a result of the current amendment, use the updated number of expected participants to estimate the current percentage of enrollment. Estimates are adequate, as precise enrollment figures will likely be changing while an amendment is being prepared. • For a global or single-country amendment, provide the estimated total enrollment at the time the sponsor approved the amendment. • For global amendments providing (or consolidating) only country/region-specific requirements, list approximate local enrollment (total or percentage) at the time of the amendment and select “locally”. • If consolidating a series of local amendments, list the status of all the relevant locations. For a country/regional amendment, provide the estimated local or regional enrollment at the time the sponsor approved the amendment.", + "conformance": "Conditional if Original Protocol =No", + "cardinality": "One to Amendment Number", + "relationship": "Amendment Details", + "value": "Code List C217275: ICH OID 2.16.840.1.113883.3.989.2.3.1.2\nGlobally (C68846); Locally (C41065); By Cohort (C218489)", + "business_rules": "Value Allowed: Yes\nRelationship: Amendment Identifier; Sponsor Approval Date\nConcept: C218695 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, reuse from the title page or other previous amendment" + }, + { + "page": 238, + "term": "{The Overview of Changes from each prior protocol amendment is {provided\nbelow} or .}", + "data_type": "Text", + "dvh": "Universal text and V, D", + "definition": "N/A", + "user_guidance": "Move the Overview of Changes table from the previous amendments to this section in reverse chronological order (most recent first).", + "conformance": "Conditional: if not original protocol or first amendment", + "cardinality": "One to one", + "relationship": "12.3", + "value": "The Overview of Changes from each prior protocol amendment is\nChoose\nprovided below\nor\n.", + "business_rules": "Value Allowed: Yes\nRelationship: 12.3 Prior Protocol Amendment(s); {The Overview of Changes\nfrom each prior protocol amendment is {provided below} or .}\nConcept: Universal text", + "repeating_reuse_rules": "No" + }, + { + "page": 239, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218836", + "user_guidance": "N/A", + "conformance": "Conditional: when a specify alternative location is selected", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Text Location where information can be found", + "business_rules": "Value Allowed: Yes\nRelationship: Location for previous amendments\nConcept: C218836 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, reuse from the title page" + }, + { + "page": 239, + "term": "{Overview of Changes in Amendment ()}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "Move the Overview of Changes table from the previous amendments to this section in reverse chronological order (most recent first). (Add rows as needed) Add additional Overview of Changes tables as protocol amendments accrue.", + "conformance": "Conditional: when there is an amendment", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Overview of Changes in Amendment:", + "business_rules": "Value Allowed: No\nRelationship: {The Overview of Changes from each prior protocol amendment\nis {provided below} or .}\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable one table per amendment" + }, + { + "page": 240, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218477", + "user_guidance": "Move the Overview of Changes table from the previous amendments to this section in reverse chronological order (most recent first).", + "conformance": "Conditional: if amendment", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: {The Overview of Changes from each prior protocol amendment\nis {provided below} or .}\nConcept: C218477 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable one table per amendment identifier" + }, + { + "page": 240, + "term": "", + "data_type": "Date", + "dvh": "D", + "definition": "C132352", + "user_guidance": "Move the Overview of Changes table from the previous amendments to this section in reverse chronological order (most recent first).", + "conformance": "Conditional: if amendment", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Date", + "business_rules": "Value Allowed: Yes\nRelationship: {The Overview of Changes from each prior protocol amendment\nis {provided below} or .}\nConcept: C132352 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable one table per amendment" + }, + { + "page": 240, + "term": "{Description of Change}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a previous amendment", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Description of Change", + "business_rules": "Value Allowed: No\nRelationship: Table; 12.3 Prior Protocol Amendment(s)\nConcept: Table Column Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 241, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218483", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a previous amendment. Table optional", + "cardinality": "Column Heading\nRow Content", + "relationship": "12.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Table Column Heading “Description of Change”; 12.3 Prior\nProtocol Amendment(s)\nConcept: C218483 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable for each Description of Change in the amendment" + }, + { + "page": 241, + "term": "{Brief Rationale for Change}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a previous amendment", + "cardinality": "Column Heading\nTable", + "relationship": "12.3", + "value": "Brief Rationale for Change", + "business_rules": "Value Allowed: No\nRelationship: Table; 12.3 Prior Protocol Amendment(s)\nConcept: Table Column Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 242, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C181233", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a previous amendment. Table optional", + "cardinality": "One to Column Heading\nRow description of change\nSection # and Name", + "relationship": "12.3", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: Table Column Heading {Brief Rationale for Change} and\n\nConcept: C181233 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable for each Description of Change in the amendment" + }, + { + "page": 242, + "term": "{Section # and Name}", + "data_type": "Text", + "dvh": "H", + "definition": "Table Column Heading", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a previous amendment", + "cardinality": "Column Heading\nTable", + "relationship": "12.3", + "value": "Section # and Name", + "business_rules": "Value Allowed: No\nRelationship: Table; 12.3 Prior Protocol Amendment(s)\nConcept: Table Column Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 242, + "term": "
", + "data_type": "Valid Value", + "dvh": "V", + "definition": "C218479", + "user_guidance": "N/A", + "conformance": "Conditional: if there is a previous amendment. Table optional", + "cardinality": "One to one", + "relationship": "12.3", + "value": "Code List C217272: ICH OID 2.16.840.1.113883.3.989.2.3.13\nC217342 Section 1\nC217343 Section 2\nC217344 Section 3\nC217345 Section 4\nC217346 Section 5\nC217347 Section 6\nC217348 Section 7\nC217349 Section 8\nC217350 Section 9\nC217351 Section 10\nC217352 Section 11\nC217353 Section 12\nC217354 Section 13\nC217355 Section 14\nC217356 Section Title Page\nC217357 Section Amendment Details", + "business_rules": "Value Allowed: Yes\nRelationship: Table Column Heading {Section # and Name} and \nConcept: C218479 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable for each Description of Change in the amendment" + }, + { + "page": 243, + "term": "12.X {Additional Appendices}", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "12 X\nwhere X is a unique number for each Additional Appendix", + "value": "Title of Appendix", + "business_rules": "Value Allowed: Yes\nRelationship: 12 APPENDIX: SUPPORTING DETAILS; Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "Yes, repeatable for each Additional Appendix" + }, + { + "page": 243, + "term": "{}", + "data_type": "Text", + "dvh": "D", + "definition": "C220640", + "user_guidance": "N/A", + "conformance": "Conditional", + "cardinality": "One to one", + "relationship": "12.X\nwhere X is a unique number for each Additional Appendix", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 12.X Additional Appendices\nConcept: C220640 ICH OID 2.16.840.1.113883.3.989.2.3.3.12", + "repeating_reuse_rules": "Yes, repeatable for each additional Appendix" + }, + { + "page": 244, + "term": "13 APPENDIX: GLOSSARY OF TERMS AND ABBREVIATIONS", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "13", + "value": "APPENDIX: GLOSSARY OF TERMS AND ABBREVIATIONS", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 244, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C218837", + "user_guidance": "Define abbreviations and other terms used in the protocol. A tabular presentation is common and may serve as the definition at first use.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "13", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 13 APPENDIX: GLOSSARY OF TERMS AND\nABBREVIATIONS\nConcept: C218837 ICH OID 2.16.840.1.113883.3.989.2.3.3.13", + "repeating_reuse_rules": "No" + }, + { + "page": 245, + "term": "14 APPENDIX: REFERENCES", + "data_type": "Text", + "dvh": "H", + "definition": "Heading", + "user_guidance": "N/A", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "14", + "value": "APPENDIX: REFERENCES", + "business_rules": "Value Allowed: No\nRelationship: Table of Contents\nConcept: Heading", + "repeating_reuse_rules": "No" + }, + { + "page": 245, + "term": "", + "data_type": "Text", + "dvh": "D", + "definition": "C184397", + "user_guidance": "References should be listed in a common format that includes all relevant information to identify the source and date published. If a reference is not published, this should be clearly indicated.", + "conformance": "Required", + "cardinality": "One to one", + "relationship": "14", + "value": "Text", + "business_rules": "Value Allowed: Yes\nRelationship: 14 APPENDIX: REFERENCES\nConcept: C184397 ICH OID 2.16.840.1.113883.3.989.2.3.3.14", + "repeating_reuse_rules": "No" + } +] \ No newline at end of file diff --git a/clinical-mdr-api/m11-templates/m11-template.html b/clinical-mdr-api/m11-templates/m11-template.html index 7ce5052e..438d824c 100644 --- a/clinical-mdr-api/m11-templates/m11-template.html +++ b/clinical-mdr-api/m11-templates/m11-template.html @@ -1,24 +1,29 @@ + - ICH M11 Template - Study {{ study_name }} - - - + -

ICH M11 Template - Study {{ study_name }}

-


-
+
+ Loading M11 specifications... +
+ + + +

ICH M11 Template / Final version Adopted on 19 November 2025 - Study {{ study_name }}

+
+
+
+ +
+ +
- - + - - + - + - - + - + + + + + - + - + - + + + + + - + + + + + - + - + - + + + + + + - + - + + + +
Protocol Full Title: - {{ protocol_full_title }}
[Protocol Full Title] -
The protocol should have a descriptive title that identifies the scientific aspects of the trial sufficiently to ensure it is immediately evident what the trial is investigating and on whom, and to allow retrieval from literature or internet searches.
+ 		+ Sponsor Confidentiality Statement: + + + {{ missing_sponsor_confidentiality_statement }}
+ <Enter Sponsor Confidentiality Statement> +
Insert the Sponsor's confidentiality statement, if applicable; otherwise + delete.
Sponsor Confidentiality Statement: -
[Sponsor Confidentiality Statement] -
Insert the Sponsor's confidentiality statement, if applicable, otherwise delete.
+ 		+ Full Title: + + + {{ protocol_full_title }}
+ <Enter Full Title> +
The protocol should have a descriptive title that identifies the scientific + aspects of the trial sufficiently to ensure it is immediately evident what the trial is investigating and on + whom, and to allow retrieval from literature or internet searches.
Protocol Number: + Trial Acronym: + + - {{ study_name }} - {{ protocol_version }}
[version] -
A unique alphanumeric identifier for the trial, designated by the Sponsor, is a standard part of trial data, and should be included for most trials.
+ {{ trial_acronym }}
+ <Enter Trial Acronym> +
Acronym or abbreviation used publicly to identify the clinical trial. Delete + this line from the table if not applicable.
Amendment Number: - [Amendment Number] -
Enter the amendment number. If this is the original instance of the protocol, indicate Not Applicable.
+ 		+ Sponsor Protocol Identifier: + + {{ sponsor_protocol_identifier }}
+ <Enter Sponsor Protocol Identifier> +
A unique alphanumeric identifier for the trial, designated by the sponsor. +
Amendment Scope: + Original Protocol: + + - [Amendment Scope] [Country/Region Identifer] -
Acceptable entries for amendment scope are: "global" or "Country-specific/Regional"
Use the ISO-3166 region or country identifier (for example, DE or EU). For global trials delete the Country/Region Identifier field.
+ {{ original_protocol }}
+ [Original Protocol Indicator] +
+ Version Number: + + + {{ study_name }} - {{ protocol_version }}
+ <Enter Version Number> +
For use by the sponsor at their discretion.
Compound Number(s): + Version Date: + + - [Compound Number] -
Enter the Sponsor's unique identifier for investigational compound(s) in the trial. Add or delete additional fields as needed.
+ {{ version_date }}
+ <Enter Version Date> +
For use by the sponsor at their discretion.
Compound Name(s): + {Amendment Identifier:} + + - [Nonproprietary Name], [Proprietary Name], [Additional Proprietary Name] -
Delete this line from the table if a nonproprietary name has not yet been assigned. Omit proprietary name fields if not yet established.
+ {{ amendment_identifier }}
+ {[Amendment Identifier]} +
Enter the amendment identifier (e.g., amendment number). If this is the + original instance of the protocol, delete this row or enter "Not applicable".
Trial Phase: + {Amendment Scope:} + + - {{ trial_phase.decode }}
[Trial Phase], [Description of Trial Phase Other] -
Acceptable entries are: "Early Phase 1", "Phase 1", "Phase 1/Phase 2", "Phase 2", "Phase 2/Phase 3", "Phase 3", "Phase 4", or "Other". For trials combining investigational drugs or vaccines with devices, classify according to the phase of drug development.
+ + {[Amendment Scope]} {[Country Identifer] or [Region Identifier] or <Enter Site Identifier>} + + +
If this is the original instance of the protocol, delete this row or enter + "Not applicable". For an amendment that applies to all sites in the trial, enter “Global” and delete the + Country, Region and Site Identifier fields. If amending a single-country trial, enter “Global”.
For an + amendment that does not apply to all sites in the trial, select "Not Global" and utilise one of the + identifiers based on amemdment scope.
+
+ Sponsor's Investigational Product Code(s): + + + {{ missing_sponsor_investigational_product_code }}
+ <Enter Sponsor's Investigational Product Code(s)> +
Enter the sponsor’s unique identifier for investigational product(s) in the + trial. Add fields as needed.
Acronym: + Investigational Product Name(s): + + - {{ study_name }}
[Protocol Acronym] -
Acronym or abbreviation used publicly to identify the clinical trial, if any. The acronym may include numerals, such as -1, -2, or I, II, III, or IV. Delete this line from the table if not applicable.
+ {{ missing_investigational_product_name }}
+ + <Enter Nonproprietary Name(s)> + + +
+ + <Enter proprietary Name(s)> + + +
Omit nonproprietary name field if a nonproprietary name has not yet been + assigned. Omit proprietary name field if not yet established.
+
+ Trial Phase: + + + {{ trial_phase.decode }}
+ [Trial Phase] +
For trials combining investigational drugs or vaccines with devices, classify + according to the phase of drug development.
Short Title: + Short Title: + + - {{ protocol_short_title }}
[Protocol Short Title] -
Short title should convey in plain language what the trial is about and is suitable for use as "Brief Title" or "Title in Plain Language" in global clinical trial registries. It can also be suitable for use with informed consents and ethics committee submissions.
+ {{ protocol_short_title }}
+ <Protocol Short Title> +
Short title should convey in plain language what the trial is about and + should be suitable for use as “Brief Title” or “Title in Plain Language” in global clinical trial + registries. It can also be suitable for use with informed consent forms (ICF) and ethics committee + submissions.
Sponsor Name and Address: + Sponsor Name and Address: + + - {{ sponsor_name }}
{{ sponsor_legal_address }}
[Sponsor Name]
[Sponsor Legal Address] -
Provide the legal name of the individual or pharmaceutical or medical device company, governmental agency, academic institution, private organisation, or other organisation who takes primary responsability for and initiates a clinical investigation. If more than on Sponsor, list the Primary Sponsor in this field.
- Local Sponsor Name and Address:
- [Sponsor Local Name]
[Sponsor Local Address] -
In some countries, the clinical trial Sponsor may be the local affiliate company (or designee). In such cases, indicate in the Sponsor Local Name and Address field.
+ {{ sponsor_name }}
+ {{ sponsor_legal_address }}
+ <Enter Sponsor Name> +
+ <Enter Sponsor Legal Address> +
+ Co-Sponsor Name and Address: +
+ <Enter Co-Sponsor Name> +
+ <Enter Co-Sponsor Legal Address> +
Provide the legal name and address of the individual or pharmaceutical or + medical device company, governmental agency, academic institution, private organisation, or other + organisation who takes primary responsibility for and initiates a clinical investigation. If more than one + sponsor, list the primary sponsor in the Sponsor Name and Sponsor Legal Address fields. If co-sponsor is + applicable, enter co-sponsor name and legal address. Add additional fields if more than one co-sponsor is + applicable.
+ + Local Sponsor Name and Address: +
+ + <Enter Local Sponsor Name>
+ <Enter Local Sponsor Legal Address> + +
In some countries, the clinical trial sponsor may be the local affiliate + company (or designee). In such cases, indicate this in the Local Sponsor Name and Local Sponsor Legal + Address Fields.
Manufacturer Name and Address: + Device Manufacturer Name and Address: + + - [Device Manufacturer Name]
[Device Manufacturer Address] -
Manufacturer name and address information is required only for protocols that include investigational device(s) and should not be included for other protocols. Include the manufacturer address only if the manufacturer is different than the Sponsor listed above.
- Add additional fields as needed if multiple investigational devices will be used in the trial. Delete this line from the table if not applicable.
+ {{ missing_device_manufacturer_name_and_address }}
+ + <Enter Device Manufacturer Name> + +
+ <Enter Device Manufacturer Legal Address> + + +
Manufacturer name and address information is required only for drug/device + combination protocols that include investigational device(s) and should not be included for other + protocols. Include the manufacturer address only if the manufacturer is different than the sponsor listed + above. +
+ Add additional fields as needed if multiple investigational devices will be used in the trial or if there + are multiple manufacturers for a single device. Delete this line if not applicable. +
+
+ Regulatory or Clinical Trial Identifier(s): + + + {% if eu_trial_number %}EU CT Number: {{ eudract_id }}{% endif %} + + <EU CT Number> + + +
+ {% if ct_gov_id %}FDA IND Number: {{ ct_gov_id }}{% endif %} + + <FDA IND Number> + + +
+ {% if investigational_device_exemption_ide_number %}IDE Number: {{ investigational_device_exemption_ide_number + }}{% endif %} + + <IDE Number> + + +
+ {% if japanese_trial_registry_number_jrct %}jRCT Number: {{ japanese_trial_registry_number_jrct }}{% endif + %}<jRCT Number Number>
+ {% if national_clinical_trial_number %}NCT Number: {{ national_clinical_trial_number }}{% endif %}<NCT Number>
+ {% if national_medical_products_administration_nmpa_number %}NMPA IND Number: {{ + national_medical_products_administration_nmpa_number }}{% endif %}<NMPA IND + Number>
+ {% if who_number %}WHO/UTN Number: {{ who_number }}{% endif %}<WHO/UTN + Number>
+ {% if other_identifier_number %}Other: {{ other_identifier_number }}{% endif %}<Other Regulatory or Clinical Trial Identifier>
+
+ {% if eudamed_srn_number %}EUDAMED: {{ eudamed_srn_number }}{% endif %}[EUDAMED + Number]
+ + {% if eu_trial_number %}EU Trial Number: {{ eu_trial_number }}{% endif %}[EU + Trial Number]
+ + {% if investigational_new_drug_application_number_ind %}IND Number: {{ + investigational_new_drug_application_number_ind }}{% endif %}[IND + Number]
+ +
Include all identifiers that are applicable for the trial and available at the + time of protocol or amendment finalisation. Delete prompts for identifiers not available at the time of + document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.
Regulatory Agency Identifier Number(s): + Sponsor Approval: + - {% if ct_gov_id %}ClinicalTrials.gov ID: {{ ct_gov_id }}{% endif %}[ClinicalTrials.gov ID]
- {% if eudamed_srn_number %}EUDAMED: {{ eudamed_srn_number }}{% endif %}[EUDAMED Number]
- {% if eu_trial_number %}EudraCT Number: {{ eudract_id }}{% endif %}[EudraCT Number]
- {% if eu_trial_number %}EU Trial Number: {{ eu_trial_number }}{% endif %}[EU Trial Number]
- {% if investigational_device_exemption_ide_number %}IDE Number: {{ investigational_device_exemption_ide_number }}{% endif %}[IDE Number]
- {% if investigational_new_drug_application_number_ind %}IND Number: {{ investigational_new_drug_application_number_ind }}{% endif %}[IND Number]
- {% if japanese_trial_registry_number_jrct %}jRCT Number: {{ japanese_trial_registry_number_jrct }}{% endif %}[jRCT Number Number]
- {% if national_clinical_trial_number %}NCT Number: {{ national_clinical_trial_number }}{% endif %}[NCT Number]
- {% if national_medical_products_administration_nmpa_number %}NMPA IND: {{ national_medical_products_administration_nmpa_number }}{% endif %}[NMPA IND Number]
- {% if who_number %}WHO Number: {{ who_number }}{% endif %}[WHO Number]
- {% if other_identifier_number %}Other: {{ other_identifier_number }}{% endif %}[Other Regulatory Agency Identifier Number]
-
Include all numbers that are applicable for the trial and available at the time of protocol or amendment finalisation. Delete prompts for numbers not available at the time of document finalisation. Delete unused fields. Add fields for “other” if more than one is needed.
+ {{ missing_sponsor_approval_date }} + {<Enter Sponsor Approval Date> or <State location where + sponsor approval information can be found>} +
All versions should be uniquely identifiable.
Sponsor Approval Date: + Sponsor Signatory: + - [Approval Date] or [The approval date is included with the electronic signature, located {describe location}.] -
All versions should be uniquely identifiable. Use the CDISC date format (dd/mmm/yyyy, for example 07/JUN/2015) to indicate the date the protocol (or amendment) was approved by the Sponsor.
+ {{ missing_sponsor_signature }} + {<Enter sponsor signatory (e.g.,name, title, signature and + date)> or <State location where sponsor signatory information can be found (e.g., electronic + signature)>}
+ Medical Expert Contact: + + {{ missing_medical_expert_contact }} + {< Medical Expert contact information (as designated by + sponsor)> or <state location where Medical Expert contact information can be found>} +
- -

Sponsor Signatory:

- - - - - - - - - -
________________________________________________________________________________________________
[Name]
[Title of Sponsor Signatory]		[Sponsor Signature Date]
- -
Or
- [This protocol was approved via {describe method} as described on the approval page appended to the document] -
Where allowed, an electronic/digital signature may be used for approval rather than a wet signature. In such cases, replace the signature block with appropriate description of the electronic/digital approval and the location of relevant information for traceability.
- -
-
Medical Monitor Name and Contact Information:
- [Medical Monitor Institution Name], [Medical Monitor Institution Address] or [ is provided separately/can be found in {describe location}]. -
Report Serious Adverse Events within 24 hours {via E-mail/fax provided in the site -manual. /per the options below:}
-
E-mail: [Rapid Alert E-mail Address]
-
Fax: [Rapid Alert Fax Number]
- -
-
Amendment Details
-
Delete this entire section for an original protocol.
- -
-
History of Amendments
-
{ #/A total of # } prior {global} amendments have occurred, as shown in the table below:
-
- +


+
Amendment Details
+
Choose the applicable statement below. For an original protocol that has not been + amended, retain the first statement below and delete the remainder of this entire section.

+ {This protocol has not been amended.}
+
Or

+ {This is the first protocol amendment.}
+
Or include the below

+ {This protocol has been amended previously. Details of prior amendments are presented in Section 12.3 Prior Protocol + Amendment(s).}
+ +
{Current Amendment}
+
{The table below describes the current amendment.}
+ +
+ - - - - - - - - - - - - - - - - -
DocumentSponsor Approval Date (dd/mmm/yyyy)Approximate {(#/%)} Enrolled
 [Amendment x] [Amendment x Date] {(#/%)} {globally/locally}}
 Original Protocol [Original Protocol Date] 0
+ + Approximate <#/%> Enrolled at Time of Sponsor + Approval: + + + {{ missing_approximately_enrolled }} enrolled {{ missing_amendment_scope_enrollment_definition }}
+ Approximate <#/%> enrolled <enter Amendment Scope Enrollment Definition> +
Enter the approximate number or percentage of participants enrolled as a + percentage of the expected total. If the number of expected participants is changing as a result of the + current amendment, use the updated number of expected participants to estimate the current percentage of + enrollment. Estimates are adequate, as precise enrollment figures will likely be changing while an amendment + is being prepared. +
    +
  • For a global or single-country amendment, provide the estimated total enrollment at the time + the sponsor approved the amendment.
    • +
  • For global amendments providing (or consolidating) only country/region-specific requirements, + list approximate local enrollment (total or percentage) at the time of the amendment and select + “locally”.
    • +
  • If consolidating a series of local amendments, list the status of all the relevant locations.
    • +
+ For a country/regional amendment, provide the estimated local or regional enrollment at the time the + sponsor approved the amendment. +
+ + + + {Reason(s) for Amendment:} + Primary: {[Primary Reason for Amendment]} +
*
+ + Secondary: {[Secondary Reason for Amendment]} +
*
+ + + + + {Amendment Summary:} + + + {{ missing_amendment_summary }} + {<Amendment Summary>} +
Briefly describe key changes. Changes that are included in the amendment but + unrelated to the key changes do not need to be described here.

+ + + + + {Is this amendment likely to have a substantial impact on the safety or rights of the participants?} + + + {{ missing_amendment_to_have_substantial_impact_on_safety }} + {[Yes/No]} + + {<If Yes, briefly explain>} +
+ + + + + {Is this amendment likely to have a substantial impact on the reliability and robustness of the data generated + in the clinical trial?} + + + {{ missing_amendment_to_have_substantial_impact_on_reliability }} + {[Yes/No]} + + {<If Yes, briefly explain>} +
+ + + + +
* Choose from the available categories the primary reason and secondary reason(s) for + the amendment. Select the closest match among the choices. Changes to primary estimand, endpoints, or related + measures should be listed as a change of strategy. If none of the choices apply, choose “other” and provide a + description. If no secondary reason, indicate “Not applicable” for the secondary reason.
+ +

+
{Overview of Changes in the Current Amendment}
-
Do not include the current amendment in the table above, as final approval dates are often difficult to predict during document preparation. Previous amendments should appear in reverse chronological order with the most recent at the top (for example, Amendment 3, 2, 1). Delete lines not needed, add lines as needed. Inclusion of regional-, country-, and site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable from global amendments.
-
If including the column with enrollment numbers, follow the instructions below. +
Instructions for the Overview of Changes:

+
    -
  • For global amendments, list approximate global enrollment total or percentage at the time of the amendment and select “globally”.
    • -
  • For country/region amendments, list the approximate local enrollment total or percentage at the time of the amendment and select “locally”.
    • +
  • +
    If an Overview of Changes already exists from a prior amendment, move it to + Section 12.3 Prior Protocol Amendment(s), and populate a new Overview of Changes table for the current + amendment.
    +
    • +
  • +
    List the changes that apply to the current amendment. Provide a brief + description of the change(s) and a concise scientific rationale for specific changes (e.g., change to + inclusion/exclusion criteria).
    +
    • +
  • +
    If the same change affects multiple parts of the protocol, it is acceptable to + list multiple locations in the right column.
    +
    • +
  • +
    Table can be sorted in any order preferred by the sponsor.
    +
    • +
  • +
    Minor edits such as clarifications and corrections to typographical errors do + not need to be itemised in this table.
    +
    • +
  • +
    The changes listed in the table do not need to be detailed in revision marks, as + these can be provided in a separate supporting document.
    +
    • +
  • +
    Tabular presentation is common but not required. The page can be changed to + landscape orientation if necessary. (Add rows as needed)
    +
-
Current Amendment
-
The table below provides an overview of the current amendment.
+
- +
- - + + + - - - - - - - - - - - - - - - + + +
Amendment Number: [Amendment Number] + {Description of Change} + + + {Brief Rationale for Change} + + + {Section # and Name} + +
 Approximate { %/# } Enrolled: [Estimated % or # Enrolled] enrolled [Globally/Locally]
Enter the approximate number or percentage of participants enrolled as a percentage of the expected total. If the number of expected participants is changing as a result of the current amendment, use the updated number of expected participants to estimate the current percent of enrollment. Estimates are adequate, as precise enrollment figures will likely be changing while an amendment is being prepared. For a global amendment, provide the estimated global enrollment at the time of the Sponsor approved the amendment. For a country/regional amendment, provide the estimated local or regional enrollment at the time the Sponsor approved the amendment.
 Reason(s) for Amendment: Primary: [Primary Reason for Amendment]
*
Select from the following (multiple selections allowed): -
    -
  • Regulatory agency request to amend
    • -
  • New regulatory guidance
    • -
  • IRB/IEC feedback
    • -
  • New safety information available
    • -
  • Manufacturing change
    • -
  • Adaptive clinical trial IMP addition
    • -
  • Change in strategy
    • -
  • Change in standard of care
    • -
  • New data available (other than safety data)
    • -
  • Investigator/site feedback
    • -
  • Recruitment difficulty
    • -
  • Inconsistency and/or error in the protocol
    • -
  • Protocol design error
    • -
  • Other:
    • -
-
[Describe]		 Other: [Other Reason for Amendment]
*
Select from the following (multiple selections allowed): -
    -
  • Regulatory agency request to amend
    • -
  • New regulatory guidance
    • -
  • IRB/IEC feedback
    • -
  • New safety information available
    • -
  • Manufacturing change
    • -
  • Adaptive clinical trial IMP addition
    • -
  • Change in strategy
    • -
  • Change in standard of care
    • -
  • New data available (other than safety data)
    • -
  • Investigator/site feedback
    • -
  • Recruitment difficulty
    • -
  • Inconsistency and/or error in the protocol
    • -
  • Protocol design error
    • -
  • Not applicable
    • -
  • Other:
    • -
-
[Describe]
Summary of the Amendment: [Summary of Amendment]
Specify on the primary reason for the amendment with details specific to the trial. If more than one key change prompted the amendment, discuss briefly. Incidental changes which are included in the amendment but unrelated to the key changes do not need to be described here.
 Is this amendment likely to have a: -
    -
  • safety or rights of the participants, or
    • -
  • on the reliability and robustness of the data generated in the clinical trial?
    • -
- 		 [Yes/No]
Indicate whether the current amendment is likely to have a significant impact on either of the criteria listed.
 <Enter Description of Change>  <Enter Brief Rationale for Change>  <Enter Section # and Name>
-
* Choose from the available categories as the primary reason and secondary reason(s) for the amendment. Select the closest match among the choices. Changes to key measures or endpoints should be listed as a change of strategy. If none of the choices apply, choose “other” and provide a description. If no secondary reason, indicate “not applicable” for the secondary reason.
+
(Add rows as needed)
-
-
Summary of Changes in the Current Amendment:
-
- - - - - - - - - - - - - -
Section # and NameDescription of ChangeBrief Rationale for Change
 [Location of Change] [Description of Change] [Rationale for Amendment Change]
-
-
(Add lines as needed)
-
Follow the steps below to prepare the summary of changes. -
    -
  • If a Summary of Changes already exists from a prior amendment, move it to Section 13.4, History of Previous Amendments, and populate a clean summary table for the present amendment.
    • -
  • List the changes that apply to the current amendment. Provide a brief description of the change(s) and a brief scientific rationale for specific changes (for example, change to individual inclusion/exclusion criteria).
    • -
-
-
Tabular presentation is common but not required. The page can be changed to landscape orientation if necessary.
- +
-

Table of Contents

+
+

Table of Contents

+
-

1. PROTOCOL SUMMARY

-

No text is intended here (header only).

-

1.1. Protocol Synopsis

-

The protocol synopsis is a short summary of the key points of the trial. No text is intended here (header only).
-

-

Primary and Secondary Objectives and Endpoints

-

Include a copy of the Objectives/Endpoints Table including primary and secondary endpoints only from Section 3 of the protocol and follow all the same instructions. Not all trials will have a complete estimand. Do not include exploratory endpoints in the synopsis.
-

- [Primary and Secondary Objectives and Endpoints] - - - - - +
+

1 PROTOCOL SUMMARY

+
+
No text is intended here (header only).
+
+

1.1 Protocol Synopsis

+
+
The protocol synopsis is a short summary of the key points of the trial. In order to + keep the synopsis brief, cross references to full details in the main body of the protocol are acceptable.
No + text is intended here (heading only).
+
+

1.1.1 Primary and Secondary Objectives and Estimands

+
+
Summarise the primary and secondary objectives and any associated estimands in + natural, nontechnical (layperson) language.
For trials intended to estimate a treatment effect or test a + hypothesis related to a treatment effect, include the primary and secondary objectives and any associated + estimands using a nontechnical summary describing the objective and treatment effect of interest + (estimand).
For other types of trials not intended to estimate a treatment effect or test a hypothesis related + to a treatment effect, define trial objectives and describe additional information relevant to the clinical + question(s) of interest (e.g., the endpoint(s) associated with each objective).
For trials with numerous + objectives in which the description of objectives will exceed half a page, consider including the most important + objectives and estimands in the synopsis and refer to Section 3 Trial Objectives and Associated Estimands, which + covers the objectives and estimands in technical detail. For considerations on estimands, refer to ICH E9(R1). +
+ + <Enter Primary and Secondary Objectives and Estimands> + + +
+
ObjectivesEndpoints
+ + + + + + {% for primary_objective in primary_objectives %} - + {% endfor %} @@ -447,992 +926,3437 @@

Primary and Secondary Objectives and Endpoints

{% for secondary_objective in secondary_objectives %} - + {% endfor %}
ObjectivesEndpoints
Primary
{{ primary_objective.description|safe }} [{{ primary_objective.name }}]{{ primary_objective.description|safe }} [{{ + primary_objective.name }}]
    {% for endpoint in primary_objective.endpoints %} -
  • {{ endpoint.description|safe }} [{{ endpoint.name }}]
    • - {% endfor %}
+
  • {{ endpoint.description|safe }} [{{ endpoint.name + }}]
    • + {% endfor %} +
    {{ secondary_objective.description|safe }} [{{ secondary_objective.name }}]{{ secondary_objective.description|safe }} [{{ + secondary_objective.name }}]
      {% for endpoint in secondary_objective.endpoints %} -
    • {{ endpoint.description|safe }} [{{ endpoint.name }}]
      • - {% endfor %}
    +
  • {{ endpoint.description|safe }} [{{ endpoint.name + }}]
    • + {% endfor %} +
    -

    Overall Design

    -

    Several key aspects of the trial design are summarised below.

    - +
    +

    1.1.2 Overall Design

    +
    +

    Key aspects of the trial design are summarised below.

    +
    - - - - + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + - - - - + + - - - - + + + +
    Intervention Model:{{ intervention_model }} [intervention model]Population Type:{% if population_healthy_subjects %} Healthy volunteers {% endif %}[population type] + Intervention: + + {{ intervention_model }} + {<Enter Sponsor's Investigational Product Code(s)>} + +
    And/or
    + {{ non_proprietary_names }} + {<Enter Nonproprietary Name(s)>} + +     		+ Population Type: + + {% if population_healthy_subjects %} Healthy volunteers {% endif %} + [Population Type] + +
    + Intervention Model: + + {{ intervention_model }} + [Intervention Model] + + + Population Diagnosis or Condition: + + {% if population_healthy_subjects %} N/A {% else %} {% for indication in study_indications %} + {{indication.name}} {% endfor %} {% endif %} + [Population Diagnosis or Condition] + +
    + Control Type: + + {{ control }} + [Control Type] + + + Population Age: + + + - Minimum: {{ population_planned_minimum_age }} {{ population_planned_minimum_age_unit }} + <Enter Minimum Age> + + [Units of Age] + +
    + - Maximum: {{ population_planned_maximum_age }} {{ population_planned_maximum_age_unit }} + <Enter Maximum Age> + + [Units of Age] + +
    Control: {{ control }} [control]Population Diagnosis or Condition: {% if population_healthy_subjects %} N/A {% else %} {% for indication in study_indications %} {{indication.name}} {% endfor %} {% endif %}[diagnosis or condition] + Control Description: + + {{ missing_nonproprietary_name }} + {[Nonproprietary Name] + + or + [INN] + + or + <Enter "Not applicable">} + + + Site Distribution and Geographic Scope: + + + {{ missing_site_distribution }} {{ missing_site_geographic_scope }} + [Site Distribution] + + [Site Geographic Scope] + +
    + Intervention Assignment Method: + + + [Intervention Assignment Method] + + If Intervention Assigment Method is "Randomisation" then enter + + {<Randomisation Type>} + + If Intervention Assigment Method is "Other" then enter + {<Other Intervention Assignment Method>} + + + Master Protocol: + + + [Master Protocol Indicator] + +
    Active Comparator: {{study_interventions.type.decode}} [comparator]Population Age: - Minimum: {{ population_planned_minimum_age }} {{ population_planned_minimum_age_unit }} [minimum age]
    - Maximum: {{ population_planned_maximum_age }} {{ population_planned_maximum_age_unit }} [maximum age]    		 + Stratification: + + + [Stratification Indicator] + +
    Trial Intervention Assignment Method: [intervention assignment method]Site Distribution: [geographic scope] + Drug/Device Combination Product Indicator: + + + [Drug/Device Combination Product Indicator] + + Adaptive Trial Design: + + + [Adaptive Trial Design Indicator] + +
    -

    Briefly state the following:
    -

    -

    -
      -
    • Intervention model (for example, single group, parallel group, cross-over, factorial, sequential).
      • -
    • Control (for example, placebo, active comparator, low dose, historical, standard of care, sham procedure, or none [uncontrolled]).
      • -
    • Active comparator, if applicable; indicate N/A if not applicable.
      • -
    • Trial intervention assignment method (for example, randomisation, stratification, or both). Do NOT state block size. If assignment to intervention is by randomisation, describe when randomisation occurs relative to screening.
      • -
    • Trial population type (for example, healthy volunteers, adult patients, paediatric patients).
      • -
    • Population Diagnosis or Condition (for example, “acute lung injury,” or a specific biomarker profile); indicate “N/A – Healthy” for trials in healthy volunteers.
      • -
    • Population age range (for example ≤3 mos, ≥18 to ≤80 years old). List N/A if a maximum or minimum age limit does not apply. For trials in which multiple age ranges may be eligible (for example, a younger cohort and an older cohort), indicate the minimum and maximum ages for the trial overall, with an additional comment for any excluded age ranges.
      • -
    • Site distribution (select from: single-site, multi-site, or multi-site and multi-regional). If none of these applies, indicate other and describe.
      • -
    -
    +
    Further clarification:

    - -

    Number of arms: {{ number_of_arms }} [Number of Arms]

    -

    Enter the numeric value for the number of arms in the trial. For trials with a different number of arms in different periods, populate this field based on the period with the greatest number of arms.

    - -

    Blinding: The following roles indicated below will not be made aware of the treatment group assignment during the trial: {{ blinded_roles }} [blinded roles].

    -

    Select from the following blinded roles: +

    +

      -
    • Participant
      • -
    • Care Provider
      • -
    • Investigator
      • -
    • Outcomes Assessor: the individual who evaluates the outcome(s) of interest
      • -
    • Not applicable (No blinding).
      • +
    • +
      Control Description: if active comparator or low dose, pick nonproprietary + name or International Nonproprietary Name; indicate "Not applicable” if not applicable.
      +
      • +
    • +
      Intervention Assignment Method: If applicable, describe the type of + randomisation to be used (e.g., simple randomisation, block randomisation). If applicable,, describe the + other intervention assignment method.
      +
      • +
    • +
      Population Diagnosis or Condition: MedDRA Preferred Term(s) or indicate + “other” and describe.
      +
      • +
    • +
      Population Age: for trials in which multiple age ranges may be eligible (e.g., + a younger cohort and an older cohort), indicate the minimum and maximum ages for the trial overall, with an + additional comment for any excluded age ranges.
      +
    - For designs in which these details may differ in one or more trial periods, answer according to the portion of the trial in which the greatest blinding occurs. More details can be provided in Section 6.6 of the protocol. Note that this list does not include Sponsor staff or their designees who may be unblinded to complete ongoing safety oversight and surveillance reporting.
    -
    “Not Applicable (No blinding)” indicates an open-label trial.

    -

    Number of Participants: {{ population_planned_enrollment_number_quantity_value }} participants

    {randomly assigned to trial intervention/ enrolled}: {x} participants
    [{Target/Maximum}]

    -
    State the expected number of participants to be assigned to trial intervention/enrolled. Indicate whether the number provided is the target or maximum number of individuals to be randomly assigned to trial intervention/enrolled.
    +

    + Number of Arms: {{ number_of_arms }} [Number of + Arms] + + +

    +

    +

    Select the numeric value for the number of arms in the trial. For trials with a + different number of arms in different periods, populate this field based on the total number of arms.
    +

    -

    Arms and Duration

    -

    Total duration of trial intervention for each participant: {{ trial_intervention_total_duration if trial_intervention_total_duration is not none else '' }}
    - [Approximately] [x] Year(s)/[x] Month(s)/[x] Day(s) -
    Or
    -
    Duration will vary [Reason duration of trial intervention will vary]
    + Trial Blind Schema: {{ blinded_roles }} [Trial + Blind Schema] +

    -

    -

    Total duration of trial participation for each participant:
    - [Approximately] [x] Year(s)/[x] Month(s)/[x] Day(s) -
    Or
    -
    Duration will vary [Reason duration of trial intervention will vary]
    -
    Select the text that applies to the trial. Note that total duration of participation should include any washout and any follow-up periods in which the participant is not receiving trial intervention. Where the total durations can be provided, indicate whether the duration is approximate, and delete terms that are not applicable (for example, for a trial of only a few days, delete the years and months terms). When duration cannot be approximated, provide a short explanation (for example, “event-driven” or “adaptive design”).
    +
    For designs in which these details may differ in one or more trial periods, answer + according to the portion of the trial in which the highest number of blinded roles occurs. Additional details can + be provided in Section 6.7.3 Measures to Maintain Blinding.

    - [Arms and Duration Description] -

    Briefly state: -
      -
    • Total duration of participation for each participant with sequence and duration of trial periods (for example, screening, run-in, fixed dose/titration, follow-up/washout periods)
      • -
    • Dose regimens in each trial period and stage (if applicable) including frequency (for example, twice daily) and route of administration and criteria for individualised dosing (for example, participant weight or plasma concentrations), if applicable
      • -
    • Rules/procedures for any dose changes/adjustments including flexible dosing; dose reductions, dose interruptions, or tapering; discontinuation; and any circumstances for resuming trial intervention, as applicable
      • -
    - If sufficiently detailed, a cross-reference to the trial schema is appropriate in lieu of text description. -
    + Blinded Roles: The following roles indicated will not be made aware of the + treatment group assignment during the trial: + {{ blinded_roles }} [Blinded Roles] + + +

    +

    “Not applicable (no blinding)” indicates an open-label trial.
    +

    +

    + +

    + Number of Participants: + +

    State the expected number of participants to be assigned to trial + intervention/enrolled. Indicate whether the number provided is the target or maximum number of individuals to be + randomly assigned to trial intervention/enrolled.
    + {{ population_planned_enrollment_number_quantity_value }} participants
    {randomly + assigned to trial intervention/ enrolled}: {x} participants
    + A [Target/Maximum] of <Enter Number of Participants> participants + will be [randomly assigned to trial intervention/enrolled]. + + + +

    + +

    + Duration: + +

    Select one of the two options for total planned duration of trial intervention and + trial participation for each participant. Note that the total duration of trial participation should include any + washout and any follow-up periods in which the participant is not receiving a trial intervention. When duration + will vary, provide a short explanation (e.g., “event-driven” or “adaptive design”).
    +

    +

    + Total planned duration of trial intervention for each participant: + +
    + {<Enter total planned duration of trial intervention> [total planned duration + of trial unit of time]} + +

    Or, if duration will vary
    + {<Enter alternate description of planned duration of trial intervention>} + +

    +
    +

    + Total planned duration of trial participation for each participant: +
    + {<total planned duration of trial participation> [Total planned + duration of trial participation unit of time]} + +

    Or, if duration will vary
    + {<Enter alternate description of planned duration of trial participation>} + +
    If necessary, include any clarifications or cross-references to details in the main + body of the protocol in the optional field below.
    + <Enter Additional Description of Duration> + +

    + +

    + Committees: + +

    Indicate whether any committee(s) will be reviewing data while the trial is ongoing, + and the type of committee. Common examples include Data Monitoring Committee, Dose Escalation Committee, or + Endpoint Adjudication Committee; describe others, if applicable. List independent committees in the space + indicated. Other committees may be included in the separate space provided. Committees listed here should be fully + described in Section 11.4 Committees.
    +

    +

    + Independent Committees: +
    + <Enter Independent Committees> +
    + Other Committees: +
    + <Other Committees> + +

    Delete “Other Committees” if not applicable.

    Committees: -

    Indicate whether any committee(s) will be reviewing data while the trial is ongoing, and the type of committee. Common examples include Data Monitoring Committee, Dose Escalation Committee, or Endpoint Adjudication Committee; describe others, if applicable. List independent committees in the space indicated. Other committees may be included at the Sponsor’s discretion in the separate space provided. Committees listed here should be fully described in Section 10.3, Committees Structure.
    -
    Independent Committees: [Independent Committees]
    -
    Indicate “N/A” if no independent committees will be involved in the trial.
    -
    Other Committees: [Other Committees]
    -
    Delete “Other Committees” if not applicable.
    +
    Indicate whether any committee(s) will be reviewing data while the trial is ongoing, + and the type of committee. Common examples include Data Monitoring Committee, Dose Escalation Committee, or + Endpoint Adjudication Committee; describe others, if applicable. List independent committees in the space + indicated. Other committees may be included at the Sponsor’s discretion in the separate space provided. Committees + listed here should be fully described in Section 10.3, Committees Structure.
    +
    Independent Committees: [Independent Committees]
    +
    Indicate “N/A” if no independent committees will be involved in the trial.
    +
    Other Committees: [Other Committees]
    +
    Delete “Other Committees” if not applicable.

    -

    1.2. Trial Schema

    -
    The purpose of this section is to provide a visual depiction of the trial design, orienting users of the protocol to the key features of the design. The schema depicts the trial arms, the flow of individual participants through the progression of trial period(s)/epochs (such as screening, washout/run-in, intervention, and key milestones [for example, randomisation, cross-over, end of treatment]). For complex trials, additional schemas may be added to describe activities or trial periods in greater detail.
    +
    +

    1.2 Trial Schema

    +
    +
    The purpose of this section is to provide a visual depiction of the trial design, + orienting users of the protocol to the key features of the design. The schema depicts the trial arms, the flow of + individual participant through the progression of trial period(s)/epochs (such as screening, washout/run-in, + intervention, and key milestones [e.g., randomisation, cross-over, end of treatment, end of study, post-treatment + follow-up]). For complex trials, additional schemas may be added to describe activities or trial periods in + greater detail.
    {{ study_design_figure_svg|safe }}
    -
    - [Schema] +
    <Enter Trial Schema>
    +
    <Enter Schema Notes>
    + +
    +

    1.3 Schedule of Activities

    - -

    1.3. Schedule of Activities

    -
    The schedule of activities must capture the procedures that will be accomplished at each trial visit, and all contact with participants, for example, telephone contacts. This includes any tests that are used for eligibility, participant randomisation or stratification, or decisions on trial intervention discontinuation. Allowable windows should be stated for all visits.
    +
    The schedule of activities must capture the procedures that will be accomplished at + each trial visit, and all contact with participants (e.g., telephone contacts). This includes any tests that are + used for eligibility, participant randomisation or stratification, or decisions on trial intervention + discontinuation. Allowable windows should be stated for all visits and procedures. A tabular format is + recommended.
    When applicable for studies with extensive sampling (e.g., serial PK sampling), a separate table + may be added.
    {{ study_flowchart_html_table|safe }}
    - [Schedule of Activities] +
    <Enter Schedule of Activities>
    + +
    +

    2 INTRODUCTION

    +
    +
    No text is intended here (header only).
    +
    +

    2.1 Purpose of Trial

    +
    +
    Explain why the trial is needed, and why the research questions being asked are + important. Do not restate the objectives or estimands. Do not restate the IB; rather, cross reference to the IB as + applicable to the description.
    +
    <Enter Purpose of Trial>
    + +
    +

    2.2 Assessment of Risks and Benefits

    +
    +
    Include an assessment of known and potential risks and benefits, if any, as a result + of participating in the trial from the perspective of an individual participant, including the basis of the risk + (e.g., nonclinical trials or prior clinical trials). This section may be structured under one single heading 2.2 + Assessment of Risks and Benefits, or if applicable under 3 subheadings as 2.2.1 Risk Summary and Mitigation + Strategy, 2.2.2 Benefit Summary and 2.2.3 Overall Risk-Benefit Assessment.
    + +
    +

    2.2.1 Risk Summary and Mitigation Strategy

    +
    +
    Trial Intervention – Describe risks related to trial-specific + treatments and interventions. For the protocol, focus on the relevant key risks for this + trial. Provide a brief description of strategies to mitigate identified risks or provide a cross reference to the + relevant protocol section.
    + +
    {{ missing_trial_specific_intervention_risks_and_mitigations }}
    + +
    <Enter Trial-specific Intervention Risks and Mitigations>
    + +
    Trial Procedures – Describe risks associated with the design (e.g., + placebo arm) and procedures specific to this trial (e.g., biopsies), and any measures to control or mitigate the + risks. Provide a brief description of strategies to mitigate identified risks or provide a cross-reference to the + relevant protocol section. This is not intended to be an exhaustive list of all possible risks associated with + trial procedures but should focus on the unique risks inherent in the design or less common or high-risk + procedures.
    + +
    {{ missing_trial_specific_procedure_risks_and_mitigations }}
    + +
    <Enter Trial-specific Procedure Risks and Mitigations>
    + +
    Other – Consider risks associated with other items (e.g., challenge + agents, imaging agents, medical devices). This could include discussion of risk mitigation for special + populations, if not described elsewhere. Insert a line for each, as needed.
    + +
    {{ missing_trial_specific_other_risks_and_mitigations }}
    -

    2. INTRODUCTION

    +
    <Enter Trial-specific Other Risks and Mitigations>
    + +
    +

    2.2.2 Benefit Summary

    +
    +
    The benefit summary should describe any physical, psychological, social, or other + potential benefits to individual participants as a result of participating in the trial, addressing immediate + potential benefits and/or long-range potential benefits. Clearly state if no benefits to an individual participant + can be anticipated, or if potential benefits are unknown. For early clinical trials such as Phase 1 or trials in + healthy participants, benefits for an individual participant (other than those of altruism) are expected to be + minimal.
    Benefits to society in general may also be included but should be described separately from the + individual participant perspective.
    + +
    {{ missing_benefit_summary }}
    + +
    <Enter Benefit Summary>
    + +
    +

    2.2.3 Overall Risk-Benefit Assessment

    +
    +
    Provide a succinct, concluding statement on the perceived balance between risks that + have been identified from cumulative safety data, protocol procedures, and anticipated efficacy/benefits within + the context of the proposed trial.
    + +
    {{ missing_overall_risk_benefit_assessment }}
    + +
    <Enter Overall Risk-Benefit Assessment>
    + + +
    +

    3 TRIAL OBJECTIVES AND ASSOCIATED ESTIMANDS

    +
    +
    In this section, precisely define each trial objective and refine each trial + objective into a precise clinical question of interest by defining the associated estimand. For considerations on + estimands, refer to ICH E9(R1). Ensure alignment with every other section of the protocol. Include additional + level 3 headings (e.g., add a new level 3 heading for each secondary objective as needed). If there is more than + one objective in a category (e.g., more than one secondary objective), number each objective consecutively as the + level 3 heading (e.g., Secondary Objective 1, Secondary Objective 2, etc.).
    No text is intended here (header only).
    -

    2.1. Purpose of Trial

    -
    Explain why the trial is needed, why the research questions being asked are important. Do not restate the IB.
    - [Purpose] -
    Refer to the Section 1.2, Trial Schema, and Section 1.3, Schedule of Activities, for 369 more information about the trial design.
    - -

    2.2. Summary of Benefits and Risks

    -
    Include an assessment of known benefits and potential risks, including the basis of the risk (for 372 example, preclinical studies or prior clinical trials).
    -
    Benefit Summary
    -
    The benefit summary should be written from the perspective of an individual participant, and 375 should describe any physical, psychological, social, legal, or any other potential benefits to 376 individual participants as a result of participating in the trial, addressing immediate potential 377 benefits and/or long-range potential benefits. Clearly state if no benefits to an individual 378 participant can be anticipated, or if potential benefits are unknown. For early clinical trials such 379 as Phase 1, benefits for an individual participant (other than those of altruism) are expected to 380 be minimal.
    -
    Benefits to society in general may also be included but should be discussed separately.
    -
    [Benefit Summary]
    -
    Risk Summary and Mitigation Strategy
    -
    Trial Intervention – Discuss risks related to trial-specific treatments and interventions. For the 385 protocol, focus discussion only on the relevant key risks for THIS trial. Provide a brief 386 description of strategies to mitigate identified risks or provide a cross-reference to the relevant 387 protocol section.
    -
    [Trial-specific Discussion of Intervention Risks and Mitigations]
    -
    Trial Procedures – Consider risks associated with the design (for example, placebo arm) and procedures specific to THIS trial (for example, biopsies), and any measures to control the risks. Provide a brief description of strategies to mitigate identified risks or provide a cross-reference to the relevant protocol section. This is not intended to be an exhaustive list of all possible risks associated with trial procedures but should focus on the unique risks inherent in the design or less common or high-risk procedures. As above, provide a brief description of strategies to mitigate identified risks or provide a cross-reference to the relevant protocol section.
    -
    [Trial-specific Discussion of Procedure Risks and Mitigations]
    -
    Other – Consider risks associated with other items (for example, comparators, challenge agents, imaging agents, medical devices). Insert a line for each, as needed.
    -
    [Trial-specific Discussion of Other Risks and Mitigations]
    -
    Overall Benefit:Risk Conclusion
    -
    Provide a succinct, concluding statement on the perceived balance between risks that have been identified from cumulative safety data, protocol procedures, and anticipated efficacy/benefits within the context of the proposed trial. Risks need to be assessed against the benefits for the individual participant at least once a year.
    -
    [Overall Benefit:Risk Conclusion]
    - -

    3. TRIAL OBJECTIVES, ENDPOINTS AND ESTIMANDS

    -
    In this section, precisely define each clinical question of interest by stating each trial objective and specifying the endpoint(s) and estimand(s) that correspond to each objective. Ensure alignment with every other section of the protocol.
    -
    Include additional level 2 headers under Section 3 Trial Objectives, Endpoints, and Estimands as needed.
    + +
    +

    3.1 Primary Objective(s) and Associated Estimand(s)

    +
    +
    For all trials, precisely state each primary trial objective by providing a + meaningful and concise description of the treatment effect of interest using natural, nontechnical language for + clear understanding by sponsors, investigators, clinical site personnel, trial participants, ethics committees, + and regulators. For trials intended to estimate a treatment effect or test a hypothesis related to a treatment + effect, use the table to precisely describe the associated estimand(s). This includes specification of the + population targeted by the clinical question, the treatment condition(s), the endpoint (or variable), and the + population-level summary. Precise specifications of treatment, population, and variable are likely to address many + of the intercurrent events. Other intercurrent events not already addressed in the clinical question of interest + by the aforementioned attributes should be described with their associated strategies. For other types of trials + not intended to estimate a treatment effect or test a hypothesis related to a treatment effect, describe + additional information relevant to the clinical question(s) of interest (at a minimum, present the endpoint(s) + associated with each objective).
    No text is intended here (header only).
    + -

    3.1. {Primary/Secondary/Exploratory} Objective + Associated Endpoint {and Estimand}

    +
    +

    3.1.1 Primary Objective {{ primary_objective_number }} <#>

    +
    +
    {{ missing_primary_objective }}
    - - - - - +
    Enter information in table of estimand characteristics below including endpoint at a + minimum.
    +
    <Enter Primary Objective>
    + +
    {Primary/Secondary/Exploratory} Objective{Primary/Secondary/Exploratory} Endpoint
    - + + - {% for primary_objective in primary_objectives %} - - + - {% endfor %} - + + - {% for secondary_objective in secondary_objectives %} - - + + + + + + + + + + + + + - {% endfor %}
    Primary + Estimand Characteristic + + + Description + +
    {{ primary_objective.description|safe }} [{{ primary_objective.name }}] -
      {% for endpoint in primary_objective.endpoints %} -
    • {{ endpoint.description|safe }} [{{ endpoint.name }}]
      • - {% endfor %}
    +     		+ {Population} + + +
    List of key characteristics, such as demographic characteristics (e.g., age, + sex) and clinical characteristics (e.g., prior therapies, symptoms, severity, biomarker status)
    + +
    {{ missing_population }}
    +
    {<Enter Population>}
    Secondary + {Treatment} + + +
    List of key aspects of treatment regimens in each treatment group, including + at least investigational agents, dosage, and administration route
    + +
    {{ missing_treatment }}
    +
    {<Enter Treatment>}
    +
    {{ secondary_objective.description|safe }} [{{ secondary_objective.name }}] -
      {% for endpoint in secondary_objective.endpoints %} -
    • {{ endpoint.description|safe }} [{{ endpoint.name }}]
      • - {% endfor %}
    +     		+ Endpoint + + +
    Definition of the endpoint
    + +
    {{ missing_endpoint }}
    +
    <Enter Endpoint>
    +
    + {Population-level Summary} + + + +
    {{ missing_population_level_summary }}
    +
    {<Population-level Summary>}
    +
    + {Other Intercurrent Event} + + + +
    {{ missing_strategy }}
    +
    {Strategy}
    +
    + {<Enter Description of Intercurrent Event>} + + +
    Description of the strategy to address the intercurrent event (e.g., a + treatment policy strategy); cross reference the justification in Section 4 Trial Design. If there is >1 + intercurrent event for an objective, add additional intercurrent event rows
    + +
    {{ missing_intercurrent_event_strategy }}
    +
    <Enter Intercurrent Event Strategy>
    -
    {Primary/Secondary/Exploratory} Estimand
    -
    Describe the attributes that construct the estimand: the treatment condition of interest, the population of participants targeted by the clinical question of interest, other intercurrent events (if applicable), a population level summary, and the endpoint (or variable) specified in the table above.
    - [Estimand Description] -

    4. TRIAL DESIGN

    -
    In this section, describe the trial design with specific mention, as applicable, of the components of an adequate and well-controlled trial and reflect the principles of Quality by Design. The description of the design should be concise and consistent across Section 1.1, Protocol Synopsis and Section 1.2, Trial Schema.
    -
    No text is intended here (header only).
    +
    +

    3.2 Secondary Objective(s) and Associated Estimand(s)

    +
    +
    Describe the secondary objective(s) and associated estimand(s) as outlined in + Section 3.1 Primary Objective(s) and Associated Estimand(s). Use the same approach as above and include table for + a precise estimand description.
    +
    No text is intended here (heading only) unless there is no secondary objective, in + which case indicate “Not applicable”.
    + + +
    +

    3.2.1 {Secondary Objective <#>} {{ secondary_objective_number }} <#>

    + +
    +
    {{ missing_secondary_objective }}
    +
    {<Enter Secondary Objective>}
    +
    If a Secondary Objective has been entered, enter information in table of estimand + characteristics below including endpoint at a minimum}
    +
    {{ missing_table_of_estimand_characteristics }}
    +
    {<Table of Estimand Characteristics including Endpoint at a minimum>}
    + + +
    +

    3.3 Exploratory Objective(s)

    +
    +
    State each exploratory objective. This should generally include documentation of + associated exploratory endpoints. It may be helpful in some cases to describe precise estimands to provide clarity + on what is being estimated. Use the same approach as above and include table for a precise estimand description. +
    +
    No text is intended here (heading only) unless there is no exploratory objective, in + which case indicate “Not applicable”.
    + + +
    +

    3.3.1 {Exploratory Objective <#>} {{ exploratory_objective_number }} <#> +

    +
    +
    {{ missing_exploratory_objective }}
    +
    {<Enter Exploratory Objective>}
    +
    If an Exploratory Objective has been entered, enter information in table of estimand + characteristics below including endpoint at a minimum:
    +
    {{ missing_table_of_estimand_characteristics }}
    +
    {<Enter Table of Estimand Characteristics>}
    + +
    +

    4 TRIAL DESIGN

    +
    +
    In the subsections below, describe the trial design with specific mention, as + applicable, of the components of an adequate and well-controlled trial and reflect the principles of Quality by + Design. The description of the design should be concise and consistent with Section 1.1 Protocol Synopsis and + Section 1.2 Trial Schema. The trial design should align with objectives/estimand(s) described in Section 3 Trial + Objectives and Associated Estimands.
    +
    This section is intended to provide a description for the important aspects of the + trial design and rationale for its key attributes. Operational details needed to implement the trial design should + be covered in more detail in subsequent sections. No text is intended here (heading only).
    +
    No text is intended here (heading only).
    + +
    +

    4.1 Description of Trial Design

    +
    +
    Describe the overall trial design and intervention model (e.g., single group, + parallel group, cross-over, factorial, sequential), the expected number of participants, and the control method + (e.g., placebo, active comparator, low dose, external, standard of care, sham procedure, or none [uncontrolled]). + If there are any key aspects of the investigational trial intervention that inform the selection of the + intervention model, this should be described.
    +
    If applicable, indicate other design characteristics (e.g., superiority, + noninferiority, dose escalation, or equivalence).
    +
    If the trial will have an adaptive or novel design (e.g., the trial will be + conducted under a master protocol), provide a summary of these design aspects.
    +
    If applicable, describe within-trial transition rules (e.g., transitions involving + cohorts or trial parts). Dose escalation or dose-ranging details should also be described.
    +
    {{ missing_overall_description_of_trial_design_and_description_of_intervention_model }}
    +
    <Enter Overall Description of Trial Design and Description of + Intervention Model>
    + +
    Describe the trial duration with reference to Section 1.2 Trial Schema. Explain what + the overall duration for an individual participant is anticipated to be and why, including the sequence and + duration of trial periods (e.g., screening, run-in, randomisation, treatment [fixed dose/titration], + follow-up/washout periods). Where applicable, include discussion of sentinel dosing (or lack thereof), dose + escalation, and cohort expansion. If dose modification decisions are dependent upon review by a committee, include + details in Section 11.4 Committees.
    +
    {{ missing_description_of_trial_duration }}
    +
    <Enter Description of Trial Duration>
    + +
    State the method of assignment to trial intervention and the level and method of + blinding that will be used, with cross reference to Section 6.7 Investigational Trial Intervention Assignment, + Randomisation and Blinding.
    +
    {{ missing_description_of_method_of_assignment_to_trial_intervention }}
    +
    <Enter Description of Method of Assignment to Trial Intervention> + +
    + +
    {{ missing_description_of_level_and_method_of_blinding }}
    +
    <Enter Description of Level and Method of Blinding>
    -

    4.1. Description of Trial Design

    -
    Describe the trial intervention model (for example, single group, parallel group, cross-over, factorial, sequential), the expected number of participants, and the control method (for example, placebo, active comparator, low dose, historical, standard of care, sham procedure, or none [uncontrolled]).
    -
    If applicable, indicate the type of trial (for example, superiority, non-inferiority, dose escalation, or equivalence).
    -
    If the trial will have an adaptive or novel design (for example, the trial will be conducted under a master protocol), provide a summary of these design aspects.
    -
    [Description of Intervention Model]
    -
    Describe the trial duration with reference to Section 1.2, Trial Schema. Explain what the overall duration for an individual participant is anticipated to be and why, including the sequence and duration of trial periods (for example, screening, run-in, randomisation, treatment [fixed dose/titration], follow-up/washout periods). Where applicable, include discussion of sentinel dosing (or lack thereof), dose escalation, and cohort expansion. If dose modification decisions are dependent upon review by a committee, include details in Section 10.2, Committees Structure.
    -
    [Description of Trial Duration]
    -
    Describe the method of assignment to trial intervention (for example, stratified randomisation). If assignment to trial intervention is by randomisation, describe when randomisation occurs relative to screening.
    -
    Describe the level and method of blinding; for example, single-blind, double-blind, [including Sponsor unblinded], matching placebo, double-dummy, or open-label). Include mention of measures taken to minimise bias on the part of participants, investigators, and analysts.
    -
    If applicable, describe within-trial transition rules, for example, transitions involving cohorts or trial parts. Dose escalation or dose-ranging details should also be described.
    -
    [Method of Assignment to Trial Intervention]
    -
    Discuss any other important aspects of the design, including but not limited to the following, where applicable:
    +
    Describe any other important aspects of the design, e.g.:
      -
    • Geographic scope of trial (for example, single-centre, multi-centre, or multi-centre and multi-national)
      • -
    • Use of decentralised processes, tools, or features in the trial
      • -
    • Planned use of a Data Monitoring Committee, or similar review group and cross reference Section 10.2, Committees, for details,
      • -
    • Whether an interim analysis is planned and, if so, refer to details in Section 9.7, Interim Analysis, and/or
      • -
    • Any planned extension trial, long-term follow-up/registry, or post-trial sample analysis or other data-related activities.
      • +
    • geographic scope of trial (e.g., single-centre, multicentre, or multicentre and multinational)
      • +
    • use of decentralised elements in the trial
      • +
    • planned use of a Data Monitoring Committee, or similar review group and cross reference Section 11.4 + Committees, for details
      • +
    • whether an interim analysis is planned; if so, refer to details in Section 10.9 Interim Analyses
      • +
    • any planned extension trial, long-term follow-up/registry, future use of samples or data, or post-trial + sample analysis or other data-related activities
    -
    [Additional Description of Design]
    +
    {{ missing_additional_description_of_trial_design }}
    +
    <Enter Additional Description of Trial Design>
    -

    4.1.1. Participant Input into Design

    -
    If applicable, describe any participant involvement in the design of the trial and any participant suggestions implemented.
    -
    [Participant Input]
    - -

    4.2. Rationale for Trial Design

    -
    Provide a rationale for the trial intervention model selected in Section 4.1, Description of Trial Design. A rationale for the choice of comparator, if applicable, should be described separately in Section 4.2.1, Rationale for Comparator.
    -
    [Rationale for Intervention Model]
    -
    Provide a rationale that the trial duration is appropriate to show a reliable and relevant effect of the trial intervention per the trial objective(s).
    -
    [Rationale for Duration]
    -
    Provide a rationale that the trial endpoint(s) described in Section 3, Trial Objectives, Endpoints, and Estimands, are clinically relevant and provide a reliable and valid measurement of the intended intervention effect.
    -
    [Rationale for Endpoints]
    -
    If applicable, provide a rationale for any interim analysis planned with respect to its purpose (for example, stopping the trial early for efficacy or futility) and timing.
    -
    [Interim Analysis]
    - -

    4.2.1. Rationale for Comparator

    -
    If applicable, provide a rationale for the type of control selected for the trial (for example, placebo, active drug, combination, historical). Discuss any known or potential problems associated with the control group selected in light of the specific disease and intervention(s) being studied. If comparators will differ by region, describe. Describe prior trials that support the dose and/or dose regimen.
    -
    [Rationale for Comparator]
    +
    +

    4.1.1 Stakeholder Input into Design

    +
    +
    If applicable, describe any stakeholder (e.g., patient, healthcare professional and + patient advocacy groups) involvement in the design of the trial and any suggestions implemented.
    +
    {{ missing_stakeholder_input_into_design }}
    +
    <Enter Stakeholder Input into Design>
    + +
    +

    4.2 Rationale for Trial Design

    +
    +
    {<Enter Rationale for Trial Design>} +
    +
    if not using below optional subheadings.
    +
    OR
    -

    4.2.2. Rationale for Adaptive or Novel Trial Design

    +
    +

    4.2.1 Rationale for Estimand(s)

    +
    +
    When estimands are associated with the Primary and Secondary Objectives described in + Section 3 Trial Objectives and Associated Estimands, provide a rationale for the estimand(s) not described + elsewhere in the document. This should include a rationale that the selected endpoint(s) are clinically relevant + and provide a reliable and valid measurement of the intended intervention effect(s). It should also include a + rationale for the selected strategies for handling intercurrent events.
    +
    {{ missing_rational_for_estimands }}
    +
    <Enter Rationale for Estimand(s)>
    + +
    +

    4.2.2 Rationale for Intervention Model

    +
    +
    Provide a rationale for the trial intervention model described in Section 4.1 + Description of Trial Design with a cross reference to Section 6.2 Rationale for Investigational Trial Intervention + Dose and Regimen. Rationale for choice of comparator, if applicable, should be described separately in Section + 4.2.3 Rationale for Control Type. A rationale for the choice of trial population should be described separately in + Section 5.1 Description of Trial Population and Rationale.
    +
    {{ missing_rational_for_intervention_model }}
    +
    <Enter Rationale for Intervention Model>
    + +
    +

    4.2.3 Rationale for Control Type

    +
    +
    If applicable, provide a rationale for the type and choice of control selected for + the trial (e.g., placebo, active drug, combination, external). Describe any known or potential problems associated + with the control group selected in light of the specific disease and intervention(s) being studied. If comparators + will differ by region, describe. The rationale for dose and/or dose regimen is explained in Section 6.2 Rationale + for Investigational Trial Intervention Dose and Regimen.
    +
    {{ missing_rational_for_control_type }}
    +
    <Enter Rationale for Control Type>
    + +
    +

    4.2.4 Rationale for Trial Duration

    +
    +
    Provide a rationale that the trial duration is appropriate for a reliable and + relevant evaluation of the trial intervention per the trial objective(s).
    +
    {{ missing_rational_for_trial_duration }}
    +
    <Enter Rationale for Trial Duration>
    + +
    +

    4.2.5 Rationale for Adaptive or Novel Trial Design

    +
    If applicable, provide a rationale for the use of an adaptive or novel design.
    -
    [Rationale for Adaptive or Novel Design]
    - -

    4.2.3. Other Trial Design Considerations

    -
    Discuss rationale for any additional aspects of the design not addressed above.
    -
    [Other Design Considerations]
    - -

    4.3. Access to Trial Intervention After End of Trial

    -
    If applicable, describe any possibilities for access to trial intervention, if any, beyond completion of the trial. Planned extension trials, if described above in Section 4.1 do not need to be repeated.
    -
    [Access to Trial Intervention after End of Trial]
    - -

    4.4. Start of Trial and End of Trial

    -
    Define key timepoints in the trial, such as the start date, first act of recruitment, and site closure. These definitions should consider local regulatory requirements. Delineate sponsor and investigator decision rights to close a site or end the trial, including criteria for early closure of a site. List responsibilities of the sponsor and investigator following termination or suspension of the trial. Provide a cross-reference to Section 10.5, Early Site Closure or Trial Termination for criteria and responsibilities related to early site closure or trial termination.
    -
    [Trial Start and End]
    - -

    5. TRIAL POPULATION

    -
    In this section, describe the trial population. Use the following guidance when developing participant eligibility criteria to be listed in Section 5.3, Inclusion Criteria, and Section 5.4, Exclusion Criteria.
    +
    {{ missing_rational_for_adaptative_or_novel_trial_design }}
    +
    <Enter Rationale for Adaptive or Novel Trial Design>
    + +
    +

    4.2.6 Rationale for Interim Analysis

    +
    +
    If applicable, provide a rationale for the use of an adaptive or novel design.
    +
    {{ missing_rational_for_interim_analysis }}
    +
    <Enter Rationale for Interim Analysis>
    + +
    +

    4.2.7 Rationale for Other Trial Design Aspects

    +
    +
    Discuss rationale for any additional aspects of the design not addressed above. +
    +
    {{ missing_rational_for_other_trial_design_aspects }}
    +
    <Enter Rationale for Other Trial Design Aspects>
    + +
    +

    4.3 Trial Stopping Rules

    +
    +
    If applicable, describe any trial-specific stopping rules, including guidance on + when the trial should be stopped for efficacy or safety reasons, when a cohort or dose escalation should be + terminated, and/or when a given treatment arm should be terminated. If applicable, describe any rules that may + result in a temporary pause of dosing and/or enrollment into the trial and criteria for restarting enrollment. + Ensure that the trial-specific stopping rules are aligned with the specifications that are described in Section + 10.9 Interim Analyses.
    +
    {{ missing_trial_stopping_rules }}
    +
    <Enter Trial Stopping Rules>
    + +
    +

    4.4 Start of Trial and End of Trial

    +
    +
    Define key timepoints in the trial, including trial start and end definitions (e.g., + a key timepoint definition for start of trial might be when the ICF is signed by the first participant, and a key + timepoint definition for end of trial might be when participants are no longer being examined or the last + participant’s last trial assessment has occurred). Consider local regulatory requirements for these and other + definitions (e.g., the first act of recruitment).
    +
    If appropriate, provide a cross reference to Section 11.11 Early Site Closure.
    +
    {{ missing_start_of_trial }}
    +
    <Enter Start of Trial>
    +
    {{ missing_end_of_trial }}
    +
    <Enter End of Trial>
    + +
    +

    4.5 Access to Trial Intervention After End of Trial

    +
    +
    If applicable, describe any possibilities for access to trial intervention, if any, + beyond completion of the trial. Planned extension trials, if described in Section 4.1 Description of Trial Design, + do not need to be repeated in this section.
    +
    {{ missing_start_of_trial }}
    +
    <Enter Access to Trial Intervention After End of Trial>
    + +
    +

    5 TRIAL POPULATION

    +
    +
    In the subsections below, describe the trial population: inclusion and exclusion + criteria, contraception requirements and lifestyle restrictions. The trial population should generally be aligned + with the population attribute of the primary estimand that was defined in Section 3 Trial Objectives and + Associated Estimands.
    +
    Consider the following when developing participant eligibility criteria to be listed + in Section 5.2 Inclusion Criteria and Section 5.3 Exclusion Criteria:
      -
    • List the criteria necessary for participation in the trial. Ensure that each criterion can be easily assessed definitively and answered with yes/no responses.
      • -
    • If participants require screening, distinguish between screening vs enrolling participants. Identify specific laboratory tests or clinical characteristics that will be used as criteria for inclusion or exclusion. If permitting existing medical diagnosis, imaging, genetic tests, or laboratory results, state any required window or acceptable test type.
      • -
    • If measures to enrich the trial population for pre-specified subgroups of interest are used, these should be described.
      • +
    • List the criteria necessary for participation in the trial. Ensure that each criterion can be easily + assessed definitively and answered with yes/no responses.
      • +
    • Criteria should be written to avoid protocol waivers or exemptions.
      • +
    • If participants require screening, distinguish between screening vs enrolling participants.
      • +
    • Identify specific laboratory tests or clinical characteristics that will be used as criteria for inclusion + or exclusion and any documentation needed to demonstrate the criterion is met (e.g., laboratory tests or + imaging). If permitting existing medical diagnosis, imaging, genetic tests, or laboratory results, state any + required window or acceptable test type.
      • +
    • If measures to enrich the trial population for pre-specified subgroups of interest are used, these should be + described.
    -
    No text is intended here (header only).
    - -

    5.1. Selection of Trial Population

    -
    Describe the population selected (for example, healthy volunteers, adult participants, paediatric participants) and how the enrollment criteria reflect the populations that are likely to use the drug if approved. Specify the population age range (for example, ≤3 months, ≥18 to ≤80 years old) and any key diagnostic criteria for the population (for example, “acute lung injury”, or a specific biomarker profile). If applicable, describe similar conditions or diseases and their differential diagnosis.
    -
    [Selection of Trial Population]
    - -

    5.2. Rationale for Trial Population

    -
    Provide a rationale for the trial population ensuring that the population selected is well defined and clinically recognisable. Justify whether the trial intervention is to be evaluated in children, in adults unable to consent for themselves, other vulnerable participant populations, or those that may respond to the trial intervention differently (for example, elderly, hepatic or renally impaired, or immunocompromised participants).
    -
    [Rationale for Trial Population]
    -
    Individuals who do not meet criteria for trial eligibility must not be enrolled via protocol waivers or exemptions
    - -

    5.3. Inclusion Criteria

    -
    Inclusion criteria are characteristics that define the trial population, for example, those criteria that every potential participant must satisfy, to qualify for trial entry.
    -
    To be eligible to participate in this trial, an individual must meet all the following criteria:
    - # [Inclusion Criterion] -
    Add criteria as needed. Number sequentially.
    - -

    5.4. Exclusion Criteria

    -
    Exclusion criteria are characteristics that make an individual ineligible for participation.
    -
    An individual who meets any of the following criteria will be excluded from participation in this trial:
    - # [Exclusion Criterion] -
    Add criteria as needed.
    - -

    5.5. Lifestyle Considerations

    -
    In the following subsections, describe any restrictions during the trial pertaining to lifestyle and/or diet, intake of caffeine, alcohol, or tobacco, or physical and other activities. If not applicable, include a statement that no restrictions are required.
    -
    [Lifestyle Considerations]
    - -

    5.5.1. Meals and Dietary Restrictions

    -
    If applicable, describe any restrictions on diet (for example, food and drink restrictions, timing of meals relative to dosing).
    -
    [Meals and Dietary Restrictions]
    - -

    5.5.2. Caffeine, Alcohol, Tobacco, and Other Habits

    -
    If applicable, describe any restrictions on the intake of caffeine, alcohol, tobacco, or other restrictions.
    -
    [Caffeine, Alcohol, Tobacco, and Other Habits]
    - -

    5.5.3. Physical Activity

    -
    If applicable, describe any restrictions on activity (for example, in first-in-human trials, activity may be restricted by ensuring participants remain in bed for 4 to 6 hours after dosing).
    -
    [Physical Activity]
    - -

    5.5.4. Other Activity

    -
    If applicable, describe restrictions on any other activity (for example, blood or tissue donation); or any other activity restrictions, such as on driving, heavy machinery use, or sun exposure.
    -
    [Other Activity]
    - -

    5.6. Screen Failures

    -
    Indicate how screen failure will be handled in the trial, including conditions and criteria upon which rescreening is acceptable. If applicable, indicate the circumstances and time window under which a repeat procedure is allowed for screen failure relating to specific inclusion/exclusion criteria for the trial.
    -
    [Screen Failure]
    - -

    6. TRIAL INTERVENTION AND CONCOMITANT THERAPY

    -
    In this section, describe the trial intervention being tested and any control product being used. If multiple trial interventions are to be evaluated, Section 6.1, Description of Trial Intervention, Section 6.3, Dosing and Administration, and Section 6.5, Preparation, Handling, Storage, and Accountability should differentiate between each product.
    -
    No text is intended here (header only).
    +
    No text is intended here (heading only).
    -

    6.1. Description of Trial Intervention

    -
    Describe the intervention to be administered in each arm of the trial and for each period of the trial including route and mode of administration, dose, dosage regimen, duration of intervention, packaging, labelling, and storage co interventions (experimental, placebo, active comparator, sham comparator).
    -
    The trial intervention should be designated as an investigational medicinal product (IMP) or non-investigational medicinal product (NIMP)/auxiliary medicinal product (AxMP).
    -
    It is suggested that the trial intervention(s) be described concisely in a table.
    -
    [Table of Trial Interventions]
    -
    Indicate whether an additional product will be provided as part of the trial and its intended use (background intervention, challenge agent, rescue medication, diagnostic, or other). If use of an additional product is planned, include dosing information. Refer to approved regional labelling or describe any differences.
    -
    For drug/device combination products, include details on the configuration and use of the device and device manufacturer. A device user manual may be referenced in this section.
    -
    [Additional Text, if Needed]
    - -

    6.2. Rationale for Trial Intervention

    -
    Provide a rationale for the selection of the dose(s) or dose range, the route of administration, and dosing regimen (including starting dose, dose titration, dose interval) of the trial intervention and any control product. This rationale should include relevant results from previous preclinical studies and clinical trials that support selection of the dose and regimen. Include any information about age or sex-based pharmacokinetic or pharmacodynamic differences known from previous trials. If applicable, justify any differences in specifications, dose regimen, or therapeutic use relative to approved labelling.
    -
    Include a rationale for prospective dose adjustments incorporated in the trial, if any; for example, as a result of interim analysis.
    -
    [Rationale for Dose and Regimen]
    - -

    6.3. Dosing and Administration

    -
    Describe the detailed procedures for administration of each participant’s dose of trial intervention and control product. This may include the timing of dosing (for example, time of day, interval), the duration (for example, the length of time participants will be administered the trial intervention), the planned route of administration (for example, oral, nasal, intramuscular), and the timing of dosing relative to meals.
    -
    Include any specific instructions to trial participants about when or how to prepare and take the dose(s) and how delayed or missed doses should be handled.
    -
    For an individual participant, describe dose modifications allowed. State any minimum period required before a participant’s dose might be raised to the next higher dose or dose range. Include whether it is permissible to start and stop treatment and how dose reductions (if permitted) are to be managed.
    -
    Discussion of dose escalation or cohort expansion as part of the overall design should be covered in Section 4.2 (Rationale for Trial Design).
    -
    [Dosing and Administration]
    - -

    6.3.1. Trial Intervention Dose Modification

    -
    If applicable, the protocol should state the conditions under which a dose modification will be made for an individual participant, particularly regarding failure to respond or to toxic or untoward changes in stipulated indicators. This section can also include discussion of dose titration. Do not include information on stopping trial intervention for individual participants due to safety/other reasons as this is detailed in Section 7, Discontinuation of Trial Intervention and Participant Discontinuation/Withdrawal from the Trial.
    -
    [Dose Modification]
    - -

    6.4. Treatment of Overdose

    -
    Specify what is meant by trial intervention overdose and any known antidote or therapies. Although clinical experience with overdose is often limited in early phases of development, provide any available project-specific guidance and information; however, ensure consistency with and avoid unnecessary duplication with any overdose information in the Investigator’s Brochure /package insert. Cross-reference these documents if appropriate. Refer to the approved product label of the comparator (as applicable) for advice on overdose.
    -
    [Treatment of Overdose]
    - -

    6.5. Preparation, Handling, Storage and Accountability

    -
    No text is intended here (header only).
    - -

    6.5.1. Preparation of Trial Intervention

    -
    Describe any preparation of the trial intervention and control product and by whom. Discuss the maximum hold time once thawed/mixed, if appropriate, before administration. Include thawing, diluting, mixing, and reconstitution/preparation instructions in this section, as applicable. For drug/device combination products, include any relevant assembly or use instructions.
    -
    If the instructions are lengthy or complicated, it is acceptable to reference the label (if applicable) or include them as a separate document(s) provided to the site (for example, a pharmacy manual). If instructions are provided to the site as a separate document(s), this should be noted in here.
    -
    [Trial Intervention Preparation]
    - -

    6.5.2. Handling and Storage of Trial Intervention

    -
    Describe storage and handling requirements (for example, protection from light, temperature, humidity) for the trial intervention and control product. For trials in which multi-dose vials are utilised, provide additional information regarding stability and expiration time after initial use (for example, the seal is broken).
    -
    [Trial Intervention Storage and Handling]
    -
    State how the trial intervention and control product will be provided to the Investigator. If applicable, describe the kits, packaging, or other material of the trial intervention for blinding purposes.
    +
    +

    5.1 Description of Trial Population and Rationale

    +
    +
    Describe the population selected (e.g., healthy participants, adult participants, + paediatric participants, pregnant participants, or breastfeeding participants) and how the enrollment criteria + reflect the populations that are likely to use the drug if approved. Specify the population age range (e.g., ≤ 3 + months, ≥ 18 to ≤ 80 years old) including the timepoint at which qualification for age criteria is determined + (e.g., at time of screening vs randomisation for paediatric trials). Specify any key diagnostic criteria for the + population (e.g., “acute lung injury”, or a specific biomarker profile). If applicable, describe similar + conditions or diseases and their differential diagnosis.
    +
    Provide a rationale for the trial population ensuring that the population selected + is well defined and clinically recognisable. Describe how the selected population can meet the trial objectives + and how the enrollment criteria reflect the population of interest.
    +
    If a clinical question targets a subset of the entire trial population, such as one + defined by a particular baseline characteristic (e.g., a specific biomarker), the rationale for selecting this + subset should be provided in this section.
    +
    Justify whether the trial intervention is to be evaluated in paediatric + participants, in adults unable to consent for themselves, other vulnerable participant populations, or those that + may respond to the trial intervention differently (e.g., elderly, hepatic or renally impaired, or + immunocompromised participants).
    +
    {{ missing_description_of_trial_population_and_rationale }}
    +
    <Enter Description of Trial Population and Rationale>
    +
    Prospective approval of protocol deviations to recruitment and enrollment criteria, also known as protocol + waivers or exemptions, is not permitted.
    + + + + +
    +

    5.2 Inclusion Criteria

    +
    +
    Describe the population selected (e.g., healthy participants, adult participants, + paediatric participants, pregnant participants, or breastfeeding participants) and how the enrollment criteria + reflect the populations that are likely to use the drug if approved. Specify the population age range (e.g., ≤ 3 + months, ≥ 18 to ≤ 80 years old) including the timepoint at which qualification for age criteria is determined + (e.g., at time of screening vs randomisation for paediatric trials). Specify any key diagnostic criteria for the + population (e.g., “acute lung injury”, or a specific biomarker profile). If applicable, describe similar + conditions or diseases and their differential diagnosis.
    +
    To be eligible to participate in this trial, an individual must meet all the following criteria:
    +
    <#>
    +
    {{ missing_inclusion_criterion }}
    +
    <Enter Inclusion Criterion>
    +
    Add criteria as needed. Consider numbering the criteria sequentially.
    + +
    +

    5.3 Exclusion Criteria

    +
    +
    Exclusion criteria are characteristics that make an individual ineligible for + participation.
    +
    An individual who meets any of the following criteria will be excluded from participation in this trial: + +
    +
    <#>
    +
    {{ missing_exclusion_criterion }}
    +
    <Enter Exclusion Criterion>
    +
    Add criteria as needed. Consider numbering the criteria sequentially.
    + +
    +

    5.4 Contraception

    +
    +
    No text is intended here (heading only).
    -

    6.5.3. Accountability of Trial Intervention

    -
    Describe the method by which the accountability will be achieved, including trial intervention will be distributed and related details, including: +
    +

    5.4.1 Definitions Related to Childbearing Potential

    +
    +
    Specify the definitions of:
    +
      -
    • how and by whom the trial intervention will be distributed
      • -
    • participation of a drug repository or pharmacy, if applicable,
      • -
    • plans for disposal or return of unused product, and
      • -
    • expectations for reconciliation.
      • +
    • participant of childbearing potential
      • +
    • participant of nonchildbearing potential
    -
    [Accountability]
    - -

    6.6. Participant Assignment, Randomisation and Blinding

    -
    No text is intended here (header only).
    - -

    6.6.1. Participant Assignment

    -
    Describe the method of assigning participants to trial intervention without being so specific that blinding or randomisation might be compromised. If assignment to trial intervention is by randomisation, describe when randomisation occurs relative to screening. If participants will be assigned to intervention sequences as in a cross-over trial, then describe these sequences.
    -
    If adaptive randomisation or other methods of covariate balancing/minimisation are employed, include a cross-reference to the methods of analysis in Section 9, Statistical Considerations. As applicable, details regarding the implementation of procedures to minimise bias should be described.
    -
    [Participant Assignment]
    - -

    6.6.2. Randomisation

    -
    Describe the randomisation procedures (for example, central randomisation procedures), the method used to generate the randomisation schedule (for example, computer generated), the source of the randomisation schedule (for example, sponsor, investigator, or other), and whether or not IVRS/IWRS will be used. To maintain the integrity of the blinding, do not include the block size. Describe the use and validation of any computer systems or programmes in randomisation, stratification, and unblinding.
    -
    [Randomisation]
    +
    {{ missing_definitions_related_to_childbearing_potential }}
    +
    <Enter Definitions Related to Childbearing Potential>
    + +
    +

    5.4.2 Contraception Requirements

    +
    +
    Specify the:
    +
    +
      +
    • contraceptive methods required
      • +
    • duration of use
      • +
    +
    +
    {{ missing_contraception_requirements }}
    +
    <Enter Contraception Requirements>
    -

    6.6.3. Blinding and Unblinding

    -
    Describe efforts to ensure that the trial intervention and control products are as indistinguishable as possible. Plans for the maintenance of randomisation codes and appropriate blinding for the trial should be discussed. Procedures for planned and unplanned breaking of randomisation codes should be provided.
    -
    If the trial allows for some investigators or other designated staff to remain unblinded (for example, to allow them to adjust medication), the means of maintaining the blinding for other investigators or staff should be explained. Measures to prevent unblinding by laboratory measurements, if used, should be described.
    -
    [Blinding and Unblinding]
    -
    Emergency Unblinding
    -
    Describe the criteria for breaking the trial blind or participant code. Discuss the circumstances in which the blinding would be broken for an individual or for all participants (for example, for SAEs) and who has responsibility. Include the procedure for emergency unblinding such as via IVRS/IWRS or code envelopes as well as documentation of unblinding. Indicate to whom the intentional and unintentional unblinding should be reported.
    -
    [Emergency Unblinding]
    +
    +

    5.5 Lifestyle Restrictions

    +
    +
    In the following subsections, describe any restrictions during the trial pertaining + to lifestyle and/or diet, intake of caffeine, alcohol, or tobacco, or physical and other activities. If not + applicable, include a statement that no restrictions are required.
    +
    {{ missing_exclusion_criterion }}
    +
    {<Enter Lifestyle Restrictions>}
    + +
    +

    5.5.1 Meals and Dietary Restrictions

    +
    +
    If applicable, describe any restrictions on diet (e.g., food and drink restrictions, + timing of meals relative to dosing, etc.).
    +
    {{ missing_meals_and_dietary_restrictions }}
    +
    <Enter Meals and Dietary Restrictions>
    + +
    +

    5.5.2 Caffeine, Alcohol, Tobacco, and Other Restrictions

    +
    +
    If applicable, describe any restrictions on the intake of caffeine, alcohol, + tobacco, or other restrictions.
    +
    {{ missing_caffeine_alcohol_tobacco_and_other_restrictions }}
    +
    <Enter Caffeine, Alcohol, Tobacco, and Other Restrictions>
    + +
    +

    5.5.3 Physical Activity Restrictions

    +
    +
    If applicable, describe any restrictions on physical activity (e.g., participants + may be required to remain in bed for 4 to 6 hours after dosing).
    +
    {{ missing_physical_activity_restrictions }}
    +
    <Enter Physical Activity Restrictions>
    + +
    +

    5.5.4 Other Activity Restrictions

    +
    +
    If applicable, describe restrictions on any other activity (e.g., blood or tissue + donation, driving, heavy machinery use, or sun exposure).
    +
    {{ missing_other_activity_restrictions }}
    +
    <Enter Other Activity Restrictions>
    + +
    +

    5.6 Screen Failure and Rescreening

    +
    +
    Describe screen failure and indicate how screen failure will be handled in the + trial, including conditions and criteria under which rescreening is acceptable. If applicable, indicate the + circumstances and time window under which a repeat procedure is allowed for screen failure relating to specific + inclusion/exclusion criteria for the trial.
    +
    {{ missing_screen_failure }}
    +
    <Enter Screen Failure>
    +
    {{ missing_rescreening }}
    +
    <Enter Rescreening>
    + +
    +

    6 TRIAL INTERVENTION AND CONCOMITANT THERAPY

    +
    +
    Trial interventions are all pre-specified investigational and noninvestigational + medicinal products, medical devices or other interventions intended for the participants during the trial. The + investigational trial intervention is the product(s) used in the trial as part of trial objectives, including + control(s) (e.g., active comparator, placebo). Description of the investigational trial intervention is provided + in Section 6.1 Description of Investigational Trial Intervention. Other trial interventions that are not part of + trial objectives or do not have an investigational role in this trial are described in Section 6.9 Description of + Noninvestigational Trial Intervention.
    +
    Any regional requirements should be noted in the appropriate subsections.
    +
    Provide an overview of investigational and noninvestigational trial interventions. + Designate the trial intervention as IMP or NIMP/AxMP based on trial design and regional requirements. Consider the + optional table below.
    +
    {{ missing_description_of_the_overview_of_trial_interventions_or_a_heading_for_the_optional_table }}
    +
    <Enter description of the overview of trial interventions or a heading + for the optional table>
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Arm Name Arm Type Intervention Name Intervention Type Pharmaceutical Dose Form Dosage Strength(s) Dosage Level(s) Route of Administration Regimen/Treatment Period/Vaccination Regimen Use IMP/NIMP Sourcing
    {{ missing_arm_name }} +
    <Enter Arm Name>
    +     		{{ missing_arm_type }} +
    [Select Arm Type]
    +     		{{ missing_intervention_name }}
    <Enter Intervention Name> + +
    +     		{{ missing_intervention_type }}
    [Select Intervention Type] + +
    +     		{{ missing_arm_name }}
    [Select Pharmaceutical Dose Form]
    +     		{{ missing_dosage_strengths }}
    <Enter Dosage Strength(s)> + +
    +     		{{ missing_dosage_levels }}
    <Enter Dosage Level(s)> + +
    +     		{{ missing_route_of_administation }}
    [Select Route of + Administration]
    +     		{{ missing_regimen_treatment_period_vaccination_regimen }}
    + <Enter Regimen/Treatment Period/Vaccination Regimen>
    +     		{{ missing_use }}
    [Select Use]
    +     		{{ missing_imp_nimp }}
    [Select IMP or NIMP] +
    +     		{{ missing_sourcing }}
    [Select Sourcing] +
    +
    +
    IMP=Investigational Medicinal Product; NIMP=Non Investigational/Auxilliary Medicinal + Product
    -

    6.7. Trial Intervention Compliance

    -
    Describe measures employed to ensure and document dosing information and trial intervention compliance (for example, accountability records, diary cards, or concentration measurements). Include a discussion of what documents are mandatory to complete (for example, participant drug log) and what source data/records will be used to document trial intervention compliance.
    -
    [Additional Trial Intervention Compliance]
    +
    +

    6.1 Description of Investigational Trial Intervention

    +
    +
    Describe the investigational trial intervention to be administered in each arm of + the trial and for each period of the trial including route and mode of administration, dose, dosage regimen, + duration of intervention, use, packaging and labelling. Refer to approved regional labelling, as appropriate. For + investigational drug/device combination products, include details on the configuration and use of the device and + device manufacturer. A device user manual may be referenced in this section.
    +
    {{ missing_description_of_investigational_trial_intervention }}
    +
    <Enter Description of Investigational Trial Intervention>
    + +
    +

    6.2 Rationale for Investigational Trial Intervention Dose and Regimen

    +
    +
    Provide a rationale for the selection of the dose(s) or dose range, pharmaceutical + dose form, route of administration, and dosing regimen of the investigational trial interventions, as applicable. + This rationale should include relevant results from nonclinical studies and clinical trials that support selection + of the dose and regimen. Discuss impact of differences in trial population characteristics (e.g., age, sex, race) + that could lead to differences in pharmacokinetics and pharmacodynamics in this trial as compared to previous + trials. If applicable, justify any differences in dose regimen or therapeutic use relative to approved labelling. + Describe prior trials and other information that support the dose and/or dose regimen of the investigational trial + intervention.
    +
    Include a rationale for prospective dose adjustments incorporated in the trial, if + any.
    +
    {{ missing_rationale_for_investigational_trial_intervention_dose_and_regimen }}
    +
    <Enter Rationale for Investigational Trial Intervention Dose and Regimen>
    + +
    +

    6.3 Investigational Trial Intervention Administration

    +
    +
    Describe the detailed procedures for administration of each participant’s dose of + each investigational trial intervention. This may include the timing of dosing (e.g., time of day, interval), the + duration (e.g., the length of time participants will be administered the investigational trial intervention), and + the timing of dosing relative to meals.
    +
    Include any specific instructions on who, when or how to prepare and take the + dose(s) and how to handle any delayed or missed doses.
    +
    Dose escalation or cohort expansion as part of the overall design should be covered + in Section 4.1 Description of Trial Design.
    +
    {{ missing_investigational_trial_intervention_administration }}
    +
    <Enter Investigational Trial Intervention Administration>
    + +
    +

    6.4 Investigational Trial Intervention Dose Modification

    +
    +
    For each participant, describe any dose modifications allowed, including conditions + for such dose modifications, particularly regarding failure to respond or safety concerns. State any minimum + period required before a participant’s dose might be raised to the next higher dose or dose range. Include whether + it is permissible to start and stop treatment and how dose reductions (if permitted) are to be managed.
    +
    Information on stopping investigational trial intervention for participants due to + safety/other reasons should be described in Section 7 Participant Discontinuation of Trial Intervention and + Discontinuation or Withdrawal from Trial.
    +
    {{ missing_investigational_trial_intervention_dose_modification }}
    +
    <Enter Investigational Trial Intervention Dose Modification>
    + +
    +

    6.5 Management of Investigational Trial Intervention Overdose

    +
    +
    Describe what is meant by investigational trial intervention overdose. Provide any + available information on managing overdose and ensure it is consistent with the Investigator’s Brochure or product + labelling. Cross reference these documents as applicable.
    +
    {{ missing_investigational_trial_intervention_overdose }}
    +
    <Enter Management of Investigational Trial Intervention Overdose>
    + +
    +

    6.6 Preparation, Storage, Handling and Accountability of Investigational Trial Intervention

    +
    +
    No text is intended here (heading only).
    -

    6.8. Concomitant Therapy

    -
    This section should be consistent with the medication restrictions in the inclusion/exclusion criteria previously listed. Describe the concomitant medications, supplements, complementary and alternative therapies, treatments, and/or procedures which are allowed or prohibited during the trial, and include details about when the information will be collected (for example, screening, all visits).
    -
    [Concomitant Therapy]
    +
    +

    6.6.1 Preparation of Investigational Trial Intervention

    +
    +
    Describe any preparation of the investigational trial intervention, and when + necessary, who should prepare it. When applicable, describe the maximum hold time once thawed/mixed before + administration. Include thawing, diluting, mixing, and reconstitution/preparation instructions. For drug/device + combination products, include any relevant assembly or use instructions and reference the package insert that is + provided separately.
    +
    If the instructions are lengthy or complicated, it is acceptable to reference the + package insert (if applicable) or include instructions in separate documents provided to the site (e.g., a + pharmacy manual) and reference the separate documents.
    +
    {{ missing_preparation_of_investigational_trial_intervention }}
    +
    <Enter Preparation of Investigational Trial Intervention>
    + +
    +

    6.6.2 Storage and Handling of Investigational Trial Intervention

    +
    +
    Describe storage and handling requirements (e.g., protection from light, + temperature, humidity) for the investigational trial intervention(s). For trials in which multidose vials are + utilised, provide additional information regarding stability and expiration time after initial use (e.g., if the + seal is broken).
    +
    Explain how the investigational trial intervention will be provided to the + investigator. If applicable, include details about kits, packaging, or other material of the investigational trial + intervention for blinding purposes.
    +
    If the instructions are lengthy or complicated, it is acceptable to reference the + package insert (if applicable) or include instructions in separate documents provided to the site (e.g., a + pharmacy manual) and reference the separate documents.
    +
    {{ missing_storage_and_handling_of_investigational_trial_intervention }}
    +
    <Enter Storage and Handling of Investigational Trial Intervention>
    + +
    +

    6.6.3 Accountability of Investigational Trial Intervention

    +
    +
    Describe the accountability method, including:
    +
    +
      +
    • how the investigational trial intervention will be distributed
      • +
    • who will distribute the investigational trial intervention
      • +
    • participation of a drug storage repository or pharmacy, if applicable
      • +
    • plans for disposal or return of unused product
      • +
    • plans for reconciliation of investigational trial intervention, if applicable
      • +
    +
    +
    {{ missing_accountability_of_investigational_trial_intervention }}
    +
    <Enter Accountability of Investigational Trial Intervention>
    + +
    +

    6.7 Investigational Trial Intervention Assignment, Randomisation and Blinding

    +
    +
    No text is intended here (heading only).
    -

    6.8.1. Prohibited Concomitant Therapy

    +
    +

    6.7.1 Participant Assignment to Investigational Trial Intervention

    +
    +
    State that at enrollment, participant identification codes should be assigned. + Describe the method of assigning participants to investigational trial intervention without being so specific that + blinding or randomisation might be compromised. If assignment to investigational trial intervention is by + randomisation, describe when randomisation will occur relative to screening.
    +
    IIf permuted block randomisation is employed, do not state the block size in the + protocol. If adaptive randomisation or other methods of covariate balancing/minimisation are employed, include a + cross reference to the methods of analysis in Section 10 Statistical Considerations. As applicable, details + regarding the implementation of procedures to minimise bias should be described.
    +
    {{ missing_participant_assignment_to_investigational_trial_intervention }}
    +
    <Enter Participant Assignment to Investigational Trial Intervention>
    + +
    +

    6.7.2 {Randomisation}

    +
    +
    Describe the randomisation procedures (e.g., central randomisation procedures), the + method used to generate the randomisation schedule (e.g., computer generated), the source of the randomisation + schedule (e.g., sponsor, investigator, or other), and whether IRT(s) will be used. To maintain the integrity of + the blinding, do not include the block size.
    +
    {{ missing_randomisation }}
    +
    {<Enter Randomisation>}
    + +
    +

    6.7.3 {Measures to Maintain Blinding}

    +
    +
    Describe measures that will be used to maintain blinding:
    +
    +
      +
    • The investigational trial interventions are as indistinguishable as possible
      • +
    • Plans for the maintenance of randomisation codes and appropriate blinding for the trial
      • +
    • Procedures for planned (e.g., interim analysis) and unintentional (e.g., breach of procedure) breaking of + randomisation codes
      • +
    +
    +
    For unplanned but intentional actions (e.g., safety events), refer to Section 6.7.4 + Emergency Unblinding at the Site.
    +
    If the trial allows for some investigators or other designated staff to remain + unblinded (e.g., to allow them to adjust investigational trial intervention), the means of maintaining the + blinding for other investigators or staff should be explained. Measures to prevent unblinding by laboratory + measurements or while performing study assessments, if used, should be described.
    +
    {{ missing_measures_to_maintain_blinding }}
    +
    {<Enter Measures to Maintain Blinding>}
    + +
    +

    6.7.4 {Emergency Unblinding at the Site}

    +
    +
    Describe the criteria for breaking the trial blind or participant code. Describe the + circumstances that would require breaking the blind, either for an individual participant or for all participants, + and specify who will be responsible for this decision. Include the procedure for emergency unblinding as well as + documentation of unblinding. Indicate to whom the intentional and unplanned unblinding should be reported.
    +
    {{ missing_emergency_unblinding_at_the_site }}
    +
    {<Enter Emergency Unblinding at the Site>}
    + +
    +

    6.8 Investigational Trial Intervention Adherence

    +
    +
    Describe the measures to monitor and document participants’ adherence to + investigational trial intervention (e.g., trial intervention accountability records, paper or electronic diaries, + or investigational trial intervention concentration measurements).
    +
    List what documents are mandatory to complete (e.g., participant drug log) and + identify which records will be used as the source records for documenting investigational trial intervention + adherence.
    +
    {{ missing_investigational_trial_intervention_adherence }}
    +
    <Enter Investigational Trial Intervention Adherence>
    + +
    +

    6.9 Description of Noninvestigational Trial Intervention

    +
    +
    As stated in Section 6 Trial Intervention and Concomitant Therapy, + noninvestigational interventions are pre-specified products used in the trial but are not part of trial objectives + and hence, are not investigational trial interventions.
    +
    {{ missing_description_of_noninvestigational_trial_intervention }}
    +
    <Enter Description of Noninvestigational Trial Intervention>
    + +
    +

    6.9.1 {Background Trial Intervention}

    +
    +
    Describe any background intervention(s), including administration and any conditions + for use.
    +
    {{ missing_background_trial_intervention }}
    +
    {<Enter Background Trial Intervention>}
    + +
    +

    6.9.2 {Rescue Therapy}

    +
    +
    List all permitted rescue medications, treatments, and/or procedures, including any + relevant instructions on administration and any conditions of use.
    +
    If administration of rescue therapy leads to the temporary or permanent + discontinuation of trial intervention, refer to Section 7 Participant Discontinuation of Trial Intervention and + Discontinuation or Withdrawal from Trial.
    +
    {{ missing_rescue_therapy }}
    +
    {<Enter Rescue Therapy>}
    + +
    +

    6.9.3 {Other Noninvestigational Trial Intervention}

    +
    +
    List all permitted rescue medications, treatments, and/or procedures, including any + relevant instructions on administration and any conditions of use.
    +
    If administration of rescue therapy leads to the temporary or permanent + discontinuation of trial intervention, refer to Section 7 Participant Discontinuation of Trial Intervention and + Discontinuation or Withdrawal from Trial.
    +
    {{ missing_other_noninvestigational_trial_intervention }}
    +
    {<Enter Other Noninvestigational Trial Intervention>}
    + +
    +

    6.10 Concomitant Therapy

    +
    +
    Specify the concomitant medications, supplements, complementary and alternative + therapies, treatments, and/or procedures that are prohibited or permitted during the trial and include details + about when the information will be collected (e.g., during screening, at each visit).
    +
    When appropriate to separate the content, the below subheadings may be used.
    +
    {{ missing_concomitant_therapy }}
    +
    <Enter Concomitant Therapy>
    + +
    +

    6.10.1 {Prohibited Concomitant Therapy}

    +
    If applicable, describe any prohibited concomitant therapy.
    -
    [Prohibited Concomitant Therapy]
    +
    {{ missing_prohibited_concomitant_therapy }}
    +
    {<Enter Prohibited Concomitant Therapy>}
    -

    6.8.2. Permitted Concomitant Therapy

    +
    +

    6.10.2 {Permitted Concomitant Therapy}

    +
    If applicable, describe any permitted concomitant therapy.
    -
    [Permitted Concomitant Therapy]
    - -

    6.8.3. Rescue Therapy

    -
    List all medications, treatments, and/or procedures which may be provided during the trial for rescue therapy and provide relevant instructions about the administration of rescue medications. Describe the circumstances under which use of rescue therapy is permitted.
    -
    If administration of rescue therapy leads to the temporary discontinuation of trial intervention or a participant’s withdrawal from the trial, refer to Section 7, Discontinuation of Trial Intervention and Participant Discontinuation/Withdrawal from the Trial.
    -
    [Rescue Therapy]
    - -

    6.8.4. Other Therapy

    -
    If applicable, describe the use of other non-investigational or auxiliary therapy, for example, challenge agents.
    -
    [Other Therapy]
    - -

    7. DISCONTINUATION OF TRIAL INTERVENTION AND PARTICIPANT WITHDRAWAL FROM TRIAL

    -
    This section must align with the intercurrent events introduced in Section 3, Trial Objectives, Endpoints, and Estimands, and the treatment described in Section 6 Trial Intervention and Concomitant Therapy.
    -
    No text is intended here (header only).
    - -

    7.1. Discontinuation of Trial Intervention

    -
    Discontinuation of trial intervention for a participant occurs when trial intervention is stopped earlier than the protocol planned duration.
    - -

    7.1.1. Criteria for Permanent Discontinuation of Trial Intervention

    -
    Describe the criteria for discontinuation of a participant from trial intervention, carefully evaluating which are appropriate for the participant population and therapy being studied.
    -
    Specify whether participants who discontinue trial intervention can or cannot continue the trial (continue trial visits). Refer to the SoA for assessments to be performed at the time of and following discontinuation of trial intervention.
    -
    [Criteria for Permanent Discontinuation of Trial Intervention]
    +
    {{ missing_permitted_concomitant_therapy }}
    +
    {<Enter Permitted Concomitant Therapy>}
    + +
    +

    7 PARTICIPANT DISCONTINUATION OF TRIAL INTERVENTION AND DISCONTINUATION OR WITHDRAWAL FROM TRIAL

    +
    +
    This section must align with the intercurrent events and their handling strategies + introduced in Section 3 Trial Objectives and Associated Estimands, and with the investigational trial intervention + described in Section 6 Trial Intervention and Concomitant Therapy.
    +
    No text is intended here (heading only).
    + +
    +

    7.1 Discontinuation of Trial Intervention for Individual Participants

    +
    +
    No text is intended here (heading only).
    -

    7.1.2. Temporary Discontinuation or Interruption of Trial Intervention

    -
    Describe +
    +

    7.1.1 Permanent Discontinuation of Trial Intervention

    +
    +
    Describe:
    +
      -
    • the criteria for temporary discontinuation or interruption of trial intervention for an individual participant
      • -
    • what to do and which restrictions still apply if the participant needs to temporarily discontinue or interrupt trial intervention
      • -
    • whether they will continue in the trial, and
      • -
    • whether all, or specify which, assessments will be performed for the stated duration of the trial.
      • +
    • the criteria for discontinuation of a participant from any trial intervention, carefully evaluating which + are appropriate for the trial population and therapy being studied
      • +
    • how participants who discontinue trial intervention will be followed after discontinuation. Depending on the + chosen intercurrent event handling strategy, it will be important to continue to follow and ascertain outcomes + in participants who discontinue trial intervention through the end of the trial to prevent missing data in + important analyses. Refer to Section 1.3 Schedule of Activities for assessments to be performed at the time of + and following discontinuation of trial intervention
      • +
    • the process for collecting and recording the detailed reasons for discontinuing trial intervention if not + described elsewhere
    -
    Details of any rechallenge or restart after a safety-related event should be included in Section 7.1.3, Rechallenge.
    -
    [Temporary Discontinuation/Interruption of Trial Intervention]
    - -

    7.1.3. Rechallenge

    -
    Describe the criteria for rechallenge/restarting trial intervention, how to perform rechallenge, number of rechallenges allowed during the trial, and whether all, or specify which, assessments will be performed for the stated duration of the trial.
    -
    If rechallenge is not allowed, state this.
    -
    [Rechallenge]
    - -

