From 0b606d32216e7b957478b0613821f9282c299e78 Mon Sep 17 00:00:00 2001 From: OpenStudyBuilder Date: Tue, 14 Apr 2026 10:34:30 +0000 Subject: [PATCH] v2.8.0 --- CHANGE-LOG.md | 42 + README.md | 3 + clinical-mdr-api/.pre-commit-config.yaml | 2 +- clinical-mdr-api/Pipfile | 9 +- clinical-mdr-api/Pipfile.lock | 658 +-- clinical-mdr-api/apiVersion | 2 +- .../activity_instance_class_repository.py | 54 + .../activity_item_class_repository.py | 33 +- .../activities/activity_group_repository.py | 4 + .../activity_instance_repository.py | 1957 ++++++--- .../activities/activity_repository.py | 368 +- .../activity_sub_group_repository.py | 6 + .../concepts/concept_generic_repository.py | 13 +- .../ct_codelist_aggregated_repository.py | 128 +- .../library_item_repository.py | 50 +- .../domain_repositories/models/activities.py | 79 +- .../study_definition_repository.py | 62 +- .../study_definition_repository_impl.py | 52 +- .../study_selections/study_soa_repository.py | 1 + .../domains/concepts/activities/activity.py | 14 +- .../concepts/activities/activity_group.py | 7 + .../concepts/activities/activity_instance.py | 938 ++++- .../concepts/activities/activity_item.py | 3 + .../concepts/activities/activity_sub_group.py | 6 + .../ct_codelist_term.py | 112 +- .../clinical_mdr_api/domains/odms/item.py | 2 +- .../study_metadata.py | 21 +- .../domains/study_selections/study_visit.py | 4 +- .../activity_instance_class.py | 40 +- .../activity_item_class.py | 16 + .../concepts/activities/activity_group.py | 13 + .../concepts/activities/activity_instance.py | 588 ++- .../concepts/activities/activity_item.py | 15 + .../concepts/activities/activity_sub_group.py | 15 + .../controlled_terminologies/ct_codelist.py | 95 +- .../controlled_terminologies/ct_term.py | 3 +- .../models/study_selections/study.py | 31 +- .../clinical_mdr_api/repositories/_utils.py | 4 + .../activity_instance_classes.py | 57 + .../activity_item_classes.py | 57 + .../concepts/activities/activity_instances.py | 416 +- .../controlled_terminologies/ct_codelists.py | 45 + .../clinical_mdr_api/routers/odms/forms.py | 5 +- .../routers/odms/item_groups.py | 5 +- .../routers/odms/study_events.py | 5 +- .../routers/studies/study_flowchart.py | 11 +- .../routers/studies/study_visits.py | 16 +- .../services/_meta_repository.py | 255 +- .../activity_instance_class.py | 16 + .../activity_item_class.py | 2 + .../activities/activity_group_service.py | 6 + .../activities/activity_instance_service.py | 393 +- .../concepts/activities/activity_service.py | 19 +- .../activities/activity_sub_group_service.py | 6 + .../concepts/concept_generic_service.py | 25 +- .../controlled_terminologies/ct_codelist.py | 50 + .../services/ddf/usdm_mapper.py | 264 +- .../clinical_mdr_api/services/odms/forms.py | 9 +- .../services/odms/generic_service.py | 15 + .../services/odms/item_groups.py | 9 +- .../services/odms/study_events.py | 9 +- .../services/studies/study.py | 30 +- .../study_activity_instance_selection.py | 2 +- .../services/studies/study_flowchart.py | 457 ++- .../services/studies/study_selection_base.py | 30 - .../services/studies/study_visit.py | 32 +- .../services/utils/table_f.py | 34 +- .../tests/auth/integration/routes.py | 64 +- .../auth/integration/test_endpoints_rbac.py | 6 +- .../clinical_mdr_api/tests/data/odm_xml.py | 8 +- .../biomedical_concepts/test_activities.py | 332 +- .../test_activity_groups.py | 18 +- .../test_activity_instance_classes.py | 72 + .../test_activity_instances.py | 814 +++- .../test_activity_item_classes.py | 70 + .../test_activity_subgroups.py | 18 +- .../test_paired_codelist_terms.py | 248 ++ .../api/ddf/test_ddf_adapter_mappings.py | 7 +- .../api/odms/test_odm_versioning.py | 4 +- .../api/old/test_activity_group.py | 4 + .../api/old/test_activity_sub_group.py | 4 + .../integration/api/old/test_odm_forms.py | 16 +- .../api/old/test_odm_item_groups.py | 14 +- .../api/old/test_odm_study_events.py | 14 +- .../integration/api/old/test_study_fields.py | 30 +- .../test_adam_listings_mdvisit.py | 1 + .../test_study_metadata_listings.py | 4 +- .../study_selections/test_study_activities.py | 4 +- .../test_study_activity_instances.py | 312 +- .../study_selections/test_study_flowchart.py | 464 ++- .../tests/integration/api/test_studies.py | 30 +- .../test_study_definition_repository.py | 69 +- .../integration/services/test_studies.py | 2 +- .../services/test_study_flowchart.py | 253 ++ .../tests/integration/utils/factory_soa.py | 6 +- .../tests/integration/utils/utils.py | 18 +- .../activity_aggregates/test_activity.py | 8 +- .../test_activity_instance.py | 4 + .../tests/unit/models/test_table_f.py | 279 ++ .../unit/services/test_study_flowchart.py | 608 ++- clinical-mdr-api/common/config.py | 6 +- clinical-mdr-api/consumer_api/apiVersion | 2 +- clinical-mdr-api/consumer_api/openapi.json | 330 +- .../requirements/fs/fs-library.md | 18 +- .../requirements/fs/fs-studies.md | 1 + .../tests/v1/test_api_audit_trail.py | 6 +- .../consumer_api/tests/v1/test_api_library.py | 295 +- .../tests/v1/test_api_library_ct.py | 71 +- .../consumer_api/tests/v1/test_api_studies.py | 54 +- .../consumer_api/tests/v2/test_api.py | 2 +- clinical-mdr-api/consumer_api/v1/db.py | 123 +- clinical-mdr-api/consumer_api/v1/main.py | 24 +- clinical-mdr-api/consumer_api/v1/models.py | 175 +- clinical-mdr-api/openapi.json | 3281 +++++++++++---- clinical-mdr-api/sbom.md | 21 +- clinical-mdr-api/templates/odm/crf.html | 34 +- db-schema-migration/Pipfile | 12 +- .../data_corrections/correction_019.py | 208 + .../correction_019_overview.md | 43 + .../migrations/migration_022.py | 104 + .../migrations/migration_overview_022.md | 58 + .../tests/test_correction_019.py | 168 + .../tests/test_migration_022.py | 131 + .../correction_verification_019.py | 69 + .../verifications/verification_022.py | 34 + .../userguide/studies/manage_studies.md | 9 +- .../packages/cdisc_ct/ddfct-2024-09-27.json | 3528 +++++++++++++++++ .../physical_data_model/neo4j-model.graphml | 184 +- .../datafiles/configuration/feature_flags.csv | 32 +- .../configuration/feature_flags.csv | 32 +- .../importers/run_import_activities.py | 241 +- .../importers/run_import_feature_flags.py | 2 + .../importers/run_import_mockdatajson.py | 509 ++- studybuilder/config/config.json | 10 +- studybuilder/package.json | 2 +- studybuilder/public/config.json | 10 +- studybuilder/public/sbom-clinical-mdr-api.md | 55 +- studybuilder/public/sbom-studybuilder.md | 2 +- studybuilder/sbom.md | 2 +- studybuilder/src/App.vue | 1 + studybuilder/src/api/activities.js | 58 +- .../api/controlledTerminology/codelists.js | 6 + .../controlledTerminology/pairedCodelists.js | 9 + .../src/api/controlledTerminology/terms.js | 10 +- studybuilder/src/api/crfs.js | 42 - studybuilder/src/api/study.js | 8 +- studybuilder/src/components/layout/TopBar.vue | 12 +- .../components/layout/UnderConstruction.vue | 2 +- .../library/ActiveSubstanceForm.vue | 2 +- .../library/ActiveSubstancesTable.vue | 2 +- ...tivitiesCreateSponsorFromRequestedForm.vue | 6 +- .../library/ActivitiesGroupsForm.vue | 365 +- .../library/ActivitiesInstantiationsForm.vue | 534 --- .../components/library/ActivitiesTable.vue | 264 +- .../components/library/ActivityGroupings.vue | 10 +- .../library/ActivityGroupingsSummary.vue | 185 + .../library/ActivityInstanceClassOverview.vue | 2 +- .../library/ActivityInstanceClassTable.vue | 7 +- .../library/ActivityInstanceForm.vue | 1114 +++++- .../library/ActivityInstanceOverview.vue | 645 ++- .../ActivityInstanceParentClassOverview.vue | 4 +- .../library/ActivityItemClassField.vue | 208 +- .../library/ActivityItemClassOverview.vue | 4 +- .../library/ActivityItemClassTable.vue | 7 +- .../components/library/ActivityItemsTable.vue | 25 +- .../components/library/ActivityOverview.vue | 21 +- .../components/library/ActivitySummary.vue | 55 +- .../library/BaseActivityOverview.vue | 31 +- .../components/library/BaseTemplateForm.vue | 4 +- .../components/library/CodelistSummary.vue | 2 +- .../src/components/library/CodelistTable.vue | 22 +- .../components/library/CompoundAliasTable.vue | 2 +- .../src/components/library/CompoundTable.vue | 2 +- .../components/library/CtPackageHistory.vue | 2 +- .../DataExchangeStandardsGuideView.vue | 7 +- .../DataExchangeStandardsModelsView.vue | 5 +- .../components/library/FormulationField.vue | 2 +- .../src/components/library/GroupOverview.vue | 8 +- .../library/MedicinalProductForm.vue | 6 +- .../library/MedicinalProductOverview.vue | 8 +- .../library/PharmaceuticalProductForm.vue | 2 +- .../library/PharmaceuticalProductTable.vue | 6 +- .../library/SelectActivityItemTermField.vue | 241 +- .../library/StandardsCodelistTermsDialog.vue | 2 +- .../components/library/SubgroupOverview.vue | 10 +- .../library/TermsSelectionField.vue | 108 - .../components/library/TermsSelectionForm.vue | 375 +- .../library/TestActivityItemClassField.vue | 154 +- .../crfs/CrfActivityInstanceManagement.vue | 2 +- .../library/crfs/CrfAliasSelection.vue | 4 +- .../components/library/crfs/CrfFormForm.vue | 4 +- .../components/library/crfs/CrfItemForm.vue | 35 +- .../library/crfs/CrfItemGroupForm.vue | 42 +- .../components/library/crfs/CrfItemTable.vue | 41 +- .../library/crfs/CrfReferencesForm.vue | 4 +- .../crfs/CrfTranslatedTextSelection.vue | 4 +- .../library/crfs/OdmBuildingViewer.vue | 11 +- .../library/crfs/OdmReferencesTree.vue | 2 +- .../src/components/library/crfs/OdmViewer.vue | 15 +- .../crfs/crfTreeComponents/CrfTreeMain.vue | 2 +- .../src/components/studies/CohortsStepper.vue | 24 +- .../components/studies/CompoundDosingForm.vue | 4 +- .../components/studies/DesignMatrixTable.vue | 2 +- .../studies/EligibilityCriteriaEditForm.vue | 2 +- .../studies/EligibilityCriteriaForm.vue | 6 +- .../components/studies/EndpointEditForm.vue | 8 +- .../src/components/studies/EndpointForm.vue | 10 +- .../studies/InterventionOverview.vue | 5 +- .../components/studies/ObjectiveEditForm.vue | 2 +- .../src/components/studies/ObjectiveForm.vue | 6 +- .../ProtocolElementsObjectiveTable.vue | 2 +- ...rotocolElementsProceduresAndActivities.vue | 2 +- .../studies/ProtocolElementsStudyDesign.vue | 2 +- .../ProtocolElementsStudyIntervention.vue | 4 +- ...ProtocolElementsStudyPopulationSummary.vue | 4 +- .../components/studies/ProtocolFlowchart.vue | 53 +- .../components/studies/ProtocolTitlePage.vue | 2 +- .../ScheduleOfActivities/EmptySoATbody.vue | 4 +- .../ReorderingDetailedSoATbody.vue | 8 +- .../ScheduleOfActivities.vue | 94 +- .../components/studies/SoaSettingsForm.vue | 6 +- .../SpecificationDashboardOverview.vue | 18 +- .../components/studies/StudyActivityForm.vue | 161 +- .../studies/StudyActivityInstancesTable.vue | 13 +- .../StudyActivityInstructionBatchForm.vue | 8 +- .../components/studies/StudyActivityTable.vue | 3 +- .../studies/StudyDisclosureTable.vue | 5 +- .../studies/StudyDraftedActivityEditForm.vue | 21 +- .../studies/StudyFootnoteEditForm.vue | 2 +- .../components/studies/StudyFootnoteForm.vue | 6 +- .../src/components/studies/StudyForm.vue | 2 +- .../src/components/studies/StudyOdmViewer.vue | 57 +- .../studies/StudyQuickSelectForm.vue | 4 +- .../studies/StudySelectionEditForm.vue | 2 +- .../components/studies/StudySelectorField.vue | 24 +- .../studies/StudyStructureOverview.vue | 48 +- .../studies/StudySubpartEditForm.vue | 12 +- .../components/studies/StudySubpartForm.vue | 23 +- .../components/studies/StudySubpartsTable.vue | 47 +- .../src/components/studies/StudyTable.vue | 4 + .../src/components/studies/StudyTitleForm.vue | 2 +- .../src/components/studies/StudyVisitForm.vue | 8 +- .../components/studies/StudyVisitTable.vue | 4 +- .../overviews/StudyCompoundOverview.vue | 10 +- .../src/components/tools/ActionsMenu.vue | 6 +- .../components/tools/CommentThreadList.vue | 4 +- .../src/components/tools/ConfirmDialog.vue | 2 +- .../tools/ExpandableHeaderContent.vue | 4 +- .../tools/FeatureDisabledDialog.vue | 34 + .../components/tools/FilterAutocomplete.vue | 27 +- .../tools/HorizontalStepperForm.vue | 2 +- studybuilder/src/components/tools/NNTable.vue | 1 + .../tools/ParameterValueSelector.vue | 4 +- .../src/components/tools/RedirectHandler.vue | 4 +- .../components/tools/SelectCTTermField.vue | 52 +- .../src/components/tools/SelectMenuSearch.vue | 28 + .../src/components/tools/SimpleFormDialog.vue | 2 +- .../src/components/tools/StepperForm.vue | 8 +- .../ui/notification/NotificationAlert.vue | 5 +- .../ui/notification/NotificationPanel.vue | 6 +- .../src/constants/activityItemClasses.js | 16 + studybuilder/src/locales/en/api.json | 52 +- studybuilder/src/locales/en/app.json | 104 +- studybuilder/src/plugins/formRules.js | 8 + studybuilder/src/plugins/i18n.js | 1 + studybuilder/src/plugins/vuetify.js | 3 + studybuilder/src/stores/studies-general.js | 14 +- studybuilder/src/styles/global.scss | 21 +- studybuilder/src/utils/soaDownloads.js | 4 +- studybuilder/src/views/HomePage.vue | 6 +- .../administration/DataCompletenessTags.vue | 10 +- .../administration/SystemAnnouncements.vue | 4 +- .../src/views/library/ActivitiesPage.vue | 70 +- studybuilder/src/views/library/SdtmPage.vue | 7 +- .../src/views/library/SummaryPage.vue | 9 +- studybuilder/src/views/library/UniiPage.vue | 4 +- studybuilder/src/views/studies/CtrOdmXml.vue | 2 +- .../src/views/studies/ProtocolProcess.vue | 6 +- .../src/views/studies/SelectOrAddStudy.vue | 4 +- .../src/views/studies/StudyDataSuppliers.vue | 12 +- .../views/studies/StudyDataSuppliersEdit.vue | 18 +- .../src/views/studies/StudyDisclosure.vue | 2 +- .../src/views/studies/StudyStatus.vue | 8 +- studybuilder/src/views/studies/StudyTitle.vue | 5 +- .../src/views/studies/SummaryPage.vue | 9 +- .../src/views/user/UserPreferences.vue | 2 +- studybuilder/yarn.lock | 8 +- .../administration_feature_flags.feature | 2 +- .../data_completness_tags.feature | 41 + .../activities-extended_scope.feature | 15 +- .../activities/activity-groups.feature | 10 +- .../activities/activity-subgroups.feature | 9 +- .../activities/requested-activities.feature | 21 +- ...nces-wizard-stepper-extended-scope.feature | 19 +- ...es-wizard-stepper-numeric-findings.feature | 2 - .../activity-instances.feature | 213 +- ...rview-page-activity-instance-class.feature | 14 +- .../overview-page-activity-instance.feature | 29 +- .../overview-page-activity-item-class.feature | 14 +- .../overview-page-activity.feature | 6 +- .../compounds/compound-aliases.feature | 138 - .../concepts/compounds/compounds.feature | 152 - ...on.feature => concepts-navigation.feature} | 32 +- .../library/concepts/units/units.feature | 16 +- .../crf-item-activity-instance-links.feature | 147 + ...-tree-item-activity-instance-links.feature | 104 + .../parent-activity-templates.feature | 231 -- ...criteria-sponsor-standards-actions.feature | 171 - ...criteria-sponsor-standards-actions.feature | 172 - ...criteria-sponsor-standards-actions.feature | 171 - ...criteria-sponsor-standards-actions.feature | 171 - ...criteria-sponsor-standards-actions.feature | 172 - ...criteria-sponsor-standards-actions.feature | 172 - .../parent-endpoint-templates-actions.feature | 149 - .../objective-pre-instance-templates.feature | 16 - ...parent-objective-templates-actions.feature | 146 - ...ture => parent-activity-templates.feature} | 183 +- ... parent-criteria-dosing-templates.feature} | 194 +- ...rent-criteria-exclusion-templates.feature} | 201 +- ...rent-criteria-inclusion-templates.feature} | 200 +- ...-criteria-randomisation-templates.feature} | 194 +- ... parent-criteria-run-in-templates.feature} | 195 +- ...ent-criteria-withdrawal-templates.feature} | 194 +- .../parent-endpoint-templates.feature | 187 +- .../parent-objective-templates.feature | 195 +- ...ure => parent-timeframe-templates.feature} | 105 +- .../search/criteria-dosing-search.feature | 40 + .../search/criteria-exclusion-search.feature | 40 + .../search/criteria-inclusion-search.feature | 41 + .../criteria-randomisation-search.feature | 40 + .../search/criteria-run-in-search.feature | 40 + .../search/criteria-withdrawal-search.feature | 40 + .../search/parent-activity-search.feature | 39 + .../search/parent-endpoint-search.feature | 38 + .../search/parent-objective-search.feature | 38 + .../search/parent-timeframes-search.feature | 37 + .../syntax-templates-filtering.feature | 118 + .../syntax-templates-navigation.feature | 57 + .../syntax-templates-tables.feature | 473 +++ ...eframe-templates-sponsor-standards.feature | 157 - .../study-activities-exchange.feature | 61 +- .../study-activities-placeholder.feature | 263 +- ...tudy-activities-shared-placeholder.feature | 236 ++ .../study_activities/study-activities.feature | 73 +- .../study-detailed-soa.feature | 26 +- .../study-activity-instances-edition.feature | 3 + .../study-activity-instances.feature | 30 +- .../study-operational-soa.feature | 26 +- .../study_visits/study-visit.feature | 33 + .../manage_studies/study/study-status.feature | 12 +- .../study/study-subparts.feature | 110 +- ...inistration_data_completness_tags_steps.js | 136 + .../administration_feature_flags_steps.js | 8 + .../global_filtering_steps.js | 4 +- .../global_table_specific_steps.js | 18 + .../library_activities_instances_steps.js | 7 +- ...tivities_instances_wizard_stepper_steps.js | 12 +- .../library_activity_overview_page_common.js | 43 +- .../library_requested_activities_steps.js | 4 +- .../study_activities_steps.js | 44 +- .../study_detailed_soa_steps.js | 8 +- .../step_definitions/study_status_steps.js | 15 +- .../step_definitions/study_subparts_steps.js | 55 + .../step_definitions/study_visits_steps.js | 9 +- .../api_requests/library_activities.js | 69 +- .../api_requests/library_syntax_templates.js | 12 +- .../api_requests/study_epochs_requests.js | 11 +- .../front_end_commands/drop_down_commands.js | 5 + update_process.md | 110 + 369 files changed, 25932 insertions(+), 8640 deletions(-) create mode 100644 clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelist_terms.py create mode 100644 db-schema-migration/data_corrections/correction_019.py create mode 100644 db-schema-migration/data_corrections/correction_019_overview.md create mode 100644 db-schema-migration/migrations/migration_022.py create mode 100644 db-schema-migration/migrations/migration_overview_022.md create mode 100644 db-schema-migration/tests/test_correction_019.py create mode 100644 db-schema-migration/tests/test_migration_022.py create mode 100644 db-schema-migration/verifications/correction_verification_019.py create mode 100644 db-schema-migration/verifications/verification_022.py create mode 100644 mdr-standards-import/mdr_standards_import/container_booting/packages/cdisc_ct/ddfct-2024-09-27.json create mode 100644 studybuilder/src/api/controlledTerminology/pairedCodelists.js delete mode 100644 studybuilder/src/components/library/ActivitiesInstantiationsForm.vue create mode 100644 studybuilder/src/components/library/ActivityGroupingsSummary.vue delete mode 100644 studybuilder/src/components/library/TermsSelectionField.vue create mode 100644 studybuilder/src/components/tools/FeatureDisabledDialog.vue create mode 100644 studybuilder/src/components/tools/SelectMenuSearch.vue create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/administration/data_completness_tags.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/compounds/compound-aliases.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/compounds/compounds.feature rename system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/{activities/concepts-activities-navigation.feature => concepts-navigation.feature} (50%) create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-item-activity-instance-links.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/data_collection_standards/crf_builder/crf-tree-item-activity-instance-links.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/activity_templates/parent-activity-templates.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/criteria_templates/dosing_criteria/dosing-criteria-sponsor-standards-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/criteria_templates/exclusion_criteria/exclusion-criteria-sponsor-standards-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/criteria_templates/inclusion_criteria/inclusion-criteria-sponsor-standards-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/criteria_templates/randomisation_criteria/randomisation-criteria-sponsor-standards-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/criteria_templates/run_in_criteria/run-in-criteria-sponsor-standards-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/criteria_templates/withdrawal_criteria/withdrawal-criteria-sponsor-standards-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/endpoint_templates/parent-endpoint-templates-actions.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/objective_templates/parent-objective-templates-actions.feature rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{activity_templates/parent-activity-templates-actions.feature => parent-activity-templates.feature} (61%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{criteria_templates/dosing_criteria/dosing-criteria-sponsor-standards.feature => parent-criteria-dosing-templates.feature} (57%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{criteria_templates/exclusion_criteria/exclusion-criteria-sponsor-standards.feature => parent-criteria-exclusion-templates.feature} (55%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{criteria_templates/inclusion_criteria/inclusion-criteria-sponsor-standards.feature => parent-criteria-inclusion-templates.feature} (55%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{criteria_templates/randomisation_criteria/randomisation-criteria-sponsor-standards.feature => parent-criteria-randomisation-templates.feature} (57%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{criteria_templates/run_in_criteria/run-in-criteria-sponsor-standards.feature => parent-criteria-run-in-templates.feature} (57%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{criteria_templates/withdrawal_criteria/withdrawal-criteria-sponsor-standards.feature => parent-criteria-withdrawal-templates.feature} (57%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{endpoint_templates => }/parent-endpoint-templates.feature (60%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{objective_templates => }/parent-objective-templates.feature (59%) rename system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/{timeframe_templates/timeframe-templates-sponsor-standards-actions.feature => parent-timeframe-templates.feature} (68%) create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/criteria-dosing-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/criteria-exclusion-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/criteria-inclusion-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/criteria-randomisation-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/criteria-run-in-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/criteria-withdrawal-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/parent-activity-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/parent-endpoint-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/parent-objective-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/search/parent-timeframes-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/syntax-templates-filtering.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/syntax-templates-navigation.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/syntax-templates-tables.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/syntax_templates/timeframe_templates/timeframe-templates-sponsor-standards.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/studies/define_study/study_activities/study-activities-shared-placeholder.feature create mode 100644 system-tests/ui-tests/cypress/e2e/step_definitions/administration_data_completness_tags_steps.js create mode 100644 system-tests/ui-tests/cypress/e2e/step_definitions/study_subparts_steps.js create mode 100644 update_process.md diff --git a/CHANGE-LOG.md b/CHANGE-LOG.md index 5958d4ff..0335c5bc 100644 --- a/CHANGE-LOG.md +++ b/CHANGE-LOG.md @@ -1,5 +1,47 @@ # OpenStudyBuilder (OSB) Commits changelog +## V 2.8 + +New Features and Enhancements +============ + +### Fixes and Enhancements + +- The rule for generating subpart study IDs is changed so this will be the main study ID concatenated with the study subpart acronym. Rule for study subpart acronym is changed to be in upper case, no blanks or special characters and a max length of 10. On the Studies, Study List an additional column is added displaying the main study ID. +- Creating placeholder activities is now much more streamlined - Users no longer need to choose whether they want to submit their placeholders or not, as we'll only have one type of placeholder activities going forward. It is now also possible to re-use placeholders with identical naming across studies. All placeholders can still be used in the SoA and will be processed by Standards Developers like they are today. +- Aligned naming of unscheduled study visits with SDTM standard +- On Studies, Manage Study, Study menu on Protocol Versions tab the distinct protocol document main versions are listed. This now include a column for the original first study definition version related to each protocol document version as well as the latest version. The modified dates and by columns are removed, as they do not reflect the protocol document version, and they are available on the study status tab for the study definition versions. + +### New Feature + +- Split of the activity instance model, to keep separate versioning of the instance groupings (activity, group, and subgroup), and all other properties. This will allow standards developers to only update the part that needs changes, like when adding a new grouping, while leaving everything related to the data specification unchanged. The result will be less time spent on maintaining the library, and a cleaner library with fewer versions of each instance. +- New slider switch added to Library - Concepts - Activities page with label Archived library off by default. + +### Consumer API +- GET `/v1/library/activity-instances` endpoint: added information about activity instance class and activity items to response. +- GET `/v1/library/ct/codelist-terms` endpoint: added optional filtering by `codelist_uid`; added `codelist_uid`, `order` and `ordinal` fields to response. + +### End-to-End Automated test enhancements + +- Various code improvements to ensure easier maintenance and overall tests stability. +- Administration > Data Completness Tags: Defined and Implemented tests for adding, updating and removing data completness tags from studies. +- Library > Concepts > Activities: Adjusted tests to the Split of the activity instance model. +- Library > Syntax Templates: Moved generic checks on table level (table structure, search, filtering, pagination) to separate feature files. +- Library > Data Collection Standards > CRF Builder > CRF Items: Defined tests for Activity Instance linkage. +- Library > Data Collection Standards > CRF Builder > CRF Tree: Defined tests for Activity Instance linkage. +- Studies > Define Study > Study Activities: Adjusted and implemented new tests for Activity Placeholders. +- Studies > Define Study > Study Structure > Study Visits: Defined and implemented tests for unscheduled visits. +- Studies > Manage Study > Study Subparts: Defined and implemented tests for adding, updating and removing study subparts. + +Solved Bugs +============ + +### Reports + + **Activity Library Dashboard > ReadMe** + +- laboratory_data_specification issues + ## V 2.7 New Features and Enhancements diff --git a/README.md b/README.md index 43f1d3ad..86e94b7c 100644 --- a/README.md +++ b/README.md @@ -225,6 +225,9 @@ docker compose down --remove-orphans --volumes # DESTROYS THE DATABASE volume docker compose up -d # the database service re-creates the database volume on the first start ``` +For hosted environments with database migrations and sequential upgrades, +see the [Environment Update Process](./update_process.md). + ## Cleaning up the Docker environment To clean up the entire Docker environment use the following commands: diff --git a/clinical-mdr-api/.pre-commit-config.yaml b/clinical-mdr-api/.pre-commit-config.yaml index 0e147557..94c2a9bf 100644 --- a/clinical-mdr-api/.pre-commit-config.yaml +++ b/clinical-mdr-api/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: black - repo: https://github.com/PyCQA/isort - rev: 8.0.1 + rev: 5.13.2 hooks: - id: isort - repo: local diff --git a/clinical-mdr-api/Pipfile b/clinical-mdr-api/Pipfile index 15b7d830..d5917cc0 100644 --- a/clinical-mdr-api/Pipfile +++ b/clinical-mdr-api/Pipfile @@ -8,7 +8,7 @@ fastapi = "~=0.131.0" uvicorn = "~=0.32.0" pydantic = "~=2.12.5" pydantic-settings = "~=2.7.1" -requests = "*" +requests = "~=2.33.0" openpyxl = "~=3.1.5" dict2xml = "~=1.7.6" hypothesis = "~=6.115.6" @@ -37,7 +37,8 @@ annotated-types = "~=0.6.0" jinja2 = "*" nh3 = "~=0.2.21" neomodel = "==6.1.0" -deepdiff = "~=8.6.1" +deepdiff = "~=8.6.2" +pyasn1 = "~=0.6.3" [dev-packages] pytest = "~=8.4.1" @@ -75,7 +76,7 @@ test = "pytest -s" dist = "python setup.py bdist_wheel" package = "pip wheel -r requirements.txt -w dist" testunit = "pytest -s --cov-report html:reports/coverage-unit-html --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/unit_report.xml clinical_mdr_api/tests/unit/ common/tests/unit" -testint = "pytest -s -n 4 --dist loadfile --cov-report html:reports/coverage-int-html --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/int_report.xml clinical_mdr_api/tests/integration/" +testint = "pytest -s -n auto --dist loadfile --cov-report html:reports/coverage-int-html --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/int_report.xml clinical_mdr_api/tests/integration/" testauth = "pytest -s --cov-report html:reports/coverage-auth-html --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/auth_report.xml clinical_mdr_api/tests/auth/ common/tests/auth extensions/tests/auth/" test-telemetry = "pytest -s --cov-report html:reports/coverage-telemetry-html --cov-report xml:reports/coverage.xml --cov-append --cov --junitxml=reports/telemetry_report.xml clinical_mdr_api/tests/telemetry/" testunitallure = "pytest -s --cov-report html:reports/coverage-unit --cov-report xml:reports/coverage.xml --cov-append --cov=clinical_mdr_api --junitxml=reports/unit_report.xml --alluredir reports/allure-results clinical_mdr_api/tests/unit/" @@ -90,7 +91,7 @@ format = """sh -c " && python -m black clinical_mdr_api consumer_api common extensions \ " """ -audit = "python -m pip_audit" +audit = "python -m pip_audit --ignore-vuln CVE-2026-4539" openapi = "python generate_openapi_json.py" schemathesis = """ schemathesis diff --git a/clinical-mdr-api/Pipfile.lock b/clinical-mdr-api/Pipfile.lock index a3720dec..6ab72d58 100644 --- a/clinical-mdr-api/Pipfile.lock +++ b/clinical-mdr-api/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "552f687cdd8d960893eee6ed5b620e574a86c2de5bac9f72079813a2f951aba3" + "sha256": "4695f36491a01fd3b75aa5cf4050ce72043a343738c3156f07853956df03a013" }, "pipfile-spec": 6, "requires": { @@ -35,11 +35,11 @@ }, "anyio": { "hashes": [ - "sha256:41cfcc3a4c85d3f05c932da7c26d0201ac36f72abd4435ba90d0464a3ffed703", - "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c" + "sha256:08b310f9e24a9594186fd75b4f73f4a4152069e3853f1ed8bfbf58369f4ad708", + "sha256:334b70e641fd2221c1505b3890c69882fe4a2df910cba14d97019b90b24439dc" ], - "markers": "python_version >= '3.9'", - "version": "==4.12.1" + "markers": "python_version >= '3.10'", + "version": "==4.13.0" }, "asyncache": { "hashes": [ @@ -52,11 +52,11 @@ }, "attrs": { "hashes": [ - "sha256:16d5969b87f0859ef33a48b35d55ac1be6e42ae49d5e853b597db70c35c57e11", - "sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373" + "sha256:c647aa4a12dfbad9333ca4e71fe62ddc36f4e63b2d260a37a8b83d2f043ac309", + "sha256:d03ceb89cb322a8fd706d4fb91940737b6642aa36998fe130a9bc96c985eff32" ], "markers": "python_version >= '3.9'", - "version": "==25.4.0" + "version": "==26.1.0" }, "authlib": { "hashes": [ @@ -69,11 +69,11 @@ }, "azure-core": { "hashes": [ - "sha256:a7931fd445cb4af8802c6f39c6a326bbd1e34b115846550a8245fa656ead6f8e", - "sha256:bf59d29765bf4748ab9edf25f98a30b7ea9797f43e367c06d846a30b29c1f845" + "sha256:4ac7b70fab5438c3f68770649a78daf97833caa83827f91df9c14e0e0ea7d34f", + "sha256:8a90a562998dd44ce84597590fff6249701b98c0e8797c95fcdd695b54c35d74" ], "markers": "python_version >= '3.9'", - "version": "==1.38.3" + "version": "==1.39.0" }, "azure-identity": { "hashes": [ @@ -458,59 +458,59 @@ }, "cryptography": { "hashes": [ - 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a/clinical-mdr-api/apiVersion b/clinical-mdr-api/apiVersion index 919b10de..bd5605d8 100644 --- a/clinical-mdr-api/apiVersion +++ b/clinical-mdr-api/apiVersion @@ -1 +1 @@ -3.0.628 +3.0.642 diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_instance_class_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_instance_class_repository.py index 0c1b4eb6..882fd532 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_instance_class_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_instance_class_repository.py @@ -36,6 +36,7 @@ ActivityInstanceClass, ActivityInstanceClassWithDataset, ) +from common.utils import validate_page_number_and_page_size class ActivityInstanceClassRepository( # type: ignore[misc] @@ -81,6 +82,59 @@ def get_neomodel_extension_query(self) -> NodeSet: ) ) + def find_all_versions( + self, + sort_by: dict[str, bool] | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, + ) -> tuple[list[ActivityInstanceClass], int]: + validate_page_number_and_page_size(page_number=page_number, page_size=page_size) + skip = (page_number - 1) * page_size + sort_order = "DESC" if sort_by and sort_by.get("start_date") is False else "ASC" + + query = f""" + MATCH (lib:Library)-[:CONTAINS]->(root:ActivityInstanceClassRoot)-[ver:HAS_VERSION]->(val:ActivityInstanceClassValue) + OPTIONAL MATCH (author:User) + WHERE author.user_id = ver.author_id + WITH root, val, ver, lib, author + ORDER BY ver.start_date {sort_order} + SKIP $skip LIMIT $limit + RETURN + root.uid AS uid, + val.name AS name, + val.order AS order_val, + val.definition AS definition, + val.is_domain_specific AS is_domain_specific, + val.level AS level, + lib.name AS library_name, + ver.start_date AS start_date, + ver.end_date AS end_date, + ver.status AS status, + ver.version AS version, + ver.change_description AS change_description, + COALESCE(author.username, ver.author_id) AS author_username + """ + + count_query = """ + MATCH (root:ActivityInstanceClassRoot)-[ver:HAS_VERSION]->(val:ActivityInstanceClassValue) + RETURN count(*) AS total + """ + + results, meta = db.cypher_query(query, {"skip": skip, "limit": page_size}) + + items = [ + ActivityInstanceClass.from_cypher_row(dict(zip(meta, row))) + for row in results + ] + + total = 0 + if total_count: + count_result, _ = db.cypher_query(count_query) + total = count_result[0][0] if count_result else 0 + + return items, total + def extend_distinct_headers_query( self, nodeset: NodeSet, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_item_class_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_item_class_repository.py index 20682000..b3d6d892 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_item_class_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/biomedical_concepts/activity_item_class_repository.py @@ -52,12 +52,18 @@ class ActivityItemClassRepository(ConceptGenericRepository[ActivityItemClassAR]) value_object_class = ActivityItemClassVO return_model = ActivityItemClass - def generic_alias_clause(self, **kwargs): + def generic_alias_clause(self, *, return_all_versions: bool = False, **kwargs): """Override to use ActivityItemClass-specific library relationship.""" - return """ + version_return = ( + "RETURN hv AS version_rel" + if return_all_versions + else """WITH collect(hv) as hvs + RETURN last(hvs) AS version_rel""" + ) + return f""" DISTINCT concept_root, concept_value, head([(library:Library)-[:CONTAINS]->(concept_root) | library]) AS library - CALL { + CALL {{ WITH concept_root, concept_value MATCH (concept_root)-[hv:HAS_VERSION]-(concept_value) WITH hv @@ -66,9 +72,8 @@ def generic_alias_clause(self, **kwargs): toInteger(split(hv.version, '.')[1]) ASC, hv.end_date ASC, hv.start_date ASC - WITH collect(hv) as hvs - RETURN last(hvs) AS version_rel - } + {version_return} + }} WITH concept_root, concept_root.uid AS uid, @@ -76,12 +81,12 @@ def generic_alias_clause(self, **kwargs): library.name AS library_name, library.is_editable AS is_library_editable, version_rel - CALL { + CALL {{ WITH version_rel OPTIONAL MATCH (author: User) WHERE author.user_id = version_rel.author_id RETURN author - } + }} WITH uid, concept_root, @@ -101,6 +106,9 @@ def generic_alias_clause(self, **kwargs): COALESCE(author.username, version_rel.author_id) AS author_username """ + def generic_alias_clause_all_versions(self): + return self.generic_alias_clause(return_all_versions=True) + def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> ActivityItemClassAR: @@ -245,7 +253,12 @@ def get_all_for_activity_instance_class( ) """ - return_clause = "RETURN DISTINCT aicr, aicv, has_activity_instance_class" + data_type_match = """ + OPTIONAL MATCH (aicv)-[:HAS_DATA_TYPE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(data_type_root:CTTermRoot) + -[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(data_type_name_value) + """ + + return_clause = "RETURN DISTINCT aicr, aicv, has_activity_instance_class, data_type_root.uid AS data_type_uid, data_type_name_value.name AS data_type_name" query_elements = [base_match] filter_clause = "" @@ -260,12 +273,14 @@ def get_all_for_activity_instance_class( filter_clause = "WHERE " + " AND ".join(filter_elements) query_elements.append(filter_clause) + query_elements.append(data_type_match) query_elements.append(return_clause) query_elements.append("UNION") query_elements.append(base_parent_match) if filter_clause: query_elements.append(match_for_filter) query_elements.append(filter_clause) + query_elements.append(data_type_match) query_elements.append(return_clause) query = " ".join(query_elements) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py index a763cf62..34f2930b 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py @@ -45,6 +45,8 @@ def _create_aggregate_root_instance_from_cypher_result( name_sentence_case=input_dict.get("name_sentence_case"), definition=input_dict.get("definition"), abbreviation=input_dict.get("abbreviation"), + nci_concept_id=input_dict.get("nci_concept_id"), + nci_concept_name=input_dict.get("nci_concept_name"), ), library=LibraryVO.from_input_values_2( library_name=input_dict["library_name"], @@ -79,6 +81,8 @@ def _create_ar( name_sentence_case=value.name_sentence_case, definition=value.definition, abbreviation=value.abbreviation, + nci_concept_id=value.nci_concept_id, + nci_concept_name=value.nci_concept_name, ), library=LibraryVO.from_input_values_2( library_name=library.name, 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 4767c94c..5db99260 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 db +from neomodel import NodeClassNotDefined, db from clinical_mdr_api.domain_repositories.concepts.concept_generic_repository import ( ConceptGenericRepository, @@ -12,6 +12,8 @@ from clinical_mdr_api.domain_repositories.models._utils import ListDistinct from clinical_mdr_api.domain_repositories.models.activities import ( ActivityGrouping, + ActivityInstanceGroupingRoot, + ActivityInstanceGroupingValue, ActivityInstanceRoot, ActivityInstanceValue, ActivityItem, @@ -29,9 +31,15 @@ from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, + VersionRoot, + VersionValue, ) from clinical_mdr_api.domains.concepts.activities.activity_instance import ( ActivityInstanceAR, + ActivityInstanceAttributesAR, + ActivityInstanceAttributesVO, + ActivityInstanceGroupingsAR, + ActivityInstanceGroupingsVO, ActivityInstanceGroupingVO, ActivityInstanceVO, ) @@ -47,12 +55,15 @@ ) from clinical_mdr_api.models.concepts.activities.activity_instance import ( ActivityInstance, + ActivityInstanceAttributes, + ActivityInstanceGroupings, ) from clinical_mdr_api.models.concepts.activities.activity_item import ( CompactUnitDefinition, ) +from clinical_mdr_api.services.user_info import UserInfoService from common.config import settings -from common.exceptions import BusinessLogicException +from common.exceptions import BusinessLogicException, NotFoundException from common.utils import convert_to_datetime, version_string_to_tuple @@ -65,22 +76,23 @@ class ActivityInstanceRepository(ConceptGenericRepository[ActivityInstanceAR]): def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValue: value_node: ActivityInstanceValue = super()._create_new_value_node(ar=ar) - value_node.is_research_lab = ar.concept_vo.is_research_lab - if ar.concept_vo.molecular_weight: - value_node.molecular_weight = ar.concept_vo.molecular_weight - if ar.concept_vo.topic_code: - value_node.topic_code = ar.concept_vo.topic_code - if ar.concept_vo.adam_param_code: - value_node.adam_param_code = ar.concept_vo.adam_param_code - value_node.is_required_for_activity = ar.concept_vo.is_required_for_activity + attrs = ar.concept_vo.activity_instance_attributes + value_node.is_research_lab = attrs.is_research_lab + if attrs.molecular_weight: + value_node.molecular_weight = attrs.molecular_weight + if attrs.topic_code: + value_node.topic_code = attrs.topic_code + if attrs.adam_param_code: + value_node.adam_param_code = attrs.adam_param_code + value_node.is_required_for_activity = attrs.is_required_for_activity value_node.is_default_selected_for_activity = ( - ar.concept_vo.is_default_selected_for_activity + attrs.is_default_selected_for_activity ) - value_node.is_data_sharing = ar.concept_vo.is_data_sharing - value_node.is_legacy_usage = ar.concept_vo.is_legacy_usage - value_node.is_derived = ar.concept_vo.is_derived - if ar.concept_vo.legacy_description: - value_node.legacy_description = ar.concept_vo.legacy_description + value_node.is_data_sharing = attrs.is_data_sharing + value_node.is_legacy_usage = attrs.is_legacy_usage + value_node.is_derived = attrs.is_derived + if attrs.legacy_description: + value_node.legacy_description = attrs.legacy_description value_node.save() @@ -98,6 +110,31 @@ def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValu msg="Activity instances are not allowed to link to activity requests or placeholders", ) + # Set up the GroupingRoot and GroupingValue nodes + # This method is only called when creating a new ActivityInstanceRoot & Value + # node pair, so we need to create the GroupingRoot and GroupingValue nodes here. + # Get the root node + root_node = ActivityInstanceRoot.nodes.get(uid=ar.uid) + grouping_root_node = ActivityInstanceGroupingRoot() + grouping_root_node.save() + root_node.has_grouping_root.connect(grouping_root_node) + + # Create a new grouping value node + grouping_value_node = ActivityInstanceGroupingValue() + grouping_value_node.save() + grouping_root_node.has_latest_value.connect(grouping_value_node) + grouping_root_node.latest_draft.connect(grouping_value_node) + version_properties = { + "start_date": datetime.datetime.now(datetime.timezone.utc), + "status": "Draft", + "author_id": self.author_id, + "version": "0.1", + "change_description": "Initial draft", + } + grouping_root_node.has_version.connect( + grouping_value_node, properties=version_properties + ) + for activity_grouping in ar.concept_vo.activity_groupings: # find related ActivityGrouping node activity_grouping_node = ListDistinct( @@ -114,14 +151,14 @@ def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValu ) activity_grouping_node = activity_grouping_node[0] # link ActivityInstanceValue with ActivityGrouping node - value_node.has_activity.connect(activity_grouping_node) + grouping_value_node.has_activity.connect(activity_grouping_node) activity_instance_class = ActivityInstanceClassRoot.nodes.get( - uid=ar.concept_vo.activity_instance_class_uid + uid=attrs.activity_instance_class_uid ) value_node.activity_instance_class.connect(activity_instance_class) - for item in ar.concept_vo.activity_items: + for item in attrs.activity_items: activity_item_class = ActivityItemClassRoot.nodes.get_or_none( uid=item.activity_item_class_uid ) @@ -138,6 +175,7 @@ def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValu ) activity_item_node = ActivityItem( is_adam_param_specific=is_adam_param_specific, + is_activity_instance_id_specific=item.is_activity_instance_id_specific, text_value=item.text_value, ) activity_item_node.save() @@ -164,206 +202,6 @@ def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValu value_node.contains_activity_item.connect(activity_item_node) return value_node - def _has_item_data_changed(self, ar_items, value_item_nodes): - ar_activity_items = [] - for item in ar_items: - ar_activity_items.append( - { - "is_adam_param_specific": item.is_adam_param_specific, - "class": item.activity_item_class_uid, - "units": {unit.uid for unit in item.unit_definitions}, - "codelist": item.ct_codelist, - "terms": {(term.uid, term.codelist_uid) for term in item.ct_terms}, - "text_value": item.text_value, - } - ) - - value_activity_items = [] - for activity_item_node in value_item_nodes: - item_class_uid = activity_item_node.has_activity_item_class.get().uid - unit_nodes = activity_item_node.has_unit_definition.all() - ct_terms = [ - { - "uid": term_context.has_selected_term.single().uid, - "codelist_uid": term_context.has_selected_codelist.single().uid, - } - for term_context in activity_item_node.has_ct_term.all() - ] - - if codelist := activity_item_node.has_codelist.get_or_none(): - name_root = codelist.has_name_root.get() - name_value = name_root.has_latest_value.get() - codelist = {"uid": codelist.uid, "name": name_value.name} - else: - codelist = None - - value_activity_items.append( - { - "is_adam_param_specific": activity_item_node.is_adam_param_specific, - "class": item_class_uid, - "units": {unit_node.uid for unit_node in unit_nodes}, - "codelist": codelist, - "terms": { - (ct_term["uid"], ct_term["codelist_uid"]) - for ct_term in ct_terms - }, - "text_value": activity_item_node.text_value, - } - ) - for item in ar_activity_items: - if item not in value_activity_items: - return True - for item in value_activity_items: - if item not in ar_activity_items: - return True - return False - - def _has_grouping_data_changed(self, ar_groupings, activity_instance_value): - value_group_pairs = [] - for activity_grouping_node in activity_instance_value.has_activity.all(): - if not activity_grouping_node.has_grouping.get().has_latest_value.single(): - # The linked ActivityValue is not the latest. - # We need to return True, so that the ActivityInstanceValue - # gets updated to use the new ActivityValue. - return True - value_group_pairs.append( - ( - activity_grouping_node.has_grouping.get().has_version.single().uid, - activity_grouping_node.has_selected_group.get() - .has_version.single() - .uid, - activity_grouping_node.has_selected_subgroup.get() - .has_version.single() - .uid, - ) - ) - - ar_group_pairs = [ - ( - grouping.activity_uid, - grouping.activity_subgroup_uid, - grouping.activity_group_uid, - ) - for grouping in ar_groupings - ] - for pair in ar_group_pairs: - if pair not in value_group_pairs: - return True - for pair in value_group_pairs: - if pair not in ar_group_pairs: - return True - return False - - def _has_data_changed( - self, ar: ActivityInstanceAR, value: ActivityInstanceValue - ) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) - are_props_changed = ( - ar.concept_vo.molecular_weight != value.molecular_weight - or ar.concept_vo.topic_code != value.topic_code - or ar.concept_vo.adam_param_code != value.adam_param_code - or bool(ar.concept_vo.is_research_lab) != bool(value.is_research_lab) - or bool(ar.concept_vo.is_required_for_activity) - != bool(value.is_required_for_activity) - or bool(ar.concept_vo.is_default_selected_for_activity) - != bool(value.is_default_selected_for_activity) - or bool(ar.concept_vo.is_data_sharing) != bool(value.is_data_sharing) - or bool(ar.concept_vo.is_legacy_usage) != bool(value.is_legacy_usage) - or bool(ar.concept_vo.is_derived) != bool(value.is_derived) - or ar.concept_vo.legacy_description != value.legacy_description - ) - - item_data_changed = self._has_item_data_changed( - ar.concept_vo.activity_items, value.contains_activity_item.all() - ) - - # Is this a final version? If yes, we skip the grouping data check - # to avoid creating new values nodes when just creating a new draft. - root_for_final_value = value.has_version.match( - status__in=[LibraryItemStatus.FINAL.value, LibraryItemStatus.RETIRED.value], - end_date__isnull=True, - ) - - if not root_for_final_value: - grouping_data_changed = self._has_grouping_data_changed( - ar.concept_vo.activity_groupings, value - ) - else: - grouping_data_changed = False - - are_rels_changed = ( - ar.concept_vo.activity_instance_class_uid - != value.activity_instance_class.get().uid - or grouping_data_changed - or item_data_changed - ) - return are_concept_properties_changed or are_props_changed or are_rels_changed - - def copy_activity_instance_and_recreate_activity_groupings( - self, activity_instance: ActivityInstanceAR, author_id: str - ) -> None: - query = """ - MATCH (concept_root:ActivityInstanceRoot {uid:$activity_instance_uid})-[status_relationship:LATEST]->(concept_value:ActivityInstanceValue) - CALL apoc.refactor.cloneNodes([concept_value]) - YIELD input, output, error""" - merge_query = f""" - MERGE (concept_root)-[:LATEST]->(output) - MERGE (concept_root)-[:LATEST_{activity_instance.item_metadata.status.value.upper()}]->(output) - MERGE (concept_root)-[new_has_version:HAS_VERSION]->(output)""" - query += self._update_versioning_relationship_query( - status=activity_instance.item_metadata.status.value, merge_query=merge_query - ) - query += """ - - WITH library, concept_root, concept_value, output - MATCH (concept_value)-[:ACTIVITY_INSTANCE_CLASS]->(activity_instance_class:ActivityInstanceClassRoot) - OPTIONAL MATCH (concept_value)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item:ActivityItem) - WITH library, concept_root, activity_item, activity_instance_class, output - MERGE (output)-[:ACTIVITY_INSTANCE_CLASS]->(activity_instance_class) - WITH library, concept_root, output, activity_item - CALL apoc.do.case([ - activity_item IS NOT NULL, - 'MERGE (output)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item) RETURN output' - ], - '', - { - activity_item: activity_item, - output: output - }) - YIELD value - UNWIND range(0, size($activity_uids)-1) AS idx - MATCH (activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(:ActivityValue)<-[:LATEST_FINAL]-(:ActivityRoot {uid:$activity_uids[idx]}) - MATCH (activity_grouping)-[:HAS_SELECTED_GROUP]->(:ActivityGroupValue)<-[:HAS_VERSION]-(:ActivityGroupRoot {uid:$activity_group_uids[idx]}) - MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(:ActivitySubGroupValue)<-[:HAS_VERSION]-(:ActivitySubGroupRoot {uid:$activity_subgroup_uids[idx]}) - WITH library, concept_root, output, activity_grouping - MERGE (output)-[:HAS_ACTIVITY]->(activity_grouping) - RETURN concept_root, output, library - """ - - db.cypher_query( - query, - params={ - "activity_instance_uid": activity_instance.uid, - "new_status": activity_instance.item_metadata.status.value, - "new_version": activity_instance.item_metadata.version, - "start_date": datetime.datetime.now(datetime.timezone.utc), - "change_description": "Copying previous ActivityInstanceValue node and updating ActivityGrouping nodes", - "author_id": author_id, - "activity_uids": [ - activity_instance.activity_uid - for activity_instance in activity_instance.concept_vo.activity_groupings - ], - "activity_subgroup_uids": [ - activity_instance.activity_subgroup_uid - for activity_instance in activity_instance.concept_vo.activity_groupings - ], - "activity_group_uids": [ - activity_instance.activity_group_uid - for activity_instance in activity_instance.concept_vo.activity_groupings - ], - }, - ) - def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> ActivityInstanceAR: @@ -455,6 +293,9 @@ def _create_aggregate_root_instance_from_cypher_result( for unit in activity_item.get("unit_definitions") ], text_value=activity_item.get("text_value"), + is_activity_instance_id_specific=activity_item.get( + "is_activity_instance_id_specific" + ), ) for activity_item in input_dict.get("activity_items", []) ], @@ -476,6 +317,30 @@ def _create_aggregate_root_instance_from_cypher_result( major_version=int(major), minor_version=int(minor), ), + groupings_item_metadata=LibraryItemMetadataVO.from_repository_values( + change_description=input_dict.get("groupings_version", {}).get( + "change_description" + ), + status=LibraryItemStatus( + input_dict.get("groupings_version", {}).get("status") + ), + author_id=input_dict.get("groupings_version", {}).get("author_id"), + author_username=UserInfoService.get_author_username_from_id( + input_dict.get("groupings_version", {}).get("author_id", "") + ), + start_date=convert_to_datetime( + value=input_dict.get("groupings_version", {}).get("start_date") + ), + end_date=convert_to_datetime( + value=input_dict.get("groupings_version", {}).get("end_date") + ), + major_version=int( + input_dict.get("groupings_version", {}).get("major_version", "0") + ), + minor_version=int( + input_dict.get("groupings_version", {}).get("minor_version", "0") + ), + ), ) return activity_instance_ar @@ -542,9 +407,20 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=activity_item.text_value, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, ) ) - activity_groupings_nodes = value.has_activity.all() + groupings_root = root.has_grouping_root.single() + groupings_value = groupings_root.has_latest_value.single() + activity_groupings_nodes = groupings_value.has_activity.all() + groupings_relationships = groupings_value.has_version.all_relationships( + groupings_root + ) + + groupings_relationship = max( + groupings_relationships, + key=lambda r: r.start_date, + ) activity_groupings = [] activity_name = None for activity_grouping in activity_groupings_nodes: @@ -634,190 +510,171 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( is_library_editable_callback=lambda _: library.is_editable, ), item_metadata=self._library_item_metadata_vo_from_relation(relationship), + groupings_item_metadata=self._library_item_metadata_vo_from_relation( + groupings_relationship + ), ) - def _create_ar( + def specific_alias_clause(self, **kwargs) -> str: + return """ + WITH *, + concept_value.nci_concept_name AS nci_concept_name, + concept_value.molecular_weight AS molecular_weight, + concept_value.topic_code AS topic_code, + concept_value.adam_param_code AS adam_param_code, + coalesce(concept_value.is_research_lab, false) AS is_research_lab, + coalesce(concept_value.is_required_for_activity, false) AS is_required_for_activity, + coalesce(concept_value.is_default_selected_for_activity, false) AS is_default_selected_for_activity, + coalesce(concept_value.is_data_sharing, false) AS is_data_sharing, + coalesce(concept_value.is_legacy_usage, false) AS is_legacy_usage, + coalesce(concept_value.is_derived, false) AS is_derived, + concept_value.legacy_description AS legacy_description, + + head([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]-> + (activity_instance_class_root:ActivityInstanceClassRoot)-[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) + | {uid:activity_instance_class_root.uid, name:activity_instance_class_value.name}]) AS activity_instance_class, + [(concept_value)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item:ActivityItem) + <-[:HAS_ACTIVITY_ITEM]-(activity_item_class_root:ActivityItemClassRoot)-[:LATEST]-> + (activity_item_class_value:ActivityItemClassValue) + | { + activity_item_class_uid: activity_item_class_root.uid, + activity_item_class_name: activity_item_class_value.name, + ct_terms: COLLECT { + MATCH (activity_item)-[:HAS_CT_TERM]->(ct_term_context:CTTermContext) + -[:HAS_SELECTED_TERM]->(term_root:CTTermRoot) + -[:HAS_NAME_ROOT]->(term_name_root:CTTermNameRoot) + -[:LATEST]->(term_name_value:CTTermNameValue) + MATCH (ct_term_context)-[:HAS_SELECTED_CODELIST]->(codelist_root:CTCodelistRoot) + MATCH (ct_codelist_term:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root) + RETURN {uid: term_root.uid, name: term_name_value.name, codelist_uid: codelist_root.uid, submission_value: ct_codelist_term.submission_value} + }, + ct_codelist: head([(activity_item)-[:HAS_CODELIST]->(ccr:CTCodelistRoot)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)-[:LATEST]-(ccnv:CTCodelistNameValue) | {uid: ccr.uid, name: ccnv.name}]), + unit_definitions: [(activity_item)-[:HAS_UNIT_DEFINITION]->(unit_definition_root:UnitDefinitionRoot)-[:LATEST]->(unit_definition_value:UnitDefinitionValue)-[:HAS_CT_DIMENSION]-(:CTTermRoot)-[:HAS_NAME_ROOT]->(CTTermNamesRoot)-[:LATEST]->(dimension_value:CTTermNameValue) | {uid: unit_definition_root.uid, name: unit_definition_value.name, dimension_name: dimension_value.name}], + is_adam_param_specific: activity_item.is_adam_param_specific, + is_activity_instance_id_specific: activity_item.is_activity_instance_id_specific, + text_value: activity_item.text_value + }] AS activity_items, + head([(concept_root)-[:HAS_GROUPING_ROOT]-(groupings_root:ActivityInstanceGroupingRoot)-[:LATEST]->(groupings_value:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(activity_value) | activity_value.name]) as activity_name, + apoc.coll.toSet([(concept_root)-[:HAS_GROUPING_ROOT]-(groupings_root:ActivityInstanceGroupingRoot)-[:LATEST]->(groupings_value:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping) + | { + activity: head(apoc.coll.sortMulti([(activity_grouping)<-[:HAS_GROUPING]-(activity_value:ActivityValue)<-[has_version:HAS_VERSION]- + (activity_root:ActivityRoot) | + { + uid: activity_root.uid, + name: activity_value.name, + major_version: toInteger(split(has_version.version,'.')[0]), + minor_version: toInteger(split(has_version.version,'.')[1]) + }], ['major_version', 'minor_version'])), + activity_subgroup: head(apoc.coll.sortMulti([(activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue)<-[has_version:HAS_VERSION]- + (activity_subgroup_root:ActivitySubGroupRoot) | + { + uid: activity_subgroup_root.uid, + name: activity_subgroup_value.name, + major_version: toInteger(split(has_version.version,'.')[0]), + minor_version: toInteger(split(has_version.version,'.')[1]) + }], ['major_version', 'minor_version'])), + activity_group: head(apoc.coll.sortMulti([(activity_grouping)-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue)<-[has_version:HAS_VERSION]- + (activity_group_root:ActivityGroupRoot) | + { + uid: activity_group_root.uid, + name: activity_group_value.name, + major_version: toInteger(split(has_version.version,'.')[0]), + minor_version: toInteger(split(has_version.version,'.')[1]) + }], ['major_version', 'minor_version'])) + }]) AS activity_groupings, + head( + apoc.coll.sortMulti([ + (concept_root)-[:HAS_GROUPING_ROOT]-(groupings_root:ActivityInstanceGroupingRoot)-[groupings_has_version:HAS_VERSION]-> + (groupings_value:ActivityInstanceGroupingValue) WHERE (groupings_root)-[:LATEST]->(groupings_value) + | { + status: groupings_has_version.status, + author_id: groupings_has_version.author_id, + version: groupings_has_version.version, + major_version: toInteger(split(groupings_has_version.version,'.')[0]), + minor_version: toInteger(split(groupings_has_version.version,'.')[1]), + change_description: groupings_has_version.change_description, + start_date: groupings_has_version.start_date, + end_date: groupings_has_version.end_date + } + ], ['major_version', 'minor_version', 'start_date']) + ) AS groupings_version + """ + + def minimal_count_query( self, - root: ActivityInstanceRoot, - library: Library, - relationship: VersionRelationship, - value: ActivityInstanceValue, - **_kwargs, - ) -> ActivityInstanceAR: - activity_instance_objects = _kwargs["activity_instance_root"] - activity_instance_class = activity_instance_objects["activity_instance_class"] - activity_item_vos = [] - for activity_item in activity_instance_objects["activity_items"]: - ct_terms = [] - unit_definitions = [] - for unit in activity_item["unit_definitions"]: - unit_definitions.append( - CompactUnitDefinition( - uid=unit["uid"], - name=unit["name"], - ) - ) - for term in activity_item["ct_terms"]: - ct_terms.append( - CTTermItem( - uid=term["uid"], - name=term["name"], - codelist_uid=term["codelist_uid"], - ) - ) - if codelist := activity_item["ct_codelist"]: - ct_codelist = CTCodelistItem(uid=codelist["uid"], name=codelist["name"]) - else: - ct_codelist = None + filter_by: dict[str, dict[str, Any]] | None, + return_all_versions: bool, + **kwargs, + ) -> tuple[str | None, dict[str, Any]]: + """Provide a fast count path for status query param on activity instances. - activity_item_vos.append( - ActivityItemVO.from_repository_values( - is_adam_param_specific=activity_item["is_adam_param_specific"], - activity_item_class_uid=activity_item["activity_item_class_uid"], - activity_item_class_name=activity_item["activity_item_class_name"], - ct_codelist=ct_codelist, - ct_terms=ct_terms, - unit_definitions=unit_definitions, - text_value=activity_item.get("text_value"), - ) + The endpoint-level `status` query parameter should match either the activity + instance status or the latest groupings status. + """ + status = kwargs.get("status") + if status is None: + return super().minimal_count_query( + filter_by=filter_by, + return_all_versions=return_all_versions, + **kwargs, ) - activity_groupings = [] - for activity_grouping in activity_instance_objects[ - "activity_instance_groupings" - ]: - activity_groupings.append( - ActivityInstanceGroupingVO( - activity_group_uid=activity_grouping["activity_group"].get("uid"), - activity_group_name=activity_grouping["activity_group"].get("name"), - activity_group_version=f"{activity_grouping['activity_group'].get('major_version')}.{activity_grouping['activity_group'].get('minor_version')}", - activity_subgroup_uid=activity_grouping["activity_subgroup"].get( - "uid" - ), - activity_subgroup_name=activity_grouping["activity_subgroup"].get( - "name" - ), - activity_subgroup_version=f"{activity_grouping['activity_subgroup'].get('major_version')}.{activity_grouping['activity_subgroup'].get('minor_version')}", - activity_uid=activity_grouping["activity"].get("uid"), - activity_name=activity_grouping["activity"].get("name"), - activity_version=f"{activity_grouping['activity'].get('major_version')}.{activity_grouping['activity'].get('minor_version')}", - ) + + # Keep generic path for non-latest queries and for additional filters that + # this fast count query does not include. + if kwargs.get("version", None) is not None or return_all_versions: + return None, {} + if filter_by and len(filter_by) > 0: + return None, {} + if any( + kwargs.get(filter_name) is not None + for filter_name in ( + "activity_instance_names", + "activity_names", + "activity_subgroup_names", + "activity_group_names", + "activity_instance_class_names", ) - return self.aggregate_class.from_repository_values( - uid=root.uid, - concept_vo=self.value_object_class.from_repository_values( - nci_concept_id=value.nci_concept_id, - nci_concept_name=value.nci_concept_name, - name=value.name, - name_sentence_case=value.name_sentence_case, - activity_instance_class_uid=activity_instance_class[ - "activity_instance_class_uid" - ], - activity_instance_class_name=activity_instance_class[ - "activity_instance_class_name" - ], - definition=value.definition, - abbreviation=value.abbreviation, - is_research_lab=( - value.is_research_lab if value.is_research_lab else False - ), - molecular_weight=value.molecular_weight, - topic_code=value.topic_code, - adam_param_code=value.adam_param_code, - is_required_for_activity=( - value.is_required_for_activity - if value.is_required_for_activity - else False - ), - is_default_selected_for_activity=( - value.is_default_selected_for_activity - if value.is_default_selected_for_activity - else False - ), - is_data_sharing=( - value.is_data_sharing if value.is_data_sharing else False - ), - is_legacy_usage=( - value.is_legacy_usage if value.is_legacy_usage else False - ), - is_derived=value.is_derived if value.is_derived else False, - legacy_description=value.legacy_description, - activity_groupings=activity_groupings, - activity_items=activity_item_vos, - ), - library=LibraryVO.from_input_values_2( - library_name=library.name, - is_library_editable_callback=lambda _: library.is_editable, - ), - item_metadata=self._library_item_metadata_vo_from_relation(relationship), - ) + ): + return None, {} - def specific_alias_clause(self, **kwargs) -> str: - return """ - WITH *, - concept_value.nci_concept_name AS nci_concept_name, - concept_value.molecular_weight AS molecular_weight, - concept_value.topic_code AS topic_code, - concept_value.adam_param_code AS adam_param_code, - coalesce(concept_value.is_research_lab, false) AS is_research_lab, - coalesce(concept_value.is_required_for_activity, false) AS is_required_for_activity, - coalesce(concept_value.is_default_selected_for_activity, false) AS is_default_selected_for_activity, - coalesce(concept_value.is_data_sharing, false) AS is_data_sharing, - coalesce(concept_value.is_legacy_usage, false) AS is_legacy_usage, - coalesce(concept_value.is_derived, false) AS is_derived, - concept_value.legacy_description AS legacy_description, - - head([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]-> - (activity_instance_class_root:ActivityInstanceClassRoot)-[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) - | {uid:activity_instance_class_root.uid, name:activity_instance_class_value.name}]) AS activity_instance_class, - [(concept_value)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item:ActivityItem) - <-[:HAS_ACTIVITY_ITEM]-(activity_item_class_root:ActivityItemClassRoot)-[:LATEST]-> - (activity_item_class_value:ActivityItemClassValue) - | { - activity_item_class_uid: activity_item_class_root.uid, - activity_item_class_name: activity_item_class_value.name, - ct_terms: COLLECT { - MATCH (activity_item)-[:HAS_CT_TERM]->(ct_term_context:CTTermContext) - -[:HAS_SELECTED_TERM]->(term_root:CTTermRoot) - -[:HAS_NAME_ROOT]->(term_name_root:CTTermNameRoot) - -[:LATEST]->(term_name_value:CTTermNameValue) - MATCH (ct_term_context)-[:HAS_SELECTED_CODELIST]->(codelist_root:CTCodelistRoot) - MATCH (ct_codelist_term:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root) - RETURN {uid: term_root.uid, name: term_name_value.name, codelist_uid: codelist_root.uid, submission_value: ct_codelist_term.submission_value} - }, - ct_codelist: head([(activity_item)-[:HAS_CODELIST]->(ccr:CTCodelistRoot)-[:HAS_NAME_ROOT]->(:CTCodelistNameRoot)-[:LATEST]-(ccnv:CTCodelistNameValue) | {uid: ccr.uid, name: ccnv.name}]), - unit_definitions: [(activity_item)-[:HAS_UNIT_DEFINITION]->(unit_definition_root:UnitDefinitionRoot)-[:LATEST]->(unit_definition_value:UnitDefinitionValue)-[:HAS_CT_DIMENSION]-(:CTTermRoot)-[:HAS_NAME_ROOT]->(CTTermNamesRoot)-[:LATEST]->(dimension_value:CTTermNameValue) | {uid: unit_definition_root.uid, name: unit_definition_value.name, dimension_name: dimension_value.name}], - is_adam_param_specific: activity_item.is_adam_param_specific, - text_value: activity_item.text_value - }] AS activity_items, - head([(concept_value)-[:HAS_ACTIVITY]->(activity_grouping)<-[:HAS_GROUPING]-(activity_value) | activity_value.name]) as activity_name, - apoc.coll.toSet([(concept_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping) - | { - activity: head(apoc.coll.sortMulti([(activity_grouping)<-[:HAS_GROUPING]-(activity_value:ActivityValue)<-[has_version:HAS_VERSION]- - (activity_root:ActivityRoot) | - { - uid: activity_root.uid, - name: activity_value.name, - major_version: toInteger(split(has_version.version,'.')[0]), - minor_version: toInteger(split(has_version.version,'.')[1]) - }], ['major_version', 'minor_version'])), - activity_subgroup: head(apoc.coll.sortMulti([(activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue)<-[has_version:HAS_VERSION]- - (activity_subgroup_root:ActivitySubGroupRoot) | - { - uid: activity_subgroup_root.uid, - name: activity_subgroup_value.name, - major_version: toInteger(split(has_version.version,'.')[0]), - minor_version: toInteger(split(has_version.version,'.')[1]) - }], ['major_version', 'minor_version'])), - activity_group: head(apoc.coll.sortMulti([(activity_grouping)-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue)<-[has_version:HAS_VERSION]- - (activity_group_root:ActivityGroupRoot) | - { - uid: activity_group_root.uid, - name: activity_group_value.name, - major_version: toInteger(split(has_version.version,'.')[0]), - minor_version: toInteger(split(has_version.version,'.')[1]) - }], ['major_version', 'minor_version'])) - }]) AS activity_groupings + concept_label = self.root_class.__label__ + concept_value_label = self.value_class.__label__ + + where_clauses = [ + "hv.end_date IS NULL", + """ + ( + hv.status = $status + OR EXISTS { + MATCH (concept_root)-[:HAS_GROUPING_ROOT]->(groupings_root:ActivityInstanceGroupingRoot) + -[groupings_has_version:HAS_VERSION]->(groupings_value:ActivityInstanceGroupingValue) + WHERE (groupings_root)-[:LATEST]->(groupings_value) + AND groupings_has_version.end_date IS NULL + AND groupings_has_version.status = $status + } + ) + """, + ] + params: dict[str, Any] = {"status": status} + + library_name = self.filter_query_parameters.get("library_name") + if library_name is not None: + where_clauses.append( + "EXISTS { MATCH (:Library {name: $library_name})-[:CONTAINS_CONCEPT]->(concept_root) }" + ) + params["library_name"] = library_name + + uids = self.filter_query_parameters.get("uids") + if uids is not None: + where_clauses.append("concept_root.uid IN $uids") + params["uids"] = uids + + query = f""" + MATCH (concept_root:{concept_label})-[hv:HAS_VERSION]->(concept_value:{concept_value_label}) + WHERE {' AND '.join(where_clauses)} + RETURN count(DISTINCT concept_root) AS count """ + return query, params def create_query_filter_statement( self, library: str | None = None, **kwargs @@ -837,15 +694,19 @@ def create_query_filter_statement( if kwargs.get("activity_names") is not None: activity_names = kwargs.get("activity_names") filter_by_activity_names = ( - "size([(concept_value)-[:HAS_ACTIVITY]->(:ActivityGrouping)<-[:HAS_GROUPING]-(activity_hierarchy_value) " - "WHERE activity_hierarchy_value.name IN $activity_names | activity_hierarchy_value.name]) > 0" + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)" + "-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)" + "<-[:HAS_GROUPING]-(activity_value:ActivityValue) " + "WHERE activity_value.name IN $activity_names | activity_value.name]) > 0" ) filter_parameters.append(filter_by_activity_names) filter_query_parameters["activity_names"] = activity_names if kwargs.get("activity_subgroup_names") is not None: activity_subgroup_names = kwargs.get("activity_subgroup_names") filter_by_activity_subgroup_names = ( - "size([(concept_value)-[:HAS_ACTIVITY]->(:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue) " + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)" + "-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)" + "-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue) " "WHERE activity_subgroup_value.name IN $activity_subgroup_names | activity_subgroup_value.name]) > 0" ) filter_parameters.append(filter_by_activity_subgroup_names) @@ -853,7 +714,9 @@ def create_query_filter_statement( if kwargs.get("activity_group_names") is not None: activity_group_names = kwargs.get("activity_group_names") filter_by_activity_group_names = ( - "size([(concept_value)-[:HAS_ACTIVITY]->(:ActivityGrouping)-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue) " + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)" + "-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)" + "-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue) " "WHERE activity_group_value.name IN $activity_group_names | activity_group_value.name]) > 0" ) filter_parameters.append(filter_by_activity_group_names) @@ -869,6 +732,23 @@ def create_query_filter_statement( filter_query_parameters["activity_instance_class_names"] = ( instance_class_names ) + if kwargs.get("status") is not None: + status = kwargs.get("status") + filter_by_status_or_groupings_status = ( + "(" + "size([(concept_root)-[concept_has_version:HAS_VERSION]->(concept_value) " + "WHERE concept_has_version.end_date IS NULL " + "AND concept_has_version.status = $status | concept_has_version]) > 0 " + "OR " + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(groupings_root:ActivityInstanceGroupingRoot)" + "-[groupings_has_version:HAS_VERSION]->(groupings_value:ActivityInstanceGroupingValue) " + "WHERE (groupings_root)-[:LATEST]->(groupings_value) " + "AND groupings_has_version.end_date IS NULL " + "AND groupings_has_version.status = $status | groupings_has_version]) > 0" + ")" + ) + filter_parameters.append(filter_by_status_or_groupings_status) + filter_query_parameters["status"] = status extended_filter_statements = " AND ".join(filter_parameters) if filter_statements_from_concept != "": if len(extended_filter_statements) > 0: @@ -885,6 +765,22 @@ def create_query_filter_statement( ) return filter_statements_to_return, filter_query_parameters + @classmethod + def format_filter_sort_keys(cls, key: str) -> str: + """Map API keys to Cypher aliases used by the activity instance list query.""" + groupings_version_key_map = { + "groupings_status": "groupings_version.status", + "groupings_version": "groupings_version.version", + "groupings_author_username": "groupings_version.author_id", + "groupings_author_id": "groupings_version.author_id", + "groupings_major_version": "groupings_version.major_version", + "groupings_minor_version": "groupings_version.minor_version", + "groupings_change_description": "groupings_version.change_description", + "groupings_start_date": "groupings_version.start_date", + "groupings_end_date": "groupings_version.end_date", + } + return groupings_version_key_map.get(key, key) + def get_activity_instance_overview( self, uid: str, version: str | None = None ) -> dict[str, Any]: @@ -930,78 +826,17 @@ def get_activity_instance_overview( | activity_instance_class_value]) AS activity_instance_class, [(activity_instance_root)-[versions:HAS_VERSION]->(:ActivityInstanceValue) | versions.version] as all_versions CALL { - WITH activity_instance_value - MATCH (activity_instance_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping) - // Get the latest activity version for this grouping - CALL { - WITH activity_grouping - MATCH (activity_grouping)<-[:HAS_GROUPING]-(av:ActivityValue)<-[hav:HAS_VERSION]-(ar:ActivityRoot) - WITH av, hav, ar - ORDER BY - toInteger(split(hav.version, '.')[0]) DESC, - toInteger(split(hav.version, '.')[1]) DESC, - hav.start_date DESC - WITH ar, collect(av) AS avs, collect(hav) AS havs - WITH ar, head(avs) AS activity_value, head(havs) AS latest_version - CALL { - WITH latest_version - OPTIONAL MATCH (author:User) - WHERE author.user_id = latest_version.author_id - RETURN author - } - RETURN ar.uid AS activity_uid, activity_value, - latest_version { .version, .status, .start_date, .end_date, author_username: coalesce(author.username, latest_version.author_id)} AS activity_version_info - } - WITH activity_grouping, activity_uid, activity_value, activity_version_info, - [(activity_value)<-[hav:HAS_VERSION]-(activity_root:ActivityRoot) | hav { .version, .status, .start_date, .end_date}] AS activity_versions, - head([(activity_value)<-[:HAS_VERSION]-(:ActivityRoot)<-[:CONTAINS_CONCEPT]-(library) | library.name]) AS activity_library_name - - // Get the latest subgroup version using subquery - CALL { - WITH activity_grouping - OPTIONAL MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(sgv:ActivitySubGroupValue)<-[sgv_rel:HAS_VERSION]-(sgr:ActivitySubGroupRoot) - WITH sgr, sgv, sgv_rel - ORDER BY - toInteger(split(sgv_rel.version, '.')[0]) DESC, - toInteger(split(sgv_rel.version, '.')[1]) DESC, - sgv_rel.start_date DESC - WITH sgr.uid AS subgroup_uid, - collect(sgv)[0] AS subgroup_value, - collect(sgv_rel { .version, .status, .start_date, .end_date})[0] AS subgroup_version - RETURN subgroup_uid, subgroup_value, subgroup_version - } - - // Get the latest group version using subquery - CALL { - WITH activity_grouping - OPTIONAL MATCH (activity_grouping)-[:HAS_SELECTED_GROUP]->(agv:ActivityGroupValue)<-[agv_rel:HAS_VERSION]-(agr:ActivityGroupRoot) - WITH agr, agv, agv_rel - ORDER BY - toInteger(split(agv_rel.version, '.')[0]) DESC, - toInteger(split(agv_rel.version, '.')[1]) DESC, - agv_rel.start_date DESC - WITH agr.uid AS group_uid, - collect(agv)[0] AS group_value, - collect(agv_rel { .version, .status, .start_date, .end_date})[0] AS group_version - RETURN group_uid, group_value, group_version - } - - WITH activity_grouping, { - uid: activity_uid, - activity_value: activity_value, - activity_versions: activity_versions, - activity_library_name: activity_library_name, - selected_activity_version: activity_version_info, - activity_subgroup_value: subgroup_value, - activity_subgroup_uid: subgroup_uid, - activity_subgroup_versions: CASE WHEN subgroup_version IS NULL THEN [] ELSE [subgroup_version] END, - selected_subgroup_version: subgroup_version, - activity_group_value: group_value, - activity_group_uid: group_uid, - activity_group_versions: CASE WHEN group_version IS NULL THEN [] ELSE [group_version] END, - selected_group_version: group_version - } AS hierarchy_item - RETURN collect(hierarchy_item) AS hierarchy + WITH activity_instance_root, has_version + MATCH (activity_instance_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)-[groupings_has_version:HAS_VERSION]->(:ActivityInstanceGroupingValue) + WHERE (groupings_has_version.start_date < coalesce(has_version.end_date, datetime()) + AND has_version.start_date < coalesce(groupings_has_version.end_date, datetime())) + WITH groupings_has_version + ORDER BY + toInteger(split(groupings_has_version.version, '.')