    7.2. Participant Withdrawal from the Trial

    -
    Describe the criteria for participant withdrawal from the trial.
    -
    [Participant Withdrawal from Trial]
    - -

    7.3. Lost to Follow-Up

    -
    Describe how the trial will define and address participants who are lost to follow-up to help limit the amount and impact of missing data. Describe the nature and duration of follow-up, as appropriate.
    -
    [Lost to Follow-Up]
    - -

    7.4. Trial Stopping Rules

    -
    If applicable, describe any trial-specific stopping rules, including guidance on when the trial should be stopped for safety reasons, when a cohort or dose escalation should be terminated, and/or when a given treatment arm should be terminated.
    -
    [Trial Stopping Rules]
    - -

    8. TRIAL ASSESSMENTS AND PROCEDURES

    +
    {{ missing_permanent_discontinuation_of_trial_intervention }}
    +
    <Enter Permanent Discontinuation of Trial Intervention>
    + +
    +

    7.1.2 Temporary Discontinuation of Trial Intervention

    +
    +
    Describe:
      -
    • Describe the assessments and procedures required during each phase of the trial that are relevant to the stated endpoints. Provide details that are not already presented in the SoA, taking care not to duplicate information.
      • -
    • Describe methods, training, tools, instruments/questionnaires, calibration methods, etc. that will be used to record and assess data and ensure consistency across centres and participants. Include instructions on timing/conditions of assessments and if a specifically qualified person should be performing these assessments. Describe whether centralised readings and measurements will be utilised. Describe procedures to be used to maintain the blind.
      • +
    • the criteria for temporary discontinuation or interruption of trial intervention for an individual + participant
      • +
    • what to do and which restrictions still apply if the participant has to temporarily discontinue or interrupt + trial intervention
      • +
    • which assessments will be performed for the stated duration of the trial
      • +
    +
    +
    Details of any rechallenge or restart after temporary discontinuation of trial + intervention due to a safety-related event should be included in Section 7.1.3 Rechallenge.
    +
    {{ missing_temporary_discontinuation_of_trial_intervention }}
    +
    <Enter Temporary Discontinuation of Trial Intervention>
    + +
    +

    7.1.3 Rechallenge

    +
    +
    Describe the criteria for rechallenge/restarting trial intervention, how and when to + perform rechallenge, the number of rechallenges allowed during the trial, and whether all, or specify which, + assessments will be performed for the stated duration of the trial.
    +
    If rechallenge is not allowed, state this.
    +
    {{ missing_rechallenge }}
    +
    <Enter Rechallenge>
    + +
    +

    7.2 Participant Discontinuation or Withdrawal from the Trial

    +
    +
    Describe the criteria for participant discontinuation or withdrawal from the trial. +
    +
    Describe the reason for withdrawal and the type of data to be collected for the + final assessments with reference to the schedule of activities for the participant’s end of study visit unless + provided in another section.
    +
    In many cases, the only reason for a participant being considered withdrawn from the + trial should be a participant’s withdrawal of consent to continue to participate in the trial. All other + participants, including those who discontinue trial intervention, should remain in the trial and continue to be + followed to prevent missing data in important analyses. Refer to Section 10 Statistical Considerations for the + data that must be collected for the trial estimands.
    +
    {{ missing_participant_discontinuation_or_withdrawal_from_trial }}
    +
    <Enter Participant Discontinuation or Withdrawal from Trial>
    + +
    +

    7.3 Management of Loss to Follow-Up

    +
    +
    Describe how the trial will define how participants are lost to follow-up. In + general, participants should be considered lost to follow-up only if they cannot be reached despite multiple + attempts to contact them. Also describe approaches that will be used to minimise loss to follow-up, such as + multiple, diverse methods to remain in contact with participants (e.g., telephone calls, texts, and emails to the + participant) and how contacts will be recorded.
    +
    {{ missing_management_of_loss_to_follow_up }}
    +
    <Enter Management of Loss to Follow-Up>
    + +
    +

    8 TRIAL ASSESSMENTS AND PROCEDURES

    +
    +
    In this section: +
      +
    • Describe the assessments and procedures required during each phase of the trial that are relevant to the + stated endpoints and related intercurrent events (e.g., surgery or use of rescue therapy). Provide details + that are not already presented in the SoA, taking care not to duplicate information.
      • +
    • Ensure alignment with every other section of the protocol. In particular, this section must align with:
      • +
        +
      • the intercurrent events and associated strategies for handling them described in Section 3 Trial + Objectives and Associated Estimands
        • +
      • the intercurrent events and associated strategies for handling them described in Section 3 Trial + Objectives and Associated Estimands
        • +
      • trial intervention and therapies outlined in Section 6 Trial Intervention and Concomitant Therapy
        • +
      • discontinuation and withdrawal procedures in Section 7 Participant Discontinuation of Trial Intervention + and Discontinuation or Withdrawal From Trial
        • +
      • the statistical analysis that is defined in Section 10 Statistical Considerations
        • +
    • Reference the literature for the validation of scales/instruments/questionnaires/assays.
      • -
    • Instructions or protocols for specialised tests may be presented in an appendix or a separate document and cross-referenced.
      • -
    • If the trial includes qualitative interviews, describe these evaluations
      • -
    • If COA measures are utilised, include instructions for the investigators per local guidance. All COA parameters should be fully integrated into the appropriate sections of the protocol; separate COA sections should not be created in the protocol.
      • -
    • Include minimums and limits for procedures (for example, volume of blood draws, number of imaging procedures/biopsies, radiation exposure, etc.) if appropriate to the trial.
      • +
    • Instructions or protocols for specialised tests and scales/instruments/questionnaires/assays may be + presented in an appendix or a separate document and cross referenced.
      • +
    • If the trial includes qualitative interviews, describe these evaluations.
      • +
    • Include minimums and limits for procedures (e.g., number of imaging procedures/biopsies, radiation exposure, + etc.) if appropriate to the trial.
    +
    No text is intended here (heading only).
    -

    8.1. Screening/Baseline Assessments and Procedures

    -
    Describe any assessments and procedures that are unique to screening/baseline (for example, collection of data on participant characteristics, assessments/procedures performed for the purpose of determining eligibility or for stratification) in this section.
    -
    [Screening/Baseline Assessments and Procedures]
    - -

    8.2. Efficacy Assessments and Procedures

    -
    Describe efficacy assessments and procedures in this section.
    -
    [Efficacy Assessments and Procedures]
    +
    +

    8.1 Trial Assessments and Procedures Considerations

    +
    +
    Describe general considerations applicable across trial assessments and procedures. +
    +
    {{ missing_trial_assessments_and_procedures_considerations }}
    +
    <Enter Trial Assessments and Procedures Considerations>
    + +
    +

    8.2 Screening/Baseline Assessments and Procedures

    +
    +
    Describe any assessments and procedures that are unique to screening/baseline (e.g., + collection of data on participant characteristics, assessments/procedures performed for the purpose of determining + eligibility or for stratification) in this section. Describe screening and baseline assessments and procedures + separately when screening and baseline are different or performed at different visits.
    +
    {{ missing_screening_assessments_and_procedures }}
    +
    <Screening Assessments and Procedures> +
    +
    {{ missing_baseline_assessments_and_procedures }}
    +
    {<Baseline Assessments and Procedures>} +
    -

    8.3. Safety Assessments and Procedures

    -
    Describe safety assessments and procedures in this section. Level 3 headings can be added as needed. +
    +

    8.3 Efficacy Assessments and Procedures

    +
    +
    Describe efficacy assessments and procedures in this section. Cross reference + Section 8.7 Immunogenicity Assessments if immunogenicity assessments are used in efficacy determination.
    +
    {{ missing_efficacy_assessments_and_procedures }}
    +
    <Efficacy Assessments and Procedures>
    + +
    +

    8.4 Safety Assessments and Procedures

    +
    +
    Describe safety assessments and procedures utilising the following subsections as + applicable. Add level 3 headings as needed.
      -
    • Identify any non-investigator party responsible for evaluation of laboratory or other safety assessments (for example, Sponsor or external Independent Data Monitoring Committee).
      • -
    • Include guidelines for the management of relevant laboratory or other safety assessment abnormalities.
      • +
    • Identify any noninvestigator party involved in the evaluation of laboratory or other safety assessments + (e.g., sponsor or external Independent Data Monitoring Committee; cross reference Section 11.4 Committees for + details as applicable).
      • +
    • Include guidelines for the medical management of relevant laboratory or other safety assessment + abnormalities.
    -
    [Safety Assessments and Procedures]
    - -

    8.3.1. Physical Examination

    -
    Include any specific instructions for the collection and interpretation of physical examinations.
    -
    [Physical Examination]
    +
    {{ missing_safety_assessments_and_procedures }}
    +
    <Safety Assessments and Procedures>
    -

    8.3.2. Vital Signs

    -
    Include any specific instructions for the collection and interpretation of vital signs.
    -
    [Vital Signs]
    - -

    8.3.3. Electrocardiograms

    -
    Include any specific instructions for the collection, interpretation, and archiving of ECGs.
    -
    [Electrocardiograms]
    +
    +

    8.4.1 {Physical Examination}

    +
    +
    Include any specific instructions for the collection and interpretation of physical + examinations.
    +
    {{ missing_physical_examination }}
    +
    {<Enter Physical Examination>}
    + +
    +

    8.4.2 {Vital Signs}

    +
    +
    Include any specific instructions for the collection and interpretation of vital + signs.
    +
    {{ missing_vital_signs }}
    +
    {<Enter Vital Signs>}
    + +
    +

    8.4.3 {Electrocardiograms}

    +
    +
    Include any specific instructions for the collection, interpretation, and archiving + of ECGs.
    +
    {{ missing_electrocardiograms }}
    +
    {<Enter Electrocardiograms>}
    + +
    +

    8.4.4 {Clinical Laboratory Assessments}

    +
    +
    Describe any specific instructions for the collection and interpretation of clinical + laboratory assessments, including: +
      +
    • type of laboratory (central/local/hybrid)
      • +
    • acceptability of additional tests deemed necessary by the investigator or local regulations
      • +
    • instructions for situations in which central laboratory results are not available in time for trial + intervention and/or response evaluation, or in the event of a severe disruption (e.g., a pandemic or natural + disaster)
      • +
    • treatment algorithms for results out of normal range
      • +
    • cross reference Section 12.1 Clinical Laboratory Tests for laboratory assessment panels
      • +
    +
    +
    {{ missing_clinical_laboratory_assessments }}
    +
    {<Enter Clinical Laboratory Assessments>}
    -

    8.3.4. Clinical Laboratory Assessments

    -
    Include any specific instructions for the collection and interpretation of clinical laboratory assessments. +
    +

    8.4.5 {Pregnancy Testing}

    +
    +
    Include any specific instructions for the collection and interpretation of pregnancy + testing.
    +
    {{ missing_pregnancy_testing }}
    +
    {<Enter Pregnancy Testing>}
    + +
    +

    8.4.6 {Suicidal Ideation and Behaviour Risk Monitoring}

    +
    +
    If the trial meets any of the criteria requiring suicidal ideation and behaviour + risk monitoring by the guidance/guideline in each region, include justification for the need for suicidal ideation + and behaviour risk monitoring in the study and add any specific instructions for the collection and interpretation + of the assessment. In case this is an AESI in the study, justification should also be provided in Section 9.2.4 + Adverse Events of Special Interest.
    +
    {{ missing_suicidal_ideation_and_behaviour_risk_monitoring }}
    +
    {<Enter Suicidal Ideation and Behaviour Risk Monitoring>}
    + +
    +

    8.5 Pharmacokinetics

    +
    +
    Include any specific instructions for the collection and assay of samples and + interpretation of PK assessments.
      -
    • Specify if and when the use of local laboratories is allowed.
      • -
    • Specify which laboratory parameters should be included in each panel (for example, for haematology, chemistry, urinalysis).
      • +
    • Describe the biological samples collected, the handling of samples, and the assay method.
      • +
        +
      • Specific sample collection and processing instructions can be described in an appendix or a separate + document and cross referenced.
        • +
      +
    • Describe the retention time for the samples (ensuring alignment with the ICF).
      • +
    • Indicate the types of analyses for each sample.
      • +
    • Define the PK parameters to be calculated and the calculation methods.
    -
    [Clinical Safety Laboratory Assessments]
    +
    {{ missing_pharmacokinetics }}
    +
    <Safety Pharmacokinetics>
    -

    8.3.5. Suicidal Ideation and Behaviour Risk Monitoring

    -
    If the trial meets any of the criteria requiring suicidal ideation and behaviour risk monitoring by the guidance/guideline in each region, include any specific instructions for the collection and interpretation of the assessment
    -
    [Suicidal Ideation and Behaviour Risk Monitoring]
    +
    +

    8.6 Biomarkers

    +
    +
    Include any specific instructions for the collection of samples and interpretation + of biomarkers in the subsections below as applicable. Safety biomarkers should be included in Section 8.4 Safety + Assessments and Procedures, and immunogenicity biomarkers should be included in Section 8.7 Immunogenicity + Assessments.
    +
    No text is intended here (heading only).
    + +
    +

    8.6.1 Genetics, Genomics, Pharmacogenetics, and Pharmacogenomics

    +
    +
    Include any specific instructions for the collection and assay of samples for + genetic, genomics, pharmacogenetics and/or pharmacogenomic analysis. +
      +
    • Describe the biological samples that will be collected (e.g., tissue, serum, plasma), handling of samples, + and the assay method.
      • +
        +
      • Specific sample collection and processing instructions can be described in an appendix or a separate + document and cross referenced.
        • +
      +
    • Describe the retention time for the samples (ensuring alignment with the ICF).
      • +
    • Indicate the types of analyses that may be studied for each sample.
      • +
    +
    +
    {{ missing_genetics_genomics_pharmacogenetics_and_pharmacogenomics }}
    +
    <Enter Genetics, Genomics, Pharmacogenetics and Pharmacogenomics>
    + +
    +

    8.6.2 Pharmacodynamic Biomarkers

    +
    +
    Include any specific instructions for the collection of samples and assessment of + pharmacodynamic biomarkers. +
      +
    • Describe the biological samples that will be collected (e.g., tissue, serum, plasma).
      • +
        +
      • Specific sample collection and processing instructions can be described in an appendix or a separate + document and cross referenced.
        • +
      +
    • Describe the retention time for the samples (ensuring alignment with the ICF).
      • +
    • Indicate the types of biomarkers that will be studied for each sample.
      • +
    • Specify whether each sample is optional or required. Required samples must be based on a protocol objective. +
      • +
    +
    +
    {{ missing_pharmacodynamix_biomarkers }}
    +
    <Enter Pharmacodynamic Biomarkers>
    -

    8.4. Adverse Events and Serious Adverse Events

    -
    No text is intended here (header only).
    +
    +

    8.6.3 {Other Biomarkers}

    +
    +
    Include any specific instructions for the collection of samples and assessment of + other biomarkers. +
      +
    • Describe the biological samples that will be collected (e.g., tissue, serum, plasma).
      • +
        +
      • Specific sample collection and processing instructions can be described in an appendix or a separate + document and cross referenced.
        • +
      +
    • Describe the retention time for the samples (ensuring alignment with the ICF).
      • +
    • Indicate the types of biomarkers that will be studied for each sample.
      • +
    • Specify whether each sample is optional or required. Required samples must be based on a protocol objective. +
      • +
    +
    +
    {{ missing_other_biomarkers }}
    +
    {<Enter Other Biomarkers>}
    -

    8.4.1. Definitions of AE and SAE

    -
    Specify the AE and SAE definitions.
    -
    [AE definition]
    -
    [SAE definition]
    -
    Additional details and clarifications for AEs and SAEs are in Appendices 12.1 and 12.2.
    +
    +

    8.7 Immunogenicity Assessments

    +
    +
    Include any specific instructions for the collection of samples and interpretation + of immunogenicity. If immunogenicity assessments are included within Section 8.3 Efficacy Assessments and + Procedures or Section 8.4 Safety Assessments and Procedures, cross reference that section. +
      +
    • Describe the biological samples that will be collected (e.g., tissue, serum, plasma).
      • +
        +
      • Specific sample collection and processing instructions can be described in an appendix or a separate + document and cross referenced.
        • +
      +
    • Describe the retention time for the samples (ensuring alignment with the ICF).
      • +
    • Indicate the types of biomarkers that will be studied for each sample.
      • +
    • Specify whether each sample is optional or required. Required samples must be based on a protocol objective. +
      • +
    +
    +
    {{ missing_immunogenicity_assessments }}
    +
    <Enter Immunogenicity Assessments>
    + +
    +

    8.8 Medical Resource Utilisation and Health Economics

    +
    +
    This section does not apply to COAs. Include this section only for any value + evidence and outcomes assessments not included in either the efficacy or safety sections.
    +
    Describe the health outcome measures, collection method (e.g., diary, physician + interview), and participant burden.
    +
    {{ missing_medical_resource_utilisation_and_health_economics }}
    +
    <Enter Medical Resource Utilisation and Health Economics>
    + +
    +

    9 ADVERSE EVENTS, SERIOUS ADVERSE EVENTS, PRODUCT COMPLAINTS, PREGNANCY AND POSTPARTUM INFORMATION, AND + SPECIAL SAFETY SITUATIONS

    +
    -

    8.4.2. Time Period and Frequency for Collecting AE and SAE Information

    -
    Specify the starting and ending time periods for collecting AEs and SAEs.
    -
    [Time period and/or frequency for collecting AEs and SAEs]
    +
    +

    9.1 Definitions

    +
    +
    No text is intended here (heading only).
    -

    8.4.3. Identifying AEs and SAEs

    -
    Specify how AEs and SAEs will be identified (for example, spontaneous reporting, solicited questions).
    -
    [Identifying AEs and SAEs]
    +
    +

    9.1.1 Definitions of Adverse Events

    +
    +
    Specify the AE definitions, including: +
      +
    • any relevant regional AE requirements
      • +
    • any events that meet and do not meet the AE definition
      • +
    • any trial-specific AE clarifications
      • +
    • if applicable, any clarifications on the AE and SAE definitions for efficacy trials (e.g., lack of efficacy + or failure of pharmacological actions)
      • +
    +
    +
    {{ missing_definitions_of_adverse_events }}
    +
    <Enter Definitions of Adverse Events>
    -

    8.4.4. Recording of AEs and SAEs

    -
    Specify the Investigator’s actions for recording AEs and SAEs, including severity, causality, and the final outcome.
    -
    [Recording of AEs and SAEs]
    -
    Further details on assessing severity and causality of AEs and SAEs are in Appendices 12.3 and 12.4.
    +
    +

    9.1.2 Definitions of Serious Adverse Events

    +
    +
    Specify the SAE definitions, including: +
      +
    • any relevant regional SAE requirements
      • +
    • any events that meet and do not meet the SAE definition
      • +
    • any trial-specific SAE clarifications
      • +
    +
    +
    {{ missing_definitions_serious_of_adverse_events }}
    +
    <Enter Definitions of Serious Adverse Events> +
    -

    8.4.5. Follow-up of AEs and SAEs

    -
    Specify the procedures for follow-up of AEs and SAEs until they are resolved or considered stable. Include the assessment tools that will be used to monitor the events and the duration of follow-up after appearance of the events. Specify any procedures to be used for trials in which death is not an endpoint.
    -
    [Follow-up of AEs and SAEs]
    +
    +

    9.1.3 Definitions of Product Complaints

    +
    +
    Specify the definitions of product complaints in the context of the trial.
    +
    {{ missing_definitions_of_product_complaints }}
    +
    <Enter Definitions of Product Complaints>
    + +
    +

    9.1.3.1 {Definitions of Medical Device Product Complaints}

    +
    +
    Specify the definitions of product complaints in the context of the trial.
    +
    {{ missing_definitions_of_product_complaints }}
    +
    {<Enter Definitions of Medical Device Product Complaints>}
    + +
    +

    9.2 Timing and Procedures for Collection and Reporting

    +
    +
    Specify timing and procedures for collection and reporting of AEs, SAEs, product + complaints (including medical device product complaints if applicable) and pregnancy and postpartum information in + the sections below. This information may be summarised in a tabular format as shown in the example table below. +
    +
    This table describes the timing and procedures for collecting and reporting events. + +
    -

    8.4.6. Reporting of SAEs

    -
    Specify the SAE reporting method (for example, an electronic data collection tool or a paper CRF) to the Sponsor.
    -
    [Reporting of SAEs]
    + + + + + + + + + + + + + + + + + + + + + + + +
    Event Type Situational Scope Reportable Period Start Reportable Period End Timing for Reporting to Sponsor or Designee Method for Reporting Back-up Method for Reporting
    {{ missing_event_type }} {{ missing_other_event_type }} +
    <Event Type>
    +
    <Other Event Type>
    +     		{{ missing_situational_scope }} +
    <Situational Scope>
    +     		{{ missing_reportable_period_start }} +
    <Reportable Period Start>
    +     		{{ missing_reportable_period_end }} +
    <Reportable Period End>
    +     		{{ missing_timing_for_reporting_to_sponsor_or_designee }} +
    <Timing for Reporting to Sponsor or Designee>
    +     		{{ missing_method_for_reporting }} +
    <Method for Reporting>
    +     		{{ missing_back_up_method_for_reporting }} +
    <Back-up Method for Reporting> +
    +
    -

    8.4.7. Regulatory Reporting Requirements for SAEs

    -
    Specify: +
    +

    9.2.1 Timing

    +
    +
    Specify timing for collection and reporting, including:
      -
    • The Sponsor’s legal/regulatory responsibilities to report SAEs to regulatory authorities, ethics committees, and investigators.
      • -
    • The investigators’ responsibilities for promptly reporting SAEs to the Sponsor (and to Ethics Committees, where required) to allow the Sponsor to meet their responsibilities.
      • +
    • start and end dates for collection and reporting
      • +
    • frequency of collection and reporting
      • +
    • cross reference to the Schedule of Assessments as appropriate
    +
    {{ missing_event_collection_and_reporting_timing }}
    +
    <Enter Event Collection and Reporting Timing> +
    -

    8.4.8. Serious and Unexpected Adverse Reaction Reporting

    -
    Include this section, if applicable.
    -
    [Serious and Unexpected Adverse Reaction Reporting]
    - -

    8.4.9. Adverse Events of Special Interest

    -
    Include this section, if applicable.
    -
    Specify any Adverse Events of Special Interest (AESI): +
    +

    9.2.2 Collection Procedures

    +
    +
    Specify procedures for collection and recording of AEs, SAEs, product complaints + (including medical device product complaints if applicable) and pregnancy and postpartum information in the + sections below.
    + Identification +
    Specify how information will be identified (e.g., self-reported, solicited + questions).
    +
    {{ missing_identification }}
    +
    <Enter Identification>
    + Severity +
    Specify the intensity rating categories/scale.
    +
    {{ missing_severity }}
    +
    <Enter Severity>
    + Causality +
    Specify:
      -
    • Other events that merit reporting to the Sponsor, trial leadership, IRB, and regulatory agencies (for example, secondary malignancies in oncology trials).
      • -
    • Other reportable events not already included in the previous sections, such as cardiovascular and death events, medical device incidents (including malfunctions), laboratory test abnormalities, and trial intervention overdose.
      • +
    • the causality categories/scale
      • +
    • procedures for assessing causality
    -
    Include the following for each AESI: +
    {{ missing_causality }}
    +
    <Enter Causality>
    + Recording +
    Specify procedures for recording.
    +
    {{ missing_recording }}
    +
    <Enter Recording>
    + Follow-up +
    Specify the procedures for follow-up. Include the assessment tools that will be used + to monitor the events and the duration of follow-up after appearance of the events.
    +
    {{ missing_recording }}
    +
    <Enter Follow-up>
    + +
    +

    9.2.3 Reporting

    +
    +
    Specify the reporting method (e.g., an electronic data collection tool or a paper + CRF), backup reporting method, if applicable, and reporting timeline to the sponsor.
    +
    {{ missing_reporting }}
    +
    <Enter Reporting>
    + +
    +

    9.2.3.1 Regulatory Reporting Requirements

    +
    +
    Specify:
      -
    • The definition of the event. Specify the MedDRA preferred terms to use to report the AESI.
      • -
    • If it is a measurable quantity, specify how will the measurement be done.
      • -
    • If it is a clinical event, specify how will it be confirmed.
      • +
    • the investigator’s responsibilities for reporting to the sponsor (and to ethics committees, where required), + specifying timing of reporting to allow the sponsor to meet their responsibilities
      • +
    • the sponsor’s legal/regulatory responsibilities for reporting to regulatory authorities, ethics committees, + and investigators
      • +
    • suspected unexpected serious adverse reaction reporting
    -
    [Adverse Events of Special Interest]
    +
    {{ missing_definitions_of_product_complaints }}
    +
    <Enter Regulatory Reporting Requirements>
    -

    8.4.10. Disease-related Events or Outcomes Not Qualifying as AEs or SAEs

    -
    Specify any Disease-Related Events (DREs), disease-related outcomes, or both that will not be reported as AEs or SAEs (for example, seizures in anticonvulsant trials).
    -
    [Disease-related Events or Outcomes not Qualifying as AEs or SAEs]
    - -

    8.5. Pregnancy and Postpartum Information

    -
    No text is intended here (header only).
    +
    +

    9.2.4 Adverse Events of Special Interest

    +
    +
    Specify any AESI, including: +
      +
    • any event (serious or nonserious) of scientific and medical concern relative to the trial intervention, for + which ongoing monitoring and rapid communication by the investigator to the sponsor can be appropriate
      • +
    • other events that merit reporting to the sponsor, trial leadership, IRB, and regulatory agencies
      • +
    + Include the following for each AESI: +
      +
    • the definition
      • +
    • the approach for ascertaining information
      • +
    • if applicable, any approach to confirm or adjudicate the event
      • +
    +
    +
    {{ missing_adverse_events_of_special_interest }}
    +
    {<Enter Adverse Events of Special Interest>}
    +
    Or
    +
    {<Enter Not Applicable>}
    + +
    +

    9.2.5 Disease-related Events or Outcomes Not Qualifying as AEs or SAEs

    +
    +
    Specify any DREs, DROs, or both that will not be reported as AEs or SAEs (e.g., + seizures in anticonvulsant trials) or state “Not applicable.
    +
    {{ missing_disease_related_events_or_outcomes_not_qualifying_as_aes_or_saes }}
    +
    <Enter Disease-related Events or Outcomes Not Qualifying as AEs or SAEs>
    + +
    +

    9.3 Pregnancy and Postpartum Information

    +
    +
    Whenever possible, pregnancy (direct or via partner) should be documented and + followed up to collect relevant pregnancy outcomes. Any negative or consequential outcome(s) in the pregnant + participant/partner or foetus, neonate or infant should be reported as an AE or SAE. Refer to Section 9.2 Timing + and Procedures for Collection and Reporting for AE and SAE related procedures as applicable. If the negative event + meets the seriousness criteria, then this is considered an SAE (e.g., spontaneous abortion, foetal death, + stillbirth, congenital anomalies, ectopic pregnancy, or pre-eclampsia) and reported per Section 9.2.3 Reporting. +
    +
    No text is intended here (heading only).
    -

    8.5.1. Participants Who Become Pregnant During the Trial

    -
    Specify +
    +

    9.3.1 {Participants Who Become Pregnant During the Trial}

    +
    +
    Specify:
      -
    • the assessments to be performed,
      • -
    • type and duration of monitoring, and
      • -
    • what information will be collected for a participant who becomes pregnant during the trial (for example, recording and reporting to the Sponsor, postpartum follow-up, trial intervention discontinuation or continuation, or trial withdrawal).
      • +
    • the assessments to be performed
      • +
    • type and duration of monitoring
      • +
    • whether participants who become pregnant during the trial may continue with trial intervention or must be + discontinued from trial intervention (refer to Section 7 Participant Discontinuation of Trial Intervention and + Discontinuation or Withdrawal from Trial as applicable)
      • +
    • any trial modifications that need to be made for participants who become pregnant
      • +
    • what information will be collected about a participant who becomes pregnant during the trial (e.g., + recording and reporting to the sponsor, postpartum follow-up, trial intervention discontinuation or + continuation, or trial withdrawal)
    + For postpartum follow-up, include the time period (e.g., initial child development) with justification.
    + If exposure to trial intervention during breastfeeding is applicable, specify: +
      +
    • the assessments to be performed
      • +
    • type and duration of monitoring
      • +
    • information to be collected for both the participant and child
      • +
    +
    +
    {{ missing_participants_who_become_pregnant_during_the_trial }}
    +
    {<Enter Participants Who Become Pregnant During the Trial>}
    + +
    +

    9.3.2 {Participants Whose Partners Become Pregnant During the Trial}

    -
    For postpartum follow-up, include the time period (for example, initial child development) with the justification.
    -
    If exposure to trial intervention during breastfeeding is applicable, specify +
    Specify:
      -
    • the assessments to be performed,
      • -
    • type and duration of monitoring, and
      • -
    • what information will be collected for both the participant and child.
      • +
    • whether the investigator will attempt to collect pregnancy information about a participant’s partner who + becomes pregnant during the specified period in the trial
      • +
    • whether the participant whose partner becomes pregnant should be discontinued from trial intervention (refer + to Section 7 Participant Discontinuation of Trial Intervention and Discontinuation or Withdrawal from Trial as + applicable)
      • +
    • the assessments to be performed, type and duration of monitoring, and the information to be collected
    -
    Specify that pregnancy is not an AE, unless a negative or consequential outcome occurs in the participant or child/foetus. If the negative event meets the seriousness criteria, then this is considered an SAE (for example, spontaneous abortion, foetal death, stillbirth, congenital anomalies, ectopic pregnancy, or pre-eclampsia) and reported per Section 8.4.5, Reporting of SAEs.
    -
    [Participants Who Become Pregnant During the Trial]
    - -

    8.5.2. Participants Whose Partners Become Pregnant

    -
    Specify: +
    {{ missing_participants_whose_partners_become_pregnant_during_the_trial }}
    +
    {<Enter Participants Whose Partners Become Pregnant During the Trial>}
    + +
    +

    9.4 Special Safety Situations

    +
    +
    Specify special safety situations associated with the trial intervention(s) that do + not qualify as an AE or SAE but require regulatory reporting. Examples include:
      -
    • If the investigator will attempt to collect pregnancy information for a participant’s partner, who becomes pregnant while the participant is in the trial.
      • -
    • The assessments to be performed, type and duration of monitoring, and what information will be collected.
      • +
    • misuse or abuse
      • +
    • off-label use (if applicable)
      • +
    • medication error (prescription or dispensing error)
      • +
    • occupational exposure
      • +
    • use outside of what is foreseen in the protocol
      • +
    • unintended exposure of embryo, foetus, or child via maternal exposure (pregnancy or breastfeeding) or via + paternal exposure (semen)
      • +
    • lack of therapeutic efficacy; this is not applicable for studies that measure efficacy as a study endpoint +
      • +
    • suspected transmission of an infectious agent; this is only applicable for injected or biologic medicinal + products
      • +
    • product complaint, including falsified or counterfeit products
      • +
    • suspected drug-food or drug-drug interaction
    -
    [Participants Whose Partners Become Pregnant]
    +
    {{ missing_participants_who_become_pregnant_during_the_trial }}
    +
    <Enter Special Safety Situations>
    -

    8.6. Medical Device Product Complaints for Drug/Device Combination Products

    -
    Optional section to include for drug/device combination products.
    -

    8.6.1. Definition of Medical Device Product Complaints

    -
    [Definition of Medical Device Product Complaints]
    -

    8.6.2. Recording of Medical Device Product Complaints

    -
    Optional section to specify the investigator’s actions for recording product complaints, including the final complaint outcome
    -
    [Recording of Medical Device Product Complaints]
    - -

    8.6.3. Time Period and Frequency for Collecting Medical Device Product Complaints

    -
    Optional section to specify the start and ending time periods for collecting Medical Device Product Complaints (for example, from when the medical device use begins to end of trial participation).
    -
    [Time Period and Frequency for Collecting Medical Device Product Complaints]
    +
    +

    10 STATISTICAL CONSIDERATIONS

    +
    +
    Ensure that the planned data analysis complies with ICH E9 and ICH E9(R1) + guidelines.
    +
    In general, all relevant data collected in the trial should be considered in this + section.
    +
    No text is intended here (heading only)
    + +
    +

    10.1 General Considerations

    +
    +
    Provide general statements related to statistical considerations, such as whether a + separate statistical analysis plan exists, which summary statistics will be provided, and the timing of analyses + (e.g., “The analysis will include all participant data at trial completion”).
    +
    {{ missing_general_considerations }}
    +
    <Enter General Considerations>
    + +
    +

    10.2 Analysis Sets

    +
    +
    Describe analysis sets to be considered at the trial level, i.e., the set of + participants whose data are to be included in the analyses, aligned with estimands. Clearly specify the analysis + set to be used for each analysis described in Section 10 Statistical Considerations.
    +
    {{ missing_analysis_sets }}
    +
    <Enter Analysis Sets>
    + +
    +

    10.3 Analyses of Demographics and Other Baseline Variables

    +
    +
    Describe the summary statistics that will be used to characterise the distribution + of demographic and other relevant variables at baseline. Specify when the variables will be measured (e.g., at + trial inclusion, prior to randomisation, or at the time of randomisation). Relevant variables include but are not + limited to: stratification variables specified in Section 6.7 Investigational Trial Intervention Assignment, + Randomisation and Blinding, covariates for the statistical models specified in Section 10.4 Analyses Associated + with the Primary Objective(s), other suspected predictive or prognostic variables, and variables used for planned + subgroup analyses.
    +
    {{ missing_analysis_of_demographics_and_other_baseline_variables }}
    +
    <Enter Analyses of Demographics and Other Baseline Variables>
    + +
    +

    10.4 Analyses Associated with the Primary Objective(s)

    +
    +
    Include additional level 3 headings for each primary objective as needed. If there + is more than one primary objective, number each objective consecutively as the level 3 heading (e.g., Primary + Objective 1, Primary Objective 2, etc.).
    +
    No text is intended here (heading only).
    + +
    +

    10.4.1 Primary Objective <#>

    +
    +
    No text is intended here (heading only).
    -

    8.6.4. Follow-Up of Medical Device Product Complaints

    -
    [Follow-up of Medical Device Product Complaints]
    +
    +

    10.4.1.1 Statistical Analysis Method

    +
    +
    Describe the statistical analysis methods that will be used to evaluate the primary + objective(s) and associated estimand(s) in Section 3.1 Primary Objective(s) and Associated Estimand(s). Ensure + that the statistical hypothesis/model/analysis (and corresponding assumptions) is aligned with the primary + estimand(s).
    +
    For each objective, when applicable, state the null and alternative hypotheses, + including the pre-planned type 1 error rate, or alternative criteria for evaluating whether the objective has been + met, and relevant operating characteristics if appropriate. Describe the statistical model used and the factors + that will be included (e.g., covariates and interactions) and any rules for handling these factors (e.g., pooling + of centres).
    +
    If modelling and simulation methods are to be used, describe the model (inputs and + outputs), the underlying assumptions, and the method of model fitting.
    +
    {{ missing_statistical_analysis_method }}
    +
    <Enter Statistical Analysis Method>
    + +
    +

    10.4.1.2 Handling of Data in Relation to Primary Estimand(s)

    +
    +
    For each intercurrent event of the primary estimand(s) defined in Section 3.1 + Primary Objective(s) and Associated Estimand(s), explain how data will be handled for the statistical analysis in + line with the primary estimand. The handling of intercurrent events in the statistical analysis should be aligned + with the specific estimand strategies being used.
    +
    FThis section should describe in more detail the rationale and handling of the data + rather than repeating information from the preceding sections.
    +
    {{ missing_handling_of_data_in_relation_to_primary_estimands }}
    +
    <Enter Handling of Data in Relation to Primary Estimand(s)>
    + +
    +

    10.4.1.3 Handling of Missing Data in Relation to Primary Estimand(s)

    +
    +
    Describe how missing data will be addressed (e.g., imputation method and model), + state the underlying assumptions, and provide a rationale for the approach.
    +
    {{ missing_handling_of_missing_data_in_relation_to_primary_estimands }}
    +
    <Enter Handling of Missing Data in Relation to Primary Estimand(s)>
    + +
    +

    10.4.1.4 {Sensitivity Analysis}

    +
    +
    Describe any sensitivity analyses and how their assumptions changed from the + assumptions of the main statistical analysis. Sensitivity analyses are a series of analyses conducted with the + intent to explore the robustness of inferences from the main estimator to deviations from its underlying modelling + assumptions and limitations in the data.
    +
    {{ missing_sensitivity_analysis }}
    +
    {<Enter Sensitivity Analysis>}
    + +
    +

    10.4.1.5 {Supplementary Analysis}

    +
    +
    Describe any supplementary analysis, if applicable. Supplementary analyses are + conducted in addition to the main and sensitivity analyses with the intent to provide additional insights into the + understanding of the treatment effect.
    +
    {{ missing_supplementary_analysis }}
    +
    {<Enter Supplementary Analysis>}
    + +
    +

    10.5 Analyses Associated with the Secondary Objective(s)

    +
    +
    Describe the statistical analysis methods that will be used to evaluate the + secondary objective(s) and associated estimand(s) in Section 3.2 Secondary Objective(s) and Associated + Estimand(s). Use the same section structure as Section 10.4 Analyses Associated with the Primary Objective(s). + Include additional level 3 headings for each secondary objective as needed. If there is more than one secondary + objective, number each objective consecutively as the level 3 heading (e.g., Secondary Objective 1, Secondary + Objective 2, etc.).
    +
    No text is intended here (heading only) unless there is no secondary objective, in + which case indicate “Not applicable.
    + +
    +

    10.5.1 {Secondary Objective <#>}

    +
    +
    No text is intended here (heading only).
    -

    8.6.5. Regulatory Reporting Requirements for Medical Device Product Complaints

    -
    Optional section to specify the investigators’ responsibilities for reporting Medical Device Product Complaints (for example, within 24 hours) to the Sponsor.
    -
    [Reporting of Medical Device Product Complaints]
    +
    +

    10.5.1.1 {Statistical Analysis Method}

    +
    +
    Clearly specify any secondary hypotheses that will be tested for confirmatory + purposes.
    +
    {{ missing_statistical_analysis_method_2 }}
    +
    {<Enter Statistical Analysis Method>}
    + +
    +

    10.5.1.2 {Handling of Data in Relation to Secondary Estimand(s)}

    +
    +
    {{ missing_handling_of_data_in_relation_to_secondary_estimands }}
    +
    {<Enter Handling of Data in Relation to Secondary Estimand(s)>}
    + +
    +

    10.5.1.3 {Handling of Missing Data in Relation to Secondary Estimand(s)}

    +
    +
    {{ missing_handling_of_missing_data_in_relation_to_secondary_estimands }}
    +
    {<Enter Handling of Missing Data in Relation to Secondary Estimand(s)>}
    + +
    +

    10.5.1.4 {Sensitivity Analysis}

    +
    +
    {{ missing_sensitivity_analysis }}
    +
    {<Enter Sensitivity Analysis>}
    -

    8.7. Pharmacokinetics

    -
    Include any specific instructions for the collection of samples and interpretation of PK assessments. +
    +

    10.5.1.5 {Supplementary Analysis}

    +
    +
    {{ missing_supplementary_analysis }}
    +
    {<Enter Supplementary Analysis>}
    + +
    +

    10.6 Analyses Associated with the Exploratory Objective(s)

    +
    +
    Describe any exploratory analyses, if applicable. Additional subsections may be + created to describe the analyses for each exploratory objective, as needed. If there is no exploratory objective, + indicate “Not applicable”.
    +
    {{ missing_analyses_associated_with_the_exploratory_objectives }}
    +
    <Enter Analyses Associated with the Exploratory Objective(s)>
    + +
    +

    10.7 Safety Analyses

    +
    +
    If safety is a primary and/or secondary objective, describe the corresponding safety + analyses in the appropriate section above (Section 10.4 Analyses Associated with the Primary Objective[s] or + Section 10.5 Analyses Associated with the Secondary Objective[s]). In this section, describe statistical methods + that will be used to analyse relevant safety outcomes, including any AESI. This should typically include + specification of a measure to estimate risk within treatment arms, a measure to compare risks across treatment + arms, and a measure of statistical uncertainty around the comparison (e.g., a confidence interval).
    +
    {{ missing_safety_analyses }}
    +
    <Enter Safety Analyses>
    + +
    +

    10.8 Other Analyses

    +
    +
    Describe other analyses not included in Sections 10.3-10.7, such as subgroup + analyses.
    +
    {{ missing_other_analyses }}
    +
    <Enter Other Analyses>
    + +
    +

    10.9 Interim Analyses

    +
    +
    Describe any interim analyses and criteria for stopping or adapting the trial. + Ensure alignment with Section 4.3 Trial Stopping Rules.
    +
    The description should include, but is not limited to, the following. Under + circumstances where interim analysis details could impede the integrity of the trial, some of the information can + be added in other documents outside of the protocol.
      -
    • Specific sample collection and processing instructions can be described in an appendix or a separate document and cross-referenced.
      • -
    • Describe the biological sample(s) collected, the handling of samples, and the assay method.
      • +
    • any planned interim analysis, even if it is only to be performed at the request of an oversight body (for + example, DMC)
      • +
    • the purpose of the interim analysis, including whether the interim analysis may be used for stopping and/or + other trial adaptations (e.g., sample size re- estimation, alteration to the proportion of participants + allocated to each trial group, or changes to eligibility criteria)
      • +
    • the applied statistical method (e.g., group sequential test) and spending function (e.g., O’Brien-Fleming), + as applicable
      • +
    • the parties responsible for performing and reviewing the results of the analyses (e.g., DMC, independent + statistician)
      • +
    • when the analyses will be conducted (timing and/or triggers)
      • +
    • the decision criteria—statistical or other—that will be adopted to judge the interim results as part of a + guideline for early stopping or other adaptations
      • +
    • who will see the outcome data while the trial is ongoing
      • +
    • whether these individuals will remain blinded to trial groups
      • +
    • how the integrity of the trial will be protected (e.g., maintaining blinding) when decisions are made after + interim analyses (e.g., a decision to continue the trial or implement a specific adaptation)
    -
    [Pharmacokinetics]
    +
    {{ missing_interim_analyses }}
    +
    <Enter Interim Analyses>
    -

    8.8. Genetics

    -
    Include any specific instructions for the collection of samples for genetic analysis. +
    +

    10.10 Multiplicity Adjustments

    +
    +
    Multiple testing procedures may be needed to limit the probability of false positive + findings in a trial. Reasons for carrying out multiple statistical tests include, but are not restricted to, + multiple endpoints, multiple treatment groups, multiple hypotheses, subgroups, and multiple timepoints.
    +
    Describe any approaches to multiplicity control for the trial. This description + might go beyond the analysis of primary objectives.
    +
    Specify the statistical approach to control the overall type I error rate as well as + the (adjusted) significance levels to test specific hypotheses, as applicable. Clarify whether the + tests/confidence intervals are one- or two-sided. State the circumstances under which a trial will be considered + to have met its primary objective(s). For example, in a study with two primary efficacy endpoints, this section + should state whether the study would be expected to provide statistical evidence on at least one or on both of the + endpoints in order to confirm the efficacy of the treatment.
    +
    For some statistical approaches it might be helpful to include a graphical + depiction, as visualisation will be helpful for understanding, coupled with the clinical translation of the + mathematical choices.
    +
    Details regarding interim analyses should be provided in Section 10.9 Interim + Analyses.
    +
    {{ missing_omultiplicity_adjustments }}
    +
    <Enter Multiplicity Adjustments>
    + +
    +

    10.11 Sample Size Determination

    +
    +
    This section should detail the methods used for the determination of the sample + size.
    +
    The sample size calculation should be aligned with the primary estimand(s) and the + primary analysis; otherwise, a justification is needed. Details of sample size calculation should include all + relevant information to enable reproduction of the sample size, e.g.:
      -
    • Include the biological samples that will be collected (for example, serum, plasma, etc.) and the retention time for the samples (ensuring alignment with the ICF).
      • -
    • Indicate the types of analyses that may be studied for each sample.
      • -
    • Specific sample collection and processing instructions can be described in an appendix or a separate document and cross-referenced.
      • +
    • references to any prior studies on which assumptions were based
      • +
    • significance level (including information on the choice of one- or two-sided level)
      • +
    • power
      • +
    • assumed treatment effect and variability
      • +
    • how dropout rate and intercurrent events have been incorporated into sample size calculation
      • +
    • precision of estimator/length of confidence interval
    -
    [Genetics]
    +
    Any assumptions made should be stated and justified. Further analysis of how + deviations from the assumptions will affect the sample size should be included.
    +
    If complex simulations were used to calculate the sample size, consider including + details in a separate simulation report as an appendix to the protocol.
    +
    If the planned sample size is not derived statistically, then this should be + explicitly stated along with a rationale for the intended sample size (e.g., exploratory nature of pilot trials; + pragmatic considerations for trials in rare diseases).
    +
    {{ missing_sample_size_determination }}
    +
    <Enter Sample Size Determination>
    + + + +
    +

    11 TRIAL OVERSIGHT AND OTHER GENERAL CONSIDERATIONS

    +
    +
    No text is intended here (heading only)
    -

    8.9. Biomarkers

    -
    Include any specific instructions for the collection of samples and interpretation of biomarkers, including pharmacodynamics. -
      -
    • Include the biological samples that will be collected (for example, serum, plasma, etc.) and the retention time for the samples (ensuring alignment with the ICF).
      • -
    • Indicate the types of biomarkers that will be studied for each sample.
      • -
    • Specific sample collection and processing instructions can be described in an appendix or a separate document and cross-referenced.
      • -
    • Specify whether optional or required. Required samples must be based on a protocol objective.
      • -
    +
    +

    11.1 Regulatory and Ethical Considerations

    -
    [Biomarkers]
    - -

    8.10. Immunogenicity Assessments

    -
    Include any specific instructions for the collection of samples and interpretation of immunogenicity. If immunogenicity assessments are included within Efficacy Assessments or Safety Assessments, cross-reference to that section.
    -
    [Immunogenicity Assessments]
    - -

    8.11. Medical Resource Utilisation and Health Economics

    -
    This section does not apply to COAs. Include this section only for any value evidence and outcomes assessments not included in either the efficacy or safety sections.
    -
    Describe the health outcome measures, collection method (for example, diary, physician interview), and participant burden.
    -
    [Medical Resource Utilisation and Health Economics]
    - -

    9. STATISTICAL CONSIDERATIONS

    -
    Ensure that the data analysis complies with ICH E9 Guideline and ICH E9(R1) Guideline.
    -
    In general, all relevant data collected in the trial should be considered in this statistical considerations section.
    -
    Provide a statement with regard to when the primary analyses will be conducted. For example: The analysis will be conducted on all participant data at the time the trial ends.
    -
    [Statistical Considerations]
    - -

    9.1. Analysis Sets

    -
    Analysis sets to support each analysis will be specified here and described in the Statistical Analysis Plan.
    -
    [Analysis Datasets]
    - -

    9.2. Analyses Supporting Primary Objective(s)

    -
    This section introduces the Statistical Analysis Plan, with the detail to be provided in the subsequent subsections. This includes describing the methods of estimation (analytic approach) in alignment with how the estimands are defined. Sensitivity analyses should be aligned with how the estimands and estimators are defined.
    -
    [Analysis Supporting Primary Objectives]
    - -

    9.2.1. Statistical Model, Hypothesis, and Method of Analysis

    -
    Ensure that the statistical hypothesis/model (and corresponding assumptions)/analysis is aligned with the primary estimand(s).
    -
    For all applicable objectives (for example, primary, secondary), under the appropriate header, state the null and alternative hypotheses, including the pre-planned type 1 error, or alternative criteria to define trial success and relevant operating characteristics if appropriate. Describe the statistical model used and the factors that will be included (covariates and interactions) and any rules for handling these factors (for example, pooling of centres). If applicable, state and discuss any adjustments to account for multiplicity.
    -
    If modelling and simulation methods are to be used, please describe the model (inputs and outputs), the underlying assumptions, and the method of model fitting.
    -
    [Statistical Model, Hypothesis, and Method of Analysis]
    - -

    9.2.2. Handling of Intercurrent Events of Primary Estimand(s)

    -
    For each intercurrent event of the primary estimand(s) (Section 3.1, Estimand[s] for the Primary Objective[s]), explain how data will be handled for the statistical analysis in line with the primary estimand. The handling of intercurrent events in statistical analysis should be aligned with the specific estimand strategies being used.
    -
    This section should describe with more detail the rationale and handling of the data rather than repeating the guidance from the preceding sections.
    -
    [Handling of Intercurrent Events of Primary Estimand]
    - -

    9.2.3. Handling of Missing Data

    -
    This section should describe how missing data will be dealt with. Refer to the E9(R1) addendum when estimand framework is used.
    -
    The protocol should describe how missing data will be handled (for example, type of imputation technique, if any, and provide justification)
    -
    In cases where the Primary Objective is related to safety, this section should also be completed. It may also be helpful to include additional statements regarding handling of missing data in general for other important efficacy or safety endpoints or this information can be included in the analysis of secondary endpoint section below.
    -
    [Handling of Missing Data]
    - -

    9.2.4. Sensitivity Analysis

    -
    Sensitivity analyses are a series of analyses conducted with the intent to explore the robustness of inferences from the main estimator to deviations from its underlying modelling assumptions and limitations in the data.
    -
    [Sensitivity Analysis]
    - -

    9.2.5. Supplementary Analysis

    -
    Describe any supplementary analysis if applicable.
    -
    [Supplementary Analysis]
    - -

    9.3. Analysis Supporting Secondary Objective(s)

    -
    This section should focus on estimands for Secondary Objectives.
    -
    In this section describe the statistical analysis, handling of intercurrent events, handling of missing data, and if applicable, sensitivity analysis corresponding to each secondary estimand.
    -
    [Analyses Supporting Secondary Objectives]
    - -

    9.4. Analysis of Exploratory Objective(s)

    -
    [Analyses Supporting Tertiary/Exploratory Objective(s)]
    - -

    9.5. Safety Analyses

    -
    If safety is a primary and/or secondary objective, describe the corresponding safety analyses in the appropriate section above (Section 9.2 or Section 9.3).
    -
    [Safety Analyses]
    - -

    9.6. Other Analyses

    -
    Describe Other Analyses such as Subgroup analyses, Adjusted analysis if needed.
    -
    [Other Analyses]
    - -

    9.7. Interim Analyses

    -
    Describe any interim analysis and criteria for stopping or adapting the trial.
    -
    The description should include, but is not limited to, the following: +
    Provide a high-level statement on the prevailing ethical, legal, and regulatory + guidelines that will be applied throughout the trial.
    +
    This trial will be conducted in accordance with the protocol and with + the following:
      -
    • Any interim analysis plan, even if it is only to be performed at the request of an oversight body (for example, DMC).
      • -
    • Describe (briefly and concisely) and reference the applied statistical method, for example, group sequential test and spending function (for example, O’Brien-Fleming), as applicable.
      • -
    • Who will perform the analyses.
      • -
    • When they will be conducted (timing and/or triggers).
      • -
    • The decision criteria—statistical or other—that will be adopted to judge the interim results as part of a guideline for early stopping or other adaptations.
      • -
    • Who will see the outcome data while the trial is ongoing.
      • -
    • Whether these individuals will remain blinded to trial groups.
      • -
    • How the integrity of the trial implementation will be protected (for example, maintaining blinding) when any adaptations to the trial are made.
      • -
    • Who has the ultimate authority to stop or modify the trial, for example, investigator, principal investigator, Data Monitoring Committee, or sponsor.
      • -
    • The stopping guidelines.
      • -
    • If pre-specified interim analyses are to be used for other trial adaptations such as sample size re-estimation, alteration to the proportion of participants allocated to each trial group, and changes to eligibility criteria.
      • +
    • Ethical principles that have their origin in the Declaration of Helsinki for medical research involving + human subjects
      • +
    • Consensus ethical principles derived from international guidelines including the Declaration of Helsinki and + the Council for International Organisations of Medical Sciences (CIOMS) International Ethical Guidelines
      • +
    • ICH Good Clinical Practice (GCP) Guidelines
      • +
    • Applicable laws and regulations
    -
    [Interim Analyses]
    +
    {{ missing_regulatory_and_ethical_considerations }}
    +
    <Enter Regulatory and Ethical Considerations> +
    -

    9.8. Sample Size Determination

    -
    This section should detail the methods used for the determination of the sample size and a reference to tables or statistical software used to carry out the calculation. Sufficient information should be provided so that the sample size calculation can be reproduced or described.
    -
    If the planned sample size is not derived statistically, then this should be explicitly stated along with a rationale for the intended sample size (for example, exploratory nature of pilot trials; pragmatic considerations for trials in rare diseases).
    -
    [Sample Size Determination]
    +
    +

    11.2 Trial Oversight

    +
    +
    Concisely summarise the trial oversight, listing the investigator and sponsor + responsibilities not covered in other sections of the protocol that are essential for trial conduct, specifying + the ones related to quality assurance. if not using below optional subheadings.
    +
    {{ missing_trial_oversight }}
    +
    {<Enter Trial Oversight>}
    +
    if not using the optional subheadings.
    +
    OR
    + +
    +

    11.2.1 Investigator Responsibilities

    +
    +
    Describe the investigator responsibilities, including the oversight of trial-related + activities delegated to a third party that may impact the trial conduct at sites, if applicable and if not + addressed elsewhere.
    +
    {{ missing_investigator_responsibilities }}
    +
    <Enter Investigator Responsibilities>
    + +
    +

    11.2.2 Sponsor Responsibilities

    +
    +
    Describe the sponsor responsibilities, including activities to be transferred to a + third party that may impact the investigator sites, if applicable.
    +
    {{ missing_sponsor_responsibilities }}
    +
    <Enter Sponsor Responsibilities>
    + +
    +

    11.3 Informed Consent Process

    +
    +
    Specify the key elements of the informed consent process, including any special + needs and how these are addressed (e.g., assent, capacity, legally acceptable representative, adolescents who may + reach age of majority during the trial, pregnant participants and pregnant partners of participants).
    +
    {{ missing_description_of_informed_consent_process }}
    +
    <Enter Description of Informed Consent Process> +
    +
    {{ missing_description_of_assent_process }}
    +
    <Enter Description of Assent Process>
    +
    If enrollment in the trial may occur during an emergency in which the participant or + their legally acceptable representative is not able or available to give consent, describe the consent process. +
    +
    {{ missing_description_of_emergency_consent_process }}
    +
    <Enter Description of Emergency Consent Process>
    + +
    +

    11.3.1 {Informed Consent for Rescreening}

    +
    +
    If participants can be rescreened as described in Section 5.6 Screen Failure and + Rescreening, state whether the participant needs to complete a new ICF. Screen failure and rescreening should be + clearly defined in the protocol, with a cross reference to those definitions.
    +
    {{ missing_informed_consent_for_rescreening }}
    +
    {<Enter Informed Consent for Rescreening>}
    + +
    +

    11.3.2 {Informed Consent for Use of Remaining Samples in Exploratory Research}

    +
    +
    If participants will be asked to consent to optional exploratory research using the + remainder of mandatory samples, describe the use of remaining samples for optional exploratory research.
    +
    If any exploratory research is planned and additional written consent regarding the + use of remaining samples for exploratory research will be obtained, describe the consent process.
    +
    {{ missing_informed_consent_for_use_of_remaining_samples_in_exploratory_research }}
    +
    {<Enter Informed Consent for Use of Remaining Samples in Exploratory Research>} + +
    + +
    +

    11.4 Committees

    +
    +
    Briefly describe the administrative structure of committees that will be reviewing + data while the trial is ongoing, and the type of committee (e.g., Dose Escalation Committee, Data Monitoring + Committee or Data Safety Monitoring Board). Note that specific details may be required depending on local law or + regulation. If applicable, committee charters may be cross referenced. If no committees are involved, state “Not + applicable.
    +
    {{ missing_committees }}
    +
    <Enter Committees>
    + +
    +

    11.5 Insurance and Indemnity

    +
    +
    Concisely summarise the arrangements for participant insurance and indemnity if not + addressed in a separate agreement, if required by the applicable regulatory requirements.
    +
    {{ missing_insurance_and_indemnity }}
    +
    <Enter Insurance and Indemnity>
    + +
    +

    11.6 Risk-Based Quality Management

    +
    +
    Describe the identified critical to quality factors, associated risks and risk + mitigation strategies for the trial or refer to the location where this is described and updated during the trial + based on emerging data.
    +
    {{ missing_risk_based_quality_management }}
    +
    <Enter Risk-Based Quality Management>
    + +
    +

    11.7 Data Governance

    +
    +
    Describe the key systems and processes for critical trial integrity, traceability + and security including a summary of the approaches enabling accurate data collection, reporting, monitoring, + transfer, retention, and access if not addressed in separate agreement(s).
    +
    {{ missing_data_governance }}
    +
    <Enter Data Governance>
    + +
    +

    11.8 Data Protection

    +
    +
    Describe the measures to protect the privacy and confidentiality of personal + information of trial participants in accordance with applicable regulatory requirements on personal data + protection and any measures that should be taken in case of a data security breach.
    +
    {{ missing_data_protection }}
    +
    <Enter Data Protection>
    + +
    +

    11.9 Source Records

    +
    +
    State the importance of source records and expectation for traceability. Delineate + expectations for investigators (e.g., maintain and ensure availability of essential records) and trial monitors + (e.g., ensure participant protections, ensure that the trial is conducted according to GCP). Identify what + constitutes source records and its origin or provide a reference to the location of this information, if contained + in a separate document.
    +
    Describe the provision for direct access to source records enabling clinical trial- + related monitoring, audits and regulatory inspections, if not included in separate agreement(s).
    +
    {{ missing_data_protection }}
    +
    <Enter Source Records Introduction>
    +
    {{ missing_investigator_expectations_for_source_records }}
    +
    <Enter Investigator Expectations for Source Records>
    +
    {{ missing_trial_monitor_expectations_for_source_records }}
    +
    <Enter Trial Monitor Expectations for Source Records>
    +
    {{ missing_identification_for_source_records }}
    +
    <Enter Identification of Source Records>
    + +
    +

    11.10 Protocol Deviations

    +
    +
    Describe plans for detecting, reviewing, and reporting any deviations from the + protocol or include reference to a separate document.
    +
    {{ missing_protocol_deviations }}
    +
    <Enter Protocol Deviations>
    + +
    +

    11.11 Early Site Closure

    +
    +
    List the sponsor’s rights to close a site early. Likewise, list the investigator’s + rights to initiate early site closure.
    +
    {{ missing_decision_rights_for_site_closure }}
    +
    <Enter Decision Rights for Site Closure>
    +
    List the criteria for early closure of a site by the sponsor or investigator.
    +
    {{ missing_criteria_for_early_closure }}
    +
    <Enter Criteria for Early Closure>
    +
    List the responsibilities of the sponsor and investigator following early site + closure (e.g., informing the ethics committee[s], and prompt notification of the participant and their transition + to appropriate therapy and/or follow-up).
    +
    {{ missing_responsibilities_following_early_site_closure }}
    +
    <Enter Responsibilities Following Early Site Closure>
    + +
    +

    11.12 Data Dissemination

    +
    +
    Describe whether the clinical trial will be registered in public databases, + including reporting of results, if applicable.
    +
    {{ missing_data_dissemination }}
    +
    <Enter Data Dissemination>
    -

    9.9. Protocol Deviations

    -
    Plans for detecting, reviewing, and reporting any deviations from the protocol should be described.
    -
    [Protocol Deviations Plans]
    -

    10. GENERAL CONSIDERATIONS: REGULATORY, ETHICAL, AND TRIAL OVERSIGHT

    -
    No text is intended here (header only).
    +
    +

    12 APPENDIX: SUPPORTING DETAILS

    +
    +
    No text is intended here (heading only)
    +
    Additional supporting detail appendices may be added at the end of the existing + level 2 headings as needed.
    -

    10.1. Regulatory and Ethical Considerations

    -
    List the prevailing ethical, legal, and regulatory guidelines that will be applied throughout the trial.
    -
    This trial will be conducted in accordance with the protocol and with the following:
    -
    +
    +

    12.1 Clinical Laboratory Tests

    +
    +
    Specify which laboratory parameters should be included in each clinical laboratory + assessment panel (e.g., haematology, chemistry, urinalysis). A tabular presentation for such information is + common. If applicable, include equations and references for locally calculated laboratory results.
    +
    If not applicable, retain heading and enter “Not applicable.”
    +
    {{ missing_clinical_laboratory_tests }}
    +
    <Enter Clinical Laboratory Tests>
    + +
    +

    12.2 Country/Region-Specific Differences

    +
    +
    Although global clinical trial practices are increasingly harmonised, some country/ + region-specific differences in requirements do exist (e.g., document retention periods, contraception + requirements). Where differences in requirements cannot be reconciled, the sponsor should explain how + country/region-specific differences will be documented and communicated (e.g., by country/region-specific + amendments or addenda).
    +
    An alternative to country/region-specific amendments is to list the specific + differences by country or countries in this section, including a reference to the relevant section of the protocol + where each differing requirement applies.
    +
    If not applicable, retain the heading and enter “Not applicable.
    +
    {{ missing_not_applicable }}
    +
    <Not applicable>
    +
    Or
    +
    {{ missing_country_region_identifier }}
    +
    [Country/Region Identifier]
    +
    {{ missing_country_region_specific_requirements }}
    +
    <Enter Country/Region-Specific Requirements>
    +
    {{ missing_country_region_specific_protocol_clarifications }}
    +
    <Enter Country/Region-Specific Protocol Clarifications>
    + +
    +

    12.3 Prior Protocol Amendment(s)

    +
    +
    Choose the applicable statement below. For an original protocol that has not been + amended, retain the first statement below and delete the remainder of this entire section.
    +
    {{ missing_not_applicable }}
    +
    {This protocol has not been amended.}
    +
    Or
    +
    {This is the first protocol amendment.}
    +
    Or include the below as applicable.
    +
    {This protocol has been amended previously. The Protocol Amendment Summary of Changes for the current amendment + is located directly before the Table of Contents. Prior amendment(s) to this protocol are listed in the table + below, beginning with the most recent.}
    +
    Previous amendments should appear in reverse chronological order with the most + recent at the top (e.g., Amendment 3, 2, 1). Delete or add lines as needed. Inclusion of region-, country-, and + site-specific amendments in the table is optional. If included, ensure that the scope is clearly distinguishable + from global amendments.
    +
    If including the column with enrollment numbers, follow the instructions below.
      -
    • Consensus ethical principles derived from international guidelines including the Declaration of Helsinki and Council for International Organisations of Medical Sciences (CIOMS) International Ethical Guidelines
      • -
    • ICH Good Clinical Practice (GCP) Guidelines
      • -
    • Applicable laws and regulations
      • +
    • For global amendments to international clinical trials or amendments to a single-country trial, list the + approximate global enrollment total or percentage at the time of the amendment and select “globally”.
      • +
    • For global amendments consolidating only country/region-specific requirements, list approximate local + enrollment total or percentage at the time of the amendment and select “locally”. If consolidating a series of + local amendments, list the status of all the relevant locations.
      • +
    • For country/region-specific amendments to international clinical trials, list the approximate local + enrollment total or percentage at the time of the amendment and select “locally”.
      • +
    • For trials in which enrollment status by cohort is more meaningful, such as for single-site or early-phase + studies, listing the approximate enrollment by cohort is an option. If multiple cohorts are ongoing at the + time of the amendment, list the status of all the ongoing cohorts.
      • +
    • Enter the approximate number or percentage of participants enrolled as a percentage of the expected total. +
    -
    List the investigators’ and sponsor’s responsibilities in this regard.
    -
    Investigator Responsibilities [Investigator Responsibilities]
    -
    Sponsor Responsibilities [Sponsor Responsibilities]
    - -

    10.2. Committees

    -
    Briefly describe the administrative structure of committees that will be reviewing data while the trial is ongoing, and the type of committee (for example, Dose Escalation Committee, Data Monitoring Committee or Data Safety Monitoring Board). Note that specific details may be required depending on local law or regulation. If applicable, Committee Charters may be cross referenced.
    -
    [Committees Structure]
    - -

    10.3. Informed Consent Process

    -
    Specify the key elements of the informed consent process, including any special needs and how these are addressed (for example, assent, capacity, legally acceptable representative).
    -
    [Informed Consent Process]
    -
    If enrollment in the trial may occur during an emergency in which the participant or their legally authorised representative is not able or available to give consent, describe the consent process.
    -
    [Emergency Consent Process]
    -
    Rescreening
    -
    If participants can be rescreened, add the text to state whether the participant needs to complete a new consent. Screen failure and rescreening should be clearly defined in the protocol, with cross-reference to those definitions.
    -
    [Consent Requirements for Rescreening]
    -
    [Additional ICF text for Use of Remaining Samples in Optional Exploratory Research]
    - -

    10.4. Data Protection

    -
    Describe how personal data will be protected and any measures that should be taken in case of a data security breach.
    -
    [Data Protection]
    - -

    10.5. Early Site Closure or Trial Termination

    -
    List the decision rights of sponsor or designee to close a site or terminate the trial. Likewise, list the investigator’s right to initiate site closure.
    -
    [Decision Rights for Site Closure and Trial Termination]
    -
    List the criteria for early closure of a site by the sponsor or investigator.
    -
    [Criteria for Early Closure]
    -
    List the responsibilities of the sponsor and investigator following termination or suspension, such as informing the ethics committee(s), and prompt notification of the participant and transition to appropriate therapy and/or follow-up.
    -
    [Responsibilities following Termination or Suspension]
    -

    11. GENERAL CONSIDERATIONS: RISK MANAGEMENT AND QUALITY ASSURANCE

    -
    No text is intended here (header only).
    + + + + + + + + + + + + + + + + + + + + +
    Document Sponsor Approval Date Approximate Enrollment when Sponsor Approved Amendment
    {{ missing_amendment_identifier }} +
    <Enter Amendment Identifier>
    +     		+ {{ missing_sponsor_approval_date }} +
    <Enter Sponsor Approval Date>
    +     		{{ missing_approximately_enrolled }} +
    Approximately <#/%> enrolled
    +
    <Enter Amendment Scope Enrollment Description>
    +
    +
    Original Protocol
    +     		+
    <Enter Sponsor Approval Date>
    +     		+
    0
    +
    -

    11.1. Quality Tolerance Limits

    -
    Indicate where Quality Tolerance Limits will be predefined, how they will be monitored during the trial, and expected discussion in the clinical trial report.
    -
    [QTL]
    +
    {{ missing_not_applicable }}
    +
    {The Overview of Changes from each prior protocol amendment is {provided\nbelow}
    +
    or
    +
    <specify alternative location>.}
    +
    Move the Overview of Changes table from the previous amendments to this section in + reverse chronological order (most recent first).
    +
    {{ missing_country_region_specific_protocol_clarifications }}
    +
    {Overview of Changes in Amendment
    +
    <Enter Amendment Identifier>
    +
    (<Enter Sponsor Approval Date>)}
    -

    11.2. Data Quality Assurance

    -
    Delineate the responsibilities of the Sponsor with respect to data quality assurance.
    -
    [Sponsor or Designee Responsibilities for Data Quality Assurance]
    -
    [Investigator Responsibilities for Data Quality Assurance]
    -

    11.3. Source Data

    -
    Establish the importance of source data and expectation for traceability of transcribed information back to source. Delineate expectations for investigators (for example, maintain source data at the site, ensure availability of current records) and trial monitors (for example, verify CRF data relative to source, safety of participants is being protected, conduct is in accordance with GCP). Define what constitutes source data and its origin or provide a reference to the location of these definitions, if contained in a separate document, such as a monitoring guideline or source data acknowledgement).
    -
    [Source Data Introduction]
    -
    [Investigator Expectations for Source Data]
    -
    [Trial Monitor Expectations for Source Data]
    -
    [Definition of Source Data]
    -

    12. APPENDIX: ADVERSE EVENTS AND SERIOUS ADVERSE EVENTS – DEFINITIONS, SEVERITY, AND CAUSALITY

    -
    No text is intended here (header only).
    -

    12.1. Further Details and Clarifications on the AE Definition

    -
    Specify: -
      -
    • Any relevant regional AE requirements.
      • -
    • Any events that meet and do not meet the AE definition.
      • -
    • Any trial-specific AE clarifications.
      • -
    • The trial-specific definition for an overdose.
      • -
    • If applicable, any clarifications on the AE and SAE definitions for efficacy trials (for example, lack of efficacy or failure of pharmacological actions reporting).
      • -
    + + + + + + + + + + + + + + + + + + + + +
    {Description of Change} {Brief Rationale for Change} {Section # and Name}
    {{ missing_description_of_change }} +
    <Enter Description of Change>
    +     		+ {{ missing_brief_rationale_for_change }} +
    <Enter Brief Rationale for Change>
    +     		{{ missing_approximately_enrolled }} +
    <Enter Section # and Name>
    +
    +
    Original Protocol
    +     		+
    <Enter Sponsor Approval Date>
    +     		+
    0
    +
    + +
    (Add rows as needed)
    +
    Add additional Overview of Changes tables as protocol amendments accrue.
    + +
    +

    12.X {Additional Appendices}

    +
    {{ missing_clinical_laboratory_tests }}
    +
    {<Enter Additional Appendices>}
    -

    12.2. Further Details and Clarifications on the SAE Definition

    -
    Specify: -
      -
    • Any relevant regional SAE requirements.
      • -
    • Any events that meet and do not meet the SAE definition.
      • -
    • Any trial-specific SAE clarifications.
      • -
    +
    +

    13 APPENDIX: GLOSSARY OF TERMS AND ABBREVIATIONS

    +
    +
    Define abbreviations and other terms used in the protocol. A tabular presentation is + common and may serve as the definition at first use.
    +
    {{ missing_glossary_of_terms_and_abbreviations }}
    +
    <Enter Glossary of Terms and Abbreviations>
    + +
    +

    14 APPENDIX: REFERENCES

    +
    +
    References should be listed in a common format that includes all relevant + information to identify the source and date published. If a reference is not published, this should be clearly + indicated.
    +
    {{ missing_references }}
    +
    <Enter References>
    + + + + -

    12.3. Severity

    -
    Specify the severity rating categories/scale.
    -
    [Severity]
    -

    12.4. Causality

    -
    Specify: -
      -
    • The causality categories/scale.
      • -
    • Procedures for assessing causality.
      • -
    -
    -
    [Causality]
    + + + - \ No newline at end of file diff --git a/clinical-mdr-api/openapi.json b/clinical-mdr-api/openapi.json index 53a2fe3e..f3c439dc 100644 --- a/clinical-mdr-api/openapi.json +++ b/clinical-mdr-api/openapi.json @@ -3,7 +3,7 @@ "info": { "title": "OpenStudyBuilder API", "description": "\n## NOTICE\n\nThis license information is applicable to the swagger documentation of the clinical-mdr-api, that is the openapi.json.\n\n## License Terms (MIT)\n\nCopyright (C) 2025 Novo Nordisk A/S, Danish company registration no. 24256790\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n\n## Licenses and Acknowledgements for Incorporated Software\n\nThis component contains software licensed under different licenses when compiled, please refer to the third-party-licenses.md file for further information and full license texts.\n\n## Authentication\n\nSupports OAuth2 [Authorization Code Flow](https://datatracker.ietf.org/doc/html/rfc6749#section-4.1),\nat paths described in the OpenID Connect Discovery metadata document (whose URL is defined by the `OAUTH_METADATA_URL` environment variable).\n\nMicrosoft Identity Platform documentation can be read \n([here](https://docs.microsoft.com/en-us/azure/active-directory/develop/v2-oauth2-auth-code-flow)).\n\nAuthentication can be turned off with `OAUTH_ENABLED=false` environment variable. \n\nWhen authentication is turned on, all requests to protected API endpoints must provide a valid bearer (JWT) token inside the `Authorization` http header. \n", - "version": "3.0.642" + "version": "3.0.657" }, "paths": { "/": { @@ -38439,6 +38439,67 @@ } } }, + "/ct/paired-codelists": { + "post": { + "tags": [ + "CT Codelists" + ], + "summary": "Creates a new set of paired codelists.", + "description": "Creates two codelists (one for names, one for codes) and links them as paired codelists.\nEach codelist gets its own name, submission_value, nci_preferred_name, definition, and sponsor_preferred_name\nvia the name_information and code_information fields respectively.", + "operationId": "create_paired_codelists_ct_paired_codelists_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/CTPairedCodelistCreateInput", + "description": "Properties to create a set of paired codelists (names and codes)." + } + } + }, + "required": true + }, + "responses": { + "201": { + "description": "Created - The paired codelists were successfully created.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/CTCodelistPaired" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The catalogue doesn't exist.\n- The library doesn't exist.\n- The library doesn't allow to add new items.\n", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + } + }, "/ct/paired-codelists/{codelist_uid}/terms": { "get": { "tags": [ @@ -49095,14 +49156,14 @@ } } }, - "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations": { + "/concepts/activities/activity-instances/{activity_instance_uid}/activations": { "delete": { "tags": [ "Activity Instances" ], - "summary": " Inactivate final version of an activity instance attributes", - "description": "State before:\n - uid must exist and activity instance must be in status Final.\n \nBusiness logic:\n - The latest 'Final' version will remain the same as before.\n - The status will be automatically set to 'Retired'.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n \nState after:\n - Activity instance changed status to Retired.\n - Audit trail entry must be made with action of inactivating to retired version.\n \nPossible errors:\n - Invalid uid or status not Final.", - "operationId": "inactivate_concepts_activities_activity_instances__activity_instance_uid__attributes_activations_delete", + "summary": "Inactivate final version of an activity instance (attributes and groupings)", + "description": "State before:\n - uid must exist and both the activity instance attributes and groupings must be in status Final.\n\nBusiness logic:\n - The latest 'Final' version will remain the same as before (for both attributes and groupings).\n - The status will be automatically set to 'Retired' for both attributes and groupings.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n\nState after:\n - Activity instance attributes and groupings changed status to Retired.\n - Audit trail entries must be made with action of inactivating to retired version.\n\nPossible errors:\n - Invalid uid, or attributes/groupings status not Final.", + "operationId": "inactivate_concepts_activities_activity_instances__activity_instance_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -49146,7 +49207,7 @@ } }, "400": { - "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in final status.", + "description": "Forbidden - Reasons include e.g.: \n- The activity instance attributes are not in final status.\n- The activity instance groupings are not in final status.", "content": { "application/json": { "schema": { @@ -49171,9 +49232,9 @@ "tags": [ "Activity Instances" ], - "summary": "Reactivate retired version of an activity instance attributes", - "description": "State before:\n - uid must exist and activity instance must be in status Retired.\n \nBusiness logic:\n - The latest 'Retired' version will remain the same as before.\n - The status will be automatically set to 'Final'.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n\nState after:\n - Activity instance changed status to Final.\n - An audit trail entry must be made with action of reactivating to final version.\n \nPossible errors:\n - Invalid uid or status not Retired.", - "operationId": "reactivate_concepts_activities_activity_instances__activity_instance_uid__attributes_activations_post", + "summary": "Reactivate retired version of an activity instance (attributes and groupings)", + "description": "State before:\n - uid must exist and both the activity instance attributes and groupings must be in status Retired.\n\nBusiness logic:\n - The latest 'Retired' version will remain the same as before (for both attributes and groupings).\n - The status will be automatically set to 'Final' for both attributes and groupings.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n\nState after:\n - Activity instance attributes and groupings changed status to Final.\n - Audit trail entries must be made with action of reactivating to final version.\n\nPossible errors:\n - Invalid uid, or attributes/groupings status not Retired.", + "operationId": "reactivate_concepts_activities_activity_instances__activity_instance_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -49217,7 +49278,7 @@ } }, "400": { - "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in retired status.", + "description": "Forbidden - Reasons include e.g.: \n- The activity instance attributes are not in retired status.\n- The activity instance groupings are not in retired status.", "content": { "application/json": { "schema": { @@ -49460,14 +49521,14 @@ } } }, - "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/activations": { - "delete": { + "/activity-instance-classes": { + "get": { "tags": [ - "Activity Instances" + "Activity Instance Classes" ], - "summary": " Inactivate final version of an activity instance groupings", - "description": "State before:\n - uid must exist and activity instance must be in status Final.\n \nBusiness logic:\n - The latest 'Final' version will remain the same as before.\n - The status will be automatically set to 'Retired'.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n \nState after:\n - Activity instance changed status to Retired.\n - Audit trail entry must be made with action of inactivating to retired version.\n \nPossible errors:\n - Invalid uid or status not Final.", - "operationId": "inactivate_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_activations_delete", + "summary": "List all activity-instance-classes (for a given library)", + "description": "State before:\n - The library must exist (if specified)\n\nBusiness logic:\n - List all activity-instance-classes in their latest version, including properties derived from theirs parent classes.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid library name specified.\n\n\n\nResponse format:\n\n- In addition to retrieving data in JSON format (default behaviour), \nit is possible to request data to be returned in CSV, XML or Excel formats \nby sending the `Accept` http request header with one of the following values:\n - `text/csv`\n\n - `text/xml`\n\n - `application/vnd.openxmlformats-officedocument.spreadsheetml.sheet`", + "operationId": "get_activity_instance_classes_activity_instance_classes_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -49478,24 +49539,117 @@ ], "parameters": [ { - "name": "activity_instance_uid", - "in": "path", - "required": true, + "name": "sort_by", + "in": "query", + "required": false, + "schema": { + "description": "\nJSON dictionary of field names and boolean flags specifying the sort order. Supported values for sort order are:\n- `true` - ascending order\n\n- `false` - descending order\n\n\nDefault: `{}` (no sorting).\n\nFormat: `{\"field_1\": true, \"field_2\": false, ...}`.\n\nFunctionality: Sorts the results by `field_1` with sort order indicated by its boolean value, then by `field_2` etc.\n\nExample: `{\"topic_code\": true, \"name\": false}` sorts the returned list by `topic_code ascending`, then by `name descending`.\n", + "title": "Sort By" + }, + "description": "\nJSON dictionary of field names and boolean flags specifying the sort order. Supported values for sort order are:\n- `true` - ascending order\n\n- `false` - descending order\n\n\nDefault: `{}` (no sorting).\n\nFormat: `{\"field_1\": true, \"field_2\": false, ...}`.\n\nFunctionality: Sorts the results by `field_1` with sort order indicated by its boolean value, then by `field_2` etc.\n\nExample: `{\"topic_code\": true, \"name\": false}` sorts the returned list by `topic_code ascending`, then by `name descending`.\n" + }, + { + "name": "page_number", + "in": "query", + "required": false, + "schema": { + "type": "integer", + "maximum": 1000000000, + "minimum": 1, + "description": "\nPage number of the returned list of entities.\n\nFunctionality : provided together with `page_size`, selects a page to retrieve for paginated results.\n\nErrors: `page_size` not provided, `page_number` must be equal or greater than 1.\n", + "default": 1, + "title": "Page Number" + }, + "description": "\nPage number of the returned list of entities.\n\nFunctionality : provided together with `page_size`, selects a page to retrieve for paginated results.\n\nErrors: `page_size` not provided, `page_number` must be equal or greater than 1.\n" + }, + { + "name": "page_size", + "in": "query", + "required": false, + "schema": { + "type": "integer", + "maximum": 1000, + "minimum": 0, + "description": "\nNumber of items to be returned per page.\n\nDefault: 10\n\nFunctionality: Provided together with `page_number`, selects the number of results per page.\n\nIn case the value is set to `0`, all rows will be returned.\n\nErrors: `page_number` not provided.\n", + "default": 10, + "title": "Page Size" + }, + "description": "\nNumber of items to be returned per page.\n\nDefault: 10\n\nFunctionality: Provided together with `page_number`, selects the number of results per page.\n\nIn case the value is set to `0`, all rows will be returned.\n\nErrors: `page_number` not provided.\n" + }, + { + "name": "filters", + "in": "query", + "required": false, + "schema": { + "description": "\nJSON dictionary of field names and search strings, with a choice of operators for building complex filtering queries.\n\nDefault: `{}` (no filtering).\n\nFunctionality: filters the queried entities based on the provided search strings and operators.\n\nFormat:\n`{\"field_name\":{\"v\":[\"search_str_1\", \"search_str_1\"], \"op\":\"comparison_operator\"}, \"other_field_name\":{...}}`\n\n- `v` specifies the list of values to match against the specified `field_name` field\n\n - If multiple values are provided in the `v` list, a logical OR filtering operation will be performed using these values.\n\n- `op` specifies the type of string match/comparison operation to perform on the specified `field_name` field. Supported values are:\n\n - `eq` (default, equals)\n\n - `ne` (not equals)\n\n - `co` (string contains)\n\n - `ge` (greater or equal to)\n\n - `gt` (greater than)\n\n - `le` (less or equal to)\n\n - `lt` (less than)\n\n - `bw` (between - exactly two values are required)\n\n - `in` (value in list).\n\n\nNote that filtering can also be performed on non-string field types. \nFor example, this works as filter on a boolean field: `{\"is_global_standard\": {\"v\": [false]}}`.\n\n\nWildcard filtering is also supported. To do this, provide `*` value for `field_name`, for example: `{\"*\":{\"v\":[\"search_string\"]}}`.\n\nWildcard only supports string search (with implicit `contains` operator) on fields of type string.\n\n\nFinally, you can filter on items that have an empty value for a field. To achieve this, set the value of `v` list to an empty array - `[]`.\n\n\nComplex filtering example:\n\n`{\"name\":{\"v\": [\"Jimbo\", \"Jumbo\"], \"op\": \"co\"}, \"start_date\": {\"v\": [\"2021-04-01T12:00:00+00.000\"], \"op\": \"ge\"}, \"*\":{\"v\": [\"wildcard_search\"], \"op\": \"co\"}}`\n\n", + "title": "Filters" + }, + "description": "\nJSON dictionary of field names and search strings, with a choice of operators for building complex filtering queries.\n\nDefault: `{}` (no filtering).\n\nFunctionality: filters the queried entities based on the provided search strings and operators.\n\nFormat:\n`{\"field_name\":{\"v\":[\"search_str_1\", \"search_str_1\"], \"op\":\"comparison_operator\"}, \"other_field_name\":{...}}`\n\n- `v` specifies the list of values to match against the specified `field_name` field\n\n - If multiple values are provided in the `v` list, a logical OR filtering operation will be performed using these values.\n\n- `op` specifies the type of string match/comparison operation to perform on the specified `field_name` field. Supported values are:\n\n - `eq` (default, equals)\n\n - `ne` (not equals)\n\n - `co` (string contains)\n\n - `ge` (greater or equal to)\n\n - `gt` (greater than)\n\n - `le` (less or equal to)\n\n - `lt` (less than)\n\n - `bw` (between - exactly two values are required)\n\n - `in` (value in list).\n\n\nNote that filtering can also be performed on non-string field types. \nFor example, this works as filter on a boolean field: `{\"is_global_standard\": {\"v\": [false]}}`.\n\n\nWildcard filtering is also supported. To do this, provide `*` value for `field_name`, for example: `{\"*\":{\"v\":[\"search_string\"]}}`.\n\nWildcard only supports string search (with implicit `contains` operator) on fields of type string.\n\n\nFinally, you can filter on items that have an empty value for a field. To achieve this, set the value of `v` list to an empty array - `[]`.\n\n\nComplex filtering example:\n\n`{\"name\":{\"v\": [\"Jimbo\", \"Jumbo\"], \"op\": \"co\"}, \"start_date\": {\"v\": [\"2021-04-01T12:00:00+00.000\"], \"op\": \"ge\"}, \"*\":{\"v\": [\"wildcard_search\"], \"op\": \"co\"}}`\n\n", + "examples": { + "none": { + "summary": "No Filters", + "description": "No filters are applied.", + "value": "{}" + }, + "wildcard": { + "summary": "Wildcard Filter", + "description": "Apply a wildcard filter.", + "value": "{\"*\":{ \"v\": [\"\"], \"op\": \"co\"}}" + }, + "uid__contains": { + "summary": "Partial Match on UID", + "description": "Apply a filter to display records **containing** specified UIDs.", + "value": "{\"uid\":{ \"v\": [\"\"], \"op\": \"co\"}}" + }, + "uid": { + "summary": "Exact Match on UID", + "description": "Apply a filter to display only those records with **exact** matching UIDs.", + "value": "{\"uid\":{ \"v\": [\"\"], \"op\": \"eq\"}}" + }, + "name__contains": { + "summary": "Partial Match on Name", + "description": "Apply a filter to display records **containing** specified names.", + "value": "{\"name\":{ \"v\": [\"\"], \"op\": \"co\"}}" + }, + "name": { + "summary": "Exact Match on Name", + "description": "Apply a filter to display only those records with **exact** matching names.", + "value": "{\"name\":{ \"v\": [\"\"], \"op\": \"eq\"}}" + } + } + }, + { + "name": "operator", + "in": "query", + "required": false, "schema": { "type": "string", - "description": "The unique id of the ActivityInstance", - "title": "Activity Instance Uid" + "description": "Specifies which logical operation - `and` or `or` - should be used in case filtering is done on several fields.\n\nDefault: `and` (all fields have to match their filter).\n\nFunctionality: `and` will return entities having all filters matching, `or` will return entities with any matches.\n\n", + "default": "and", + "title": "Operator" }, - "description": "The unique id of the ActivityInstance" + "description": "Specifies which logical operation - `and` or `or` - should be used in case filtering is done on several fields.\n\nDefault: `and` (all fields have to match their filter).\n\nFunctionality: `and` will return entities having all filters matching, `or` will return entities with any matches.\n\n" + }, + { + "name": "total_count", + "in": "query", + "required": false, + "schema": { + "type": "boolean", + "description": "Boolean flag to include the total count of entities in the response.\n\nDefault: `false`\n\nFunctionality: When set to `true`, returns the total number of entities that match the query.\n\nWhen combined with filters, the count reflects only the entities matching those filters.\n\nNote: This operation can be expensive for large datasets.\n\nSpecial case: A value of `-1` indicates that the exact count is unavailable due to performance constraints, but confirms that at least one more entity exists beyond the current page.", + "default": false, + "title": "Total Count" + }, + "description": "Boolean flag to include the total count of entities in the response.\n\nDefault: `false`\n\nFunctionality: When set to `true`, returns the total number of entities that match the query.\n\nWhen combined with filters, the count reflects only the entities matching those filters.\n\nNote: This operation can be expensive for large datasets.\n\nSpecial case: A value of `-1` indicates that the exact count is unavailable due to performance constraints, but confirms that at least one more entity exists beyond the current page." } ], "responses": { "200": { - "description": "OK.", + "description": "Successful Response", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ActivityInstanceGroupings" + "$ref": "#/components/schemas/CustomPage_ActivityInstanceClass_" } } } @@ -49510,8 +49664,8 @@ } } }, - "400": { - "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in final status.", + "404": { + "description": "Entity not found", "content": { "application/json": { "schema": { @@ -49520,8 +49674,8 @@ } } }, - "404": { - "description": "Not Found - The activity instance with the specified 'activity_instance_uid' could not be found.", + "400": { + "description": "Bad Request", "content": { "application/json": { "schema": { @@ -49534,11 +49688,11 @@ }, "post": { "tags": [ - "Activity Instances" + "Activity Instance Classes" ], - "summary": "Reactivate retired version of an activity instance groupings", - "description": "State before:\n - uid must exist and activity instance must be in status Retired.\n \nBusiness logic:\n - The latest 'Retired' version will remain the same as before.\n - The status will be automatically set to 'Final'.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n\nState after:\n - Activity instance changed status to Final.\n - An audit trail entry must be made with action of reactivating to final version.\n \nPossible errors:\n - Invalid uid or status not Retired.", - "operationId": "reactivate_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_activations_post", + "summary": "Creates new activity instance class.", + "description": "State before:\n - The specified library allows creation of concepts (the 'is_editable' property of the library needs to be true).\n\nBusiness logic:\n - New node is created for the activity instance class with the set properties.\n - relationships to specified parent classes are created (as in the model).\n - The status of the new created version will be automatically set to 'Draft'.\n - The 'version' property of the new version will be automatically set to 0.1.\n - The 'change_description' property will be set automatically to 'Initial version'.\n\nState after:\n - ActivityInstanceClass is created in status Draft and assigned an initial minor version number as 0.1.\n - Audit trail entry must be made with action of creating new Draft version.\n\nPossible errors:\n - Invalid library or control terminology uid's specified.", + "operationId": "create_activity_instance_classes_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -49547,26 +49701,23 @@ "BearerJwtAuth": [] } ], - "parameters": [ - { - "name": "activity_instance_uid", - "in": "path", - "required": true, - "schema": { - "type": "string", - "description": "The unique id of the ActivityInstance", - "title": "Activity Instance Uid" - }, - "description": "The unique id of the ActivityInstance" + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceClassInput" + } + } } - ], + }, "responses": { - "200": { - "description": "OK.", + "201": { + "description": "Created - The activity was successfully created.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ActivityInstanceGroupings" + "$ref": "#/components/schemas/ActivityInstanceClass" } } } @@ -49582,17 +49733,7 @@ } }, "400": { - "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in retired status.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "404": { - "description": "Not Found - The activity instance with the specified 'activity_instance_uid' could not be found.", + "description": "Forbidden - Reasons include e.g.: \n- The library doesn't exist.\n- The library doesn't allow to add new items.\n", "content": { "application/json": { "schema": { @@ -49604,238 +49745,14 @@ } } }, - "/activity-instance-classes": { + "/activity-instance-classes/versions": { "get": { "tags": [ "Activity Instance Classes" ], - "summary": "List all activity-instance-classes (for a given library)", - "description": "State before:\n - The library must exist (if specified)\n\nBusiness logic:\n - List all activity-instance-classes in their latest version, including properties derived from theirs parent classes.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid library name specified.\n\n\n\nResponse format:\n\n- In addition to retrieving data in JSON format (default behaviour), \nit is possible to request data to be returned in CSV, XML or Excel formats \nby sending the `Accept` http request header with one of the following values:\n - `text/csv`\n\n - `text/xml`\n\n - `application/vnd.openxmlformats-officedocument.spreadsheetml.sheet`", - "operationId": "get_activity_instance_classes_activity_instance_classes_get", - "security": [ - { - "OAuth2AuthorizationCodeBearer": [] - }, - { - "BearerJwtAuth": [] - } - ], - "parameters": [ - { - "name": "sort_by", - "in": "query", - "required": false, - "schema": { - "description": "\nJSON dictionary of field names and boolean flags specifying the sort order. Supported values for sort order are:\n- `true` - ascending order\n\n- `false` - descending order\n\n\nDefault: `{}` (no sorting).\n\nFormat: `{\"field_1\": true, \"field_2\": false, ...}`.\n\nFunctionality: Sorts the results by `field_1` with sort order indicated by its boolean value, then by `field_2` etc.\n\nExample: `{\"topic_code\": true, \"name\": false}` sorts the returned list by `topic_code ascending`, then by `name descending`.\n", - "title": "Sort By" - }, - "description": "\nJSON dictionary of field names and boolean flags specifying the sort order. Supported values for sort order are:\n- `true` - ascending order\n\n- `false` - descending order\n\n\nDefault: `{}` (no sorting).\n\nFormat: `{\"field_1\": true, \"field_2\": false, ...}`.\n\nFunctionality: Sorts the results by `field_1` with sort order indicated by its boolean value, then by `field_2` etc.\n\nExample: `{\"topic_code\": true, \"name\": false}` sorts the returned list by `topic_code ascending`, then by `name descending`.\n" - }, - { - "name": "page_number", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "maximum": 1000000000, - "minimum": 1, - "description": "\nPage number of the returned list of entities.\n\nFunctionality : provided together with `page_size`, selects a page to retrieve for paginated results.\n\nErrors: `page_size` not provided, `page_number` must be equal or greater than 1.\n", - "default": 1, - "title": "Page Number" - }, - "description": "\nPage number of the returned list of entities.\n\nFunctionality : provided together with `page_size`, selects a page to retrieve for paginated results.\n\nErrors: `page_size` not provided, `page_number` must be equal or greater than 1.\n" - }, - { - "name": "page_size", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "maximum": 1000, - "minimum": 0, - "description": "\nNumber of items to be returned per page.\n\nDefault: 10\n\nFunctionality: Provided together with `page_number`, selects the number of results per page.\n\nIn case the value is set to `0`, all rows will be returned.\n\nErrors: `page_number` not provided.\n", - "default": 10, - "title": "Page Size" - }, - "description": "\nNumber of items to be returned per page.\n\nDefault: 10\n\nFunctionality: Provided together with `page_number`, selects the number of results per page.\n\nIn case the value is set to `0`, all rows will be returned.\n\nErrors: `page_number` not provided.\n" - }, - { - "name": "filters", - "in": "query", - "required": false, - "schema": { - "description": "\nJSON dictionary of field names and search strings, with a choice of operators for building complex filtering queries.\n\nDefault: `{}` (no filtering).\n\nFunctionality: filters the queried entities based on the provided search strings and operators.\n\nFormat:\n`{\"field_name\":{\"v\":[\"search_str_1\", \"search_str_1\"], \"op\":\"comparison_operator\"}, \"other_field_name\":{...}}`\n\n- `v` specifies the list of values to match against the specified `field_name` field\n\n - If multiple values are provided in the `v` list, a logical OR filtering operation will be performed using these values.\n\n- `op` specifies the type of string match/comparison operation to perform on the specified `field_name` field. Supported values are:\n\n - `eq` (default, equals)\n\n - `ne` (not equals)\n\n - `co` (string contains)\n\n - `ge` (greater or equal to)\n\n - `gt` (greater than)\n\n - `le` (less or equal to)\n\n - `lt` (less than)\n\n - `bw` (between - exactly two values are required)\n\n - `in` (value in list).\n\n\nNote that filtering can also be performed on non-string field types. \nFor example, this works as filter on a boolean field: `{\"is_global_standard\": {\"v\": [false]}}`.\n\n\nWildcard filtering is also supported. To do this, provide `*` value for `field_name`, for example: `{\"*\":{\"v\":[\"search_string\"]}}`.\n\nWildcard only supports string search (with implicit `contains` operator) on fields of type string.\n\n\nFinally, you can filter on items that have an empty value for a field. To achieve this, set the value of `v` list to an empty array - `[]`.\n\n\nComplex filtering example:\n\n`{\"name\":{\"v\": [\"Jimbo\", \"Jumbo\"], \"op\": \"co\"}, \"start_date\": {\"v\": [\"2021-04-01T12:00:00+00.000\"], \"op\": \"ge\"}, \"*\":{\"v\": [\"wildcard_search\"], \"op\": \"co\"}}`\n\n", - "title": "Filters" - }, - "description": "\nJSON dictionary of field names and search strings, with a choice of operators for building complex filtering queries.\n\nDefault: `{}` (no filtering).\n\nFunctionality: filters the queried entities based on the provided search strings and operators.\n\nFormat:\n`{\"field_name\":{\"v\":[\"search_str_1\", \"search_str_1\"], \"op\":\"comparison_operator\"}, \"other_field_name\":{...}}`\n\n- `v` specifies the list of values to match against the specified `field_name` field\n\n - If multiple values are provided in the `v` list, a logical OR filtering operation will be performed using these values.\n\n- `op` specifies the type of string match/comparison operation to perform on the specified `field_name` field. Supported values are:\n\n - `eq` (default, equals)\n\n - `ne` (not equals)\n\n - `co` (string contains)\n\n - `ge` (greater or equal to)\n\n - `gt` (greater than)\n\n - `le` (less or equal to)\n\n - `lt` (less than)\n\n - `bw` (between - exactly two values are required)\n\n - `in` (value in list).\n\n\nNote that filtering can also be performed on non-string field types. \nFor example, this works as filter on a boolean field: `{\"is_global_standard\": {\"v\": [false]}}`.\n\n\nWildcard filtering is also supported. To do this, provide `*` value for `field_name`, for example: `{\"*\":{\"v\":[\"search_string\"]}}`.\n\nWildcard only supports string search (with implicit `contains` operator) on fields of type string.\n\n\nFinally, you can filter on items that have an empty value for a field. To achieve this, set the value of `v` list to an empty array - `[]`.\n\n\nComplex filtering example:\n\n`{\"name\":{\"v\": [\"Jimbo\", \"Jumbo\"], \"op\": \"co\"}, \"start_date\": {\"v\": [\"2021-04-01T12:00:00+00.000\"], \"op\": \"ge\"}, \"*\":{\"v\": [\"wildcard_search\"], \"op\": \"co\"}}`\n\n", - "examples": { - "none": { - "summary": "No Filters", - "description": "No filters are applied.", - "value": "{}" - }, - "wildcard": { - "summary": "Wildcard Filter", - "description": "Apply a wildcard filter.", - "value": "{\"*\":{ \"v\": [\"\"], \"op\": \"co\"}}" - }, - "uid__contains": { - "summary": "Partial Match on UID", - "description": "Apply a filter to display records **containing** specified UIDs.", - "value": "{\"uid\":{ \"v\": [\"\"], \"op\": \"co\"}}" - }, - "uid": { - "summary": "Exact Match on UID", - "description": "Apply a filter to display only those records with **exact** matching UIDs.", - "value": "{\"uid\":{ \"v\": [\"\"], \"op\": \"eq\"}}" - }, - "name__contains": { - "summary": "Partial Match on Name", - "description": "Apply a filter to display records **containing** specified names.", - "value": "{\"name\":{ \"v\": [\"\"], \"op\": \"co\"}}" - }, - "name": { - "summary": "Exact Match on Name", - "description": "Apply a filter to display only those records with **exact** matching names.", - "value": "{\"name\":{ \"v\": [\"\"], \"op\": \"eq\"}}" - } - } - }, - { - "name": "operator", - "in": "query", - "required": false, - "schema": { - "type": "string", - "description": "Specifies which logical operation - `and` or `or` - should be used in case filtering is done on several fields.\n\nDefault: `and` (all fields have to match their filter).\n\nFunctionality: `and` will return entities having all filters matching, `or` will return entities with any matches.\n\n", - "default": "and", - "title": "Operator" - }, - "description": "Specifies which logical operation - `and` or `or` - should be used in case filtering is done on several fields.\n\nDefault: `and` (all fields have to match their filter).\n\nFunctionality: `and` will return entities having all filters matching, `or` will return entities with any matches.\n\n" - }, - { - "name": "total_count", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "description": "Boolean flag to include the total count of entities in the response.\n\nDefault: `false`\n\nFunctionality: When set to `true`, returns the total number of entities that match the query.\n\nWhen combined with filters, the count reflects only the entities matching those filters.\n\nNote: This operation can be expensive for large datasets.\n\nSpecial case: A value of `-1` indicates that the exact count is unavailable due to performance constraints, but confirms that at least one more entity exists beyond the current page.", - "default": false, - "title": "Total Count" - }, - "description": "Boolean flag to include the total count of entities in the response.\n\nDefault: `false`\n\nFunctionality: When set to `true`, returns the total number of entities that match the query.\n\nWhen combined with filters, the count reflects only the entities matching those filters.\n\nNote: This operation can be expensive for large datasets.\n\nSpecial case: A value of `-1` indicates that the exact count is unavailable due to performance constraints, but confirms that at least one more entity exists beyond the current page." - } - ], - "responses": { - "200": { - "description": "Successful Response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CustomPage_ActivityInstanceClass_" - } - } - } - }, - "403": { - "description": "Forbidden", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "404": { - "description": "Entity not found", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "400": { - "description": "Bad Request", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - } - } - }, - "post": { - "tags": [ - "Activity Instance Classes" - ], - "summary": "Creates new activity instance class.", - "description": "State before:\n - The specified library allows creation of concepts (the 'is_editable' property of the library needs to be true).\n\nBusiness logic:\n - New node is created for the activity instance class with the set properties.\n - relationships to specified parent classes are created (as in the model).\n - The status of the new created version will be automatically set to 'Draft'.\n - The 'version' property of the new version will be automatically set to 0.1.\n - The 'change_description' property will be set automatically to 'Initial version'.\n\nState after:\n - ActivityInstanceClass is created in status Draft and assigned an initial minor version number as 0.1.\n - Audit trail entry must be made with action of creating new Draft version.\n\nPossible errors:\n - Invalid library or control terminology uid's specified.", - "operationId": "create_activity_instance_classes_post", - "security": [ - { - "OAuth2AuthorizationCodeBearer": [] - }, - { - "BearerJwtAuth": [] - } - ], - "requestBody": { - "required": true, - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ActivityInstanceClassInput" - } - } - } - }, - "responses": { - "201": { - "description": "Created - The activity was successfully created.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ActivityInstanceClass" - } - } - } - }, - "403": { - "description": "Forbidden", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "400": { - "description": "Forbidden - Reasons include e.g.: \n- The library doesn't exist.\n- The library doesn't allow to add new items.\n", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - } - } - } - }, - "/activity-instance-classes/versions": { - "get": { - "tags": [ - "Activity Instance Classes" - ], - "summary": "List all versions of activity instance classes", - "description": "State before:\n - The library must exist (if specified)\n\nBusiness logic:\n - List version history of activity instance classes\n - The returned versions are ordered by version start_date descending (newest entries first).\n\nState after:\n - No change\n\nPossible errors:\n - Invalid library name specified.\n\n\n\nResponse format:\n\n- In addition to retrieving data in JSON format (default behaviour), \nit is possible to request data to be returned in CSV, XML or Excel formats \nby sending the `Accept` http request header with one of the following values:\n - `text/csv`\n\n - `text/xml`\n\n - `application/vnd.openxmlformats-officedocument.spreadsheetml.sheet`", - "operationId": "get_activity_instance_classes_versions_activity_instance_classes_versions_get", + "summary": "List all versions of activity instance classes", + "description": "State before:\n - The library must exist (if specified)\n\nBusiness logic:\n - List version history of activity instance classes\n - The returned versions are ordered by version start_date descending (newest entries first).\n\nState after:\n - No change\n\nPossible errors:\n - Invalid library name specified.\n\n\n\nResponse format:\n\n- In addition to retrieving data in JSON format (default behaviour), \nit is possible to request data to be returned in CSV, XML or Excel formats \nby sending the `Accept` http request header with one of the following values:\n - `text/csv`\n\n - `text/xml`\n\n - `application/vnd.openxmlformats-officedocument.spreadsheetml.sheet`", + "operationId": "get_activity_instance_classes_versions_activity_instance_classes_versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -72649,7 +72566,342 @@ } } } - } + } + } + }, + "/studies/template": { + "get": { + "tags": [ + "Studies" + ], + "summary": "Returns the active study template, if any.", + "operationId": "get_study_template_studies_template_get", + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "anyOf": [ + { + "$ref": "#/components/schemas/StudyTemplate" + }, + { + "type": "null" + } + ], + "title": "Response Get Study Template Studies Template Get" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + }, + "post": { + "tags": [ + "Studies" + ], + "summary": "Creates the study template configuration.", + "operationId": "create_study_template_studies_template_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyTemplateInput", + "description": "Study template target study reference." + } + } + }, + "required": true + }, + "responses": { + "201": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyTemplate" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + }, + "patch": { + "tags": [ + "Studies" + ], + "summary": "Updates the study template with a new version.", + "operationId": "patch_study_template_studies_template_patch", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyTemplatePatchInput", + "description": "Updated study template target." + } + } + }, + "required": true + }, + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyTemplate" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + } + }, + "/studies/template/activations": { + "post": { + "tags": [ + "Studies" + ], + "summary": "Reactivates a retired study template.", + "operationId": "reactivate_study_template_studies_template_activations_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "anyOf": [ + { + "$ref": "#/components/schemas/EditInputModel" + }, + { + "type": "null" + } + ], + "title": " ", + "description": "Optional change description payload." + } + } + } + }, + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyTemplate" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + }, + "delete": { + "tags": [ + "Studies" + ], + "summary": "Retires the current study template.", + "operationId": "retire_study_template_studies_template_activations_delete", + "requestBody": { + "content": { + "application/json": { + "schema": { + "anyOf": [ + { + "$ref": "#/components/schemas/EditInputModel" + }, + { + "type": "null" + } + ], + "title": " ", + "description": "Optional change description payload." + } + } + } + }, + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyTemplate" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] } }, "/studies/structure-overview": { @@ -73832,6 +74084,90 @@ } } }, + "/studies/{study_uid}/study-selection-containment/{target_study_uid}": { + "get": { + "tags": [ + "Studies" + ], + "summary": "Whether target study selection statistics are contained in the source study.", + "description": "Compares selection counts (and distinct CT term roots) for each concrete selection label that appears on **target_study_uid** against **study_uid** (source). Returns whether target counts are <= source for every such label, plus per-label figures. **StudySoAFootnote** is excluded (conditional clone rules make footnote counts incomparable).", + "operationId": "get_study_selection_containment_studies__study_uid__study_selection_containment__target_study_uid__get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + }, + { + "name": "target_study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the target study (e.g. a clone). Only selection labels that appear on this study are included in the comparison.", + "title": "Target Study Uid" + }, + "description": "The unique id of the target study (e.g. a clone). Only selection labels that appear on this study are included in the comparison." + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudySelectionContainmentResult" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - source or target study uid.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, "/studies/{study_uid}/pharma-cm": { "get": { "tags": [ @@ -74138,13 +74474,195 @@ } } }, - "/studies/{study_uid}/protocol-header-versions": { + "/studies/{study_uid}/protocol-header-versions": { + "get": { + "tags": [ + "Studies" + ], + "summary": "Returns the latest available protocol header version and whether the study contains a 'Final Protocol' locked version.", + "operationId": "get_protocol_header_version_studies__study_uid__protocol_header_versions_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StudyProtocolHeaderVersion" + } + } + } + }, + "404": { + "description": "Not Found - The study with the specified 'study_uid'", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/studies/{study_uid}/fields-audit-trail": { + "get": { + "tags": [ + "Studies" + ], + "summary": "Returns the audit trail for the fields of a specific study definition identified by 'study_uid'.", + "description": "Actions on the study are grouped by date of edit.Optionally select which subset of fields should be reflected in the audit trail.", + "operationId": "get_fields_audit_trail_studies__study_uid__fields_audit_trail_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + }, + { + "name": "include_sections", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "array", + "items": { + "$ref": "#/components/schemas/StudyComponentEnum" + } + }, + { + "type": "null" + } + ], + "description": "\n Optionally specify a list of sections to include from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned.", + "title": "Include Sections" + }, + "description": "\n Optionally specify a list of sections to include from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned." + }, + { + "name": "exclude_sections", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "array", + "items": { + "$ref": "#/components/schemas/StudyComponentEnum" + } + }, + { + "type": "null" + } + ], + "description": "\n Optionally specify a list of sections to exclude from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned.", + "title": "Exclude Sections" + }, + "description": "\n Optionally specify a list of sections to exclude from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned." + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/StudyFieldAuditTrailEntry" + }, + "title": "Response Get Fields Audit Trail Studies Study Uid Fields Audit Trail Get" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - The study with the specified 'study_uid' wasn't found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/studies/{study_uid}/audit-trail": { "get": { "tags": [ "Studies" ], - "summary": "Returns the latest available protocol header version or the one associated with specified study value version.", - "operationId": "get_protocol_header_version_studies__study_uid__protocol_header_versions_get", + "summary": "Returns the audit trail for the subparts of a specific study definition identified by 'study_uid'.", + "description": "Actions on the study are grouped by date of edit. Optionally select which subset of fields should be reflected in the audit trail.", + "operationId": "get_study_subpart_audit_trail_studies__study_uid__audit_trail_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -74164,225 +74682,75 @@ "title": "Study Uid" }, "description": "The unique id of the study." - } - ], - "responses": { - "200": { - "description": "Successful Response", - "content": { - "application/json": { - "schema": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Response Get Protocol Header Version Studies Study Uid Protocol Header Versions Get" - } - } - } - }, - "404": { - "description": "Not Found - The study with the specified 'study_uid'", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "400": { - "description": "Bad Request", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - } - } - } - }, - "/studies/{study_uid}/fields-audit-trail": { - "get": { - "tags": [ - "Studies" - ], - "summary": "Returns the audit trail for the fields of a specific study definition identified by 'study_uid'.", - "description": "Actions on the study are grouped by date of edit.Optionally select which subset of fields should be reflected in the audit trail.", - "operationId": "get_fields_audit_trail_studies__study_uid__fields_audit_trail_get", - "security": [ - { - "OAuth2AuthorizationCodeBearer": [] }, { - "BearerJwtAuth": [] - } - ], - "parameters": [ - { - "name": "study_uid", - "in": "path", - "required": true, + "name": "is_subpart", + "in": "query", + "required": false, "schema": { - "type": "string", - "description": "The unique id of the study.", - "title": "Study Uid" - }, - "description": "The unique id of the study." + "type": "boolean", + "default": false, + "title": "Is Subpart" + } }, { - "name": "include_sections", + "name": "study_value_version", "in": "query", "required": false, "schema": { "anyOf": [ { - "type": "array", - "items": { - "$ref": "#/components/schemas/StudyComponentEnum" - } + "type": "string", + "pattern": "^[0-9]+\\.?[0-9]*$" }, { "type": "null" } ], - "description": "\n Optionally specify a list of sections to include from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned.", - "title": "Include Sections" + "description": "If specified, study data with specified version is returned.\n\n Only exact matches are considered. \n\n E.g. 1, 2, 2.1, ...", + "title": "Study Value Version" }, - "description": "\n Optionally specify a list of sections to include from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned." + "description": "If specified, study data with specified version is returned.\n\n Only exact matches are considered. \n\n E.g. 1, 2, 2.1, ..." }, { - "name": "exclude_sections", + "name": "page_number", "in": "query", "required": false, "schema": { - "anyOf": [ - { - "type": "array", - "items": { - "$ref": "#/components/schemas/StudyComponentEnum" - } - }, - { - "type": "null" - } - ], - "description": "\n Optionally specify a list of sections to exclude from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned.", - "title": "Exclude Sections" + "type": "integer", + "maximum": 1000000000, + "minimum": 1, + "description": "\nPage number of the returned list of entities.\n\nFunctionality : provided together with `page_size`, selects a page to retrieve for paginated results.\n\nErrors: `page_size` not provided, `page_number` must be equal or greater than 1.\n", + "default": 1, + "title": "Page Number" }, - "description": "\n Optionally specify a list of sections to exclude from the StudyDefinition.\n\n Valid values are:\n\n - identification_metadata\n - registry_identifiers\n - version_metadata\n - high_level_study_design\n - study_population\n - study_intervention\n - study_description\n\n If no sections are specified, the whole audit trail is returned." - } - ], - "responses": { - "200": { - "description": "Successful Response", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StudyFieldAuditTrailEntry" - }, - "title": "Response Get Fields Audit Trail Studies Study Uid Fields Audit Trail Get" - } - } - } - }, - "403": { - "description": "Forbidden", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "404": { - "description": "Not Found - The study with the specified 'study_uid' wasn't found.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "400": { - "description": "Bad Request", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - } - } - } - }, - "/studies/{study_uid}/audit-trail": { - "get": { - "tags": [ - "Studies" - ], - "summary": "Returns the audit trail for the subparts of a specific study definition identified by 'study_uid'.", - "description": "Actions on the study are grouped by date of edit. Optionally select which subset of fields should be reflected in the audit trail.", - "operationId": "get_study_subpart_audit_trail_studies__study_uid__audit_trail_get", - "security": [ - { - "OAuth2AuthorizationCodeBearer": [] + "description": "\nPage number of the returned list of entities.\n\nFunctionality : provided together with `page_size`, selects a page to retrieve for paginated results.\n\nErrors: `page_size` not provided, `page_number` must be equal or greater than 1.\n" }, { - "BearerJwtAuth": [] - } - ], - "parameters": [ - { - "name": "study_uid", - "in": "path", - "required": true, + "name": "page_size", + "in": "query", + "required": false, "schema": { - "type": "string", - "description": "The unique id of the study.", - "title": "Study Uid" + "type": "integer", + "maximum": 1000, + "minimum": 0, + "description": "\nNumber of items to be returned per page.\n\nDefault: 10\n\nFunctionality: Provided together with `page_number`, selects the number of results per page.\n\nIn case the value is set to `0`, all rows will be returned.\n\nErrors: `page_number` not provided.\n", + "default": 10, + "title": "Page Size" }, - "description": "The unique id of the study." + "description": "\nNumber of items to be returned per page.\n\nDefault: 10\n\nFunctionality: Provided together with `page_number`, selects the number of results per page.\n\nIn case the value is set to `0`, all rows will be returned.\n\nErrors: `page_number` not provided.\n" }, { - "name": "is_subpart", + "name": "total_count", "in": "query", "required": false, "schema": { "type": "boolean", + "description": "Boolean flag to include the total count of entities in the response.\n\nDefault: `false`\n\nFunctionality: When set to `true`, returns the total number of entities that match the query.\n\nWhen combined with filters, the count reflects only the entities matching those filters.\n\nNote: This operation can be expensive for large datasets.\n\nSpecial case: A value of `-1` indicates that the exact count is unavailable due to performance constraints, but confirms that at least one more entity exists beyond the current page.", "default": false, - "title": "Is Subpart" - } - }, - { - "name": "study_value_version", - "in": "query", - "required": false, - "schema": { - "anyOf": [ - { - "type": "string", - "pattern": "^[0-9]+\\.?[0-9]*$" - }, - { - "type": "null" - } - ], - "description": "If specified, study data with specified version is returned.\n\n Only exact matches are considered. \n\n E.g. 1, 2, 2.1, ...", - "title": "Study Value Version" + "title": "Total Count" }, - "description": "If specified, study data with specified version is returned.\n\n Only exact matches are considered. \n\n E.g. 1, 2, 2.1, ..." + "description": "Boolean flag to include the total count of entities in the response.\n\nDefault: `false`\n\nFunctionality: When set to `true`, returns the total number of entities that match the query.\n\nWhen combined with filters, the count reflects only the entities matching those filters.\n\nNote: This operation can be expensive for large datasets.\n\nSpecial case: A value of `-1` indicates that the exact count is unavailable due to performance constraints, but confirms that at least one more entity exists beyond the current page." } ], "responses": { @@ -74391,11 +74759,7 @@ "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StudySubpartAuditTrail" - }, - "title": "Response Get Study Subpart Audit Trail Studies Study Uid Audit Trail Get" + "$ref": "#/components/schemas/CustomPage_StudySubpartAuditTrail_" } } } @@ -75445,15 +75809,114 @@ "description": "The unique id of the study." }, { - "name": "study_visit_uid", - "in": "path", - "required": true, + "name": "study_visit_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "SoA split uid", + "title": "Study Visit Uid" + }, + "description": "SoA split uid" + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/StudySoaSplit" + }, + "title": "Response Remove Soa Split Studies Study Uid Soa Splits Study Visit Uid Delete" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - study with the specified 'study_uid' doesn't exist", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/studies/{study_uid}/complexity-score": { + "get": { + "tags": [ + "Studies" + ], + "summary": "Get study complexity score", + "operationId": "get_complexity_score_studies__study_uid__complexity_score_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + }, + { + "name": "study_value_version", + "in": "query", + "required": false, "schema": { - "type": "string", - "description": "SoA split uid", - "title": "Study Visit Uid" + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Study Version Number", + "title": "Study Value Version" }, - "description": "SoA split uid" + "description": "Study Version Number", + "examples": { + "2.1": { + "value": "2.1" + } + } } ], "responses": { @@ -75462,21 +75925,8 @@ "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StudySoaSplit" - }, - "title": "Response Remove Soa Split Studies Study Uid Soa Splits Study Visit Uid Delete" - } - } - } - }, - "403": { - "description": "Forbidden", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" + "type": "number", + "title": "Response Get Complexity Score Studies Study Uid Complexity Score Get" } } } @@ -75504,13 +75954,13 @@ } } }, - "/studies/{study_uid}/complexity-score": { + "/studies/{study_uid}/complexity-score-details": { "get": { "tags": [ "Studies" ], - "summary": "Get study complexity score", - "operationId": "get_complexity_score_studies__study_uid__complexity_score_get", + "summary": "Get detailed study complexity score breakdown", + "operationId": "get_complexity_score_details_studies__study_uid__complexity_score_details_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -75561,8 +76011,7 @@ "content": { "application/json": { "schema": { - "type": "number", - "title": "Response Get Complexity Score Studies Study Uid Complexity Score Get" + "$ref": "#/components/schemas/ComplexityScoreDetails" } } } @@ -122870,28 +123319,15 @@ "attributes": { "$ref": "#/components/schemas/CTCodelistAttributes" }, - "paired_codes_codelist_uid": { + "paired_codelist": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/CTPairedCodelistInfo" }, { "type": "null" } ], - "title": "Paired Codes Codelist Uid", - "nullable": true - }, - "paired_names_codelist_uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Paired Names Codelist Uid", "nullable": true }, "term_uids": { @@ -125394,6 +125830,50 @@ "title": "CTCodelistAttributesVersion", "description": "Class for storing CTCodelistAttributes and calculation of differences" }, + "CTCodelistCodelistInformation": { + "properties": { + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "submission_value": { + "type": "string", + "minLength": 1, + "title": "Submission Value" + }, + "nci_preferred_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Preferred Name" + }, + "definition": { + "type": "string", + "minLength": 1, + "title": "Definition" + }, + "sponsor_preferred_name": { + "type": "string", + "minLength": 1, + "title": "Sponsor Preferred Name" + } + }, + "type": "object", + "required": [ + "name", + "submission_value", + "definition", + "sponsor_preferred_name" + ], + "title": "CTCodelistCodelistInformation" + }, "CTCodelistCompact": { "properties": { "uid": { @@ -125748,28 +126228,15 @@ "attributes": { "$ref": "#/components/schemas/CTCodelistAttributes" }, - "paired_codes_codelist_uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Paired Codes Codelist Uid", - "nullable": true - }, - "paired_names_codelist_uid": { + "paired_codelist": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/CTPairedCodelistInfo" }, { "type": "null" } ], - "title": "Paired Names Codelist Uid", "nullable": true } }, @@ -126952,6 +127419,93 @@ ], "title": "CTPackageDates" }, + "CTPairedCodelistCreateInput": { + "properties": { + "catalogue_names": { + "items": { + "type": "string" + }, + "type": "array", + "title": "Catalogue Names" + }, + "name_information": { + "$ref": "#/components/schemas/CTCodelistCodelistInformation" + }, + "code_information": { + "$ref": "#/components/schemas/CTCodelistCodelistInformation" + }, + "extensible": { + "type": "boolean", + "title": "Extensible" + }, + "is_ordinal": { + "type": "boolean", + "title": "Is Ordinal" + }, + "codelist_type": { + "type": "string", + "title": "Codelist Type", + "default": "Standard" + }, + "template_parameter": { + "type": "boolean", + "title": "Template Parameter" + }, + "parent_codelist_uid": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Parent Codelist Uid" + }, + "library_name": { + "type": "string", + "minLength": 1, + "title": "Library Name" + } + }, + "type": "object", + "required": [ + "catalogue_names", + "name_information", + "code_information", + "extensible", + "is_ordinal", + "template_parameter", + "library_name" + ], + "title": "CTPairedCodelistCreateInput" + }, + "CTPairedCodelistInfo": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name", + "nullable": true + } + }, + "type": "object", + "required": [ + "uid" + ], + "title": "CTPairedCodelistInfo" + }, "CTPairedCodelistTerm": { "properties": { "term_uid": { @@ -129963,6 +130517,76 @@ "type": "object", "title": "CompactUnitDefinition" }, + "ComplexityScoreAssessment": { + "properties": { + "type": { + "type": "string", + "title": "Type" + }, + "count": { + "type": "integer", + "title": "Count" + }, + "burden": { + "type": "number", + "title": "Burden" + } + }, + "type": "object", + "required": [ + "type", + "count", + "burden" + ], + "title": "ComplexityScoreAssessment" + }, + "ComplexityScoreDetails": { + "properties": { + "visits": { + "items": { + "$ref": "#/components/schemas/ComplexityScoreVisit" + }, + "type": "array", + "title": "Visits" + }, + "assessments": { + "items": { + "$ref": "#/components/schemas/ComplexityScoreAssessment" + }, + "type": "array", + "title": "Assessments" + } + }, + "type": "object", + "required": [ + "visits", + "assessments" + ], + "title": "ComplexityScoreDetails" + }, + "ComplexityScoreVisit": { + "properties": { + "type": { + "type": "string", + "title": "Type" + }, + "count": { + "type": "integer", + "title": "Count" + }, + "burden": { + "type": "number", + "title": "Burden" + } + }, + "type": "object", + "required": [ + "type", + "count", + "burden" + ], + "title": "ComplexityScoreVisit" + }, "Compound": { "properties": { "start_date": { @@ -136166,13 +136790,47 @@ "page", "size" ], - "title": "CustomPage[StudySelectionCompound]" + "title": "CustomPage[StudySelectionCompound]" + }, + "CustomPage_StudySelectionCriteria_": { + "properties": { + "items": { + "items": { + "$ref": "#/components/schemas/StudySelectionCriteria" + }, + "type": "array", + "title": "Items" + }, + "total": { + "type": "integer", + "minimum": -1.0, + "title": "Total" + }, + "page": { + "type": "integer", + "minimum": 0.0, + "title": "Page" + }, + "size": { + "type": "integer", + "minimum": 0.0, + "title": "Size" + } + }, + "type": "object", + "required": [ + "items", + "total", + "page", + "size" + ], + "title": "CustomPage[StudySelectionCriteria]" }, - "CustomPage_StudySelectionCriteria_": { + "CustomPage_StudySelectionDataSupplier_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySelectionCriteria" + "$ref": "#/components/schemas/StudySelectionDataSupplier" }, "type": "array", "title": "Items" @@ -136200,13 +136858,13 @@ "page", "size" ], - "title": "CustomPage[StudySelectionCriteria]" + "title": "CustomPage[StudySelectionDataSupplier]" }, - "CustomPage_StudySelectionDataSupplier_": { + "CustomPage_StudySelectionElement_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySelectionDataSupplier" + "$ref": "#/components/schemas/StudySelectionElement" }, "type": "array", "title": "Items" @@ -136234,13 +136892,13 @@ "page", "size" ], - "title": "CustomPage[StudySelectionDataSupplier]" + "title": "CustomPage[StudySelectionElement]" }, - "CustomPage_StudySelectionElement_": { + "CustomPage_StudySelectionEndpoint_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySelectionElement" + "$ref": "#/components/schemas/StudySelectionEndpoint" }, "type": "array", "title": "Items" @@ -136268,13 +136926,13 @@ "page", "size" ], - "title": "CustomPage[StudySelectionElement]" + "title": "CustomPage[StudySelectionEndpoint]" }, - "CustomPage_StudySelectionEndpoint_": { + "CustomPage_StudySelectionObjective_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySelectionEndpoint" + "$ref": "#/components/schemas/StudySelectionObjective" }, "type": "array", "title": "Items" @@ -136302,13 +136960,13 @@ "page", "size" ], - "title": "CustomPage[StudySelectionEndpoint]" + "title": "CustomPage[StudySelectionObjective]" }, - "CustomPage_StudySelectionObjective_": { + "CustomPage_StudySoAFootnote_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySelectionObjective" + "$ref": "#/components/schemas/StudySoAFootnote" }, "type": "array", "title": "Items" @@ -136336,13 +136994,13 @@ "page", "size" ], - "title": "CustomPage[StudySelectionObjective]" + "title": "CustomPage[StudySoAFootnote]" }, - "CustomPage_StudySoAFootnote_": { + "CustomPage_StudySoAGroup_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySoAFootnote" + "$ref": "#/components/schemas/StudySoAGroup" }, "type": "array", "title": "Items" @@ -136370,13 +137028,13 @@ "page", "size" ], - "title": "CustomPage[StudySoAFootnote]" + "title": "CustomPage[StudySoAGroup]" }, - "CustomPage_StudySoAGroup_": { + "CustomPage_StudyStructureOverview_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudySoAGroup" + "$ref": "#/components/schemas/StudyStructureOverview" }, "type": "array", "title": "Items" @@ -136404,13 +137062,13 @@ "page", "size" ], - "title": "CustomPage[StudySoAGroup]" + "title": "CustomPage[StudyStructureOverview]" }, - "CustomPage_StudyStructureOverview_": { + "CustomPage_StudySubpartAuditTrail_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudyStructureOverview" + "$ref": "#/components/schemas/StudySubpartAuditTrail" }, "type": "array", "title": "Items" @@ -136438,7 +137096,7 @@ "page", "size" ], - "title": "CustomPage[StudyStructureOverview]" + "title": "CustomPage[StudySubpartAuditTrail]" }, "CustomPage_StudySummaryListing_": { "properties": { @@ -139105,6 +139763,20 @@ "type": "object", "title": "Duration model to store ISO8601 duration" }, + "EditInputModel": { + "properties": { + "change_description": { + "type": "string", + "minLength": 1, + "title": "Change Description" + } + }, + "type": "object", + "required": [ + "change_description" + ], + "title": "EditInputModel" + }, "Endpoint": { "properties": { "uid": { @@ -141146,6 +141818,14 @@ "type": "integer", "title": "Sn" }, + "section": { + "type": "string", + "title": "Section" + }, + "feature": { + "type": "string", + "title": "Feature" + }, "name": { "type": "string", "title": "Name" @@ -141170,6 +141850,8 @@ "type": "object", "required": [ "sn", + "section", + "feature", "name", "enabled" ], @@ -141177,6 +141859,20 @@ }, "FeatureFlagInput": { "properties": { + "section": { + "type": "string", + "enum": [ + "admin", + "library", + "studies" + ], + "title": "Section" + }, + "feature": { + "type": "string", + "minLength": 1, + "title": "Feature" + }, "name": { "type": "string", "minLength": 1, @@ -141201,6 +141897,8 @@ }, "type": "object", "required": [ + "section", + "feature", "name", "enabled" ], @@ -141208,10 +141906,44 @@ }, "FeatureFlagPatchInput": { "properties": { + "section": { + "anyOf": [ + { + "type": "string", + "enum": [ + "admin", + "library", + "studies" + ] + }, + { + "type": "null" + } + ], + "title": "Section" + }, + "feature": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Feature" + }, "enabled": { - "type": "boolean", - "title": "Enabled", - "default": false + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Enabled" } }, "type": "object", @@ -158148,6 +158880,36 @@ "title": "Copy Study Design Matrix", "default": false }, + "copy_study_soa_group": { + "type": "boolean", + "title": "Copy Study Soa Group", + "default": false + }, + "copy_study_activity": { + "type": "boolean", + "title": "Copy Study Activity", + "default": false + }, + "copy_study_activity_instance": { + "type": "boolean", + "title": "Copy Study Activity Instance", + "default": false + }, + "copy_study_activity_group": { + "type": "boolean", + "title": "Copy Study Activity Group", + "default": false + }, + "copy_study_activity_subgroup": { + "type": "boolean", + "title": "Copy Study Activity Subgroup", + "default": false + }, + "copy_study_activity_schedule": { + "type": "boolean", + "title": "Copy Study Activity Schedule", + "default": false + }, "validation_mode": { "$ref": "#/components/schemas/ValidationMode", "default": "strict" @@ -162923,6 +163685,31 @@ ], "title": "StudyPreferredTimeUnitInput" }, + "StudyProtocolHeaderVersion": { + "properties": { + "protocol_header_version": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Protocol Header Version", + "description": "The latest available protocol header version.", + "nullable": true + }, + "has_final_protocol_locked_version": { + "type": "boolean", + "title": "Has Final Protocol Locked Version", + "description": "Indicates whether the study contains a locked version with 'Final Protocol' as the reason for lock.", + "default": false + } + }, + "type": "object", + "title": "StudyProtocolHeaderVersion" + }, "StudyProtocolTitle": { "properties": { "study_uid": { @@ -168301,6 +169088,84 @@ ], "title": "StudySelectionCompoundNewOrder" }, + "StudySelectionContainmentLabelRow": { + "properties": { + "label": { + "type": "string", + "title": "Label", + "description": "Concrete study selection label" + }, + "target_selection_count": { + "type": "integer", + "title": "Target Selection Count", + "description": "Selections on target" + }, + "source_selection_count": { + "type": "integer", + "title": "Source Selection Count", + "description": "Selections on source" + }, + "target_distinct_ct_term_root_count": { + "type": "integer", + "title": "Target Distinct Ct Term Root Count", + "description": "Distinct CT term roots on target (via CTTermContext on selections)" + }, + "source_distinct_ct_term_root_count": { + "type": "integer", + "title": "Source Distinct Ct Term Root Count", + "description": "Distinct CT term roots on source (via CTTermContext on selections)" + }, + "label_contained": { + "type": "boolean", + "title": "Label Contained", + "description": "True if target selection and term counts are <= source for this label" + } + }, + "type": "object", + "required": [ + "label", + "target_selection_count", + "source_selection_count", + "target_distinct_ct_term_root_count", + "source_distinct_ct_term_root_count", + "label_contained" + ], + "title": "StudySelectionContainmentLabelRow", + "description": "Per-label comparison when checking if target is contained in source." + }, + "StudySelectionContainmentResult": { + "properties": { + "target_contained_in_source": { + "type": "boolean", + "title": "Target Contained In Source", + "description": "True if containment holds for every compared label present on target" + }, + "labels_from_target": { + "items": { + "type": "string" + }, + "type": "array", + "title": "Labels From Target", + "description": "Concrete selection labels on the target used in the comparison (excludes StudySoAFootnote)" + }, + "per_label": { + "items": { + "$ref": "#/components/schemas/StudySelectionContainmentLabelRow" + }, + "type": "array", + "title": "Per Label", + "description": "Breakdown per label" + } + }, + "type": "object", + "required": [ + "target_contained_in_source", + "labels_from_target", + "per_label" + ], + "title": "StudySelectionContainmentResult", + "description": "Whether the **target** study's selection statistics are contained in the **source**.\n\nOnly labels that appear on the **target** study are considered (except\n``StudySoAFootnote``, which is skipped because SoA footnotes are copied\nconditionally). Containment means for each such label, target counts are less\nthan or equal to source counts (selection nodes and distinct CT term roots via\nCTTermContext)." + }, "StudySelectionCriteria": { "properties": { "study_uid": { @@ -171075,6 +171940,18 @@ "title": "Title", "nullable": true }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description", + "nullable": true + }, "subpart_id": { "anyOf": [ { @@ -172400,6 +173277,16 @@ "type": "integer", "title": "Visit Footnote Count", "description": "Number of connected footnotes (visit level)" + }, + "study_activity_count": { + "type": "integer", + "title": "Study Activity Count", + "description": "Number of connected study activities" + }, + "study_activity_schedule_count": { + "type": "integer", + "title": "Study Activity Schedule Count", + "description": "Number of connected study activity schedules" } }, "type": "object", @@ -172411,7 +173298,9 @@ "epoch_count", "epoch_footnote_count", "visit_count", - "visit_footnote_count" + "visit_footnote_count", + "study_activity_count", + "study_activity_schedule_count" ], "title": "StudyStructureStatistics" }, @@ -172691,6 +173580,97 @@ ], "title": "StudySummaryListing" }, + "StudyTemplate": { + "properties": { + "uid": { + "type": "string", + "title": "Uid", + "description": "Uid of study template root" + }, + "study_uid": { + "type": "string", + "title": "Study Uid", + "description": "Uid of template study" + }, + "study_value_version": { + "type": "string", + "title": "Study Value Version", + "description": "Study value version" + }, + "status": { + "$ref": "#/components/schemas/LibraryItemStatus", + "description": "Template item status" + }, + "version": { + "type": "string", + "title": "Version", + "description": "Template item version" + }, + "change_description": { + "type": "string", + "title": "Change Description", + "description": "Version change description" + } + }, + "type": "object", + "required": [ + "uid", + "study_uid", + "study_value_version", + "status", + "version", + "change_description" + ], + "title": "StudyTemplate" + }, + "StudyTemplateInput": { + "properties": { + "study_uid": { + "type": "string", + "minLength": 1, + "title": "Study Uid", + "description": "Uid of template study" + }, + "study_value_version": { + "type": "string", + "minLength": 1, + "title": "Study Value Version", + "description": "Study value version of template study, e.g. '1.0'" + } + }, + "type": "object", + "required": [ + "study_uid", + "study_value_version" + ], + "title": "StudyTemplateInput" + }, + "StudyTemplatePatchInput": { + "properties": { + "change_description": { + "type": "string", + "minLength": 1, + "title": "Change Description" + }, + "study_uid": { + "type": "string", + "title": "Study Uid", + "description": "Uid of template study; empty string clears the configured target" + }, + "study_value_version": { + "type": "string", + "title": "Study Value Version", + "description": "Released study value version; required when study_uid is non-empty" + } + }, + "type": "object", + "required": [ + "change_description", + "study_uid", + "study_value_version" + ], + "title": "StudyTemplatePatchInput" + }, "StudyTypeListingModel": { "properties": { "stype": { diff --git a/clinical-mdr-api/pyproject.toml b/clinical-mdr-api/pyproject.toml index 04de5d23..abaf839f 100644 --- a/clinical-mdr-api/pyproject.toml +++ b/clinical-mdr-api/pyproject.toml @@ -36,7 +36,13 @@ max-line-length = 200 max-module-lines = 6500 [tool.pylint.'BASIC'] -good-names = '_,c,e,i,j,k,l,r,v,x,y,z,ar,ex,rs,_AggregateRootType,db' +good-names = '_,c,e,i,j,k,l,r,v,x,y,z,ar,ex,rs,_AggregateRootType,db,studyUID' +# Allow UPPER_CASE and PascalCase for classes, with optional leading underscore +class-rgx = '_?([A-Z][a-zA-Z0-9]*|[A-Z_][A-Z0-9_]*)$' +# Allow UPPER_CASE, PascalCase, and snake_case for constants (Path descriptors, test globals) +const-rgx = '([A-Z_][A-Z0-9_]*|[A-Z][a-zA-Z0-9]*|[a-z_][a-z0-9_]*)$' +# Allow UPPER_CASE in addition to snake_case for variables (test constants at function scope) +variable-rgx = '([a-z_][a-z0-9_]*|[A-Z_][A-Z0-9_]*)$' [tool.pylint.'DESIGN'] max-args = 50 diff --git a/clinical-mdr-api/sbom.md b/clinical-mdr-api/sbom.md index 87b0b8fa..b123eef1 100644 --- a/clinical-mdr-api/sbom.md +++ b/clinical-mdr-api/sbom.md @@ -16,10 +16,10 @@ | cachetools | 5.5.2 | [MIT](#cachetools) | | certifi | 2026.2.25 | [MPL-2.0](#certifi) | | cffi | 2.0.0 | [MIT](#cffi) | -| charset-normalizer | 3.4.6 | [MIT](#charset-normalizer) | -| click | 8.3.1 | [BSD-3-Clause](#click) | +| charset-normalizer | 3.4.7 | [MIT](#charset-normalizer) | +| click | 8.3.2 | [BSD-3-Clause](#click) | | colour | 0.1.5 | [BSD 3-Clause License](#colour) | -| cryptography | 46.0.6 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | +| cryptography | 46.0.7 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | | cssselect2 | 0.9.0 | [see below](#cssselect2) | | deepdiff | 8.6.2 | [see below](#deepdiff) | | dict2xml | 1.7.8 | [MIT](#dict2xml) | @@ -29,9 +29,9 @@ | fhir_core | 1.1.7 | [BSD license](#fhir_core) | | fhir.resources | 8.2.0 | [BSD license](#fhirresources) | | fonttools | 4.62.1 | [MIT](#fonttools) | -| google-api-core | 2.30.0 | [Apache 2.0](#google-api-core) | -| google-auth | 2.49.1 | [Apache 2.0](#google-auth) | -| googleapis-common-protos | 1.73.0 | [Apache 2.0](#googleapis-common-protos) | +| google-api-core | 2.30.3 | [Apache 2.0](#google-api-core) | +| google-auth | 2.49.2 | [Apache 2.0](#google-auth) | +| googleapis-common-protos | 1.74.0 | [Apache 2.0](#googleapis-common-protos) | | h11 | 0.16.0 | [MIT](#h11) | | httpcore | 1.0.9 | [BSD-3-Clause](#httpcore) | | httpx | 0.27.2 | [BSD-3-Clause](#httpx) | @@ -40,21 +40,21 @@ | Jinja2 | 3.1.6 | [see below](#jinja2) | | lxml | 5.3.2 | [BSD-3-Clause](#lxml) | | MarkupSafe | 3.0.3 | [BSD-3-Clause](#markupsafe) | -| msal | 1.35.1 | [MIT](#msal) | +| msal | 1.36.0 | [MIT](#msal) | | msal-extensions | 1.3.1 | [MIT License](#msal-extensions) | | neo4j | 6.1.0 | [Apache-2.0 AND Python-2.0](#neo4j) | | neomodel | 6.1.0 | [MIT](#neomodel) | | nh3 | 0.2.22 | [MIT](#nh3) | -| numpy | 2.4.3 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | +| numpy | 2.4.4 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | | opencensus | 0.11.4 | [Apache-2.0](#opencensus) | | opencensus-context | 0.1.3 | [Apache-2.0](#opencensus-context) | | opencensus-ext-azure | 1.1.15 | [Apache-2.0](#opencensus-ext-azure) | | openpyxl | 3.1.5 | [MIT](#openpyxl) | | orderly-set | 5.5.0 | [see below](#orderly-set) | -| pandas | 3.0.1 | [see below](#pandas) | -| pillow | 12.1.1 | [MIT-CMU](#pillow) | -| proto-plus | 1.27.1 | [Apache 2.0](#proto-plus) | -| protobuf | 6.33.6 | [3-Clause BSD License](#protobuf) | +| pandas | 3.0.2 | [see below](#pandas) | +| pillow | 12.2.0 | [MIT-CMU](#pillow) | +| proto-plus | 1.27.2 | [Apache 2.0](#proto-plus) | +| protobuf | 7.34.1 | [3-Clause BSD License](#protobuf) | | psutil | 7.2.2 | [BSD-3-Clause](#psutil) | | pyasn1 | 0.6.3 | [BSD-2-Clause](#pyasn1) | | pyasn1_modules | 0.4.2 | [BSD](#pyasn1_modules) | @@ -68,10 +68,10 @@ | python-dateutil | 2.9.0.post0 | [Dual License](#python-dateutil) | | python-docx | 1.1.2 | [MIT](#python-docx) | | python-dotenv | 1.2.2 | [BSD-3-Clause](#python-dotenv) | -| python-multipart | 0.0.22 | [Apache-2.0](#python-multipart) | +| python-multipart | 0.0.24 | [Apache-2.0](#python-multipart) | | pytz | 2026.1.post1 | [MIT](#pytz) | | PyYAML | 6.0.3 | [MIT](#pyyaml) | -| requests | 2.33.0 | [Apache-2.0](#requests) | +| requests | 2.33.1 | [Apache-2.0](#requests) | | six | 1.17.0 | [MIT](#six) | | sniffio | 1.3.1 | [MIT OR Apache-2.0](#sniffio) | | sortedcontainers | 2.4.0 | [Apache 2.0](#sortedcontainers) | @@ -6944,7 +6944,7 @@ Pillow is the friendly PIL fork. It is - Copyright © 2010 by Jeffrey A. Clark and contributors + Copyright © 2010 by Jeffrey 'Alex' Clark and contributors Like PIL, Pillow is licensed under the open source MIT-CMU License: diff --git a/db-schema-migration/Pipfile b/db-schema-migration/Pipfile index 24efb7cf..331d220e 100644 --- a/db-schema-migration/Pipfile +++ b/db-schema-migration/Pipfile @@ -30,12 +30,12 @@ python_version = "3.14" [scripts] build-sbom = "pipenv run python3 assbom.py --pipfile --fallback-dir doc/licenses --level 2 --output sbom.md" -test = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml tests/test_migration_022.py" -verify = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml verifications/verification_022.py" -migrate = "python -m migrations.migration_022" -test_corrections = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml tests/test_correction_019.py" -verify_corrections = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml verifications/correction_verification_019.py" -apply_corrections = "python -m data_corrections.correction_019" +test = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml tests/test_migration_023.py" +verify = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml verifications/verification_023.py" +migrate = "python -m migrations.migration_023" +test_corrections = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml tests/test_correction_020.py" +verify_corrections = "python -m pytest -s --cov-report html:test_coverage --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/test_report.xml verifications/correction_verification_020.py" +apply_corrections = "python -m data_corrections.correction_020" wipe_single_study = "python -m data_corrections.correction_wipe_study" token = "python -m migrations.auth" lint = "pylint migrations tests verifications data_corrections" diff --git a/db-schema-migration/data_corrections/change_logs/remove_veeva_codelists.correction.json b/db-schema-migration/data_corrections/change_logs/remove_veeva_codelists.correction.json new file mode 100644 index 00000000..3a07d2d1 --- /dev/null +++ b/db-schema-migration/data_corrections/change_logs/remove_veeva_codelists.correction.json @@ -0,0 +1,587643 @@ +[ + [ + "EGcd7MhuWPmkAAAAAAARVzIAAAAAAAAAAAAAAZ1Ie0vq", + 1136434, + 0, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + 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+ "labels": [ + "CTCodelistAttributesValue" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistAttributesValue" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWsAAAAZ1Ie00G", + 1136435, + 5808, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392956", + "eventType": "n", + "state": { + "before": { + "properties": { + "uid": "CTCodelist_000273" + }, + "labels": [ + "CTCodelistRoot" + ] + }, + "after": null + }, + "operation": "d", + "keys": { + "CTCodelistRoot": [ + { + "uid": "CTCodelist_000273" + } + ] + }, + "labels": [ + "CTCodelistRoot" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWsQAAAZ1Ie00G", + 1136435, + 5809, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392957", + "eventType": "n", + "state": { + "before": { + "properties": {}, + "labels": [ + "CTCodelistNameRoot" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistNameRoot" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWsgAAAZ1Ie00G", + 1136435, + 5810, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392958", + "eventType": "n", + "state": { + "before": { + "properties": { + "name": "SUTRT_ECIGARET" + }, + "labels": [ + "CTCodelistNameValue" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistNameValue" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWswAAAZ1Ie00G", + 1136435, + 5811, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392994", + "eventType": "n", + "state": { + "before": { + "properties": {}, + "labels": [ + "CTCodelistAttributesRoot" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistAttributesRoot" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWtAAAAZ1Ie00G", + 1136435, + 5812, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392995", + "eventType": "n", + "state": { + "before": { + "properties": { + "preferred_term": "SUTRT_NICOTINE", + "name": "SUTRT_NICOTINE", + "definition": "Created by Veeva Library Importer", + "extensible": true, + "codelist_type": "Standard", + "submission_value": "SUTRT_NICOTINE" + }, + "labels": [ + "CTCodelistAttributesValue" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistAttributesValue" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWtQAAAZ1Ie00G", + 1136435, + 5813, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392996", + "eventType": "n", + "state": { + "before": { + "properties": { + "uid": "CTCodelist_000274" + }, + "labels": [ + "CTCodelistRoot" + ] + }, + "after": null + }, + "operation": "d", + "keys": { + "CTCodelistRoot": [ + { + "uid": "CTCodelist_000274" + } + ] + }, + "labels": [ + "CTCodelistRoot" + ] + } + ], + [ + "EGcd7MhuWPmkAAAAAAARVzMAAAAAAAAWtgAAAZ1Ie00G", + 1136435, + 5814, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392997", + "eventType": "n", + "state": { + "before": { + "properties": {}, + "labels": [ + "CTCodelistNameRoot" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistNameRoot" + ] + } + ], + [ + "EWcd7MhuWPmkAAAAAAARVzMAAAAAAAAWtwAAAZ1Ie00G", + 1136435, + 5815, + { + "txMetadata": {}, + "executingUser": "neo4j", + "databaseName": "neo4j", + "connectionClient": "10.192.3.247:36046", + "authenticatedUser": "neo4j", + "captureMode": "FULL", + "serverId": "81e16dcf", + "connectionType": "bolt", + "connectionServer": "10.192.3.52:17688", + "txStartTime": "2026-04-01T09:58:53.328000000+00:00", + "txCommitTime": "2026-04-01T09:58:53.446000000+00:00" + }, + { + "elementId": "4:60fb5341-ed71-4e60-b8fe-1e641d2d6354:2392998", + "eventType": "n", + "state": { + "before": { + "properties": { + "name": "SUTRT_NICOTINE" + }, + "labels": [ + "CTCodelistNameValue" + ] + }, + "after": null + }, + "operation": "d", + "keys": {}, + "labels": [ + "CTCodelistNameValue" + ] + } + ] +] \ No newline at end of file diff --git a/db-schema-migration/data_corrections/correction_020.py b/db-schema-migration/data_corrections/correction_020.py new file mode 100644 index 00000000..f87c7cfe --- /dev/null +++ b/db-schema-migration/data_corrections/correction_020.py @@ -0,0 +1,270 @@ +"""PRD Data Corrections: Fix Non and Unscheduled visit labels and visibility, restore CTCodelistTerm nodes""" + +import json +import os + +from data_corrections.utils.utils import ( + capture_changes, + get_db_driver, + print_counters_table, + run_cypher_query, + save_md_title, +) +from migrations.utils.utils import get_logger +from verifications import correction_verification_020 + +LOGGER = get_logger(os.path.basename(__file__)) +DB_DRIVER = get_db_driver() +CORRECTION_DESC = "data-correction-fix-visit-label-and-visibility" +CHANGE_LOG_FILE = os.path.join( + os.path.dirname(__file__), + "change_logs", + "remove_veeva_codelists.correction.json", +) + + +def main(run_label="correction"): + desc = f"Running data corrections on DB '{os.environ['DATABASE_NAME']}'" + LOGGER.info(desc) + save_md_title(run_label, __doc__, desc) + + fix_non_and_unscheduled_visit_label_and_visibility(DB_DRIVER, LOGGER, run_label) + restore_codelist_term_nodes(DB_DRIVER, LOGGER, run_label) + + +@capture_changes( + verify_func=correction_verification_020.test_non_and_unscheduled_visits_label_and_visibility +) +def fix_non_and_unscheduled_visit_label_and_visibility(db_driver, log, run_label): + """ + ### Problem description + Non-visit and Unscheduled-visit StudyVisit nodes have `short_visit_label` values + that are not prefixed with "V", and their `show_visit` property is not set to `false`. + ### Change description + - Prefix `short_visit_label` with "V" for all current Non and Unscheduled visits + whose label does not already start with "V". + - Set `show_visit` to `false` for all current Non and Unscheduled visits. + ### Nodes and relationships affected + - `StudyVisit` node properties: `short_visit_label`, `show_visit` + ### Expected changes: Non and Unscheduled visits updated with "V" prefix and show_visit=false + """ + log.info( + f"Run: {run_label}, Fixing short_visit_label prefix and show_visit for Non and Unscheduled visits" + ) + query = """ + MATCH (visit:StudyVisit) + WHERE visit.visit_class IN ['NON_VISIT', 'UNSCHEDULED_VISIT'] + AND (NOT visit.short_visit_label STARTS WITH 'V' OR visit.show_visit <> false) + SET visit.short_visit_label = 'V' + visit.short_visit_label + SET visit.show_visit = false + """ + _, summary = run_cypher_query(db_driver, query) + counters = summary.counters + print_counters_table(counters) + return counters.contains_updates + + +def parse_change_log(change_log_path): + """Parse the correction 019 change log and extract deleted CTCodelistTerm data. + + The change log contains two transactions, one for each phase of the correction. + In the first transaction (phase A) the CTCodelistTerm nodes that link the terms + to codelists were removed, and in the second (phase B) the Veeva codelists + themselves were removed. The changes to be undone are all in the first phase. + + Returns a list of dicts, one per deleted CTCodelistTerm node: + { + "submission_value": str, + "term_root_uid": str, + "has_term_from": [{"codelist_uid": str, "rel_props": dict}], + "contains_sv_from": [str], + } + """ + with open(change_log_path, encoding="utf-8") as f: + data = json.load(f) + + if not data: + return [] + + # Build set of ALL deleted node elementIds (across all transactions) + # so we can skip relationships to nodes that were also deleted (e.g. Veeva + # codelists removed in Phase B). + deleted_node_ids = { + r[4]["elementId"] + for r in data + if r[4].get("eventType") == "n" and r[4].get("operation") == "d" + } + + # Phase A is the first (earliest) transaction + commit_times = sorted({r[3].get("txCommitTime") for r in data}) + phase_a_time = commit_times[0] + phase_a = [r for r in data if r[3].get("txCommitTime") == phase_a_time] + + # Collect deleted CTCodelistTerm nodes + clt_nodes = {} + for r in phase_a: + event = r[4] + if event.get("operation") == "d" and event.get("eventType") == "n": + labels = event.get("state", {}).get("before", {}).get("labels", []) + if "CTCodelistTerm" in labels: + eid = event.get("elementId") + props = event.get("state", {}).get("before", {}).get("properties", {}) + clt_nodes[eid] = { + "submission_value": props.get("submission_value"), + "term_root_uid": None, + "has_term_from": [], + "contains_sv_from": [], + } + + # Collect relationships, skipping any where the other end was also deleted + for r in phase_a: + event = r[4] + if event.get("operation") != "d" or event.get("eventType") != "r": + continue + + start = event.get("start", {}) + end = event.get("end", {}) + rel_type = event.get("type") + rel_props = event.get("state", {}).get("before", {}).get("properties", {}) + + if rel_type == "HAS_TERM_ROOT": + start_eid = start.get("elementId") + if start_eid in clt_nodes: + for kd in end.get("keys", {}).get("CTTermRoot", []): + clt_nodes[start_eid]["term_root_uid"] = kd.get("uid") + + elif rel_type == "HAS_TERM": + end_eid = end.get("elementId") + start_eid = start.get("elementId") + if end_eid in clt_nodes and start_eid not in deleted_node_ids: + for kd in start.get("keys", {}).get("CTCodelistRoot", []): + clt_nodes[end_eid]["has_term_from"].append( + {"codelist_uid": kd.get("uid"), "rel_props": rel_props} + ) + + elif rel_type == "CONTAINS_SUBMISSION_VALUE": + end_eid = end.get("elementId") + start_eid = start.get("elementId") + if end_eid in clt_nodes and start_eid not in deleted_node_ids: + for kd in start.get("keys", {}).get("CTPackageTerm", []): + clt_nodes[end_eid]["contains_sv_from"].append(kd.get("uid")) + + # Skip entries where all codelists and package terms were also deleted + # (i.e. the term was exclusively on Veeva codelists removed in Phase B). + # Restoring these would create dangling CTCodelistTerm nodes with no purpose. + return [ + j for j in clt_nodes.values() if j["has_term_from"] or j["contains_sv_from"] + ] + + +def build_restore_query(clt_entry): + """Build a Cypher statement to restore a single CTCodelistTerm node. + + Pattern: + 1. MATCH CTTermRoot, MERGE CTCodelistTerm + HAS_TERM_ROOT + 2. For each CTPackageTerm: WITH term, MATCH, MERGE CONTAINS_SUBMISSION_VALUE + 3. For each CTCodelistRoot: WITH term, MATCH, MERGE HAS_TERM with properties + """ + sv = clt_entry["submission_value"] + tr_uid = clt_entry["term_root_uid"] + + parts = [ + f'MATCH (termRoot:CTTermRoot {{uid: "{tr_uid}"}})', + f'MERGE (termRoot)<-[:HAS_TERM_ROOT]-(term:CTCodelistTerm {{submission_value: "{sv}"}})', + ] + + for pkg_uid in clt_entry["contains_sv_from"]: + parts.append("WITH term") + parts.append(f'MATCH (other:CTPackageTerm {{uid: "{pkg_uid}"}})') + parts.append("MERGE (other)-[:CONTAINS_SUBMISSION_VALUE]->(term)") + + for ht in clt_entry["has_term_from"]: + cl_uid = ht["codelist_uid"] + props = ht["rel_props"] + + prop_parts = [] + if "author_id" in props: + prop_parts.append(f'author_id: "{props["author_id"]}"') + if "start_date" in props: + prop_parts.append(f'start_date: datetime("{props["start_date"]}")') + if "end_date" in props: + prop_parts.append(f'end_date: datetime("{props["end_date"]}")') + if "order" in props: + prop_parts.append(f"order: {props['order']}") + + prop_str = ", ".join(prop_parts) + parts.append("WITH term") + parts.append(f'MATCH (other:CTCodelistRoot {{uid: "{cl_uid}"}})') + parts.append(f"MERGE (other)-[:HAS_TERM {{{prop_str}}}]->(term)") + + return "\n".join(parts) + + +@capture_changes( + verify_func=correction_verification_020.test_no_orphaned_correction_019_terms +) +def restore_codelist_term_nodes(db_driver, log, run_label): + """ + ### Problem description + Correction 019 Phase A (unlink non-Veeva terms from Veeva codelists) used + `DETACH DELETE clt` on CTCodelistTerm nodes. Because these nodes are shared + across multiple codelists (HAS_TERM from both Veeva and CDISC codelists), + deleting the node severed terms from ALL codelists, not just the + Veeva ones. This left 84 CDISC terms fully orphaned and destroyed 5,670 + CONTAINS_SUBMISSION_VALUE relationships from CTPackageTerm nodes. + ### Change description + - Read the correction 019 change log to identify deleted CTCodelistTerm nodes + and their original relationships (skipping 13 whose codelists were all deleted) + - Recreate each CTCodelistTerm node with its submission_value + - Restore HAS_TERM_ROOT relationships to CTTermRoot + - Restore HAS_TERM relationships to CTCodelistRoot nodes that still exist + - Restore CONTAINS_SUBMISSION_VALUE relationships from CTPackageTerm nodes + ### Nodes and relationships affected + - `CTCodelistTerm` (recreated via MERGE) + - `HAS_TERM_ROOT` (CTCodelistTerm -> CTTermRoot) + - `HAS_TERM` (CTCodelistRoot -> CTCodelistTerm, with author_id/start_date/order/end_date) + - `CONTAINS_SUBMISSION_VALUE` (CTPackageTerm -> CTCodelistTerm) + ### Expected changes: up to 95 CTCodelistTerm nodes restored with all relationships + """ + change_log_path = CHANGE_LOG_FILE + if not os.path.exists(change_log_path): + log.warning(f"Change log not found at {change_log_path}, skipping") + return False + + log.info(f"Run: {run_label}, Parsing change log from {change_log_path}") + clt_entries = parse_change_log(change_log_path) + if not clt_entries: + log.info( + f"Run: {run_label}, No CTCodelistTerm nodes to restore (empty change log)" + ) + return False + + log.info(f"Run: {run_label}, Restoring {len(clt_entries)} CTCodelistTerm nodes") + + contains_updates = False + for i, clt_entry in enumerate(clt_entries): + query = build_restore_query(clt_entry) + _, summary = run_cypher_query(db_driver, query, quiet=True) + if summary.counters.contains_updates: + contains_updates = True + if (i + 1) % 20 == 0 or i == len(clt_entries) - 1: + log.info( + f"Run: {run_label}, Processed {i + 1}/{len(clt_entries)} CTCodelistTerm nodes" + ) + + # Print final summary by running a count query + log.info(f"Run: {run_label}, Verifying restored CTCodelistTerm nodes") + query_count = """ + MATCH (tr:CTTermRoot) + WHERE NOT EXISTS { MATCH (:CTCodelistTerm)-[:HAS_TERM_ROOT]->(tr) } + RETURN COUNT(tr) AS orphaned_terms + """ + records, _ = run_cypher_query(db_driver, query_count) + orphaned = records[0]["orphaned_terms"] if records else -1 + log.info(f"Run: {run_label}, Remaining orphaned terms: {orphaned}") + + return contains_updates + + +if __name__ == "__main__": + main() diff --git a/db-schema-migration/data_corrections/correction_019_overview.md b/db-schema-migration/data_corrections/corrections_overview_019.md similarity index 99% rename from db-schema-migration/data_corrections/correction_019_overview.md rename to db-schema-migration/data_corrections/corrections_overview_019.md index 646e17e4..ff113edd 100644 --- a/db-schema-migration/data_corrections/correction_019_overview.md +++ b/db-schema-migration/data_corrections/corrections_overview_019.md @@ -40,4 +40,3 @@ be preserved. - `CTTermContext` (orphaned nodes with no incoming relationships) #### Expected changes: 646 terms deleted, 6 terms preserved - diff --git a/db-schema-migration/data_corrections/corrections_overview_020.md b/db-schema-migration/data_corrections/corrections_overview_020.md new file mode 100644 index 00000000..ba403dc9 --- /dev/null +++ b/db-schema-migration/data_corrections/corrections_overview_020.md @@ -0,0 +1,44 @@ +## Data corrections: overview of data_corrections.correction_020 + +PRD Data Corrections: Fix Non and Unscheduled visit labels and visibility, restore CTCodelistTerm nodes + + + +## 1. Correction: fix_non_and_unscheduled_visit_label_and_visibility + +#### Problem description +Non-visit and Unscheduled-visit StudyVisit nodes have `short_visit_label` values +that are not prefixed with "V", and their `show_visit` property is not set to `false`. +#### Change description +- Prefix `short_visit_label` with "V" for all current Non and Unscheduled visits + whose label does not already start with "V". +- Set `show_visit` to `false` for all current Non and Unscheduled visits. +#### Nodes and relationships affected +- `StudyVisit` node properties: `short_visit_label`, `show_visit` +#### Expected changes: Non and Unscheduled visits updated with "V" prefix and show_visit=false + + +## 2. Correction: restore_codelist_term_nodes + +#### Problem description +Correction 019 Phase A (unlink non-Veeva terms from Veeva codelists) used +`DETACH DELETE clt` on CTCodelistTerm nodes. Because these nodes are shared +across multiple codelists (HAS_TERM from both Veeva and CDISC codelists), +deleting the node severed terms from ALL codelists, not just the +Veeva ones. This left 84 CDISC terms fully orphaned and destroyed 5,670 +CONTAINS_SUBMISSION_VALUE relationships from CTPackageTerm nodes. +#### Change description +- Read the correction 019 change log to identify deleted CTCodelistTerm nodes + and their original relationships (skipping 13 whose codelists were all deleted) +- Recreate each CTCodelistTerm node with its submission_value +- Restore HAS_TERM_ROOT relationships to CTTermRoot +- Restore HAS_TERM relationships to CTCodelistRoot nodes that still exist +- Restore CONTAINS_SUBMISSION_VALUE relationships from CTPackageTerm nodes +#### Nodes and relationships affected +- `CTCodelistTerm` (recreated via MERGE) +- `HAS_TERM_ROOT` (CTCodelistTerm -> CTTermRoot) +- `HAS_TERM` (CTCodelistRoot -> CTCodelistTerm, with author_id/start_date/order/end_date) +- `CONTAINS_SUBMISSION_VALUE` (CTPackageTerm -> CTCodelistTerm) +#### Expected changes: up to 95 CTCodelistTerm nodes restored with all relationships + + diff --git a/db-schema-migration/migrations/migration_023.py b/db-schema-migration/migrations/migration_023.py new file mode 100644 index 00000000..fe8914d4 --- /dev/null +++ b/db-schema-migration/migrations/migration_023.py @@ -0,0 +1,58 @@ +"""Schema migrations needed to release 2.9 in PROD""" + +import os + +from migrations.common import migrate_ct_config_values, migrate_indexes_and_constraints +from migrations.utils.utils import ( + get_db_connection, + get_db_driver, + get_logger, + print_counters_table, + run_cypher_query, +) + +logger = get_logger(os.path.basename(__file__)) +DB_DRIVER = get_db_driver() +DB_CONNECTION = get_db_connection() +MIGRATION_DESC = "schema-migration-release-2.9" + + +def migrate_feature_flags(db_driver, log) -> bool: + """ + Add 2 new fields to FeatureFlag node: section and feature. + """ + log.info( + "Adding new fields section and feature with dummy values to `FeatureFlag` nodes" + ) + _, summary1 = run_cypher_query( + db_driver, + """ + MATCH (ff:FeatureFlag) WHERE ff.section IS NULL + SET ff.section = 'admin' + """, + ) + print_counters_table(summary1.counters) + + _, summary2 = run_cypher_query( + db_driver, + """ + MATCH (ff:FeatureFlag) WHERE ff.feature IS NULL + SET ff.feature = 'FIXME' + """, + ) + print_counters_table(summary2.counters) + return summary1.counters.contains_updates or summary2.counters.contains_updates + + +def main(): + logger.info("Running migration on DB '%s'", os.environ["DATABASE_NAME"]) + + ### Common migrations + migrate_indexes_and_constraints(DB_CONNECTION, logger) + migrate_ct_config_values(DB_CONNECTION, logger) + ### FeatureFlag migration + migrate_feature_flags(DB_DRIVER, logger) + + +if __name__ == "__main__": + main() diff --git a/db-schema-migration/migrations/migration_overview_023.md b/db-schema-migration/migrations/migration_overview_023.md new file mode 100644 index 00000000..29af13dd --- /dev/null +++ b/db-schema-migration/migrations/migration_overview_023.md @@ -0,0 +1,33 @@ +# Release 2.9 (x 2026) + +## Common migrations + +### 1. Indexes and Constraints +------------------------------------- +#### Change Description +- Re-create all db indexes and constraints according to [db schema definition](https://orgremoved.visualstudio.com/Clinical-MDR/_git/neo4j-mdr-db?path=/db_schema.py&version=GBmain&_a=contents). + + +### 2. CT Config Values (Study Fields Configuration) +------------------------------------- +#### Change Description +- Re-create all `CTConfigValue` nodes according to values defined in [this file](https://orgremoved.visualstudio.com/Clinical-MDR/_git/studybuilder-import?path=/datafiles/configuration/study_fields_configuration.csv). + +#### Nodes Affected +- CTConfigValue + + +## Release specific migrations + +### 1. Add section and feature properties to FeatureFlags +------------------------------------- +#### Change description +- Add a `section` property to all `FeatureFlag` nodes with default value being `'admin'` +- Add a `feature` property to all `FeatureFlag` nodes with default value being `'FIXME'` + +#### Nodes affected +- `FeatureFlag` + +#### Relationships affected +- None + diff --git a/db-schema-migration/tests/test_correction_020.py b/db-schema-migration/tests/test_correction_020.py new file mode 100644 index 00000000..c9bd4a1e --- /dev/null +++ b/db-schema-migration/tests/test_correction_020.py @@ -0,0 +1,359 @@ +"""Data corrections for PROD: Test fix Non and Unscheduled visit labels and visibility, and restore CTCodelistTerm nodes.""" + +import json +import os +import tempfile +from unittest.mock import patch + +import pytest + +from data_corrections import correction_020 +from data_corrections.utils.utils import get_db_driver, run_cypher_query, save_md_title +from migrations.utils.utils import execute_statements, get_logger +from tests.data.db_before_correction_020 import ( + STUDY_000083_STUDY_VISITS, + TEST_DATA_RESTORE_CLT_NODES, +) +from tests.utils.utils import clear_db +from verifications import correction_verification_020 + +LOGGER = get_logger(os.path.basename(__file__)) +DB_DRIVER = get_db_driver() + +VERIFY_RUN_LABEL = "test_verification" +CORRECTION_ARGS = (DB_DRIVER, LOGGER, VERIFY_RUN_LABEL) + + +@pytest.fixture(scope="session", autouse=True) +def setup_logging(): + """Initialize logging once at the start of the test session""" + desc = f"Running verification for data corrections on DB '{os.environ['DATABASE_NAME']}'" + save_md_title(VERIFY_RUN_LABEL, correction_020.__doc__, desc) + yield + + +def _setup_test_data(test_data): + """Helper to set up test data for a test""" + clear_db() + execute_statements(test_data) + + +def test_fix_non_and_unscheduled_visit_label_and_visibility(): + """Test that Non and Unscheduled visits get 'V' prefix and show_visit=false""" + # Setup test data + _setup_test_data(STUDY_000083_STUDY_VISITS) + + # Verify initial state (should fail — visits have wrong label/visibility) + with pytest.raises(AssertionError): + correction_verification_020.test_non_and_unscheduled_visits_label_and_visibility() + + # Run correction + correction_020.fix_non_and_unscheduled_visit_label_and_visibility(*CORRECTION_ARGS) + + # Verify correction worked + correction_verification_020.test_non_and_unscheduled_visits_label_and_visibility() + + +@pytest.mark.order(after="test_fix_non_and_unscheduled_visit_label_and_visibility") +def test_repeat_fix_non_and_unscheduled_visit_label_and_visibility(): + """Test that visit label/visibility fix is idempotent""" + assert not correction_020.fix_non_and_unscheduled_visit_label_and_visibility( + *CORRECTION_ARGS + ) + + +def _build_test_change_log(): + """Build a synthetic change log matching the CDC format for test data.""" + tx_meta = { + "txCommitTime": "2026-04-01T09:58:53.162000000+00:00", + "executingUser": "neo4j", + "databaseName": "test", + "captureMode": "DIFF", + } + tx_id = "TEST_TX_001" + seq = [0] + + def seq_next(): + seq[0] += 1 + return seq[0] + + records = [] + + def add_node_delete(element_id, labels, properties): + records.append( + [ + tx_id, + seq_next(), + 0, + tx_meta, + { + "elementId": element_id, + "eventType": "n", + "operation": "d", + "state": { + "before": {"labels": labels, "properties": properties}, + "after": None, + }, + }, + ] + ) + + def add_rel_delete( # pylint: disable=too-many-arguments,too-many-positional-arguments + rel_type, start_labels, start_keys, end_labels, end_keys, props=None + ): + records.append( + [ + tx_id, + seq_next(), + 0, + tx_meta, + { + "elementId": f"5:test:{seq[0]}", + "eventType": "r", + "operation": "d", + "type": rel_type, + "start": { + "elementId": f"4:test:start_{seq[0]}", + "labels": start_labels, + "keys": start_keys, + }, + "end": { + "elementId": f"4:test:end_{seq[0]}", + "labels": end_labels, + "keys": end_keys, + }, + "state": { + "before": {"properties": props or {}}, + "after": None, + }, + }, + ] + ) + + # CTCodelistTerm A: C70543 / "NEVER" - with 2 CTPackageTerm + 2 CTCodelistRoot + clt_a_eid = "4:test:clt_a" + add_node_delete(clt_a_eid, ["CTCodelistTerm"], {"submission_value": "NEVER"}) + add_rel_delete( + "HAS_TERM_ROOT", + ["CTCodelistTerm"], + {}, + ["CTTermRoot"], + {"CTTermRoot": [{"uid": "C70543"}]}, + ) + # Override start elementId to match clt_a + records[-1][4]["start"]["elementId"] = clt_a_eid + + add_rel_delete( + "HAS_TERM", + ["CTCodelistRoot"], + {"CTCodelistRoot": [{"uid": "C78738"}]}, + ["CTCodelistTerm"], + {}, + props={ + "author_id": "fd909732-bc9e-492b-a1ed-6e27757a4f00", + "start_date": "2014-09-26T00:00:00.000000000+00:00", + }, + ) + records[-1][4]["end"]["elementId"] = clt_a_eid + + add_rel_delete( + "HAS_TERM", + ["CTCodelistRoot"], + {"CTCodelistRoot": [{"uid": "C83004"}]}, + ["CTCodelistTerm"], + {}, + props={ + "author_id": "fd909732-bc9e-492b-a1ed-6e27757a4f00", + "start_date": "2014-09-26T00:00:00.000000000+00:00", + }, + ) + records[-1][4]["end"]["elementId"] = clt_a_eid + + add_rel_delete( + "CONTAINS_SUBMISSION_VALUE", + ["CTPackageTerm"], + {"CTPackageTerm": [{"uid": "SDTM__CT__2021-12-17_C70543"}]}, + ["CTCodelistTerm"], + {}, + ) + records[-1][4]["end"]["elementId"] = clt_a_eid + + add_rel_delete( + "CONTAINS_SUBMISSION_VALUE", + ["CTPackageTerm"], + {"CTPackageTerm": [{"uid": "SDTM__CT__2022-03-25_C70543"}]}, + ["CTCodelistTerm"], + {}, + ) + records[-1][4]["end"]["elementId"] = clt_a_eid + + # CTCodelistTerm B: CTTerm_000108 / "OBESITY" - with 1 CTCodelistRoot, no CTPackageTerm + clt_b_eid = "4:test:clt_b" + add_node_delete(clt_b_eid, ["CTCodelistTerm"], {"submission_value": "OBESITY"}) + add_rel_delete( + "HAS_TERM_ROOT", + ["CTCodelistTerm"], + {}, + ["CTTermRoot"], + {"CTTermRoot": [{"uid": "CTTerm_000108"}]}, + ) + records[-1][4]["start"]["elementId"] = clt_b_eid + + add_rel_delete( + "HAS_TERM", + ["CTCodelistRoot"], + {"CTCodelistRoot": [{"uid": "CTCodelist_000005"}]}, + ["CTCodelistTerm"], + {}, + props={ + "author_id": "fd909732-bc9e-492b-a1ed-6e27757a4f00", + "order": 95, + "start_date": "2022-09-21T19:39:41.255386000+00:00", + }, + ) + records[-1][4]["end"]["elementId"] = clt_b_eid + + # Add a second transaction to simulate Phase B (so Phase A is correctly identified) + phase_b_meta = dict(tx_meta, txCommitTime="2026-04-01T09:58:53.446000000+00:00") + records.append( + [ + "TEST_TX_002", + seq_next(), + 0, + phase_b_meta, + { + "elementId": "4:test:dummy", + "eventType": "n", + "operation": "d", + "state": { + "before": { + "labels": ["CTCodelistRoot"], + "properties": {"uid": "deleted_codelist"}, + }, + "after": None, + }, + }, + ] + ) + + return records + + +def _write_test_change_log(): + """Write the test change log to a temporary file and return the path.""" + with tempfile.NamedTemporaryFile( + mode="w", suffix=".json", delete=False, prefix="correction_020_test_" + ) as tmpfile: + json.dump(_build_test_change_log(), tmpfile) + return tmpfile.name + + +def test_restore_codelist_term_nodes(): + """Test restoration of CTCodelistTerm nodes from change log""" + _setup_test_data(TEST_DATA_RESTORE_CLT_NODES) + + # Verify initial orphaned state - verification should fail before correction + with pytest.raises(AssertionError): + correction_verification_020.test_no_orphaned_correction_019_terms() + + # Write test change log and patch the constant to point at it + change_log_path = _write_test_change_log() + + try: + with patch.object(correction_020, "CHANGE_LOG_FILE", change_log_path): + # Run correction + result = correction_020.restore_codelist_term_nodes(*CORRECTION_ARGS) + assert result, "Correction should report changes were made" + + # Verification should pass after correction + correction_verification_020.test_no_orphaned_correction_019_terms() + + # Verify CTCodelistTerm A: C70543 / "NEVER" + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (tr:CTTermRoot {uid: 'C70543'}) + <-[:HAS_TERM_ROOT]-(clt:CTCodelistTerm {submission_value: 'NEVER'}) + RETURN clt + """, + ) + assert ( + len(res) == 1 + ), "CTCodelistTerm 'NEVER' should be created with HAS_TERM_ROOT to C70543" + + # Verify HAS_TERM from C78738 + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'C78738'}) + -[ht:HAS_TERM]->(clt:CTCodelistTerm {submission_value: 'NEVER'}) + RETURN ht.author_id AS author_id, ht.start_date AS start_date + """, + ) + assert len(res) == 1, "HAS_TERM from C78738 to 'NEVER' should be restored" + assert res[0]["author_id"] == "fd909732-bc9e-492b-a1ed-6e27757a4f00" + + # Verify HAS_TERM from C83004 + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'C83004'}) + -[ht:HAS_TERM]->(clt:CTCodelistTerm {submission_value: 'NEVER'}) + RETURN ht + """, + ) + assert len(res) == 1, "HAS_TERM from C83004 to 'NEVER' should be restored" + + # Verify CONTAINS_SUBMISSION_VALUE + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (pt:CTPackageTerm)-[:CONTAINS_SUBMISSION_VALUE]-> + (clt:CTCodelistTerm {submission_value: 'NEVER'}) + RETURN pt.uid AS uid ORDER BY uid + """, + ) + assert len(res) == 2, "Two CONTAINS_SUBMISSION_VALUE should be restored" + assert res[0]["uid"] == "SDTM__CT__2021-12-17_C70543" + assert res[1]["uid"] == "SDTM__CT__2022-03-25_C70543" + + # Verify CTCodelistTerm B: CTTerm_000108 / "OBESITY" + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'CTCodelist_000005'}) + -[ht:HAS_TERM]->(clt:CTCodelistTerm {submission_value: 'OBESITY'}) + -[:HAS_TERM_ROOT]->(tr:CTTermRoot {uid: 'CTTerm_000108'}) + RETURN ht.order AS order + """, + ) + assert len(res) == 1, "CTCodelistTerm B should be fully restored" + assert res[0]["order"] == 95, "HAS_TERM order property should be preserved" + + # Verify scenario C: existing CTCodelistTerm is not duplicated + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'C78738'}) + -[:HAS_TERM]->(clt:CTCodelistTerm {submission_value: 'EXISTING_SV'}) + -[:HAS_TERM_ROOT]->(tr:CTTermRoot {uid: 'CTTermRoot_existing'}) + RETURN clt + """, + ) + assert len(res) == 1, "Existing CTCodelistTerm should still be intact" + + finally: + os.unlink(change_log_path) + + +@pytest.mark.order(after="test_restore_codelist_term_nodes") +def test_repeat_restore_is_idempotent(): + """Test that running the correction again makes no changes (MERGE idempotency)""" + change_log_path = _write_test_change_log() + + try: + with patch.object(correction_020, "CHANGE_LOG_FILE", change_log_path): + result = correction_020.restore_codelist_term_nodes(*CORRECTION_ARGS) + assert not result, "Second run should report no changes (idempotent)" + finally: + os.unlink(change_log_path) diff --git a/db-schema-migration/tests/test_migration_023.py b/db-schema-migration/tests/test_migration_023.py new file mode 100644 index 00000000..9cf3134c --- /dev/null +++ b/db-schema-migration/tests/test_migration_023.py @@ -0,0 +1,85 @@ +import os + +import pytest + +from migrations import migration_023 +from migrations.utils.utils import ( + execute_statements, + get_db_connection, + get_db_driver, + get_logger, + run_cypher_query, +) +from tests import common +from tests.utils.utils import clear_db + +try: + from tests.data.db_before_migration_023 import TEST_DATA +except ImportError: + TEST_DATA = "" + + +# pylint: disable=unused-argument +# pylint: disable=redefined-outer-name +# pylint: disable=too-many-arguments +# pylint: disable=protected-access +# pylint: disable=broad-except + +# pytest fixture functions have other fixture functions as arguments, +# which pylint interprets as unused arguments + +db = get_db_connection() +DB_DRIVER = get_db_driver() +logger = get_logger(os.path.basename(__file__)) + + +@pytest.fixture(scope="module") +def initial_data(): + """Insert test data""" + clear_db() + execute_statements(TEST_DATA) + + +@pytest.fixture(scope="module") +def migration(initial_data): + # Run migration + migration_023.main() + + +def test_indexes_and_constraints(migration): + common.test_indexes_and_constraints(db, logger) + + +def test_ct_config_values(migration): + common.test_ct_config_values(db, logger) + + +def test_migrate_featureflag_nodes(migration): + logger.info("Verify migrate_feature_flags results") + + records, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (n:FeatureFlag) WHERE n.section IS NULL + RETURN count(n) AS count + """, + ) + assert ( + records[0]["count"] == 0 + ), "All FeatureFlag nodes must have a section property after migration" + + records, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (n:FeatureFlag) WHERE n.feature IS NULL + RETURN count(n) AS count + """, + ) + assert ( + records[0]["count"] == 0 + ), "All FeatureFlag nodes must have a feature property after migration" + + +@pytest.mark.order(after="test_migrate_featureflag_nodes") +def test_repeat_migrate_featureflag_nodes(migration): + assert not migration_023.migrate_feature_flags(DB_DRIVER, logger) diff --git a/db-schema-migration/verifications/correction_verification_020.py b/db-schema-migration/verifications/correction_verification_020.py new file mode 100644 index 00000000..9181c018 --- /dev/null +++ b/db-schema-migration/verifications/correction_verification_020.py @@ -0,0 +1,136 @@ +""" +This modules verifies that database nodes/relations and API endpoints look and behave as expected. + +It utilizes tests written for verifying a specific migration, +without inserting any test data and without running any migration script on the target database. +""" + +import os + +from data_corrections.utils.utils import get_db_driver, run_cypher_query +from migrations.utils.utils import get_logger + +LOGGER = get_logger(os.path.basename(__file__)) +DB_DRIVER = get_db_driver() + + +def test_non_and_unscheduled_visits_label_and_visibility(): + """Verify that all Non and Unscheduled visits have 'V'-prefixed short_visit_label and show_visit=False.""" + LOGGER.info( + "Checking Non and Unscheduled visits for correct short_visit_label prefix and show_visit" + ) + query = """ + MATCH (visit:StudyVisit) + WHERE visit.visit_class IN ['NON_VISIT', 'UNSCHEDULED_VISIT'] + AND (NOT visit.short_visit_label STARTS WITH 'V' OR visit.show_visit <> false) + RETURN visit.uid AS uid, visit.visit_class AS visit_class, + visit.short_visit_label AS short_visit_label, visit.show_visit AS show_visit + """ + res, _ = run_cypher_query(DB_DRIVER, query) + assert ( + len(res) == 0 + ), f"Found {len(res)} Non/Unscheduled visits with incorrect short_visit_label or show_visit: {res}" + + +# 79 CTTermRoot UIDs that were completely orphaned by correction 019 Phase A +# (i.e. lost ALL their CTCodelistTerm nodes, leaving the CTTermRoot with zero +# HAS_TERM_ROOT connections). The correction restores additional terms too, but +# those were only partially affected and still had other CTCodelistTerm nodes. +ORPHANED_TERM_UIDS = [ + "C101589", + "C101888", + "C105519", + "C111092", + "C116244", + "C116246", + "C12366", + "C12377", + "C12392", + "C12393", + "C12402", + "C12415", + "C12416", + "C12432", + "C12434", + "C12438", + "C12470", + "C12722", + "C12745", + "C12971", + "C13056", + "C132424", + "C132447", + "C139186", + "C14143", + "C14172", + "C15262", + "C15632", + "C165873", + "C166074", + "C16929", + "C17822", + "C182672", + "C182680", + "C182681", + "C182736", + "C182742", + "C182743", + "C183001", + "C183002", + "C183035", + "C25613", + "C25742", + "C26784", + "C28161", + "C3036", + "C32525", + "C33010", + "C33012", + "C33763", + "C33837", + "C33839", + "C3390", + "C38276", + "C38299", + "C42678", + "C48508", + "C51998", + "C53287", + "C64387", + "C64777", + "C64783", + "C67015", + "C67255", + "C67326", + "C67376", + "C67399", + "C67432", + "C67452", + "C67456", + "C67474", + "C70543", + "C73721", + "C80383", + "C94522", + "C99521", + "CTTerm_000101", + "CTTerm_000107", + "CTTerm_000108", +] + + +def test_no_orphaned_correction_019_terms(): + """Verify that none of the 79 terms orphaned by correction 019 remain orphaned.""" + query = """ + UNWIND $term_uids AS uid + MATCH (tr:CTTermRoot {uid: uid}) + WHERE NOT EXISTS { MATCH (:CTCodelistTerm)-[:HAS_TERM_ROOT]->(tr) } + RETURN COLLECT(tr.uid) AS orphaned_uids + """ + records, _ = run_cypher_query( + DB_DRIVER, query, params={"term_uids": ORPHANED_TERM_UIDS} + ) + orphaned = records[0]["orphaned_uids"] if records else [] + assert ( + len(orphaned) == 0 + ), f"Found {len(orphaned)} orphaned terms that should have been restored: {orphaned}" diff --git a/db-schema-migration/verifications/verification_023.py b/db-schema-migration/verifications/verification_023.py new file mode 100644 index 00000000..6d767195 --- /dev/null +++ b/db-schema-migration/verifications/verification_023.py @@ -0,0 +1,30 @@ +""" +This modules verifies that database nodes/relations and API endpoints look and behave as expected. + +It utilizes tests written for verifying a specific migration, +without inserting any test data and without running any migration script on the target database. +""" + +import pytest + +from tests import test_migration_023 + + +@pytest.fixture(scope="module") +def migration(): + """ + This method is empty as we do not want to run any migration script here. + We just wish to run all tests related to a specific migration. + """ + + +def test_ct_config_values(): + test_migration_023.test_ct_config_values(migration) + + +def test_indexes_and_constraints(): + test_migration_023.test_indexes_and_constraints(migration) + + +def test_migrate_featureflag_nodes(): + test_migration_023.test_migrate_featureflag_nodes(migration) diff --git a/documentation-portal/docs/.vuepress/config.js b/documentation-portal/docs/.vuepress/config.js index bac14389..e867d1c1 100644 --- a/documentation-portal/docs/.vuepress/config.js +++ b/documentation-portal/docs/.vuepress/config.js @@ -23,8 +23,9 @@ module.exports = { 'userguide/studies/guide_visits', 'userguide/studies/protocol_SoA_Milestone_row', 'userguide/studies/userguide_activities', - 'userguide/userguides_crf', 'userguide/studies/data_specifications', + 'userguide/library/activity_concepts', + 'userguide/userguides_crf', 'userguide/reports/userguides_reports' ] }, diff --git a/documentation-portal/docs/guides/cdisc/test-cases.md b/documentation-portal/docs/guides/cdisc/test-cases.md index 98746e43..13f97a1d 100644 --- a/documentation-portal/docs/guides/cdisc/test-cases.md +++ b/documentation-portal/docs/guides/cdisc/test-cases.md @@ -26,7 +26,7 @@ and are considered to be **consistent**/**valid**: If we have that codelist in the DB already: -> update with the rules below including all terms. Check for inconsistencies across all package files. Even if the codelist was imported and deactivated before, we will create a new final version and - therefore re-activate the codelist. In that case, we will also re-activate the Novo Nordisk managed name. + therefore re-activate the codelist. In that case, we will also re-activate the managed name. If we don't have the codelist in the DB: Create the codelist including all terms. > Example: We have imported the package 'ADaM CT 2014-09-26'. The next time we import from CDISC, diff --git a/documentation-portal/docs/guides/datamodel/physical/control-terminology.md b/documentation-portal/docs/guides/datamodel/physical/control-terminology.md index 2cf95c81..a5da874f 100644 --- a/documentation-portal/docs/guides/datamodel/physical/control-terminology.md +++ b/documentation-portal/docs/guides/datamodel/physical/control-terminology.md @@ -5,7 +5,7 @@ date: 2021-08-06 # Control Terminology Model At its core, Control Terminology provides a standardized set of values required for generating CDISC-compliant datasets. -In our model, Control Terminology can also be extended with Sponsor defined values - in particular, Novo Nordisk specific naming for certain values. +In our model, Control Terminology can also be extended with Sponsor defined values. The two main building blocks of control terminology are: - **Terms**: standardized names for terminology used in a clinical context. E.g. "100mg/L", "Weight", "Intravenously". diff --git a/documentation-portal/docs/guides/userguide/library/activity_concepts.md b/documentation-portal/docs/guides/userguide/library/activity_concepts.md new file mode 100644 index 00000000..aa1b1b3c --- /dev/null +++ b/documentation-portal/docs/guides/userguide/library/activity_concepts.md @@ -0,0 +1,272 @@ +# Activity Concepts + +## Introduction + +An ***Activity*** is by CDISC defined as an action, undertaking, or event, which is anticipated to be performed or observed, or was performed or observed, according to the study protocol during the execution of the study. + +CDISC defines a ***Biomedical Concept*** as a unit of biomedical knowledge created from a unique combination of characteristics that include implementation details like variables and terminologies, used as building blocks for standardized, hierarchically structured clinical research information. + +In OSB we support biomedical concepts of different types, and we see the concepts as definitions in more complex structures consisting of a set of related elements as opposed to controlled terminologies that can be represented as simpler term definitions in code lists. The term biomedical concepts has been difficult to grasp as it can cover many different things. In OSB we have therefore decided to simply name them **Concepts** as a broad term, and you can find the management of these under the menu **Library** > **Concepts**. The most important type of concept in OSB is concepts detailing activities, therefore simply named as **Activity Concepts**. + +An Activity Concept in OpenStudyBuilder is made to support both the protocol specification (electronically) as well as the down-stream data flow (Forms, SDTM). An activity can be a clinical data recording (like measurement of body weight), but it can also be an activity performed during the study that is not leading to collection of data (like administration of study drug). + +The OpenStudyBuilder activity concepts model consists of the following main elements each represented in tabs under the menu **Library** > **Concepts** > **Activities**: + +- **Activities** are, as described in the introduction, actions, undertakings, or events that are anticipated to be performed or observed, or were performed or observed, according to the study protocol during the execution of the study. An activity related to data collection results in a semantic logical observation — meaning a formally defined, meaningful data point — which can have different identifications depending on context and qualifiers. An activity not related to data collection refers to a semantically specific activity, i.e. an activity with a precise definition but without resulting data (e.g. administration of study drug). Activities are represented at the most detailed level as needed in the protocol SoA, and are referred to in protocol section 8 and protocol appendixes. + +- **Activity Groups** is high-level grouping of activities. The Activity Group can be what you decide to show in the protocol SoA. The Activity Group can be similar to CRF form names, but not necessarily. It is basically the clinical term relevant to show in the protocol both in overview section one as well as sub headings in section 8. + +- **Activity Subgroups** is a second grouping level of activities similar to the Activity Groups. + +- **Activity Instances** are similar to the CDISC BC SDTM specialisation, but defined semantically to an ADaM PARAM/PARAMCD specialisation. +The identification is for a specific semantic logical observation, this includes reference to context and qualifier values (like fasting plasma glucose). Primary identification is for ADaM BDS PARAM/PARAMCD, identification in occurrence datasets or column name in ADSL as well as identification in SDTM dataset. The Activity Instance can also include reference to external dictionaries (like NCI Thesaurus) and sponsor identification (like topic code). This will enable unique identification of source data, representation in SDTM by several qualifiers, and representation in ADaM BDS by PARAMCD value. The Activity Instance will always have a relationship to one Activity. The Activity Instance can have relationship to one or more Activity Instance Classes. The Activity Instance is the data collection specification of an activity to be used to link the operational SoA with data collection instruments such as CRFs and external data specifications. + +> Note, coming in OSB later is support for derived Activity Instances as derivation concepts. + +- **Activity Instance Classes** define the type of logical observation for an Activity Instance, and determine which Activity Item Classes (i.e. variable types) are relevant. For example, a numeric finding expects variables such as collection unit, collection value, standard unit, and value in standard unit — these are common characteristics of logical observations measuring numeric assessments. The Activity Instance Class has a recursive self-relationship describing the hierarchical relationship from general classes to more specific ones, where properties from the general ones are inherited by the sub classes (e.g. Subject Observation -> Finding -> Numeric Finding). The Activity Instance Class also has a relationship to zero or more Activity Item Classes. + +- **Activity Item Classes** are the semantically defined generic types of variables related to a specific Activity Instance Class. Each Activity Item Class is related to a Semantic Item Role and a Semantic Item Data Type. Most Activity Item Classes will be related to an Activity Instance via an Activity Item. The Activity Item Class holds the relationship to Variable Class representations in various Data Models and Implementation Guides, connecting the semantic definition of a variable to its various representations in connected data models. The Activity Item Classes are typically defined based on general SDTM and ADaM model understanding, but are independent of any specific data models. + +> NOTE, Each of the activity concepts main elements are individually versioned library objects in the OpenStudyBuilder repository solution. You can read more on the different versioning approaches in the user guide introduction section and other sections. + +The following sections describe each of the tabs where you manage and browse the main elements of the activity concepts model. Note, within each section you have an expandable section with attribute details. + +Each row in the display tables for activity concepts has hyper links into a detailed overview page for relevant column values. So e.g. a specific activity name will have a hyper link that opens a detailed overview of that specific activity, with relevant actions, different display views, and hyper links to related elements. + +## Activities + +On the Activities tab you have fast filtering between activities in status Final, Retired, Draft or All. You have standard free search, filtering, column displays, history, export as well as add, edit and delete actions. + +
    + Activities table + +| Column | Description | +|---------|---------------------| +| Library | Reference to which library the activity belongs to. This is Sponsor for activities defined and approved as standard within OSB; it can be set to CDISC if imported from CDISC Library; and it can be Requested if this activity is part of a user request. | +| Activity group | Sponsor name for the high-level grouping of activities. The activity group name can be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Activity subgroup | Sponsor name for the second level grouping of activities. The activity subgroup name can also be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Activity name | Sponsor name for the activity in title case. This can be chosen to be displayed in protocol SoA, will be the name being referenced in protocol section 8 and appendixes. | +| Sentence case name | Same name for the activity in lower case, but with correct casing in abbreviations if these are part of the name. This sentence case name is intended to be used in text generation for protocol section 8 and other sections when in-text references are made to activities so these occur in correct case. | +| Synonyms | Array of synonyms, these are defined to support flexible search and selection of standardised activity names. | +| Definition | The sponsor definition of the activity, this can be made with input from external definitions. | +| NCI Concept ID | NCI Thesaurus concept code identifier | +| NCI Concept name | NCI Thesaurus preferred name. As OSB currently does not have reference to the full NCI Thesaurus then we beside the NCI concept ID also keep a direct reference to the NCI Thesaurus preferred name. | +| Abbreviation | A sponsor defined abbreviation for the activity. | +| Data collection | Boolean flag to indicate if this activity relates to data collection. If not, the activity refers to reminders and procedures without data collection. | +| Legacy usage | Boolean flag to indicate if this activity is created for legacy data migration usage, and should not be used for new study specifications. | + +