[0]) DESC, + toInteger(split(groupings_has_version.version, '.')[1]) DESC, + groupings_has_version.start_date DESC + WITH collect(DISTINCT groupings_has_version.version) as groupings_versions + RETURN groupings_versions } WITH *, apoc.coll.toSet([(activity_instance_value)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item) @@ -1028,6 +863,7 @@ def get_activity_instance_overview( | {uid: unit_definition_root.uid, name: unit_definition_value.name, dimension_name: dimension_value.name} ], is_adam_param_specific: activity_item.is_adam_param_specific, + is_activity_instance_id_specific: activity_item.is_activity_instance_id_specific, text_value: activity_item.text_value } ]) AS activity_items @@ -1042,7 +878,7 @@ def get_activity_instance_overview( activity_instance_value, instance_library_name, activity_instance_class, - hierarchy, + groupings_versions, activity_items, has_version { .*, @@ -1069,23 +905,19 @@ def get_activity_instance_overview( overview_dict = {} for overview_prop, attribute_name in zip(overview, attribute_names): overview_dict[attribute_name] = overview_prop - for item in overview_dict["hierarchy"]: - # Use the selected versions from the subqueries - item["version"] = item.get("selected_activity_version") - item["activity_group_version"] = item.get("selected_group_version") - item["activity_subgroup_version"] = item.get("selected_subgroup_version") return overview_dict def get_cosmos_activity_instance_overview(self, uid: str) -> dict[str, Any]: query = """ MATCH (activity_instance_root:ActivityInstanceRoot {uid:$uid})-[:LATEST]->(activity_instance_value:ActivityInstanceValue) - WITH activity_instance_root,activity_instance_value, + MATCH (activity_instance_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)-[:LATEST]->(activity_instance_groupings_value:ActivityInstanceGroupingValue) + WITH activity_instance_root,activity_instance_value, activity_instance_groupings_value, head([(library)-[:CONTAINS_CONCEPT]->(activity_instance_root) | library.name]) AS instance_library_name, head([(activity_instance_value)-[:ACTIVITY_INSTANCE_CLASS]-> (activity_instance_class_root:ActivityInstanceClassRoot)-[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) | activity_instance_class_value.name]) AS activity_instance_class_name WITH *, - [(activity_instance_value)-[:HAS_ACTIVITY]->(:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue) | activity_subgroup_value.name] AS activity_subgroups, + [(activity_instance_groupings_value)-[:HAS_ACTIVITY]->(:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue) | activity_subgroup_value.name] AS activity_subgroups, apoc.coll.toSet([(activity_instance_value)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item) <-[HAS_ACTIVITY_ITEM]-(activity_item_class_root)-[:LATEST]->(activity_item_class_value) | { @@ -1126,7 +958,6 @@ def get_cosmos_activity_instance_overview(self, uid: str) -> dict[str, Any]: def generic_match_clause_all_versions(self): return """ MATCH (concept_root:ActivityInstanceRoot)-[version:HAS_VERSION]->(concept_value:ActivityInstanceValue) - -[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(activity_value:ActivityValue) """ def get_all_activity_instances_for_activity_grouping( @@ -1141,7 +972,8 @@ def get_all_activity_instances_for_activity_grouping( 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_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(:ActivityValue)<-[:HAS_VERSION]-(:ActivityRoot {uid:$activity_uid}) + MATCH (activity_instance_root)-[:HAS_GROUPING_ROOT]->(activity_instance_groupings_root:ActivityInstanceGroupingRoot)-[:LATEST_FINAL]->(activity_instance_groupings_value:ActivityInstanceGroupingValue) + MATCH (activity_instance_groupings_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(:ActivityValue)<-[:HAS_VERSION]-(:ActivityRoot {uid:$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 @@ -1186,10 +1018,41 @@ def specific_header_match_clause_lite(self, field_name: str) -> str | None: It should fetch only the required field, without supporting wildcard filtering. """ + if field_name in [ + "groupings_status", + "groupings_version", + "groupings_author_username", + "groupings_start_date", + "groupings_end_date", + ]: + groupings_value_alias = { + "groupings_status": "latest_groupings_version.status", + "groupings_version": "latest_groupings_version.version", + "groupings_author_username": "coalesce(author.username, latest_groupings_version.author_id)", + "groupings_start_date": "latest_groupings_version.start_date", + "groupings_end_date": "latest_groupings_version.end_date", + }[field_name] + return f""" + CALL {{ + WITH concept_root + MATCH (concept_root)-[:HAS_GROUPING_ROOT]->(groupings_root:ActivityInstanceGroupingRoot)-[groupings_has_version:HAS_VERSION]->(:ActivityInstanceGroupingValue) + WHERE (groupings_root)-[:LATEST]->(:ActivityInstanceGroupingValue) + WITH groupings_has_version + ORDER BY + toInteger(split(groupings_has_version.version, '.')[0]) DESC, + toInteger(split(groupings_has_version.version, '.')[1]) DESC, + groupings_has_version.start_date DESC + RETURN head(collect(groupings_has_version)) AS latest_groupings_version + }} + OPTIONAL MATCH (author:User) + WHERE author.user_id = latest_groupings_version.author_id + WITH concept_root, concept_value, {groupings_value_alias} AS {field_name} + """ + if field_name == "activity_name": return """ - WITH concept_value, - head([(concept_value)-[:HAS_ACTIVITY]->(activity_grouping)<-[:HAS_GROUPING]-(activity_value) | activity_value.name]) as activity_name + WITH concept_root, concept_value, + head([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(activity_grouping)<-[:HAS_GROUPING]-(activity_value) | activity_value.name]) as activity_name """ if field_name == "activity_instance_class.name": @@ -1201,3 +1064,1129 @@ def specific_header_match_clause_lite(self, field_name: str) -> str | None: """ return None + + +class ActivityInstanceAttributesRepository( + ConceptGenericRepository[ActivityInstanceAttributesAR] +): + root_class = ActivityInstanceRoot + value_class = ActivityInstanceValue + aggregate_class = ActivityInstanceAttributesAR + value_object_class = ActivityInstanceAttributesVO + return_model = ActivityInstanceAttributes + + def _create_new_value_node( + self, ar: ActivityInstanceAttributesAR + ) -> ActivityInstanceValue: + value_node: ActivityInstanceValue = super()._create_new_value_node(ar=ar) + value_node.is_research_lab = ar.concept_vo.is_research_lab + if ar.concept_vo.molecular_weight: + value_node.molecular_weight = ar.concept_vo.molecular_weight + if ar.concept_vo.topic_code: + value_node.topic_code = ar.concept_vo.topic_code + if ar.concept_vo.adam_param_code: + value_node.adam_param_code = ar.concept_vo.adam_param_code + value_node.is_required_for_activity = ar.concept_vo.is_required_for_activity + value_node.is_default_selected_for_activity = ( + ar.concept_vo.is_default_selected_for_activity + ) + value_node.is_data_sharing = ar.concept_vo.is_data_sharing + value_node.is_legacy_usage = ar.concept_vo.is_legacy_usage + value_node.is_derived = ar.concept_vo.is_derived + if ar.concept_vo.legacy_description: + value_node.legacy_description = ar.concept_vo.legacy_description + + value_node.save() + + activity_instance_class = ActivityInstanceClassRoot.nodes.get( + uid=ar.concept_vo.activity_instance_class_uid + ) + value_node.activity_instance_class.connect(activity_instance_class) + + for item in ar.concept_vo.activity_items: + activity_item_class = ActivityItemClassRoot.nodes.get_or_none( + uid=item.activity_item_class_uid + ) + is_adam_param_specific = ( + item.is_adam_param_specific + if getattr( + activity_item_class.has_activity_instance_class.relationship( + activity_instance_class + ), + "is_adam_param_specific_enabled", + False, + ) + else False + ) + activity_item_node = ActivityItem( + is_adam_param_specific=is_adam_param_specific, + is_activity_instance_id_specific=item.is_activity_instance_id_specific, + text_value=item.text_value, + ) + activity_item_node.save() + activity_item_node.has_activity_item_class.connect(activity_item_class) + + for term in item.ct_terms: + ct_term_root = CTTermRoot.nodes.get_or_none(uid=term.uid) + selected_term_node = ( + CTCodelistAttributesRepository().get_or_create_selected_term( + ct_term_root, + codelist_uid=term.codelist_uid, + ) + ) + activity_item_node.has_ct_term.connect(selected_term_node) + + if item.ct_codelist: + codelist = CTCodelistRoot.nodes.get_or_none(uid=item.ct_codelist.uid) + activity_item_node.has_codelist.connect(codelist) + + for unit in item.unit_definitions: + unit_definition = UnitDefinitionRoot.nodes.get_or_none(uid=unit.uid) + activity_item_node.has_unit_definition.connect(unit_definition) + + value_node.contains_activity_item.connect(activity_item_node) + return value_node + + def _has_item_data_changed(self, ar_items, value_item_nodes): + ar_activity_items = [] + for item in ar_items: + ar_activity_items.append( + { + "is_adam_param_specific": item.is_adam_param_specific, + "is_activity_instance_id_specific": item.is_activity_instance_id_specific, + "class": item.activity_item_class_uid, + "units": {unit.uid for unit in item.unit_definitions}, + "terms": {(term.uid, term.codelist_uid) for term in item.ct_terms}, + "text_value": item.text_value, + "ct_codelist": item.ct_codelist.uid if item.ct_codelist else None, + } + ) + + value_activity_items = [] + for activity_item_node in value_item_nodes: + item_class_uid = activity_item_node.has_activity_item_class.get().uid + unit_nodes = activity_item_node.has_unit_definition.all() + ct_terms = [ + { + "uid": term_context.has_selected_term.single().uid, + "codelist_uid": term_context.has_selected_codelist.single().uid, + } + for term_context in activity_item_node.has_ct_term.all() + ] + codelist_node = activity_item_node.has_codelist.get_or_none() + + value_activity_items.append( + { + "is_adam_param_specific": activity_item_node.is_adam_param_specific, + "is_activity_instance_id_specific": activity_item_node.is_activity_instance_id_specific, + "class": item_class_uid, + "units": {unit_node.uid for unit_node in unit_nodes}, + "terms": { + (ct_term["uid"], ct_term["codelist_uid"]) + for ct_term in ct_terms + }, + "text_value": activity_item_node.text_value, + "ct_codelist": codelist_node.uid if codelist_node else None, + } + ) + for item in ar_activity_items: + if item not in value_activity_items: + return True + for item in value_activity_items: + if item not in ar_activity_items: + return True + return False + + def _has_data_changed( + self, ar: ActivityInstanceAttributesAR, value: ActivityInstanceValue + ) -> bool: + are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_props_changed = ( + ar.concept_vo.molecular_weight != value.molecular_weight + or ar.concept_vo.topic_code != value.topic_code + or ar.concept_vo.adam_param_code != value.adam_param_code + or bool(ar.concept_vo.is_research_lab) != bool(value.is_research_lab) + or bool(ar.concept_vo.is_required_for_activity) + != bool(value.is_required_for_activity) + or bool(ar.concept_vo.is_default_selected_for_activity) + != bool(value.is_default_selected_for_activity) + or bool(ar.concept_vo.is_data_sharing) != bool(value.is_data_sharing) + or bool(ar.concept_vo.is_legacy_usage) != bool(value.is_legacy_usage) + or bool(ar.concept_vo.is_derived) != bool(value.is_derived) + or ar.concept_vo.legacy_description != value.legacy_description + ) + + item_data_changed = self._has_item_data_changed( + ar.concept_vo.activity_items, value.contains_activity_item.all() + ) + + are_rels_changed = ( + ar.concept_vo.activity_instance_class_uid + != value.activity_instance_class.get().uid + or item_data_changed + ) + return are_concept_properties_changed or are_props_changed or are_rels_changed + + def _create_aggregate_root_instance_from_cypher_result( + self, input_dict: dict[str, Any] + ) -> ActivityInstanceAttributesAR: + major, minor = input_dict["version"].split(".") + activity_instance_ar = self.aggregate_class.from_repository_values( + uid=input_dict["uid"], + concept_vo=self.value_object_class.from_repository_values( + nci_concept_id=input_dict.get("nci_concept_id"), + nci_concept_name=input_dict.get("nci_concept_name"), + name=input_dict["name"], + name_sentence_case=input_dict["name_sentence_case"], + activity_instance_class_uid=input_dict.get( + "activity_instance_class" + ).get("uid"), + activity_instance_class_name=input_dict.get( + "activity_instance_class" + ).get("name"), + definition=input_dict["definition"], + abbreviation=input_dict.get("abbreviation"), + is_research_lab=input_dict.get("is_research_lab", False), + molecular_weight=input_dict.get("molecular_weight"), + topic_code=input_dict["topic_code"], + adam_param_code=input_dict.get("adam_param_code"), + is_required_for_activity=input_dict.get( + "is_required_for_activity", False + ), + is_default_selected_for_activity=input_dict.get( + "is_default_selected_for_activity", False + ), + is_data_sharing=input_dict.get("is_data_sharing", False), + is_legacy_usage=input_dict.get("is_legacy_usage", False), + is_derived=input_dict.get("is_derived", False), + legacy_description=input_dict.get("legacy_description"), + activity_items=[ + ActivityItemVO.from_repository_values( + is_adam_param_specific=activity_item.get( + "is_adam_param_specific" + ), + activity_item_class_uid=activity_item.get( + "activity_item_class_uid" + ), + activity_item_class_name=activity_item.get( + "activity_item_class_name" + ), + ct_terms=[ + CTTermItem( + uid=term["uid"], + name=term["name"], + codelist_uid=term["codelist_uid"], + ) + for term in activity_item.get("ct_terms") + ], + ct_codelist=( + CTCodelistItem( + uid=activity_item.get("ct_codelist", {}).get("uid"), + name=activity_item.get("ct_codelist", {}).get("name"), + ) + if activity_item.get("ct_codelist") + else None + ), + unit_definitions=[ + CompactUnitDefinition( + uid=unit["uid"], + name=unit["name"], + dimension_name=unit["dimension_name"], + ) + for unit in activity_item.get("unit_definitions") + ], + is_activity_instance_id_specific=activity_item.get( + "is_activity_instance_id_specific" + ), + ) + for activity_item in input_dict.get("activity_items", []) + ], + ), + library=LibraryVO.from_input_values_2( + library_name=input_dict["library_name"], + is_library_editable_callback=( + lambda _: input_dict["is_library_editable"] + ), + ), + item_metadata=LibraryItemMetadataVO.from_repository_values( + change_description=input_dict["change_description"], + status=LibraryItemStatus(input_dict.get("status")), + author_id=input_dict["author_id"], + author_username=input_dict.get("author_username"), + start_date=convert_to_datetime(value=input_dict["start_date"]), + end_date=convert_to_datetime(value=input_dict.get("end_date")), + major_version=int(major), + minor_version=int(minor), + ), + ) + return activity_instance_ar + + def _create_aggregate_root_instance_from_version_root_relationship_and_value( + self, + root: ActivityInstanceRoot, + library: Library, + relationship: VersionRelationship, + value: ActivityInstanceValue, + **_kwargs, + ) -> ActivityInstanceAttributesAR: + activity_instance_class = value.activity_instance_class.get() + activity_items = value.contains_activity_item.all() + activity_item_vos = [] + for activity_item in activity_items: + activity_item_class_root = ( + activity_item.has_activity_item_class.get_or_none() + ) + ct_terms = [] + unit_definitions = [] + for unit in activity_item.has_unit_definition.all(): + if ( + ct_dimension := unit.has_version.single() + .has_ct_dimension.single() + .has_selected_term.single() + ): + dimension_name = ( + ct_dimension.has_name_root.single() + .has_latest_value.single() + .name + ) + else: + dimension_name = None + + unit_definitions.append( + CompactUnitDefinition( + uid=unit.uid, + name=unit.has_version.single().name, + dimension_name=dimension_name, + ) + ) + for term_context in activity_item.has_ct_term.all(): + term_root = term_context.has_selected_term.single() + ct_terms.append( + CTTermItem( + uid=term_root.uid, + name=term_root.has_name_root.single().has_version.single().name, + codelist_uid=term_context.has_selected_codelist.single().uid, + ) + ) + if codelist := activity_item.has_codelist.get_or_none(): + name_root = codelist.has_name_root.get() + name_value = name_root.has_latest_value.get() + ct_codelist = CTCodelistItem(uid=codelist.uid, name=name_value.name) + else: + ct_codelist = None + activity_item_vos.append( + ActivityItemVO.from_repository_values( + is_adam_param_specific=activity_item.is_adam_param_specific, + activity_item_class_uid=activity_item_class_root.uid, + activity_item_class_name=activity_item_class_root.has_latest_value.get_or_none().name, + ct_terms=ct_terms, + ct_codelist=ct_codelist, + unit_definitions=unit_definitions, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, + ) + ) + + return self.aggregate_class.from_repository_values( + uid=root.uid, + concept_vo=self.value_object_class.from_repository_values( + nci_concept_id=value.nci_concept_id, + nci_concept_name=value.nci_concept_name, + name=value.name, + name_sentence_case=value.name_sentence_case, + activity_instance_class_uid=activity_instance_class.uid, + activity_instance_class_name=activity_instance_class.has_latest_value.get().name, + definition=value.definition, + abbreviation=value.abbreviation, + is_research_lab=( + value.is_research_lab if value.is_research_lab else False + ), + molecular_weight=value.molecular_weight, + topic_code=value.topic_code, + adam_param_code=value.adam_param_code, + is_required_for_activity=( + value.is_required_for_activity + if value.is_required_for_activity + else False + ), + is_default_selected_for_activity=( + value.is_default_selected_for_activity + if value.is_default_selected_for_activity + else False + ), + is_data_sharing=( + value.is_data_sharing if value.is_data_sharing else False + ), + is_legacy_usage=( + value.is_legacy_usage if value.is_legacy_usage else False + ), + is_derived=value.is_derived if value.is_derived else False, + legacy_description=value.legacy_description, + activity_items=activity_item_vos, + ), + library=LibraryVO.from_input_values_2( + library_name=library.name, + is_library_editable_callback=lambda _: library.is_editable, + ), + item_metadata=self._library_item_metadata_vo_from_relation(relationship), + ) + + def _create_ar( + self, + root: ActivityInstanceRoot, + library: Library, + relationship: VersionRelationship, + value: ActivityInstanceValue, + **_kwargs, + ) -> ActivityInstanceAttributesAR: + activity_instance_objects = _kwargs["activity_instance_root"] + activity_instance_class = activity_instance_objects["activity_instance_class"] + activity_item_vos = [] + for activity_item in activity_instance_objects["activity_items"]: + ct_terms = [] + unit_definitions = [] + for unit in activity_item["unit_definitions"]: + unit_definitions.append( + CompactUnitDefinition( + uid=unit["uid"], + name=unit["name"], + ) + ) + for term in activity_item["ct_terms"]: + ct_terms.append( + CTTermItem( + uid=term["uid"], + name=term["name"], + codelist_uid=term["codelist_uid"], + ) + ) + if codelist := activity_item.has_codelist.get_or_none(): + name_root = codelist.has_name_root.get() + name_value = name_root.has_latest_value.get() + ct_codelist = CTCodelistItem(uid=codelist.uid, name=name_value.name) + else: + ct_codelist = None + activity_item_vos.append( + ActivityItemVO.from_repository_values( + is_adam_param_specific=activity_item["is_adam_param_specific"], + activity_item_class_uid=activity_item["activity_item_class_uid"], + activity_item_class_name=activity_item["activity_item_class_name"], + ct_terms=ct_terms, + ct_codelist=ct_codelist, + unit_definitions=unit_definitions, + is_activity_instance_id_specific=activity_item.get( + "is_activity_instance_id_specific" + ), + ) + ) + + return self.aggregate_class.from_repository_values( + uid=root.uid, + concept_vo=self.value_object_class.from_repository_values( + nci_concept_id=value.nci_concept_id, + nci_concept_name=value.nci_concept_name, + name=value.name, + name_sentence_case=value.name_sentence_case, + activity_instance_class_uid=activity_instance_class[ + "activity_instance_class_uid" + ], + activity_instance_class_name=activity_instance_class[ + "activity_instance_class_name" + ], + definition=value.definition, + abbreviation=value.abbreviation, + is_research_lab=( + value.is_research_lab if value.is_research_lab else False + ), + molecular_weight=value.molecular_weight, + topic_code=value.topic_code, + adam_param_code=value.adam_param_code, + is_required_for_activity=( + value.is_required_for_activity + if value.is_required_for_activity + else False + ), + is_default_selected_for_activity=( + value.is_default_selected_for_activity + if value.is_default_selected_for_activity + else False + ), + is_data_sharing=( + value.is_data_sharing if value.is_data_sharing else False + ), + is_legacy_usage=( + value.is_legacy_usage if value.is_legacy_usage else False + ), + is_derived=value.is_derived if value.is_derived else False, + legacy_description=value.legacy_description, + activity_items=activity_item_vos, + ), + library=LibraryVO.from_input_values_2( + library_name=library.name, + is_library_editable_callback=lambda _: library.is_editable, + ), + item_metadata=self._library_item_metadata_vo_from_relation(relationship), + ) + + def specific_alias_clause(self, **kwargs) -> str: + return """ + WITH *, + concept_value.nci_concept_name AS nci_concept_name, + concept_value.molecular_weight AS molecular_weight, + concept_value.topic_code AS topic_code, + concept_value.adam_param_code AS adam_param_code, + coalesce(concept_value.is_research_lab, false) AS is_research_lab, + coalesce(concept_value.is_required_for_activity, false) AS is_required_for_activity, + coalesce(concept_value.is_default_selected_for_activity, false) AS is_default_selected_for_activity, + coalesce(concept_value.is_data_sharing, false) AS is_data_sharing, + coalesce(concept_value.is_legacy_usage, false) AS is_legacy_usage, + coalesce(concept_value.is_derived, false) AS is_derived, + concept_value.legacy_description AS legacy_description, + + head([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]-> + (activity_instance_class_root:ActivityInstanceClassRoot)-[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) + | {uid:activity_instance_class_root.uid, name:activity_instance_class_value.name}]) AS activity_instance_class, + [(concept_value)-[:CONTAINS_ACTIVITY_ITEM]->(activity_item:ActivityItem) + <-[:HAS_ACTIVITY_ITEM]-(activity_item_class_root:ActivityItemClassRoot)-[:LATEST]-> + (activity_item_class_value:ActivityItemClassValue) + | { + activity_item_class_uid: activity_item_class_root.uid, + activity_item_class_name: activity_item_class_value.name, + ct_terms: COLLECT { + MATCH (activity_item)-[:HAS_CT_TERM]->(ct_term_context:CTTermContext) + -[:HAS_SELECTED_TERM]->(term_root:CTTermRoot) + -[:HAS_NAME_ROOT]->(term_name_root:CTTermNameRoot) + -[:LATEST]->(term_name_value:CTTermNameValue) + MATCH (ct_term_context)-[:HAS_SELECTED_CODELIST]->(codelist_root:CTCodelistRoot) + MATCH (ct_codelist_term:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root) + RETURN {uid: term_root.uid, name: term_name_value.name, codelist_uid: codelist_root.uid, submission_value: ct_codelist_term.submission_value} + }, + unit_definitions: [(activity_item)-[:HAS_UNIT_DEFINITION]->(unit_definition_root:UnitDefinitionRoot)-[:LATEST]->(unit_definition_value:UnitDefinitionValue)-[:HAS_CT_DIMENSION]-(:CTTermRoot)-[:HAS_NAME_ROOT]->(CTTermNamesRoot)-[:LATEST]->(dimension_value:CTTermNameValue) | {uid: unit_definition_root.uid, name: unit_definition_value.name, dimension_name: dimension_value.name}], + is_adam_param_specific: activity_item.is_adam_param_specific, + is_activity_instance_id_specific: activity_item.is_activity_instance_id_specific + }] AS activity_items + """ + + def create_query_filter_statement( + self, library: str | None = None, **kwargs + ) -> tuple[str, dict[Any, Any]]: + ( + filter_statements_from_concept, + filter_query_parameters, + ) = super().create_query_filter_statement(library=library, **kwargs) + filter_parameters = [] + if kwargs.get("activity_instance_names") is not None: + activity_instance_names = kwargs.get("activity_instance_names") + filter_by_activity_instance_names = ( + "concept_value.name IN $activity_instance_names" + ) + filter_parameters.append(filter_by_activity_instance_names) + filter_query_parameters["activity_instance_names"] = activity_instance_names + + if kwargs.get("activity_instance_class_names") is not None: + instance_class_names = kwargs.get("activity_instance_class_names") + filter_by_instance_classes = ( + "size([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)" + "-[:LATEST]->(instance_class_value:ActivityInstanceClassValue)" + "WHERE instance_class_value.name IN $activity_instance_class_names | instance_class_value.name]) > 0" + ) + filter_parameters.append(filter_by_instance_classes) + filter_query_parameters["activity_instance_class_names"] = ( + instance_class_names + ) + extended_filter_statements = " AND ".join(filter_parameters) + if filter_statements_from_concept != "": + if len(extended_filter_statements) > 0: + filter_statements_to_return = " AND ".join( + [filter_statements_from_concept, extended_filter_statements] + ) + else: + filter_statements_to_return = filter_statements_from_concept + else: + filter_statements_to_return = ( + "WHERE " + extended_filter_statements + if len(extended_filter_statements) > 0 + else "" + ) + return filter_statements_to_return, filter_query_parameters + + def generic_match_clause_all_versions(self): + return """ + MATCH (concept_root:ActivityInstanceRoot)-[version:HAS_VERSION]->(concept_value:ActivityInstanceValue) + """ + + +class ActivityInstanceGroupingsRepository( + ConceptGenericRepository[ActivityInstanceGroupingsAR] +): + root_class = ActivityInstanceGroupingRoot + parent_root_class = ActivityInstanceRoot + parent_root_relationship = "has_grouping_root" + value_class = ActivityInstanceGroupingValue + aggregate_class = ActivityInstanceGroupingsAR + value_object_class = ActivityInstanceGroupingsVO + return_model = ActivityInstanceGroupings + + def _has_uid_and_library_on_parent_root(self) -> bool: + return True + + def _lock_object(self, uid: str) -> None: + itm = self.parent_root_class.nodes.get_or_none(uid=uid) + if itm is not None: + itm.__WRITE_LOCK__ = None + itm.save() + + def copy_activity_instance_groupings_and_recreate( + self, + activity_instance_groupings: ActivityInstanceGroupingsAR, + author_id: str, + ) -> None: + """ + Creates a new ActivityInstanceGroupingValue node by cloning the current one, + updates the versioning relationships, and links the new value node to the + correct ActivityGrouping nodes. + + This is used during cascade edits to persist new groupings versions + without requiring repository_closure_data (which ActivityInstanceGroupingsAR + does not have). + """ + status = activity_instance_groupings.item_metadata.status.value + query = """ + MATCH (parent_root:ActivityInstanceRoot {uid: $activity_instance_uid}) + -[:HAS_GROUPING_ROOT]->(concept_root:ActivityInstanceGroupingRoot) + -[status_relationship:LATEST]->(concept_value:ActivityInstanceGroupingValue) + CALL apoc.refactor.cloneNodes([concept_value]) + YIELD input, output, error + + WITH parent_root, concept_root, concept_value, output, status_relationship + + MATCH (concept_root)-[latest_has_version:HAS_VERSION]->(concept_value) + WHERE latest_has_version.end_date IS NULL + """ + query += f""" + MATCH (concept_root)-[latest_status_relationship:LATEST_{status.upper()}]->(:{self.value_class.__label__}) + WITH parent_root, concept_root, concept_value, output, status_relationship, + latest_has_version, latest_status_relationship + + MERGE (concept_root)-[:LATEST]->(output) + MERGE (concept_root)-[:LATEST_{status.upper()}]->(output) + MERGE (concept_root)-[new_has_version:HAS_VERSION]->(output) + + SET new_has_version.start_date = $start_date + SET new_has_version.end_date = null + SET new_has_version.change_description = $change_description + SET new_has_version.version = $new_version + SET new_has_version.status = $new_status + SET new_has_version.author_id = $author_id + SET latest_has_version.end_date = $start_date + + WITH parent_root, concept_root, concept_value, output, status_relationship, latest_status_relationship + DELETE status_relationship, latest_status_relationship + + WITH parent_root, concept_root, concept_value, output + + // Remove cloned HAS_ACTIVITY relationships from the new value node + // (they were copied by cloneNodes but point to old ActivityGrouping nodes) + OPTIONAL MATCH (output)-[old_rel:HAS_ACTIVITY]->() + DELETE old_rel + + WITH parent_root, concept_root, output + + // Link new value node to the correct ActivityGrouping nodes + UNWIND range(0, size($activity_uids)-1) AS idx + MATCH (activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(:ActivityValue)<-[:LATEST_FINAL]-(:ActivityRoot {{uid: $activity_uids[idx]}}) + MATCH (activity_grouping)-[:HAS_SELECTED_GROUP]->(:ActivityGroupValue)<-[:HAS_VERSION]-(:ActivityGroupRoot {{uid: $activity_group_uids[idx]}}) + MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(:ActivitySubGroupValue)<-[:HAS_VERSION]-(:ActivitySubGroupRoot {{uid: $activity_subgroup_uids[idx]}}) + WITH output, activity_grouping + MERGE (output)-[:HAS_ACTIVITY]->(activity_grouping) + RETURN output + """ + + db.cypher_query( + query, + params={ + "activity_instance_uid": activity_instance_groupings.uid, + "new_status": status, + "new_version": activity_instance_groupings.item_metadata.version, + "start_date": datetime.datetime.now(datetime.timezone.utc), + "change_description": "Cascade edit: updating activity instance groupings", + "author_id": author_id, + "activity_uids": [ + grouping.activity_uid + for grouping in activity_instance_groupings.concept_vo.activity_groupings + ], + "activity_subgroup_uids": [ + grouping.activity_subgroup_uid + for grouping in activity_instance_groupings.concept_vo.activity_groupings + ], + "activity_group_uids": [ + grouping.activity_group_uid + for grouping in activity_instance_groupings.concept_vo.activity_groupings + ], + }, + ) + + def generic_match_clause(self, **kwargs): + concept_label = self.root_class.__label__ + parent_root_label = self.parent_root_class.__label__ + concept_value_label = self.value_class.__label__ + + version = kwargs.get("version", None) + rel = ( + "hv:HAS_VERSION WHERE hv.version = $requested_version" + if version is not None + else ":LATEST" + ) + + return f"""CYPHER runtime=slotted MATCH (parent_root:{parent_root_label})-[:HAS_GROUPING_ROOT]->(concept_root:{concept_label})-[{rel}]->(concept_value:{concept_value_label})""" + + def generic_alias_clause(self, **kwargs): + version = kwargs.get("version", None) + where_version = ( + "WHERE hv.version = $requested_version" if version is not None else "" + ) + + return f""" + DISTINCT parent_root, concept_root, concept_value, + head([(library)-[:CONTAINS_CONCEPT]->(parent_root) | library]) AS library + CALL {{ + WITH concept_root, concept_value + MATCH (concept_root)-[hv:HAS_VERSION]-(concept_value) + {where_version} + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.end_date ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS version_rel + }} + WITH + parent_root, + concept_root, + parent_root.uid AS uid, + concept_value as concept_value, + library, + version_rel + CALL {{ + WITH version_rel + OPTIONAL MATCH (author: User) + WHERE author.user_id = version_rel.author_id + RETURN author + }} + WITH + uid, + parent_root, + concept_root, + library, + library.name AS library_name, + library.is_editable AS is_library_editable, + version_rel.start_date AS start_date, + version_rel.end_date AS end_date, + version_rel.status AS status, + version_rel.version AS version, + version_rel.change_description AS change_description, + version_rel.author_id AS author_id, + coalesce(author.username, version_rel.author_id) AS author_username, + concept_value + """ + + def generic_alias_clause_all_versions(self): + return """ + DISTINCT parent_root, concept_root, concept_value, + head([(library)-[:CONTAINS_CONCEPT]->(parent_root) | library]) AS library + CALL { + WITH parent_root, concept_root, concept_value + MATCH (concept_root)-[hv:HAS_VERSION]-(concept_value) + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.end_date ASC, + hv.start_date ASC + RETURN hv AS version_rel + } + WITH + parent_root, + concept_root, + parent_root.uid AS uid, + concept_value as concept_value, + library.name AS library_name, + library.is_editable AS is_library_editable, + version_rel + CALL { + WITH version_rel + OPTIONAL MATCH (author: User) + WHERE author.user_id = version_rel.author_id + RETURN author + } + WITH + uid, + parent_root, + concept_root, + library_name, + is_library_editable, + version_rel.start_date AS start_date, + version_rel.end_date AS end_date, + version_rel.status AS status, + version_rel.version AS version, + version_rel.change_description AS change_description, + version_rel.author_id AS author_id, + coalesce(author.username, version_rel.author_id) AS author_username, + concept_value + """ + + 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) + root: VersionRoot | None = parent_root.has_grouping_root.get() + except NodeClassNotDefined as exc: + raise NotFoundException( + msg="Resource doesn't exist - it was likely deleted in a concurrent transaction." + ) from exc + if parent_root is None: + return None, None + library: Library | None + if self.has_library: + library = parent_root.has_library.get() + else: + library = None + return root, library + + def _maintain_parameters( + self, + versioned_object, + root: VersionRoot, + value: VersionValue, + ) -> None: + # No parameters to maintain for ActivityInstanceGroupings + pass + + def _create_new_value_node( + self, ar: ActivityInstanceGroupingsAR + ) -> ActivityInstanceGroupingValue: + value_node = ActivityInstanceGroupingValue() + value_node.save() + + activity_uids = {ag.activity_uid for ag in ar.concept_vo.activity_groupings} + BusinessLogicException.raise_if( + len(activity_uids) > 1, + msg="Instances are not allowed to link to several different activities", + ) + requested = ActivityRoot.nodes.filter( + uid=next(iter(activity_uids)), + has_library__name=settings.requested_library_name, + ) + BusinessLogicException.raise_if( + len(requested) > 0, + msg="Activity instances are not allowed to link to activity requests or placeholders", + ) + + for activity_grouping in ar.concept_vo.activity_groupings: + # find related ActivityGrouping node + activity_grouping_node = ListDistinct( + ActivityGrouping.nodes.filter( + has_selected_group__has_version__uid=activity_grouping.activity_group_uid, + has_selected_subgroup__has_version__uid=activity_grouping.activity_subgroup_uid, + has_grouping__latest_final__uid=activity_grouping.activity_uid, + ).resolve_subgraph() + ).distinct() + BusinessLogicException.raise_if( + len(activity_grouping_node) == 0, + msg=f"The ActivityGrouping node wasn't found for Activity Subgroup with UID '{activity_grouping.activity_subgroup_uid}'" + f" and Activity Group with UID '{activity_grouping.activity_group_uid}'.", + ) + activity_grouping_node = activity_grouping_node[0] + # link ActivityInstanceValue with ActivityGrouping node + value_node.has_activity.connect(activity_grouping_node) + + return value_node + + def _has_grouping_data_changed(self, ar_groupings, activity_instance_value): + value_group_pairs = [] + for activity_grouping_node in activity_instance_value.has_activity.all(): + if not activity_grouping_node.has_grouping.get().has_latest_value.single(): + # The linked ActivityValue is not the latest. + # We need to return True, so that the ActivityInstanceValue + # gets updated to use the new ActivityValue. + return True + value_group_pairs.append( + ( + activity_grouping_node.has_grouping.get().has_version.single().uid, + activity_grouping_node.has_selected_group.get() + .has_version.single() + .uid, + activity_grouping_node.has_selected_subgroup.get() + .has_version.single() + .uid, + ) + ) + + ar_group_pairs = [ + ( + grouping.activity_uid, + grouping.activity_subgroup_uid, + grouping.activity_group_uid, + ) + for grouping in ar_groupings + ] + for pair in ar_group_pairs: + if pair not in value_group_pairs: + return True + for pair in value_group_pairs: + if pair not in ar_group_pairs: + return True + return False + + def _has_data_changed( + self, ar: ActivityInstanceGroupingsAR, value: ActivityInstanceGroupingValue + ) -> bool: + # are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + + # Is this a final version? If yes, we skip the grouping data check + # to avoid creating new values nodes when just creating a new draft. + root_for_final_value = value.has_version.match( + status__in=[LibraryItemStatus.FINAL.value, LibraryItemStatus.RETIRED.value], + end_date__isnull=True, + ) + + if not root_for_final_value: + grouping_data_changed = self._has_grouping_data_changed( + ar.concept_vo.activity_groupings, value + ) + else: + grouping_data_changed = False + + return grouping_data_changed + + def _create_aggregate_root_instance_from_cypher_result( + self, input_dict: dict[str, Any] + ) -> ActivityInstanceGroupingsAR: + major, minor = input_dict["version"].split(".") + activity_instance_ar = self.aggregate_class.from_repository_values( + uid=input_dict["uid"], + library=LibraryVO.from_input_values_2( + library_name=input_dict["library_name"], + is_library_editable_callback=lambda _: input_dict[ + "is_library_editable" + ], + ), + concept_vo=self.value_object_class.from_repository_values( + activity_groupings=[ + ActivityInstanceGroupingVO( + activity_group_uid=activity_grouping.get("activity_group").get( + "uid" + ), + activity_group_name=activity_grouping.get("activity_group").get( + "name" + ), + activity_group_version=f"{activity_grouping.get('activity_group').get('major_version')}.{activity_grouping.get('activity_group').get('minor_version')}", + activity_subgroup_uid=activity_grouping.get( + "activity_subgroup" + ).get("uid"), + activity_subgroup_name=activity_grouping.get( + "activity_subgroup" + ).get("name"), + activity_subgroup_version=f"{activity_grouping.get('activity_subgroup').get('major_version')}.{activity_grouping.get('activity_subgroup').get('minor_version')}", + activity_uid=activity_grouping.get("activity").get("uid"), + activity_name=activity_grouping.get("activity").get("name"), + activity_version=f"{activity_grouping.get('activity').get('major_version')}.{activity_grouping.get('activity').get('minor_version')}", + ) + for activity_grouping in input_dict.get("activity_groupings") + ], + activity_name=input_dict.get("activity_name"), + ), + item_metadata=LibraryItemMetadataVO.from_repository_values( + change_description=input_dict["change_description"], + status=LibraryItemStatus(input_dict.get("status")), + author_id=input_dict["author_id"], + author_username=input_dict.get("author_username"), + start_date=convert_to_datetime(value=input_dict["start_date"]), + end_date=convert_to_datetime(value=input_dict.get("end_date")), + major_version=int(major), + minor_version=int(minor), + ), + ) + return activity_instance_ar + + def _create_aggregate_root_instance_from_version_root_relationship_and_value( + self, + root: ActivityInstanceGroupingRoot, + library: Library, + relationship: VersionRelationship, + value: ActivityInstanceGroupingValue, + **_kwargs, + ) -> ActivityInstanceGroupingsAR: + + parent_root = root.has_grouping_root.single() + activity_groupings_nodes = value.has_activity.all() + + activity_groupings = [] + activity_name = None + for activity_grouping in activity_groupings_nodes: + activity_value_node = activity_grouping.has_grouping.get() + # 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 + # 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) + ) + # ActivityGroup + activity_group_value = activity_grouping.has_selected_group.get() + activity_group_root = activity_group_value.has_version.single() + all_group_rels = activity_group_value.has_version.all_relationships( + activity_group_root + ) + latest_group = max( + all_group_rels, key=lambda r: version_string_to_tuple(r.version) + ) + # ActivitySubGroup + activity_subgroup_value = activity_grouping.has_selected_subgroup.get() + activity_subgroup_root = activity_subgroup_value.has_version.single() + all_subgroup_rels = activity_subgroup_value.has_version.all_relationships( + activity_subgroup_root + ) + latest_subgroup = max( + all_subgroup_rels, key=lambda r: version_string_to_tuple(r.version) + ) + + activity_groupings.append( + ActivityInstanceGroupingVO( + activity_group_uid=activity_group_root.uid, + activity_group_version=latest_group.version, + activity_subgroup_uid=activity_subgroup_root.uid, + activity_subgroup_version=latest_subgroup.version, + activity_uid=activity_root.uid, + activity_version=latest_activity.version, + ) + ) + + return self.aggregate_class.from_repository_values( + uid=parent_root.uid, + library=LibraryVO.from_input_values_2( + library_name=library.name, + is_library_editable_callback=lambda _: library.is_editable, + ), + concept_vo=self.value_object_class.from_repository_values( + activity_groupings=activity_groupings, + activity_name=activity_name, + ), + item_metadata=self._library_item_metadata_vo_from_relation(relationship), + ) + + def specific_alias_clause(self, **kwargs) -> str: + return """ + WITH *, + head([(concept_root)-[:LATEST]->(groupings_value:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping)<-[:HAS_GROUPING]-(activity_value) | activity_value.name]) as activity_name, + apoc.coll.toSet([(concept_root)-[:LATEST]->(groupings_value:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping) + | { + activity: head(apoc.coll.sortMulti([(activity_grouping)<-[:HAS_GROUPING]-(activity_value:ActivityValue)<-[has_version:HAS_VERSION]- + (activity_root:ActivityRoot) | + { + uid: activity_root.uid, + name: activity_value.name, + major_version: toInteger(split(has_version.version,'.')[0]), + minor_version: toInteger(split(has_version.version,'.')[1]) + }], ['major_version', 'minor_version'])), + activity_subgroup: head(apoc.coll.sortMulti([(activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue)<-[has_version:HAS_VERSION]- + (activity_subgroup_root:ActivitySubGroupRoot) | + { + uid: activity_subgroup_root.uid, + name: activity_subgroup_value.name, + major_version: toInteger(split(has_version.version,'.')[0]), + minor_version: toInteger(split(has_version.version,'.')[1]) + }], ['major_version', 'minor_version'])), + activity_group: head(apoc.coll.sortMulti([(activity_grouping)-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue)<-[has_version:HAS_VERSION]- + (activity_group_root:ActivityGroupRoot) | + { + uid: activity_group_root.uid, + name: activity_group_value.name, + major_version: toInteger(split(has_version.version,'.')[0]), + minor_version: toInteger(split(has_version.version,'.')[1]) + }], ['major_version', 'minor_version'])) + }]) AS activity_groupings + """ + + def create_query_filter_statement( + self, library: str | None = None, **kwargs + ) -> tuple[str, dict[Any, Any]]: + ( + filter_statements_from_concept, + filter_query_parameters, + ) = super().create_query_filter_statement(library=library, **kwargs) + filter_parameters = [] + if kwargs.get("activity_instance_names") is not None: + activity_instance_names = kwargs.get("activity_instance_names") + filter_by_activity_instance_names = ( + "concept_value.name IN $activity_instance_names" + ) + filter_parameters.append(filter_by_activity_instance_names) + filter_query_parameters["activity_instance_names"] = activity_instance_names + if kwargs.get("activity_names") is not None: + activity_names = kwargs.get("activity_names") + filter_by_activity_names = ( + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)" + "-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)" + "<-[:HAS_GROUPING]-(activity_value:ActivityValue) " + "WHERE activity_value.name IN $activity_names | activity_value.name]) > 0" + ) + filter_parameters.append(filter_by_activity_names) + filter_query_parameters["activity_names"] = activity_names + if kwargs.get("activity_subgroup_names") is not None: + activity_subgroup_names = kwargs.get("activity_subgroup_names") + filter_by_activity_subgroup_names = ( + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)" + "-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)" + "-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue) " + "WHERE activity_subgroup_value.name IN $activity_subgroup_names | activity_subgroup_value.name]) > 0" + ) + filter_parameters.append(filter_by_activity_subgroup_names) + filter_query_parameters["activity_subgroup_names"] = activity_subgroup_names + if kwargs.get("activity_group_names") is not None: + activity_group_names = kwargs.get("activity_group_names") + filter_by_activity_group_names = ( + "size([(concept_root)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot)" + "-[:LATEST]->(:ActivityInstanceGroupingValue)-[:HAS_ACTIVITY]->(:ActivityGrouping)" + "-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue) " + "WHERE activity_group_value.name IN $activity_group_names | activity_group_value.name]) > 0" + ) + filter_parameters.append(filter_by_activity_group_names) + filter_query_parameters["activity_group_names"] = activity_group_names + if kwargs.get("activity_instance_class_names") is not None: + instance_class_names = kwargs.get("activity_instance_class_names") + filter_by_instance_classes = ( + "size([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)" + "-[:LATEST]->(instance_class_value:ActivityInstanceClassValue)" + "WHERE instance_class_value.name IN $activity_instance_class_names | instance_class_value.name]) > 0" + ) + filter_parameters.append(filter_by_instance_classes) + filter_query_parameters["activity_instance_class_names"] = ( + instance_class_names + ) + extended_filter_statements = " AND ".join(filter_parameters) + if filter_statements_from_concept != "": + if len(extended_filter_statements) > 0: + filter_statements_to_return = " AND ".join( + [filter_statements_from_concept, extended_filter_statements] + ) + else: + filter_statements_to_return = filter_statements_from_concept + else: + filter_statements_to_return = ( + "WHERE " + extended_filter_statements + if len(extended_filter_statements) > 0 + else "" + ) + return filter_statements_to_return, filter_query_parameters + + def generic_match_clause_all_versions(self): + return """ + MATCH (concept_root:ActivityInstanceRoot)-[:HAS_GROUPING_ROOT]->(groupings_root:ActivityInstanceGroupingRoot)-[version:HAS_VERSION]->(concept_value:ActivityInstanceGroupingValue) + """ diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_repository.py index 54710e7f..b2ea3a31 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_repository.py @@ -66,6 +66,62 @@ class ActivityRepository(ConceptGenericRepository[ActivityAR]): return_model = Activity filter_query_parameters: dict[Any, Any] = {} + def latest_concept_in_library_exists_by_name( + self, + library_name: str, + concept_name: str, + activity_groupings: list[ActivityGroupingVO] | None = None, + ) -> bool: + if not activity_groupings or library_name != settings.requested_library_name: + return super().latest_concept_in_library_exists_by_name( + library_name, concept_name + ) + # Check if an activity with the same name AND same groupings exists + grouping_clauses = [] + params: dict[str, Any] = { + "concept_name": concept_name, + "library_name": library_name, + } + for i, grouping in enumerate(activity_groupings): + group_uid = ( + grouping.activity_group_uid + if hasattr(grouping, "activity_group_uid") + else grouping.get("activity_group_uid") + ) + subgroup_uid = ( + grouping.activity_subgroup_uid + if hasattr(grouping, "activity_subgroup_uid") + else grouping.get("activity_subgroup_uid") + ) + if group_uid and subgroup_uid: + grouping_clauses.append(f"""EXISTS {{ + MATCH (concept_value)-[:HAS_GROUPING]->(ag:ActivityGrouping) + -[:HAS_SELECTED_GROUP]->(gv:ActivityGroupValue) + <-[:HAS_VERSION]-(gr:ActivityGroupRoot {{uid: $group_uid_{i}}}) + WHERE EXISTS {{ + MATCH (ag)-[:HAS_SELECTED_SUBGROUP]->(sv:ActivitySubGroupValue) + <-[:HAS_VERSION]-(sr:ActivitySubGroupRoot {{uid: $subgroup_uid_{i}}}) + }} + }}""") + params[f"group_uid_{i}"] = group_uid + params[f"subgroup_uid_{i}"] = subgroup_uid + + if not grouping_clauses: + return super().latest_concept_in_library_exists_by_name( + library_name, concept_name + ) + + where_clause = " AND ".join(grouping_clauses) + query = f""" + MATCH (l:Library {{name: $library_name}})-[:CONTAINS_CONCEPT]-> + (concept_root:ActivityRoot)-[:LATEST]-> + (concept_value:ActivityValue{{name: $concept_name}}) + WHERE {where_clause} + RETURN concept_root + """ + result, _ = db.cypher_query(query, params) + return len(result) > 0 and len(result[0]) > 0 + def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> ActivityAR: @@ -228,7 +284,13 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( activity_instances = [] _activity_instance_uids = set() for activity_grouping in activity_groupings_nodes: - for activity_instance_value in activity_grouping.has_activity.all(): + for instance_groupings_value in activity_grouping.has_activity.all(): + activity_instance_root = ( + instance_groupings_value.has_version.single().has_grouping_root.single() + ) + activity_instance_value = ( + activity_instance_root.has_latest_value.single() + ) has_version = activity_instance_value.has_version for activity_instance_root in has_version.all(): if activity_instance_root.uid in _activity_instance_uids: @@ -297,9 +359,9 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( query = """ MATCH (ar:ActivityRoot {uid:$uid})-[:HAS_VERSION]->(:ActivityValue)<-[:HAS_SELECTED_ACTIVITY]-(sa:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(sv:StudyValue) WHERE NOT (sa)-[:BEFORE]-() AND NOT (sa)--(:Delete) - WITH CASE sv.subpart_id + WITH CASE sv.study_subpart_acronym WHEN IS NULL THEN COALESCE(sv.study_id_prefix, '') + '-' + COALESCE(sv.study_number, '') - ELSE COALESCE(sv.study_id_prefix, '') + '-' + COALESCE(sv.study_number, '') + '-' + sv.subpart_id + ELSE COALESCE(sv.study_id_prefix, '') + '-' + COALESCE(sv.study_number, '') + '-' + sv.study_subpart_acronym END AS study_id RETURN apoc.coll.toSet(apoc.coll.sort(collect(distinct study_id))) AS used_by_studies """ @@ -670,7 +732,7 @@ def specific_alias_clause(self, **kwargs) -> str: THEN apoc.coll.toSet(apoc.coll.sort( [(concept_root)-[:HAS_VERSION]->(:{self.value_class.__label__})<-[:HAS_SELECTED_ACTIVITY]->(sa:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(study_value:StudyValue) WHERE NOT (sa)-[:BEFORE]-() AND NOT (sa)--(:Delete) | COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '') + - CASE WHEN study_value.subpart_id IS NOT NULL AND study_value.subpart_id <> '' THEN "-" + study_value.subpart_id ELSE "" END])) + CASE WHEN study_value.study_subpart_acronym IS NOT NULL AND study_value.study_subpart_acronym <> '' THEN "-" + study_value.study_subpart_acronym ELSE "" END])) ELSE [] END AS used_by_studies, coalesce(concept_value.is_data_collected, False) AS is_data_collected, @@ -702,31 +764,38 @@ def specific_alias_clause(self, **kwargs) -> str: RETURN grouping }} AS activity_groupings, - apoc.coll.toSet([({activity_grouping_query_text})<-[:HAS_ACTIVITY]-(activity_instance_value:ActivityInstanceValue) - <-[has_version:HAS_VERSION]-(activity_instance_root:ActivityInstanceRoot) | {{uid: activity_instance_root.uid, name: activity_instance_value.name}}]) AS activity_instances, - head([(concept_value)-[:REPLACED_BY_ACTIVITY]->(replacing_activity_root:ActivityRoot) | replacing_activity_root.uid]) AS replaced_by_activity, - apoc.coll.sortMulti([({activity_grouping_query_text})<-[:HAS_ACTIVITY]-(activity_instance_value:ActivityInstanceValue) - <-[instance_version:HAS_VERSION WHERE instance_version.status='Final' and instance_version.end_date IS NULL]-(activity_instance_root) | - {{ - uid:activity_instance_root.uid, - legacy_code:activity_instance_value.is_legacy_usage, - major_version: toInteger(split(instance_version.version,'.')[0]), - minor_version: toInteger(split(instance_version.version,'.')[1]) - }}], ['^uid', 'major_version', 'minor_version']) AS all_legacy_codes - WITH *, - // Sort by uid and instance_version in descending order and leave only latest version of same ActivityInstances - [ - i in range(0, size(all_legacy_codes) -1) - WHERE i=0 OR all_legacy_codes[i].uid <> all_legacy_codes[i-1].uid | all_legacy_codes[i].legacy_code ] as all_legacy_codes - WITH *, - CASE - WHEN NOT is_request_rejected and replaced_by_activity IS NULL THEN false - ELSE true - END as is_finalized, - CASE WHEN size(all_legacy_codes) > 0 - THEN all(is_legacy_usage IN all_legacy_codes where is_legacy_usage=true and is_legacy_usage IS NOT NULL) - ELSE false - END as is_used_by_legacy_instances + apoc.coll.toSet([({activity_grouping_query_text})<-[:HAS_ACTIVITY]-(activity_instance_groupings_value:ActivityInstanceGroupingValue) + <-[groupings_has_version:HAS_VERSION]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot) + <-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot)-[:LATEST]->(activity_instance_value:ActivityInstanceValue) + | {{uid: activity_instance_root.uid, name: activity_instance_value.name}}]) AS activity_instances, + + head([(concept_value)-[:REPLACED_BY_ACTIVITY]->(replacing_activity_root:ActivityRoot) | replacing_activity_root.uid]) AS replaced_by_activity, + + apoc.coll.sortMulti([({activity_grouping_query_text})<-[:HAS_ACTIVITY]-(activity_instance_groupings_value:ActivityInstanceGroupingValue) + <-[groupings_has_version:HAS_VERSION]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot) + <-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot)-[instance_version:HAS_VERSION WHERE instance_version.status='Final' and instance_version.end_date IS NULL]->(activity_instance_value:ActivityInstanceValue) | + {{ + uid:activity_instance_root.uid, + legacy_code:activity_instance_value.is_legacy_usage, + major_version: toInteger(split(instance_version.version,'.')[0]), + minor_version: toInteger(split(instance_version.version,'.')[1]) + }}], ['^uid', 'major_version', 'minor_version']) AS all_legacy_codes + + WITH *, + // Sort by uid and instance_version in descending order and leave only latest version of same ActivityInstances + [ + i in range(0, size(all_legacy_codes) -1) + WHERE i=0 OR all_legacy_codes[i].uid <> all_legacy_codes[i-1].uid | all_legacy_codes[i].legacy_code ] as all_legacy_codes + + WITH *, + CASE + WHEN NOT is_request_rejected and replaced_by_activity IS NULL THEN false + ELSE true + END as is_finalized, + CASE WHEN size(all_legacy_codes) > 0 + THEN all(is_legacy_usage IN all_legacy_codes where is_legacy_usage=true and is_legacy_usage IS NOT NULL) + ELSE false + END as is_used_by_legacy_instances """ def replace_request_with_sponsor_activity( @@ -801,36 +870,39 @@ def get_activity_overview( } """ query = match + """ - WITH DISTINCT activity_root,activity_value, has_version, - head([(library)-[:CONTAINS_CONCEPT]->(activity_root) | library.name]) AS activity_library_name, - [(activity_root)-[versions:HAS_VERSION]->(:ActivityValue) | versions.version] as all_versions, - apoc.coll.sortMulti([(activity_value)-[:HAS_GROUPING]->(:ActivityGrouping)<-[:HAS_ACTIVITY]- - (activity_instance_value:ActivityInstanceValue)<-[aihv:HAS_VERSION]-(activity_instance_root:ActivityInstanceRoot) - WHERE NOT EXISTS ((activity_instance_value)<--(:DeletedActivityInstanceRoot)) - AND aihv.end_date IS NULL - | { - activity_instance_library_name: head([(library)-[:CONTAINS_CONCEPT]->(activity_instance_root) | library.name]), - uid: activity_instance_root.uid, - version: - { - major_version: toInteger(split(aihv.version,'.')[0]), - minor_version: toInteger(split(aihv.version,'.')[1]), - status:aihv.status - }, - name:activity_instance_value.name, - name_sentence_case:activity_instance_value.name_sentence_case, - abbreviation:activity_instance_value.abbreviation, - definition:activity_instance_value.definition, - adam_param_code:activity_instance_value.adam_param_code, - is_required_for_activity:coalesce(activity_instance_value.is_required_for_activity, false), - is_default_selected_for_activity:coalesce(activity_instance_value.is_default_selected_for_activity, false), - is_data_sharing:coalesce(activity_instance_value.is_data_sharing, false), - is_legacy_usage:coalesce(activity_instance_value.is_legacy_usage, false), - is_derived:coalesce(activity_instance_value.is_derived, false), - topic_code:activity_instance_value.topic_code, - activity_instance_class: head([(activity_instance_value)-[:ACTIVITY_INSTANCE_CLASS]->(activity_instance_class_root:ActivityInstanceClassRoot) - -[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) | activity_instance_class_value]) - }], ['^uid', 'version.major_version', 'version.minor_version']) AS activity_instances, + WITH DISTINCT + activity_root,activity_value, has_version, + head([(library)-[:CONTAINS_CONCEPT]->(activity_root) | library.name]) AS activity_library_name, + [(activity_root)-[versions:HAS_VERSION]->(:ActivityValue) | versions.version] as all_versions, + apoc.coll.sortMulti([(activity_value)-[:HAS_GROUPING]->(:ActivityGrouping)<-[:HAS_ACTIVITY]- + (activity_instance_groupings_value:ActivityInstanceGroupingValue)<-[aighv:HAS_VERSION]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot)-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot) + -[aihv:HAS_VERSION]->(activity_instance_value:ActivityInstanceValue) + WHERE NOT EXISTS ((activity_instance_value)<--(:DeletedActivityInstanceRoot)) + AND datetime(has_version.start_date) <= datetime(aihv.start_date) + AND (has_version.end_date IS NULL OR datetime(has_version.end_date) > datetime(aihv.start_date)) + | { + activity_instance_library_name: head([(library)-[:CONTAINS_CONCEPT]->(activity_instance_root) | library.name]), + uid: activity_instance_root.uid, + version: + { + major_version: toInteger(split(aihv.version,'.')[0]), + minor_version: toInteger(split(aihv.version,'.')[1]), + status:aihv.status + }, + name:activity_instance_value.name, + name_sentence_case:activity_instance_value.name_sentence_case, + abbreviation:activity_instance_value.abbreviation, + definition:activity_instance_value.definition, + adam_param_code:activity_instance_value.adam_param_code, + is_required_for_activity:coalesce(activity_instance_value.is_required_for_activity, false), + is_default_selected_for_activity:coalesce(activity_instance_value.is_default_selected_for_activity, false), + is_data_sharing:coalesce(activity_instance_value.is_data_sharing, false), + is_legacy_usage:coalesce(activity_instance_value.is_legacy_usage, false), + is_derived:coalesce(activity_instance_value.is_derived, false), + topic_code:activity_instance_value.topic_code, + activity_instance_class: head([(activity_instance_value)-[:ACTIVITY_INSTANCE_CLASS]->(activity_instance_class_root:ActivityInstanceClassRoot) + -[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) | activity_instance_class_value]) + }], ['^uid', 'version.major_version', 'version.minor_version']) AS activity_instances, apoc.coll.toSet([(activity_value)-[:HAS_GROUPING]->(activity_grouping:ActivityGrouping) | { activity_subgroup_value: head([(activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue) @@ -887,7 +959,9 @@ def get_cosmos_activity_overview(self, uid: str) -> dict[str, Any]: MATCH (activity_root:ActivityRoot {uid:$uid})-[:LATEST]->(activity_value:ActivityValue) WITH DISTINCT activity_root,activity_value, apoc.coll.toSet([(activity_value)-[:HAS_GROUPING]->(:ActivityGrouping)<-[:HAS_ACTIVITY]- - (activity_instance_value:ActivityInstanceValue)-[:ACTIVITY_INSTANCE_CLASS]-> + (activity_instance_groupings_value:ActivityInstanceGroupingValue)<-[:HAS_VERSION]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot) + <-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot)-[:LATEST]->(activity_instance_value:ActivityInstanceValue) + -[:ACTIVITY_INSTANCE_CLASS]-> (activity_instance_class_root:ActivityInstanceClassRoot)-[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) WHERE NOT EXISTS ((activity_instance_value)<--(:DeletedActivityInstanceRoot)) AND (:ActivityInstanceRoot)-[:HAS_VERSION {end_date: null}]->(activity_instance_value) @@ -903,7 +977,8 @@ def get_cosmos_activity_overview(self, uid: str) -> dict[str, Any]: activity_subgroups, apoc.coll.sortMaps(activity_instances, '^name') as activity_instances OPTIONAL MATCH (activity_value)-[:HAS_GROUPING]->(:ActivityGrouping)<-[:HAS_ACTIVITY]- - (activity_instance_value)-[:CONTAINS_ACTIVITY_ITEM]-> + (activity_instance_groupings_value:ActivityInstanceGroupingValue)<-[:HAS_VERSION]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot) + <-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot)-[:LATEST]->(activity_instance_value:ActivityInstanceValue)-[:CONTAINS_ACTIVITY_ITEM]-> (activity_item:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-(activity_item_class_root:ActivityItemClassRoot)-[:LATEST]-> (activity_item_class_value:ActivityItemClassValue) OPTIONAL MATCH (activity_item)-[]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]->(CTTermAttributesRoot)-[:LATEST]->(activity_item_term_attr_value) @@ -1045,40 +1120,28 @@ def get_linked_upgradable_activity_instances( query = match + """ MATCH (activity_value)-[:HAS_GROUPING]->(activity_grouping:ActivityGrouping)<-[:HAS_ACTIVITY]- - (activity_instance_value:ActivityInstanceValue)<-[aihv:HAS_VERSION]-(activity_instance_root:ActivityInstanceRoot) + (activity_instance_groupings_value:ActivityInstanceGroupingValue)<-[aighv:HAS_VERSION]-(activity_instance_groupings_root:ActivityInstanceGroupingRoot) + <-[:HAS_GROUPING_ROOT]-(activity_instance_root:ActivityInstanceRoot) OPTIONAL MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue)<-[:HAS_VERSION]-(activity_subgroup_root:ActivitySubGroupRoot) OPTIONAL MATCH (activity_grouping)-[:HAS_SELECTED_GROUP]->(activity_group_value:ActivityGroupValue)<-[:HAS_VERSION]-(activity_group_root:ActivityGroupRoot) - WITH DISTINCT activity_root, activity_value, activity_instance_root, activity_instance_value, aihv, COLLECT(DISTINCT { + WITH DISTINCT activity_root, activity_value, activity_instance_root, activity_instance_groupings_root, aighv, COLLECT(DISTINCT { activity_uid: activity_root.uid, activity_group_uid: activity_group_root.uid, activity_subgroup_uid: activity_subgroup_root.uid }) AS activity_groupings - WHERE aihv.end_date IS NULL AND NOT EXISTS ((activity_instance_value)<--(:DeletedActivityInstanceRoot)) + WHERE aighv.end_date IS NULL AND NOT EXISTS ((activity_instance_groupings_root)<--(:DeletedActivityInstanceRoot)) WITH *, { activity_instance_library_name: head([(library)-[:CONTAINS_CONCEPT]->(activity_instance_root) | library.name]), uid: activity_instance_root.uid, version: { - major_version: toInteger(split(aihv.version,'.')[0]), - minor_version: toInteger(split(aihv.version,'.')[1]), - status:aihv.status + major_version: toInteger(split(aighv.version,'.')[0]), + minor_version: toInteger(split(aighv.version,'.')[1]), + status:aighv.status }, - name:activity_instance_value.name, - name_sentence_case:activity_instance_value.name_sentence_case, - abbreviation:activity_instance_value.abbreviation, - definition:activity_instance_value.definition, - adam_param_code:activity_instance_value.adam_param_code, - is_required_for_activity:coalesce(activity_instance_value.is_required_for_activity, false), - is_default_selected_for_activity:coalesce(activity_instance_value.is_default_selected_for_activity, false), - is_data_sharing:coalesce(activity_instance_value.is_data_sharing, false), - is_legacy_usage:coalesce(activity_instance_value.is_legacy_usage, false), - is_derived:coalesce(activity_instance_value.is_derived, false), - topic_code:activity_instance_value.topic_code, - activity_instance_class: head([(activity_instance_value)-[:ACTIVITY_INSTANCE_CLASS]->(activity_instance_class_root:ActivityInstanceClassRoot) - -[:LATEST]->(activity_instance_class_value:ActivityInstanceClassValue) | activity_instance_class_value]), activity_groupings: activity_groupings - } AS activity_instance ORDER BY activity_instance.uid, activity_instance.name + } AS activity_instance ORDER BY activity_instance.uid RETURN collect(activity_instance) as activity_instances """ @@ -1167,8 +1230,17 @@ def get_specific_activity_version_groupings( } CALL { WITH agrp - MATCH (agrp)<-[:HAS_ACTIVITY]-(aiv:ActivityInstanceValue)<-[hv:HAS_VERSION]-(air:ActivityInstanceRoot) + MATCH (agrp)<-[:HAS_ACTIVITY]-(aigv:ActivityInstanceGroupingValue) + <-[ghv:HAS_VERSION]-(:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(air:ActivityInstanceRoot)-[hv:HAS_VERSION]->(aiv:ActivityInstanceValue) WHERE NOT EXISTS((aiv)<--(:DeletedActivityInstanceRoot)) + AND ( + // both versions are the latest: no further checks needed + (ghv.end_date IS NULL AND hv.end_date IS NULL) + // grouping has an end date, instance is latest: instance start date is before grouping end date + OR (ghv.end_date IS NOT NULL AND hv.end_date IS NULL AND datetime(hv.start_date) < datetime(ghv.end_date)) + // grouping has an end date, instance has an end date: instance start date is before grouping end date and instance end date is after grouping end date + OR (ghv.end_date IS NOT NULL AND hv.end_date IS NOT NULL AND datetime(hv.start_date) < datetime(ghv.end_date) AND datetime(hv.end_date) >= datetime(ghv.end_date)) + ) WITH aiv, hv, air ORDER BY hv.start_date WITH DISTINCT air, collect({aiv: aiv, version: hv.version}) AS aiv_versions @@ -1324,6 +1396,136 @@ def get_activity_instances_for_version( For each relevant activity instance, it returns the latest linked version as the parent, along with older linked versions as children. + Args: + activity_uid (str): The UID of the parent activity. + version (str): The specific version of the parent activity (e.g., "16.0"). + skip (int): Number of records to skip for pagination (0-based). + limit (int): Maximum number of records to return. + + Returns: + tuple[list[dict], int]: A tuple containing the list of activity instance + dictionaries and the total count of unique relevant instances. + """ + # Ensure skip and limit are non-negative integers + if not isinstance(skip, int) or skip < 0: + skip = 0 + + if not isinstance(limit, int) or limit < 0: + # Default to a reasonable value for negative or invalid values + limit = 10 + + # Collect linked instances + linked_instances_query = """ + MATCH (activity_root:ActivityRoot {uid: $uid})-[:HAS_VERSION {version: $version}]->(activity_value:ActivityValue) + WITH activity_root, activity_value + MATCH (activity_value)-[:HAS_GROUPING]->(:ActivityGrouping)<-[:HAS_ACTIVITY]-(:ActivityInstanceGroupingValue)<-[ghv:HAS_VERSION]-(:ActivityInstanceGroupingRoot)<-[:HAS_GROUPING_ROOT]-(ai_root:ActivityInstanceRoot) + WITH DISTINCT ai_root, activity_value, collect(ghv) AS ghvs ORDER BY ai_root.uid + CALL { + WITH ai_root, activity_value, ghvs + UNWIND ghvs AS ghv + MATCH (ai_root)-[hv:HAS_VERSION]->(aiv:ActivityInstanceValue) + WHERE NOT (aiv)<--(:DeletedActivityInstanceRoot) + AND ( + // both versions are the latest: no further checks needed + (ghv.end_date IS NULL AND hv.end_date IS NULL) + // grouping has an end date, instance is latest: instance start date is before grouping end date + OR (ghv.end_date IS NOT NULL AND hv.end_date IS NULL AND datetime(hv.start_date) < datetime(ghv.end_date)) + // grouping is the latest, instance has an end date: instance end date is after grouping start date + OR (ghv.end_date IS NULL AND hv.end_date IS NOT NULL AND datetime(hv.end_date) > datetime(ghv.start_date)) + // grouping has an end date, instance has an end date: instance start date is before grouping end date and instance end date is after grouping start date + OR (ghv.end_date IS NOT NULL AND hv.end_date IS NOT NULL AND datetime(hv.start_date) < datetime(ghv.end_date) AND datetime(hv.end_date) >= datetime(ghv.start_date)) + ) + OPTIONAL MATCH (aiv)-[:ACTIVITY_INSTANCE_CLASS]->(aic_root:ActivityInstanceClassRoot)-[:LATEST]->(aic_value:ActivityInstanceClassValue) + WITH {uid: ai_root.uid, name: aiv.name, version: hv.version, activity_instance_class: {uid: aic_root.uid, name: aic_value.name}, status: hv.status, topic_code: aiv.topic_code, adam_param_code: aiv.adam_param_code} AS instance_info + ORDER BY hv.start_date DESC + WITH COLLECT(DISTINCT instance_info) AS instance_versions + WITH instance_versions[0].uid AS uid, + instance_versions[0].name AS name, + instance_versions[0].version AS version, + instance_versions[0].activity_instance_class AS activity_instance_class, + instance_versions[0].status AS status, + instance_versions[0].topic_code AS topic_code, + instance_versions[0].adam_param_code AS adam_param_code, + instance_versions[1..] AS children + RETURN * + } + """ + + instances_return_query = """ + WITH { + uid: uid, + version: version, + status: status, + name: name, + adam_param_code: adam_param_code, + topic_code: topic_code, + activity_instance_class: activity_instance_class, + children: children + } AS instance + RETURN instance SKIP $skip LIMIT $limit + """ + + count_return_query = "RETURN count(uid) as total_count" + + count_query = linked_instances_query + count_return_query + params: dict[str, str | int | None] = {"uid": activity_uid, "version": version} + try: + count_result, _ = db.cypher_query( + query=count_query, + params=params, + resolve_objects=False, + ) + if not count_result or not count_result[0]: + # This case might mean the activity/version doesn't exist or has no linked instances + return [], 0 + total_count = count_result[0][0] + + # Handle case where activity/version exists but no instances meet criteria + if total_count == 0: + return [], 0 + + except IndexError: + # Handle case where query returns empty results unexpectedly + return [], 0 + except Exception as e: + # Log error or raise a more specific exception + print(f"Error executing count/end_date query: {e}") + raise # Re-raise for now, or handle appropriately + + # Query 2: Fetch details for paginated roots + + full_query = linked_instances_query + instances_return_query + params.update({"skip": skip, "limit": limit}) + try: + instances_results, _ = db.cypher_query( + query=full_query, params=params, resolve_objects=False + ) + instances = [row[0] for row in instances_results] + except Exception as e: + # Log error or raise a more specific exception + print(f"Error executing details query: {e}") + raise # Re-raise for now, or handle appropriately + + return instances, total_count + + def get_activity_instances_for_version_deleteme( + self, + activity_uid: str, + version: str | None, + skip: int = 0, + limit: int = 10, + ) -> tuple[list[dict[Any, Any]], int]: + """ + Retrieves a paginated list of activity instances that are linked to a specific + activity version via HAS_ACTIVITY relationships. + + Only returns instance versions that have a direct HAS_ACTIVITY relationship to + this activity's groupings. If an instance was later moved to a different activity, + only the versions that were linked to THIS activity are returned. + + For each relevant activity instance, it returns the latest linked version as the + parent, along with older linked versions as children. + Args: activity_uid (str): The UID of the parent activity. version (str): The specific version of the parent activity (e.g., "16.0"). @@ -1554,7 +1756,7 @@ def specific_header_match_clause_lite(self, field_name: str) -> str | None: WHEN exists((concept_root)<-[:CONTAINS_CONCEPT]-(:Library {name:'Requested'})) THEN apoc.coll.toSet(apoc.coll.sort([(concept_root)-[:HAS_VERSION]->(:ActivityValue)<-[:HAS_SELECTED_ACTIVITY]->(sa:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(study_value:StudyValue) WHERE NOT (sa)-[:BEFORE]-() AND NOT (sa)--(:Delete) | COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '') + - CASE WHEN study_value.subpart_id IS NOT NULL AND study_value.subpart_id <> '' THEN "-" + study_value.subpart_id ELSE "" END])) + CASE WHEN study_value.study_subpart_acronym IS NOT NULL AND study_value.study_subpart_acronym <> '' THEN "-" + study_value.study_subpart_acronym ELSE "" END])) ELSE [] END AS used_by_studies""" return header_query diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py index f3b09602..f6245fdd 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py @@ -47,6 +47,8 @@ def _create_aggregate_root_instance_from_cypher_result( name_sentence_case=input_dict["name_sentence_case"], definition=input_dict.get("definition"), abbreviation=input_dict.get("abbreviation"), + nci_concept_id=input_dict.get("nci_concept_id"), + nci_concept_name=input_dict.get("nci_concept_name"), ), library=LibraryVO.from_input_values_2( library_name=input_dict["library_name"], @@ -82,6 +84,8 @@ def _create_ar( name_sentence_case=value.name_sentence_case, definition=value.definition, abbreviation=value.abbreviation, + nci_concept_id=value.nci_concept_id, + nci_concept_name=value.nci_concept_name, ), library=LibraryVO.from_input_values_2( library_name=library.name, @@ -106,6 +110,8 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( name_sentence_case=value.name_sentence_case, definition=value.definition, abbreviation=value.abbreviation, + nci_concept_id=value.nci_concept_id, + nci_concept_name=value.nci_concept_name, ), library=LibraryVO.from_input_values_2( library_name=library.name, 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 b26d00cf..f6f7f10b 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 @@ -278,13 +278,17 @@ def create_query_filter_statement( filter_parameters = [] filter_query_parameters = {} uids = kwargs.get("uids") + if self._has_uid_and_library_on_parent_root(): + concept_root_alias = "parent_root" + else: + concept_root_alias = "concept_root" if library: - filter_by_library_name = """ - head([(library:Library)-[:CONTAINS_CONCEPT]->(concept_root) | library.name])=$library_name""" + filter_by_library_name = f""" + head([(library:Library)-[:CONTAINS_CONCEPT]->({concept_root_alias}) | library.name])=$library_name""" filter_parameters.append(filter_by_library_name) filter_query_parameters["library_name"] = library if uids: - filter_by_uids = "concept_root.uid IN $uids" + filter_by_uids = f"{concept_root_alias}.uid IN $uids" filter_parameters.append(filter_by_uids) filter_query_parameters["uids"] = uids @@ -493,8 +497,9 @@ def get_distinct_headers( query.parameters.update(filter_query_parameters) + header_alias = self.format_filter_sort_keys(field_name) query.full_query = query.build_header_query( - header_alias=field_name, page_size=page_size + header_alias=header_alias, page_size=page_size ) result_array, _ = query.execute() 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 a0c649c2..7eef78e6 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 @@ -22,8 +22,12 @@ ) from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_term import ( CTCodelistTermAR, + CTPairedCodelistTermAR, +) +from clinical_mdr_api.models.controlled_terminologies.ct_codelist import ( + CTCodelistTerm, + CTPairedCodelistTerm, ) -from clinical_mdr_api.models.controlled_terminologies.ct_codelist import CTCodelistTerm from clinical_mdr_api.models.controlled_terminologies.ct_stats import CodelistCount from clinical_mdr_api.repositories._utils import ( ComparisonOperator, @@ -1076,3 +1080,125 @@ def get_paired_codelist_uids( """ result, _ = db.cypher_query(query, {"codelist_uid": codelist_uid}) return result[0] if result else (None, None) + + def find_paired_codelist_terms( + self, + names_codelist_uid: str, + codes_codelist_uid: str, + sort_by: dict[str, bool] | None = None, + page_number: int = 1, + page_size: int = 0, + filter_by: dict[str, dict[str, Any]] | None = None, + filter_operator: FilterOperator = FilterOperator.AND, + total_count: bool = False, + ) -> tuple[list[CTPairedCodelistTermAR], int]: + match_clause = """ + CALL { + MATCH (:CTCodelistRoot {uid: $names_codelist_uid})-[ht:HAS_TERM]->(:CTCodelistTerm)-[:HAS_TERM_ROOT]->(tr:CTTermRoot) + WHERE ht.end_date IS NULL + RETURN tr + UNION + MATCH (:CTCodelistRoot {uid: $codes_codelist_uid})-[ht:HAS_TERM]->(:CTCodelistTerm)-[:HAS_TERM_ROOT]->(tr:CTTermRoot) + WHERE ht.end_date IS NULL + RETURN tr + } + WITH DISTINCT tr AS term_root + OPTIONAL MATCH (:CTCodelistRoot {uid: $names_codelist_uid})-[names_ht:HAS_TERM]->(names_clt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root) + WHERE names_ht.end_date IS NULL + OPTIONAL MATCH (:CTCodelistRoot {uid: $codes_codelist_uid})-[codes_ht:HAS_TERM]->(codes_clt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(term_root) + WHERE codes_ht.end_date IS NULL + MATCH (term_root)<-[:CONTAINS_TERM]-(library:Library) + MATCH (term_root)-[:HAS_NAME_ROOT]->(tnr:CTTermNameRoot)-[:LATEST]->(tnv:CTTermNameValue) + MATCH (term_root)-[:HAS_ATTRIBUTES_ROOT]->(tar:CTTermAttributesRoot)-[:LATEST]->(tav:CTTermAttributesValue) + """ + + alias_clause = """ + DISTINCT term_root, names_ht, codes_ht, names_clt, codes_clt, tnr, tnv, tar, tav, library + CALL { + WITH tar, tav + MATCH (tar)-[hv:HAS_VERSION]->(tav) + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.end_date ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS rel_data_attributes + } + CALL { + WITH tnr, tnv + MATCH (tnr)-[hv:HAS_VERSION]->(tnv) + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.end_date ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS rel_data_name + } + WITH + term_root.uid AS term_uid, + names_clt.submission_value AS name_submission_value, + codes_clt.submission_value AS code_submission_value, + COALESCE(names_ht.order, codes_ht.order) AS order, + COALESCE(names_ht.ordinal, codes_ht.ordinal) AS ordinal, + COALESCE(names_ht.start_date, codes_ht.start_date) AS start_date, + COALESCE(names_ht.end_date, codes_ht.end_date) AS end_date, + tav.definition AS definition, + tav.concept_id AS concept_id, + tav.preferred_term AS nci_preferred_name, + rel_data_attributes.start_date AS attributes_date, + rel_data_attributes.status AS attributes_status, + tnv.name AS sponsor_preferred_name, + tnv.name_sentence_case AS sponsor_preferred_name_sentence_case, + rel_data_name.start_date AS name_date, + rel_data_name.status AS name_status, + library.name AS library_name + """ + + if sort_by is None: + sort_by = {"order": True} + + query = CypherQueryBuilder( + filter_by=FilterDict.model_validate({"elements": filter_by}), + filter_operator=filter_operator, + match_clause=match_clause, + alias_clause=alias_clause, + wildcard_properties_list=list_codelist_wildcard_properties( + target_model=CTPairedCodelistTerm, transform=False + ), + sort_by=sort_by, + page_number=page_number, + page_size=page_size, + total_count=total_count, + ) + query.parameters.update( + { + "names_codelist_uid": names_codelist_uid, + "codes_codelist_uid": codes_codelist_uid, + } + ) + + result_array, attributes_names = query.execute() + + paired_term_ars = [] + for term in result_array: + term_dictionary = {} + for term_property, attribute_name in zip(term, attributes_names): + term_dictionary[attribute_name] = term_property + paired_term_ars.append( + CTPairedCodelistTermAR.from_result_dict(term_dictionary) + ) + + total = calculate_total_count_from_query_result( + len(paired_term_ars), page_number, page_size, total_count + ) + if total is None: + count_result, _ = db.cypher_query( + query=query.count_query, params=query.parameters + ) + total = count_result[0][0] if len(count_result) > 0 else 0 + + return paired_term_ars, total diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/library_item_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/library_item_repository.py index e57880e0..7efb593f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/library_item_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/library_item_repository.py @@ -74,6 +74,9 @@ class LibraryItemRepositoryImplBase( lock_store_term_by_uid_and_submval = Lock() has_library = True + def _has_uid_and_library_on_parent_root(self) -> bool: + return False + @abc.abstractmethod def _create_aggregate_root_instance_from_version_root_relationship_and_value( self, @@ -278,8 +281,11 @@ def _update( if self._is_repository_related_to_ct(): root = root.has_root.single() + # updating library connection if necessary + # Skip if we have uid and library on a parent root if ( - self.has_library + not self._has_uid_and_library_on_parent_root() + and self.has_library and versioned_object.library.name != root.has_library.get().name ): self._db_remove_relationship(root.has_library) @@ -655,9 +661,6 @@ def _get_item_versions( ) itm: VersionValue for itm in traversal.all(): - assert isinstance( - itm, (VersionValue, ControlledTerminology) - ) # PIWQ: juts to check whether I understand what's going here if itm in managed: continue @@ -684,15 +687,19 @@ def get_all_versions_2( # these two nodes don't contain uids but serves as a roots for versioned relationships # Connection to the Library node is attached to the 'main' root not the root that owns versioned relationships # this is why we need the following condition - if not self._is_repository_related_to_ct(): - root: VersionRoot | None = self.root_class.nodes.get_or_none(uid=uid) - if root is not None: - - if self.has_library: - library = root.has_library.get() - else: - library = None - else: + if self._has_uid_and_library_on_parent_root(): + # This object has a parent root that contains the uid + parent_root: VersionRoot | None = self.parent_root_class.nodes.get_or_none( + uid=uid + ) + if parent_root is not None: + root: VersionRoot | None = getattr( + parent_root, self.parent_root_relationship + ).single() + library = parent_root.has_library.get() + else: + root = None + elif self._is_repository_related_to_ct(): # ControlledTerminology version root items don't contain uid - then we have to get object by it's id _result, _ = db.cypher_query( MATCH_NODE_BY_ID, @@ -705,6 +712,14 @@ def get_all_versions_2( library = root.has_root.single().has_library.get() else: library = None + else: + root = self.root_class.nodes.get_or_none(uid=uid) + if root is not None: + + if self.has_library: + library = root.has_library.get() + else: + library = None result: list[_AggregateRootType] = [] if root is not None: @@ -1051,7 +1066,11 @@ def _get_version_data_from_db( if not self.has_library: library = None elif not self._is_repository_related_to_ct(): - library = item.has_library.get() + if self._has_uid_and_library_on_parent_root(): + parent_root = getattr(item, self.parent_root_relationship).single() + library = parent_root.has_library.get() + else: + library = item.has_library.get() else: library = item.has_root.single().has_library.get() data = value.to_dict() @@ -2642,6 +2661,7 @@ def _activity_instance_root_match_return_stmt(self): ct_terms:ct_terms, unit_definitions: unit_definitions, is_adam_param_specific: activity_item.is_adam_param_specific, + is_activity_instance_id_specific: activity_item.is_activity_instance_id_specific, text_value: activity_item.text_value, odm_items: odm_items }) as activity_items @@ -2704,7 +2724,7 @@ def _activity_root_match_return_stmt(self): <-[:HAS_SELECTED_ACTIVITY]-(sa:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(study_value:StudyValue) WHERE library.name="Requested" AND NOT (sa)-[:BEFORE]-() AND NOT (sa)--(:Delete) | COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '') + - CASE WHEN study_value.subpart_id IS NOT NULL AND study_value.subpart_id <> '' THEN "-" + study_value.subpart_id ELSE "" END])) AS used_by_studies + CASE WHEN study_value.study_subpart_acronym IS NOT NULL AND study_value.study_subpart_acronym <> '' THEN "-" + study_value.study_subpart_acronym ELSE "" END])) AS used_by_studies RETURN activity_groupings, used_by_studies } """ diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/activities.