    + + +## Activity Groups + +On the Activity Groups tab you have fast filtering between Activity Groups in status Final, Retired, Draft or All. You have standard free search, filtering, column displays, history, export as well as add, edit and delete actions. + +
    + Activity Groups table + +| Column | Description | +|---------|---------------------| +| Activity group | Sponsor name for the high-level grouping of activities. The activity group name can be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Sentence case name | Same name for the activity group in lower case, but with correct casing in abbreviations if these are part of the name. This sentence case name is intended to be used in text generation for protocol section 8 and other sections when in-text references are made to activity groups so these occur in correct case. | +| Abbreviation | A sponsor defined abbreviation for the activity. | +| Definition | The sponsor definition of the activity group, this can be made with input from external definitions. | +| NCI Concept ID | NCI Thesaurus concept code identifier | +| NCI Concept name | NCI Thesaurus preferred name. As OSB currently does not have reference to the full NCI Thesaurus then we beside the NCI concept ID also keep a direct reference to the NCI Thesaurus preferred name. | + +
    + + +## Activity Subgroups + +On the Activity Subgroups tab you have fast filtering between Activity Subgroups in status Final, Retired, Draft or All. You have standard free search, filtering, column displays, history, export as well as add, edit and delete actions. + +
    + Activity Subgroups table + +| Column | Description | +|---------|---------------------| +| Activity subgroup | Sponsor name for the second level grouping of activities. The activity subgroup name can also be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Sentence case name | Same name for the activity subgroup in lower case, but with correct casing in abbreviations if these are part of the name. This sentence case name is intended to be used in text generation for protocol section 8 and other sections when in-text references are made to activity subgroups so these occur in correct case. | +| Abbreviation | A sponsor defined abbreviation for the activity. | +| Definition | The sponsor definition of the activity subgroup, this can be made with input from external definitions. | +| NCI Concept ID | NCI Thesaurus concept code identifier | +| NCI Concept name | NCI Thesaurus preferred name. As OSB currently does not have reference to the full NCI Thesaurus then we beside the NCI concept ID also keep a direct reference to the NCI Thesaurus preferred name. | + +
    + + +## Activities by Grouping + +On the Activity by Groupings tab you can browse activities top-down by the grouping hierarchy. This page does not offer any searching, filtering or actions on managing activities or groupings. + +
    + Activities by Groupings table + +| Column | Description | +|---------|---------------------| +| Group/subgroup/activity | Nested hierarchy of sponsor name for the activity group, subgroup and activities. Note the same activity can exist multiple times if it is included in multiple groupings. | + +
    + + +## Activity Instances + +On the Activity Instances tab you have fast filtering between Activity Instances in status Final, Retired, Draft or All. You have standard free search, filtering, column displays, history, export as well as add, edit and delete actions. + +
    + Activity Instances table + +| Column | Description | +|---------|---------------------| +| Library | Reference to which library the activity instance belongs to. This is Sponsor for activity instances defined and approved as standard within OSB; it can be set to CDISC if imported from CDISC Library. | +| Activity group | Sponsor name for the high-level grouping of activities. The activity group name can be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Activity subgroup | Sponsor name for the second level grouping of activities. The activity subgroup name can also be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Activity name | Sponsor name for the activity in title case. This can be chosen to be displayed in protocol SoA, will be the name being referenced in protocol section 8 and appendixes. | +| Activity instance class | Name for the activity instance class. The activity instance class define the type of logical observation for an activity instance, and determine relevant activity item classes (i.e. variable types). | +| Activity instance | Sponsor name for the activity instance. | +| NCI Concept ID | NCI Thesaurus concept code identifier | +| NCI Concept name | NCI Thesaurus preferred name. As OSB currently does not have reference to the full NCI Thesaurus then we beside the NCI concept ID also keep a direct reference to the NCI Thesaurus preferred name. | +| Research lab | Boolean flag that indicate if the analysis for this activity instance is performed by a dedicated research lab. | +| Molecular weight | | +| Topic code | Internal unique identifier for the activity instance. It is made so it is readable and can be a longer text string (as opposite to the ADaM parameter). | +| ADaM parameter code | The related unique ADaM parameter code for the activity instance. The definition of an activity instance is made to be specific for an ADaM parameter code, thereby the ADaM parameter code is by definition also an unique identifier for the activity instance. The ADaM parameter code have a maximum length of 8 characters. | +| Required for activity | A Boolean flag that indicate if this activity is required to be included in the operational SoA if it's related parent activity is included in the detailed SoA. If so, the system will automatically add this to the operational SoA when the parent activity is added to the detailed SoA. | +| Default selected for activity | A Boolean flag that indicate this activity instance by default is selected to the operational SoA when the parent activity is added to the detailed SoA. But it is no mandatory and can be removed without giving error notifications. | +| Data sharing | A Boolean flag that indicate this activity instance not is sponsor specific or confidential and therefore generally can be shared with standards organisations (like CDISC), partners and publicly. | +| Legacy usage | A Boolean flag indicating this activity instance is defined to support data migrations for legacy study specifications and should as such not be used in new studies (even as the activity instance is available in final status). | + +
    + +### Create Activity Instance + + 1. Select **Library** > **Concepts** > **Activities** > **Activity Instances** tab, click the **'Add activity instance'** icon. + + [Add screen dump]: # + + 1. Search and select the Activity this Activity Instance is related to including the grouping. Once selected the header info box will show the selected Activity and Activity grouping. Then click Continue. + + 1. First select the Activity Instance Class (see values and related definitions in following step). For all classes the following shared attributes must be made: + - Related data domain (will map to CDISC SDTM dataset) + - Data category and subcategory (will map to content categories in CDISC SDTM datasets) + + [Add screen dump]: # + + 1. Depending on what Activity Instance Class is selected the following selections must be made: + - For **NumericFindings** class: + - Test code and test name (will map to the finding test code and test name variables in CDISC SDTM datasets). Note, this selection is a paired selection, and you have the option to use an advanced search by clicking the search icon next to the drop down controls. + - Unit dimension (grouping of a set of units where conversions can be made between these units) + - Standard unit for the numeric finding (this will control the unit for the standard value in the CDISC SDTM dataset) + + [Add screen dump]: # + + - For **CategoricFinding** class: + - Test code and test name (will map to the finding test code and test name variables in CDISC SDTM datasets). Note, this selection is a paired selection, and you have the option to use an advanced search by clicking the search icon next to the drop down controls. + - Code list for categoric finding original result and either all terms in this code list or a selected subset of terms as the valid response terms for the categoric finding. Note here you also have the option to use an advanced search by clicking the search icon next to the term value drop down control. + + [Add screen dump]: # + + - For **TextualFindings** class: + - Test code and test name (will map to the finding test code and test name variables in CDISC SDTM datasets). Note, this selection is a paired selection, and you have the option to use an advanced search by clicking the search icon next to the drop down controls. + + [Add screen dump]: # + + > Note, Other Activity Instance Classes are still to be specified. + + 1. Next is for the finding classes to specify optional potential Activity Item values that will drive the identification and name for the Activity Instance: + - Depending on the selections made on the previous step the system will suggest default values for Activity Instance name attributes, the ADaM PARAM/PARAMCD values, and the sponsor topic code identifier. + - If additional Activity Item Classes are added where their qualifier values are part of identifying the Activity Instance then those values will also be part of the system defaulted identifier values. + - Click the '+ Activity Item Class' control, select an Activity Item Class, and if applicable a qualifier term value. + - You have the option to override the system defaulted values by clicking the 'Customize' control. + - Enter the NCI Thesaurus preferred name and code ID. NCI values have to be looked up manually as OSB does not yet support dynamic search and reference to the NCI Thesaurus. + - For the findings classes it is possible to flag if data from the Activity Instance will come from a research lab. + + [Add screen dump]: # + + 1. Last is to specify optional Activity Items that are not part of identifying the Activity Instance. These values are used to specify data that can be collected on a CRF or an external specification. Examples are methods, anatomical locations or evaluator information. + - Click the '+ Activity Item Class' control, select an Activity Item Class, and if applicable a qualifier term value. + + 1. Click **SAVE**. + + 1. Approve the new Activity Instance by clicking the **Approve** icon or via the table row 3 actions dots menu. + + +### Edit Activity Instance + + 1. Select **Library** > **Concepts** > **Activities** > **Activity Instances** tab, search and select the row to be edited, click the 3 action dots on the row, **New version (attributes)**, then select to display **Draft** rows, select **Edit attributes** on the 3 action dots menu. + + [Add screen dump]: # + + > Note, you cannot edit the related activity for an Activity Instance. If this is needed you need to retire the Activity Instance and then create a new one for the correct activity. + > If you need to edit the groupings, then this is done by a dedicated versioning and edit action on the row menu. + + 1. Edit the Activity Instance attributes. + + > Note, the Activity Instance Class, data domain and Activity Item Classes related to the identification of PARAM/PARAMCD cannot be edited. + + 1. Enter a short change description. + + 1. Click **SAVE**. + + 1. Approve the changes by clicking the **Approve** icon or via the table row 3 actions dots menu. + + +### Edit Groupings for an Activity Instance + + [TO BE WRITTEN]: # + + +## Requested Activities + +On the Requested Activities tab you have fast filtering between activities that are handled or archived. You have standard free search, filtering, column displays, history, export as well as action for handling an activity request. + +
    + Requested Activities table + +| Column | Description | +|---------|---------------------| +| Activity group | Sponsor name for the high-level grouping of activities. The activity group name can be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Activity subgroup | Sponsor name for the second level grouping of activities. The activity subgroup name can also be used to be displayed in protocol SoA, as sub-section in protocol section 8, and as grouping in appendix 2 for lab assessments. | +| Activity name | Sponsor name for the activity in title case. This can be chosen to be displayed in protocol SoA, will be the name being referenced in protocol section 8 and appendixes. | +| Sentence case name | Same name for the activity in lower case, but with correct casing in abbreviations if these are part of the name. This sentence case name is intended to be used in text generation for protocol section 8 and other sections when in-text references are made to activities so these occur in correct case. | +| Definition | The sponsor definition of the activity, this can be made with input from external definitions. | +| Rationale for activity request | The rationale for the new activity as given by the requester. | +| Study ID | The study ID from where the request was made. | + +
    + + +## Activity Instance Classes + +On the Activity Instance Classes tab you can browse the nested definition of Activity Instance Classes by their hierarchy. This page only offers export and history. Management of Activity Instance Classes needs to be performed via the API directly. + +
    + Activity Instance Classes table + +| Column | Description | +|---------|---------------------| +| Name | Sponsor name for the activity instance class. | +| Definition | The sponsor definition of the activity instance class. | +| Domain specific | | +| Library | Reference to which library the activity instance class belongs to. This can at the moment only be the sponsor library as the class model is OSB specific. | | | + +
    + + +## Activity Item Classes + +On the Activity Item Classes tab you can browse, free search, filtering, column display, history, and export. Management of Activity Item Classes needs to be performed via the API directly. + +
    + Activity Item Classes table + +| Column | Description | +|---------|---------------------| +| Name | Sponsor name for the activity item class. | +| Definition | The sponsor definition of the activity item class. | +| NCI Code | | +| Library | Reference to which library the activity item class belongs to. This can at the moment only be the sponsor library as the class model is OSB specific. | | | + +
    + + diff --git a/documentation-portal/docs/guides/userguide/studies/userguide_activities.md b/documentation-portal/docs/guides/userguide/studies/userguide_activities.md index 1d0ca10e..2dcd8a2d 100644 --- a/documentation-portal/docs/guides/userguide/studies/userguide_activities.md +++ b/documentation-portal/docs/guides/userguide/studies/userguide_activities.md @@ -29,7 +29,7 @@ If baseline shown as time 0 is selected then the study visit duration time is us Study activities can be added to a study from the library standards, from other studies or they can be added as an activity placeholder that also will act as an activity request. -[![Study Activities](~@source/images/user_guides/guide_activities_study activities.png)](../../../images/user_guides/guide_activities_study activities.png) +[![Study Activities](~@source/images/user_guides/guide_activities_study_activities.png)](../../../images/user_guides/guide_activities_study_activities.png) In the library definition of an activity, the activity can exist within a possible set of activity groups and activity subgroups, and the display of these groupings can be controlled for the protocol SoA. Unfortunately, the groupings can only be selected when you add an activity to a study, it is currently not possible to change the grouping (this we will change in a coming release). diff --git a/documentation-portal/docs/images/user_guides/guide_activities_study activities.png b/documentation-portal/docs/images/user_guides/guide_activities_study_activities.png similarity index 100% rename from documentation-portal/docs/images/user_guides/guide_activities_study activities.png rename to documentation-portal/docs/images/user_guides/guide_activities_study_activities.png diff --git a/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable.csv b/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable.csv index 49df5924..0b69afe4 100644 --- a/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable.csv +++ b/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable.csv @@ -9,7 +9,7 @@ LAB,--REFID,7,LBREFID,Character,80,Mandatory,"Unique sample identifier: Sample LAB,TOPICCD,8,TOPICCD,Character,80,Mandatory,"Topic code, see 'Lab, content' sheet." LAB,SUPTEST,9,SUPTEST,Character,100,Optional,Supplier assessment name. LAB,--ORRES,10,LBORRES,Character,200,Mandatory when a result is obtained,Result. LBORRES should be NULL if a result is not obtained. -LAB,--STRESC,11,LBSTRESC,Character,200,Mandatory when a result is obtained and the result is categorical,Character result in standardised format. LBSTRESC should be compliant with CDISC CT codelist LBSTRESC (e.g. 'NEGATIVE') or Novo Nordisk-defined extensions. LBSTRESC should be NULL for numeric results. +LAB,--STRESC,11,LBSTRESC,Character,200,Mandatory when a result is obtained and the result is categorical,Character result in standardised format. LBSTRESC should be compliant with CDISC CT codelist LBSTRESC (e.g. 'NEGATIVE') or custom defined extensions. LBSTRESC should be NULL for numeric results. LAB,UNITCOLL,12,UNITCOLL,Character,40,Mandatory when a result is obtained for numeric assessments except for unitless data,"Collected unit. UNITCOLL should be compliant with CDISC CT codelist UNIT (e.g. 'mmol/L') or Novo Nordisk-defined extensions. Supplier should not perform unit-based conversion of results. UNITCOLL should be NULL for unitless data, e.g. pH." LAB,--ORNRLO,13,LBORNRLO,Character,40,Mandatory if there is a reference range with a lower limit,Lower limit of supplier reference range applicable to the subject in same unit as the result. LBORNRLO should be NULL if there is no lower limit. See 'Supplier guidance' sheet. LAB,--ORNRHI,14,LBORNRHI,Character,40,Mandatory if there is a reference range with an upper limit,Upper limit of supplier reference range applicable to the subject in same unit as the result. LBORNRHI should be NULL if there is no upper limit. See 'Supplier guidance' sheet. diff --git a/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable_class.csv b/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable_class.csv index c094db66..837d33dd 100644 --- a/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable_class.csv +++ b/mdr-standards-import/cdisc_data/packages/cdisc_data_models/FBDE/9-0/variable_class.csv @@ -9,7 +9,7 @@ Finding,,--REFID,7,Character,80,"Unique sample identifier: Sample ID, requisiti Finding,,TOPICCD,8,Character,80,"Topic code, see 'Lab, content' sheet." Finding,,SUPTEST,9,Character,100,Supplier assessment name. Finding,original_result,--ORRES,10,Character,200,Result. LBORRES should be NULL if a result is not obtained. -Finding,,--STRESC,11,Character,200,Character result in standardised format. LBSTRESC should be compliant with CDISC CT codelist LBSTRESC (e.g. 'NEGATIVE') or Novo Nordisk-defined extensions. LBSTRESC should be NULL for numeric results. +Finding,,--STRESC,11,Character,200,Character result in standardised format. LBSTRESC should be compliant with CDISC CT codelist LBSTRESC (e.g. 'NEGATIVE') or custom defined extensions. LBSTRESC should be NULL for numeric results. Finding,original_unit,UNITCOLL,12,Character,40,"Collected unit. UNITCOLL should be compliant with CDISC CT codelist UNIT (e.g. 'mmol/L') or Novo Nordisk-defined extensions. Supplier should not perform unit-based conversion of results. UNITCOLL should be NULL for unitless data, e.g. pH." Finding,normal_range_lower_limit,--ORNRLO,13,Character,40,Lower limit of supplier reference range applicable to the subject in same unit as the result. LBORNRLO should be NULL if there is no lower limit. See 'Supplier guidance' sheet. Finding,normal_range_upper_limit,--ORNRHI,14,Character,40,Upper limit of supplier reference range applicable to the subject in same unit as the result. LBORNRHI should be NULL if there is no upper limit. See 'Supplier guidance' sheet. diff --git a/neo4j-mdr-db/model/logical_data_model/old/ct_mt_proposal.graphml b/neo4j-mdr-db/model/logical_data_model/old/ct_mt_proposal.graphml index 40bb197a..1a7a13c1 100644 --- a/neo4j-mdr-db/model/logical_data_model/old/ct_mt_proposal.graphml +++ b/neo4j-mdr-db/model/logical_data_model/old/ct_mt_proposal.graphml @@ -481,7 +481,7 @@ is_testname_codelist: Boolean CTTermNameValue - Novo Nordisk preferred name + Preferred name diff --git a/neo4j-mdr-db/model/logical_data_model/old/logical-model-compound-bc-sample.graphml b/neo4j-mdr-db/model/logical_data_model/old/logical-model-compound-bc-sample.graphml index 6e789028..e9d56447 100644 --- a/neo4j-mdr-db/model/logical_data_model/old/logical-model-compound-bc-sample.graphml +++ b/neo4j-mdr-db/model/logical_data_model/old/logical-model-compound-bc-sample.graphml @@ -1057,7 +1057,7 @@ N0000175944< - Insulatard + DrugA diff --git a/neo4j-mdr-db/model/physical_data_model/neo4j-model.graphml b/neo4j-mdr-db/model/physical_data_model/neo4j-model.graphml index 7767d3eb..65d3a9b9 100644 --- a/neo4j-mdr-db/model/physical_data_model/neo4j-model.graphml +++ b/neo4j-mdr-db/model/physical_data_model/neo4j-model.graphml @@ -1688,7 +1688,7 @@ DeletedActivityInstructionRoot - Written documentation for this model is present in the Novo Nordisk Clinical MDR Documentation Portal. + Written documentation for this model is present in the Clinical MDR Documentation Portal. diff --git a/neo4j-mdr-db/neodash/neo4j_custom_procedures/background_queries/activity_instance_export.cypher b/neo4j-mdr-db/neodash/neo4j_custom_procedures/background_queries/activity_instance_export.cypher new file mode 100644 index 00000000..a46749c1 --- /dev/null +++ b/neo4j-mdr-db/neodash/neo4j_custom_procedures/background_queries/activity_instance_export.cypher @@ -0,0 +1,74 @@ +// Activity Instance Export +// Parameters needed: +// $neodash_activity_instance_value_name - list of activity instance names (set via :param in Neo4j Browser) +// $input - text filter for activity instance lookup + +// --- Query 1: Select Activity Instances --- +MATCH (n:`ActivityInstanceValue`)-[:LATEST_FINAL]->() +WHERE toLower(toString(n.`name`)) CONTAINS toLower($input) +RETURN DISTINCT n.`name` as value, n.`name` as display +ORDER BY size(toString(value)) ASC LIMIT 20; + +:param neodash_activity_instance_value_name => ["Albumin Urine"]; +// --- Query 2: Activity items --- +MATCH (n1:ActivityInstanceValue)<-[:LATEST_FINAL]-() +WHERE n1.name IN $neodash_activity_instance_value_name +MATCH (n1)-[r1:CONTAINS_ACTIVITY_ITEM]-(ai:ActivityItem) + +MATCH + (ai)-[r2:HAS_ACTIVITY_ITEM]- + (i1:ActivityItemClassRoot)-[r3:LATEST_FINAL]- + (k1:ActivityItemClassValue) +MATCH (n1)-[r4:LATEST_FINAL]-(i2:ActivityInstanceRoot) +MATCH + (i2)-[r5:HAS_GROUPING_ROOT]-> + (aigr:ActivityInstanceGroupingRoot)-[r30:LATEST]-> + (aigv:ActivityInstanceGroupingValue)-[r6:HAS_ACTIVITY]- + (n10:ActivityGrouping)<-[r7:HAS_GROUPING]- + (n11:ActivityValue) + +MATCH + (n1)-[r8:ACTIVITY_INSTANCE_CLASS]- + (i5:ActivityInstanceClassRoot)-[r9:LATEST_FINAL]- + (k3:ActivityInstanceClassValue) +OPTIONAL MATCH + (ai)-[r10:HAS_CT_TERM]->(context:CTTermContext), + (context)-[r11:HAS_SELECTED_TERM]-> + (i_term_root:CTTermRoot)<-[r12:HAS_TERM_ROOT]- + (cl_term:CTCodelistTerm), + (context)-[r13:HAS_SELECTED_CODELIST]-> + (cl_root:CTCodelistRoot)-[r14:HAS_TERM]-> + (cl_term), + (cl_root)-[r22:HAS_ATTRIBUTES_ROOT]- + (i_cl_attr_root:CTCodelistAttributesRoot)-[r88:LATEST_FINAL]- + (cl_attr:CTCodelistAttributesValue) + +OPTIONAL MATCH + (ai)-[r21:HAS_UNIT_DEFINITION]-> + (udr:UnitDefinitionRoot)-[r22:LATEST_FINAL]-> + (udv:UnitDefinitionValue) + +WITH + n1.name AS ACTIVITY_INSTANCE_NAME, + k3.name AS ACTIVITY_ITEM_CLASS_NAME, + k1.name AS ACTIVITY_ITEM_TYPE, + cl_attr.submission_value AS codelist, + cl_term.submission_value AS term, + "" AS IS_ADAM_PARAM_SPECIFIC +WITH + ACTIVITY_INSTANCE_NAME, + ACTIVITY_ITEM_CLASS_NAME, + ACTIVITY_ITEM_TYPE, + codelist, + apoc.text.join(collect(DISTINCT term), '|') AS terms, + IS_ADAM_PARAM_SPECIFIC +RETURN + ACTIVITY_INSTANCE_NAME, + ACTIVITY_ITEM_CLASS_NAME, + ACTIVITY_ITEM_TYPE, + CASE codelist + WHEN codelist THEN apoc.text.join([codelist, terms], ':') + ELSE "" + END AS ACTIVITY_ITEM_VALUE, + IS_ADAM_PARAM_SPECIFIC +ORDER BY ACTIVITY_INSTANCE_NAME, ACTIVITY_ITEM_TYPE; \ No newline at end of file diff --git a/neo4j-mdr-db/neodash/neodash_reports/activity_instance_export.json b/neo4j-mdr-db/neodash/neodash_reports/activity_instance_export.json index b8e91335..d90f3bc2 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/activity_instance_export.json +++ b/neo4j-mdr-db/neodash/neodash_reports/activity_instance_export.json @@ -1,96 +1,93 @@ -{ - "title": "Activity Instance Export", - "version": "2.4", - "settings": { - "pagenumber": 0, - "editable": true, - "fullscreenEnabled": false, - "parameters": { - "neodash_activityinstancevalue_name": [ - - ], - "neodash_activityinstancevalue_name_display": [ - - ], - "neodash_": "" - }, - "theme": "light" - }, - "pages": [ - { - "title": "New page", - "reports": [ - { - "id": "fd7ccd21-1a54-4645-ae33-a3c455e0b449", - "title": "Activity items", - "query": "MATCH (n1:ActivityInstanceValue)\nWHERE n1.name in $neodash_activityinstancevalue_name\nMATCH (n1)-[r1:CONTAINS_ACTIVITY_ITEM]-(ai:ActivityItem)\n\nMATCH\n (ai)-[r2:HAS_ACTIVITY_ITEM]-\n (n6:ActivityItemClassRoot)-[r3:LATEST_FINAL]-\n (n7:ActivityItemClassValue)\nMATCH (n1)-[r4:LATEST_FINAL]-(n8:ActivityInstanceRoot)\nMATCH\n (n1)-[r5:HAS_ACTIVITY]-\n (n9:ActivityGrouping)-[r6:HAS_GROUPING]-\n (n10:ActivityValue)-[r7:LATEST_FINAL]-\n (n11:ActivityRoot)\nMATCH\n (n1)-[r8:ACTIVITY_INSTANCE_CLASS]-\n (n12:ActivityInstanceClassRoot)-[r9:LATEST_FINAL]-\n (n13:ActivityInstanceClassValue)\n\n\n\n// Make sure that the query works in both previous (PRD) and new (DEV) model\n// Previous model: ActivityGrouping-[r10:IN_SUBGROUP]-(ActivityValidGroup)-[r11:IN_GROUP]-(ActivityGroupValue)\nOPTIONAL MATCH\n (n9)-[r12:IN_SUBGROUP]-\n (old_avg:ActivityValidGroup)-[r13:IN_GROUP]-\n (old_agv:ActivityGroupValue)\nOPTIONAL MATCH (old_avg)-[r14:HAS_GROUP]-(old_asgv:ActivitySubGroupValue)\n// New model: ActivityGrouping-[r15:HAS_SELECTED_GROUP]-(ActivityGroupValue)\nOPTIONAL MATCH\n (n9)-[r16:HAS_SELECTED_GROUP]-\n (new_agv:ActivityGroupValue)\nOPTIONAL MATCH (n9)-[r17:HAS_SELECTED_SUBGROUP]-(new_asgv:ActivitySubGroupValue)\n\nOPTIONAL MATCH\n (ai)-[r18:HAS_CT_TERM]->\n (n3:CTTermRoot)-[r19:HAS_ATTRIBUTES_ROOT]->\n (n4:CTTermAttributesRoot)-[r20:LATEST_FINAL]-\n (n5:CTTermAttributesValue)\nOPTIONAL MATCH\n (ai)-[r21:HAS_UNIT_DEFINITION]->\n (udr:UnitDefinitionRoot)-[r22:LATEST_FINAL]->\n (udv:UnitDefinitionValue)\n\nWITH\n COALESCE(collect(new_agv.name)[0], collect(old_agv.name)[0]) AS `Assm. group`,\n COALESCE(collect(new_asgv.name)[0], collect(old_asgv.name)[0]) AS `Assm. subgroup`,\n n10.name AS activity,\n n1.name AS activity_instance,\n n13.name AS ActivityInstanceClassValue,\n n1.topic_code AS TOPIC_CD,\n n7.name AS activity_item_type,\n COALESCE(n5.name_submission_value, n5.code_submission_value, udv.name) AS term\nRETURN\n `Assm. group`,\n `Assm. subgroup`,\n activity,\n activity_instance,\n ActivityInstanceClassValue,\n TOPIC_CD,\n activity_item_type,\n \"\" as codelist,\n apoc.text.join(collect(DISTINCT term), '|') AS activity_item_value\nORDER BY TOPIC_CD\n", - "width": 21, - "height": 6, - "x": 0, - "y": 2, - "type": "table", - "selection": {}, - "settings": { - "compact": true, - "wrapContent": true, - "allowDownload": true, - "actionsRules": [ - { - "condition": "Click", - "field": "", - "value": "", - "customization": "set variable", - "customizationValue": "" - } - ], - "styleRules": [ - { - "field": "", - "condition": "=", - "value": "", - "customization": "row color", - "customizationValue": "black" - } - ] - } - }, - { - "id": "972e858e-4a51-4465-ab27-8fca527465f2", - "title": "Select Activity Instances", - "query": "MATCH (n:`ActivityInstanceValue`) \nWHERE toLower(toString(n.`name`)) CONTAINS toLower($input) \nRETURN DISTINCT n.`name` as value, n.`name` as display ORDER BY size(toString(value)) ASC LIMIT 5", - "width": 21, - "height": 2, - "x": 0, - "y": 0, - "type": "select", - "selection": {}, - "settings": { - "type": "Node Property", - "entityType": "ActivityInstanceValue", - "propertyType": "name", - "propertyTypeDisplay": "name", - "parameterName": "neodash_activityinstancevalue_name", - "multiSelector": true, - "multiSelectLimit": 20 - }, - "schema": [] - } - ] - } - ], - "parameters": {}, - "extensions": { - "active": true, - "activeReducers": [], - "advanced-charts": { - "active": true - }, - "styling": { - "active": true - }, - "actions": { - "active": true - } - }, - "uuid": "be1726c5-b9a1-4b07-ab16-5eb7c6a69345" +{ + "title": "Activity Instance Export", + "version": "2.4", + "settings": { + "pagenumber": 0, + "editable": true, + "fullscreenEnabled": false, + "parameters": { + "neodash_activity_instance_value_name": [], + "neodash_activity_instance_value_name_display": [], + "neodash_": "" + }, + "theme": "light" + }, + "pages": [ + { + "title": "New page", + "reports": [ + { + "id": "fd7ccd21-1a54-4645-ae33-a3c455e0b449", + "title": "Activity items", + "query": "MATCH (n1:ActivityInstanceValue)<-[:LATEST_FINAL]-()\nWHERE n1.name IN $neodash_activity_instance_value_name\nMATCH (n1)-[r1:CONTAINS_ACTIVITY_ITEM]-(ai:ActivityItem)\nMATCH\n (ai)-[r2:HAS_ACTIVITY_ITEM]-\n (i1:ActivityItemClassRoot)-[r3:LATEST_FINAL]-\n (k1:ActivityItemClassValue)\n MATCH (n1)-[r4:LATEST_FINAL]-(i2:ActivityInstanceRoot)\nMATCH\n (i2)-[r5:HAS_GROUPING_ROOT]->\n (aigr:ActivityInstanceGroupingRoot)-[r30:LATEST]->\n (aigv:ActivityInstanceGroupingValue)-[r6:HAS_ACTIVITY]-\n (n10:ActivityGrouping)<-[r7:HAS_GROUPING]-\n (n11:ActivityValue)\n MATCH\n (n1)-[r8:ACTIVITY_INSTANCE_CLASS]-\n (i5:ActivityInstanceClassRoot)-[r9:LATEST_FINAL]-\n (k3:ActivityInstanceClassValue)\n OPTIONAL MATCH\n (ai)-[r10:HAS_CT_TERM]->(context:CTTermContext),\n (context)-[r11:HAS_SELECTED_TERM]->\n (i_term_root:CTTermRoot)<-[r12:HAS_TERM_ROOT]-\n (cl_term:CTCodelistTerm),\n (context)-[r13:HAS_SELECTED_CODELIST]->\n (cl_root:CTCodelistRoot)-[r14:HAS_TERM]->\n (cl_term),\n (cl_root)-[r22:HAS_ATTRIBUTES_ROOT]-\n (i_cl_attr_root:CTCodelistAttributesRoot)-[r88:LATEST_FINAL]-\n (cl_attr:CTCodelistAttributesValue)\n OPTIONAL MATCH\n (ai)-[r21:HAS_UNIT_DEFINITION]->\n (udr:UnitDefinitionRoot)-[r22:LATEST_FINAL]->\n (udv:UnitDefinitionValue)\n WITH\n n1.name AS ACTIVITY_INSTANCE_NAME,\n k3.name AS ACTIVITY_ITEM_CLASS_NAME,\n k1.name AS ACTIVITY_ITEM_TYPE,\n cl_attr.submission_value AS codelist,\n cl_term.submission_value AS term,\n '' AS IS_ADAM_PARAM_SPECIFIC\n WITH\n ACTIVITY_INSTANCE_NAME,\n ACTIVITY_ITEM_CLASS_NAME,\n ACTIVITY_ITEM_TYPE,\n codelist,\n apoc.text.join(collect(DISTINCT term), '|') AS terms,\n IS_ADAM_PARAM_SPECIFIC\n RETURN\n ACTIVITY_INSTANCE_NAME,\n ACTIVITY_ITEM_CLASS_NAME,\n ACTIVITY_ITEM_TYPE,\n CASE codelist\n WHEN codelist THEN apoc.text.join([codelist, terms], ':')\n ELSE ''\n END AS ACTIVITY_ITEM_VALUE,\n IS_ADAM_PARAM_SPECIFIC\n ORDER BY ACTIVITY_INSTANCE_NAME, ACTIVITY_ITEM_TYPE;\n ", + "width": 21, + "height": 6, + "x": 0, + "y": 2, + "type": "table", + "selection": {}, + "settings": { + "compact": true, + "wrapContent": true, + "allowDownload": true, + "actionsRules": [ + { + "condition": "Click", + "field": "", + "value": "", + "customization": "set variable", + "customizationValue": "" + } + ], + "styleRules": [ + { + "field": "", + "condition": "=", + "value": "", + "customization": "row color", + "customizationValue": "black" + } + ], + "noDataMessage": "Select Activity Instances above" + } + }, + { + "id": "972e858e-4a51-4465-ab27-8fca527465f2", + "title": "Select Activity Instances", + "query": "MATCH (n:`ActivityInstanceValue`) \nWHERE toLower(toString(n.`name`)) CONTAINS toLower($input) \nRETURN DISTINCT n.`name` as value, n.`name` as display ORDER BY size(toString(value)) ASC LIMIT 5", + "width": 21, + "height": 2, + "x": 0, + "y": 0, + "type": "select", + "selection": {}, + "settings": { + "type": "Node Property", + "entityType": "ActivityInstanceValue", + "propertyType": "name", + "propertyTypeDisplay": "name", + "parameterName": "neodash_activity_instance_value_name", + "multiSelector": true, + "multiSelectLimit": 20 + }, + "schema": [] + } + ] + } + ], + "parameters": {}, + "extensions": { + "active": true, + "activeReducers": [], + "advanced-charts": { + "active": true + }, + "styling": { + "active": true + }, + "actions": { + "active": true + } + }, + "uuid": "be1726c5-b9a1-4b07-ab16-5eb7c6a69345" } \ No newline at end of file diff --git a/neo4j-mdr-db/neodash/neodash_reports/activity_library_content_dashboard.json b/neo4j-mdr-db/neodash/neodash_reports/activity_library_content_dashboard.json index 36a8573d..489e0824 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/activity_library_content_dashboard.json +++ b/neo4j-mdr-db/neodash/neodash_reports/activity_library_content_dashboard.json @@ -57,11 +57,13 @@ "neodash_ai_display": [], "neodash_operator": "AND", "neodash_operator_display": "AND", - "neodash_study_act_select": 1301509, + "neodash_study_act_select": { }, "neodash_study_activity": [], - "neodash_study_activity_display": [], + "neodash_study_activity_display":[], "neodash_show_latest": "N", - "neodash_show_latest_display": "N" + "neodash_show_latest_display": "N", + "neodash_activityvalue_name": [], + "neodash_activityvalue_name_display": [] }, "resizing": "bottom-right", "disableRowLimiting": false, @@ -90,7 +92,7 @@ { "id": "7f7a7cda-2fa3-413d-bac7-40bda540d74e", "title": "Number of Activities and Instances by Group and Subgroup", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),(act)<-[:LATEST]-()\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nreturn distinct agrp.name as `Activity Group`, \nasgrp.name as `Activity Subgroup`,\ncount(distinct act.name) as `Number of Activities`,\ncount(distinct ai.name) as `Number of Activity Instances`", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),(act)<-[:LATEST]-()\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nreturn distinct agrp.name as `Activity Group`, \nasgrp.name as `Activity Subgroup`,\ncount(distinct act.name) as `Number of Activities`,\ncount(distinct ai.name) as `Number of Activity Instances`", "width": 12, "height": 6, "x": 0, @@ -107,7 +109,7 @@ { "id": "119873c7-f120-4db1-ac52-64d55a3bb120", "title": "Number of Activities and Instances by Type and Subtype", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),(act)<-[:LATEST]-()\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nOPTIONAL MATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nOPTIONAL MATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nreturn \naicp.name as `Activity Type`,\naic.name as `Activity Subtype`,\ncount(distinct ai.name) as `Number of Activity Instances`,\ncount(distinct act.name) as `Number of Activities`\n\n\n\n\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),(act)<-[:LATEST]-()\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nOPTIONAL MATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nOPTIONAL MATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nreturn \naicp.name as `Activity Type`,\naic.name as `Activity Subtype`,\ncount(distinct ai.name) as `Number of Activity Instances`,\ncount(distinct act.name) as `Number of Activities`\n\n\n\n\n\n", "width": 12, "height": 6, "x": 12, @@ -125,7 +127,7 @@ { "id": "e5b87c60-b072-4f8a-955a-9cc1e778f251", "title": "Number of Activities and Instances", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(), (act)-[:LATEST]-()\nreturn count(distinct act) as `Number of Activities`, count(distinct ai) as `Number of Activity Instances`\n\n\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue), (act)-[:LATEST]-()\nreturn count(distinct act) as `Number of Activities`, count(distinct ai) as `Number of Activity Instances`\n\n\n\n", "width": 12, "height": 4, "x": 12, @@ -143,7 +145,7 @@ { "id": "1402a2c5-8cdf-406e-858d-96bc0bf0c933", "title": "Groupings of Activities", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),(act)<-[:LATEST]-()\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\n[aicp.name,aic.name,agrp.name,asgrp.name] as Grouping,\ncount(distinct act.name) as N_act\nreturn Grouping, N_act as Activities", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),(act)<-[:LATEST]-()\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\n[aicp.name,aic.name,agrp.name,asgrp.name] as Grouping,\ncount(distinct act.name) as N_act\nreturn Grouping, N_act as Activities", "width": 12, "height": 4, "x": 0, @@ -172,7 +174,7 @@ "reports": [ { "title": "Activity Subgroup", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[HSSG:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[HSG:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH (g)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name =$neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT asgrp.`name` as value, asgrp.`name` as display ORDER BY size(toString(value)) ASC", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[HSSG:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[HSG:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH (g)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name =$neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT asgrp.`name` as value, asgrp.`name` as display ORDER BY size(toString(value)) ASC", "width": 6, "height": 2, "x": 18, @@ -191,7 +193,7 @@ }, { "title": "Number of Activities (Instances per Activity, when Subgroup is Selected)", - "query": "// only instance class selected\nCALL apoc.case([not $neodash_activityinstanceclassvalue_name='' and $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn aic.name as Category,\ncount(distinct act) as `Number of Activities` order by Category' ,\n\n// instance class and subclass selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn agrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n\n// instance class, subclass and group selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c]\nMATCH (g)-[:HAS_SELECTED_SUBGROUP]-(asgrp:ActivitySubGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn asgrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n\n// all fields selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and not $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c] and asgrp.name in[$d]\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn act.name as Category,\ncount(distinct ai) as `Number of Activities` order by Category'],\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) \nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) \nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nreturn aicp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n{a:$neodash_activityinstanceclassvalue_name,\nb:$neodash_activityinstanceclassvalue_name_subtype,\nc:$neodash_activitygroupvalue_name, \nd:$neodash_activitysubgroupvalue_name}) YIELD value \nreturn value.Category as Category,\nvalue.`Number of Activities` as`Number of Activities/Instances` order by Category\n\n", + "query": "// only instance class selected\nCALL apoc.case([not $neodash_activityinstanceclassvalue_name='' and $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn aic.name as Category,\ncount(distinct act) as `Number of Activities` order by Category' ,\n\n// instance class and subclass selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn agrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n\n// instance class, subclass and group selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c]\nMATCH (g)-[:HAS_SELECTED_SUBGROUP]-(asgrp:ActivitySubGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn asgrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n\n// all fields selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and not $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c] and asgrp.name in[$d]\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn act.name as Category,\ncount(distinct ai) as `Number of Activities` order by Category'],\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) \nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) \nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nreturn aicp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n{a:$neodash_activityinstanceclassvalue_name,\nb:$neodash_activityinstanceclassvalue_name_subtype,\nc:$neodash_activitygroupvalue_name, \nd:$neodash_activitysubgroupvalue_name}) YIELD value \nreturn value.Category as Category,\nvalue.`Number of Activities` as`Number of Activities/Instances` order by Category\n\n", "width": 24, "height": 6, "x": 0, @@ -226,7 +228,7 @@ }, { "title": "Activity Group", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name = $neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT agrp.`name` as value, agrp.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name = $neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT agrp.`name` as value, agrp.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 12, @@ -246,7 +248,7 @@ }, { "title": "Activity Class", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) return distinct aicp.name as value, aicp.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) return distinct aicp.name as value, aicp.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 0, @@ -267,7 +269,7 @@ }, { "title": "Activity as a Graph View (Logical View) - $neodash_activity", - "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", + "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", "width": 12, "height": 6, "x": 0, @@ -275,9 +277,9 @@ "type": "graph", "selection": { "ActivityGrouping": "(label)", - "TemplateParameterTermValue": "name", - "ConceptValue": "name", "ActivityGroupValue": "name", + "ConceptValue": "name", + "TemplateParameterTermValue": "name", "ActivitySubGroupValue": "name", "ActivityValue": "name", "ActivityInstance": "name", @@ -285,7 +287,16 @@ "ActivityItem": "(label)", "ActivityItemClass": "name", "CTTerm": "name", - "CTCodeList": "(label)" + "HAS": "(label)", + "HAS_ACTIVITY": "(label)", + "OF_CLASS": "(label)", + "HAS_ROLE": "(label)", + "HAS_TYPE": "(label)", + "HAS_GROUPING": "(label)", + "HAS_SELECTED_SUBGROUP": "(label)", + "HAS_SELECTED_GROUP": "(label)", + "CTCodeList": "name", + "FOR": "(label)" }, "settings": { "nodePositions": {}, @@ -311,32 +322,29 @@ "uid" ], [ - "TemplateParameterTermValue", + "ActivityGroupValue", "name", - "name_sentence_case", - "definition", - "synonyms", - "is_request_rejected", - "is_data_collected", - "is_request_final", - "is_multiple_selection_allowed" + "name_sentence_case" ], [ "ConceptValue", "name", "name_sentence_case", - "definition", "synonyms", "is_request_rejected", - "is_data_collected", "is_request_final", + "is_data_collected", "is_multiple_selection_allowed" ], [ - "ActivityGroupValue", + "TemplateParameterTermValue", "name", "name_sentence_case", - "definition" + "synonyms", + "is_request_rejected", + "is_request_final", + "is_data_collected", + "is_multiple_selection_allowed" ], [ "ActivitySubGroupValue", @@ -349,8 +357,8 @@ "name", "is_request_rejected", "name_sentence_case", - "is_data_collected", "is_request_final", + "is_data_collected", "is_multiple_selection_allowed" ], [ @@ -358,14 +366,13 @@ "topic_code", "is_derived", "adam_param_code", - "name_sentence_case", - "is_legacy_usage", "name", - "definition", + "name_sentence_case", "is_default_selected_for_activity", "is_data_sharing", "is_required_for_activity", "legacy_description", + "is_legacy_usage", "is_research_lab" ], [ @@ -384,33 +391,24 @@ "ActivityItemClass", "name", "definition", + "display_name", "nci_concept_id", "order" ], [ "CTTerm", + "name", + "name_sentence_case", "us_conventional_unit", "display_unit", "si_unit", "master_unit", - "name", - "definition", "use_complex_unit_conversion", "use_molecular_weight", "conversion_factor_to_master", "convertible_unit", "order", - "legacy_code", - "name_sentence_case" - ], - [ - "CTCodeList", - "preferred_term", - "name", - "definition", - "extensible", - "submission_value", - "ordinal" + "legacy_code" ], [ "HAS", @@ -424,10 +422,6 @@ "OF_CLASS", "type" ], - [ - "FOR", - "type" - ], [ "HAS_ROLE", "type" @@ -444,12 +438,25 @@ ], [ "HAS_SELECTED_GROUP" + ], + [ + "CTCodeList", + "preferred_term", + "name", + "definition", + "codelist_type", + "extensible", + "submission_value" + ], + [ + "FOR", + "type" ] ] }, { "title": "Activity Subclass", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name = $neodash_activityinstanceclassvalue_name return distinct aic.`name` as value, aic.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name = $neodash_activityinstanceclassvalue_name return distinct aic.`name` as value, aic.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 6, @@ -470,7 +477,7 @@ }, { "title": "Activity in Tabular Format - $neodash_activity", - "query": "CALL\n apoc.when(\n NOT $neodash_activity = '',\n \"\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n apoc.convert.toSet(collect(agrp.name)) AS ActivityGroup,\n apoc.convert.toSet(collect(asgrp.name)) AS ActivitySubGroup,\n act.name AS Activity,\n aitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nWITH\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivityGroup))) AS ActivityGroup,\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivitySubGroup))) AS ActivitySubGroup,\n Activity,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Terms,\n `Code List`,\n Role,\n `Data Type`\nRETURN\n ActivityGroup,\n ActivitySubGroup,\n Activity,\n `Activity Item Class`,\n Terms,\n `Code List`,\n Role,\n `Data Type`\",\n \"match(x:blbla) return *\",\n {neodash_activity: $neodash_activity}\n )\n YIELD value\nRETURN\n value.ActivityGroup AS `Activity Group`,\n value.ActivitySubGroup AS `Activity Subgroup`,\n value.Activity AS Activity,\n value.`Activity Item Class` AS `Activity Item Class`,\n value.Terms AS Terms,\n value.`Code List` AS `Code List`,\n value.Role AS Role,\n value.`Data Type` AS `Data Type`", + "query": "// Skip entirely if parameter is empty\nWITH $neodash_activity AS actName\nWHERE actName <> ''\n\n// Anchor on the specific ActivityValue first (uses index)\nMATCH (act:ActivityValue {name: actName})\n\n// Core traversal from anchor\nMATCH (act)-[:HAS_GROUPING]->(g:ActivityGrouping)\n -[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[:LATEST]-(:ActivityInstanceGroupingRoot)\n <-[:HAS_GROUPING_ROOT]-(:ActivityInstanceRoot)\n -[:LATEST]->(ai:ActivityInstanceValue)\n -[:CONTAINS_ACTIVITY_ITEM]->(aitm1:ActivityItem)\n\nMATCH (ai)-[:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[:LATEST]->(aic:ActivityInstanceClassValue)\n\n// Require ActivityItemClass — was MATCH so keep as MATCH\nMATCH (aitmc1r:ActivityItemClassRoot)-[:HAS_ACTIVITY_ITEM]->(aitm1),\n (aitmc1r)-[:LATEST]->(aitmc1:ActivityItemClassValue)\n\n// Require DataType — was MATCH so keep as MATCH\nMATCH (aitmc1)-[:HAS_DATA_TYPE]->(:CTTermContext)\n -[:HAS_SELECTED_TERM]->(dtype_r:CTTermRoot)\n -[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(dtype_val)\n\n// Optional parent class traversals\nOPTIONAL MATCH (aicr)-[:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aicrp)-[:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicpp:ActivityInstanceClassValue)\n\n// Optional item class membership checks\nOPTIONAL MATCH (aitmc1r)<-[:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[:HAS_ITEM_CLASS]-(aicrpp)\n\n// Optional Role\nOPTIONAL MATCH (aitmc1)-[:HAS_ROLE]->(:CTTermContext)\n -[:HAS_SELECTED_TERM]->(role_r:CTTermRoot)\n -[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(role_val)\n\n// Optional CT Terms\nOPTIONAL MATCH (aitm1)-[:HAS_CT_TERM]->(ct_context:CTTermContext)\n -[:HAS_SELECTED_TERM]->(ct2cd:CTTermRoot)\n -[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(ct2_sponsor),\n (ct2cd)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)\n -[:LATEST]->(ct2_cdisc),\n (ct2cd)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)\n <-[:HAS_TERM]-(clr:CTCodelistRoot)\n <-[:HAS_SELECTED_CODELIST]-(ct_context),\n (ct2cd)<-[:CONTAINS_TERM]-(:Library)\n\n// Optional codelist attributes\nOPTIONAL MATCH (clr)-[:HAS_ATTRIBUTES_ROOT]->(clatt:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (clr)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_sponsor)\n\n// Optional unit dimension on context\nOPTIONAL MATCH (ct_context)<-[:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\n\n// Optional unit definition\nOPTIONAL MATCH (aitm1)-[:HAS_UNIT_DEFINITION]->(:UnitDefinitionRoot)\n -[:LATEST]->(unit_term:UnitDefinitionValue)\n -[:HAS_CT_DIMENSION]->(:CTTermContext)\n -[:HAS_SELECTED_CODELIST]->(cl_unit_root:CTCodelistRoot)\n -[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (cl_unit_root)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_unit_sponsor)\n\n// Resolve CT term and codelist values once\nWITH\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n act.name AS Activity,\n aitmc1.name AS ActivityItemClass,\n role_val.name AS Role,\n dtype_val.name AS DataType,\n // Resolve CT2 with priority: pos_units_in_dim > unit_term > merged ct term\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim.name\n WHEN unit_term IS NOT NULL THEN unit_term.name\n WHEN ct2cd IS NOT NULL\n THEN apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor)).name\n ELSE null\n END AS term,\n // Resolve codelist with priority: clr > cl_unit_root\n CASE\n WHEN clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor)).name\n WHEN cl_unit_root IS NOT NULL\n THEN apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor)).preferred_term\n ELSE null\n END AS CodeList\n\n// Aggregate per Activity + ActivityItemClass combination\nWITH\n Activity,\n ActivityItemClass,\n Role,\n DataType,\n CodeList,\n collect(DISTINCT ActivityGroup) AS ActivityGroups,\n collect(DISTINCT ActivitySubGroup) AS ActivitySubGroups,\n collect(DISTINCT term) AS Terms\n\nRETURN\n ActivityGroups AS `Activity Group`,\n ActivitySubGroups AS `Activity Subgroup`,\n Activity,\n ActivityItemClass AS `Activity Item Class`,\n Terms,\n CodeList AS `Code List`,\n Role,\n DataType AS `Data Type`", "width": 24, "height": 4, "x": 0, @@ -490,38 +497,60 @@ }, { "title": "Activity as a Graph View (Physical View) - $neodash_activity", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nreturn *", + "query": "// Anchor on indexed ActivityValue node first\nMATCH (act:ActivityValue {name: $neodash_activity})\n\n// Core grouping traversal from anchor\nMATCH (act)-[R1:HAS_GROUPING]->(g:ActivityGrouping)\n -[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\n\n// Activity instance traversal - all relationships now captured\nMATCH (g)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[R_LATEST_AIGV:LATEST]-(aigr:ActivityInstanceGroupingRoot)\n <-[R_HAS_GROUPING_ROOT:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)\n -[R_LATEST_AIR:LATEST]->(ai:ActivityInstanceValue)\n -[R6:CONTAINS_ACTIVITY_ITEM]->(aitm1:ActivityItem)\n\n// Activity instance class\nMATCH (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[R8:LATEST]->(aic:ActivityInstanceClassValue)\n\n// Optional item class\nOPTIONAL MATCH (aitmc1r:ActivityItemClassRoot)-[R9:HAS_ACTIVITY_ITEM]->(aitm1)\nOPTIONAL MATCH (aitmc1r)-[R10:LATEST]->(aitmc1:ActivityItemClassValue)\n\n// Optional parent class hierarchy\nOPTIONAL MATCH (aicr)-[R11:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)\n -[R12:LATEST]->(aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aicrp)-[R13:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)\n -[R14:LATEST]->(aicpp:ActivityInstanceClassValue)\n\n// Optional item class membership checks\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n\n// Optional CT Terms\nOPTIONAL MATCH (aitm1)-[R18:HAS_CT_TERM]->(ct_context:CTTermContext)\nOPTIONAL MATCH (ct_context)-[R19:HAS_SELECTED_TERM]->(ct2cd:CTTermRoot)\nOPTIONAL MATCH (ct2cd)-[R20:HAS_NAME_ROOT]->(ct2cdr:CTTermNameRoot)\n -[R21:LATEST]->(ct2_sponsor)\nOPTIONAL MATCH (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->(ct2att:CTTermAttributesRoot)\n -[R23:LATEST]->(ct2_cdisc)\nOPTIONAL MATCH (ct2cd)<-[x1:HAS_TERM_ROOT]-(term:CTCodelistTerm)\nOPTIONAL MATCH (term)<-[x2:HAS_TERM]-(clr:CTCodelistRoot)\nOPTIONAL MATCH (clr)<-[x3:HAS_SELECTED_CODELIST]-(ct_context)\nOPTIONAL MATCH (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\n\n// Optional unit dimension on CT context\nOPTIONAL MATCH (ct_context)<-[x12:HAS_CT_DIMENSION]\n -(pos_units_in_dim:UnitDefinitionValue)\n\n// Optional unit definition\nOPTIONAL MATCH (aitm1)-[x6:HAS_UNIT_DEFINITION]->(unit_def_root:UnitDefinitionRoot)\nOPTIONAL MATCH (unit_def_root)-[x7:LATEST]->(unit_term:UnitDefinitionValue)\nOPTIONAL MATCH (unit_term)-[x8:HAS_CT_DIMENSION]->(ct_context2)\nOPTIONAL MATCH (ct_context2)-[x9:HAS_SELECTED_CODELIST]->(cl_unit_root:CTCodelistRoot)\nOPTIONAL MATCH (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-(cl_unit_att:CTCodelistAttributesRoot)\n -[x11:LATEST]->(cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (cl_unit_root)-[x13:HAS_NAME_ROOT]->(clunit_attr:CTCodelistNameRoot)\n -[x14:LATEST]-(cl_unit_sponsor)\n\n// Optional codelist attributes\nOPTIONAL MATCH (clr)-[R27:HAS_ATTRIBUTES_ROOT]->(clatt:CTCodelistAttributesRoot)\n -[R28:LATEST]->(cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (clr)-[R29:HAS_NAME_ROOT]->(clattr:CTCodelistNameRoot)\n -[R30:LATEST]-(cl_sponsor)\n\n// Optional role\nOPTIONAL MATCH (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)\nOPTIONAL MATCH (ct_context_role)-[y1:HAS_SELECTED_TERM]->(role_r:CTTermRoot)\nOPTIONAL MATCH (role_r)-[R40:HAS_NAME_ROOT]->(ctnr_role)\n -[R41:LATEST]->(role_val)\n\n// DataType\nOPTIONAL MATCH (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)\nOPTIONAL MATCH (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r)\nOPTIONAL MATCH (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)\n -[R45:LATEST]->(dtype_val)\n\nRETURN\n // Core Activity nodes\n act, agrp, asgrp, g, aigv, aigr, air, ai, aitm1,\n\n // Activity Instance Class nodes\n aicr, aic, aitmc1r, aitmc1, aicrp, aicp, aicrpp, aicpp,\n\n // CT Term nodes\n ct_context, ct2cd, ct2cdr, ct2_sponsor, ct2att, ct2_cdisc,\n\n // Codelist nodes\n term, clr, lib, pos_units_in_dim,\n\n // Unit Definition nodes\n unit_def_root, unit_term, ct_context2, cl_unit_root,\n cl_unit_att, cl_unit_cdisc, clunit_attr, cl_unit_sponsor,\n\n // Codelist attribute nodes\n clatt, cl_cdisc, clattr, cl_sponsor,\n\n // Role nodes\n ct_context_role, role_r, ctnr_role, role_val,\n\n // DataType nodes\n ct_context_dtype, dtype_r, ctnr_dtype, dtype_val,\n\n // Core relationships\n R1, R2, R4, R5, R6, R7, R8, R9, R10,\n R11, R12, R13, R14, R15, R16, R17, R18, R19, R20,\n R21, R22, R23, R27, R28, R29, R30, R39, R40, R41,\n R43, R44, R45,\n\n // Previously missing activity instance traversal relationships\n R_LATEST_AIGV, R_HAS_GROUPING_ROOT, R_LATEST_AIR,\n\n // Unit / CT Term relationships\n x1, x2, x3, x4,\n x6, x7, x8, x9, x10,\n x11, x12, x13, x14,\n\n // Role / DataType relationships\n y1, y2", "width": 12, "height": 6, "x": 12, "y": 18, "type": "graph", "selection": { - "TemplateParameterTermValue": "name", - "ConceptValue": "name", "ActivityValue": "name", + "ConceptValue": "name", + "TemplateParameterTermValue": "name", "ActivityGroupValue": "name", + "ActivitySubGroupValue": "name", + "ActivityGrouping": "uid", + "ActivityInstanceGroupingValue": "(label)", + "ActivityInstanceGroupingRoot": "(label)", + "ConceptRoot": "uid", + "ActivityInstanceRoot": "uid", + "TemplateParameterTermRoot": "uid", "ActivityInstanceValue": "name", - "ActivityInstanceClassValue": "name", - "ActivityInstanceClassRoot": "uid", "ActivityItem": "(label)", - "ActivityItemClassValue": "name", + "ActivityInstanceClassRoot": "uid", + "ActivityInstanceClassValue": "name", "ActivityItemClassRoot": "uid", - "ActivitySubGroupValue": "name", - "CTCodelistAttributesRoot": "(label)", - "CTCodelistAttributesValue": "name", - "CTCodelistRoot": "uid", - "CTCodelistNameValue": "name", - "CTCodelistNameRoot": "(label)", + "ActivityItemClassValue": "name", "CTTermContext": "(label)", - "TemplateParameterTermRoot": "uid", - "CTTermNameRoot": "uid", "CTTermRoot": "uid", + "CTTermNameRoot": "uid", "CTTermNameValue": "name", - "ActivityGrouping": "uid", - "ConceptRoot": "uid", + "HAS_GROUPING": "(label)", + "HAS_SELECTED_SUBGROUP": "(label)", + "HAS_SELECTED_GROUP": "(label)", + "HAS_ACTIVITY": "(label)", + "CONTAINS_ACTIVITY_ITEM": "(label)", + "ACTIVITY_INSTANCE_CLASS": "(label)", + "LATEST": "(label)", + "HAS_ACTIVITY_ITEM": "(label)", + "PARENT_CLASS": "(label)", + "HAS_ITEM_CLASS": "(label)", + "HAS_ROLE": "(label)", + "HAS_NAME_ROOT": "(label)", + "HAS_DATA_TYPE": "(label)", + "HAS_GROUPING_ROOT": "(label)", + "HAS_SELECTED_TERM": "(label)", "UnitDefinitionRoot": "uid", - "UnitDefinitionValue": "name" + "UnitDefinitionValue": "name", + "CTCodelistRoot": "uid", + "CTCodelistAttributesRoot": "(label)", + "CTCodelistAttributesValue": "name", + "CTCodelistNameRoot": "(label)", + "CTCodelistNameValue": "name", + "HAS_UNIT_DEFINITION": "(label)", + "HAS_CT_DIMENSION": "(label)", + "HAS_SELECTED_CODELIST": "(label)", + "HAS_ATTRIBUTES_ROOT": "(label)" }, "settings": { "hideSelections": true, @@ -537,56 +566,24 @@ "id": "823d3dfb-bce1-4719-9843-cb30524e20f6", "schema": [ [ - "HAS_GROUPING" - ], - [ - "LATEST" - ], - [ - "PARENT_CLASS" - ], - [ - "HAS_ITEM_CLASS", - "is_adam_param_specific_enabled", - "mandatory" - ], - [ - "HAS_SELECTED_SUBGROUP" - ], - [ - "HAS_ROLE" - ], - [ - "HAS_SELECTED_GROUP" - ], - [ - "HAS_NAME_ROOT" - ], - [ - "HAS_DATA_TYPE" - ], - [ - "HAS_ACTIVITY" - ], - [ - "CONTAINS_ACTIVITY_ITEM" - ], - [ - "ACTIVITY_INSTANCE_CLASS" - ], - [ - "HAS_ACTIVITY_ITEM" + "ActivityValue", + "synonyms", + "name", + "is_request_rejected", + "name_sentence_case", + "is_request_final", + "is_data_collected", + "is_multiple_selection_allowed" ], [ - "TemplateParameterTermValue", + "ConceptValue", "synonyms", "name", "is_request_rejected", "name_sentence_case", - "is_data_collected", "is_request_final", + "is_data_collected", "is_multiple_selection_allowed", - "definition", "topic_code", "is_derived", "adam_param_code", @@ -594,8 +591,8 @@ "is_data_sharing", "is_required_for_activity", "legacy_description", - "is_research_lab", "is_legacy_usage", + "is_research_lab", "us_conventional_unit", "display_unit", "si_unit", @@ -608,15 +605,14 @@ "legacy_code" ], [ - "ConceptValue", + "TemplateParameterTermValue", "synonyms", "name", "is_request_rejected", "name_sentence_case", - "is_data_collected", "is_request_final", + "is_data_collected", "is_multiple_selection_allowed", - "definition", "topic_code", "is_derived", "adam_param_code", @@ -624,8 +620,8 @@ "is_data_sharing", "is_required_for_activity", "legacy_description", - "is_research_lab", "is_legacy_usage", + "is_research_lab", "us_conventional_unit", "display_unit", "si_unit", @@ -638,20 +634,36 @@ "legacy_code" ], [ - "ActivityValue", - "synonyms", + "ActivityGroupValue", "name", - "is_request_rejected", - "name_sentence_case", - "is_data_collected", - "is_request_final", - "is_multiple_selection_allowed" + "name_sentence_case" ], [ - "ActivityGroupValue", + "ActivitySubGroupValue", "name", - "name_sentence_case", - "definition" + "name_sentence_case" + ], + [ + "ActivityGrouping", + "uid" + ], + [ + "ActivityInstanceGroupingValue" + ], + [ + "ActivityInstanceGroupingRoot" + ], + [ + "ConceptRoot", + "uid" + ], + [ + "ActivityInstanceRoot", + "uid" + ], + [ + "TemplateParameterTermRoot", + "uid" ], [ "ActivityInstanceValue", @@ -660,13 +672,20 @@ "adam_param_code", "name", "name_sentence_case", - "definition", "is_default_selected_for_activity", "is_data_sharing", "is_required_for_activity", "legacy_description", - "is_research_lab", - "is_legacy_usage" + "is_legacy_usage", + "is_research_lab" + ], + [ + "ActivityItem", + "is_adam_param_specific" + ], + [ + "ActivityInstanceClassRoot", + "uid" ], [ "ActivityInstanceClassValue", @@ -677,79 +696,81 @@ "order" ], [ - "ActivityInstanceClassRoot", + "ActivityItemClassRoot", "uid" ], - [ - "ActivityItem", - "is_adam_param_specific" - ], [ "ActivityItemClassValue", "nci_concept_id", "name", "definition", + "display_name", "order" ], [ - "ActivityItemClassRoot", + "CTTermContext" + ], + [ + "CTTermRoot", "uid" ], [ - "ActivitySubGroupValue", + "CTTermNameRoot", + "uid" + ], + [ + "CTTermNameValue", "name", "name_sentence_case" ], [ - "CTCodelistAttributesRoot" + "HAS_GROUPING" ], [ - "CTCodelistAttributesValue", - "preferred_term", - "name", - "definition", - "extensible", - "submission_value", - "ordinal" + "HAS_SELECTED_SUBGROUP" ], [ - "CTCodelistRoot", - "uid" + "HAS_SELECTED_GROUP" ], [ - "CTCodelistNameValue", - "name" + "HAS_ACTIVITY" ], [ - "CTCodelistNameRoot" + "CONTAINS_ACTIVITY_ITEM" ], [ - "CTTermContext" + "ACTIVITY_INSTANCE_CLASS" ], [ - "TemplateParameterTermRoot", - "uid" + "LATEST" ], [ - "CTTermNameRoot", - "uid" + "HAS_ACTIVITY_ITEM" ], [ - "CTTermRoot", - "uid" + "PARENT_CLASS" ], [ - "CTTermNameValue", - "name", - "name_sentence_case" + "HAS_ITEM_CLASS", + "is_adam_param_specific_enabled", + "mandatory", + "is_additional_optional", + "is_default_linked" ], [ - "ActivityGrouping", - "uid" + "HAS_ROLE" ], [ - "ConceptRoot", - "uid" + "HAS_NAME_ROOT" + ], + [ + "HAS_DATA_TYPE" + ], + [ + "HAS_GROUPING_ROOT" + ], + [ + "HAS_SELECTED_TERM" ], [ "UnitDefinitionRoot", @@ -762,16 +783,35 @@ "si_unit", "master_unit", "name", + "use_complex_unit_conversion", + "use_molecular_weight", + "conversion_factor_to_master", + "convertible_unit", + "order", + "legacy_code" + ], + [ + "CTCodelistRoot", + "uid" + ], + [ + "CTCodelistAttributesRoot" + ], + [ + "CTCodelistAttributesValue", + "preferred_term", + "codelist_type", + "name", "definition", - "use_complex_unit_conversion", - "use_molecular_weight", - "conversion_factor_to_master", - "convertible_unit", - "order", - "legacy_code" + "extensible", + "submission_value" ], [ - "HAS_ATTRIBUTES_ROOT" + "CTCodelistNameRoot" + ], + [ + "CTCodelistNameValue", + "name" ], [ "HAS_UNIT_DEFINITION" @@ -783,14 +823,14 @@ "HAS_SELECTED_CODELIST" ], [ - "HAS_SELECTED_TERM" + "HAS_ATTRIBUTES_ROOT" ] ] }, { "id": "c1bb190a-b3a9-4e65-843d-c0ab8c42ba42", "title": "List of Activities", - "query": "CALL apoc.case([not $neodash_activityinstanceclassvalue_name='' \n and $neodash_activityinstanceclassvalue_name_subtype='' \n and $neodash_activitygroupvalue_name='' \n and $neodash_activitysubgroupvalue_name='', \n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity', \n\nnot $neodash_activityinstanceclassvalue_name='' \nand not $neodash_activityinstanceclassvalue_name_subtype='' \nand $neodash_activitygroupvalue_name='' \nand $neodash_activitysubgroupvalue_name='', \n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] and aic.name in [$b] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity', \n\nnot $neodash_activityinstanceclassvalue_name='' \nand not $neodash_activityinstanceclassvalue_name_subtype='' \nand not $neodash_activitygroupvalue_name='' \nand $neodash_activitysubgroupvalue_name='', \n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] and aic.name in [$b] and agrp.name in [$c] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity', \n\nnot $neodash_activityinstanceclassvalue_name='' \nand not $neodash_activityinstanceclassvalue_name_subtype='' \nand not $neodash_activitygroupvalue_name='' \nand not $neodash_activitysubgroupvalue_name='',\n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] and aic.name in [$b] and agrp.name in [$c] and asgrp.name in [$d] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity'],\n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue) \nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity',{\na:$neodash_activityinstanceclassvalue_name, \nb:$neodash_activityinstanceclassvalue_name_subtype,\nc:$neodash_activitygroupvalue_name, \nd:$neodash_activitysubgroupvalue_name}) YIELD value return value.ActivityType as `Activity Type`,value.ActivitySubType as `Activity Subtype`, value.ActivityGroup as `Activity Group` ,value.ActivitySubGroup as `Activity Subgroup` , value.Activity as Activity order by Activity", + "query": "// Build the core pattern ONCE, then apply conditional filters\nMATCH (act:ActivityValue)-[:HAS_GROUPING]->(g:ActivityGrouping)\n -[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)\n <-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)\n -[:LATEST]->(ai:ActivityInstanceValue),\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[:LATEST]->(aic:ActivityInstanceClassValue),\n (aicr)-[:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicp:ActivityInstanceClassValue),\n (aicrp)-[:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicpp:ActivityInstanceClassValue)\n\n// Apply filters conditionally using WHERE with CASE logic\nWHERE\n // Filter on ActivityType (aicp.name) — only when param is not empty\n (\n $neodash_activityinstanceclassvalue_name = ''\n OR aicp.name = $neodash_activityinstanceclassvalue_name\n )\n AND\n // Filter on ActivitySubType (aic.name) — only when param is not empty\n (\n $neodash_activityinstanceclassvalue_name_subtype = ''\n OR aic.name = $neodash_activityinstanceclassvalue_name_subtype\n )\n AND\n // Filter on ActivityGroup (agrp.name) — only when param is not empty\n (\n $neodash_activitygroupvalue_name = ''\n OR agrp.name = $neodash_activitygroupvalue_name\n )\n AND\n // Filter on ActivitySubGroup (asgrp.name) — only when param is not empty\n (\n $neodash_activitysubgroupvalue_name = ''\n OR asgrp.name = $neodash_activitysubgroupvalue_name\n )\n\nRETURN DISTINCT\n aicp.name AS `Activity Type`,\n aic.name AS `Activity Subtype`,\n agrp.name AS `Activity Group`,\n asgrp.name AS `Activity Subgroup`,\n act.name AS Activity\n\nORDER BY Activity", "width": 24, "height": 4, "x": 0, @@ -839,7 +879,7 @@ { "id": "2a328d78-132e-49c6-b4a5-884d1fdaa015", "title": "Select Instance - $neodash_activity", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-() \nwhere act.name = $neodash_activity \nreturn ai.name as Instance, ai.adam_param_code as `ADaM Param Code`", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) \nwhere act.name = $neodash_activity \nreturn ai.name as Instance, ai.adam_param_code as `ADaM Param Code`", "width": 7, "height": 5, "x": 0, @@ -855,7 +895,7 @@ "entityType": "instance", "parameterName": "neodash_instance" }, - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue) \nwhere act.name = $neodash_activity return ai.name as Instance" + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) \nwhere act.name = $neodash_activity return ai.name as Instance" } ], "runButtonText": "Show detail", @@ -876,7 +916,7 @@ { "id": "bf2468d0-bf4e-4aa2-93e5-2f7e78ba4203", "title": "Instance Detail - $neodash_instance", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-() where ai.adam_param_code=$neodash_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aic,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\naic.name as Class,\nagrp.name as ActivityGroup,\nasgrp.name as ActivitySubGroup,\nai.name as Instance,\nai.adam_param_code as ADAM_CODE,\naitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nreturn distinct \nClass,\nInstance,\nADAM_CODE,\n`Activity Item Class`,\napoc.convert.toSet(collect(terms)) AS Term,\n`Code List`,\nRole,\n`Data Type`\n", + "query": "// 1. Anchor on indexed ActivityValue node first\nMATCH (act:ActivityValue {name: $neodash_activity})\n\n// 2. Core grouping traversal\nMATCH (act)-[:HAS_GROUPING]->(g:ActivityGrouping)\n -[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\n\n// 3. Activity instance traversal - filter early on adam_param_code\nMATCH (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[:LATEST]-(:ActivityInstanceGroupingRoot)\n <-[:HAS_GROUPING_ROOT]-(:ActivityInstanceRoot)\n -[:LATEST]->(ai:ActivityInstanceValue {adam_param_code: $neodash_instance})\n -[:CONTAINS_ACTIVITY_ITEM]->(aitm1:ActivityItem)\n\n// 4. Activity instance class\nMATCH (ai)-[:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[:LATEST]->(aic:ActivityInstanceClassValue)\n\n// 5. Early WITH DISTINCT to reduce cardinality before expensive optional lookups\nWITH DISTINCT\n agrp, asgrp, ai, aitm1, aicr, aic\n\n// 6. Optional item class\nOPTIONAL MATCH (aitmc1r:ActivityItemClassRoot)-[:HAS_ACTIVITY_ITEM]->(aitm1)\nOPTIONAL MATCH (aitmc1r)-[:LATEST]->(aitmc1:ActivityItemClassValue)\n\n// 7. Optional parent class hierarchy\nOPTIONAL MATCH (aicr)-[:PARENT_CLASS]->(:ActivityInstanceClassRoot)\n -[:LATEST]->(aicp:ActivityInstanceClassValue)\n\n// 8. Optional DataType - resolved early to reduce rows\nOPTIONAL MATCH (aitmc1)-[:HAS_DATA_TYPE]->(ct_context_dtype)\nOPTIONAL MATCH (ct_context_dtype)-[:HAS_SELECTED_TERM]->(dtype_r)\nOPTIONAL MATCH (dtype_r)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(dtype_val)\n\n// 9. Optional Role\nOPTIONAL MATCH (aitmc1)-[:HAS_ROLE]->(ct_context_role)\nOPTIONAL MATCH (ct_context_role)-[:HAS_SELECTED_TERM]->(role_r:CTTermRoot)\nOPTIONAL MATCH (role_r)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(role_val)\n\n// 10. Second WITH DISTINCT before expensive CT term lookups\nWITH DISTINCT\n agrp, asgrp, ai, aitm1, aicr, aic,\n aitmc1r, aitmc1, aicp,\n dtype_val, role_val\n\n// 11. Optional CT Terms\nOPTIONAL MATCH (aitm1)-[:HAS_CT_TERM]->(ct_context:CTTermContext)\nOPTIONAL MATCH (ct_context)-[:HAS_SELECTED_TERM]->(ct2cd:CTTermRoot)\nOPTIONAL MATCH (ct2cd)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(ct2_sponsor)\nOPTIONAL MATCH (ct2cd)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)\n -[:LATEST]->(ct2_cdisc)\n\n// 12. Optional unit dimension on CT context\nOPTIONAL MATCH (ct_context)<-[:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\n\n// 13. Optional unit definition\nOPTIONAL MATCH (aitm1)-[:HAS_UNIT_DEFINITION]->(unit_def_root:UnitDefinitionRoot)\nOPTIONAL MATCH (unit_def_root)-[:LATEST]->(unit_term:UnitDefinitionValue)\n\n// 14. Optional codelist\nOPTIONAL MATCH (ct2cd)<-[:HAS_TERM_ROOT]-(term:CTCodelistTerm)\n <-[:HAS_TERM]-(clr:CTCodelistRoot)\n <-[:HAS_SELECTED_CODELIST]-(ct_context)\nOPTIONAL MATCH (clr)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (clr)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_sponsor)\n\n// 15. Optional unit codelist\nOPTIONAL MATCH (unit_term)-[:HAS_CT_DIMENSION]->(ct_context2)\nOPTIONAL MATCH (ct_context2)-[:HAS_SELECTED_CODELIST]->(cl_unit_root:CTCodelistRoot)\nOPTIONAL MATCH (cl_unit_root)-[:HAS_ATTRIBUTES_ROOT]-(:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (cl_unit_root)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_unit_sponsor)\n\n// 16. Resolve final CT2 and CL values\nWITH DISTINCT\n aic.name AS Class,\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n ai.name AS Instance,\n ai.adam_param_code AS ADAM_CODE,\n aitmc1.name AS `Activity Item Class`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`,\n COALESCE(\n pos_units_in_dim.name,\n unit_term.name,\n ct2_sponsor.name,\n ct2_cdisc.name\n ) AS terms,\n COALESCE(\n cl_sponsor.preferred_term,\n cl_cdisc.name,\n cl_unit_sponsor.preferred_term,\n cl_unit_cdisc.name\n ) AS `Code List`\n\n// 17. Final aggregation\nRETURN DISTINCT\n Class,\n Instance,\n ADAM_CODE,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Term,\n `Code List`,\n Role,\n `Data Type`", "width": 17, "height": 5, "x": 7, @@ -892,7 +932,7 @@ { "id": "0a3ffebe-ca79-43bb-a06b-46cb158e4d9d", "title": "Instance (Logical View) - $neodash_instance", - "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-() where ai.adam_param_code=$neodash_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", + "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) where ai.adam_param_code=$neodash_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", "width": 24, "height": 10, "x": 0, @@ -900,9 +940,9 @@ "type": "graph", "selection": { "ActivityGrouping": "(label)", - "TemplateParameterTermValue": "name", - "ConceptValue": "name", "ActivityGroupValue": "name", + "ConceptValue": "name", + "TemplateParameterTermValue": "name", "ActivitySubGroupValue": "name", "ActivityValue": "name", "ActivityInstance": "name", @@ -910,7 +950,16 @@ "ActivityItem": "(label)", "ActivityItemClass": "name", "CTTerm": "name", - "CTCodeList": "name" + "HAS": "(label)", + "HAS_ACTIVITY": "(label)", + "OF_CLASS": "(label)", + "HAS_ROLE": "(label)", + "HAS_TYPE": "(label)", + "HAS_GROUPING": "(label)", + "HAS_SELECTED_SUBGROUP": "(label)", + "HAS_SELECTED_GROUP": "(label)", + "CTCodeList": "name", + "FOR": "(label)" }, "settings": { "nodeColorScheme": "set3", @@ -926,32 +975,29 @@ "uid" ], [ - "TemplateParameterTermValue", + "ActivityGroupValue", "name", - "name_sentence_case", - "definition", - "synonyms", - "is_request_rejected", - "is_data_collected", - "is_request_final", - "is_multiple_selection_allowed" + "name_sentence_case" ], [ "ConceptValue", "name", "name_sentence_case", - "definition", "synonyms", "is_request_rejected", - "is_data_collected", "is_request_final", + "is_data_collected", "is_multiple_selection_allowed" ], [ - "ActivityGroupValue", + "TemplateParameterTermValue", "name", "name_sentence_case", - "definition" + "synonyms", + "is_request_rejected", + "is_request_final", + "is_data_collected", + "is_multiple_selection_allowed" ], [ "ActivitySubGroupValue", @@ -964,8 +1010,8 @@ "name", "is_request_rejected", "name_sentence_case", - "is_data_collected", "is_request_final", + "is_data_collected", "is_multiple_selection_allowed" ], [ @@ -973,14 +1019,13 @@ "topic_code", "is_derived", "adam_param_code", - "name_sentence_case", - "is_legacy_usage", "name", - "definition", + "name_sentence_case", "is_default_selected_for_activity", "is_data_sharing", "is_required_for_activity", "legacy_description", + "is_legacy_usage", "is_research_lab" ], [ @@ -999,33 +1044,24 @@ "ActivityItemClass", "name", "definition", + "display_name", "nci_concept_id", "order" ], [ "CTTerm", + "name", + "name_sentence_case", "us_conventional_unit", "display_unit", "si_unit", "master_unit", - "name", - "definition", "use_complex_unit_conversion", "use_molecular_weight", "conversion_factor_to_master", "convertible_unit", "order", - "legacy_code", - "name_sentence_case" - ], - [ - "CTCodeList", - "preferred_term", - "name", - "definition", - "extensible", - "submission_value", - "ordinal" + "legacy_code" ], [ "HAS", @@ -1039,10 +1075,6 @@ "OF_CLASS", "type" ], - [ - "FOR", - "type" - ], [ "HAS_ROLE", "type" @@ -1059,6 +1091,19 @@ ], [ "HAS_SELECTED_GROUP" + ], + [ + "CTCodeList", + "preferred_term", + "name", + "definition", + "codelist_type", + "extensible", + "submission_value" + ], + [ + "FOR", + "type" ] ] } @@ -1095,7 +1140,7 @@ { "id": "e0a486e2-b652-4375-b36f-57acf318277c", "title": "Groups for Selected Activity/Activities", - "query": "MATCH(p_act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(p_asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(p_agrp:ActivityGroupValue) where p_act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(p_ai:ActivityInstanceValue)<-[:LATEST]-()\nreturn p_act.name as Activity,\np_agrp.name as Group,\np_asgrp.name as `Subgroup`,\np_ai.adam_param_code as `Activity Instance (ADAM PARAM CODE)`,\np_ai.topic_code as `Activity Instance (TOPIC CODE)`,\n'Show Detail' as Select order by Activity, Group, `Subgroup`", + "query": "MATCH(p_act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(p_asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(p_agrp:ActivityGroupValue) where p_act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(p_ai:ActivityInstanceValue)\nreturn p_act.name as Activity,\np_agrp.name as Group,\np_asgrp.name as `Subgroup`,\np_ai.adam_param_code as `Activity Instance (ADAM PARAM CODE)`,\np_ai.topic_code as `Activity Instance (TOPIC CODE)`,\n'Show Detail' as Select order by Activity, Group, `Subgroup`", "width": 24, "height": 4, "x": 0, @@ -1124,7 +1169,7 @@ { "id": "51ddc5ee-2e17-44e1-99f1-8b2f95a8ba21", "title": "Activity Instance Detail - $neodash_detail", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-() where ai.adam_param_code=$neodash_detail\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n apoc.convert.toSet(collect(agrp.name)) AS ActivityGroup,\n apoc.convert.toSet(collect(asgrp.name)) AS ActivitySubGroup,\n act.name AS Activity,\n ai.adam_param_code as `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nWITH\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivityGroup))) AS `Activity Group`,\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivitySubGroup))) AS `Activity Subgroup`,\n Activity,\n `Activity Instance`,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Terms,\n `Code List`,\n Role,\n `Data Type`\nreturn `Activity Group`,\n`Activity Subgroup`,\nActivity,\n`Activity Instance`,\n`Activity Item Class`,\napoc.text.join(Terms, \",\") as Term,\n`Code List`,\nRole,\n`Data Type`", + "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nWHERE ai.adam_param_code=$neodash_detail\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n apoc.convert.toSet(collect(agrp.name)) AS ActivityGroup,\n apoc.convert.toSet(collect(asgrp.name)) AS ActivitySubGroup,\n act.name AS Activity,\n ai.adam_param_code as `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nWITH\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivityGroup))) AS `Activity Group`,\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivitySubGroup))) AS `Activity Subgroup`,\n Activity,\n `Activity Instance`,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Terms,\n `Code List`,\n Role,\n `Data Type`\nreturn `Activity Group`,\n`Activity Subgroup`,\nActivity,\n`Activity Instance`,\n`Activity Item Class`,\napoc.text.join(Terms, \",\") as Term,\n`Code List`,\nRole,\n`Data Type`", "width": 24, "height": 4, "x": 0, @@ -1144,7 +1189,7 @@ { "id": "97dd35f9-9411-4b89-9bcd-9bdebdb027f0", "title": "Number of Subgroups for Selected Activity", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", "width": 12, "height": 4, "x": 12, @@ -1177,7 +1222,7 @@ { "id": "c39ce16b-7619-4118-b1e2-cc65efadd267", "title": "Number of Groups for Selected Activity", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", "width": 12, "height": 4, "x": 0, @@ -1248,7 +1293,7 @@ }, { "title": "Activity Mapped to SDTM - $neodash_activity_instance_sdtm", - "query": "//Activity mapped to SDTM\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nWHERE ai.adam_param_code = $neodash_activity_instance_sdtm\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\n\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[r1:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[r2:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[r3:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[:HAS_CT_TERM]->\n (:CTTermContext)-[:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[r4:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [r5:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [r6:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[r7:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\n\nOPTIONAL MATCH\n (aitm1:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-\n (aitmc1r)-[R46:MAPS_VARIABLE_CLASS]->\n (varcl:VariableClass)-[R47:HAS_INSTANCE]->\n (varcli:VariableClassInstance),\n (varcli)<-[R48:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dci:DatasetVariableInstance)<-\n [R49:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dsi:DatasetInstance)<-[R50:HAS_INSTANCE]-\n (ds:Dataset)<-[R51:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R52:CONTAINS_VERSION]->\n (dmig:DataModelVersion),\n (dsi)<-[R53:HAS_DATASET]-\n (dmigv:DataModelIGValue)<-[R54:CONTAINS_DATA_MODEL_IG]-\n (dmig),\n (dci)<-[:HAS_INSTANCE]-(ds_var:DatasetVariable)\nWHERE dmigv.version_number = $neodash_sdtmversion\nWITH DISTINCT\n act.name AS Activity,\n ai.name AS `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n varcl.uid AS `Variable Class`,\n ds_var.uid AS `SDTMIG Variable`,\n dci.label AS `SDTMIG Variable Label`,\n ds.uid AS `SDTMIG Dataset`,\n dsi.label AS `SDTMIG Dataset Label`,\n aitmc1.order AS item_order\nRETURN\n Activity,\n `Activity Instance`,\n `Activity Item Class`,\n `Variable Class`,\n `SDTMIG Variable`,\n `SDTMIG Variable Label`,\n `SDTMIG Dataset`,\n `SDTMIG Dataset Label`\nORDER BY `Activity Instance`, item_order", + "query": "//Activity mapped to SDTM\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nWHERE ai.adam_param_code = $neodash_activity_instance_sdtm\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\n\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[r1:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[r2:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[r3:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[:HAS_CT_TERM]->\n (:CTTermContext)-[:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[r4:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [r5:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [r6:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[r7:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\n\nOPTIONAL MATCH\n (aitm1:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-\n (aitmc1r)-[R46:MAPS_VARIABLE_CLASS]->\n (varcl:VariableClass)-[R47:HAS_INSTANCE]->\n (varcli:VariableClassInstance),\n (varcli)<-[R48:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dci:DatasetVariableInstance)<-\n [R49:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dsi:DatasetInstance)<-[R50:HAS_INSTANCE]-\n (ds:Dataset)<-[R51:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R52:CONTAINS_VERSION]->\n (dmig:DataModelVersion),\n (dsi)<-[R53:HAS_DATASET]-\n (dmigv:DataModelIGValue)<-[R54:CONTAINS_DATA_MODEL_IG]-\n (dmig),\n (dci)<-[:HAS_INSTANCE]-(ds_var:DatasetVariable)\nWHERE dmigv.version_number = $neodash_sdtmversion\nWITH DISTINCT\n act.name AS Activity,\n ai.name AS `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n varcl.uid AS `Variable Class`,\n ds_var.uid AS `SDTMIG Variable`,\n dci.label AS `SDTMIG Variable Label`,\n ds.uid AS `SDTMIG Dataset`,\n dsi.label AS `SDTMIG Dataset Label`,\n aitmc1.order AS item_order\nRETURN\n Activity,\n `Activity Instance`,\n `Activity Item Class`,\n `Variable Class`,\n `SDTMIG Variable`,\n `SDTMIG Variable Label`,\n `SDTMIG Dataset`,\n `SDTMIG Dataset Label`\nORDER BY `Activity Instance`, item_order", "width": 24, "height": 6, "x": 0, @@ -1267,7 +1312,7 @@ { "id": "0894bb17-3aaa-4c4a-9372-93e95422f362", "title": "Select Activity Instance", - "query": "MATCH(p_act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(p_asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(p_agrp:ActivityGroupValue) where p_asgrp.name=$neodash_activitysubgroupvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(p_ai:ActivityInstanceValue)<-[:LATEST]-()\nreturn p_agrp.name as `Activity Group`, p_asgrp.name as `Activity Subgroup`, p_act.name as Activity, p_ai.adam_param_code as `Activity Instance` order by Activity\n", + "query": "MATCH(p_act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(p_asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(p_agrp:ActivityGroupValue) where p_asgrp.name=$neodash_activitysubgroupvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(p_ai:ActivityInstanceValue)\nreturn p_agrp.name as `Activity Group`, p_asgrp.name as `Activity Subgroup`, p_act.name as Activity, p_ai.adam_param_code as `Activity Instance` order by Activity\n", "width": 10, "height": 4, "x": 0, @@ -1296,36 +1341,74 @@ { "id": "93059873-3ac9-464e-bc2b-72f5fb9ddcdf", "title": "Activity with Links to SDTM - $neodash_activity_instance_sdtm", - "query": "//Activity mapped to SDTM\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nWHERE ai.adam_param_code = $neodash_detail\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[R30:LATEST]->\n (unit_term:UnitDefinitionValue)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\n\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R49:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[R50:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[R51:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[R52:HAS_CT_TERM]->\n (:CTTermContext)-[R53:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[R54:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[R55:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [R56:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [R57:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[R58:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\n\nOPTIONAL MATCH\n (aitm1:ActivityItem)<-[R59:HAS_ACTIVITY_ITEM]-\n (aitmc1r)-[R60:MAPS_VARIABLE_CLASS]->\n (varcl:VariableClass)-[R61:HAS_INSTANCE]->\n (varcli:VariableClassInstance),\n (varcli)<-[R62:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dci:DatasetVariableInstance)<-\n [R63:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dsi:DatasetInstance)<-[R64:HAS_INSTANCE]-\n (ds:Dataset)<-[R51:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R65:CONTAINS_VERSION]->\n (dmig:DataModelVersion),\n (dsi)<-[R66:HAS_DATASET]-\n (dmigv:DataModelIGValue)<-[R67:CONTAINS_DATA_MODEL_IG]-\n (dmig),\n (dci)<-[R69:HAS_INSTANCE]-(ds_var:DatasetVariable)\nWHERE dmigv.version_number = $neodash_sdtmversion\nreturn *", + "query": "//Activity mapped to SDTM\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nWHERE ai.adam_param_code = $neodash_detail\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[R30:LATEST]->\n (unit_term:UnitDefinitionValue)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\n\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R49:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[R50:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[R51:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[R52:HAS_CT_TERM]->\n (:CTTermContext)-[R53:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[R54:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[R55:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [R56:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [R57:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[R58:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\n\nOPTIONAL MATCH\n (aitm1:ActivityItem)<-[R59:HAS_ACTIVITY_ITEM]-\n (aitmc1r)-[R60:MAPS_VARIABLE_CLASS]->\n (varcl:VariableClass)-[R61:HAS_INSTANCE]->\n (varcli:VariableClassInstance),\n (varcli)<-[R62:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dci:DatasetVariableInstance)<-\n [R63:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dsi:DatasetInstance)<-[R64:HAS_INSTANCE]-\n (ds:Dataset)<-[R51:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R65:CONTAINS_VERSION]->\n (dmig:DataModelVersion),\n (dsi)<-[R66:HAS_DATASET]-\n (dmigv:DataModelIGValue)<-[R67:CONTAINS_DATA_MODEL_IG]-\n (dmig),\n (dci)<-[R69:HAS_INSTANCE]-(ds_var:DatasetVariable)\nWHERE dmigv.version_number = $neodash_sdtmversion\nreturn *", "width": 24, "height": 8, "x": 0, "y": 12, "type": "graph", "selection": { - "TemplateParameterTermValue": "name", - "ConceptValue": "name", + "HAS_GROUPING": "(label)", + "LATEST": "(label)", + "PARENT_CLASS": "(label)", + "HAS_ITEM_CLASS": "(label)", + "HAS_SELECTED_SUBGROUP": "(label)", + "HAS_SELECTED_GROUP": "(label)", + "HAS_ROLE": "(label)", + "HAS_SELECTED_TERM": "(label)", + "HAS_NAME_ROOT": "(label)", + "HAS_DATA_TYPE": "(label)", + "CONTAINS_ACTIVITY_ITEM": "(label)", + "HAS_ACTIVITY": "(label)", + "HAS_ACTIVITY_ITEM": "(label)", + "MAPS_VARIABLE_CLASS": "(label)", + "HAS_CT_TERM": "(label)", + "HAS_TERM_ROOT": "(label)", + "HAS_INSTANCE": "(label)", + "IMPLEMENTS_VARIABLE": "(label)", + "HAS_DATASET_VARIABLE": "(label)", + "ACTIVITY_INSTANCE_CLASS": "(label)", "ActivityValue": "name", + "ConceptValue": "name", + "TemplateParameterTermValue": "name", "ActivityGroupValue": "name", "ActivityInstanceValue": "name", "ActivityInstanceClassValue": "name", "ActivityInstanceClassRoot": "uid", + "ActivityInstanceGroupingRoot": "(label)", + "ActivityInstanceGroupingValue": "(label)", + "ConceptRoot": "uid", + "ActivityInstanceRoot": "uid", + "TemplateParameterTermRoot": "uid", "ActivityItem": "(label)", "ActivityItemClassValue": "name", "ActivityItemClassRoot": "uid", "ActivitySubGroupValue": "name", - "CTCodelistAttributesRoot": "(label)", - "CTCodelistAttributesValue": "name", - "CTCodelistRoot": "uid", - "CTCodelistNameValue": "name", - "CTCodelistNameRoot": "(label)", + "CTCodelistTerm": "(label)", "CTTermContext": "(label)", - "TemplateParameterTermRoot": "uid", "CTTermNameRoot": "uid", + "VariableClass": "uid", + "Dataset": "uid", "CTTermRoot": "uid", "CTTermNameValue": "name", "ActivityGrouping": "uid", - "ConceptRoot": "uid", + "VariableClassInstance": "title", + "DatasetVariableInstance": "title", + "DatasetInstance": "title", + "HAS_ATTRIBUTES_ROOT": "(label)", + "HAS_TERM": "(label)", + "HAS_SELECTED_CODELIST": "(label)", + "CONTAINS_TERM": "(label)", + "CTCodelistAttributesValue": "name", + "CTCodelistNameValue": "name", + "CTCodelistAttributesRoot": "(label)", + "CTCodelistNameRoot": "(label)", + "CTCodelistRoot": "uid", + "CTTermAttributesValue": "(label)", + "CTTermAttributesRoot": "(label)", + "Library": "name", + "HAS_UNIT_DEFINITION": "(label)", + "HAS_CT_DIMENSION": "(label)", "UnitDefinitionRoot": "uid", "UnitDefinitionValue": "name" }, @@ -1351,72 +1434,86 @@ [ "HAS_ITEM_CLASS", "is_adam_param_specific_enabled", - "mandatory" + "is_additional_optional", + "mandatory", + "is_default_linked" ], [ "HAS_SELECTED_SUBGROUP" ], [ - "HAS_UNIT_DEFINITION" + "HAS_SELECTED_GROUP" ], [ - "HAS_CT_DIMENSION" + "HAS_ROLE" ], [ - "HAS_SELECTED_CODELIST" + "HAS_SELECTED_TERM" ], [ - "HAS_ATTRIBUTES_ROOT" + "HAS_NAME_ROOT" ], [ - "HAS_NAME_ROOT" + "HAS_DATA_TYPE" ], [ - "HAS_SELECTED_GROUP" + "CONTAINS_ACTIVITY_ITEM" ], [ - "HAS_ROLE" + "HAS_ACTIVITY" ], [ - "HAS_SELECTED_TERM" + "HAS_ACTIVITY_ITEM" ], [ - "HAS_DATA_TYPE" + "MAPS_VARIABLE_CLASS" ], [ - "HAS_ACTIVITY" + "HAS_CT_TERM" ], [ - "CONTAINS_ACTIVITY_ITEM" + "HAS_TERM_ROOT" + ], + [ + "HAS_INSTANCE" + ], + [ + "IMPLEMENTS_VARIABLE", + "version_number", + "catalogue" + ], + [ + "HAS_DATASET_VARIABLE", + "version_number", + "ordinal" ], [ "ACTIVITY_INSTANCE_CLASS" ], [ - "HAS_ACTIVITY_ITEM" + "ActivityValue", + "name", + "name_sentence_case", + "is_data_collected" ], [ - "TemplateParameterTermValue", - "synonyms", + "ConceptValue", "name", - "is_request_rejected", "name_sentence_case", "is_data_collected", - "is_request_final", - "is_multiple_selection_allowed", - "definition", "topic_code", "is_derived", "adam_param_code", + "definition", "is_default_selected_for_activity", "is_data_sharing", "is_required_for_activity", "legacy_description", - "is_research_lab", "is_legacy_usage", + "is_research_lab", "us_conventional_unit", - "display_unit", "si_unit", + "display_unit", "master_unit", "use_complex_unit_conversion", "use_molecular_weight", @@ -1426,27 +1523,23 @@ "legacy_code" ], [ - "ConceptValue", - "synonyms", + "TemplateParameterTermValue", "name", - "is_request_rejected", "name_sentence_case", "is_data_collected", - "is_request_final", - "is_multiple_selection_allowed", - "definition", "topic_code", "is_derived", "adam_param_code", + "definition", "is_default_selected_for_activity", "is_data_sharing", "is_required_for_activity", "legacy_description", - "is_research_lab", "is_legacy_usage", + "is_research_lab", "us_conventional_unit", - "display_unit", "si_unit", + "display_unit", "master_unit", "use_complex_unit_conversion", "use_molecular_weight", @@ -1455,21 +1548,10 @@ "order", "legacy_code" ], - [ - "ActivityValue", - "synonyms", - "name", - "is_request_rejected", - "name_sentence_case", - "is_data_collected", - "is_request_final", - "is_multiple_selection_allowed" - ], [ "ActivityGroupValue", "name", - "name_sentence_case", - "definition" + "name_sentence_case" ], [ "ActivityInstanceValue", @@ -1483,8 +1565,8 @@ "is_data_sharing", "is_required_for_activity", "legacy_description", - "is_research_lab", - "is_legacy_usage" + "is_legacy_usage", + "is_research_lab" ], [ "ActivityInstanceClassValue", @@ -1498,6 +1580,24 @@ "ActivityInstanceClassRoot", "uid" ], + [ + "ActivityInstanceGroupingRoot" + ], + [ + "ActivityInstanceGroupingValue" + ], + [ + "ConceptRoot", + "uid" + ], + [ + "ActivityInstanceRoot", + "uid" + ], + [ + "TemplateParameterTermRoot", + "uid" + ], [ "ActivityItem", "is_adam_param_specific" @@ -1507,6 +1607,7 @@ "nci_concept_id", "name", "definition", + "display_name", "order" ], [ @@ -1519,55 +1620,124 @@ "name_sentence_case" ], [ - "CTCodelistAttributesRoot" + "CTCodelistTerm", + "submission_value" + ], + [ + "CTTermContext" + ], + [ + "CTTermNameRoot", + "uid" + ], + [ + "VariableClass", + "uid" + ], + [ + "Dataset", + "uid" + ], + [ + "CTTermRoot", + "uid" + ], + [ + "CTTermNameValue", + "name", + "name_sentence_case" + ], + [ + "ActivityGrouping", + "uid" + ], + [ + "VariableClassInstance", + "role", + "simple_datatype", + "description", + "label", + "title", + "role_description" + ], + [ + "DatasetVariableInstance", + "core", + "role", + "simple_datatype", + "description", + "label", + "value_list", + "title" + ], + [ + "DatasetInstance", + "description", + "label", + "title" + ], + [ + "HAS_ATTRIBUTES_ROOT" + ], + [ + "HAS_TERM", + "end_date", + "author_id", + "order", + "start_date" + ], + [ + "HAS_SELECTED_CODELIST" + ], + [ + "CONTAINS_TERM" ], [ "CTCodelistAttributesValue", "preferred_term", + "codelist_type", "name", "definition", "extensible", "submission_value", - "ordinal" - ], - [ - "CTCodelistRoot", - "uid" + "concept_id", + "synonyms" ], [ "CTCodelistNameValue", - "name" + "name", + "name_sentence_case" ], [ - "CTCodelistNameRoot" + "CTCodelistAttributesRoot" ], [ - "CTTermContext" + "CTCodelistNameRoot" ], [ - "TemplateParameterTermRoot", + "CTCodelistRoot", "uid" ], [ - "CTTermNameRoot", - "uid" + "CTTermAttributesValue", + "definition", + "preferred_term", + "concept_id", + "synonyms" ], [ - "CTTermRoot", - "uid" + "CTTermAttributesRoot" ], [ - "CTTermNameValue", + "Library", "name", - "name_sentence_case" + "is_editable" ], [ - "ActivityGrouping", - "uid" + "HAS_UNIT_DEFINITION" ], [ - "ConceptRoot", - "uid" + "HAS_CT_DIMENSION" ], [ "UnitDefinitionRoot", @@ -1576,8 +1746,8 @@ [ "UnitDefinitionValue", "us_conventional_unit", - "display_unit", "si_unit", + "display_unit", "master_unit", "name", "definition", @@ -1617,7 +1787,7 @@ "reports": [ { "title": "Select Activity", - "query": "CALL apoc.when($neodash_limit_list='','MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nreturn agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity, ai.name as `Instance Name`,ai.adam_param_code as ActivityInstance','MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue) where asgrp.name in [$a] \nreturn agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity, ai.name as `Instance Name`, ai.adam_param_code as ActivityInstance ', {a:$neodash_limit_list}) YIELD value\nreturn distinct value.ActivityGroup as `Activity Group`,\nvalue.ActivitySubGroup as `Activity Subgroup`,\nvalue.Activity as Activity, 'click' as `Select Activity` order by Activity", + "query": "CALL apoc.when($neodash_limit_list='','MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nreturn agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity, ai.name as `Instance Name`,ai.adam_param_code as ActivityInstance','MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) where asgrp.name in [$a] \nreturn agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity, ai.name as `Instance Name`, ai.adam_param_code as ActivityInstance ', {a:$neodash_limit_list}) YIELD value\nreturn distinct value.ActivityGroup as `Activity Group`,\nvalue.ActivitySubGroup as `Activity Subgroup`,\nvalue.Activity as Activity, 'click' as `Select Activity` order by Activity", "width": 16, "height": 4, "x": 8, @@ -1688,7 +1858,7 @@ { "id": "3d05187e-4292-40e2-a9dc-0ed8f0d54392", "title": "Activity as COSMOS SDTM Dataset Specialization - $neodash_cosmos_instance", - "query": "///SDTM specialiation\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nWHERE ai.adam_param_code = $neodash_cosmos_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data1:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data2:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data3:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[R30:LATEST]->\n (unitdef:UnitDefinitionValue)-[:HAS_CT_UNIT]->\n (ct_context_unit:CTTermContext)-[:HAS_SELECTED_TERM]->\n (unit_code:CTTermRoot)-[:HAS_NAME_ROOT]->\n (:CTTermNameRoot)-[:LATEST]->\n (unit_sponsor),\n (unit_code)-[:HAS_ATTRIBUTES_ROOT]->\n (:CTTermAttributesRoot)-[:LATEST]->\n (unit_cdisc),\n (unitdef)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nOPTIONAL MATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R49:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[R50:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[R51:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[R52:HAS_CT_TERM]->\n (:CTTermContext)-[R53:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[R54:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[R55:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [R56:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [R57:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[R58:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\nOPTIONAL MATCH\n (aitmc1r)-[R59:MAPS_VARIABLE_CLASS]->\n (varcl:VariableClass)-[R60:HAS_INSTANCE]->\n (varcli:VariableClassInstance),\n (varcli)<-[R61:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (var:DatasetVariableInstance)<-\n [R62:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dsi:DatasetInstance)<-[R63:HAS_INSTANCE]-\n (ds:Dataset)<-[R64:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R65:CONTAINS_VERSION]->\n (dmig:DataModelVersion),\n (dsi)<-[R66:HAS_DATASET]-\n (dmigv:DataModelIGValue)<-[R67:CONTAINS_DATA_MODEL_IG]-\n (dmig),\n (dmcat)-[R68:HAS_DATASET_VARIABLE]->\n (dsv:DatasetVariable)-[R69:HAS_INSTANCE]->\n (var)\nWHERE dmigv.version_number = $neodash_sdtmversion\nOPTIONAL MATCH\n (ds)-[R70:HAS_DATASET_VARIABLE]->\n (sdv:SponsorModelDatasetVariableInstance)<-[R71:HAS_INSTANCE]-\n (dsv:DatasetVariable)-[R72:HAS_INSTANCE]->\n (dci)<-[R73:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R74:CONTAINS_VERSION]->\n (dmig:DataModelVersion)\nWITH DISTINCT\n asgrp,\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role_val,\n dtype_val,\n clr,\n cl_cdisc,\n cl_sponsor,\n ct2cd,\n ct2_cdisc,\n ct2_sponsor,\n unit_code.uid AS unit_code,\n unit_cdisc,\n unit_sponsor,\n ct_context2,\n sdv,\n coalesce(\n is_mandatory_data1.mandatory,\n is_mandatory_data2.mandatory,\n is_mandatory_data3.mandatory\n ) AS mandatory_variable\nWHERE NOT aitmc1.name IN ['unit_dimension', 'domain']\nWITH\n asgrp,\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role_val,\n dtype_val,\n clr,\n cl_cdisc,\n cl_sponsor,\n ct2cd,\n ct2_cdisc,\n ct2_sponsor,\n unit_code,\n unit_cdisc,\n unit_sponsor,\n sdv,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n CASE\n WHEN\n var.role = 'Topic'\n THEN\n apoc.map.fromPairs([\n ['code', ct2cd.uid],\n [\n 'value',\n coalesce(\n ct2_cdisc.submission_value,\n toUpper(ct2_sponsor.name)\n )\n ],\n ['shortName', ct2_cdisc.preferred_term]\n ])\n WHEN\n varcl.uid = \"--TEST\"\n THEN\n apoc.map.fromPairs([\n ['code', ct2cd.uid],\n [\n 'value',\n coalesce(ct2_cdisc.preferred_term, toUpper(ct2_sponsor.name))\n ]\n ])\n ELSE\n apoc.map.fromPairs([\n ['code', ct2cd.uid],\n [\n 'value',\n coalesce(ct2_cdisc.submission_value, toUpper(ct2_sponsor.name))\n ]\n ])\n END\n WHEN\n unit_code IS NOT NULL\n THEN\n apoc.map.fromPairs([\n ['code', unit_code],\n [\n 'value',\n coalesce(unit_cdisc.submission_value, toUpper(unit_sponsor.name))\n ]\n ])\n ELSE\n CASE\n WHEN\n varcl.uid = \"--CAT\"\n THEN apoc.map.fromPairs([['value', asgrp.name]])\n END\n END AS val_list,\n mandatory_variable\nWITH\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role_val,\n dtype_val,\n clr,\n cl_cdisc,\n cl_sponsor,\n sdv,\n collect(DISTINCT val_list) AS terms,\n {\n DATETIME: 'datetime',\n FLOAT: 'float',\n INTEGER: 'integer',\n CTTERM: 'text',\n TEXT: 'text'\n } AS dtype_map,\n mandatory_variable\nWITH\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n sdv,\n var,\n role_val,\n [\n x IN ['Identifier', 'Qualifier', 'Timing', 'Topic']\n WHERE var.role CONTAINS x\n ][0] AS role,\n dtype_val,\n dtype_map[toUpper(dtype_val.name)] AS dtype,\n clr,\n cl_cdisc,\n cl_sponsor,\n terms,\n CASE\n WHEN var.role = 'Topic' THEN apoc.text.join([ds.uid, dsv.uid], '.')\n END AS source,\n CASE\n WHEN\n clr IS NOT NULL\n THEN\n apoc.map.fromPairs([\n ['conceptId', clr.uid],\n [\n 'href',\n 'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' +\n clr.uid\n ],\n [\n 'submissionValue',\n coalesce(cl_cdisc.submission_value, toUpper(cl_sponsor.name))\n ]\n ])\n END AS cdlist,\n CASE\n WHEN\n size(terms) = 1\n THEN\n CASE\n WHEN\n any(term IN terms WHERE 'code' IN keys(term))\n THEN\n [\n term IN terms\n | apoc.map.fromPairs([\n ['conceptId', term['code']],\n ['value', term['value']]\n ])\n ]\n ELSE [term IN terms | term['value']]\n END\n END AS assignedTerms,\n CASE\n WHEN size(terms) > 1 THEN [v IN terms | v['value']]\n END AS valueList,\n CASE\n WHEN aitmc1.is_data_collected = 'Yes' THEN 'Collected'\n ELSE 'Not Collected'\n END AS collected,\n mandatory_variable\nWITH\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role,\n dtype_val,\n dtype,\n assignedTerms,\n valueList,\n cdlist,\n source,\n terms,\n sdv,\n CASE\n WHEN\n assignedTerms IS NOT NULL\n THEN\n CASE\n WHEN\n var.role = 'Topic' AND dsv.uid = cdlist['submissionValue']\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['assignedTerm', assignedTerms[0]],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n ELSE\n CASE\n WHEN\n varcl.uid = '--TEST' AND dsv.uid = cdlist['submissionValue']\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['assignedTerm', assignedTerms[0]],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n ELSE\n CASE\n WHEN\n NOT varcl.uid CONTAINS 'TEST'\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['dataElementConceptId', aitmc1.nci_concept_id],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['assignedTerm', assignedTerms[0]],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n END\n END\n END\n ELSE\n CASE\n WHEN\n valueList IS NOT NULL\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['dataElementConceptId', aitmc1.nci_concept_id],\n ['isNonStandard', false],\n ['codelist', cdlist],\n ['valueList', valueList],\n ['role', role],\n ['originType', collected],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n ELSE\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['dataElementConceptId', aitmc1.nci_concept_id],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['valueList', valueList],\n ['originType', collected],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n END\n END AS dataElement,\n ai.adam_param_code AS datasetSpecializationId,\n CASE\n WHEN var.role = 'Topic' THEN [v IN terms | v['shortName']][0]\n END AS shortName\nWITH\n aic,\n ai,\n apoc.coll.toSet(collect(shortName))[0] AS shortName,\n dmigv,\n ds,\n apoc.coll.toSet(collect(source))[0] AS source,\n apoc.coll.toSet(collect(datasetSpecializationId))[0] AS datasetSpecializationId,\n collect(DISTINCT dataElement) AS vars\nWITH\n aic,\n ai,\n shortName,\n dmigv,\n ds,\n source,\n datasetSpecializationId,\n vars,\n apoc.map.fromPairs([\n ['datasetSpecializationId', datasetSpecializationId],\n ['domain', ds.uid],\n ['shortName', shortName],\n ['source', source],\n ['sdtmigStartVersion', dmigv.version_number],\n ['sdtmigEndVersion', \"\"],\n ['variables', vars]\n ]) AS activity\nRETURN activity", + "query": "///SDTM specialiation\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nWHERE ai.adam_param_code = $neodash_cosmos_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data1:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data2:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data3:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[R30:LATEST]->\n (unitdef:UnitDefinitionValue)-[:HAS_CT_UNIT]->\n (ct_context_unit:CTTermContext)-[:HAS_SELECTED_TERM]->\n (unit_code:CTTermRoot)-[:HAS_NAME_ROOT]->\n (:CTTermNameRoot)-[:LATEST]->\n (unit_sponsor),\n (unit_code)-[:HAS_ATTRIBUTES_ROOT]->\n (:CTTermAttributesRoot)-[:LATEST]->\n (unit_cdisc),\n (unitdef)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nOPTIONAL MATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R49:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[R50:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[R51:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[R52:HAS_CT_TERM]->\n (:CTTermContext)-[R53:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[R54:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[R55:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [R56:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [R57:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[R58:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\nOPTIONAL MATCH\n (aitmc1r)-[R59:MAPS_VARIABLE_CLASS]->\n (varcl:VariableClass)-[R60:HAS_INSTANCE]->\n (varcli:VariableClassInstance),\n (varcli)<-[R61:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (var:DatasetVariableInstance)<-\n [R62:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (dsi:DatasetInstance)<-[R63:HAS_INSTANCE]-\n (ds:Dataset)<-[R64:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R65:CONTAINS_VERSION]->\n (dmig:DataModelVersion),\n (dsi)<-[R66:HAS_DATASET]-\n (dmigv:DataModelIGValue)<-[R67:CONTAINS_DATA_MODEL_IG]-\n (dmig),\n (dmcat)-[R68:HAS_DATASET_VARIABLE]->\n (dsv:DatasetVariable)-[R69:HAS_INSTANCE]->\n (var)\nWHERE dmigv.version_number = $neodash_sdtmversion\nOPTIONAL MATCH\n (ds)-[R70:HAS_DATASET_VARIABLE]->\n (sdv:SponsorModelDatasetVariableInstance)<-[R71:HAS_INSTANCE]-\n (dsv:DatasetVariable)-[R72:HAS_INSTANCE]->\n (dci)<-[R73:HAS_DATASET]-\n (dmcat:DataModelCatalogue)-[R74:CONTAINS_VERSION]->\n (dmig:DataModelVersion)\nWITH DISTINCT\n asgrp,\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role_val,\n dtype_val,\n clr,\n cl_cdisc,\n cl_sponsor,\n ct2cd,\n ct2_cdisc,\n ct2_sponsor,\n unit_code.uid AS unit_code,\n unit_cdisc,\n unit_sponsor,\n ct_context2,\n sdv,\n coalesce(\n is_mandatory_data1.mandatory,\n is_mandatory_data2.mandatory,\n is_mandatory_data3.mandatory\n ) AS mandatory_variable\nWHERE NOT aitmc1.name IN ['unit_dimension', 'domain']\nWITH\n asgrp,\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role_val,\n dtype_val,\n clr,\n cl_cdisc,\n cl_sponsor,\n ct2cd,\n ct2_cdisc,\n ct2_sponsor,\n unit_code,\n unit_cdisc,\n unit_sponsor,\n sdv,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n CASE\n WHEN\n var.role = 'Topic'\n THEN\n apoc.map.fromPairs([\n ['code', ct2cd.uid],\n [\n 'value',\n coalesce(\n ct2_cdisc.submission_value,\n toUpper(ct2_sponsor.name)\n )\n ],\n ['shortName', ct2_cdisc.preferred_term]\n ])\n WHEN\n varcl.uid = \"--TEST\"\n THEN\n apoc.map.fromPairs([\n ['code', ct2cd.uid],\n [\n 'value',\n coalesce(ct2_cdisc.preferred_term, toUpper(ct2_sponsor.name))\n ]\n ])\n ELSE\n apoc.map.fromPairs([\n ['code', ct2cd.uid],\n [\n 'value',\n coalesce(ct2_cdisc.submission_value, toUpper(ct2_sponsor.name))\n ]\n ])\n END\n WHEN\n unit_code IS NOT NULL\n THEN\n apoc.map.fromPairs([\n ['code', unit_code],\n [\n 'value',\n coalesce(unit_cdisc.submission_value, toUpper(unit_sponsor.name))\n ]\n ])\n ELSE\n CASE\n WHEN\n varcl.uid = \"--CAT\"\n THEN apoc.map.fromPairs([['value', asgrp.name]])\n END\n END AS val_list,\n mandatory_variable\nWITH\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role_val,\n dtype_val,\n clr,\n cl_cdisc,\n cl_sponsor,\n sdv,\n collect(DISTINCT val_list) AS terms,\n {\n DATETIME: 'datetime',\n FLOAT: 'float',\n INTEGER: 'integer',\n CTTERM: 'text',\n TEXT: 'text'\n } AS dtype_map,\n mandatory_variable\nWITH\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n sdv,\n var,\n role_val,\n [\n x IN ['Identifier', 'Qualifier', 'Timing', 'Topic']\n WHERE var.role CONTAINS x\n ][0] AS role,\n dtype_val,\n dtype_map[toUpper(dtype_val.name)] AS dtype,\n clr,\n cl_cdisc,\n cl_sponsor,\n terms,\n CASE\n WHEN var.role = 'Topic' THEN apoc.text.join([ds.uid, dsv.uid], '.')\n END AS source,\n CASE\n WHEN\n clr IS NOT NULL\n THEN\n apoc.map.fromPairs([\n ['conceptId', clr.uid],\n [\n 'href',\n 'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' +\n clr.uid\n ],\n [\n 'submissionValue',\n coalesce(cl_cdisc.submission_value, toUpper(cl_sponsor.name))\n ]\n ])\n END AS cdlist,\n CASE\n WHEN\n size(terms) = 1\n THEN\n CASE\n WHEN\n any(term IN terms WHERE 'code' IN keys(term))\n THEN\n [\n term IN terms\n | apoc.map.fromPairs([\n ['conceptId', term['code']],\n ['value', term['value']]\n ])\n ]\n ELSE [term IN terms | term['value']]\n END\n END AS assignedTerms,\n CASE\n WHEN size(terms) > 1 THEN [v IN terms | v['value']]\n END AS valueList,\n CASE\n WHEN aitmc1.is_data_collected = 'Yes' THEN 'Collected'\n ELSE 'Not Collected'\n END AS collected,\n mandatory_variable\nWITH\n aic,\n ai,\n aitmc1,\n dmigv,\n ds,\n varcl,\n dsv,\n var,\n role,\n dtype_val,\n dtype,\n assignedTerms,\n valueList,\n cdlist,\n source,\n terms,\n sdv,\n CASE\n WHEN\n assignedTerms IS NOT NULL\n THEN\n CASE\n WHEN\n var.role = 'Topic' AND dsv.uid = cdlist['submissionValue']\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['assignedTerm', assignedTerms[0]],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n ELSE\n CASE\n WHEN\n varcl.uid = '--TEST' AND dsv.uid = cdlist['submissionValue']\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['assignedTerm', assignedTerms[0]],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n ELSE\n CASE\n WHEN\n NOT varcl.uid CONTAINS 'TEST'\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['dataElementConceptId', aitmc1.nci_concept_id],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['assignedTerm', assignedTerms[0]],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n END\n END\n END\n ELSE\n CASE\n WHEN\n valueList IS NOT NULL\n THEN\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['dataElementConceptId', aitmc1.nci_concept_id],\n ['isNonStandard', false],\n ['codelist', cdlist],\n ['valueList', valueList],\n ['role', role],\n ['originType', collected],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n ELSE\n apoc.map.fromPairs([\n ['name', dsv.uid],\n ['dataElementConceptId', aitmc1.nci_concept_id],\n ['isNonStandard', false],\n ['role', role],\n ['dataType', dtype],\n ['codelist', cdlist],\n ['valueList', valueList],\n ['originType', collected],\n ['mandatoryVariable', mandatory_variable],\n ['mandatoryValue', false]\n ])\n END\n END AS dataElement,\n ai.adam_param_code AS datasetSpecializationId,\n CASE\n WHEN var.role = 'Topic' THEN [v IN terms | v['shortName']][0]\n END AS shortName\nWITH\n aic,\n ai,\n apoc.coll.toSet(collect(shortName))[0] AS shortName,\n dmigv,\n ds,\n apoc.coll.toSet(collect(source))[0] AS source,\n apoc.coll.toSet(collect(datasetSpecializationId))[0] AS datasetSpecializationId,\n collect(DISTINCT dataElement) AS vars\nWITH\n aic,\n ai,\n shortName,\n dmigv,\n ds,\n source,\n datasetSpecializationId,\n vars,\n apoc.map.fromPairs([\n ['datasetSpecializationId', datasetSpecializationId],\n ['domain', ds.uid],\n ['shortName', shortName],\n ['source', source],\n ['sdtmigStartVersion', dmigv.version_number],\n ['sdtmigEndVersion', \"\"],\n ['variables', vars]\n ]) AS activity\nRETURN activity", "width": 15, "height": 7, "x": 9, @@ -1729,7 +1899,7 @@ { "id": "4b986a7e-91bd-447e-9a23-41036b6795b6", "title": "Activity as COSMOS BC Concept - $neodash_cosmos_activity", - "query": "//Activity mapped to SDTM\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_cosmos_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[R30:LATEST]->\n (unitdef:UnitDefinitionValue)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R49:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[R50:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[R51:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[R52:HAS_CT_TERM]->\n (:CTTermContext)-[R53:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[R54:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[R55:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [R56:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [R57:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[R58:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\nWITH DISTINCT\n act.name AS ActivityName,\n aic AS aic,\n asgrp,\n aitmc1,\n ai,\n ct2cd,\n unitdef AS unit_ct,\n role_val AS role,\n dtype_val AS dtype,\n CASE\n WHEN unitdefr IS NOT NULL THEN unitdef\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END AS ct2,\n term.submission_value AS term_submission_value,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n ActivityName,\n aic,\n asgrp,\n aitmc1,\n ai,\n unit_ct,\n ct2,\n ct2cd,\n role,\n dtype,\n cl,\n term_submission_value,\n CASE\n WHEN role.name = 'Topic' THEN ct2cd.uid\n END AS conceptId,\n CASE\n WHEN aitmc1.name = 'domain' THEN term_submission_value\n END AS domain\nWITH DISTINCT\n ActivityName,\n aic,\n asgrp,\n aitmc1,\n ai,\n unit_ct,\n ct2,\n role,\n dtype,\n conceptId,\n domain,\n cl,\n term_submission_value,\n CASE\n WHEN (apoc.any.property(aic, 'name') = 'NumericFinding') THEN 'Quantitative'\n ELSE\n CASE\n WHEN\n (apoc.any.property(aic, 'name') = 'CategoricFinding')\n THEN 'Ordinal'\n ELSE 'Nominal'\n END\n END AS aiclass\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp.name AS asgrp,\n domain,\n aitmc1,\n unit_ct,\n ct2,\n term_submission_value,\n role,\n dtype,\n cl,\n collect(\n DISTINCT\n (coalesce(term_submission_value, ct2.preferred_term, unit_ct.name))) AS val_lst\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n aitmc1,\n dtype.name AS dtype,\n apoc.coll.flatten(collect(val_lst)) AS val_list,\n toInteger(aitmc1.order) AS var_order,\n cl\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n cl\nCALL\n apoc.load.json(\n 'https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/C82590?include=minimal%2CinverseAssociations'\n )\n YIELD value\nWITH DISTINCT\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n cl,\n value['inverseAssociations'] AS class_concepts\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n cl,\n aitmc1,\n val_list,\n var_order,\n class_concepts,\n {\n PERCENTAGE: \"Unit of Fraction\",\n `RESPIRATORY RATE`: \"Unit Respiratory Rate\",\n CONCENTRATION: \"Unit of Concentration\",\n `U_IU Concentration`: \"Unit of Concentration\",\n TEMPERATURE: \"Unit of Temperature\",\n WEIGHT: \"Unit of Weight\",\n PRESSURE: \"Unit of Pressure\",\n FLOW: \"Unit of Flow Rate\",\n `VOLUMETRIC FLOW RATE`: \"Unit of Volumetric Flow Rate\",\n `CELL COUNT`: \"Unit of Cell Count\",\n LENGTH: \"Unit of Length\",\n `NO UNIT`: \"No Unit\",\n TIME: \"Unit of Time\",\n `BEAT RATE`: \"Unit of Beat Rate\"\n } AS unit_dimension_dict,\n {\n DATETIME: 'datetime',\n FLOAT: 'decimal',\n INTEGER: 'integer',\n CTTERM: 'string',\n TEXT: 'string'\n } AS dtype_map\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n aitmc1,\n val_list,\n cl,\n var_order,\n class_concepts,\n unit_dimension_dict,\n dtype_map,\n CASE\n WHEN\n aitmc1.name = 'standard_unit'\n THEN apoc.text.join(['Unit of', cl.name], ' ')\n ELSE\n CASE\n WHEN\n aitmc1.name = 'unit_dimension'\n THEN unit_dimension_dict[apoc.text.join(val_list, '')]\n ELSE\n CASE\n WHEN aitmc1.name = 'test_code' THEN \"Test Code\"\n ELSE\n CASE\n WHEN aitmc1.name CONTAINS 'category' THEN 'Category'\n ELSE\n CASE\n WHEN aitmc1.name = 'domain' THEN 'Submission Domain'\n ELSE\n CASE\n WHEN aitmc1.name = 'specimen' THEN 'Biospecimen Type'\n ELSE\n apoc.text.join(\n [\n c IN class_concepts\n WHERE\n toUpper(c.relatedName) = toUpper(aitmc1.name)\n | c.relatedName\n ],\n ''\n )\n END\n END\n END\n END\n END\n END AS aitmc1_term,\n dtype_map[toUpper(dtype)] AS dtype\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n apoc.text.replace(aitmc1_term, \" \", \"%20\") AS aitmc1_term\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n aitmc1_term\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/search?fromRecord=0&include=minimal&pageSize=10&term=\" +\n aitmc1_term +\n \"&type=match&value=term\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n aitmc1.nci_concept_id AS item_concept_id,\n aitmc1_term\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n item_concept_id,\n aitmc1_term\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/search?fromRecord=0&include=minimal&pageSize=10&term=\" +\n aitmc1_term +\n \"&type=startsWith&value=term\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n item_concept_id,\n apoc.text.join([v IN value.concepts | v.code], ',') AS alt_item_concept_id\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n CASE\n WHEN\n item_concept_id IS NULL AND NOT alt_item_concept_id IS NULL\n THEN alt_item_concept_id\n ELSE item_concept_id\n END AS item_concept_id\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n item_concept_id,\n CASE\n WHEN item_concept_id IS NULL THEN null\n ELSE\n 'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' +\n item_concept_id\n END AS href\nWITH DISTINCT\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n aitmc1.name AS aitmc1Name,\n apoc.text.join(collect(DISTINCT dtype), ',') AS dtypes,\n apoc.coll.flatten(collect(val_list)) AS val_list,\n var_order,\n href,\n item_concept_id\nWITH DISTINCT\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n val_list,\n var_order,\n href,\n item_concept_id\nWITH DISTINCT\n collect(conceptId) AS conceptId,\n ActivityName,\n aiclass,\n asgrp,\n collect(domain) AS domain,\n collect(\n apoc.map.fromPairs([\n ['dtypes', dtypes],\n ['aitmc1Name', aitmc1Name],\n ['val_list', val_list],\n ['var_order', var_order],\n ['href', href],\n ['item_concept_id', item_concept_id]\n ])) AS var_map\nWITH\n conceptId,\n ActivityName,\n apoc.coll.toSet(collect(aiclass)) AS aiclass,\n apoc.coll.toSet(collect(asgrp)) AS asgrp,\n apoc.coll.toSet(domain) AS domain,\n apoc.coll.toSet(apoc.coll.flatten(collect(var_map))) AS var_maps\nWITH conceptId, ActivityName, aiclass, asgrp, domain, var_maps\nUNWIND var_maps AS var_map\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n var_map['dtypes'] AS dtypes,\n var_map['aitmc1Name'] AS aitmc1Name,\n var_map['val_list'] AS val_list,\n var_map['var_order'] AS var_order,\n var_map['href'] AS href,\n var_map['item_concept_id'] AS item_concept_id\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n apoc.coll.toSet(collect(href)) AS href,\n apoc.coll.toSet(collect(item_concept_id)) AS item_concept_id,\n apoc.coll.toSet(apoc.coll.flatten(collect(val_list))) AS val_list,\n var_order\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n href,\n item_concept_id,\n val_list,\n var_order\nWHERE NOT aitmc1Name IN ['domain', 'test_code', 'test_name','unit_dimension']\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n CASE\n WHEN size(href) = 0 THEN null\n ELSE apoc.text.join(href, '')\n END AS href,\n CASE\n WHEN size(item_concept_id) = 0 THEN null\n ELSE apoc.text.join(item_concept_id, '')\n END AS item_concept_id,\n val_list,\n var_order\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n collect(\n apoc.map.fromPairs([\n ['conceptId', item_concept_id],\n ['href', href],\n ['shortName', aitmc1Name],\n ['dataType', dtypes],\n ['exampleSet', val_list]\n ])) AS vars\nWITH conceptId, ActivityName, aiclass, asgrp, domain, vars\nWHERE size(conceptId) < 2\nWITH\n apoc.text.join(conceptId, ',') AS conceptId,\n ActivityName,\n aiclass,\n asgrp,\n apoc.text.join(domain, ';') AS domain,\n vars\nWITH\n CASE\n WHEN conceptId = \"\" THEN 'C17998'\n ELSE conceptId\n END AS conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"?limit=100&include=minimal\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n value.name AS conceptName\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"/parents\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n collect(value.code)[0] AS parentConceptId\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"?include=definitions\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n value,\n [def IN value.definitions WHERE def.source = \"NCI\"] AS def\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n def[0][\"definition\"] AS conceptDefinition\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n conceptDefinition\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"?include=synonyms\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n conceptDefinition,\n value,\n apoc.coll.toSet(\n [\n sym IN value.synonyms\n WHERE sym.source = \"CDISC\" AND sym.termType = \"PT\"\n | sym.name\n ]) AS conceptSynonyms\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n apoc.coll.sortMaps(vars, '^var_order') AS vars,\n conceptName,\n parentConceptId,\n conceptDefinition,\n conceptSynonyms\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n conceptDefinition,\n conceptSynonyms,\n apoc.map.fromPairs([\n ['packageDate', toString(date())],\n ['packageType', 'bc'],\n ['conceptId', conceptId],\n [\n 'href',\n 'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' +\n conceptId\n ],\n ['parentConceptId', parentConceptId],\n ['category', asgrp],\n ['shortName', conceptName],\n ['activityName', ActivityName],\n ['synonym', conceptSynonyms],\n ['resultScale', aiclass],\n ['definition', conceptDefinition],\n ['domain', domain],\n ['dataElementConcepts', vars]\n ]) AS activity\nRETURN DISTINCT activity", + "query": "//Activity mapped to SDTM\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_cosmos_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[R30:LATEST]->\n (unitdef:UnitDefinitionValue)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R49:CONTAINS_ACTIVITY_ITEM]->\n (aitm1_dom:ActivityItem)<-[R50:HAS_ACTIVITY_ITEM]-\n (n1:ActivityItemClassRoot)-[R51:MAPS_VARIABLE_CLASS]->\n (dom_class:VariableClass {uid: 'DOMAIN'}),\n (aitm1_dom)-[R52:HAS_CT_TERM]->\n (:CTTermContext)-[R53:HAS_SELECTED_TERM]->\n (:CTTermRoot)<-[R54:HAS_TERM_ROOT]-\n (ct2_dom:CTCodelistTerm),\n (dom_class)-[R55:HAS_INSTANCE]->\n (n3:VariableClassInstance)<-\n [R56:IMPLEMENTS_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n4:DatasetVariableInstance)<-\n [R57:HAS_DATASET_VARIABLE {version_number: $neodash_sdtmversion}]-\n (n5:DatasetInstance)<-[R58:HAS_INSTANCE]-\n (ds:Dataset)\nWHERE ds.uid = ct2_dom.submission_value\nWITH DISTINCT\n act.name AS ActivityName,\n aic AS aic,\n asgrp,\n aitmc1,\n ai,\n ct2cd,\n unitdef AS unit_ct,\n role_val AS role,\n dtype_val AS dtype,\n CASE\n WHEN unitdefr IS NOT NULL THEN unitdef\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END AS ct2,\n term.submission_value AS term_submission_value,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n ActivityName,\n aic,\n asgrp,\n aitmc1,\n ai,\n unit_ct,\n ct2,\n ct2cd,\n role,\n dtype,\n cl,\n term_submission_value,\n CASE\n WHEN role.name = 'Topic' THEN ct2cd.uid\n END AS conceptId,\n CASE\n WHEN aitmc1.name = 'domain' THEN term_submission_value\n END AS domain\nWITH DISTINCT\n ActivityName,\n aic,\n asgrp,\n aitmc1,\n ai,\n unit_ct,\n ct2,\n role,\n dtype,\n conceptId,\n domain,\n cl,\n term_submission_value,\n CASE\n WHEN (apoc.any.property(aic, 'name') = 'NumericFinding') THEN 'Quantitative'\n ELSE\n CASE\n WHEN\n (apoc.any.property(aic, 'name') = 'CategoricFinding')\n THEN 'Ordinal'\n ELSE 'Nominal'\n END\n END AS aiclass\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp.name AS asgrp,\n domain,\n aitmc1,\n unit_ct,\n ct2,\n term_submission_value,\n role,\n dtype,\n cl,\n collect(\n DISTINCT\n (coalesce(term_submission_value, ct2.preferred_term, unit_ct.name))) AS val_lst\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n aitmc1,\n dtype.name AS dtype,\n apoc.coll.flatten(collect(val_lst)) AS val_list,\n toInteger(aitmc1.order) AS var_order,\n cl\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n cl\nCALL\n apoc.load.json(\n 'https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/C82590?include=minimal%2CinverseAssociations'\n )\n YIELD value\nWITH DISTINCT\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n cl,\n value['inverseAssociations'] AS class_concepts\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n cl,\n aitmc1,\n val_list,\n var_order,\n class_concepts,\n {\n PERCENTAGE: \"Unit of Fraction\",\n `RESPIRATORY RATE`: \"Unit Respiratory Rate\",\n CONCENTRATION: \"Unit of Concentration\",\n `U_IU Concentration`: \"Unit of Concentration\",\n TEMPERATURE: \"Unit of Temperature\",\n WEIGHT: \"Unit of Weight\",\n PRESSURE: \"Unit of Pressure\",\n FLOW: \"Unit of Flow Rate\",\n `VOLUMETRIC FLOW RATE`: \"Unit of Volumetric Flow Rate\",\n `CELL COUNT`: \"Unit of Cell Count\",\n LENGTH: \"Unit of Length\",\n `NO UNIT`: \"No Unit\",\n TIME: \"Unit of Time\",\n `BEAT RATE`: \"Unit of Beat Rate\"\n } AS unit_dimension_dict,\n {\n DATETIME: 'datetime',\n FLOAT: 'decimal',\n INTEGER: 'integer',\n CTTERM: 'string',\n TEXT: 'string'\n } AS dtype_map\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n aitmc1,\n val_list,\n cl,\n var_order,\n class_concepts,\n unit_dimension_dict,\n dtype_map,\n CASE\n WHEN\n aitmc1.name = 'standard_unit'\n THEN apoc.text.join(['Unit of', cl.name], ' ')\n ELSE\n CASE\n WHEN\n aitmc1.name = 'unit_dimension'\n THEN unit_dimension_dict[apoc.text.join(val_list, '')]\n ELSE\n CASE\n WHEN aitmc1.name = 'test_code' THEN \"Test Code\"\n ELSE\n CASE\n WHEN aitmc1.name CONTAINS 'category' THEN 'Category'\n ELSE\n CASE\n WHEN aitmc1.name = 'domain' THEN 'Submission Domain'\n ELSE\n CASE\n WHEN aitmc1.name = 'specimen' THEN 'Biospecimen Type'\n ELSE\n apoc.text.join(\n [\n c IN class_concepts\n WHERE\n toUpper(c.relatedName) = toUpper(aitmc1.name)\n | c.relatedName\n ],\n ''\n )\n END\n END\n END\n END\n END\n END AS aitmc1_term,\n dtype_map[toUpper(dtype)] AS dtype\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n apoc.text.replace(aitmc1_term, \" \", \"%20\") AS aitmc1_term\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n aitmc1_term\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/search?fromRecord=0&include=minimal&pageSize=10&term=\" +\n aitmc1_term +\n \"&type=match&value=term\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n aitmc1.nci_concept_id AS item_concept_id,\n aitmc1_term\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n item_concept_id,\n aitmc1_term\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/search?fromRecord=0&include=minimal&pageSize=10&term=\" +\n aitmc1_term +\n \"&type=startsWith&value=term\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n item_concept_id,\n apoc.text.join([v IN value.concepts | v.code], ',') AS alt_item_concept_id\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n CASE\n WHEN\n item_concept_id IS NULL AND NOT alt_item_concept_id IS NULL\n THEN alt_item_concept_id\n ELSE item_concept_id\n END AS item_concept_id\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtype,\n aitmc1,\n val_list,\n var_order,\n item_concept_id,\n CASE\n WHEN item_concept_id IS NULL THEN null\n ELSE\n 'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' +\n item_concept_id\n END AS href\nWITH DISTINCT\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n aitmc1.name AS aitmc1Name,\n apoc.text.join(collect(DISTINCT dtype), ',') AS dtypes,\n apoc.coll.flatten(collect(val_list)) AS val_list,\n var_order,\n href,\n item_concept_id\nWITH DISTINCT\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n val_list,\n var_order,\n href,\n item_concept_id\nWITH DISTINCT\n collect(conceptId) AS conceptId,\n ActivityName,\n aiclass,\n asgrp,\n collect(domain) AS domain,\n collect(\n apoc.map.fromPairs([\n ['dtypes', dtypes],\n ['aitmc1Name', aitmc1Name],\n ['val_list', val_list],\n ['var_order', var_order],\n ['href', href],\n ['item_concept_id', item_concept_id]\n ])) AS var_map\nWITH\n conceptId,\n ActivityName,\n apoc.coll.toSet(collect(aiclass)) AS aiclass,\n apoc.coll.toSet(collect(asgrp)) AS asgrp,\n apoc.coll.toSet(domain) AS domain,\n apoc.coll.toSet(apoc.coll.flatten(collect(var_map))) AS var_maps\nWITH conceptId, ActivityName, aiclass, asgrp, domain, var_maps\nUNWIND var_maps AS var_map\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n var_map['dtypes'] AS dtypes,\n var_map['aitmc1Name'] AS aitmc1Name,\n var_map['val_list'] AS val_list,\n var_map['var_order'] AS var_order,\n var_map['href'] AS href,\n var_map['item_concept_id'] AS item_concept_id\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n apoc.coll.toSet(collect(href)) AS href,\n apoc.coll.toSet(collect(item_concept_id)) AS item_concept_id,\n apoc.coll.toSet(apoc.coll.flatten(collect(val_list))) AS val_list,\n var_order\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n href,\n item_concept_id,\n val_list,\n var_order\nWHERE NOT aitmc1Name IN ['domain', 'test_code', 'test_name','unit_dimension']\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n dtypes,\n aitmc1Name,\n CASE\n WHEN size(href) = 0 THEN null\n ELSE apoc.text.join(href, '')\n END AS href,\n CASE\n WHEN size(item_concept_id) = 0 THEN null\n ELSE apoc.text.join(item_concept_id, '')\n END AS item_concept_id,\n val_list,\n var_order\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n collect(\n apoc.map.fromPairs([\n ['conceptId', item_concept_id],\n ['href', href],\n ['shortName', aitmc1Name],\n ['dataType', dtypes],\n ['exampleSet', val_list]\n ])) AS vars\nWITH conceptId, ActivityName, aiclass, asgrp, domain, vars\nWHERE size(conceptId) < 2\nWITH\n apoc.text.join(conceptId, ',') AS conceptId,\n ActivityName,\n aiclass,\n asgrp,\n apoc.text.join(domain, ';') AS domain,\n vars\nWITH\n CASE\n WHEN conceptId = \"\" THEN 'C17998'\n ELSE conceptId\n END AS conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"?limit=100&include=minimal\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n value.name AS conceptName\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"/parents\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n collect(value.code)[0] AS parentConceptId\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"?include=definitions\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n value,\n [def IN value.definitions WHERE def.source = \"NCI\"] AS def\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n def[0][\"definition\"] AS conceptDefinition\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n conceptDefinition\nCALL\n apoc.load.json(\n \"https://api-evsrest.nci.nih.gov/api/v1/concept/ncit/\" +\n conceptId +\n \"?include=synonyms\"\n )\n YIELD value\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n conceptDefinition,\n value,\n apoc.coll.toSet(\n [\n sym IN value.synonyms\n WHERE sym.source = \"CDISC\" AND sym.termType = \"PT\"\n | sym.name\n ]) AS conceptSynonyms\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n apoc.coll.sortMaps(vars, '^var_order') AS vars,\n conceptName,\n parentConceptId,\n conceptDefinition,\n conceptSynonyms\nWITH\n conceptId,\n ActivityName,\n aiclass,\n asgrp,\n domain,\n vars,\n conceptName,\n parentConceptId,\n conceptDefinition,\n conceptSynonyms,\n apoc.map.fromPairs([\n ['packageDate', toString(date())],\n ['packageType', 'bc'],\n ['conceptId', conceptId],\n [\n 'href',\n 'https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=' +\n conceptId\n ],\n ['parentConceptId', parentConceptId],\n ['category', asgrp],\n ['shortName', conceptName],\n ['activityName', ActivityName],\n ['synonym', conceptSynonyms],\n ['resultScale', aiclass],\n ['definition', conceptDefinition],\n ['domain', domain],\n ['dataElementConcepts', vars]\n ]) AS activity\nRETURN DISTINCT activity", "width": 24, "height": 6, "x": 0, @@ -1747,7 +1917,7 @@ { "id": "1b17908f-5b7f-41e5-a4dc-735c9cf356b2", "title": "Select Instance", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-() \nwhere act.name = $neodash_cosmos_activity \nreturn ai.name as Instance, ai.adam_param_code as `ADaM Param Code`\n\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) \nwhere act.name = $neodash_cosmos_activity \nreturn ai.name as Instance, ai.adam_param_code as `ADaM Param Code`\n\n\n", "width": 9, "height": 3, "x": 0, @@ -1899,7 +2069,7 @@ { "id": "473fee31-bf53-421f-9e1e-553063c9d8aa", "title": "SoA (Activity Instances)", - "query": "match(s:StudyValue) where id(s) = toInteger($neodash_study_act_select )\noptional match(s)-[:HAS_STUDY_VISIT]->(v:StudyVisit)\nwith s, v order by v.visit_number, v.short_visit_label\nwith s, collect(distinct v.short_visit_label) as vis_total\noptional match(s)-[:HAS_STUDY_VISIT]->(vis:StudyVisit)\noptional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\noptional match(vis)-[:STUDY_VISIT_HAS_SCHEDULE]->(schedule:StudyActivitySchedule)\noptional match (s)-[:HAS_STUDY_ACTIVITY_SCHEDULE]->(schedule),\n(schedule)<-[:STUDY_ACTIVITY_HAS_SCHEDULE]-(s_act:StudyActivity),\n(s_act)-[:HAS_SELECTED_ACTIVITY]->(act_val:ActivityValue),(s_act)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_INSTANCE]->(ai_s:StudyActivityInstance)-[:HAS_SELECTED_ACTIVITY_INSTANCE]-(ai:ActivityInstanceValue),\n(ai)-[r1]->(g)<-[r2]-(act_val) where act_val.name in $neodash_study_activity\nwith distinct schedule, ai.topic_code as TOPIC_CODE, vis_total, vis.short_visit_label as `Visit Short Label`,vis.visit_number as `Visit ID`\nwhere TOPIC_CODE is not null \nWith schedule,TOPIC_CODE, `Visit Short Label` as Visits order by `Visit ID`, `Visit Short Label`, schedule.uid\nwith Visits, collect(TOPIC_CODE) as `TOPIC CODES`\nreturn Visits, `TOPIC CODES`", + "query": "match(s:StudyValue) where id(s) = toInteger($neodash_study_act_select )\noptional match(s)-[:HAS_STUDY_VISIT]->(v:StudyVisit)\nwith s, v order by v.visit_number, v.short_visit_label\nwith s, collect(distinct v.short_visit_label) as vis_total\noptional match(s)-[:HAS_STUDY_VISIT]->(vis:StudyVisit)\noptional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\noptional match(vis)-[:STUDY_VISIT_HAS_SCHEDULE]->(schedule:StudyActivitySchedule)\noptional match (s)-[:HAS_STUDY_ACTIVITY_SCHEDULE]->(schedule),\n(schedule)<-[:STUDY_ACTIVITY_HAS_SCHEDULE]-(s_act:StudyActivity),\n(s_act)-[:HAS_SELECTED_ACTIVITY]->(act_val:ActivityValue),(s_act)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_INSTANCE]->(ai_s:StudyActivityInstance)-[:HAS_SELECTED_ACTIVITY_INSTANCE]-(ai:ActivityInstanceValue),\n(ai)<-[:LATEST]-(air:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(aigr:ActivityInstanceGroupingRoot)-[:LATEST]->(aigv:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(g:ActivityGrouping)<-[:HAS_GROUPING]-(act_val) where act_val.name in $neodash_study_activity\nwith distinct schedule, ai.topic_code as TOPIC_CODE, vis_total, vis.short_visit_label as `Visit Short Label`,vis.visit_number as `Visit ID`\nwhere TOPIC_CODE is not null \nWith schedule,TOPIC_CODE, `Visit Short Label` as Visits order by `Visit ID`, `Visit Short Label`, schedule.uid\nwith Visits, collect(TOPIC_CODE) as `TOPIC CODES`\nreturn Visits, `TOPIC CODES`", "width": 24, "height": 8, "x": 0, @@ -1960,7 +2130,7 @@ { "id": "a8d99ae6-9c80-44e5-b480-49e768f3732b", "title": "Detail of Selected Instances", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nWHERE ai.name IN $neodash_ai\nOPTIONAL MATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data1:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data2:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data3:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[R30:LATEST]->\n (unitdef:UnitDefinitionValue)-[:HAS_CT_UNIT]->\n (ct_context_unit:CTTermContext)-[:HAS_SELECTED_TERM]->\n (unit_code:CTTermRoot)-[:HAS_NAME_ROOT]->\n (:CTTermNameRoot)-[:LATEST]->\n (unit_sponsor),\n (unit_code)-[:HAS_ATTRIBUTES_ROOT]->\n (:CTTermAttributesRoot)-[:LATEST]->\n (unit_cdisc),\n (unitdef)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nOPTIONAL MATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\nWITH\n agrp.name AS `Activity Group`,\n asgrp.name AS `Activity Subgroup`,\n act.name AS Activity,\n ai.adam_param_code AS `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n CASE\n WHEN aitmc1.name = \"unit_dimension\" THEN pos_units_in_dim.name\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN coalesce(ct2_cdisc.preferred_term, ct2_sponsor.name)\n ELSE\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN coalesce(unit_cdisc.preferred_term, unit_sponsor.name)\n END\n END\n END AS terms,\n CASE\n WHEN clr IS NOT NULL THEN coalesce(cl_cdisc.preferred_term, cl_sponsor.name)\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN coalesce(cl_unit_cdisc.preferred_term, cl_unit_sponsor.name)\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nRETURN\n `Activity Instance`,\n `Activity Item Class`,\n apoc.text.join(collect(DISTINCT terms), \",\") AS Term,\n `Code List`,\n Role,\n `Data Type`,\n Activity,\n `Activity Subgroup`,\n `Activity Group`", + "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nWHERE ai.name IN $neodash_ai\nOPTIONAL MATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data1:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data2:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[is_mandatory_data3:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[R24:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[R25:HAS_TERM]-\n (clr:CTCodelistRoot)<-[R26:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[R27:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[R28:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[R29:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[R30:LATEST]->\n (unitdef:UnitDefinitionValue)-[:HAS_CT_UNIT]->\n (ct_context_unit:CTTermContext)-[:HAS_SELECTED_TERM]->\n (unit_code:CTTermRoot)-[:HAS_NAME_ROOT]->\n (:CTTermNameRoot)-[:LATEST]->\n (unit_sponsor),\n (unit_code)-[:HAS_ATTRIBUTES_ROOT]->\n (:CTTermAttributesRoot)-[:LATEST]->\n (unit_cdisc),\n (unitdef)-[R31:HAS_CT_DIMENSION]->\n (ct_context2)-[R32:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[R33:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[R34:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[R35:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[R36:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R37:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R38:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R39:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R40:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R41:HAS_ROLE]->\n (ct_context_role)-[R42:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R43:HAS_NAME_ROOT]->\n (ctnr_role)-[R44:LATEST]->\n (role_val)\nOPTIONAL MATCH\n (aitmc1)-[R45:HAS_DATA_TYPE]->\n (ct_context_dtype)-[R46:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R47:HAS_NAME_ROOT]->(ctnr_dtype)-[R48:LATEST]->(dtype_val)\nWITH\n agrp.name AS `Activity Group`,\n asgrp.name AS `Activity Subgroup`,\n act.name AS Activity,\n ai.adam_param_code AS `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n CASE\n WHEN aitmc1.name = \"unit_dimension\" THEN pos_units_in_dim.name\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN coalesce(ct2_cdisc.preferred_term, ct2_sponsor.name)\n ELSE\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN coalesce(unit_cdisc.preferred_term, unit_sponsor.name)\n END\n END\n END AS terms,\n CASE\n WHEN clr IS NOT NULL THEN coalesce(cl_cdisc.preferred_term, cl_sponsor.name)\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN coalesce(cl_unit_cdisc.preferred_term, cl_unit_sponsor.name)\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nRETURN\n `Activity Instance`,\n `Activity Item Class`,\n apoc.text.join(collect(DISTINCT terms), \",\") AS Term,\n `Code List`,\n Role,\n `Data Type`,\n Activity,\n `Activity Subgroup`,\n `Activity Group`", "width": 24, "height": 7, "x": 0, diff --git a/neo4j-mdr-db/neodash/neodash_reports/activity_metadata_check.json b/neo4j-mdr-db/neodash/neodash_reports/activity_metadata_check.json index 62fe587f..f126bb94 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/activity_metadata_check.json +++ b/neo4j-mdr-db/neodash/neodash_reports/activity_metadata_check.json @@ -87,7 +87,7 @@ "reports": [ { "title": "Activity Subgroup", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name =$neodash_activityinstanceclassvalue_name_subtype \nand agrp.name = $neodash_activitygroupvalue_name\nRETURN DISTINCT asgrp.