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/activities.py index fb116d19..1c864dc1 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/activities.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/activities.py @@ -114,7 +114,7 @@ class ActivityGrouping(ClinicalMdrNodeWithUID): "ActivityValue", "HAS_GROUPING", model=ClinicalMdrRel, cardinality=One ) has_activity = RelationshipFrom( - "ActivityInstanceValue", + "ActivityInstanceGroupingValue", "HAS_ACTIVITY", model=ClinicalMdrRel, cardinality=ZeroOrMore, @@ -175,6 +175,7 @@ class ActivityRoot(ConceptRoot): class ActivityItem(ClinicalMdrNode): is_adam_param_specific = BooleanProperty(False) + is_activity_instance_id_specific = BooleanProperty() text_value = StringProperty() has_activity_item_class = RelationshipFrom( ActivityItemClassRoot, @@ -207,9 +208,6 @@ class ActivityInstanceValue(ConceptValue): is_derived = BooleanProperty(default=False) legacy_description = StringProperty() - has_activity = RelationshipTo( - ActivityGrouping, "HAS_ACTIVITY", model=ClinicalMdrRel, cardinality=OneOrMore - ) activity_instance_class = RelationshipTo( ActivityInstanceClassRoot, "ACTIVITY_INSTANCE_CLASS", @@ -236,6 +234,72 @@ class ActivityInstanceValue(ConceptValue): ) +class ActivityInstanceGroupingRoot(ClinicalMdrNode): + has_version = RelationshipTo( + "ActivityInstanceGroupingValue", "HAS_VERSION", model=VersionRelationship + ) + has_latest_value = RelationshipTo( + "ActivityInstanceGroupingValue", "LATEST", model=ClinicalMdrRel + ) + latest_draft = RelationshipTo( + "ActivityInstanceGroupingValue", "LATEST_DRAFT", model=ClinicalMdrRel + ) + latest_final = RelationshipTo( + "ActivityInstanceGroupingValue", "LATEST_FINAL", model=ClinicalMdrRel + ) + latest_retired = RelationshipTo( + "ActivityInstanceGroupingValue", "LATEST_RETIRED", model=ClinicalMdrRel + ) + has_grouping_root = RelationshipFrom( + "ActivityInstanceRoot", + "HAS_GROUPING_ROOT", + model=ClinicalMdrRel, + cardinality=One, + ) + + def get_value_for_version(self, version: str | None): + matching_values = self.has_version.match(version=version) + if len(matching_values) > 0: + return matching_values[0] + return None + + def get_relation_for_version(self, version: str): + value = self.get_value_for_version(version) + relationships = self.has_version.all_relationships(value) + all_matching = [rel for rel in relationships if rel.version == version] + all_without_end = [rel for rel in all_matching if rel.end_date is None] + if len(all_without_end) == 1: + # There is only one relationship without end date + return all_without_end[0] + if len(all_without_end) > 1: + # There are several relationships without end date, return the latest one based on start date + return max(all_without_end, key=lambda d: d.start_date) + # There are no relationships without end date, return the latest one based on end date + return max(all_matching, key=lambda d: d.end_date) + + +class ActivityInstanceGroupingValue(ClinicalMdrNode): + has_latest_value = RelationshipFrom( + ActivityInstanceGroupingRoot, "LATEST", model=ClinicalMdrRel + ) + has_version = RelationshipFrom( + ActivityInstanceGroupingRoot, "HAS_VERSION", model=VersionRelationship + ) + latest_draft = RelationshipFrom( + ActivityInstanceGroupingRoot, "LATEST_DRAFT", model=ClinicalMdrRel + ) + latest_final = RelationshipFrom( + ActivityInstanceGroupingRoot, "LATEST_FINAL", model=ClinicalMdrRel + ) + latest_retired = RelationshipFrom( + ActivityInstanceGroupingRoot, "LATEST_RETIRED", model=ClinicalMdrRel + ) + + has_activity = RelationshipTo( + ActivityGrouping, "HAS_ACTIVITY", model=ClinicalMdrRel, cardinality=OneOrMore + ) + + class ActivityInstanceRoot(ConceptRoot): has_version = RelationshipTo( ActivityInstanceValue, "HAS_VERSION", model=VersionRelationship @@ -252,3 +316,10 @@ class ActivityInstanceRoot(ConceptRoot): latest_retired = RelationshipTo( ActivityInstanceValue, "LATEST_RETIRED", model=ClinicalMdrRel ) + + has_grouping_root = RelationshipTo( + ActivityInstanceGroupingRoot, + "HAS_GROUPING_ROOT", + model=ClinicalMdrRel, + cardinality=One, + ) 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 76dc4fae..1515cb49 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 @@ -761,6 +761,7 @@ def save( def get_studies_list( self, + minimal_response: bool = True, has_study_objective: bool | None = None, has_study_footnote: bool | None = None, has_study_endpoint: bool | None = None, @@ -805,6 +806,29 @@ def where_stmt(): return f"WHERE {' AND '.join(conditions)}" if conditions else "" self._check_not_closed() + + if minimal_response: + query = f""" + MATCH (sr:StudyRoot)-[:LATEST]->(sv:StudyValue) + {where_stmt()} + + RETURN sr.uid AS uid, + sv.study_id_prefix + '-' + sv.study_number + COALESCE(nullif('-' + sv.study_subpart_acronym, '-'), '') as id, + sv.study_acronym, + sv.study_subpart_acronym + ORDER BY uid + """ + rs = db.cypher_query(query) + return [ + { + "uid": row[0], + "id": row[1], + "acronym": row[2], + "subpart_acronym": row[3], + } + for row in rs[0] + ] + query = f""" MATCH (sr:StudyRoot)-[:LATEST]->(sv:StudyValue)-[:HAS_PROJECT]-(:StudyProjectField)<-[:HAS_FIELD]-(p:Project)<-[:HOLDS_PROJECT]-(cp:ClinicalProgramme) {where_stmt()} @@ -830,14 +854,15 @@ def where_stmt(): head(latest_released) as latest_released_version, head(latest_locked) as latest_locked_version OPTIONAL MATCH (author:User {{user_id: current_version.author_id}}) - RETURN sr.uid AS uid, + RETURN sr.uid AS uid, sv.study_acronym, - sv.study_id_prefix + '-' + sv.study_number + COALESCE(nullif('-' + sv.subpart_id, '-'), '') as id, + sv.study_id_prefix + '-' + sv.study_number + COALESCE(nullif('-' + sv.study_subpart_acronym, '-'), '') as id, + sv.study_id_prefix + '-' + sv.study_number as main_id, sv.study_number, sv.subpart_id, sv.study_subpart_acronym, stf.value as study_title, - cp.name as clinical_progamme, + cp.name as clinical_programme, p.project_number as project_number, p.name as project_name, current_version.author_id as version_author_id, @@ -856,21 +881,22 @@ def where_stmt(): "uid": row[0], "acronym": row[1], "id": row[2], - "study_number": row[3], - "subpart_id": row[4], - "subpart_acronym": row[5], - "title": row[6], - "clinical_programme_name": row[7], - "project_number": row[8], - "project_name": row[9], - "version_author_id": row[10], - "version_status": row[11], - "version_start_date": convert_to_datetime(row[12]), - "version_number": row[13], - "version_author": row[14], - "latest_locked_version": row[15], - "latest_released_version": row[16], - "data_completeness_tags": row[17], + "main_id": row[3], + "study_number": row[4], + "subpart_id": row[5], + "subpart_acronym": row[6], + "title": row[7], + "clinical_programme_name": row[8], + "project_number": row[9], + "project_name": row[10], + "version_author_id": row[11], + "version_status": row[12], + "version_start_date": convert_to_datetime(row[13]), + "version_number": row[14], + "version_author": row[15], + "latest_locked_version": row[16], + "latest_released_version": row[17], + "data_completeness_tags": row[18], } for row in rs[0] ] 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 73ef4cee..f514ddeb 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 @@ -2124,6 +2124,52 @@ def _create(self, snapshot: StudyDefinitionSnapshot) -> None: date=date, ) + # Persist study fields and registry identifiers that are inherited + # from a parent study (e.g. when creating a subpart). Only call the + # maintain helpers when there are actual values to persist. + metadata = snapshot.current_metadata + has_study_description = ( + metadata.study_title is not None or metadata.study_short_title is not None + ) + has_registry_ids = any( + getattr(metadata, cfg.study_field_name, None) is not None + for cfg in FieldConfiguration.default_field_config() + if cfg.study_field_data_type == StudyFieldType.REGISTRY + ) + if has_study_description or has_registry_ids: + empty_snapshot = StudyDefinitionSnapshot( + uid=snapshot.uid, + study_parent_part_uid=snapshot.study_parent_part_uid, + study_subpart_uids=snapshot.study_subpart_uids, + current_metadata=StudyDefinitionSnapshot.StudyMetadataSnapshot( + study_number=metadata.study_number, + project_number=metadata.project_number, + ), + draft_metadata=None, + released_metadata=None, + locked_metadata_versions=[], + study_status=snapshot.study_status, + deleted=False, + ) + if has_study_description: + self._maintain_study_fields_relationships( + study_root=root, + previous_snapshot=empty_snapshot, + current_snapshot=snapshot, + previous_value=value, + expected_latest_value=value, + date=date, + ) + if has_registry_ids: + self._maintain_study_registry_id_fields_relationships( + study_root=root, + previous_snapshot=empty_snapshot, + current_snapshot=snapshot, + previous_value=value, + expected_latest_value=value, + date=date, + ) + @staticmethod def _generate_study_value_audit_node( study_root_node: StudyRoot, @@ -2841,9 +2887,13 @@ def get_study_id( study_id_prefix = study_value.get("study_id_prefix") study_number = study_value.get("study_number") + study_subpart_acronym = study_value.get("study_subpart_acronym") if study_number and study_id_prefix: - return f"{study_id_prefix}-{study_number}" + study_id = f"{study_id_prefix}-{study_number}" + if study_subpart_acronym: + study_id += f"-{study_subpart_acronym}" + return study_id return None diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_repository.py index f070b22f..6a78c57f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_repository.py @@ -47,6 +47,7 @@ class SoALayout(Enum): PROTOCOL = "protocol" + PROTOCOL_LAB_TABLE = "protocol_lab_table" DETAILED = "detailed" OPERATIONAL = "operational" diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity.py b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity.py index 4bcef37c..578e13b5 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity.py @@ -105,7 +105,7 @@ def from_repository_values( def validate( self, - activity_exists_by_name_callback: Callable[[str, str], bool], + activity_exists_by_name_callback: Callable[..., bool], activity_subgroup_exists: Callable[[str], bool], activity_group_exists: Callable[[str], bool], get_activity_uids_by_synonyms_callback: Callable[ @@ -121,7 +121,9 @@ def validate( self.validate_name_sentence_case() if self.name and library_name is not None: - existing_name = activity_exists_by_name_callback(library_name, self.name) + existing_name = activity_exists_by_name_callback( + library_name, self.name, self.activity_groupings + ) AlreadyExistsException.raise_if( existing_name and previous_name != self.name, @@ -185,8 +187,8 @@ def from_input_values( [str, str, bool], bool ] = lambda x, y, z: True, concept_exists_by_library_and_name_callback: Callable[ - [str, str], bool - ] = lambda x, y: True, + ..., bool + ] = lambda x, y, z: True, activity_subgroup_exists: Callable[[str], bool] = lambda _: False, activity_group_exists: Callable[[str], bool] = lambda _: False, get_activity_uids_by_synonyms_callback: Callable[ @@ -226,8 +228,8 @@ def edit_draft( [str, str, bool], bool ] = lambda x, y, z: True, concept_exists_by_library_and_name_callback: Callable[ - [str, str], bool - ] = lambda x, y: True, + ..., bool + ] = lambda x, y, z: True, activity_subgroup_exists: Callable[[str], bool] = lambda _: False, activity_group_exists: Callable[[str], bool] = lambda _: False, get_activity_uids_by_synonyms_callback: Callable[ diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_group.py b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_group.py index 9fb932fb..22adcd33 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_group.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_group.py @@ -15,6 +15,9 @@ class ActivityGroupVO(ConceptVO): The ActivityGroupVO acts as the value object for a single ActivityGroup aggregate """ + nci_concept_id: str | None = None + nci_concept_name: str | None = None + @classmethod def from_repository_values( cls, @@ -22,6 +25,8 @@ def from_repository_values( name_sentence_case: str | None, definition: str | None, abbreviation: str | None, + nci_concept_id: str | None = None, + nci_concept_name: str | None = None, ) -> Self: activity_group_vo = cls( name=name, @@ -29,6 +34,8 @@ def from_repository_values( definition=definition, abbreviation=abbreviation, is_template_parameter=True, + nci_concept_id=nci_concept_id, + nci_concept_name=nci_concept_name, ) return activity_group_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_instance.py b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_instance.py index f1dcc519..2bc768a1 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_instance.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_instance.py @@ -1,5 +1,5 @@ -from dataclasses import dataclass -from typing import Callable, Self +from dataclasses import dataclass, field +from typing import AbstractSet, Callable, Self from neo4j.graph import Node @@ -12,9 +12,11 @@ from clinical_mdr_api.domains.concepts.activities.activity import ActivityGroupingVO from clinical_mdr_api.domains.concepts.activities.activity_item import ActivityItemVO from clinical_mdr_api.domains.concepts.concept_base import ConceptARBase, ConceptVO +from clinical_mdr_api.domains.enums import LibraryItemStatus, ObjectAction from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, + VersioningActionMixin, ) from common.exceptions import ( AlreadyExistsException, @@ -31,9 +33,9 @@ class ActivityInstanceGroupingVO(ActivityGroupingVO): @dataclass(frozen=True) -class ActivityInstanceVO(ConceptVO): +class ActivityInstanceAttributesVO(ConceptVO): """ - The ActivityInstanceVO acts as the value object for a single ActivityInstance aggregate + The ActivityInstanceAttributesVO acts as the value object for a single ActivityInstanceAttributes aggregate """ nci_concept_id: str | None @@ -48,8 +50,6 @@ class ActivityInstanceVO(ConceptVO): is_legacy_usage: bool is_derived: bool legacy_description: str | None - activity_name: str | None - activity_groupings: list[ActivityInstanceGroupingVO] activity_instance_class_uid: str activity_instance_class_name: str | None activity_items: list[ActivityItemVO] @@ -73,11 +73,9 @@ def from_repository_values( is_legacy_usage: bool, is_derived: bool, legacy_description: str | None, - activity_groupings: list[ActivityInstanceGroupingVO], activity_instance_class_uid: str, activity_instance_class_name: str | None, activity_items: list[ActivityItemVO], - activity_name: str | None = None, ) -> Self: activity_instance_vo = cls( nci_concept_id=nci_concept_id, @@ -99,20 +97,13 @@ def from_repository_values( is_legacy_usage=is_legacy_usage, is_derived=is_derived, legacy_description=legacy_description, - activity_groupings=( - activity_groupings if activity_groupings is not None else [] - ), activity_items=activity_items if activity_items is not None else [], - activity_name=activity_name, ) return activity_instance_vo def validate( # pylint: disable=too-many-locals self, - get_final_activity_value_by_uid_callback: Callable[[str], Node | None], - activity_subgroup_exists: Callable[[str], bool], - activity_group_exists: Callable[[str], bool], ct_term_exists_by_uid_callback: Callable[[str], bool], unit_definition_exists_by_uid_callback: Callable[[str], bool], find_activity_item_class_by_uid_callback: Callable[ @@ -129,10 +120,6 @@ def validate( # pylint: disable=too-many-locals previous_topic_code: str | None = None, library_name: str | None = None, preview: bool = False, - activity_subgroup_latest_is_final: Callable[[str], bool] = lambda x: True, - activity_group_latest_is_final: Callable[[str], bool] = lambda x: True, - get_activity_subgroup_name: Callable[[str], str | None] = lambda x: None, - get_activity_group_name: Callable[[str], str | None] = lambda x: None, get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, strict_mode: bool = False, ) -> None: @@ -160,71 +147,6 @@ def validate( # pylint: disable=too-many-locals "Topic Code", ) - if not self.activity_groupings: - raise BusinessLogicException( - msg="Activity Instance must have at least one grouping", - ) - - for activity_grouping in self.activity_groupings: - if activity_grouping.activity_uid is None: - raise BusinessLogicException( - msg="Activity UID missing for one of the Activity Groupings" - ) - activity = get_final_activity_value_by_uid_callback( - activity_grouping.activity_uid - ) - if activity is None: - raise BusinessLogicException( - msg=f"{type(self).__name__} tried to connect to non-existent or non-final Activity with UID '{activity_grouping.activity_uid}'.", - ) - BusinessLogicException.raise_if_not( - activity["is_data_collected"], - msg=f"{type(self).__name__} tried to connect to Activity without data collection", - ) - - # Check that the selected subgroup and group exist - BusinessLogicException.raise_if_not( - activity_subgroup_exists(activity_grouping.activity_subgroup_uid), - msg=f"{type(self).__name__} tried to connect to non-existent Activity Sub Group with UID '{activity_grouping.activity_subgroup_uid}'.", - ) - BusinessLogicException.raise_if_not( - activity_group_exists(activity_grouping.activity_group_uid), - msg=f"{type(self).__name__} tried to connect to non-existent Activity Group with UID '{activity_grouping.activity_group_uid}'.", - ) - - # Check that the LATEST version of the selected subgroup and group are Final (only during creation) - if previous_name is None: # This is a creation, not an edit - if not activity_subgroup_latest_is_final( - activity_grouping.activity_subgroup_uid - ): - # Get the subgroup name for a better error message - name = get_activity_subgroup_name( - activity_grouping.activity_subgroup_uid - ) - if name: - subgroup_str = ( - f"'{name}' ({activity_grouping.activity_subgroup_uid})" - ) - else: - subgroup_str = f"'{activity_grouping.activity_subgroup_uid}'" - - raise BusinessLogicException( - msg=f"Cannot create activity instance: Activity Sub Group {subgroup_str} is currently not in Final status." - ) - if not activity_group_latest_is_final( - activity_grouping.activity_group_uid - ): - # Get the group name for a better error message - name = get_activity_group_name(activity_grouping.activity_group_uid) - if name: - group_str = f"'{name}' ({activity_grouping.activity_group_uid})" - else: - group_str = f"'{activity_grouping.activity_group_uid}'" - - raise BusinessLogicException( - msg=f"Cannot create activity instance: Activity Group {group_str} is currently not in Final status." - ) - activity_item_class_uids = [ item.activity_item_class_uid for item in self.activity_items ] @@ -292,6 +214,19 @@ def validate( # pylint: disable=too-many-locals unit.uid and unit_definition_exists_by_uid_callback(unit.uid), msg=f"{type(self).__name__} tried to connect to non-existent or non-final Unit Definition with UID '{unit.uid}'.", ) + if activity_item.is_activity_instance_id_specific: + BusinessLogicException.raise_if( + activity_item.ct_codelist is not None, + msg="An ActivityItem with 'is_activity_instance_id_specific' set to true must not have a ct_codelist.", + ) + BusinessLogicException.raise_if( + len(activity_item.ct_terms) > 1, + msg="An ActivityItem with 'is_activity_instance_id_specific' set to true must not have more than one ct_term.", + ) + BusinessLogicException.raise_if( + len(activity_item.unit_definitions) > 1, + msg="An ActivityItem with 'is_activity_instance_id_specific' set to true must not have more than one unit_definition.", + ) activity_instance_class = find_activity_instance_class_by_uid_callback( self.activity_instance_class_uid @@ -423,148 +358,449 @@ def validate( # pylint: disable=too-many-locals ) -@dataclass -class ActivityInstanceAR(ConceptARBase): - _concept_vo: ActivityInstanceVO - - @property - def concept_vo(self) -> ActivityInstanceVO: - return self._concept_vo - - @concept_vo.setter - def concept_vo(self, value: ActivityInstanceVO) -> None: - self._concept_vo = value - - @property - def name(self) -> str: - return self._concept_vo.name +@dataclass(frozen=True) +class ActivityInstanceGroupingsVO: + """ + The ActivityInstanceGroupingsVO acts as the value object for a single ActivityInstanceGroupings aggregate + """ - @property - def name_sentence_case(self) -> str: - return self._concept_vo.name_sentence_case + activity_name: str | None + activity_groupings: list[ActivityInstanceGroupingVO] @classmethod def from_repository_values( cls, - uid: str, - concept_vo: ActivityInstanceVO, - library: LibraryVO, - item_metadata: LibraryItemMetadataVO, + activity_groupings: list[ActivityInstanceGroupingVO], + activity_name: str | None = None, ) -> Self: - activity_ar = cls( - _uid=uid, - _concept_vo=concept_vo, - _item_metadata=item_metadata, - _library=library, + activity_instance_vo = cls( + activity_groupings=( + activity_groupings if activity_groupings is not None else [] + ), + activity_name=activity_name, ) - return activity_ar - @classmethod - def from_input_values( - cls, - *, - author_id: str, - concept_vo: ActivityInstanceVO, - library: LibraryVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, - concept_exists_by_library_and_property_value_callback: Callable[ - [str, str, str], bool - ] = lambda x, y, z: True, + return activity_instance_vo + + def validate( # pylint: disable=too-many-locals + self, get_final_activity_value_by_uid_callback: Callable[[str], Node | None], activity_subgroup_exists: Callable[[str], bool], activity_group_exists: Callable[[str], bool], - ct_term_exists_by_uid_callback: Callable[[str], bool] = lambda _: False, - unit_definition_exists_by_uid_callback: Callable[[str], bool] = lambda _: False, - find_activity_item_class_by_uid_callback: Callable[[str], ActivityItemClassAR], - find_activity_instance_class_by_uid_callback: Callable[ - [str], ActivityInstanceClassAR - ], - get_dimension_names_by_unit_definition_uids: Callable[ - [list[str]], list[str] - ] = lambda _: [], activity_subgroup_latest_is_final: Callable[[str], bool] = lambda x: True, activity_group_latest_is_final: Callable[[str], bool] = lambda x: True, get_activity_subgroup_name: Callable[[str], str | None] = lambda x: None, get_activity_group_name: Callable[[str], str | None] = lambda x: None, - get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, - strict_mode: bool = False, - generate_uid_callback: Callable[[], str | None] = lambda: None, - preview: bool = False, - ) -> Self: - item_metadata = LibraryItemMetadataVO.get_initial_item_metadata( - author_id=author_id - ) + update: bool = False, + ) -> None: - BusinessLogicException.raise_if_not( - library.is_editable, - msg=f"Library with Name '{library.name}' doesn't allow creation of objects.", - ) + if not self.activity_groupings: + raise BusinessLogicException( + msg="Activity Instance must have at least one grouping", + ) - concept_vo.validate( - get_final_activity_value_by_uid_callback=get_final_activity_value_by_uid_callback, - activity_subgroup_exists=activity_subgroup_exists, - activity_group_exists=activity_group_exists, - ct_term_exists_by_uid_callback=ct_term_exists_by_uid_callback, - unit_definition_exists_by_uid_callback=unit_definition_exists_by_uid_callback, - find_activity_item_class_by_uid_callback=find_activity_item_class_by_uid_callback, - find_activity_instance_class_by_uid_callback=find_activity_instance_class_by_uid_callback, - get_dimension_names_by_unit_definition_uids=get_dimension_names_by_unit_definition_uids, - library_name=library.name, - preview=preview, - activity_subgroup_latest_is_final=activity_subgroup_latest_is_final, - activity_group_latest_is_final=activity_group_latest_is_final, - get_activity_subgroup_name=get_activity_subgroup_name, - get_activity_group_name=get_activity_group_name, - get_parent_class_uid_callback=get_parent_class_uid_callback, - strict_mode=strict_mode, - activity_instance_exists_by_property_value=concept_exists_by_library_and_property_value_callback, - ) + for activity_grouping in self.activity_groupings: + if activity_grouping.activity_uid is None: + raise BusinessLogicException( + msg="Activity UID missing for one of the Activity Groupings" + ) + activity = get_final_activity_value_by_uid_callback( + activity_grouping.activity_uid + ) + if activity is None: + raise BusinessLogicException( + msg=f"{type(self).__name__} tried to connect to non-existent or non-final Activity with UID '{activity_grouping.activity_uid}'.", + ) + BusinessLogicException.raise_if_not( + activity["is_data_collected"], + msg=f"{type(self).__name__} tried to connect to Activity without data collection", + ) - activity_ar = cls( - _uid=generate_uid_callback(), - _item_metadata=item_metadata, - _library=library, - _concept_vo=concept_vo, - ) - return activity_ar + # Check that the selected subgroup and group exist + BusinessLogicException.raise_if_not( + activity_subgroup_exists(activity_grouping.activity_subgroup_uid), + msg=f"{type(self).__name__} tried to connect to non-existent Activity Sub Group with UID '{activity_grouping.activity_subgroup_uid}'.", + ) + BusinessLogicException.raise_if_not( + activity_group_exists(activity_grouping.activity_group_uid), + msg=f"{type(self).__name__} tried to connect to non-existent Activity Group with UID '{activity_grouping.activity_group_uid}'.", + ) - def edit_draft( - self, - author_id: str, - change_description: str, - concept_vo: ActivityInstanceVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, - concept_exists_by_library_and_property_value_callback: Callable[ - [str, str, str], bool - ] = lambda x, y, z: True, - get_final_activity_value_by_uid_callback: Callable[ - [str], Node | None - ] = lambda _: None, - activity_subgroup_exists: Callable[[str], bool] = lambda _: True, - activity_group_exists: Callable[[str], bool] = lambda _: True, - ct_term_exists_by_uid_callback: Callable[[str], bool] = lambda _: True, - unit_definition_exists_by_uid_callback: Callable[[str], bool] = lambda _: True, - find_activity_item_class_by_uid_callback: Callable[ - ..., ActivityItemClassAR | None - ] = lambda _: None, - find_activity_instance_class_by_uid_callback: Callable[ - ..., ActivityInstanceClassAR | None - ] = lambda _: None, - get_dimension_names_by_unit_definition_uids: Callable[ - [list[str]], list[str] - ] = lambda _: [], - get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, - strict_mode: bool = False, - perform_validation: bool = True, - ) -> None: - """ - Creates a new draft version for the object. - """ - if perform_validation: + # Check that the LATEST version of the selected subgroup and group are Final (only during creation) + if not update: # This is a creation, not an edit + if not activity_subgroup_latest_is_final( + activity_grouping.activity_subgroup_uid + ): + # Get the subgroup name for a better error message + name = get_activity_subgroup_name( + activity_grouping.activity_subgroup_uid + ) + if name: + subgroup_str = ( + f"'{name}' ({activity_grouping.activity_subgroup_uid})" + ) + else: + subgroup_str = f"'{activity_grouping.activity_subgroup_uid}'" + + raise BusinessLogicException( + msg=f"Cannot create activity instance: Activity Sub Group {subgroup_str} is currently not in Final status." + ) + if not activity_group_latest_is_final( + activity_grouping.activity_group_uid + ): + # Get the group name for a better error message + name = get_activity_group_name(activity_grouping.activity_group_uid) + if name: + group_str = f"'{name}' ({activity_grouping.activity_group_uid})" + else: + group_str = f"'{activity_grouping.activity_group_uid}'" + + raise BusinessLogicException( + msg=f"Cannot create activity instance: Activity Group {group_str} is currently not in Final status." + ) + + +@dataclass(frozen=True) +class ActivityInstanceVO(ConceptVO): + """ + The ActivityInstanceVO acts as the value object for a single ActivityInstance aggregate. + Combines ActivityInstanceAttributesVO with grouping information. + """ + + activity_instance_attributes: ActivityInstanceAttributesVO + activity_name: str | None + activity_groupings: list[ActivityInstanceGroupingVO] + + @property + def nci_concept_id(self) -> str | None: + return self.activity_instance_attributes.nci_concept_id + + @property + def nci_concept_name(self) -> str | None: + return self.activity_instance_attributes.nci_concept_name + + @classmethod + def from_repository_values( + cls, + nci_concept_id: str | None, + nci_concept_name: str | None, + name: str, + name_sentence_case: str, + definition: str | None, + abbreviation: str | None, + is_research_lab: bool, + molecular_weight: float | None, + topic_code: str | None, + adam_param_code: str | None, + is_required_for_activity: bool, + is_default_selected_for_activity: bool, + is_data_sharing: bool, + is_legacy_usage: bool, + is_derived: bool, + legacy_description: str | None, + activity_groupings: list[ActivityInstanceGroupingVO], + activity_instance_class_uid: str, + activity_instance_class_name: str | None, + activity_items: list[ActivityItemVO], + activity_name: str | None = None, + ) -> Self: + attributes_vo = ActivityInstanceAttributesVO.from_repository_values( + nci_concept_id=nci_concept_id, + nci_concept_name=nci_concept_name, + name=name, + name_sentence_case=name_sentence_case, + definition=definition, + abbreviation=abbreviation, + is_research_lab=is_research_lab, + molecular_weight=molecular_weight, + topic_code=topic_code, + adam_param_code=adam_param_code, + is_required_for_activity=is_required_for_activity, + is_default_selected_for_activity=is_default_selected_for_activity, + is_data_sharing=is_data_sharing, + is_legacy_usage=is_legacy_usage, + is_derived=is_derived, + legacy_description=legacy_description, + activity_instance_class_uid=activity_instance_class_uid, + activity_instance_class_name=activity_instance_class_name, + activity_items=activity_items if activity_items is not None else [], + ) + + activity_instance_vo = cls( + name=name, + name_sentence_case=name_sentence_case, + definition=definition, + abbreviation=abbreviation, + is_template_parameter=True, + activity_instance_attributes=attributes_vo, + activity_groupings=( + activity_groupings if activity_groupings is not None else [] + ), + activity_name=activity_name, + ) + + return activity_instance_vo + + def validate( # pylint: disable=too-many-locals + self, + get_final_activity_value_by_uid_callback: Callable[[str], Node | None], + activity_subgroup_exists: Callable[[str], bool], + activity_group_exists: Callable[[str], bool], + ct_term_exists_by_uid_callback: Callable[[str], bool], + unit_definition_exists_by_uid_callback: Callable[[str], bool], + find_activity_item_class_by_uid_callback: Callable[ + ..., ActivityItemClassAR | None + ], + find_activity_instance_class_by_uid_callback: Callable[ + ..., ActivityInstanceClassAR | None + ], + get_dimension_names_by_unit_definition_uids: Callable[[list[str]], list[str]], + activity_instance_exists_by_property_value: Callable[ + [str, str, str], bool + ] = lambda x, y, z: True, + previous_name: str | None = None, + previous_topic_code: str | None = None, + library_name: str | None = None, + preview: bool = False, + activity_subgroup_latest_is_final: Callable[[str], bool] = lambda x: True, + activity_group_latest_is_final: Callable[[str], bool] = lambda x: True, + get_activity_subgroup_name: Callable[[str], str | None] = lambda x: None, + get_activity_group_name: Callable[[str], str | None] = lambda x: None, + get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, + strict_mode: bool = False, + ) -> None: + # Delegate attributes validation to the embedded ActivityInstanceAttributesVO + self.activity_instance_attributes.validate( + ct_term_exists_by_uid_callback=ct_term_exists_by_uid_callback, + unit_definition_exists_by_uid_callback=unit_definition_exists_by_uid_callback, + find_activity_item_class_by_uid_callback=find_activity_item_class_by_uid_callback, + find_activity_instance_class_by_uid_callback=find_activity_instance_class_by_uid_callback, + get_dimension_names_by_unit_definition_uids=get_dimension_names_by_unit_definition_uids, + activity_instance_exists_by_property_value=activity_instance_exists_by_property_value, + previous_name=previous_name, + previous_topic_code=previous_topic_code, + library_name=library_name, + preview=preview, + get_parent_class_uid_callback=get_parent_class_uid_callback, + strict_mode=strict_mode, + ) + + if not self.activity_groupings: + raise BusinessLogicException( + msg="Activity Instance must have at least one grouping", + ) + + for activity_grouping in self.activity_groupings: + if activity_grouping.activity_uid is None: + raise BusinessLogicException( + msg="Activity UID missing for one of the Activity Groupings" + ) + activity = get_final_activity_value_by_uid_callback( + activity_grouping.activity_uid + ) + if activity is None: + raise BusinessLogicException( + msg=f"{type(self).__name__} tried to connect to non-existent or non-final Activity with UID '{activity_grouping.activity_uid}'.", + ) + BusinessLogicException.raise_if_not( + activity["is_data_collected"], + msg=f"{type(self).__name__} tried to connect to Activity without data collection", + ) + + # Check that the selected subgroup and group exist + BusinessLogicException.raise_if_not( + activity_subgroup_exists(activity_grouping.activity_subgroup_uid), + msg=f"{type(self).__name__} tried to connect to non-existent Activity Sub Group with UID '{activity_grouping.activity_subgroup_uid}'.", + ) + BusinessLogicException.raise_if_not( + activity_group_exists(activity_grouping.activity_group_uid), + msg=f"{type(self).__name__} tried to connect to non-existent Activity Group with UID '{activity_grouping.activity_group_uid}'.", + ) + + # Check that the LATEST version of the selected subgroup and group are Final (only during creation) + if previous_name is None: # This is a creation, not an edit + if not activity_subgroup_latest_is_final( + activity_grouping.activity_subgroup_uid + ): + # Get the subgroup name for a better error message + name = get_activity_subgroup_name( + activity_grouping.activity_subgroup_uid + ) + if name: + subgroup_str = ( + f"'{name}' ({activity_grouping.activity_subgroup_uid})" + ) + else: + subgroup_str = f"'{activity_grouping.activity_subgroup_uid}'" + + raise BusinessLogicException( + msg=f"Cannot create activity instance: Activity Sub Group {subgroup_str} is currently not in Final status." + ) + if not activity_group_latest_is_final( + activity_grouping.activity_group_uid + ): + # Get the group name for a better error message + name = get_activity_group_name(activity_grouping.activity_group_uid) + if name: + group_str = f"'{name}' ({activity_grouping.activity_group_uid})" + else: + group_str = f"'{activity_grouping.activity_group_uid}'" + + raise BusinessLogicException( + msg=f"Cannot create activity instance: Activity Group {group_str} is currently not in Final status." + ) + + +@dataclass +class ActivityInstanceAR(ConceptARBase): + _concept_vo: ActivityInstanceVO + _groupings_item_metadata: LibraryItemMetadataVO + + @property + def concept_vo(self) -> ActivityInstanceVO: + return self._concept_vo + + @concept_vo.setter + def concept_vo(self, value: ActivityInstanceVO) -> None: + self._concept_vo = value + + @property + def name(self) -> str: + return self._concept_vo.name + + @property + def name_sentence_case(self) -> str: + return self._concept_vo.name_sentence_case + + @property + def groupings_item_metadata(self) -> LibraryItemMetadataVO: + return self._groupings_item_metadata + + @classmethod + def from_repository_values( + cls, + uid: str, + concept_vo: ActivityInstanceVO, + library: LibraryVO, + item_metadata: LibraryItemMetadataVO, + groupings_item_metadata: LibraryItemMetadataVO, + ) -> Self: + activity_ar = cls( + _uid=uid, + _concept_vo=concept_vo, + _item_metadata=item_metadata, + _groupings_item_metadata=groupings_item_metadata, + _library=library, + ) + return activity_ar + + @classmethod + def from_input_values( + cls, + *, + author_id: str, + concept_vo: ActivityInstanceVO, + library: LibraryVO, + concept_exists_by_callback: Callable[ + [str, str, bool], bool + ] = lambda x, y, z: True, + concept_exists_by_library_and_property_value_callback: Callable[ + [str, str, str], bool + ] = lambda x, y, z: True, + get_final_activity_value_by_uid_callback: Callable[[str], Node | None], + activity_subgroup_exists: Callable[[str], bool], + activity_group_exists: Callable[[str], bool], + ct_term_exists_by_uid_callback: Callable[[str], bool] = lambda _: False, + unit_definition_exists_by_uid_callback: Callable[[str], bool] = lambda _: False, + find_activity_item_class_by_uid_callback: Callable[[str], ActivityItemClassAR], + find_activity_instance_class_by_uid_callback: Callable[ + [str], ActivityInstanceClassAR + ], + get_dimension_names_by_unit_definition_uids: Callable[ + [list[str]], list[str] + ] = lambda _: [], + activity_subgroup_latest_is_final: Callable[[str], bool] = lambda x: True, + activity_group_latest_is_final: Callable[[str], bool] = lambda x: True, + get_activity_subgroup_name: Callable[[str], str | None] = lambda x: None, + get_activity_group_name: Callable[[str], str | None] = lambda x: None, + get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, + strict_mode: bool = False, + generate_uid_callback: Callable[[], str | None] = lambda: None, + preview: bool = False, + ) -> Self: + item_metadata = LibraryItemMetadataVO.get_initial_item_metadata( + author_id=author_id + ) + + BusinessLogicException.raise_if_not( + library.is_editable, + msg=f"Library with Name '{library.name}' doesn't allow creation of objects.", + ) + + concept_vo.validate( + get_final_activity_value_by_uid_callback=get_final_activity_value_by_uid_callback, + activity_subgroup_exists=activity_subgroup_exists, + activity_group_exists=activity_group_exists, + ct_term_exists_by_uid_callback=ct_term_exists_by_uid_callback, + unit_definition_exists_by_uid_callback=unit_definition_exists_by_uid_callback, + find_activity_item_class_by_uid_callback=find_activity_item_class_by_uid_callback, + find_activity_instance_class_by_uid_callback=find_activity_instance_class_by_uid_callback, + get_dimension_names_by_unit_definition_uids=get_dimension_names_by_unit_definition_uids, + library_name=library.name, + preview=preview, + activity_subgroup_latest_is_final=activity_subgroup_latest_is_final, + activity_group_latest_is_final=activity_group_latest_is_final, + get_activity_subgroup_name=get_activity_subgroup_name, + get_activity_group_name=get_activity_group_name, + get_parent_class_uid_callback=get_parent_class_uid_callback, + strict_mode=strict_mode, + activity_instance_exists_by_property_value=concept_exists_by_library_and_property_value_callback, + ) + + activity_ar = cls( + _uid=generate_uid_callback(), + _item_metadata=item_metadata, + _groupings_item_metadata=item_metadata, + _library=library, + _concept_vo=concept_vo, + ) + return activity_ar + + def edit_draft( + self, + author_id: str, + change_description: str, + concept_vo: ActivityInstanceVO, + concept_exists_by_callback: Callable[ + [str, str, bool], bool + ] = lambda x, y, z: True, + concept_exists_by_library_and_property_value_callback: Callable[ + [str, str, str], bool + ] = lambda x, y, z: True, + get_final_activity_value_by_uid_callback: Callable[ + [str], Node | None + ] = lambda _: None, + activity_subgroup_exists: Callable[[str], bool] = lambda _: True, + activity_group_exists: Callable[[str], bool] = lambda _: True, + ct_term_exists_by_uid_callback: Callable[[str], bool] = lambda _: True, + unit_definition_exists_by_uid_callback: Callable[[str], bool] = lambda _: True, + find_activity_item_class_by_uid_callback: Callable[ + ..., ActivityItemClassAR | None + ] = lambda _: None, + find_activity_instance_class_by_uid_callback: Callable[ + ..., ActivityInstanceClassAR | None + ] = lambda _: None, + get_dimension_names_by_unit_definition_uids: Callable[ + [list[str]], list[str] + ] = lambda _: [], + get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, + strict_mode: bool = False, + perform_validation: bool = True, + ) -> None: + """ + Creates a new draft version for the object. + """ + if perform_validation: concept_vo.validate( get_final_activity_value_by_uid_callback=get_final_activity_value_by_uid_callback, activity_subgroup_exists=activity_subgroup_exists, @@ -586,3 +822,291 @@ def edit_draft( change_description=change_description, author_id=author_id ) self._concept_vo = concept_vo + + def get_groupings_possible_actions(self) -> AbstractSet[ObjectAction]: + """ + Returns list of possible actions for the groupings versioning track. + """ + md = self._groupings_item_metadata + if md.status == LibraryItemStatus.DRAFT and md.major_version == 0: + return {ObjectAction.APPROVE, ObjectAction.EDIT, ObjectAction.DELETE} + if md.status == LibraryItemStatus.DRAFT: + return {ObjectAction.APPROVE, ObjectAction.EDIT} + if md.status == LibraryItemStatus.FINAL: + return {ObjectAction.NEWVERSION, ObjectAction.INACTIVATE} + if md.status == LibraryItemStatus.RETIRED: + return {ObjectAction.REACTIVATE} + return frozenset() + + def soft_delete(self) -> None: + BusinessLogicException.raise_if( + self._groupings_item_metadata.major_version != 0, + msg="Object has been accepted", + ) + super().soft_delete() + + +@dataclass +class ActivityInstanceAttributesAR(ConceptARBase): + _concept_vo: ActivityInstanceAttributesVO + + @property + def concept_vo(self) -> ActivityInstanceAttributesVO: + return self._concept_vo + + @concept_vo.setter + def concept_vo(self, value: ActivityInstanceAttributesVO) -> None: + self._concept_vo = value + + @property + def name(self) -> str: + return self._concept_vo.name + + @property + def name_sentence_case(self) -> str: + return self._concept_vo.name_sentence_case + + @property + def groupings_item_metadata(self) -> LibraryItemMetadataVO: + return self._groupings_item_metadata + + @classmethod + def from_repository_values( + cls, + uid: str, + concept_vo: ActivityInstanceAttributesVO, + library: LibraryVO, + item_metadata: LibraryItemMetadataVO, + ) -> Self: + activity_ar = cls( + _uid=uid, + _concept_vo=concept_vo, + _item_metadata=item_metadata, + _library=library, + ) + return activity_ar + + @classmethod + def from_input_values( + cls, + *, + author_id: str, + concept_vo: ActivityInstanceAttributesVO, + library: LibraryVO, + concept_exists_by_callback: Callable[ + [str, str, bool], bool + ] = lambda x, y, z: True, + concept_exists_by_library_and_property_value_callback: Callable[ + [str, str, str], bool + ] = lambda x, y, z: True, + ct_term_exists_by_uid_callback: Callable[[str], bool] = lambda _: False, + unit_definition_exists_by_uid_callback: Callable[[str], bool] = lambda _: False, + find_activity_item_class_by_uid_callback: Callable[[str], ActivityItemClassAR], + find_activity_instance_class_by_uid_callback: Callable[ + [str], ActivityInstanceClassAR + ], + get_dimension_names_by_unit_definition_uids: Callable[ + [list[str]], list[str] + ] = lambda _: [], + get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, + strict_mode: bool = False, + generate_uid_callback: Callable[[], str | None] = lambda: None, + preview: bool = False, + ) -> Self: + item_metadata = LibraryItemMetadataVO.get_initial_item_metadata( + author_id=author_id + ) + + BusinessLogicException.raise_if_not( + library.is_editable, + msg=f"Library with Name '{library.name}' doesn't allow creation of objects.", + ) + + concept_vo.validate( + ct_term_exists_by_uid_callback=ct_term_exists_by_uid_callback, + unit_definition_exists_by_uid_callback=unit_definition_exists_by_uid_callback, + find_activity_item_class_by_uid_callback=find_activity_item_class_by_uid_callback, + find_activity_instance_class_by_uid_callback=find_activity_instance_class_by_uid_callback, + get_dimension_names_by_unit_definition_uids=get_dimension_names_by_unit_definition_uids, + library_name=library.name, + preview=preview, + get_parent_class_uid_callback=get_parent_class_uid_callback, + strict_mode=strict_mode, + activity_instance_exists_by_property_value=concept_exists_by_library_and_property_value_callback, + ) + + activity_ar = cls( + _uid=generate_uid_callback(), + _item_metadata=item_metadata, + _library=library, + _concept_vo=concept_vo, + ) + return activity_ar + + def edit_draft( + self, + author_id: str, + change_description: str, + concept_vo: ActivityInstanceAttributesVO, + concept_exists_by_callback: Callable[ + [str, str, bool], bool + ] = lambda x, y, z: True, + concept_exists_by_library_and_property_value_callback: Callable[ + [str, str, str], bool + ] = lambda x, y, z: True, + get_final_activity_value_by_uid_callback: Callable[ + [str], Node | None + ] = lambda _: None, + ct_term_exists_by_uid_callback: Callable[[str], bool] = lambda _: True, + unit_definition_exists_by_uid_callback: Callable[[str], bool] = lambda _: True, + find_activity_item_class_by_uid_callback: Callable[ + ..., ActivityItemClassAR | None + ] = lambda _: None, + find_activity_instance_class_by_uid_callback: Callable[ + ..., ActivityInstanceClassAR | None + ] = lambda _: None, + get_dimension_names_by_unit_definition_uids: Callable[ + [list[str]], list[str] + ] = lambda _: [], + get_parent_class_uid_callback: Callable[[str], str | None] = lambda _: None, + strict_mode: bool = False, + perform_validation: bool = True, + ) -> None: + """ + Creates a new draft version for the object. + """ + _ = get_final_activity_value_by_uid_callback + if perform_validation: + concept_vo.validate( + ct_term_exists_by_uid_callback=ct_term_exists_by_uid_callback, + unit_definition_exists_by_uid_callback=unit_definition_exists_by_uid_callback, + find_activity_item_class_by_uid_callback=find_activity_item_class_by_uid_callback, + find_activity_instance_class_by_uid_callback=find_activity_instance_class_by_uid_callback, + get_dimension_names_by_unit_definition_uids=get_dimension_names_by_unit_definition_uids, + get_parent_class_uid_callback=get_parent_class_uid_callback, + strict_mode=strict_mode, + activity_instance_exists_by_property_value=concept_exists_by_library_and_property_value_callback, + previous_name=self.name, + previous_topic_code=self._concept_vo.topic_code, + library_name=self.library.name, + ) + if self._concept_vo != concept_vo: + super()._edit_draft( + change_description=change_description, author_id=author_id + ) + self._concept_vo = concept_vo + + +@dataclass +class ActivityInstanceGroupingsAR(VersioningActionMixin): + _concept_vo: ActivityInstanceGroupingsVO + _item_metadata: LibraryItemMetadataVO + + # used for soft delete + _is_deleted: bool = field(init=False, default=False) + + # Properties from ActivityInstanceRoot + _uid: str | None + _library: LibraryVO + + @property + def uid(self) -> str | None: + return self._uid + + @property + def library(self) -> LibraryVO: + return self._library + + @property + def is_deleted(self) -> bool: + return self._is_deleted + + @property + def concept_vo(self) -> ActivityInstanceGroupingsVO: + return self._concept_vo + + @concept_vo.setter + def concept_vo(self, value: ActivityInstanceGroupingsVO) -> None: + self._concept_vo = value + + @property + def item_metadata(self) -> LibraryItemMetadataVO: + return self._item_metadata + + @property + def name(self) -> str: + return self._concept_vo.name + + @property + def name_sentence_case(self) -> str: + return self._concept_vo.name_sentence_case + + def _is_edit_allowed_in_non_editable_library(self): + return True + + @classmethod + def from_repository_values( + cls, + uid: str, + concept_vo: ActivityInstanceGroupingsVO, + library: LibraryVO, + item_metadata: LibraryItemMetadataVO, + ) -> Self: + activity_ar = cls( + _uid=uid, + _library=library, + _concept_vo=concept_vo, + _item_metadata=item_metadata, + ) + return activity_ar + + def create_new_version(self, author_id: str) -> None: + """ + Puts object into DRAFT status with relevant changes to version numbers. + """ + super()._create_new_version(author_id=author_id) + + def edit_draft( + self, + author_id: str, + change_description: str, + concept_vo: ActivityInstanceGroupingsVO, + get_final_activity_value_by_uid_callback: Callable[ + [str], Node | None + ] = lambda _: None, + activity_subgroup_exists: Callable[[str], bool] = lambda _: True, + activity_group_exists: Callable[[str], bool] = lambda _: True, + perform_validation: bool = True, + ) -> None: + """ + Creates a new draft version for the object. + """ + if perform_validation: + concept_vo.validate( + get_final_activity_value_by_uid_callback=get_final_activity_value_by_uid_callback, + activity_subgroup_exists=activity_subgroup_exists, + activity_group_exists=activity_group_exists, + update=True, + ) + if self._concept_vo != concept_vo: + super()._edit_draft( + change_description=change_description, author_id=author_id + ) + self._concept_vo = concept_vo + + def get_possible_actions(self) -> AbstractSet[ObjectAction]: + """ + Returns list of possible actions + """ + if ( + self._item_metadata.status == LibraryItemStatus.DRAFT + and self._item_metadata.major_version == 0 + ): + return {ObjectAction.APPROVE, ObjectAction.EDIT, ObjectAction.DELETE} + if self._item_metadata.status == LibraryItemStatus.DRAFT: + return {ObjectAction.APPROVE, ObjectAction.EDIT} + if self._item_metadata.status == LibraryItemStatus.FINAL: + return {ObjectAction.NEWVERSION, ObjectAction.INACTIVATE} + if self._item_metadata.status == LibraryItemStatus.RETIRED: + return {ObjectAction.REACTIVATE} + return frozenset() diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_item.py b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_item.py index 3a4ee8e8..eb4fbdb8 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_item.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_item.py @@ -28,6 +28,7 @@ class ActivityItemVO: """ is_adam_param_specific: bool + is_activity_instance_id_specific: bool | None activity_item_class_uid: str activity_item_class_name: str | None ct_codelist: CTCodelistItem | None @@ -45,9 +46,11 @@ def from_repository_values( ct_terms: list[CTTermItem], unit_definitions: list[CompactUnitDefinition], text_value: str | None = None, + is_activity_instance_id_specific: bool | None = None, ) -> Self: activity_item_vo = cls( is_adam_param_specific=is_adam_param_specific, + is_activity_instance_id_specific=is_activity_instance_id_specific, activity_item_class_uid=activity_item_class_uid, activity_item_class_name=activity_item_class_name, ct_codelist=ct_codelist, diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_sub_group.py b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_sub_group.py index d27bd19b..dab14673 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_sub_group.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/concepts/activities/activity_sub_group.py @@ -17,6 +17,8 @@ class ActivitySubGroupVO(ConceptVO): name: str name_sentence_case: str + nci_concept_id: str | None = None + nci_concept_name: str | None = None @classmethod def from_repository_values( @@ -25,6 +27,8 @@ def from_repository_values( name_sentence_case: str, definition: str | None, abbreviation: str | None, + nci_concept_id: str | None = None, + nci_concept_name: str | None = None, ) -> Self: activity_subgroup_vo = cls( name=name, @@ -32,6 +36,8 @@ def from_repository_values( definition=definition, abbreviation=abbreviation, is_template_parameter=True, + nci_concept_id=nci_concept_id, + nci_concept_name=nci_concept_name, ) return activity_subgroup_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_term.py b/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_term.py index fe18762b..b18b760f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_term.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/controlled_terminologies/ct_codelist_term.py @@ -1,16 +1,14 @@ from dataclasses import dataclass from datetime import datetime -from typing import Any, Self +from typing import Any, Generic, Self, TypeVar from clinical_mdr_api.domain_repositories.models._utils import convert_to_datetime from clinical_mdr_api.domains.versioned_object_aggregate import LibraryItemStatus @dataclass(frozen=True) -class CTCodelistTermVO: - """ - The CTCodelistNameVO acts as the value object for a single CTCodelist name - """ +class CTCodelistTermBaseVO: + """Base value object with fields common to all codelist term variants.""" term_uid: str sponsor_preferred_name: str @@ -21,7 +19,6 @@ class CTCodelistTermVO: end_date: datetime | None attributes_status: LibraryItemStatus attributes_date: datetime - submission_value: str order: int | None ordinal: float | None concept_id: str | None @@ -30,52 +27,97 @@ class CTCodelistTermVO: library_name: str | None @classmethod - def from_result_dict(cls, result: dict[str, Any]) -> Self: - ct_codelist_term_vo = cls( - term_uid=result["term_uid"], - sponsor_preferred_name=result["sponsor_preferred_name"], - sponsor_preferred_name_sentence_case=result[ + def _common_kwargs_from_result_dict(cls, result: dict[str, Any]) -> dict[str, Any]: + return { + "term_uid": result["term_uid"], + "sponsor_preferred_name": result["sponsor_preferred_name"], + "sponsor_preferred_name_sentence_case": result[ "sponsor_preferred_name_sentence_case" ], - name_status=LibraryItemStatus(result["name_status"]), - name_date=convert_to_datetime(result["name_date"]), - attributes_status=LibraryItemStatus(result["attributes_status"]), - attributes_date=convert_to_datetime(result["attributes_date"]), + "name_status": LibraryItemStatus(result["name_status"]), + "name_date": convert_to_datetime(result["name_date"]), + "attributes_status": LibraryItemStatus(result["attributes_status"]), + "attributes_date": convert_to_datetime(result["attributes_date"]), + "order": result.get("order"), + "ordinal": result.get("ordinal"), + "start_date": convert_to_datetime(result["start_date"]), + "end_date": convert_to_datetime(result.get("end_date")), + "concept_id": result.get("concept_id"), + "nci_preferred_name": result.get("nci_preferred_name"), + "definition": result["definition"], + "library_name": result.get("library_name"), + } + + +@dataclass(frozen=True) +class CTCodelistTermVO(CTCodelistTermBaseVO): + submission_value: str + + @classmethod + def from_result_dict(cls, result: dict[str, Any]) -> Self: + return cls( + **cls._common_kwargs_from_result_dict(result), submission_value=result["submission_value"], - order=result.get("order"), - ordinal=result.get("ordinal"), - start_date=convert_to_datetime(result["start_date"]), - end_date=convert_to_datetime(result.get("end_date")), - concept_id=result.get("concept_id"), - nci_preferred_name=result.get("nci_preferred_name"), - definition=result["definition"], - library_name=result.get("library_name"), ) - return ct_codelist_term_vo + +_VOType = TypeVar("_VOType", bound=CTCodelistTermBaseVO) # pylint: disable=invalid-name @dataclass -class CTCodelistTermAR: - _ct_codelist_term_vo: CTCodelistTermVO +class CTCodelistTermBaseAR(Generic[_VOType]): + _vo: _VOType + + @property + def vo(self) -> _VOType: + return self._vo + + @classmethod + def from_repository_values(cls, vo: _VOType) -> Self: + return cls(_vo=vo) + +@dataclass +class CTCodelistTermAR(CTCodelistTermBaseAR[CTCodelistTermVO]): @property def ct_codelist_term_vo(self) -> CTCodelistTermVO: - return self._ct_codelist_term_vo + return self._vo @classmethod - def from_repository_values( - cls, - ct_codelist_term_vo: CTCodelistTermVO, - ) -> Self: - ct_codelist_term_ar = cls( - _ct_codelist_term_vo=ct_codelist_term_vo, + def from_result_dict(cls, result: dict[str, Any]) -> Self: + return cls.from_repository_values(CTCodelistTermVO.from_result_dict(result)) + + +@dataclass(frozen=True) +class CTPairedCodelistTermVO(CTCodelistTermBaseVO): + """ + Value object for a term in a paired codelist context, + containing submission values from both the names and codes codelists. + """ + + code_submission_value: str | None + name_submission_value: str | None + + @classmethod + def from_result_dict(cls, result: dict[str, Any]) -> Self: + return cls( + **cls._common_kwargs_from_result_dict(result), + code_submission_value=result.get("code_submission_value"), + name_submission_value=result.get("name_submission_value"), ) - return ct_codelist_term_ar + + +@dataclass +class CTPairedCodelistTermAR(CTCodelistTermBaseAR[CTPairedCodelistTermVO]): + @property + def ct_paired_codelist_term_vo(self) -> CTPairedCodelistTermVO: + return self._vo @classmethod def from_result_dict(cls, result: dict[str, Any]) -> Self: - return cls.from_repository_values(CTCodelistTermVO.from_result_dict(result)) + return cls.from_repository_values( + CTPairedCodelistTermVO.from_result_dict(result) + ) @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/odms/item.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/item.py index 1fb69274..a37b74b9 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/odms/item.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/item.py @@ -155,7 +155,7 @@ def validate( if activity_instance["activity_item_class_uid"] not in [ activity_item.activity_item_class_uid - for activity_item in db_activity_instance.concept_vo.activity_items + for activity_item in db_activity_instance.concept_vo.activity_instance_attributes.activity_items ]: raise BusinessLogicException( msg=( diff --git a/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_metadata.py b/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_metadata.py index ac233ffb..1022843d 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_metadata.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/study_metadata.py @@ -58,6 +58,7 @@ class StudyCompactComponentEnum(str, Enum): _STUDY_NUMBER_PATTERN = re.compile(r"\d{1,4}") +_STUDY_SUBPART_ACRONYM_PATTERN = re.compile(r"[A-Z0-9]+") FIX_SOME_VALUE_DEFAULT = """ @@ -97,7 +98,11 @@ def __init__( study_number=normalize_string(study_number), subpart_id=normalize_string(subpart_id), study_acronym=normalize_string(study_acronym), - study_subpart_acronym=normalize_string(study_subpart_acronym), + study_subpart_acronym=normalize_string( + study_subpart_acronym.upper() + if study_subpart_acronym + else study_subpart_acronym + ), study_id_prefix=normalize_string(_study_id_prefix), description=normalize_string(description), registry_identifiers=registry_identifiers, @@ -182,6 +187,20 @@ def validate( msg="Study Subpart Acronym must be provided for Study Subpart.", ) + exceptions.ValidationException.raise_if( + self.study_subpart_acronym is not None + and len(self.study_subpart_acronym) > 10, + msg=f"Study Subpart Acronym must not exceed 10 characters, got {len(self.study_subpart_acronym) if self.study_subpart_acronym else 0}.", + ) + + exceptions.ValidationException.raise_if( + self.study_subpart_acronym is not None + and not _STUDY_SUBPART_ACRONYM_PATTERN.fullmatch( + self.study_subpart_acronym + ), + msg=f"Study Subpart Acronym must contain only alphanumeric characters (no blanks or special characters), got '{self.study_subpart_acronym}'.", + ) + exceptions.ValidationException.raise_if( not is_subpart and self.study_number is not None 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 b11df641..d68168b8 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 @@ -128,6 +128,8 @@ def visit_name(self): def derive_visit_name(self): if self.visit_class != VisitClass.MANUALLY_DEFINED_VISIT: + if self.visit_class == VisitClass.UNSCHEDULED_VISIT: + return settings.unscheduled_visit_name if self.visit_subclass == VisitSubclass.REPEATING_VISIT: return f"Visit {int(self.visit_number)}.n" return f"Visit {int(self.visit_number)}" @@ -197,7 +199,7 @@ def visit_short_name(self): self.special_visit_number - 1 ] return visit_short_name + chosen_letter - if self.visit_class in (VisitClass.NON_VISIT, VisitClass.UNSCHEDULED_VISIT): + if self.visit_class in [VisitClass.UNSCHEDULED_VISIT, VisitClass.NON_VISIT]: return visit_number return visit_short_name return self.vis_short_name diff --git a/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_instance_class.py b/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_instance_class.py index 0a826efc..d20a749b 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_instance_class.py +++ b/clinical-mdr-api/clinical_mdr_api/models/biomedical_concepts/activity_instance_class.py @@ -1,4 +1,4 @@ -from typing import Annotated, Callable, Self +from typing import Annotated, Any, Callable, Self from pydantic import ConfigDict, Field, ValidationInfo, field_validator @@ -13,6 +13,7 @@ from clinical_mdr_api.models.concepts.concept import VersionProperties from clinical_mdr_api.models.libraries.library import Library from clinical_mdr_api.models.utils import BaseModel, InputModel, PatchInputModel +from common.utils import convert_to_datetime class ParentActivityItemClass(BaseModel): @@ -140,6 +141,24 @@ class CompactActivityItemClassForInstanceClass(BaseModel): } ), ] = False + data_type_uid: Annotated[ + str | None, + Field( + json_schema_extra={ + "source": "has_activity_item_class.has_latest_value.has_data_type.has_selected_term.uid", + "nullable": True, + } + ), + ] = None + data_type_name: Annotated[ + str | None, + Field( + json_schema_extra={ + "source": "has_activity_item_class.has_latest_value.has_data_type.has_selected_term.has_name_root.has_latest_value.name", + "nullable": True, + } + ), + ] = None class CompactActivityInstanceClass(BaseModel): @@ -273,6 +292,25 @@ def from_activity_instance_class_ar( ), ) + @classmethod + def from_cypher_row(cls, row: dict[str, Any]) -> Self: + return cls( + uid=row["uid"], + name=row["name"], + order=row.get("order_val"), + definition=row.get("definition"), + is_domain_specific=row.get("is_domain_specific"), + level=row.get("level"), + library_name=row.get("library_name"), + start_date=convert_to_datetime(row.get("start_date")), + end_date=convert_to_datetime(row.get("end_date")), + status=row.get("status"), + version=row.get("version"), + change_description=row.get("change_description"), + author_username=row.get("author_username"), + possible_actions=[], + ) + class ActivityInstanceClassInput(InputModel): name: Annotated[str | None, Field(min_length=1)] = None 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 9c2c7690..25dcc524 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 @@ -373,6 +373,22 @@ class CompactActivityItemClass(BaseModel): } ), ] = False + data_type_uid: Annotated[ + str | None, + Field( + json_schema_extra={ + "nullable": True, + } + ), + ] = None + data_type_name: Annotated[ + str | None, + Field( + json_schema_extra={ + "nullable": True, + } + ), + ] = None class ActivityInstanceClassRelInput(InputModel): diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_group.py b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_group.py index 42b294e7..16705ad4 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_group.py +++ b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_group.py @@ -11,6 +11,13 @@ class ActivityGroup(ActivityBase): + nci_concept_id: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + nci_concept_name: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + @classmethod def from_activity_ar(cls, activity_group_ar: ActivityGroupAR) -> Self: return cls( @@ -19,6 +26,8 @@ def from_activity_ar(cls, activity_group_ar: ActivityGroupAR) -> Self: name_sentence_case=activity_group_ar.concept_vo.name_sentence_case, definition=activity_group_ar.concept_vo.definition, abbreviation=activity_group_ar.concept_vo.abbreviation, + nci_concept_id=activity_group_ar.concept_vo.nci_concept_id, + nci_concept_name=activity_group_ar.concept_vo.nci_concept_name, library_name=Library.from_library_vo(activity_group_ar.library).name, start_date=activity_group_ar.item_metadata.start_date, end_date=activity_group_ar.item_metadata.end_date, @@ -41,6 +50,8 @@ class BaseActivityGroupInput(ExtendedConceptPostInput): ), ] name_sentence_case: Annotated[str, Field(min_length=1)] + nci_concept_id: Annotated[str | None, Field(min_length=1)] = None + nci_concept_name: Annotated[str | None, Field(min_length=1)] = None class ActivityGroupEditInput(BaseActivityGroupInput, EditInputModel): @@ -64,6 +75,8 @@ class ActivityGroupDetail(BaseModel): name: Annotated[str, Field()] name_sentence_case: Annotated[str | None, Field()] = None + nci_concept_id: Annotated[str | None, Field()] = None + nci_concept_name: Annotated[str | None, Field()] = None library_name: Annotated[str | None, Field()] = None start_date: Annotated[str | None, Field()] = None end_date: Annotated[str | None, Field()] = None 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 2ec29e55..ba80c8d5 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 @@ -8,6 +8,8 @@ from clinical_mdr_api.domains.concepts.activities.activity_group import ActivityGroupAR from clinical_mdr_api.domains.concepts.activities.activity_instance import ( ActivityInstanceAR, + ActivityInstanceAttributesAR, + ActivityInstanceGroupingsAR, ) from clinical_mdr_api.domains.concepts.activities.activity_item import ( CTCodelistItem, @@ -23,11 +25,9 @@ ActivityBase, ActivityGrouping, ActivityHierarchySimpleModel, - SimpleActivityGroup, SimpleActivityGrouping, SimpleActivityInstance, SimpleActivityInstanceClassForActivity, - SimpleActivitySubGroup, ) from clinical_mdr_api.models.concepts.activities.activity_item import ( ActivityItem, @@ -42,7 +42,7 @@ ExtendedConceptPostInput, ) from clinical_mdr_api.models.libraries.library import Library -from clinical_mdr_api.models.utils import BaseModel +from clinical_mdr_api.models.utils import BaseModel, PatchInputModel from common.utils import convert_to_datetime @@ -56,7 +56,7 @@ class ActivityInstanceGrouping(ActivityGrouping): activity_uid: Annotated[str, Field()] -class ActivityInstance(ActivityBase): +class ActivityInstanceAttributes(ActivityBase): nci_concept_id: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None @@ -82,12 +82,357 @@ class ActivityInstance(ActivityBase): legacy_description: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None + activity_instance_class: Annotated[ + CompactActivityInstanceClass, + Field(description="The uid and the name of the linked activity instance class"), + ] + activity_items: Annotated[ + list[ActivityItem] | None, + Field( + description="List of activity items", + ), + ] = None + start_date: Annotated[datetime | None, Field()] = None + end_date: Annotated[ + datetime | None, Field(json_schema_extra={"nullable": True}) + ] = None + status: Annotated[str | None, Field()] = None + version: Annotated[str | None, Field()] = None + change_description: Annotated[str | None, Field()] = None + author_username: Annotated[ + str | None, + Field( + json_schema_extra={"nullable": True}, + ), + ] = None + possible_actions: Annotated[ + list[str] | None, + Field( + description=( + "Holds those actions that can be performed on the ActivityInstances. " + "Actions are: 'approve', 'edit', 'new_version'." + ), + ), + ] = None + + @classmethod + def from_activity_ar( + cls, + activity_ar: ActivityInstanceAttributesAR, + ) -> Self: + activity_items = [] + for activity_item in activity_ar.concept_vo.activity_items: + ct_terms = [] + unit_definitions = [] + for unit in activity_item.unit_definitions: + unit_definitions.append( + CompactUnitDefinition( + uid=unit.uid, name=unit.name, dimension_name=unit.dimension_name + ) + ) + unit_definitions.sort(key=lambda x: x.uid or "") + for term in activity_item.ct_terms: + ct_terms.append( + CompactCTTerm( + uid=term.uid, + name=term.name, + submission_value=term.submission_value, + codelist_uid=term.codelist_uid, + ) + ) + ct_terms.sort(key=lambda x: x.uid or "") + + activity_items.append( + ActivityItem( + activity_item_class=CompactActivityItemClassForActivityItem( + uid=activity_item.activity_item_class_uid, + name=activity_item.activity_item_class_name, + ), + ct_terms=ct_terms, + unit_definitions=unit_definitions, + is_adam_param_specific=activity_item.is_adam_param_specific, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, + ) + ) + + return cls( + uid=activity_ar.uid, + nci_concept_id=activity_ar.concept_vo.nci_concept_id, + nci_concept_name=activity_ar.concept_vo.nci_concept_name, + name=activity_ar.name, + name_sentence_case=activity_ar.concept_vo.name_sentence_case, + definition=activity_ar.concept_vo.definition, + abbreviation=activity_ar.concept_vo.abbreviation, + topic_code=activity_ar.concept_vo.topic_code, + is_research_lab=activity_ar.concept_vo.is_research_lab, + molecular_weight=activity_ar.concept_vo.molecular_weight, + adam_param_code=activity_ar.concept_vo.adam_param_code, + is_required_for_activity=activity_ar.concept_vo.is_required_for_activity, + is_default_selected_for_activity=activity_ar.concept_vo.is_default_selected_for_activity, + is_data_sharing=activity_ar.concept_vo.is_data_sharing, + is_legacy_usage=activity_ar.concept_vo.is_legacy_usage, + is_derived=activity_ar.concept_vo.is_derived, + legacy_description=activity_ar.concept_vo.legacy_description, + activity_instance_class=CompactActivityInstanceClass( + uid=activity_ar.concept_vo.activity_instance_class_uid, + name=activity_ar.concept_vo.activity_instance_class_name, + ), + activity_items=activity_items, + library_name=Library.from_library_vo(activity_ar.library).name, + start_date=activity_ar.item_metadata.start_date, + end_date=activity_ar.item_metadata.end_date, + status=activity_ar.item_metadata.status.value, + version=activity_ar.item_metadata.version, + change_description=activity_ar.item_metadata.change_description, + author_username=activity_ar.item_metadata.author_username, + possible_actions=sorted( + [_.value for _ in activity_ar.get_possible_actions()] + ), + ) + + @classmethod + def from_activity_instance_ar_objects( + cls, activity_instance_ar: ActivityInstanceAttributesAR + ) -> Self: + activity_items = [] + for activity_item in activity_instance_ar.concept_vo.activity_items: + unit_definitions = sorted( + [ + CompactUnitDefinition(uid=unit.uid, name=unit.name) + for unit in activity_item.unit_definitions + ], + key=lambda x: x.uid or "", + ) + + ct_terms = sorted( + [ + CompactCTTerm( + uid=term.uid, + name=term.name, + submission_value=term.submission_value, + ) + for term in activity_item.ct_terms + ], + key=lambda x: x.uid or "", + ) + + activity_items.append( + ActivityItem( + activity_item_class=CompactActivityItemClassForActivityItem( + uid=activity_item.activity_item_class_uid, + name=activity_item.activity_item_class_name, + ), + ct_terms=ct_terms, + unit_definitions=unit_definitions, + is_adam_param_specific=activity_item.is_adam_param_specific, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, + ) + ) + + return cls( + uid=activity_instance_ar.uid, + nci_concept_id=activity_instance_ar.concept_vo.nci_concept_id, + nci_concept_name=activity_instance_ar.concept_vo.nci_concept_name, + name=activity_instance_ar.name, + name_sentence_case=activity_instance_ar.concept_vo.name_sentence_case, + definition=activity_instance_ar.concept_vo.definition, + abbreviation=activity_instance_ar.concept_vo.abbreviation, + topic_code=activity_instance_ar.concept_vo.topic_code, + is_research_lab=activity_instance_ar.concept_vo.is_research_lab, + molecular_weight=activity_instance_ar.concept_vo.molecular_weight, + adam_param_code=activity_instance_ar.concept_vo.adam_param_code, + is_required_for_activity=activity_instance_ar.concept_vo.is_required_for_activity, + is_default_selected_for_activity=activity_instance_ar.concept_vo.is_default_selected_for_activity, + is_data_sharing=activity_instance_ar.concept_vo.is_data_sharing, + is_legacy_usage=activity_instance_ar.concept_vo.is_legacy_usage, + is_derived=activity_instance_ar.concept_vo.is_derived, + legacy_description=activity_instance_ar.concept_vo.legacy_description, + activity_instance_class=CompactActivityInstanceClass( + uid=activity_instance_ar.concept_vo.activity_instance_class_uid, + name=activity_instance_ar.concept_vo.activity_instance_class_name, + ), + activity_items=activity_items, + library_name=Library.from_library_vo(activity_instance_ar.library).name, + start_date=activity_instance_ar.item_metadata.start_date, + end_date=activity_instance_ar.item_metadata.end_date, + status=activity_instance_ar.item_metadata.status.value, + version=activity_instance_ar.item_metadata.version, + change_description=activity_instance_ar.item_metadata.change_description, + author_username=activity_instance_ar.item_metadata.author_username, + possible_actions=sorted( + [_.value for _ in activity_instance_ar.get_possible_actions()] + ), + ) + + +# ActivityInstance is a complete view of an Activity Instance +# that combines both the instance attributes and the groupings. +class ActivityInstanceGroupings(BaseModel): + start_date: Annotated[datetime | None, Field()] = None + end_date: Annotated[ + datetime | None, Field(json_schema_extra={"nullable": True}) + ] = None + status: Annotated[str | None, Field()] = None + version: Annotated[str | None, Field()] = None + change_description: Annotated[str | None, Field()] = None + author_username: Annotated[ + str | None, + Field( + json_schema_extra={"nullable": True}, + ), + ] = None + possible_actions: Annotated[ + list[str] | None, + Field( + description=( + "Holds those actions that can be performed on the ActivityInstances. " + "Actions are: 'approve', 'edit', 'new_version'." + ), + ), + ] = None + + # These properties are related to the separately versioned activity instance groupings activity_groupings: Annotated[ list[ActivityInstanceHierarchySimpleModel] | None, Field() ] = None activity_name: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None + + @classmethod + def from_activity_ar( + cls, + activity_ar: ActivityInstanceGroupingsAR, + find_activity_hierarchy_by_uid: Callable[[str], ActivityAR | None], + find_activity_subgroup_by_uid: Callable[[str], ActivitySubGroupAR | None], + find_activity_group_by_uid: Callable[[str], ActivityGroupAR | None], + ) -> Self: + + activity_groupings = [] + for activity_grouping in activity_ar.concept_vo.activity_groupings: + if activity_grouping.activity_name: + # Activity name is there, it means we are building for a GET query + translation = ActivityInstanceHierarchySimpleModel( + activity_group=ActivityHierarchySimpleModel( + uid=activity_grouping.activity_group_uid, + name=activity_grouping.activity_group_name, + ), + activity_subgroup=ActivityHierarchySimpleModel( + uid=activity_grouping.activity_subgroup_uid, + name=activity_grouping.activity_subgroup_name, + ), + activity=ActivityHierarchySimpleModel( + uid=activity_grouping.activity_uid or "", + name=activity_grouping.activity_name, + ), + ) + else: + translation = ActivityInstanceHierarchySimpleModel( + activity_group=ActivityHierarchySimpleModel.from_activity_uid( + uid=activity_grouping.activity_group_uid, + find_activity_by_uid=find_activity_group_by_uid, + version=activity_grouping.activity_group_version, + ), + activity_subgroup=ActivityHierarchySimpleModel.from_activity_uid( + uid=activity_grouping.activity_subgroup_uid, + find_activity_by_uid=find_activity_subgroup_by_uid, + version=activity_grouping.activity_subgroup_version, + ), + activity=ActivityHierarchySimpleModel.from_activity_uid( + uid=activity_grouping.activity_uid or "", + find_activity_by_uid=find_activity_hierarchy_by_uid, + version=activity_grouping.activity_version, + ), + ) + activity_groupings.append(translation) + + return cls( + activity_groupings=activity_groupings, + activity_name=activity_ar.concept_vo.activity_name, + start_date=activity_ar.item_metadata.start_date, + end_date=activity_ar.item_metadata.end_date, + status=activity_ar.item_metadata.status.value, + version=activity_ar.item_metadata.version, + change_description=activity_ar.item_metadata.change_description, + author_username=activity_ar.item_metadata.author_username, + possible_actions=sorted( + [_.value for _ in activity_ar.get_possible_actions()] + ), + ) + + @classmethod + def from_activity_instance_ar_objects( + cls, activity_instance_ar: ActivityInstanceAR + ) -> Self: + + activity_instance_groupings = [ + ActivityInstanceHierarchySimpleModel( + activity_group=ActivityHierarchySimpleModel( + uid=activity_instance_grouping_vo.activity_group_uid, + name=activity_instance_grouping_vo.activity_group_name, + ), + activity_subgroup=ActivityHierarchySimpleModel( + uid=activity_instance_grouping_vo.activity_subgroup_uid, + name=activity_instance_grouping_vo.activity_subgroup_name, + ), + activity=ActivityHierarchySimpleModel( + uid=activity_instance_grouping_vo.activity_uid or "", + name=activity_instance_grouping_vo.activity_name, + ), + ) + for activity_instance_grouping_vo in activity_instance_ar.concept_vo.activity_groupings + ] + + return cls( + activity_groupings=sorted( + activity_instance_groupings, + key=lambda item: ( + item.activity_subgroup.name, + item.activity_group.name, + item.activity.name, + ), + ), + activity_name=activity_instance_ar.concept_vo.activity_name, + start_date=activity_instance_ar.item_metadata.start_date, + end_date=activity_instance_ar.item_metadata.end_date, + status=activity_instance_ar.item_metadata.status.value, + version=activity_instance_ar.item_metadata.version, + change_description=activity_instance_ar.item_metadata.change_description, + author_username=activity_instance_ar.item_metadata.author_username, + possible_actions=sorted( + [_.value for _ in activity_instance_ar.get_possible_actions()] + ), + ) + + +# ActivityInstance is a complete view of an Activity Instance +# that combines both the instance attributes and the groupings. +class ActivityInstance(ActivityBase): + nci_concept_id: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + nci_concept_name: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + + topic_code: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( + None + ) + adam_param_code: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + is_research_lab: Annotated[bool, Field()] = False + molecular_weight: Annotated[ + float | None, Field(json_schema_extra={"nullable": True}) + ] = None + is_required_for_activity: Annotated[bool, Field()] = False + is_default_selected_for_activity: Annotated[bool, Field()] = False + is_data_sharing: Annotated[bool, Field()] = False + is_legacy_usage: Annotated[bool, Field()] = False + is_derived: Annotated[bool, Field()] = False + legacy_description: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None activity_instance_class: Annotated[ CompactActivityInstanceClass, Field(description="The uid and the name of the linked activity instance class"), @@ -121,6 +466,46 @@ class ActivityInstance(ActivityBase): ), ] = None + # These properties are related to the separately versioned activity instance groupings + activity_groupings: Annotated[ + list[ActivityInstanceHierarchySimpleModel] | None, Field() + ] = None + activity_name: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + groupings_status: Annotated[ + str | None, Field(json_schema_extra={"remove_from_wildcard": True}) + ] = None + groupings_version: Annotated[ + str | None, Field(json_schema_extra={"remove_from_wildcard": True}) + ] = None + groupings_start_date: Annotated[ + datetime | None, Field(json_schema_extra={"remove_from_wildcard": True}) + ] = None + groupings_end_date: Annotated[ + datetime | None, + Field(json_schema_extra={"nullable": True, "remove_from_wildcard": True}), + ] = None + groupings_change_description: Annotated[ + str | None, Field(json_schema_extra={"remove_from_wildcard": True}) + ] = None + groupings_author_username: Annotated[ + str | None, + Field( + json_schema_extra={"nullable": True, "remove_from_wildcard": True}, + ), + ] = None + groupings_possible_actions: Annotated[ + list[str] | None, + Field( + description=( + "Holds those actions that can be performed on the ActivityInstance groupings. " + "Actions are: 'approve', 'edit', 'new_version'." + ), + json_schema_extra={"remove_from_wildcard": True}, + ), + ] = None + @classmethod def from_activity_ar( cls, @@ -129,8 +514,9 @@ def from_activity_ar( find_activity_subgroup_by_uid: Callable[[str], ActivitySubGroupAR | None], find_activity_group_by_uid: Callable[[str], ActivityGroupAR | None], ) -> Self: + attrs = activity_ar.concept_vo.activity_instance_attributes activity_items = [] - for activity_item in activity_ar.concept_vo.activity_items: + for activity_item in attrs.activity_items: ct_terms = [] unit_definitions = [] for unit in activity_item.unit_definitions: @@ -169,6 +555,7 @@ def from_activity_ar( ct_terms=ct_terms, unit_definitions=unit_definitions, is_adam_param_specific=activity_item.is_adam_param_specific, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, text_value=activity_item.text_value, ) ) @@ -213,27 +600,27 @@ def from_activity_ar( return cls( uid=activity_ar.uid, - nci_concept_id=activity_ar.concept_vo.nci_concept_id, - nci_concept_name=activity_ar.concept_vo.nci_concept_name, + nci_concept_id=attrs.nci_concept_id, + nci_concept_name=attrs.nci_concept_name, name=activity_ar.name, - name_sentence_case=activity_ar.concept_vo.name_sentence_case, - definition=activity_ar.concept_vo.definition, - abbreviation=activity_ar.concept_vo.abbreviation, - topic_code=activity_ar.concept_vo.topic_code, - is_research_lab=activity_ar.concept_vo.is_research_lab, - molecular_weight=activity_ar.concept_vo.molecular_weight, - adam_param_code=activity_ar.concept_vo.adam_param_code, - is_required_for_activity=activity_ar.concept_vo.is_required_for_activity, - is_default_selected_for_activity=activity_ar.concept_vo.is_default_selected_for_activity, - is_data_sharing=activity_ar.concept_vo.is_data_sharing, - is_legacy_usage=activity_ar.concept_vo.is_legacy_usage, - is_derived=activity_ar.concept_vo.is_derived, - legacy_description=activity_ar.concept_vo.legacy_description, + name_sentence_case=attrs.name_sentence_case, + definition=attrs.definition, + abbreviation=attrs.abbreviation, + topic_code=attrs.topic_code, + is_research_lab=attrs.is_research_lab, + molecular_weight=attrs.molecular_weight, + adam_param_code=attrs.adam_param_code, + is_required_for_activity=attrs.is_required_for_activity, + is_default_selected_for_activity=attrs.is_default_selected_for_activity, + is_data_sharing=attrs.is_data_sharing, + is_legacy_usage=attrs.is_legacy_usage, + is_derived=attrs.is_derived, + legacy_description=attrs.legacy_description, activity_groupings=activity_groupings, activity_name=activity_ar.concept_vo.activity_name, activity_instance_class=CompactActivityInstanceClass( - uid=activity_ar.concept_vo.activity_instance_class_uid, - name=activity_ar.concept_vo.activity_instance_class_name, + uid=attrs.activity_instance_class_uid, + name=attrs.activity_instance_class_name, ), activity_items=activity_items, library_name=Library.from_library_vo(activity_ar.library).name, @@ -246,14 +633,24 @@ def from_activity_ar( possible_actions=sorted( [_.value for _ in activity_ar.get_possible_actions()] ), + groupings_status=activity_ar.groupings_item_metadata.status.value, + groupings_version=activity_ar.groupings_item_metadata.version, + groupings_start_date=activity_ar.groupings_item_metadata.start_date, + groupings_end_date=activity_ar.groupings_item_metadata.end_date, + groupings_change_description=activity_ar.groupings_item_metadata.change_description, + groupings_author_username=activity_ar.groupings_item_metadata.author_username, + groupings_possible_actions=sorted( + [_.value for _ in activity_ar.get_groupings_possible_actions()] + ), ) @classmethod def from_activity_instance_ar_objects( cls, activity_instance_ar: ActivityInstanceAR ) -> Self: + attrs = activity_instance_ar.concept_vo.activity_instance_attributes activity_items = [] - for activity_item in activity_instance_ar.concept_vo.activity_items: + for activity_item in attrs.activity_items: unit_definitions = sorted( [ CompactUnitDefinition(uid=unit.uid, name=unit.name) @@ -283,6 +680,7 @@ def from_activity_instance_ar_objects( ct_terms=ct_terms, unit_definitions=unit_definitions, is_adam_param_specific=activity_item.is_adam_param_specific, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, text_value=activity_item.text_value, ) ) @@ -307,22 +705,22 @@ def from_activity_instance_ar_objects( return cls( uid=activity_instance_ar.uid, - nci_concept_id=activity_instance_ar.concept_vo.nci_concept_id, - nci_concept_name=activity_instance_ar.concept_vo.nci_concept_name, + nci_concept_id=attrs.nci_concept_id, + nci_concept_name=attrs.nci_concept_name, name=activity_instance_ar.name, - name_sentence_case=activity_instance_ar.concept_vo.name_sentence_case, - definition=activity_instance_ar.concept_vo.definition, - abbreviation=activity_instance_ar.concept_vo.abbreviation, - topic_code=activity_instance_ar.concept_vo.topic_code, - is_research_lab=activity_instance_ar.concept_vo.is_research_lab, - molecular_weight=activity_instance_ar.concept_vo.molecular_weight, - adam_param_code=activity_instance_ar.concept_vo.adam_param_code, - is_required_for_activity=activity_instance_ar.concept_vo.is_required_for_activity, - is_default_selected_for_activity=activity_instance_ar.concept_vo.is_default_selected_for_activity, - is_data_sharing=activity_instance_ar.concept_vo.is_data_sharing, - is_legacy_usage=activity_instance_ar.concept_vo.is_legacy_usage, - is_derived=activity_instance_ar.concept_vo.is_derived, - legacy_description=activity_instance_ar.concept_vo.legacy_description, + name_sentence_case=attrs.name_sentence_case, + definition=attrs.definition, + abbreviation=attrs.abbreviation, + topic_code=attrs.topic_code, + is_research_lab=attrs.is_research_lab, + molecular_weight=attrs.molecular_weight, + adam_param_code=attrs.adam_param_code, + is_required_for_activity=attrs.is_required_for_activity, + is_default_selected_for_activity=attrs.is_default_selected_for_activity, + is_data_sharing=attrs.is_data_sharing, + is_legacy_usage=attrs.is_legacy_usage, + is_derived=attrs.is_derived, + legacy_description=attrs.legacy_description, activity_groupings=sorted( activity_instance_groupings, key=lambda item: ( @@ -333,8 +731,8 @@ def from_activity_instance_ar_objects( ), activity_name=activity_instance_ar.concept_vo.activity_name, activity_instance_class=CompactActivityInstanceClass( - uid=activity_instance_ar.concept_vo.activity_instance_class_uid, - name=activity_instance_ar.concept_vo.activity_instance_class_name, + uid=attrs.activity_instance_class_uid, + name=attrs.activity_instance_class_name, ), activity_items=activity_items, library_name=Library.from_library_vo(activity_instance_ar.library).name, @@ -412,6 +810,35 @@ class ActivityInstanceEditInput(ExtendedConceptPatchInput): change_description: Annotated[str, Field(min_length=1)] +class ActivityInstanceAttributesEditInput(ExtendedConceptPatchInput): + nci_concept_id: Annotated[str | None, Field(min_length=1)] = None + nci_concept_name: Annotated[str | None, Field(min_length=1)] = None + topic_code: Annotated[str | None, Field(min_length=1)] = None + is_research_lab: Annotated[bool, Field()] = False + molecular_weight: Annotated[float | None, Field()] = None + adam_param_code: Annotated[str | None, Field(min_length=1)] = None + is_required_for_activity: Annotated[bool | None, Field()] = None + is_default_selected_for_activity: Annotated[bool | None, Field()] = None + is_data_sharing: Annotated[bool | None, Field()] = None + is_legacy_usage: Annotated[bool | None, Field()] = None + is_derived: Annotated[bool | None, Field()] = None + legacy_description: Annotated[str | None, Field(min_length=1)] = None + activity_instance_class_uid: Annotated[str | None, Field(min_length=1)] = None + activity_items: Annotated[list[ActivityItemCreateInput] | None, Field()] = None + strict_mode: Annotated[ + bool | None, + Field( + description="If True, enforces strict validation for parent mandatory activity item classes. Defaults to False (relaxed mode) when not provided." + ), + ] = None + change_description: Annotated[str, Field(min_length=1)] + + +class ActivityInstanceGroupingsEditInput(PatchInputModel): + activity_groupings: Annotated[list[ActivityInstanceGrouping] | None, Field()] = None + change_description: Annotated[str, Field(min_length=1)] + + class ActivityInstanceVersion(ActivityInstance): """ Class for storing ActivityInstance and calculation of differences @@ -420,6 +847,22 @@ class ActivityInstanceVersion(ActivityInstance): changes: list[str] = Field(description=CHANGES_FIELD_DESC, default_factory=list) +class ActivityInstanceAttributesVersion(ActivityInstanceAttributes): + """ + Class for storing ActivityInstanceAttributes and calculation of differences + """ + + changes: list[str] = Field(description=CHANGES_FIELD_DESC, default_factory=list) + + +class ActivityInstanceGroupingsVersion(ActivityInstanceGroupings): + """ + Class for storing ActivityInstanceGroupings and calculation of differences + """ + + changes: list[str] = Field(description=CHANGES_FIELD_DESC, default_factory=list) + + class SimpleActivityForActivityInstance(BaseModel): uid: Annotated[str, Field()] nci_concept_id: Annotated[ @@ -468,6 +911,7 @@ class SimplifiedActivityItem(BaseModel): unit_definitions: list[CompactUnitDefinition] = Field(default_factory=list) activity_item_class: Annotated[SimpleActivityItemClassForActivityInstance, Field()] is_adam_param_specific: Annotated[bool, Field()] + is_activity_instance_id_specific: Annotated[bool | None, Field()] = None text_value: Annotated[str | None, Field()] = None @@ -476,7 +920,7 @@ class SimpleActivityInstanceGrouping(SimpleActivityGrouping): class ActivityInstanceOverview(BaseModel): - activity_groupings: Annotated[list[SimpleActivityInstanceGrouping], Field()] + activity_groupings_versions: Annotated[list[str], Field()] activity_instance: Annotated[SimpleActivityInstance, Field()] activity_items: Annotated[list[SimplifiedActivityItem], Field()] all_versions: Annotated[list[str], Field()] @@ -544,69 +988,15 @@ def from_repository_input(cls, overview: dict[str, Any]): is_adam_param_specific=activity_item.get( "is_adam_param_specific", False ), + is_activity_instance_id_specific=activity_item.get( + "is_activity_instance_id_specific" + ), text_value=activity_item.get("text_value"), ) ) return cls( - activity_groupings=[ - SimpleActivityInstanceGrouping( - activity=SimpleActivityForActivityInstance( - uid=activity_grouping.get("uid"), - name=activity_grouping.get("activity_value").get("name"), - definition=activity_grouping.get("activity_value").get( - "definition" - ), - nci_concept_id=activity_grouping.get("activity_value").get( - "nci_concept_id" - ), - nci_concept_name=activity_grouping.get("activity_value").get( - "nci_concept_name" - ), - synonyms=activity_grouping.get("activity_value").get( - "synonyms", [] - ), - is_data_collected=activity_grouping.get("activity_value").get( - "is_data_collected", False - ), - is_multiple_selection_allowed=activity_grouping.get( - "activity_value" - ).get("is_multiple_selection_allowed", True), - library_name=activity_grouping.get("activity_library_name"), - version=(activity_grouping.get("version") or {}).get("version"), - status=(activity_grouping.get("version") or {}).get("status"), - ), - activity_group=SimpleActivityGroup( - uid=activity_grouping.get("activity_group_uid"), - name=activity_grouping.get("activity_group_value").get("name"), - definition=activity_grouping.get("activity_group_value").get( - "definition" - ), - version=( - activity_grouping.get("activity_group_version") or {} - ).get("version"), - status=( - activity_grouping.get("activity_group_version") or {} - ).get("status"), - ), - activity_subgroup=SimpleActivitySubGroup( - uid=activity_grouping.get("activity_subgroup_uid"), - name=activity_grouping.get("activity_subgroup_value").get( - "name" - ), - definition=activity_grouping.get("activity_subgroup_value").get( - "definition" - ), - version=( - activity_grouping.get("activity_subgroup_version") or {} - ).get("version"), - status=( - activity_grouping.get("activity_subgroup_version") or {} - ).get("status"), - ), - ) - for activity_grouping in overview.get("hierarchy") - ], + activity_groupings_versions=overview["groupings_versions"], activity_instance=SimpleActivityInstance( uid=overview.get("activity_instance_root").get("uid"), name=overview.get("activity_instance_value").get("name"), diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_item.py b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_item.py index 3c6a1ced..3c96e8c0 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_item.py +++ b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_item.py @@ -121,6 +121,7 @@ class ActivityItem(BaseModel): ct_terms: list[CompactCTTerm] = Field(default_factory=list) unit_definitions: list[CompactUnitDefinition] = Field(default_factory=list) is_adam_param_specific: Annotated[bool, Field()] + is_activity_instance_id_specific: Annotated[bool | None, Field()] = None text_value: Annotated[str | None, Field()] = None @@ -134,6 +135,7 @@ class CTTermsInput(PostInputModel): ct_terms: Annotated[list[CTTermsInput], Field()] unit_definition_uids: Annotated[list[str], Field()] is_adam_param_specific: Annotated[bool, Field()] + is_activity_instance_id_specific: Annotated[bool | None, Field()] = None text_value: Annotated[str | None, Field()] = None @model_validator(mode="after") @@ -142,4 +144,17 @@ def validate_codelist_and_terms(self): raise ValueError( "Both ct_terms and ct_codelist cannot be provided at the same time for an ActivityItem." ) + if self.is_activity_instance_id_specific: + if self.ct_codelist_uid: + raise ValueError( + "An ActivityItem with 'is_activity_instance_id_specific' set to true must not have a ct_codelist_uid." + ) + if len(self.ct_terms) > 1: + raise ValueError( + "An ActivityItem with 'is_activity_instance_id_specific' set to true must not have more than one ct_term." + ) + if len(self.unit_definition_uids) > 1: + raise ValueError( + "An ActivityItem with 'is_activity_instance_id_specific' set to true must not have more than one unit_definition." + ) return self diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_sub_group.py b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_sub_group.py index f9e72682..b030f1c1 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_sub_group.py +++ b/clinical-mdr-api/clinical_mdr_api/models/concepts/activities/activity_sub_group.py @@ -15,6 +15,13 @@ class ActivitySubGroup(ActivityBase): + nci_concept_id: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + nci_concept_name: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + @classmethod def from_activity_ar( cls, @@ -27,6 +34,8 @@ def from_activity_ar( name_sentence_case=activity_subgroup_ar.concept_vo.name_sentence_case, definition=activity_subgroup_ar.concept_vo.definition, abbreviation=activity_subgroup_ar.concept_vo.abbreviation, + nci_concept_id=activity_subgroup_ar.concept_vo.nci_concept_id, + nci_concept_name=activity_subgroup_ar.concept_vo.nci_concept_name, library_name=Library.from_library_vo(activity_subgroup_ar.library).name, start_date=activity_subgroup_ar.item_metadata.start_date, end_date=activity_subgroup_ar.item_metadata.end_date, @@ -49,6 +58,8 @@ class ActivitySubGroupCreateInput(ExtendedConceptPostInput): ), ] name_sentence_case: Annotated[str, Field(min_length=1)] + nci_concept_id: Annotated[str | None, Field(min_length=1)] = None + nci_concept_name: Annotated[str | None, Field(min_length=1)] = None library_name: Annotated[str, Field(min_length=1)] @@ -74,6 +85,8 @@ class ActivityGroupForActivitySubGroup(BaseModel): class ActivitySubGroupDetail(BaseModel): name: Annotated[str | None, Field()] = None name_sentence_case: Annotated[str | None, Field()] = None + nci_concept_id: Annotated[str | None, Field()] = None + nci_concept_name: Annotated[str | None, Field()] = None library_name: Annotated[str | None, Field()] = None definition: Annotated[str | None, Field()] = None start_date: Annotated[datetime | None, Field()] = None @@ -104,6 +117,8 @@ def from_repository_input(cls, overview: dict[str, Any]): # Map basic fields from subgroup_value name=subgroup_value.get("name"), name_sentence_case=subgroup_value.get("name_sentence_case"), + nci_concept_id=subgroup_value.get("nci_concept_id"), + nci_concept_name=subgroup_value.get("nci_concept_name"), definition=subgroup_value.get("definition"), # Get library name from library node library_name=library_info.get("name"), 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 734b1c48..80c18aba 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 @@ -12,6 +12,7 @@ ) from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_term import ( CTCodelistTermAR, + CTPairedCodelistTermAR, ) from clinical_mdr_api.models.controlled_terminologies.ct_codelist_attributes import ( CTCodelistAttributes, @@ -271,35 +272,8 @@ class CTCodelistCompact(BaseModel): library_name: Annotated[str, Field()] -class CTCodelistTerm(BaseModel): - @classmethod - def from_ct_codelist_term_ar( - cls, - ct_codelist_term_ar: CTCodelistTermAR, - ) -> Self: - codelist_terms = cls( - term_uid=ct_codelist_term_ar.ct_codelist_term_vo.term_uid, - submission_value=ct_codelist_term_ar.ct_codelist_term_vo.submission_value, - order=ct_codelist_term_ar.ct_codelist_term_vo.order, - ordinal=ct_codelist_term_ar.ct_codelist_term_vo.ordinal, - library_name=ct_codelist_term_ar.ct_codelist_term_vo.library_name, - sponsor_preferred_name=ct_codelist_term_ar.ct_codelist_term_vo.sponsor_preferred_name, - sponsor_preferred_name_sentence_case=ct_codelist_term_ar.ct_codelist_term_vo.sponsor_preferred_name_sentence_case, - concept_id=ct_codelist_term_ar.ct_codelist_term_vo.concept_id, - nci_preferred_name=ct_codelist_term_ar.ct_codelist_term_vo.nci_preferred_name, - definition=ct_codelist_term_ar.ct_codelist_term_vo.definition, - name_date=ct_codelist_term_ar.ct_codelist_term_vo.name_date, - name_status=ct_codelist_term_ar.ct_codelist_term_vo.name_status.value, - attributes_date=ct_codelist_term_ar.ct_codelist_term_vo.attributes_date, - attributes_status=ct_codelist_term_ar.ct_codelist_term_vo.attributes_status.value, - start_date=ct_codelist_term_ar.ct_codelist_term_vo.start_date, - end_date=ct_codelist_term_ar.ct_codelist_term_vo.end_date, - ) - - return codelist_terms - +class CTCodelistTermBase(BaseModel): term_uid: Annotated[str, Field()] - submission_value: Annotated[str, Field()] order: Annotated[ int | None, Field(json_schema_extra={"nullable": True}), @@ -330,3 +304,68 @@ def from_ct_codelist_term_ar( start_date: datetime end_date: Annotated[datetime | None, Field(json_schema_extra={"nullable": True})] + + +class CTCodelistTerm(CTCodelistTermBase): + @classmethod + def from_ct_codelist_term_ar( + cls, + ct_codelist_term_ar: CTCodelistTermAR, + ) -> Self: + codelist_terms = cls( + term_uid=ct_codelist_term_ar.ct_codelist_term_vo.term_uid, + submission_value=ct_codelist_term_ar.ct_codelist_term_vo.submission_value, + order=ct_codelist_term_ar.ct_codelist_term_vo.order, + ordinal=ct_codelist_term_ar.ct_codelist_term_vo.ordinal, + library_name=ct_codelist_term_ar.ct_codelist_term_vo.library_name, + sponsor_preferred_name=ct_codelist_term_ar.ct_codelist_term_vo.sponsor_preferred_name, + sponsor_preferred_name_sentence_case=ct_codelist_term_ar.ct_codelist_term_vo.sponsor_preferred_name_sentence_case, + concept_id=ct_codelist_term_ar.ct_codelist_term_vo.concept_id, + nci_preferred_name=ct_codelist_term_ar.ct_codelist_term_vo.nci_preferred_name, + definition=ct_codelist_term_ar.ct_codelist_term_vo.definition, + name_date=ct_codelist_term_ar.ct_codelist_term_vo.name_date, + name_status=ct_codelist_term_ar.ct_codelist_term_vo.name_status.value, + attributes_date=ct_codelist_term_ar.ct_codelist_term_vo.attributes_date, + attributes_status=ct_codelist_term_ar.ct_codelist_term_vo.attributes_status.value, + start_date=ct_codelist_term_ar.ct_codelist_term_vo.start_date, + end_date=ct_codelist_term_ar.ct_codelist_term_vo.end_date, + ) + + return codelist_terms + + submission_value: Annotated[str, Field()] + + +class CTPairedCodelistTerm(CTCodelistTermBase): + @classmethod + def from_ct_paired_codelist_term_ar( + cls, + ct_paired_codelist_term_ar: CTPairedCodelistTermAR, + ) -> Self: + vo = ct_paired_codelist_term_ar.ct_paired_codelist_term_vo + return cls( + term_uid=vo.term_uid, + code_submission_value=vo.code_submission_value, + name_submission_value=vo.name_submission_value, + order=vo.order, + ordinal=vo.ordinal, + library_name=vo.library_name, + sponsor_preferred_name=vo.sponsor_preferred_name, + sponsor_preferred_name_sentence_case=vo.sponsor_preferred_name_sentence_case, + concept_id=vo.concept_id, + nci_preferred_name=vo.nci_preferred_name, + definition=vo.definition, + name_date=vo.name_date, + name_status=vo.name_status.value, + attributes_date=vo.attributes_date, + attributes_status=vo.attributes_status.value, + start_date=vo.start_date, + end_date=vo.end_date, + ) + + code_submission_value: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] + name_submission_value: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] diff --git a/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_term.py b/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_term.py index 575adb21..335320dc 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_term.py +++ b/clinical-mdr-api/clinical_mdr_api/models/controlled_terminologies/ct_term.py @@ -23,6 +23,7 @@ from clinical_mdr_api.models.controlled_terminologies.ct_term_name import CTTermName from clinical_mdr_api.models.libraries.library import Library from clinical_mdr_api.models.utils import BaseModel, PostInputModel +from common.config import settings class CTTerm(BaseModel): @@ -229,7 +230,7 @@ def from_ct_term_ars( class CTTermNewCodelist(BaseModel): codelist_uid: Annotated[str, Field()] - order: Annotated[int, Field()] + order: Annotated[int, Field(ge=0, le=settings.max_int_neo4j)] submission_value: Annotated[str, Field()] 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 35832e2f..14771098 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 @@ -54,12 +54,13 @@ def update_study_subpart_properties(study: "Study | CompactStudy"): if ( study.study_parent_part and study.study_parent_part.study_id - and study.current_metadata.identification_metadata.subpart_id is not None + and study.current_metadata.identification_metadata.study_subpart_acronym + is not None ): study.current_metadata.identification_metadata.study_id = ( study.study_parent_part.study_id + "-" - + study.current_metadata.identification_metadata.subpart_id + + study.current_metadata.identification_metadata.study_subpart_acronym ) @@ -113,6 +114,11 @@ class StudySoaPreferencesInput(PatchInputModel): description="Show the baseline visit as time 0 in all SoA layouts", alias=settings.study_field_soa_baseline_as_time_zero, ) + show_all_visits_lab_table: bool = Field( # type: ignore[literal-required] + False, + description="Show all visits in protocol lab table SoA (incl. those without lab assessments)", + alias=settings.study_field_soa_show_all_visits_lab_table, + ) class StudySoaPreferences(StudySoaPreferencesInput): @@ -380,7 +386,10 @@ class StudyIdentificationMetadataJsonModel(BaseModel): str | None, Field(json_schema_extra={"nullable": True}) ] = None study_subpart_acronym: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) + str | None, + Field( + json_schema_extra={"nullable": True}, + ), ] = None project_number: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) @@ -1727,6 +1736,9 @@ class StudyMinimal(BaseModel): ), ] = None acronym: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None + subpart_acronym: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None @classmethod def from_input( @@ -1736,6 +1748,7 @@ def from_input( return cls( uid=val["uid"], acronym=val["acronym"], + subpart_acronym=val["subpart_acronym"], id=val["id"], ) @@ -1749,6 +1762,13 @@ class VersionInfo(BaseModel): str | None, Field(json_schema_extra={"nullable": True}) ] = None + main_id: Annotated[ + str | None, + Field( + description="Main ID of the study, e.g. 'NN1234-56789'", + json_schema_extra={"nullable": True}, + ), + ] = None number: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None title: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None subpart_id: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( @@ -1788,6 +1808,7 @@ def from_input( acronym=val.get("acronym"), number=val.get("study_number"), id=val["id"], + main_id=val["main_id"], title=val.get("title"), subpart_id=val.get("subpart_id"), subpart_acronym=val.get("subpart_acronym"), @@ -1941,7 +1962,9 @@ class StudyCloneInput(StudyCreateInput): class StudySubpartCreateInput(PostInputModel): - study_subpart_acronym: Annotated[str, Field(min_length=1)] + study_subpart_acronym: Annotated[ + str, Field(min_length=1, max_length=10, pattern=r"^[A-Za-z0-9]+$") + ] description: Annotated[str | None, Field()] = None diff --git a/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py b/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py index b7495a8f..a23d0fa9 100644 --- a/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py +++ b/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py @@ -828,6 +828,10 @@ def build_filter_clause(self) -> None: attribute, attr_desc, ) in self.return_model.model_fields.items(): + # Skip fields explicitly excluded from wildcard filtering + jse = attr_desc.json_schema_extra or {} + if jse.get("remove_from_wildcard", False): + continue # Wildcard filtering only searches in properties of type string if ( get_field_type(attr_desc.annotation) is str diff --git a/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_instance_classes.py b/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_instance_classes.py index a8a13f58..b6ab862d 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_instance_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_instance_classes.py @@ -100,6 +100,63 @@ def get_activity_instance_classes( ) +@router.get( + "/versions", + dependencies=[security, rbac.LIBRARY_READ], + summary="List all versions of activity instance classes", + description=f""" +State before: + - The library must exist (if specified) + +Business logic: + - List version history of activity instance classes + - The returned versions are ordered by version start_date descending (newest entries first). + +State after: + - No change + +Possible errors: + - Invalid library name specified. + +{_generic_descriptions.DATA_EXPORTS_HEADER} +""", + response_model_exclude_unset=True, + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +@decorators.allow_exports( + { + "defaults": ["uid", "name", "start_date", "status", "version"], + "formats": [ + "text/csv", + "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", + "text/xml", + "application/json", + ], + } +) +# pylint: disable=unused-argument +def get_activity_instance_classes_versions( + request: Request, # request is actually required by the allow_exports decorator + 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[ActivityInstanceClass]: + activity_instance_class_service = ActivityInstanceClassService() + results = activity_instance_class_service.get_all_item_versions( + sort_by={"start_date": False}, + page_number=page_number, + page_size=page_size, + total_count=total_count, + ) + return CustomPage( + items=results.items, total=results.total, page=page_number, size=page_size + ) + + @router.get( "/headers", dependencies=[security, rbac.LIBRARY_READ], diff --git a/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_item_classes.py b/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_item_classes.py index b6dda45e..e14af044 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_item_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/biomedical_concepts/activity_item_classes.py @@ -94,6 +94,63 @@ def get_activity_item_classes( ) +@router.get( + "/versions", + dependencies=[security, rbac.LIBRARY_READ], + summary="List all versions of activity item classes", + description=f""" +State before: + - The library must exist (if specified) + +Business logic: + - List version history of activity item classes + - The returned versions are ordered by version start_date descending (newest entries first). + +State after: + - No change + +Possible errors: + - Invalid library name specified. + +{_generic_descriptions.DATA_EXPORTS_HEADER} +""", + response_model_exclude_unset=True, + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +@decorators.allow_exports( + { + "defaults": ["uid", "name", "start_date", "status", "version"], + "formats": [ + "text/csv", + "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", + "text/xml", + "application/json", + ], + } +) +# pylint: disable=unused-argument +def get_activity_item_classes_versions( + request: Request, # request is actually required by the allow_exports decorator + 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[ActivityItemClass]: + activity_item_class_service = ActivityItemClassService() + results = activity_item_class_service.get_all_concept_versions( + sort_by={"start_date": False}, + page_number=page_number, + page_size=page_size, + total_count=total_count, + ) + return CustomPage( + items=results.items, total=results.total, page=page_number, size=page_size + ) + + @router.get( "/headers", dependencies=[security, rbac.LIBRARY_READ], 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 c5093c89..6ae289a9 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 @@ -7,11 +7,13 @@ from clinical_mdr_api.models.concepts.activities.activity_instance import ( ActivityInstance, + ActivityInstanceAttributes, + ActivityInstanceAttributesEditInput, ActivityInstanceCreateInput, - ActivityInstanceEditInput, + ActivityInstanceGroupings, + ActivityInstanceGroupingsEditInput, ActivityInstanceOverview, ActivityInstancePreviewInput, - SimpleActivityInstanceGrouping, SimplifiedActivityItem, ) from clinical_mdr_api.models.utils import CustomPage @@ -19,6 +21,8 @@ from clinical_mdr_api.routers import _generic_descriptions, decorators from clinical_mdr_api.routers.responses import YAMLResponse from clinical_mdr_api.services.concepts.activities.activity_instance_service import ( + ActivityInstanceAttributesService, + ActivityInstanceGroupingsService, ActivityInstanceService, ) from common.auth import rbac @@ -127,6 +131,12 @@ def get_activities( alias="activity_instance_class_names[]", ), ] = None, + status: Annotated[ + str | None, + Query( + description="Filter by status, matching either activity instance status or groupings status", + ), + ] = None, sort_by: _generic_descriptions.SORT_BY_QUERY = None, page_number: _generic_descriptions.PAGE_NUMBER_QUERY = settings.default_page_number, page_size: _generic_descriptions.PAGE_SIZE_QUERY = settings.default_page_size, @@ -142,6 +152,7 @@ def get_activities( activity_group_names=activity_group_names, activity_instance_class_names=activity_instance_class_names, activity_instance_names=names, + status=status, sort_by=sort_by, page_number=page_number, page_size=page_size, @@ -155,7 +166,7 @@ def get_activities( @router.get( - "/versions", + "/attributes/versions", dependencies=[security, rbac.LIBRARY_READ], summary="List all versions of all activity instances (for a given library)", description=f""" @@ -235,8 +246,8 @@ def get_activity_instances_versions( filters: _generic_descriptions.FILTERS_QUERY = None, operator: _generic_descriptions.FILTER_OPERATOR_QUERY = settings.default_filter_operator, total_count: _generic_descriptions.TOTAL_COUNT_QUERY = False, -) -> CustomPage[ActivityInstance]: - activity_instance_service = ActivityInstanceService() +) -> CustomPage[ActivityInstanceAttributes]: + activity_instance_service = ActivityInstanceAttributesService() results = activity_instance_service.get_all_concept_versions( library=library_name, activity_names=activity_names, @@ -398,57 +409,72 @@ def get_activity_instance_overview( @router.get( - "/{activity_instance_uid}/activity-groupings", + "/{activity_instance_uid}/attributes", dependencies=[security, rbac.LIBRARY_READ], - summary="Get activity groupings for a specific activity instance", - status_code=200, + summary="Get details on a specific activity instance attributes (in a specific version)", description=""" -Returns activity groupings (hierarchy) for an activity instance, including: - - Activity information with version and library details - - Activity groups with name and definition - - Activity subgroups with name and definition - State before: - - an activity instance with uid must exist. + - a activity instance with uid must exist. + +Business logic: + - If parameter at_specified_date_time is specified then the latest/newest representation of the concept at this point in time is returned. The point in time needs to be specified in ISO 8601 format including the timezone, e.g.: '2020-10-31T16:00:00+02:00' for October 31, 2020 at 4pm in UTC+2 timezone. If the timezone is ommitted, UTC�0 is assumed. + - If parameter status is specified then the representation of the concept in that status is returned (if existent). This is useful if the concept has a status 'Draft' and a status 'Final'. + - If parameter version is specified then the latest/newest representation of the concept in that version is returned. Only exact matches are considered. The version is specified in the following format: . where and are digits. E.g. '0.1', '0.2', '1.0', ... State after: - No change Possible errors: - - Invalid uid. + - Invalid uid, at_specified_date_time, status or version. + """, + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def get_activity_instance_attributes( + activity_instance_uid: Annotated[str, ActivityInstanceUID], +) -> ActivityInstanceAttributes: + activity_instance_service = ActivityInstanceAttributesService() + return activity_instance_service.get_by_uid(uid=activity_instance_uid) -{_generic_descriptions.DATA_EXPORTS_HEADER} + +@router.get( + "/{activity_instance_uid}/groupings", + dependencies=[security, rbac.LIBRARY_READ], + summary="Get details on a specific activity instance groupings (in a specific version)", + description=""" +State before: + - a activity instance with uid must exist. + +Business logic: + - If parameter at_specified_date_time is specified then the latest/newest representation of the concept at this point in time is returned. The point in time needs to be specified in ISO 8601 format including the timezone, e.g.: '2020-10-31T16:00:00+02:00' for October 31, 2020 at 4pm in UTC+2 timezone. If the timezone is ommitted, UTC�0 is assumed. + - If parameter status is specified then the representation of the concept in that status is returned (if existent). This is useful if the concept has a status 'Draft' and a status 'Final'. + - If parameter version is specified then the latest/newest representation of the concept in that version is returned. Only exact matches are considered. The version is specified in the following format: . where and are digits. E.g. '0.1', '0.2', '1.0', ... + +State after: + - No change + +Possible errors: + - Invalid uid, at_specified_date_time, status or version. """, + status_code=200, responses={ 403: _generic_descriptions.ERROR_403, - 200: {"model": list[SimpleActivityInstanceGrouping]}, 404: _generic_descriptions.ERROR_404, }, ) @decorators.allow_exports( { "defaults": [ - "activity_group_uid=activity_group.uid", - "activity_group_name=activity_group.name", - "activity_group_definition=activity_group.definition", - "activity_group_version=activity_group.version", - "activity_group_status=activity_group.status", - "activity_subgroup_uid=activity_subgroup.uid", - "activity_subgroup_name=activity_subgroup.name", - "activity_subgroup_definition=activity_subgroup.definition", - "activity_subgroup_version=activity_subgroup.version", - "activity_subgroup_status=activity_subgroup.status", - "activity_uid=activity.uid", - "activity_name=activity.name", - "activity_definition=activity.definition", - "activity_nci_concept_id=activity.nci_concept_id", - "activity_nci_concept_name=activity.nci_concept_name", - "activity_is_data_collected=activity.is_data_collected", - "activity_library_name=activity.library_name", - "activity_version=activity.version", - "activity_status=activity.status", + "status=activity_instance.status", + "version=activity_instance.version", + "activity_groupings_count=activity_groupings", + "all_versions", ], "formats": [ + "application/x-yaml", "text/csv", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "text/xml", @@ -461,10 +487,10 @@ def get_activity_instance_groupings( request: Request, # request is actually required by the allow_exports decorator activity_instance_uid: Annotated[str, ActivityInstanceUID], version: Annotated[str | None, Query()] = None, -): - activity_instance_service = ActivityInstanceService() - return activity_instance_service.get_activity_instance_groupings( - activity_instance_uid=activity_instance_uid, version=version +) -> ActivityInstanceGroupings: + activity_instance_service = ActivityInstanceGroupingsService() + return activity_instance_service.get_by_uid( + uid=activity_instance_uid, version=version ) @@ -576,9 +602,9 @@ def get_cosmos_activity_instance_overview( @router.get( - "/{activity_instance_uid}/versions", + "/{activity_instance_uid}/attributes/versions", dependencies=[security, rbac.LIBRARY_READ], - summary="List version history for activity instance", + summary="List version history for activity instance attributes", description=""" State before: - uid must exist. @@ -604,8 +630,8 @@ def get_cosmos_activity_instance_overview( ) def get_versions( activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> list[ActivityInstance]: - activity_instance_service = ActivityInstanceService() +) -> list[ActivityInstanceAttributes]: + activity_instance_service = ActivityInstanceAttributesService() return activity_instance_service.get_version_history(uid=activity_instance_uid) @@ -709,12 +735,12 @@ def preview( @router.patch( - "/{activity_instance_uid}", + "/{activity_instance_uid}/attributes", dependencies=[security, rbac.LIBRARY_WRITE], - summary="Update activity instance", + summary="Update activity instance attributes", description=""" State before: - - uid must exist and activity instance must exist in status draft. + - uid must exist and activity instance attributes must exist in status draft. - The activity instance must belongs to a library that allows deleting (the 'is_editable' property of the library needs to be true). Business logic: @@ -748,9 +774,11 @@ def preview( ) def edit( activity_instance_uid: Annotated[str, ActivityInstanceUID], - activity_instance_edit_input: Annotated[ActivityInstanceEditInput, Body()], -) -> ActivityInstance: - activity_instance_service = ActivityInstanceService() + activity_instance_edit_input: Annotated[ + ActivityInstanceAttributesEditInput, Body() + ], +) -> ActivityInstanceAttributes: + activity_instance_service = ActivityInstanceAttributesService() return activity_instance_service.edit_draft( uid=activity_instance_uid, concept_edit_input=activity_instance_edit_input, @@ -759,9 +787,9 @@ def edit( @router.post( - "/{activity_instance_uid}/versions", + "/{activity_instance_uid}/attributes/versions", dependencies=[security, rbac.LIBRARY_WRITE], - summary=" Create a new version of an activity instance", + summary=" Create a new version of an activity instance attributes", description=""" State before: - uid must exist and the activity instance must be in status Final. @@ -795,15 +823,15 @@ def edit( ) def create_new_version( activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> ActivityInstance: - activity_instance_service = ActivityInstanceService() +) -> ActivityInstanceAttributes: + activity_instance_service = ActivityInstanceAttributesService() return activity_instance_service.create_new_version(uid=activity_instance_uid) @router.post( - "/{activity_instance_uid}/approvals", + "/{activity_instance_uid}/attributes/approvals", dependencies=[security, rbac.LIBRARY_WRITE], - summary="Approve draft version of an activity instance", + summary="Approve draft version of an activity instance attributes", description=""" State before: - uid must exist and activity instance must be in status Draft. @@ -839,15 +867,15 @@ def create_new_version( ) def approve( activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> ActivityInstance: - activity_instance_service = ActivityInstanceService() +) -> ActivityInstanceAttributes: + activity_instance_service = ActivityInstanceAttributesService() return activity_instance_service.approve(uid=activity_instance_uid) @router.delete( - "/{activity_instance_uid}/activations", + "/{activity_instance_uid}/attributes/activations", dependencies=[security, rbac.LIBRARY_WRITE], - summary=" Inactivate final version of an activity instance", + summary=" Inactivate final version of an activity instance attributes", description=""" State before: - uid must exist and activity instance must be in status Final. @@ -882,15 +910,15 @@ def approve( ) def inactivate( activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> ActivityInstance: - activity_instance_service = ActivityInstanceService() +) -> ActivityInstanceAttributes: + activity_instance_service = ActivityInstanceAttributesService() return activity_instance_service.inactivate_final(uid=activity_instance_uid) @router.post( - "/{activity_instance_uid}/activations", + "/{activity_instance_uid}/attributes/activations", dependencies=[security, rbac.LIBRARY_WRITE], - summary="Reactivate retired version of an activity instance", + summary="Reactivate retired version of an activity instance attributes", description=""" State before: - uid must exist and activity instance must be in status Retired. @@ -925,8 +953,264 @@ def inactivate( ) def reactivate( activity_instance_uid: Annotated[str, ActivityInstanceUID], -) -> ActivityInstance: - activity_instance_service = ActivityInstanceService() +) -> ActivityInstanceAttributes: + activity_instance_service = ActivityInstanceAttributesService() + return activity_instance_service.reactivate_retired(uid=activity_instance_uid) + + +@router.patch( + "/{activity_instance_uid}/groupings", + dependencies=[security, rbac.LIBRARY_WRITE], + summary="Update activity instance groupings", + description=""" +State before: + - uid must exist and activity instance groupings must exist in status draft. + - The activity instance must belongs to a library that allows deleting (the 'is_editable' property of the library needs to be true). + +Business logic: + - If activity instance exist in status draft then groupings are updated. +- If the linked activity instance is updated, the relationships are updated to point to the activity instance value node. + +State after: + - groupings are updated for the activity instance. + - Audit trail entry must be made with update of groupings. + +Possible errors: + - Invalid uid. + +""", + 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 draft status.\n" + "- The activity instance had been in 'Final' status before.\n" + "- The library doesn't allow to edit draft versions.\n", + }, + 404: { + "model": ErrorResponse, + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", + }, + }, +) +def edit_groupings( + activity_instance_uid: Annotated[str, ActivityInstanceUID], + activity_instance_edit_input: Annotated[ActivityInstanceGroupingsEditInput, Body()], +) -> ActivityInstanceGroupings: + activity_instance_service = ActivityInstanceGroupingsService() + return activity_instance_service.edit_draft( + uid=activity_instance_uid, + concept_edit_input=activity_instance_edit_input, + patch_mode=True, + ) + + +@router.get( + "/{activity_instance_uid}/groupings/versions", + dependencies=[security, rbac.LIBRARY_READ], + summary="List version history for activity instance groupings", + description=""" +State before: + - uid must exist. + +Business logic: + - List version history for activity instance groupings. + - The returned versions are ordered by start_date descending (newest entries first). + +State after: + - No change + +Possible errors: + - Invalid uid. + """, + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: { + "model": ErrorResponse, + "description": "Not Found - The activity isntance with the specified 'activity_instance_uid' wasn't found.", + }, + }, +) +def get_groupings_versions( + activity_instance_uid: Annotated[str, ActivityInstanceUID], +) -> list[ActivityInstanceGroupings]: + activity_instance_service = ActivityInstanceGroupingsService() + return activity_instance_service.get_version_history(uid=activity_instance_uid) + + +@router.post( + "/{activity_instance_uid}/groupings/versions", + dependencies=[security, rbac.LIBRARY_WRITE], + summary=" Create a new version of an activity instance groupings", + description=""" +State before: + - uid must exist and the activity instance must be in status Final. + +Business logic: +- The activity instance is changed to a draft state. + +State after: + - Activity instance changed status to Draft and assigned a new minor version number. + - Audit trail entry must be made with action of creating a new draft version. + +Possible errors: + - Invalid uid or status not Final. +""", + status_code=201, + responses={ + 403: _generic_descriptions.ERROR_403, + 201: {"description": "OK."}, + 400: { + "model": ErrorResponse, + "description": "Forbidden - Reasons include e.g.: \n" + "- The library doesn't allow to create activity instances.\n", + }, + 404: { + "model": ErrorResponse, + "description": "Not Found - Reasons include e.g.: \n" + "- The activity instance is not in final status.\n" + "- The activity instance with the specified 'activity_instance_uid' could not be found.", + }, + }, +) +def create_new_groupings_version( + activity_instance_uid: Annotated[str, ActivityInstanceUID], +) -> ActivityInstanceGroupings: + activity_instance_service = ActivityInstanceGroupingsService() + return activity_instance_service.create_new_version(uid=activity_instance_uid) + + +@router.post( + "/{activity_instance_uid}/groupings/approvals", + dependencies=[security, rbac.LIBRARY_WRITE], + summary="Approve draft version of an activity instance groupings", + description=""" +State before: + - uid must exist and activity instance must be in status Draft. + +Business logic: + - The latest 'Draft' version will remain the same as before. + - The status of the new approved version will be automatically set to 'Final'. + - The 'version' property of the new version will be automatically set to the version of the latest 'Final' version increased by +1.0. + - The 'change_description' property will be set automatically 'Approved version'. + +State after: + - Activity instance changed status to Final and assigned a new major version number. + - Audit trail entry must be made with action of approving to new Final version. + +Possible errors: + - Invalid uid or status not Draft. + """, + status_code=201, + responses={ + 403: _generic_descriptions.ERROR_403, + 201: {"description": "OK."}, + 400: { + "model": ErrorResponse, + "description": "Forbidden - Reasons include e.g.: \n" + "- The activity instance is not in draft status.\n" + "- The library doesn't allow to approve activity instance.\n", + }, + 404: { + "model": ErrorResponse, + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", + }, + }, +) +def approve_groupings( + activity_instance_uid: Annotated[str, ActivityInstanceUID], +) -> ActivityInstanceGroupings: + activity_instance_service = ActivityInstanceGroupingsService() + 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) 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 afa5f73f..f9698091 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, + CTPairedCodelistTerm, ) from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator @@ -383,6 +384,50 @@ def update_paired_codelist( return results +@router.get( + "/paired-codelists/{codelist_uid}/terms", + dependencies=[security, rbac.LIBRARY_READ], + summary="Returns terms from the paired codelists identified by the given codelist UID.", + description="Returns the list of all terms coming from the codelist specified by the given UID and its paired codelist. " + "Each term includes both the code_submission_value (from the codes codelist) and " + "the name_submission_value (from the names codelist).", + response_model=CustomPage[CTPairedCodelistTerm], + status_code=200, + responses={ + 400: { + "model": ErrorResponse, + "description": "Bad Request - The codelist does not have a paired codelist.", + }, + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def get_paired_codelist_terms( + codelist_uid: str = CTCodelistUID, + sort_by: _generic_descriptions.SORT_BY_QUERY = None, + page_number: _generic_descriptions.PAGE_NUMBER_QUERY = settings.default_page_number, + page_size: _generic_descriptions.PAGE_SIZE_QUERY = settings.default_page_size, + filters: _generic_descriptions.FILTERS_QUERY = None, + operator: str | None = Query( + "and", description=_generic_descriptions.FILTER_OPERATOR + ), + total_count: _generic_descriptions.TOTAL_COUNT_QUERY = False, +): + ct_codelist_service = CTCodelistService() + results = ct_codelist_service.get_paired_codelist_terms( + codelist_uid=codelist_uid, + sort_by=sort_by, + page_number=page_number, + page_size=page_size, + total_count=total_count, + filter_by=filters, + filter_operator=FilterOperator.from_str(operator), + ) + return CustomPage.create( + items=results.items, total=results.total, page=page_number, size=page_size + ) + + @router.get( "/codelists/headers", dependencies=[security, rbac.LIBRARY_READ], diff --git a/clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py index dd79cbdb..13f22ca0 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py @@ -477,7 +477,10 @@ def add_item_groups_to_odm_form( override: Annotated[ bool, Query( - description="If true, all existing item group relationships will be replaced with the provided item group relationships.", + description=""" +When true, replaces all existing item relationships with the provided ones. +When false, appends the provided item relationships to existing ones, continuing the order sequence. + """, ), ] = False, ) -> OdmForm: diff --git a/clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py index 4193b1e7..17f2ca91 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py @@ -488,7 +488,10 @@ def add_item_to_odm_item_group( override: Annotated[ bool, Query( - description="If true, all existing item relationships will be replaced with the provided item relationships.", + description=""" +When true, replaces all existing item relationships with the provided ones. +When false, appends the provided item relationships to existing ones, continuing the order sequence. + """, ), ] = False, ) -> OdmItemGroup: diff --git a/clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py index 721aa6d2..9705a515 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py @@ -415,7 +415,10 @@ def add_forms_to_odm_study_event( override: Annotated[ bool, Query( - description="If true, all existing form relationships will be replaced with the provided form relationships.", + description=""" +When true, replaces all existing item relationships with the provided ones. +When false, appends the provided item relationships to existing ones, continuing the order sequence. + """, ), ] = False, ) -> OdmStudyEvent: diff --git a/clinical-mdr-api/clinical_mdr_api/routers/studies/study_flowchart.py b/clinical-mdr-api/clinical_mdr_api/routers/studies/study_flowchart.py index ab49a3f5..d93dceae 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/studies/study_flowchart.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/studies/study_flowchart.py @@ -124,6 +124,9 @@ def get_study_flowchart_html( debug_propagation: Annotated[ bool, Query(description="Debug propagations without hiding rows") ] = False, + include_uids: Annotated[ + bool, Query(description="Include uids in the HTML as data attributes") + ] = False, ) -> HTMLResponse: return HTMLResponse( StudyFlowchartService().get_study_flowchart_html( @@ -134,6 +137,7 @@ def get_study_flowchart_html( debug_uids=debug_uids, debug_coordinates=debug_coordinates, debug_propagation=debug_propagation, + include_uids=include_uids, ) ) @@ -514,11 +518,16 @@ def export_protocol_soa_content( study_value_version: Annotated[ str | None, _generic_descriptions.STUDY_VALUE_VERSION_QUERY ] = None, + protocol_lab_table: Annotated[ + bool, + Query(description="Whether to export Protocol Lab table SoA"), + ] = False, ) -> list[dict[str, Any]]: soa_content = StudyFlowchartService().download_detailed_soa_content( study_uid=study_uid, study_value_version=study_value_version, - protocol_flowchart=True, + protocol_flowchart=not protocol_lab_table, + protocol_lab_table=protocol_lab_table, ) return soa_content diff --git a/clinical-mdr-api/clinical_mdr_api/routers/studies/study_visits.py b/clinical-mdr-api/clinical_mdr_api/routers/studies/study_visits.py index 3c0bb914..c7fe6080 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/studies/study_visits.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/studies/study_visits.py @@ -415,7 +415,7 @@ def delete_study_visit( study_uid: Annotated[str, studyUID], study_visit_uid: Annotated[str, study_visit_uid_description], ): - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) service.delete(study_uid=study_uid, study_visit_uid=study_visit_uid) @@ -575,7 +575,7 @@ def get_amount_of_visits_in_given_epoch( str, Path(description="The unique uid of the study epoch") ], ) -> int: - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) return service.get_amount_of_visits_in_given_epoch( study_uid=study_uid, study_epoch_uid=study_epoch_uid ) @@ -608,7 +608,7 @@ def get_amount_of_visits_in_given_epoch( def get_global_anchor_visit( study_uid: Annotated[str, studyUID], ) -> SimpleStudyVisit | None: - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) return service.get_global_anchor_visit(study_uid=study_uid) @@ -639,7 +639,7 @@ def get_global_anchor_visit( def get_anchor_visits_in_group_of_subvisits( study_uid: Annotated[str, studyUID], ) -> list[SimpleStudyVisit]: - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) return service.get_anchor_visits_in_a_group_of_subvisits(study_uid=study_uid) @@ -674,7 +674,7 @@ def get_anchor_visits_for_special_visit( description="The uid of StudyEpoch from which StudyVisits are returned.", ), ) -> list[SimpleStudyVisit]: - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) return service.get_anchor_for_special_visit( study_uid=study_uid, study_epoch_uid=study_epoch_uid ) @@ -700,7 +700,7 @@ def get_study_visits_for_specific_activity_instance( str, Path(description="The unique id of the study activity instance.") ], ) -> list[SimpleStudyVisit]: - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) return service.get_study_visits_for_specific_activity_instance( study_uid=study_uid, study_activity_instance_uid=study_activity_instance_uid, @@ -747,7 +747,7 @@ def assign_consecutive_visit_group_for_selected_study_visit( ), ] = False, ) -> list[StudyVisit]: - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) return service.assign_visit_consecutive_group( study_uid=study_uid, visits_to_assign=consecutive_visit_group_input.visits_to_assign, @@ -787,7 +787,7 @@ def remove_consecutive_group( str, Path(description="The name of the consecutive-visit-group that is removed") ], ): - service = StudyVisitService(study_uid=study_uid) + service = StudyVisitService(study_uid=study_uid, load_terms=False) service.remove_visit_consecutive_group( study_uid=study_uid, consecutive_visit_group_uid=consecutive_visit_group_uid ) 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 61ffabbf..77c03725 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py @@ -20,6 +20,8 @@ ActivityGroupRepository, ) from clinical_mdr_api.domain_repositories.concepts.activities.activity_instance_repository import ( + ActivityInstanceAttributesRepository, + ActivityInstanceGroupingsRepository, ActivityInstanceRepository, ) from clinical_mdr_api.domain_repositories.concepts.activities.activity_repository import ( @@ -320,13 +322,14 @@ def __init__(self, author_id: str = "unknown-user"): def close(self) -> None: for repo in self._repositories.values(): - repo.close() + if hasattr(repo, "close"): + repo.close() self._repositories = {} def __del__(self): self.close() - def _build_repository_instance(self, repo_interface: type) -> Any: + def _build_repository_instance(self, repo_interface: type, **kwargs) -> Any: """ here we put code for build different repo classes. :param repo_interface: An interface to retrieve a configured implementation. @@ -343,16 +346,14 @@ def _build_repository_instance(self, repo_interface: type) -> Any: } if repo_interface not in repository_configuration: - raise NotImplementedError( - f"This class doesn't know how to provide {repo_interface} implementation." - ) + return repo_interface(**kwargs) - return repository_configuration[repo_interface]() + return repository_configuration[repo_interface](**kwargs) - def get_repository_instance(self, repo_interface: type) -> Any: + def get_repository_instance(self, repo_interface: type, **kwargs) -> Any: if repo_interface not in self._repositories: self._repositories[repo_interface] = self._build_repository_instance( - repo_interface + repo_interface, **kwargs ) return self._repositories[repo_interface] @@ -360,275 +361,309 @@ def get_repository_instance(self, repo_interface: type) -> Any: @property def activity_instance_repository(self) -> ActivityInstanceRepository: - return ActivityInstanceRepository() + return self.get_repository_instance(ActivityInstanceRepository) + + @property + def activity_instance_groupings_repository( + self, + ) -> ActivityInstanceGroupingsRepository: + return ActivityInstanceGroupingsRepository() + + @property + def activity_instance_attributes_repository( + self, + ) -> ActivityInstanceAttributesRepository: + return ActivityInstanceAttributesRepository() @property def activity_instance_class_repository(self) -> ActivityInstanceClassRepository: - return ActivityInstanceClassRepository() + return self.get_repository_instance(ActivityInstanceClassRepository) @property def data_supplier_repository(self) -> DataSupplierRepository: - return DataSupplierRepository() + return self.get_repository_instance(DataSupplierRepository) @property def data_model_ig_repository(self) -> DataModelIGRepository: - return DataModelIGRepository() + return self.get_repository_instance(DataModelIGRepository) @property def dataset_repository(self) -> DatasetRepository: - return DatasetRepository() + return self.get_repository_instance(DatasetRepository) @property def dataset_class_repository(self) -> DatasetClassRepository: - return DatasetClassRepository() + return self.get_repository_instance(DatasetClassRepository) @property def dataset_variable_repository(self) -> DatasetVariableRepository: - return DatasetVariableRepository() + return self.get_repository_instance(DatasetVariableRepository) @property def activity_item_class_repository(self) -> ActivityItemClassRepository: - return ActivityItemClassRepository() + return self.get_repository_instance(ActivityItemClassRepository) @property def compound_repository(self) -> CompoundRepository: - return CompoundRepository() + return self.get_repository_instance(CompoundRepository) @property def compound_alias_repository(self) -> CompoundAliasRepository: - return CompoundAliasRepository() + return self.get_repository_instance(CompoundAliasRepository) @property def medicinal_product_repository(self) -> MedicinalProductRepository: - return MedicinalProductRepository() + return self.get_repository_instance(MedicinalProductRepository) @property def active_substance_repository(self) -> ActiveSubstanceRepository: - return ActiveSubstanceRepository() + return self.get_repository_instance(ActiveSubstanceRepository) @property def pharmaceutical_product_repository(self) -> PharmaceuticalProductRepository: - return PharmaceuticalProductRepository() + return self.get_repository_instance(PharmaceuticalProductRepository) @property def activity_repository(self) -> ActivityRepository: - return ActivityRepository() + return self.get_repository_instance(ActivityRepository) @property def activity_subgroup_repository(self) -> ActivitySubGroupRepository: - return ActivitySubGroupRepository() + return self.get_repository_instance(ActivitySubGroupRepository) @property def activity_group_repository(self) -> ActivityGroupRepository: - return ActivityGroupRepository() + return self.get_repository_instance(ActivityGroupRepository) @property def numeric_value_repository(self) -> NumericValueRepository: - return NumericValueRepository() + return self.get_repository_instance(NumericValueRepository) @property def numeric_value_with_unit_repository(self) -> NumericValueWithUnitRepository: - return NumericValueWithUnitRepository() + return self.get_repository_instance(NumericValueWithUnitRepository) @property def lag_time_repository(self) -> LagTimeRepository: - return LagTimeRepository() + return self.get_repository_instance(LagTimeRepository) @property def text_value_repository(self) -> TextValueRepository: - return TextValueRepository() + return self.get_repository_instance(TextValueRepository) @property def visit_name_repository(self) -> VisitNameRepository: - return VisitNameRepository() + return self.get_repository_instance(VisitNameRepository) @property def study_day_repository(self) -> StudyDayRepository: - return StudyDayRepository() + return self.get_repository_instance(StudyDayRepository) @property def study_week_repository(self) -> StudyWeekRepository: - return StudyWeekRepository() + return self.get_repository_instance(StudyWeekRepository) @property def study_duration_days_repository(self) -> StudyDurationDaysRepository: - return StudyDurationDaysRepository() + return self.get_repository_instance(StudyDurationDaysRepository) @property def study_duration_weeks_repository(self) -> StudyDurationWeeksRepository: - return StudyDurationWeeksRepository() + return self.get_repository_instance(StudyDurationWeeksRepository) @property def week_in_study_repository(self) -> WeekInStudyRepository: - return WeekInStudyRepository() + return self.get_repository_instance(WeekInStudyRepository) @property def time_point_repository(self) -> TimePointRepository: - return TimePointRepository() + return self.get_repository_instance(TimePointRepository) @property def unit_definition_repository(self) -> UnitDefinitionRepository: - return UnitDefinitionRepository() + return self.get_repository_instance(UnitDefinitionRepository) @property def odm_method_repository(self) -> MethodRepository: - return MethodRepository() + return self.get_repository_instance(MethodRepository) @property def odm_condition_repository(self) -> ConditionRepository: - return ConditionRepository() + return self.get_repository_instance(ConditionRepository) @property def odm_form_repository(self) -> FormRepository: - return FormRepository() + return self.get_repository_instance(FormRepository) @property def odm_item_group_repository(self) -> ItemGroupRepository: - return ItemGroupRepository() + return self.get_repository_instance(ItemGroupRepository) @property def odm_item_repository(self) -> ItemRepository: - return ItemRepository() + return self.get_repository_instance(ItemRepository) @property def odm_study_event_repository(self) -> StudyEventRepository: - return StudyEventRepository() + return self.get_repository_instance(StudyEventRepository) @property def odm_vendor_namespace_repository(self) -> VendorNamespaceRepository: - return VendorNamespaceRepository() + return self.get_repository_instance(VendorNamespaceRepository) @property def odm_vendor_element_repository(self) -> VendorElementRepository: - return VendorElementRepository() + return self.get_repository_instance(VendorElementRepository) @property def odm_vendor_attribute_repository(self) -> VendorAttributeRepository: - return VendorAttributeRepository() + return self.get_repository_instance(VendorAttributeRepository) @property def criteria_repository(self) -> CriteriaRepository: - return CriteriaRepository() + return self.get_repository_instance(CriteriaRepository) @property def objective_repository(self) -> ObjectiveRepository: - return ObjectiveRepository() + return self.get_repository_instance(ObjectiveRepository) @property def endpoint_repository(self) -> EndpointRepository: - return EndpointRepository() + return self.get_repository_instance(EndpointRepository) @property def timeframe_repository(self) -> TimeframeRepository: - return TimeframeRepository() + return self.get_repository_instance(TimeframeRepository) @property def footnote_repository(self) -> FootnoteRepository: - return FootnoteRepository() + return self.get_repository_instance(FootnoteRepository) @property def parameter_repository(self) -> TemplateParameterRepository: - return TemplateParameterRepository() + return self.get_repository_instance(TemplateParameterRepository) @property def footnote_template_repository( self, ) -> FootnoteTemplateRepository: - return FootnoteTemplateRepository(self._author_id) + return self.get_repository_instance( + FootnoteTemplateRepository, user=self._author_id + ) @property def activity_instruction_template_repository( self, ) -> ActivityInstructionTemplateRepository: - return ActivityInstructionTemplateRepository(self._author_id) + return self.get_repository_instance( + ActivityInstructionTemplateRepository, user=self._author_id + ) @property def criteria_template_repository(self) -> CriteriaTemplateRepository: - return CriteriaTemplateRepository(self._author_id) + return self.get_repository_instance( + CriteriaTemplateRepository, user=self._author_id + ) @property def endpoint_template_repository(self) -> EndpointTemplateRepository: - return EndpointTemplateRepository(self._author_id) + return self.get_repository_instance( + EndpointTemplateRepository, user=self._author_id + ) @property def objective_template_repository(self) -> ObjectiveTemplateRepository: - return ObjectiveTemplateRepository(self._author_id) + return self.get_repository_instance( + ObjectiveTemplateRepository, user=self._author_id + ) @property def timeframe_template_repository(self) -> TimeframeTemplateRepository: - return TimeframeTemplateRepository(self._author_id) + return self.get_repository_instance( + TimeframeTemplateRepository, user=self._author_id + ) @property def activity_instruction_pre_instance_repository( self, ) -> ActivityInstructionPreInstanceRepository: - return ActivityInstructionPreInstanceRepository(self._author_id) + return self.get_repository_instance( + ActivityInstructionPreInstanceRepository, user=self._author_id + ) @property def footnote_pre_instance_repository(self) -> FootnotePreInstanceRepository: - return FootnotePreInstanceRepository(self._author_id) + return self.get_repository_instance( + FootnotePreInstanceRepository, user=self._author_id + ) @property def criteria_pre_instance_repository(self) -> CriteriaPreInstanceRepository: - return CriteriaPreInstanceRepository(self._author_id) + return self.get_repository_instance( + CriteriaPreInstanceRepository, user=self._author_id + ) @property def endpoint_pre_instance_repository(self) -> EndpointPreInstanceRepository: - return EndpointPreInstanceRepository(self._author_id) + return self.get_repository_instance( + EndpointPreInstanceRepository, user=self._author_id + ) @property def objective_pre_instance_repository(self) -> ObjectivePreInstanceRepository: - return ObjectivePreInstanceRepository(self._author_id) + return self.get_repository_instance( + ObjectivePreInstanceRepository, user=self._author_id + ) @property def library_repository(self) -> LibraryRepository: - return LibraryRepository() + return self.get_repository_instance(LibraryRepository) @property def ct_catalogue_repository(self) -> CTCatalogueRepository: - return CTCatalogueRepository() + return self.get_repository_instance(CTCatalogueRepository) @property def ct_package_repository(self) -> CTPackageRepository: - return CTPackageRepository() + return self.get_repository_instance(CTPackageRepository) @property def ct_codelist_name_repository(self) -> CTCodelistNameRepository: - return CTCodelistNameRepository() + return self.get_repository_instance(CTCodelistNameRepository) @property def ct_codelist_attribute_repository(self) -> CTCodelistAttributesRepository: - return CTCodelistAttributesRepository() + return self.get_repository_instance(CTCodelistAttributesRepository) @property def ct_codelist_aggregated_repository(self) -> CTCodelistAggregatedRepository: - return CTCodelistAggregatedRepository() + return self.get_repository_instance(CTCodelistAggregatedRepository) @property def ct_term_name_repository(self) -> CTTermNameRepository: - return CTTermNameRepository() + return self.get_repository_instance(CTTermNameRepository) @property def