`name` as value, asgrp.`name` as display ORDER BY size(toString(value)) ASC", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[HSSG:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[HSG:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH (g)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name =$neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT asgrp.`name` as value, asgrp.`name` as display ORDER BY size(toString(value)) ASC", "width": 6, "height": 2, "x": 18, @@ -106,7 +106,7 @@ }, { "title": "Number of Activities (Instances per Activity, when Subgroup is Selected)", - "query": "CALL apoc.case([not $neodash_activityinstanceclassvalue_name='' and $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn aic.name as Category,\ncount(distinct act) as `Number of Activities` order by Category' , \nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn agrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category', \nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c]\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn asgrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and not $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c] and asgrp.name in[$d]\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn act.name as Category,\ncount(distinct ai) as `Number of Activities` order by Category'],\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) \nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) \nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nreturn aicp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n{a:$neodash_activityinstanceclassvalue_name,\nb:$neodash_activityinstanceclassvalue_name_subtype,\nc:$neodash_activitygroupvalue_name, \nd:$neodash_activitysubgroupvalue_name}) YIELD value \nreturn value.Category as Category,\nvalue.`Number of Activities` as`Number of Activities/Instances` order by Category\n\n", + "query": "// only instance class selected\nCALL apoc.case([not $neodash_activityinstanceclassvalue_name='' and $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn aic.name as Category,\ncount(distinct act) as `Number of Activities` order by Category' ,\n\n// instance class and subclass selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn agrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n\n// instance class, subclass and group selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R3:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c]\nMATCH (g)-[:HAS_SELECTED_SUBGROUP]-(asgrp:ActivitySubGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn asgrp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n\n// all fields selected\nnot $neodash_activityinstanceclassvalue_name='' and not $neodash_activityinstanceclassvalue_name_subtype='' and not $neodash_activitygroupvalue_name='' and not $neodash_activitysubgroupvalue_name='', \n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where agrp.name in [$c] and asgrp.name in[$d]\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) where aic.name in [$b]\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name in [$a]\nreturn act.name as Category,\ncount(distinct ai) as `Number of Activities` order by Category'],\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) \nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue) \nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nreturn aicp.name as Category,\ncount(distinct act) as `Number of Activities` order by Category',\n{a:$neodash_activityinstanceclassvalue_name,\nb:$neodash_activityinstanceclassvalue_name_subtype,\nc:$neodash_activitygroupvalue_name, \nd:$neodash_activitysubgroupvalue_name}) YIELD value \nreturn value.Category as Category,\nvalue.`Number of Activities` as`Number of Activities/Instances` order by Category\n\n", "width": 24, "height": 6, "x": 0, @@ -141,7 +141,7 @@ }, { "title": "Activity Group", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name = $neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT agrp.`name` as value, agrp.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nand aic.name = $neodash_activityinstanceclassvalue_name_subtype \nRETURN DISTINCT agrp.`name` as value, agrp.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 12, @@ -161,7 +161,7 @@ }, { "title": "Activity Class", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) return distinct aicp.name as value, aicp.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) return distinct aicp.name as value, aicp.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 0, @@ -182,7 +182,7 @@ }, { "title": "Activity as a Graph View (Logical View) - $neodash_activity", - "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", + "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", "width": 12, "height": 6, "x": 0, @@ -373,7 +373,7 @@ }, { "title": "Activity Subclass", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name = $neodash_activityinstanceclassvalue_name return distinct aic.`name` as value, aic.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) where aicp.name = $neodash_activityinstanceclassvalue_name return distinct aic.`name` as value, aic.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 6, @@ -394,7 +394,7 @@ }, { "title": "Activity in Tabular Format - $neodash_activity", - "query": "CALL\n apoc.when(\n NOT $neodash_activity = '',\n \"\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n apoc.convert.toSet(collect(agrp.name)) AS ActivityGroup,\n apoc.convert.toSet(collect(asgrp.name)) AS ActivitySubGroup,\n act.name AS Activity,\n aitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nWITH\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivityGroup))) AS ActivityGroup,\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivitySubGroup))) AS ActivitySubGroup,\n Activity,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Terms,\n `Code List`,\n Role,\n `Data Type`\nRETURN\n ActivityGroup,\n ActivitySubGroup,\n Activity,\n `Activity Item Class`,\n Terms,\n `Code List`,\n Role,\n `Data Type`\",\n \"match(x:blbla) return *\",\n {neodash_activity: $neodash_activity}\n )\n YIELD value\nRETURN\n value.ActivityGroup AS `Activity Group`,\n value.ActivitySubGroup AS `Activity Subgroup`,\n value.Activity AS Activity,\n value.`Activity Item Class` AS `Activity Item Class`,\n value.Terms AS Terms,\n value.`Code List` AS `Code List`,\n value.Role AS Role,\n value.`Data Type` AS `Data Type`", + "query": "// Skip entirely if parameter is empty\nWITH $neodash_activity AS actName\nWHERE actName <> ''\n\n// Anchor on the specific ActivityValue first (uses index)\nMATCH (act:ActivityValue {name: actName})\n\n// Core traversal from anchor\nMATCH (act)-[:HAS_GROUPING]->(g:ActivityGrouping)\n -[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[:LATEST]-(:ActivityInstanceGroupingRoot)\n <-[:HAS_GROUPING_ROOT]-(:ActivityInstanceRoot)\n -[:LATEST]->(ai:ActivityInstanceValue)\n -[:CONTAINS_ACTIVITY_ITEM]->(aitm1:ActivityItem)\n\nMATCH (ai)-[:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[:LATEST]->(aic:ActivityInstanceClassValue)\n\n// Require ActivityItemClass — was MATCH so keep as MATCH\nMATCH (aitmc1r:ActivityItemClassRoot)-[:HAS_ACTIVITY_ITEM]->(aitm1),\n (aitmc1r)-[:LATEST]->(aitmc1:ActivityItemClassValue)\n\n// Require DataType — was MATCH so keep as MATCH\nMATCH (aitmc1)-[:HAS_DATA_TYPE]->(:CTTermContext)\n -[:HAS_SELECTED_TERM]->(dtype_r:CTTermRoot)\n -[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(dtype_val)\n\n// Optional parent class traversals\nOPTIONAL MATCH (aicr)-[:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aicrp)-[:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicpp:ActivityInstanceClassValue)\n\n// Optional item class membership checks\nOPTIONAL MATCH (aitmc1r)<-[:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[:HAS_ITEM_CLASS]-(aicrpp)\n\n// Optional Role\nOPTIONAL MATCH (aitmc1)-[:HAS_ROLE]->(:CTTermContext)\n -[:HAS_SELECTED_TERM]->(role_r:CTTermRoot)\n -[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(role_val)\n\n// Optional CT Terms\nOPTIONAL MATCH (aitm1)-[:HAS_CT_TERM]->(ct_context:CTTermContext)\n -[:HAS_SELECTED_TERM]->(ct2cd:CTTermRoot)\n -[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(ct2_sponsor),\n (ct2cd)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)\n -[:LATEST]->(ct2_cdisc),\n (ct2cd)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)\n <-[:HAS_TERM]-(clr:CTCodelistRoot)\n <-[:HAS_SELECTED_CODELIST]-(ct_context),\n (ct2cd)<-[:CONTAINS_TERM]-(:Library)\n\n// Optional codelist attributes\nOPTIONAL MATCH (clr)-[:HAS_ATTRIBUTES_ROOT]->(clatt:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (clr)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_sponsor)\n\n// Optional unit dimension on context\nOPTIONAL MATCH (ct_context)<-[:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\n\n// Optional unit definition\nOPTIONAL MATCH (aitm1)-[:HAS_UNIT_DEFINITION]->(:UnitDefinitionRoot)\n -[:LATEST]->(unit_term:UnitDefinitionValue)\n -[:HAS_CT_DIMENSION]->(:CTTermContext)\n -[:HAS_SELECTED_CODELIST]->(cl_unit_root:CTCodelistRoot)\n -[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (cl_unit_root)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_unit_sponsor)\n\n// Resolve CT term and codelist values once\nWITH\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n act.name AS Activity,\n aitmc1.name AS ActivityItemClass,\n role_val.name AS Role,\n dtype_val.name AS DataType,\n // Resolve CT2 with priority: pos_units_in_dim > unit_term > merged ct term\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim.name\n WHEN unit_term IS NOT NULL THEN unit_term.name\n WHEN ct2cd IS NOT NULL\n THEN apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor)).name\n ELSE null\n END AS term,\n // Resolve codelist with priority: clr > cl_unit_root\n CASE\n WHEN clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor)).name\n WHEN cl_unit_root IS NOT NULL\n THEN apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor)).preferred_term\n ELSE null\n END AS CodeList\n\n// Aggregate per Activity + ActivityItemClass combination\nWITH\n Activity,\n ActivityItemClass,\n Role,\n DataType,\n CodeList,\n collect(DISTINCT ActivityGroup) AS ActivityGroups,\n collect(DISTINCT ActivitySubGroup) AS ActivitySubGroups,\n collect(DISTINCT term) AS Terms\n\nRETURN\n ActivityGroups AS `Activity Group`,\n ActivitySubGroups AS `Activity Subgroup`,\n Activity,\n ActivityItemClass AS `Activity Item Class`,\n Terms,\n CodeList AS `Code List`,\n Role,\n DataType AS `Data Type`", "width": 24, "height": 4, "x": 0, @@ -415,7 +415,7 @@ }, { "title": "Activity as a Graph View (Physical View) - $neodash_activity", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-()\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nreturn *", + "query": "// Anchor on indexed ActivityValue node first\nMATCH (act:ActivityValue {name: $neodash_activity})\n\n// Core grouping traversal from anchor\nMATCH (act)-[R1:HAS_GROUPING]->(g:ActivityGrouping)\n -[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\n\n// Activity instance traversal - all relationships now captured\nMATCH (g)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[R_LATEST_AIGV:LATEST]-(aigr:ActivityInstanceGroupingRoot)\n <-[R_HAS_GROUPING_ROOT:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)\n -[R_LATEST_AIR:LATEST]->(ai:ActivityInstanceValue)\n -[R6:CONTAINS_ACTIVITY_ITEM]->(aitm1:ActivityItem)\n\n// Activity instance class\nMATCH (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[R8:LATEST]->(aic:ActivityInstanceClassValue)\n\n// Optional item class\nOPTIONAL MATCH (aitmc1r:ActivityItemClassRoot)-[R9:HAS_ACTIVITY_ITEM]->(aitm1)\nOPTIONAL MATCH (aitmc1r)-[R10:LATEST]->(aitmc1:ActivityItemClassValue)\n\n// Optional parent class hierarchy\nOPTIONAL MATCH (aicr)-[R11:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)\n -[R12:LATEST]->(aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aicrp)-[R13:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)\n -[R14:LATEST]->(aicpp:ActivityInstanceClassValue)\n\n// Optional item class membership checks\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n\n// Optional CT Terms\nOPTIONAL MATCH (aitm1)-[R18:HAS_CT_TERM]->(ct_context:CTTermContext)\nOPTIONAL MATCH (ct_context)-[R19:HAS_SELECTED_TERM]->(ct2cd:CTTermRoot)\nOPTIONAL MATCH (ct2cd)-[R20:HAS_NAME_ROOT]->(ct2cdr:CTTermNameRoot)\n -[R21:LATEST]->(ct2_sponsor)\nOPTIONAL MATCH (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->(ct2att:CTTermAttributesRoot)\n -[R23:LATEST]->(ct2_cdisc)\nOPTIONAL MATCH (ct2cd)<-[x1:HAS_TERM_ROOT]-(term:CTCodelistTerm)\nOPTIONAL MATCH (term)<-[x2:HAS_TERM]-(clr:CTCodelistRoot)\nOPTIONAL MATCH (clr)<-[x3:HAS_SELECTED_CODELIST]-(ct_context)\nOPTIONAL MATCH (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\n\n// Optional unit dimension on CT context\nOPTIONAL MATCH (ct_context)<-[x12:HAS_CT_DIMENSION]\n -(pos_units_in_dim:UnitDefinitionValue)\n\n// Optional unit definition\nOPTIONAL MATCH (aitm1)-[x6:HAS_UNIT_DEFINITION]->(unit_def_root:UnitDefinitionRoot)\nOPTIONAL MATCH (unit_def_root)-[x7:LATEST]->(unit_term:UnitDefinitionValue)\nOPTIONAL MATCH (unit_term)-[x8:HAS_CT_DIMENSION]->(ct_context2)\nOPTIONAL MATCH (ct_context2)-[x9:HAS_SELECTED_CODELIST]->(cl_unit_root:CTCodelistRoot)\nOPTIONAL MATCH (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-(cl_unit_att:CTCodelistAttributesRoot)\n -[x11:LATEST]->(cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (cl_unit_root)-[x13:HAS_NAME_ROOT]->(clunit_attr:CTCodelistNameRoot)\n -[x14:LATEST]-(cl_unit_sponsor)\n\n// Optional codelist attributes\nOPTIONAL MATCH (clr)-[R27:HAS_ATTRIBUTES_ROOT]->(clatt:CTCodelistAttributesRoot)\n -[R28:LATEST]->(cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (clr)-[R29:HAS_NAME_ROOT]->(clattr:CTCodelistNameRoot)\n -[R30:LATEST]-(cl_sponsor)\n\n// Optional role\nOPTIONAL MATCH (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)\nOPTIONAL MATCH (ct_context_role)-[y1:HAS_SELECTED_TERM]->(role_r:CTTermRoot)\nOPTIONAL MATCH (role_r)-[R40:HAS_NAME_ROOT]->(ctnr_role)\n -[R41:LATEST]->(role_val)\n\n// DataType\nOPTIONAL MATCH (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)\nOPTIONAL MATCH (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r)\nOPTIONAL MATCH (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)\n -[R45:LATEST]->(dtype_val)\n\nRETURN\n // Core Activity nodes\n act, agrp, asgrp, g, aigv, aigr, air, ai, aitm1,\n\n // Activity Instance Class nodes\n aicr, aic, aitmc1r, aitmc1, aicrp, aicp, aicrpp, aicpp,\n\n // CT Term nodes\n ct_context, ct2cd, ct2cdr, ct2_sponsor, ct2att, ct2_cdisc,\n\n // Codelist nodes\n term, clr, lib, pos_units_in_dim,\n\n // Unit Definition nodes\n unit_def_root, unit_term, ct_context2, cl_unit_root,\n cl_unit_att, cl_unit_cdisc, clunit_attr, cl_unit_sponsor,\n\n // Codelist attribute nodes\n clatt, cl_cdisc, clattr, cl_sponsor,\n\n // Role nodes\n ct_context_role, role_r, ctnr_role, role_val,\n\n // DataType nodes\n ct_context_dtype, dtype_r, ctnr_dtype, dtype_val,\n\n // Core relationships\n R1, R2, R4, R5, R6, R7, R8, R9, R10,\n R11, R12, R13, R14, R15, R16, R17, R18, R19, R20,\n R21, R22, R23, R27, R28, R29, R30, R39, R40, R41,\n R43, R44, R45,\n\n // Previously missing activity instance traversal relationships\n R_LATEST_AIGV, R_HAS_GROUPING_ROOT, R_LATEST_AIR,\n\n // Unit / CT Term relationships\n x1, x2, x3, x4,\n x6, x7, x8, x9, x10,\n x11, x12, x13, x14,\n\n // Role / DataType relationships\n y1, y2", "width": 12, "height": 6, "x": 12, @@ -732,7 +732,7 @@ { "id": "c1bb190a-b3a9-4e65-843d-c0ab8c42ba42", "title": "List of Activities", - "query": "CALL apoc.case([not $neodash_activityinstanceclassvalue_name='' \n and $neodash_activityinstanceclassvalue_name_subtype='' \n and $neodash_activitygroupvalue_name='' \n and $neodash_activitysubgroupvalue_name='', \n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity', \n\nnot $neodash_activityinstanceclassvalue_name='' \nand not $neodash_activityinstanceclassvalue_name_subtype='' \nand $neodash_activitygroupvalue_name='' \nand $neodash_activitysubgroupvalue_name='', \n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] and aic.name in [$b] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity', \n\nnot $neodash_activityinstanceclassvalue_name='' \nand not $neodash_activityinstanceclassvalue_name_subtype='' \nand not $neodash_activitygroupvalue_name='' \nand $neodash_activitysubgroupvalue_name='', \n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] and aic.name in [$b] and agrp.name in [$c] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity', \n\nnot $neodash_activityinstanceclassvalue_name='' \nand not $neodash_activityinstanceclassvalue_name_subtype='' \nand not $neodash_activitygroupvalue_name='' \nand not $neodash_activitysubgroupvalue_name='',\n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue)\nwhere aicp.name in [$a] and aic.name in [$b] and agrp.name in [$c] and asgrp.name in [$d] \n\nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity'],\n\n'MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue),\n(aitm1)<-[R8:HAS_ACTIVITY_ITEM]-(aitmc1r:ActivityItemClassRoot)-[R9:LATEST]->(aitmc1:ActivityItemClassValue),\n(aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue),\n(aicrp)-[R12:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)-[R13:LATEST]->(aicpp:ActivityInstanceClassValue) \nreturn distinct aicp.name as ActivityType, aic.name as ActivitySubType, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity',{\na:$neodash_activityinstanceclassvalue_name, \nb:$neodash_activityinstanceclassvalue_name_subtype,\nc:$neodash_activitygroupvalue_name, \nd:$neodash_activitysubgroupvalue_name}) YIELD value return value.ActivityType as `Activity Type`,value.ActivitySubType as `Activity Subtype`, value.ActivityGroup as `Activity Group` ,value.ActivitySubGroup as `Activity Subgroup` , value.Activity as Activity order by Activity", + "query": "// Build the core pattern ONCE, then apply conditional filters\nMATCH (act:ActivityValue)-[:HAS_GROUPING]->(g:ActivityGrouping)\n -[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue),\n (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)\n <-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)\n -[:LATEST]->(ai:ActivityInstanceValue),\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[:LATEST]->(aic:ActivityInstanceClassValue),\n (aicr)-[:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicp:ActivityInstanceClassValue),\n (aicrp)-[:PARENT_CLASS]->(aicrpp:ActivityInstanceClassRoot)\n -[:LATEST]->(aicpp:ActivityInstanceClassValue)\n\n// Apply filters conditionally using WHERE with CASE logic\nWHERE\n // Filter on ActivityType (aicp.name) — only when param is not empty\n (\n $neodash_activityinstanceclassvalue_name = ''\n OR aicp.name = $neodash_activityinstanceclassvalue_name\n )\n AND\n // Filter on ActivitySubType (aic.name) — only when param is not empty\n (\n $neodash_activityinstanceclassvalue_name_subtype = ''\n OR aic.name = $neodash_activityinstanceclassvalue_name_subtype\n )\n AND\n // Filter on ActivityGroup (agrp.name) — only when param is not empty\n (\n $neodash_activitygroupvalue_name = ''\n OR agrp.name = $neodash_activitygroupvalue_name\n )\n AND\n // Filter on ActivitySubGroup (asgrp.name) — only when param is not empty\n (\n $neodash_activitysubgroupvalue_name = ''\n OR asgrp.name = $neodash_activitysubgroupvalue_name\n )\n\nRETURN DISTINCT\n aicp.name AS `Activity Type`,\n aic.name AS `Activity Subtype`,\n agrp.name AS `Activity Group`,\n asgrp.name AS `Activity Subgroup`,\n act.name AS Activity\n\nORDER BY Activity", "width": 24, "height": 4, "x": 0, @@ -783,7 +783,7 @@ { "id": "2a328d78-132e-49c6-b4a5-884d1fdaa015", "title": "Select Instance - $neodash_activity", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-() \nwhere act.name = $neodash_activity \nreturn ai.name as Instance, ai.adam_param_code as `ADaM Param Code`", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) \nwhere act.name = $neodash_activity \nreturn ai.name as Instance, ai.adam_param_code as `ADaM Param Code`", "width": 7, "height": 5, "x": 0, @@ -799,7 +799,7 @@ "entityType": "instance", "parameterName": "neodash_instance" }, - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue) \nwhere act.name = $neodash_activity return ai.name as Instance" + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) \nwhere act.name = $neodash_activity return ai.name as Instance" } ], "runButtonText": "Show detail", @@ -820,7 +820,7 @@ { "id": "bf2468d0-bf4e-4aa2-93e5-2f7e78ba4203", "title": "Instance Detail - $neodash_instance", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE act.name = $neodash_activity\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-() where ai.adam_param_code=$neodash_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aic,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\naic.name as Class,\nagrp.name as ActivityGroup,\nasgrp.name as ActivitySubGroup,\nai.name as Instance,\nai.adam_param_code as ADAM_CODE,\naitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nreturn distinct \nClass,\nInstance,\nADAM_CODE,\n`Activity Item Class`,\napoc.convert.toSet(collect(terms)) AS Term,\n`Code List`,\nRole,\n`Data Type`\n", + "query": "// 1. Anchor on indexed ActivityValue node first\nMATCH (act:ActivityValue {name: $neodash_activity})\n\n// 2. Core grouping traversal\nMATCH (act)-[:HAS_GROUPING]->(g:ActivityGrouping)\n -[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\n\n// 3. Activity instance traversal - filter early on adam_param_code\nMATCH (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)\n <-[:LATEST]-(:ActivityInstanceGroupingRoot)\n <-[:HAS_GROUPING_ROOT]-(:ActivityInstanceRoot)\n -[:LATEST]->(ai:ActivityInstanceValue {adam_param_code: $neodash_instance})\n -[:CONTAINS_ACTIVITY_ITEM]->(aitm1:ActivityItem)\n\n// 4. Activity instance class\nMATCH (ai)-[:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)\n -[:LATEST]->(aic:ActivityInstanceClassValue)\n\n// 5. Early WITH DISTINCT to reduce cardinality before expensive optional lookups\nWITH DISTINCT\n agrp, asgrp, ai, aitm1, aicr, aic\n\n// 6. Optional item class\nOPTIONAL MATCH (aitmc1r:ActivityItemClassRoot)-[:HAS_ACTIVITY_ITEM]->(aitm1)\nOPTIONAL MATCH (aitmc1r)-[:LATEST]->(aitmc1:ActivityItemClassValue)\n\n// 7. Optional parent class hierarchy\nOPTIONAL MATCH (aicr)-[:PARENT_CLASS]->(:ActivityInstanceClassRoot)\n -[:LATEST]->(aicp:ActivityInstanceClassValue)\n\n// 8. Optional DataType - resolved early to reduce rows\nOPTIONAL MATCH (aitmc1)-[:HAS_DATA_TYPE]->(ct_context_dtype)\nOPTIONAL MATCH (ct_context_dtype)-[:HAS_SELECTED_TERM]->(dtype_r)\nOPTIONAL MATCH (dtype_r)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(dtype_val)\n\n// 9. Optional Role\nOPTIONAL MATCH (aitmc1)-[:HAS_ROLE]->(ct_context_role)\nOPTIONAL MATCH (ct_context_role)-[:HAS_SELECTED_TERM]->(role_r:CTTermRoot)\nOPTIONAL MATCH (role_r)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(role_val)\n\n// 10. Second WITH DISTINCT before expensive CT term lookups\nWITH DISTINCT\n agrp, asgrp, ai, aitm1, aicr, aic,\n aitmc1r, aitmc1, aicp,\n dtype_val, role_val\n\n// 11. Optional CT Terms\nOPTIONAL MATCH (aitm1)-[:HAS_CT_TERM]->(ct_context:CTTermContext)\nOPTIONAL MATCH (ct_context)-[:HAS_SELECTED_TERM]->(ct2cd:CTTermRoot)\nOPTIONAL MATCH (ct2cd)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)\n -[:LATEST]->(ct2_sponsor)\nOPTIONAL MATCH (ct2cd)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)\n -[:LATEST]->(ct2_cdisc)\n\n// 12. Optional unit dimension on CT context\nOPTIONAL MATCH (ct_context)<-[:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\n\n// 13. Optional unit definition\nOPTIONAL MATCH (aitm1)-[:HAS_UNIT_DEFINITION]->(unit_def_root:UnitDefinitionRoot)\nOPTIONAL MATCH (unit_def_root)-[:LATEST]->(unit_term:UnitDefinitionValue)\n\n// 14. Optional codelist\nOPTIONAL MATCH (ct2cd)<-[:HAS_TERM_ROOT]-(term:CTCodelistTerm)\n <-[:HAS_TERM]-(clr:CTCodelistRoot)\n <-[:HAS_SELECTED_CODELIST]-(ct_context)\nOPTIONAL MATCH (clr)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (clr)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_sponsor)\n\n// 15. Optional unit codelist\nOPTIONAL MATCH (unit_term)-[:HAS_CT_DIMENSION]->(ct_context2)\nOPTIONAL MATCH (ct_context2)-[:HAS_SELECTED_CODELIST]->(cl_unit_root:CTCodelistRoot)\nOPTIONAL MATCH (cl_unit_root)-[:HAS_ATTRIBUTES_ROOT]-(:CTCodelistAttributesRoot)\n -[:LATEST]->(cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH (cl_unit_root)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)\n -[:LATEST]->(cl_unit_sponsor)\n\n// 16. Resolve final CT2 and CL values\nWITH DISTINCT\n aic.name AS Class,\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n ai.name AS Instance,\n ai.adam_param_code AS ADAM_CODE,\n aitmc1.name AS `Activity Item Class`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`,\n COALESCE(\n pos_units_in_dim.name,\n unit_term.name,\n ct2_sponsor.name,\n ct2_cdisc.name\n ) AS terms,\n COALESCE(\n cl_sponsor.preferred_term,\n cl_cdisc.name,\n cl_unit_sponsor.preferred_term,\n cl_unit_cdisc.name\n ) AS `Code List`\n\n// 17. Final aggregation\nRETURN DISTINCT\n Class,\n Instance,\n ADAM_CODE,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Term,\n `Code List`,\n Role,\n `Data Type`", "width": 17, "height": 5, "x": 7, @@ -839,7 +839,7 @@ { "id": "0a3ffebe-ca79-43bb-a06b-46cb158e4d9d", "title": "Instance (Logical View) - $neodash_instance", - "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-() where ai.adam_param_code=$neodash_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", + "query": "//Logical view of Activity and intances\nMATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)<-[:LATEST]-()\nWHERE act.name = $neodash_activity\nMATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue) where ai.adam_param_code=$neodash_instance\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n apoc.create.vNode([\"ActivityInstance\"], properties(ai)) AS v_ai,\n apoc.create.vNode([\"ActivityInstanceClass\"], properties(aic)) AS v_aic,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n apoc.create.vRelationship(act, \"HAS\", {type: \"logical\"}, v_ai) AS r1,\n apoc.create.vRelationship(v_ai, \"HAS_ACTIVITY\", {type: \"logical\"}, g) AS r2,\n apoc.create.vRelationship(v_ai, \"OF_CLASS\", {type: \"logical\"}, v_aic) AS r3,\n R1,\n R2,\n R4,\n R5\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aicr,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\n//Items\nOPTIONAL MATCH\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n aicp,\n aicpp,\n v_ai,\n v_aic,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vNode([\"ActivityItemClass\"], properties(aitmc1)) AS v_aitmc1,\n CASE\n WHEN\n R16 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicp))\n END AS v_aicp,\n CASE\n WHEN\n R17 IS NOT NULL\n THEN apoc.create.vNode([\"ActivityInstanceClass\"], properties(aicpp))\n END AS v_aicpp\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17,\n apoc.create.vRelationship(v_ai, \"HAS\", {type: \"logical\"}, aitm1) AS r4,\n apoc.create.vRelationship(aitm1, \"OF_CLASS\", {type: \"logical\"}, v_aitmc1) AS r5,\n CASE\n WHEN\n (R15 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aic\n )\n END AS r6,\n CASE\n WHEN\n (R16 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicp\n )\n END AS r7,\n CASE\n WHEN\n (R17 IS NOT NULL)\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"OF_CLASS\",\n {type: \"logical\"},\n v_aicpp\n )\n END AS r8\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n R15,\n R16,\n R17\n//Role and Type\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->\n (ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->\n (ct_context_dtype)-[y2:HAS_SELECTED_TERM]->\n (dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n role_val,\n dtype_val,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(role_val))\n END AS v_role,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(dtype_val))\n END AS v_dtype\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n R1,\n R2,\n R4,\n R5,\n R6,\n role_r,\n dtype_r,\n CASE\n WHEN\n role_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_ROLE\",\n {type: \"logical\"},\n v_role\n )\n END AS r11,\n CASE\n WHEN\n dtype_r IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_aitmc1,\n \"HAS_TYPE\",\n {type: \"logical\"},\n v_dtype\n )\n END AS r12\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unitdefr:UnitDefinitionRoot)-[x7:LATEST]->\n (unitdef:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n ct2_cdisc,\n ct2_sponsor,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTTerm\"],\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n )\n END AS v_ct,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vNode([\"CTTerm\"], properties(unitdef))\n END AS v_unit_ct\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n cl_cdisc,\n cl_sponsor,\n cl_unit_cdisc,\n cl_unit_sponsor,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_ct)\n END AS r9,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN apoc.create.vRelationship(aitm1, \"FOR\", {type: \"logical\"}, v_unit_ct)\n END AS r10\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n ct2cd,\n unitdefr,\n unitdef,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n )\n END AS v_cl,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vNode(\n [\"CTCodeList\"],\n apoc.map.merge(properties(cl_unit_cdisc), properties(cl_unit_sponsor))\n )\n END AS v_unit_cl\nWITH\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n ct2cd,\n unitdefr,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_cl,\n v_unit_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n R1,\n R2,\n R4,\n R5,\n R6,\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN apoc.create.vRelationship(v_cl, \"HAS\", {type: \"logical\"}, v_ct)\n END AS r13,\n CASE\n WHEN\n unitdefr IS NOT NULL\n THEN\n apoc.create.vRelationship(\n v_unit_ct,\n \"HAS\",\n {type: \"logical\"},\n v_unit_cl\n )\n END AS r14\nRETURN\n g,\n agrp,\n asgrp,\n act,\n v_ai,\n v_aic,\n v_aicp,\n v_aicpp,\n aitm1,\n v_aitmc1,\n v_ct,\n v_unit_ct,\n v_role,\n v_dtype,\n v_unit_cl,\n v_cl,\n r1,\n r2,\n r3,\n r4,\n r5,\n r6,\n r7,\n r8,\n r9,\n r10,\n r11,\n r12,\n r13,\n r14,\n R1,\n R2,\n R4,\n R5", "width": 24, "height": 10, "x": 0, @@ -1052,7 +1052,7 @@ { "id": "e0a486e2-b652-4375-b36f-57acf318277c", "title": "Groups for Selected Activity/Activities", - "query": "MATCH(p_act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(p_asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(p_agrp:ActivityGroupValue) where p_act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(p_ai:ActivityInstanceValue)<-[:LATEST]-()\nreturn p_act.name as Activity,\np_agrp.name as Group,\np_asgrp.name as `Subgroup`,\np_ai.adam_param_code as `Activity Instance (ADAM PARAM CODE)`,\np_ai.topic_code as `Activity Instance (TOPIC CODE)`,\n'Show Detail' as Select order by Activity, Group, `Subgroup`", + "query": "MATCH(p_act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(p_asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(p_agrp:ActivityGroupValue) where p_act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(p_ai:ActivityInstanceValue)\nreturn p_act.name as Activity,\np_agrp.name as Group,\np_asgrp.name as `Subgroup`,\np_ai.adam_param_code as `Activity Instance (ADAM PARAM CODE)`,\np_ai.topic_code as `Activity Instance (TOPIC CODE)`,\n'Show Detail' as Select order by Activity, Group, `Subgroup`", "width": 24, "height": 4, "x": 0, @@ -1082,7 +1082,7 @@ { "id": "51ddc5ee-2e17-44e1-99f1-8b2f95a8ba21", "title": "Activity Instance Detail - $neodash_detail", - "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-\n (ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem),\n (ai)<-[:LATEST]-() where ai.adam_param_code=$neodash_detail\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n apoc.convert.toSet(collect(agrp.name)) AS ActivityGroup,\n apoc.convert.toSet(collect(asgrp.name)) AS ActivitySubGroup,\n act.name AS Activity,\n ai.adam_param_code as `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nWITH\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivityGroup))) AS `Activity Group`,\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivitySubGroup))) AS `Activity Subgroup`,\n Activity,\n `Activity Instance`,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Terms,\n `Code List`,\n Role,\n `Data Type`\nreturn `Activity Group`,\n`Activity Subgroup`,\nActivity,\n`Activity Instance`,\n`Activity Item Class`,\napoc.text.join(Terms, \",\") as Term,\n`Code List`,\nRole,\n`Data Type`", + "query": "MATCH\n (act:ActivityValue)-[R1:HAS_GROUPING]->\n (g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue),\n (g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH\n (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)-[R6:CONTAINS_ACTIVITY_ITEM]->\n (aitm1:ActivityItem)\nWHERE ai.adam_param_code=$neodash_detail\nMATCH\n (ai)-[R7:ACTIVITY_INSTANCE_CLASS]->\n (aicr:ActivityInstanceClassRoot)-[R8:LATEST]->\n (aic:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aitm1)<-[R9:HAS_ACTIVITY_ITEM]-\n (aitmc1r:ActivityItemClassRoot)-[R10:LATEST]->\n (aitmc1:ActivityItemClassValue)\nOPTIONAL MATCH\n (aicr)-[R11:PARENT_CLASS]->\n (aicrp:ActivityInstanceClassRoot)-[R12:LATEST]->\n (aicp:ActivityInstanceClassValue)\nOPTIONAL MATCH\n (aicrp)-[R13:PARENT_CLASS]->\n (aicrpp:ActivityInstanceClassRoot)-[R14:LATEST]->\n (aicpp:ActivityInstanceClassValue)\nOPTIONAL MATCH (aitmc1r)<-[R15:HAS_ITEM_CLASS]-(aicr)\nOPTIONAL MATCH (aitmc1r)<-[R16:HAS_ITEM_CLASS]-(aicrp)\nOPTIONAL MATCH (aitmc1r)<-[R17:HAS_ITEM_CLASS]-(aicrpp)\n//Terms\nOPTIONAL MATCH\n (aitm1)-[R18:HAS_CT_TERM]->\n (ct_context:CTTermContext)-[R19:HAS_SELECTED_TERM]->\n (ct2cd:CTTermRoot)-[R20:HAS_NAME_ROOT]->\n (ct2cdr:CTTermNameRoot)-[R21:LATEST]->\n (ct2_sponsor),\n (ct2cd)-[R22:HAS_ATTRIBUTES_ROOT]->\n (ct2att:CTTermAttributesRoot)-[R23:LATEST]->\n (ct2_cdisc),\n (ct2cd)<-[x1:HAS_TERM_ROOT]-\n (term:CTCodelistTerm)<-[x2:HAS_TERM]-\n (clr:CTCodelistRoot)<-[x3:HAS_SELECTED_CODELIST]-\n (ct_context),\n (ct2cd)<-[x4:CONTAINS_TERM]-(lib:Library)\nOPTIONAL MATCH\n (ct_context)<-[x12:HAS_CT_DIMENSION]-(pos_units_in_dim:UnitDefinitionValue)\nOPTIONAL MATCH\n (aitm1)-[x6:HAS_UNIT_DEFINITION]->\n (unit_def_root:UnitDefinitionRoot)-[x7:LATEST]->\n (unit_term:UnitDefinitionValue)-[x8:HAS_CT_DIMENSION]->\n (ct_context2)-[x9:HAS_SELECTED_CODELIST]->\n (cl_unit_root:CTCodelistRoot),\n (cl_unit_root)-[x10:HAS_ATTRIBUTES_ROOT]-\n (cl_unit_att:CTCodelistAttributesRoot)-[x11:LATEST]->\n (cl_unit_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (cl_unit_root)-[x13:HAS_NAME_ROOT]->\n (clunit_attr:CTCodelistNameRoot)-[x14:LATEST]-\n (cl_unit_sponsor)\nOPTIONAL MATCH\n (clr:CTCodelistRoot)-[R27:HAS_ATTRIBUTES_ROOT]->\n (clatt:CTCodelistAttributesRoot)-[R28:LATEST]->\n (cl_cdisc:CTCodelistAttributesValue)\nOPTIONAL MATCH\n (clr)-[R29:HAS_NAME_ROOT]->\n (clattr:CTCodelistNameRoot)-[R30:LATEST]-\n (cl_sponsor)\nOPTIONAL MATCH\n (aitmc1)-[R39:HAS_ROLE]->(ct_context_role)-[y1:HAS_SELECTED_TERM]->\n (role_r:CTTermRoot)-[R40:HAS_NAME_ROOT]->\n (ctnr_role)-[R41:LATEST]->\n (role_val)\nMATCH\n (aitmc1)-[R43:HAS_DATA_TYPE]->(ct_context_dtype)-[y2:HAS_SELECTED_TERM]->(dtype_r),\n (dtype_r)-[R44:HAS_NAME_ROOT]->(ctnr_dtype)-[R45:LATEST]->(dtype_val)\nWITH DISTINCT\n g,\n agrp,\n asgrp,\n act,\n ai,\n aitm1,\n aitmc1r,\n aitmc1,\n aicrp,\n aicp,\n aicrpp,\n aicpp,\n ct2cd,\n ct2cdr,\n ct2_sponsor,\n ct2att,\n ct2_cdisc,\n unit_def_root,\n unit_term,\n clr,\n clatt,\n clattr,\n cl_sponsor,\n cl_cdisc,\n cl_unit_cdisc,\n cl_unit_sponsor,\n pos_units_in_dim,\n role_r,\n ctnr_role,\n role_val,\n dtype_r,\n dtype_val,\n CASE\n WHEN pos_units_in_dim IS NOT NULL THEN pos_units_in_dim\n ELSE\n CASE\n WHEN unit_term IS NOT NULL THEN unit_term\n ELSE\n CASE\n WHEN\n ct2cd IS NOT NULL\n THEN\n apoc.map.merge(properties(ct2_cdisc), properties(ct2_sponsor))\n END\n END\n END AS ct2,\n CASE\n WHEN\n clr IS NOT NULL\n THEN apoc.map.merge(properties(cl_cdisc), properties(cl_sponsor))\n ELSE\n CASE\n WHEN\n cl_unit_root IS NOT NULL\n THEN\n apoc.map.merge(\n properties(cl_unit_cdisc),\n properties(cl_unit_sponsor)\n )\n END\n END AS cl\nWITH DISTINCT\n apoc.convert.toSet(collect(agrp.name)) AS ActivityGroup,\n apoc.convert.toSet(collect(asgrp.name)) AS ActivitySubGroup,\n act.name AS Activity,\n ai.adam_param_code as `Activity Instance`,\n aitmc1.name AS `Activity Item Class`,\n ct2.name as terms,\n CASE\n WHEN ct2 IS NOT NULL THEN cl.name\n ELSE\n CASE\n WHEN cl IS NOT NULL THEN cl.preferred_term\n END\n END AS `Code List`,\n role_val.name AS Role,\n dtype_val.name AS `Data Type`\nWITH\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivityGroup))) AS `Activity Group`,\n apoc.convert.toSet(apoc.coll.flatten(collect(ActivitySubGroup))) AS `Activity Subgroup`,\n Activity,\n `Activity Instance`,\n `Activity Item Class`,\n apoc.convert.toSet(collect(terms)) AS Terms,\n `Code List`,\n Role,\n `Data Type`\nreturn `Activity Group`,\n`Activity Subgroup`,\nActivity,\n`Activity Instance`,\n`Activity Item Class`,\napoc.text.join(Terms, \",\") as Term,\n`Code List`,\nRole,\n`Data Type`", "width": 24, "height": 4, "x": 0, @@ -1103,7 +1103,7 @@ { "id": "97dd35f9-9411-4b89-9bcd-9bdebdb027f0", "title": "Number of Subgroups for Selected Activity", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", "width": 12, "height": 4, "x": 12, @@ -1136,7 +1136,7 @@ { "id": "c39ce16b-7619-4118-b1e2-cc65efadd267", "title": "Number of Groups for Selected Activity", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as Activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,Activity,N_groups,N_subgroups\n\n", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue) where act.name in $neodash_activityvalue_name\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n(ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue)\nwith distinct aicp.name as ActivityType,\naic.name as ActivitySubType,\nagrp.name as ActivityGroup, \nasgrp.name as ActiviySubGroup,\nact.name as activity,\n[agrp.name] as Groups,\n[asgrp.name] as SubGroups,\ncount(distinct asgrp.name) as N_subgroups,\ncount(distinct agrp.name) as N_groups\nreturn Groups,SubGroups,activity,N_groups,N_subgroups\n\n", "width": 12, "height": 4, "x": 0, @@ -1174,7 +1174,7 @@ { "id": "6eba64b3-890f-46b1-80a6-5d630525df46", "title": "Results", - "query": "WITH\n [\n $neodash_activityinstanceclassvalue_name,\n $neodash_activityinstanceclassvalue_name_subtype\n ] AS activity_filter,\n $neodash_activitygroupvalue_name AS activity_group,\n $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH\n ()-[:LATEST]->\n (act:ActivityValue)-[:HAS_GROUPING]->\n (g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH\n activity_filter,\n g,\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n act.name AS Activity\n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH\n (g)<-[:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (root:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass:ActivityInstanceClassValue),\n (root)-[:PARENT_CLASS]->{0,1}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass_parent:ActivityInstanceClassValue)\nWITH\n ActivityGroup,\n ActivitySubGroup,\n Activity,\n ai,\n [aiclass_parent.name, aiclass.name] AS type_filter,\n apoc.coll.removeAll(activity_filter, ['']) AS activity_filter\nWITH ActivityGroup, ActivitySubGroup, Activity, ai, type_filter\nWHERE\n (activity_filter = [\"\"] OR\n apoc.coll.containsAll(type_filter, activity_filter))\nMATCH\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,1}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aicp:ActivityInstanceClassValue)\nMATCH\n (aicp)<-[:LATEST]-\n (aicr_mandatory:ActivityInstanceClassRoot)-\n [:HAS_ITEM_CLASS {mandatory: true}]->\n (aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->\n (aitmv_mandatory:ActivityItemClassValue)\nWHERE\n (NOT (ai)-\n [:CONTAINS_ACTIVITY_ITEM]->\n (:ActivityItem)<-\n [:HAS_ACTIVITY_ITEM]-\n (aitmrp_mandatory))\nRETURN DISTINCT\n ActivityGroup AS `Activity Group`,\n ActivitySubGroup AS `Activity Subgroup`,\n Activity,\n ai.name AS `Activity Instance`,\n type_filter AS `Activity Instance Class`,\n aitmv_mandatory.name AS `Missing Activity Item`,\n aicp.name AS `Class of Missing Activity Item`", + "query": "WITH\n [\n $neodash_activityinstanceclassvalue_name,\n $neodash_activityinstanceclassvalue_name_subtype\n ] AS activity_filter,\n $neodash_activitygroupvalue_name AS activity_group,\n $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH\n ()-[:LATEST]->\n (act:ActivityValue)-[:HAS_GROUPING]->\n (g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH\n activity_filter,\n g,\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n act.name AS Activity\n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH\n (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (root:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass:ActivityInstanceClassValue),\n (root)-[:PARENT_CLASS]->{0,1}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass_parent:ActivityInstanceClassValue)\nWITH\n ActivityGroup,\n ActivitySubGroup,\n Activity,\n ai,\n [aiclass_parent.name, aiclass.name] AS type_filter,\n apoc.coll.removeAll(activity_filter, ['']) AS activity_filter\nWITH ActivityGroup, ActivitySubGroup, Activity, ai, type_filter\nWHERE\n (activity_filter = [\"\"] OR\n apoc.coll.containsAll(type_filter, activity_filter))\nMATCH\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,1}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aicp:ActivityInstanceClassValue)\nMATCH\n (aicp)<-[:LATEST]-\n (aicr_mandatory:ActivityInstanceClassRoot)-\n [:HAS_ITEM_CLASS {mandatory: true}]->\n (aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->\n (aitmv_mandatory:ActivityItemClassValue)\nWHERE\n (NOT (ai)-\n [:CONTAINS_ACTIVITY_ITEM]->\n (:ActivityItem)<-\n [:HAS_ACTIVITY_ITEM]-\n (aitmrp_mandatory))\nRETURN DISTINCT\n ActivityGroup AS `Activity Group`,\n ActivitySubGroup AS `Activity Subgroup`,\n Activity,\n ai.name AS `Activity Instance`,\n type_filter AS `Activity Instance Class`,\n aitmv_mandatory.name AS `Missing Activity Item`,\n aicp.name AS `Class of Missing Activity Item`", "width": 24, "height": 8, "x": 0, @@ -1192,7 +1192,7 @@ { "id": "77c78c45-27cf-4aa3-bc87-ea74c82cdf2a", "title": "Used terms for Activity Item Class", - "query": "WITH [$neodash_activityinstanceclassvalue_name,$neodash_activityinstanceclassvalue_name_subtype] AS activity_filter, $neodash_activitygroupvalue_name AS activity_group, $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH ()-[:LATEST]->(act:ActivityValue)-[:HAS_GROUPING]->(g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH activity_filter, g, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity \n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH (g)<-[:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(), \n(ai)-[:ACTIVITY_INSTANCE_CLASS]->(root:ActivityInstanceClassRoot)-[:LATEST]->(aiclass:ActivityInstanceClassValue),\n(root)-[:PARENT_CLASS]->{0,1}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aiclass_parent:ActivityInstanceClassValue)\nWITH ActivityGroup, ActivitySubGroup, Activity, ai, [aiclass_parent.name,aiclass.name] as type_filter, apoc.coll.removeAll(activity_filter,['']) as activity_filter\nWITH ActivityGroup, ActivitySubGroup, Activity, ai,type_filter where (activity_filter = [\"\"] OR apoc.coll.containsAll(type_filter,activity_filter))\nMATCH(ai)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,1}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aicp:ActivityInstanceClassValue)\nMATCH (aicp)<-[:LATEST]-(aicr_mandatory:ActivityInstanceClassRoot)-[:HAS_ITEM_CLASS{mandatory: TRUE}]->(aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->(aitmv_mandatory:ActivityItemClassValue)\nwhere (not (ai)-[:CONTAINS_ACTIVITY_ITEM]->(:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-(aitmrp_mandatory))\nWITH aitmv_mandatory, aitmrp_mandatory, aicp,aicr\nOPTIONAL Match(aitmrp_mandatory)-[:HAS_ACTIVITY_ITEM]->(aitm:ActivityItem)<-[:CONTAINS_ACTIVITY_ITEM]-(inst)<-[:LATEST]-(),(aitmrp_mandatory)<-[:HAS_ITEM_CLASS]-(aicr)-[:LATEST]->(aicp) \nOPTIONAL MATCH(aitm)-[:HAS_CT_TERM]->(term_root:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]-(attrib_root:CTTermAttributesRoot)-[:LATEST]->(cdisc_term:CTTermAttributesValue), (term_root)-[:HAS_NAME_ROOT]->(name_root:CTTermNameRoot)-[:LATEST]->(sponsor_term:CTTermNameValue)\nOPTIONAL MATCH (aitm)-[:HAS_UNIT_DEFINITION]->(unitdefr:UnitDefinitionRoot)-[R22:LATEST]->(unitdef:UnitDefinitionValue)\nOPTIONAL MATCH(unitdef)-[:HAS_CT_UNIT]->(cdisc_unit:CTTermRoot)\nWITH distinct aitmv_mandatory, aicp, cdisc_term, sponsor_term, unitdef,cdisc_unit\nWITH distinct aitmv_mandatory, aicp, cdisc_term,coalesce(cdisc_term.concept_id,cdisc_unit.concept_id) as term_concept_id,coalesce(cdisc_term.preferred_term,sponsor_term.name,unitdef.name) as term_label\nWITH distinct aitmv_mandatory, aicp, cdisc_term, term_label, term_concept_id\nWITH distinct aitmv_mandatory, aicp, cdisc_term, term_label, term_concept_id, \nCASE WHEN cdisc_term.code_submission_value is null and term_concept_id is not null then\napoc.text.join([term_concept_id,':','(',term_label,')'],\"\") ELSE CASE WHEN term_concept_id is not null THEN apoc.text.join([term_concept_id,':',cdisc_term.code_submission_value,'(',term_label,')'],\"\") ELSE term_label END END as terms\nWITH distinct aitmv_mandatory.name as `Missing Activity Item Type`, \naicp.name as `Class of Missing Activity Item`,terms\n WITH `Missing Activity Item Type`,`Class of Missing Activity Item`, collect(terms) as Terms\nWITH DISTINCT `Missing Activity Item Type`,`Class of Missing Activity Item`, size(Terms) as NumberOfTerms, Terms\nreturn `Missing Activity Item Type`,`Class of Missing Activity Item`, NumberOfTerms, Terms\n", + "query": "WITH [$neodash_activityinstanceclassvalue_name,$neodash_activityinstanceclassvalue_name_subtype] AS activity_filter, $neodash_activitygroupvalue_name AS activity_group, $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH ()-[:LATEST]->(act:ActivityValue)-[:HAS_GROUPING]->(g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH activity_filter, g, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity \n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue), \n(ai)-[:ACTIVITY_INSTANCE_CLASS]->(root:ActivityInstanceClassRoot)-[:LATEST]->(aiclass:ActivityInstanceClassValue),\n(root)-[:PARENT_CLASS]->{0,1}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aiclass_parent:ActivityInstanceClassValue)\nWITH ActivityGroup, ActivitySubGroup, Activity, ai, [aiclass_parent.name,aiclass.name] as type_filter, apoc.coll.removeAll(activity_filter,['']) as activity_filter\nWITH ActivityGroup, ActivitySubGroup, Activity, ai,type_filter where (activity_filter = [\"\"] OR apoc.coll.containsAll(type_filter,activity_filter))\nMATCH(ai)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,1}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aicp:ActivityInstanceClassValue)\nMATCH (aicp)<-[:LATEST]-(aicr_mandatory:ActivityInstanceClassRoot)-[:HAS_ITEM_CLASS{mandatory: TRUE}]->(aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->(aitmv_mandatory:ActivityItemClassValue)\nwhere (not (ai)-[:CONTAINS_ACTIVITY_ITEM]->(:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-(aitmrp_mandatory))\nWITH aitmv_mandatory, aitmrp_mandatory, aicp,aicr\nOPTIONAL Match(aitmrp_mandatory)-[:HAS_ACTIVITY_ITEM]->(aitm:ActivityItem)<-[:CONTAINS_ACTIVITY_ITEM]-(inst)<-[:LATEST]-(),(aitmrp_mandatory)<-[:HAS_ITEM_CLASS]-(aicr)-[:LATEST]->(aicp) \nOPTIONAL MATCH(aitm)-[:HAS_CT_TERM]->(term_root:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]-(attrib_root:CTTermAttributesRoot)-[:LATEST]->(cdisc_term:CTTermAttributesValue), (term_root)-[:HAS_NAME_ROOT]->(name_root:CTTermNameRoot)-[:LATEST]->(sponsor_term:CTTermNameValue)\nOPTIONAL MATCH (aitm)-[:HAS_UNIT_DEFINITION]->(unitdefr:UnitDefinitionRoot)-[R22:LATEST]->(unitdef:UnitDefinitionValue)\nOPTIONAL MATCH(unitdef)-[:HAS_CT_UNIT]->(cdisc_unit:CTTermRoot)\nWITH distinct aitmv_mandatory, aicp, cdisc_term, sponsor_term, unitdef,cdisc_unit\nWITH distinct aitmv_mandatory, aicp, cdisc_term,coalesce(cdisc_term.concept_id,cdisc_unit.concept_id) as term_concept_id,coalesce(cdisc_term.preferred_term,sponsor_term.name,unitdef.name) as term_label\nWITH distinct aitmv_mandatory, aicp, cdisc_term, term_label, term_concept_id\nWITH distinct aitmv_mandatory, aicp, cdisc_term, term_label, term_concept_id, \nCASE WHEN cdisc_term.code_submission_value is null and term_concept_id is not null then\napoc.text.join([term_concept_id,':','(',term_label,')'],\"\") ELSE CASE WHEN term_concept_id is not null THEN apoc.text.join([term_concept_id,':',cdisc_term.code_submission_value,'(',term_label,')'],\"\") ELSE term_label END END as terms\nWITH distinct aitmv_mandatory.name as `Missing Activity Item Type`, \naicp.name as `Class of Missing Activity Item`,terms\n WITH `Missing Activity Item Type`,`Class of Missing Activity Item`, collect(terms) as Terms\nWITH DISTINCT `Missing Activity Item Type`,`Class of Missing Activity Item`, size(Terms) as NumberOfTerms, Terms\nreturn `Missing Activity Item Type`,`Class of Missing Activity Item`, NumberOfTerms, Terms\n", "width": 24, "height": 7, "x": 0, @@ -1231,7 +1231,7 @@ { "id": "eec86f8e-a93e-43f4-92eb-69da05b6e49a", "title": "Results (Mandatory)", - "query": "WITH\n [\n $neodash_activityinstanceclassvalue_name,\n $neodash_activityinstanceclassvalue_name_subtype\n ] AS activity_filter,\n $neodash_activitygroupvalue_name AS activity_group,\n $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH\n ()-[:LATEST]->\n (act:ActivityValue)-[:HAS_GROUPING]->\n (g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH\n activity_filter,\n g,\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n act.name AS Activity\n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH\n (g)<-[:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(),\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (root:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass:ActivityInstanceClassValue),\n (root)-[:PARENT_CLASS]->{0,3}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass_parent:ActivityInstanceClassValue)\nWITH\n ActivityGroup,\n ActivitySubGroup,\n Activity,\n ai,\n [aiclass_parent.name, aiclass.name] AS type_filter,\n apoc.coll.removeAll(activity_filter, ['']) AS activity_filter\nWITH activity_filter, ActivityGroup, ActivitySubGroup, Activity, ai, type_filter\nWHERE\n (apoc.coll.containsAll(type_filter, activity_filter) AND\n size(activity_filter) = 2)\nMATCH\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,3}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aicp:ActivityInstanceClassValue)\nMATCH\n (aicp)<-[:LATEST]-\n (aicr_mandatory:ActivityInstanceClassRoot)-\n [:HAS_ITEM_CLASS {mandatory: true}]->\n (aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->\n (aitmv_mandatory:ActivityItemClassValue)\nWHERE\n (NOT (ai)-\n [:CONTAINS_ACTIVITY_ITEM]->\n (:ActivityItem)<-\n [:HAS_ACTIVITY_ITEM]-\n (aitmrp_mandatory))\nRETURN DISTINCT\n ActivityGroup AS `Activity Group`,\n ActivitySubGroup AS `Activity Subgroup`,\n Activity,\n ai.name AS `Activity Instance`,\n type_filter AS `Activity Instance Class`,\n aitmv_mandatory.name AS `Missing Activity Item`,\n aicp.name AS `Class of Missing Activity Item`", + "query": "WITH\n [\n $neodash_activityinstanceclassvalue_name,\n $neodash_activityinstanceclassvalue_name_subtype\n ] AS activity_filter,\n $neodash_activitygroupvalue_name AS activity_group,\n $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH\n ()-[:LATEST]->\n (act:ActivityValue)-[:HAS_GROUPING]->\n (g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->\n (asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH\n activity_filter,\n g,\n agrp.name AS ActivityGroup,\n asgrp.name AS ActivitySubGroup,\n act.name AS Activity\n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH\n (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue),\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (root:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass:ActivityInstanceClassValue),\n (root)-[:PARENT_CLASS]->{0,3}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aiclass_parent:ActivityInstanceClassValue)\nWITH\n ActivityGroup,\n ActivitySubGroup,\n Activity,\n ai,\n [aiclass_parent.name, aiclass.name] AS type_filter,\n apoc.coll.removeAll(activity_filter, ['']) AS activity_filter\nWITH activity_filter, ActivityGroup, ActivitySubGroup, Activity, ai, type_filter\nWHERE\n (apoc.coll.containsAll(type_filter, activity_filter) AND\n size(activity_filter) = 2)\nMATCH\n (ai)-[:ACTIVITY_INSTANCE_CLASS]->\n (:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,3}\n (aicr:ActivityInstanceClassRoot)-[:LATEST]->\n (aicp:ActivityInstanceClassValue)\nMATCH\n (aicp)<-[:LATEST]-\n (aicr_mandatory:ActivityInstanceClassRoot)-\n [:HAS_ITEM_CLASS {mandatory: true}]->\n (aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->\n (aitmv_mandatory:ActivityItemClassValue)\nWHERE\n (NOT (ai)-\n [:CONTAINS_ACTIVITY_ITEM]->\n (:ActivityItem)<-\n [:HAS_ACTIVITY_ITEM]-\n (aitmrp_mandatory))\nRETURN DISTINCT\n ActivityGroup AS `Activity Group`,\n ActivitySubGroup AS `Activity Subgroup`,\n Activity,\n ai.name AS `Activity Instance`,\n type_filter AS `Activity Instance Class`,\n aitmv_mandatory.name AS `Missing Activity Item`,\n aicp.name AS `Class of Missing Activity Item`", "width": 24, "height": 4, "x": 0, @@ -1248,7 +1248,7 @@ { "id": "c9c1f804-fde1-4515-8bf4-3fb9e163c40d", "title": "Activity Class", - "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) return distinct aicp.name as value, aicp.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH(act:ActivityValue)-[R1:HAS_GROUPING]->(g:ActivityGrouping)-[R2:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue),\n(g)-[R4:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nMATCH(g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) return distinct aicp.name as value, aicp.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 12, @@ -1265,7 +1265,7 @@ { "id": "acaf0a95-cf39-40a4-a1e3-572ca898eaf8", "title": "Activity Subclass", - "query": "MATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nWHERE exists { (aicr)-[:HAS_ITEM_CLASS{mandatory: TRUE}]->(:ActivityItemClassRoot)-[:LATEST]->(:ActivityItemClassValue) }\nWITH aicr, aic\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nreturn distinct aic.`name` as value, aic.`name` as display ORDER BY size(toString(value)) ASC ", + "query": "MATCH (g:ActivityGrouping)<-[R5:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue)\nMATCH (ai)-[R42:ACTIVITY_INSTANCE_CLASS]->(aicr:ActivityInstanceClassRoot)-[R43:LATEST]->(aic:ActivityInstanceClassValue)\nWHERE exists { (aicr)-[:HAS_ITEM_CLASS{mandatory: TRUE}]->(:ActivityItemClassRoot)-[:LATEST]->(:ActivityItemClassValue) }\nWITH aicr, aic\nMATCH (aicr)-[R10:PARENT_CLASS]->(aicrp:ActivityInstanceClassRoot)-[R11:LATEST]->(aicp:ActivityInstanceClassValue) \nwhere aicp.name = $neodash_activityinstanceclassvalue_name \nreturn distinct aic.`name` as value, aic.`name` as display ORDER BY size(toString(value)) ASC ", "width": 6, "height": 2, "x": 18, @@ -1282,7 +1282,7 @@ { "id": "75709134-8427-4d0e-9e2c-a457bcb069c3", "title": "Results (All)", - "query": "WITH [$neodash_activityinstanceclassvalue_name,$neodash_activityinstanceclassvalue_name_subtype] AS activity_filter, $neodash_activitygroupvalue_name AS activity_group, $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH ()-[:LATEST]->(act:ActivityValue)-[:HAS_GROUPING]->(g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH activity_filter, g, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity \n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH (g)<-[:HAS_ACTIVITY]-(ai:ActivityInstanceValue)<-[:LATEST]-(), \n(ai)-[:ACTIVITY_INSTANCE_CLASS]->(root:ActivityInstanceClassRoot)-[:LATEST]->(aiclass:ActivityInstanceClassValue),\n(root)-[:PARENT_CLASS]->{0,3}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aiclass_parent:ActivityInstanceClassValue)\nWITH ActivityGroup, ActivitySubGroup, Activity, ai, [aiclass_parent.name,aiclass.name] as type_filter, apoc.coll.removeAll(activity_filter,['']) as activity_filter\nWITH activity_filter, ActivityGroup, ActivitySubGroup, Activity, ai,type_filter where (apoc.coll.containsAll(type_filter,activity_filter) AND size(activity_filter) = 2)\nMATCH(ai)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,3}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aicp:ActivityInstanceClassValue)\nMATCH (aicp)<-[:LATEST]-(aicr_mandatory:ActivityInstanceClassRoot)-[R1:HAS_ITEM_CLASS]->(aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->(aitmv_mandatory:ActivityItemClassValue)\nWHERE (not (ai)-[:CONTAINS_ACTIVITY_ITEM]->(:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-(aitmrp_mandatory))\nRETURN DISTINCT ActivityGroup as `Activity Group`, ActivitySubGroup as `Activity Subgroup`, Activity, ai.name as `Activity Instance`, type_filter as `Activity Instance Class`, aitmv_mandatory.name as `Missing Activity Item`, aicp.name as `Class of Missing Activity Item`, R1.mandatory AS Mandatory", + "query": "WITH [$neodash_activityinstanceclassvalue_name,$neodash_activityinstanceclassvalue_name_subtype] AS activity_filter, $neodash_activitygroupvalue_name AS activity_group, $neodash_activitysubgroupvalue_name AS activity_subgroup\nMATCH ()-[:LATEST]->(act:ActivityValue)-[:HAS_GROUPING]->(g:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(asgrp:ActivitySubGroupValue)\nWHERE (activity_subgroup = \"\" OR asgrp.name = activity_subgroup)\nMATCH (g)-[:HAS_SELECTED_GROUP]->(agrp:ActivityGroupValue)\nWHERE (activity_group = \"\" OR agrp.name = activity_group)\nWITH activity_filter, g, agrp.name as ActivityGroup, asgrp.name as ActivitySubGroup, act.name as Activity \n//get the activity instances ParentInstanceClass - aiclass_parent. Also getting the immediate class of the instance(aiclass)\nMATCH (g)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(ai:ActivityInstanceValue), \n(ai)-[:ACTIVITY_INSTANCE_CLASS]->(root:ActivityInstanceClassRoot)-[:LATEST]->(aiclass:ActivityInstanceClassValue),\n(root)-[:PARENT_CLASS]->{0,3}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aiclass_parent:ActivityInstanceClassValue)\nWITH ActivityGroup, ActivitySubGroup, Activity, ai, [aiclass_parent.name,aiclass.name] as type_filter, apoc.coll.removeAll(activity_filter,['']) as activity_filter\nWITH activity_filter, ActivityGroup, ActivitySubGroup, Activity, ai,type_filter where (apoc.coll.containsAll(type_filter,activity_filter) AND size(activity_filter) = 2)\nMATCH(ai)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)-[:PARENT_CLASS]->{0,3}(aicr:ActivityInstanceClassRoot)-[:LATEST]->(aicp:ActivityInstanceClassValue)\nMATCH (aicp)<-[:LATEST]-(aicr_mandatory:ActivityInstanceClassRoot)-[R1:HAS_ITEM_CLASS]->(aitmrp_mandatory:ActivityItemClassRoot)-[:LATEST]->(aitmv_mandatory:ActivityItemClassValue)\nWHERE (not (ai)-[:CONTAINS_ACTIVITY_ITEM]->(:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-(aitmrp_mandatory))\nRETURN DISTINCT ActivityGroup as `Activity Group`, ActivitySubGroup as `Activity Subgroup`, Activity, ai.name as `Activity Instance`, type_filter as `Activity Instance Class`, aitmv_mandatory.name as `Missing Activity Item`, aicp.name as `Class of Missing Activity Item`, R1.mandatory AS Mandatory", "width": 24, "height": 4, "x": 0, @@ -1324,7 +1324,7 @@ { "id": "edd46367-a94b-48f7-889d-938d32dc52f9", "title": "Activities and their Activity Instances", - "query": "WITH $neodash_activityvalue_name AS activity_val_name\nMATCH (aig)<-[:HAS_GROUPING]-(av:ActivityValue)<-[:LATEST]-(:ActivityRoot)\nWHERE (activity_val_name = [] OR av.name IN activity_val_name)\nWITH DISTINCT aig, av.name AS `Activity Value`\nOPTIONAL MATCH (:ActivityInstanceRoot)-[:LATEST]->(aiv:ActivityInstanceValue)-[:HAS_ACTIVITY]->(aig)\nWITH DISTINCT `Activity Value`, aig.uid AS `Grouping`, count(aiv) AS `Instance Value Count`, collect(aiv.name) AS `Activity Instance Values` \nRETURN `Activity Value`, `Grouping`, `Instance Value Count`, `Activity Instance Values`", + "query": "WITH $neodash_activityvalue_name AS activity_val_name\nMATCH (aig)<-[:HAS_GROUPING]-(av:ActivityValue)<-[:LATEST]-(:ActivityRoot)\nWHERE (activity_val_name = [] OR av.name IN activity_val_name)\nWITH DISTINCT aig, av.name AS `Activity Value`\nOPTIONAL MATCH (:ActivityInstanceRoot)-[:LATEST]->(aiv:ActivityInstanceValue)<-[:LATEST]-(air:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(aigr:ActivityInstanceGroupingRoot)-[:LATEST]->(aigv:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(aig:ActivityGrouping)\nWITH DISTINCT `Activity Value`, aig.uid AS `Grouping`, count(aiv) AS `Instance Value Count`, collect(aiv.name) AS `Activity Instance Values` \nRETURN `Activity Value`, `Grouping`, `Instance Value Count`, `Activity Instance Values`", "width": 24, "height": 4, "x": 0, @@ -1358,7 +1358,7 @@ { "id": "bf2db8d8-9c58-4e75-8039-fce233d8052f", "title": "Number of Activity Instances Without Grouping", - "query": "MATCH (:ActivityInstanceRoot)-[LATEST]->(aiv:ActivityInstanceValue)\nWHERE not exists {(aiv)-[:HAS_ACTIVITY]->(:ActivityGrouping)}\nRETURN count(aiv)", + "query": "MATCH (:ActivityInstanceRoot)-[LATEST]->(aiv:ActivityInstanceValue)\nWHERE not exists {(aiv)<-[:LATEST]-(air_exists:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)}\nRETURN count(aiv)", "width": 8, "height": 2, "x": 16, @@ -1388,7 +1388,7 @@ { "id": "3323a73e-bcd2-4de4-afb7-527c14bc89a6", "title": "Activity Instances Without Grouping", - "query": "MATCH (:ActivityInstanceRoot)-[LATEST]->(aiv:ActivityInstanceValue)\nWHERE not exists {(aiv)-[:HAS_ACTIVITY]->(:ActivityGrouping)}\nRETURN aiv.name AS `Activity Instance`", + "query": "MATCH (:ActivityInstanceRoot)-[LATEST]->(aiv:ActivityInstanceValue)\nWHERE not exists {(aiv)<-[:LATEST]-(air_exists:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)}\nRETURN aiv.name AS `Activity Instance`", "width": 8, "height": 3, "x": 16, @@ -1473,7 +1473,7 @@ { "id": "09238485-3910-4321-a6af-21b438a7880c", "title": "[:LATEST] Activity Instances with a Grouping", - "query": "MATCH (act_ins_root:ActivityInstanceRoot)-[:LATEST]->(act_ins_val:ActivityInstanceValue)-[:HAS_ACTIVITY]->(act_grping:ActivityGrouping)\nRETURN count(DISTINCT act_ins_val)", + "query": "MATCH (act_ins_root:ActivityInstanceRoot)-[:LATEST]->(act_ins_val:ActivityInstanceValue)<-[:LATEST]-(air:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(aigr:ActivityInstanceGroupingRoot)-[:LATEST]->(aigv:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(act_grping:ActivityGrouping)\nRETURN count(DISTINCT act_ins_val)", "width": 12, "height": 2, "x": 12, @@ -1499,7 +1499,7 @@ { "id": "d191a65b-ba0f-40a4-9a98-6ade995fd4e2", "title": "[:LATEST] Activity Instances with All Conditions Met", - "query": "MATCH (act_ins_root:ActivityInstanceRoot)-[:LATEST]->(act_ins_val:ActivityInstanceValue)-[:HAS_ACTIVITY]->(act_grping:ActivityGrouping)<-[:HAS_GROUPING]-(act_val:ActivityValue)\nMATCH (act_grping)-[:HAS_SELECTED_GROUP]->(:ActivityGroupValue)\nMATCH (act_grping)-[:HAS_SELECTED_SUBGROUP]->(:ActivitySubGroupValue)\nRETURN count(DISTINCT act_ins_val)", + "query": "MATCH (act_ins_root:ActivityInstanceRoot)-[:LATEST]->(act_ins_val:ActivityInstanceValue)<-[:LATEST]-(air:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(aigr:ActivityInstanceGroupingRoot)-[:LATEST]->(aigv:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(act_grping:ActivityGrouping)<-[:HAS_GROUPING]-(act_val:ActivityValue)\nMATCH (act_grping)-[:HAS_SELECTED_GROUP]->(:ActivityGroupValue)\nMATCH (act_grping)-[:HAS_SELECTED_SUBGROUP]->(:ActivitySubGroupValue)\nRETURN count(DISTINCT act_ins_val)", "width": 12, "height": 2, "x": 0, diff --git a/neo4j-mdr-db/neodash/neodash_reports/data_exchange_data_models.json b/neo4j-mdr-db/neodash/neodash_reports/data_exchange_data_models.json index 7fad175c..ee34e6d9 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/data_exchange_data_models.json +++ b/neo4j-mdr-db/neodash/neodash_reports/data_exchange_data_models.json @@ -44,7 +44,7 @@ { "id": "9b95c45f-de92-43fb-a753-fda680813992", "title": "Guide", - "query": "This report is for exploring \n- CDISC models\n- Implementation Guides (SDTM & SEND, CDASH, ADaM) \n- Novo Nordisk Sponsor Models\n\n\nNote that CDASH and ADaM Implementation Guides are in their own section because they have a slightly different structure\n", + "query": "This report is for exploring \n- CDISC models\n- Implementation Guides (SDTM & SEND, CDASH, ADaM) \n- Sponsor Models\n\n\nNote that CDASH and ADaM Implementation Guides are in their own section because they have a slightly different structure\n", "width": 15, "height": 4, "x": 0, diff --git a/neo4j-mdr-db/neodash/neodash_reports/draft_reports/schema_update_activity_intance_grouping.json b/neo4j-mdr-db/neodash/neodash_reports/draft_reports/schema_update_activity_intance_grouping.json new file mode 100644 index 00000000..6b281348 --- /dev/null +++ b/neo4j-mdr-db/neodash/neodash_reports/draft_reports/schema_update_activity_intance_grouping.json @@ -0,0 +1,243 @@ +[ + { + "nodes": [ + { + "identity": -5, + "labels": [ + "ActivityGrouping" + ], + "properties": { + "name": "ActivityGrouping", + "count": 750 + }, + "elementId": "-5" + }, + { + "identity": -2, + "labels": [ + "ActivityInstanceGroupingRoot" + ], + "properties": { + "name": "ActivityInstanceGroupingRoot", + "count": 231 + }, + "elementId": "-2" + }, + { + "identity": -6, + "labels": [ + "ActivityInstanceGroupingValue" + ], + "properties": { + "name": "ActivityInstanceGroupingValue", + "count": 1383 + }, + "elementId": "-6" + }, + { + "identity": -3, + "labels": [ + "ActivityInstanceRoot" + ], + "properties": { + "name": "ActivityInstanceRoot", + "count": 231 + }, + "elementId": "-3" + }, + { + "identity": -4, + "labels": [ + "ActivityInstanceValue" + ], + "properties": { + "name": "ActivityInstanceValue", + "count": 1792 + }, + "elementId": "-4" + } + ], + "relationships": [ + { + "identity": -20, + "start": -3, + "end": -4, + "type": "LATEST_RETIRED", + "properties": { + "count": 8, + "type": "LATEST_RETIRED", + "in": 2, + "out": 2 + }, + "elementId": "84ade306-3caa-447a-9830-587d5fae3b37", + "startNodeElementId": "-3", + "endNodeElementId": "-4" + }, + { + "identity": -7, + "start": -3, + "end": -4, + "type": "LATEST", + "properties": { + "count": 73699, + "type": "LATEST", + "in": 231, + "out": 231 + }, + "elementId": "5df0865e-d110-41c3-b927-c14efe33b448", + "startNodeElementId": "-3", + "endNodeElementId": "-4" + }, + { + "identity": -6, + "start": -2, + "end": -6, + "type": "LATEST", + "properties": { + "count": 73699, + "type": "LATEST", + "in": 250, + "out": 250 + }, + "elementId": "9a2f4c80-c4b0-420b-83e9-efc9c539e050", + "startNodeElementId": "-2", + "endNodeElementId": "-6" + }, + { + "identity": -19, + "start": -2, + "end": -6, + "type": "LATEST_RETIRED", + "properties": { + "count": 8, + "type": "LATEST_RETIRED", + "in": 2, + "out": 2 + }, + "elementId": "5b094681-5457-4ca0-b11f-84dabbcf943d", + "startNodeElementId": "-2", + "endNodeElementId": "-6" + }, + { + "identity": -22, + "start": -3, + "end": -2, + "type": "HAS_GROUPING_ROOT", + "properties": { + "count": 231, + "type": "HAS_GROUPING_ROOT", + "in": 231, + "out": 231 + }, + "elementId": "9b522cc0-914c-4e18-9246-18ab30a37f6d", + "startNodeElementId": "-3", + "endNodeElementId": "-2" + }, + { + "identity": -2, + "start": -2, + "end": -6, + "type": "HAS_VERSION", + "properties": { + "count": 107879, + "type": "HAS_VERSION", + "in": 4431, + "out": 4431 + }, + "elementId": "d2d277b3-d569-4de6-80b3-75123cd8059d", + "startNodeElementId": "-2", + "endNodeElementId": "-6" + }, + { + "identity": -3, + "start": -3, + "end": -4, + "type": "HAS_VERSION", + "properties": { + "count": 107879, + "type": "HAS_VERSION", + "in": 6810, + "out": 6810 + }, + "elementId": "b963be4c-6061-4a08-8085-f24984ae8724", + "startNodeElementId": "-3", + "endNodeElementId": "-4" + }, + { + "identity": -15, + "start": -3, + "end": -4, + "type": "LATEST_DRAFT", + "properties": { + "count": 8295, + "type": "LATEST_DRAFT", + "in": 231, + "out": 231 + }, + "elementId": "91ec465e-93c2-4e32-a0e2-5df65de3847c", + "startNodeElementId": "-3", + "endNodeElementId": "-4" + }, + { + "identity": -11, + "start": -3, + "end": -4, + "type": "LATEST_FINAL", + "properties": { + "count": 72766, + "type": "LATEST_FINAL", + "in": 217, + "out": 217 + }, + "elementId": "244d014f-9901-4fd3-b113-7d32b4260be6", + "startNodeElementId": "-3", + "endNodeElementId": "-4" + }, + { + "identity": -14, + "start": -2, + "end": -6, + "type": "LATEST_DRAFT", + "properties": { + "count": 8295, + "type": "LATEST_DRAFT", + "in": 250, + "out": 250 + }, + "elementId": "f7cd440e-d5ad-408b-80a1-af202329bc15", + "startNodeElementId": "-2", + "endNodeElementId": "-6" + }, + { + "identity": -17, + "start": -6, + "end": -5, + "type": "HAS_ACTIVITY", + "properties": { + "count": 1793, + "type": "HAS_ACTIVITY", + "in": 1499, + "out": 1499 + }, + "elementId": "d8ed6125-eee0-4844-80ed-982f5f2cd161", + "startNodeElementId": "-6", + "endNodeElementId": "-5" + }, + { + "identity": -10, + "start": -2, + "end": -6, + "type": "LATEST_FINAL", + "properties": { + "count": 72766, + "type": "LATEST_FINAL", + "in": 234, + "out": 234 + }, + "elementId": "a4e50c02-d139-44c1-ab7f-aa4d7930bea7", + "startNodeElementId": "-2", + "endNodeElementId": "-6" + } + ] + } +] \ No newline at end of file diff --git a/neo4j-mdr-db/neodash/neodash_reports/laboratory_data_specification.json b/neo4j-mdr-db/neodash/neodash_reports/laboratory_data_specification.json index b47824d0..cdc5eba6 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/laboratory_data_specification.json +++ b/neo4j-mdr-db/neodash/neodash_reports/laboratory_data_specification.json @@ -219,7 +219,7 @@ { "id": "7e95f560-0407-471a-a533-0900b23367f7", "title": "Types of visits", - "query": "Consider if **UNSCHEDULED** and/or **NON-VISIT** options should be included in the Visits sheet. \n\nData from unscheduled samples (see section 1.2.1 in https://novonordisk.sharepoint.com/:w:/r/sites/ClinicalDataManagement/DMTGDocs/Laboratory%20Process%20Guideline%20for%20Data%20Management%20V.2.0.docx?d=wd8b84eb397fe406f97220ecc4cbdc08c&csf=1&web=1&e=Qol6Yu&isSPOFile=1&xsdata=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%3D&sdata=MXNOUnlLYmlXREhvTlZKUlFHWDdJLzFGczd2YjVMTUZhU1BoNlhMMW5BYz0%3D&ovuser=fdfed7bd-9f6a-44a1-b694-6e39c468c150%2CBAPU%40novonordisk.com) allowed per protocol can be received from the laboratory with “VISIT = UNSCHEDULED” or ”VISIT = NON-VISIT”. \n\nIt is recommended that “VISIT = NON-VISIT” is used for data from samples that is taken due to AE requiring additional data collection or similar, e.g., a systemic hypersensitivity sample or an extra blood test in case of suspected pregnancy. \n\n”VISIT = NON-VISIT” will serve as an identifier for these special cases, also in cases where a parameter is analysed for both via a scheduled sample and an unscheduled sample, if topiccd (and therefore also CAT and SUBCAT) is the same. \n\nAn example of this could be an AB that should be analysed for both on a normal visit and also in case of hypersensitivity.\n\nFor phase 2-4 it should also be considered to include “VISIT = UNSCHEDULED”, to enable transfer of samples where the CL cannot assign it to a specific visit (e.g., site forgot to mark at which visit sample was taken).\n\n\n", + "query": "Consider if **UNSCHEDULED** and/or **NON-VISIT** options should be included in the Visits sheet. \n\nData from unscheduled samples (see section 1.2.1 in Laboratory Process Guideline for Data Management V.2.0) allowed per protocol can be received from the laboratory with “VISIT = UNSCHEDULED” or ”VISIT = NON-VISIT”. \n\nIt is recommended that “VISIT = NON-VISIT” is used for data from samples that is taken due to AE requiring additional data collection or similar, e.g., a systemic hypersensitivity sample or an extra blood test in case of suspected pregnancy. \n\n”VISIT = NON-VISIT” will serve as an identifier for these special cases, also in cases where a parameter is analysed for both via a scheduled sample and an unscheduled sample, if topiccd (and therefore also CAT and SUBCAT) is the same. \n\nAn example of this could be an AB that should be analysed for both on a normal visit and also in case of hypersensitivity.\n\nFor phase 2-4 it should also be considered to include “VISIT = UNSCHEDULED”, to enable transfer of samples where the CL cannot assign it to a specific visit (e.g., site forgot to mark at which visit sample was taken).\n\n\n", "width": 9, "height": 6, "x": 15, diff --git a/neo4j-mdr-db/neodash/neodash_reports/pre_define.json b/neo4j-mdr-db/neodash/neodash_reports/pre_define.json index b4bff317..94b91a64 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/pre_define.json +++ b/neo4j-mdr-db/neodash/neodash_reports/pre_define.json @@ -1,176 +1,176 @@ { - "title": "Pre-Define", - "version": "2.4", - "settings": { - "pagenumber": 0, - "editable": true, - "fullscreenEnabled": false, - "parameters": { - "neodash_studyid": "4467", - "neodash_sponsor_model": "sdtmig_mastermodel_3.2_NN15", - "neodash_dataset": "VS", - "neodash_sponsor_version_number": "Select", - "neodash_sponsor_version_number_display": [], - "neodash_codelist": "VSTEST" - } - }, - "pages": [ + "title": "Pre-Define", + "version": "2.4", + "settings": { + "pagenumber": 0, + "editable": true, + "fullscreenEnabled": false, + "parameters": { + "neodash_studyid": "0", + "neodash_sponsor_model": "", + "neodash_dataset": "", + "neodash_sponsor_version_number": "Select", + "neodash_sponsor_version_number_display": [], + "neodash_codelist": "" + } + }, + "pages": [ + { + "title": "Pre-Define.xml", + "reports": [ + { + "id": "b596c443-a056-4810-808d-99d0b28e2737", + "title": "Study Selection", + "query": "MATCH (n1:StudyRoot)-[r1]->(n2:StudyValue)\nRETURN DISTINCT 'Select' AS Select,\nn2.study_number AS StudyID,\nn2.study_id_prefix AS StudyName,\nn2.study_acronym AS StudyAcronym,\nCOALESCE(n2.study_subpart_acronym,\"No sub study\") AS StudySubpart;\n\n\n", + "width": 8, + "height": 4, + "x": 0, + "y": 0, + "type": "table", + "selection": {}, + "settings": { + "compact": true, + "columnWidths": "[2,1,1,2,2]", + "allowDownload": true, + "actionsRules": [ + { + "condition": "Click", + "field": "Select", + "value": "StudyID", + "customization": "set variable", + "customizationValue": "studyid" + } + ], + "wrapContent": true + } + }, { - "title": "Pre-Define.xml", - "reports": [ - { - "id": "b596c443-a056-4810-808d-99d0b28e2737", - "title": "Study Selection", - "query": "MATCH (n1:StudyRoot)-[r1]->(n2:StudyValue)\nRETURN DISTINCT 'Select' AS Select,\nn2.study_number AS StudyID,\nn2.study_id_prefix AS StudyName,\nn2.study_acronym AS StudyAcronym,\nCOALESCE(n2.study_subpart_acronym,\"No sub study\") AS StudySubpart;\n\n\n", - "width": 8, - "height": 4, - "x": 0, - "y": 0, - "type": "table", - "selection": {}, - "settings": { - "compact": true, - "columnWidths": "[2,1,1,2,2]", - "allowDownload": true, - "actionsRules": [ - { - "condition": "Click", - "field": "Select", - "value": "StudyID", - "customization": "set variable", - "customizationValue": "studyid" - } - ], - "wrapContent": true - } - }, - { - "id": "24612f46-711b-4eac-92d1-c397cc25847c", - "title": "Study", - "query": "MATCH (n1:StudyRoot)-[r1]->(n2:StudyValue) WHERE n2.study_number = $neodash_studyid\n RETURN 'Study Name' AS label,\n n2.study_id_prefix AS Value\n UNION\nMATCH (n2)-[r2]->(n3:StudyTextField) WHERE n2.study_number = $neodash_studyid AND n3.field_name = \"study_title\"\n RETURN 'Study Description' AS label,\n n3.value AS Value\n UNION\nMATCH (n1:StudyRoot)-[r1]->(n2:StudyValue) WHERE n2.study_number = $neodash_studyid\n RETURN 'Protocol Name' AS label,\n n2.study_acronym AS Value;\n\n\n", - "width": 8, - "height": 4, - "x": 8, - "y": 0, - "type": "table", - "selection": {}, - "settings": { - "compact": false, - "columnWidths": "[1,5]", - "allowDownload": true, - "wrapContent": true - } - }, - { - "id": "caeab539-3978-4ec3-97a8-2da59c8ef20b", - "title": "Standard selection", - "query": "MATCH (n1:SponsorModelValue)-[r1:EXTENDS_VERSION]->(n2:DataModelIGValue)\nRETURN \"Select\" AS Select,\nn1.name AS SponsorModelIg,\nn2.name AS CdiscModelIg,\nn2.effective_date AS EffectiveDate,\nn2.version_number AS Version;\n\n\n", - "width": 8, - "height": 4, - "x": 16, - "y": 0, - "type": "table", - "selection": {}, - "settings": { - "wrapContent": true, - "columnWidths": "[2,3,1,2,1]", - "allowDownload": true, - "actionsRules": [ - { - "condition": "Click", - "field": "Select", - "value": "SponsorModelIg", - "customization": "set variable", - "customizationValue": "sponsor_model" - }, - { - "condition": "Click", - "field": "Select", - "value": "15", - "customization": "set variable", - "customizationValue": "sponsor_version_number" - } - ] - } - }, - { - "id": "93fc9ba4-5ac9-419b-a242-72acebbd6043", - "title": "Datasets - Using $neodash_sponsor_model", - "query": "// Study selection with applicable Visits and Study Activities and Grouping New Version\nMATCH ()-[r1:LATEST]->(n2:StudyValue {study_number: $neodash_studyid})-[r2:HAS_STUDY_VISIT]->(n3:StudyVisit)-[r3:STUDY_VISIT_HAS_SCHEDULE]->(n4:StudyActivitySchedule)<-[r4:STUDY_ACTIVITY_HAS_SCHEDULE]-(n5:StudyActivity)\n// Connection between Study Activities to Library Activities and back to the Study Visits\nWITH DISTINCT n5\nMATCH (n5)-[r9:HAS_SELECTED_ACTIVITY]->(n10:ActivityValue)-[r10:HAS_GROUPING]->(n11:ActivityGrouping)<-[r11:HAS_ACTIVITY]-(n12:ActivityInstanceValue)<-[r12:HAS_SELECTED_ACTIVITY_INSTANCE]-(n13:StudyActivityInstance)\nWITH DISTINCT n12\n// Looking at the SDTMIG and the connected MasterModel\nMATCH (n27:DataModelIGValue)<-[r28:EXTENDS_VERSION]-(n28:SponsorModelValue) \nWHERE n28.name=$neodash_sponsor_model\n// Display the Domain connected to the ActivityInstance\nOPTIONAL MATCH (n12)-[r29:CONTAINS_ACTIVITY_ITEM]->(n29:ActivityItem)<-[r30:HAS_ACTIVITY_ITEM]-(n30:ActivityItemClassRoot)-[r31:MAPS_VARIABLE_CLASS]->(n31:VariableClass {uid:'DOMAIN'})-[r32:HAS_INSTANCE]->(n32:VariableClassInstance)<-[r33:IMPLEMENTS_VARIABLE{version_number:n27.version_number}]-(n33:DatasetVariableInstance)<-[r34:HAS_DATASET_VARIABLE {version_number:n27.version_number}]-(n34:DatasetInstance)<-[r35:HAS_INSTANCE]-(n35:Dataset) ,\n (n29)-[r36:HAS_CT_TERM]->(n36:CTTermRoot)-[r37:HAS_ATTRIBUTES_ROOT]->(n37:CTTermAttributesRoot)-[r38:LATEST]->(n38:CTTermAttributesValue) \nWHERE n35.uid = n38.code_submission_value\nWITH DISTINCT n34, n35\nMATCH (n35)-[r57:HAS_INSTANCE]->(n48:SponsorModelDatasetInstance)\nMATCH (n34)-[r58:IMPLEMENTS_DATASET_CLASS]->(n54:DatasetClassInstance)\nRETURN DISTINCT n35.uid AS Dataset, n48.label AS Description, n54.label AS Class, n48.structure AS Structure, \"Tabulation\" AS Purpose, \"To be Specify\" AS Keys, n34.description AS Documentation, TOLOWER(n35.uid)||\".xpt\" AS Location;", - "width": 24, - "height": 4, - "x": 0, - "y": 4, - "type": "table", - "selection": {}, - "settings": { - "columnWidths": "[1,2,2,3,1,1,5,1]", - "allowDownload": true, - "actionsRules": [ - { - "condition": "Click", - "field": "Dataset", - "value": "Dataset", - "customization": "set variable", - "customizationValue": "dataset" - } - ], - "wrapContent": true - } - }, - { - "id": "fdd27b48-0ea9-4ee1-bbb8-fb2a5033de42", - "title": "$neodash_dataset Using $neodash_sponsor_model", - "query": "MATCH (n1:SponsorModelValue)-[r1:HAS_DATASET]->(n2:SponsorModelDatasetInstance)<-[r2:HAS_INSTANCE]-(n3:Dataset)\nWHERE n1.name=$neodash_sponsor_model AND n3.uid=$neodash_dataset\nMATCH (n2)-[r3:HAS_DATASET_VARIABLE]->(n4:SponsorModelDatasetVariableInstance)<-[r4:HAS_INSTANCE]-(n5:DatasetVariable)\n//WHERE r3.version_number=toString($neodash_sponsor_version_number)\nOPTIONAL MATCH (n5)<-[r5:HAS_KEY]-(n2)\n\nRETURN DISTINCT\n n5.uid AS Variable,\n n4.is_basic_std AS Cdisc,\n n4.label AS `Label/Description`,\n (n4.xml_datatype+\" [\"+n4.variable_type+\"]\") AS Type,\n n4.length AS Length,\n n4.display_format AS DisplayFormat,\n n4.xml_codelist AS Codelist,\n n4.term AS Term,\n n4.core AS Core,\n n4.origin AS Origin,\n n4.role AS Role,\n n4.ig_comment AS Comment,\n r3.ordinal AS Order\nORDER BY toInteger(Order);", - "width": 24, - "height": 4, - "x": 0, - "y": 8, - "type": "table", - "selection": {}, - "settings": { - "columnWidths": "[2,1,3,1,1,1,1,1,1,1,2,3,1]", - "allowDownload": true, - "fullscreenEnabled": true, - "actionsRules": [ - { - "condition": "Click", - "field": "Codelist", - "value": "Codelist", - "customization": "set variable", - "customizationValue": "codelist" - } - ], - "compact": true - } - }, - { - "id": "21683f6d-bce3-4e01-ac1f-4ddcd5e7a16a", - "title": "Codelist/Terms - $neodash_codelist", - "query": "// Cypher to export the full CT as a JSON file\nMATCH (n1:CTCodelistRoot)-[r1]->(n2:CTCodelistAttributesRoot)-[r2:LATEST]->(n3:CTCodelistAttributesValue)\nWHERE n3.submission_value = $neodash_codelist\nMATCH (n1)-[r3]->(n4:CTTermRoot)-[r4]->(n5:CTTermAttributesRoot)-[r5:LATEST]->(n6:CTTermAttributesValue)\nRETURN DISTINCT n1.uid AS ConceptID,\nn3.submission_value AS SubmissionValue,\nn3.name AS Name,\nn3.extensible AS Extensible,\n//COALESCE(n4.concept_id,n4.uid) AS TermConceptID,\nn4.uid AS SBTermConceptID,\nn6.code_submission_value AS TermSubmissionValue,\nn6.preferred_term AS TermName\n//n6.preferred_term AS TermPreferredTerm\nORDER BY SubmissionValue, \nTermSubmissionValue;\n\n\n", - "width": 24, - "height": 4, - "x": 0, - "y": 12, - "type": "table", - "selection": {}, - "settings": { - "compact": true, - "columnWidths": "[1,1,2,1,3,3,2]", - "allowDownload": true, - "fullscreenEnabled": true - } - } + "id": "24612f46-711b-4eac-92d1-c397cc25847c", + "title": "Study", + "query": "MATCH (n1:StudyRoot)-[r1]->(n2:StudyValue) WHERE n2.study_number = $neodash_studyid\n RETURN 'Study Name' AS label,\n n2.study_id_prefix AS Value\n UNION\nMATCH (n2)-[r2]->(n3:StudyTextField) WHERE n2.study_number = $neodash_studyid AND n3.field_name = \"study_title\"\n RETURN 'Study Description' AS label,\n n3.value AS Value\n UNION\nMATCH (n1:StudyRoot)-[r1]->(n2:StudyValue) WHERE n2.study_number = $neodash_studyid\n RETURN 'Protocol Name' AS label,\n n2.study_acronym AS Value;\n\n\n", + "width": 8, + "height": 4, + "x": 8, + "y": 0, + "type": "table", + "selection": {}, + "settings": { + "compact": false, + "columnWidths": "[1,5]", + "allowDownload": true, + "wrapContent": true + } + }, + { + "id": "caeab539-3978-4ec3-97a8-2da59c8ef20b", + "title": "Standard selection", + "query": "MATCH (n1:SponsorModelValue)-[r1:EXTENDS_VERSION]->(n2:DataModelIGValue)\nRETURN \"Select\" AS Select,\nn1.name AS SponsorModelIg,\nn2.name AS CdiscModelIg,\nn2.effective_date AS EffectiveDate,\nn2.version_number AS Version;\n\n\n", + "width": 8, + "height": 4, + "x": 16, + "y": 0, + "type": "table", + "selection": {}, + "settings": { + "wrapContent": true, + "columnWidths": "[2,3,1,2,1]", + "allowDownload": true, + "actionsRules": [ + { + "condition": "Click", + "field": "Select", + "value": "SponsorModelIg", + "customization": "set variable", + "customizationValue": "sponsor_model" + }, + { + "condition": "Click", + "field": "Select", + "value": "15", + "customization": "set variable", + "customizationValue": "sponsor_version_number" + } ] + } + }, + { + "id": "93fc9ba4-5ac9-419b-a242-72acebbd6043", + "title": "Datasets - Using $neodash_sponsor_model", + "query": "// Study selection with applicable Visits and Study Activities and Grouping New Version\nMATCH ()-[r1:LATEST]->(n2:StudyValue {study_number: $neodash_studyid})-[r2:HAS_STUDY_VISIT]->(n3:StudyVisit)-[r3:STUDY_VISIT_HAS_SCHEDULE]->(n4:StudyActivitySchedule)<-[r4:STUDY_ACTIVITY_HAS_SCHEDULE]-(n5:StudyActivity)\n// Connection between Study Activities to Library Activities and back to the Study Visits\nWITH DISTINCT n5\nMATCH (n5)-[r9:HAS_SELECTED_ACTIVITY]->(n10:ActivityValue)-[r10:HAS_GROUPING]->(n11:ActivityGrouping)<-[r11:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue)<-[:LATEST]-(aigr:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[:LATEST]->(n12:ActivityInstanceValue)<-[r12:HAS_SELECTED_ACTIVITY_INSTANCE]-(n13:StudyActivityInstance)\nWITH DISTINCT n12\n// Looking at the SDTMIG and the connected MasterModel\nMATCH (n27:DataModelIGValue)<-[r28:EXTENDS_VERSION]-(n28:SponsorModelValue) \nWHERE n28.name=$neodash_sponsor_model\n// Display the Domain connected to the ActivityInstance\n// Updated: replaced HAS_CT_TERM->CTTermRoot with HAS_CT_TERM->CTTermContext->HAS_SELECTED_TERM->CTTermRoot\nOPTIONAL MATCH (n12:ActivityInstanceValue)-[r29:CONTAINS_ACTIVITY_ITEM]->(n29:ActivityItem)<-[r30:HAS_ACTIVITY_ITEM]-(n30:ActivityItemClassRoot)-[r31:MAPS_VARIABLE_CLASS]->(n31:VariableClass {uid:'DOMAIN'})-[r32:HAS_INSTANCE]->(n32:VariableClassInstance)<-[r33:IMPLEMENTS_VARIABLE {version_number:n27.version_number}]-(n33:DatasetVariableInstance)<-[r34:HAS_DATASET_VARIABLE {version_number:n27.version_number}]-(n34:DatasetInstance)<-[r35:HAS_INSTANCE]-(n35:Dataset),(n29)-[r36:HAS_CT_TERM]->(n36:CTTermContext)-[r37:HAS_SELECTED_TERM]->(n37:CTTermRoot)<-[r38]-(n39:CTCodelistTerm)\nWHERE n35.uid = n39.submission_value\nWITH DISTINCT n34, n35\nMATCH (n35)-[r57:HAS_INSTANCE]->(n48:SponsorModelDatasetInstance)\nMATCH (n34)-[r58:IMPLEMENTS_DATASET_CLASS]->(n54:DatasetClassInstance)\nRETURN DISTINCT n35.uid AS Dataset, n48.label AS Description, n54.label AS Class, n48.structure AS Structure, \"Tabulation\" AS Purpose, \"To be Specify\" AS Keys, n34.description AS Documentation, TOLOWER(n35.uid)||\".xpt\" AS Location;", + "width": 24, + "height": 4, + "x": 0, + "y": 4, + "type": "table", + "selection": {}, + "settings": { + "columnWidths": "[1,2,2,3,1,1,5,1]", + "allowDownload": true, + "actionsRules": [ + { + "condition": "Click", + "field": "Dataset", + "value": "Dataset", + "customization": "set variable", + "customizationValue": "dataset" + } + ], + "wrapContent": true + } + }, + { + "id": "fdd27b48-0ea9-4ee1-bbb8-fb2a5033de42", + "title": "$neodash_dataset Using $neodash_sponsor_model", + "query": "MATCH (n1:SponsorModelValue)-[r1:HAS_DATASET]->(n2:SponsorModelDatasetInstance)<-[r2:HAS_INSTANCE]-(n3:Dataset)\nWHERE n1.name=$neodash_sponsor_model AND n3.uid=$neodash_dataset\nMATCH (n2)-[r3:HAS_DATASET_VARIABLE]->(n4:SponsorModelDatasetVariableInstance)<-[r4:HAS_INSTANCE]-(n5:DatasetVariable)\n//WHERE r3.version_number=toString($neodash_sponsor_version_number)\nOPTIONAL MATCH (n5)<-[r5:HAS_KEY]-(n2)\n\nRETURN DISTINCT\n n5.uid AS Variable,\n n4.is_basic_std AS Cdisc,\n n4.label AS `Label/Description`,\n (n4.xml_datatype+\" [\"+n4.variable_type+\"]\") AS Type,\n n4.length AS Length,\n n4.display_format AS DisplayFormat,\n CASE WHEN n5.uid = 'DOMAIN' THEN 'DOMAIN' ELSE CASE WHEN NOT n4.term ='*' THEN replace(replace(n4.term, '(', ''), ')', '') ELSE '' END END AS Codelist,\n n4.term AS Term,\n n4.core AS Core,\n n4.origin AS Origin,\n n4.role AS Role,\n n4.ig_comment AS Comment,\n r3.ordinal AS Order\nORDER BY toInteger(Order);", + "width": 24, + "height": 4, + "x": 0, + "y": 8, + "type": "table", + "selection": {}, + "settings": { + "columnWidths": "[2,1,3,1,1,1,1,1,1,1,2,3,1]", + "allowDownload": true, + "fullscreenEnabled": true, + "actionsRules": [ + { + "condition": "Click", + "field": "Codelist", + "value": "Codelist", + "customization": "set variable", + "customizationValue": "codelist" + } + ], + "compact": true + } + }, + { + "id": "21683f6d-bce3-4e01-ac1f-4ddcd5e7a16a", + "title": "Codelist/Terms - $neodash_codelist", + "query": "// Cypher to export the full CT as a JSON file\nMATCH (n1:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(n2:CTCodelistAttributesRoot)-[:LATEST]->(n3:CTCodelistAttributesValue)\nWHERE n3.submission_value = $neodash_codelist\nMATCH (n1)-[:HAS_TERM]->(n39:CTCodelistTerm)-[:HAS_TERM_ROOT]->(n4:CTTermRoot)\nMATCH (n4)-[:HAS_ATTRIBUTES_ROOT]->(n5:CTTermAttributesRoot)-[:LATEST]->(n6:CTTermAttributesValue)\nRETURN DISTINCT \n n1.uid AS ConceptID,\n n3.submission_value AS SubmissionValue,\n n3.name AS Name,\n n3.extensible AS Extensible,\n n4.uid AS SBTermConceptID,\n n39.submission_value AS TermSubmissionValue,\n n6.preferred_term AS TermName\nORDER BY SubmissionValue, TermSubmissionValue;", + "width": 24, + "height": 4, + "x": 0, + "y": 12, + "type": "table", + "selection": {}, + "settings": { + "compact": true, + "columnWidths": "[1,1,2,1,3,3,2]", + "allowDownload": true, + "fullscreenEnabled": true + } } - ], - "parameters": {}, - "extensions": { - "active": true, - "activeReducers": [], - "actions": { - "active": true - } - }, - "uuid": "8c7c0c94-b0ed-4383-bcd2-a4b5b10b1c54" + ] + } + ], + "parameters": {}, + "extensions": { + "active": true, + "activeReducers": [], + "actions": { + "active": true + } + }, + "uuid": "8c7c0c94-b0ed-4383-bcd2-a4b5b10b1c54" } \ No newline at end of file diff --git a/neo4j-mdr-db/neodash/neodash_reports/study_metadata_compare.json b/neo4j-mdr-db/neodash/neodash_reports/study_metadata_compare.json index 4f57fcd6..e08b375f 100644 --- a/neo4j-mdr-db/neodash/neodash_reports/study_metadata_compare.json +++ b/neo4j-mdr-db/neodash/neodash_reports/study_metadata_compare.json @@ -16,11 +16,6 @@ "neodash_versiondate_studya_display": "", "neodash_versiondate_studyb": "", "neodash_versiondate_studyb_display": "", - "neodash_sstdtc": { - "year": 2024, - "month": 10, - "day": 29 - }, "neodash_differences_only": "No", "neodash_differences_only_display": "No", "neodash_diff_only": "On", @@ -75,7 +70,7 @@ { "id": "5e333e2c-6067-4875-95a0-d6e239821fdd", "title": "Select Base", - "query": "CALL apoc.when(size($neodash_project)=0,\"match(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid \nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,sact.date as date order by StudyRoot, sact.date\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Base' as Select, id(s) as id_a\",\n\"match(p:Project)-[:HAS_FIELD]->(:StudyProjectField)<-[:HAS_PROJECT]-(s:StudyValue) \nwhere p.project_number in $a\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,sact.date as date order by StudyRoot, sact.date\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Base' as Select, id(s) as id_a\",{a:$neodash_project}) YIELD value \nRETURN value.StudyRoot as StudyRoot, \nvalue.TrialID as `Trial ID`,\nvalue.Acronym as Acronym,\nvalue.Date as Date,\nvalue.Version as Version,\nvalue.Status as Status,\nvalue.Latest as Latest, \nvalue.Select as Select,\nvalue.id_a as __id_a order by `Trial ID`, Date", + "query": "CALL apoc.when(size($neodash_project)=0,\"match(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by StudyRoot, date, Latest DESC\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest\nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Base' as Select, id(s) as id_a\",\n\"match(p:Project)-[:HAS_FIELD]->(:StudyProjectField)<-[:HAS_PROJECT]-(s:StudyValue) \nwhere p.project_number in $a\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by StudyRoot, date, Latest DESC\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest\nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Base' as Select, id(s) as id_a\",{a:$neodash_project}) YIELD value \nRETURN value.StudyRoot as StudyRoot, \nvalue.TrialID as `Trial ID`,\nvalue.Acronym as Acronym,\nvalue.Date as Date,\nvalue.Version as Version,\nvalue.Status as Status,\nvalue.Latest as Latest, \nvalue.Select as Select,\nvalue.id_a as __id_a order by `Trial ID`, Date", "width": 24, "height": 4, "x": 0, @@ -102,7 +97,7 @@ { "id": "232befa7-93ac-49d8-a73f-ae5bc308b011", "title": "Select Compare", - "query": "CALL apoc.when(size($neodash_project)=0,\"match(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid \nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,sact.date as date order by StudyRoot, sact.date\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Compare' as Select, id(s) as id_b\",\n\"match(p:Project)-[:HAS_FIELD]->(:StudyProjectField)<-[:HAS_PROJECT]-(s:StudyValue) \nwhere p.project_number in $a\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,sact.date as date order by StudyRoot, sact.date\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Compare' as Select, id(s) as id_b\",{a:$neodash_project}) YIELD value \nRETURN value.StudyRoot as StudyRoot, \nvalue.TrialID as `Trial ID`,\nvalue.Acronym as Acronym,\nvalue.Date as Date,\nvalue.Version as Version,\nvalue.Status as Status,\nvalue.Latest as Latest, \nvalue.Select as Select,\nvalue.id_b as __id_b order by `Trial ID`, Date", + "query": "CALL apoc.when(size($neodash_project)=0,\"match(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by StudyRoot, date, Latest DESC\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest\nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Compare' as Select, id(s) as id_b\",\n\"match(p:Project)-[:HAS_FIELD]->(:StudyProjectField)<-[:HAS_PROJECT]-(s:StudyValue) \nwhere p.project_number in $a\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nwith r0, s, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid\nwith s, trialid\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct s,trialid,sr.uid as StudyRoot, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by StudyRoot, date, Latest DESC\nwith s,StudyRoot, s.study_acronym as acronym, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest\nreturn StudyRoot, trialid as TrialID, acronym as Acronym, Date, Version, Latest,Status, 'Compare' as Select, id(s) as id_b\",{a:$neodash_project}) YIELD value \nRETURN value.StudyRoot as StudyRoot, \nvalue.TrialID as `Trial ID`,\nvalue.Acronym as Acronym,\nvalue.Date as Date,\nvalue.Version as Version,\nvalue.Status as Status,\nvalue.Latest as Latest, \nvalue.Select as Select,\nvalue.id_b as __id_b order by `Trial ID`, Date", "width": 24, "height": 4, "x": 0, @@ -128,7 +123,7 @@ { "id": "b2cda169-8f28-48c2-b83b-718696fad031", "title": "Selected Studies", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", "width": 24, "height": 3, "x": 0, @@ -213,7 +208,7 @@ { "id": "8d648671-d1eb-458a-8b09-90b8cf10ed4d", "title": "Current Study Selection", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", "width": 24, "height": 3, "x": 0, @@ -235,7 +230,7 @@ { "id": "9fddd824-7a71-4ad5-a73b-389c94f87dc1", "title": "Current Study Selection", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", "width": 24, "height": 3, "x": 0, @@ -329,7 +324,7 @@ { "id": "a27b17d9-032d-4bd9-939b-09099d10b49c", "title": "Current Study Selection", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", "width": 24, "height": 3, "x": 0, @@ -346,7 +341,7 @@ { "id": "fd6d2fa7-8639-4db1-ada2-fce7103a0739", "title": "Study Criteria", - "query": "call apoc.when($neodash_differences_only contains 'Yes',\"match(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[r3]->(endp:StudyCriteria)-[r3_1]->(crit_val:CriteriaValue)\nwith study, crit_val, \ncrit_val.name_plain as Criteria\nwith apoc.map.fromPairs(collect([study,Criteria])) as map\nwith map['Base'] as `Base - Criteria`, map['Compare'] as `Compare - Criteria`,\nCASE WHEN map['Base'] = map['Compare'] THEN 'no' ELSE CASE WHEN map['Base'] is null and map['Compare'] is null THEN 'no' ELSE 'yes' END END as Diff\nwith `Base - Criteria`,`Compare - Criteria`, Diff where Diff='yes'\nreturn `Base - Criteria`,`Compare - Criteria`, Diff\",\"match(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[r3]->(endp:StudyCriteria)-[r3_1]->(crit_val:CriteriaValue)\nwith study, crit_val, \ncrit_val.name_plain as Criteria\nwith apoc.map.fromPairs(collect([study,Criteria])) as map\nwith map['Base'] as `Base - Criteria`, map['Compare'] as `Compare - Criteria`,\nCASE WHEN map['Base'] = map['Compare'] THEN 'no' ELSE CASE WHEN map['Base'] is null and map['Compare'] is null THEN 'no' ELSE 'yes' END END as Diff \nreturn `Base - Criteria`,`Compare - Criteria`, Diff\",{neodash_studya:$neodash_studya, neodash_studyb:$neodash_studyb}) YIELD value\nreturn value.`Base - Criteria` as `Base - Criteria`,\nvalue.`Compare - Criteria` as `Compare - Criteria`, \nvalue.Diff as __Diff", + "query": "call apoc.when($neodash_differences_only contains 'Yes',\"match(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[r3]->(endp:StudyCriteria)-[r3_1]->(crit_val:CriteriaValue)\nOPTIONAL MATCH(crit_val)<-[x1]-(crit_root:CriteriaRoot)<-[x2]-(crit_temp_root:CriteriaTemplateRoot)-[x3:HAS_TYPE]->(context:CTTermContext)-[x4]->(term_root:CTTermRoot)<-[x5]-(crit_cat:CTCodelistTerm)<-[x6]-(cl_root:CTCodelistRoot)<-[x7]-(catalog:CTCatalogue{name:'PROTOCOL CT'})\nwith study, crit_cat, endp.order as crit_order, crit_val.name_plain as Criteria order by crit_order\nwith crit_cat, crit_order, Criteria, apoc.map.fromPairs(collect([study,Criteria])) as map\nwith crit_cat, crit_order, map['Base'] as `Base - Criteria`, map['Compare'] as `Compare - Criteria`,\nCASE WHEN map['Base'] = map['Compare'] THEN 'no' ELSE CASE WHEN map['Base'] is null and map['Compare'] is null THEN 'no' ELSE 'yes' END END as Diff\nwith crit_cat, crit_order, `Base - Criteria`,`Compare - Criteria`, Diff where Diff='yes'\nreturn crit_cat.submission_value as Category, `Base - Criteria`,`Compare - Criteria`, Diff order by crit_order\",\n\"match(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[r3]->(endp:StudyCriteria)-[r3_1]->(crit_val:CriteriaValue)\nOPTIONAL MATCH(crit_val)<-[x1]-(crit_root:CriteriaRoot)<-[x2]-(crit_temp_root:CriteriaTemplateRoot)-[x3:HAS_TYPE]->(context:CTTermContext)-[x4]->(term_root:CTTermRoot)<-[x5]-(crit_cat:CTCodelistTerm)<-[x6]-(cl_root:CTCodelistRoot)<-[x7]-(catalog:CTCatalogue{name:'PROTOCOL CT'})\nwith study, crit_cat, endp.order as crit_order, crit_val.name_plain as Criteria\nwith crit_cat, crit_order,Criteria, apoc.map.fromPairs(collect([study,Criteria])) as map\nwith crit_cat, crit_order, map['Base'] as `Base - Criteria`, map['Compare'] as `Compare - Criteria`,\nCASE WHEN map['Base'] = map['Compare'] THEN 'no' ELSE CASE WHEN map['Base'] is null and map['Compare'] is null THEN 'no' ELSE 'yes' END END as Diff\nwith crit_cat, crit_order, `Base - Criteria`,`Compare - Criteria`, Diff\nreturn crit_cat.submission_value as Category, crit_order, `Base - Criteria`,`Compare - Criteria`, Diff order by crit_order\",{neodash_studya:$neodash_studya, neodash_studyb:$neodash_studyb}) YIELD value\nreturn value.Category as Category, \nvalue.crit_order as `#`,\nvalue.`Base - Criteria` as `Base - Criteria`,\nvalue.`Compare - Criteria` as `Compare - Criteria`, \nvalue.Diff as __Diff order by Category desc", "width": 24, "height": 4, "x": 0, @@ -375,7 +370,7 @@ "fullscreenEnabled": true, "refreshButtonEnabled": true, "noDataMessage": "No differences found", - "columnWidths": "[8,8,1]", + "columnWidths": "[1,1,8,8,1]", "wrapContent": true } } @@ -385,47 +380,88 @@ "title": "Planned Visits", "reports": [ { - "id": "3f881d70-89ad-4326-bff5-b623eb6f4d24", - "title": "Planned Study Start Date", - "query": "RETURN true;", - "width": 12, + "id": "405fb205-c5e2-4e1d-841a-bfb85182e7cf", + "title": "Change Type", + "query": "with [\"Added\", \"No Change\", \"Deleted\", \"Changed\"] as list\nunwind(list) as Status\nreturn Status\n\n", + "width": 6, "height": 3, - "x": 12, + "x": 0, "y": 0, - "type": "select", + "type": "table", "selection": {}, "settings": { - "type": "Date Picker", - "entityType": "SSTDTC", - "parameterName": "neodash_sstdtc" - }, - "schema": [] + "compact": true, + "styleRules": [ + { + "field": "Status", + "condition": "=", + "value": "Added", + "customization": "row color", + "customizationValue": "#00B5FF6E" + }, + { + "field": "Status", + "condition": "=", + "value": "No Change", + "customization": "row color", + "customizationValue": "#5FE8866E" + }, + { + "field": "Status", + "condition": "=", + "value": "Deleted", + "customization": "row color", + "customizationValue": "#FF11116E" + }, + { + "field": "Status", + "condition": "=", + "value": "Changed", + "customization": "row color", + "customizationValue": "#FFA4006E" + } + ] + } }, { "id": "f7b1ef51-afc4-4baf-a7fb-7b4a5a9becba", "title": "Visit Attribute Changes", - "query": "call apoc.when($neodash_differences_only contains 'Yes', \n//First\n\"match(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[:HAS_STUDY_VISIT]->(vis)\noptional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\noptional match(vis)-[r]->(x_r)-[:HAS_VERSION]->(x) where not type(r)='HAS_VISIT_NAME' \n with study, x, [k in keys(vis) where not k='uid'] as vis_keys, properties(vis) as vis_props, vis_name.name as `Visit Name`, vis.visit_number as `Visit Number`, [i in labels(x) where not (i contains 'ConceptValue' or i contains 'Template' or i contains 'Numeric' or i contains 'VisitName') ][0] as types\nwith study, `Visit Name`, `Visit Number`, substring(types,0, size(types)-5) as type, x, vis_keys, vis_props, CASE when not vis_keys is null THEN range(0,size(vis_keys)-1,1) else [0] END AS coll_size \nwith study, `Visit Name`, `Visit Number`, type, CASE when x.value is null then x.name ELSE x.value+' ('+x.name+')' END as value, vis_keys, vis_props, coll_size \nwith study, `Visit Name`, `Visit Number`, collect(apoc.map.fromPairs([[type,value]])) as map, [k in vis_keys | apoc.map.fromPairs([[apoc.text.capitalize(replace(k,'_',' ')),apoc.text.capitalize(toLower(replace(toString(vis_props[k]),'_',' ')))]])] as add_maps\nwith study, `Visit Name`, `Visit Number`, CASE WHEN not add_maps is null THEN apoc.map.mergeList(apoc.coll.flatten([map,add_maps])) ELSE apoc.map.mergeList(map) END as map \nwith study, `Visit Name`, `Visit Number`, map, CASE when not map is null THEN range(0,size(keys(map))-1,1) ELSE [0] END AS coll_size \nUNWIND coll_size AS idx\nwith study, `Visit Name`, `Visit Number`, \nCASE WHEN not isEmpty(map) THEN keys(map)[idx] ElSE null END as type, CASE WHEN not isEmpty(map) THEN map[keys(map)[idx]] ELSE null END as value\nwith `Visit Name`, `Visit Number`, type, apoc.map.fromPairs(collect([study,value])) as visit_info_map\nWITH\n`Visit Name`, \n`Visit Number`, \ntype as `Visit Property Type`, \nvisit_info_map['Base'] as Base, \nvisit_info_map['Compare'] as Compare,\nCASE WHEN visit_info_map['Base'] = visit_info_map['Compare'] THEN 'no' ELSE 'yes' END as Changed order by `Visit Number`,`Visit Property Type` \nWITH `Visit Name`, `Visit Number`,`Visit Property Type`, Base, Compare, Changed where Changed='yes'\nreturn `Visit Name`, `Visit Number`,`Visit Property Type`, Base, Compare, Changed\",\n//second\n\"\nmatch(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[:HAS_STUDY_VISIT]->(vis)\noptional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\noptional match(vis)-[r]->(x_r)-[:HAS_VERSION]->(x) where not type(r)='HAS_VISIT_NAME' \n with study, x, [k in keys(vis) where not k='uid'] as vis_keys, properties(vis) as vis_props, vis_name.name as `Visit Name`, vis.visit_number as `Visit Number`, [i in labels(x) where not (i contains 'ConceptValue' or i contains 'Template' or i contains 'Numeric' or i contains 'VisitName') ][0] as types\nwith study, `Visit Name`, `Visit Number`, substring(types,0, size(types)-5) as type, x, vis_keys, vis_props, CASE when not vis_keys is null THEN range(0,size(vis_keys)-1,1) else [0] END AS coll_size \nwith study, `Visit Name`, `Visit Number`, type, CASE when x.value is null then x.name ELSE x.value+' ('+x.name+')' END as value, vis_keys, vis_props, coll_size \nwith study, `Visit Name`, `Visit Number`, collect(apoc.map.fromPairs([[type,value]])) as map, [k in vis_keys | apoc.map.fromPairs([[apoc.text.capitalize(replace(k,'_',' ')),apoc.text.capitalize(toLower(replace(toString(vis_props[k]),'_',' ')))]])] as add_maps\nwith study, `Visit Name`, `Visit Number`, CASE WHEN not add_maps is null THEN apoc.map.mergeList(apoc.coll.flatten([map,add_maps])) ELSE apoc.map.mergeList(map) END as map \nwith study, `Visit Name`, `Visit Number`, map, CASE when not map is null THEN range(0,size(keys(map))-1,1) ELSE [0] END AS coll_size \nUNWIND coll_size AS idx\nwith study, `Visit Name`, `Visit Number`, \nCASE WHEN not isEmpty(map) THEN keys(map)[idx] ElSE null END as type, CASE WHEN not isEmpty(map) THEN map[keys(map)[idx]] ELSE null END as value\nwith `Visit Name`, `Visit Number`, type, apoc.map.fromPairs(collect([study,value])) as visit_info_map\nWITH\n`Visit Name`, \n`Visit Number`, \ntype as `Visit Property Type`, \nvisit_info_map['Base'] as Base, \nvisit_info_map['Compare'] as Compare,\nCASE WHEN visit_info_map['Base'] = visit_info_map['Compare'] THEN 'no' ELSE 'yes' END as Changed order by `Visit Number`,`Visit Property Type` \nWITH `Visit Name`, `Visit Number`,`Visit Property Type`, Base, Compare, Changed\nreturn `Visit Name`, `Visit Number`,`Visit Property Type`, Base, Compare, Changed\n\",{neodash_studya:$neodash_studya, neodash_studyb:$neodash_studyb}) YIELD value\nreturn value.`Visit Name` as`Visit Name`, \nvalue.`Visit Number` as `Visit Number`, \nvalue.`Visit Property Type` as `Visit Property Type`, \nvalue.Base as Base, \nvalue.Compare as Compare,\nvalue.Changed as __Diff order by `Visit Number`,`Visit Property Type`", + "query": "CALL\n apoc.when(\n $neodash_differences_only CONTAINS 'Yes',\n //First\n \"match(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[:HAS_STUDY_VISIT]->(vis)\noptional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\noptional match(vis)-[r]->(x_r)-[:HAS_VERSION]->(x) where not type(r)='HAS_VISIT_NAME' \nwith study, x, [k in keys(vis) where not k='uid'] as vis_keys, properties(vis) as vis_props, vis.unique_visit_number as `Unique #`, vis_name.name as `Visit Name`, vis.short_visit_label as `Short Name`,vis.visit_number as `Visit Number`, [i in labels(x) where not (i contains 'ConceptValue' or i contains 'Template' or i contains 'Numeric' or i contains 'VisitName') ][0] as types\nwith study, `Unique #`,`Visit Name`, `Short Name`, `Visit Number`, substring(types,0, size(types)-5) as type, x, vis_keys, vis_props, CASE when not vis_keys is null THEN range(0,size(vis_keys)-1,1) else [0] END AS coll_size \nwith study, `Unique #`, `Visit Name`, `Short Name`, `Visit Number`, type, CASE when x.value is null then x.name ELSE x.value+' ('+x.name+')' END as value, vis_keys, vis_props, coll_size \nwith study, `Unique #`, `Visit Name`, `Short Name`, `Visit Number`, collect(apoc.map.fromPairs([[type,value]])) as map, [k in vis_keys | apoc.map.fromPairs([[apoc.text.capitalize(replace(k,'_',' ')),apoc.text.capitalize(toLower(replace(toString(vis_props[k]),'_',' ')))]])] as add_maps\nwith study, `Unique #`, `Visit Name`, `Short Name`, `Visit Number`, CASE WHEN not add_maps is null THEN apoc.map.mergeList(apoc.coll.flatten([map,add_maps])) ELSE apoc.map.mergeList(map) END as map \nwith study, `Unique #`, `Visit Name`, `Short Name`, `Visit Number`, map, CASE when not map is null THEN range(0,size(keys(map))-1,1) ELSE [0] END AS coll_size \nUNWIND coll_size AS idx\nwith study, `Unique #`, `Visit Name`, `Short Name`,`Visit Number`, \nCASE WHEN not isEmpty(map) THEN keys(map)[idx] ElSE null END as type, CASE WHEN not isEmpty(map) THEN map[keys(map)[idx]] ELSE null END as value\nwith `Unique #`, `Visit Name`, `Short Name`,`Visit Number`, type, apoc.map.fromPairs(collect([study,value])) as visit_info_map\nWITH `Unique #`,\n`Visit Name`, \n`Short Name`,\n`Visit Number`, \ntype as `Visit Property Type`, \nvisit_info_map['Base'] as Base, \nvisit_info_map['Compare'] as Compare,\nCASE WHEN visit_info_map['Base'] IS NULL AND visit_info_map['Compare'] IS NOT NULL THEN 'Added' WHEN visit_info_map['Base'] IS NOT NULL AND visit_info_map['Compare'] IS NULL THEN 'Deleted' WHEN visit_info_map['Base'] = visit_info_map['Compare'] THEN 'No Change' ELSE 'Changed' END as `Change Type` order by `Visit Number`,`Visit Property Type` \nWITH `Unique #`, `Visit Name`, `Short Name`, `Visit Number`,`Visit Property Type`, Base, Compare, `Change Type` where `Change Type`<>'No Change'\nreturn `Unique #`, `Visit Name`, `Short Name`, `Visit Number`,`Visit Property Type`, Base, Compare, `Change Type`\",\n //second\n \"\nmatch(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[:HAS_STUDY_VISIT]->(vis)\noptional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\noptional match(vis)-[r]->(x_r)-[:HAS_VERSION]->(x) where not type(r)='HAS_VISIT_NAME' \nwith study, x, [k in keys(vis) where not k='uid'] as vis_keys, properties(vis) as vis_props, vis.unique_visit_number as `Unique #`,vis_name.name as `Visit Name`, vis.short_visit_label as `Short Name`,vis.visit_number as `Visit Number`, [i in labels(x) where not (i contains 'ConceptValue' or i contains 'Template' or i contains 'Numeric' or i contains 'VisitName') ][0] as types\nwith study, `Unique #`,`Visit Name`, `Short Name`, `Visit Number`, substring(types,0, size(types)-5) as type, x, vis_keys, vis_props, CASE when not vis_keys is null THEN range(0,size(vis_keys)-1,1) else [0] END AS coll_size \nwith study, `Unique #`,`Visit Name`, `Short Name`, `Visit Number`, type, CASE when x.value is null then x.name ELSE x.value+' ('+x.name+')' END as value, vis_keys, vis_props, coll_size \nwith study, `Unique #`,`Visit Name`, `Short Name`, `Visit Number`, collect(apoc.map.fromPairs([[type,value]])) as map, [k in vis_keys | apoc.map.fromPairs([[apoc.text.capitalize(replace(k,'_',' ')),apoc.text.capitalize(toLower(replace(toString(vis_props[k]),'_',' ')))]])] as add_maps\nwith study, `Unique #`,`Visit Name`, `Short Name`, `Visit Number`, CASE WHEN not add_maps is null THEN apoc.map.mergeList(apoc.coll.flatten([map,add_maps])) ELSE apoc.map.mergeList(map) END as map \nwith study, `Unique #`,`Visit Name`, `Short Name`, `Visit Number`, map, CASE when not map is null THEN range(0,size(keys(map))-1,1) ELSE [0] END AS coll_size \nUNWIND coll_size AS idx\nwith study, `Unique #`,`Visit Name`, `Short Name`,`Visit Number`, \nCASE WHEN not isEmpty(map) THEN keys(map)[idx] ElSE null END as type, CASE WHEN not isEmpty(map) THEN map[keys(map)[idx]] ELSE null END as value\nwith `Unique #`,`Visit Name`, `Short Name`,`Visit Number`, type, apoc.map.fromPairs(collect([study,value])) as visit_info_map\nWITH `Unique #`,\n`Visit Name`, \n`Short Name`,\n`Visit Number`, \ntype as `Visit Property Type`, \nvisit_info_map['Base'] as Base, \nvisit_info_map['Compare'] as Compare,\nCASE WHEN visit_info_map['Base'] IS NULL AND visit_info_map['Compare'] IS NOT NULL THEN 'Added' WHEN visit_info_map['Base'] IS NOT NULL AND visit_info_map['Compare'] IS NULL THEN 'Deleted' WHEN visit_info_map['Base'] = visit_info_map['Compare'] THEN 'No Change' ELSE 'Changed' END as `Change Type` order by `Visit Number`,`Visit Property Type` \nWITH `Unique #`, `Visit Name`, `Short Name`, `Visit Number`,`Visit Property Type`, Base, Compare, `Change Type` \nreturn `Unique #`, `Visit Name`, `Short Name`, `Visit Number`,`Visit Property Type`, Base, Compare, `Change Type`\",\n {neodash_studya: $neodash_studya, neodash_studyb: $neodash_studyb}\n )\n YIELD value\nRETURN\n value.`Unique #` as `Unique #`,\n value.`Visit Name` AS `Visit Name`,\n value.`Short Name` AS `Short Name`,\n value.`Visit Number` AS `Visit Number`,\n value.`Visit Property Type` AS `Visit Property Type`,\n value.Base AS Base,\n value.Compare AS Compare,\n value.`Change Type` AS __Diff\nORDER BY toInteger(`Unique #`), `Visit Number`, `Short Name`, `Visit Property Type`", "width": 24, - "height": 4, + "height": 3, "x": 0, - "y": 8, + "y": 3, "type": "table", "selection": {}, "settings": { "refreshButtonEnabled": true, - "columnWidths": "[1,1,2,2,2,0.5]", + "columnWidths": "[0.5,1,1,0.7,2,2,2]", "styleRules": [ { "field": "__Diff", "condition": "=", - "value": "yes", + "value": "Added", + "customization": "row color", + "customizationValue": "#00B5FF6E" + }, + { + "field": "__Diff", + "condition": "=", + "value": "Deleted", "customization": "row color", "customizationValue": "#FF11116E" }, { "field": "__Diff", "condition": "=", - "value": "no", + "value": "Changed", + "customization": "row color", + "customizationValue": "#FFA4006E" + }, + { + "field": "__Diff", + "condition": "=", + "value": "No Change", "customization": "row color", "customizationValue": "#5FE8866E" } @@ -439,10 +475,10 @@ { "id": "71058c94-7543-428d-b272-b6befaea92f8", "title": "Current Study Selection", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", - "width": 12, + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", + "width": 18, "height": 3, - "x": 0, + "x": 6, "y": 0, "type": "table", "selection": {}, @@ -451,53 +487,6 @@ "transposed": true, "compact": true } - }, - { - "id": "63a77779-13f2-4e2b-a8d9-b6f9fd765e92", - "title": "Visit Timeline Differences", - "query": "match(st:StudyValue) where id(st) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith collect(st) as st\ncall apoc.when(size(st)>0,\n\"with $t as t\nUNWIND t as s \nwith s, CASE when id(s)=toInteger($studya) then 'Base' ELSE 'Compare' END as study\noptional match (s)-[:HAS_STUDY_VISIT]->(vis) \nWITH distinct s, apoc.coll.toSet(collect(vis.short_visit_label)) as vis, study\ncall apoc.when(size(vis)=0,\\\"return $study as Study, 'FALSE' as HasVisit\\\",\\\"return $study as Study, 'TRUE' as HasVisit\\\",{study:study,vis:vis}) yield value \nwith apoc.map.fromPairs(collect([value.Study,value.HasVisit])) as visitmap\nwith visitmap\ncall apoc.case([\n visitmap['Base']='TRUE' and visitmap['Compare']='TRUE', \n \\\"with $t as t\n UNWIND t as s \n with s, CASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as study\n // optional match (s)-[:HAS_STUDY_VISIT]->(vis) where not vis.visit_class ='SPECIAL_VISIT'\n optional match(s)-[:HAS_STUDY_VISIT]->(vis)-[:HAS_STUDY_DURATION_DAYS]->(dur_day_root:StudyDurationDaysRoot)-[:HAS_VERSION]->(dur_days:StudyDurationDaysValue)\n optional match(vis)-[:HAS_STUDY_DURATION_WEEKS]->(dur_wk_root:StudyDurationWeeksRoot)-[:HAS_VERSION]->(dur_week:StudyDurationWeeksValue)\n optional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\n with s, study, vis, dur_days, vis_name order by id(s), vis.visit_number\n with distinct s, study, dur_days.value as duration,vis, \n CASE WHEN study='Base' THEN {duration:dur_days.value,visit_name:vis_name.name+'; Day: '+toString(toInteger(dur_days.value)), endDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), startDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), visit_number:vis.visit_number,study_id:study} ELSE {duration:dur_days.value,visit_name:vis_name.name+'; Day: '+toString(toInteger(dur_days.value)), endDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), startDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), visit_number:vis.visit_number,study_id:study} END as prop order by duration, study\n with duration, collect(distinct prop) as props\n with duration, [x in range(0,size(props)-1,1) |\n CASE WHEN size(props)=2 and not props[0].visit_number = props[1].visit_number \n THEN apoc.create.vNode([\\\\\\\"Visit\\\\\\\"],\n {visit_number:(\\\\\\\"