ct_term_attributes_repository(self) -> CTTermAttributesRepository: - return CTTermAttributesRepository() + return self.get_repository_instance(CTTermAttributesRepository) @property def ct_term_aggregated_repository(self) -> CTTermAggregatedRepository: - return CTTermAggregatedRepository() + return self.get_repository_instance(CTTermAggregatedRepository) @property def dictionary_codelist_generic_repository( self, ) -> DictionaryCodelistGenericRepository: - return DictionaryCodelistGenericRepository() + return self.get_repository_instance(DictionaryCodelistGenericRepository) @property def dictionary_term_generic_repository(self) -> DictionaryTermGenericRepository: - return DictionaryTermGenericRepository() + return self.get_repository_instance(DictionaryTermGenericRepository) @property def dictionary_term_substance_repository(self) -> DictionaryTermSubstanceRepository: - return DictionaryTermSubstanceRepository() + return self.get_repository_instance(DictionaryTermSubstanceRepository) @property def study_definition_repository(self) -> StudyDefinitionRepository: @@ -636,150 +671,154 @@ def study_definition_repository(self) -> StudyDefinitionRepository: @property def study_definition_document_repository(self) -> StudyDefinitionDocumentRepository: - return StudyDefinitionDocumentRepository() + return self.get_repository_instance(StudyDefinitionDocumentRepository) @property def study_version_repository(self) -> StudyVersionRepository: - return StudyVersionRepository() + return self.get_repository_instance(StudyVersionRepository) @property def project_repository(self) -> ProjectRepository: - return ProjectRepository() + return self.get_repository_instance(ProjectRepository) @property def brand_repository(self) -> BrandRepository: - return BrandRepository() + return self.get_repository_instance(BrandRepository) @property def comments_repository(self) -> CommentsRepository: - return CommentsRepository() + return self.get_repository_instance(CommentsRepository) @property def clinical_programme_repository(self) -> ClinicalProgrammeRepository: - return ClinicalProgrammeRepository() + return self.get_repository_instance(ClinicalProgrammeRepository) @property def study_data_supplier_repository(self) -> StudyDataSupplierRepository: - return StudyDataSupplierRepository() + return self.get_repository_instance(StudyDataSupplierRepository) @property def study_objective_repository(self) -> StudySelectionObjectiveRepository: - return StudySelectionObjectiveRepository() + return self.get_repository_instance(StudySelectionObjectiveRepository) @property def study_endpoint_repository(self) -> StudySelectionEndpointRepository: - return StudySelectionEndpointRepository() + return self.get_repository_instance(StudySelectionEndpointRepository) @property def study_compound_repository(self) -> StudySelectionCompoundRepository: - return StudySelectionCompoundRepository() + return self.get_repository_instance(StudySelectionCompoundRepository) @property def study_compound_dosing_repository(self) -> StudyCompoundDosingRepository: - return StudyCompoundDosingRepository() + return self.get_repository_instance(StudyCompoundDosingRepository) @property def study_criteria_repository(self) -> StudySelectionCriteriaRepository: - return StudySelectionCriteriaRepository() + return self.get_repository_instance(StudySelectionCriteriaRepository) @property def study_activity_instance_repository( self, ) -> StudySelectionActivityInstanceRepository: - return StudySelectionActivityInstanceRepository() + return self.get_repository_instance(StudySelectionActivityInstanceRepository) @property def study_activity_repository( self, ) -> StudySelectionActivityRepository: - return StudySelectionActivityRepository() + return self.get_repository_instance(StudySelectionActivityRepository) @property def study_activity_subgroup_repository( self, ) -> StudySelectionActivitySubGroupRepository: - return StudySelectionActivitySubGroupRepository() + return self.get_repository_instance(StudySelectionActivitySubGroupRepository) @property def study_activity_group_repository( self, ) -> StudySelectionActivityGroupRepository: - return StudySelectionActivityGroupRepository() + return self.get_repository_instance(StudySelectionActivityGroupRepository) @property def study_soa_group_repository( self, ) -> StudySoAGroupRepository: - return StudySoAGroupRepository() + return self.get_repository_instance(StudySoAGroupRepository) @property def study_activity_schedule_repository(self) -> StudyActivityScheduleRepository: - return StudyActivityScheduleRepository() + return self.get_repository_instance(StudyActivityScheduleRepository) @property def study_soa_footnote_repository(self) -> StudySoAFootnoteRepository: - return StudySoAFootnoteRepository() + return self.get_repository_instance(StudySoAFootnoteRepository) @property def study_design_cell_repository(self) -> StudyDesignCellRepository: - return StudyDesignCellRepository() + return self.get_repository_instance(StudyDesignCellRepository) @property def study_activity_instruction_repository( self, ) -> StudyActivityInstructionRepository: - return StudyActivityInstructionRepository() + return self.get_repository_instance(StudyActivityInstructionRepository) @property def study_title_repository(self) -> StudyTitleRepository: - return StudyTitleRepository() + return self.get_repository_instance(StudyTitleRepository) @property def study_epoch_repository(self) -> StudyEpochRepository: - return StudyEpochRepository() + return self.get_repository_instance(StudyEpochRepository) @property def study_disease_milestone_repository(self) -> StudyDiseaseMilestoneRepository: - return StudyDiseaseMilestoneRepository(self._author_id) + return self.get_repository_instance( + StudyDiseaseMilestoneRepository, author_id=self._author_id + ) @property def study_standard_version_repository(self) -> StudyStandardVersionRepository: - return StudyStandardVersionRepository(self._author_id) + return self.get_repository_instance( + StudyStandardVersionRepository, author_id=self._author_id + ) @property def study_visit_repository(self) -> StudyVisitRepository: - return StudyVisitRepository() + return self.get_repository_instance(StudyVisitRepository) @property def ct_config_repository(self) -> CTConfigRepository: - return CTConfigRepository(self._author_id) + return self.get_repository_instance(CTConfigRepository, user=self._author_id) @property def study_arm_repository(self) -> StudySelectionArmRepository: - return StudySelectionArmRepository() + return self.get_repository_instance(StudySelectionArmRepository) @property def study_element_repository(self) -> StudySelectionElementRepository: - return StudySelectionElementRepository() + return self.get_repository_instance(StudySelectionElementRepository) @property def study_branch_arm_repository( self, ) -> StudySelectionBranchArmRepository: - return StudySelectionBranchArmRepository() + return self.get_repository_instance(StudySelectionBranchArmRepository) @property def study_cohort_repository(self) -> StudySelectionCohortRepository: - return StudySelectionCohortRepository() + return self.get_repository_instance(StudySelectionCohortRepository) @property def study_design_class_repository(self) -> StudyDesignClassRepository: - return StudyDesignClassRepository() + return self.get_repository_instance(StudyDesignClassRepository) @property def study_source_variable_repository(self) -> StudySourceVariableRepository: - return StudySourceVariableRepository() + return self.get_repository_instance(StudySourceVariableRepository) @property def user_repository(self) -> UserRepository: - return UserRepository() + return self.get_repository_instance(UserRepository) diff --git a/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_instance_class.py b/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_instance_class.py index 2a116e53..30b90d66 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_instance_class.py +++ b/clinical-mdr-api/clinical_mdr_api/services/biomedical_concepts/activity_instance_class.py @@ -40,6 +40,22 @@ class ActivityInstanceClassService(NeomodelExtGenericService[ActivityInstanceCla api_model_class = ActivityInstanceClass version_class = ActivityInstanceClassVersion + @ensure_transaction(db) + def get_all_item_versions( + self, + sort_by: dict[str, bool] | None = None, + page_number: int = 1, + page_size: int = 0, + total_count: bool = False, + ) -> GenericFilteringReturn[ActivityInstanceClass]: + items, total = self.repository.find_all_versions( + sort_by=sort_by, + page_number=page_number, + page_size=page_size, + total_count=total_count, + ) + return GenericFilteringReturn(items=items, total=total) + def _transform_aggregate_root_to_pydantic_model( self, item_ar: ActivityInstanceClassAR ) -> ActivityInstanceClass: 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 4a94da8d..720d27a5 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 @@ -304,6 +304,8 @@ def get_all_for_activity_instance_class( is_default_linked=item_class["has_activity_instance_class"][ "is_default_linked" ], + data_type_uid=item_class.get("data_type_uid"), + data_type_name=item_class.get("data_type_name"), ) # Order the results by name return sorted(seen_uids.values(), key=lambda x: x.name or "") diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_group_service.py b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_group_service.py index dd7f9c49..ff722231 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_group_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_group_service.py @@ -53,6 +53,8 @@ def _create_aggregate_root( name_sentence_case=concept_input.name_sentence_case, definition=concept_input.definition, abbreviation=concept_input.abbreviation, + nci_concept_id=concept_input.nci_concept_id, + nci_concept_name=concept_input.nci_concept_name, ), library=library, generate_uid_callback=self.repository.generate_uid, @@ -70,6 +72,8 @@ def _edit_aggregate( name_sentence_case=concept_edit_input.name_sentence_case, definition=concept_edit_input.definition, abbreviation=concept_edit_input.abbreviation, + nci_concept_id=concept_edit_input.nci_concept_id, + nci_concept_name=concept_edit_input.nci_concept_name, ), concept_exists_by_library_and_name_callback=self._repos.activity_group_repository.latest_concept_in_library_exists_by_name, ) @@ -104,6 +108,8 @@ def get_group_details( return ActivityGroupDetail( name=group.name, name_sentence_case=group.name_sentence_case, + nci_concept_id=group.nci_concept_id, + nci_concept_name=group.nci_concept_name, library_name=group.library_name, start_date=start_date, end_date=end_date, 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 1970fabb..146d967c 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 @@ -2,10 +2,16 @@ from typing import Any from clinical_mdr_api.domain_repositories.concepts.activities.activity_instance_repository import ( + ActivityInstanceAttributesRepository, + ActivityInstanceGroupingsRepository, ActivityInstanceRepository, ) from clinical_mdr_api.domains.concepts.activities.activity_instance import ( ActivityInstanceAR, + ActivityInstanceAttributesAR, + ActivityInstanceAttributesVO, + ActivityInstanceGroupingsAR, + ActivityInstanceGroupingsVO, ActivityInstanceGroupingVO, ActivityInstanceVO, ) @@ -17,16 +23,21 @@ from clinical_mdr_api.domains.versioned_object_aggregate import LibraryVO from clinical_mdr_api.models.concepts.activities.activity_instance import ( ActivityInstance, + ActivityInstanceAttributes, + ActivityInstanceAttributesVersion, ActivityInstanceCreateInput, ActivityInstanceEditInput, + ActivityInstanceGroupings, + ActivityInstanceGroupingsEditInput, + ActivityInstanceGroupingsVersion, ActivityInstanceOverview, ActivityInstanceVersion, - SimpleActivityInstanceGrouping, SimplifiedActivityItem, ) from clinical_mdr_api.models.concepts.activities.activity_item import ( CompactUnitDefinition, ) +from clinical_mdr_api.models.utils import BaseModel from clinical_mdr_api.services.concepts import constants from clinical_mdr_api.services.concepts.concept_generic_service import ( ConceptGenericService, @@ -92,6 +103,7 @@ def _create_aggregate_root( ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=item.text_value, + is_activity_instance_id_specific=item.is_activity_instance_id_specific, ) ) @@ -157,9 +169,196 @@ def _create_aggregate_root( def _edit_aggregate( self, item: ActivityInstanceAR, + concept_edit_input: BaseModel, + ) -> ActivityInstanceAR: + # Editing happens on the different aggregate roots for attributes and groupings, + # so this method is never used. + raise NotImplementedError + + def get_activity_instance_overview( + self, activity_instance_uid: str, version: str | None = None + ) -> ActivityInstanceOverview: + NotFoundException.raise_if_not( + self.repository.exists_by("uid", activity_instance_uid, True), + "Activity Instance", + activity_instance_uid, + ) + overview = ( + self._repos.activity_instance_repository.get_activity_instance_overview( + uid=activity_instance_uid, version=version + ) + ) + return ActivityInstanceOverview.from_repository_input(overview=overview) + + def get_activity_instance_items( + self, activity_instance_uid: str, version: str | None = None + ) -> list[SimplifiedActivityItem]: + NotFoundException.raise_if_not( + self.repository.exists_by("uid", activity_instance_uid, True), + "Activity Instance", + activity_instance_uid, + ) + overview = self.repository.get_activity_instance_overview( + uid=activity_instance_uid, version=version + ) + return ActivityInstanceOverview.from_repository_input( + overview=overview + ).activity_items + + def get_cosmos_activity_instance_overview( + self, activity_instance_uid: str + ) -> dict[str, Any]: + NotFoundException.raise_if_not( + self.repository.exists_by("uid", activity_instance_uid, True), + "Activity Instance", + activity_instance_uid, + ) + data: dict[Any, Any] = self.repository.get_cosmos_activity_instance_overview( + uid=activity_instance_uid + ) + result: dict[str, Any] = { + "packageDate": datetime.date.today().isoformat(), + "packageType": "bc", + "conceptId": data["activity_instance_value"]["nci_concept_id"], + "ncitCode": data["activity_instance_value"]["nci_concept_id"], + "href": constants.COSM0S_BASE_ITEM_HREF.format( + data["activity_instance_value"]["nci_concept_id"] + ), + "categories": data["activity_subgroups"], + "shortName": data["activity_instance_value"]["name"], + "synonyms": data["activity_instance_value"]["abbreviation"], + "resultScales": [ + constants.COSM0S_RESULT_SCALES_MAP.get( + data["activity_instance_class_name"], "" + ) + ], + "definition": data["activity_instance_value"]["definition"], + "dataElementConcepts": [], + } + for activity_item in data["activity_items"]: + result["dataElementConcepts"].append( + { + "conceptId": activity_item["nci_concept_id"], + "ncitCode": activity_item["nci_concept_id"], + "href": constants.COSM0S_BASE_ITEM_HREF.format( + activity_item["nci_concept_id"] + ), + "shortName": activity_item["name"], + "dataType": constants.COSMOS_DEC_TYPES_MAP.get( + activity_item["type"], activity_item["type"] + ), + "exampleSet": activity_item["example_set"], + } + ) + return result + + +class ActivityInstanceAttributesService( + ConceptGenericService[ActivityInstanceAttributesAR] +): + aggregate_class = ActivityInstanceAttributesAR + repository_interface = ActivityInstanceAttributesRepository + version_class = ActivityInstanceAttributesVersion + + def _get_parent_class_uid(self, uid: str) -> str | None: + """Get parent class UID for a given activity instance class UID""" + parent = self._repos.activity_instance_class_repository.get_parent_class(uid) + return parent[0] if parent else None + + def _transform_aggregate_root_to_pydantic_model( + self, item_ar: ActivityInstanceAttributesAR + ) -> ActivityInstanceAttributes: + return ActivityInstanceAttributes.from_activity_ar( + activity_ar=item_ar, + ) + + def _create_aggregate_root( + self, + concept_input: ActivityInstanceCreateInput, + library: LibraryVO, + preview: bool = False, + ) -> ActivityInstanceAttributesAR: + activity_items = [] + if ( + getattr(concept_input, "activity_items", None) + and concept_input.activity_items is not None + ): + for item in concept_input.activity_items: + unit_definitions = [ + CompactUnitDefinition(uid=unit_uid, name=None, dimension_name=None) + for unit_uid in item.unit_definition_uids + ] + ct_terms = [ + CTTermItem( + uid=ct_term.term_uid, + name=None, + codelist_uid=ct_term.codelist_uid, + ) + for ct_term in item.ct_terms + ] + ct_codelist = ( + CTCodelistItem(uid=item.ct_codelist_uid) + if item.ct_codelist_uid + else None + ) + activity_items.append( + ActivityItemVO.from_repository_values( + is_adam_param_specific=item.is_adam_param_specific, + activity_item_class_uid=item.activity_item_class_uid, + activity_item_class_name=None, + ct_codelist=ct_codelist, + ct_terms=ct_terms, + unit_definitions=unit_definitions, + is_activity_instance_id_specific=item.is_activity_instance_id_specific, + ) + ) + + return ActivityInstanceAttributesAR.from_input_values( + author_id=self.author_id, + concept_vo=ActivityInstanceAttributesVO.from_repository_values( + nci_concept_id=concept_input.nci_concept_id, + nci_concept_name=concept_input.nci_concept_name, + name=concept_input.name or "", + name_sentence_case=concept_input.name_sentence_case or "", + definition=concept_input.definition, + abbreviation=concept_input.abbreviation, + is_research_lab=concept_input.is_research_lab, + molecular_weight=concept_input.molecular_weight, + topic_code=concept_input.topic_code, + adam_param_code=concept_input.adam_param_code, + is_required_for_activity=concept_input.is_required_for_activity, + is_default_selected_for_activity=concept_input.is_default_selected_for_activity, + is_data_sharing=concept_input.is_data_sharing, + is_legacy_usage=concept_input.is_legacy_usage, + is_derived=concept_input.is_derived, + legacy_description=concept_input.legacy_description, + activity_instance_class_uid=concept_input.activity_instance_class_uid, + activity_instance_class_name=None, + activity_items=activity_items, + ), + library=library, + generate_uid_callback=( + self.repository.generate_uid + if not preview + else lambda: "PreviewTemporalUid" + ), + concept_exists_by_library_and_property_value_callback=self._repos.activity_instance_repository.latest_concept_in_library_exists_by_property_value, + ct_term_exists_by_uid_callback=self._repos.ct_term_name_repository.term_exists, + unit_definition_exists_by_uid_callback=self._repos.unit_definition_repository.final_concept_exists, + find_activity_item_class_by_uid_callback=self._repos.activity_item_class_repository.find_by_uid_2, + find_activity_instance_class_by_uid_callback=self._repos.activity_instance_class_repository.find_by_uid_2, + preview=preview, + get_dimension_names_by_unit_definition_uids=self._repos.unit_definition_repository.get_dimension_names_by_unit_definition_uids, + get_parent_class_uid_callback=self._get_parent_class_uid, + strict_mode=getattr(concept_input, "strict_mode", False), + ) + + def _edit_aggregate( + self, + item: ActivityInstanceAttributesAR, concept_edit_input: ActivityInstanceEditInput, perform_validation: bool = True, - ) -> ActivityInstanceAR: + ) -> ActivityInstanceAttributesAR: fields_set = concept_edit_input.model_fields_set # Validate that restricted fields cannot be modified @@ -228,31 +427,6 @@ def _edit_aggregate( msg="Activity items with param/paramcd cannot have their terms (ct_terms) modified after creation.", ) - if "activity_groupings" in fields_set: - if concept_edit_input.activity_groupings: - activity_groupings = [ - ActivityInstanceGroupingVO( - activity_uid=activity_grouping.activity_uid, - activity_group_uid=activity_grouping.activity_group_uid, - activity_subgroup_uid=activity_grouping.activity_subgroup_uid, - ) - for activity_grouping in concept_edit_input.activity_groupings - ] - else: - activity_groupings = [] - else: - if item.concept_vo.activity_groupings: - activity_groupings = [ - ActivityInstanceGroupingVO( - activity_uid=activity_grouping.activity_uid, - activity_group_uid=activity_grouping.activity_group_uid, - activity_subgroup_uid=activity_grouping.activity_subgroup_uid, - ) - for activity_grouping in item.concept_vo.activity_groupings - ] - else: - activity_groupings = [] - if "activity_items" in fields_set: activity_items = [] if concept_edit_input.activity_items is not None: @@ -284,6 +458,7 @@ def _edit_aggregate( ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=activity_item.text_value, + is_activity_instance_id_specific=activity_item.is_activity_instance_id_specific, ) ) else: @@ -292,7 +467,7 @@ def _edit_aggregate( item.edit_draft( author_id=self.author_id, change_description=concept_edit_input.change_description, - concept_vo=ActivityInstanceVO.from_repository_values( + concept_vo=ActivityInstanceAttributesVO.from_repository_values( nci_concept_id=get_edit_input_or_previous_value( concept_edit_input, item.concept_vo, @@ -347,7 +522,6 @@ def _edit_aggregate( legacy_description=get_edit_input_or_previous_value( concept_edit_input, item.concept_vo, "legacy_description" ), - activity_groupings=activity_groupings, activity_instance_class_uid=concept_edit_input.activity_instance_class_uid or item.concept_vo.activity_instance_class_uid, activity_instance_class_name=None, @@ -356,9 +530,6 @@ def _edit_aggregate( concept_exists_by_library_and_property_value_callback=self._repos.activity_instance_repository.latest_concept_in_library_exists_by_property_value, ct_term_exists_by_uid_callback=self._repos.ct_term_name_repository.term_exists, unit_definition_exists_by_uid_callback=self._repos.unit_definition_repository.final_concept_exists, - get_final_activity_value_by_uid_callback=self._repos.activity_repository.final_concept_value, - activity_group_exists=self._repos.activity_group_repository.final_concept_exists, - activity_subgroup_exists=self._repos.activity_subgroup_repository.final_concept_exists, find_activity_item_class_by_uid_callback=self._repos.activity_item_class_repository.find_by_uid_2, find_activity_instance_class_by_uid_callback=self._repos.activity_instance_class_repository.find_by_uid_2, get_dimension_names_by_unit_definition_uids=self._repos.unit_definition_repository.get_dimension_names_by_unit_definition_uids, @@ -372,94 +543,80 @@ def _edit_aggregate( ) return item - def get_activity_instance_overview( - self, activity_instance_uid: str, version: str | None = None - ) -> ActivityInstanceOverview: - NotFoundException.raise_if_not( - self.repository.exists_by("uid", activity_instance_uid, True), - "Activity Instance", - activity_instance_uid, - ) - overview = ( - self._repos.activity_instance_repository.get_activity_instance_overview( - uid=activity_instance_uid, version=version - ) - ) - return ActivityInstanceOverview.from_repository_input(overview=overview) - def get_activity_instance_groupings( - self, activity_instance_uid: str, version: str | None = None - ) -> list[SimpleActivityInstanceGrouping]: - NotFoundException.raise_if_not( - self.repository.exists_by("uid", activity_instance_uid, True), - "Activity Instance", - activity_instance_uid, - ) - overview = self.repository.get_activity_instance_overview( - uid=activity_instance_uid, version=version - ) - return ActivityInstanceOverview.from_repository_input( - overview=overview - ).activity_groupings +class ActivityInstanceGroupingsService( + ConceptGenericService[ActivityInstanceGroupingsAR] +): + aggregate_class = ActivityInstanceGroupingsAR + repository_interface = ActivityInstanceGroupingsRepository + version_class = ActivityInstanceGroupingsVersion - def get_activity_instance_items( - self, activity_instance_uid: str, version: str | None = None - ) -> list[SimplifiedActivityItem]: - NotFoundException.raise_if_not( - self.repository.exists_by("uid", activity_instance_uid, True), - "Activity Instance", - activity_instance_uid, - ) - overview = self.repository.get_activity_instance_overview( - uid=activity_instance_uid, version=version - ) - return ActivityInstanceOverview.from_repository_input( - overview=overview - ).activity_items + def _get_parent_class_uid(self, uid: str) -> str | None: + """Get parent class UID for a given activity instance class UID""" + parent = self._repos.activity_instance_class_repository.get_parent_class(uid) + return parent[0] if parent else None - def get_cosmos_activity_instance_overview( - self, activity_instance_uid: str - ) -> dict[str, Any]: - NotFoundException.raise_if_not( - self.repository.exists_by("uid", activity_instance_uid, True), - "Activity Instance", - activity_instance_uid, - ) - data: dict[Any, Any] = self.repository.get_cosmos_activity_instance_overview( - uid=activity_instance_uid + def _transform_aggregate_root_to_pydantic_model( + self, item_ar: ActivityInstanceGroupingsAR + ) -> ActivityInstanceGroupings: + return ActivityInstanceGroupings.from_activity_ar( + activity_ar=item_ar, + find_activity_hierarchy_by_uid=self._repos.activity_repository.find_by_uid_2, + find_activity_subgroup_by_uid=self._repos.activity_subgroup_repository.find_by_uid_2, + find_activity_group_by_uid=self._repos.activity_group_repository.find_by_uid_2, ) - result: dict[str, Any] = { - "packageDate": datetime.date.today().isoformat(), - "packageType": "bc", - "conceptId": data["activity_instance_value"]["nci_concept_id"], - "ncitCode": data["activity_instance_value"]["nci_concept_id"], - "href": constants.COSM0S_BASE_ITEM_HREF.format( - data["activity_instance_value"]["nci_concept_id"] + + def _create_aggregate_root( + self, + concept_input: ActivityInstanceCreateInput, + library: LibraryVO, + preview: bool = False, + ) -> ActivityInstanceGroupingsAR: + # Groupings are never created by themselves, creation only happens together with attributes, + # so we can raise NotImplementedError here and use the del + raise NotImplementedError + + def _edit_aggregate( + self, + item: ActivityInstanceGroupingsAR, + concept_edit_input: ActivityInstanceGroupingsEditInput, + perform_validation: bool = True, + ) -> ActivityInstanceGroupingsAR: + fields_set = concept_edit_input.model_fields_set + if "activity_groupings" in fields_set: + if concept_edit_input.activity_groupings: + activity_groupings = [ + ActivityInstanceGroupingVO( + activity_uid=activity_grouping.activity_uid, + activity_group_uid=activity_grouping.activity_group_uid, + activity_subgroup_uid=activity_grouping.activity_subgroup_uid, + ) + for activity_grouping in concept_edit_input.activity_groupings + ] + else: + activity_groupings = [] + else: + if item.concept_vo.activity_groupings: + activity_groupings = [ + ActivityInstanceGroupingVO( + activity_uid=activity_grouping.activity_uid, + activity_group_uid=activity_grouping.activity_group_uid, + activity_subgroup_uid=activity_grouping.activity_subgroup_uid, + ) + for activity_grouping in item.concept_vo.activity_groupings + ] + else: + activity_groupings = [] + + item.edit_draft( + author_id=self.author_id, + change_description=concept_edit_input.change_description, + concept_vo=ActivityInstanceGroupingsVO.from_repository_values( + activity_groupings=activity_groupings, ), - "categories": data["activity_subgroups"], - "shortName": data["activity_instance_value"]["name"], - "synonyms": data["activity_instance_value"]["abbreviation"], - "resultScales": [ - constants.COSM0S_RESULT_SCALES_MAP.get( - data["activity_instance_class_name"], "" - ) - ], - "definition": data["activity_instance_value"]["definition"], - "dataElementConcepts": [], - } - for activity_item in data["activity_items"]: - result["dataElementConcepts"].append( - { - "conceptId": activity_item["nci_concept_id"], - "ncitCode": activity_item["nci_concept_id"], - "href": constants.COSM0S_BASE_ITEM_HREF.format( - activity_item["nci_concept_id"] - ), - "shortName": activity_item["name"], - "dataType": constants.COSMOS_DEC_TYPES_MAP.get( - activity_item["type"], activity_item["type"] - ), - "exampleSet": activity_item["example_set"], - } - ) - return result + get_final_activity_value_by_uid_callback=self._repos.activity_repository.final_concept_value, + activity_group_exists=self._repos.activity_group_repository.final_concept_exists, + activity_subgroup_exists=self._repos.activity_subgroup_repository.final_concept_exists, + perform_validation=perform_validation, + ) + return item 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 64bcd73f..f636a438 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 @@ -28,14 +28,14 @@ ) from clinical_mdr_api.models.concepts.activities.activity_instance import ( ActivityInstanceDetail, - ActivityInstanceEditInput, ActivityInstanceGrouping, + ActivityInstanceGroupingsEditInput, ) from clinical_mdr_api.models.utils import GenericFilteringReturn from clinical_mdr_api.services._utils import is_library_editable from clinical_mdr_api.services.concepts import constants from clinical_mdr_api.services.concepts.activities.activity_instance_service import ( - ActivityInstanceService, + ActivityInstanceGroupingsService, ) from clinical_mdr_api.services.concepts.concept_generic_service import ( ConceptGenericService, @@ -460,7 +460,7 @@ def cascade_edit_and_approve(self, item: ActivityAR): self.batch_cascade_update(item, linked_instances) def batch_cascade_update(self, item: ActivityAR, linked_instances: dict[str, Any]): - activity_instance_service = ActivityInstanceService() + activity_instance_groupings_service = ActivityInstanceGroupingsService() linked_instances_map = { activity_instance["uid"]: activity_instance for activity_instance in linked_instances.get("activity_instances", []) @@ -471,7 +471,7 @@ def batch_cascade_update(self, item: ActivityAR, linked_instances: dict[str, Any uids=activity_instance_uids ) activity_instance_ars, _ = ( - self._repos.activity_instance_repository.find_all( + self._repos.activity_instance_groupings_repository.find_all( uids=activity_instance_uids, ) ) @@ -513,21 +513,20 @@ def batch_cascade_update(self, item: ActivityAR, linked_instances: dict[str, Any # For FINAL activity instances: create new version, edit, and approve activity_instance.create_new_version(author_id=self.author_id) - edit_input = ActivityInstanceEditInput( + edit_input = ActivityInstanceGroupingsEditInput( change_description="Cascade edit", activity_groupings=instance_groupings, - name=activity_instance.concept_vo.name, - name_sentence_case=activity_instance.concept_vo.name_sentence_case, ) - activity_instance = activity_instance_service._edit_aggregate( + activity_instance = activity_instance_groupings_service._edit_aggregate( item=activity_instance, concept_edit_input=edit_input, perform_validation=False, ) activity_instance.approve(author_id=self.author_id) - self._repos.activity_instance_repository.copy_activity_instance_and_recreate_activity_groupings( - activity_instance=activity_instance, author_id=self.author_id + self._repos.activity_instance_groupings_repository.copy_activity_instance_groupings_and_recreate( + activity_instance_groupings=activity_instance, + author_id=self.author_id, ) def get_specific_activity_version_groupings( diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_sub_group_service.py b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_sub_group_service.py index aea5188c..bddef1f9 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_sub_group_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/concepts/activities/activity_sub_group_service.py @@ -60,6 +60,8 @@ def _create_aggregate_root( name_sentence_case=concept_input.name_sentence_case, definition=concept_input.definition, abbreviation=concept_input.abbreviation, + nci_concept_id=concept_input.nci_concept_id, + nci_concept_name=concept_input.nci_concept_name, ), library=library, generate_uid_callback=self.repository.generate_uid, @@ -79,6 +81,8 @@ def _edit_aggregate( name_sentence_case=concept_edit_input.name_sentence_case, definition=concept_edit_input.definition, abbreviation=concept_edit_input.abbreviation, + nci_concept_id=concept_edit_input.nci_concept_id, + nci_concept_name=concept_edit_input.nci_concept_name, ), concept_exists_by_library_and_name_callback=self._repos.activity_subgroup_repository.latest_concept_in_library_exists_by_name, ) @@ -111,6 +115,8 @@ def get_subgroup_overview( activity_subgroup_detail = ActivitySubGroupDetail( name=subgroup.name, name_sentence_case=subgroup.name_sentence_case, + nci_concept_id=subgroup.nci_concept_id, + nci_concept_name=subgroup.nci_concept_name, library_name=subgroup.library_name, definition=subgroup.definition, start_date=subgroup.start_date, diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/concept_generic_service.py b/clinical-mdr-api/clinical_mdr_api/services/concepts/concept_generic_service.py index 211ae018..5bb8a012 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/concept_generic_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/concepts/concept_generic_service.py @@ -16,6 +16,10 @@ from clinical_mdr_api.models.concepts.activities.activity import ( ActivityHierarchySimpleModel, ) +from clinical_mdr_api.models.concepts.activities.activity_instance import ( + ActivityInstanceGrouping, + ActivityInstanceHierarchySimpleModel, +) from clinical_mdr_api.models.concepts.unit_definitions.unit_definition import ( UnitDefinitionModel, ) @@ -142,6 +146,24 @@ def _fill_missing_values_in_base_model_from_reference_base_model( for term in getattr(reference_base_model, field_name) ], ) + elif ( + get_field_type( + reference_base_model.model_fields[field_name].annotation + ) + is ActivityInstanceHierarchySimpleModel + ): + setattr( + base_model_with_missing_values, + field_name, + [ + ActivityInstanceGrouping( + activity_uid=term.activity.uid, + activity_group_uid=term.activity_group.uid, + activity_subgroup_uid=term.activity_subgroup.uid, + ) + for term in getattr(reference_base_model, field_name) + ], + ) else: setattr( base_model_with_missing_values, @@ -587,8 +609,7 @@ def generate_default_adam_code(self, response_model): MATCH (lib:Library)-[:CONTAINS_TERM]-> (ctterm_root:CTTermRoot) where - lib.name="CDISC" - AND ctterm_root.uid = $ct_uid + ctterm_root.uid = $ct_uid MATCH (ctterm_root)<-[:HAS_TERM_ROOT]- (codelist_term:CTCodelistTerm)<-[:HAS_TERM]- (:CTCodelistRoot)<-[:REFERENCES_CODELIST]- 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 d922464b..a253ea0c 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 @@ -23,6 +23,7 @@ CTCodelistPaired, CTCodelistPairedInput, CTCodelistTerm, + CTPairedCodelistTerm, ) from clinical_mdr_api.models.utils import GenericFilteringReturn from clinical_mdr_api.repositories._utils import FilterOperator @@ -787,3 +788,52 @@ def update_paired_codelists( ) return self.get_paired_codelists(codelist_uid) + + def get_paired_codelist_terms( + self, + codelist_uid: str, + sort_by: dict[str, bool] | None = None, + page_number: int = 1, + page_size: int = 0, + filter_by: dict[str, dict[str, Any]] | None = None, + filter_operator: FilterOperator = FilterOperator.AND, + total_count: bool = False, + ) -> GenericFilteringReturn[CTPairedCodelistTerm]: + paired_codes_uid, paired_names_uid = ( + self._repos.ct_codelist_aggregated_repository.get_paired_codelist_uids( + codelist_uid + ) + ) + + BusinessLogicException.raise_if( + paired_codes_uid is None and paired_names_uid is None, + msg=f"Codelist with UID '{codelist_uid}' does not have a paired codelist.", + ) + + if paired_codes_uid is not None: + names_codelist_uid = codelist_uid + codes_codelist_uid = paired_codes_uid + else: + assert paired_names_uid is not None + codes_codelist_uid = codelist_uid + names_codelist_uid = paired_names_uid + + all_paired_terms, count = ( + self._repos.ct_codelist_aggregated_repository.find_paired_codelist_terms( + names_codelist_uid=names_codelist_uid, + codes_codelist_uid=codes_codelist_uid, + sort_by=sort_by, + page_number=page_number, + page_size=page_size, + total_count=total_count, + filter_by=filter_by, + filter_operator=filter_operator, + ) + ) + + items = [ + CTPairedCodelistTerm.from_ct_paired_codelist_term_ar(paired_term_ar) + for paired_term_ar in all_paired_terms + ] + + return GenericFilteringReturn.create(items=items, total=count) diff --git a/clinical-mdr-api/clinical_mdr_api/services/ddf/usdm_mapper.py b/clinical-mdr-api/clinical_mdr_api/services/ddf/usdm_mapper.py index 62d2b937..6e050350 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/ddf/usdm_mapper.py +++ b/clinical-mdr-api/clinical_mdr_api/services/ddf/usdm_mapper.py @@ -1,6 +1,6 @@ import re import uuid -from datetime import date +from datetime import date, datetime, timezone from itertools import chain from typing import Any, Callable @@ -13,6 +13,7 @@ from usdm_model import Endpoint as USDMEndpoint from usdm_model import Indication as USDMIndication from usdm_model import Objective as USDMObjective +from usdm_model import Organization as USDMOrganization from usdm_model import Procedure as USDMProcedure from usdm_model import Quantity as USDMQuantity from usdm_model import Range as USDMRange @@ -43,7 +44,8 @@ from clinical_mdr_api.services.ddf.usdm_utils import IdManager from common.telemetry import trace_calls -DDF_CT_PACKAGE_EFFECTIVE_DATE = "2023-12-15" +DDF_ORGANIZATION_TYPE_STUDY_REGISTRY = "C93453" +DDF_ORGANIZATION_TYPE_REGULATORY_AGENCY = "C188863" DDF_STUDY_ARM_DATA_ORIGIN_TYPE_GENERATED_WITHIN_STUDY = "C188866" DDF_STUDY_POPULATION_DURATION_UNIT_DAYS = "C25301" DDF_STUDY_POPULATION_DURATION_UNIT_WEEKS = "C29844" @@ -131,6 +133,64 @@ def __init__( self._get_osb_study_activities = get_osb_study_activities self._get_osb_activity_schedules = get_osb_activity_schedules self._id_manager = IdManager() + self._ct_package_effective_date: str = str(date.today()) + self._ct_terms_datetime: datetime | None = None + self._registid_labels: dict[str, str] = {} + + @staticmethod + def _effective_date_to_str(effective_date) -> str: + """Convert a Neo4j date value to a date-only string (YYYY-MM-DD).""" + # Neo4j may return neo4j.time.Date or datetime — ensure date-only format + return str(effective_date)[:10] + + @staticmethod + def _effective_date_to_datetime(effective_date_str: str) -> datetime: + """Convert effective date string (YYYY-MM-DD) to a timezone-aware datetime for version-aware CT term resolution.""" + d = date.fromisoformat(effective_date_str) + return datetime(d.year, d.month, d.day, 23, 59, 59, 999999, tzinfo=timezone.utc) + + @staticmethod + def _resolve_ct_package_effective_date(study_uid: str) -> str: + """Resolve CT package effective date from study's selected CT package, falling back to latest CDISC CT package.""" + # Try study's own CT package first + query = """ + MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue) + -[:HAS_STUDY_STANDARD_VERSION]->(ssv:StudyStandardVersion) + -[:HAS_CT_PACKAGE]->(ct_pkg:CTPackage) + RETURN ct_pkg.effective_date AS effective_date + ORDER BY ct_pkg.effective_date DESC + LIMIT 1 + """ + result, _ = db.cypher_query(query, {"study_uid": study_uid}) + if result and result[0][0] is not None: + return USDMMapper._effective_date_to_str(result[0][0]) + + # Fallback: latest CDISC CT package (from DDF CT or SDTM CT catalogues, excluding sponsor extensions) + fallback_query = """ + MATCH (cat:CTCatalogue)-[:CONTAINS_PACKAGE]->(ct_pkg:CTPackage) + WHERE cat.name IN ['DDF CT', 'SDTM CT'] AND NOT (ct_pkg)-[:EXTENDS_PACKAGE]->() + RETURN ct_pkg.effective_date AS effective_date + ORDER BY ct_pkg.effective_date DESC + LIMIT 1 + """ + result, _ = db.cypher_query(fallback_query) + if result and result[0][0] is not None: + return USDMMapper._effective_date_to_str(result[0][0]) + + # Ultimate fallback + return str(date.today()) + + @staticmethod + def _load_registid_labels() -> dict[str, str]: + """Load registry identifier term labels from the REGISTID sponsor codelist (CTCodelist_000038).""" + query = """ + MATCH (cl:CTCodelistRoot {uid: 'CTCodelist_000038'})-[:HAS_TERM]->(clt:CTCodelistTerm) + -[:HAS_TERM_ROOT]->(tr:CTTermRoot) + MATCH (tr)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(tnv:CTTermNameValue) + RETURN tr.uid AS term_uid, tnv.name AS term_name + """ + result, _ = db.cypher_query(query) + return {row[0]: row[1] for row in result} def get_void_usdm_code(self): return USDMCode( @@ -146,15 +206,26 @@ def get_void_usdm_code(self): def get_ct_package_term_as_usdm_code(self, concept_id: str | None) -> USDMCode: if concept_id is None: return self.get_void_usdm_code() + # Version-aware term resolution: resolve term name at the study's CT package effective date. + # Uses the ct_term_name_at_datetime pattern from common/queries.py — orders by dates_match DESC + # so an exact version match is preferred, but falls back gracefully to the latest version. query = """ - MATCH (l:Library)-[:CONTAINS_TERM]->(cttr:CTTermRoot)-[:HAS_NAME_ROOT]->()-[:LATEST]->(cttav) + MATCH (l:Library)-[:CONTAINS_TERM]->(cttr:CTTermRoot) WHERE cttr.uid STARTS WITH $concept_id - RETURN l, cttav + MATCH (cttr)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[version:HAS_VERSION]->(value:CTTermNameValue) + WHERE version.status IN ['Final', 'Retired'] + WITH l, cttr, version, value, + ($ct_terms_datetime IS NULL OR version.start_date <= $ct_terms_datetime + AND (version.end_date IS NULL OR version.end_date > $ct_terms_datetime)) AS dates_match + ORDER BY dates_match DESC, version.start_date DESC + LIMIT 1 + RETURN l, value """ result, _ = db.cypher_query( query, { "concept_id": concept_id, + "ct_terms_datetime": self._ct_terms_datetime, }, ) if len(result) == 0: @@ -165,7 +236,7 @@ def get_ct_package_term_as_usdm_code(self, concept_id: str | None) -> USDMCode: id=self._id_manager.get_id(USDMCode.__name__, concept_id), code=concept_id, codeSystem=library["name"], - codeSystemVersion=str(date.today()), + codeSystemVersion=self._ct_package_effective_date, decode=ct_term_name_value["name"], instanceType="Code", ) @@ -263,7 +334,7 @@ def get_dictionary_term_as_usdm_code(self, term_uid: str) -> USDMCode: id=self._id_manager.get_id(USDMCode.__name__, term_uid), code=term_uid, codeSystem=library["name"], - codeSystemVersion=str(date.today()), + codeSystemVersion=self._ct_package_effective_date, decode=ct_term_attributes_value["name"], instanceType="Code", ) @@ -271,6 +342,14 @@ def get_dictionary_term_as_usdm_code(self, term_uid: str) -> USDMCode: @trace_calls def map(self, study: OSBStudy) -> dict[str, Any]: + self._ct_package_effective_date = self._resolve_ct_package_effective_date( + study.uid + ) + self._ct_terms_datetime = self._effective_date_to_datetime( + self._ct_package_effective_date + ) + self._registid_labels = self._load_registid_labels() + usdm_study = USDMStudy(name=self._get_study_name(study), instanceType="Study") usdm_study.id = uuid.uuid4() usdm_study.label = self._get_study_label(study) @@ -290,10 +369,15 @@ def map(self, study: OSBStudy) -> dict[str, Any]: instanceType="StudyTitle", ) + study_identifiers, organizations = ( + self._get_study_identifiers_and_organizations(study) + ) + usdm_version = USDMStudyVersion( id=self._id_manager.get_id(USDMStudyVersion.__name__), titles=[ddf_study_title], - studyIdentifiers=self._get_study_identifiers(study), + studyIdentifiers=study_identifiers, + organizations=organizations, versionIdentifier="", rationale="Missing metadata", instanceType="StudyVersion", @@ -562,8 +646,107 @@ def _get_study_name(self, study: OSBStudy): osb_study_id = getattr(osb_identification_metadata, "study_id", "") return osb_study_id + # Registry identifier field names mapped to organization metadata. + # Organization type codes (from DDF CT codelist C188724): C93453 = Study Registry, C188863 = Regulatory Agency + # Labels are resolved at runtime from the REGISTID sponsor codelist (CTCodelist_000038) in the database. + # org_name and id_scheme have no DB source and remain as configuration. + REGISTRY_ORGANIZATIONS: dict[str, tuple[str, str | None, str, str, str]] = { + # field_name: (org_name, registid_term_uid, id_scheme, org_type_code, fallback_label) + "ct_gov_id": ( + "CT-GOV", + "CTTerm_000212", + "USGOV", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "ClinicalTrials.gov ID", + ), + "eudract_id": ( + "EUDRACT", + "CTTerm_000215", + "EU", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "EUDRACT ID", + ), + "eu_trial_number": ( + "EU-CT", + "CTTerm_000218", + "EU", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "EU Trial Number", + ), + "universal_trial_number_utn": ( + "WHO-UTN", + "CTTerm_000214", + "UTN", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "Universal Trial Number (UTN)", + ), + "japanese_trial_registry_id_japic": ( + "JAPIC", + "CTTerm_000213", + "JAPIC", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "Japanese Trial Registry ID (JAPIC)", + ), + "japanese_trial_registry_number_jrct": ( + "JRCT", + "CTTerm_000221", + "JRCT", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "Japanese Trial Registry Number (jRCT)", + ), + "investigational_new_drug_application_number_ind": ( + "FDA-IND", + "CTTerm_000217", + "USGOV", + DDF_ORGANIZATION_TYPE_REGULATORY_AGENCY, + "Investigational New Drug Application (IND) Number", + ), + "investigational_device_exemption_ide_number": ( + "FDA-IDE", + "CTTerm_000224", + "USGOV", + DDF_ORGANIZATION_TYPE_REGULATORY_AGENCY, + "Investigational Device Exemption (IDE) Number", + ), + "civ_id_sin_number": ( + "CIV-SIN", + "CTTerm_000216", + "EU", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "CIV-ID/SIN Number", + ), + "national_clinical_trial_number": ( + "NCT-REG", + "CTTerm_000220", + "NATIONAL", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "National Clinical Trial Number", + ), + "national_medical_products_administration_nmpa_number": ( + "NMPA", + "CTTerm_000222", + "NMPA", + DDF_ORGANIZATION_TYPE_REGULATORY_AGENCY, + "National Medical Products Administration (NMPA) Number", + ), + "eudamed_srn_number": ( + "EUDAMED", + "CTTerm_000223", + "EU", + DDF_ORGANIZATION_TYPE_REGULATORY_AGENCY, + "EUDAMED SRN Number", + ), + "eu_pas_number": ( + "EU-PAS", + None, + "EU", + DDF_ORGANIZATION_TYPE_STUDY_REGISTRY, + "EU PAS Register", + ), + } + @trace_calls - def _get_study_identifiers(self, study: OSBStudy): + def _get_study_identifiers_and_organizations(self, study: OSBStudy): osb_identification_metadata = getattr( getattr(study, "current_metadata", None), "identification_metadata", None ) @@ -571,32 +754,49 @@ def _get_study_identifiers(self, study: OSBStudy): osb_identification_metadata, "registry_identifiers", [] ) - selected_registry_identifiers = [ - "civ_id_sin_number", - "ct_gov_id", - "eudamed_srn_number", - "eudract_id", - "eu_trial_number", - "investigational_device_exemption_ide_number", - "investigational_new_drug_application_number_ind", - "japanese_trial_registry_id_japic", - "japanese_trial_registry_number_jrct", - "national_clinical_trial_number", - "national_medical_products_administration_nmpa_number", - "universal_trial_number_utn", - "eu_pas_number", - ] + study_identifiers = [] + organizations = [] + + for field_name, ( + org_name, + registid_term_uid, + id_scheme, + org_type_concept_id, + fallback_label, + ) in self.REGISTRY_ORGANIZATIONS.items(): + value = getattr(osb_registry_identifiers, field_name, None) + if not value: + continue + + # Resolve label from REGISTID codelist in DB, falling back to static label + org_label = ( + self._registid_labels.get(registid_term_uid, fallback_label) + if registid_term_uid + else fallback_label + ) - return [ - USDMStudyIdentifier( - id=self._id_manager.get_id(USDMStudyIdentifier.__name__), - text=osb_curr_id, - scopeId=selected_id, - instanceType="StudyIdentifier", + org_id = self._id_manager.get_id(USDMOrganization.__name__) + organizations.append( + USDMOrganization( + id=org_id, + name=org_name, + label=org_label, + type=self.get_ct_package_term_as_usdm_code(org_type_concept_id), + identifierScheme=id_scheme, + identifier=org_name, + instanceType="Organization", + ) ) - for selected_id in selected_registry_identifiers - if (osb_curr_id := getattr(osb_registry_identifiers, selected_id, None)) - ] + study_identifiers.append( + USDMStudyIdentifier( + id=self._id_manager.get_id(USDMStudyIdentifier.__name__), + text=value, + scopeId=org_id, + instanceType="StudyIdentifier", + ) + ) + + return study_identifiers, organizations @trace_calls def _get_study_indications(self, study: OSBStudy): diff --git a/clinical-mdr-api/clinical_mdr_api/services/odms/forms.py b/clinical-mdr-api/clinical_mdr_api/services/odms/forms.py index 4d4dd250..0afe7ba2 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/odms/forms.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/forms.py @@ -129,6 +129,8 @@ def add_item_groups( ) -> OdmForm: odm_form_ar = self._find_by_uid_or_raise_not_found(normalize_string(uid)) + renumbering_start = len(odm_form_ar.odm_vo.item_group_uids) or 1 + BusinessLogicException.raise_if( odm_form_ar.item_metadata.status != LibraryItemStatus.DRAFT, msg=self.OBJECT_NOT_IN_DRAFT, @@ -141,6 +143,7 @@ def add_item_groups( relationship_type=RelationType.ITEM_GROUP, disconnect_all=True, ) + renumbering_start = 1 vendor_attribute_patterns = self.get_regex_patterns_of_attributes( [ @@ -159,7 +162,11 @@ def add_item_groups( VendorAttributeCompatibleType.ITEM_GROUP_REF, ) - for item_group in odm_form_item_group_post_input: + post_input = self.renumber_items_sequentially( + odm_form_item_group_post_input, "order_number", renumbering_start + ) + + for item_group in post_input: if item_group.vendor: self.can_connect_vendor_attributes(item_group.vendor.attributes) self.attribute_values_matches_their_regex( diff --git a/clinical-mdr-api/clinical_mdr_api/services/odms/generic_service.py b/clinical-mdr-api/clinical_mdr_api/services/odms/generic_service.py index b9eb430d..04e264ea 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/odms/generic_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/generic_service.py @@ -1064,6 +1064,21 @@ def manage_vendors( return self.get_by_uid(uid) + def renumber_items_sequentially( + self, items: Sequence[BaseModel], order_field_name: str, start: int = 1 + ): + sorted_items = sorted(items, key=lambda x: getattr(x, order_field_name)) + + for idx, item in enumerate(sorted_items, start=start): + if isinstance(item, BaseModel): + if getattr(item, order_field_name, None) != idx: + setattr(item, order_field_name, idx) + else: + raise ValueError( + f"Items must be a Pydantic model. Found item of type {type(item)}." + ) + return sorted_items + def cascade_inactivate(self, item: _AggregateRootType): pass diff --git a/clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py b/clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py index b971b8d8..bc8eaf0e 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py @@ -147,6 +147,8 @@ def add_items( ) -> OdmItemGroup: odm_item_group_ar = self._find_by_uid_or_raise_not_found(normalize_string(uid)) + renumbering_start = len(odm_item_group_ar.odm_vo.item_uids) or 1 + BusinessLogicException.raise_if( odm_item_group_ar.item_metadata.status != LibraryItemStatus.DRAFT, msg=self.OBJECT_NOT_IN_DRAFT, @@ -159,6 +161,7 @@ def add_items( relationship_type=RelationType.ITEM, disconnect_all=True, ) + renumbering_start = 1 vendor_attribute_patterns = self.get_regex_patterns_of_attributes( [ @@ -177,7 +180,11 @@ def add_items( VendorAttributeCompatibleType.ITEM_REF, ) - for item in odm_item_group_item_post_input: + post_input = self.renumber_items_sequentially( + odm_item_group_item_post_input, "order_number", renumbering_start + ) + + for item in post_input: if item.vendor: self.can_connect_vendor_attributes(item.vendor.attributes) self.attribute_values_matches_their_regex( diff --git a/clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py b/clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py index f31daed6..b68b78dc 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py @@ -80,6 +80,8 @@ def add_forms( ) -> OdmStudyEvent: odm_study_event_ar = self._find_by_uid_or_raise_not_found(normalize_string(uid)) + renumbering_start = len(odm_study_event_ar.odm_vo.form_uids) or 1 + BusinessLogicException.raise_if( odm_study_event_ar.item_metadata.status != LibraryItemStatus.DRAFT, msg=self.OBJECT_NOT_IN_DRAFT, @@ -92,8 +94,13 @@ def add_forms( relationship_type=RelationType.FORM, disconnect_all=True, ) + renumbering_start = 1 + + post_input = self.renumber_items_sequentially( + odm_study_event_form_post_input, "order_number", renumbering_start + ) - for form in odm_study_event_form_post_input: + for form in post_input: self._repos.odm_study_event_repository.add_relation( uid=uid, relation_uid=form.uid, 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 6a8da0f4..379ada73 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study.py @@ -36,6 +36,7 @@ StudyDefinitionAR, ) from clinical_mdr_api.domains.study_definition_aggregates.study_metadata import ( + _STUDY_SUBPART_ACRONYM_PATTERN, HighLevelStudyDesignVO, StudyCompactComponentEnum, StudyComponentEnum, @@ -139,6 +140,19 @@ def wrapper(*args, **kwargs): return decorator +def validate_study_subpart_acronym(study_subpart_acronym: str): + """Check if provided study subpart acronym respects business rules.""" + BusinessLogicException.raise_if( + study_subpart_acronym is not None and len(study_subpart_acronym) > 10, + msg=f"Study Subpart Acronym must not exceed 10 characters, got {len(study_subpart_acronym) if study_subpart_acronym else 0}.", + ) + BusinessLogicException.raise_if( + study_subpart_acronym is not None + and not _STUDY_SUBPART_ACRONYM_PATTERN.fullmatch(study_subpart_acronym), + msg=f"Study Subpart Acronym must contain only alphanumeric characters (no blanks or special characters), got '{study_subpart_acronym}'.", + ) + + class StudyService: _repos: MetaRepository @@ -994,6 +1008,7 @@ def get_studies_list( deleted: bool = False, ) -> list[StudySimple | StudyMinimal]: items = self._repos.study_definition_repository.get_studies_list( + minimal_response, has_study_objective, has_study_footnote, has_study_endpoint, @@ -1358,6 +1373,9 @@ def create( parent_part_ar.study_parent_part_uid, msg=f"Provided study_parent_part_uid '{study_create_input.study_parent_part_uid}' is a Study Subpart UID.", ) + study_subpart_acronym = study_create_input.study_subpart_acronym + validate_study_subpart_acronym(study_subpart_acronym) + project_number = ( parent_part_ar.current_metadata.id_metadata.project_number ) @@ -1458,7 +1476,10 @@ def create( self._repos.study_definition_repository.post_soa_preferences( study_uid=study_definition.uid, soa_preferences=StudySoaPreferencesInput( - baseline_as_time_zero=True, show_epochs=True, show_milestones=False + baseline_as_time_zero=True, + show_epochs=True, + show_milestones=False, + show_all_visits_lab_table=True, ), ) @@ -1977,6 +1998,13 @@ def patch( != parent_part_ar.current_metadata.id_metadata.project_number, msg="Project number of Study Parent Part and Study Subpart must be same.", ) + if ( + study_patch_request.current_metadata.identification_metadata + and study_patch_request.current_metadata.identification_metadata.study_subpart_acronym + ): + validate_study_subpart_acronym( + study_patch_request.current_metadata.identification_metadata.study_subpart_acronym + ) if not study_patch_request.current_metadata: study_patch_request.current_metadata = StudyMetadataJsonModel( 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 b89630ff..422d21f1 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 @@ -265,7 +265,7 @@ def _create_value_object( activity_subgroup_uid=study_activity_selection.activity_subgroup_uid, activity_group_uid=study_activity_selection.activity_group_uid, generate_uid_callback=self.repository.generate_uid, - is_reviewed=activity_instance_ar.concept_vo.is_required_for_activity + is_reviewed=activity_instance_ar.concept_vo.activity_instance_attributes.is_required_for_activity or selection_create_input.is_reviewed, study_data_supplier_uid=selection_create_input.study_data_supplier_uid, origin_type_uid=selection_create_input.origin_type_uid, diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_flowchart.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_flowchart.py index f2615a21..f8fc1092 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_flowchart.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_flowchart.py @@ -81,11 +81,15 @@ NUM_OPERATIONAL_CODE_COLS = 2 SOA_CHECK_MARK = "X" +LAB_TABLE_INCLUDE_ACTIVITY_GROUP = "Laboratory Assessments" # Strings prepared for localization _T = { "study_epoch": "", "procedure_label": "Procedure", + "lab_assessments": "Laboratory assessments", + "parameters": "Parameters", + "visits_list": "Visits and timing of visits", "study_milestone": "", "protocol_section": "Protocol Section", "visit_short_name": "Visit short name", @@ -93,6 +97,7 @@ "study_day": "Study day", "visit_window": "Visit window ({unit_name})", "protocol_flowchart": "Protocol Flowchart", + "protocol_lab_table": "Protocol - Lab table", "operational_soa": "Operational SoA", "detailed_soa": "Detailed SoA", "no_study_group": "(not selected)", @@ -118,6 +123,7 @@ "soaGroup": ("Table lvl 1", WD_STYLE_TYPE.PARAGRAPH), "group": ("Table lvl 2", WD_STYLE_TYPE.PARAGRAPH), "subGroup": ("Table lvl 3", WD_STYLE_TYPE.PARAGRAPH), + "subGroupLabTable": ("Table lvl 2", WD_STYLE_TYPE.PARAGRAPH), "activity": ("Table lvl 4", WD_STYLE_TYPE.PARAGRAPH), "activityRequest": ("Table lvl 4", WD_STYLE_TYPE.PARAGRAPH), "activityRequestFinal": ("Table lvl 4", WD_STYLE_TYPE.PARAGRAPH), @@ -624,6 +630,146 @@ def get_flowchart_table( return table + @trace_calls + def get_flowchart_table_lab_table( + self, + study_uid: str, + study_value_version: str | None, + time_unit: str | None = None, + ) -> TableWithFootnotes: + """ + Returns internal TableWithFootnotes representation of Protocol Lab table SoA. + + This table includes: + - An additional first column displaying activity subgroup names + - Only activities whose activity group name is "Laboratory Assessments" + + Args: + study_uid (str): The unique identifier of the study. + study_value_version (str | None): The version of the study to check. Defaults to None. + time_unit (str | None): The preferred time unit, either "day" or "week". Defaults to None. + + Returns: + TableWithFootnotes: Protocol Lab table SoA flowchart table with footnotes. + """ + + if not time_unit: + time_unit = self.get_preferred_time_unit( + study_uid, study_value_version=study_value_version + ) + + self._validate_parameters( + study_uid, study_value_version=study_value_version, time_unit=time_unit + ) + + # Fetch database objects in parallel + with ThreadPoolExecutor() as executor: + soa_preferences_future = executor.submit( + RuntimeContext.with_current_context(self._get_soa_preferences), + study_uid, + study_value_version=study_value_version, + ) + + activities_future = executor.submit( + RuntimeContext.with_current_context(self.fetch_study_activities), + study_uid, + study_value_version=study_value_version, + ) + + activity_schedules_future = executor.submit( + RuntimeContext.with_current_context(self._get_study_activity_schedules), + study_uid, + study_value_version=study_value_version, + operational=False, + ) + + visits_future = executor.submit( + RuntimeContext.with_current_context( + self._get_study_visits_dict_filtered + ), + study_uid, + study_value_version, + ) + + footnotes_future = executor.submit( + RuntimeContext.with_current_context(self._get_study_footnotes), + study_uid, + study_value_version=study_value_version, + ) + + soa_preferences: StudySoaPreferences = soa_preferences_future.result() + all_activities: list[StudySelectionActivity] = activities_future.result() + activity_schedules: list[StudyActivitySchedule] = ( + activity_schedules_future.result() + ) + visits: dict[str, StudyVisitLite] = visits_future.result() + + # Filter for Laboratory Assessments group + selection_activities = [ + activity + for activity in all_activities + if ( + activity.study_activity_group.activity_group_name + and activity.study_activity_group.activity_group_name.lower().strip() + == LAB_TABLE_INCLUDE_ACTIVITY_GROUP.lower().strip() + ) + ] + + # Sort the filtered activities + self._sort_study_activities(selection_activities, hide_soa_groups=True) + + # Filter visits to only those with a lab activity schedule assigned (aka 'X') + lab_activity_uids = {sa.study_activity_uid for sa in selection_activities} + scheduled_visit_uids = { + sas.study_visit_uid + for sas in activity_schedules + if sas.study_activity_uid in lab_activity_uids + } + visits = {uid: v for uid, v in visits.items() if uid in scheduled_visit_uids} + + # group visits in nested dict: study_epoch_uid -> [ consecutive_visit_group | visit_uid ] -> [Visits] + grouped_visits = self._group_visits(visits.values(), collapse_visit_groups=True) + + # Build header rows with extra column for subgroup names + header_rows = self._get_header_rows_lab_table( + grouped_visits, time_unit, soa_preferences + ) + + # Build activity rows with subgroup name column + activity_rows = self._get_activity_rows_lab_table( + selection_activities, + activity_schedules, + grouped_visits, + ) + + table = TableWithFootnotes( + rows=header_rows + activity_rows, + num_header_rows=len(header_rows), + num_header_cols=2, # Two header columns: subgroup name + activity name + title=_T("protocol_lab_table"), + ) + + # Filter rows without checkmarks + self._hide_rows_without_checkmarks( + table.rows, len(header_rows), table.num_header_cols + ) + + # Group rows by activity subgroup name so same-subgroup rows are consecutive + self._group_rows_by_subgroup(table.rows, len(header_rows)) + + # Do not repeat the activity subgroup name on subsequent rows + self._hide_repeated_subgroup_names(table.rows) + + # In case show_all_visits_lab_table is False, keep only the first two columns (subgroup name + activity name) and remove the rest of the visit columns + if not soa_preferences.show_all_visits_lab_table: + for row in table.rows: + row.cells = row.cells[:2] + + footnotes: list[StudySoAFootnote] = footnotes_future.result() + self.add_footnotes(table, footnotes) + + return table + @staticmethod @trace_calls def split_flowchart_table( @@ -888,7 +1034,16 @@ def get_study_flowchart_html( debug_uids: bool = False, debug_coordinates: bool = False, debug_propagation: bool = False, + include_uids: bool = False, ) -> str: + if layout == SoALayout.PROTOCOL_LAB_TABLE: + table = self.get_flowchart_table_lab_table( + study_uid=study_uid, + study_value_version=study_value_version, + time_unit=time_unit, + ) + return tables_to_html([table], include_uids=include_uids) + # build internal representation of flowchart table = self.get_flowchart_table( study_uid=study_uid, @@ -922,7 +1077,7 @@ def get_study_flowchart_html( tables = [table] # convert flowchart to HTML document - return tables_to_html(tables) + return tables_to_html(tables, include_uids=include_uids) def split_soa(self, study_uid: str, study_value_version: str | None, table) -> Any: # Get StudyVisit.uids for slicing the SoA table @@ -947,6 +1102,15 @@ def get_study_flowchart_docx( ) -> DocxBuilder: """Returns a DOCX document with SoA table and footnotes""" + if layout == SoALayout.PROTOCOL_LAB_TABLE: + # Lab table uses its own table builder with different filtering and structure + table = self.get_flowchart_table_lab_table( + study_uid=study_uid, + study_value_version=study_value_version, + time_unit=time_unit, + ) + return tables_to_docx([table], styles=DOCX_STYLES) + # build internal representation of flowchart table = self.get_flowchart_table( study_uid=study_uid, @@ -992,6 +1156,16 @@ def get_study_flowchart_xlsx( layout: SoALayout, time_unit: str | None, ) -> Workbook: + if layout == SoALayout.PROTOCOL_LAB_TABLE: + table = self.get_flowchart_table_lab_table( + study_uid=study_uid, + study_value_version=study_value_version, + time_unit=time_unit, + ) + return table_to_xlsx( + table, styles=OPERATIONAL_XLSX_STYLES, hide_rows_without_checkmarks=True + ) + # build internal representation of flowchart table = self.get_flowchart_table( study_uid=study_uid, @@ -1546,6 +1720,108 @@ def _get_header_rows( return rows + @classmethod + @trace_calls + def _get_header_rows_lab_table( + cls, + grouped_visits: dict[str, dict[str, list[StudyVisitLite]]], + time_unit: str, + soa_preferences: StudySoaPreferencesInput, + ) -> list[TableRow]: + """Builds the header rows for Protocol Lab table SoA flowchart with subgroup name column""" + + visit_timing_prop = cls._get_visit_timing_property(time_unit, soa_preferences) + + rows = [] + + # Calculate total number of visit columns + total_visit_columns = sum( + len(visit_groups) for visit_groups in grouped_visits.values() + ) + + # Header line 1 + rows.append(header_row_1 := TableRow()) + header_row_1.cells.append( + TableCell(text=_T("lab_assessments"), style="header1") + ) + header_row_1.cells.append(TableCell(text=_T("parameters"), style="header1")) + + if soa_preferences.show_all_visits_lab_table: + header_row_1.cells.append( + TableCell(_T("visits_list"), span=total_visit_columns, style="header1") + ) + + # Header line 2: Visit names + rows.append(visits_row := TableRow()) + visits_row.cells.append( + TableCell(text=_T("visit_short_name"), style="header2") + ) + visits_row.cells.append(TableCell()) # Empty cell for activity column + + # Header line 3: Visit timing + rows.append(timing_row := TableRow()) + if time_unit == "day": + timing_row.cells.append( + TableCell(text=_T("study_day"), style="header3") + ) + else: + timing_row.cells.append( + TableCell(text=_T("study_week"), style="header3") + ) + timing_row.cells.append(TableCell()) # Empty cell for activity column + + # Header line 4: Visit window + rows.append(window_row := TableRow()) + visit_window_unit = next( + ( + group[0].visit_window_unit_name + for visit_groups in grouped_visits.values() + for group in visit_groups.values() + ), + "", + ) + # Append window unit used for all StudyVisits + window_row.cells.append( + TableCell( + text=_T("visit_window").format(unit_name=visit_window_unit), + style="header4", + ) + ) + window_row.cells.append(TableCell()) # Empty cell for activity column + + for _study_epoch_uid, visit_groups in grouped_visits.items(): + for group in visit_groups.values(): + visit: StudyVisitLite = group[0] + + # Add empty cells with span=0 for the "List of visits" spanning cell + header_row_1.cells.append(TableCell(span=0)) + + visit_name = cls._get_visit_name(group) + visit_timing = cls._get_visit_timing(group, visit_timing_prop) + + # Visit name cell + visits_row.cells.append( + TableCell( + visit_name, + style="header2", + refs=[ + Ref(type_=SoAItemType.STUDY_VISIT.value, uid=vis.uid) + for vis in group + ], + ) + ) + + # Visit timing cell + timing_row.cells.append(TableCell(visit_timing, style="header3")) + + # Visit window + visit_window = cls._get_visit_window(visit) + + # Visit window cell + window_row.cells.append(TableCell(visit_window, style="header4")) + + return rows + @staticmethod def _get_visit_timing_property( time_unit: str | None, soa_preferences: StudySoaPreferencesInput @@ -1847,6 +2123,85 @@ def _get_activity_rows( return rows + @classmethod + @trace_calls + def _get_activity_rows_lab_table( + cls, + study_selection_activities: Sequence[StudySelectionActivity], + study_activity_schedules: Sequence[StudyActivitySchedule], + grouped_visits: dict[str, dict[str, list[StudyVisitLite]]], + ) -> list[TableRow]: + """Builds activity rows for Protocol Lab table with subgroup name column""" + + # Ordered StudyVisit.uids of visits to show + visit_groups: list[list[StudyVisitLite]] = [ + visit_group + for epochs_group in grouped_visits.values() + for visit_group in epochs_group.values() + ] + + # StudyActivitySchedules indexed by tuple of [uid, StudyVisit.uid] + study_activity_schedules_mapping = { + (sas.study_activity_uid, sas.study_visit_uid): sas + for sas in study_activity_schedules + } + + rows = [] + prev_study_selection_id = None + + for study_selection_activity in study_selection_activities: + study_selection_id = study_selection_activity.study_activity_uid + + if ( + prev_study_selection_id != study_selection_id + and study_selection_activity.study_activity_uid + ): + prev_study_selection_id = study_selection_id + + # Create row with subgroup name as first cell + row = TableRow( + order=study_selection_activity.order, + level=4, + ) + + # Determine if we should show the subgroup name + current_subgroup_name = ( + study_selection_activity.study_activity_subgroup.activity_subgroup_name + ) + + # Add subgroup name cell + row.cells.append( + TableCell( + text=current_subgroup_name, + style="subGroupLabTable", + refs=( + [ + Ref( + type_=SoAItemType.STUDY_ACTIVITY_SUBGROUP.value, + uid=study_selection_activity.study_activity_subgroup.study_activity_subgroup_uid, + ) + ] + if study_selection_activity.study_activity_subgroup.study_activity_subgroup_uid + else [] + ), + ) + ) + + # Add activity name cell + row.cells.append(cls._get_study_activity_cell(study_selection_activity)) + + # Add crosses for visits + cls._append_activity_crosses( + row, + visit_groups, + study_activity_schedules_mapping, + study_selection_activity.study_activity_uid, + ) + + rows.append(row) + + return rows + @classmethod def _get_activity_row( cls, @@ -2214,7 +2569,41 @@ def add_footnotes( table: TableWithFootnotes, footnotes: list[StudySoAFootnote], ): - """Adds footnote symbols to table rows based on the referenced uids""" + """Adds footnote symbols to table rows based on the referenced uids. + + Only footnotes whose referenced items appear in at least one visible (non-hidden) + row are included. Footnotes that exclusively reference items in hidden rows are + silently dropped before symbols are assigned, so they do not appear in the + rendered footnote listing. + """ + # Keep only footnotes that are referenced in the table, visible rows only + visible_rows = [row for row in table.rows if not row.hide] + + # Collect referenced UIDs preserving the order they appear in the table + referenced_uids: dict[str, int] = {} + for row in visible_rows: + for cell in row.cells: + for ref in cell.refs or []: + if ref.uid not in referenced_uids: + referenced_uids[ref.uid] = len(referenced_uids) + + footnotes = [ + fn + for fn in footnotes + if any(ref.item_uid in referenced_uids for ref in fn.referenced_items) + ] + + # Sort footnotes by the earliest table position of their referenced items + footnotes.sort( + key=lambda fn: min( + ( + referenced_uids[ref.item_uid] + for ref in fn.referenced_items + if ref.item_uid in referenced_uids + ), + default=len(referenced_uids), + ) + ) ( footnote_symbols_by_ref_uid, @@ -2228,6 +2617,7 @@ def add_footnotes( cell.footnotes = ( sorted(str(_footnote) for _footnote in _footnotes) if _footnotes + and cell.text # Only show footnote symbols if there is cell text to attach them to else None ) @@ -2243,6 +2633,51 @@ def show_hidden_rows(rows: Iterable[TableRow]): # unhide all rows row.hide = False + @staticmethod + @trace_calls + def _hide_rows_without_checkmarks( + rows: list[TableRow], num_header_rows: int, num_header_cols: int = 2 + ): + """ + Hides activity rows that don't contain any checkmarks in visit cells. + + Args: + rows: List of table rows + num_header_rows: Number of header rows to skip + num_header_cols: Number of leading header columns to skip when checking for checkmarks + """ + for row in rows[num_header_rows:]: + has_checkmark = any( + cell.text == SOA_CHECK_MARK for cell in row.cells[num_header_cols:] + ) + if not has_checkmark: + row.hide = True + + @staticmethod + @trace_calls + def _group_rows_by_subgroup(rows: list[TableRow], num_header_rows: int): + """Reorders activity rows in place so rows with the same subgroup name (first cell) are consecutive.""" + activity_rows = rows[num_header_rows:] + groups: dict[str, list[TableRow]] = {} + for row in activity_rows: + key = row.cells[0].text if row.cells else "" + groups.setdefault(key, []).append(row) + rows[num_header_rows:] = [row for group in groups.values() for row in group] + + @staticmethod + @trace_calls + def _hide_repeated_subgroup_names(rows: list[TableRow]): + """Clears the activity subgroup name (first cell) on subsequent rows where it repeats.""" + prev_subgroup_name = None + for row in rows: + if row.hide or not row.cells: + continue + cell = row.cells[0] + if cell.text == prev_subgroup_name: + cell.text = "" + else: + prev_subgroup_name = cell.text + @staticmethod @trace_calls def remove_hidden_rows(table: TableWithFootnotes): @@ -2386,6 +2821,7 @@ def download_detailed_soa_content( study_uid: str, study_value_version: str | None = None, protocol_flowchart: bool = False, + protocol_lab_table: bool = False, ) -> list[dict[Any, Any]]: if not study_value_version: query = "MATCH (study_root:StudyRoot{uid:$study_uid})-[has_version:LATEST]-(study_value:StudyValue)" @@ -2431,6 +2867,13 @@ def download_detailed_soa_content( is_soa_milestone:study_visit.is_soa_milestone, milestone_name:visity_type_term.name }]) as milestone + """ + query += ( + "WHERE trim(toLower(study_activity_group.activity_group_value.name)) = $activity_group_filter" + if protocol_lab_table + else "" + ) + query += """ ORDER BY study_soa_group.order, study_activity_group.order, study_activity_subgroup.order, study_activity.order, study_visit.visit_number RETURN CASE @@ -2452,7 +2895,15 @@ def download_detailed_soa_content( result_array, attribute_names = db.cypher_query( query, - params={"study_uid": study_uid, "study_value_version": study_value_version}, + params={ + "study_uid": study_uid, + "study_value_version": study_value_version, + "activity_group_filter": ( + LAB_TABLE_INCLUDE_ACTIVITY_GROUP.lower().strip() + if protocol_lab_table + else None + ), + }, ) soa_preferences = self._get_soa_preferences( study_uid, study_value_version=study_value_version 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 bcbdf886..21c5aca5 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 @@ -10,9 +10,6 @@ from clinical_mdr_api.models.concepts.activities.activity import ( ActivityForStudyActivity, ) -from clinical_mdr_api.models.concepts.activities.activity_instance import ( - ActivityInstance, -) from clinical_mdr_api.models.concepts.compound import Compound from clinical_mdr_api.models.concepts.compound_alias import CompoundAlias from clinical_mdr_api.models.concepts.medicinal_product import MedicinalProduct @@ -364,33 +361,6 @@ def _transform_activity_model( ) ) - def _transform_latest_activity_instance_model( - self, activity_instance_uid: str - ) -> ActivityInstance: - """Finds the activity instance with a given UID.""" - - return ActivityInstance.from_activity_ar( - activity_ar=self._repos.activity_instance_repository.find_by_uid_optimized( - activity_instance_uid - ), - find_activity_hierarchy_by_uid=self._repos.activity_repository.find_by_uid_optimized, - find_activity_subgroup_by_uid=self._repos.activity_subgroup_repository.find_by_uid_optimized, - find_activity_group_by_uid=self._repos.activity_group_repository.find_by_uid_optimized, - ) - - def _transform_activity_instance_model( - self, activity_instance_uid: str, activity_instance_version: str | None - ) -> ActivityInstance: - """Finds the activity instance with given UID and version.""" - return ActivityInstance.from_activity_ar( - activity_ar=self._repos.activity_instance_repository.find_by_uid_optimized( - activity_instance_uid, version=activity_instance_version - ), - find_activity_hierarchy_by_uid=self._repos.activity_repository.find_by_uid_optimized, - find_activity_subgroup_by_uid=self._repos.activity_subgroup_repository.find_by_uid_optimized, - find_activity_group_by_uid=self._repos.activity_group_repository.find_by_uid_optimized, - ) - def _transform_compound_model(self, compound_uid: str) -> Compound: """ Finds the compound template parameter value with a given UID. 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 2d2a4919..eefe11a9 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 @@ -123,22 +123,25 @@ def __init__( self, study_uid: str, study_value_version: str | None = None, + load_terms: bool = True, ): self._repos = MetaRepository() self.repo = self._repos.study_visit_repository self.author = user().id() self.check_if_study_exists(study_uid=study_uid) - self.terms_at_specific_datetime = ( - self.get_study_standard_version_ct_terms_datetime( - study_uid=study_uid, - study_value_version=study_value_version, + + if load_terms: + self.terms_at_specific_datetime = ( + self.get_study_standard_version_ct_terms_datetime( + study_uid=study_uid, + study_value_version=study_value_version, + ) ) - ) - self.update_ctterm_maps(self.terms_at_specific_datetime) + self.update_ctterm_maps(self.terms_at_specific_datetime) - self._day_unit, self._week_unit = self.repo.get_day_week_units() + self._day_unit, self._week_unit = self.repo.get_day_week_units() def get_allowed_time_references_for_study(self, study_uid: str): resp = [] @@ -198,8 +201,11 @@ def get_amount_of_visits_in_given_epoch( def get_global_anchor_visit(self, study_uid: str) -> SimpleStudyVisit | None: global_anchor_visit = ( StudyVisitNeoModel.nodes.traverse( - "has_visit_name__has_latest_value", - "has_visit_type__has_selected_term__has_name_root__has_latest_value", + Path("has_visit_name__has_latest_value", include_rels_in_return=False), + Path( + "has_visit_type__has_selected_term__has_name_root__has_latest_value", + include_rels_in_return=False, + ), ) .filter( has_study_visit__latest_value__uid=study_uid, @@ -269,7 +275,7 @@ def get_study_visits_for_specific_activity_instance( Path( "has_study_visit__latest_value", include_rels_in_return=False, - include_nodes_in_return=True, # Set to False when migrating to neomodel 6.x + include_nodes_in_return=False, ), Path( "has_study_activity_schedule__study_value__latest_value", @@ -1037,7 +1043,11 @@ def _from_input_values( window_unit_object=window_unit_object, time_unit_object=time_unit_object, description=create_input.description, - start_rule=create_input.start_rule, + start_rule=( + settings.unscheduled_visit_start_rule + if create_input.visit_class == VisitClass.UNSCHEDULED_VISIT + else create_input.start_rule + ), end_rule=create_input.end_rule, visit_contact_mode=visit_contact_mode, epoch_allocation=( diff --git a/clinical-mdr-api/clinical_mdr_api/services/utils/table_f.py b/clinical-mdr-api/clinical_mdr_api/services/utils/table_f.py index 180d6646..b2c95e63 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/utils/table_f.py +++ b/clinical-mdr-api/clinical_mdr_api/services/utils/table_f.py @@ -328,7 +328,9 @@ def table_to_html(table: TableWithFootnotes, css_style: str | None = None) -> st @trace_calls def tables_to_html( - tables: Iterable[TableWithFootnotes], css_style: str | None = None + tables: Iterable[TableWithFootnotes], + css_style: str | None = None, + include_uids: bool = False, ) -> str: """Renders a list of TableWithFootnotes into an HTML document with multiple tables @@ -356,7 +358,7 @@ def render_table(): if cell.span == 0: continue - with tag("th", **_cell_to_attrs(cell)): + with tag("th", **_cell_to_attrs(cell, include_uids)): render_cell_contents(cell) with tag("tbody"): @@ -371,7 +373,7 @@ def render_table(): with tag( ("th" if i < table.num_header_cols else "td"), - **_cell_to_attrs(cell), + **_cell_to_attrs(cell, include_uids), ): render_cell_contents(cell) @@ -417,7 +419,7 @@ def add_footnote_symbols(symbols): return yattag.indent(doc.getvalue()) -def _cell_to_attrs(cell): +def _cell_to_attrs(cell, include_uids: bool = False): attrs = {} if cell.style: @@ -426,6 +428,15 @@ def _cell_to_attrs(cell): if cell.span > 1: attrs["colspan"] = cell.span + if include_uids and cell.refs: + # add data attributes for each reference in the cell + for i, ref in enumerate(cell.refs): + prefix = "object" + suffix = f"-{i}" if len(cell.refs) > 1 else "" + if ref.type: + attrs[f"{prefix}-type{suffix}"] = ref.type + attrs[f"{prefix}-uid{suffix}"] = ref.uid + return attrs @@ -434,6 +445,7 @@ def table_to_xlsx( table: TableWithFootnotes, styles: Mapping[str, str] | None = None, template: str | None = None, + hide_rows_without_checkmarks: bool = False, ) -> Workbook: if template: template = os.path.join(os.path.dirname(__file__), template) @@ -447,8 +459,12 @@ def table_to_xlsx( if table.title: worksheet.title = table.title + visible_rows = [ + row for row in table.rows if not (hide_rows_without_checkmarks and row.hide) + ] + column_widths = defaultdict(list) - for r, row in enumerate(table.rows, start=1): + for r, row in enumerate(visible_rows, start=1): worksheet.append([cell.text for cell in row.cells]) for c, cell in enumerate(row.cells, start=1): @@ -479,17 +495,17 @@ def table_to_xlsx( for r, row in enumerate(worksheet.iter_rows()): for c, rowcell in enumerate(row): if ( - c < len(table.rows[r].cells) - and table.rows[r].cells[c].style in styles + c < len(visible_rows[r].cells) + and visible_rows[r].cells[c].style in styles ): - style_index = table.rows[r].cells[c].style + style_index = visible_rows[r].cells[c].style if style_index is not None: rowcell.style = styles[style_index] # define table tab = Table( displayName="Table1", - ref=f"A1:{get_column_letter(len(table.rows[-1].cells))}{len(table.rows)}", + ref=f"A1:{get_column_letter(len(visible_rows[-1].cells))}{len(visible_rows)}", ) tab.tableStyleInfo = TableStyleInfo(name="TableStyleMedium2") 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 e88a406d..43dff0da 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/{codelist_uid}/terms", "GET", {"Library.Read"}), ("/ct/terms", "POST", {"Library.Write"}), ("/ct/terms", "GET", {"Library.Read"}), ("/ct/terms/headers", "GET", {"Library.Read"}), @@ -1079,7 +1080,6 @@ ("/template-parameters/{name}/terms", "GET", {"Library.Read"}), ("/concepts/activities/activity-instances", "GET", {"Library.Read"}), ("/concepts/activities/activity-instances/preview", "POST", {"Library.Write"}), - ("/concepts/activities/activity-instances/versions", "GET", {"Library.Read"}), ("/concepts/activities/activity-instances/headers", "GET", {"Library.Read"}), ( "/concepts/activities/activities/{activity_uid}/versions/{version}/groupings", @@ -1102,7 +1102,7 @@ {"Library.Read"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/activity-groupings", + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings", "GET", {"Library.Read"}, ), @@ -1116,43 +1116,84 @@ "GET", {"Library.Read"}, ), + ("/concepts/activities/activity-instances", "POST", {"Library.Write"}), + ( + "/concepts/activities/activity-instances/{activity_instance_uid}", + "DELETE", + {"Library.Write"}, + ), + ( + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings", + "PATCH", + {"Library.Write"}, + ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/versions", + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/versions", "GET", {"Library.Read"}, ), - ("/concepts/activities/activity-instances", "POST", {"Library.Write"}), ( - "/concepts/activities/activity-instances/{activity_instance_uid}", - "PATCH", + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/versions", + "POST", {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/versions", + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/approvals", "POST", {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/approvals", + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/activations", "POST", {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/activations", + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/activations", "DELETE", {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}/activations", + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes", + "GET", + {"Library.Read"}, + ), + ( + "/concepts/activities/activity-instances/attributes/versions", + "GET", + {"Library.Read"}, + ), + ( + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes", + "PATCH", + {"Library.Write"}, + ), + ( + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/versions", + "GET", + {"Library.Read"}, + ), + ( + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/versions", "POST", {"Library.Write"}, ), ( - "/concepts/activities/activity-instances/{activity_instance_uid}", + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/approvals", + "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"}), ( "/activity-instance-classes/{activity_instance_class_uid}", @@ -1231,6 +1272,7 @@ {"Library.Write"}, ), ("/activity-item-classes", "GET", {"Library.Read"}), + ("/activity-item-classes/versions", "GET", {"Library.Read"}), ("/activity-item-classes/headers", "GET", {"Library.Read"}), ("/activity-item-classes/{activity_item_class_uid}", "GET", {"Library.Read"}), ( diff --git a/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/test_endpoints_rbac.py b/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/test_endpoints_rbac.py index 38744dde..266e1027 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/test_endpoints_rbac.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/auth/integration/test_endpoints_rbac.py @@ -201,8 +201,12 @@ def test_endpoints_rbac_correct_roles( is_json, content_type, ) + # We allow 500 because this test may be running against a database with an outdated data model. + # A 500 error still means that the authentication has passed and the request reached the application code. + # This is acceptable because this test is only for the authentication part, + # and the application logic is covered by other tests. assert_response_status_code( - response, (200, 201, 202, 204, 207, 400, 403, 404, 409) + response, (200, 201, 202, 204, 207, 400, 403, 404, 409, 500) ) if response.status_code == 400: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/data/odm_xml.py b/clinical-mdr-api/clinical_mdr_api/tests/data/odm_xml.py index 69ff4227..3fa727b7 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/data/odm_xml.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/data/odm_xml.py @@ -7119,7 +7119,7 @@ "oid": "IG.153", "name": "Body Measurements 1", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "", "vendor": {"attributes": []}, @@ -8252,7 +8252,7 @@ "oid": "I.355", "name": "VS_syst_blood_pres_ORRES_SYSBP 1", "version": "1.0", - "order_number": 4, + "order_number": 3, "mandatory": "Yes", "key_sequence": "None", "method_oid": None, @@ -8267,7 +8267,7 @@ "oid": "I.356", "name": "VS_diast_blood_pres_ORRES_DIABP 1", "version": "1.0", - "order_number": 5, + "order_number": 4, "mandatory": "Yes", "key_sequence": "None", "method_oid": None, @@ -8282,7 +8282,7 @@ "oid": "I.347", "name": "VS_pulse_ORRES_PULSE 1", "version": "1.0", - "order_number": 6, + "order_number": 5, "mandatory": "Yes", "key_sequence": "None", "method_oid": None, 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 98db6a6c..8751c2d3 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 @@ -648,16 +648,6 @@ def test_get_activity_versions(api_client): pytest.param('{"*": {"v": ["zzzz"]}}', None, None), pytest.param('{"*": {"v": ["Final"]}}', "status", "Final"), pytest.param('{"*": {"v": ["1.0"]}}', "version", "1.0"), - pytest.param( - '{"*": {"v": ["activity_group"]}}', - "activity_groupings.activity_group_name", - "activity_group", - ), - pytest.param( - '{"*": {"v": ["activity_subgroup"]}}', - "activity_groupings.activity_subgroup_name", - "activity_subgroup", - ), ], ) def test_filtering_versions_wildcard( @@ -1289,7 +1279,7 @@ def test_cascade_edit_activities(api_client): assert res["version"] == "1.0" assert res["status"] == "Final" - # ==== Update activity with cascade edit&approve, instance should be updated also ==== + # ==== Update activity with cascade edit&approve, instance groupings should be updated also ==== # Create new version of activity response = api_client.post( @@ -1386,8 +1376,8 @@ def test_cascade_edit_activities(api_client): assert_response_status_code(response, 200) res = response.json() assert len(res["activity_groupings"]) == 1 - assert res["version"] == "3.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "3.0" + assert res["groupings_status"] == "Final" # Update the activity by removing activity grouping api_client.post(f"/concepts/activities/activities/{activity.uid}/versions") @@ -1427,13 +1417,13 @@ def test_cascade_edit_activities(api_client): assert_response_status_code(response, 200) res = response.json() assert len(res["activity_groupings"]) == 1 - assert res["version"] == "3.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "3.0" + assert res["groupings_status"] == "Final" # Get the instance versions and assert that there is one new version created. # There should be a new final version 2.0 that links to activity version 2.0 response = api_client.get( - f"/concepts/activities/activity-instances/{activity_instance.uid}/versions" + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions" ) assert_response_status_code(response, 200) res = response.json() @@ -1488,8 +1478,314 @@ def test_cascade_edit_activities(api_client): assert_response_status_code(response, 200) res = response.json() - assert res["version"] == "3.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "3.0" + assert res["groupings_status"] == "Final" + + +def test_get_specific_activity_version_groupings(api_client): + """Test that the /groupings endpoint returns activity instances linked to an activity, + and that updating the activity/instance shows correct data per version.""" + + # ==== Setup: create fresh group, subgroup, activity, and instance ==== + grp = TestUtils.create_activity_group(name="groupings_test_group") + subgrp = TestUtils.create_activity_subgroup(name="groupings_test_subgroup") + + activity = TestUtils.create_activity( + name="Groupings Test Activity", + activity_subgroups=[subgrp.uid], + activity_groups=[grp.uid], + approve=True, + is_data_collected=True, + ) + + instance = TestUtils.create_activity_instance( + name="Groupings Test Instance", + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case="groupings test instance", + topic_code="groupings_tc", + activities=[activity.uid], + activity_subgroups=[subgrp.uid], + activity_groups=[grp.uid], + activity_items=[activity_items[0]], + approve=True, + ) + + # ==== 1: check groupings for the initial approved version ==== + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/1.0/groupings" + ) + assert_response_status_code(response, 200) + res = response.json() + + assert res["total"] >= 1 + items = res["items"] + assert len(items) >= 1 + + item = items[0] + assert item["activity_uid"] == activity.uid + assert item["activity_version"] == "1.0" + + assert len(item["activity_groupings"]) == 1 + grouping = item["activity_groupings"][0] + assert grouping["group"]["uid"] == grp.uid + assert grouping["group"]["name"] == grp.name + assert grouping["subgroup"]["uid"] == subgrp.uid + assert grouping["subgroup"]["name"] == subgrp.name + + instance_uids = [inst["uid"] for inst in grouping["activity_instances"]] + assert instance.uid in instance_uids + + # ==== 2: update the activity with a new name, approve, and check that the groupings endpoint for v2.0 returns the updated data ==== + response = api_client.post( + f"/concepts/activities/activities/{activity.uid}/versions", + json={}, + ) + assert_response_status_code(response, 201) + response = api_client.put( + f"/concepts/activities/activities/{activity.uid}", + json={ + "name": "Updated Groupings Test Activity", + "name_sentence_case": "updated groupings test activity", + "change_description": "test update for v2.0", + "library_name": activity.library_name, + "is_data_collected": True, + "activity_groupings": [ + {"activity_group_uid": grp.uid, "activity_subgroup_uid": subgrp.uid} + ], + }, + ) + assert_response_status_code(response, 200) + + response = api_client.post( + f"/concepts/activities/activities/{activity.uid}/approvals", + params={"cascade_edit_and_approve": True}, + ) + assert_response_status_code(response, 201) + + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/2.0/groupings" + ) + assert_response_status_code(response, 200) + res = response.json() + + assert res["total"] >= 1 + items = res["items"] + assert len(items) >= 1 + + item = items[0] + assert item["activity_uid"] == activity.uid + assert item["activity_version"] == "2.0" + + assert len(item["activity_groupings"]) == 1 + grouping = item["activity_groupings"][0] + assert grouping["group"]["uid"] == grp.uid + assert grouping["group"]["name"] == grp.name + assert grouping["subgroup"]["uid"] == subgrp.uid + assert grouping["subgroup"]["name"] == subgrp.name + + assert grouping["activity_instances"][0]["uid"] == instance.uid + assert grouping["activity_instances"][0]["name"] == "Groupings Test Instance" + + # 3a: Update the instance with a new name, approve + response = api_client.post( + f"/concepts/activities/activity-instances/{instance.uid}/attributes/versions", + json={}, + ) + assert_response_status_code(response, 201) + response = api_client.patch( + f"/concepts/activities/activity-instances/{instance.uid}/attributes", + json={ + "name": "Updated Groupings Test Instance", + "name_sentence_case": "updated groupings test instance", + "change_description": "test update for instance", + "topic_code": instance.topic_code, + "nci_concept_id": instance.nci_concept_id, + "library_name": instance.library_name, + }, + ) + assert_response_status_code(response, 200) + response = api_client.post( + f"/concepts/activities/activity-instances/{instance.uid}/attributes/approvals", + ) + assert_response_status_code(response, 201) + + # 3b: Undate the instance groupings to link it to the new activity version, approve + response = api_client.post( + f"/concepts/activities/activity-instances/{instance.uid}/groupings/versions", + json={}, + ) + assert_response_status_code(response, 201) + response = api_client.patch( + f"/concepts/activities/activity-instances/{instance.uid}/groupings", + json={ + "change_description": "link instance to new activity version", + }, + ) + assert_response_status_code(response, 200) + response = api_client.post( + f"/concepts/activities/activity-instances/{instance.uid}/groupings/approvals", + ) + assert_response_status_code(response, 201) + + # 4: Get the activity groupings for the activity v2.0 again and assert that the instance data is updated + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/2.0/groupings" + ) + assert_response_status_code(response, 200) + res = response.json() + items = res["items"] + item = items[0] + assert len(item["activity_groupings"]) == 1 + grouping = item["activity_groupings"][0] + assert len(grouping["activity_instances"]) == 1 + assert grouping["activity_instances"][0]["uid"] == instance.uid + assert ( + grouping["activity_instances"][0]["name"] == "Updated Groupings Test Instance" + ) + + # 5: Get the activity groupings for the activity v1.0 and assert that the instance data is NOT updated in the old version + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/1.0/groupings" + ) + assert_response_status_code(response, 200) + res = response.json() + items = res["items"] + item = items[0] + assert len(item["activity_groupings"]) == 1 + grouping = item["activity_groupings"][0] + assert len(grouping["activity_instances"]) == 1 + assert grouping["activity_instances"][0]["uid"] == instance.uid + assert grouping["activity_instances"][0]["name"] == "Groupings Test Instance" + + +def test_get_instances_for_version(api_client): + # Create activity and instance + activity = TestUtils.create_activity( + name="Linked Instances Test Activity", + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + approve=True, + ) + instance = TestUtils.create_activity_instance( + name="Linked Instances Test Instance", + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case="linked instances test instance", + topic_code="linked_instances_tc", + activities=[activity.uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=True, + ) + # Get instances linked to the activity version + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/1.0/instances" + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["total"] == 1 + assert res["items"][0]["uid"] == instance.uid + assert res["items"][0]["name"] == "Linked Instances Test Instance" + all_linked_versions = [child["version"] for child in res["items"][0]["children"]] + all_linked_versions.append(res["items"][0]["version"]) + assert len(all_linked_versions) == 2 + assert "1.0" in all_linked_versions + assert "0.1" in all_linked_versions + + # Make a new Ativity version + response = api_client.post( + f"/concepts/activities/activities/{activity.uid}/versions", + json={}, + ) + assert_response_status_code(response, 201) + response = api_client.put( + f"/concepts/activities/activities/{activity.uid}", + json={ + "name": "Edited Linked Instances Test Activity", + "name_sentence_case": "edited linked instances test activity", + "change_description": "test update for new version", + "library_name": activity.library_name, + "is_data_collected": True, + "activity_groupings": [ + { + "activity_group_uid": activity_group.uid, + "activity_subgroup_uid": activity_subgroup.uid, + } + ], + }, + ) + assert_response_status_code(response, 200) + response = api_client.post( + f"/concepts/activities/activities/{activity.uid}/approvals", + params={"cascade_edit_and_approve": True}, + ) + assert_response_status_code(response, 201) + + # Get instances linked to the new activity version + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/2.0/instances" + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["total"] == 1 + assert res["items"][0]["uid"] == instance.uid + assert res["items"][0]["name"] == "Linked Instances Test Instance" + all_linked_versions = [child["version"] for child in res["items"][0]["children"]] + all_linked_versions.append(res["items"][0]["version"]) + assert len(all_linked_versions) == 1 + assert "1.0" in all_linked_versions + + # Make a new instance attributes version + response = api_client.post( + f"/concepts/activities/activity-instances/{instance.uid}/attributes/versions", + json={}, + ) + assert_response_status_code(response, 201) + response = api_client.patch( + f"/concepts/activities/activity-instances/{instance.uid}/attributes", + json={ + "name": "Edited Linked Instances Test Instance", + "name_sentence_case": "edited linked instances test instance", + "change_description": "test update for instance", + }, + ) + assert_response_status_code(response, 200) + response = api_client.post( + f"/concepts/activities/activity-instances/{instance.uid}/attributes/approvals", + ) + assert_response_status_code(response, 201) + + # Get instances linked to the new activity version again, should include the new instance version as well + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/2.0/instances" + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["total"] == 1 + assert res["items"][0]["uid"] == instance.uid + assert res["items"][0]["name"] == "Edited Linked Instances Test Instance" + all_linked_versions = [child["version"] for child in res["items"][0]["children"]] + all_linked_versions.append(res["items"][0]["version"]) + assert len(all_linked_versions) == 4 + assert "1.0" in all_linked_versions + assert "1.1" in all_linked_versions + assert "1.2" in all_linked_versions + assert "2.0" in all_linked_versions + + # Get the instances linked to the old activity version, should still be linked to the old version + response = api_client.get( + f"/concepts/activities/activities/{activity.uid}/versions/1.0/instances" + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["total"] == 1 + assert res["items"][0]["uid"] == instance.uid + assert res["items"][0]["name"] == "Linked Instances Test Instance" + all_linked_versions = [child["version"] for child in res["items"][0]["children"]] + all_linked_versions.append(res["items"][0]["version"]) + assert len(all_linked_versions) == 2 + assert "1.0" in all_linked_versions + assert "0.1" in all_linked_versions def test_create_activity_without_groupings_not_allowed(api_client): diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_groups.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_groups.py index c71761b8..412e6729 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_groups.py @@ -67,6 +67,8 @@ def test_data(): "uid", "name", "name_sentence_case", + "nci_concept_id", + "nci_concept_name", "definition", "abbreviation", "library_name", @@ -321,11 +323,15 @@ def test_cascade_edit_activity_groups(api_client): # Update the activity group updated_activity_group_name = "Edited Cascade Activity Group" + concept_id = "CONCEPT_ID" + concept_name = "concept name" response = api_client.put( f"/concepts/activities/activity-groups/{activity_group.uid}", json={ "name": updated_activity_group_name, "name_sentence_case": updated_activity_group_name.lower(), + "nci_concept_id": concept_id, + "nci_concept_name": concept_name, "change_description": "test cascade edit", "library_name": activity_group.library_name, }, @@ -347,6 +353,8 @@ def test_cascade_edit_activity_groups(api_client): res = response.json() assert res["name"] == updated_activity_group_name assert res["name_sentence_case"] == updated_activity_group_name.lower() + assert res["nci_concept_id"] == concept_id + assert res["nci_concept_name"] == concept_name assert res["status"] == "Final" assert res["version"] == "2.0" @@ -375,8 +383,8 @@ def test_cascade_edit_activity_groups(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res["version"] == "2.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "2.0" + assert res["groupings_status"] == "Final" assert len(res["activity_groupings"]) == 1 assert res["activity_groupings"][0]["activity_group"]["uid"] == activity_group.uid assert ( @@ -416,7 +424,7 @@ def test_cascade_edit_activity_groups(api_client): # Get the activity instance versions and assert that one new version was created. # There should be a new final version 2.0 that links to activity version 2.0 response = api_client.get( - f"/concepts/activities/activity-instances/{activity_instance.uid}/versions" + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions" ) assert_response_status_code(response, 200) res = response.json() @@ -481,8 +489,8 @@ def test_cascade_edit_activity_groups(api_client): ) assert_response_status_code(response, 200) res = response.json() - assert res["version"] == "2.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "2.0" + assert res["groupings_status"] == "Final" assert len(res["activity_groupings"]) == 1 assert ( res["activity_groupings"][0]["activity_subgroup"]["uid"] diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instance_classes.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instance_classes.py index 7d456a12..d3a464ea 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instance_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instance_classes.py @@ -784,6 +784,8 @@ def test_get_activity_item_classes_for_instance_class(api_client): res = response.json() assert len(res) == 1 assert res[0]["name"] == "name A" + assert res[0]["data_type_uid"] == data_type_term.term_uid + assert res[0]["data_type_name"] == "Data type" response = api_client.get( f"/activity-instance-classes/{activity_instance_classes_all[20].uid}/activity-item-classes" @@ -1149,3 +1151,73 @@ def test_get_item_classes_paginated(api_client: TestClient) -> None: f"/activity-instance-classes/{instance_class.uid}/item-classes?version=0.1" ) assert_response_status_code(response, 200) + + +def test_get_activity_instance_classes_versions(api_client): + """Test GET /activity-instance-classes/versions endpoint""" + # First, create a new version of one class so we have multiple versions + response = api_client.post( + f"/activity-instance-classes/{activity_instance_classes_all[0].uid}/versions" + ) + assert_response_status_code(response, 201) + + # Get all versions + response = api_client.get( + "/activity-instance-classes/versions?page_size=100&total_count=true" + ) + res = response.json() + + assert_response_status_code(response, 200) + + # Check response structure + assert set(res.keys()) == {"items", "total", "page", "size"} + assert res["total"] > 0 + + # Should have more versions than unique classes (since we created a new version above) + assert res["total"] > len(activity_instance_classes_all) + + # Check that the items are sorted by start_date descending + start_dates = [item["start_date"] for item in res["items"] if item["start_date"]] + assert start_dates == sorted(start_dates, reverse=True) + + # Check that the class updated in this test has multiple versions + versions_of_class = [ + item["version"] + for item in res["items"] + if item["uid"] == activity_instance_classes_all[0].uid + ] + assert len(versions_of_class) >= 2 + + # Check fields on first item + item = res["items"][0] + assert "uid" in item + assert "name" in item + assert "version" in item + assert "status" in item + assert "start_date" in item + assert "library_name" in item + + +def test_get_activity_instance_classes_versions_pagination(api_client): + """Test pagination on /activity-instance-classes/versions""" + # Get first page + response = api_client.get( + "/activity-instance-classes/versions?page_size=5&page_number=1&total_count=true" + ) + assert_response_status_code(response, 200) + page1 = response.json() + assert len(page1["items"]) == 5 + assert page1["total"] > 5 + + # Get second page + response = api_client.get( + "/activity-instance-classes/versions?page_size=5&page_number=2&total_count=true" + ) + assert_response_status_code(response, 200) + page2 = response.json() + assert len(page2["items"]) > 0 + + # Pages should not overlap + page1_uids_versions = {(i["uid"], i["version"]) for i in page1["items"]} + page2_uids_versions = {(i["uid"], i["version"]) for i in page2["items"]} + assert page1_uids_versions.isdisjoint(page2_uids_versions) 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 7edf5aac..2504fd99 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 @@ -237,6 +237,7 @@ def test_data(): base_test_data["day_unit"].uid, ], "is_adam_param_specific": True, + "is_activity_instance_id_specific": True, }, { "activity_item_class_uid": activity_item_classes[1].uid, @@ -248,6 +249,7 @@ def test_data(): ], "unit_definition_uids": [], "is_adam_param_specific": False, + "is_activity_instance_id_specific": False, }, { "activity_item_class_uid": activity_item_classes[2].uid, @@ -263,6 +265,7 @@ def test_data(): ], "unit_definition_uids": [], "is_adam_param_specific": False, + "is_activity_instance_id_specific": False, }, { "activity_item_class_uid": activity_item_classes[3].uid, @@ -270,6 +273,7 @@ def test_data(): "ct_codelist_uid": codelist.codelist_uid, "unit_definition_uids": [], "is_adam_param_specific": False, + "is_activity_instance_id_specific": False, }, ] global activity_instances_all @@ -438,6 +442,43 @@ def test_data(): "change_description", "author_username", "possible_actions", + "groupings_version", + "groupings_end_date", + "groupings_start_date", + "groupings_change_description", + "groupings_status", + "groupings_author_username", + "groupings_possible_actions", +] + +ACTIVITY_INSTANCE_ATTRIBUTES_FIELDS_ALL = [ + "uid", + "nci_concept_id", + "nci_concept_name", + "name", + "name_sentence_case", + "definition", + "abbreviation", + "topic_code", + "is_research_lab", + "molecular_weight", + "adam_param_code", + "is_required_for_activity", + "is_default_selected_for_activity", + "is_data_sharing", + "is_legacy_usage", + "is_derived", + "legacy_description", + "activity_instance_class", + "activity_items", + "library_name", + "start_date", + "end_date", + "status", + "version", + "change_description", + "author_username", + "possible_actions", ] ACTIVITY_INSTANCES_FIELDS_NOT_NULL = [ @@ -488,6 +529,7 @@ def test_get_activity_instance(api_client): assert res["activity_instance_class"]["name"] == activity_instance_classes[0].name assert len(res["activity_items"]) == 1 assert res["activity_items"][0]["is_adam_param_specific"] is True + assert res["activity_items"][0]["is_activity_instance_id_specific"] is True assert ( res["activity_items"][0]["activity_item_class"]["uid"] == activity_item_classes[0].uid @@ -557,6 +599,10 @@ def test_get_activity_instances_pagination(api_client): pytest.param(10, 1, True, '{"name": false}', 10), pytest.param(10, 2, True, '{"name": true}', 10), pytest.param(10, 1, True, '{"activity_name": true}', 10), + pytest.param(10, 1, True, '{"status": true}', 10), + pytest.param(10, 1, True, '{"start_date": true}', 10), + pytest.param(10, 1, True, '{"groupings_status": true}', 10), + pytest.param(10, 1, True, '{"groupings_start_date": true}', 10), ], ) def test_get_activity_instances( @@ -608,6 +654,89 @@ def test_get_activity_instances( # assert result_vals == result_vals_sorted_locally +def test_get_activity_instances_status_query_matches_status_or_groupings_status( + api_client, +): + status_on_attributes_name = f"status-attributes-{uuid.uuid4().hex[:8]}" + status_on_groupings_name = f"status-groupings-{uuid.uuid4().hex[:8]}" + + status_on_attributes = TestUtils.create_activity_instance( + name=status_on_attributes_name, + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case=status_on_attributes_name, + topic_code=f"topic-{uuid.uuid4().hex[:8]}", + is_required_for_activity=True, + activities=[activities[0].uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=False, + ) + response = api_client.post( + f"/concepts/activities/activity-instances/{status_on_attributes.uid}/attributes/approvals" + ) + assert_response_status_code(response, 201) + + status_on_groupings = TestUtils.create_activity_instance( + name=status_on_groupings_name, + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case=status_on_groupings_name, + topic_code=f"topic-{uuid.uuid4().hex[:8]}", + is_required_for_activity=True, + activities=[activities[0].uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=False, + ) + response = api_client.post( + f"/concepts/activities/activity-instances/{status_on_groupings.uid}/groupings/approvals" + ) + assert_response_status_code(response, 201) + + response = api_client.get( + "/concepts/activities/activity-instances", + params={ + "status": "Draft", + "page_size": 100, + "names[]": [status_on_attributes_name, status_on_groupings_name], + }, + ) + assert_response_status_code(response, 200) + res = response.json() + + returned_items = {item["name"]: item for item in res["items"]} + assert set(returned_items.keys()) == { + status_on_attributes_name, + status_on_groupings_name, + } + assert returned_items[status_on_attributes_name]["status"] == "Final" + assert returned_items[status_on_attributes_name]["groupings_status"] == "Draft" + assert returned_items[status_on_groupings_name]["status"] == "Draft" + assert returned_items[status_on_groupings_name]["groupings_status"] == "Final" + + # Status-only query should use repository minimal_count_query and still count + # both rows matched via status OR groupings_status. + response = api_client.get( + "/concepts/activities/activity-instances", + params={ + "status": "Draft", + "page_size": 100, + "total_count": True, + }, + ) + assert_response_status_code(response, 200) + res = response.json() + + matching_names = { + item["name"] + for item in res["items"] + if item["name"] in {status_on_attributes_name, status_on_groupings_name} + } + assert matching_names == {status_on_attributes_name, status_on_groupings_name} + assert res["total"] == len(res["items"]) + + @pytest.mark.parametrize( "export_format", [ @@ -735,16 +864,16 @@ def test_filtering_exact( assert len(res["items"]) == 0 -def test_get_activity_instances_versions(api_client): +def test_get_activity_instance_attributes_versions(api_client): # Create a new version of an activity - response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instances_all[0].uid}/versions" + test_instance_response = api_client.post( + f"/concepts/activities/activity-instances/{activity_instances_all[0].uid}/attributes/versions" ) - assert_response_status_code(response, 201) + assert_response_status_code(test_instance_response, 201) # Get all versions of all activities response = api_client.get( - "/concepts/activities/activity-instances/versions?page_size=100" + "/concepts/activities/activity-instances/attributes/versions?page_size=100" ) res = response.json() @@ -753,9 +882,10 @@ def test_get_activity_instances_versions(api_client): # Check fields included in the response assert set(res.keys()) == set(["items", "total", "page", "size"]) - assert len(res["items"]) == len(activity_instances_all) * 2 + 1 + # Check that at least all the versions created by the test data fixture are returned + assert len(res["items"]) >= len(activity_instances_all) * 2 for item in res["items"]: - assert set(list(item.keys())) == set(ACTIVITY_INSTANCES_FIELDS_ALL) + assert set(list(item.keys())) == set(ACTIVITY_INSTANCE_ATTRIBUTES_FIELDS_ALL) for key in ACTIVITY_INSTANCES_FIELDS_NOT_NULL: assert item[key] is not None @@ -763,6 +893,15 @@ def test_get_activity_instances_versions(api_client): sorted_items = sorted(res["items"], key=itemgetter("start_date"), reverse=True) assert sorted_items == res["items"] + # Check that the instance updated in this test is listed as three versions + versions_of_instance = [ + item["version"] + for item in res["items"] + if item["uid"] == activity_instances_all[0].uid + ] + assert len(versions_of_instance) == 3 + assert set(versions_of_instance) == {"0.1", "1.0", "1.1"} + @pytest.mark.parametrize( "filter_by, expected_matched_field, expected_result_prefix", @@ -774,10 +913,10 @@ def test_get_activity_instances_versions(api_client): pytest.param('{"*": {"v": ["1.0"]}}', "version", "1.0"), ], ) -def test_filtering_versions_wildcard( +def test_filtering_attributes_versions_wildcard( api_client, filter_by, expected_matched_field, expected_result_prefix ): - url = f"/concepts/activities/activity-instances/versions?filters={filter_by}" + url = f"/concepts/activities/activity-instances/attributes/versions?filters={filter_by}" response = api_client.get(url) res = response.json() @@ -840,10 +979,10 @@ def test_filtering_versions_wildcard( ), ], ) -def test_filtering_versions_exact( +def test_filtering_attributes_versions_exact( api_client, filter_by, expected_matched_field, expected_result ): - url = f"/concepts/activities/activity-instances/versions?filters={filter_by}" + url = f"/concepts/activities/activity-instances/attributes/versions?filters={filter_by}" response = api_client.get(url) res = response.json() @@ -876,8 +1015,65 @@ def test_filtering_versions_exact( assert len(res["items"]) == 0 -def test_edit_activity_instance(api_client): +def test_preview_activity_instance_with_multiple_versions(api_client): + """ + Test preview functionality with an activity instance that has multiple versions. + This ensures sequential numbering works correctly when there are existing versions. + """ + # Create an actual activity instance (not preview) + activity_instance = TestUtils.create_activity_instance( + name="Activity Instance for Preview", + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case="activity instance for preview", + nci_concept_id="C-999", + topic_code="ACTIVITY", + activities=[activities[0].uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=False, + ) + + # Verify initial version + response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instance.uid}" + ) + res = response.json() + assert_response_status_code(response, 200) + assert res["version"] == "0.1" + assert res["status"] == "Draft" + + # First Edit - creates version 0.2 + response = api_client.patch( + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", + json={ + "name": "Activity Instance for Preview - Edited", + "name_sentence_case": "activity instance for preview - edited", + "change_description": "First edit", + }, + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["version"] == "0.2" + + # Second Edit - creates version 0.3 + # Set name to "Activity" to test preview numbering + response = api_client.patch( + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", + json={ + "name": "Activity", + "name_sentence_case": "activity", + "change_description": "Second edit", + }, + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["version"] == "0.3" + + # Now test preview functionality with the instance that has multiple versions + # This ensures sequential numbering is considered when there are existing versions activity_instance_preview = TestUtils.create_activity_instance( + name="", activity_instance_class_uid=activity_instance_classes[0].uid, nci_concept_id="C-123", activities=[activities[0].uid], @@ -888,10 +1084,28 @@ def test_edit_activity_instance(api_client): preview=True, ) assert activity_instance_preview.adam_param_code == "" - assert activity_instance_preview.name == "Activity" - assert activity_instance_preview.name_sentence_case == "activity" - assert activity_instance_preview.topic_code == "ACTIVITY" + assert activity_instance_preview.name == "Activity 1" + assert activity_instance_preview.name_sentence_case == "activity 1" + assert activity_instance_preview.topic_code == "ACTIVITY_1" + + # Create an actual activity instance with research lab set to true + _activity_instance_research = TestUtils.create_activity_instance( + name="Activity Research", + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case="activity research", + nci_concept_id="C-999", + topic_code="ACTIVITY_REASEARCH", + activities=[activities[0].uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=False, + is_research_lab=True, + ) + + # Test preview with is_research_lab=True activity_instance_preview = TestUtils.create_activity_instance( + name="", activity_instance_class_uid=activity_instance_classes[0].uid, nci_concept_id="C-123", activities=[activities[0].uid], @@ -903,11 +1117,13 @@ def test_edit_activity_instance(api_client): preview=True, ) assert activity_instance_preview.adam_param_code == "" - assert activity_instance_preview.name == "Activity Research" - assert activity_instance_preview.name_sentence_case == "activity research" - assert activity_instance_preview.topic_code == "ACTIVITY_RESEARCH" + assert activity_instance_preview.name == "Activity Research 1" + assert activity_instance_preview.name_sentence_case == "activity research 1" + assert activity_instance_preview.topic_code == "ACTIVITY_RESEARCH_1" + + # Test preview with custom name activity_instance_preview = TestUtils.create_activity_instance( - name="Activity (BU)", + name="Custom Activity Name", activity_instance_class_uid=activity_instance_classes[0].uid, nci_concept_id="C-123", activities=[activities[0].uid], @@ -918,34 +1134,139 @@ def test_edit_activity_instance(api_client): preview=True, ) assert activity_instance_preview.adam_param_code == "" - assert activity_instance_preview.name == "Activity (BU)" - # TODO: standard_unit detection disabled for now, it will be added in the future, so the response should be in lower case - assert activity_instance_preview.name_sentence_case == "activity (bu)" - assert activity_instance_preview.topic_code == "ACTIVITY_BU" + assert activity_instance_preview.name == "Custom Activity Name" + assert activity_instance_preview.name_sentence_case == "custom activity name" + assert activity_instance_preview.topic_code == "CUSTOM_ACTIVITY_NAME" + + +def test_get_activity_instance_groupings_versions(api_client): + activity = TestUtils.create_activity( + name="Activity For Instance Groupings Versions", + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + ) activity_instance = TestUtils.create_activity_instance( - name="Activity Instance", + name="Instance for Groupings Versions", activity_instance_class_uid=activity_instance_classes[0].uid, - name_sentence_case="activity instance", + name_sentence_case="instance for groupings versions", + nci_concept_id="C123456", + topic_code="GROUPINGS_VERSIONS", + activities=[activity.uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=True, + ) + + # Create a new version of the instance, create a second Draft version + response = api_client.post( + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions" + ) + assert_response_status_code(response, 201) + + # Approve the grouping to create a Final version + response = api_client.post( + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/approvals" + ) + assert_response_status_code(response, 201) + + # Get all versions of the instance + response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions" + ) + res = response.json() + + assert_response_status_code(response, 200) + assert len(res) == 4 + + # check that all versions have start date, status and version fields + for item in res: + assert item["start_date"] is not None + assert item["status"] is not None + assert item["version"] is not None + + # Check that the items are sorted by start_date descending + sorted_items = sorted(res, key=itemgetter("start_date"), reverse=True) + assert sorted_items == res + + assert res[0]["status"] == "Final" + assert res[0]["version"] == "2.0" + assert res[0]["start_date"] == res[1]["end_date"] + assert res[1]["status"] == "Draft" + assert res[1]["version"] == "1.1" + assert res[1]["start_date"] == res[2]["end_date"] + assert res[2]["status"] == "Final" + assert res[2]["version"] == "1.0" + assert res[2]["start_date"] == res[3]["end_date"] + assert res[3]["status"] == "Draft" + assert res[3]["version"] == "0.1" + + +def test_edit_activity_instance_groupings(api_client): + activity = TestUtils.create_activity( + name="Activity For Instance Groupings Edit", + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + ) + activity2 = TestUtils.create_activity( + name="Other Activity For Instance Groupings Edit", + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + ) + activity_instance = TestUtils.create_activity_instance( + name="Activity Instance For Grouping Edit", + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case="activity instance for grouping edit", nci_concept_id="C-123", - topic_code="activity instance tc 2", - activities=[activities[0].uid], + topic_code="activity instance grouping tc 2", + activities=[activity.uid], activity_subgroups=[activity_subgroup.uid], activity_groups=[activity_group.uid], activity_items=[activity_items[0]], approve=False, ) response = api_client.get( - f"/concepts/activities/activity-instances/{activity_instance.uid}" + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings" ) res = response.json() assert_response_status_code(response, 200) - assert res["name"] == "Activity Instance" - assert res["name_sentence_case"] == "activity instance" - assert res["nci_concept_id"] == "C-123" - assert res["topic_code"] == "activity instance tc 2" assert len(res["activity_groupings"]) == 1 - assert res["activity_groupings"][0]["activity"]["uid"] == activities[0].uid - assert res["activity_groupings"][0]["activity"]["name"] == activities[0].name + assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid + assert res["activity_groupings"][0]["activity"]["name"] == activity.name + assert ( + res["activity_groupings"][0]["activity_subgroup"]["uid"] + == activity_subgroup.uid + ) + assert ( + res["activity_groupings"][0]["activity_subgroup"]["name"] + == activity_subgroup.name + ) + assert res["activity_groupings"][0]["activity_group"]["uid"] == activity_group.uid + assert res["activity_groupings"][0]["activity_group"]["name"] == activity_group.name + + assert res["version"] == "0.1" + assert res["status"] == "Draft" + assert res["possible_actions"] == ["approve", "delete", "edit"] + + # Edit + response = api_client.patch( + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings", + json={ + "activity_groupings": [ + { + "activity_uid": activity2.uid, + "activity_subgroup_uid": activity_subgroup.uid, + "activity_group_uid": activity_group.uid, + } + ], + "change_description": "modifying activity instance", + }, + ) + res = response.json() + assert_response_status_code(response, 200) + 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_subgroup"]["uid"] == activity_subgroup.uid @@ -956,16 +1277,68 @@ def test_edit_activity_instance(api_client): ) assert res["activity_groupings"][0]["activity_group"]["uid"] == activity_group.uid assert res["activity_groupings"][0]["activity_group"]["name"] == activity_group.name + + assert res["version"] == "0.2" + assert res["status"] == "Draft" + assert res["possible_actions"] == ["approve", "delete", "edit"] + + # Get version 0.1 + response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings", + params={"version": "0.1"}, + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["version"] == "0.1" + assert len(res["activity_groupings"]) == 1 + assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid + + # Get version 0.2 + response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings", + params={"version": "0.2"}, + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["version"] == "0.2" + assert len(res["activity_groupings"]) == 1 + assert res["activity_groupings"][0]["activity"]["uid"] == activity2.uid + + +def test_edit_activity_instance_attributes(api_client): + + activity_instance = TestUtils.create_activity_instance( + name="Activity Instance Attributes Edit", + activity_instance_class_uid=activity_instance_classes[0].uid, + name_sentence_case="activity instance attributes edit", + nci_concept_id="C-123", + topic_code="activity instance attributes edit tc 2", + activities=[activities[0].uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[0]], + approve=False, + ) + response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes" + ) + res = response.json() + assert_response_status_code(response, 200) + assert res["name"] == "Activity Instance Attributes Edit" + assert res["name_sentence_case"] == "activity instance attributes edit" + assert res["nci_concept_id"] == "C-123" + assert res["topic_code"] == "activity instance attributes edit tc 2" assert res["activity_instance_class"]["uid"] == activity_instance_classes[0].uid assert len(res["activity_items"]) == 1 assert res["activity_items"][0]["is_adam_param_specific"] is True + assert res["activity_items"][0]["is_activity_instance_id_specific"] is True assert res["version"] == "0.1" assert res["status"] == "Draft" assert res["possible_actions"] == ["approve", "delete", "edit"] # First Edit without activity-items explicitly sent response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "name": "some new name", "name_sentence_case": "some new name", @@ -976,18 +1349,11 @@ def test_edit_activity_instance(api_client): # Second Edit with more properties sent response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "name": "new name", "name_sentence_case": "new name", "nci_concept_id": "C-123NEW", - "activity_groupings": [ - { - "activity_uid": activities[1].uid, - "activity_subgroup_uid": activity_subgroup.uid, - "activity_group_uid": activity_group.uid, - } - ], "activity_instance_class_uid": activity_instance_classes[0].uid, "activity_items": [activity_items[0], activity_items[1]], "change_description": "modifying activity instance", @@ -998,25 +1364,15 @@ def test_edit_activity_instance(api_client): assert res["name"] == "new name" assert res["name_sentence_case"] == "new name" assert res["nci_concept_id"] == "C-123NEW" - assert res["topic_code"] == "activity instance tc 2" - assert len(res["activity_groupings"]) == 1 - assert res["activity_groupings"][0]["activity"]["uid"] == activities[1].uid - assert res["activity_groupings"][0]["activity"]["name"] == activities[1].name - assert ( - res["activity_groupings"][0]["activity_subgroup"]["uid"] - == activity_subgroup.uid - ) - assert ( - res["activity_groupings"][0]["activity_subgroup"]["name"] - == activity_subgroup.name - ) - assert res["activity_groupings"][0]["activity_group"]["uid"] == activity_group.uid - assert res["activity_groupings"][0]["activity_group"]["name"] == activity_group.name + assert res["topic_code"] == "activity instance attributes edit tc 2" + assert res["activity_instance_class"]["uid"] == activity_instance_classes[0].uid items = res["activity_items"] assert len(items) == 2 assert items[0]["is_adam_param_specific"] is True + assert items[0]["is_activity_instance_id_specific"] is True assert items[1]["is_adam_param_specific"] is False + assert items[1]["is_activity_instance_id_specific"] is False items = sorted(items, key=lambda x: x["activity_item_class"]["uid"]) @@ -1053,86 +1409,6 @@ def test_edit_activity_instance(api_client): assert res["status"] == "Draft" assert res["possible_actions"] == ["approve", "delete", "edit"] - activity_instance_preview = TestUtils.create_activity_instance( - name="", - activity_instance_class_uid=activity_instance_classes[0].uid, - nci_concept_id="C-123", - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0]], - approve=False, - preview=True, - ) - activity_instance = TestUtils.create_activity_instance( - name=activity_instance_preview.name, - activity_instance_class_uid=activity_instance_classes[0].uid, - name_sentence_case=activity_instance_preview.name_sentence_case, - nci_concept_id="C-124", - topic_code=activity_instance_preview.topic_code, - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0]], - approve=False, - ) - activity_instance_preview = TestUtils.create_activity_instance( - name="", - activity_instance_class_uid=activity_instance_classes[0].uid, - nci_concept_id="C-123", - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0]], - approve=False, - preview=True, - ) - assert activity_instance_preview.adam_param_code == "" - assert activity_instance_preview.name == "Activity 1" - assert activity_instance_preview.name_sentence_case == "activity 1" - assert activity_instance_preview.topic_code == "ACTIVITY_1" - - activity_instance_preview = TestUtils.create_activity_instance( - name="", - activity_instance_class_uid=activity_instance_classes[0].uid, - nci_concept_id="C-123", - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0]], - approve=False, - is_research_lab=True, - preview=True, - ) - activity_instance = TestUtils.create_activity_instance( - name=activity_instance_preview.name, - activity_instance_class_uid=activity_instance_classes[0].uid, - name_sentence_case=activity_instance_preview.name_sentence_case, - nci_concept_id="C-124", - topic_code=activity_instance_preview.topic_code, - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0]], - approve=False, - ) - activity_instance_preview = TestUtils.create_activity_instance( - name="", - activity_instance_class_uid=activity_instance_classes[0].uid, - nci_concept_id="C-123", - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0]], - is_research_lab=True, - approve=False, - preview=True, - ) - assert activity_instance_preview.adam_param_code == "" - assert activity_instance_preview.name == "Activity Research 1" - assert activity_instance_preview.name_sentence_case == "activity research 1" - assert activity_instance_preview.topic_code == "ACTIVITY_RESEARCH_1" - def test_cannot_edit_activity_instance_class_uid(api_client): """Test that editing activity_instance_class_uid raises BusinessLogicException""" @@ -1151,7 +1427,7 @@ def test_cannot_edit_activity_instance_class_uid(api_client): # Try to edit activity_instance_class_uid response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "activity_instance_class_uid": activity_instance_classes[1].uid, "change_description": "trying to change instance class", @@ -1180,7 +1456,7 @@ def test_cannot_edit_topic_code(api_client): # Try to edit topic_code response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "topic_code": "NEW_TOPIC_CODE", "change_description": "trying to change topic code", @@ -1210,7 +1486,7 @@ def test_cannot_edit_is_research_lab(api_client): # Try to edit is_research_lab from False to True response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "is_research_lab": True, "change_description": "trying to change research lab flag", @@ -1240,20 +1516,11 @@ def test_can_edit_allowed_fields(api_client): # Edit allowed fields (keep the same activity to avoid interfering with other tests) response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "name": "Updated Name", "name_sentence_case": "updated name", "adam_param_code": "UPDATED_ADAM_CODE", - "activity_groupings": [ - { - "activity_uid": activities[ - 0 - ].uid, # Keep same activity to avoid test isolation issues - "activity_subgroup_uid": activity_subgroup.uid, - "activity_group_uid": activity_group.uid, - } - ], "change_description": "updating allowed fields", }, ) @@ -1264,8 +1531,6 @@ def test_can_edit_allowed_fields(api_client): assert res["adam_param_code"] == "UPDATED_ADAM_CODE" assert res["topic_code"] == unique_topic_code # Should remain unchanged assert res["is_research_lab"] is False # Should remain unchanged - assert len(res["activity_groupings"]) == 1 - assert res["activity_groupings"][0]["activity"]["uid"] == activities[0].uid def test_cannot_edit_ct_terms_for_param_paramcd_activity_items(api_client): @@ -1312,7 +1577,7 @@ def test_cannot_edit_ct_terms_for_param_paramcd_activity_items(api_client): } response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "activity_items": [modified_activity_item], "change_description": "trying to change ct_terms for param/paramcd item", @@ -1367,7 +1632,7 @@ def test_can_edit_ct_terms_for_non_param_paramcd_activity_items(api_client): } response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes", json={ "activity_items": [modified_activity_item], "change_description": "changing ct_terms for non-param/paramcd item", @@ -1427,6 +1692,7 @@ def test_post_activity_instance(api_client): assert res["activity_instance_class"]["uid"] == activity_instance_classes[0].uid assert len(res["activity_items"]) == 2 assert res["activity_items"][0]["is_adam_param_specific"] is False + assert res["activity_items"][0]["is_activity_instance_id_specific"] is False assert ( res["activity_items"][0]["activity_item_class"]["uid"] == activity_item_classes[1].uid @@ -1462,7 +1728,7 @@ def test_post_activity_instance(api_client): assert res["possible_actions"] == ["approve", "delete", "edit"] -def test_activity_instance_versioning(api_client): +def test_activity_instance_attributes_versioning(api_client): response = api_client.post( "/concepts/activities/activity-instances", json={ @@ -1489,46 +1755,46 @@ def test_activity_instance_versioning(api_client): activity_instance_uid = res["uid"] response = api_client.get( - f"/concepts/activities/activity-instances/{activity_instance_uid}/versions" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/versions" ) res = response.json() assert_response_status_code(response, 200) for item in res: - assert set(list(item.keys())) == set(ACTIVITY_INSTANCES_FIELDS_ALL) + assert set(list(item.keys())) == set(ACTIVITY_INSTANCE_ATTRIBUTES_FIELDS_ALL) for key in ACTIVITY_INSTANCES_FIELDS_NOT_NULL: assert item[key] is not None response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/versions" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/versions" ) assert_response_status_code(response, 400) res = response.json() assert res["message"] == "New draft version can be created only for FINAL versions." response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/approvals" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/approvals" ) assert_response_status_code(response, 201) response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/approvals" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/approvals" ) assert_response_status_code(response, 400) res = response.json() assert res["message"] == "The object isn't in draft status." response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/activations" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations" ) assert_response_status_code(response, 400) res = response.json() assert res["message"] == "Only RETIRED version can be reactivated." response = api_client.delete( - f"/concepts/activities/activity-instances/{activity_instance_uid}/activations" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations" ) assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance_uid}/activations" + f"/concepts/activities/activity-instances/{activity_instance_uid}/attributes/activations" ) assert_response_status_code(response, 200) @@ -1563,36 +1829,25 @@ def test_activity_instance_with_codelist(api_client): def test_activity_instance_overview(api_client): - response = api_client.get( + # this is done in two steps, start with the overview endpoint + overview_response = api_client.get( f"/concepts/activities/activity-instances/{activity_instances_all[3].uid}/overview", ) - assert_response_status_code(response, 200) - res = response.json() - verify_instance_overview_content(res=res) - - -def verify_instance_overview_content(res: dict[Any, Any]): - print(json.dumps(res, indent=2, default=str)) - - assert len(res["activity_groupings"]) == 1 - # activity - assert res["activity_groupings"][0]["activity"]["uid"] == activities[0].uid - assert res["activity_groupings"][0]["activity"]["name"] == activities[0].name - assert res["activity_groupings"][0]["activity"]["definition"] is None - assert ( - res["activity_groupings"][0]["activity"]["library_name"] == SPONSOR_LIBRARY_NAME - ) + assert_response_status_code(overview_response, 200) + overview_res = overview_response.json() + verify_instance_overview_content(res=overview_res) - # activity subgroups - assert ( - res["activity_groupings"][0]["activity_subgroup"]["name"] == "activity_subgroup" + # then get the groupings for the same instance to verify the grouping content as well + groupings_response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instances_all[3].uid}/groupings", ) - assert res["activity_groupings"][0]["activity_subgroup"]["definition"] is None + assert_response_status_code(groupings_response, 200) + groupings_res = groupings_response.json() + verify_instance_groupings_content(res=groupings_res) - # activity groups - assert res["activity_groupings"][0]["activity_group"]["name"] == "activity_group" - assert res["activity_groupings"][0]["activity_group"]["definition"] is None +def verify_instance_overview_content(res: dict[Any, Any]): + print(json.dumps(res, indent=2, default=str)) # activity instance assert res["activity_instance"]["uid"] is not None assert res["activity_instance"]["name"] == "name XXX" @@ -1659,7 +1914,25 @@ def verify_instance_overview_content(res: dict[Any, Any]): assert items[2]["activity_item_class"]["order"] == 3 +def verify_instance_groupings_content(res: dict[Any, Any]): + print(json.dumps(res, indent=2, default=str)) + + assert len(res["activity_groupings"]) == 1 + # activity + assert res["activity_groupings"][0]["activity"]["uid"] == activities[0].uid + assert res["activity_groupings"][0]["activity"]["name"] == activities[0].name + + # activity subgroups + assert ( + res["activity_groupings"][0]["activity_subgroup"]["name"] == "activity_subgroup" + ) + + # activity groups + assert res["activity_groupings"][0]["activity_group"]["name"] == "activity_group" + + def test_activity_instance_overview_export_to_yaml(api_client): + # Done in two steps, first the overview endpoint: url = f"/concepts/activities/activity-instances/{activity_instances_all[3].uid}/overview" export_format = "application/x-yaml" headers = {"Accept": export_format} @@ -1671,6 +1944,15 @@ def test_activity_instance_overview_export_to_yaml(api_client): res = yaml.load(response.text, Loader=yaml.SafeLoader) verify_instance_overview_content(res=res) + # Now the groupings endpoint to verify the grouping content as well + url = f"/concepts/activities/activity-instances/{activity_instances_all[3].uid}/groupings" + response = api_client.get(url, headers=headers) + assert_response_status_code(response, 200) + assert export_format in response.headers["content-type"] + + groupings_res = yaml.load(response.text, Loader=yaml.SafeLoader) + verify_instance_groupings_content(res=groupings_res) + def test_activity_instance_cosmos_overview(api_client): url = f"/concepts/activities/activity-instances/{activity_instances_all[3].uid}/overview.cosmos" @@ -1987,15 +2269,10 @@ def test_updating_parents(api_client): assert_response_status_code(response, 200) res = response.json() assert res["activity_instance"]["name"] == original_instance_name - assert len(res["activity_groupings"]) == 1 - assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid - assert res["activity_groupings"][0]["activity"]["name"] == original_activity_name - - assert ( - res["activity_groupings"][0]["activity_subgroup"]["name"] - == original_subgroup_name - ) - assert res["activity_groupings"][0]["activity_group"]["name"] == original_group_name + # there should be only two groupings versions, 0.1 and 1.0 + assert len(res["activity_groupings_versions"]) == 2 + assert "0.1" in res["activity_groupings_versions"] + assert "1.0" in res["activity_groupings_versions"] assert res["activity_instance"]["version"] == "1.0" assert res["activity_instance"]["status"] == "Final" @@ -2110,28 +2387,28 @@ def test_updating_instance_to_new_activity(api_client): # ==== Update instance to updated activity ==== # Create new version of instance response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance.uid}/versions", + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions", json={}, ) assert_response_status_code(response, 201) # Patch the activity instance, no changes response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings", json={ "change_description": "string", - "name": "updatetest original instance name", }, ) assert_response_status_code(response, 200) # Approve the activity instance response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance.uid}/approvals" + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/approvals" ) assert_response_status_code(response, 201) - # Get the instance by uid and assert that it is not conncted to the new activity + # Get the instance by uid and assert that it is still connected to the original activity + # and that the activity name is updated in the instance overview response = api_client.get( f"/concepts/activities/activity-instances/{activity_instance.uid}" ) @@ -2147,20 +2424,22 @@ def test_updating_instance_to_new_activity(api_client): assert res["activity_groupings"][0]["activity_group"]["uid"] == group.uid assert res["activity_groupings"][0]["activity_group"]["name"] == group_name - assert res["version"] == "2.0" + assert res["version"] == "1.0" assert res["status"] == "Final" + assert res["groupings_version"] == "2.0" + assert res["groupings_status"] == "Final" # ==== Update instance to another activity ==== # Create new version of instance response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance.uid}/versions", + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions", json={}, ) assert_response_status_code(response, 201) # Patch the activity instance to another activity, no other changes response = api_client.patch( - f"/concepts/activities/activity-instances/{activity_instance.uid}", + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings", json={ "activity_groupings": [ { @@ -2169,7 +2448,6 @@ def test_updating_instance_to_new_activity(api_client): "activity_uid": other_activity.uid, } ], - "name": "updatetest original instance name", "change_description": "string2", }, ) @@ -2177,7 +2455,7 @@ def test_updating_instance_to_new_activity(api_client): # Approve the activity instance response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance.uid}/approvals" + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/approvals" ) assert_response_status_code(response, 201) @@ -2197,8 +2475,10 @@ def test_updating_instance_to_new_activity(api_client): assert res["activity_groupings"][0]["activity_group"]["uid"] == group.uid assert res["activity_groupings"][0]["activity_group"]["name"] == group_name - assert res["version"] == "3.0" + assert res["version"] == "1.0" assert res["status"] == "Final" + assert res["groupings_version"] == "3.0" + assert res["groupings_status"] == "Final" def test_instance_to_activity_without_data_collection(api_client): @@ -2354,6 +2634,10 @@ def test_cannot_provide_is_adam_param_specific_if_is_adam_param_specific_enabled ("is_default_selected_for_activity", "f"), ("is_data_sharing", "f"), ("is_legacy_usage", "f"), + ("groupings_author_username", "unknown-user"), + ("groupings_version", "1.0"), + ("groupings_status", "Final"), + ("groupings_start_date", "20"), ], ) def test_get_activity_instances_headers(api_client, field_name, search_string): @@ -2758,3 +3042,119 @@ def test_cannot_provide_ct_terms_and_ct_codelist(api_client): "msg": "Value error, Both ct_terms and ct_codelist cannot be provided at the same time for an ActivityItem.", "ctx": {"error": {}}, } + + +def test_cannot_provide_ct_codelist_with_is_activity_instance_id_specific(api_client): + """Test that providing ct_codelist_uid together with is_activity_instance_id_specific=True raises validation error""" + response = api_client.post( + "/concepts/activities/activity-instances", + json={ + "name": "id specific with ct codelist", + "name_sentence_case": "id specific with ct codelist", + "activity_groupings": [ + { + "activity_uid": activities[0].uid, + "activity_subgroup_uid": activity_subgroup.uid, + "activity_group_uid": activity_group.uid, + } + ], + "activity_instance_class_uid": activity_instance_classes[0].uid, + "activity_items": [ + { + "activity_item_class_uid": activity_item_classes[0].uid, + "ct_codelist_uid": codelist.codelist_uid, + "ct_terms": [], + "unit_definition_uids": [], + "is_adam_param_specific": False, + "is_activity_instance_id_specific": True, + }, + ], + "library_name": "Sponsor", + }, + ) + assert_response_status_code(response, 400) + res = response.json() + assert res["type"] == "RequestValidationError" + assert "must not have a ct_codelist_uid" in res["details"][0]["msg"] + + +def test_cannot_provide_multiple_ct_terms_with_is_activity_instance_id_specific( + api_client, +): + """Test that providing more than one ct_term with is_activity_instance_id_specific=True raises validation error""" + response = api_client.post( + "/concepts/activities/activity-instances", + json={ + "name": "id specific with multiple terms", + "name_sentence_case": "id specific with multiple terms", + "activity_groupings": [ + { + "activity_uid": activities[0].uid, + "activity_subgroup_uid": activity_subgroup.uid, + "activity_group_uid": activity_group.uid, + } + ], + "activity_instance_class_uid": activity_instance_classes[0].uid, + "activity_items": [ + { + "activity_item_class_uid": activity_item_classes[0].uid, + "ct_terms": [ + { + "term_uid": ct_terms[0].term_uid, + "codelist_uid": codelist.codelist_uid, + }, + { + "term_uid": ct_terms[1].term_uid, + "codelist_uid": codelist.codelist_uid, + }, + ], + "unit_definition_uids": [], + "is_adam_param_specific": False, + "is_activity_instance_id_specific": True, + }, + ], + "library_name": "Sponsor", + }, + ) + assert_response_status_code(response, 400) + res = response.json() + assert res["type"] == "RequestValidationError" + assert "must not have more than one ct_term" in res["details"][0]["msg"] + + +def test_cannot_provide_multiple_unit_definitions_with_is_activity_instance_id_specific( + api_client, +): + """Test that providing more than one unit_definition with is_activity_instance_id_specific=True raises validation error""" + response = api_client.post( + "/concepts/activities/activity-instances", + json={ + "name": "id specific with multiple units", + "name_sentence_case": "id specific with multiple units", + "activity_groupings": [ + { + "activity_uid": activities[0].uid, + "activity_subgroup_uid": activity_subgroup.uid, + "activity_group_uid": activity_group.uid, + } + ], + "activity_instance_class_uid": activity_instance_classes[0].uid, + "activity_items": [ + { + "activity_item_class_uid": activity_item_classes[0].uid, + "ct_terms": [], + "unit_definition_uids": [ + base_test_data["day_unit"].uid, + base_test_data["day_unit"].uid, + ], + "is_adam_param_specific": False, + "is_activity_instance_id_specific": True, + }, + ], + "library_name": "Sponsor", + }, + ) + assert_response_status_code(response, 400) + res = response.json() + assert res["type"] == "RequestValidationError" + assert "must not have more than one unit_definition" in res["details"][0]["msg"] diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_item_classes.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_item_classes.py index b0784483..db3f644a 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_item_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_item_classes.py @@ -1027,3 +1027,73 @@ def test_get_activity_instance_classes_using_item(api_client: TestClient) -> Non result = response.json() assert result["items"] == [] assert result["total"] == 0 + + +def test_get_activity_item_classes_versions(api_client): + """Test GET /activity-item-classes/versions endpoint""" + # First, create a new version of one item class so we have multiple versions + response = api_client.post( + f"/activity-item-classes/{activity_item_classes_all[0].uid}/versions" + ) + assert_response_status_code(response, 201) + + # Get all versions + response = api_client.get( + "/activity-item-classes/versions?page_size=100&total_count=true" + ) + res = response.json() + + assert_response_status_code(response, 200) + + # Check response structure + assert set(res.keys()) == {"items", "total", "page", "size"} + assert res["total"] > 0 + + # Should have more versions than unique classes (since we created a new version above) + assert res["total"] > len(activity_item_classes_all) + + # Check that the items are sorted by start_date descending + start_dates = [item["start_date"] for item in res["items"] if item["start_date"]] + assert start_dates == sorted(start_dates, reverse=True) + + # Check that the class updated in this test has multiple versions + versions_of_class = [ + item["version"] + for item in res["items"] + if item["uid"] == activity_item_classes_all[0].uid + ] + assert len(versions_of_class) >= 2 + + # Check fields on first item + item = res["items"][0] + assert "uid" in item + assert "name" in item + assert "version" in item + assert "status" in item + assert "start_date" in item + assert "library_name" in item + + +def test_get_activity_item_classes_versions_pagination(api_client): + """Test pagination on /activity-item-classes/versions""" + # Get first page + response = api_client.get( + "/activity-item-classes/versions?page_size=2&page_number=1&total_count=true" + ) + assert_response_status_code(response, 200) + page1 = response.json() + assert len(page1["items"]) == 2 + assert page1["total"] > 2 + + # Get second page + response = api_client.get( + "/activity-item-classes/versions?page_size=2&page_number=2&total_count=true" + ) + assert_response_status_code(response, 200) + page2 = response.json() + assert len(page2["items"]) > 0 + + # Pages should not overlap + page1_uids_versions = {(i["uid"], i["version"]) for i in page1["items"]} + page2_uids_versions = {(i["uid"], i["version"]) for i in page2["items"]} + assert page1_uids_versions.isdisjoint(page2_uids_versions) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_subgroups.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_subgroups.py index 164311b1..f66f2002 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_subgroups.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_subgroups.py @@ -66,6 +66,8 @@ def test_data(): "uid", "name", "name_sentence_case", + "nci_concept_id", + "nci_concept_name", "definition", "abbreviation", "library_name", @@ -345,11 +347,15 @@ def test_cascade_edit_activity_subgroups(api_client): # Update the activity subgroup updated_activity_subgroup_name = "Edited Cascade Activity SubGroup" + concept_id = "CONCEPT_ID" + concept_name = "concept name" response = api_client.put( f"/concepts/activities/activity-sub-groups/{activity_subgroup.uid}", json={ "name": updated_activity_subgroup_name, "name_sentence_case": updated_activity_subgroup_name.lower(), + "nci_concept_id": concept_id, + "nci_concept_name": concept_name, "change_description": "test cascade edit", "library_name": activity_subgroup.library_name, }, @@ -371,6 +377,8 @@ def test_cascade_edit_activity_subgroups(api_client): res = response.json() assert res["name"] == updated_activity_subgroup_name assert res["name_sentence_case"] == updated_activity_subgroup_name.lower() + assert res["nci_concept_id"] == concept_id + assert res["nci_concept_name"] == concept_name assert res["status"] == "Final" assert res["version"] == "2.0" @@ -426,8 +434,8 @@ def test_cascade_edit_activity_subgroups(api_client): ) assert res["activity_groupings"][0]["activity"]["uid"] == activity.uid assert res["activity_groupings"][0]["activity"]["name"] == activity.name - assert res["version"] == "2.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "2.0" + assert res["groupings_status"] == "Final" # Get the activity subgroup versions and assert that two new versions were created. # There should be a draft version 1.1 that still links to activity group version 1.0 & 1.1, @@ -477,7 +485,7 @@ def test_cascade_edit_activity_subgroups(api_client): # Get the activity instance versions and assert that there is one new version created. # There should be a new final version 2.0 that links to activity version 2.0 response = api_client.get( - f"/concepts/activities/activity-instances/{activity_instance.uid}/versions" + f"/concepts/activities/activity-instances/{activity_instance.uid}/groupings/versions" ) assert_response_status_code(response, 200) res = response.json() @@ -550,8 +558,8 @@ def test_cascade_edit_activity_subgroups(api_client): assert_response_status_code(response, 200) res = response.json() assert len(res["activity_groupings"]) == 1 - assert res["version"] == "2.0" - assert res["status"] == "Final" + assert res["groupings_version"] == "2.0" + assert res["groupings_status"] == "Final" assert ( res["activity_groupings"][0]["activity_subgroup"]["name"] == updated_activity_subgroup_name diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelist_terms.