    Base: \\\\\\\" + props[0].visit_number + \\\\\\\"

    Comp: \\\\\\\" + props[1].visit_number + \\\\\\\"

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:(\\\\\\\"

    Base: \\\\\\\" + props[0].visit_name + \\\\\\\"

    Comp: \\\\\\\" + props[1].visit_name + \\\\\\\"

    \\\\\\\"),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) \n ELSE \n CASE WHEN size(props)=2 and props[0].visit_number = props[1].visit_number\n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number: props[0].visit_number,\n duration:toInteger(duration),\n visit_name:substring(props[x].study_id,0,4)+': '+props[0].visit_name,\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) ELSE \n CASE WHEN size(props)<2 and props[x].study_id='Base' \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: \\\\\\\" + props[x].visit_number + \\\\\\\"

    Comp: Null

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:( \\\\\\\"

    Base: \\\\\\\" + props[x].visit_name + \\\\\\\"

    Comp: Null

    \\\\\\\"),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) ELSE\n CASE WHEN size(props)<2 and props[x].study_id='Compare' \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: Null

    Comp: \\\\\\\" + props[x].visit_number + \\\\\\\"

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:( \\\\\\\"

    Base: Null

    Comp: \\\\\\\" + props[x].visit_name),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n })END END END END] as v_visits\n with duration, v_visits\n UNWIND v_visits as v_visit\n with duration, apoc.any.property(v_visit,'study_id') as study, v_visit\n with study, collect(duration) as durations, collect(v_visit) as v_visits\n with study, durations, v_visits, [n in RANGE(0,size(v_visits)-2) | apoc.create.vRelationship(v_visits[n], \\\\\\\"FOLLOWS \\\\\\\",{type: \\\\\\\"logical \\\\\\\"},v_visits[n+1]) ]as v_rels, range(0,size(v_visits)-1,1) AS coll_size \n with study, durations, v_visits,v_rels, coll_size \n UNWIND coll_size AS idx\n WITH study, durations[idx] as duration,\n v_visits[idx] as v_visit, v_rels[idx] as v_rel\n return v_visit,v_rel\\\",\n visitmap['Base']='TRUE' and visitmap['Compare']='FALSE', \n \\\"with $t as t\n UNWIND t as s \n with s, CASE when id(s)=toInteger($neodash_studya) THEN 'Base' END as study\n // optional match (s)-[:HAS_STUDY_VISIT]->(vis) where not vis.visit_class ='SPECIAL_VISIT'\n optional match(s)-[:HAS_STUDY_VISIT]->(vis)-[:HAS_STUDY_DURATION_DAYS]->(dur_day_root:StudyDurationDaysRoot)-[:HAS_VERSION]->(dur_days:StudyDurationDaysValue)\n optional match(vis)-[:HAS_STUDY_DURATION_WEEKS]->(dur_wk_root:StudyDurationWeeksRoot)-[:HAS_VERSION]->(dur_week:StudyDurationWeeksValue)\n optional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\n with s, study, vis, dur_days, vis_name order by id(s), vis.visit_number\n with distinct s, study, dur_days.value as duration,vis, \n CASE WHEN study='Base' THEN {duration:dur_days.value,visit_name:vis_name.name+'; Day: '+toString(toInteger(dur_days.value)), endDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), startDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), visit_number:vis.visit_number,study_id:study} END as prop order by duration, study\n with duration, collect(distinct prop) as props\n with duration, [x in range(0,size(props)-1,1) |\n CASE WHEN size(props)=2 and not props[0].visit_number = props[1].visit_number \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: \\\\\\\" + props[0].visit_number + \\\\\\\"

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:( \\\\\\\"

    Base: \\\\\\\" + props[0].visit_name),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) \n ELSE \n CASE WHEN size(props)=2 and props[0].visit_number = props[1].visit_number\n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number: props[0].visit_number,\n duration:toInteger(duration),\n visit_name:substring(props[x].study_id,0,4)+': '+props[0].visit_name,\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) ELSE \n CASE WHEN size(props)<2 and props[x].study_id='Base' \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: \\\\\\\" + props[x].visit_number + \\\\\\\"

    Comp: Null

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:( \\\\\\\"

    Base: \\\\\\\" + props[x].visit_name + \\\\\\\"

    Comp: Null

    \\\\\\\"),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) ELSE\n CASE WHEN size(props)<2 and props[x].study_id='Compare' \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: Null

    Comp: \\\\\\\" + props[x].visit_number + \\\\\\\"

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:(\\\\\\\"

    Base: Null

    Comp: \\\\\\\" + props[x].visit_name),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n })END END END END] as v_visits\n with distinct duration, v_visits\n UNWIND v_visits as v_visit\n with duration, apoc.any.property(v_visit,'study_id') as study, v_visit\n with study, collect(duration) as durations, collect(v_visit) as v_visits\n with study, durations, v_visits, [n in RANGE(0,size(v_visits)-2) | apoc.create.vRelationship(v_visits[n], \\\\\\\"FOLLOWS \\\\\\\",{type: \\\\\\\"logical \\\\\\\"},v_visits[n+1]) ]as v_rels, range(0,size(v_visits)-1,1) AS coll_size \n with study, durations, v_visits,v_rels, coll_size \n UNWIND coll_size AS idx\n WITH study, durations[idx] as duration,\n v_visits[idx] as v_visit, v_rels[idx] as v_rel\n return v_visit,v_rel\\\",\n visitmap['Base']='FALSE' and visitmap['Compare']='TRUE', \n \\\"with $t as t\n UNWIND t as s \n with s, CASE when id(s)=toInteger($neodash_studyb) then 'Compare' END as study\n // optional match (s)-[:HAS_STUDY_VISIT]->(vis) where not vis.visit_class ='SPECIAL_VISIT'\n optional match(s)-[:HAS_STUDY_VISIT]->(vis)-[:HAS_STUDY_DURATION_DAYS]->(dur_day_root:StudyDurationDaysRoot)-[:HAS_VERSION]->(dur_days:StudyDurationDaysValue)\n optional match(vis)-[:HAS_STUDY_DURATION_WEEKS]->(dur_wk_root:StudyDurationWeeksRoot)-[:HAS_VERSION]->(dur_week:StudyDurationWeeksValue)\n optional match(vis)-[:HAS_VISIT_NAME]->(vis_name_root)-[:HAS_VERSION]->(vis_name:VisitNameValue)\n with s, study, vis, dur_days, vis_name order by id(s), vis.visit_number\n with distinct s, study, dur_days.value as duration,vis, \n CASE WHEN study='Compare' THEN {duration:dur_days.value,visit_name:vis_name.name+'; Day: '+toString(toInteger(dur_days.value)), endDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), startDate:date($neodash_sstdtc)+Duration({days:(dur_days.value)}), visit_number:vis.visit_number,study_id:study} END as prop order by duration, study\n with duration, collect(distinct prop) as props\n with duration, [x in range(0,size(props)-1,1) |\n CASE WHEN size(props)=2 and not props[0].visit_number = props[1].visit_number \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: \\\\\\\" + props[0].visit_number + \\\\\\\"

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:( \\\\\\\"

    Base: \\\\\\\" + props[0].visit_name),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) \n ELSE \n CASE WHEN size(props)=2 and props[0].visit_number = props[1].visit_number\n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number: props[0].visit_number,\n duration:toInteger(duration),\n visit_name:substring(props[x].study_id,0,4)+': '+props[0].visit_name,\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) ELSE \n CASE WHEN size(props)<2 and props[x].study_id='Base' \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: \\\\\\\" + props[x].visit_number + \\\\\\\"

    Comp: Null

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:( \\\\\\\"

    Base: \\\\\\\" + props[x].visit_name + \\\\\\\"

    Comp: Null

    \\\\\\\"),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n }) ELSE\n CASE WHEN size(props)<2 and props[x].study_id='Compare' \n THEN apoc.create.vNode([ \\\\\\\"Visit \\\\\\\"],\n {visit_number:( \\\\\\\"

    Base: Null

    Comp: \\\\\\\" + props[x].visit_number + \\\\\\\"

    \\\\\\\"),\n duration:toInteger(duration),\n visit_name:(\\\\\\\"

    Base: Null

    Comp: \\\\\\\" + props[x].visit_name),\n startDate:date($neodash_sstdtc)+Duration({days:(duration)}), \n endDate:date($neodash_sstdtc)+Duration({days:(duration)}),\n study_id:props[x].study_id,\n visit_label:substring(props[x].study_id,0,4)+': '+props[x].visit_name\n })END END END END] as v_visits\n with distinct duration, v_visits\n UNWIND v_visits as v_visit\n with duration, apoc.any.property(v_visit,'study_id') as study, v_visit\n with study, collect(duration) as durations, collect(v_visit) as v_visits\n with study, durations, v_visits, [n in RANGE(0,size(v_visits)-2) | apoc.create.vRelationship(v_visits[n], \\\\\\\"FOLLOWS \\\\\\\",{type: \\\\\\\"logical \\\\\\\"},v_visits[n+1]) ]as v_rels, range(0,size(v_visits)-1,1) AS coll_size \n with study, durations, v_visits,v_rels, coll_size \n UNWIND coll_size AS idx\n WITH study, durations[idx] as duration,\n v_visits[idx] as v_visit, v_rels[idx] as v_rel\n return v_visit,v_rel\\\"],\n \\\"RETURN NULL as v_visit, NULL as v_rel\\\",{t:$t,neodash_studya:$studya,neodash_studyb:$studyb,neodash_sstdtc:$sstdtc}) YIELD value \nwith distinct value\nMATCH (n:Library) where value.v_visit is not null\nreturn distinct value.v_visit as v_visit,value.v_rel as v_rel\" \n,\n\"RETURN NULL as v_visit, NULL as v_rel\",{t:st,sstdtc:$neodash_sstdtc, studya:$neodash_studya, studyb:$neodash_studyb}) YIELD value \nwith distinct value\nMATCH (n:Library) where value.v_visit is not null\nreturn distinct value.v_visit as v_visit, value.v_rel as v_rel", - "width": 24, - "height": 5, - "x": 0, - "y": 3, - "type": "gantt", - "selection": { - "Visit ": "(label)" - }, - "settings": { - "refreshButtonEnabled": true, - "viewMode": "auto", - "styleRules": [ - { - "field": "FOLLOWS.study", - "condition": "=", - "value": "$neodash_studya", - "customization": "node color", - "customizationValue": "blue" - } - ], - "barColor": "#10276F", - "fullscreenEnabled": true, - "nameProperty": "visit_label", - "orderProperty": "study_id", - "downloadImageEnabled": true - }, - "schema": [ - [ - "Visit ", - "duration", - "visit_label", - "endDate", - "study_id", - "visit_number", - "visit_name", - "startDate" - ], - [ - "FOLLOWS ", - "type" - ] - ] } ] }, @@ -556,7 +545,7 @@ { "id": "a25cbf27-c432-4b66-a6ab-103b7358087c", "title": "Current Study Selection", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", "width": 18, "height": 3, "x": 6, @@ -679,7 +668,7 @@ { "id": "07ad5bb7-ad85-4d87-b56b-838995557506", "title": "Current Study Selection", - "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, s.study_id_prefix+'-'+s.study_number as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\noptional match(s)<-[r:AFTER]-(sact:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, sact.date as date order by trialid, sact.date\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version \nreturn Study,\ntrialid as TrialID, Date, Version, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version\n\n\n", + "query": "MATCH (sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue)\nWHERE id(s) IN [toInteger($neodash_studya), toInteger($neodash_studyb)]\nWITH\n CASE\n WHEN count(distinct sr) > 1 THEN 'Across Study'\n ELSE 'Within Study'\n END AS compare_type\nWITH compare_type\nmatch(sr:StudyRoot)-[r0:HAS_VERSION]->(s:StudyValue) where id(s) in[toInteger($neodash_studya),toInteger($neodash_studyb)]\nwith compare_type,r0, s, sr, CASE WHEN s.subpart_id is not null THEN s.study_id_prefix+'-'+s.study_number+'-'+s.subpart_id ELSE s.study_id_prefix+'-'+s.study_number END as trialid, \nCASE when id(s)=toInteger($neodash_studya) then 'Base' ELSE 'Compare' END as Study\nwith compare_type,s, sr, trialid, Study\nmatch (sr:StudyRoot)-[r0:HAS_VERSION]->(s)\nOPTIONAL MATCH (sr)-[r1:LATEST]->(s)\noptional match(s)<-[r_b:BEFORE]-(sact_before:StudyAction)\noptional match(s)<-[r_a:AFTER]-(sact_after:StudyAction)\nwith distinct compare_type,s,sr.uid as StudyRoot,Study, trialid, collect(r0.status) as statuses ,collect(r0.version) as versions, type(r1) as Latest,coalesce(sact_before.date,sact_after.date) as date order by trialid, date, Latest DESC\nwith compare_type,s,StudyRoot,Study, trialid, split(apoc.temporal.format(date, 'iso_local_date_time'),'.')[0] as Date, case when 'LOCKED' in statuses then 'LOCKED' else 'DRAFT' END as Status,\napoc.text.join(apoc.coll.toSet(versions),'') as Version,Latest \nreturn Study,\ntrialid as TrialID, Date, Version, Latest, Status, compare_type as `Compare Type`, StudyRoot order by Study, Version", "width": 18, "height": 3, "x": 6, diff --git a/neo4j-mdr-db/project_documentation/odm_csv_metadata.md b/neo4j-mdr-db/project_documentation/odm_csv_metadata.md index 0e213a15..c56b97a4 100644 --- a/neo4j-mdr-db/project_documentation/odm_csv_metadata.md +++ b/neo4j-mdr-db/project_documentation/odm_csv_metadata.md @@ -10,7 +10,7 @@ The csv form is collecting the following information: | oid | Provide here a Unique Object Identifier like for example F.DM for the Informed Consent & Demography form | | name | Please report here the name of the form as written in the dark bleue cell on the first page of the Form (example: Informed Consent and Demography) | | prompt | Please provide a short value that could be used instead of the name or the description | -| repeating | Is this form repeating or not - Reply with a Yes or No. In the Novo Nordisk form this info is at the right end of the dark bleue cell on the first page, on the same level as the title of the form | +| repeating | Is this form repeating or not - Reply with a Yes or No. | | language | Provide by default the ENG value here. To have more translation, please add new row with the same OID but with additional language like FRA for French | | description | Please provide here the description of the Form. You can take here the information from the Design Notes or at the end of the form or even from the Guidance documentation. For multilingual, please provide additional lines | | instruction | Please provide here also every instruction that could help the end user in filling this Form | diff --git a/studybuilder-import/datafiles/configuration/feature_flags.csv b/studybuilder-import/datafiles/configuration/feature_flags.csv index cfb3cb38..2e67d60a 100644 --- a/studybuilder-import/datafiles/configuration/feature_flags.csv +++ b/studybuilder-import/datafiles/configuration/feature_flags.csv @@ -8,10 +8,11 @@ library,Wizard Stepper,activity_instance_wizard_stepper_edit_mode,0,This flag to library,Compounds v2,compounds_library,0,This flag toggles on/off the whole subpage found at Library/Concepts/Compounds studies,Compounds v2,compounds_studies,0,This flag toggles on/off the whole subpage found at Studies/Define Study/Study Interventions studies,Complexity score,complexity_score_calculation,1,Enables complexity score calculation on the Detailed SoA page +studies,Complexity score details,complexity_score_details,0,Enables complexity score details dialog on the Detailed SoA page studies,Study Data Suppliers,study_data_suppliers,0,This flag toggles on/off the Study Data Suppliers page found at Studies/Manage/Study Data Suppliers studies,Study Data Suppliers,study_data_suppliers_create_from_study,0,This flag toggles on/off the ability to create a user-defined data supplier from study level (Add a user defined data supplier button) admin,Prodex Extension,prodex_extension,1,Show/hide admin menu for managing extracts and loads of ProdEx data into OSB library,Dictionaries,meddra_dictionary,0,This flag toggles on/off the MedDRA dictionary page found at Library/Dictionaries/MedDRA library,Dictionaries,loinc_dictionary,0,This flag toggles on/off the LOINC dictionary page found at Library/Dictionaries/LOINC studies,Protocol – Lab,soa_protocol_lab_table,0,Show/hide 'Protocol - Lab Table' tab on 'Studies > Study Activities' -studies,Placeholder Activities,streamline_placeholder_activities,0,When enabled restores the old placeholder activity workflow: shows the Requested Activities tab and submit option and request type choice +studies,Placeholder Activities,streamline_placeholder_activities,1,When enabled uses the streamlined placeholder activity workflow and hides the Requested Activities tab diff --git a/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv b/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv index cfb3cb38..2e67d60a 100644 --- a/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv +++ b/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv @@ -8,10 +8,11 @@ library,Wizard Stepper,activity_instance_wizard_stepper_edit_mode,0,This flag to library,Compounds v2,compounds_library,0,This flag toggles on/off the whole subpage found at Library/Concepts/Compounds studies,Compounds v2,compounds_studies,0,This flag toggles on/off the whole subpage found at Studies/Define Study/Study Interventions studies,Complexity score,complexity_score_calculation,1,Enables complexity score calculation on the Detailed SoA page +studies,Complexity score details,complexity_score_details,0,Enables complexity score details dialog on the Detailed SoA page studies,Study Data Suppliers,study_data_suppliers,0,This flag toggles on/off the Study Data Suppliers page found at Studies/Manage/Study Data Suppliers studies,Study Data Suppliers,study_data_suppliers_create_from_study,0,This flag toggles on/off the ability to create a user-defined data supplier from study level (Add a user defined data supplier button) admin,Prodex Extension,prodex_extension,1,Show/hide admin menu for managing extracts and loads of ProdEx data into OSB library,Dictionaries,meddra_dictionary,0,This flag toggles on/off the MedDRA dictionary page found at Library/Dictionaries/MedDRA library,Dictionaries,loinc_dictionary,0,This flag toggles on/off the LOINC dictionary page found at Library/Dictionaries/LOINC studies,Protocol – Lab,soa_protocol_lab_table,0,Show/hide 'Protocol - Lab Table' tab on 'Studies > Study Activities' -studies,Placeholder Activities,streamline_placeholder_activities,0,When enabled restores the old placeholder activity workflow: shows the Requested Activities tab and submit option and request type choice +studies,Placeholder Activities,streamline_placeholder_activities,1,When enabled uses the streamlined placeholder activity workflow and hides the Requested Activities tab diff --git a/studybuilder-import/importers/run_import_activities.py b/studybuilder-import/importers/run_import_activities.py index 9f3a4cf2..d476a045 100644 --- a/studybuilder-import/importers/run_import_activities.py +++ b/studybuilder-import/importers/run_import_activities.py @@ -1037,6 +1037,46 @@ def _split_activity_instance_payload(self, body): groupings_payload = {"activity_groupings": body.get("activity_groupings", [])} return attributes_payload, groupings_payload + async def _approve_activity_instance_part( + self, activity_instance_name, activity_instance_uid, part, session + ): + part_path = path_join( + ACTIVITY_INSTANCES_PATH, activity_instance_uid, part, "approvals" + ) + status, _ = await self.api.approve_async(part_path, session=session) + if status >= 400: + self.log.error( + f"Failed to approve activity instance '{activity_instance_name}' ({part})" + ) + + async def _post_and_approve_activity_instance(self, data, session): + """Post a new activity instance and approve both attributes and groupings separately.""" + self.log.debug(f"Post to {data['path']}") + status, response = await self.api.post_to_api_async( + url=data["path"], body=data["body"], session=session + ) + if status >= 400: + error_message = ( + response.get("message") or response.get("detail") or str(response) + ) + name = data["body"].get("name", str(data["body"])) + self.log.error( + f"Failed to post '{name}' to '{data['path']}', error: {error_message}" + ) + return + uid = response.get("uid") + if uid is None: + self.log.error("No uid returned, unable to approve") + return response + activity_instance_name = data["body"].get("name", uid) + await self._approve_activity_instance_part( + activity_instance_name, uid, "attributes", session + ) + await self._approve_activity_instance_part( + activity_instance_name, uid, "groupings", session + ) + return response + async def _patch_activity_instance_part( self, activity_instance_name, @@ -1374,8 +1414,8 @@ async def handle_activity_instances(self, csvfile, session): ): self.log.info(f"Adding activity instance '{activity_instance_name}'") api_tasks.append( - self.api.post_then_approve( - data=activity_instance_data, session=session, approve=True + self._post_and_approve_activity_instance( + data=activity_instance_data, session=session ) ) elif ( diff --git a/studybuilder-import/importers/run_import_mockdatajson.py b/studybuilder-import/importers/run_import_mockdatajson.py index fe3f40f4..402873f2 100644 --- a/studybuilder-import/importers/run_import_mockdatajson.py +++ b/studybuilder-import/importers/run_import_mockdatajson.py @@ -3602,14 +3602,22 @@ def handle_activity_instances(self, jsonfile): activity_instance_data["body"], ) if response is not None: - if self.api.approve_item(response["uid"], ACTIVITY_INSTANCES_PATH): - self.log.info("Approve ok") - self.metrics.icrement(ACTIVITY_INSTANCES_PATH + "--Approve") - else: - self.log.error("Approve failed") - self.metrics.icrement( - ACTIVITY_INSTANCES_PATH + "--ApproveError" + uid = response["uid"] + # Approve attributes and groupings separately + for part in ("attributes", "groupings"): + approve_path = path_join( + ACTIVITY_INSTANCES_PATH, uid, part, "approvals" ) + if self.api.simple_approve(approve_path): + self.log.info(f"Approve {part} ok") + self.metrics.icrement( + ACTIVITY_INSTANCES_PATH + f"--Approve-{part}" + ) + else: + self.log.error(f"Approve {part} failed") + self.metrics.icrement( + ACTIVITY_INSTANCES_PATH + f"--ApproveError-{part}" + ) else: self.log.warning( "Failed to add activity instance '%s'", diff --git a/studybuilder/config/config.json b/studybuilder/config/config.json index de92775b..45686627 100644 --- a/studybuilder/config/config.json +++ b/studybuilder/config/config.json @@ -25,15 +25,15 @@ "AUTH_CLIENT_ID": "", "AUTH_ENABLED": "", - "API_BUILD_NUMBER" : "OSB v2.8.0", + "API_BUILD_NUMBER" : "OSB v2.9.0", "DATA_IMPORT_BUILD_NUMBER": "N/A", - "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.8.0", - "FRONTEND_BUILD_NUMBER" : "OSB v2.8.0", + "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.9.0", + "FRONTEND_BUILD_NUMBER" : "OSB v2.9.0", "NEO4J_MDR_BUILD_NUMBER": "N/A", "NEODASH_BUILD_NUMBER": "N/A", - "RELEASE_VERSION_NUMBER" : "OSB v2.8.0", + "RELEASE_VERSION_NUMBER" : "OSB v2.9.0", "STANDARDS_IMPORT_BUILD_NUMBER": "N/A", "STUDYBUILDER_EXPORT_BUILD_NUMBER": "N/A", - "STUDYBUILDER_VERSION" : "OSB v2.8.0" + "STUDYBUILDER_VERSION" : "OSB v2.9.0" } diff --git a/studybuilder/package.json b/studybuilder/package.json index dae10707..6976fbcc 100644 --- a/studybuilder/package.json +++ b/studybuilder/package.json @@ -22,10 +22,10 @@ "@microsoft/applicationinsights-clickanalytics-js": "^3.2.0", "@microsoft/applicationinsights-web": "^3.2.0", "@vueup/vue-quill": "^1.2.0", - "axios": "^1.13.5", + "axios": "^1.15.0", "buffer": "^6.0.3", "chart.js": "^4.4.0", - "dompurify": "^3.2.5", + "dompurify": "^3.3.2", "exceljs": "^4.4.0", "html2canvas": "^1.4.1", "luxon": "^3.4.4", @@ -39,7 +39,7 @@ "vue-i18n": "11.1.10", "vue-router": "^4.2.5", "vuetify": "4.0.2", - "yaml": "^2.3.4" + "yaml": "^2.8.3" }, "devDependencies": { "@mdi/font": "^7.3.67", @@ -50,10 +50,10 @@ "husky": "^9.1.7", "license-checker": "^25.0.1", "prettier": "^3.2.5", - "sass": "1.97.3", + "sass": "^1.99.0", "sass-embedded": "^1.86.0", - "vite": "^5.4.21", - "vite-plugin-vuetify": "^2.0.1" + "vite": "^6.4.2", + "vite-plugin-vuetify": "^2.1.3" }, "resolutions": { "quill": "^2.0.2", @@ -64,7 +64,14 @@ "exceljs/**/minimatch": "^9.0.7", "eslint/**/minimatch": "^3.1.4", "license-checker/**/minimatch": "^3.1.4", - "**/immutable": "^5.1.5" + "**/immutable": "^5.1.5", + "**/flatted": "^3.4.2", + "eslint/**/brace-expansion": "^1.1.13", + "license-checker/**/brace-expansion": "^1.1.13", + "exceljs/**/brace-expansion": "^2.0.3", + "**/picomatch": "^4.0.4", + "**/lodash": "^4.18.1", + "**/lodash-es": "^4.18.1" }, "packageManager": "yarn@1.22.22" } diff --git a/studybuilder/public/config.json b/studybuilder/public/config.json index de92775b..45686627 100644 --- a/studybuilder/public/config.json +++ b/studybuilder/public/config.json @@ -25,15 +25,15 @@ "AUTH_CLIENT_ID": "", "AUTH_ENABLED": "", - "API_BUILD_NUMBER" : "OSB v2.8.0", + "API_BUILD_NUMBER" : "OSB v2.9.0", "DATA_IMPORT_BUILD_NUMBER": "N/A", - "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.8.0", - "FRONTEND_BUILD_NUMBER" : "OSB v2.8.0", + "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.9.0", + "FRONTEND_BUILD_NUMBER" : "OSB v2.9.0", "NEO4J_MDR_BUILD_NUMBER": "N/A", "NEODASH_BUILD_NUMBER": "N/A", - "RELEASE_VERSION_NUMBER" : "OSB v2.8.0", + "RELEASE_VERSION_NUMBER" : "OSB v2.9.0", "STANDARDS_IMPORT_BUILD_NUMBER": "N/A", "STUDYBUILDER_EXPORT_BUILD_NUMBER": "N/A", - "STUDYBUILDER_VERSION" : "OSB v2.8.0" + "STUDYBUILDER_VERSION" : "OSB v2.9.0" } diff --git a/studybuilder/public/sbom-clinical-mdr-api.md b/studybuilder/public/sbom-clinical-mdr-api.md index 87b0b8fa..b123eef1 100644 --- a/studybuilder/public/sbom-clinical-mdr-api.md +++ b/studybuilder/public/sbom-clinical-mdr-api.md @@ -16,10 +16,10 @@ | cachetools | 5.5.2 | [MIT](#cachetools) | | certifi | 2026.2.25 | [MPL-2.0](#certifi) | | cffi | 2.0.0 | [MIT](#cffi) | -| charset-normalizer | 3.4.6 | [MIT](#charset-normalizer) | -| click | 8.3.1 | [BSD-3-Clause](#click) | +| charset-normalizer | 3.4.7 | [MIT](#charset-normalizer) | +| click | 8.3.2 | [BSD-3-Clause](#click) | | colour | 0.1.5 | [BSD 3-Clause License](#colour) | -| cryptography | 46.0.6 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | +| cryptography | 46.0.7 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | | cssselect2 | 0.9.0 | [see below](#cssselect2) | | deepdiff | 8.6.2 | [see below](#deepdiff) | | dict2xml | 1.7.8 | [MIT](#dict2xml) | @@ -29,9 +29,9 @@ | fhir_core | 1.1.7 | [BSD license](#fhir_core) | | fhir.resources | 8.2.0 | [BSD license](#fhirresources) | | fonttools | 4.62.1 | [MIT](#fonttools) | -| google-api-core | 2.30.0 | [Apache 2.0](#google-api-core) | -| google-auth | 2.49.1 | [Apache 2.0](#google-auth) | -| googleapis-common-protos | 1.73.0 | [Apache 2.0](#googleapis-common-protos) | +| google-api-core | 2.30.3 | [Apache 2.0](#google-api-core) | +| google-auth | 2.49.2 | [Apache 2.0](#google-auth) | +| googleapis-common-protos | 1.74.0 | [Apache 2.0](#googleapis-common-protos) | | h11 | 0.16.0 | [MIT](#h11) | | httpcore | 1.0.9 | [BSD-3-Clause](#httpcore) | | httpx | 0.27.2 | [BSD-3-Clause](#httpx) | @@ -40,21 +40,21 @@ | Jinja2 | 3.1.6 | [see below](#jinja2) | | lxml | 5.3.2 | [BSD-3-Clause](#lxml) | | MarkupSafe | 3.0.3 | [BSD-3-Clause](#markupsafe) | -| msal | 1.35.1 | [MIT](#msal) | +| msal | 1.36.0 | [MIT](#msal) | | msal-extensions | 1.3.1 | [MIT License](#msal-extensions) | | neo4j | 6.1.0 | [Apache-2.0 AND Python-2.0](#neo4j) | | neomodel | 6.1.0 | [MIT](#neomodel) | | nh3 | 0.2.22 | [MIT](#nh3) | -| numpy | 2.4.3 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | +| numpy | 2.4.4 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | | opencensus | 0.11.4 | [Apache-2.0](#opencensus) | | opencensus-context | 0.1.3 | [Apache-2.0](#opencensus-context) | | opencensus-ext-azure | 1.1.15 | [Apache-2.0](#opencensus-ext-azure) | | openpyxl | 3.1.5 | [MIT](#openpyxl) | | orderly-set | 5.5.0 | [see below](#orderly-set) | -| pandas | 3.0.1 | [see below](#pandas) | -| pillow | 12.1.1 | [MIT-CMU](#pillow) | -| proto-plus | 1.27.1 | [Apache 2.0](#proto-plus) | -| protobuf | 6.33.6 | [3-Clause BSD License](#protobuf) | +| pandas | 3.0.2 | [see below](#pandas) | +| pillow | 12.2.0 | [MIT-CMU](#pillow) | +| proto-plus | 1.27.2 | [Apache 2.0](#proto-plus) | +| protobuf | 7.34.1 | [3-Clause BSD License](#protobuf) | | psutil | 7.2.2 | [BSD-3-Clause](#psutil) | | pyasn1 | 0.6.3 | [BSD-2-Clause](#pyasn1) | | pyasn1_modules | 0.4.2 | [BSD](#pyasn1_modules) | @@ -68,10 +68,10 @@ | python-dateutil | 2.9.0.post0 | [Dual License](#python-dateutil) | | python-docx | 1.1.2 | [MIT](#python-docx) | | python-dotenv | 1.2.2 | [BSD-3-Clause](#python-dotenv) | -| python-multipart | 0.0.22 | [Apache-2.0](#python-multipart) | +| python-multipart | 0.0.24 | [Apache-2.0](#python-multipart) | | pytz | 2026.1.post1 | [MIT](#pytz) | | PyYAML | 6.0.3 | [MIT](#pyyaml) | -| requests | 2.33.0 | [Apache-2.0](#requests) | +| requests | 2.33.1 | [Apache-2.0](#requests) | | six | 1.17.0 | [MIT](#six) | | sniffio | 1.3.1 | [MIT OR Apache-2.0](#sniffio) | | sortedcontainers | 2.4.0 | [Apache 2.0](#sortedcontainers) | @@ -6944,7 +6944,7 @@ Pillow is the friendly PIL fork. It is - Copyright © 2010 by Jeffrey A. Clark and contributors + Copyright © 2010 by Jeffrey 'Alex' Clark and contributors Like PIL, Pillow is licensed under the open source MIT-CMU License: diff --git a/studybuilder/public/sbom-studybuilder.md b/studybuilder/public/sbom-studybuilder.md index da5aca4b..49d39b60 100644 --- a/studybuilder/public/sbom-studybuilder.md +++ b/studybuilder/public/sbom-studybuilder.md @@ -5,11 +5,11 @@ |--------------------------------------------------|----------|----------------------------------------------------------| | @babel/helper-string-parser | 7.27.1 | [MIT](#@babel/helper-string-parser) | | @babel/helper-validator-identifier | 7.28.5 | [MIT](#@babel/helper-validator-identifier) | -| @babel/parser | 7.29.0 | [MIT](#@babel/parser) | -| @babel/runtime | 7.28.6 | [MIT](#@babel/runtime) | +| @babel/parser | 7.29.2 | [MIT](#@babel/parser) | +| @babel/runtime | 7.29.2 | [MIT](#@babel/runtime) | | @babel/types | 7.29.0 | [MIT](#@babel/types) | | @bufbuild/protobuf | 2.11.0 | [(Apache-2.0 AND BSD-3-Clause)](#@bufbuild/protobuf) | -| @esbuild/linux-x64 | 0.21.5 | [MIT](#@esbuild/linux-x64) | +| @esbuild/linux-x64 | 0.25.12 | [MIT](#@esbuild/linux-x64) | | @fast-csv/format | 4.3.5 | [MIT](#@fast-csv/format) | | @fast-csv/parse | 4.3.6 | [MIT](#@fast-csv/parse) | | @formkit/drag-and-drop | 0.5.3 | [MIT](#@formkit/drag-and-drop) | @@ -21,16 +21,15 @@ | @jaames/iro | 5.5.2 | [MPL-2.0](#@jaames/iro) | | @jridgewell/sourcemap-codec | 1.5.5 | [MIT](#@jridgewell/sourcemap-codec) | | @kurkle/color | 0.3.4 | [MIT](#@kurkle/color) | -| @microsoft/applicationinsights-analytics-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-analytics-js) | -| @microsoft/applicationinsights-cfgsync-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-cfgsync-js) | -| @microsoft/applicationinsights-channel-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-channel-js) | -| @microsoft/applicationinsights-clickanalytics-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-clickanalytics-js) | -| @microsoft/applicationinsights-common | 3.3.11 | [MIT](#@microsoft/applicationinsights-common) | -| @microsoft/applicationinsights-core-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-core-js) | -| @microsoft/applicationinsights-dependencies-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-dependencies-js) | -| @microsoft/applicationinsights-properties-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-properties-js) | +| @microsoft/applicationinsights-analytics-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-analytics-js) | +| @microsoft/applicationinsights-cfgsync-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-cfgsync-js) | +| @microsoft/applicationinsights-channel-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-channel-js) | +| @microsoft/applicationinsights-clickanalytics-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-clickanalytics-js) | +| @microsoft/applicationinsights-core-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-core-js) | +| @microsoft/applicationinsights-dependencies-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-dependencies-js) | +| @microsoft/applicationinsights-properties-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-properties-js) | | @microsoft/applicationinsights-shims | 3.0.1 | [MIT](#@microsoft/applicationinsights-shims) | -| @microsoft/applicationinsights-web | 3.3.11 | [MIT](#@microsoft/applicationinsights-web) | +| @microsoft/applicationinsights-web | 3.4.1 | [MIT](#@microsoft/applicationinsights-web) | | @microsoft/dynamicproto-js | 2.0.3 | [MIT](#@microsoft/dynamicproto-js) | | @nevware21/ts-async | 0.5.5 | [MIT](#@nevware21/ts-async) | | @nevware21/ts-utils | 0.13.0 | [MIT](#@nevware21/ts-utils) | @@ -38,23 +37,23 @@ | @parcel/watcher-linux-x64-musl | 2.5.6 | [MIT](#@parcel/watcher-linux-x64-musl) | | @parcel/watcher | 2.5.6 | [MIT](#@parcel/watcher) | | @pkgjs/parseargs | 0.11.0 | [MIT](#@pkgjs/parseargs) | -| @rollup/rollup-linux-x64-gnu | 4.59.0 | [MIT](#@rollup/rollup-linux-x64-gnu) | -| @rollup/rollup-linux-x64-musl | 4.59.0 | [MIT](#@rollup/rollup-linux-x64-musl) | +| @rollup/rollup-linux-x64-gnu | 4.60.1 | [MIT](#@rollup/rollup-linux-x64-gnu) | +| @rollup/rollup-linux-x64-musl | 4.60.1 | [MIT](#@rollup/rollup-linux-x64-musl) | | @types/estree | 1.0.8 | [MIT](#@types/estree) | | @types/lodash.merge | 4.6.9 | [MIT](#@types/lodashmerge) | | @types/lodash | 4.17.24 | [MIT](#@types/lodash) | | @types/node | 14.18.63 | [MIT](#@types/node) | | @types/trusted-types | 2.0.7 | [MIT](#@types/trusted-types) | -| @vue/compiler-core | 3.5.29 | [MIT](#@vue/compiler-core) | -| @vue/compiler-dom | 3.5.29 | [MIT](#@vue/compiler-dom) | -| @vue/compiler-sfc | 3.5.29 | [MIT](#@vue/compiler-sfc) | -| @vue/compiler-ssr | 3.5.29 | [MIT](#@vue/compiler-ssr) | +| @vue/compiler-core | 3.5.32 | [MIT](#@vue/compiler-core) | +| @vue/compiler-dom | 3.5.32 | [MIT](#@vue/compiler-dom) | +| @vue/compiler-sfc | 3.5.32 | [MIT](#@vue/compiler-sfc) | +| @vue/compiler-ssr | 3.5.32 | [MIT](#@vue/compiler-ssr) | | @vue/devtools-api | 6.6.4 | [MIT](#@vue/devtools-api) | -| @vue/reactivity | 3.5.29 | [MIT](#@vue/reactivity) | -| @vue/runtime-core | 3.5.29 | [MIT](#@vue/runtime-core) | -| @vue/runtime-dom | 3.5.29 | [MIT](#@vue/runtime-dom) | -| @vue/server-renderer | 3.5.29 | [MIT](#@vue/server-renderer) | -| @vue/shared | 3.5.29 | [MIT](#@vue/shared) | +| @vue/reactivity | 3.5.32 | [MIT](#@vue/reactivity) | +| @vue/runtime-core | 3.5.32 | [MIT](#@vue/runtime-core) | +| @vue/runtime-dom | 3.5.32 | [MIT](#@vue/runtime-dom) | +| @vue/server-renderer | 3.5.32 | [MIT](#@vue/server-renderer) | +| @vue/shared | 3.5.32 | [MIT](#@vue/shared) | | @vuetify/loader-shared | 2.1.2 | [MIT](#@vuetify/loader-shared) | | @vueup/vue-quill | 1.2.0 | [MIT](#@vueup/vue-quill) | | abort-controller | 3.0.0 | [MIT](#abort-controller) | @@ -64,19 +63,19 @@ | archiver | 7.0.1 | [MIT](#archiver) | | async | 3.2.6 | [MIT](#async) | | asynckit | 0.4.0 | [MIT](#asynckit) | -| axios | 1.13.6 | [MIT](#axios) | +| axios | 1.15.0 | [MIT](#axios) | | b4a | 1.8.0 | [Apache-2.0](#b4a) | | balanced-match | 1.0.2 | [MIT](#balanced-match) | | bare-events | 2.8.2 | [Apache-2.0](#bare-events) | -| bare-fs | 4.5.5 | [Apache-2.0](#bare-fs) | -| bare-os | 3.7.1 | [Apache-2.0](#bare-os) | +| bare-fs | 4.7.0 | [Apache-2.0](#bare-fs) | +| bare-os | 3.8.7 | [Apache-2.0](#bare-os) | | bare-path | 3.0.0 | [Apache-2.0](#bare-path) | -| bare-stream | 2.8.0 | [Apache-2.0](#bare-stream) | -| bare-url | 2.3.2 | [Apache-2.0](#bare-url) | +| bare-stream | 2.13.0 | [Apache-2.0](#bare-stream) | +| bare-url | 2.4.0 | [Apache-2.0](#bare-url) | | base64-arraybuffer | 1.0.2 | [MIT](#base64-arraybuffer) | | base64-js | 1.5.1 | [MIT](#base64-js) | | bluebird | 3.7.2 | [MIT](#bluebird) | -| brace-expansion | 2.0.2 | [MIT](#brace-expansion) | +| brace-expansion | 2.1.0 | [MIT](#brace-expansion) | | buffer-crc32 | 1.0.0 | [MIT](#buffer-crc32) | | buffer | 6.0.3 | [MIT](#buffer) | | call-bind-apply-helpers | 1.0.2 | [MIT](#call-bind-apply-helpers) | @@ -94,11 +93,11 @@ | cross-spawn | 7.0.6 | [MIT](#cross-spawn) | | css-line-break | 2.1.0 | [MIT](#css-line-break) | | csstype | 3.2.3 | [MIT](#csstype) | -| dayjs | 1.11.19 | [MIT](#dayjs) | +| dayjs | 1.11.20 | [MIT](#dayjs) | | debug | 4.4.3 | [MIT](#debug) | | delayed-stream | 1.0.0 | [MIT](#delayed-stream) | | detect-libc | 2.1.2 | [Apache-2.0](#detect-libc) | -| dompurify | 3.3.1 | [(MPL-2.0 OR Apache-2.0)](#dompurify) | +| dompurify | 3.3.3 | [(MPL-2.0 OR Apache-2.0)](#dompurify) | | dunder-proto | 1.0.1 | [MIT](#dunder-proto) | | duplexer2 | 0.1.4 | [BSD-3-Clause](#duplexer2) | | eastasianwidth | 0.2.0 | [MIT](#eastasianwidth) | @@ -108,7 +107,7 @@ | es-errors | 1.3.0 | [MIT](#es-errors) | | es-object-atoms | 1.1.1 | [MIT](#es-object-atoms) | | es-set-tostringtag | 2.1.0 | [MIT](#es-set-tostringtag) | -| esbuild | 0.21.5 | [MIT](#esbuild) | +| esbuild | 0.25.12 | [MIT](#esbuild) | | estree-walker | 2.0.2 | [MIT](#estree-walker) | | event-target-shim | 5.0.1 | [MIT](#event-target-shim) | | eventemitter3 | 5.0.4 | [MIT](#eventemitter3) | @@ -118,6 +117,7 @@ | fast-csv | 4.3.6 | [MIT](#fast-csv) | | fast-diff | 1.2.0 | [Apache-2.0](#fast-diff) | | fast-fifo | 1.3.2 | [MIT](#fast-fifo) | +| fdir | 6.5.0 | [MIT](#fdir) | | flat | 5.0.2 | [BSD-3-Clause](#flat) | | follow-redirects | 1.15.11 | [MIT](#follow-redirects) | | foreground-child | 3.3.1 | [ISC](#foreground-child) | @@ -152,7 +152,7 @@ | kind-of | 6.0.3 | [MIT](#kind-of) | | lazystream | 1.0.1 | [MIT](#lazystream) | | lie | 3.3.0 | [MIT](#lie) | -| lodash-es | 4.17.23 | [MIT](#lodash-es) | +| lodash-es | 4.18.1 | [MIT](#lodash-es) | | lodash.clonedeep | 4.5.0 | [MIT](#lodashclonedeep) | | lodash.escaperegexp | 4.1.2 | [MIT](#lodashescaperegexp) | | lodash.groupby | 4.6.0 | [MIT](#lodashgroupby) | @@ -163,7 +163,7 @@ | lodash.isundefined | 3.0.1 | [MIT](#lodashisundefined) | | lodash.merge | 4.6.2 | [MIT](#lodashmerge) | | lodash.uniq | 4.5.0 | [MIT](#lodashuniq) | -| lodash | 4.17.23 | [MIT](#lodash) | +| lodash | 4.18.1 | [MIT](#lodash) | | lru-cache | 10.4.3 | [ISC](#lru-cache) | | luxon | 3.7.2 | [MIT](#luxon) | | magic-string | 0.30.21 | [MIT](#magic-string) | @@ -177,33 +177,33 @@ | node-addon-api | 7.1.1 | [MIT](#node-addon-api) | | node-int64 | 0.4.0 | [MIT](#node-int64) | | normalize-path | 3.0.0 | [MIT](#normalize-path) | -| oidc-client-ts | 3.4.1 | [Apache-2.0](#oidc-client-ts) | +| oidc-client-ts | 3.5.0 | [Apache-2.0](#oidc-client-ts) | | package-json-from-dist | 1.0.1 | [BlueOak-1.0.0](#package-json-from-dist) | | pako | 1.0.11 | [(MIT AND Zlib)](#pako) | | parchment | 3.0.0 | [BSD-3-Clause](#parchment) | | path-key | 3.1.1 | [MIT](#path-key) | | path-scurry | 1.11.1 | [BlueOak-1.0.0](#path-scurry) | | picocolors | 1.1.1 | [ISC](#picocolors) | -| picomatch | 4.0.3 | [MIT](#picomatch) | +| picomatch | 4.0.4 | [MIT](#picomatch) | | pinia | 2.3.1 | [MIT](#pinia) | -| postcss | 8.5.8 | [MIT](#postcss) | -| preact | 10.28.4 | [MIT](#preact) | +| postcss | 8.5.9 | [MIT](#postcss) | +| preact | 10.29.1 | [MIT](#preact) | | process-nextick-args | 2.0.1 | [MIT](#process-nextick-args) | | process | 0.11.10 | [MIT](#process) | -| proxy-from-env | 1.1.0 | [MIT](#proxy-from-env) | +| proxy-from-env | 2.1.0 | [MIT](#proxy-from-env) | | quill-delta | 4.2.2 | [MIT](#quill-delta) | | quill-table-better | 1.2.3 | [MIT](#quill-table-better) | | quill | 2.0.3 | [BSD-3-Clause](#quill) | | readable-stream | 4.7.0 | [MIT](#readable-stream) | | readdir-glob | 1.1.3 | [Apache-2.0](#readdir-glob) | | readdirp | 4.1.2 | [MIT](#readdirp) | -| rollup | 4.59.0 | [MIT](#rollup) | +| rollup | 4.60.1 | [MIT](#rollup) | | rxjs | 7.8.2 | [Apache-2.0](#rxjs) | | safe-buffer | 5.1.2 | [MIT](#safe-buffer) | -| sass-embedded-linux-musl-x64 | 1.97.3 | [MIT](#sass-embedded-linux-musl-x64) | -| sass-embedded-linux-x64 | 1.97.3 | [MIT](#sass-embedded-linux-x64) | -| sass-embedded | 1.97.3 | [MIT](#sass-embedded) | -| sass | 1.97.3 | [MIT](#sass) | +| sass-embedded-linux-musl-x64 | 1.99.0 | [MIT](#sass-embedded-linux-musl-x64) | +| sass-embedded-linux-x64 | 1.99.0 | [MIT](#sass-embedded-linux-x64) | +| sass-embedded | 1.99.0 | [MIT](#sass-embedded) | +| sass | 1.99.0 | [MIT](#sass) | | saxes | 5.0.1 | [ISC](#saxes) | | setimmediate | 1.0.5 | [MIT](#setimmediate) | | shallow-clone | 3.0.1 | [MIT](#shallow-clone) | @@ -211,7 +211,7 @@ | shebang-regex | 3.0.0 | [MIT](#shebang-regex) | | signal-exit | 4.1.0 | [ISC](#signal-exit) | | source-map-js | 1.2.1 | [BSD-3-Clause](#source-map-js) | -| streamx | 2.23.0 | [MIT](#streamx) | +| streamx | 2.25.0 | [MIT](#streamx) | | string-width-cjs | 4.2.3 | [MIT](#string-width-cjs) | | string-width | 5.1.2 | [MIT](#string-width) | | string_decoder | 1.3.0 | [MIT](#string_decoder) | @@ -224,6 +224,7 @@ | teex | 1.0.1 | [MIT](#teex) | | text-decoder | 1.2.7 | [Apache-2.0](#text-decoder) | | text-segmentation | 1.0.3 | [MIT](#text-segmentation) | +| tinyglobby | 0.2.16 | [MIT](#tinyglobby) | | tmp | 0.2.5 | [MIT](#tmp) | | tslib | 2.8.1 | [0BSD](#tslib) | | universalify | 2.0.1 | [MIT](#universalify) | @@ -234,12 +235,12 @@ | uuid | 8.3.2 | [MIT](#uuid) | | varint | 6.0.0 | [MIT](#varint) | | vite-plugin-vuetify | 2.1.3 | [MIT](#vite-plugin-vuetify) | -| vite | 5.4.21 | [MIT](#vite) | +| vite | 6.4.2 | [MIT](#vite) | | vue-chartjs | 5.3.3 | [MIT](#vue-chartjs) | | vue-demi | 0.14.10 | [MIT](#vue-demi) | | vue-i18n | 11.1.10 | [MIT](#vue-i18n) | | vue-router | 4.6.4 | [MIT](#vue-router) | -| vue | 3.5.29 | [MIT](#vue) | +| vue | 3.5.32 | [MIT](#vue) | | vuetify | 4.0.2 | [MIT](#vuetify) | | webpack-merge | 5.10.0 | [MIT](#webpack-merge) | | which | 2.0.2 | [ISC](#which) | @@ -247,7 +248,7 @@ | wrap-ansi-cjs | 7.0.0 | [MIT](#wrap-ansi-cjs) | | wrap-ansi | 8.1.0 | [MIT](#wrap-ansi) | | xmlchars | 2.2.0 | [MIT](#xmlchars) | -| yaml | 2.8.2 | [ISC](#yaml) | +| yaml | 2.8.3 | [ISC](#yaml) | | zip-stream | 6.0.1 | [MIT](#zip-stream) | @@ -1665,31 +1666,6 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ---- -### @microsoft/applicationinsights-common - - The MIT License (MIT) - - Copyright (c) Microsoft Corporation - - Permission is hereby granted, free of charge, to any person obtaining a copy - of this software and associated documentation files (the "Software"), to deal - in the Software without restriction, including without limitation the rights - to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - copies of the Software, and to permit persons to whom the Software is - furnished to do so, subject to the following conditions: - - The above copyright notice and this permission notice shall be included in all - copies or substantial portions of the Software. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - SOFTWARE. - --- ### @microsoft/applicationinsights-core-js @@ -7908,6 +7884,17 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +--- +### fdir + + Copyright 2023 Abdullah Atta + + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + --- ### flat @@ -10662,7 +10649,7 @@ The MIT License (MIT) - Copyright 2013 Andrey Sitnik + Copyright 2013 Andrey Sitnik Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in @@ -14518,6 +14505,31 @@ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +--- +### tinyglobby + + MIT License + + Copyright (c) 2024 Madeline Gurriarán + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + --- ### tmp @@ -14753,7 +14765,7 @@ # Licenses of bundled dependencies The published Vite artifact additionally contains code with the following licenses: - Apache-2.0, BSD-2-Clause, BlueOak-1.0.0, CC0-1.0, ISC, MIT + Apache-2.0, BSD-2-Clause, CC0-1.0, ISC, MIT # Bundled dependencies: ## @ampproject/remapping @@ -14965,10 +14977,10 @@ --------------------------------------- - ## @jridgewell/gen-mapping + ## @jridgewell/gen-mapping, @jridgewell/set-array License: MIT By: Justin Ridgewell - Repository: https://github.com/jridgewell/gen-mapping + Repositories: https://github.com/jridgewell/gen-mapping, https://github.com/jridgewell/set-array > Copyright 2022 Justin Ridgewell > @@ -15019,33 +15031,6 @@ --------------------------------------- - ## @jridgewell/set-array - License: MIT - By: Justin Ridgewell - Repository: https://github.com/jridgewell/set-array - - > Copyright 2022 Justin Ridgewell - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - ## @jridgewell/sourcemap-codec License: MIT By: Rich Harris @@ -15102,13 +15087,39 @@ --------------------------------------- - ## @nodelib/fs.scandir + ## @polka/compression + License: MIT + Repository: lukeed/polka + + --------------------------------------- + + ## @polka/url + License: MIT + By: Luke Edwards + Repository: lukeed/polka + + --------------------------------------- + + ## @rollup/plugin-alias, @rollup/plugin-commonjs, @rollup/plugin-dynamic-import-vars, @rollup/pluginutils + License: MIT + By: Johannes Stein + Repository: rollup/plugins + + License: MIT + By: Rich Harris + Repository: rollup/plugins + + License: MIT + By: LarsDenBakker + Repository: rollup/plugins + License: MIT - Repository: https://github.com/nodelib/nodelib/tree/master/packages/fs/fs.scandir + By: Rich Harris + Repository: rollup/plugins > The MIT License (MIT) > - > Copyright (c) Denis Malinochkin + > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15117,54 +15128,51 @@ > copies of the Software, and to permit persons to whom the Software is > furnished to do so, subject to the following conditions: > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. + > The above copyright notice and this permission notice shall be included in + > all copies or substantial portions of the Software. > > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. + > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + > THE SOFTWARE. --------------------------------------- - ## @nodelib/fs.stat - License: MIT - Repository: https://github.com/nodelib/nodelib/tree/master/packages/fs/fs.stat + ## anymatch + License: ISC + By: Elan Shanker + Repository: https://github.com/micromatch/anymatch - > The MIT License (MIT) - > - > Copyright (c) Denis Malinochkin + > The ISC License > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: + > Copyright (c) 2019 Elan Shanker, Paul Miller (https://paulmillr.com) > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. + > Permission to use, copy, modify, and/or distribute this software for any + > purpose with or without fee is hereby granted, provided that the above + > copyright notice and this permission notice appear in all copies. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. + > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR + > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. --------------------------------------- - ## @nodelib/fs.walk + ## artichokie License: MIT - Repository: https://github.com/nodelib/nodelib/tree/master/packages/fs/fs.walk + By: sapphi-red, Evan You + Repository: git+https://github.com/sapphi-red/artichokie.git - > The MIT License (MIT) + > MIT License > - > Copyright (c) Denis Malinochkin + > Copyright (c) 2020-present, Yuxi (Evan) You + > Copyright (c) 2023-present, sapphi-red > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15186,27 +15194,40 @@ --------------------------------------- - ## @polka/compression + ## binary-extensions License: MIT - Repository: lukeed/polka + By: Sindre Sorhus + Repository: sindresorhus/binary-extensions + + > MIT License + > + > Copyright (c) Sindre Sorhus (https://sindresorhus.com) + > Copyright (c) Paul Miller (https://paulmillr.com) + > + > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + > + > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + > + > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. --------------------------------------- - ## @polka/url + ## braces, fill-range, is-number License: MIT - By: Luke Edwards - Repository: lukeed/polka + By: Jon Schlinkert, Brian Woodward, Elan Shanker, Eugene Sharygin, hemanth.hm + Repository: micromatch/braces - --------------------------------------- + License: MIT + By: Jon Schlinkert, Edo Rivai, Paul Miller, Rouven Weßling + Repository: jonschlinkert/fill-range - ## @rollup/plugin-alias License: MIT - By: Johannes Stein - Repository: rollup/plugins + By: Jon Schlinkert, Olsten Larck, Rouven Weßling + Repository: jonschlinkert/is-number > The MIT License (MIT) > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) 2014-present, Jon Schlinkert. > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15228,43 +15249,31 @@ --------------------------------------- - ## @rollup/plugin-commonjs + ## bundle-name, default-browser, default-browser-id, define-lazy-prop, is-docker, is-inside-container, is-wsl, open, run-applescript License: MIT - By: Rich Harris - Repository: rollup/plugins + By: Sindre Sorhus + Repositories: sindresorhus/bundle-name, sindresorhus/default-browser, sindresorhus/default-browser-id, sindresorhus/define-lazy-prop, sindresorhus/is-docker, sindresorhus/is-inside-container, sindresorhus/is-wsl, sindresorhus/open, sindresorhus/run-applescript - > The MIT License (MIT) + > MIT License > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) Sindre Sorhus (https://sindresorhus.com) > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: + > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. + > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. + > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. --------------------------------------- - ## @rollup/plugin-dynamic-import-vars + ## cac License: MIT - By: LarsDenBakker - Repository: rollup/plugins + By: egoist + Repository: egoist/cac > The MIT License (MIT) > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) EGOIST <0x142857@gmail.com> (https://github.com/egoist) > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15286,17 +15295,17 @@ --------------------------------------- - ## @rollup/pluginutils + ## chokidar License: MIT - By: Rich Harris - Repository: rollup/plugins + By: Paul Miller, Elan Shanker + Repository: git+https://github.com/paulmillr/chokidar.git > The MIT License (MIT) > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) 2012-2019 Paul Miller (https://paulmillr.com), Elan Shanker > > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal + > of this software and associated documentation files (the “Software”), to deal > in the Software without restriction, including without limitation the rights > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell > copies of the Software, and to permit persons to whom the Software is @@ -15305,7 +15314,7 @@ > The above copyright notice and this permission notice shall be included in > all copies or substantial portions of the Software. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + > THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER @@ -15315,286 +15324,27 @@ --------------------------------------- - ## ansi-regex + ## commondir, shell-quote License: MIT - By: Sindre Sorhus - Repository: chalk/ansi-regex + By: James Halliday + Repositories: http://github.com/substack/node-commondir.git, http://github.com/ljharb/shell-quote.git - > MIT License + > The MIT License > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) + > Copyright (c) 2013 James Halliday (mail@substack.net) > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + > Permission is hereby granted, free of charge, + > to any person obtaining a copy of this software and + > associated documentation files (the "Software"), to + > deal in the Software without restriction, including + > without limitation the rights to use, copy, modify, + > merge, publish, distribute, sublicense, and/or sell + > copies of the Software, and to permit persons to whom + > the Software is furnished to do so, + > subject to the following conditions: > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## anymatch - License: ISC - By: Elan Shanker - Repository: https://github.com/micromatch/anymatch - - > The ISC License - > - > Copyright (c) 2019 Elan Shanker, Paul Miller (https://paulmillr.com) - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## artichokie - License: MIT - By: sapphi-red, Evan You - Repository: git+https://github.com/sapphi-red/artichokie.git - - > MIT License - > - > Copyright (c) 2020-present, Yuxi (Evan) You - > Copyright (c) 2023-present, sapphi-red - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## astring - License: MIT - By: David Bonnet - Repository: https://github.com/davidbonnet/astring.git - - > Copyright (c) 2015, David Bonnet - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## balanced-match - License: MIT - By: Julian Gruber - Repository: git://github.com/juliangruber/balanced-match.git - - > (MIT) - > - > Copyright (c) 2013 Julian Gruber <julian@juliangruber.com> - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies - > of the Software, and to permit persons to whom the Software is furnished to do - > so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## binary-extensions - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/binary-extensions - - > MIT License - > - > Copyright (c) 2019 Sindre Sorhus (https://sindresorhus.com), Paul Miller (https://paulmillr.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## brace-expansion - License: MIT - By: Julian Gruber - Repository: git://github.com/juliangruber/brace-expansion.git - - > MIT License - > - > Copyright (c) 2013 Julian Gruber - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## braces - License: MIT - By: Jon Schlinkert, Brian Woodward, Elan Shanker, Eugene Sharygin, hemanth.hm - Repository: micromatch/braces - - > The MIT License (MIT) - > - > Copyright (c) 2014-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## cac - License: MIT - By: egoist - Repository: egoist/cac - - > The MIT License (MIT) - > - > Copyright (c) EGOIST <0x142857@gmail.com> (https://github.com/egoist) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## chokidar - License: MIT - By: Paul Miller, Elan Shanker - Repository: git+https://github.com/paulmillr/chokidar.git - - > The MIT License (MIT) - > - > Copyright (c) 2012-2019 Paul Miller (https://paulmillr.com), Elan Shanker - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the “Software”), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## commondir - License: MIT - By: James Halliday - Repository: http://github.com/substack/node-commondir.git - - > The MIT License - > - > Copyright (c) 2013 James Halliday (mail@substack.net) - > - > Permission is hereby granted, free of charge, - > to any person obtaining a copy of this software and - > associated documentation files (the "Software"), to - > deal in the Software without restriction, including - > without limitation the rights to use, copy, modify, - > merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom - > the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice - > shall be included in all copies or substantial portions of the Software. + > The above copyright notice and this permission notice + > shall be included in all copies or substantial portions of the Software. > > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, > EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES @@ -15784,23 +15534,6 @@ --------------------------------------- - ## define-lazy-prop - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/define-lazy-prop - - > MIT License - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## dotenv License: BSD-2-Clause Repository: git://github.com/motdotla/dotenv.git @@ -16063,85 +15796,6 @@ --------------------------------------- - ## fast-glob - License: MIT - By: Denis Malinochkin - Repository: mrmlnc/fast-glob - - > The MIT License (MIT) - > - > Copyright (c) Denis Malinochkin - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## fastq - License: ISC - By: Matteo Collina - Repository: git+https://github.com/mcollina/fastq.git - - > Copyright (c) 2015-2020, Matteo Collina - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF - > OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## fill-range - License: MIT - By: Jon Schlinkert, Edo Rivai, Paul Miller, Rouven Weßling - Repository: jonschlinkert/fill-range - - > The MIT License (MIT) - > - > Copyright (c) 2014-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - ## finalhandler License: MIT By: Douglas Christopher Wilson @@ -16175,7 +15829,7 @@ ## follow-redirects License: MIT By: Ruben Verborgh, Olivier Lalonde, James Talmage - Repository: git@github.com:follow-redirects/follow-redirects.git + Repository: git+ssh://git@github.com/follow-redirects/follow-redirects.git > Copyright 2014–present Olivier Lalonde , James Talmage , Ruben Verborgh > @@ -16227,29 +15881,6 @@ --------------------------------------- - ## glob - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/node-glob.git - - > The ISC License - > - > Copyright (c) 2009-2023 Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - ## glob-parent License: ISC By: Gulp Team, Elan Shanker, Blaine Bublitz @@ -16334,23 +15965,6 @@ --------------------------------------- - ## is-docker - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/is-docker - - > MIT License - > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## is-extglob License: MIT By: Jon Schlinkert @@ -16380,43 +15994,14 @@ --------------------------------------- - ## is-glob - License: MIT - By: Jon Schlinkert, Brian Woodward, Daniel Perez - Repository: micromatch/is-glob - - > The MIT License (MIT) - > - > Copyright (c) 2014-2017, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## is-number + ## is-glob License: MIT - By: Jon Schlinkert, Olsten Larck, Rouven Weßling - Repository: jonschlinkert/is-number + By: Jon Schlinkert, Brian Woodward, Daniel Perez + Repository: micromatch/is-glob > The MIT License (MIT) > - > Copyright (c) 2014-present, Jon Schlinkert. + > Copyright (c) 2014-2017, Jon Schlinkert. > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -16445,27 +16030,10 @@ --------------------------------------- - ## is-wsl - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/is-wsl - - > MIT License - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## isexe + ## isexe, which License: ISC By: Isaac Z. Schlueter - Repository: git+https://github.com/isaacs/isexe.git + Repositories: git+https://github.com/isaacs/isexe.git, git://github.com/isaacs/node-which.git > The ISC License > @@ -16514,39 +16082,10 @@ --------------------------------------- - ## launch-editor - License: MIT - By: Evan You - Repository: git+https://github.com/yyx990803/launch-editor.git - - > The MIT License (MIT) - > - > Copyright (c) 2017-present, Yuxi (Evan) You - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## launch-editor-middleware + ## launch-editor, launch-editor-middleware License: MIT By: Evan You - Repository: git+https://github.com/yyx990803/launch-editor.git + Repositories: git+https://github.com/yyx990803/launch-editor.git, git+https://github.com/yyx990803/launch-editor.git > The MIT License (MIT) > @@ -16684,29 +16223,6 @@ --------------------------------------- - ## lru-cache - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/node-lru-cache.git - - > The ISC License - > - > Copyright (c) 2010-2023 Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - ## magic-string License: MIT By: Rich Harris @@ -16722,112 +16238,9 @@ --------------------------------------- - ## merge2 - License: MIT - Repository: git@github.com:teambition/merge2.git - - > The MIT License (MIT) - > - > Copyright (c) 2014-2020 Teambition - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## micromatch - License: MIT - By: Jon Schlinkert, Amila Welihinda, Bogdan Chadkin, Brian Woodward, Devon Govett, Elan Shanker, Fabrício Matté, Martin Kolárik, Olsten Larck, Paul Miller, Tom Byrer, Tyler Akins, Peter Bright, Kuba Juszczyk - Repository: micromatch/micromatch - - > The MIT License (MIT) - > - > Copyright (c) 2014-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## minimatch - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/minimatch.git - - > The ISC License - > - > Copyright (c) 2011-2023 Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## minipass - License: ISC - By: Isaac Z. Schlueter - Repository: https://github.com/isaacs/minipass - - > The ISC License - > - > Copyright (c) 2017-2023 npm, Inc., Isaac Z. Schlueter, and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## mlly + ## mlly, ufo License: MIT - Repository: unjs/mlly + Repositories: unjs/mlly, unjs/ufo > MIT License > @@ -16884,11 +16297,11 @@ ## ms License: MIT - Repository: zeit/ms + Repository: vercel/ms > The MIT License (MIT) > - > Copyright (c) 2016 Zeit, Inc. + > Copyright (c) 2020 Vercel, Inc. > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -16999,23 +16412,6 @@ --------------------------------------- - ## open - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/open - - > MIT License - > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## parse5 License: MIT By: Ivan Nikulin, https://github.com/inikulin/parse5/graphs/contributors @@ -17074,10 +16470,10 @@ --------------------------------------- - ## path-key + ## path-key, shebang-regex License: MIT By: Sindre Sorhus - Repository: sindresorhus/path-key + Repositories: sindresorhus/path-key, sindresorhus/shebang-regex > MIT License > @@ -17091,69 +16487,6 @@ --------------------------------------- - ## path-scurry - License: BlueOak-1.0.0 - By: Isaac Z. Schlueter - Repository: git+https://github.com/isaacs/path-scurry - - > # Blue Oak Model License - > - > Version 1.0.0 - > - > ## Purpose - > - > This license gives everyone as much permission to work with - > this software as possible, while protecting contributors - > from liability. - > - > ## Acceptance - > - > In order to receive this license, you must agree to its - > rules. The rules of this license are both obligations - > under that agreement and conditions to your license. - > You must not do anything with this software that triggers - > a rule that you cannot or will not follow. - > - > ## Copyright - > - > Each contributor licenses you to do everything with this - > software that would otherwise infringe that contributor's - > copyright in it. - > - > ## Notices - > - > You must ensure that everyone who gets a copy of - > any part of this software from you, with or without - > changes, also gets the text of this license or a link to - > . - > - > ## Excuse - > - > If anyone notifies you in writing that you have not - > complied with [Notices](#notices), you can keep your - > license by taking all practical steps to comply within 30 - > days after the notice. If you do not do so, your license - > ends immediately. - > - > ## Patent - > - > Each contributor licenses you to do everything with this - > software that would otherwise infringe any patent claims - > they can license or become able to license. - > - > ## Reliability - > - > No contributor can revoke this license. - > - > ## No Liability - > - > ***As far as the law allows, this software comes as is, - > without any warranty or condition, and no contributor - > will be liable to anyone for any damages related to this - > software or this license, under any kind of legal claim.*** - - --------------------------------------- - ## periscopic License: MIT Repository: Rich-Harris/periscopic @@ -17175,77 +16508,19 @@ > ISC License > - > Copyright (c) 2021 Alexey Raspopov, Kostiantyn Denysov, Anton Verinov + > Copyright (c) 2021-2024 Oleksii Raspopov, Kostiantyn Denysov, Anton Verinov > > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF - > OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## picomatch - License: MIT - By: Jon Schlinkert - Repository: micromatch/picomatch - - > The MIT License (MIT) - > - > Copyright (c) 2017-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## pify - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/pify - - > The MIT License (MIT) - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. + > purpose with or without fee is hereby granted, provided that the above + > copyright notice and this permission notice appear in all copies. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. + > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + > OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. --------------------------------------- @@ -17464,62 +16739,6 @@ --------------------------------------- - ## queue-microtask - License: MIT - By: Feross Aboukhadijeh - Repository: git://github.com/feross/queue-microtask.git - - > The MIT License (MIT) - > - > Copyright (c) Feross Aboukhadijeh - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of - > the Software, and to permit persons to whom the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS - > FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR - > COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## read-cache - License: MIT - By: Bogdan Chadkin - Repository: git+https://github.com/TrySound/read-cache.git - - > The MIT License (MIT) - > - > Copyright 2016 Bogdan Chadkin - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of - > the Software, and to permit persons to whom the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS - > FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR - > COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## readdirp License: MIT By: Thorsten Lorenz, Paul Miller @@ -17578,10 +16797,10 @@ --------------------------------------- - ## resolve.exports + ## resolve.exports, totalist License: MIT By: Luke Edwards - Repository: lukeed/resolve.exports + Repositories: lukeed/resolve.exports, lukeed/totalist > The MIT License (MIT) > @@ -17607,63 +16826,6 @@ --------------------------------------- - ## reusify - License: MIT - By: Matteo Collina - Repository: git+https://github.com/mcollina/reusify.git - - > The MIT License (MIT) - > - > Copyright (c) 2015 Matteo Collina - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## run-parallel - License: MIT - By: Feross Aboukhadijeh - Repository: git://github.com/feross/run-parallel.git - - > The MIT License (MIT) - > - > Copyright (c) Feross Aboukhadijeh - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of - > the Software, and to permit persons to whom the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS - > FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR - > COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## shebang-command License: MIT By: Kevin Mårtensson @@ -17681,55 +16843,6 @@ --------------------------------------- - ## shebang-regex - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/shebang-regex - - > MIT License - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## shell-quote - License: MIT - By: James Halliday - Repository: http://github.com/ljharb/shell-quote.git - - > The MIT License - > - > Copyright (c) 2013 James Halliday (mail@substack.net) - > - > Permission is hereby granted, free of charge, - > to any person obtaining a copy of this software and - > associated documentation files (the "Software"), to - > deal in the Software without restriction, including - > without limitation the rights to use, copy, modify, - > merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom - > the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice - > shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - > EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - > OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. - > IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR - > ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, - > TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE - > SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## sirv License: MIT By: Luke Edwards @@ -17774,23 +16887,6 @@ --------------------------------------- - ## strip-ansi - License: MIT - By: Sindre Sorhus - Repository: chalk/strip-ansi - - > MIT License - > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## strip-literal License: MIT By: Anthony Fu @@ -17849,35 +16945,6 @@ --------------------------------------- - ## totalist - License: MIT - By: Luke Edwards - Repository: lukeed/totalist - - > The MIT License (MIT) - > - > Copyright (c) Luke Edwards (lukeed.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - ## tsconfck License: MIT By: dominikg @@ -17932,34 +16999,6 @@ --------------------------------------- - ## ufo - License: MIT - Repository: unjs/ufo - - > MIT License - > - > Copyright (c) Pooya Parsa - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - ## unpipe License: MIT By: Douglas Christopher Wilson @@ -18080,29 +17119,6 @@ --------------------------------------- - ## which - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/node-which.git - - > The ISC License - > - > Copyright (c) Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - ## ws License: MIT By: Einar Otto Stangvik @@ -18129,27 +17145,6 @@ > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - --------------------------------------- - - ## yaml - License: ISC - By: Eemeli Aro - Repository: github:eemeli/yaml - - > Copyright Eemeli Aro - > - > Permission to use, copy, modify, and/or distribute this software for any purpose - > with or without fee is hereby granted, provided that the above copyright notice - > and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH - > REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND - > FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, - > INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS - > OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER - > TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF - > THIS SOFTWARE. - --- ### vue-chartjs diff --git a/studybuilder/sbom.md b/studybuilder/sbom.md index da5aca4b..49d39b60 100644 --- a/studybuilder/sbom.md +++ b/studybuilder/sbom.md @@ -5,11 +5,11 @@ |--------------------------------------------------|----------|----------------------------------------------------------| | @babel/helper-string-parser | 7.27.1 | [MIT](#@babel/helper-string-parser) | | @babel/helper-validator-identifier | 7.28.5 | [MIT](#@babel/helper-validator-identifier) | -| @babel/parser | 7.29.0 | [MIT](#@babel/parser) | -| @babel/runtime | 7.28.6 | [MIT](#@babel/runtime) | +| @babel/parser | 7.29.2 | [MIT](#@babel/parser) | +| @babel/runtime | 7.29.2 | [MIT](#@babel/runtime) | | @babel/types | 7.29.0 | [MIT](#@babel/types) | | @bufbuild/protobuf | 2.11.0 | [(Apache-2.0 AND BSD-3-Clause)](#@bufbuild/protobuf) | -| @esbuild/linux-x64 | 0.21.5 | [MIT](#@esbuild/linux-x64) | +| @esbuild/linux-x64 | 0.25.12 | [MIT](#@esbuild/linux-x64) | | @fast-csv/format | 4.3.5 | [MIT](#@fast-csv/format) | | @fast-csv/parse | 4.3.6 | [MIT](#@fast-csv/parse) | | @formkit/drag-and-drop | 0.5.3 | [MIT](#@formkit/drag-and-drop) | @@ -21,16 +21,15 @@ | @jaames/iro | 5.5.2 | [MPL-2.0](#@jaames/iro) | | @jridgewell/sourcemap-codec | 1.5.5 | [MIT](#@jridgewell/sourcemap-codec) | | @kurkle/color | 0.3.4 | [MIT](#@kurkle/color) | -| @microsoft/applicationinsights-analytics-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-analytics-js) | -| @microsoft/applicationinsights-cfgsync-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-cfgsync-js) | -| @microsoft/applicationinsights-channel-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-channel-js) | -| @microsoft/applicationinsights-clickanalytics-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-clickanalytics-js) | -| @microsoft/applicationinsights-common | 3.3.11 | [MIT](#@microsoft/applicationinsights-common) | -| @microsoft/applicationinsights-core-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-core-js) | -| @microsoft/applicationinsights-dependencies-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-dependencies-js) | -| @microsoft/applicationinsights-properties-js | 3.3.11 | [MIT](#@microsoft/applicationinsights-properties-js) | +| @microsoft/applicationinsights-analytics-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-analytics-js) | +| @microsoft/applicationinsights-cfgsync-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-cfgsync-js) | +| @microsoft/applicationinsights-channel-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-channel-js) | +| @microsoft/applicationinsights-clickanalytics-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-clickanalytics-js) | +| @microsoft/applicationinsights-core-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-core-js) | +| @microsoft/applicationinsights-dependencies-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-dependencies-js) | +| @microsoft/applicationinsights-properties-js | 3.4.1 | [MIT](#@microsoft/applicationinsights-properties-js) | | @microsoft/applicationinsights-shims | 3.0.1 | [MIT](#@microsoft/applicationinsights-shims) | -| @microsoft/applicationinsights-web | 3.3.11 | [MIT](#@microsoft/applicationinsights-web) | +| @microsoft/applicationinsights-web | 3.4.1 | [MIT](#@microsoft/applicationinsights-web) | | @microsoft/dynamicproto-js | 2.0.3 | [MIT](#@microsoft/dynamicproto-js) | | @nevware21/ts-async | 0.5.5 | [MIT](#@nevware21/ts-async) | | @nevware21/ts-utils | 0.13.0 | [MIT](#@nevware21/ts-utils) | @@ -38,23 +37,23 @@ | @parcel/watcher-linux-x64-musl | 2.5.6 | [MIT](#@parcel/watcher-linux-x64-musl) | | @parcel/watcher | 2.5.6 | [MIT](#@parcel/watcher) | | @pkgjs/parseargs | 0.11.0 | [MIT](#@pkgjs/parseargs) | -| @rollup/rollup-linux-x64-gnu | 4.59.0 | [MIT](#@rollup/rollup-linux-x64-gnu) | -| @rollup/rollup-linux-x64-musl | 4.59.0 | [MIT](#@rollup/rollup-linux-x64-musl) | +| @rollup/rollup-linux-x64-gnu | 4.60.1 | [MIT](#@rollup/rollup-linux-x64-gnu) | +| @rollup/rollup-linux-x64-musl | 4.60.1 | [MIT](#@rollup/rollup-linux-x64-musl) | | @types/estree | 1.0.8 | [MIT](#@types/estree) | | @types/lodash.merge | 4.6.9 | [MIT](#@types/lodashmerge) | | @types/lodash | 4.17.24 | [MIT](#@types/lodash) | | @types/node | 14.18.63 | [MIT](#@types/node) | | @types/trusted-types | 2.0.7 | [MIT](#@types/trusted-types) | -| @vue/compiler-core | 3.5.29 | [MIT](#@vue/compiler-core) | -| @vue/compiler-dom | 3.5.29 | [MIT](#@vue/compiler-dom) | -| @vue/compiler-sfc | 3.5.29 | [MIT](#@vue/compiler-sfc) | -| @vue/compiler-ssr | 3.5.29 | [MIT](#@vue/compiler-ssr) | +| @vue/compiler-core | 3.5.32 | [MIT](#@vue/compiler-core) | +| @vue/compiler-dom | 3.5.32 | [MIT](#@vue/compiler-dom) | +| @vue/compiler-sfc | 3.5.32 | [MIT](#@vue/compiler-sfc) | +| @vue/compiler-ssr | 3.5.32 | [MIT](#@vue/compiler-ssr) | | @vue/devtools-api | 6.6.4 | [MIT](#@vue/devtools-api) | -| @vue/reactivity | 3.5.29 | [MIT](#@vue/reactivity) | -| @vue/runtime-core | 3.5.29 | [MIT](#@vue/runtime-core) | -| @vue/runtime-dom | 3.5.29 | [MIT](#@vue/runtime-dom) | -| @vue/server-renderer | 3.5.29 | [MIT](#@vue/server-renderer) | -| @vue/shared | 3.5.29 | [MIT](#@vue/shared) | +| @vue/reactivity | 3.5.32 | [MIT](#@vue/reactivity) | +| @vue/runtime-core | 3.5.32 | [MIT](#@vue/runtime-core) | +| @vue/runtime-dom | 3.5.32 | [MIT](#@vue/runtime-dom) | +| @vue/server-renderer | 3.5.32 | [MIT](#@vue/server-renderer) | +| @vue/shared | 3.5.32 | [MIT](#@vue/shared) | | @vuetify/loader-shared | 2.1.2 | [MIT](#@vuetify/loader-shared) | | @vueup/vue-quill | 1.2.0 | [MIT](#@vueup/vue-quill) | | abort-controller | 3.0.0 | [MIT](#abort-controller) | @@ -64,19 +63,19 @@ | archiver | 7.0.1 | [MIT](#archiver) | | async | 3.2.6 | [MIT](#async) | | asynckit | 0.4.0 | [MIT](#asynckit) | -| axios | 1.13.6 | [MIT](#axios) | +| axios | 1.15.0 | [MIT](#axios) | | b4a | 1.8.0 | [Apache-2.0](#b4a) | | balanced-match | 1.0.2 | [MIT](#balanced-match) | | bare-events | 2.8.2 | [Apache-2.0](#bare-events) | -| bare-fs | 4.5.5 | [Apache-2.0](#bare-fs) | -| bare-os | 3.7.1 | [Apache-2.0](#bare-os) | +| bare-fs | 4.7.0 | [Apache-2.0](#bare-fs) | +| bare-os | 3.8.7 | [Apache-2.0](#bare-os) | | bare-path | 3.0.0 | [Apache-2.0](#bare-path) | -| bare-stream | 2.8.0 | [Apache-2.0](#bare-stream) | -| bare-url | 2.3.2 | [Apache-2.0](#bare-url) | +| bare-stream | 2.13.0 | [Apache-2.0](#bare-stream) | +| bare-url | 2.4.0 | [Apache-2.0](#bare-url) | | base64-arraybuffer | 1.0.2 | [MIT](#base64-arraybuffer) | | base64-js | 1.5.1 | [MIT](#base64-js) | | bluebird | 3.7.2 | [MIT](#bluebird) | -| brace-expansion | 2.0.2 | [MIT](#brace-expansion) | +| brace-expansion | 2.1.0 | [MIT](#brace-expansion) | | buffer-crc32 | 1.0.0 | [MIT](#buffer-crc32) | | buffer | 6.0.3 | [MIT](#buffer) | | call-bind-apply-helpers | 1.0.2 | [MIT](#call-bind-apply-helpers) | @@ -94,11 +93,11 @@ | cross-spawn | 7.0.6 | [MIT](#cross-spawn) | | css-line-break | 2.1.0 | [MIT](#css-line-break) | | csstype | 3.2.3 | [MIT](#csstype) | -| dayjs | 1.11.19 | [MIT](#dayjs) | +| dayjs | 1.11.20 | [MIT](#dayjs) | | debug | 4.4.3 | [MIT](#debug) | | delayed-stream | 1.0.0 | [MIT](#delayed-stream) | | detect-libc | 2.1.2 | [Apache-2.0](#detect-libc) | -| dompurify | 3.3.1 | [(MPL-2.0 OR Apache-2.0)](#dompurify) | +| dompurify | 3.3.3 | [(MPL-2.0 OR Apache-2.0)](#dompurify) | | dunder-proto | 1.0.1 | [MIT](#dunder-proto) | | duplexer2 | 0.1.4 | [BSD-3-Clause](#duplexer2) | | eastasianwidth | 0.2.0 | [MIT](#eastasianwidth) | @@ -108,7 +107,7 @@ | es-errors | 1.3.0 | [MIT](#es-errors) | | es-object-atoms | 1.1.1 | [MIT](#es-object-atoms) | | es-set-tostringtag | 2.1.0 | [MIT](#es-set-tostringtag) | -| esbuild | 0.21.5 | [MIT](#esbuild) | +| esbuild | 0.25.12 | [MIT](#esbuild) | | estree-walker | 2.0.2 | [MIT](#estree-walker) | | event-target-shim | 5.0.1 | [MIT](#event-target-shim) | | eventemitter3 | 5.0.4 | [MIT](#eventemitter3) | @@ -118,6 +117,7 @@ | fast-csv | 4.3.6 | [MIT](#fast-csv) | | fast-diff | 1.2.0 | [Apache-2.0](#fast-diff) | | fast-fifo | 1.3.2 | [MIT](#fast-fifo) | +| fdir | 6.5.0 | [MIT](#fdir) | | flat | 5.0.2 | [BSD-3-Clause](#flat) | | follow-redirects | 1.15.11 | [MIT](#follow-redirects) | | foreground-child | 3.3.1 | [ISC](#foreground-child) | @@ -152,7 +152,7 @@ | kind-of | 6.0.3 | [MIT](#kind-of) | | lazystream | 1.0.1 | [MIT](#lazystream) | | lie | 3.3.0 | [MIT](#lie) | -| lodash-es | 4.17.23 | [MIT](#lodash-es) | +| lodash-es | 4.18.1 | [MIT](#lodash-es) | | lodash.clonedeep | 4.5.0 | [MIT](#lodashclonedeep) | | lodash.escaperegexp | 4.1.2 | [MIT](#lodashescaperegexp) | | lodash.groupby | 4.6.0 | [MIT](#lodashgroupby) | @@ -163,7 +163,7 @@ | lodash.isundefined | 3.0.1 | [MIT](#lodashisundefined) | | lodash.merge | 4.6.2 | [MIT](#lodashmerge) | | lodash.uniq | 4.5.0 | [MIT](#lodashuniq) | -| lodash | 4.17.23 | [MIT](#lodash) | +| lodash | 4.18.1 | [MIT](#lodash) | | lru-cache | 10.4.3 | [ISC](#lru-cache) | | luxon | 3.7.2 | [MIT](#luxon) | | magic-string | 0.30.21 | [MIT](#magic-string) | @@ -177,33 +177,33 @@ | node-addon-api | 7.1.1 | [MIT](#node-addon-api) | | node-int64 | 0.4.0 | [MIT](#node-int64) | | normalize-path | 3.0.0 | [MIT](#normalize-path) | -| oidc-client-ts | 3.4.1 | [Apache-2.0](#oidc-client-ts) | +| oidc-client-ts | 3.5.0 | [Apache-2.0](#oidc-client-ts) | | package-json-from-dist | 1.0.1 | [BlueOak-1.0.0](#package-json-from-dist) | | pako | 1.0.11 | [(MIT AND Zlib)](#pako) | | parchment | 3.0.0 | [BSD-3-Clause](#parchment) | | path-key | 3.1.1 | [MIT](#path-key) | | path-scurry | 1.11.1 | [BlueOak-1.0.0](#path-scurry) | | picocolors | 1.1.1 | [ISC](#picocolors) | -| picomatch | 4.0.3 | [MIT](#picomatch) | +| picomatch | 4.0.4 | [MIT](#picomatch) | | pinia | 2.3.1 | [MIT](#pinia) | -| postcss | 8.5.8 | [MIT](#postcss) | -| preact | 10.28.4 | [MIT](#preact) | +| postcss | 8.5.9 | [MIT](#postcss) | +| preact | 10.29.1 | [MIT](#preact) | | process-nextick-args | 2.0.1 | [MIT](#process-nextick-args) | | process | 0.11.10 | [MIT](#process) | -| proxy-from-env | 1.1.0 | [MIT](#proxy-from-env) | +| proxy-from-env | 2.1.0 | [MIT](#proxy-from-env) | | quill-delta | 4.2.2 | [MIT](#quill-delta) | | quill-table-better | 1.2.3 | [MIT](#quill-table-better) | | quill | 2.0.3 | [BSD-3-Clause](#quill) | | readable-stream | 4.7.0 | [MIT](#readable-stream) | | readdir-glob | 1.1.3 | [Apache-2.0](#readdir-glob) | | readdirp | 4.1.2 | [MIT](#readdirp) | -| rollup | 4.59.0 | [MIT](#rollup) | +| rollup | 4.60.1 | [MIT](#rollup) | | rxjs | 7.8.2 | [Apache-2.0](#rxjs) | | safe-buffer | 5.1.2 | [MIT](#safe-buffer) | -| sass-embedded-linux-musl-x64 | 1.97.3 | [MIT](#sass-embedded-linux-musl-x64) | -| sass-embedded-linux-x64 | 1.97.3 | [MIT](#sass-embedded-linux-x64) | -| sass-embedded | 1.97.3 | [MIT](#sass-embedded) | -| sass | 1.97.3 | [MIT](#sass) | +| sass-embedded-linux-musl-x64 | 1.99.0 | [MIT](#sass-embedded-linux-musl-x64) | +| sass-embedded-linux-x64 | 1.99.0 | [MIT](#sass-embedded-linux-x64) | +| sass-embedded | 1.99.0 | [MIT](#sass-embedded) | +| sass | 1.99.0 | [MIT](#sass) | | saxes | 5.0.1 | [ISC](#saxes) | | setimmediate | 1.0.5 | [MIT](#setimmediate) | | shallow-clone | 3.0.1 | [MIT](#shallow-clone) | @@ -211,7 +211,7 @@ | shebang-regex | 3.0.0 | [MIT](#shebang-regex) | | signal-exit | 4.1.0 | [ISC](#signal-exit) | | source-map-js | 1.2.1 | [BSD-3-Clause](#source-map-js) | -| streamx | 2.23.0 | [MIT](#streamx) | +| streamx | 2.25.0 | [MIT](#streamx) | | string-width-cjs | 4.2.3 | [MIT](#string-width-cjs) | | string-width | 5.1.2 | [MIT](#string-width) | | string_decoder | 1.3.0 | [MIT](#string_decoder) | @@ -224,6 +224,7 @@ | teex | 1.0.1 | [MIT](#teex) | | text-decoder | 1.2.7 | [Apache-2.0](#text-decoder) | | text-segmentation | 1.0.3 | [MIT](#text-segmentation) | +| tinyglobby | 0.2.16 | [MIT](#tinyglobby) | | tmp | 0.2.5 | [MIT](#tmp) | | tslib | 2.8.1 | [0BSD](#tslib) | | universalify | 2.0.1 | [MIT](#universalify) | @@ -234,12 +235,12 @@ | uuid | 8.3.2 | [MIT](#uuid) | | varint | 6.0.0 | [MIT](#varint) | | vite-plugin-vuetify | 2.1.3 | [MIT](#vite-plugin-vuetify) | -| vite | 5.4.21 | [MIT](#vite) | +| vite | 6.4.2 | [MIT](#vite) | | vue-chartjs | 5.3.3 | [MIT](#vue-chartjs) | | vue-demi | 0.14.10 | [MIT](#vue-demi) | | vue-i18n | 11.1.10 | [MIT](#vue-i18n) | | vue-router | 4.6.4 | [MIT](#vue-router) | -| vue | 3.5.29 | [MIT](#vue) | +| vue | 3.5.32 | [MIT](#vue) | | vuetify | 4.0.2 | [MIT](#vuetify) | | webpack-merge | 5.10.0 | [MIT](#webpack-merge) | | which | 2.0.2 | [ISC](#which) | @@ -247,7 +248,7 @@ | wrap-ansi-cjs | 7.0.0 | [MIT](#wrap-ansi-cjs) | | wrap-ansi | 8.1.0 | [MIT](#wrap-ansi) | | xmlchars | 2.2.0 | [MIT](#xmlchars) | -| yaml | 2.8.2 | [ISC](#yaml) | +| yaml | 2.8.3 | [ISC](#yaml) | | zip-stream | 6.0.1 | [MIT](#zip-stream) | @@ -1665,31 +1666,6 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ---- -### @microsoft/applicationinsights-common - - The MIT License (MIT) - - Copyright (c) Microsoft Corporation - - Permission is hereby granted, free of charge, to any person obtaining a copy - of this software and associated documentation files (the "Software"), to deal - in the Software without restriction, including without limitation the rights - to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - copies of the Software, and to permit persons to whom the Software is - furnished to do so, subject to the following conditions: - - The above copyright notice and this permission notice shall be included in all - copies or substantial portions of the Software. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - SOFTWARE. - --- ### @microsoft/applicationinsights-core-js @@ -7908,6 +7884,17 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +--- +### fdir + + Copyright 2023 Abdullah Atta + + Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + --- ### flat @@ -10662,7 +10649,7 @@ The MIT License (MIT) - Copyright 2013 Andrey Sitnik + Copyright 2013 Andrey Sitnik Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in @@ -14518,6 +14505,31 @@ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +--- +### tinyglobby + + MIT License + + Copyright (c) 2024 Madeline Gurriarán + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + --- ### tmp @@ -14753,7 +14765,7 @@ # Licenses of bundled dependencies The published Vite artifact additionally contains code with the following licenses: - Apache-2.0, BSD-2-Clause, BlueOak-1.0.0, CC0-1.0, ISC, MIT + Apache-2.0, BSD-2-Clause, CC0-1.0, ISC, MIT # Bundled dependencies: ## @ampproject/remapping @@ -14965,10 +14977,10 @@ --------------------------------------- - ## @jridgewell/gen-mapping + ## @jridgewell/gen-mapping, @jridgewell/set-array License: MIT By: Justin Ridgewell - Repository: https://github.com/jridgewell/gen-mapping + Repositories: https://github.com/jridgewell/gen-mapping, https://github.com/jridgewell/set-array > Copyright 2022 Justin Ridgewell > @@ -15019,33 +15031,6 @@ --------------------------------------- - ## @jridgewell/set-array - License: MIT - By: Justin Ridgewell - Repository: https://github.com/jridgewell/set-array - - > Copyright 2022 Justin Ridgewell - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - ## @jridgewell/sourcemap-codec License: MIT By: Rich Harris @@ -15102,13 +15087,39 @@ --------------------------------------- - ## @nodelib/fs.scandir + ## @polka/compression + License: MIT + Repository: lukeed/polka + + --------------------------------------- + + ## @polka/url + License: MIT + By: Luke Edwards + Repository: lukeed/polka + + --------------------------------------- + + ## @rollup/plugin-alias, @rollup/plugin-commonjs, @rollup/plugin-dynamic-import-vars, @rollup/pluginutils + License: MIT + By: Johannes Stein + Repository: rollup/plugins + + License: MIT + By: Rich Harris + Repository: rollup/plugins + + License: MIT + By: LarsDenBakker + Repository: rollup/plugins + License: MIT - Repository: https://github.com/nodelib/nodelib/tree/master/packages/fs/fs.scandir + By: Rich Harris + Repository: rollup/plugins > The MIT License (MIT) > - > Copyright (c) Denis Malinochkin + > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15117,54 +15128,51 @@ > copies of the Software, and to permit persons to whom the Software is > furnished to do so, subject to the following conditions: > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. + > The above copyright notice and this permission notice shall be included in + > all copies or substantial portions of the Software. > > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. + > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN + > THE SOFTWARE. --------------------------------------- - ## @nodelib/fs.stat - License: MIT - Repository: https://github.com/nodelib/nodelib/tree/master/packages/fs/fs.stat + ## anymatch + License: ISC + By: Elan Shanker + Repository: https://github.com/micromatch/anymatch - > The MIT License (MIT) - > - > Copyright (c) Denis Malinochkin + > The ISC License > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: + > Copyright (c) 2019 Elan Shanker, Paul Miller (https://paulmillr.com) > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. + > Permission to use, copy, modify, and/or distribute this software for any + > purpose with or without fee is hereby granted, provided that the above + > copyright notice and this permission notice appear in all copies. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. + > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR + > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. --------------------------------------- - ## @nodelib/fs.walk + ## artichokie License: MIT - Repository: https://github.com/nodelib/nodelib/tree/master/packages/fs/fs.walk + By: sapphi-red, Evan You + Repository: git+https://github.com/sapphi-red/artichokie.git - > The MIT License (MIT) + > MIT License > - > Copyright (c) Denis Malinochkin + > Copyright (c) 2020-present, Yuxi (Evan) You + > Copyright (c) 2023-present, sapphi-red > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15186,27 +15194,40 @@ --------------------------------------- - ## @polka/compression + ## binary-extensions License: MIT - Repository: lukeed/polka + By: Sindre Sorhus + Repository: sindresorhus/binary-extensions + + > MIT License + > + > Copyright (c) Sindre Sorhus (https://sindresorhus.com) + > Copyright (c) Paul Miller (https://paulmillr.com) + > + > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + > + > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + > + > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. --------------------------------------- - ## @polka/url + ## braces, fill-range, is-number License: MIT - By: Luke Edwards - Repository: lukeed/polka + By: Jon Schlinkert, Brian Woodward, Elan Shanker, Eugene Sharygin, hemanth.hm + Repository: micromatch/braces - --------------------------------------- + License: MIT + By: Jon Schlinkert, Edo Rivai, Paul Miller, Rouven Weßling + Repository: jonschlinkert/fill-range - ## @rollup/plugin-alias License: MIT - By: Johannes Stein - Repository: rollup/plugins + By: Jon Schlinkert, Olsten Larck, Rouven Weßling + Repository: jonschlinkert/is-number > The MIT License (MIT) > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) 2014-present, Jon Schlinkert. > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15228,43 +15249,31 @@ --------------------------------------- - ## @rollup/plugin-commonjs + ## bundle-name, default-browser, default-browser-id, define-lazy-prop, is-docker, is-inside-container, is-wsl, open, run-applescript License: MIT - By: Rich Harris - Repository: rollup/plugins + By: Sindre Sorhus + Repositories: sindresorhus/bundle-name, sindresorhus/default-browser, sindresorhus/default-browser-id, sindresorhus/define-lazy-prop, sindresorhus/is-docker, sindresorhus/is-inside-container, sindresorhus/is-wsl, sindresorhus/open, sindresorhus/run-applescript - > The MIT License (MIT) + > MIT License > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) Sindre Sorhus (https://sindresorhus.com) > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: + > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. + > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. + > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. --------------------------------------- - ## @rollup/plugin-dynamic-import-vars + ## cac License: MIT - By: LarsDenBakker - Repository: rollup/plugins + By: egoist + Repository: egoist/cac > The MIT License (MIT) > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) EGOIST <0x142857@gmail.com> (https://github.com/egoist) > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -15286,17 +15295,17 @@ --------------------------------------- - ## @rollup/pluginutils + ## chokidar License: MIT - By: Rich Harris - Repository: rollup/plugins + By: Paul Miller, Elan Shanker + Repository: git+https://github.com/paulmillr/chokidar.git > The MIT License (MIT) > - > Copyright (c) 2019 RollupJS Plugin Contributors (https://github.com/rollup/plugins/graphs/contributors) + > Copyright (c) 2012-2019 Paul Miller (https://paulmillr.com), Elan Shanker > > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal + > of this software and associated documentation files (the “Software”), to deal > in the Software without restriction, including without limitation the rights > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell > copies of the Software, and to permit persons to whom the Software is @@ -15305,7 +15314,7 @@ > The above copyright notice and this permission notice shall be included in > all copies or substantial portions of the Software. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + > THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER @@ -15315,286 +15324,27 @@ --------------------------------------- - ## ansi-regex + ## commondir, shell-quote License: MIT - By: Sindre Sorhus - Repository: chalk/ansi-regex + By: James Halliday + Repositories: http://github.com/substack/node-commondir.git, http://github.com/ljharb/shell-quote.git - > MIT License + > The MIT License > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) + > Copyright (c) 2013 James Halliday (mail@substack.net) > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + > Permission is hereby granted, free of charge, + > to any person obtaining a copy of this software and + > associated documentation files (the "Software"), to + > deal in the Software without restriction, including + > without limitation the rights to use, copy, modify, + > merge, publish, distribute, sublicense, and/or sell + > copies of the Software, and to permit persons to whom + > the Software is furnished to do so, + > subject to the following conditions: > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## anymatch - License: ISC - By: Elan Shanker - Repository: https://github.com/micromatch/anymatch - - > The ISC License - > - > Copyright (c) 2019 Elan Shanker, Paul Miller (https://paulmillr.com) - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## artichokie - License: MIT - By: sapphi-red, Evan You - Repository: git+https://github.com/sapphi-red/artichokie.git - - > MIT License - > - > Copyright (c) 2020-present, Yuxi (Evan) You - > Copyright (c) 2023-present, sapphi-red - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## astring - License: MIT - By: David Bonnet - Repository: https://github.com/davidbonnet/astring.git - - > Copyright (c) 2015, David Bonnet - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## balanced-match - License: MIT - By: Julian Gruber - Repository: git://github.com/juliangruber/balanced-match.git - - > (MIT) - > - > Copyright (c) 2013 Julian Gruber <julian@juliangruber.com> - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies - > of the Software, and to permit persons to whom the Software is furnished to do - > so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## binary-extensions - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/binary-extensions - - > MIT License - > - > Copyright (c) 2019 Sindre Sorhus (https://sindresorhus.com), Paul Miller (https://paulmillr.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## brace-expansion - License: MIT - By: Julian Gruber - Repository: git://github.com/juliangruber/brace-expansion.git - - > MIT License - > - > Copyright (c) 2013 Julian Gruber - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## braces - License: MIT - By: Jon Schlinkert, Brian Woodward, Elan Shanker, Eugene Sharygin, hemanth.hm - Repository: micromatch/braces - - > The MIT License (MIT) - > - > Copyright (c) 2014-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## cac - License: MIT - By: egoist - Repository: egoist/cac - - > The MIT License (MIT) - > - > Copyright (c) EGOIST <0x142857@gmail.com> (https://github.com/egoist) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## chokidar - License: MIT - By: Paul Miller, Elan Shanker - Repository: git+https://github.com/paulmillr/chokidar.git - - > The MIT License (MIT) - > - > Copyright (c) 2012-2019 Paul Miller (https://paulmillr.com), Elan Shanker - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the “Software”), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## commondir - License: MIT - By: James Halliday - Repository: http://github.com/substack/node-commondir.git - - > The MIT License - > - > Copyright (c) 2013 James Halliday (mail@substack.net) - > - > Permission is hereby granted, free of charge, - > to any person obtaining a copy of this software and - > associated documentation files (the "Software"), to - > deal in the Software without restriction, including - > without limitation the rights to use, copy, modify, - > merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom - > the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice - > shall be included in all copies or substantial portions of the Software. + > The above copyright notice and this permission notice + > shall be included in all copies or substantial portions of the Software. > > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, > EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES @@ -15784,23 +15534,6 @@ --------------------------------------- - ## define-lazy-prop - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/define-lazy-prop - - > MIT License - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## dotenv License: BSD-2-Clause Repository: git://github.com/motdotla/dotenv.git @@ -16063,85 +15796,6 @@ --------------------------------------- - ## fast-glob - License: MIT - By: Denis Malinochkin - Repository: mrmlnc/fast-glob - - > The MIT License (MIT) - > - > Copyright (c) Denis Malinochkin - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## fastq - License: ISC - By: Matteo Collina - Repository: git+https://github.com/mcollina/fastq.git - - > Copyright (c) 2015-2020, Matteo Collina - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF - > OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## fill-range - License: MIT - By: Jon Schlinkert, Edo Rivai, Paul Miller, Rouven Weßling - Repository: jonschlinkert/fill-range - - > The MIT License (MIT) - > - > Copyright (c) 2014-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - ## finalhandler License: MIT By: Douglas Christopher Wilson @@ -16175,7 +15829,7 @@ ## follow-redirects License: MIT By: Ruben Verborgh, Olivier Lalonde, James Talmage - Repository: git@github.com:follow-redirects/follow-redirects.git + Repository: git+ssh://git@github.com/follow-redirects/follow-redirects.git > Copyright 2014–present Olivier Lalonde , James Talmage , Ruben Verborgh > @@ -16227,29 +15881,6 @@ --------------------------------------- - ## glob - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/node-glob.git - - > The ISC License - > - > Copyright (c) 2009-2023 Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - ## glob-parent License: ISC By: Gulp Team, Elan Shanker, Blaine Bublitz @@ -16334,23 +15965,6 @@ --------------------------------------- - ## is-docker - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/is-docker - - > MIT License - > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## is-extglob License: MIT By: Jon Schlinkert @@ -16380,43 +15994,14 @@ --------------------------------------- - ## is-glob - License: MIT - By: Jon Schlinkert, Brian Woodward, Daniel Perez - Repository: micromatch/is-glob - - > The MIT License (MIT) - > - > Copyright (c) 2014-2017, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## is-number + ## is-glob License: MIT - By: Jon Schlinkert, Olsten Larck, Rouven Weßling - Repository: jonschlinkert/is-number + By: Jon Schlinkert, Brian Woodward, Daniel Perez + Repository: micromatch/is-glob > The MIT License (MIT) > - > Copyright (c) 2014-present, Jon Schlinkert. + > Copyright (c) 2014-2017, Jon Schlinkert. > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -16445,27 +16030,10 @@ --------------------------------------- - ## is-wsl - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/is-wsl - - > MIT License - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## isexe + ## isexe, which License: ISC By: Isaac Z. Schlueter - Repository: git+https://github.com/isaacs/isexe.git + Repositories: git+https://github.com/isaacs/isexe.git, git://github.com/isaacs/node-which.git > The ISC License > @@ -16514,39 +16082,10 @@ --------------------------------------- - ## launch-editor - License: MIT - By: Evan You - Repository: git+https://github.com/yyx990803/launch-editor.git - - > The MIT License (MIT) - > - > Copyright (c) 2017-present, Yuxi (Evan) You - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## launch-editor-middleware + ## launch-editor, launch-editor-middleware License: MIT By: Evan You - Repository: git+https://github.com/yyx990803/launch-editor.git + Repositories: git+https://github.com/yyx990803/launch-editor.git, git+https://github.com/yyx990803/launch-editor.git > The MIT License (MIT) > @@ -16684,29 +16223,6 @@ --------------------------------------- - ## lru-cache - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/node-lru-cache.git - - > The ISC License - > - > Copyright (c) 2010-2023 Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - ## magic-string License: MIT By: Rich Harris @@ -16722,112 +16238,9 @@ --------------------------------------- - ## merge2 - License: MIT - Repository: git@github.com:teambition/merge2.git - - > The MIT License (MIT) - > - > Copyright (c) 2014-2020 Teambition - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## micromatch - License: MIT - By: Jon Schlinkert, Amila Welihinda, Bogdan Chadkin, Brian Woodward, Devon Govett, Elan Shanker, Fabrício Matté, Martin Kolárik, Olsten Larck, Paul Miller, Tom Byrer, Tyler Akins, Peter Bright, Kuba Juszczyk - Repository: micromatch/micromatch - - > The MIT License (MIT) - > - > Copyright (c) 2014-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## minimatch - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/minimatch.git - - > The ISC License - > - > Copyright (c) 2011-2023 Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## minipass - License: ISC - By: Isaac Z. Schlueter - Repository: https://github.com/isaacs/minipass - - > The ISC License - > - > Copyright (c) 2017-2023 npm, Inc., Isaac Z. Schlueter, and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## mlly + ## mlly, ufo License: MIT - Repository: unjs/mlly + Repositories: unjs/mlly, unjs/ufo > MIT License > @@ -16884,11 +16297,11 @@ ## ms License: MIT - Repository: zeit/ms + Repository: vercel/ms > The MIT License (MIT) > - > Copyright (c) 2016 Zeit, Inc. + > Copyright (c) 2020 Vercel, Inc. > > Permission is hereby granted, free of charge, to any person obtaining a copy > of this software and associated documentation files (the "Software"), to deal @@ -16999,23 +16412,6 @@ --------------------------------------- - ## open - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/open - - > MIT License - > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## parse5 License: MIT By: Ivan Nikulin, https://github.com/inikulin/parse5/graphs/contributors @@ -17074,10 +16470,10 @@ --------------------------------------- - ## path-key + ## path-key, shebang-regex License: MIT By: Sindre Sorhus - Repository: sindresorhus/path-key + Repositories: sindresorhus/path-key, sindresorhus/shebang-regex > MIT License > @@ -17091,69 +16487,6 @@ --------------------------------------- - ## path-scurry - License: BlueOak-1.0.0 - By: Isaac Z. Schlueter - Repository: git+https://github.com/isaacs/path-scurry - - > # Blue Oak Model License - > - > Version 1.0.0 - > - > ## Purpose - > - > This license gives everyone as much permission to work with - > this software as possible, while protecting contributors - > from liability. - > - > ## Acceptance - > - > In order to receive this license, you must agree to its - > rules. The rules of this license are both obligations - > under that agreement and conditions to your license. - > You must not do anything with this software that triggers - > a rule that you cannot or will not follow. - > - > ## Copyright - > - > Each contributor licenses you to do everything with this - > software that would otherwise infringe that contributor's - > copyright in it. - > - > ## Notices - > - > You must ensure that everyone who gets a copy of - > any part of this software from you, with or without - > changes, also gets the text of this license or a link to - > . - > - > ## Excuse - > - > If anyone notifies you in writing that you have not - > complied with [Notices](#notices), you can keep your - > license by taking all practical steps to comply within 30 - > days after the notice. If you do not do so, your license - > ends immediately. - > - > ## Patent - > - > Each contributor licenses you to do everything with this - > software that would otherwise infringe any patent claims - > they can license or become able to license. - > - > ## Reliability - > - > No contributor can revoke this license. - > - > ## No Liability - > - > ***As far as the law allows, this software comes as is, - > without any warranty or condition, and no contributor - > will be liable to anyone for any damages related to this - > software or this license, under any kind of legal claim.*** - - --------------------------------------- - ## periscopic License: MIT Repository: Rich-Harris/periscopic @@ -17175,77 +16508,19 @@ > ISC License > - > Copyright (c) 2021 Alexey Raspopov, Kostiantyn Denysov, Anton Verinov + > Copyright (c) 2021-2024 Oleksii Raspopov, Kostiantyn Denysov, Anton Verinov > > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF - > OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - - ## picomatch - License: MIT - By: Jon Schlinkert - Repository: micromatch/picomatch - - > The MIT License (MIT) - > - > Copyright (c) 2017-present, Jon Schlinkert. - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - - ## pify - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/pify - - > The MIT License (MIT) - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. + > purpose with or without fee is hereby granted, provided that the above + > copyright notice and this permission notice appear in all copies. > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. + > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + > OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. --------------------------------------- @@ -17464,62 +16739,6 @@ --------------------------------------- - ## queue-microtask - License: MIT - By: Feross Aboukhadijeh - Repository: git://github.com/feross/queue-microtask.git - - > The MIT License (MIT) - > - > Copyright (c) Feross Aboukhadijeh - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of - > the Software, and to permit persons to whom the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS - > FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR - > COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## read-cache - License: MIT - By: Bogdan Chadkin - Repository: git+https://github.com/TrySound/read-cache.git - - > The MIT License (MIT) - > - > Copyright 2016 Bogdan Chadkin - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of - > the Software, and to permit persons to whom the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS - > FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR - > COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## readdirp License: MIT By: Thorsten Lorenz, Paul Miller @@ -17578,10 +16797,10 @@ --------------------------------------- - ## resolve.exports + ## resolve.exports, totalist License: MIT By: Luke Edwards - Repository: lukeed/resolve.exports + Repositories: lukeed/resolve.exports, lukeed/totalist > The MIT License (MIT) > @@ -17607,63 +16826,6 @@ --------------------------------------- - ## reusify - License: MIT - By: Matteo Collina - Repository: git+https://github.com/mcollina/reusify.git - - > The MIT License (MIT) - > - > Copyright (c) 2015 Matteo Collina - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - - ## run-parallel - License: MIT - By: Feross Aboukhadijeh - Repository: git://github.com/feross/run-parallel.git - - > The MIT License (MIT) - > - > Copyright (c) Feross Aboukhadijeh - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of - > this software and associated documentation files (the "Software"), to deal in - > the Software without restriction, including without limitation the rights to - > use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of - > the Software, and to permit persons to whom the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS - > FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR - > COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN - > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## shebang-command License: MIT By: Kevin Mårtensson @@ -17681,55 +16843,6 @@ --------------------------------------- - ## shebang-regex - License: MIT - By: Sindre Sorhus - Repository: sindresorhus/shebang-regex - - > MIT License - > - > Copyright (c) Sindre Sorhus (sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - - ## shell-quote - License: MIT - By: James Halliday - Repository: http://github.com/ljharb/shell-quote.git - - > The MIT License - > - > Copyright (c) 2013 James Halliday (mail@substack.net) - > - > Permission is hereby granted, free of charge, - > to any person obtaining a copy of this software and - > associated documentation files (the "Software"), to - > deal in the Software without restriction, including - > without limitation the rights to use, copy, modify, - > merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom - > the Software is furnished to do so, - > subject to the following conditions: - > - > The above copyright notice and this permission notice - > shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - > EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - > OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. - > IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR - > ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, - > TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE - > SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## sirv License: MIT By: Luke Edwards @@ -17774,23 +16887,6 @@ --------------------------------------- - ## strip-ansi - License: MIT - By: Sindre Sorhus - Repository: chalk/strip-ansi - - > MIT License - > - > Copyright (c) Sindre Sorhus (https://sindresorhus.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - --------------------------------------- - ## strip-literal License: MIT By: Anthony Fu @@ -17849,35 +16945,6 @@ --------------------------------------- - ## totalist - License: MIT - By: Luke Edwards - Repository: lukeed/totalist - - > The MIT License (MIT) - > - > Copyright (c) Luke Edwards (lukeed.com) - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in - > all copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN - > THE SOFTWARE. - - --------------------------------------- - ## tsconfck License: MIT By: dominikg @@ -17932,34 +16999,6 @@ --------------------------------------- - ## ufo - License: MIT - Repository: unjs/ufo - - > MIT License - > - > Copyright (c) Pooya Parsa - > - > Permission is hereby granted, free of charge, to any person obtaining a copy - > of this software and associated documentation files (the "Software"), to deal - > in the Software without restriction, including without limitation the rights - > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - > copies of the Software, and to permit persons to whom the Software is - > furnished to do so, subject to the following conditions: - > - > The above copyright notice and this permission notice shall be included in all - > copies or substantial portions of the Software. - > - > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - > SOFTWARE. - - --------------------------------------- - ## unpipe License: MIT By: Douglas Christopher Wilson @@ -18080,29 +17119,6 @@ --------------------------------------- - ## which - License: ISC - By: Isaac Z. Schlueter - Repository: git://github.com/isaacs/node-which.git - - > The ISC License - > - > Copyright (c) Isaac Z. Schlueter and Contributors - > - > Permission to use, copy, modify, and/or distribute this software for any - > purpose with or without fee is hereby granted, provided that the above - > copyright notice and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES - > WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF - > MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR - > ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES - > WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN - > ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR - > IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - - --------------------------------------- - ## ws License: MIT By: Einar Otto Stangvik @@ -18129,27 +17145,6 @@ > IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN > CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - --------------------------------------- - - ## yaml - License: ISC - By: Eemeli Aro - Repository: github:eemeli/yaml - - > Copyright Eemeli Aro - > - > Permission to use, copy, modify, and/or distribute this software for any purpose - > with or without fee is hereby granted, provided that the above copyright notice - > and this permission notice appear in all copies. - > - > THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH - > REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND - > FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, - > INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS - > OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER - > TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF - > THIS SOFTWARE. - --- ### vue-chartjs diff --git a/studybuilder/src/api/controlledTerminology/pairedCodelists.js b/studybuilder/src/api/controlledTerminology/pairedCodelists.js index 186aa9cf..533733ca 100644 --- a/studybuilder/src/api/controlledTerminology/pairedCodelists.js +++ b/studybuilder/src/api/controlledTerminology/pairedCodelists.js @@ -3,6 +3,9 @@ import repository from '../repository' const resource = 'ct/paired-codelists' export default { + create(data) { + return repository.post(resource, data) + }, getCodelistTerms(codelistUid, params) { return repository.get(`${resource}/${codelistUid}/terms`, { params }) }, diff --git a/studybuilder/src/api/study.js b/studybuilder/src/api/study.js index 51650aa7..9d4a15f2 100644 --- a/studybuilder/src/api/study.js +++ b/studybuilder/src/api/study.js @@ -978,6 +978,9 @@ export default { getComplexityScore(studyUid) { return repository.get(`${resource}/${studyUid}/complexity-score`) }, + getComplexityScoreDetails(studyUid) { + return repository.get(`${resource}/${studyUid}/complexity-score-details`) + }, // Study Data Suppliers getAllStudyDataSuppliers(params) { return repository.get('study-data-suppliers', { params }) diff --git a/studybuilder/src/api/studyTemplate.js b/studybuilder/src/api/studyTemplate.js new file mode 100644 index 00000000..f0fccca4 --- /dev/null +++ b/studybuilder/src/api/studyTemplate.js @@ -0,0 +1,15 @@ +import repository from './repository' + +const resource = 'studies' + +export default { + getStudyTemplate() { + return repository.get(`${resource}/template`) + }, + setStudyTemplate(data) { + return repository.post(`${resource}/template`, data) + }, + updateStudyTemplate(data) { + return repository.patch(`${resource}/template`, data) + }, +} diff --git a/studybuilder/src/components/layout/TopBar.vue b/studybuilder/src/components/layout/TopBar.vue index 4e5e180c..5fd6138f 100644 --- a/studybuilder/src/components/layout/TopBar.vue +++ b/studybuilder/src/components/layout/TopBar.vue @@ -93,6 +93,7 @@