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelist_terms.py new file mode 100644 index 00000000..7462196b --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_paired_codelist_terms.py @@ -0,0 +1,248 @@ +""" +Tests for paired codelist terms endpoint +""" + +# pylint: disable=unused-argument +# pylint: disable=redefined-outer-name +# pylint: disable=too-many-arguments + +# pytest fixture functions have other fixture functions as arguments, +# which pylint interprets as unused arguments + +import logging + +import pytest +from fastapi.testclient import TestClient + +from clinical_mdr_api.main import app +from clinical_mdr_api.models.controlled_terminologies.ct_codelist import CTCodelist +from clinical_mdr_api.models.controlled_terminologies.ct_term import CTTerm +from clinical_mdr_api.services.controlled_terminologies.ct_codelist import ( + CTCodelistService, +) +from clinical_mdr_api.tests.integration.utils.api import ( + inject_and_clear_db, + inject_base_data, +) +from clinical_mdr_api.tests.integration.utils.utils import TestUtils +from clinical_mdr_api.tests.utils.checks import assert_response_status_code + +log = logging.getLogger(__name__) + +# Global variables shared between fixtures and tests +names_codelist: CTCodelist +codes_codelist: CTCodelist +unpaired_codelist: CTCodelist +term_a: CTTerm +term_b: CTTerm +term_c: CTTerm + +CATALOGUE = "SDTM CT" +URL = "/ct/paired-codelists" + + +@pytest.fixture(scope="module") +def api_client(test_data): + """Create FastAPI test client + using the database name set in the `test_data` fixture""" + yield TestClient(app) + + +@pytest.fixture(scope="module") +def test_data(): + """Initialize test data: + - A names codelist paired with a codes codelist + - 3 terms in the names codelist + - Same 3 terms added to the codes codelist with different submission values + - An unpaired codelist for the 400 error test + """ + db_name = "ct-paired-codelist-terms.api" + inject_and_clear_db(db_name) + inject_base_data(inject_unit_subset=False) + + # Create the two codelists that will be paired + global codes_codelist + codes_codelist = TestUtils.create_ct_codelist( + catalogue_name=CATALOGUE, + name="Codes CL", + sponsor_preferred_name="Codes CL", + submission_value="CODES_CL", + library_name="Sponsor", + approve=True, + extensible=True, + ) + global names_codelist + names_codelist = TestUtils.create_ct_codelist( + catalogue_name=CATALOGUE, + name="Names CL", + sponsor_preferred_name="Names CL", + submission_value="NAMES_CL", + library_name="Sponsor", + approve=True, + extensible=True, + paired_codes_codelist_uid=codes_codelist.codelist_uid, + ) + + # Create terms in the names codelist + global term_a + term_a = TestUtils.create_ct_term( + codelist_uid=names_codelist.codelist_uid, + sponsor_preferred_name="Term A", + submission_value="NAME_A", + order=1, + library_name="Sponsor", + approve=True, + ) + global term_b + term_b = TestUtils.create_ct_term( + codelist_uid=names_codelist.codelist_uid, + sponsor_preferred_name="Term B", + submission_value="NAME_B", + order=2, + library_name="Sponsor", + approve=True, + ) + global term_c + term_c = TestUtils.create_ct_term( + codelist_uid=names_codelist.codelist_uid, + sponsor_preferred_name="Term C", + submission_value="NAME_C", + order=3, + library_name="Sponsor", + approve=True, + ) + + # Add the same terms to the codes codelist with different submission values + codelist_service = CTCodelistService() + codelist_service.add_term( + codelist_uid=codes_codelist.codelist_uid, + term_uid=term_a.term_uid, + order=1, + submission_value="CODE_A", + ) + codelist_service.add_term( + codelist_uid=codes_codelist.codelist_uid, + term_uid=term_b.term_uid, + order=2, + submission_value="CODE_B", + ) + codelist_service.add_term( + codelist_uid=codes_codelist.codelist_uid, + term_uid=term_c.term_uid, + order=3, + submission_value="CODE_C", + ) + + # Create an unpaired codelist for the 400 error test + global unpaired_codelist + unpaired_codelist = TestUtils.create_ct_codelist( + catalogue_name=CATALOGUE, + sponsor_preferred_name="Unpaired CL", + submission_value="UNPAIRED_CL", + library_name="Sponsor", + approve=True, + ) + + yield + + +def test_get_paired_terms_from_names_codelist(api_client): + """Requesting paired terms using the names codelist UID should return + all terms with both name and code submission values.""" + response = api_client.get(f"{URL}/{names_codelist.codelist_uid}/terms") + assert_response_status_code(response, 200) + + res = response.json() + terms = res["items"] + assert len(terms) == 3 + + # Default sort is by order ascending + assert terms[0]["term_uid"] == term_a.term_uid + assert terms[1]["term_uid"] == term_b.term_uid + assert terms[2]["term_uid"] == term_c.term_uid + + assert terms[0]["name_submission_value"] == "NAME_A" + assert terms[0]["code_submission_value"] == "CODE_A" + assert terms[1]["name_submission_value"] == "NAME_B" + assert terms[1]["code_submission_value"] == "CODE_B" + assert terms[2]["name_submission_value"] == "NAME_C" + assert terms[2]["code_submission_value"] == "CODE_C" + + assert terms[0]["sponsor_preferred_name"] == "Term A" + assert terms[1]["sponsor_preferred_name"] == "Term B" + assert terms[2]["sponsor_preferred_name"] == "Term C" + + +def test_get_paired_terms_from_codes_codelist(api_client): + """Requesting paired terms using the codes codelist UID should return + the same results as requesting from the names codelist.""" + response = api_client.get(f"{URL}/{codes_codelist.codelist_uid}/terms") + assert_response_status_code(response, 200) + + terms = response.json()["items"] + assert len(terms) == 3 + + assert terms[0]["name_submission_value"] == "NAME_A" + assert terms[0]["code_submission_value"] == "CODE_A" + assert terms[1]["name_submission_value"] == "NAME_B" + assert terms[1]["code_submission_value"] == "CODE_B" + assert terms[2]["name_submission_value"] == "NAME_C" + assert terms[2]["code_submission_value"] == "CODE_C" + + +def test_get_paired_terms_returns_400_for_unpaired_codelist(api_client): + """Requesting paired terms for a codelist without a paired codelist + should return a 400 error.""" + response = api_client.get(f"{URL}/{unpaired_codelist.codelist_uid}/terms") + assert_response_status_code(response, 400) + + +def test_get_paired_terms_pagination(api_client): + """Pagination should work correctly on the paired terms endpoint.""" + response = api_client.get( + f"{URL}/{names_codelist.codelist_uid}/terms", + params={"page_size": 2, "page_number": 1}, + ) + assert_response_status_code(response, 200) + + res = response.json() + assert len(res["items"]) == 2 + assert res["items"][0]["term_uid"] == term_a.term_uid + assert res["items"][1]["term_uid"] == term_b.term_uid + + response = api_client.get( + f"{URL}/{names_codelist.codelist_uid}/terms", + params={"page_size": 2, "page_number": 2}, + ) + assert_response_status_code(response, 200) + + res = response.json() + assert len(res["items"]) == 1 + assert res["items"][0]["term_uid"] == term_c.term_uid + + +def test_get_paired_terms_total_count(api_client): + """The total_count parameter should return the total number of items.""" + response = api_client.get( + f"{URL}/{names_codelist.codelist_uid}/terms", + params={"page_size": 2, "page_number": 1, "total_count": True}, + ) + assert_response_status_code(response, 200) + + res = response.json() + assert len(res["items"]) == 2 + assert res["total"] == 3 + + +def test_get_paired_terms_sort_by_name(api_client): + """Sorting by sponsor_preferred_name descending should reverse the order.""" + response = api_client.get( + f"{URL}/{names_codelist.codelist_uid}/terms", + params={"sort_by": '{"sponsor_preferred_name": false}'}, + ) + assert_response_status_code(response, 200) + + terms = response.json()["items"] + assert terms[0]["sponsor_preferred_name"] == "Term C" + assert terms[1]["sponsor_preferred_name"] == "Term B" + assert terms[2]["sponsor_preferred_name"] == "Term A" diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/ddf/test_ddf_adapter_mappings.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/ddf/test_ddf_adapter_mappings.py index c21cff7e..4323f99e 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/ddf/test_ddf_adapter_mappings.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/ddf/test_ddf_adapter_mappings.py @@ -153,5 +153,8 @@ def test_study_identifier(ddf_mapper, tst_study): study_patch_request=study_patch_request, ) - ddf_study_identifier = ddf_mapper._get_study_identifiers(patched_study) - assert ddf_study_identifier is not None + ddf_study_identifiers, ddf_organizations = ( + ddf_mapper._get_study_identifiers_and_organizations(patched_study) + ) + assert ddf_study_identifiers is not None + assert ddf_organizations is not None diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_versioning.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_versioning.py index 72c2fe8b..b865c078 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_versioning.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_versioning.py @@ -357,7 +357,7 @@ def test_add_odm_items_to_odm_item_group(api_client): "oid": "I2", "name": "Item 2", "version": "0.1", - "order_number": 2, + "order_number": 1, "mandatory": "No", "key_sequence": "None", "method_oid": "None", @@ -523,7 +523,7 @@ def test_approve_study_event_with_cascade_effect(api_client): "oid": "I2", "name": "Item 2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "No", "key_sequence": "None", "method_oid": "None", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_group.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_group.py index bb0084bc..67b0b031 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_group.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_group.py @@ -41,6 +41,8 @@ def test_post_create_activity_group(api_client): "definition": "definition", "abbreviation": "abbv", "library_name": "Sponsor", + "nci_concept_id": "CONCEPT_ID", + "nci_concept_name": "CONCEPT_NAME", } response = api_client.post("/concepts/activities/activity-groups", json=data) @@ -54,6 +56,8 @@ def test_post_create_activity_group(api_client): assert res["definition"] == "definition" assert res["abbreviation"] == "abbv" assert res["library_name"] == "Sponsor" + assert res["nci_concept_id"] == data["nci_concept_id"] + assert res["nci_concept_name"] == data["nci_concept_name"] assert res["end_date"] is None assert res["status"] == "Draft" assert res["version"] == "0.1" diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_sub_group.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_sub_group.py index f226571e..46cadfff 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_sub_group.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_activity_sub_group.py @@ -41,6 +41,8 @@ def test_post_create_activity_sub_group(api_client): "definition": "definition", "abbreviation": "abbv", "library_name": "Sponsor", + "nci_concept_id": "CONCEPT_ID", + "nci_concept_name": "CONCEPT_NAME", } response = api_client.post("/concepts/activities/activity-sub-groups", json=data) @@ -54,6 +56,8 @@ def test_post_create_activity_sub_group(api_client): assert res["definition"] == "definition" assert res["abbreviation"] == "abbv" assert res["library_name"] == "Sponsor" + assert res["nci_concept_id"] == data["nci_concept_id"] + assert res["nci_concept_name"] == data["nci_concept_name"] assert res["end_date"] is None assert res["status"] == "Draft" assert res["version"] == "0.1" diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms.py index 56514d92..ae0ed50b 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms.py @@ -804,7 +804,7 @@ def test_overriding_odm_item_groups_from_a_specific_odm_form(api_client): data = [ { "uid": "odm_item_group2", - "order_number": 2, + "order_number": 2, # this order number should be overridden by the API to 1, since it's the only form in the request "mandatory": "Yes", "locked": "No", "collection_exception_condition_oid": "collection_exception_condition_oid2", @@ -879,7 +879,7 @@ def test_overriding_odm_item_groups_from_a_specific_odm_form(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { @@ -1045,7 +1045,7 @@ def test_managing_odm_vendors_of_a_specific_odm_form(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { @@ -1155,7 +1155,7 @@ def test_approving_an_odm_form(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { @@ -1265,7 +1265,7 @@ def test_inactivating_a_specific_odm_form(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { @@ -1375,7 +1375,7 @@ def test_reactivating_a_specific_odm_form(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { @@ -1485,7 +1485,7 @@ def test_creating_a_new_odm_form_version(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { @@ -1731,7 +1731,7 @@ def test_updating_an_existing_odm_form_with_relations(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "collection_exception_condition_oid": "collection_exception_condition_oid2", "vendor": { diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups.py index 4c28f783..7fb8d743 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups.py @@ -979,7 +979,7 @@ def test_overriding_odm_items_from_a_specific_odm_item_group(api_client): data = [ { "uid": "odm_item2", - "order_number": 2, + "order_number": 2, # this order number should be overridden by the API to 1, since it's the only form in the request "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", @@ -1087,7 +1087,7 @@ def test_overriding_odm_items_from_a_specific_odm_item_group(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", @@ -1220,7 +1220,7 @@ def test_approving_an_odm_item_group(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", @@ -1353,7 +1353,7 @@ def test_inactivating_a_specific_odm_item_group(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", @@ -1486,7 +1486,7 @@ def test_reactivating_a_specific_odm_item_group(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", @@ -1619,7 +1619,7 @@ def test_creating_a_new_odm_item_group_version(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", @@ -1913,7 +1913,7 @@ def test_updating_an_existing_odm_item_group_with_relations(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "key_sequence": "key_sequence2", "method_oid": "method_oid2", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events.py index 6eb79bfe..8fd45784 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events.py @@ -260,11 +260,11 @@ def test_overriding_odm_forms_from_a_specific_odm_study_event(api_client): data = [ { "uid": "odm_form2", - "order_number": 2, + "order_number": 2, # this order number should be overridden by the API to 1, since it's the only form in the request "mandatory": "Yes", "locked": "Yes", "collection_exception_condition_oid": "None", - } + }, ] response = api_client.post( "odms/study-events/OdmStudyEvent_000001/forms?override=true", json=data @@ -293,7 +293,7 @@ def test_overriding_odm_forms_from_a_specific_odm_study_event(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "locked": "Yes", "collection_exception_condition_oid": "None", @@ -328,7 +328,7 @@ def test_approving_an_odm_study_event(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "locked": "Yes", "collection_exception_condition_oid": "None", @@ -363,7 +363,7 @@ def test_inactivating_a_specific_odm_study_event(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "locked": "Yes", "collection_exception_condition_oid": "None", @@ -398,7 +398,7 @@ def test_reactivating_a_specific_odm_study_event(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "locked": "Yes", "collection_exception_condition_oid": "None", @@ -433,7 +433,7 @@ def test_creating_a_new_odm_study_event_version(api_client): "oid": "oid2", "name": "name2", "version": "1.0", - "order_number": 2, + "order_number": 1, "mandatory": "Yes", "locked": "Yes", "collection_exception_condition_oid": "None", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_study_fields.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_study_fields.py index 7d19c1e1..338d56b6 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_study_fields.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_study_fields.py @@ -2037,7 +2037,7 @@ def test_get_complete_audit_trail_for_study_fields(api_client): assert res[7]["actions"] == [ { "section": "Unknown", - "field": "baseline_as_time_zero", + "field": "soa_show_all_visits_lab_table", "before_value": None, "after_value": {"term_uid": "true", "name": None}, "action": "Create", @@ -2049,9 +2049,9 @@ def test_get_complete_audit_trail_for_study_fields(api_client): assert res[8]["actions"] == [ { "section": "Unknown", - "field": "soa_show_milestones", + "field": "baseline_as_time_zero", "before_value": None, - "after_value": {"term_uid": "false", "name": None}, + "after_value": {"term_uid": "true", "name": None}, "action": "Create", } ] @@ -2061,9 +2061,9 @@ def test_get_complete_audit_trail_for_study_fields(api_client): assert res[9]["actions"] == [ { "section": "Unknown", - "field": "soa_show_epochs", + "field": "soa_show_milestones", "before_value": None, - "after_value": {"term_uid": "true", "name": None}, + "after_value": {"term_uid": "false", "name": None}, "action": "Create", } ] @@ -2073,9 +2073,9 @@ def test_get_complete_audit_trail_for_study_fields(api_client): assert res[10]["actions"] == [ { "section": "Unknown", - "field": "soa_preferred_time_unit", + "field": "soa_show_epochs", "before_value": None, - "after_value": {"term_uid": "UnitDefinition_000003", "name": None}, + "after_value": {"term_uid": "true", "name": None}, "action": "Create", } ] @@ -2085,9 +2085,9 @@ def test_get_complete_audit_trail_for_study_fields(api_client): assert res[11]["actions"] == [ { "section": "Unknown", - "field": "preferred_time_unit", + "field": "soa_preferred_time_unit", "before_value": None, - "after_value": {"term_uid": "UnitDefinition_000002", "name": None}, + "after_value": {"term_uid": "UnitDefinition_000003", "name": None}, "action": "Create", } ] @@ -2095,6 +2095,18 @@ def test_get_complete_audit_trail_for_study_fields(api_client): assert res[12]["author_username"] == "unknown-user@example.com" assert res[12]["date"] assert res[12]["actions"] == [ + { + "section": "Unknown", + "field": "preferred_time_unit", + "before_value": None, + "after_value": {"term_uid": "UnitDefinition_000002", "name": None}, + "action": "Create", + } + ] + assert res[13]["study_uid"] == "Study_000001" + assert res[13]["author_username"] == "unknown-user@example.com" + assert res[13]["date"] + assert res[13]["actions"] == [ { "section": "identification_metadata", "field": "project_number", 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 4fec9953..8a36ffda 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 @@ -5,6 +5,7 @@ # pylint: disable=unused-argument # pylint: disable=redefined-outer-name # pylint: disable=too-many-arguments +# pylint: disable=invalid-name # pytest fixture functions have other fixture functions as arguments, # which pylint interprets as unused arguments diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_study_metadata_listings.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_study_metadata_listings.py index 1c0162c4..de593a6a 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_study_metadata_listings.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_study_metadata_listings.py @@ -763,7 +763,7 @@ def test_study_metadata_listing_api(api_client): def test_study_metadata_listing_with_subpart(api_client): - subpart_acronym = "test" + subpart_acronym = "TEST" # create parent study parent_study = TestUtils.create_study(project_number=project_id) TestUtils.set_study_standard_version(study_uid=parent_study.uid) @@ -819,7 +819,7 @@ def test_study_metadata_listing_with_subpart(api_client): expected_output = { "api_ver": "TBA", - "study_id": f"123-{p_study_number}test", + "study_id": f"123-{p_study_number}{subpart_acronym}", "study_ver": 2.0, "specified_dt": "2099-12-30", "request_dt": "2024-04-05T09:55:55", 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 7a9b46b3..e932e310 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 @@ -4216,7 +4216,6 @@ def test_cross_soa_group_duplicate_study_activity_blocked_on_patch(api_client): assert_response_status_code(response, 201) # Second study activity: subgroup B under a *different* SoA group (Safety) - # Different SoA group → different study_activity_subgroup_uid → invisible to AR validate() response = api_client.post( f"/studies/{test_study.uid}/study-activities", json={ @@ -4229,8 +4228,7 @@ def test_cross_soa_group_duplicate_study_activity_blocked_on_patch(api_client): assert_response_status_code(response, 201) second_study_activity_uid = response.json()["study_activity_uid"] - # Patch second: subgroup B → A. Now both share (activity, subgroup A, group) - # but they remain under separate SoA groups so AR validate() still can't see them. + # Patch second: subgroup B → A. Same groupings but different SoA groups → 409 response = api_client.patch( f"/studies/{test_study.uid}/study-activities/{second_study_activity_uid}", json={ 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 0aca806b..851b39b4 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 @@ -1474,13 +1474,13 @@ def test_sync_to_latest_version_activity_instance(api_client): assert study_activity_instances[0]["keep_old_version"] is False response = api_client.post( - f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/versions", + f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/attributes/versions", ) assert_response_status_code(response, 201) # PATCH underling activity-instance changed_definition = "new activity instance definition for sync test" response = api_client.patch( - f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}", + f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/attributes", json={ "definition": changed_definition, "change_description": "Sync to latest version test", @@ -1489,7 +1489,7 @@ def test_sync_to_latest_version_activity_instance(api_client): assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/approvals", + f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/attributes/approvals", ) assert_response_status_code(response, 201) @@ -1514,14 +1514,14 @@ def test_sync_to_latest_version_activity_instance(api_client): ) response = api_client.post( - f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/versions", + f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/attributes/versions", ) assert_response_status_code(response, 201) # PATCH underling activity-instance - use a modifiable field instead of activity_instance_class_uid # DUE TO THE activity_instance_class_uid is not modifiable after creation updated_name = "Updated activity instance name for sync test" response = api_client.patch( - f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}", + f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/attributes", json={ "name": updated_name, "name_sentence_case": updated_name.lower(), @@ -1531,7 +1531,7 @@ def test_sync_to_latest_version_activity_instance(api_client): assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/approvals", + f"/concepts/activities/activity-instances/{new_test_activity_instance.uid}/attributes/approvals", ) assert_response_status_code(response, 201) @@ -1825,11 +1825,11 @@ def test_study_activity_instances_return_proper_activity_instance_versionsing_da activity_items=[], ) response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance.uid}/versions", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes/versions", ) assert_response_status_code(response, 201) response = api_client.post( - f"/concepts/activities/activity-instances/{activity_instance.uid}/approvals", + f"/concepts/activities/activity-instances/{activity_instance.uid}/attributes/approvals", ) assert_response_status_code(response, 201) # After creating a new draft and immidiately approving it, we'll have two Final (1.0, 2.0) versions linked between single root-value nodes @@ -1975,7 +1975,7 @@ def test_study_activity_instances_review_changes_batch(api_client): ) response = api_client.delete( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" ) assert_response_status_code(response, 200) @@ -2021,19 +2021,19 @@ 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}/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" ) assert_response_status_code(response, 200) # update library activity instance response = api_client.post( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/versions" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/versions" ) assert_response_status_code(response, 201) randomized_activity_name_after_update = "Randomized activity name after update" response = api_client.patch( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}", + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes", json={ "name": randomized_activity_name_after_update, "name_sentence_case": randomized_activity_name_after_update.lower(), @@ -2042,13 +2042,13 @@ def test_study_activity_instances_review_changes_batch(api_client): ) assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/approvals" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/approvals" ) assert_response_status_code(response, 201) # update library activity response = api_client.post( - f"/concepts/activities/activity-instances/{second_randomized_activity_instance.uid}/versions" + f"/concepts/activities/activity-instances/{second_randomized_activity_instance.uid}/attributes/versions" ) assert_response_status_code(response, 201) @@ -2056,7 +2056,7 @@ def test_study_activity_instances_review_changes_batch(api_client): "Second Randomized activity name after update" ) response = api_client.patch( - f"/concepts/activities/activity-instances/{second_randomized_activity_instance.uid}", + f"/concepts/activities/activity-instances/{second_randomized_activity_instance.uid}/attributes", json={ "name": second_randomized_activity_name_after_update, "name_sentence_case": second_randomized_activity_name_after_update.lower(), @@ -2065,7 +2065,7 @@ def test_study_activity_instances_review_changes_batch(api_client): ) assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{second_randomized_activity_instance.uid}/approvals" + f"/concepts/activities/activity-instances/{second_randomized_activity_instance.uid}/attributes/approvals" ) assert_response_status_code(response, 201) @@ -2144,7 +2144,7 @@ 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}/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" ) assert_response_status_code(response, 200) @@ -2177,18 +2177,18 @@ 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}/activations" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/activations" ) assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/versions" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/versions" ) assert_response_status_code(response, 201) updated_name = randomized_activity_instance.name + " updated" response = api_client.patch( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}", + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes", json={ "name": updated_name, "name_sentence_case": updated_name.lower(), @@ -2198,7 +2198,7 @@ def test_study_activity_instances_invalidate_keep_old_version(api_client): assert_response_status_code(response, 200) response = api_client.post( - f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/approvals" + f"/concepts/activities/activity-instances/{randomized_activity_instance.uid}/attributes/approvals" ) assert_response_status_code(response, 201) @@ -2817,3 +2817,273 @@ def test_study_activity_instance_origin_term_not_in_codelist(api_client): res = response.json() assert "was not found in the codelist" in res["message"] TestUtils.delete_study(test_study.uid) + + +# ──────────────────────────────────────────────────────────────────────────── +# Tests for StudyActivityInstance state field +# ──────────────────────────────────────────────────────────────────────────── + + +def test_state_not_applicable_for_non_data_collection_activity(api_client): + """ + Requirement: User must be presented with 'Not applicable' state for every + non-data collection study activity. + """ + test_study = TestUtils.create_study(project_number=project.project_number) + + non_dc_activity_group = TestUtils.create_activity_group(name="NonDC Group") + non_dc_activity_subgroup = TestUtils.create_activity_subgroup(name="NonDC SubGroup") + non_dc_activity = TestUtils.create_activity( + name="Non Data Collection Activity", + activity_subgroups=[non_dc_activity_subgroup.uid], + activity_groups=[non_dc_activity_group.uid], + library_name="Sponsor", + is_data_collected=False, + ) + + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": non_dc_activity.uid, + "activity_subgroup_uid": non_dc_activity_subgroup.uid, + "activity_group_uid": non_dc_activity_group.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + + response = api_client.get( + f"/studies/{test_study.uid}/study-activity-instances", + ) + assert_response_status_code(response, 200) + items = response.json()["items"] + assert len(items) >= 1 + for item in items: + assert item["state"] == StudyActivityInstanceState.NOT_APPLICABLE.value + + TestUtils.delete_study(test_study.uid) + + +def test_state_review_needed_for_default_activity_instance(api_client): + """ + Requirement: User must be presented with 'Review needed' state when + activity instance selected for study activity is default (not mandatory). + """ + test_study = TestUtils.create_study(project_number=project.project_number) + + default_activity_group = TestUtils.create_activity_group(name="Default AI Group") + default_activity_subgroup = TestUtils.create_activity_subgroup( + name="Default AI SubGroup" + ) + default_activity = TestUtils.create_activity( + name="Activity With Default Instance", + activity_subgroups=[default_activity_subgroup.uid], + activity_groups=[default_activity_group.uid], + library_name="Sponsor", + is_data_collected=True, + ) + default_instance_class = TestUtils.create_activity_instance_class( + name="Default Instance Class" + ) + TestUtils.create_activity_instance( + name="Default selected instance", + activity_instance_class_uid=default_instance_class.uid, + name_sentence_case="default selected instance", + topic_code="default_selected_topic", + is_required_for_activity=False, + is_default_selected_for_activity=True, + activities=[default_activity.uid], + activity_subgroups=[default_activity_subgroup.uid], + activity_groups=[default_activity_group.uid], + activity_items=[], + ) + + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": default_activity.uid, + "activity_subgroup_uid": default_activity_subgroup.uid, + "activity_group_uid": default_activity_group.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + + response = api_client.get( + f"/studies/{test_study.uid}/study-activity-instances", + ) + assert_response_status_code(response, 200) + items = response.json()["items"] + assert len(items) == 1 + assert items[0]["state"] == StudyActivityInstanceState.REVIEW_NEEDED.value + assert items[0]["is_reviewed"] is False + + TestUtils.delete_study(test_study.uid) + + +def test_state_review_not_needed_for_mandatory_activity_instance(api_client): + """ + Requirement: User must be presented with 'Review not needed' and checked + Reviewed checkbox when activity instance selected for study activity is mandatory. + """ + test_study = TestUtils.create_study(project_number=project.project_number) + + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": randomized_activity.uid, + "activity_subgroup_uid": randomisation_activity_subgroup.uid, + "activity_group_uid": general_activity_group.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + + response = api_client.get( + f"/studies/{test_study.uid}/study-activity-instances", + ) + assert_response_status_code(response, 200) + items = response.json()["items"] + # The auto-created instance corresponds to randomized_activity_instance which is mandatory + mandatory_items = [ + item + for item in items + if item.get("activity_instance") + and item["activity_instance"]["is_required_for_activity"] + ] + assert len(mandatory_items) >= 1 + for item in mandatory_items: + assert item["state"] == StudyActivityInstanceState.REVIEW_NOT_NEEDED.value + assert item["is_reviewed"] is True + + TestUtils.delete_study(test_study.uid) + + +def test_state_add_instance_when_no_activity_instance_linked(api_client): + """ + Requirement: User must be presented with 'Add instance' and disabled Reviewed + checkbox when study activity is not linked to any activity instance. + """ + test_study = TestUtils.create_study(project_number=project.project_number) + + # Create an activity that has no linked activity instances + orphan_activity_group = TestUtils.create_activity_group(name="Orphan Group") + orphan_activity_subgroup = TestUtils.create_activity_subgroup( + name="Orphan SubGroup" + ) + orphan_activity = TestUtils.create_activity( + name="Activity Without Instances", + activity_subgroups=[orphan_activity_subgroup.uid], + activity_groups=[orphan_activity_group.uid], + library_name="Sponsor", + is_data_collected=True, + ) + + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": orphan_activity.uid, + "activity_subgroup_uid": orphan_activity_subgroup.uid, + "activity_group_uid": orphan_activity_group.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + + response = api_client.get( + f"/studies/{test_study.uid}/study-activity-instances", + ) + assert_response_status_code(response, 200) + items = response.json()["items"] + assert len(items) == 1 + assert items[0]["state"] == StudyActivityInstanceState.ADD_INSTANCE.value + assert items[0]["activity_instance"] is None + assert items[0]["is_reviewed"] is False + + TestUtils.delete_study(test_study.uid) + + +def test_state_remove_instance_when_too_many_instances(api_client): + """ + Requirement: User must be presented with 'Remove instance' and disabled Reviewed + checkbox when study activity has more linked activity instances than allowed + for that study activity (is_multiple_selection_allowed=False with >1 instance). + """ + test_study = TestUtils.create_study(project_number=project.project_number) + + single_select_group = TestUtils.create_activity_group(name="SingleSelect Group") + single_select_subgroup = TestUtils.create_activity_subgroup( + name="SingleSelect SubGroup" + ) + single_select_activity = TestUtils.create_activity( + name="Single Select Activity", + activity_subgroups=[single_select_subgroup.uid], + activity_groups=[single_select_group.uid], + library_name="Sponsor", + is_data_collected=True, + is_multiple_selection_allowed=False, + ) + single_select_instance_class = TestUtils.create_activity_instance_class( + name="SingleSelect Instance Class" + ) + TestUtils.create_activity_instance( + name="SingleSelect required instance", + activity_instance_class_uid=single_select_instance_class.uid, + name_sentence_case="singleselect required instance", + topic_code="single_select_required_topic", + is_required_for_activity=True, + activities=[single_select_activity.uid], + activity_subgroups=[single_select_subgroup.uid], + activity_groups=[single_select_group.uid], + activity_items=[], + ) + extra_instance = TestUtils.create_activity_instance( + name="SingleSelect extra instance", + activity_instance_class_uid=single_select_instance_class.uid, + name_sentence_case="singleselect extra instance", + topic_code="single_select_extra_topic", + is_required_for_activity=False, + activities=[single_select_activity.uid], + activity_subgroups=[single_select_subgroup.uid], + activity_groups=[single_select_group.uid], + activity_items=[], + ) + + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": single_select_activity.uid, + "activity_subgroup_uid": single_select_subgroup.uid, + "activity_group_uid": single_select_group.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + study_activity_uid = response.json()["study_activity_uid"] + + # Auto-creation should have created one instance (the required one). + # Now manually add a second instance to exceed the allowed count. + response = api_client.post( + f"/studies/{test_study.uid}/study-activity-instances/batch", + json=[ + { + "method": "POST", + "content": { + "activity_instance_uid": extra_instance.uid, + "study_activity_uid": study_activity_uid, + }, + } + ], + ) + assert_response_status_code(response, 207) + + response = api_client.get( + f"/studies/{test_study.uid}/study-activity-instances", + ) + assert_response_status_code(response, 200) + items = response.json()["items"] + assert len(items) == 2 + for item in items: + assert item["state"] == StudyActivityInstanceState.REMOVE_INSTANCE.value + + TestUtils.delete_study(test_study.uid) 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 c53747fa..320500fb 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 @@ -5,11 +5,6 @@ from io import BytesIO import docx -import docx.enum.section -import docx.enum.text -import docx.section -import docx.table -import docx.text.paragraph import lxml.etree import openpyxl import pytest @@ -193,13 +188,18 @@ def test_integrity_checks_for_all_studies(api_client): (None, SoALayout.DETAILED), (None, SoALayout.DETAILED), (None, SoALayout.OPERATIONAL), + (None, SoALayout.PROTOCOL), + (None, SoALayout.PROTOCOL_LAB_TABLE), ("day", SoALayout.DETAILED), ("day", SoALayout.DETAILED), ("day", SoALayout.OPERATIONAL), + ("day", SoALayout.PROTOCOL), + ("day", SoALayout.PROTOCOL_LAB_TABLE), ("week", SoALayout.DETAILED), ("week", SoALayout.DETAILED), ("week", SoALayout.OPERATIONAL), - (None, SoALayout.PROTOCOL), + ("week", SoALayout.PROTOCOL), + ("week", SoALayout.PROTOCOL_LAB_TABLE), ], ) def test_flowchart( @@ -346,6 +346,7 @@ def test_flowchart_coordinates(soa_test_data: SoATestData, api_client): (SoALayout.PROTOCOL, "day"), (SoALayout.PROTOCOL, "week"), (SoALayout.PROTOCOL, "week"), + (SoALayout.PROTOCOL_LAB_TABLE, "week"), (SoALayout.DETAILED, "day"), (SoALayout.DETAILED, "week"), (SoALayout.OPERATIONAL, "day"), @@ -368,15 +369,23 @@ def test_flowchart_html( service = StudyFlowchartService() # SoA table for comparison base - soa_table: TableWithFootnotes = service.build_flowchart_table( - study_uid=soa_test_data.study.uid, - study_value_version=None, - layout=layout, - time_unit=time_unit, - ) + if layout == SoALayout.PROTOCOL_LAB_TABLE: + # Lab table uses its own table builder with different filtering and structure + soa_table: TableWithFootnotes = service.get_flowchart_table_lab_table( + study_uid=soa_test_data.study.uid, + study_value_version=None, + time_unit=time_unit, + ) + else: + soa_table: TableWithFootnotes = service.build_flowchart_table( + study_uid=soa_test_data.study.uid, + study_value_version=None, + layout=layout, + time_unit=time_unit, + ) # Layout alterations from get_flowchart_table - if layout == SoALayout.PROTOCOL: + if layout in (SoALayout.PROTOCOL, SoALayout.PROTOCOL_LAB_TABLE): service.propagate_hidden_rows(soa_table.rows) service.remove_hidden_rows(soa_table) @@ -414,7 +423,7 @@ def test_flowchart_html( # Although table_f.table_to_html() has it's unit tests, we also run them on this SoA table # to increase the number of cases and to test on real-world scenarios. - if layout != SoALayout.PROTOCOL: + if layout not in (SoALayout.PROTOCOL, SoALayout.PROTOCOL_LAB_TABLE): # Detailed and Operation SoA show all rows StudyFlowchartService.show_hidden_rows(soa_table.rows) @@ -432,6 +441,9 @@ def test_flowchart_html( (SoALayout.PROTOCOL, "day"), (SoALayout.PROTOCOL, "week"), (SoALayout.PROTOCOL, None), + (SoALayout.PROTOCOL_LAB_TABLE, "day"), + (SoALayout.PROTOCOL_LAB_TABLE, "week"), + (SoALayout.PROTOCOL_LAB_TABLE, None), (SoALayout.DETAILED, "day"), (SoALayout.DETAILED, "week"), (SoALayout.DETAILED, None), @@ -455,23 +467,28 @@ def test_flowchart_docx( service = StudyFlowchartService() # SoA table for comparison base - soa_table: TableWithFootnotes = service.build_flowchart_table( - study_uid=soa_test_data.study.uid, - study_value_version=None, - layout=layout, - time_unit=time_unit, - ) - - # Layout alterations from get_flowchart_table - if layout == SoALayout.PROTOCOL: - service.propagate_hidden_rows(soa_table.rows) - service.remove_hidden_rows(soa_table) - - # Layout alterations from get_study_flowchart_docx - service.add_protocol_section_column(soa_table) - + if layout == SoALayout.PROTOCOL_LAB_TABLE: + # Lab table uses its own table builder with different filtering and structure + soa_table: TableWithFootnotes = service.get_flowchart_table_lab_table( + study_uid=soa_test_data.study.uid, + study_value_version=None, + time_unit=time_unit, + ) else: - service.show_hidden_rows(soa_table.rows) + soa_table: TableWithFootnotes = service.build_flowchart_table( + study_uid=soa_test_data.study.uid, + study_value_version=None, + layout=layout, + time_unit=time_unit, + ) + + # Layout alterations from get_flowchart_table / get_study_flowchart_docx + if layout == SoALayout.PROTOCOL: + service.propagate_hidden_rows(soa_table.rows) + service.remove_hidden_rows(soa_table) + service.add_protocol_section_column(soa_table) + else: + service.show_hidden_rows(soa_table.rows) # Query parameters params = {"layout": layout.value} @@ -517,6 +534,9 @@ def test_flowchart_docx( (SoALayout.PROTOCOL, "day"), (SoALayout.PROTOCOL, "week"), (SoALayout.PROTOCOL, None), + (SoALayout.PROTOCOL_LAB_TABLE, "day"), + (SoALayout.PROTOCOL_LAB_TABLE, "week"), + (SoALayout.PROTOCOL_LAB_TABLE, None), (SoALayout.DETAILED, "day"), (SoALayout.DETAILED, "week"), (SoALayout.DETAILED, None), @@ -575,13 +595,33 @@ def test_flowchart_xlsx( assert len(workbook.worksheets) == 1, "expected exactly 1 worksheet in XLSX file" worksheet = workbook.worksheets[0] - # THEN worksheet has the same number of rows as SoA table xlsx_rows = list(worksheet.rows) - assert len(xlsx_rows) == len(soa_table.rows), "number of rows mismatch" + if layout == SoALayout.PROTOCOL_LAB_TABLE: + # For Lab table layouts: + # only activities from the "Laboratory Assessments" activity group which are assigned to some visits are shown in XLSX. + # With show_all_visits_lab_table=False (default), there is only 1 header row and no visit columns. + expected_num_rows = 1 # starts with 1 to account for header rows in the Lab table layout (show_all_visits_lab_table defaults to False) + for activity_data in soa_test_data.ACTIVITIES.values(): + if ( + activity_data.get("group", "").lower() == "laboratory assessments" + and len(activity_data.get("visits", [])) > 0 + ): + expected_num_rows += 1 + + assert ( + len(xlsx_rows) == expected_num_rows + ), "number of rows mismatch for Lab table layout" + + else: + + # For non-Lab table layouts, all rows are shown in XLSX, so we compare with all rows in the SoA table + assert len(xlsx_rows) == len(soa_table.rows), "number of rows mismatch" - # THEN worksheet has the same number of columns as SoA table - num_xlsx_cols = sum(1 for _ in worksheet.columns) - assert num_xlsx_cols == len(soa_table.rows[-1].cells), "number of columns mismatch" + # THEN worksheet has the same number of columns as SoA table + num_xlsx_cols = sum(1 for _ in worksheet.columns) + assert num_xlsx_cols == len( + soa_table.rows[-1].cells + ), "number of columns mismatch" @pytest.mark.parametrize( @@ -688,50 +728,50 @@ def soa_test_data_for_exports( "/studies/{study_uid}/detailed-soa-exports", "text/csv", DETAILED_SOA_EXPORT_COLUMN_HEADERS, - [False, False], + [False, False, True], ), ( "/studies/{study_uid}/detailed-soa-exports", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", DETAILED_SOA_EXPORT_COLUMN_HEADERS, - [False, True], + [False, True, False], ), ( "/studies/{study_uid}/detailed-soa-exports", "text/xml", DETAILED_SOA_EXPORT_COLUMN_HEADERS, - [True, False], + [True, False, False], ), ( "/studies/{study_uid}/detailed-soa-exports", "application/json", DETAILED_SOA_JSON_EXPORT_COLUMN_HEADERS, - [True, True], + [True, True, False], ), ( "/studies/{study_uid}/protocol-soa-exports", "text/csv", PROTOCOL_SOA_EXPORT_COLUMN_HEADERS, - [True, True], + [True, True, False], ), ( "/studies/{study_uid}/protocol-soa-exports", "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", PROTOCOL_SOA_EXPORT_COLUMN_HEADERS, - [True, False], + [True, False, False], ), ( "/studies/{study_uid}/protocol-soa-exports", "text/xml", PROTOCOL_SOA_EXPORT_COLUMN_HEADERS, - [False, True], + [False, True, False], ), ( "/studies/{study_uid}/protocol-soa-exports", "application/json", # for JSON output, the exported properties are not filtered DETAILED_SOA_JSON_EXPORT_COLUMN_HEADERS, - [False, False], + [False, False, False], ), ( "/studies/{study_uid}/operational-soa-exports", @@ -770,15 +810,20 @@ def test_soa_exports( """Test the export endpoints return the expected data format""" expected_column_headers = column_headers.copy() if soa_preferences: - show_epochs, show_milestones = soa_preferences + show_epochs, show_milestones, show_all_visits_lab_table = soa_preferences response = api_client.patch( f"/studies/{soa_test_data_for_exports.study.uid}/soa-preferences", - json={"show_epochs": show_epochs, "show_milestones": show_milestones}, + json={ + "show_epochs": show_epochs, + "show_milestones": show_milestones, + "show_all_visits_lab_table": show_all_visits_lab_table, + }, ) assert_response_status_code(response, 200) res = response.json() assert res["show_epochs"] == show_epochs assert res["show_milestones"] == show_milestones + assert res["show_all_visits_lab_table"] == show_all_visits_lab_table if show_epochs: expected_column_headers.append("epoch") if show_milestones: @@ -859,6 +904,140 @@ def test_soa_exports( assert num_rows > 1, f"worksheet 0 has only {num_rows} rows" +@pytest.mark.parametrize("data_format", ["text/csv", "application/json"]) +def test_protocol_soa_exports_default_filters_by_protocol_flowchart( + api_client: TestClient, + soa_test_data_for_exports: SoATestData, + data_format: str, +): + """With no parameters, protocol-soa-exports returns the full Protocol SoA export""" + study_uid = soa_test_data_for_exports.study.uid + + response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + headers={"Accept": data_format}, + ) + + assert_response_status_code(response, 200) + assert_response_content_type(response, data_format) + + if data_format == "application/json": + data = response.json() + assert isinstance(data, list) + # THEN returns data (protocol flowchart filter is active by default) + assert len(data) > 0, "expected non-empty results for protocol SoA export" + + +@pytest.mark.parametrize("data_format", ["text/csv", "application/json"]) +def test_protocol_soa_exports_lab_table_filters_laboratory_assessments( + api_client: TestClient, + soa_test_data_for_exports: SoATestData, + data_format: str, +): + """protocol_lab_table=true restricts results to Laboratory Assessments group only""" + study_uid = soa_test_data_for_exports.study.uid + + # Get default protocol export (all activities in protocol flowchart) + default_response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + headers={"Accept": data_format}, + ) + # Get Lab table export + lab_table_response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + params={"protocol_lab_table": "true"}, + headers={"Accept": data_format}, + ) + + assert_response_status_code(default_response, 200) + assert_response_status_code(lab_table_response, 200) + + if data_format == "application/json": + default_data = default_response.json() + lab_table_data = lab_table_response.json() + assert ( + len(default_data) > 0 + ), "expected non-empty results for default protocol SoA export" + assert ( + len(lab_table_data) > 0 + ), "expected non-empty results for Lab table protocol SoA export" + + # THEN all Lab table records belong to the Laboratory Assessments group + for record in lab_table_data: + assert ( + record.get("activity_group", "").lower() == "laboratory assessments" + ), f"Unexpected activity_group in Lab table export: {record.get('activity_group')!r}" + + +def test_protocol_soa_exports_lab_table_and_default_are_mutually_exclusive( + api_client: TestClient, + soa_test_data_for_exports: SoATestData, +): + """protocol_lab_table=false (default) and protocol_lab_table=true return disjoint activity sets""" + study_uid = soa_test_data_for_exports.study.uid + + default_response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + params={"protocol_lab_table": "false"}, + headers={"Accept": "application/json"}, + ) + lab_table_response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + params={"protocol_lab_table": "true"}, + headers={"Accept": "application/json"}, + ) + + assert_response_status_code(default_response, 200) + assert_response_status_code(lab_table_response, 200) + + default_groups = {r["activity_group"] for r in default_response.json()} + lab_table_groups = {r["activity_group"] for r in lab_table_response.json()} + + # THEN default export does NOT contain Laboratory Assessments + # (because protocol_flowchart filter applies, and Lab table filter does not) + assert ( + "Laboratory Assessments" not in default_groups or len(default_groups) > 1 + ), "Default export should not be restricted to Laboratory Assessments only" + + # THEN Lab table export ONLY contains Laboratory Assessments + assert lab_table_groups <= { + "Laboratory Assessments" + }, f"Lab table export should only contain Laboratory Assessments, got: {lab_table_groups}" + + +def test_protocol_soa_exports_column_headers_consistent_for_lab_table( + api_client: TestClient, + soa_test_data_for_exports: SoATestData, +): + """Lab table export returns the same column structure as regular protocol export""" + study_uid = soa_test_data_for_exports.study.uid + + default_response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + headers={"Accept": "text/csv"}, + ) + lab_table_response = api_client.get( + f"/studies/{study_uid}/protocol-soa-exports", + params={"protocol_lab_table": "true"}, + headers={"Accept": "text/csv"}, + ) + + assert_response_status_code(default_response, 200) + assert_response_status_code(lab_table_response, 200) + + def _csv_headers(response): + reader = csv.reader(response.iter_lines(), dialect=csv.excel) + return next(reader, []) + + default_headers = _csv_headers(default_response) + lab_table_headers = _csv_headers(lab_table_response) + + # THEN both exports have identical column headers + assert ( + default_headers == lab_table_headers + ), f"Column headers differ: default={default_headers}, lab_table={lab_table_headers}" + + def test_get_study_flowchart_versioned(api_client, temp_database_populated): """Test study flowchart endpoint with versioning for Protocol SoA @@ -1273,3 +1452,198 @@ def test_detailed_soa_xlsx( for cell in row[num_header_cols:] ) assert num_checkmarks == len(soa_test_data.study_activity_schedules) + + +# Tests for Protocol Lab table functionality + + +def test_study_flowchart_protocol_lab_table_layout( + soa_test_data: SoATestData, + api_client: TestClient, + temp_database_populated: TempDatabasePopulated, +): + """Test Protocol Lab table layout returns correct HTML structure""" + + study_uid = soa_test_data.study.uid + + response = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params={"layout": "protocol_lab_table", "time_unit": "week"}, + ) + + assert response.status_code == 200 + assert response.headers["content-type"] == "text/html; charset=utf-8" + + # Parse HTML to validate structure + soup = BeautifulSoup(response.content, "html.parser") + + # THEN should contain a table + table = soup.find("table") + assert table is not None, "HTML should contain a table" + + # THEN should have header structure for Lab table + # With show_all_visits_lab_table=False (default), there is only 1 header row and 2 columns (no visit columns). + header_rows = table.find("thead").find_all("tr") + assert len(header_rows) >= 1, "Should have at least 1 header row" + + # THEN first header row should have correct structure + first_row_cells = header_rows[0].find_all(["th", "td"]) + assert ( + len(first_row_cells) >= 2 + ), "Should have at least 2 columns (subgroup + activity)" + + +def test_study_flowchart_protocol_lab_table_filters_activities( + soa_test_data: SoATestData, + api_client: TestClient, + temp_database_populated: TempDatabasePopulated, +): + """Test that Protocol Lab table filters activities correctly""" + study_uid = soa_test_data.study.uid + + # Get regular detailed layout for comparison + detailed_response = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params={"layout": "detailed", "time_unit": "week"}, + ) + + # Get Protocol Lab table layout + lab_table_response = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params={"layout": "protocol_lab_table", "time_unit": "week"}, + ) + + assert detailed_response.status_code == 200 + assert lab_table_response.status_code == 200 + + detailed_soup = BeautifulSoup(detailed_response.content, "html.parser") + lab_table_soup = BeautifulSoup(lab_table_response.content, "html.parser") + + # Count activity rows (non-header rows in tbody) + detailed_activity_rows = len(detailed_soup.find("tbody").find_all("tr")) + lab_table_activity_rows = len(lab_table_soup.find("tbody").find_all("tr")) + + # THEN Protocol Lab table should have fewer or equal activity rows + # (since it filters to only Laboratory Assessments) + assert lab_table_activity_rows <= detailed_activity_rows + + +@pytest.mark.parametrize( + "layout, time_unit", + [ + (SoALayout.PROTOCOL, "day"), + (SoALayout.PROTOCOL, "week"), + (SoALayout.PROTOCOL, None), + (SoALayout.PROTOCOL_LAB_TABLE, "day"), + (SoALayout.PROTOCOL_LAB_TABLE, "week"), + (SoALayout.PROTOCOL_LAB_TABLE, None), + (SoALayout.DETAILED, "day"), + (SoALayout.DETAILED, "week"), + (SoALayout.DETAILED, None), + (SoALayout.OPERATIONAL, "day"), + (SoALayout.OPERATIONAL, "week"), + (SoALayout.OPERATIONAL, None), + ], +) +def test_study_flowchart_include_uids_parameter_html( + soa_test_data: SoATestData, + api_client: TestClient, + temp_database_populated: TempDatabasePopulated, + layout: SoALayout, + time_unit: str | None, +): + """Test include_uids parameter adds data attributes to HTML""" + + study_uid = soa_test_data.study.uid + + params = {"layout": layout.value} + if time_unit is not None: + params["time_unit"] = time_unit + + # Test without include_uids (default) + response_without_uids = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params=params, + ) + + # Test with include_uids=true + response_with_uids = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params={**params, "include_uids": "true"}, + ) + + assert response_without_uids.status_code == 200 + assert response_with_uids.status_code == 200 + + soup_without = BeautifulSoup(response_without_uids.content, "html.parser") + soup_with = BeautifulSoup(response_with_uids.content, "html.parser") + + # Count cells with object-* attributes + cells_without_attrs = soup_without.find_all( + lambda tag: tag.name in ("th", "td") + and any(k.startswith("object-") for k in tag.attrs), + ) + cells_with_attrs = soup_with.find_all( + lambda tag: tag.name in ("th", "td") + and any(k.startswith("object-") for k in tag.attrs), + ) + + # THEN default response should not have UID attributes + assert ( + len(cells_without_attrs) == 0 + ), "Default response should not include UID attributes" + + # THEN response with include_uids should have UID attributes + assert ( + len(cells_with_attrs) > 0 + ), "Response with include_uids should have UID attributes" + + +def test_study_flowchart_include_uids_with_protocol_lab_table_html( + soa_test_data: SoATestData, + api_client: TestClient, + temp_database_populated: TempDatabasePopulated, +): + """Test include_uids parameter works with Protocol Lab table layout""" + + study_uid = soa_test_data.study.uid + + response = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params={ + "layout": "protocol_lab_table", + "time_unit": "week", + "include_uids": "true", + }, + ) + + assert response.status_code == 200 + + soup = BeautifulSoup(response.content, "html.parser") + + # THEN should have cells with UID attributes + cells_with_uids = soup.find_all( + lambda tag: tag.name in ("th", "td") + and any(k.startswith("object-uid") for k in tag.attrs), + ) + + # Should have at least some cells with UIDs (visits, activities, etc.) + assert len(cells_with_uids) > 0, "Should have cells with UID attributes" + + +def test_study_flowchart_invalid_layout_parameter( + soa_test_data: SoATestData, + api_client: TestClient, + temp_database_populated: TempDatabasePopulated, +): + """Test that invalid layout parameter returns error""" + + study_uid = soa_test_data.study.uid + + response = api_client.get( + f"/studies/{study_uid}/flowchart.html", + params={"layout": "invalid-layout", "time_unit": "week"}, + ) + + # Should return validation error + assert response.status_code == 400 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 b209e9c9..a0fe33dd 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 @@ -815,7 +815,7 @@ def test_create_study_subpart(api_client): response = api_client.post( "/studies", json={ - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", "description": "desc", "study_parent_part_uid": study.uid, }, @@ -865,12 +865,12 @@ def test_create_study_subpart(api_client): "study_number": study.current_metadata.identification_metadata.study_number, "subpart_id": "a", "study_acronym": "new acronym", - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", "project_number": "123", "project_name": "Project ABC", "description": "desc", "clinical_programme_name": "CP", - "study_id": f"{study.current_metadata.identification_metadata.study_id}-a", + "study_id": f"{study.current_metadata.identification_metadata.study_id}-SUB1", "registry_identifiers": { "ct_gov_id": None, "ct_gov_id_null_value_code": None, @@ -957,12 +957,12 @@ def test_create_study_subpart(api_client): "study_number": study.current_metadata.identification_metadata.study_number, "subpart_id": "a", "study_acronym": "new acronym", - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", "project_number": "123", "project_name": "Project ABC", "description": "desc", "clinical_programme_name": "CP", - "study_id": f"{study.current_metadata.identification_metadata.study_id}-a", + "study_id": f"{study.current_metadata.identification_metadata.study_id}-SUB1", "registry_identifiers": { "ct_gov_id": None, "ct_gov_id_null_value_code": None, @@ -1027,7 +1027,7 @@ def test_use_an_already_existing_study_as_a_study_subpart(api_client): "current_metadata": { "identification_metadata": { "study_acronym": "something", - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", } }, }, @@ -1078,11 +1078,11 @@ def test_use_an_already_existing_study_as_a_study_subpart(api_client): "subpart_id": "a", "project_number": "123", "study_acronym": parent_study.current_metadata.identification_metadata.study_acronym, - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", "project_name": new_study.current_metadata.identification_metadata.project_name, "description": new_study.current_metadata.identification_metadata.description, "clinical_programme_name": "CP", - "study_id": f"{parent_study.current_metadata.identification_metadata.study_id}-a", + "study_id": f"{parent_study.current_metadata.identification_metadata.study_id}-SUB1", "registry_identifiers": { "ct_gov_id": None, "ct_gov_id_null_value_code": None, @@ -1183,11 +1183,11 @@ def test_use_an_already_existing_study_as_a_study_subpart(api_client): "subpart_id": "a", "project_number": "123", "study_acronym": parent_study.current_metadata.identification_metadata.study_acronym, - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", "project_name": new_study.current_metadata.identification_metadata.project_name, "description": new_study.current_metadata.identification_metadata.description, "clinical_programme_name": "CP", - "study_id": f"{parent_study.current_metadata.identification_metadata.study_id}-a", + "study_id": f"{parent_study.current_metadata.identification_metadata.study_id}-SUB1", "registry_identifiers": { "ct_gov_id": None, "ct_gov_id_null_value_code": None, @@ -1586,7 +1586,7 @@ def test_remove_study_subpart_from_parent_part(api_client): "study_parent_part_uid": parent_part.uid, "current_metadata": { "identification_metadata": { - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", } }, }, @@ -1637,11 +1637,11 @@ def test_remove_study_subpart_from_parent_part(api_client): "subpart_id": "a", "project_number": "123", "study_acronym": parent_part.current_metadata.identification_metadata.study_acronym, - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", "project_name": new_study.current_metadata.identification_metadata.project_name, "description": None, "clinical_programme_name": "CP", - "study_id": f"{parent_part.current_metadata.identification_metadata.study_id}-a", + "study_id": f"{parent_part.current_metadata.identification_metadata.study_id}-SUB1", "registry_identifiers": { "ct_gov_id": None, "ct_gov_id_null_value_code": None, @@ -2257,7 +2257,7 @@ def test_cannot_remove_study_subpart_from_parent_part_and_provide_an_existing_st "study_parent_part_uid": parent_part.uid, "current_metadata": { "identification_metadata": { - "study_subpart_acronym": "sub something", + "study_subpart_acronym": "SUB1", } }, }, @@ -3006,6 +3006,7 @@ def test_get_studies_list(api_client): "uid", "id", "acronym", + "subpart_acronym", ] STUDY_MINIMAL_FIELDS_NOT_NULL = [ "uid", @@ -3013,6 +3014,7 @@ def test_get_studies_list(api_client): STUDY_SIMPLE_FIELDS = [ "uid", "id", + "main_id", "acronym", "number", "title", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_study_definition_repository.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_study_definition_repository.py index d6d62984..42f24c5c 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_study_definition_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_study_definition_repository.py @@ -1065,7 +1065,7 @@ def test__get_study_id__with_missing_study_number__returns_none(self): assert study_id is None def test__get_study_id__with_subpart__returns_study_id_with_subpart(self): - """Test that get_study_id returns study_id including subpart_id when present""" + """Test that get_study_id returns study_id including study_subpart_acronym when present""" # given with db.transaction: repo = StudyDefinitionRepositoryImpl(current_function_name()) @@ -1080,21 +1080,21 @@ def test__get_study_id__with_subpart__returns_study_id_with_subpart(self): repo.save(created_study) repo.close() - # Manually add subpart_id to the study - subpart_id = "SP1" + # Manually add study_subpart_acronym to the study + study_subpart_acronym = "SUB1" db.cypher_query( """ MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) - SET sv.subpart_id = $subpart_id + SET sv.study_subpart_acronym = $study_subpart_acronym """, - {"uid": created_study.uid, "subpart_id": subpart_id}, + {"uid": created_study.uid, "study_subpart_acronym": study_subpart_acronym}, ) # when study_id = StudyDefinitionRepositoryImpl.get_study_id(created_study.uid) # then - expected_id = f"{created_study.current_metadata.id_metadata.study_id_prefix}-{created_study.current_metadata.id_metadata.study_number}" + expected_id = f"{created_study.current_metadata.id_metadata.study_id_prefix}-{created_study.current_metadata.id_metadata.study_number}-{study_subpart_acronym}" assert study_id == expected_id def test__get_study_id__after_release__returns_study_id(self): @@ -1138,6 +1138,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, ), ( # 1 @@ -1146,6 +1147,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": True, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, ), ( # 2 @@ -1156,6 +1158,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": False, "soa_show_milestones": True, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, ), ( # 3 @@ -1164,6 +1167,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, ), ( # 4 @@ -1174,6 +1178,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": False, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, ), ( # 5 @@ -1182,6 +1187,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": True, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, ), ( # 6 @@ -1190,6 +1196,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, ), ( # 7 @@ -1200,6 +1207,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, ), ( # 8 @@ -1208,6 +1216,7 @@ def test__get_study_id__after_release__returns_study_id(self): "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, ), ), @@ -1222,9 +1231,9 @@ def test_post_soa_preferences( study = TestUtils.create_study(project_number=tst_project.project_number) - # should have two StudySoaPreferencesInput created at Study creation + # should have four StudySoaPreferencesInput created at Study creation nodes = repo.get_soa_preferences(study.uid) - assert len(nodes) == 3 + assert len(nodes) == 4 unlink_study_soa_properties(study.uid, repo) @@ -1245,7 +1254,7 @@ def test_post_soa_preferences( "expected_num_actions", ), ( - (None, StudySoaPreferencesInput(), {}, 3), # 0 + (None, StudySoaPreferencesInput(), {}, 4), # 0 ( # 1 StudySoaPreferencesInput(show_epochs=False, show_milestones=True), StudySoaPreferencesInput(), @@ -1253,8 +1262,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": True, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 2 StudySoaPreferencesInput( @@ -1265,8 +1275,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 3 StudySoaPreferencesInput( @@ -1277,8 +1288,9 @@ def test_post_soa_preferences( "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 4 StudySoaPreferencesInput( @@ -1289,8 +1301,9 @@ def test_post_soa_preferences( "soa_show_epochs": True, "soa_show_milestones": True, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 5 StudySoaPreferencesInput(), @@ -1299,8 +1312,9 @@ def test_post_soa_preferences( "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 6 StudySoaPreferencesInput(show_milestones=False), @@ -1309,8 +1323,9 @@ def test_post_soa_preferences( "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 7 StudySoaPreferencesInput(show_milestones=True, show_epochs=False), @@ -1319,8 +1334,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": True, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 8 StudySoaPreferencesInput(show_epochs=True), @@ -1329,8 +1345,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 7, + 9, ), ( # 9 StudySoaPreferencesInput(show_epochs=True), @@ -1339,8 +1356,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 7, + 9, ), ( # 10 StudySoaPreferencesInput(show_milestones=True, show_epochs=False), @@ -1349,8 +1367,9 @@ def test_post_soa_preferences( "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 8, + 10, ), ( # 11 StudySoaPreferencesInput( @@ -1361,8 +1380,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": True, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, - 6, + 8, ), ( # 12 StudySoaPreferencesInput(show_epochs=True, baseline_as_time_zero=False), @@ -1371,8 +1391,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 7, + 9, ), ( # 13 StudySoaPreferencesInput(show_epochs=True, baseline_as_time_zero=True), @@ -1381,8 +1402,9 @@ def test_post_soa_preferences( "soa_show_epochs": False, "soa_show_milestones": False, "baseline_as_time_zero": False, + "soa_show_all_visits_lab_table": False, }, - 8, + 10, ), ( # 14 StudySoaPreferencesInput(show_milestones=True, show_epochs=False), @@ -1393,8 +1415,9 @@ def test_post_soa_preferences( "soa_show_epochs": True, "soa_show_milestones": False, "baseline_as_time_zero": True, + "soa_show_all_visits_lab_table": False, }, - 9, + 11, ), ), ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_studies.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_studies.py index 3754cc6d..2a4a3983 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_studies.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_studies.py @@ -285,7 +285,7 @@ def test_get_study_id__for_subpart__returns_study_id( study_id = study_service.get_study_id(subpart_study.uid) # THEN - expected_id = f"{tst_project.project_number}-{study_number}" + expected_id = f"{tst_project.project_number}-{study_number}-SUB1" assert study_id == expected_id diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_flowchart.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_flowchart.py index a5544121..2a0308b3 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_flowchart.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_flowchart.py @@ -1830,3 +1830,256 @@ def _to_list_of_dicts(items: Sequence[pydantic.BaseModel]) -> list[dict[str, Any ) for item in items ] + + +# Tests for Protocol Lab table functionality + + +def test_get_flowchart_table_lab_table_integration( + soa_test_data: SoATestData, +): + """Integration test for get_flowchart_table_lab_table with real database""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + table = service.get_flowchart_table_lab_table( + study_uid=study_uid, study_value_version=None, time_unit="week" + ) + + # THEN should return a valid table + assert isinstance(table, TableWithFootnotes) + + # THEN should have correct structure for Lab table + assert table.num_header_cols == 2 # Subgroup + Activity columns + + # THEN should have header rows + assert table.num_header_rows > 0 + + # THEN should have at least header rows + assert len(table.rows) >= table.num_header_rows + + +def test_get_flowchart_table_lab_table_filters_laboratory_assessments( + soa_test_data: SoATestData, +): + """Test that Protocol Lab table filters to Laboratory Assessments only""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + # Get regular flowchart for comparison + regular_table = service.get_flowchart_table( + study_uid=study_uid, + study_value_version=None, + layout=SoALayout.DETAILED, + time_unit="week", + ) + + # Get Lab table table + lab_table = service.get_flowchart_table_lab_table( + study_uid=study_uid, study_value_version=None, time_unit="week" + ) + + # Count activity rows (excluding headers) + regular_activity_rows = len(regular_table.rows) - regular_table.num_header_rows + lab_table_activity_rows = len(lab_table.rows) - lab_table.num_header_rows + + # THEN Lab table should have fewer or equal activities (filtered subset) + assert lab_table_activity_rows <= regular_activity_rows + + # THEN all lab table visits should also be present in the regular table + def _visit_uids_from_header(table): + uids = set() + for row in table.rows[: table.num_header_rows]: + for cell in row.cells: + if cell.refs: + for ref in cell.refs: + if ref.type == SoAItemType.STUDY_VISIT.value: + uids.add(ref.uid) + return uids + + regular_visit_uids = _visit_uids_from_header(regular_table) + lab_table_visit_uids = _visit_uids_from_header(lab_table) + + assert lab_table_visit_uids.issubset( + regular_visit_uids + ), f"Lab table visits {lab_table_visit_uids - regular_visit_uids} not found in regular table" + + +def test_get_study_flowchart_html_with_protocol_lab_table_layout( + soa_test_data: SoATestData, +): + """Test HTML generation for Protocol Lab table layout""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + html = service.get_study_flowchart_html( + study_uid=study_uid, + study_value_version=None, + layout=SoALayout.PROTOCOL_LAB_TABLE, + time_unit="week", + ) + + # THEN should return valid HTML + assert isinstance(html, str) + assert len(html) > 0 + assert "" in html + assert "
" in html + + +def test_get_study_flowchart_html_with_include_uids( + soa_test_data: SoATestData, +): + """Test HTML generation with include_uids parameter""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + # Get HTML without UIDs + html_without_uids = service.get_study_flowchart_html( + study_uid=study_uid, + study_value_version=None, + layout=SoALayout.PROTOCOL, + time_unit="week", + include_uids=False, + ) + + # Get HTML with UIDs + html_with_uids = service.get_study_flowchart_html( + study_uid=study_uid, + study_value_version=None, + layout=SoALayout.PROTOCOL, + time_unit="week", + include_uids=True, + ) + + # THEN both should be valid HTML + assert isinstance(html_without_uids, str) + assert isinstance(html_with_uids, str) + assert "" in html_without_uids + assert "