    newItemVersion(item, 'activity-instances', 'attributes'), }, { - label: t('ActivitiesTable.inactivate_attributes'), + label: t('ActivitiesTable.inactivate'), icon: 'mdi-close-octagon-outline', iconColor: 'primary', - condition: (item) => item.possible_actions?.includes('inactivate'), + condition: (item) => + item.possible_actions?.includes('inactivate') || + item.groupings_possible_actions?.includes('inactivate'), accessRole: roles.LIBRARY_WRITE, - click: (item) => inactivateItem(item, 'activity-instances', 'attributes'), + click: (item) => inactivateInstance(item), }, { - label: t('ActivitiesTable.reactivate_attributes'), + label: t('ActivitiesTable.reactivate'), icon: 'mdi-undo-variant', iconColor: 'primary', - condition: (item) => item.possible_actions?.includes('reactivate'), + condition: (item) => + item.status === statuses.RETIRED && + item.possible_actions?.includes('reactivate'), accessRole: roles.LIBRARY_WRITE, - click: (item) => reactivateItem(item, 'activity-instances', 'attributes'), + click: (item) => reactivateInstance(item), }, // --- Groupings actions --- { @@ -787,24 +791,6 @@ const instanceActions = [ accessRole: roles.LIBRARY_WRITE, click: (item) => newItemVersion(item, 'activity-instances', 'groupings'), }, - { - label: t('ActivitiesTable.inactivate_groupings'), - icon: 'mdi-close-octagon-outline', - iconColor: 'primary', - condition: (item) => - item.groupings_possible_actions?.includes('inactivate'), - accessRole: roles.LIBRARY_WRITE, - click: (item) => inactivateItem(item, 'activity-instances', 'groupings'), - }, - { - label: t('ActivitiesTable.reactivate_groupings'), - icon: 'mdi-undo-variant', - iconColor: 'primary', - condition: (item) => - item.groupings_possible_actions?.includes('reactivate'), - accessRole: roles.LIBRARY_WRITE, - click: (item) => reactivateItem(item, 'activity-instances', 'groupings'), - }, // --- Shared actions --- { label: t('_global.delete'), @@ -1257,14 +1243,8 @@ function transformItems(items) { : item.activities || [] for (const grouping of item.activity_groupings) { - groups.push({ - name: grouping.activity_group.name, - uid: grouping.activity_group.uid, - }) - subgroups.push({ - name: grouping.activity_subgroup.name, - uid: grouping.activity_subgroup.uid, - }) + groups.push(grouping.activity_group.name) + subgroups.push(grouping.activity_subgroup.name) } // Remove existing activity_group and activity_subgroup to avoid conflicts const cleanItem = { ...item } @@ -1467,14 +1447,10 @@ function fetchActivities(filters, options, filtersUpdated) { } if (props.source === 'activities') { - const filtersObj = normalizeFiltersObject(params.filters) - if (!filtersObj.library_name) { - filtersObj.library_name = { - v: [libConstants.LIBRARY_ARCHIVED], - op: onlyArchivedLibrary.value ? 'eq' : 'ne', - } + params.filters = normalizeFiltersObject(params.filters) + if (onlyArchivedLibrary.value) { + params.library_name = libConstants.LIBRARY_ARCHIVED } - params.filters = filtersObj } // Ensure filters are stringified if they're objects @@ -1644,6 +1620,16 @@ function inactivateItem(item, source, subitem) { }) } +function inactivateInstance(item) { + activitiesApi.inactivate(item.uid, 'activity-instances').then(() => { + notificationHub.add({ + msg: t(`ActivitiesTable.inactivate_${props.source}_success`), + type: 'success', + }) + tableRef.value.filterTable() + }) +} + function reactivateItem(item, source, subitem) { source = source === undefined ? props.source : source activitiesApi.reactivate(item.uid, source, subitem).then(() => { @@ -1655,6 +1641,16 @@ function reactivateItem(item, source, subitem) { }) } +function reactivateInstance(item) { + activitiesApi.reactivate(item.uid, 'activity-instances').then(() => { + notificationHub.add({ + msg: t(`ActivitiesTable.reactivate_${props.source}_success`), + type: 'success', + }) + tableRef.value.filterTable() + }) +} + function deleteItem(item, source) { source = source === undefined ? props.source : source activitiesApi.delete(item.uid, source).then(() => { @@ -1811,7 +1807,7 @@ function getSubgroupActivities(items) { function updateArchivedView() { if (onlyArchivedLibrary.value) { - selectedStatusTab.value = 'retired' + selectedStatusTab.value = 'all' } else { selectedStatusTab.value = 'final' } diff --git a/studybuilder/src/components/library/ActivityGroupingsSummary.vue b/studybuilder/src/components/library/ActivityGroupingsSummary.vue index fba40d88..bf010a74 100644 --- a/studybuilder/src/components/library/ActivityGroupingsSummary.vue +++ b/studybuilder/src/components/library/ActivityGroupingsSummary.vue @@ -27,7 +27,13 @@
    {{ $t('_global.status') }}
    -
    {{ summaryData.status || '-' }}
    +
    + + - +
    {{ $t('_global.author') }}
    @@ -61,6 +67,7 @@ + + diff --git a/studybuilder/src/components/library/ActivitySummary.vue b/studybuilder/src/components/library/ActivitySummary.vue index 17a471e4..9e131e40 100644 --- a/studybuilder/src/components/library/ActivitySummary.vue +++ b/studybuilder/src/components/library/ActivitySummary.vue @@ -170,7 +170,7 @@ const activityInfo = computed(() => { return { uid: firstGrouping.activity.uid, name: firstGrouping.activity.name, - version: firstGrouping.activity.version || '1.0', + version: firstGrouping.activity.version, } }) diff --git a/studybuilder/src/components/library/BaseActivityOverview.vue b/studybuilder/src/components/library/BaseActivityOverview.vue index e75692e0..5351ee09 100644 --- a/studybuilder/src/components/library/BaseActivityOverview.vue +++ b/studybuilder/src/components/library/BaseActivityOverview.vue @@ -20,6 +20,7 @@ ({}), }, + hiddenActions: { + type: Array, + default: () => [], + }, }, emits: ['closePage', 'refresh'], setup() { @@ -203,6 +208,7 @@ export default { actions() { return [ { + key: 'approve', label: this.$t('_global.approve'), icon: 'mdi-check-decagram', iconColor: 'success', @@ -214,6 +220,7 @@ export default { click: this.approveItem, }, { + key: 'edit', label: this.$t('_global.edit'), icon: 'mdi-pencil-outline', iconColor: 'nnBaseBlue', @@ -224,6 +231,7 @@ export default { click: this.editItem, }, { + key: 'new_version', label: this.$t('_global.new_version'), icon: 'mdi-plus-circle-outline', iconColor: 'nnBaseBlue', @@ -236,6 +244,7 @@ export default { click: this.newItemVersion, }, { + key: 'inactivate', label: this.$t('_global.inactivate'), icon: 'mdi-close-octagon-outline', iconColor: 'nnBaseBlue', @@ -248,6 +257,7 @@ export default { click: this.inactivateItem, }, { + key: 'reactivate', label: this.$t('_global.reactivate'), icon: 'mdi-undo-variant', iconColor: 'nnBaseBlue', @@ -260,6 +270,7 @@ export default { click: this.reactivateItem, }, { + key: 'delete', label: this.$t('_global.delete'), icon: 'mdi-delete-outline', iconColor: 'error', @@ -270,6 +281,7 @@ export default { click: this.deleteItem, }, { + key: 'history', label: this.$t('_global.history'), iconColor: 'nnBaseBlue', icon: 'mdi-history', @@ -278,6 +290,7 @@ export default { click: this.openHistory, }, { + key: 'close', label: this.$t('_global.close'), iconColor: 'nnBaseBlue', icon: 'mdi-close', @@ -418,7 +431,11 @@ export default { await this.fetchItem() }, async openHistory() { - const resp = await activities.getVersions(this.source, this.itemUid) + const resp = await activities.getVersions( + this.source, + this.itemUid, + this.resolveActionSubitem('history') + ) this.historyItems = this.transformItems(resp.data) this.showHistory = true }, diff --git a/studybuilder/src/components/library/CodelistCreationForm.vue b/studybuilder/src/components/library/CodelistCreationForm.vue index 4a1a32f7..e1092cd2 100644 --- a/studybuilder/src/components/library/CodelistCreationForm.vue +++ b/studybuilder/src/components/library/CodelistCreationForm.vue @@ -8,6 +8,28 @@ @close="cancel" @save="submit" > + diff --git a/studybuilder/src/components/tools/HorizontalStepperForm.vue b/studybuilder/src/components/tools/HorizontalStepperForm.vue index 60ccd50a..44f0b39b 100644 --- a/studybuilder/src/components/tools/HorizontalStepperForm.vue +++ b/studybuilder/src/components/tools/HorizontalStepperForm.vue @@ -17,6 +17,7 @@ color="secondary" class="ml-2 text-label-large" size="small" + data-cy="copy-url" @click="copyUrl" > {{ $t('_global.copy_link') }} @@ -67,6 +68,7 @@ {{ value[0].name.length > 25 - ? value[0].name.replace(/<\/?[^>]+(>)/g, '').substring(0, 25) + - '...' - : value[0].name.replace(/<\/?[^>]+(>)/g, '') + ? value[0].name.replace(/[<>]/g, '').substring(0, 25) + '...' + : value[0].name.replace(/[<>]/g, '') }}
    diff --git a/studybuilder/src/components/tools/ParameterValueSelector.vue b/studybuilder/src/components/tools/ParameterValueSelector.vue index 4c59d4e3..db1183a6 100644 --- a/studybuilder/src/components/tools/ParameterValueSelector.vue +++ b/studybuilder/src/components/tools/ParameterValueSelector.vue @@ -440,7 +440,7 @@ export default { }, cleanItemName(item) { // Return the name without any html tags such as

    or

    - return `${item.name.replace(/<\/?[^>]+(>)/g, '')}` + return `${item.name.replace(/[<>]/g, '')}` }, getNamePreview(hideEmptyParams) { if (!this.template) { diff --git a/studybuilder/src/locales/en/api.json b/studybuilder/src/locales/en/api.json index 253e4e79..86f7efc7 100644 --- a/studybuilder/src/locales/en/api.json +++ b/studybuilder/src/locales/en/api.json @@ -694,8 +694,9 @@ "body,codes,a,name,b,status": "Status of Name #{b} of Codes #{a}", "body,codes,a,name,b,template_parameter": "Template Parameter of Name #{b} of Codes #{a}", "body,codes,a,name,b,version": "Version of Name #{b} of Codes #{a}", - "body,codes,a,paired_codes_codelist_uid": "Paired Codes Codelist UID of Codes #{a}", - "body,codes,a,paired_names_codelist_uid": "Paired Names Codelist UID of Codes #{a}", + "body,codes,a,paired_codelist": "Paired Codelist of Codes #{a}", + "body,codes,a,paired_codelist,b,name": "Name of Paired Codelist #{b} of Codes #{a}", + "body,codes,a,paired_codelist,b,uid": "UID of Paired Codelist #{b} of Codes #{a}", "body,codes,a,parent_codelist_uid": "Parent Codelist UID of Codes #{a}", "body,cohort_count": "Cohort Count", "body,cohort_uid": "Cohort UID", @@ -1126,6 +1127,11 @@ "body,content,a,uid": "UID of Content #{a}", "body,conversion_factor_to_master": "Conversion Factor To Master", "body,convertible_unit": "Convertible Unit", + "body,copy_study_activity": "Copy Study Activity", + "body,copy_study_activity_group": "Copy Study Activity Group", + "body,copy_study_activity_instance": "Copy Study Activity Instance", + "body,copy_study_activity_schedule": "Copy Study Activity Schedule", + "body,copy_study_activity_subgroup": "Copy Study Activity Subgroup", "body,copy_study_arm": "Copy Study Arm", "body,copy_study_branch_arm": "Copy Study Branch Arm", "body,copy_study_cohort": "Copy Study Cohort", @@ -1133,6 +1139,7 @@ "body,copy_study_element": "Copy Study Element", "body,copy_study_epoch": "Copy Study Epoch", "body,copy_study_epochs_study_footnote": "Copy Study Epochs Study Footnote", + "body,copy_study_soa_group": "Copy Study Soa Group", "body,copy_study_visit": "Copy Study Visit", "body,copy_study_visits_study_footnote": "Copy Study Visits Study Footnote", "body,core": "Core", @@ -2019,6 +2026,7 @@ "body,groupings_status": "Groupings Status", "body,groupings_version": "Groupings Version", "body,guidance_text": "Guidance Text", + "body,has_final_protocol_locked_version": "Has Final Protocol Locked Version", "body,has_mapping_target": "Has Mapping Target", "body,has_mapping_target,a,name": "Name of Has Mapping Target #{a}", "body,has_mapping_target,a,uid": "UID of Has Mapping Target #{a}", @@ -3411,8 +3419,9 @@ "body,items,a,other_info": "Other Info of Items #{a}", "body,items,a,other_reason_for_locking_releasing": "Other Reason For Locking Releasing of Items #{a}", "body,items,a,other_reason_for_unlocking": "Other Reason For Unlocking of Items #{a}", - "body,items,a,paired_codes_codelist_uid": "Paired Codes Codelist UID of Items #{a}", - "body,items,a,paired_names_codelist_uid": "Paired Names Codelist UID of Items #{a}", + "body,items,a,paired_codelist": "Paired Codelist of Items #{a}", + "body,items,a,paired_codelist,b,name": "Name of Paired Codelist #{b} of Items #{a}", + "body,items,a,paired_codelist,b,uid": "UID of Paired Codelist #{b} of Items #{a}", "body,items,a,parameter_terms": "Parameter Terms of Items #{a}", "body,items,a,parameter_terms,b,conjunction": "Conjunction of Parameter Terms #{b} of Items #{a}", "body,items,a,parameter_terms,b,position": "Position of Parameter Terms #{b} of Items #{a}", @@ -3568,6 +3577,7 @@ "body,items,a,status_modified_at": "Status Modified At of Items #{a}", "body,items,a,status_modified_by": "Status Modified By of Items #{a}", "body,items,a,structure": "Structure of Items #{a}", + "body,items,a,study_acronym": "Study Acronym of Items #{a}", "body,items,a,study_activity_group": "Study Activity Group of Items #{a}", "body,items,a,study_activity_group_uid": "Study Activity Group UID of Items #{a}", "body,items,a,study_activity_group_uids": "Study Activity Group UIDs of Items #{a}", @@ -4021,6 +4031,7 @@ "body,items,a,study_soa_group,b,soa_group_term_uid": "Soa Group Term UID of Study Soa Group #{b} of Items #{a}", "body,items,a,study_soa_group,b,study_soa_group_uid": "Study Soa Group UID of Study Soa Group #{b} of Items #{a}", "body,items,a,study_status": "Study Status of Items #{a}", + "body,items,a,study_subpart_acronym": "Study Subpart Acronym of Items #{a}", "body,items,a,study_subpart_uids": "Study Subpart UIDs of Items #{a}", "body,items,a,study_uid": "Study UID of Items #{a}", "body,items,a,study_version": "Study Version of Items #{a}", @@ -4036,6 +4047,8 @@ "body,items,a,sub_domain_class": "Sub Domain Class of Items #{a}", "body,items,a,sub_domain_type": "Sub Domain Type of Items #{a}", "body,items,a,submission_value": "Submission Value of Items #{a}", + "body,items,a,subpart_id": "Subpart Id of Items #{a}", + "body,items,a,subpart_uid": "Subpart UID of Items #{a}", "body,items,a,suppl_qual_flag": "Suppl Qual Flag of Items #{a}", "body,items,a,supplier_type": "Supplier Type of Items #{a}", "body,items,a,supplier_type,b,name": "Name of Supplier Type #{b} of Items #{a}", @@ -4347,6 +4360,7 @@ "body,key_criteria": "Key Criteria", "body,keys": "Keys", "body,label": "Label", + "body,labels_from_target": "Labels From Target", "body,latest_activity": "Latest Activity", "body,latest_activity_instance": "Latest Activity Instance", "body,latest_activity_instance,a,activity_instance_class": "Activity Instance Class of Latest Activity Instance #{a}", @@ -4439,8 +4453,9 @@ "body,latest_added_codelists,a,name,b,status": "Status of Name #{b} of Latest Added Codelists #{a}", "body,latest_added_codelists,a,name,b,template_parameter": "Template Parameter of Name #{b} of Latest Added Codelists #{a}", "body,latest_added_codelists,a,name,b,version": "Version of Name #{b} of Latest Added Codelists #{a}", - "body,latest_added_codelists,a,paired_codes_codelist_uid": "Paired Codes Codelist UID of Latest Added Codelists #{a}", - "body,latest_added_codelists,a,paired_names_codelist_uid": "Paired Names Codelist UID of Latest Added Codelists #{a}", + "body,latest_added_codelists,a,paired_codelist": "Paired Codelist of Latest Added Codelists #{a}", + "body,latest_added_codelists,a,paired_codelist,b,name": "Name of Paired Codelist #{b} of Latest Added Codelists #{a}", + "body,latest_added_codelists,a,paired_codelist,b,uid": "UID of Paired Codelist #{b} of Latest Added Codelists #{a}", "body,latest_added_codelists,a,parent_codelist_uid": "Parent Codelist UID of Latest Added Codelists #{a}", "body,latest_criteria": "Latest Criteria", "body,latest_criteria,a,author_username": "Author Username of Latest Criteria #{a}", @@ -4721,8 +4736,9 @@ "body,names,a,name,b,status": "Status of Name #{b} of Names #{a}", "body,names,a,name,b,template_parameter": "Template Parameter of Name #{b} of Names #{a}", "body,names,a,name,b,version": "Version of Name #{b} of Names #{a}", - "body,names,a,paired_codes_codelist_uid": "Paired Codes Codelist UID of Names #{a}", - "body,names,a,paired_names_codelist_uid": "Paired Names Codelist UID of Names #{a}", + "body,names,a,paired_codelist": "Paired Codelist of Names #{a}", + "body,names,a,paired_codelist,b,name": "Name of Paired Codelist #{b} of Names #{a}", + "body,names,a,paired_codelist,b,uid": "UID of Paired Codelist #{b} of Names #{a}", "body,names,a,parent_codelist_uid": "Parent Codelist UID of Names #{a}", "body,nci_concept_id": "Nci Concept Id", "body,nci_concept_name": "Nci Concept Name", @@ -4938,6 +4954,13 @@ "body,pclass,a,dictionary_id": "Dictionary Id of Pclass #{a}", "body,pclass,a,name": "Name of Pclass #{a}", "body,pclass,a,term_uid": "Term UID of Pclass #{a}", + "body,per_label": "Per Label", + "body,per_label,a,label": "Label of Per Label #{a}", + "body,per_label,a,label_contained": "Label Contained of Per Label #{a}", + "body,per_label,a,source_distinct_ct_term_root_count": "Source Distinct Ct Term Root Count of Per Label #{a}", + "body,per_label,a,source_selection_count": "Source Selection Count of Per Label #{a}", + "body,per_label,a,target_distinct_ct_term_root_count": "Target Distinct Ct Term Root Count of Per Label #{a}", + "body,per_label,a,target_selection_count": "Target Selection Count of Per Label #{a}", "body,pharmaceutical_product_uids": "Pharmaceutical Product UIDs", "body,pharmaceutical_products": "Pharmaceutical Products", "body,pharmaceutical_products,a,external_id": "External Id of Pharmaceutical Products #{a}", @@ -5137,6 +5160,7 @@ "body,strict_mode": "Strict Mode", "body,structure": "Structure", "body,study_acronym": "Study Acronym", + "body,study_activity_count": "Study Activity Count", "body,study_activity_group": "Study Activity Group", "body,study_activity_group_uid": "Study Activity Group UID", "body,study_activity_group_uids": "Study Activity Group UIDs", @@ -5146,6 +5170,7 @@ "body,study_activity_group,a,study_activity_group_uid": "Study Activity Group UID of Study Activity Group #{a}", "body,study_activity_instance_uid": "Study Activity Instance UID", "body,study_activity_instruction_uid": "Study Activity Instruction UID", + "body,study_activity_schedule_count": "Study Activity Schedule Count", "body,study_activity_schedule_uid": "Study Activity Schedule UID", "body,study_activity_subgroup": "Study Activity Subgroup", "body,study_activity_subgroup_uid": "Study Activity Subgroup UID", @@ -5693,7 +5718,6 @@ "body,study_soa_group,a,soa_group_term_uid": "Soa Group Term UID of Study Soa Group #{a}", "body,study_soa_group,a,study_soa_group_uid": "Study Soa Group UID of Study Soa Group #{a}", "body,study_status": "Study Status", - "body,study_subpart_acronym": "Study Subpart Acronym", "body,study_subpart_uids": "Study Subpart UIDs", "body,study_title": "Study Title", "body,study_type": "Study Type", @@ -5716,6 +5740,7 @@ "body,study_type,a,trial_type,b,id": "Id of Trial Type #{b} of Study Type #{a}", "body,study_type,a,trial_type,b,name": "Name of Trial Type #{b} of Study Type #{a}", "body,study_uid": "Study UID", + "body,study_value_version": "Study Value Version", "body,study_ver": "Study Ver", "body,study_version": "Study Version", "body,study_visit_count": "Study Visit Count", @@ -5738,8 +5763,6 @@ "body,subgroups,a,uid": "UID of Subgroups #{a}", "body,subgroups,a,version": "Version of Subgroups #{a}", "body,submission_value": "Submission Value", - "body,subpart_id": "Subpart Id", - "body,subpart_uid": "Subpart UID", "body,substance_name": "Substance Name", "body,subtype": "Subtype", "body,subtype_name": "Subtype Name", @@ -5753,6 +5776,7 @@ "body,suppliers,a,study_data_supplier_type_uid": "Study Data Supplier Type UID of Suppliers #{a}", "body,surname": "Surname", "body,synonyms": "Synonyms", + "body,target_contained_in_source": "Target Contained In Source", "body,template": "Template", "body,template_name": "Template Name", "body,template_parameter": "Template Parameter", @@ -6214,6 +6238,7 @@ "path,study_visit_uid,a": "study_visit_uid #{a} in path parameters", "path,study_week_uid,a": "study_week_uid #{a} in path parameters", "path,stylesheet,a": "stylesheet #{a} in path parameters", + "path,target_study_uid,a": "target_study_uid #{a} in path parameters", "path,term_uid,a": "term_uid #{a} in path parameters", "path,text_value_uid,a": "text_value_uid #{a} in path parameters", "path,time_point_uid,a": "time_point_uid #{a} in path parameters", diff --git a/studybuilder/src/locales/en/app.json b/studybuilder/src/locales/en/app.json index b830f27d..8a748202 100644 --- a/studybuilder/src/locales/en/app.json +++ b/studybuilder/src/locales/en/app.json @@ -126,6 +126,7 @@ "value": "Value", "values": "Values", "type": "Type", + "count": "Count", "day": "Day", "week": "Week", "copy_link": "Copy link", @@ -181,7 +182,8 @@ "edit_in_table": "Edit in table", "view_source": "View Source", "rich_text": "Rich Text", - "required": " (Required)" + "required": " (Required)", + "feature": "Feature" }, "_errors": { "general": "Something went wrong. Please try again later.", @@ -360,29 +362,29 @@ }, "CompoundForm": { "sponsor_compound": "Indicate if this is a sponsor compound. Tick yes if sponsor is the authorisation holder/or future authorisation holder of the compound.", - "analyte_number": "Analyte number (Non-clinical), example is AN000028 (The analyte number for semaglutide).", - "long_number": "Substance ID. Example NNC0113-0000-0217. Only applicable for Novo Nordisk compound. Leave blank for other compounds.", - "short_number": "Substance name. Example NNC0113-0217. Only applicable for Novo Nordisk compound. Leave blank for other compounds. ", - "name": "The international nonproprietary name (INN) being the official generic and non-proprietary name given to a pharmaceutical drug or an active ingredient. Example: semaglutide.", + "analyte_number": "Analyte number (Non-clinical), example is 1115-70-4 (the analyte number for metformin).", + "long_number": "Substance ID. Example SPN0001-0000-0001. Only applicable for compounds developed or manufactured by the sponsor (your company). Leave blank for other compounds.", + "short_number": "Substance name. Example SPN0001-0001. Only applicable for compounds developed or manufactured by the sponsor (your company). Leave blank for other compounds. ", + "name": "The international nonproprietary name (INN) being the official generic and non-proprietary name given to a pharmaceutical drug or an active ingredient. Example: metformin.", "is_inn": "Tick No if INN hasn't been approved/published.", "definition": "A definition/description of the compound.", "brand_name": " This is chosen by the company that makes it. Several companies may make the same generic medicine, each with their own brand name. The name is often chosen to be memorable for advertising, or to be easier to say or spell than the generic name. For example, paracetamol is a generic name. There are several companies that make this with brand names such as Panadol®, Calpol®, etc.", "substance_name": "Add one or more substances by using the + button. A compound can consist of one or more substances.", "pharmacological_class": "Pharmacological class (Auto-populated)", "medrt": "Medication Reference Terminology (Auto-populated)", - "dose": "Specify dose of the drug. Example 0.25 mg of semalgutide. If more are applicable then click + to add more.", - "strength": "Specify the strength of the drug. Example 1.34 mg/nL of semaglutide. If more are applicable then click + to add more.", - "dosing_frequency": "Select frequency from the drop-down. Example for semaglutide is Once Weekly.", - "route_of_administration": "Select route of administration from the drop-down. Example for semaglutide is Subcutaneous Route.", - "dosage_form": "Select pharmaceutical dosage form from the drop-down. Example for semaglutide is Concentrated Injectable Solution.", - "dispensed_in": "Select Dispensed in from the drop-down. Example for semaglutide is Pre-filled Pen.", - "device": "Select Device from the drop-down. Example for semaglutide is Pre-filled Pen.", + "dose": "Specify dose of the drug. Example 500 mg of metformin. If more are applicable then click + to add more.", + "strength": "Specify the strength of the drug. Example 500 mg tablet of metformin. If more are applicable then click + to add more.", + "dosing_frequency": "Select frequency from the drop-down. Example for metformin is Twice Daily.", + "route_of_administration": "Select route of administration from the drop-down. Example for metformin is Oral Route.", + "dosage_form": "Select pharmaceutical dosage form from the drop-down. Example for metformin is Film-coated Tablet.", + "dispensed_in": "Select Dispensed in from the drop-down. Example for metformin is Blister Pack.", + "device": "Select Device from the drop-down. Example for metformin is No device.", "formulation": "Short description of the Formulation (if relevant).", "formulation_details": "Detailed description of the Formulation(if relevant).", - "manufacturing_place": "Manufacturing place, e.g. for semaglutide Novo Nordisk A/S, Hallas Allé, DK-4400 Kalundborg, Denmark. Information in ANNEX of Product labeling", + "manufacturing_place": "Manufacturing place, e.g. for metformin Example Pharma Ltd., Example Street 1, City, Country. Information in ANNEX of Product labeling", "manufacturing_process": "Specify the manufacturing process, if relevant.", - "half_life": "Specify the number and unit for the Half-life. Example for semaglutide is 1 week.", - "lag_time": "Lag-time the number of days after end of treatment an observation is regarded as being influenced by the drug. E.g. for Adverse Events for semalgutide, with an elimination half-life of approximately 1 week, semaglutide will be present in the circulation for about 5 weeks after the last dose (ref. product information), i.e. lag-time is 5 weeks.", + "half_life": "Specify the number and unit for the Half-life. Example for metformin is 6 hours.", + "lag_time": "Lag-time is the number of days after end of treatment an observation is regarded as being influenced by the drug. E.g. for Adverse Events for metformin, with an elimination half-life of approximately 6 hours, metformin will be present in the circulation for about 2 days after the last dose (ref. product information), i.e. lag-time is 2 days.", "sdtm_domain": "Specify the domain where the lag-time will apply. E.g. AE " }, "CompoundAliasForm": { @@ -396,7 +398,7 @@ "analyte_number": "Sponsor identification number for the active substance.", "name": "Name of the substance can be a sponsor name when an INN name is not yet defined.", "id": "A sponsor identifier for the active substance.", - "unii": "Selection of UNII term by UNII name and ID. Start typing the INN and the INN will appear with the UNII e.g. Semaglutide (53AXN4NNHX). If the needed UNII for an INN is missing, then it must be added to the independent UNII dictionary." + "unii": "Selection of UNII term by UNII name and ID. Start typing the INN and the INN will appear with the UNII e.g. Metformin (9100L32L2N). If the needed UNII for an INN is missing, then it must be added to the independent UNII dictionary." }, "PharmaceuticalProduct": { "dosage_form": "Select dosage form (from CDISC CT codelist).", @@ -431,19 +433,30 @@ "criterion_sub_cat": "Select one or more sub-category that applies to the criterion. Tick NA if not applicable. The categorisation is used for searching when selecting criteria template for a study." }, "CodelistCreationForm": { + "codelist_creation_type": "Select whether to create a regular code list or paired code lists", "catalogue": "The new code list will be created in this catalogue" }, "CodelistSponsorValuesForm": { "pref_name": "The sponsor preferred name is used by the OpenStudyBuilder as the default display name for the code list", + "name_pref_name": "The sponsor preferred name for the name code list of the pair", + "code_pref_name": "The sponsor preferred name for the code code list of the pair", "tpl_parameter": "If set/active, the code list is used as parameter in the creation of templates." }, "CodelistAttributesForm": { "name": "Provide the code list name that represent the only allowed values for a data item", + "name_name": "Provide the code list name for the name code list of the pair", + "code_name": "Provide the code list name for the code code list of the pair", "subm_value": "Provide a unique submission value. If a duplicate exists then the application will request a unique value.", + "name_subm_value": "Provide a unique submission value for the name code list of the pair", + "code_subm_value": "Provide a unique submission value for the code code list of the pair", "nci_pref_name": "Provide if applicable a preferred name", + "name_nci_pref_name": "Provide if applicable a preferred name for the name code list of the pair", + "code_nci_pref_name": "Provide if applicable a preferred name for the code code list of the pair", "extensible": "Allow addition of new term(s)", "is_ordinal": "Mark the codelist as ordinal, meaning that the 'order' of the terms represent their numeric value.", - "definition": "Provide a complete definition of the code list" + "definition": "Provide a complete definition of the code list", + "name_definition": "Provide a complete definition for the name code list of the pair", + "code_definition": "Provide a complete definition for the code code list of the pair" }, "CodelistTermCreationForm": { "sponsor_pref_name": "Preferred name of the term", @@ -471,7 +484,7 @@ "predecessor": "Select a parent term that specifies the predecessor of this term. This is used to indicate that this term replaces the parent." }, "DictionaryTermForm": { - "dictionary_id": "Add an ID of the dictionary term. Ensure that the ID follows the nomenclature for the dictionary. Example UNII for Insulin Detemir (levemir) is 4FT78T86XV, MED-RT for Insulin analogue is N0000175453, and SNOMED ID for Diabetes Mellitus is 73211009.", + "dictionary_id": "Add an ID of the dictionary term. Ensure that the ID follows the nomenclature for the dictionary. Example UNII for Metformin is 9100L32L2N, MED-RT for Insulin analogue is N0000175453, and SNOMED ID for Diabetes Mellitus is 73211009.", "name": "The name of the term.", "lower_case_name": "Auto-populated as all lower-case of the name specified.", "abbreviation": "If any abbreviated term applies.", @@ -980,15 +993,15 @@ "select_class": "“Study with cohorts, branches and subpopulations” will bring up the full stepper, helping you set up cohorts and branches in an easy and controlled way. Study participants must be as-signed to each branch and are then automatically assigned to cohorts and arms as well. “Study with arms only” will only bring up the first page of the stepper and participants must be assigned to arms directly. It is still possible to add cohorts and branches manually after-wards.", "set_arms_for_study": "You can add as many arms as required in your study using the “Add arm” button.", "study_arm_type": "There are four options available for study arm type: Comparator arm, Investigational arm, Observational arm and Placebo arm.", - "arm_name": "Arm name can be filled in with free text but is most commonly the name of the investigation, e.g. “Semaglutide” or “Placebo”.", + "arm_name": "Arm name can be filled in with free text but is most commonly the name of the investigation, e.g. “Metformin” or “Placebo”.", "arm_short_name": "Arm short name can be filled in with free text but is most commonly the same as the arm name.", "arm_label": "Shorter version of arm name", "rand_group": "Randomisation group should be filled out when known. Randomisation group must be filled out with capital letters (e.g. A). If multiple groups apply for one arm, they must be separated using pipes (e.g. AIBID).", - "arm_code": "Arm code is generated automatically within Novo Nordisk but may be applicable for open-source users.", + "arm_code": "Arm code is generated automatically within sponsor-specific setups but may be applicable for open-source users.", "set_cohorts_for_study": "You can add as many cohorts/subpop as required in your study using the “Add Co-horts/subpop.” button.", "source_var": "There are three options available for source variable: Cohort, Subgroup or Stratum.", "cohort_code": "Cohort code must be filled out with a numerical value (e.g. 1). Most common approach is numbering each cohort in numerical order.", - "cohort_name": "Cohort/subpop. name can be filled in with free text but is most commonly the name of the investigation + dose level, e.g. “Semaglutide 2.4 mg” or “Placebo 2.4 mg”.", + "cohort_name": "Cohort/subpop. name can be filled in with free text but is most commonly the name of the investigation + dose level, e.g. “Metformin 500 mg” or “Placebo 500 mg”.", "cohort_short_name": "Cohort/subpop. short name can be filled in with free text but is most commonly the same as the cohort/subpop. name or sometimes just the dose level.", "link_arms_cohorts": "Enter the number of participants per branch. It is possible to copy the number of participants from the first row to all other rows. Branch name and branch short name is automatically generated based on the cohort and arm that the branch is assigned to. Using the Edit button, it is possible to rename the branch name and branch short name." }, @@ -1047,7 +1060,7 @@ "description_bottom": "standards used in the OpenStudyBuilder", "dashboard_description": "A simple graphical presentation of the current status and historical trends of the metadata stored in the Library", "codelist_description": "Find the CDISC controlled terminology, including the code lists, the valid values and associated definitions for each code list and the evolution in packages and terms over time. Sponsor defined list and terms are also included.", - "dictionaries_description": "Find relevant external dictionaries and thesaurus for clinical development such as SNOMED, MedDRA, MED-RT, UNII, LOINC, UCUM. Since some of these dictionaries are very large, only selected terms relevant for the Novo Nordisk pipeline are included.", + "dictionaries_description": "Find relevant external dictionaries and thesaurus for clinical development such as SNOMED, MedDRA, MED-RT, UNII, LOINC, UCUM. Since some of these dictionaries are very large, only selected terms relevant for the sponsor pipeline are included.", "concepts_description": "Find controlled listings of the terms to use for generic concepts such as units, activities, compounds and CRFs.", "syntax_templates_description": "View (or manage) the different syntax templates used for specifying the objectives, the endpoints, the eligibility, randomisation, dosing and other criteria for the individual studies. Only templates in status Final can be used under Studies.", "template_instantiations_description": "See how the different templates are used in the studies, including number of studies using a specific syntax and which studies.", @@ -1181,7 +1194,8 @@ "data_collection_standards": "Data Collection Standards", "activities_subgroups": "Activity Subgroups", "activities_groups": "Activity Groups", - "data_suppliers": "Data Suppliers" + "data_suppliers": "Data Suppliers", + "template_study": "Template Study" }, "study": { "about": "About Studies", @@ -1673,6 +1687,7 @@ "project_name": "Project name", "id": "Study ID", "main_id": "Main study ID", + "study_id": "Study ID", "acronym": "Study acronym", "subpart_acronym": "Study subpart acronym", "select": "Select", @@ -1694,6 +1709,8 @@ "creation_mode_title": "Create a new study from scratch or from an existing study?", "create_from_scratch": "Create a new study from scratch", "create_from_study": "Create a study from an existing study", + "create_from_template": "Create a new study with default settings", + "create_from_template_help": "This option creates a study that, by default, includes commonly used activities as well as non-visit and unscheduled visits.", "copy_notice": "The following information is NOT regarding the existing study, but the properties of your new study." }, "StudyStructureCopyForm": { @@ -1712,6 +1729,10 @@ "epochs_help": "An Epoch describes a time period in the study such as dose escalation of the drug. An Epoch can have a footnote attached which would be visible in the Schedule of Activities.", "visits": "Study visits ({count})", "visits_help": "A Study visit is a single point in time during the study where an activity is happening. A Study visit can have a footnote attached which would be visible in the Schedule of Activities.", + "study_activities": "Study activities ({count})", + "study_activities_help": "Copies study activity groupings, study activities and study activity instances.", + "schedules": "Schedules ({count})", + "schedules_help": "Copies study activity schedules after Study visits and Study activities are selected.", "design_matrix": "Design matrix", "design_matrix_help": "The design matrix combines the overall interventions (Study Elements) that a subject will undergo while participating in a study arm over time (Study Epochs).", "footnotes": "Include footnotes ({count})", @@ -2088,8 +2109,8 @@ "device": "Delivered in", "half_life": "Half-life", "lag_time": "Lag-time", - "nnc_number_long": "NNC Number (long)", - "nnc_number_short": "NNC Number (short)", + "nnc_number_long": "Sponsor Number (long)", + "nnc_number_short": "Sponsor Number (short)", "analyte_number": "Analyte number", "reason_for_missing": "Reason for missing", "compound_definition": "Compound definition", @@ -2211,7 +2232,8 @@ "attr_status": "Attributes status", "modified_name": "Name modified", "modified_attributes": "Attributes modified", - "remove_term": "Remove term" + "remove_term": "Remove term", + "paired_with": "Paired with" }, "ActivityTable": { "sentence_case_name": "Sentence case name", @@ -2525,6 +2547,8 @@ "CodelistSponsorValuesForm": { "title": "Edit Sponsor Code list", "pref_name": "Sponsor preferred name", + "name_pref_name": "Sponsor preferred name (Name codelist)", + "code_pref_name": "Sponsor preferred name (Code codelist)", "tpl_parameter": "Template parameter?", "update_success": "Sponsor values have been updated" }, @@ -2536,24 +2560,36 @@ "CodelistAttributesForm": { "title": "Edit code list attributes values", "name": "Code list name", + "name_name": "Code list name (Name codelist)", + "code_name": "Code list name (Code codelist)", "name_hint": "Provide the code list name that represent the only allowed values for a data item", "subm_value": "Submission value", + "name_subm_value": "Submission value (Name codelist)", + "code_subm_value": "Submission value (Code codelist)", "subm_value_hint": "Provide a unique submission value. If a duplicate exists then the application will be used instead", "nci_pref_name": "NCI preferred name", + "name_nci_pref_name": "NCI preferred name (Name codelist)", + "code_nci_pref_name": "NCI preferred name (Code codelist)", "nci_pref_name_hint": "Provide if applicable a preferred name", "extensible": "Extensible?", "extensible_hint": "Allow addition of new term(s)", "is_ordinal": "Ordinal?", "ordinal_hint": "Mark the codelist as ordinal, meaning that the 'order' of the terms represent their numeric value.", "definition": "Definition", + "name_definition": "Definition (Name codelist)", + "code_definition": "Definition (Code codelist)", "definition_hint": "Provide a complete definition of the code list", "codelist_type": "Type" }, "CodelistCreationForm": { "title": "Add sponsor code list", - "step1_title": "Select catalogue", - "step2_title": "Manage sponsor preferred name", - "step3_title": "Manage code list attribute values", + "step1_title": "Select what you want to create", + "step2_title": "Select catalogue", + "step3_title": "Manage sponsor preferred name", + "step4_title": "Manage code list attribute values", + "codelist_creation_type": "Code list type", + "regular_codelist": "Single code list", + "paired_codelists": "Paired code lists", "catalogue": "Catalogue", "add_success": "Code list added" }, @@ -4538,6 +4574,8 @@ "new_version_groupings": "New version (groupings)", "inactivate_attributes": "Inactivate attributes", "inactivate_groupings": "Inactivate groupings", + "inactivate": "Inactivate", + "reactivate": "Reactivate", "reactivate_attributes": "Reactivate attributes", "reactivate_groupings": "Reactivate groupings", "history_attributes": "History (attributes)", @@ -4625,7 +4663,10 @@ "is_default_selected_for_activity": "Default selected for activity", "is_data_sharing": "Data sharing", "is_legacy_usage": "Legacy usage", - "history_title": "History for activity instance [{uid}]" + "history_title": "History for activity instance [{uid}]", + "summary_title": "Summary", + "attributes": "Attributes", + "groupings": "Groupings" }, "ActivityInstanceClassOverview": { "domain_specific": "Domain specific", @@ -5068,7 +5109,7 @@ "required_for_activity": "Required for activity", "required_for_activity_help": "This flag is used in the standards governance process. The flag is used when some or all instances under an activity is required to be selected when that activity is selected, as an example in questionnaires", "data_sharing": "Data sharing", - "data_sharing_help": "The purpose of this flag is to enable sharing details of the instance with CDISC and other pharmaceutical companies. The flag should not be checked for activity instances which contains Novo Nordisk specific information. For e.g. but not limited to, product information or antibodies specific to products etc.", + "data_sharing_help": "The purpose of this flag is to enable sharing details of the instance with CDISC and other pharmaceutical companies. The flag should not be checked for activity instances which contain sponsor-specific information. For example, but not limited to, product information or antibodies specific to products.", "default_selected": "Default selected for activity", "default_selected_help": "The purpose of the default flag is to help the user select instances under an activity faster by flagging the instance that is used the most across all studies as the default. This is only used when more than one instance exists under an activity. The user can manually change the selection based on the need of the study", "data_from_research_lab": "Data from a Research lab", @@ -5192,6 +5233,11 @@ "remove_cohort_warning": "You are about to remove a cohort and all its participants. This will decrease the total numbers of participants in the study.", "create_arms": "Create arms" }, + "TemplateStudy": { + "title": "Template study", + "current_template": "The study template currently in use is:", + "reset": "Reset template" + }, "DataSupplierView": { "title": "Data Suppliers", "DataSupplierTable": { @@ -5225,6 +5271,7 @@ }, "ComplexityScore": { "admin_title": "Complexity Burdens", + "admin_study_scores_tab": "Study Complexity Scores", "admin_activity_burdens_info": "Mapping between activity subgroups and corresponding site/participant burdens.", "admin_activity_burdens_tab": "Activity Subgroup Burdens", "admin_burdens_tab": "Burdens Library", @@ -5235,7 +5282,18 @@ "admin_burdens_description": "Description", "admin_burdens_id": "Burden ID", "admin_burdens_site_burden": "Site burden", - "admin_burdens_patient_burden": "Participant burden" + "admin_burdens_patient_burden": "Participant burden", + "complexity_score": "Complexity Score", + "complexity_score_intro": "Complexity score is calculated as the sum of total burdens for visits and activities below.", + "visits": "Visits", + "activities": "Activities", + "activity_subgroup": "Activity subgroup", + "burden": "Burden", + "count_times_burden": "Count * Burden", + "visit_type_initial": "Initial", + "visit_type_follow_up": "Follow-up", + "visit_type_physical": "Physical", + "visit_type_virtual": "Virtual" }, "StudyDataCompleteness": { "admin_title": "Data Completeness Tags", diff --git a/studybuilder/src/plugins/vuetify.js b/studybuilder/src/plugins/vuetify.js index 1622d665..8b250af0 100644 --- a/studybuilder/src/plugins/vuetify.js +++ b/studybuilder/src/plugins/vuetify.js @@ -59,6 +59,7 @@ const NNCustomLightTheme = { tableChildRow: '#E6EFFB', nnTableRowExpanded: '#C2D8F4', nnTableRowChild: '#E6EFFB', + nnAlertRed: '#C44836', }, } diff --git a/studybuilder/src/router/index.js b/studybuilder/src/router/index.js index 1c6339b4..d65c6179 100644 --- a/studybuilder/src/router/index.js +++ b/studybuilder/src/router/index.js @@ -583,6 +583,14 @@ const routes = [ authRequired: true, }, }, + { + path: 'template_study', + name: 'TemplateStudy', + component: () => import('../views/library/TemplateStudyPage.vue'), + meta: { + authRequired: true, + }, + }, { path: 'overviews', component: () => import('../components/layout/PassThrough.vue'), diff --git a/studybuilder/src/stores/app.js b/studybuilder/src/stores/app.js index 89acc310..d89f1a33 100644 --- a/studybuilder/src/stores/app.js +++ b/studybuilder/src/stores/app.js @@ -49,13 +49,13 @@ export const useAppStore = defineStore('app', { url: { name: 'LibrarySummary' }, icon: 'mdi-information-outline', }, - { - id: 'process_overview_tile', - title: i18n.t('Sidebar.library.process_overview'), - icon: 'mdi-arrow-right-bold-outline', - url: { name: 'ProcessOverview' }, - description: i18n.t('Library.process_overview_description'), - }, + // { + // id: 'process_overview_tile', + // title: i18n.t('Sidebar.library.process_overview'), + // icon: 'mdi-arrow-right-bold-outline', + // url: { name: 'ProcessOverview' }, + // description: i18n.t('Library.process_overview_description'), + // }, { id: 'codelists_tile', title: i18n.t('Sidebar.library.code_lists'), @@ -74,10 +74,10 @@ export const useAppStore = defineStore('app', { title: i18n.t('Sidebar.library.ct_packages'), url: { name: 'CtPackages' }, }, - { - title: i18n.t('Sidebar.library.cdisc'), - url: { name: 'CDISC' }, - }, + // { + // title: i18n.t('Sidebar.library.cdisc'), + // url: { name: 'CDISC' }, + // }, { title: i18n.t('Sidebar.library.sponsor'), url: { name: 'Sponsor' }, @@ -229,26 +229,26 @@ export const useAppStore = defineStore('app', { }, ], }, - { - id: 'template_collections_tile', - title: i18n.t('Sidebar.library.template_collections'), - icon: 'mdi-folder-star-multiple-outline', - description: i18n.t('Library.template_collections_description'), - children: [ - { - title: i18n.t('Sidebar.library.project_templates'), - url: { name: 'ProjectTemplates' }, - }, - { - title: i18n.t('Sidebar.library.shared_templates'), - url: { name: 'SharedTemplates' }, - }, - { - title: i18n.t('Sidebar.library.supporting_templates'), - url: { name: 'SupportingTemplates' }, - }, - ], - }, + // { + // id: 'template_collections_tile', + // title: i18n.t('Sidebar.library.template_collections'), + // icon: 'mdi-folder-star-multiple-outline', + // description: i18n.t('Library.template_collections_description'), + // children: [ + // { + // title: i18n.t('Sidebar.library.project_templates'), + // url: { name: 'ProjectTemplates' }, + // }, + // { + // title: i18n.t('Sidebar.library.shared_templates'), + // url: { name: 'SharedTemplates' }, + // }, + // { + // title: i18n.t('Sidebar.library.supporting_templates'), + // url: { name: 'SupportingTemplates' }, + // }, + // ], + // }, { id: 'overview_pages_title', title: i18n.t('Sidebar.library.overview_pages'), @@ -279,10 +279,10 @@ export const useAppStore = defineStore('app', { title: i18n.t('Sidebar.library.sdtm_sponsor'), url: { name: 'SponsorSdtm' }, }, - { - title: i18n.t('Sidebar.library.adam'), - url: { name: 'Adam' }, - }, + // { + // title: i18n.t('Sidebar.library.adam'), + // url: { name: 'Adam' }, + // }, ], }, { @@ -311,36 +311,42 @@ export const useAppStore = defineStore('app', { icon: 'mdi-archive-outline', url: { name: 'DataSuppliers' }, }, - ], - }, - { - id: 'list_tile', - title: i18n.t('Sidebar.library.list'), - icon: 'mdi-format-list-bulleted-square', - description: i18n.t('Library.list_description'), - children: [ - { - title: i18n.t('Sidebar.library.cdash_std'), - url: { name: 'CdashStandards' }, - }, - { - title: i18n.t('Sidebar.library.sdtm_std_cst'), - url: { name: 'SdtmStdCst' }, - }, - { - title: i18n.t('Sidebar.library.sdtm_std_dmw'), - url: { name: 'SdtmStdDmw' }, - }, - { - title: i18n.t('Sidebar.library.adam_std_cst'), - url: { name: 'AdamStdCst' }, - }, { - title: i18n.t('Sidebar.library.adam_std_new'), - url: { name: 'AdamStdNew' }, + id: 'template_study', + title: i18n.t('Sidebar.library.template_study'), + icon: 'mdi-clipboard-outline', + url: { name: 'TemplateStudy' }, }, ], }, + // { + // id: 'list_tile', + // title: i18n.t('Sidebar.library.list'), + // icon: 'mdi-format-list-bulleted-square', + // description: i18n.t('Library.list_description'), + // children: [ + // { + // title: i18n.t('Sidebar.library.cdash_std'), + // url: { name: 'CdashStandards' }, + // }, + // { + // title: i18n.t('Sidebar.library.sdtm_std_cst'), + // url: { name: 'SdtmStdCst' }, + // }, + // { + // title: i18n.t('Sidebar.library.sdtm_std_dmw'), + // url: { name: 'SdtmStdDmw' }, + // }, + // { + // title: i18n.t('Sidebar.library.adam_std_cst'), + // url: { name: 'AdamStdCst' }, + // }, + // { + // title: i18n.t('Sidebar.library.adam_std_new'), + // url: { name: 'AdamStdNew' }, + // }, + // ], + // }, ], }, Studies: { diff --git a/studybuilder/src/views/administration/ComplexityBurdens.vue 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"^2.0.7" @@ -1299,34 +1297,37 @@ es-set-tostringtag@^2.1.0: has-tostringtag "^1.0.2" hasown "^2.0.2" -esbuild@^0.21.3: - version "0.21.5" - resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.21.5.tgz#9ca301b120922959b766360d8ac830da0d02997d" - integrity sha512-mg3OPMV4hXywwpoDxu3Qda5xCKQi+vCTZq8S9J/EpkhB2HzKXq4SNFZE3+NK93JYxc8VMSep+lOUSC/RVKaBqw== +esbuild@^0.25.0: + version "0.25.12" + resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.25.12.tgz#97a1d041f4ab00c2fce2f838d2b9969a2d2a97a5" + integrity sha512-bbPBYYrtZbkt6Os6FiTLCTFxvq4tt3JKall1vRwshA3fdVztsLAatFaZobhkBC8/BrPetoa0oksYoKXoG4ryJg== optionalDependencies: - "@esbuild/aix-ppc64" "0.21.5" - "@esbuild/android-arm" "0.21.5" - "@esbuild/android-arm64" "0.21.5" - "@esbuild/android-x64" "0.21.5" - "@esbuild/darwin-arm64" "0.21.5" - "@esbuild/darwin-x64" "0.21.5" - "@esbuild/freebsd-arm64" "0.21.5" - "@esbuild/freebsd-x64" "0.21.5" - "@esbuild/linux-arm" "0.21.5" - "@esbuild/linux-arm64" "0.21.5" - 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"0.25.12" + "@esbuild/linux-x64" "0.25.12" + "@esbuild/netbsd-arm64" "0.25.12" + "@esbuild/netbsd-x64" "0.25.12" + "@esbuild/openbsd-arm64" "0.25.12" + "@esbuild/openbsd-x64" "0.25.12" + "@esbuild/openharmony-arm64" "0.25.12" + "@esbuild/sunos-x64" "0.25.12" + "@esbuild/win32-arm64" "0.25.12" + "@esbuild/win32-ia32" "0.25.12" + "@esbuild/win32-x64" "0.25.12" escape-string-regexp@^1.0.5: version "1.0.5" @@ -1534,6 +1535,11 @@ fastq@^1.6.0: dependencies: reusify "^1.0.4" +fdir@^6.4.4, fdir@^6.5.0: + version "6.5.0" + resolved "https://registry.yarnpkg.com/fdir/-/fdir-6.5.0.tgz#ed2ab967a331ade62f18d077dae192684d50d350" + integrity sha512-tIbYtZbucOs0BRGqPJkshJUYdL+SDH7dVM8gjy+ERp3WAUjLEFJE+02kanyHtwjWOnwrKYBiwAmM0p4kLJAnXg== + file-entry-cache@^6.0.1: version "6.0.1" resolved "https://registry.yarnpkg.com/file-entry-cache/-/file-entry-cache-6.0.1.tgz#211b2dd9659cb0394b073e7323ac3c933d522027" @@ -1563,10 +1569,10 @@ flat@^5.0.2: resolved 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sha512-J8xewKD/Gk22OZbhpOVSwcs60zhd95ESDwezOFuA3/099925PdHJ7OFHNTGtajL3AlZkykD32HykiMo+BIBI8A== lodash.clonedeep@^4.5.0: version "4.5.0" @@ -2014,10 +2020,10 @@ lodash.uniq@^4.5.0: resolved "https://registry.yarnpkg.com/lodash.uniq/-/lodash.uniq-4.5.0.tgz#d0225373aeb652adc1bc82e4945339a842754773" integrity sha512-xfBaXQd9ryd9dlSDvnvI0lvxfLJlYAZzXomUYzLKtUeOQvOP5piqAWuGtrhWeqaXK9hhoM/iyJc5AV+XfsX3HQ== -lodash@^4.17.15, lodash@^4.17.21: - version "4.17.23" - resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.17.23.tgz#f113b0378386103be4f6893388c73d0bde7f2c5a" - integrity sha512-LgVTMpQtIopCi79SJeDiP0TfWi5CNEc/L/aRdTh3yIvmZXTnheWpKjSZhnvMl8iXbC1tFg9gdHHDMLoV7CnG+w== +lodash@^4.17.15, lodash@^4.17.21, lodash@^4.18.1: + version "4.18.1" + resolved "https://registry.yarnpkg.com/lodash/-/lodash-4.18.1.tgz#ff2b66c1f6326d59513de2407bf881439812771c" + integrity sha512-dMInicTPVE8d1e5otfwmmjlxkZoUpiVLwyeTdUsi/Caj/gfzzblBcCE5sRHV/AsjuCmxWrte2TNGSYuCeCq+0Q== lru-cache@^10.2.0: version 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+2940,14 @@ text-table@^0.2.0: resolved "https://registry.yarnpkg.com/text-table/-/text-table-0.2.0.tgz#7f5ee823ae805207c00af2df4a84ec3fcfa570b4" integrity sha512-N+8UisAXDGk8PFXP4HAzVR9nbfmVJ3zYLAWiTIoqC5v5isinhr+r5uaO8+7r3BMfuNIufIsA7RdpVgacC2cSpw== +tinyglobby@^0.2.13: + version "0.2.16" + resolved "https://registry.yarnpkg.com/tinyglobby/-/tinyglobby-0.2.16.tgz#1c3b7eb953fce42b226bc5a1ee06428281aff3d6" + integrity sha512-pn99VhoACYR8nFHhxqix+uvsbXineAasWm5ojXoN8xEwK5Kd3/TrhNn1wByuD52UxWRLy8pu+kRMniEi6Eq9Zg== + dependencies: + fdir "^6.5.0" + picomatch "^4.0.4" + tmp@^0.2.0, tmp@^0.2.5: version "0.2.5" resolved "https://registry.yarnpkg.com/tmp/-/tmp-0.2.5.tgz#b06bcd23f0f3c8357b426891726d16015abfd8f8" @@ -3023,7 +3038,7 @@ varint@^6.0.0: resolved "https://registry.yarnpkg.com/varint/-/varint-6.0.0.tgz#9881eb0ce8feaea6512439d19ddf84bf551661d0" integrity sha512-cXEIW6cfr15lFv563k4GuVuW/fiwjknytD37jIOLSdSWuOI6WnO/oKwmP2FQTU2l01LP8/M5TSAJpzUaGe3uWg== -vite-plugin-vuetify@^2.0.1: 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"^4.0.2" + postcss "^8.5.3" + rollup "^4.34.9" + tinyglobby "^0.2.13" optionalDependencies: fsevents "~2.3.3" @@ -3083,15 +3101,15 @@ vue-router@^4.2.5: "@vue/devtools-api" "^6.6.4" vue@^3.4.19: - version "3.5.29" - resolved "https://registry.yarnpkg.com/vue/-/vue-3.5.29.tgz#859a1cc5219eb1228c7ce6f355b27de080517111" - integrity sha512-BZqN4Ze6mDQVNAni0IHeMJ5mwr8VAJ3MQC9FmprRhcBYENw+wOAAjRj8jfmN6FLl0j96OXbR+CjWhmAmM+QGnA== + version "3.5.32" + resolved "https://registry.yarnpkg.com/vue/-/vue-3.5.32.tgz#9a7cbeb181aa4b2a71c3ebac4995542cf0353de3" + integrity sha512-vM4z4Q9tTafVfMAK7IVzmxg34rSzTFMyIe0UUEijUCkn9+23lj0WRfA83dg7eQZIUlgOSGrkViIaCfqSAUXsMw== dependencies: - "@vue/compiler-dom" "3.5.29" - "@vue/compiler-sfc" "3.5.29" - "@vue/runtime-dom" "3.5.29" - "@vue/server-renderer" "3.5.29" - "@vue/shared" "3.5.29" + "@vue/compiler-dom" "3.5.32" + "@vue/compiler-sfc" "3.5.32" + "@vue/runtime-dom" "3.5.32" + "@vue/server-renderer" "3.5.32" + "@vue/shared" "3.5.32" vuetify@4.0.2: version "4.0.2" @@ -3157,10 +3175,10 @@ xmlchars@^2.2.0: resolved "https://registry.yarnpkg.com/xmlchars/-/xmlchars-2.2.0.tgz#060fe1bcb7f9c76fe2a17db86a9bc3ab894210cb" integrity sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw== -yaml@^2.3.4: - version "2.8.2" - resolved "https://registry.yarnpkg.com/yaml/-/yaml-2.8.2.tgz#5694f25eca0ce9c3e7a9d9e00ce0ddabbd9e35c5" - integrity sha512-mplynKqc1C2hTVYxd0PU2xQAc22TI1vShAYGksCCfxbn/dFwnHTNi1bvYsBTkhdUNtGIf5xNOg938rrSSYvS9A== +yaml@^2.8.3: + version "2.8.3" + resolved "https://registry.yarnpkg.com/yaml/-/yaml-2.8.3.tgz#a0d6bd2efb3dd03c59370223701834e60409bd7d" + integrity sha512-AvbaCLOO2Otw/lW5bmh9d/WEdcDFdQp2Z2ZUH3pX9U2ihyUY0nvLv7J6TrWowklRGPYbB/IuIMfYgxaCPg5Bpg== yocto-queue@^0.1.0: version "0.1.0" diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/administration/administration_feature_flags.feature b/system-tests/ui-tests/cypress/e2e/features/modules/administration/administration_feature_flags.feature index 08d142b4..ef175432 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/administration/administration_feature_flags.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/administration/administration_feature_flags.feature @@ -13,13 +13,14 @@ Feature: Administration - Feature Flags Scenario: [Table][Columns][Names] User must be able to see the columns list on the main page as below Given The '/administration/featureflags' page is opened Then A table is visible with following headers - | header | - | Name | - | Description | + | header | + | Feature | + | Name | Scenario: [Feature flags] User must be able to toggle off feature flags Given The '/administration/featureflags' page is opened - And The toggle is set to off + And User switch to 'Studies' feature flags + And User disables 'studies_view_listings_analysis_study_metadata_new' feature flag When The '/studies' page is opened And Click the View Listings side-menu Then The sub-menu Analysis Study Metadata should not exist @@ -35,7 +36,8 @@ Feature: Administration - Feature Flags Scenario: [Feature flags] User must be able to toggle on feature flags Given The '/administration/featureflags' page is opened - And The toggle is set to on + And User switch to 'Studies' feature flags + And User enables 'studies_view_listings_analysis_study_metadata_new' feature flag When The '/studies' page is opened And Click the View Listings side-menu Then The sub-menu Analysis Study Metadata should exist diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/administration/data_completness_tags.feature b/system-tests/ui-tests/cypress/e2e/features/modules/administration/data_completness_tags.feature index 4106b269..6c8abb72 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/administration/data_completness_tags.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/administration/data_completness_tags.feature @@ -36,6 +36,6 @@ Feature: Administration - Data Completeness Tags Given A test study '8016' for data completion tags test exists And The '/administration/data-completeness-tags' page is opened And The user creates multiple completion tags - And The user sets multiple tags to complete for selected study + And The user sets multiple tags to completed for selected study And The '/studies/select_or_add_study/active' page is opened Then All the completed tags are visible for the study \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/about_library/about-library.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/about_library/about-library.feature index 87994b53..1f3b9a78 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/about_library/about-library.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/about_library/about-library.feature @@ -24,7 +24,7 @@ Feature: Library - About Library Given The '/library' page is opened Then A tile 'Dictionaries' is visible with following description """ - Find relevant external dictionaries and thesaurus for clinical development such as SNOMED, MedDRA, MED-RT, UNII, LOINC, UCUM. Since some of these dictionaries are very large, only selected terms relevant for the Novo Nordisk pipeline are included. + Find relevant external dictionaries and thesaurus for clinical development such as SNOMED, MedDRA, MED-RT, UNII, LOINC, UCUM. Since some of these dictionaries are very large, only selected terms relevant for the sponsor pipeline are included. """ Scenario: [Overview][Description] User must be able to view the description under 'Concepts' tile in library Module diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/code_lists/sponsor.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/code_lists/sponsor.feature index f089aa3b..a72d3633 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/code_lists/sponsor.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/code_lists/sponsor.feature @@ -48,12 +48,12 @@ Feature: Library - Code Lists - Sponsor Scenario: [Create][Positive case] User must be able to add a new Codelist Given The '/library/sponsor' page is opened When The new Codelist is added + Given The '/library/sponsor' page is opened And The codelist is search for and found And The codelist and attributes status is set to 'Draft' Scenario: [Actions][Approve] User must be able to add a new Codelist Given The '/library/sponsor' page is opened - When The new Codelist is added And The codelist is search for and found When The 'Edit' option is clicked from the three dot menu list And The codelist sponsor values are approved @@ -79,13 +79,7 @@ Feature: Library - Code Lists - Sponsor Scenario: [Actions][Availability][Draft item] User must only have access to edit, show terms, history actions for Drafted version of the codelist Given The '/library/sponsor' page is opened When The new Codelist is added - And The codelist is search for and found - Then The item actions button is clicked - Then Only actions that should be avaiable for the Codelist are displayed - - Scenario: [Actions][Availability][Final item] User must only have access to edit, show terms, history actions for Final version of the codelist - Given The '/library/sponsor' page is opened - When The new Codelist is added + Given The '/library/sponsor' page is opened And The codelist is search for and found Then The item actions button is clicked Then Only actions that should be avaiable for the Codelist are displayed diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/activity-groups.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/activity-groups.feature index 1eae26a7..7e4665a9 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/activity-groups.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/activity-groups.feature @@ -11,6 +11,7 @@ Feature: Library - Concepts - Activities - Activity Groups @smoke_test Scenario: [Create][Positive case] User must be able to add a new activity group When The add activity group button is clicked + And User waits for 1 seconds And The test activity group container is filled with data And User intercepts activity group request And Form save button is clicked diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/requested-activities.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/requested-activities.feature index 7ff5d27b..6b1ffdce 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/requested-activities.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/requested-activities.feature @@ -6,6 +6,11 @@ Feature: Library - Concepts - Activities - Requested Activities Background: User must be logged in Given The user is logged in + Scenario: [TestData] Old placeholder activity workflow feature flag is enabled + When The '/administration/featureflags' page is opened + And User switch to 'Studies' feature flags + And User disables 'streamline_placeholder_activities' feature flag + Scenario: [Create] User must not be able to create activity request from library level Given The '/library/activities/requested-activities' page is opened Then The add activity request button is not available @@ -78,3 +83,29 @@ Feature: Library - Concepts - Activities - Requested Activities And Requested activity is found And The item actions button is clicked Then Only actions that should be avaiable for the Retired item are displayed + + Scenario: [Overview Page] User must able to see the linked study on the activity placeholder overview page + Given A test study is selected + And [API] Get SoA Group 'BIOMARKERS' id + When [API] Create Unsubmitted Requested Activity + And [API] Requested Activity is added to the study + And The '/library/activities/activities' page is opened + And Activity placeholder is found + Then The Library value is set to 'Requested' + And User goes to activity placeholder overview page by clicking its name + Then The Library displayed on the summary has value 'Requested' + And The Study ID displayed on the summary has value 'CDISC DEV-9876' + + Scenario: [Overview Page] User must able unlink study from the activity placeholder and see the change on the overview page + Given A test study is selected + Given The test study '/activities/list' page is opened + And Activity placeholder is found + When The 'Remove Activity' option is clicked from the three dot menu list + And Action is confirmed by clicking continue + Then The pop up displays 'Study activity deleted' + And The '/library/activities/activities' page is opened + And Activity placeholder is found + Then The Library value is set to 'Requested' + And User goes to activity placeholder overview page by clicking its name + Then The Library displayed on the summary has value 'Requested' + And The Study ID displayed on the summary has value '-' diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-events.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-events.feature new file mode 100644 index 00000000..72f1a168 --- /dev/null +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-events.feature @@ -0,0 +1,104 @@ +@REQ_ID:1070683 +Feature: Library - Concepts - Activities - Activity instances - wizard stepper - numeric findings + As a user, I want to manage the Activity Instances in the Concepts Library with Wizard Stepper + process to ensure the data is saved and displayed correctly. + + Background: User must be logged in + Given The user is logged in + + Scenario: [Feature flag] User must be able to turn on wizard stepper for activity instance creation + When The '/administration/featureflags' page is opened + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag + And User enables 'activity_instance_wizard_stepper_events' feature flag + + Scenario: [Create][Events][Existing activity] User must be able to add a new Activity Instance with Events as Activity Instance Class + Given The '/library/activities/activity-instances' page is opened + And User intercepts available activities requests + When The Add Activity Instance button is clicked + And User waits for available activities requests + Then The Activity Instance Wizard Stepper 'Select activity' page is displayed + When First activity is selected from the activity list + And Selected Activity name is saved + And Form continue button is clicked + Then The Activity Instance Wizard Stepper 'Required' page is displayed + When The 'Events' is selected from the Activity instance class field + And The 'DE' is selected from the Activity instance domain field + And User intecepts preview request + And Form continue button is clicked + Then User waits for preview request + Then The Activity Instance Wizard Stepper 'OCCDS' page is displayed + And Automatically assigned activity instance name is saved + And Form continue button is clicked + Then The Activity Instance Wizard Stepper 'Data specification' page is displayed + And User intercepts activity instance creation request with strict_mode verification + And Form save button is clicked + And User waits for activity instance creation request with strict_mode verification + And The form is no longer available + Then The current URL is '/overview' + And Correct instance overview page is displayed + + Scenario: [Create][Events][Fields validation] User must be not be presened with required Activity Instance Classes selection + Given The '/library/activities/activity-instances' page is opened + And User intercepts available activities requests + When The Add Activity Instance button is clicked + And User waits for available activities requests + Then The Activity Instance Wizard Stepper 'Select activity' page is displayed + When First activity is selected from the activity list + And Selected Activity name is saved + And Form continue button is clicked + Then The Activity Instance Wizard Stepper 'Required' page is displayed + When The 'Events' is selected from the Activity instance class field + And The 'DE' is selected from the Activity instance domain field + Then The Activity Item Classes selection is not displayed + + Scenario: [Create][Events][Fields validation] User must be not be presened with ADaM Paramter code input + Given The '/library/activities/activity-instances' page is opened + And User intercepts available activities requests + When The Add Activity Instance button is clicked + And User waits for available activities requests + Then The Activity Instance Wizard Stepper 'Select activity' page is displayed + When First activity is selected from the activity list + And Selected Activity name is saved + And Form continue button is clicked + Then The Activity Instance Wizard Stepper 'Required' page is displayed + When The 'Events' is selected from the Activity instance class field + And The 'DE' is selected from the Activity instance domain field + And Form continue button is clicked + Then ADaM parameter code input should not exists + + Scenario: [Create][Events][Overview Page] User must be able to view all selected values in the overview page (instance class, datadomain, category, subcategory) + And [API] Study Activity is created and approved + And User saves activity name created via API + And The homepage is opened + And User sets row page to 10 in the settings menu + Given The '/library/activities/activity-instances' page is opened + And User intercepts available activities requests + When The Add Activity Instance button is clicked + And User waits for available activities requests + And Activity created via API is searched for + When First activity is selected from the activity list + And Selected Activity name is saved + And Form continue button is clicked + When The 'Events' is selected from the Activity instance class field + And The 'AE' is selected from the Activity instance domain field + And The 'ADVERSE EVENT' is selected from the Data category field + And The 'ACQUIRED' is selected from the Data SubCategory field + And User intecepts preview request + And Form continue button is clicked + Then User waits for preview request + And Automatically assigned activity instance name is saved + And Form continue button is clicked + And User intecepts activity groupings request + And User intecepts activity items request + And User intercepts activity instance creation request with strict_mode verification + And Form save button is clicked + And User waits for activity instance creation request with strict_mode verification + And The form is no longer available + Then The current URL is '/overview' + And Correct instance overview page is displayed + And User waits for activity groupings request + And User waits for activity items request + Then Activity Item Class 'event_category' with value 'ADVERSE EVENT' and type 'CTterm' is present in the table + And Activity Item Class 'event_subcategory' with value 'ACQUIRED' and type 'CTterm' is present in the table + And Activity Item Class 'domain' with value 'AE' and type 'CTterm' is present in the table \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-extended-scope.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-extended-scope.feature index 6e94d8a2..6d60c3c9 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-extended-scope.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-extended-scope.feature @@ -8,7 +8,8 @@ Feature: Library - Concepts - Activities - Activity instances - new wizard stepp Scenario: [Feature flag] User must be able to turn on wizard stepper for activity instance creation When The '/administration/featureflags' page is opened - Then Activity instance wizard feature flag is turned on + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag Scenario: [Create][Selected Activity] User must be able to see which activity has been selected in the first step And [API] Study Activity is created and approved diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-fields-validation.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-fields-validation.feature index c43fadf2..b21e8498 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-fields-validation.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-fields-validation.feature @@ -8,7 +8,8 @@ Feature: Library - Concepts - Activities - Activity instances - wizard stepper - Scenario: [Feature flag] User must be able to turn on wizard stepper for activity instance creation When The '/administration/featureflags' page is opened - Then Activity instance wizard feature flag is turned on + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag Scenario: [Create][Mandatory fields] User must not be able to continue without selecting activity Given The '/library/activities/activity-instances' page is opened diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-numeric-findings.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-numeric-findings.feature index 23fef24d..19268767 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-numeric-findings.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-numeric-findings.feature @@ -8,7 +8,8 @@ Feature: Library - Concepts - Activities - Activity instances - wizard stepper - Scenario: [Feature flag] User must be able to turn on wizard stepper for activity instance creation When The '/administration/featureflags' page is opened - Then Activity instance wizard feature flag is turned on + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag Scenario: [Create][NumericFindings][Existing activity] User must be able to add a new Activity Instance with NumericFindlings as Activity Instance Class Given The '/library/activities/activity-instances' page is opened diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-textual-findings.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-textual-findings.feature index 884cfbfd..d4eaedaa 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-textual-findings.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances-wizard-stepper-textual-findings.feature @@ -8,8 +8,9 @@ Feature: Library - Concepts - Activities - Activity instances - wizard stepper - Scenario: [Feature flag] User must be able to turn on wizard stepper for activity instance creation When The '/administration/featureflags' page is opened - Then Activity instance wizard feature flag is turned on - And Activity instance wizard textual findings feature flag is turned on + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag + And User enables 'activity_instance_wizard_stepper_textual_findings' feature flag Scenario: [Create][TextualFindings][Existing activity] User must be able to add a new Activity Instance with TextualFindings as Activity Instance Class Given The '/library/activities/activity-instances' page is opened diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances.feature index deee6b9f..91344473 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activity-instances/activity-instances.feature @@ -6,6 +6,12 @@ Feature: Library - Concepts - Activities - Activity Instances Given The user is logged in And The '/library/activities/activity-instances' page is opened + Scenario: [Test data] Wizard stepper feature flags are enabled + Given The '/administration/featureflags' page is opened + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag + And User enables 'activity_instance_wizard_stepper_edit_mode' feature flag + Scenario: [Actions][Approve] User must be able to Approve the drafted version of the Activity Instance Attributes And [API] Activity Instance in status Draft exists When User sets status filter to 'all' @@ -19,28 +25,18 @@ Feature: Library - Concepts - Activities - Activity Instances When The 'Approve groupings' option is clicked from the three dot menu list Then The activity instance groupings has status 'Final' and version '1.0' - Scenario: [Actions][Inactivate] User must be able to inactivate the approved version of the Activity Instance Attributes + Scenario: [Actions][Inactivate] User must be able to inactivate the approved version of the Activity Instance When User sets status filter to 'all' And Activity Instance is searched for and found - When The 'Inactivate attributes' option is clicked from the three dot menu list + When The 'Inactivate' option is clicked from the three dot menu list Then The item has status 'Retired' and version '1.0' - - Scenario: [Actions][Inactivate] User must be able to inactivate the approved version of the Activity Instance Groupings - When User sets status filter to 'all' - And Activity Instance is searched for and found - When The 'Inactivate groupings' option is clicked from the three dot menu list Then The activity instance groupings has status 'Retired' and version '1.0' - Scenario: [Actions][Reactivate] User must be able to reactivate the inactivated version of the Activity Instance Attributes + Scenario: [Actions][Reactivate] User must be able to reactivate the inactivated version of the Activity Instance When User sets status filter to 'all' And Activity Instance is searched for and found - When The 'Reactivate attributes' option is clicked from the three dot menu list + When The 'Reactivate' option is clicked from the three dot menu list Then The item has status 'Final' and version '1.0' - - Scenario: [Actions][Reactivate] User must be able to reactivate the inactivated version of the Activity Instance Groupings - When User sets status filter to 'all' - And Activity Instance is searched for and found - When The 'Reactivate groupings' option is clicked from the three dot menu list Then The activity instance groupings has status 'Final' and version '1.0' Scenario: [Actions][New version] User must be able to add a new version for the approved Activity Instance Attributes diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/overview-pages/overview-page-activity-instance.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/overview-pages/overview-page-activity-instance.feature index 5f655853..8eb9276e 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/overview-pages/overview-page-activity-instance.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/overview-pages/overview-page-activity-instance.feature @@ -48,6 +48,7 @@ Feature: Library - Concepts - Activities - Activity Instance Overview Page Scenario: [COSMoS YAML] Verify that the instance overview page displays all sections correctly When I click on the COSMoS YAML tab + And User waits for 1 seconds When The download button is clicked Then The 'COSMoS-overview' file without timestamp is downloaded in 'yml' format # Ad the COSMoS YAML file should be saved with correct content (this step should be tested manually) @@ -67,30 +68,36 @@ Feature: Library - Concepts - Activities - Activity Instance Overview Page | Data type | | Name | | Activity Item Class | + | Name submission value | + | Code submission value | And The Instance linked group, subgroup and instance are displayed in the Activity groupings table And The free text search field should be displayed in the 'Activity groupings' table And The free text search field should be displayed in the 'Activity Items' table - @pending_implmentation - Scenario: [History] Verify that the activity group overview page displays correctly - When The history button is clicked + Scenario: [History] Verify that the activity instance attributes history page displays correctly + When Activity instance attributes history button is clicked + Then The history page is opened + + Scenario: [History] Verify that the activity instance groupings history page displays correctly + When Activity instance groupings history button is clicked Then The history page is opened Scenario: [Linking] Verify that the activities instance overview page can link to the correct groups, subgroups and activities - When Version '0.1' is selected from the Version dropdown list + When Version '0.1' is selected from the Version dropdown list in the instance attributes section And The status displayed on the summary for Activity Instance Attributes is 'Draft' and version is '0.1' And The Start date value is saved Then The correct End date should be displayed And The Instance linked group, subgroup and instance are displayed in the Activity groupings table And The Activity Items table is empty - When Version '1.0' is selected from the Version dropdown list + When Version '1.0' is selected from the Version dropdown list in the instance attributes section And The status displayed on the summary for Activity Instance Attributes is 'Final' and version is '1.0' Then The Instance linked group, subgroup and instance are displayed in the Activity groupings table Scenario: [Edit] Edit the Instance Attributes Given The '/administration/featureflags' page is opened - And Activity instance wizard feature flag is turned on - And Activity instance wizard edit mode feature flag is turned on + And User switch to 'Library' feature flags + And User enables 'new_activity_instance_wizard_stepper' feature flag + And User enables 'activity_instance_wizard_stepper_edit_mode' feature flag And Overview page for activity instance created via API is opened And Instance overview page is opened When Activity instance attributes new version button is clicked diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-item-activity-instance-links.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-item-activity-instance-links.feature index bd6ae684..8f1294da 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-item-activity-instance-links.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-item-activity-instance-links.feature @@ -8,7 +8,6 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Items - Activit Given The user is logged in And The homepage is opened - @manual_test Scenario: [Create][Form View][Single Link][CRF Item Page] User must be able to add one Activity Instance Link to a CRF Item in Form View and verify result in CRF Viewer Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/items' page is opened @@ -18,104 +17,101 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Items - Activit Then The Edit Item page is opened and RESET button is disabled And No Activity Instance Links text is visible And The default page is Form View - When I click the plus button + When I click the Activity Instance Link plus button Then Activity Instance Item 1 table is visible - And The RESET button is enabled When User waits for Activity Instance dropdown to load And I select a value from the Activity Instance dropdown list And User waits for Activity Item Class dropdown to load And I select a value from the Activity Item Class dropdown list + Then The RESET button is enabled When The 'save-button' button is clicked Then The Edit Item window is closed And The current URL is '/library/crf-builder/items' When The '/library/crf-builder/odm-viewer' page is opened When I select created Form from the Form Name dropdown list And I click the GENERATE button - And User waits for CRF Viewer data to load Then The imported CRF view page should be displayed When I click the Activity Instance option from the right top corner Then The added Activity Instance Link is displayed under the test item name - @manual_test Scenario: [Create][Form View][Multiple Links][CRF Item Page] User must be able to add multiple Activity Instance Links to a CRF Item in Form View and verify result in CRF Viewer - Given The test CRF item is created with one Activity Instance Link + Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/items' page is opened And User waits for CRF Items data to load - And Created CRF Item is found + And Created test CRF Item is found When The 'Manage Activity Instance Links' option is clicked from the three dot menu list - Then Activity Instance Item 1 table is visible with the existing linked Activity Instance - When I click the plus button - Then Activity Instance Item 2 table is visible - When I select a value from the Activity Instance dropdown list + When I click the Activity Instance Link plus button + Then Activity Instance Item 1 table is visible + When User waits for Activity Instance dropdown to load + And I select a value from the Activity Instance dropdown list + And User waits for Activity Item Class dropdown to load And I select a value from the Activity Item Class dropdown list + When I click the Activity Instance Link plus button + Then Activity Instance Item 2 table is visible + When I select a value from the second Activity Instance dropdown list + And I select a value from the second Activity Item Class dropdown list When The 'save-button' button is clicked Then The Edit Item window is closed And The current URL is '/library/crf-builder/items' When The '/library/crf-builder/odm-viewer' page is opened When I select created Form from the Form Name dropdown list And I click the GENERATE button - And User waits for CRF Viewer data to load Then The imported CRF view page should be displayed When I click the Activity Instance option from the right top corner - Then The added Activity Instance Link is displayed under the test item name + Then All added Activity Instance Links are displayed under the test item name - @manual_test Scenario: [Create][Table View][Single Link][CRF Item Page] User must be able to add Activity Instance Links in Table View and verify result in CRF Viewer Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/items' page is opened And User waits for CRF Items data to load - And Created CRF Item is found + And Created test CRF Item is found When The 'Manage Activity Instance Links' option is clicked from the three dot menu list Then The Edit Item page is opened and RESET button is disabled And The default page is Form View When I select the Table View option Then The page is switched to Table View When I select a value from the Select an Activity Instance dropdown list - And I select a value from the Activity Item Class dropdown list + And I select an Activity Item Class from the table And The 'save-button' button is clicked Then The Edit Item window is closed And The current URL is '/library/crf-builder/items' When The '/library/crf-builder/odm-viewer' page is opened When I select created Form from the Form Name dropdown list And I click the GENERATE button - And User waits for CRF Viewer data to load Then The imported CRF view page should be displayed When I click the Activity Instance option from the right top corner Then The added Activity Instance Link is displayed under the test item name - @manual_test Scenario: [Mandatory Field Validation][Form View][CRF Item Page] User must select both Activity Instance and Activity Item Class to save Activity Instance Link Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/items' page is opened And User waits for CRF Items data to load - And Created CRF Item is found + And Created test CRF Item is found When The 'Manage Activity Instance Links' option is clicked from the three dot menu list Then The Edit Item page is opened and RESET button is disabled - And The default page is Form View - When I click the plus button + When I click the Activity Instance Link plus button Then Activity Instance Item 1 table is visible - When I do not select any values from either the Activity Instance dropdown list or the Activity Item Class dropdown list - And I click the 'save-button' button - Then I should see validation messages for both dropdown lists indicating that selection is required - When I select a value from the Activity Instance dropdown list and do not select any value from the Activity Item Class dropdown list - And I click the 'save-button' button - Then I should see a validation message for the Activity Item Class dropdown list indicating that selection is required And I am not able to select a value from the Activity Item Class dropdown list before I have selected a value from the Activity Instance dropdown list + When The 'save-button' button is clicked + Then I should see alert messages for both Activity Instance and Activity Item Class fields + When I select a value from the Activity Instance dropdown list and do not select any value from the Activity Item Class dropdown list + Then I should see a field validation message for the Activity Item Class dropdown list + When The 'save-button' button is clicked + Then I should see an alert message for the Activity Item Class field - @manual_test Scenario: [Delete][Form View][CRF Item Page] User must be able to delete Activity Instance Link from a CRF Item in Form View and verify result in CRF Viewer Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/items' page is opened And User waits for CRF Items data to load - And Created CRF Item is found + And Created test CRF Item is found When The 'Manage Activity Instance Links' option is clicked from the three dot menu list Then The Edit Item page is opened and RESET button is disabled - When I click the plus button + When I click the Activity Instance Link plus button Then Activity Instance Item 1 table is visible And The Delete button is visible When I click the Delete button Then The page returns to the initial edit item page without Activity Instance Item table - When I click the plus button + When I click the Activity Instance Link plus button Then Activity Instance Item 1 table is visible When I select a value from the Activity Instance dropdown list And I select a value from the Activity Item Class dropdown list @@ -132,16 +128,23 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Items - Activit When The 'Manage Activity Instance Links' option is clicked from the three dot menu list Then The Edit Item page is opened without any linked Activity Instance Item table - @manual_test + @manual_test Scenario: [Reset][Form View][CRF Item Page] User must be able to reset Activity Instance Link from a CRF Item and verify page state Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/items' page is opened And User waits for CRF Items data to load - And Created CRF Item is found + And Created test CRF Item is found When The 'Manage Activity Instance Links' option is clicked from the three dot menu list - When I click the plus button + Then The Edit Item page is opened and RESET button is disabled + And No Activity Instance Links text is visible + And The default page is Form View + When I click the Activity Instance Link plus button Then Activity Instance Item 1 table is visible - And The RESET button is enabled + When User waits for Activity Instance dropdown to load + And I select a value from the Activity Instance dropdown list + And User waits for Activity Item Class dropdown to load + And I select a value from the Activity Item Class dropdown list + Then The RESET button is enabled When I click the RESET button Then The Activity Instance Item table is removed and the page returns to the initial edit item page diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-tree-item-activity-instance-links.feature b/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-tree-item-activity-instance-links.feature index 005a3557..7e3f3496 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-tree-item-activity-instance-links.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-tree-item-activity-instance-links.feature @@ -8,7 +8,6 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Tree - Activity Given The user is logged in And The homepage is opened - @manual_test Scenario: [Create][Table View][Single Link][CRF Tree Page] User must be able to add one Activity Instance Link to a CRF Item in Table View and verify result in CRF Viewer Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/crf-tree' page is opened @@ -23,18 +22,15 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Tree - Activity And I select a value from the Activity Item Class table And The 'save-button' button is clicked Then The Edit Item window is closed - And The current URL is '/library/crf-builder/crf-tree' When The '/library/crf-builder/odm-viewer' page is opened When I select created Form from the Form Name dropdown list And I click the GENERATE button - And User waits for CRF Viewer data to load Then The imported CRF view page should be displayed When I click the Activity Instance option from the right top corner Then The added Activity Instance Link is displayed under the test item name - - @manual_test + Scenario: [Create][Table View][Multiple Links][CRF Tree Page] User must be able to add multiple Activity Instance Links to a CRF Item in Table View and verify result in CRF Viewer - Given The test CRF item is created with one Activity Instance Link + Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/crf-tree' page is opened When I click the expand button beside created test Collection to expand the CRF Tree And I click the expand button beside created test Form form to expand the form @@ -43,22 +39,20 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Tree - Activity When The 'Manage Activity Instance Links' option is clicked from the three dot menu list of the created test CRF item Then The Edit Item page is opened And The default page is Table View - And I can see the existing Activity Instance Link in the table - When I select another value from the Select an Activity Instance dropdown list - And I select a value from the Activity Item Class dropdown list + When I select a value from the Select an Activity Instance dropdown list + And I select a value from the Activity Item Class table + And I select another value from the Select an Activity Instance dropdown list + And I select a value from the Activity Item Class table And The 'save-button' button is clicked Then The Edit Item window is closed And The current URL is '/library/crf-builder/crf-tree' When The '/library/crf-builder/odm-viewer' page is opened When I select created Form from the Form Name dropdown list And I click the GENERATE button - And User waits for CRF Viewer data to load Then The imported CRF view page should be displayed When I click the Activity Instance option from the right top corner Then The added two Activity Instance Links are displayed under the test item name - - @manual_test Scenario: [Create][Form View][CRF Tree Page] User must be able to add Activity Instance Links in Form View and verify result in CRF Viewer Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/crf-tree' page is opened @@ -71,6 +65,8 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Tree - Activity And The default page is Table View When I select the Form View option Then The page is switched to Form View + When I click the Activity Instance Link plus button + Then Activity Instance Item 1 table is visible When I select a value from the Activity Instance dropdown list And I select a value from the Activity Item Class dropdown list And The 'save-button' button is clicked @@ -79,12 +75,11 @@ Feature: Library - Data Collection Standards - CRF Builder - CRF Tree - Activity When The '/library/crf-builder/odm-viewer' page is opened When I select created Form from the Form Name dropdown list And I click the GENERATE button - And User waits for CRF Viewer data to load Then The imported CRF view page should be displayed When I click the Activity Instance option from the right top corner Then The added Activity Instance Link is displayed under the test item name - @manual_test + @manual_test Scenario: [Mandatory Field Validation][CRF Tree Page] User must select both Activity Instance and Activity Item Class to save Activity Instance Link Given The test CRF item is created with no Activity Instance Link And The '/library/crf-builder/crf-tree' page is opened diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-exchange.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-exchange.feature index 5b9f85a8..6320256f 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-exchange.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-exchange.feature @@ -11,7 +11,8 @@ Feature: Studies - Define Study - Study Activities - Exchange Activity Scenario: [TestData] Old placeholder activity workflow feature flag is disabled When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned off + And User switch to 'Studies' feature flags + And User enables 'streamline_placeholder_activities' feature flag Scenario: [TestData] Study visits, epochs and activities are created And [API] All Activities are deleted from study diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-placeholder.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-placeholder.feature index a2f0a324..266f07f0 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-placeholder.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-placeholder.feature @@ -11,7 +11,8 @@ Scenario: [TestData] Old placeholder activity workflow feature flag is disabled and all activities are deleted from study When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned off + And User switch to 'Studies' feature flags + And User enables 'streamline_placeholder_activities' feature flag And [API] All Activities are deleted from study @smoke_test diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-shared-placeholder.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-shared-placeholder.feature index 9da95d82..4df3072f 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-shared-placeholder.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-shared-placeholder.feature @@ -8,7 +8,8 @@ Feature: Studies - Define Study - Study Activities - Study Activities Placeholde Scenario: [TestData] Old placeholder activity workflow feature flag is enabled When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned on + And User switch to 'Studies' feature flags + And User disables 'streamline_placeholder_activities' feature flag Scenario: [Update][Positive Case][Shared Activity Request] User must be able to accept changes to activity request copied from other study When Study activity add button is clicked diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities.feature index c99ec7af..d89b75e9 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities.feature @@ -11,7 +11,8 @@ Feature: Studies - Define Study - Study Activities - Study Activities Scenario: [TestData] Old placeholder activity workflow feature flag is disabled When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned off + And User switch to 'Studies' feature flags + And User enables 'streamline_placeholder_activities' feature flag Scenario: [TestData] Study visits, epochs and activities are created And [API] All Activities are deleted from study diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-detailed-soa.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-detailed-soa.feature index 730c71e5..49147017 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-detailed-soa.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-detailed-soa.feature @@ -11,7 +11,8 @@ Feature: Studies - Define Study - Study Activities - Schedule of Activities - De Scenario: [TestData] Old placeholder activity workflow feature flag is disabled When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned off + And User switch to 'Studies' feature flags + And User enables 'streamline_placeholder_activities' feature flag Scenario: [TestData] Study visits, epochs and activities are created And [API] The epoch with type 'Pre Treatment' and subtype 'Run-in' exists in selected study @@ -512,17 +513,17 @@ Feature: Studies - Define Study - Study Activities - Schedule of Activities - De When User search for non-existing activity Then No activities are found - Scenario: [Table][Search][Negative] User must not be able to search activity by activity subgroup + Scenario: [Table][Search][By subgroup] User must be able to search activity by activity subgroup Given The test study '/activities/soa' page is opened And Detailed SoA table is loaded When User search study activity by subgroup - Then No activities are found + Then Activity is found in table - Scenario: [Table][Search][Negative] User must not be able to search activity by activity group + Scenario: [Table][Search][By group] User must be able to search activity by activity group Given The test study '/activities/soa' page is opened And Detailed SoA table is loaded When User search study activity by group - Then No activities are found + Then Activity is found in table Scenario: [Export][CSV] User must be able to export the data in CSV format Given The test study '/activities/soa' page is opened diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/suty-soa-protocol-lab-table.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/suty-soa-protocol-lab-table.feature new file mode 100644 index 00000000..be1a3910 --- /dev/null +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/suty-soa-protocol-lab-table.feature @@ -0,0 +1,58 @@ +@REQ_ID:1074260 +Feature: Studies - Define Study - Study Activities - Schedule of Activities - Protocol - Lab Table + + As a system user, + I want the system to ensure [Scenario], + So that I can make complete and consistent specification of study SoA for the protocol. + + Background: User is logged in and study has been selected + Given The user is logged in + And A test study is selected + And The feature flag 'Protocol – Lab' enabled state is set to 'true' + + Scenario: [Test data] User must be able to create data needed for study protocol lab table - lab assemenents + And [API] The epoch with type 'Pre Treatment' and subtype 'Run-in' exists in selected study + And [API] The epoch with type 'Treatment' and subtype 'Intervention' exists in selected study + And [API] Study vists uids are fetched for current study + When [API] Study visits in current study are cleaned-up + And [API] The static visit data is fetched + And [API] The dynamic visit data is fetched: contact mode 'On Site Visit', time reference 'Global anchor visit', type 'Pre-screening', epoch 'Run-in' + And [API] The visit with following attributes is created: isGlobalAnchor 1, visitWeek 0 + And [API] The visit with following attributes is created: isGlobalAnchor 0, visitWeek 1, minVisitWindow -1, maxVisitWindow 1 + And [API] The dynamic visit data is fetched: contact mode 'On Site Visit', time reference 'Global anchor visit', type 'Randomisation', epoch 'Intervention' + And [API] The visit with following attributes is created: isGlobalAnchor 0, visitWeek 2, minVisitWindow 3, maxVisitWindow 7 + When [API] All Activities are deleted from study + When [API] Activity for SoA group 'BIOMARKERS' with activity group 'Laboratory Assessments' is added to the study + + Scenario: [Navigation] User must be able to navigate to Protocol SoA - Lab table page using side menu + Given The '/studies' page is opened + When The 'Study Activities' submenu is clicked in the 'Define Study' section + And The 'Schedule of Activities' tab is selected + And User switches to the 'protocol_lab_table' view + Then The current URL is '/activities/soa' + + Scenario: [Table][View] User must be presented with lab assesments activities in the Lab Table view + And The test study '/activities/soa' page is opened + When User switches to the 'protocol_lab_table' view + Then The laboratory assements activities are present in protocol lab table + + Scenario: [Export][CSV] User must be able to export the data in CSV format + Given The test study '/activities/soa' page is opened + And User switches to the 'protocol_lab_table' view + When User clicks export button + And User selects 'CSV' format to export the table content + Then The study specific 'protocol_lab_table SoA' file without timestamp is downloaded in 'csv' format + + Scenario: [Export][EXCEL] User must be able to export the data in JSON format + Given The test study '/activities/soa' page is opened + And User switches to the 'protocol_lab_table' view + When User clicks export button + And User selects 'EXCEL' format to export the table content + Then The study specific 'protocol_lab_table SoA' file without timestamp is downloaded in 'xlsx' format + + Scenario: [Export][DOCX] User must be able to export the data in XML format + Given The test study '/activities/soa' page is opened + And User switches to the 'protocol_lab_table' view + When User clicks export button + And User selects 'DOCX' format to export the table content + Then The study specific 'protocol_lab_table SoA' file without timestamp is downloaded in 'docx' format \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances-edition.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances-edition.feature index 4209fb9f..880f396b 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances-edition.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances-edition.feature @@ -48,8 +48,9 @@ Feature: Studies - Define Study - Study Data Specifications - Study Activity Ins And [API] The activity instance with isDefaultForActivity set to true is created and approved And [API] Activity is added to the study When The '/administration/featureflags' page is opened - Then Study data supplier feature flag is turned on - And Userdefined study data supplier feature flag is turned on + And User switch to 'Studies' feature flags + And User enables 'study_data_suppliers' feature flag + And User enables 'study_data_suppliers_create_from_study' feature flag When User intercepts data supplier request And The test study '/data-suppliers' page is opened And The 'Overview' tab is selected diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances.feature index 599c1351..7b198921 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-activity-instances.feature @@ -11,7 +11,8 @@ Feature: Studies - Define Study - Study Data Specifications - Study Activity Ins Scenario: [TestData] Old placeholder activity workflow feature flag is disabled When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned off + And User switch to 'Studies' feature flags + And User enables 'streamline_placeholder_activities' feature flag Scenario: [Test data] User creates test data via API And [API] The epoch with type 'Pre Treatment' and subtype 'Run-in' exists in selected study diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-operational-soa.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-operational-soa.feature index 13a3c08d..edfb6ed0 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-operational-soa.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_data_specification/study-operational-soa.feature @@ -14,7 +14,8 @@ Feature: Studies - Define Study - Study Data Specifications - Operational SoA Scenario: [TestData] Old placeholder activity workflow feature flag is disabled When The '/administration/featureflags' page is opened - Then Old placeholder workflow feature flag is turned off + And User switch to 'Studies' feature flags + And User enables 'streamline_placeholder_activities' feature flag Scenario: [TestData] All activities are deleted from test study And [API] All Activities are deleted from study diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds.feature index f1aad389..323d82fe 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds.feature @@ -5,8 +5,15 @@ Feature: Studies - Define Study - Study Interventions - Study Compounds Given The user is logged in And A test study is selected - Scenario: [Test Data] All study compounds must be removed prior to tests execution - Given The study compounds data is cleaned for testing purspose + Scenario: [Test data] Study compunds feature flag is enabled, data for compound creation is fetched and existing compounds are deleted + Given The '/administration/featureflags' page is opened + And User switch to 'Studies' feature flags + And User enables 'compounds_studies' feature flag + And [API] Study compound simple data is fetched + And [API] Study compound alias data is fetched + And [API] Study compound medical product data is fetched + And [API] Study compound type of treatment data is fetched is created + And The study compounds data is cleaned for testing purspose Scenario: [Navigaion] User must be able to navigate to the Study Compounds page Given The '/studies' page is opened @@ -46,56 +53,18 @@ Feature: Studies - Define Study - Study Interventions - Study Compounds Then The study compound is present in the compounds table Scenario: [Edit] User must be able to edit a study compound + Given [API] Study compound is created Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User select first compund - And User select first medicinal product - And Form continue button is clicked - And User fills other information - And User intercepts compund create request - When Form save button is clicked + When User searches the compound by the uid And The 'Edit' option is clicked from the three dot menu list And User select last type of treatment And Form continue button is clicked And User select last medicinal product And Form continue button is clicked - And User fills other information And User intercepts compund update request When Form save button is clicked Then The study compound is present in the compounds table - Scenario: [Create][Form behaviour] Compound alias must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts compund aliases request - And User intercepts compunds request - And User select first compund - Then The compound alias for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Other aliases must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts compund aliases request - And User intercepts compunds request - And User select first compund - Then The other aliases for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Sponsor compound must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts compund aliases request - And User intercepts compunds request - And User select first compund - Then The sponsor compound for this compound is automatically populated from library - Scenario: [Create][Form behaviour] Compound definition must be automatically populated when selecting study compound Given The test study '/study_interventions/study_compounds' page is opened When User clicks add study compund button @@ -104,20 +73,10 @@ Feature: Studies - Define Study - Study Interventions - Study Compounds And User intercepts compund aliases request And User intercepts compunds request And User select first compund - Then The compound definition for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Dispensed must be automatically populated when selecting medicinal product - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts medicial products request - And User intercepts pharmaceutical products request - And User select first compund - And User select first medicinal product - Then The dispensed in for this compound is automatically populated from library + Then The compound alias data is automatically populated from library + And The sponsor compound data is automatically populated from library - Scenario: [Create][Form behaviour] INN must be automatically populated when selecting medicinal product + Scenario: [Create][Form behaviour] Pharmacological and Medicinal Product data must be automatically populated when selecting medicinal product Given The test study '/study_interventions/study_compounds' page is opened When User clicks add study compund button And User select first type of treatment @@ -126,62 +85,8 @@ Feature: Studies - Define Study - Study Interventions - Study Compounds And User intercepts pharmaceutical products request And User select first compund And User select first medicinal product - Then The INN for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Analyte number must be automatically populated when selecting medicinal product - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts medicial products request - And User intercepts pharmaceutical products request - And User select first compund - And User select first medicinal product - Then The analyte number for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Substance ID must be automatically populated when selecting medicinal product - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts medicial products request - And User intercepts pharmaceutical products request - And User select first compund - And User select first medicinal product - Then The substance id for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Substance name must be automatically populated when selecting medicinal product - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts medicial products request - And User intercepts pharmaceutical products request - And User select first compund - And User select first medicinal product - Then The substance name for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] UNII must be automatically populated when selecting medicinal product - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts medicial products request - And User intercepts pharmaceutical products request - And User select first compund - And User select first medicinal product - Then The UNII for this compound is automatically populated from library - - Scenario: [Create][Form behaviour] Pharmacological class (MED-RT) must be automatically populated when selecting medicinal product - Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User intercepts medicial products request - And User intercepts pharmaceutical products request - And User select first compund - And User select first medicinal product - Then The pharmacological class MED-RT for this compound is automatically populated from library + Then The Pharmaceutical Product data is automatically populated from library + And The Medicinal Product data is automatically populated from library Scenario: [Create] User must not be able to create a study compound without the type of treatment selected Given The test study '/study_interventions/study_compounds' page is opened @@ -207,16 +112,9 @@ Feature: Studies - Define Study - Study Interventions - Study Compounds Then The user cannot save the form Scenario: [Delete] User must be able to delete a study compound + Given [API] Study compound is created Given The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User select first compund - And User select first medicinal product - And Form continue button is clicked - And User fills other information - And User intercepts compund create request - When Form save button is clicked + When User searches the compound by the uid When The 'Delete' option is clicked from the three dot menu list And User intercepts compund delete request And Action is confirmed by clicking continue diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds_dosings.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds_dosings.feature index 5c6de842..28e26dfe 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds_dosings.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_interventions/study_compounds_dosings.feature @@ -5,6 +5,17 @@ Feature: Studies - Define Study - Study Interventions - Study Compound Dosings Given The user is logged in And A test study is selected + Scenario: [Test data] Study compunds feature flag is enabled, data for compound creation is fetched and existing compounds are deleted + Given The '/administration/featureflags' page is opened + And User switch to 'Studies' feature flags + And User enables 'compounds_studies' feature flag + And The study compounds data is cleaned for testing purspose + And [API] Study compound simple data is fetched + And [API] Study compound alias data is fetched + And [API] Study compound medical product data is fetched + And [API] Study compound type of treatment data is fetched is created + Given [API] Study compound is created + Scenario: [Navigaion] User must be able to navigate to the Study Compound Dosings page Given The '/studies' page is opened When The 'Study Interventions' submenu is clicked in the 'Define Study' section @@ -32,17 +43,6 @@ Feature: Studies - Define Study - Study Interventions - Study Compound Dosings Scenario: [Create] User must be able to create a study compound dosings Given [API] Uids are fetched for element subtype 'Treatment' And [API] Element is created for the test study - And The study compounds data is cleaned for testing purspose - And The test study '/study_interventions/study_compounds' page is opened - When User clicks add study compund button - And User select first type of treatment - And Form continue button is clicked - And User select first compund - And User select first medicinal product - And Form continue button is clicked - And User fills other information - And User intercepts compund create request - When Form save button is clicked And The test study '/study_interventions/study_compound_dosings' page is opened When The user clicks add study compund dosing And The user select first study element @@ -56,16 +56,10 @@ Feature: Studies - Define Study - Study Interventions - Study Compound Dosings Scenario: [Edit] User must be able to edit a study compound dosing Given The study compound dosing data is cleaned for testing purspose + Given [API] Study compound data is fetched + And [API] Study compound dosing is created And The test study '/study_interventions/study_compound_dosings' page is opened - When The user clicks add study compund dosing - And The user select first study element - And Form continue button is clicked - And The user select first compund - And Form continue button is clicked - And The user select first dose value - And The user intercepts study compund dosings create request - When Form save button is clicked - And User waits for the table + And User searches the compound dosing by the uid When The 'Edit' option is clicked from the three dot menu list And The user select last study element And Form continue button is clicked @@ -76,92 +70,21 @@ Feature: Studies - Define Study - Study Interventions - Study Compound Dosings When Form save button is clicked Then The study compound dosing is present in the compound dosings table - Scenario: [Create][Form behaviour][Compound Dosings][Element] Element order must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study elements request - When The user clicks add study compund dosing - And The user select first study element - Then The element order for this element is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Element] Element type must be automatically populated when selecting study compound + Scenario: [Create][Form behaviour][Compound Dosings][Element] Element data is automatically populated when selecting study compound Given The test study '/study_interventions/study_compound_dosings' page is opened And The user intercepts study elements request When The user clicks add study compund dosing And The user select first study element - Then The element type for this element is automatically populated from library + Then The Element data is automatically populated - Scenario: [Create][Form behaviour][Compound Dosings][Element] Element subtype must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study elements request - When The user clicks add study compund dosing - And The user select first study element - Then The element subtype for this element is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Element] Element name must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study elements request - When The user clicks add study compund dosing - And The user select first study element - Then The element name for this element is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Element] Element short name be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study elements request - When The user clicks add study compund dosing - And The user select first study element - Then The element short name for this element is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Element] Element description must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study elements request - When The user clicks add study compund dosing - And The user select first study element - Then The element description for this element is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Compound] Compound order must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study compunds request - And The user clicks add study compund dosing - And The user select first study element - And Form continue button is clicked - When The user select first compund - Then The compound order in dosings from for this compound is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Compound] Type of treatment must be automatically populated when selecting study compound + Scenario: [Create][Form behaviour][Compound Dosings][Compound] Compound data is automatically populated when selecting study compound Given The test study '/study_interventions/study_compound_dosings' page is opened And The user intercepts study compunds request And The user clicks add study compund dosing And The user select first study element And Form continue button is clicked When The user select first compund - Then The type of treatment in dosings from for this compound is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Compound] Compound name must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study compunds request - And The user clicks add study compund dosing - And The user select first study element - And Form continue button is clicked - When The user select first compund - Then The compound name in dosings from for this compound is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Compound] Compound alias name be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study compunds request - And The user clicks add study compund dosing - And The user select first study element - And Form continue button is clicked - When The user select first compund - Then The compound alias name in dosings from for this compound is automatically populated from library - - Scenario: [Create][Form behaviour][Compound Dosings][Compound] Preffered synonym must be automatically populated when selecting study compound - Given The test study '/study_interventions/study_compound_dosings' page is opened - And The user intercepts study compunds request - And The user clicks add study compund dosing - And The user select first study element - And Form continue button is clicked - When The user select first compund - Then The preferred synonim in dosings from for this compound is automatically populated from library + Then The Compound data is automatically populated Scenario: [Create] User must not be able to create a study compound dosing without the study element selected Given The test study '/study_interventions/study_compound_dosings' page is opened @@ -189,16 +112,10 @@ Feature: Studies - Define Study - Study Interventions - Study Compound Dosings Scenario: [Delete] User must be able to delete a study compound Given The study compound dosing data is cleaned for testing purspose + Given [API] Study compound data is fetched + And [API] Study compound dosing is created And The test study '/study_interventions/study_compound_dosings' page is opened - When The user clicks add study compund dosing - And The user select first study element - And Form continue button is clicked - And The user select first compund - And Form continue button is clicked - And The user select first dose value - And The user intercepts study compund dosings create request - When Form save button is clicked - And User waits for the table + And User searches the compound dosing by the uid When The 'Delete' option is clicked from the three dot menu list And The user intercepts study compound dosing delete request And Action is confirmed by clicking continue diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/manage_studies/study_data_suppliers/study_data_supplier.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/manage_studies/study_data_suppliers/study_data_supplier.feature index 092c6ba1..214fcae3 100644 --- a/system-tests/ui-tests/cypress/e2e/features/modules/studies/manage_studies/study_data_suppliers/study_data_supplier.feature +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/manage_studies/study_data_suppliers/study_data_supplier.feature @@ -7,7 +7,11 @@ Feature: Study - Manage Study - Study Data Suppliers And A test study is selected And Data supplier type is set to 'EDC System' - Scenario: [Test data] User must be able delete all existing data suppliers for given study + Scenario: [Test data] User must be able to enabler feature flags and delete all existing data suppliers for given study + Given The '/administration/featureflags' page is opened + And User switch to 'Studies' feature flags + And User enables 'study_data_suppliers' feature flag + And User enables 'study_data_suppliers_create_from_study' feature flag Given User intercepts data supplier request Given The test study '/data-suppliers' page is opened And The 'Overview' tab is selected diff --git a/system-tests/ui-tests/cypress/e2e/features/modules/studies/study_list/study-list-copy-study-activities-schedules.feature b/system-tests/ui-tests/cypress/e2e/features/modules/studies/study_list/study-list-copy-study-activities-schedules.feature new file mode 100644 index 00000000..0f9ae1f4 --- /dev/null +++ b/system-tests/ui-tests/cypress/e2e/features/modules/studies/study_list/study-list-copy-study-activities-schedules.feature @@ -0,0 +1,60 @@ +@REQ_ID:987736 @development_only +Feature: Studies - Study List - Copy Study - Study activities and schedules + + As a user, I want to clone a study including study activity groupings, study activities, instances, and activity schedules. + + Background: User must be logged in + Given The user is logged in + And The '/studies/select_or_add_study/active' page is opened + + Scenario: [Create][Positive case][Study activities][Schedules] User must be able to copy study including study activities and schedules + When Get study 'CDISC DEV-9866' uid + And Select study with uid saved in previous step + And [API] Study vists uids are fetched for selected study + When [API] Study visits in selected study are cleaned-up + Given The study visits uid array is cleared + And [API] The epoch with type 'Pre Treatment' and subtype 'Run-in' exists in selected study + And [API] The epoch with type 'Treatment' and subtype 'Intervention' exists in selected study + And [API] Uid of study type 'Investigational Arm' is fetched + And [API] The Study Arm with name 'Arm1' exists within selected study + And [API] The Study Branch is created within selected study + And [API] The Study Cohort is created within selected study + And [API] Uids are fetched for element subtype 'Run-in' + And [API] Element is created for the current study + And [API] Link Study Element to Epoch and Study Arm within selected study + And [API] Uids are fetched for element subtype 'Treatment' + And [API] Element is created for the current study + And [API] The Study Arm with name 'Arm2' exists within selected study + And [API] The Study Arm with name 'Arm3' exists within selected study + And [API] The static visit data is fetched + And [API] The dynamic visit data is fetched: contact mode 'On Site Visit', time reference 'Global anchor visit', type 'Pre-screening', epoch 'Run-in' + And [API] The visit with following attributes is created: isGlobalAnchor 1, visitWeek 0 + And [API] The visit with following attributes is created: isGlobalAnchor 0, visitWeek 1, minVisitWindow -1, maxVisitWindow 1 + And [API] The dynamic visit data is fetched: contact mode 'On Site Visit', time reference 'Global anchor visit', type 'Randomisation', epoch 'Intervention' + And [API] The visit with following attributes is created: isGlobalAnchor 0, visitWeek 2, minVisitWindow 3, maxVisitWindow 7 + And [API] All Activities are deleted from selected study + And [API] Study Activity is created and approved + And [API] Get SoA Group 'INFORMED CONSENT' id + And [API] Activity is added to the selected study + And [API] Activity is assigned to the visit 0 in selected study + And [API] Activity is assigned to the visit 1 in selected study + And The '/studies/select_or_add_study/active' page is opened + Given The Add Study button is clicked + And The user selects to create study from existing study + And New study project id, study number and study acronym are filled in + And Form continue button is clicked + And The user intercepts study statistics request + When The user selects study to use for copy + When The user selects 'Arms' category to be copied + When The user selects 'Branches' category to be copied + When The user selects 'Cohorts' category to be copied + When The user selects 'Epochs' category to be copied + When The user selects 'Study visits' category to be copied + When The user selects 'Study activities' category to be copied + When The user selects 'Schedules' category to be copied + When The user selects 'Elements' category to be copied + When The user selects 'Design matrix' category to be copied + When User intercepts study clone request verifying structure and activity clone flags + And Form save button is clicked + And User waits for cloning request + Then The study clone response is successful with submitted metadata diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/administration_data_completness_tags_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/administration_data_completness_tags_steps.js index 337bdd41..66f09d72 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/administration_data_completness_tags_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/administration_data_completness_tags_steps.js @@ -1,7 +1,6 @@ const { Given, When, Then } = require("@badeball/cypress-cucumber-preprocessor"); let currentStudyNumber -let currentStudyUid let currentTag let tag1 let tag2 @@ -10,19 +9,8 @@ let tag3 Given('A test study {string} for data completion tags test exists', (study_number) => { currentStudyNumber = study_number cy.createTestStudy(study_number, `Data Completness Tags Tests ${Date.now()}`) - cy.getStudyUid(study_number).then(uid => { - currentStudyUid = uid - }) }) -When("The user selects a study to create a completness tag", () => { - cy.get(`[data-cy="select-study-to-tag"]`).within(() => cy.get('.v-field__input').click()) - cy.get('.v-overlay__content .v-list', { timeout: 20000 }) - .filter(':visible') - .should('not.contain', 'No data available') - .within(() => cy.contains('.v-list-item', currentStudyNumber).click()) -}); - When("The user provides new completness tag into the text field", () => { currentTag = Date.now() cy.fillInput('tag-name', currentTag) @@ -43,45 +31,25 @@ When("The data completness tag in uncompleted state exists", () => { }); When("The user sets the tag to completed for study", () => { - cy.get(`[data-cy="select-study-to-tag"]`).within(() => cy.get('.v-field__input').click()) - cy.get('.v-overlay__content .v-list', { timeout: 20000 }) - .filter(':visible') - .should('not.contain', 'No data available') - .within(() => cy.contains('.v-list-item', currentStudyNumber).click()) - cy.contains('.v-data-table__tr', currentTag).within(() => { - cy.get('[data-cy="set-tag"]').click() - }) + selectTagStudy(currentStudyNumber) + setTag(currentTag) }); When("The user sets the tag to uncompleted for the study", () => { - cy.get(`[data-cy="select-study-to-tag"]`).within(() => cy.get('.v-field__input').click()) - cy.get('.v-overlay__content .v-list', { timeout: 20000 }) - .filter(':visible') - .should('not.contain', 'No data available') - .within(() => cy.contains('.v-list-item', currentStudyNumber).click()) - - cy.contains('.v-data-table__tr', currentTag).within(() => { - cy.get('[data-cy="set-tag"]').click() - }) + selectTagStudy(currentStudyNumber) + setTag(currentTag) }); When("The data completness tag is visible on study list level for selected study", () => { cy.searchFor(currentStudyNumber) - cy.contains(currentTag).should('not.exist') + cy.contains(currentTag).should('exist') }); When("The data completness tag in completed state exists for the study", () => { currentTag = Date.now() - cy.get(`[data-cy="select-study-to-tag"]`).within(() => cy.get('.v-field__input').click()) - cy.get('.v-overlay__content .v-list', { timeout: 20000 }) - .filter(':visible') - .should('not.contain', 'No data available') - .within(() => cy.contains('.v-list-item', currentStudyNumber).click()) - cy.fillInput('tag-name', currentTag) - cy.clickButton('save-tag') - cy.contains('.v-data-table__tr', currentTag).within(() => { - cy.get('[data-cy="set-tag"]').click() - }) + selectTagStudy(currentStudyNumber) + createTag(currentTag) + setTag(currentTag) }); @@ -92,39 +60,25 @@ When("The data completness tag is not on study list level for selected study", ( When("The user creates multiple completion tags", () => { - cy.fillInput('tag-name', 'Tag 1') - cy.clickButton('save-tag') - cy.fillInput('tag-name', 'Tag 2') - cy.clickButton('save-tag') - cy.fillInput('tag-name', 'Tag 3') - cy.clickButton('save-tag') - cy.fillInput('tag-name', 'Tag 4') - cy.clickButton('save-tag') + tag1 = `Tag1 ${Date.now()}` + tag2 = `Tag2 ${Date.now()}` + tag3 = `Tag3 ${Date.now()}` + createTag(tag1) + createTag(tag2) + createTag(tag3) + }); When("Only the completed tag is visible on the study list level for the study", () => { cy.searchFor(currentStudyNumber) }); -When("The user sets multiple tags to complete for selected study", () => { - cy.get(`[data-cy="select-study-to-tag"]`).within(() => cy.get('.v-field__input').click()) - cy.get('.v-overlay__content .v-list', { timeout: 20000 }) - .filter(':visible') - .should('not.contain', 'No data available') - .within(() => cy.contains('.v-list-item', currentStudyNumber).click()) +When("The user sets multiple tags to completed for selected study", () => { + selectTagStudy(currentStudyNumber) + setTag(tag1) + setTag(tag2) + setTag(tag3) - cy.get('.v-data-table__tr').eq(1).within(() => { - cy.get('td').eq(1).invoke('text').then((value) => tag1 = value) - cy.get('.v-selection-control__input').click() - }) - cy.get('.v-data-table__tr').eq(2).within(() => { - cy.get('td').eq(1).invoke('text').then((value) => tag2 = value) - cy.get('.v-selection-control__input').click() - }) - cy.get('.v-data-table__tr').eq(3).within(() => { - cy.get('td').eq(1).invoke('text').then((value) => tag3 = value) - cy.get('.v-selection-control__input').click() - }) }); @@ -133,4 +87,20 @@ Then('All the completed tags are visible for the study', () => { cy.tableContains(tag1) cy.tableContains(tag2) cy.tableContains(tag3) -}) \ No newline at end of file +}) + + +function setTag(tag) { + cy.contains('.v-data-table__tr', tag).within(() => { + cy.get('input').click() + }) +} + +function createTag(tag) { + cy.fillInput('tag-name', tag) + cy.clickButton('save-tag') +} + +function selectTagStudy(study) { + cy.selectAutoComplete("select-study-to-tag", study, { defocus: false }) +} \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/administration_feature_flags_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/administration_feature_flags_steps.js index 1be0dfd5..024284cc 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/administration_feature_flags_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/administration_feature_flags_steps.js @@ -1,41 +1,20 @@ const { Given, When, Then } = require("@badeball/cypress-cucumber-preprocessor"); -Given("The toggle is set to on", () => toggleAllOnOff(true)); +Given("The feature flag {string} enabled state is set to {string}", (feature_flag, state) => enableFlag(feature_flag, state)) -Given("The toggle is set to off", () => toggleAllOnOff(false)); +When('User switch to {string} feature flags', (name) => cy.contains('.layoutSelector button', name).click()) -When("Click the View Listings side-menu", () => cy.get('.v-list-item-title').contains('View Listings').click()) +When('User enables {string} feature flag', (name) => toggleOnOff(name, true)) -Then("The sub-menu Analysis Study Metadata should exist", () => checkIfItemAvailableInMenu('Analysis Study Metadata (New)', true)) - -Then("The sub-menu Analysis Study Metadata should not exist", () => checkIfItemAvailableInMenu('Analysis Study Metadata (New)', false)) - -When('Activity instance wizard feature flag is turned off', () => toggleOnOff('create/edit Activity Instances', false)) - -When('Activity instance wizard feature flag is turned on', () => toggleOnOff('create/edit Activity Instances', true)) - -When('Activity instance wizard textual findings feature flag is turned on', () => toggleOnOff('Textual Findings use case in the new wizard stepper', true)) - -When('Activity instance wizard edit mode feature flag is turned on', () => toggleOnOff('edit mode of the new wizard', true)) - -When('Old placeholder workflow feature flag is turned on', () => toggleOnOff('enabled restores the old placeholder activity workflow: shows the Requested Activities', true)) - -When('Old placeholder workflow feature flag is turned off', () => toggleOnOff('enabled restores the old placeholder activity workflow: shows the Requested Activities', false)) - -When('Study data supplier feature flag is turned on', () => toggleOnOff('This flag toggles on/off the Study Data Suppliers page', true)) - -When('Userdefined study data supplier feature flag is turned on', () => toggleOnOff('This flag toggles on/off the ability to create a user-defined data supplier from study level', true)) - -function toggleAllOnOff(on) { - cy.wait(1000) - on ? cy.get('table .v-switch input').check() : cy.get('table .v-switch input').uncheck() -} - -function checkIfItemAvailableInMenu(name, shouldExists) { - const condition = shouldExists ? 'be.visible' : 'not.exist' - cy.get(`[data-cy="${name}"]`).should(condition); -} +When('User disables {string} feature flag', (name) => toggleOnOff(name, false)) function toggleOnOff(featureName, on) { cy.contains('table tbody tr', featureName).find('.v-switch input').then(el => on ? cy.wrap(el).check() : cy.wrap(el).uncheck()) } + +function enableFlag(flagName, state) { + cy.sendGetRequest('/feature-flags').then((response) => { + let feature_flag_sn = response.body.find(element => element.feature == flagName).sn + cy.sendUpdateRequest('PATCH',`feature-flags/${feature_flag_sn}`, { enabled: state }) + }) +} \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/global_functions_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/global_functions_steps.js index 45eaf174..51aa52fc 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/global_functions_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/global_functions_steps.js @@ -1,6 +1,12 @@ const { Given, When, Then } = require("@badeball/cypress-cucumber-preprocessor"); import { formatDateToMMMDDYYYY, getCurrentStudyId } from '../../support/helper_functions' +When("Click the View Listings side-menu", () => cy.get('.v-list-item-title').contains('View Listings').click()) + +Then("The sub-menu Analysis Study Metadata should exist", () => cy.get(`[data-cy="Analysis Study Metadata (New)"]`).should('be.visible')) + +Then("The sub-menu Analysis Study Metadata should not exist", () => cy.get(`[data-cy="Analysis Study Metadata (New)"]`).should('not.exist')) + When('User clicks table export button', () => cy.clickButton('table-export-button')) When('User clicks export button', () => cy.get('button .mdi-download-outline').click()) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/global_table_specific_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/global_table_specific_steps.js index a6191261..abdbdf9e 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/global_table_specific_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/global_table_specific_steps.js @@ -98,19 +98,19 @@ Then('Only actions that should be avaiable for the Retired item are displayed', Then('Only actions that should be avaiable for the Draft Activity Instance are displayed', () => { const allowedActions = ['Approve attributes', 'Approve groupings', 'Edit attributes', 'Edit groupings', 'Delete', 'History (attributes)', 'History (groupings)'] - const notAllowedActions = ['New version (attributes)', 'New version (groupings)', 'Inactivate attributes', 'Inactivate groupings', 'Reactivate attributes', 'Reactivate groupings'] + const notAllowedActions = ['New version (attributes)', 'New version (groupings)', 'Inactivate', 'Reactivate'] checkActionsAvailability(allowedActions, notAllowedActions) }) Then('Only actions that should be avaiable for the Final Activity Instance are displayed', () => { - const allowedActions = ['New version (attributes)', 'New version (groupings)', 'Inactivate attributes', 'Inactivate groupings', 'History (attributes)', 'History (groupings)'] - const notAllowedActions = ['Edit attributes', 'Edit groupings', 'Delete', 'Approve attributes', 'Approve groupings', 'Reactivate attributes', 'Reactivate groupings'] + const allowedActions = ['New version (attributes)', 'New version (groupings)', 'Inactivate', 'History (attributes)', 'History (groupings)'] + const notAllowedActions = ['Edit attributes', 'Edit groupings', 'Delete', 'Approve attributes', 'Approve groupings', 'Reactivate'] checkActionsAvailability(allowedActions, notAllowedActions) }) Then('Only actions that should be avaiable for the Retired Activity Instance are displayed', () => { - const allowedActions = ['Reactivate attributes', 'Reactivate groupings', 'History (attributes)', 'History (groupings)'] - const notAllowedActions = ['New version (attributes)', 'New version (groupings)', 'Inactivate attributes', 'Inactivate groupings', 'Edit attributes', 'Edit groupings', 'Delete', 'Approve attributes', 'Approve groupings'] + const allowedActions = ['Reactivate', 'History (attributes)', 'History (groupings)'] + const notAllowedActions = ['New version (attributes)', 'New version (groupings)', 'Inactivate', 'Edit attributes', 'Edit groupings', 'Delete', 'Approve attributes', 'Approve groupings'] checkActionsAvailability(allowedActions, notAllowedActions) }) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_instances_wizard_stepper_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_instances_wizard_stepper_steps.js index ccc5cf5f..1c8f3223 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_instances_wizard_stepper_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_instances_wizard_stepper_steps.js @@ -75,6 +75,8 @@ When("The {string} is selected from the Activity instance domain field", name => Then("The Activity Item Classes selection displayed", () => cy.contains('.v-overlay .v-row .dialog-title', 'Select Activity Item Classes'). should('be.visible')) +Then("The Activity Item Classes selection is not displayed", () => cy.contains('.v-overlay .v-row .dialog-title', 'Select Activity Item Classes'). should('not.exist')) + Then("Warning is displayed for mandatory field {string}", (fieldName) => warningIsDisplayed(fieldName)) Then("Warning about not matching name and sentence case name is displayed", () => warningIsDisplayed('Sentence case name', "Sentence case name can only differ in case compared to name value")) @@ -158,6 +160,10 @@ Then("ADaM parameter code is four first letters of selected Code submission valu cy.contains('.v-stepper-window-item .v-input', 'ADaM parameter code').find('input').should('contain.value', selectedCodeSubmissionValue.substring(0, 4)) }) +Then("ADaM parameter code input should not exists", () => { + cy.contains('.v-stepper-window-item .v-input', 'ADaM parameter code').should('not.exist') +}) + When("Data from research lab is checked", () => cy.get('input[aria-label="Data from a Research lab"]').check()) Then("Activity Instance Name have Research added to it", () => { diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_steps.js index 049205e2..c294fa26 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_activities_steps.js @@ -8,6 +8,8 @@ const { getShortUniqueId } = require("../../support/helper_functions"); export let activityName, synonym, currentSubgroupName, currentGroupName const nciconceptid = "NCIID", nciconceptname = "NCINAME", abbreviation = "ABB", definition = "DEF" +Then('The Library value is set to {string}', (value) => cy.checkRowByIndex(0, 'Library', value)) + Then('Activity is present in first table row', () => cy.checkRowByIndex(0, 'Activity name', activityName)) When('The Add activity button is clicked', () => cy.clickButton('add-activity')) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_activity_overview_page_common.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_activity_overview_page_common.js index 1a4a9f77..5305036d 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/library_activity_overview_page_common.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_activity_overview_page_common.js @@ -1,5 +1,6 @@ import { activityInstance_uid, activity_uid, group_uid, subgroup_uid} from "../../support/api_requests/library_activities"; import { apiSubgroupName } from "./api_library_steps" +import { activity_placeholder_name } from "./study_activities_steps"; const { When, Then, Given } = require("@badeball/cypress-cucumber-preprocessor"); @@ -10,9 +11,13 @@ When('Activity instance approve attributes button is clicked', () => cy.get('but When('Activity instance approve groupings button is clicked', () => cy.get('.activity-section').within(() => cy.get('button .mdi-check-decagram').click())) -When('Activity instance attributes new version button is clicked', () => cy.get('button .mdi-plus-circle-outline').eq(0).click()) +When('Activity instance attributes new version button is clicked', () => cy.get('.groupings-action-buttons .mdi-plus-circle-outline').eq(0).click()) -When('Activity instance groupings new version button is clicked', () => cy.get('.activity-section').within(() => cy.get('button .mdi-plus-circle-outline').click())) +When('Activity instance groupings new version button is clicked', () => cy.get('.groupings-action-buttons .mdi-plus-circle-outline').eq(1).click()) + +When('Activity instance attributes history button is clicked', () => cy.get('.groupings-action-buttons .mdi-history').eq(0).click()) + +When('Activity instance groupings history button is clicked', () => cy.get('.groupings-action-buttons .mdi-history').eq(1).click()) When('Activity name created via API is fetched', () => cy.getActivityNameByUid().then(text => activityName = text)) @@ -59,6 +64,8 @@ When('User goes to subgroup overview page by clicking its name', () => cy.get('t When('User goes to activity overview page by clicking its name', () => cy.get('table tbody tr td').contains(activityName).click()) +When('User goes to activity placeholder overview page by clicking its name', () => cy.get('table tbody tr td').contains(activity_placeholder_name).click()) + When('User goes to instance overview page by clicking its name', () => cy.get('table tbody tr td').contains(instanceName).click()) Given('{string} overview page is opened', (name) => cy.get('.d-flex.page-title').should('contain.text', name)) @@ -169,6 +176,14 @@ Then('The Instance linked activity has status {string} and version {string}', (s }) }) +Then('The Library displayed on the summary has value {string}', (value) => { + cy.contains('.summary-label', 'Library').parent().within(() => cy.get('.summary-value').should('have.text', value)) +}) + +Then('The Study ID displayed on the summary has value {string}', (value) => { + cy.contains('.summary-label', 'Study ID').parent().within(() => cy.get('.summary-value').should('have.text', value)) +}) + Then('The status displayed on the summary has value {string} and version is {string}', (status, version) => { cy.contains('.summary-label', 'Status').parent().within(() => cy.get('.summary-value').should('have.text', status)) cy.get('.v-select__selection-text').should('contain', version) @@ -193,6 +208,11 @@ When('Version {string} is selected from the Version dropdown list', (version) => cy.get('.v-list-item').contains(version).click(); }) +When('Version {string} is selected from the Version dropdown list in the instance attributes section', (version) => { + cy.get('.activity-instance-attributes-section').contains('.summary-label', 'Version').parent().within(() => cy.get('.v-field__input').click()) + cy.get('.v-list-item').contains(version).click(); +}) + Then('The Start date value is saved', () => { cy.contains('.summary-label', 'Start date').parent().within(() => { cy.get('.summary-value').invoke('text').then(startDate => trimmedStartDate = startDate.trim()) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_code_lists_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_code_lists_steps.js index 91cd43e5..3c9f3499 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/library_code_lists_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_code_lists_steps.js @@ -158,6 +158,7 @@ When('The new Codelist is added', () => { termNciValue = `NCITerm${getShortUniqueId()}` termDefinition = `Definition ${getShortUniqueId()}` cy.clickButton('add-sponsor-codelist') + cy.clickButton('step.codelist_type_selection-continue-button') cy.selectAutoComplete('catalogue-dropdown', 'ADAM CT') cy.clickButton('step.catalogue-continue-button') cy.fillInput('sponsor-preffered-name', termSponsorName) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_item_activity_instance_links_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_item_activity_instance_links_steps.js new file mode 100644 index 00000000..ed18bfcd --- /dev/null +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_item_activity_instance_links_steps.js @@ -0,0 +1,300 @@ +const { Given, When, Then } = require("@badeball/cypress-cucumber-preprocessor"); +const { generateShortUniqueName } = require("../../support/helper_functions"); + +// Shared state object (exported for use by CRF tree steps) +const state = { + collectionName: undefined, + formName: undefined, + itemGroupName: undefined, + itemName: undefined, + collectionUid: undefined, + formUid: undefined, + itemGroupUid: undefined, + itemUid: undefined, + selectedActivityInstances: [], + selectedActivityItemClasses: [] +} +module.exports = { state } + +// ==================== Setup Steps ==================== + +Given('The test CRF item is created with no Activity Instance Link', () => { + state.selectedActivityInstances = []; + state.selectedActivityItemClasses = []; + createTestItem(); +}); + +When('Created test CRF Item is found', () => cy.searchAndCheckPresence(state.itemName, true)) + +// ==================== Edit Item Page Steps ==================== + +Then('The Edit Item page is opened and RESET button is disabled', () => { + cy.get('.dialog-title').should('contain', 'Edit Item'); + cy.get('[data-cy="reset-activity-instances"]').should('be.disabled'); +}); + +Then('The default page is Form View', () => { + cy.get('[data-cy="switch-view"]').should('be.visible'); + cy.get('[data-cy="switch-view"]').find('input').should('be.checked'); +}); + +Then('No Activity Instance Links text is visible', () => { + cy.get('.v-card-text').should('contain', 'No Activity Instance Links'); + cy.get('.v-col').contains('No Activity Instance Links').should('be.visible'); +}); + +Then('Activity Instance Item {int} table is visible', (tableNumber) => { + cy.get('.v-card-title').contains(`Activity Instance Item ${tableNumber}`).should('be.visible'); +}); + +Then('The Edit Item window is closed', () => { + cy.get('.dialog-title').should('not.exist'); + cy.get('.v-dialog').should('not.exist'); + cy.get('table').should('be.visible'); +}); + +// ==================== Button Steps ==================== + +When('I click the Activity Instance Link plus button', () => { + cy.clickButton('add-activity-instances'); +}); + +When('I click the Delete button', () => { + cy.clickButton('remove-activity-instance'); +}); + +When('I click the RESET button', () => { + cy.clickButton('reset-activity-instances'); +}); + +Then('The Delete button is visible', () => { + cy.get('[data-cy="remove-activity-instance"]').should('be.visible'); +}); + +Then('The RESET button is enabled', () => { + cy.get('[data-cy="reset-activity-instances"]').should('be.visible').and('not.be.disabled'); +}); + +Then('The RESET button is disabled', () => { + cy.get('[data-cy="reset-activity-instances"]').should('be.disabled'); +}); + +// ==================== Form View - Switch & Table View ==================== + +When('I select the Table View option', () => { + cy.get('[data-cy="switch-view"]').find('input').uncheck({ force: true }); +}); + +Then('The page is switched to Table View', () => { + cy.get('[data-cy="switch-view"]').should('be.visible'); + cy.get('[data-cy="switch-view"]').find('input').should('not.be.checked'); +}); + +// ==================== Form View - Dropdown Selections ==================== + +When('I select a value from the Activity Instance dropdown list', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-instance"]').find('.v-field__input').click(); + }); + cy.get('.v-overlay__content .v-list-item').first().then($item => { + state.selectedActivityInstances.push($item.text().trim()); + cy.wrap($item).click(); + }); +}); + +When('I select a value from the Activity Item Class dropdown list', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-item-class"]').find('.v-field__input').click(); + }); + cy.get('.v-overlay__content .v-list-item').first().then($item => { + state.selectedActivityItemClasses.push($item.text().trim()); + cy.wrap($item).click(); + }); +}); + +When('I select a value from the second Activity Instance dropdown list', () => { + cy.get('.v-card-title').contains('Activity Instance Item 2').parent('.v-card').within(() => { + cy.get('[data-cy="activity-instance"]').find('.v-field__input').click(); + }); + cy.get('.v-overlay__content .v-list-item', { timeout: 10000 }).should('have.length.greaterThan', 0); + cy.get('.v-overlay__content .v-list-item').last().click(); + cy.get('.v-card-title').contains('Activity Instance Item 2').parent('.v-card').within(() => { + cy.get('[data-cy="activity-instance"]').find('.v-autocomplete__selection-text').invoke('text').then(text => { + state.selectedActivityInstances.push(text.trim()); + }); + }); +}); + +When('I select a value from the second Activity Item Class dropdown list', () => { + cy.get('.v-card-title').contains('Activity Instance Item 2').parent('.v-card').within(() => { + cy.get('[data-cy="activity-item-class"]').find('.v-field__input').click(); + }); + cy.get('.v-overlay__content .v-list-item').last().then($item => { + state.selectedActivityItemClasses.push($item.text().trim()); + cy.wrap($item).click(); + }); +}); + +When('User waits for Activity Instance dropdown to load', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-instance"]').find('.v-field__input').click(); + }); + cy.get('.v-list-item').should('have.length.greaterThan', 0); + cy.get('body').click(); +}); + +When('User waits for Activity Item Class dropdown to load', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-item-class"]').find('.v-field__input').click(); + }); + cy.get('.v-list-item').should('have.length.greaterThan', 0); + cy.get('body').click(); +}); + +// ==================== Table View - Dropdown & Table Selections ==================== + +When('I select a value from the Select an Activity Instance dropdown list', () => { + cy.selectFirstVSelect('select-activity-instance'); + cy.get('[data-cy="select-activity-instance"]').find('.v-autocomplete__selection-text').then($el => { + state.selectedActivityInstances.push($el.text().trim()); + }); +}); + +When('I select an Activity Item Class from the table', () => { + cy.get('.v-data-table__td--select-row', { timeout: 10000 }).first() + .find('input[type="checkbox"]').check({ force: true }); +}); + +// ==================== CRF Viewer - Form Selection ==================== + +When('I select created Form from the Form Name dropdown list', () => { + expect(state.formName, 'Form name should be defined from test setup').to.not.be.undefined; + expect(state.formName, 'Form name should not be empty').to.not.be.empty; + cy.get('.v-label').contains('Form Name').parent().parent().find('.v-field__input').click(); + cy.get('.v-overlay__content .v-list', { timeout: 10000 }).should('be.visible'); + cy.get('.v-overlay__content .v-list-item').contains(state.formName).scrollIntoView().click(); +}); + +When('User waits for CRF Viewer data to load', () => { + cy.intercept('/api/odms/metadata/report?*').as('getCrfViewerData'); + cy.wait('@getCrfViewerData', { timeout: 60000 }); +}); + +// ==================== CRF Viewer - Verification ==================== + +When('I click the Activity Instance option from the right top corner', () => { + cy.get('iframe.frame').its('0.contentDocument.body').should('not.be.empty') + .then(cy.wrap) + .find('button') + .contains('Activity Instance') + .click(); +}); + +Then('The added Activity Instance Link is displayed under the test item name', () => { + cy.get('iframe.frame').its('0.contentDocument.body').should('not.be.empty') + .then(cy.wrap) + .then($body => { + cy.wrap($body).contains('h4', state.itemName).should('exist'); + cy.wrap($body).contains('tr', state.itemName).within(() => { + cy.get('.activity-instance-container').should('be.visible'); + cy.get('.activity-instance-container').should('contain', state.selectedActivityInstances[state.selectedActivityInstances.length - 1]); + }); + }); +}); + +Then('All added Activity Instance Links are displayed under the test item name', () => { + cy.get('iframe.frame').its('0.contentDocument.body').should('not.be.empty') + .then(cy.wrap) + .then($body => { + cy.wrap($body).contains('h4', state.itemName).should('exist'); + cy.wrap($body).contains('tr', state.itemName).within(() => { + cy.get('.activity-instance-container').should('have.length.at.least', 2); + state.selectedActivityInstances.forEach((instance) => { + cy.get('.activity-instance-container').should('contain', instance); + }); + }); + }); +}); + +// ==================== Validation Steps ==================== + +Then('I should see alert messages for both Activity Instance and Activity Item Class fields', () => { + cy.get('.v-alert.bg-error').should('contain', 'Activity Instance UID of Activity Instances #1 must be at least 1 character(s)'); + cy.get('.v-alert.bg-error').should('contain', 'Activity Item Class UID of Activity Instances #1 must be at least 1 character(s)'); +}); + +When('I select a value from the Activity Instance dropdown list and do not select any value from the Activity Item Class dropdown list', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-instance"]').find('.v-field__input').click(); + }); + cy.get('.v-overlay__content .v-list-item').first().then($item => { + state.selectedActivityInstances.push($item.text().trim()); + cy.wrap($item).click(); + }); + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-item-class"]').find('.v-field__input').click(); + }); + cy.get('body').click(); +}); + +Then('I should see a field validation message for the Activity Item Class dropdown list', () => { + cy.checkIfValidationAppears('activity-item-class'); +}); + +Then('I should see an alert message for the Activity Item Class field', () => { + cy.get('.v-alert.bg-error').should('contain', 'Activity Item Class UID of Activity Instances #1 must be at least 1 character(s)'); +}); + +Then('I am not able to select a value from the Activity Item Class dropdown list before I have selected a value from the Activity Instance dropdown list', () => { + cy.get('[data-cy="activity-item-class"]').should('have.class', 'v-input--readonly'); +}); + +// ==================== Delete & Reset Steps ==================== + +Then('The page returns to the initial edit item page without Activity Instance Item table', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').should('not.exist'); + cy.get('.v-col').contains('No Activity Instance Links').should('be.visible'); +}); + +Then('The Edit Item page is opened with saved linked Activity Instance Item table', () => { + cy.get('.dialog-title').should('contain', 'Edit Item'); + cy.get('.v-card-title').contains('Activity Instance Item 1').should('be.visible'); + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-instance"]').find('.v-field__input').should('not.be.empty'); + }); +}); + +Then('The page returns to the initial edit item page and the RESET button is enabled', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').should('not.exist'); + cy.get('.v-col').contains('No Activity Instance Links').should('be.visible'); + cy.get('[data-cy="reset-activity-instances"]').should('be.visible').and('not.be.disabled'); +}); + +Then('The Edit Item page is opened without any linked Activity Instance Item table', () => { + cy.get('.dialog-title').should('contain', 'Edit Item'); + cy.get('.v-card-title').contains('Activity Instance Item 1').should('not.exist'); + cy.get('.v-col').contains('No Activity Instance Links').should('be.visible'); + cy.get('[data-cy="reset-activity-instances"]').should('be.disabled'); +}); + +Then('The Activity Instance Item table is removed and the page returns to the initial edit item page', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').should('not.exist'); + cy.get('.v-col').contains('No Activity Instance Links').should('be.visible'); + cy.get('[data-cy="reset-activity-instances"]').should('be.disabled'); +}); + +// ==================== Helper Functions ==================== + +function createTestItem() { + state.collectionName = generateShortUniqueName('C_'); + cy.createCrfCollection(state.collectionName).then(collectionResponse => state.collectionUid = collectionResponse.body.uid) + state.formName = generateShortUniqueName('F_'); + cy.createCrfForm(state.formName).then(formResponse => state.formUid = formResponse.body.uid) + state.itemGroupName = generateShortUniqueName('IG_'); + cy.createCrfItemGroup(state.itemGroupName).then(itemGroupResponse => state.itemGroupUid = itemGroupResponse.body.uid) + state.itemName = generateShortUniqueName('I_'); + cy.createCrfItem(state.itemName).then(itemResponse => state.itemUid = itemResponse.body.uid) + cy.then(() => cy.linkFormToCollection(state.formUid, state.collectionUid)) + cy.then(() => cy.linkItemGroupToForm(state.formUid, state.itemGroupUid)) + cy.then(() => cy.linkItemToItemGroup(state.itemGroupUid, state.itemUid)) +} diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_tree-item_activity_instance_links_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_tree-item_activity_instance_links_steps.js new file mode 100644 index 00000000..96292458 --- /dev/null +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_tree-item_activity_instance_links_steps.js @@ -0,0 +1,97 @@ +const { When, Then } = require("@badeball/cypress-cucumber-preprocessor"); +const { state } = require("./library_crf_item_activity_instance_links_steps"); + +// ==================== CRF Tree Navigation Steps ==================== + +When('I click the expand button beside created test Collection to expand the CRF Tree', () => { + cy.contains('td', state.collectionName).parent('tr').find('button').first().click(); +}); + +When('I click the expand button beside created test Form form to expand the form', () => { + cy.contains('td', state.formName).should('be.visible'); + cy.contains('td', state.formName).parent('tr').find('button').first().click(); +}); + +When('I click the expand button beside created test Item Group to expand the item group', () => { + cy.contains('td', state.itemGroupName).should('be.visible'); + cy.contains('td', state.itemGroupName).parent('tr').find('button').first().click(); +}); + +Then('I can see the Created test CRF Item in the list', () => { + cy.contains('span', state.itemName).should('be.visible'); +}); + +When('The \'Manage Activity Instance Links\' option is clicked from the three dot menu list of the created test CRF item', () => { + cy.get('.text-crfItem').parent('span').contains(state.itemName).closest('.v-row') + .find('[data-cy="table-item-action-button"]').click({ force: true }); + cy.get('[data-cy="Manage Activity Instances"]', { timeout: 10000 }).click({ force: true }); +}); + +// ==================== CRF Tree - Edit Item Page Steps ==================== + +Then('The Edit Item page is opened', () => { + cy.get('.dialog-title').should('contain', 'Edit Item'); +}); + +Then('The default page is Table View', () => { + cy.get('[data-cy="switch-view"]').should('be.visible'); + cy.get('[data-cy="switch-view"]').find('input').should('not.be.checked'); +}); + +// ==================== CRF Tree - Table View Steps ==================== + +When('I select another value from the Select an Activity Instance dropdown list', () => { + cy.selectLastVSelect('select-activity-instance'); + cy.get('[data-cy="select-activity-instance"]').find('.v-autocomplete__selection-text').then($el => { + state.selectedActivityInstances.push($el.text().trim()); + }); +}); + +When('I select a value from the Activity Item Class table', () => { + cy.get('.v-data-table__td--select-row', { timeout: 10000 }).first() + .find('input[type="checkbox"]').check({ force: true }); +}); + +// ==================== CRF Tree - Form View Switch ==================== + +When('I select the Form View option', () => { + cy.get('[data-cy="switch-view"]').find('input').check({ force: true }); +}); + +Then('The page is switched to Form View', () => { + cy.get('[data-cy="switch-view"]').should('be.visible'); + cy.get('[data-cy="switch-view"]').find('input').should('be.checked'); +}); + +When('I do not select a value from the Activity Item Class dropdown list', () => { + // No action needed - verifying empty state +}); + +Then('I can see no linked Activity Item Class in the Form View', () => { + cy.get('.v-card-title').contains('Activity Instance Item 1').parent('.v-card').within(() => { + cy.get('[data-cy="activity-item-class"]').find('.v-field__input').should('have.value', ''); + }); +}); + +// ==================== CRF Tree - Verification ==================== + +Then('The added two Activity Instance Links are displayed under the test item name', () => { + cy.get('iframe.frame').its('0.contentDocument.body').should('not.be.empty') + .then(cy.wrap) + .then($body => { + cy.wrap($body).contains('h4', state.itemName).should('exist'); + cy.wrap($body).contains('tr', state.itemName).within(() => { + cy.get('.activity-instance-container').should('have.length.at.least', 2); + }); + }); +}); + +// ==================== CRF Tree - Validation Steps ==================== + +Then('The Edit Item window remains open', () => { + cy.get('.dialog-title').should('contain', 'Edit Item'); +}); + +When('I switch to the Form View', () => { + cy.get('[data-cy="switch-view"]').find('input').check({ force: true }); +}); diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_viewer_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_viewer_steps.js index fbb57320..99b88125 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_viewer_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/library_crf_viewer_steps.js @@ -29,10 +29,7 @@ When('I select a value from the Form Name dropdown', () => { }) When ('I click the GENERATE button', () => { - cy.get('.v-btn').contains('Generate') // Find the button containing the text 'Generate' - .should('be.visible') // Ensure the button is visible - .should('not.be.disabled') // Ensure the button is not disabled - .click(); // Click the button + cy.clickButton('generate'); }) Then('I open stylesheets dropdown', () => { @@ -69,7 +66,11 @@ When("I select HTML option from the Stylesheet dropdown list", () => { }); Then('The imported CRF view page should be displayed', () => { - cy.get('body').contains(crf_form).should('be.visible'); + if (crf_form) { + cy.get('body').contains(crf_form).should('be.visible'); + } else { + cy.get('iframe.frame').should('be.visible'); + } }) When('User intercepts ODM document generation request', () => cy.intercept('/api/odms/metadata/report?targets=OdmForm*').as('generateReportDocument')) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/study_activities_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/study_activities_steps.js index 54c1ffa3..b923ba4d 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/study_activities_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/study_activities_steps.js @@ -177,10 +177,16 @@ When('The user is presented with the changes to request', () => { Then('[API] Activity is assigned to the visit {int}', (visitIndex) => cy.assignActivityToVisit(Cypress.env('TEST_STUDY_UID'), study_activity_uid, visitIndex)) +Then('[API] Activity is assigned to the visit {int} in selected study', (visitIndex) => cy.assignActivityToVisit(getCurrStudyUid(), study_activity_uid, visitIndex)) + Then('[API] All Activities are deleted from study', () => { cy.getExistingStudyActivities(Cypress.env('TEST_STUDY_UID')).then(uids => uids.forEach(uid => cy.deleteActivityFromStudy(Cypress.env('TEST_STUDY_UID'), uid))) }) +Then('[API] All Activities are deleted from selected study', () => { + cy.getExistingStudyActivities(getCurrStudyUid()).then((uids) => uids.forEach((uid) => cy.deleteActivityFromStudy(getCurrStudyUid(), uid))) +}) + Then('[API] Get SoA Group {string} id', (name) => cy.getSoaGroupUid(name)) Then('[API] Activity is added to the study', () => addActivityToStudyAndGetValues(Cypress.env('TEST_STUDY_UID'))) @@ -220,6 +226,20 @@ Then('[API] Create Submitted Requested Activity', () => { cy.approveRequestedActivity() }) +When('[API] Activity for SoA group {string} with activity group {string} is added to the study', (soa_group, activity_group) => { + let activity_group_filter_value = activity_group.replace(' ', '+') + cy.addActivityToCurrentStudyFromActivityGroup(soa_group, activity_group_filter_value).then((activity) => { + activity_sub_group = activity.body[0].content.activity.activity_groupings[0].activity_subgroup_name + new_activity_name = activity.body[0].content.activity.name + cy.assignActivityToVisit(getCurrStudyUid(), activity.body[0].content.study_activity_uid, '0') + }) +}) + +Then('The laboratory assements activities are present in protocol lab table', () => { + cy.get('.subGroupLabTable').should('contain', activity_sub_group) + cy.get('.activity').should('contain', new_activity_name) +}) + Then('[API] Requested Activity is added to the study', () => cy.addActivityToStudy(getCurrStudyUid(), requestedActivity_uid, group_uid, subgroup_uid)) When('The user accepts the changes', () => cy.contains('button', 'Accept').click()) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/study_compound_dosings.js b/system-tests/ui-tests/cypress/e2e/step_definitions/study_compound_dosings.js index ac87171a..bee0c5a3 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/study_compound_dosings.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/study_compound_dosings.js @@ -17,7 +17,7 @@ When('The user select last dose value', () => cy.selectLastVSelect('dose-value') When('The user intercepts study compund dosings create request', () => cy.intercept('POST', '**/study-compound-dosings').as('createdDosing')) -When('The user intercepts study compund dosings update request', () => cy.intercept('PATCH', '**/study-compound-dosings').as('createdDosing')) +When('The user intercepts study compund dosings update request', () => cy.intercept('PATCH', '**/study-compound-dosings/*').as('createdDosing')) When('The user intercepts study compound dosing delete request', () => cy.intercept('**/study-compound-dosings/**').as('deleteRequest')) @@ -28,84 +28,38 @@ When('The user intercepts study compunds request', () => cy.intercept('**/study- Then('The study compound dosing is present in the compound dosings table', () => { cy.wait('@createdDosing').then((req) => { let dosingData = req.response.body - cy.checkRowByIndex(dosingData.order - 1, '#', dosingData.order) - cy.checkRowByIndex(dosingData.order - 1, 'Study Element', dosingData.study_element.name) - cy.checkRowByIndex(dosingData.order - 1, 'Compound Name', dosingData.study_compound.compound.name) - cy.checkRowByIndex(dosingData.order - 1, 'Medicinal product', dosingData.study_compound.medicinal_product.name) - cy.checkRowByIndex(dosingData.order - 1, 'Compound Alias Name', dosingData.study_compound.compound_alias.name) - cy.checkRowByIndex(dosingData.order - 1, 'Preferred Alias', dosingData.study_compound.compound_alias.is_preferred_synonym ? 'Yes' : 'No') - cy.checkRowByIndex(dosingData.order - 1, 'Dose Value', `${dosingData.dose_value.value} ${dosingData.dose_value.unit_label}`) - cy.checkRowByIndex(dosingData.order - 1, 'Dose Frequency', dosingData.study_compound.dose_frequency.term_name) + cy.searchFor(dosingData.study_compound_dosing_uid) + cy.checkRowByIndex(0, '#', dosingData.order) + cy.checkRowByIndex(0, 'Study Element', dosingData.study_element.name) + cy.checkRowByIndex(0, 'Compound Name', dosingData.study_compound.compound.name) + cy.checkRowByIndex(0, 'Medicinal product', dosingData.study_compound.medicinal_product.name) + cy.checkRowByIndex(0, 'Compound Alias Name', dosingData.study_compound.compound_alias.name) + cy.checkRowByIndex(0, 'Preferred Alias', dosingData.study_compound.compound_alias.is_preferred_synonym ? 'Yes' : 'No') + cy.checkRowByIndex(0, 'Dose Value', `${dosingData.dose_value.value} ${dosingData.dose_value.unit_label}`) + cy.checkRowByIndex(0, 'Dose Frequency', dosingData.study_compound.dose_frequency.term_name) }) }) -Then('The element order for this element is automatically populated from library', () => { +Then('The Element data is automatically populated', () => { cy.wait('@elementsRequest').then((request) => { compareValue('study-element-order', request.response.body.items[0].order) - }) -}) - -Then('The element type for this element is automatically populated from library', () => { - cy.wait('@elementsRequest').then((request) => { compareValue('study-element-type', request.response.body.items[0].element_type.term_name) - }) -}) - -Then('The element subtype for this element is automatically populated from library', () => { - cy.wait('@elementsRequest').then((request) => { compareValue('study-element-subtype', request.response.body.items[0].element_subtype.term_name) - }) -}) - -Then('The element name for this element is automatically populated from library', () => { - cy.wait('@elementsRequest').then((request) => { compareValue('study-element-name', request.response.body.items[0].name) - }) -}) - -Then('The element short name for this element is automatically populated from library', () => { - cy.wait('@elementsRequest').then((request) => { compareValue('study-element-short-name', request.response.body.items[0].short_name) - }) -}) - -Then('The element description for this element is automatically populated from library', () => { - cy.wait('@elementsRequest').then((request) => { compareValue('study-element-description', request.response.body.items[0].description) }) }) -Then('The compound order in dosings from for this compound is automatically populated from library', () => { +Then('The Compound data is automatically populated', () => { cy.wait('@compoundsRequest').then((request) => { compareValue('compound-order', request.response.body.items[0].order) - }) -}) - -Then('The type of treatment in dosings from for this compound is automatically populated from library', () => { - cy.wait('@compoundsRequest').then((request) => { compareValue('type-of-treatment', request.response.body.items[0].type_of_treatment.term_name) - }) -}) - -Then('The compound name in dosings from for this compound is automatically populated from library', () => { - cy.wait('@compoundsRequest').then((request) => { compareValue('compound-name', request.response.body.items[0].compound.name) - }) -}) - -Then('The compound alias name in dosings from for this compound is automatically populated from library', () => { - cy.wait('@compoundsRequest').then((request) => { compareValue('compound-alias-name', request.response.body.items[0].compound_alias.name) - }) -}) - -Then('The preferred synonim in dosings from for this compound is automatically populated from library', () => { - cy.wait('@compoundsRequest').then((request) => { cy.get('[data-cy="is-preffered-synonym"]').within(() => { - let radioSelection = request.response.body.items[0].compound_alias.is_preferred_synonym ? '[data-cy="radio-Yes"]' : '[data-cy="radio-No"]' - cy.get(radioSelection).within(() => { - cy.get('input').should('have.attr', 'checked') - }) + let radioSelection = request.response.body.items[0].compound_alias.is_preferred_synonym ? '[data-cy="radio-Yes"] input' : '[data-cy="radio-No"] input' + cy.get(radioSelection).should('have.attr', 'checked') }) }) }) @@ -124,7 +78,5 @@ Given('The study compound dosing data is cleaned for testing purspose', () => { }) function compareValue(selector, value) { - cy.get(`[data-cy="${selector}"]`).within(() => { - cy.get('input').should('have.value', value ? value : '') - }) + cy.get(`[data-cy="${selector}"] input`).should('have.value', value ? value : '') } \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/study_compounds_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/study_compounds_steps.js index b2c1df55..33fb914e 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/study_compounds_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/study_compounds_steps.js @@ -1,6 +1,25 @@ const { Given, When, Then } = require("@badeball/cypress-cucumber-preprocessor"); +import { study_compound_dosing_uid, study_compound_uid } from '../../support/api_requests/study_compounds_request.js'; import { getCurrStudyUid } from '../../support/helper_functions.js' +Given('[API] Study compound is created', () => cy.createSimpleCompound(getCurrStudyUid())) + +Given('[API] Study compound dosing is created', () => cy.createCompoundDosing(getCurrStudyUid())) + +Given('[API] Study compound simple data is fetched', () => cy.getCompundSimpleData()) + +Given('[API] Study compound alias data is fetched', () => cy.getCompundAliasData()) + +Given('[API] Study compound medical product data is fetched', () => cy.getMedicalProductData()) + +Given('[API] Study compound type of treatment data is fetched is created', () => cy.getTypeOfTreatmentUid()) + +Given('[API] Study compound data is fetched', () => cy.getStudyCompundData(getCurrStudyUid())) + +Given('User searches the compound by the uid', () => cy.searchFor(study_compound_uid)) + +Given('User searches the compound dosing by the uid', () => cy.searchFor(study_compound_dosing_uid)) + Given('User clicks add study compund button', () => cy.clickButton('add-study-compound')) Given('User fills other information', () => cy.fillInput('other-information', 'Testing Information')) @@ -19,7 +38,7 @@ Given('User select last medicinal product', () => cy.selectLastVSelect('medicina Given('User intercepts compund create request', () => cy.intercept('POST', '**/study-compounds').as('createdCompound')) -Given('User intercepts compund update request', () => cy.intercept('PATCH', '**/study-compounds').as('createdCompound')) +Given('User intercepts compund update request', () => cy.intercept('PATCH', '**/study-compounds/*').as('createdCompound')) Given('User intercepts compund delete request', () => cy.intercept('**/study-compounds/**').as('deleteRequest')) @@ -34,109 +53,60 @@ Given('User intercepts pharmaceutical products request', () => cy.intercept('**/ Then('The study compound is present in the compounds table', () => { cy.wait('@createdCompound').then((req) => { let compoundData = req.response.body - cy.checkRowByIndex(compoundData.order - 1, 'Type of treatment', compoundData.type_of_treatment.term_name) - cy.checkRowByIndex(compoundData.order - 1, 'Compound', compoundData.compound.name) - cy.checkRowByIndex(compoundData.order - 1, 'Sponsor compound', compoundData.is_sponsor_compound ? 'Yes' : 'No') - cy.checkRowByIndex(compoundData.order - 1, 'Compound alias', compoundData.compound_alias.name) - cy.checkRowByIndex(compoundData.order - 1, 'Medicinal product', compoundData.medicinal_product.name) - cy.checkRowByIndex(compoundData.order - 1, 'Dose frequency', compoundData.dose_frequency.preferred_term) - }) -}) - -Then('The compound alias for this compound is automatically populated from library', () => { - cy.wait('@compoundAliasesRequest').then((request) => { - cy.get('[data-cy="compound-alias"]').should('contain', request.response.body.items[0].compound.name) + cy.searchFor(compoundData.study_compound_uid) + cy.checkRowByIndex(0, 'Type of treatment', compoundData.type_of_treatment.term_name) + cy.checkRowByIndex(0, 'Compound', compoundData.compound.name) + cy.checkRowByIndex(0, 'Sponsor compound', compoundData.is_sponsor_compound ? 'Yes' : 'No') + cy.checkRowByIndex(0, 'Compound alias', compoundData.compound_alias.name) + cy.checkRowByIndex(0, 'Medicinal product', compoundData.medicinal_product.name) + cy.checkRowByIndex(0, 'Dose frequency', compoundData.dose_frequency.preferred_term) }) }) -Then('The other aliases for this compound is automatically populated from library', () => { +Then('The compound alias data is automatically populated from library', () => { cy.wait('@compoundAliasesRequest').then((request) => { + let alias_name = request.response.body.items[0].compound.name let other_aliases = otherAliases(request.response.body.items) - cy.get('[data-cy="other-aliases"]').within(() => { - cy.get('input').should('have.value', other_aliases) - }) - }) -}) -Then('The sponsor compound for this compound is automatically populated from library', () => { - cy.wait('@compoundRequest').then((request) => { - let radioSelection = request.response.body.is_sponsor_compound ? '[data-cy="radio-Yes"]' : '[data-cy="radio-No"]' - cy.get(radioSelection).within(() => { - cy.get('input').should('have.attr', 'checked') - }) + cy.get('[data-cy="compound-alias"]').should('contain', alias_name) + cy.get('[data-cy="other-aliases"] input').should('have.value', other_aliases) }) }) -Then('The compound definition for this compound is automatically populated from library', () => { +Then('The sponsor compound data is automatically populated from library', () => { cy.wait('@compoundRequest').then((request) => { - cy.get('[data-cy="compound-definition"]').within(() => { - cy.get('textarea').should('have.value', request.response.body.definition ? request.response.body.definition : '-') - }) + let radioSelection = request.response.body.is_sponsor_compound ? '[data-cy="radio-Yes"]' : '[data-cy="radio-No"]' + let compoundDefinition = request.response.body.definition ? request.response.body.definition : '-' + + cy.get(`${radioSelection} input`).should('have.attr', 'checked') + cy.get('[data-cy="compound-definition"] textarea').should('have.value', compoundDefinition) }) }) -Then('The dispensed in for this compound is automatically populated from library', () => { +Then('The Medicinal Product data is automatically populated from library', () => { cy.wait('@medicinalProductRequest').then((request) => { let dispensed_in = request.response.body.items[0].dispenser.name - cy.get('[data-cy="dispensed-in"]').within(() => { - cy.get('input').should('have.value', dispensed_in ? dispensed_in : '-') - }) + cy.get('[data-cy="dispensed-in"] input').should('have.value', dispensed_in ? dispensed_in : '-') }) }) -Then('The INN for this compound is automatically populated from library', () => { +Then('The Pharmaceutical Product data is automatically populated from library', () => { cy.wait('@pharmaceuticalProductRequest').then((request) => { let active_substance = request.response.body.formulations[0].ingredients[0].active_substance.inn - cy.get('[data-cy="active-substance"]').within(() => { - cy.get('input').should('have.value', active_substance ? active_substance : '-') - }) - }) -}) - -Then('The analyte number for this compound is automatically populated from library', () => { - cy.wait('@pharmaceuticalProductRequest').then((request) => { let analyte_number = request.response.body.formulations[0].ingredients[0].active_substance.analyte_number - cy.get('[data-cy="analyte-number"]').within(() => { - cy.get('input').should('have.value', analyte_number ? analyte_number : '-') - }) - }) -}) - -Then('The substance id for this compound is automatically populated from library', () => { - cy.wait('@pharmaceuticalProductRequest').then((request) => { let long_number = request.response.body.formulations[0].ingredients[0].active_substance.long_number - cy.get('[data-cy="long-number"]').within(() => { - cy.get('input').should('have.value', long_number ? long_number : '-') - }) - }) -}) - -Then('The substance name for this compound is automatically populated from library', () => { - cy.wait('@pharmaceuticalProductRequest').then((request) => { let short_number = request.response.body.formulations[0].ingredients[0].active_substance.short_number - cy.get('[data-cy="short-number"]').within(() => { - cy.get('input').should('have.value', short_number ? short_number : '-') - }) - }) -}) - -Then('The UNII for this compound is automatically populated from library', () => { - cy.wait('@pharmaceuticalProductRequest').then((request) => { let substance_unii = request.response.body.formulations[0].ingredients[0].active_substance.unii.substance_unii - cy.get('[data-cy="substance"]').within(() => { - cy.get('input').should('have.value', substance_unii ? substance_unii : '-') - }) - }) -}) - -Then('The pharmacological class MED-RT for this compound is automatically populated from library', () => { - cy.wait('@pharmaceuticalProductRequest').then((request) => { let pclass = request.response.body.formulations[0].ingredients[0].active_substance.unii.pclass_name let id = request.response.body.formulations[0].ingredients[0].active_substance.unii.pclass_id let pharmacological_class = `${pclass} (${id})` - cy.get('[data-cy="pharmacological-class"]').within(() => { - cy.get('input').should('have.value', pharmacological_class ? pharmacological_class : '-') - }) + + cy.get('[data-cy="active-substance"] input').should('have.value', active_substance ? active_substance : '-') + cy.get('[data-cy="analyte-number"] input').should('have.value', analyte_number ? analyte_number : '-') + cy.get('[data-cy="long-number"] input').should('have.value', long_number ? long_number : '-') + cy.get('[data-cy="short-number"] input').should('have.value', short_number ? short_number : '-') + cy.get('[data-cy="substance"] input').should('have.value', substance_unii ? substance_unii : '-') + cy.get('[data-cy="pharmacological-class"] input').should('have.value', pharmacological_class ? pharmacological_class : '-') }) }) @@ -154,9 +124,7 @@ Given('The study compounds data is cleaned for testing purspose', () => { cy.sendDeleteRequest(`/studies/${currentStudy}/study-compounds/${item.study_compound_uid}`) }) } - }) - }) function otherAliases(aliases) { diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/study_list_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/study_list_steps.js index 2c4c77c1..eef91ba8 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/study_list_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/study_list_steps.js @@ -11,6 +11,32 @@ Given('The user intercepts study statistics request', () => cy.intercept('**stru When('User intercepts cloning request', () => cy.intercept('**clone').as('clone_request')) +/** + * Verifies clone POST payload in the intercept callback (payload verification best practice). + * Use with scenarios that select structure + study activities + schedules. + */ +When( + 'User intercepts study clone request verifying structure and activity clone flags', + () => { + cy.intercept({ method: 'POST', url: '**/clone' }, (req) => { + expect(req.body).to.have.property('copy_study_arm', true) + expect(req.body).to.have.property('copy_study_branch_arm', true) + expect(req.body).to.have.property('copy_study_cohort', true) + expect(req.body).to.have.property('copy_study_design_matrix', true) + expect(req.body).to.have.property('copy_study_element', true) + expect(req.body).to.have.property('copy_study_epoch', true) + expect(req.body).to.have.property('copy_study_visit', true) + expect(req.body).to.have.property('copy_study_soa_group', true) + expect(req.body).to.have.property('copy_study_activity_group', true) + expect(req.body).to.have.property('copy_study_activity_subgroup', true) + expect(req.body).to.have.property('copy_study_activity', true) + expect(req.body).to.have.property('copy_study_activity_instance', true) + expect(req.body).to.have.property('copy_study_activity_schedule', true) + expect(req.body).to.have.property('validation_mode', 'strict') + }).as('clone_request') + } +) + When('User waits for cloning request', () => cy.wait('@clone_request')) Then('The user is presented study selection dropdown', () => { @@ -44,7 +70,12 @@ Then('The user is presented with visual representation of designated study struc cy.get('line.visit-arrow').should('have.length', 2); }) -When('The user selects {string} category to be copied', (category) => cy.contains('label', category).click()) +When('The user selects {string} category to be copied', (category) => { + // Wait for structure-statistics (arm_count, etc.); long timeout for slow API. + // cy.get('@alias') reuses a completed intercept; cy.wait would only match once per request. + cy.get('@study_statistics', { timeout: 6000 }) + cy.contains('label', category, { timeout: 30000 }).should('be.visible').click() +}) Then('The {string} category with {string} derived from source study is presented for selection', (category, count) => { cy.get('@study_statistics').then((request) => { @@ -87,7 +118,6 @@ When('Study is found', () => cy.searchAndCheckPresence(studyAcronym, true)) Then('The new study is created with selected data', () => { cy.get('@clone_request').then((req) => { - expect(req.request.body.copy_study_arm).to.eq(true) expect(req.request.body.copy_study_arm).to.eq(true) expect(req.request.body.copy_study_branch_arm).to.eq(true) expect(req.request.body.copy_study_cohort).to.eq(true) @@ -95,9 +125,23 @@ Then('The new study is created with selected data', () => { expect(req.request.body.copy_study_element).to.eq(true) expect(req.request.body.copy_study_epoch).to.eq(true) expect(req.request.body.copy_study_visit).to.eq(true) + expect(req.request.body.validation_mode).to.eq('strict') expect(req.request.body.project_number).to.eq('CDISC DEV') expect(req.request.body.study_acronym).to.eq(studyAcronym) expect(req.request.body.study_number).to.eq(studyNumber) expect(req.response.statusCode).to.eq(201) }) }) + +/** + * Response-only assertion when request body was already verified in the intercept callback. + */ +Then('The study clone response is successful with submitted metadata', () => { + cy.get('@clone_request').then((req) => { + expect(req.response.statusCode).to.eq(201) + expect(req.request.body.validation_mode).to.eq('strict') + expect(req.request.body.project_number).to.eq('CDISC DEV') + expect(req.request.body.study_acronym).to.eq(studyAcronym) + expect(req.request.body.study_number).to.eq(studyNumber) + }) +}) diff --git a/system-tests/ui-tests/cypress/e2e/step_definitions/study_soa_steps.js b/system-tests/ui-tests/cypress/e2e/step_definitions/study_soa_steps.js index 3d88f1da..a7e1b392 100644 --- a/system-tests/ui-tests/cypress/e2e/step_definitions/study_soa_steps.js +++ b/system-tests/ui-tests/cypress/e2e/step_definitions/study_soa_steps.js @@ -44,6 +44,10 @@ Then('The SoA split on {string} is removed', (visitNumber) => { cy.contains('.split-class', visitNumber).should('not.exist') }) +When('the SoA View is switched to {string}', (view) => { + cy.get(`button[value="${view}]"`).click() +}) + function splitSoa(visitNumber, interceptPath) { cy.intercept(interceptPath).as('splitRequest') cy.contains('.v-btn__content', visitNumber).click() diff --git a/system-tests/ui-tests/cypress/support/api_requests/library_activities.js b/system-tests/ui-tests/cypress/support/api_requests/library_activities.js index 4ddd9082..fed604f3 100644 --- a/system-tests/ui-tests/cypress/support/api_requests/library_activities.js +++ b/system-tests/ui-tests/cypress/support/api_requests/library_activities.js @@ -22,8 +22,7 @@ const approveActivityInstanceGroupingsUrl = (activityInstance_uid) => `${activit const approveActivityGroupUrl = (group_uid) => `${activityGroupUrl}/${group_uid}/approvals` const approveActivitySubGroupUrl = (subgroup_uid) => `${activitySubGroupUrl}/${subgroup_uid}/approvals` const activateActivityUrl = (activity_uid) => `${activityUrl}/${activity_uid}/activations` -const activateActivityInstanceAttributesUrl = (activityInstance_uid) => `${activityInstanceUrl}/${activityInstance_uid}/attributes/activations` -const activateActivityInstanceGroupingsUrl = (activityInstance_uid) => `${activityInstanceUrl}/${activityInstance_uid}/groupings/activations` +const activateActivityInstanceUrl = (activityInstance_uid) => `${activityInstanceUrl}/${activityInstance_uid}/activations` const activateActivityGroupUrl = (group_uid) => `${activityGroupUrl}/${group_uid}/activations` const activateActivitySubGroupUrl = (subgroup_uid) => `${activitySubGroupUrl}/${subgroup_uid}/activations` const newVersionActivityUrl = (activity_uid) => `${activityUrl}/${activity_uid}/versions` @@ -105,10 +104,7 @@ Cypress.Commands.add('subGroupNewVersion', () => cy.sendPostRequest(newVersionAc Cypress.Commands.add('inactivateActivity', () => cy.sendDeleteRequest(activateActivityUrl(activity_uid), {})) -Cypress.Commands.add('inactivateActivityInstance', () => { - cy.sendDeleteRequest(activateActivityInstanceAttributesUrl(activityInstance_uid), {}) - cy.sendDeleteRequest(activateActivityInstanceGroupingsUrl(activityInstance_uid), {}) -}) +Cypress.Commands.add('inactivateActivityInstance', () => cy.sendDeleteRequest(activateActivityInstanceUrl(activityInstance_uid), {})) Cypress.Commands.add('inactivateGroup', () => cy.sendDeleteRequest(activateActivityGroupUrl(group_uid), {})) diff --git a/system-tests/ui-tests/cypress/support/api_requests/study_activities_requests.js b/system-tests/ui-tests/cypress/support/api_requests/study_activities_requests.js index dbd27b9b..0e999073 100644 --- a/system-tests/ui-tests/cypress/support/api_requests/study_activities_requests.js +++ b/system-tests/ui-tests/cypress/support/api_requests/study_activities_requests.js @@ -1,8 +1,11 @@ +import { getCurrStudyUid } from "../helper_functions" + let soaGroup_uid const studyActivityUrl = (study_uid, study_activity_uid) => `/studies/${study_uid}/study-activities/${study_activity_uid}` const studyActivitiesUrl = (study_uid) => `/studies/${study_uid}/study-activities?page_number=1&page_size=0` const studyActivityBatchUrl = (study_uid) => `/studies/${study_uid}/study-activities/batch` const flowchartGroupUrl = () => '/ct/codelists/terms?page_size=100&codelist_submission_value=FLWCRTGRP' +const activityWithActivityGroupFilterUrl = (activity_group_name) => `/concepts/activities/activities?library_name=Sponsor&activity_group_names%5B%5D=${activity_group_name}&filters=%7B%22status%22:%7B%22v%22:%5B%22Final%22%5D%7D%7D` Cypress.Commands.add('deleteActivityFromStudy', (study_uid, activity_uid) => cy.sendDeleteRequest(studyActivityUrl(study_uid, activity_uid))) @@ -19,9 +22,21 @@ Cypress.Commands.add('addActivityToStudy', (study_uid, activity_uid, activityGro }) Cypress.Commands.add('getSoaGroupUid', (soaGroup_name) => { - cy.sendGetRequest(flowchartGroupUrl()).then((response) => { - soaGroup_uid = response.body.items.find(item => item.sponsor_preferred_name == soaGroup_name).term_uid + cy.sendGetRequest(flowchartGroupUrl()).then((response) => { + soaGroup_uid = response.body.items.find(item => item.sponsor_preferred_name == soaGroup_name).term_uid + }) +}) + +Cypress.Commands.add('addActivityToCurrentStudyFromActivityGroup', (soa_group, group_name) => { + let activity_uid + cy.getSoaGroupUid(soa_group) + cy.sendGetRequest(activityWithActivityGroupFilterUrl(group_name)).then((response) => { + activity_uid = response.body.items[0].uid + let activityGroup_uid = response.body.items[0].activity_groupings[0].activity_group_uid + let activitySubgroup_uid = response.body.items[0].activity_groupings[0].activity_subgroup_uid + cy.addActivityToStudy(getCurrStudyUid(), activity_uid, activityGroup_uid, activitySubgroup_uid) }) + return activity_uid }) const addActivityToStudyBody = (soaGroup_uid, activity_uid, activityGroup_uid, activitySubgroup_uid) => { @@ -32,7 +47,7 @@ const addActivityToStudyBody = (soaGroup_uid, activity_uid, activityGroup_uid, a "soa_group_term_uid": soaGroup_uid, "activity_uid": activity_uid, "order": null, - "activity_group_uid":activityGroup_uid, + "activity_group_uid": activityGroup_uid, "activity_subgroup_uid": activitySubgroup_uid } } diff --git a/system-tests/ui-tests/cypress/support/api_requests/study_arm_requests.js b/system-tests/ui-tests/cypress/support/api_requests/study_arm_requests.js index 0bfc7e11..7e556484 100644 --- a/system-tests/ui-tests/cypress/support/api_requests/study_arm_requests.js +++ b/system-tests/ui-tests/cypress/support/api_requests/study_arm_requests.js @@ -19,7 +19,20 @@ Cypress.Commands.add('createTestArmIfNoneExists', (study_uid) => { }) Cypress.Commands.add('createTestArm', (study_uid, customName = '') => { - cy.sendPostRequest(createArmUrl(study_uid), createArmBody(arm_type_uid, customName)).then(response => { + if (customName != '') { + cy.sendGetRequest(studyArmsUrl(study_uid)).then((response) => { + const existing = response.body.items.find((item) => item.name === customName) + if (existing) { + arm_uid = existing.arm_uid ?? existing.uid + return + } + cy.sendPostRequest(createArmUrl(study_uid), createArmBody(arm_type_uid, customName)).then((response) => { + arm_uid = response.body[0].content.arm_uid + }) + }) + return + } + cy.sendPostRequest(createArmUrl(study_uid), createArmBody(arm_type_uid, customName)).then((response) => { arm_uid = response.body[0].content.arm_uid }) }) diff --git a/system-tests/ui-tests/cypress/support/api_requests/study_compounds_request.js b/system-tests/ui-tests/cypress/support/api_requests/study_compounds_request.js new file mode 100644 index 00000000..c85e1221 --- /dev/null +++ b/system-tests/ui-tests/cypress/support/api_requests/study_compounds_request.js @@ -0,0 +1,87 @@ +import { element_uid } from "./study_elements_requests"; + +const { getShortUniqueId } = require("../../support/helper_functions"); + +export let study_compound_uid, study_compound_dosing_uid +let compound_simple_uid, compound_simple_name +let type_of_treatment_uid +let compound_alias_data, compound_alias_uid, medical_product_data, medical_product_uid +let study_compound_data, study_compound_dose_value_uid + +const createCompoundUrl = (study_uid) => `/studies/${study_uid}/study-compounds` +const createCompoundDosingUrl = (study_uid) => `/studies/${study_uid}/study-compound-dosings` +const compoundSimpleUrl = '/concepts/compounds-simple?filters={"status":{"v":["Final"]}}&page_size=0' +const treatmentTypeUrl = '/ct/codelists/terms?page_size=100&sort_by={"sponsor_preferred_name":true}&codelist_submission_value=TPOFTRT' +const compoundAliasUrl = (compound_simple_uid) => `/concepts/compound-aliases?filters={"compound_uid":{"v":["${compound_simple_uid}"]},"status":{"v":["Final"]}}&page_size=0` +const medicalProducsUrl = (compound_simple_uid) => `/concepts/medicinal-products?filters={"compound.uid":{"v":["${compound_simple_uid}"]},"status":{"v":["Final"]}}&page_size=0` +const studyCompoundsUrl = (study_uid) => `/studies/${study_uid}/study-compounds?page_size=0` + +Cypress.Commands.add('createSimpleCompound', (study_uid) => { + cy.sendPostRequest(createCompoundUrl(study_uid), createStudyCompoundsBody()).then(response => study_compound_uid = response.body.study_compound_uid) +}) + +Cypress.Commands.add('createCompoundDosing', (study_uid) => { + cy.sendPostRequest(createCompoundDosingUrl(study_uid), createStudyCompoundsDosingBody()).then(response => study_compound_dosing_uid = response.body.study_compound_dosing_uid) +}) + +Cypress.Commands.add('getStudyCompundData', (study_uid) => { + cy.sendGetRequest(studyCompoundsUrl(study_uid)).then(response => { + study_compound_uid = response.body.items[0].study_compound_uid + study_compound_dose_value_uid = response.body.items[0].medicinal_product.dose_values[0].uid + study_compound_data = response.body.items[0] + }) +}) + +Cypress.Commands.add('getCompundSimpleData', () => { + cy.sendGetRequest(compoundSimpleUrl).then(response => { + compound_simple_uid = response.body.items[0].uid + compound_simple_name = response.body.items[0].name + }) +}) + +Cypress.Commands.add('getCompundAliasData', () => { + cy.sendGetRequest(compoundAliasUrl(compound_simple_uid)).then(response => { + compound_alias_data = response.body.items[0] + compound_alias_uid = response.body.items[0].uid + }) +}) + +Cypress.Commands.add('getMedicalProductData', () => { + cy.sendGetRequest(medicalProducsUrl(compound_simple_uid)).then(response => { + medical_product_data = response.body.items[0] + medical_product_uid = response.body.items[0].uid + }) +}) + +Cypress.Commands.add('getTypeOfTreatmentUid', () => { + cy.sendGetRequest(treatmentTypeUrl).then(response => type_of_treatment_uid = response.body.items[0].uid) +}) + +const createStudyCompoundsBody = () => { + return { + "compoundSimple": { + "uid": compound_simple_uid, + "name": compound_simple_name + }, + "compound_alias": compound_alias_data, + "medicinalProduct": medical_product_data, + "dosage_form_uid": null, + "strength_value_uid": null, + "route_of_administration_uid": null, + "dispenser_uid": null, + "delivery_device_uid": null, + "other_info": "E2E testing", + "type_of_treatment_uid": "CTTerm_000155", + "medicinal_product_uid": medical_product_uid, + "compound_alias_uid": compound_alias_uid + } +} + +const createStudyCompoundsDosingBody = () => { + return { + "study_compound": study_compound_data, + "dose_value_uid": study_compound_dose_value_uid, + "study_element_uid": element_uid, + "study_compound_uid": study_compound_uid + } +} \ No newline at end of file diff --git a/system-tests/ui-tests/cypress/support/e2e.js b/system-tests/ui-tests/cypress/support/e2e.js index 166ea9a1..81d17009 100644 --- a/system-tests/ui-tests/cypress/support/e2e.js +++ b/system-tests/ui-tests/cypress/support/e2e.js @@ -20,6 +20,7 @@ import './api_requests/study_elements_requests' import './api_requests/study_epochs_requests' import './api_requests/study_type_requests' import './api_requests/study_visits_requests' +import './api_requests/study_compounds_request' import './browser_operations/study_select_command' import './front_end_commands/buttons_commands' import './front_end_commands/drop_down_commands' diff --git a/system-tests/ui-tests/package.json b/system-tests/ui-tests/package.json index cabef2df..d7fa840c 100644 --- a/system-tests/ui-tests/package.json +++ b/system-tests/ui-tests/package.json @@ -9,6 +9,8 @@ "test:no-allure-chrome": "failsafe test:clean test:junit-chrome", "test:clean": "rimraf results", "test:run": "cypress run --env allure=true,allureResultsPath=results/allure,host=$cypresshost --spec cypress/e2e/**/*.feature --headless", + "test:run-studies": "cypress run --env allure=true,allureResultsPath=results/allure,host=$cypresshost --spec 'cypress/e2e/features/modules/library/**/*.feature' --headless", + "test:run-library": "cypress run --env allure=true,allureResultsPath=results/allure,host=$cypresshost --spec 'cypress/e2e/features/modules/studies/**/*.feature' --headless", "test:run-chrome": "cypress run --env allure=true,allureResultsPath=results/allure,host=$cypresshost --spec cypress/e2e/**/*.feature --headless --browser chrome", "test:junit": "cypress run --env allure=false,host=$cypresshost --spec cypress/e2e/**/*.feature --headless", "test:junit-chrome": "cypress run --env allure=false,host=$cypresshost --spec cypress/e2e/**/*.feature --headless --browser chrome",