" in html_with_uids + + # THEN HTML with UIDs should contain object-uid attributes + assert "object-uid" in html_with_uids + + # THEN HTML without UIDs should not contain object-uid attributes + assert "object-uid" not in html_without_uids + + +def test_protocol_lab_table_with_different_time_units( + soa_test_data: SoATestData, +): + """Test Protocol Lab table works with different time units""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + for time_unit in ["day", "week"]: + table = service.get_flowchart_table_lab_table( + study_uid=study_uid, study_value_version=None, time_unit=time_unit + ) + + # THEN should return valid table for both time units + assert isinstance(table, TableWithFootnotes) + assert table.num_header_cols == 2 + assert table.num_header_rows > 0 + + +def test_footnote_filtering_in_lab_table( + soa_test_data: SoATestData, +): + """Test that footnotes are properly filtered for visible rows in Lab table""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + table = service.get_flowchart_table_lab_table( + study_uid=study_uid, study_value_version=None, time_unit="week" + ) + + # THEN footnotes should only reference items that appear in visible rows + if table.footnotes: + # Get all referenced UIDs from visible rows + visible_rows = [row for row in table.rows if not row.hide] + referenced_uids = set() + for row in visible_rows: + for cell in row.cells: + if cell.refs: + for ref in cell.refs: + referenced_uids.add(ref.uid) + + # Check that all footnotes reference items that are in visible rows + for footnote in table.footnotes.values(): + # Note: This is a basic check - actual footnote filtering logic may be more complex + assert hasattr(footnote, "uid"), "Footnote should have uid attribute" + + +@pytest.mark.parametrize( + "layout", [SoALayout.PROTOCOL_LAB_TABLE, SoALayout.PROTOCOL, SoALayout.DETAILED] +) +def test_include_uids_parameter_across_layouts( + soa_test_data: SoATestData, layout: SoALayout +): + """Test include_uids parameter works across different layouts""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + html = service.get_study_flowchart_html( + study_uid=study_uid, + study_value_version=None, + layout=layout, + time_unit="week", + include_uids=True, + ) + + # THEN all layouts should support include_uids + assert isinstance(html, str) + assert len(html) > 0 + + # THEN HTML should contain UID attributes when include_uids is True + # (may vary based on layout and available data) + if "object-uid" in html: + # If UIDs are present, verify they follow the expected format + assert "object-type" in html, "Should also have object-type attributes" + + +def test_hide_rows_without_checkmarks_integration( + soa_test_data: SoATestData, +): + """Integration test for hiding rows without checkmarks in Lab table""" + + study_uid = soa_test_data.study.uid + service = StudyFlowchartService() + + table = service.get_flowchart_table_lab_table( + study_uid=study_uid, study_value_version=None, time_unit="week" + ) + + # Count visible activity rows + activity_rows = table.rows[table.num_header_rows :] + visible_activity_rows = [row for row in activity_rows if not row.hide] + + # THEN should have some activity rows (unless no Laboratory Assessments activities exist) + # Note: This may be 0 if test data doesn't have Laboratory Assessments activities + assert len(activity_rows) >= 0 + + # THEN if there are visible activity rows with visit columns, they should have checkmarks + # Note: when show_all_visits_lab_table is False, visit columns are stripped from the table, + # so we can only verify checkmarks when visit columns are present. + for row in visible_activity_rows: + # Check if row has checkmarks in visit columns (skip first 2 columns: subgroup + activity) + visit_cells = row.cells[2:] # Skip header columns + if not visit_cells: + # Visit columns were stripped (show_all_visits_lab_table=False), skip checkmark check + continue + has_checkmark = any(cell.text == "X" for cell in visit_cells) + + # If the row is visible, it should either have checkmarks or be a header/grouping row + if row.cells[0].text or row.cells[1].text: # Has content in header columns + # This is an activity row, so if it's visible, it should have checkmarks + assert ( + has_checkmark + ), f"Visible activity row should have checkmarks: {row.cells[:5]}" # Show first few cells for debugging diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_soa.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_soa.py index cc414036..a3cf6187 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_soa.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_soa.py @@ -642,9 +642,11 @@ def __init__(self, project: Project): self.soa_footnotes = self.create_soa_footnotes(self.FOOTNOTES) - # Patch SoA Preferences as tests do not yet support baseline_as_time_zero + # Patch SoA Preferences to keep baseline and lab table visit structure deterministic in tests. self.soa_preferences = TestUtils.patch_soa_preferences( - self.study.uid, baseline_as_time_zero=False + self.study.uid, + baseline_as_time_zero=False, + show_all_visits_lab_table=False, ) def create_codelist_with_terms( 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 40999fff..c30b52cb 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 @@ -361,6 +361,7 @@ ActivityGroupService, ) from clinical_mdr_api.services.concepts.activities.activity_instance_service import ( + ActivityInstanceGroupingsService, ActivityInstanceService, ) from clinical_mdr_api.services.concepts.activities.activity_service import ( @@ -778,7 +779,7 @@ def verify_exported_data_format( @classmethod def random_str(cls, length: int = 8, prefix: str = ""): """returns a random numerical string of `length` with optional string prefix (length excludes prefix)""" - return prefix + str(randint(1, 10**length - 1)) + return prefix + str(randint(0, 10**length - 1)).zfill(length) @classmethod def random_if_none(cls, val, length: int = 10, prefix: str = ""): @@ -1735,9 +1736,12 @@ def create_activity_instance( concept_input=activity_instance_input, preview=preview ) if approve and not preview: + groupings_service = ActivityInstanceGroupingsService() service.approve(result.uid) + groupings_service.approve(result.uid) if retire_after_approve: service.inactivate_final(result.uid) + groupings_service.inactivate_final(result.uid) return result @classmethod @@ -1865,6 +1869,8 @@ def create_activity_subgroup( definition: str | None = None, abbreviation: str | None = None, library_name: str = SPONSOR_LIBRARY_NAME, + nci_concept_id: str | None = None, + nci_concept_name: str | None = None, approve: bool = True, ) -> ActivitySubGroup: service: ActivitySubGroupService = ActivitySubGroupService() @@ -1875,6 +1881,8 @@ def create_activity_subgroup( definition=definition, abbreviation=abbreviation, library_name=library_name, + nci_concept_id=nci_concept_id, + nci_concept_name=nci_concept_name, ) ) result: ActivitySubGroup = service.create( # type: ignore[assignment] @@ -1892,6 +1900,8 @@ def create_activity_group( definition: str | None = None, abbreviation: str | None = None, library_name: str = SPONSOR_LIBRARY_NAME, + nci_concept_id: str | None = None, + nci_concept_name: str | None = None, approve: bool = True, ) -> ActivityGroup: service: ActivityGroupService = ActivityGroupService() @@ -1902,6 +1912,8 @@ def create_activity_group( definition=definition, abbreviation=abbreviation, library_name=library_name, + nci_concept_id=nci_concept_id, + nci_concept_name=nci_concept_name, ) ) result: ActivityGroup = service.create( # type: ignore[assignment] @@ -2697,7 +2709,9 @@ def create_study( ) else: payload = StudySubpartCreateInput( # type: ignore[assignment] - study_subpart_acronym=cls.random_if_none(subpart_acronym, prefix="st-"), + study_subpart_acronym=cls.random_if_none( + subpart_acronym, length=6, prefix="SUB" + ), description=cls.random_if_none(description), study_parent_part_uid=study_parent_part_uid, ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity.py index 7b0fb90b..6f15fb44 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/activity_aggregates/test_activity.py @@ -55,7 +55,7 @@ def create_random_activity_ar( library_name=library, is_editable=is_editable ), author_id=AUTHOR_ID, - concept_exists_by_library_and_name_callback=lambda _l, _c: False, + concept_exists_by_library_and_name_callback=lambda _l, _c, _g: False, activity_subgroup_exists=lambda _: True, activity_group_exists=lambda _: True, ) @@ -89,7 +89,7 @@ def test__edit_draft_version__version_created(self): author_id=AUTHOR_ID, change_description="Test", concept_vo=activity_vo, - concept_exists_by_library_and_name_callback=lambda _l, _c: False, + concept_exists_by_library_and_name_callback=lambda _l, _c, _g: False, activity_subgroup_exists=lambda _: True, activity_group_exists=lambda _: True, ) @@ -204,7 +204,7 @@ def test__init__ar_validation_failure(self): library_name="library", is_editable=True ), author_id=AUTHOR_ID, - concept_exists_by_library_and_name_callback=lambda _l, _c: False, + concept_exists_by_library_and_name_callback=lambda _l, _c, _g: False, activity_subgroup_exists=lambda _: True, activity_group_exists=lambda _: True, ) @@ -241,7 +241,7 @@ def test__edit_draft_version__name_validation_failure(self): request_rationale=random_str(), is_data_collected=True, ), - concept_exists_by_library_and_name_callback=lambda _l, _c: False, + concept_exists_by_library_and_name_callback=lambda _l, _c, _g: False, activity_subgroup_exists=lambda _: True, activity_group_exists=lambda _: True, ) 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 75511871..ff69e934 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 @@ -85,6 +85,7 @@ def create_random_activity_instance_vo() -> ActivityInstanceVO: ) ], is_adam_param_specific=False, + is_activity_instance_id_specific=False, ), ActivityItemVO.from_repository_values( activity_item_class_uid=random_str(), @@ -101,6 +102,7 @@ def create_random_activity_instance_vo() -> ActivityInstanceVO: ) ], is_adam_param_specific=False, + is_activity_instance_id_specific=True, ), ], ) @@ -325,6 +327,7 @@ def test__init__ar_validation_failure(self): ) ], is_adam_param_specific=False, + is_activity_instance_id_specific=False, ), ActivityItemVO.from_repository_values( activity_item_class_uid=random_str(), @@ -338,6 +341,7 @@ def test__init__ar_validation_failure(self): ) ], is_adam_param_specific=False, + is_activity_instance_id_specific=False, ), ], ), diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/models/test_table_f.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/models/test_table_f.py index a1f8b17e..77322ccc 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/models/test_table_f.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/models/test_table_f.py @@ -556,3 +556,282 @@ def test_table_to_xlsx(): } merged_ranges = {str(rng) for rng in worksheet.merged_cells.ranges} assert expected_merged.issubset(merged_ranges) + + +# Table for hide_rows_without_checkmarks tests: +# 2 header rows + 4 activity rows (alternating visible/hidden) +_XLSX_HIDE_TABLE = TableWithFootnotes( + rows=[ + TableRow( + hide=False, cells=[TableCell("Header A"), TableCell("V1"), TableCell("V2")] + ), + TableRow( + hide=False, cells=[TableCell("Header B"), TableCell("W1"), TableCell("W2")] + ), + TableRow( + hide=False, cells=[TableCell("Activity 1"), TableCell("X"), TableCell("")] + ), + TableRow( + hide=True, cells=[TableCell("Activity 2"), TableCell(""), TableCell("")] + ), + TableRow( + hide=False, cells=[TableCell("Activity 3"), TableCell("X"), TableCell("X")] + ), + TableRow( + hide=True, cells=[TableCell("Activity 4"), TableCell(""), TableCell("")] + ), + ], + num_header_rows=2, + num_header_cols=1, + title="Hide Test", +) + + +def test_table_to_xlsx_hide_rows_false_includes_all_rows(): + """Default behaviour: hidden rows ARE written to the worksheet""" + workbook = table_to_xlsx(_XLSX_HIDE_TABLE, hide_rows_without_checkmarks=False) + worksheet = workbook.active + + # THEN all rows (including hidden ones) appear in the sheet + assert worksheet.max_row == len(_XLSX_HIDE_TABLE.rows) + + # THEN cell text matches for every row, including hidden ones + for r, row in enumerate(_XLSX_HIDE_TABLE.rows, start=1): + for c, cell in enumerate(row.cells, start=1): + value = worksheet.cell(row=r, column=c).value or "" + assert value == cell.text, f"text mismatch at row {r} col {c}" + + +def test_table_to_xlsx_hide_rows_true_excludes_hidden_rows(): + """hide_rows_without_checkmarks=True: hidden rows must NOT appear in the worksheet""" + workbook = table_to_xlsx(_XLSX_HIDE_TABLE, hide_rows_without_checkmarks=True) + worksheet = workbook.active + + visible_rows = [row for row in _XLSX_HIDE_TABLE.rows if not row.hide] + + # THEN only visible rows appear in the sheet + assert worksheet.max_row == len(visible_rows) + + # THEN cell text of visible rows matches, in order + for r, row in enumerate(visible_rows, start=1): + for c, cell in enumerate(row.cells, start=1): + value = worksheet.cell(row=r, column=c).value or "" + assert value == cell.text, f"text mismatch at worksheet row {r} col {c}" + + +def test_table_to_xlsx_hide_rows_title_and_freeze_panes_unaffected(): + """Worksheet title and freeze_panes are unaffected by hide_rows_without_checkmarks""" + wb_all = table_to_xlsx(_XLSX_HIDE_TABLE, hide_rows_without_checkmarks=False) + wb_filtered = table_to_xlsx(_XLSX_HIDE_TABLE, hide_rows_without_checkmarks=True) + + assert wb_filtered.active.title == wb_all.active.title == _XLSX_HIDE_TABLE.title + assert wb_filtered.active.freeze_panes == wb_all.active.freeze_panes + + +# Tests for UID data attributes functionality + + +TEST_TABLE_WITH_UIDS = TableWithFootnotes( + rows=[ + TableRow( + cells=[ + TableCell(text="Visits"), + TableCell(text="V1", refs=[Ref(type_="StudyVisit", uid="visit-1")]), + TableCell(text="V2", refs=[Ref(type_="StudyVisit", uid="visit-2")]), + TableCell( + text="V3", + refs=[ + Ref(type_="StudyVisit", uid="visit-3"), + Ref(type_="StudyEpoch", uid="epoch-1"), + ], + ), + ] + ), + TableRow( + cells=[ + TableCell( + text="Lab Assessment", + refs=[Ref(type_="StudyActivity", uid="activity-1")], + ), + TableCell(text="X"), + TableCell(text=""), + TableCell(text="X"), + ] + ), + ], + num_header_rows=1, + num_header_cols=1, + title="Table with UIDs", +) + + +def test_tables_to_html_with_include_uids_false(): + """Test that tables_to_html without include_uids doesn't add data attributes""" + html = tables_to_html([TEST_TABLE_WITH_UIDS], include_uids=False) + + doc = bs4.BeautifulSoup(html, features="html.parser") + + # Find all cells with references + cells_with_refs = doc.find_all(["th", "td"]) + + for cell in cells_with_refs: + # THEN no object-uid or object-type attributes should be present + assert not any( + attr.startswith("object-") for attr in cell.attrs.keys() + ), f"Found unexpected object-* attribute in cell: {cell.attrs}" + + +def test_tables_to_html_with_include_uids_true(): + """Test that tables_to_html with include_uids=True adds data attributes""" + html = tables_to_html([TEST_TABLE_WITH_UIDS], include_uids=True) + + doc = bs4.BeautifulSoup(html, features="html.parser") + + # Find specific cells with known references + v1_cell = None + v3_cell = None + lab_cell = None + + for cell in doc.find_all(["th", "td"]): + if cell.get_text(strip=True) == "V1": + v1_cell = cell + elif cell.get_text(strip=True) == "V3": + v3_cell = cell + elif cell.get_text(strip=True) == "Lab Assessment": + lab_cell = cell + + # THEN V1 cell should have single reference attributes + assert v1_cell is not None + assert v1_cell.get("object-type") == "StudyVisit" + assert v1_cell.get("object-uid") == "visit-1" + + # THEN V3 cell should have multiple reference attributes + assert v3_cell is not None + assert v3_cell.get("object-type-0") == "StudyVisit" + assert v3_cell.get("object-uid-0") == "visit-3" + assert v3_cell.get("object-type-1") == "StudyEpoch" + assert v3_cell.get("object-uid-1") == "epoch-1" + + # THEN Lab Assessment cell should have activity reference + assert lab_cell is not None + assert lab_cell.get("object-type") == "StudyActivity" + assert lab_cell.get("object-uid") == "activity-1" + + # THEN cells without references should not have object attributes + empty_cells = [ + cell for cell in doc.find_all(["th", "td"]) if cell.get_text(strip=True) == "" + ] + for cell in empty_cells: + assert not any( + attr.startswith("object-") for attr in cell.attrs.keys() + ), f"Empty cell should not have object attributes: {cell.attrs}" + + +def test_tables_to_html_with_include_uids_single_table(): + """Test that single table also supports include_uids parameter""" + html = table_to_html(TEST_TABLE_WITH_UIDS) + + # Default behavior should not include UIDs + doc = bs4.BeautifulSoup(html, features="html.parser") + cells_with_attrs = [ + cell + for cell in doc.find_all(["th", "td"]) + if any(attr.startswith("object-") for attr in cell.attrs.keys()) + ] + assert ( + len(cells_with_attrs) == 0 + ), "Default table_to_html should not include UID attributes" + + +def test_cell_to_attrs_with_single_ref(): + """Test _cell_to_attrs function with single reference""" + from clinical_mdr_api.services.utils.table_f import _cell_to_attrs + + cell = TableCell( + text="Test Cell", + style="test-style", + span=2, + refs=[Ref(type_="StudyVisit", uid="visit-123")], + ) + + attrs = _cell_to_attrs(cell, include_uids=True) + + expected_attrs = { + "klass": "test-style", + "colspan": 2, + "object-type": "StudyVisit", + "object-uid": "visit-123", + } + + assert attrs == expected_attrs + + +def test_cell_to_attrs_with_multiple_refs(): + """Test _cell_to_attrs function with multiple references""" + from clinical_mdr_api.services.utils.table_f import _cell_to_attrs + + cell = TableCell( + text="Multi Ref Cell", + refs=[ + Ref(type_="StudyVisit", uid="visit-123"), + Ref(type_="StudyEpoch", uid="epoch-456"), + Ref(type_="StudyActivity", uid="activity-789"), + ], + ) + + attrs = _cell_to_attrs(cell, include_uids=True) + + expected_attrs = { + "object-type-0": "StudyVisit", + "object-uid-0": "visit-123", + "object-type-1": "StudyEpoch", + "object-uid-1": "epoch-456", + "object-type-2": "StudyActivity", + "object-uid-2": "activity-789", + } + + assert attrs == expected_attrs + + +def test_cell_to_attrs_without_include_uids(): + """Test _cell_to_attrs function with include_uids=False""" + from clinical_mdr_api.services.utils.table_f import _cell_to_attrs + + cell = TableCell( + text="Test Cell", + style="test-style", + span=3, + refs=[Ref(type_="StudyVisit", uid="visit-123")], + ) + + attrs = _cell_to_attrs(cell, include_uids=False) + + expected_attrs = {"klass": "test-style", "colspan": 3} + + assert attrs == expected_attrs + + +def test_cell_to_attrs_no_refs(): + """Test _cell_to_attrs function with no references""" + from clinical_mdr_api.services.utils.table_f import _cell_to_attrs + + cell = TableCell(text="No Refs Cell", style="test-style") + + attrs = _cell_to_attrs(cell, include_uids=True) + + expected_attrs = {"klass": "test-style"} + + assert attrs == expected_attrs + + +def test_cell_to_attrs_empty_refs(): + """Test _cell_to_attrs function with empty refs list""" + from clinical_mdr_api.services.utils.table_f import _cell_to_attrs + + cell = TableCell(text="Empty Refs Cell", refs=[]) + + attrs = _cell_to_attrs(cell, include_uids=True) + + expected_attrs = {} + + assert attrs == expected_attrs diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_flowchart.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_flowchart.py index bf2fa7bf..dbc08a03 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_flowchart.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_flowchart.py @@ -12,17 +12,36 @@ SoALayout, ) from clinical_mdr_api.domains.study_selections.study_selection_base import SoAItemType +from clinical_mdr_api.models.concepts.activities.activity import ( + ActivityForStudyActivity, +) from clinical_mdr_api.models.controlled_terminologies.ct_term_name import CTTermName from clinical_mdr_api.models.study_selections.study import StudySoaPreferencesInput from clinical_mdr_api.models.study_selections.study_epoch import StudyEpoch -from clinical_mdr_api.models.study_selections.study_soa_footnote import StudySoAFootnote +from clinical_mdr_api.models.study_selections.study_selection import ( + ReferencedItem, + SimpleStudyActivityGroup, + SimpleStudyActivitySubGroup, + SimpleStudySoAGroup, + StudyActivitySchedule, + StudySelectionActivity, +) +from clinical_mdr_api.models.study_selections.study_soa_footnote import ( + CompactFootnote, + StudySoAFootnote, +) from clinical_mdr_api.models.study_selections.study_visit import ( StudyVisit, StudyVisitLite, ) from clinical_mdr_api.services.studies.study_flowchart import _T as _gettext from clinical_mdr_api.services.studies.study_flowchart import StudyFlowchartService -from clinical_mdr_api.services.utils.table_f import TableRow, TableWithFootnotes +from clinical_mdr_api.services.utils.table_f import ( + Ref, + TableCell, + TableRow, + TableWithFootnotes, +) from clinical_mdr_api.tests.unit.services.soa_test_data import ( ADD_PROTOCOL_SECTION_COLUMN_CASE1, ADD_PROTOCOL_SECTION_COLUMN_CASE2, @@ -227,6 +246,8 @@ def check_flowchart_table_footnotes( symbol_ref_uid_map: dict[str, set[Any]] = defaultdict(set) soa_ref_uids = set() + # Collect ref UIDs from visible rows only, matching add_footnotes filtering logic + visible_ref_uids = set() for r_idx, row in enumerate(table.rows): for c_idx, cell in enumerate(row.cells): @@ -242,6 +263,8 @@ def check_flowchart_table_footnotes( for ref in cell.refs: soa_ref_uids.add(ref.uid) + if not row.hide: + visible_ref_uids.add(ref.uid) if has_footnotes: for symbol in cell.footnotes: @@ -265,6 +288,17 @@ def check_flowchart_table_footnotes( } for soa_footnote in soa_footnotes: + # Footnotes are excluded from the table by add_footnotes if none of their + # referenced items appear in visible rows (matching add_footnotes filtering) + has_visible_refs = any( + ref.item_uid in visible_ref_uids for ref in soa_footnote.referenced_items + ) + if not has_visible_refs: + assert ( + soa_footnote.uid not in footnote_uid_symbol_map + ), f"Footnote {soa_footnote.uid} with no visible references should not appear in table" + continue + assert ( soa_footnote.uid in footnote_uid_symbol_map ), f"No symbol found for footnote {soa_footnote.uid}" @@ -694,9 +728,19 @@ def test_build_flowchart_table(mock_study_flowchart_service): assert table.num_header_rows == DETAILED_SOA_TABLE.num_header_rows assert table.num_header_cols == DETAILED_SOA_TABLE.num_header_cols assert table.title == DETAILED_SOA_TABLE.title - assert table.footnotes == DETAILED_SOA_TABLE.footnotes - assert table.dict() == DETAILED_SOA_TABLE.model_dump() + # Expected footnotes after filtering - only 'a' and 'b' are referenced in visible rows + # Footnotes 'c' and 'd' are filtered out because they're only referenced in hidden rows + expected_footnotes = { + key: footnote + for key, footnote in DETAILED_SOA_TABLE.footnotes.items() + if key in ["a", "b"] + } + assert table.footnotes == expected_footnotes + + # Verify table structure + assert len(table.rows) == len(DETAILED_SOA_TABLE.rows) + assert isinstance(table, TableWithFootnotes) @pytest.mark.parametrize( @@ -836,7 +880,7 @@ def test_get_header_rows_with_soa_preferences( def test_add_protocol_section_column(test_table, expected_table): table = deepcopy(test_table) StudyFlowchartService.add_protocol_section_column(table) - assert table.dict() == expected_table.dict() + assert table.model_dump() == expected_table.model_dump() @pytest.mark.parametrize("uids", [[], ["nonexistent-uid"]]) @@ -957,3 +1001,557 @@ def test_split_flowchart_table_with_two_splits( orig_row.cells[4] = orig_row.cells[2] orig_row.cells[4].span = 1 assert slice_row.cells == [orig_row.cells[0], orig_row.cells[4]] + + +# Tests for Protocol Lab table functionality + + +class MockStudyFlowchartServiceLabTable(MockStudyFlowchartService): + """Extended mock service for testing Protocol Lab table functionality""" + + def fetch_study_activities(self, *_args, **_kwargs): + """Return activities with Laboratory Assessments group and subgroups""" + activities = deepcopy(STUDY_ACTIVITIES) + + # Ensure we have Laboratory Assessments activities for testing + lab_activities = [ + activity + for activity in activities + if activity.study_activity_group.activity_group_name + == "Laboratory Assessments" + ] + + # If no lab activities exist in test data, create some + if not lab_activities: + # Create test Laboratory Assessments activities + lab_group = SimpleStudyActivityGroup( + study_activity_group_uid="lab_group_uid", + activity_group_name="Laboratory Assessments", + ) + + biochemistry_subgroup = SimpleStudyActivitySubGroup( + study_activity_subgroup_uid="biochemistry_subgroup_uid", + activity_subgroup_name="Biochemistry", + ) + + hematology_subgroup = SimpleStudyActivitySubGroup( + study_activity_subgroup_uid="hematology_subgroup_uid", + activity_subgroup_name="Hematology", + ) + + activities.append( + StudySelectionActivity( + study_activity_uid="lab_activity_1", + study_activity_group=lab_group, + study_activity_subgroup=biochemistry_subgroup, + activity=ActivityForStudyActivity( + activity_name="Blood Chemistry", + uid="activity_1", + library_name="Sponsor", + ), + order=1, + ) + ) + + activities.append( + StudySelectionActivity( + study_activity_uid="lab_activity_2", + study_activity_group=lab_group, + study_activity_subgroup=hematology_subgroup, + activity=ActivityForStudyActivity( + activity_name="Complete Blood Count", + uid="activity_2", + library_name="Sponsor", + ), + order=2, + ) + ) + + return activities + + +@pytest.fixture(scope="module") +def mock_study_flowchart_service_lab_table(): + return MockStudyFlowchartServiceLabTable() + + +def test_get_flowchart_table_lab_table(mock_study_flowchart_service_lab_table): + """Test the new get_flowchart_table_lab_table method""" + + table = mock_study_flowchart_service_lab_table.get_flowchart_table_lab_table( + study_uid="test_study", study_value_version=None, time_unit="week" + ) + + # THEN table is returned + assert isinstance(table, TableWithFootnotes) + + # THEN table has correct structure for Lab table (2 header columns) + assert table.num_header_cols == 2 + + # THEN table has 1 header row (show_all_visits_lab_table defaults to False → no visit columns) + assert table.num_header_rows == 1 + + # THEN header row has correct structure (only 2 columns) + header_row = table.rows[0] + assert header_row.cells[0].text == _gettext("lab_assessments") + assert header_row.cells[1].text == _gettext("parameters") + assert len(header_row.cells) == 2 + + +def test_get_flowchart_table_lab_table_filtering( + mock_study_flowchart_service_lab_table, +): + """Test that Laboratory Assessments filtering works correctly""" + + # Get all activities first + all_activities = mock_study_flowchart_service_lab_table.fetch_study_activities() + + # Get filtered activities for Lab table + table = mock_study_flowchart_service_lab_table.get_flowchart_table_lab_table( + study_uid="test_study", study_value_version=None, time_unit="week" + ) + + # Count Laboratory Assessments activities + lab_group_activities = [ + activity + for activity in all_activities + if activity.study_activity_group.activity_group_name == "Laboratory Assessments" + ] + + # THEN all Laboratory Assessments activities are included in the table + included_activity_uids = set() + for row in table.rows[table.num_header_rows :]: + for cell in row.cells: + if cell.refs: + for ref in cell.refs: + if ref.type == SoAItemType.STUDY_ACTIVITY.value: + included_activity_uids.add(ref.uid) + + assert ( + set(activity.study_activity_uid for activity in lab_group_activities) + == included_activity_uids + ) + + +def test_get_header_rows_lab_table(): + """Test the new _get_header_rows_lab_table method""" + + # Create test data + + grouped_visits = { + "epoch1": {"visit1": [STUDY_VISITS[0]], "visit2": [STUDY_VISITS[1]]} + } + + soa_preferences = StudySoaPreferencesInput( + show_epochs=True, + show_milestones=False, + baseline_as_time_zero=False, + show_all_visits_lab_table=True, + ) + + header_rows = StudyFlowchartService._get_header_rows_lab_table( + grouped_visits=grouped_visits, time_unit="week", soa_preferences=soa_preferences + ) + + # THEN returns correct number of header rows + assert len(header_rows) == 4 # epochs, visits, timing, window + + # THEN first row has correct structure + epochs_row = header_rows[0] + assert epochs_row.cells[0].text == _gettext("lab_assessments") + assert epochs_row.cells[1].text == _gettext("parameters") + assert epochs_row.cells[2].text == _gettext("visits_list") + + # THEN subsequent rows have label in first cell and empty second cell + for row in header_rows[1:]: + assert row.cells[0].text != "" # Label column (visit name / timing / window) + assert row.cells[1].text == "" # Empty activity column + + +def test_get_activity_rows_lab_table(): + """Test the new _get_activity_rows_lab_table method""" + + # Create test activities with Laboratory Assessments + activities = MockStudyFlowchartServiceLabTable().fetch_study_activities() + lab_activities = [ + activity + for activity in activities + if activity.study_activity_group.activity_group_name == "Laboratory Assessments" + ] + + grouped_visits = { + "epoch1": {"visit1": [STUDY_VISITS[0]], "visit2": [STUDY_VISITS[1]]} + } + + activity_rows = StudyFlowchartService._get_activity_rows_lab_table( + study_selection_activities=lab_activities, + study_activity_schedules=[], + grouped_visits=grouped_visits, + ) + + # THEN returns activity rows + assert len(activity_rows) >= 0 + + if lab_activities and activity_rows: + # THEN first row has subgroup name in first cell + first_row = activity_rows[0] + assert len(first_row.cells) >= 2 + + # Check that subgroup name is present in the first cell + first_cell = first_row.cells[0] + if first_cell.text: + # Should contain a subgroup name + assert first_cell.text != "" + + # Check that second cell contains activity information + second_cell = first_row.cells[1] + assert second_cell.refs is not None + if second_cell.refs: + # Should have activity reference + activity_refs = [ + ref + for ref in second_cell.refs + if ref.type == SoAItemType.STUDY_ACTIVITY.value + ] + assert len(activity_refs) > 0 + + +def test_hide_rows_without_checkmarks(): + """Test the _hide_rows_without_checkmarks method""" + + # Create test table with some rows having checkmarks and some not + rows = [ + # Header rows + TableRow(cells=[TableCell("Header1"), TableCell("Header2")]), + TableRow(cells=[TableCell("Header1"), TableCell("Header2")]), + # Activity rows - some with checkmarks, some without + TableRow( + cells=[ + TableCell("Subgroup1"), + TableCell("Activity1"), + TableCell("X"), # Has checkmark + TableCell(""), + ] + ), + TableRow( + cells=[ + TableCell("Subgroup2"), + TableCell("Activity2"), + TableCell(""), # No checkmark + TableCell(""), + ] + ), + TableRow( + cells=[ + TableCell("Subgroup3"), + TableCell("Activity3"), + TableCell(""), # No checkmark + TableCell("X"), # Has checkmark + ] + ), + ] + + # Apply the method + StudyFlowchartService._hide_rows_without_checkmarks( + rows, num_header_rows=2, num_header_cols=2 + ) + + # THEN header rows are not hidden + assert not rows[0].hide + assert not rows[1].hide + + # THEN row with checkmark is not hidden + assert not rows[2].hide + + # THEN row without checkmarks is hidden + assert rows[3].hide + + # THEN row with checkmark is not hidden + assert not rows[4].hide + + +def test_protocol_lab_table_layout_enum(): + """Test that the PROTOCOL_LAB_TABLE enum value exists""" + + # THEN enum value exists + assert hasattr(SoALayout, "PROTOCOL_LAB_TABLE") + assert SoALayout.PROTOCOL_LAB_TABLE.value == "protocol_lab_table" + + +def test_footnote_filtering_for_visible_rows(): + """Test that footnotes are filtered to only include those referenced in visible rows""" + + # Create test footnotes + footnote1 = StudySoAFootnote( + uid="footnote1", + study_uid="test_study", + footnote=CompactFootnote( + uid="compact_footnote1", name="Footnote 1", name_plain="Footnote 1" + ), + referenced_items=[ + ReferencedItem(item_uid="activity1", item_type=SoAItemType.STUDY_ACTIVITY) + ], + ) + footnote2 = StudySoAFootnote( + uid="footnote2", + study_uid="test_study", + footnote=CompactFootnote( + uid="compact_footnote2", name="Footnote 2", name_plain="Footnote 2" + ), + referenced_items=[ + ReferencedItem(item_uid="activity2", item_type=SoAItemType.STUDY_ACTIVITY) + ], + ) + footnote3 = StudySoAFootnote( + uid="footnote3", + study_uid="test_study", + footnote=CompactFootnote( + uid="compact_footnote3", name="Footnote 3", name_plain="Footnote 3" + ), + referenced_items=[ + ReferencedItem(item_uid="activity3", item_type=SoAItemType.STUDY_ACTIVITY) + ], + ) + + # Create table with some visible and some hidden rows + table = TableWithFootnotes( + rows=[ + TableRow(cells=[TableCell("Header")]), # Header row - visible + TableRow( + cells=[ + TableCell( + "Activity1", + refs=[ + Ref(type_=SoAItemType.STUDY_ACTIVITY.value, uid="activity1") + ], + ) + ], + hide=False, + ), # Visible row referencing activity1 + TableRow( + cells=[ + TableCell( + "Activity2", + refs=[ + Ref(type_=SoAItemType.STUDY_ACTIVITY.value, uid="activity2") + ], + ) + ], + hide=True, + ), # Hidden row referencing activity2 + TableRow( + cells=[ + TableCell( + "Activity3", + refs=[ + Ref(type_=SoAItemType.STUDY_ACTIVITY.value, uid="activity3") + ], + ) + ], + hide=False, + ), # Visible row referencing activity3 + ], + num_header_rows=1, + num_header_cols=1, + ) + + all_footnotes = [footnote1, footnote2, footnote3] + + # Apply footnotes to table + StudyFlowchartService().add_footnotes(table, all_footnotes) + + # THEN only footnotes referenced in visible rows are included + actual_footnote_uids = {fn.uid for fn in table.footnotes.values()} + + # footnote1 and footnote3 are referenced in visible rows — must be present + assert ( + "footnote1" in actual_footnote_uids + ), "footnote1 (visible row) should be included" + assert ( + "footnote3" in actual_footnote_uids + ), "footnote3 (visible row) should be included" + + # footnote2 is only referenced in a hidden row — must be excluded + assert ( + "footnote2" not in actual_footnote_uids + ), "footnote2 (hidden row only) should be excluded" + + +# Tests for show_all_visits_lab_table visit filtering + + +class MockStudyFlowchartServiceLabTableVisitFilter(MockStudyFlowchartService): + """Mock service for testing show_all_visits_lab_table visit filtering. + + Setup: + - 3 visible visits: V1, V2, V3 + - 2 lab activities: lab_act_1 (scheduled on V1), lab_act_2 (scheduled on V1, V2) + - V3 has NO lab activity schedule → should be excluded when show_all_visits_lab_table=False + """ + + def __init__(self, show_all_visits_lab_table: bool = False): + super().__init__() + self._show_all_visits_lab_table = show_all_visits_lab_table + + def _get_soa_preferences(self, *_args, **_kwargs) -> StudySoaPreferencesInput: + return StudySoaPreferencesInput( + show_epochs=True, + show_milestones=False, + baseline_as_time_zero=False, + show_all_visits_lab_table=self._show_all_visits_lab_table, + ) + + def _get_study_visits_dict_filtered(self, *_args, **_kwargs): + # Return 3 visits across 2 epochs + return { + v.uid: v + for v in STUDY_VISITS[:3] + if v.show_visit # V1 (000012), V2 (000013) — V3 (000014) has show_visit=False + } | { + STUDY_VISITS[3].uid: STUDY_VISITS[3] # V4 (000015) — no lab schedule + } + + def fetch_study_activities(self, *_args, **_kwargs): + lab_group = SimpleStudyActivityGroup( + study_activity_group_uid="lab_group_uid", + activity_group_uid="ActivityGroup_Lab", + activity_group_name="Laboratory Assessments", + ) + subgroup = SimpleStudyActivitySubGroup( + study_activity_subgroup_uid="sub_uid", + activity_subgroup_uid="SubGroup_1", + activity_subgroup_name="Biochemistry", + ) + soa_group = SimpleStudySoAGroup( + study_soa_group_uid="SoAGroup_1", + soa_group_term_uid="CTTerm_Lab", + soa_group_term_name="PROCEDURES", + ) + return [ + StudySelectionActivity( + study_uid="test_study", + study_activity_uid="lab_act_1", + study_activity_group=lab_group, + study_activity_subgroup=subgroup, + study_soa_group=soa_group, + activity=ActivityForStudyActivity( + uid="Activity_Lab1", + activity_name="Blood Chemistry", + library_name="Sponsor", + ), + order=1, + ), + StudySelectionActivity( + study_uid="test_study", + study_activity_uid="lab_act_2", + study_activity_group=lab_group, + study_activity_subgroup=subgroup, + study_soa_group=soa_group, + activity=ActivityForStudyActivity( + uid="Activity_Lab2", + activity_name="Complete Blood Count", + library_name="Sponsor", + ), + order=2, + ), + ] + + def _get_study_activity_schedules(self, *_args, **_kwargs): + # lab_act_1 scheduled on V1, lab_act_2 scheduled on V1 and V2 + # V4 has no lab schedule at all + return [ + StudyActivitySchedule( + study_activity_schedule_uid="sched_1", + study_activity_uid="lab_act_1", + study_visit_uid="StudyVisit_000012", # V1 + ), + StudyActivitySchedule( + study_activity_schedule_uid="sched_2", + study_activity_uid="lab_act_2", + study_visit_uid="StudyVisit_000012", # V1 + ), + StudyActivitySchedule( + study_activity_schedule_uid="sched_3", + study_activity_uid="lab_act_2", + study_visit_uid="StudyVisit_000013", # V2 + ), + ] + + def _get_study_footnotes(self, *_args, **_kwargs): + return [] + + +def _extract_visit_uids_from_table(table: TableWithFootnotes) -> set[str]: + """Extract StudyVisit uids from visit header row refs.""" + visit_row = table.rows[1] # visits row in lab table header + uids: set[str] = set() + for cell in visit_row.cells: + if cell.refs: + for ref in cell.refs: + if ref.type == SoAItemType.STUDY_VISIT.value: + uids.add(ref.uid) + return uids + + +def test_lab_table_show_all_visits_false_filters_unscheduled_visits(): + """When show_all_visits_lab_table=False, the table has only 2 columns (no visit columns).""" + service = MockStudyFlowchartServiceLabTableVisitFilter( + show_all_visits_lab_table=False + ) + + table = service.get_flowchart_table_lab_table( + study_uid="test_study", study_value_version=None, time_unit="week" + ) + + # THEN table has only 1 header row (no visit header rows) + assert table.num_header_rows == 1 + + # THEN every row has exactly 2 cells (subgroup + activity, no visit columns) + for row in table.rows: + assert len(row.cells) == 2, f"Expected 2 columns, got {len(row.cells)}" + + +def test_lab_table_show_all_visits_true_includes_all_visits(): + """When show_all_visits_lab_table=True, only visits with lab schedules are included.""" + service = MockStudyFlowchartServiceLabTableVisitFilter( + show_all_visits_lab_table=True + ) + + table = service.get_flowchart_table_lab_table( + study_uid="test_study", study_value_version=None, time_unit="week" + ) + + visit_uids = _extract_visit_uids_from_table(table) + + # V1 and V2 have lab schedules — must be present + assert "StudyVisit_000012" in visit_uids, "V1 should be included" + assert "StudyVisit_000013" in visit_uids, "V2 should be included" + + # V4 has no lab schedule — always filtered out + assert "StudyVisit_000015" not in visit_uids, "V4 (unscheduled) should be excluded" + + +def test_lab_table_show_all_visits_false_fewer_columns_than_true(): + """When filtering is active, the table has fewer visit columns than when all visits are shown.""" + service_filtered = MockStudyFlowchartServiceLabTableVisitFilter( + show_all_visits_lab_table=False + ) + service_all = MockStudyFlowchartServiceLabTableVisitFilter( + show_all_visits_lab_table=True + ) + + table_filtered = service_filtered.get_flowchart_table_lab_table( + study_uid="test_study", study_value_version=None, time_unit="week" + ) + table_all = service_all.get_flowchart_table_lab_table( + study_uid="test_study", study_value_version=None, time_unit="week" + ) + + # Visit header row (row index 1) + filtered_visit_count = len(_extract_visit_uids_from_table(table_filtered)) + all_visit_count = len(_extract_visit_uids_from_table(table_all)) + + assert filtered_visit_count < all_visit_count, ( + f"Filtered table should have fewer visit columns ({filtered_visit_count}) " + f"than unfiltered table ({all_visit_count})" + ) diff --git a/clinical-mdr-api/common/config.py b/clinical-mdr-api/common/config.py index d0bb8a12..3fee680b 100644 --- a/clinical-mdr-api/common/config.py +++ b/clinical-mdr-api/common/config.py @@ -200,6 +200,8 @@ def swagger_ui_init_oauth(self) -> dict[str, Any] | None: non_visit_number: int = 29999 unscheduled_visit_number: int = 29500 + unscheduled_visit_name: str = "Unscheduled" + unscheduled_visit_start_rule: str = "Unplanned unscheduled" visit_0_number: int = 0 fixed_week_period: int = 7 @@ -251,12 +253,14 @@ def swagger_ui_init_oauth(self) -> dict[str, Any] | None: study_field_soa_preferred_time_unit_name: str = "soa_preferred_time_unit" study_field_soa_show_epochs: str = "soa_show_epochs" study_field_soa_show_milestones: str = "soa_show_milestones" + study_field_soa_show_all_visits_lab_table: str = "soa_show_all_visits_lab_table" study_field_soa_baseline_as_time_zero: str = "baseline_as_time_zero" - study_soa_preferences_fields: tuple[str, str, str] = ( + study_soa_preferences_fields: tuple[str, str, str, str] = ( # can't be a set: Neomodel's transform_operator_to_filter is strict for IN operator only accepts list or tuple study_field_soa_show_epochs, study_field_soa_show_milestones, study_field_soa_baseline_as_time_zero, + study_field_soa_show_all_visits_lab_table, ) study_soa_split_uids_field: str = "soa_split_uids" diff --git a/clinical-mdr-api/consumer_api/apiVersion b/clinical-mdr-api/consumer_api/apiVersion index 27f3bc3e..f3185747 100644 --- a/clinical-mdr-api/consumer_api/apiVersion +++ b/clinical-mdr-api/consumer_api/apiVersion @@ -1 +1 @@ -0.1.120 +0.1.128 diff --git a/clinical-mdr-api/consumer_api/openapi.json b/clinical-mdr-api/consumer_api/openapi.json index 7cd05cd7..79cd5a4a 100644 --- a/clinical-mdr-api/consumer_api/openapi.json +++ b/clinical-mdr-api/consumer_api/openapi.json @@ -3,7 +3,7 @@ "info": { "title": "OpenStudyBuilder Consumer 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", - "version": "0.1.120" + "version": "0.1.128" }, "paths": { "/": { @@ -186,7 +186,7 @@ "[V1] Studies" ], "summary": "Get Studies", - "description": "Returns a paginated list of studies, sorted by the specified sort criteria and order.\n\nEach returned study contains a full list of corresponding study versions, sorted by version start date in descending order.\n\nReturned `version_number` value can be used in other endpoints to retrieve study entities (e.g. visits, activities, etc.)\nassociated with a specific study version.", + "description": "Returns a paginated list of studies, sorted by the specified sort criteria and order.\n\nEach returned study contains a full list of corresponding study versions, sorted by version start date in descending order.\n\nReturned `version_number` value can be used in other endpoints to retrieve study entities (e.g. visits, activities, etc.)\nassociated with a specific study version.\n\nCodelist details can be retrieved from the `GET /v1/library/ct/codelists` endpoint.\n\nDetails related to the Data Supplier type can be retrieved from the `GET /v1/library/ct/codelist-terms?codelist_submission_value=DATA_SUPPLIER_TYPE` endpoint.", "operationId": "get_studies_v1_studies_get", "security": [ { @@ -1602,7 +1602,7 @@ "[V1] Library" ], "summary": "Get Codelist Terms", - "description": "Returns a paginated list of CT codelist terms for the specified codelist submission value,\nsorted by ascending sponsor preferred name.\n\nTerms can be filtered by `name_status` and `attributes_status` (_Final, Draft, Retired_). Both default to _Final_.", + "description": "Returns a paginated list of CT codelist terms, sorted by ascending by codelist UID, then term UID.\n\nIf neither `codelist_submission_value` nor `codelist_uid` is provided, all terms are returned.\nIf either is provided, terms are filtered accordingly.\n\nTerms can also be filtered by `name_status` and `attributes_status` (_Final, Draft, Retired_). Both default to _Final_.", "operationId": "get_codelist_terms_v1_library_ct_codelist_terms_get", "security": [ { @@ -1616,14 +1616,39 @@ { "name": "codelist_submission_value", "in": "query", - "required": true, + "required": false, "schema": { - "type": "string", + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], "description": "Codelist submission value to filter by, for example `TIMELB`, `TIMEREF`, `VISCNTMD`, `FLWCRTGRP`, `EPOCHSTP` etc.", "title": "Codelist Submission Value" }, "description": "Codelist submission value to filter by, for example `TIMELB`, `TIMEREF`, `VISCNTMD`, `FLWCRTGRP`, `EPOCHSTP` etc." }, + { + "name": "codelist_uid", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Codelist UID to filter by.", + "title": "Codelist Uid" + }, + "description": "Codelist UID to filter by." + }, { "name": "page_size", "in": "query", @@ -2086,11 +2111,42 @@ }, "CodelistTerm": { "properties": { - "uid": { + "codelist_uid": { "type": "string", - "title": "Uid", + "title": "Codelist Uid", + "description": "Codelist UID" + }, + "term_uid": { + "type": "string", + "title": "Term Uid", "description": "Codelist Term UID" }, + "order": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Order", + "description": "Term order within the codelist", + "nullable": true + }, + "ordinal": { + "anyOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Ordinal", + "description": "Term ordinal value (only for ordinal codelists)", + "nullable": true + }, "submission_value": { "type": "string", "title": "Submission Value", @@ -2156,7 +2212,8 @@ }, "type": "object", "required": [ - "uid", + "codelist_uid", + "term_uid", "submission_value", "sponsor_preferred_name", "library_name", @@ -2488,6 +2545,18 @@ "title": "Version", "description": "Activity Version" }, + "activity_instance_class": { + "anyOf": [ + { + "$ref": "#/components/schemas/LibraryActivityInstanceClass" + }, + { + "type": "null" + } + ], + "description": "Activity Instance Class", + "nullable": true + }, "groupings": { "items": { "$ref": "#/components/schemas/LibraryActivityGroupingWithActivity" @@ -2496,6 +2565,24 @@ "title": "Groupings", "description": "Activity Groups/Subgroups", "default": [] + }, + "groupings_status": { + "$ref": "#/components/schemas/LibraryItemStatus", + "description": "Activity Groupings Status" + }, + "groupings_version": { + "type": "string", + "title": "Groupings Version", + "description": "Activity Groupings Version" + }, + "activity_items": { + "items": { + "$ref": "#/components/schemas/LibraryActivityItem" + }, + "type": "array", + "title": "Activity Items", + "description": "Activity Items", + "default": [] } }, "type": "object", @@ -2505,10 +2592,173 @@ "name", "definition", "status", - "version" + "version", + "groupings_status", + "groupings_version" ], "title": "LibraryActivityInstance" }, + "LibraryActivityInstanceClass": { + "properties": { + "uid": { + "type": "string", + "title": "Uid", + "description": "Activity Instance Class UID" + }, + "name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name", + "description": "Activity Instance Class Name", + "nullable": true + } + }, + "type": "object", + "required": [ + "uid" + ], + "title": "LibraryActivityInstanceClass" + }, + "LibraryActivityItem": { + "properties": { + "activity_item_class": { + "$ref": "#/components/schemas/LibraryActivityItemClass", + "description": "Activity Item Class" + }, + "data_type": { + "type": "string", + "title": "Data Type", + "description": "Data type of the activity item" + }, + "ct_codelist": { + "anyOf": [ + { + "$ref": "#/components/schemas/LibraryActivityItemCTCodelist" + }, + { + "type": "null" + } + ], + "description": "CT Codelist", + "nullable": true + }, + "ct_terms": { + "items": { + "$ref": "#/components/schemas/SimpleCodelistTerm" + }, + "type": "array", + "title": "Ct Terms", + "description": "CT Terms", + "default": [] + }, + "unit_definitions": { + "items": { + "$ref": "#/components/schemas/LibraryActivityItemUnitDefinition" + }, + "type": "array", + "title": "Unit Definitions", + "description": "Unit Definitions", + "default": [] + }, + "text_value": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Text Value", + "description": "Text Value", + "nullable": true + }, + "is_adam_param_specific": { + "type": "boolean", + "title": "Is Adam Param Specific", + "description": "Is ADaM Parameter Specific", + "default": false + }, + "is_activity_instance_id_specific": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Activity Instance Id Specific", + "description": "Is Activity Instance ID Specific" + } + }, + "type": "object", + "required": [ + "activity_item_class", + "data_type" + ], + "title": "LibraryActivityItem" + }, + "LibraryActivityItemCTCodelist": { + "properties": { + "uid": { + "type": "string", + "title": "Uid", + "description": "CT Codelist UID" + }, + "submission_value": { + "type": "string", + "title": "Submission Value", + "description": "CT Codelist Submission Value" + } + }, + "type": "object", + "required": [ + "uid", + "submission_value" + ], + "title": "LibraryActivityItemCTCodelist" + }, + "LibraryActivityItemClass": { + "properties": { + "uid": { + "type": "string", + "title": "Uid", + "description": "Activity Item Class UID" + }, + "name": { + "type": "string", + "title": "Name", + "description": "Activity Item Class Name" + } + }, + "type": "object", + "required": [ + "uid", + "name" + ], + "title": "LibraryActivityItemClass" + }, + "LibraryActivityItemUnitDefinition": { + "properties": { + "uid": { + "type": "string", + "title": "Uid", + "description": "Unit Definition UID" + } + }, + "type": "object", + "required": [ + "uid" + ], + "title": "LibraryActivityItemUnitDefinition" + }, "LibraryItemStatus": { "type": "string", "enum": [ @@ -3093,6 +3343,26 @@ ], "title": "PapillonsSoAItem" }, + "SimpleCodelistTerm": { + "properties": { + "codelist_uid": { + "type": "string", + "title": "Codelist Uid", + "description": "Codelist Term UID" + }, + "term_uid": { + "type": "string", + "title": "Term Uid", + "description": "Codelist Term UID" + } + }, + "type": "object", + "required": [ + "codelist_uid", + "term_uid" + ], + "title": "SimpleCodelistTerm" + }, "SoaGroup": { "properties": { "uid": { @@ -3263,6 +3533,14 @@ "type": "array", "title": "Data Completeness Tags", "description": "List of data completeness tag names assigned to the study." + }, + "data_suppliers": { + "items": { + "$ref": "#/components/schemas/StudyDataSupplier" + }, + "type": "array", + "title": "Data Suppliers", + "description": "List of data suppliers of the study." } }, "type": "object", @@ -3543,6 +3821,40 @@ ], "title": "StudyAuditTrailEntity" }, + "StudyDataSupplier": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "type": { + "$ref": "#/components/schemas/SimpleCodelistTerm" + }, + "order": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Order", + "nullable": true + } + }, + "type": "object", + "required": [ + "uid", + "name", + "type" + ], + "title": "StudyDataSupplier" + }, "StudyDetailedSoA": { "properties": { "study_uid": { diff --git a/clinical-mdr-api/consumer_api/requirements/fs/fs-library.md b/clinical-mdr-api/consumer_api/requirements/fs/fs-library.md index b9ab1e0e..deaa25bf 100644 --- a/clinical-mdr-api/consumer_api/requirements/fs/fs-library.md +++ b/clinical-mdr-api/consumer_api/requirements/fs/fs-library.md @@ -53,6 +53,7 @@ Response must include basic information about each activity instance, together w | tests/v1/test_api_library.py | test_get_library_activity_instances_all | | tests/v1/test_api_library.py | test_get_library_activity_instances_filtering | | tests/v1/test_api_library.py | test_get_library_activity_instances_invalid_pagination_params | +| tests/v1/test_api_library.py | test_get_library_activity_instances_activity_items | # Library CT Codelists @@ -86,19 +87,23 @@ Items are sorted by ascending codelist name. ## FS-ConsumerApi-Library-CodelistTerms-Get-010 [`URS-ConsumerApi-Library-ControlledTerminology`] -Consumers must be able to retrieve a paginated list of CT codelist terms for a specified codelist by calling the `GET /library/ct/codelist-terms` endpoint with the required `codelist_submission_value` query parameter. +Consumers must be able to retrieve a paginated list of CT codelist terms by calling the `GET /library/ct/codelist-terms` endpoint. ### Request -The `codelist_submission_value` query parameter is required and filters terms by codelist submission value (e.g. `TIMELB`, `TIMEREF`, `VISCNTMD`, `FLWCRTGRP`, `EPOCHSTP`). +The optional `codelist_submission_value` query parameter filters terms by codelist submission value (e.g. `TIMELB`, `TIMEREF`, `VISCNTMD`, `FLWCRTGRP`, `EPOCHSTP`). + +The optional `codelist_uid` query parameter filters terms by codelist UID. + +Both `codelist_submission_value` and `codelist_uid` can be provided together. If neither is provided, all terms are returned. It must be possible to filter items by `name_status` and `attributes_status` (_Final, Draft, Retired_). Both filters default to _Final_. ### Response -Response must include basic information about each codelist term: UID, submission value, sponsor preferred name, concept ID, NCI preferred name, and library name. +Response must include basic information about each codelist term: term UID, codelist UID, order, ordinal, submission value, sponsor preferred name, concept ID, NCI preferred name, and library name. -Items are sorted by ascending sponsor preferred name. +Items are sorted by ascending codelist UID, then term UID. If the specified codelist does not exist, an empty list is returned. @@ -109,7 +114,10 @@ If the specified codelist does not exist, an empty list is returned. | tests/v1/test_api_library_ct.py | test_get_codelist_terms | | tests/v1/test_api_library_ct.py | test_get_codelist_terms_nonexistent_codelist | | tests/v1/test_api_library_ct.py | test_get_codelist_terms_pagination | -| tests/v1/test_api_library_ct.py | test_get_codelist_terms_missing_required_param | +| tests/v1/test_api_library_ct.py | test_get_codelist_terms_no_filters | +| tests/v1/test_api_library_ct.py | test_get_codelist_terms_filter_by_codelist_uid | +| tests/v1/test_api_library_ct.py | test_get_codelist_terms_filter_by_both_params | +| tests/v1/test_api_library_ct.py | test_get_codelist_terms_filter_by_nonexistent_codelist_uid | | tests/v1/test_api_library_ct.py | test_get_codelist_terms_invalid_pagination_params | | tests/v1/test_api_library_ct.py | test_get_codelist_terms_default_status_filter | | tests/v1/test_api_library_ct.py | test_get_codelist_terms_filter_name_status_draft | diff --git a/clinical-mdr-api/consumer_api/requirements/fs/fs-studies.md b/clinical-mdr-api/consumer_api/requirements/fs/fs-studies.md index 26332488..919748a2 100644 --- a/clinical-mdr-api/consumer_api/requirements/fs/fs-studies.md +++ b/clinical-mdr-api/consumer_api/requirements/fs/fs-studies.md @@ -29,6 +29,7 @@ Each item in the response must include basic information about a study (`uid`, ` | tests/v1/test_api_studies.py | test_get_studies_all | | tests/v1/test_api_studies.py | test_get_studies_filtering | | tests/v1/test_api_studies.py | test_get_studies_invalid_pagination_params | +| tests/v1/test_api_studies.py | test_get_studies_returns_data_suppliers | # Study Structure diff --git a/clinical-mdr-api/consumer_api/tests/v1/test_api_audit_trail.py b/clinical-mdr-api/consumer_api/tests/v1/test_api_audit_trail.py index 924a2fca..7d293783 100644 --- a/clinical-mdr-api/consumer_api/tests/v1/test_api_audit_trail.py +++ b/clinical-mdr-api/consumer_api/tests/v1/test_api_audit_trail.py @@ -91,7 +91,7 @@ def test_data(api_client): studies = [study] # type: ignore[list-item] for _idx in range(1, total_studies): - rand = TestUtils.random_str(4) + rand = TestUtils.random_str(10) studies.append(TestUtils.create_study(acronym=f"ACR-{rand}")) # type: ignore[arg-type] study_epoch = create_study_epoch("EpochSubType_0001", study_uid=studies[0].uid) @@ -381,8 +381,8 @@ def test_count_create_and_edit_actions_per_entity_type(api_client): print("=" * 100 + "\n") # Assertions based on expected counts per entity_type - # StudyField|StudyBooleanField: Create=76, Edit=0 - assert create_counts["StudyField|StudyBooleanField"] == 76 + # StudyField|StudyBooleanField: Create=101, Edit=0 + assert create_counts["StudyField|StudyBooleanField"] == 101 assert edit_counts["StudyField|StudyBooleanField"] == 0 # StudyField|StudyTimeField: Create=50, Edit=0 diff --git a/clinical-mdr-api/consumer_api/tests/v1/test_api_library.py b/clinical-mdr-api/consumer_api/tests/v1/test_api_library.py index a2ae0397..8c7cb480 100644 --- a/clinical-mdr-api/consumer_api/tests/v1/test_api_library.py +++ b/clinical-mdr-api/consumer_api/tests/v1/test_api_library.py @@ -6,6 +6,10 @@ import pytest from fastapi.testclient import TestClient +from clinical_mdr_api.models.biomedical_concepts.activity_item_class import ( + ActivityInstanceClassRelInput, +) +from clinical_mdr_api.models.controlled_terminologies.ct_term import CTTerm from clinical_mdr_api.tests.integration.utils.api import inject_base_data from clinical_mdr_api.tests.integration.utils.utils import TestUtils from common.config import settings @@ -51,6 +55,10 @@ "param_code", "status", "version", + "groupings_status", + "groupings_version", + "activity_instance_class", + "activity_items", ] LIBRARY_ACTIVITY_INSTANCE_FIELDS_NOT_NULL = [ @@ -62,6 +70,10 @@ "param_code", "status", "version", + "groupings_status", + "groupings_version", + "activity_instance_class", + "activity_items", ] @@ -71,6 +83,14 @@ activity_group: Any activity_subgroup: Any activity_instances: list[models.LibraryActivityInstance] +activity_instance_with_items: Any +activity_item_class: Any +activity_item_class_ct_term: Any +activity_item_class_ct_codelist: Any +activity_item_class_text: Any +activity_item_codelist: Any +activity_item_ct_terms: list[CTTerm] +activity_item_unit_definition_uid: str @pytest.fixture(scope="module") @@ -85,7 +105,7 @@ def test_data(api_client): """Initialize test data""" db_name = "consumer-api-v1-library" set_db(db_name) - inject_base_data() + inject_base_data(inject_unit_dimension=True) global activities global activity_group global activity_subgroup @@ -101,6 +121,94 @@ def test_data(api_client): activity_group = TestUtils.create_activity_group("Activity Group") activity_subgroup = TestUtils.create_activity_subgroup("Activity Sub Group") + # Create activity item class prerequisites + global activity_item_class + global activity_item_class_ct_term + global activity_item_class_ct_codelist + global activity_item_class_text + global activity_instance_with_items + global activity_item_codelist + global activity_item_ct_terms + global activity_item_unit_definition_uid + + data_type_codelist = TestUtils.create_ct_codelist( + name="DATATYPE", submission_value="DATATYPE", extensible=True, approve=True + ) + data_type_term = TestUtils.create_ct_term( + sponsor_preferred_name="Data type", codelist_uid=data_type_codelist.codelist_uid + ) + role_codelist = TestUtils.create_ct_codelist( + name="ROLE", submission_value="ROLE", extensible=True, approve=True + ) + role_term = TestUtils.create_ct_term( + sponsor_preferred_name="Role", codelist_uid=role_codelist.codelist_uid + ) + + aic_rel = ActivityInstanceClassRelInput( + uid=activity_instance_class.uid, # type: ignore[arg-type] + mandatory=True, + is_adam_param_specific_enabled=True, + is_additional_optional=False, + is_default_linked=False, + ) + + # Activity item class for unit definition type + activity_item_class = TestUtils.create_activity_item_class( + name="Test Activity Item Class", + order=1, + activity_instance_classes=[aic_rel], + role_uid=role_term.term_uid, + data_type_uid=data_type_term.term_uid, + ) + + # Activity item class for ct_term type + activity_item_class_ct_term = TestUtils.create_activity_item_class( + name="CT Term Item Class", + order=2, + activity_instance_classes=[aic_rel], + role_uid=role_term.term_uid, + data_type_uid=data_type_term.term_uid, + ) + + # Activity item class for ct_codelist type + activity_item_class_ct_codelist = TestUtils.create_activity_item_class( + name="CT Codelist Item Class", + order=3, + activity_instance_classes=[aic_rel], + role_uid=role_term.term_uid, + data_type_uid=data_type_term.term_uid, + ) + + # Activity item class for text type + activity_item_class_text = TestUtils.create_activity_item_class( + name="Text Item Class", + order=4, + activity_instance_classes=[aic_rel], + role_uid=role_term.term_uid, + data_type_uid=data_type_term.term_uid, + ) + + # Create a codelist and terms for activity items + activity_item_codelist = TestUtils.create_ct_codelist( + name="AI Codelist", + submission_value="AI_CODELIST", + extensible=True, + approve=True, + ) + activity_item_ct_terms = [ + TestUtils.create_ct_term( + codelist_uid=activity_item_codelist.codelist_uid, + sponsor_preferred_name="AI Term 1", + ), + TestUtils.create_ct_term( + codelist_uid=activity_item_codelist.codelist_uid, + sponsor_preferred_name="AI Term 2", + ), + ] + + # Use the "day" unit definition created by inject_base_data + activity_item_unit_definition_uid = TestUtils.get_unit_uid_by_name("day") + for idx in range(0, total_activities): # Create Final Activity activity = TestUtils.create_activity( @@ -152,6 +260,69 @@ def test_data(api_client): ) activities.append(activity_draft) # type: ignore[arg-type] + # Create one activity instance with all types of activity items + ai_activity = TestUtils.create_activity( + "Activity With Items", + activity_groups=[activity_group.uid], + activity_subgroups=[activity_subgroup.uid], + approve=True, + ) + activities.append(ai_activity) # type: ignore[arg-type] + activity_instance_with_items = TestUtils.create_activity_instance( + name="Activity instance with items", + activity_instance_class_uid=activity_instance_class.uid, # type: ignore[arg-type] + name_sentence_case="activity instance with items", + topic_code="TC with items", + adam_param_code="adam_param_with_items", + is_required_for_activity=True, + activities=[ai_activity.uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[ + # Unit definition type + { + "activity_item_class_uid": activity_item_class.uid, + "ct_terms": [], + "unit_definition_uids": [activity_item_unit_definition_uid], + "is_adam_param_specific": True, + }, + # CT term type + { + "activity_item_class_uid": activity_item_class_ct_term.uid, + "ct_terms": [ + { + "term_uid": activity_item_ct_terms[0].term_uid, + "codelist_uid": activity_item_codelist.codelist_uid, + }, + { + "term_uid": activity_item_ct_terms[1].term_uid, + "codelist_uid": activity_item_codelist.codelist_uid, + }, + ], + "unit_definition_uids": [], + "is_adam_param_specific": False, + }, + # CT codelist type + { + "activity_item_class_uid": activity_item_class_ct_codelist.uid, + "ct_terms": [], + "ct_codelist_uid": activity_item_codelist.codelist_uid, + "unit_definition_uids": [], + "is_adam_param_specific": False, + }, + # Text type + { + "activity_item_class_uid": activity_item_class_text.uid, + "ct_terms": [], + "unit_definition_uids": [], + "is_adam_param_specific": False, + "text_value": "Sample text value", + }, + ], + approve=True, + ) + activity_instances.append(activity_instance_with_items) # type: ignore[arg-type] + # sort activities by name activities.sort(key=lambda x: x.name) @@ -259,7 +430,7 @@ def test_get_library_activities_filtering(api_client): for key in ["self", "prev", "next"]: assert "status=Final&" in res[key] - assert len(res["items"]) == len(activities) // 2 + assert len(res["items"]) == total_activities + 1 # +1 for ai_activity for item in res["items"]: assert item["status"] == "Final" @@ -271,7 +442,7 @@ def test_get_library_activities_filtering(api_client): for key in ["self", "prev", "next"]: assert "status=Draft&" in res[key] - assert len(res["items"]) == len(activities) // 2 + assert len(res["items"]) == total_activities for item in res["items"]: assert item["status"] == "Draft" @@ -312,7 +483,7 @@ def test_get_library_activities_filtering(api_client): assert "library=Sponsor&" in res[key] assert "status=Final&" in res[key] - assert len(res["items"]) == len(activities) // 2 + assert len(res["items"]) == total_activities + 1 # +1 for ai_activity for item in res["items"]: assert item["library"] == "Sponsor" assert item["status"] == "Final" @@ -457,7 +628,9 @@ def test_get_library_activity_instances_filtering(api_client): for key in ["self", "prev", "next"]: assert "status=Final&" in res[key] - assert len(res["items"]) == len(activity_instances) // 2 + assert ( + len(res["items"]) == total_activities + 1 + ) # +1 for activity_instance_with_items for item in res["items"]: assert item["status"] == "Final" @@ -469,7 +642,7 @@ def test_get_library_activity_instances_filtering(api_client): for key in ["self", "prev", "next"]: assert "status=Draft&" in res[key] - assert len(res["items"]) == len(activity_instances) // 2 + assert len(res["items"]) == total_activities for item in res["items"]: assert item["status"] == "Draft" @@ -512,7 +685,9 @@ def test_get_library_activity_instances_filtering(api_client): assert "library=Sponsor&" in res[key] assert "status=Final&" in res[key] - assert len(res["items"]) == len(activity_instances) // 2 + assert ( + len(res["items"]) == total_activities + 1 + ) # +1 for activity_instance_with_items for item in res["items"]: assert item["library"] == "Sponsor" assert item["status"] == "Final" @@ -537,6 +712,112 @@ def test_get_library_activity_instances_filtering(api_client): assert item["groupings"][0]["activity_subgroup_uid"] == activity_subgroup.uid +def test_get_library_activity_instances_activity_items(api_client): + """Test that all types of activity items are properly returned.""" + response = api_client.get( + f"{BASE_URL}/library/activity-instances?page_size=100&status=Final" + ) + assert_response_status_code(response, 200) + res = response.json() + + # Find the activity instance that has activity items + items_with_activity_items = [ + item for item in res["items"] if len(item.get("activity_items", [])) > 0 + ] + assert ( + len(items_with_activity_items) > 0 + ), "Expected at least one activity instance with activity items" + + item = items_with_activity_items[0] + assert item["name"] == "Activity instance with items" + assert len(item["activity_items"]) == 4 + + expected_keys = { + "activity_item_class", + "data_type", + "ct_codelist", + "ct_terms", + "unit_definitions", + "text_value", + "is_adam_param_specific", + "is_activity_instance_id_specific", + } + for activity_item in item["activity_items"]: + assert set(activity_item.keys()) == expected_keys + + # Build a lookup by activity_item_class uid for easier assertions + items_by_class = { + ai["activity_item_class"]["uid"]: ai for ai in item["activity_items"] + } + + # --- Unit definition type --- + unit_item = items_by_class[activity_item_class.uid] + assert unit_item["activity_item_class"]["name"] == "Test Activity Item Class" + assert unit_item["data_type"] == "Data type" + assert len(unit_item["unit_definitions"]) == 1 + assert unit_item["unit_definitions"][0]["uid"] == activity_item_unit_definition_uid + assert unit_item["ct_terms"] == [] + assert unit_item["ct_codelist"] is None + assert unit_item["text_value"] is None + assert unit_item["is_adam_param_specific"] is True + + # --- CT term type --- + ct_term_item = items_by_class[activity_item_class_ct_term.uid] + assert ct_term_item["activity_item_class"]["name"] == "CT Term Item Class" + assert ct_term_item["data_type"] == "Data type" + assert len(ct_term_item["ct_terms"]) == 2 + ct_term_uids = {t["term_uid"] for t in ct_term_item["ct_terms"]} + assert ct_term_uids == { + activity_item_ct_terms[0].term_uid, + activity_item_ct_terms[1].term_uid, + } + for ct_term in ct_term_item["ct_terms"]: + assert ct_term["codelist_uid"] == activity_item_codelist.codelist_uid + assert ct_term_item["unit_definitions"] == [] + assert ct_term_item["ct_codelist"] is None + assert ct_term_item["text_value"] is None + assert ct_term_item["is_adam_param_specific"] is False + + # --- CT codelist type --- + codelist_item = items_by_class[activity_item_class_ct_codelist.uid] + assert codelist_item["activity_item_class"]["name"] == "CT Codelist Item Class" + assert codelist_item["data_type"] == "Data type" + assert codelist_item["ct_codelist"] is not None + assert codelist_item["ct_codelist"]["uid"] == activity_item_codelist.codelist_uid + assert codelist_item["ct_codelist"]["submission_value"] is not None + assert codelist_item["ct_terms"] == [] + assert codelist_item["unit_definitions"] == [] + assert codelist_item["text_value"] is None + assert codelist_item["is_adam_param_specific"] is False + + # --- Text type --- + text_item = items_by_class[activity_item_class_text.uid] + assert text_item["activity_item_class"]["name"] == "Text Item Class" + assert text_item["data_type"] == "Data type" + assert text_item["text_value"] == "Sample text value" + assert text_item["ct_terms"] == [] + assert text_item["ct_codelist"] is None + assert text_item["unit_definitions"] == [] + assert text_item["is_adam_param_specific"] is False + + # Verify activity_instance_class is present on the activity instance + assert item["activity_instance_class"] is not None + assert item["activity_instance_class"]["uid"] is not None + assert ( + item["activity_instance_class"]["name"] == "Randomized activity instance class" + ) + + # Verify activity instances without items have empty list + items_without_activity_items = [ + item for item in res["items"] if len(item.get("activity_items", [])) == 0 + ] + assert ( + len(items_without_activity_items) > 0 + ), "Expected some activity instances without activity items" + for item in items_without_activity_items: + assert item["activity_items"] == [] + + def test_get_library_activity_instances_invalid_pagination_params(api_client): response = api_client.get(f"{BASE_URL}/library/activity-instances?page_size=0") assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/consumer_api/tests/v1/test_api_library_ct.py b/clinical-mdr-api/consumer_api/tests/v1/test_api_library_ct.py index 917bd48f..083a791a 100644 --- a/clinical-mdr-api/consumer_api/tests/v1/test_api_library_ct.py +++ b/clinical-mdr-api/consumer_api/tests/v1/test_api_library_ct.py @@ -155,7 +155,10 @@ def test_get_codelists_filter_both_statuses_explicit(api_client): # ------- Codelist Term tests ------- CODELIST_TERM_FIELDS_ALL = [ - "uid", + "term_uid", + "codelist_uid", + "order", + "ordinal", "submission_value", "sponsor_preferred_name", "concept_id", @@ -168,7 +171,8 @@ def test_get_codelists_filter_both_statuses_explicit(api_client): ] CODELIST_TERM_FIELDS_NOT_NULL = [ - "uid", + "term_uid", + "codelist_uid", "submission_value", "sponsor_preferred_name", "library_name", @@ -178,6 +182,8 @@ def test_get_codelists_filter_both_statuses_explicit(api_client): "attributes_version", ] +CODELIST_UID = "C66737" + def test_get_codelist_terms(api_client): """Test retrieving codelist terms for the "CT Codelist" (10 final terms in test data).""" @@ -240,10 +246,65 @@ def test_get_codelist_terms_pagination(api_client): assert len(all_fetched) == 10 -def test_get_codelist_terms_missing_required_param(api_client): - """Test that omitting required codelist_submission_value returns 400.""" +def test_get_codelist_terms_no_filters(api_client): + """Calling without any filter returns all terms (200).""" response = api_client.get(f"{BASE_URL}/library/ct/codelist-terms") - assert_response_status_code(response, 400) + assert_response_status_code(response, 200) + res = response.json() + + TestUtils.assert_paginated_response_shape_ok(res, False) + assert len(res["items"]) > 0 + + for item in res["items"]: + TestUtils.assert_response_shape_ok( + item, CODELIST_TERM_FIELDS_ALL, CODELIST_TERM_FIELDS_NOT_NULL + ) + + +def test_get_codelist_terms_filter_by_codelist_uid(api_client): + """Filtering by codelist_uid returns the same terms as filtering by codelist_submission_value for the same codelist.""" + response_by_uid = api_client.get( + f"{BASE_URL}/library/ct/codelist-terms?codelist_uid={CODELIST_UID}" + ) + assert_response_status_code(response_by_uid, 200) + res_by_uid = response_by_uid.json() + + response_by_submval = api_client.get( + f"{BASE_URL}/library/ct/codelist-terms?codelist_submission_value={CODELIST_SUBMISSION_VALUE}" + ) + assert_response_status_code(response_by_submval, 200) + res_by_submval = response_by_submval.json() + + assert len(res_by_uid["items"]) == len(res_by_submval["items"]) + assert {item["term_uid"] for item in res_by_uid["items"]} == { + item["term_uid"] for item in res_by_submval["items"] + } + + +def test_get_codelist_terms_filter_by_both_params(api_client): + """Filtering by both codelist_uid and codelist_submission_value returns the same results as filtering by either alone.""" + response = api_client.get( + f"{BASE_URL}/library/ct/codelist-terms?codelist_uid={CODELIST_UID}&codelist_submission_value={CODELIST_SUBMISSION_VALUE}" + ) + assert_response_status_code(response, 200) + res = response.json() + + response_by_uid = api_client.get( + f"{BASE_URL}/library/ct/codelist-terms?codelist_uid={CODELIST_UID}" + ) + assert len(res["items"]) == len(response_by_uid.json()["items"]) + + +def test_get_codelist_terms_filter_by_nonexistent_codelist_uid(api_client): + """Filtering by a nonexistent codelist_uid returns empty list.""" + response = api_client.get( + f"{BASE_URL}/library/ct/codelist-terms?codelist_uid=NONEXISTENT" + ) + assert_response_status_code(response, 200) + res = response.json() + + TestUtils.assert_paginated_response_shape_ok(res, False) + assert len(res["items"]) == 0 def test_get_codelist_terms_invalid_pagination_params(api_client): diff --git a/clinical-mdr-api/consumer_api/tests/v1/test_api_studies.py b/clinical-mdr-api/consumer_api/tests/v1/test_api_studies.py index 4ce0319a..17e4cc13 100644 --- a/clinical-mdr-api/consumer_api/tests/v1/test_api_studies.py +++ b/clinical-mdr-api/consumer_api/tests/v1/test_api_studies.py @@ -6,8 +6,15 @@ import pytest from fastapi.testclient import TestClient +from clinical_mdr_api.models.study_selections.study_selection import ( + StudySelectionDataSupplierInput, + StudySelectionDataSupplierSyncInput, +) from clinical_mdr_api.services.data_completeness_tags import DataCompletenessTagService from clinical_mdr_api.services.studies.study import StudyService +from clinical_mdr_api.services.studies.study_data_supplier import ( + StudyDataSupplierSelectionService, +) from clinical_mdr_api.services.studies.study_flowchart import StudyFlowchartService from clinical_mdr_api.tests.integration.utils.api import inject_base_data from clinical_mdr_api.tests.integration.utils.factory_visit import ( @@ -35,6 +42,7 @@ "acronym", "versions", "data_completeness_tags", + "data_suppliers", ] STUDY_FIELDS_NOT_NULL = [ @@ -319,7 +327,7 @@ def test_data(api_client): studies = [study] # type: ignore[list-item] for _idx in range(1, total_studies): - rand = TestUtils.random_str(4) + rand = TestUtils.random_str(10) studies.append(TestUtils.create_study(acronym=f"ACR-{rand}")) # type: ignore[arg-type] study_epoch = create_study_epoch("EpochSubType_0001", study_uid=studies[0].uid) @@ -511,6 +519,50 @@ def test_get_studies_returns_data_completeness_tags(api_client): service.remove_tag_from_study(study_uid=studies[0].uid, tag_uid=tag2.uid) +def test_get_studies_returns_data_suppliers(api_client): + """Verify that data_suppliers are properly returned for studies.""" + ct_codelist = TestUtils.create_ct_codelist( + name="Data Supplier", + submission_value="DATA_SUPPLIER_TYPE", + extensible=True, + approve=True, + ) + ct_term = TestUtils.create_ct_term(codelist_uid=ct_codelist.codelist_uid) + data_supplier = TestUtils.create_data_supplier( + name="Consumer Data Supplier A", supplier_type_uid=ct_term.term_uid + ) + + service = StudyDataSupplierSelectionService() + service.sync_selections( + study_uid=studies[0].uid, + sync_input=StudySelectionDataSupplierSyncInput( + suppliers=[ + StudySelectionDataSupplierInput( + data_supplier_uid=data_supplier.uid, # type: ignore[arg-type] + ) + ] + ), + ) + + response = api_client.get(f"{BASE_URL}/studies?page_size=100") + assert_response_status_code(response, 200) + res = response.json() + + # Find the study we assigned tags to + study_item = next((s for s in res["items"] if s["uid"] == studies[0].uid), None) + assert study_item is not None + assert "data_suppliers" in study_item + assert isinstance(study_item["data_suppliers"], list) + assert study_item["data_suppliers"][0]["name"] == data_supplier.name + + # Verify a study without tags returns an empty list + study_without_data_supplier = next( + (s for s in res["items"] if s["uid"] == studies[1].uid), None + ) + assert study_without_data_supplier is not None + assert study_without_data_supplier["data_suppliers"] == [] + + def test_get_studies_pagination_sorting(api_client): page_size_default = 10 diff --git a/clinical-mdr-api/consumer_api/tests/v2/test_api.py b/clinical-mdr-api/consumer_api/tests/v2/test_api.py index 0647e160..920d4ae9 100644 --- a/clinical-mdr-api/consumer_api/tests/v2/test_api.py +++ b/clinical-mdr-api/consumer_api/tests/v2/test_api.py @@ -54,7 +54,7 @@ def test_data(): studies = [study] # type: ignore[list-item] for _idx in range(1, 5): rand = TestUtils.random_str(4) - studies.append(TestUtils.create_study(number=rand, acronym=f"ACR-{rand}")) # type: ignore[arg-type] + studies.append(TestUtils.create_study(acronym=f"ACR-{rand}")) # type: ignore[arg-type] def test_get_studies(api_client): diff --git a/clinical-mdr-api/consumer_api/v1/db.py b/clinical-mdr-api/consumer_api/v1/db.py index c7a6b3f3..a387082a 100644 --- a/clinical-mdr-api/consumer_api/v1/db.py +++ b/clinical-mdr-api/consumer_api/v1/db.py @@ -106,13 +106,14 @@ def get_studies( ORDER BY hv.start_date DESC WITH study_root, + study_value, study_root.uid as uid, study_value.study_acronym as acronym, study_value.study_id_prefix as id_prefix, study_value.study_number as number, - CASE study_value.subpart_id + CASE study_value.study_subpart_acronym WHEN IS NULL THEN COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '') - ELSE COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '') + "-" + study_value.subpart_id + ELSE COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '') + "-" + study_value.study_subpart_acronym END AS id, hv_ld as version_latest_draft, COLLECT(DISTINCT {{ @@ -131,14 +132,28 @@ def get_studies( [v IN versions_all WHERE v.version_status IN ['RELEASED', 'LOCKED'] OR (v.version_started_at = version_latest_draft.start_date AND v.version_ended_at is null)] as versions - + + OPTIONAL MATCH (study_value)-[hsds:HAS_STUDY_DATA_SUPPLIER]->(sds:StudyDataSupplier) + OPTIONAL MATCH (sds)-[hds:HAS_DATA_SUPPLIER]->(dsv:DataSupplierValue) + OPTIONAL MATCH (sds)-[:HAS_STUDY_DATA_SUPPLIER_TYPE]->(ctc:CTTermContext) + OPTIONAL MATCH (ctc)-[:HAS_SELECTED_TERM]->(ctr:CTTermRoot)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(ctnv:CTTermNameValue) + OPTIONAL MATCH (ctr)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm)<-[:HAS_TERM]-(ccr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]-> + (:CTCodelistAttributesRoot)-[:LATEST]->(:CTCodelistAttributesValue {{submission_value: "DATA_SUPPLIER_TYPE"}}) + RETURN uid, acronym, id_prefix, number, id, versions, - [(study_root)-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) | t.name] as data_completeness_tags + [(study_root)-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) | t.name] as data_completeness_tags, + [ds IN COLLECT(DISTINCT {{ + uid: sds.uid, + name: dsv.name, + type_uid: ctr.uid, + type_codelist_uid: ccr.uid, + order: sds.order + }}) WHERE ds.uid IS NOT NULL] AS study_data_suppliers """ full_query = " ".join( @@ -515,9 +530,9 @@ def get_study_operational_soa( RETURN DISTINCT study_root.uid AS study_uid, - CASE study_value.subpart_id + CASE study_value.study_subpart_acronym WHEN IS NULL THEN toUpper(COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '')) - ELSE toUpper(COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '')) + "-" + study_value.subpart_id + ELSE toUpper(COALESCE(study_value.study_id_prefix, '') + "-" + COALESCE(study_value.study_number, '')) + "-" + study_value.study_subpart_acronym END AS study_id, study_visit.uid AS visit_uid, study_visit.short_visit_label AS visit_short_name, @@ -673,10 +688,13 @@ def get_library_activity_instances( MATCH (library:Library)-[:CONTAINS_CONCEPT]->(concept_root:ActivityInstanceRoot)-[:LATEST]->(concept_value:ActivityInstanceValue) """ ) + base_query += """ + MATCH (concept_root)-[:HAS_GROUPING_ROOT]->(grouping_root:ActivityInstanceGroupingRoot)-[:LATEST]->(grouping_value:ActivityInstanceGroupingValue) + """ base_query += f""" WITH - DISTINCT concept_root, concept_value, library + DISTINCT concept_root, concept_value, grouping_root, grouping_value, library CALL {{ WITH concept_root, concept_value MATCH (concept_root)-[hv:HAS_VERSION]-(concept_value) @@ -689,7 +707,19 @@ def get_library_activity_instances( WITH collect(hv) as hvs RETURN last(hvs) AS last_version_rel }} - WITH concept_root, concept_value, last_version_rel, library + CALL {{ + WITH grouping_root, grouping_value + MATCH (grouping_root)-[hv:HAS_VERSION]-(grouping_value) + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.end_date ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS last_grouping_version_rel + }} + WITH concept_root, concept_value, grouping_root, grouping_value, last_version_rel, last_grouping_version_rel, library {status_filter} @@ -697,15 +727,20 @@ def get_library_activity_instances( concept_root.uid AS uid, library.name AS library_name, last_version_rel, + last_grouping_version_rel, concept_value.nci_concept_id AS nci_concept_id, concept_value.nci_concept_name AS nci_concept_name, concept_value.name AS name, concept_value.definition AS definition, last_version_rel.status AS status, last_version_rel.version AS version, + last_grouping_version_rel.status AS groupings_status, + last_grouping_version_rel.version AS groupings_version, concept_value.topic_code AS topic_code, concept_value.adam_param_code AS param_code, - apoc.coll.toSet([(concept_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping) + head([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]->(aic_root:ActivityInstanceClassRoot) | aic_root.uid]) AS activity_instance_class_uid, + head([(concept_value)-[:ACTIVITY_INSTANCE_CLASS]->(:ActivityInstanceClassRoot)-[:LATEST]->(aic_val:ActivityInstanceClassValue) | aic_val.name]) AS activity_instance_class_name, + apoc.coll.toSet([(grouping_value)-[:HAS_ACTIVITY]->(activity_grouping:ActivityGrouping) | {{ activity: head(apoc.coll.sortMulti([(activity_grouping)<-[:HAS_GROUPING]-(activity_value:ActivityValue)<-[has_version:HAS_VERSION]- (activity_root:ActivityRoot) | @@ -731,7 +766,28 @@ def get_library_activity_instances( major_version: toInteger(split(has_version.version,'.')[0]), minor_version: toInteger(split(has_version.version,'.')[1]) }}], ['major_version', 'minor_version'])) - }}]) AS activity_groupings + }}]) AS activity_groupings, + [(concept_value)-[:CONTAINS_ACTIVITY_ITEM]->(ai) + <-[:HAS_ACTIVITY_ITEM]-(aic_root)-[:LATEST]->(aic_val) | {{ + activity_item_class_uid: aic_root.uid, + activity_item_class_name: aic_val.name, + data_type: head([(aic_val)-[:HAS_DATA_TYPE]->(:CTTermContext) + -[:HAS_SELECTED_TERM]->(:CTTermRoot)-[:HAS_NAME_ROOT]-> + (:CTTermNameRoot)-[:LATEST]->(dtv:CTTermNameValue) | dtv.name]), + ct_codelist: head([(ai)-[:HAS_CODELIST]->(clr:CTCodelistRoot) + -[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot) + -[:LATEST]->(clav:CTCodelistAttributesValue) + | {{uid: clr.uid, submission_value: clav.submission_value}}]), + ct_terms: [(ai)-[:HAS_CT_TERM]->(:CTTermContext)-[:HAS_SELECTED_TERM]-> + (tr:CTTermRoot)<-[:HAS_TERM_ROOT]-(:CTCodelistTerm) + <-[:HAS_TERM]-(clr:CTCodelistRoot) + | {{uid: tr.uid, codelist_uid: clr.uid}}], + unit_definitions: [(ai)-[:HAS_UNIT_DEFINITION]->(udr:UnitDefinitionRoot) + | {{uid: udr.uid}}], + text_value: ai.text_value, + is_adam_param_specific: ai.is_adam_param_specific, + is_activity_instance_id_specific: ai.is_activity_instance_id_specific + }}] AS activity_items {activity_uid_filter} @@ -743,9 +799,14 @@ def get_library_activity_instances( nci_concept_name, topic_code, param_code, + activity_instance_class_uid, + activity_instance_class_name, activity_groupings, + activity_items, status, - version + version, + groupings_status, + groupings_version """ full_query = " ".join( @@ -1044,7 +1105,8 @@ def get_codelists( def get_codelist_terms( - codelist_submission_value: str, + codelist_submission_value: str | None = None, + codelist_uid: str | None = None, page_size: int = 10, page_number: int = 1, name_status: models.LibraryItemStatus | None = None, @@ -1071,15 +1133,34 @@ def get_codelist_terms( elif name_status_filter: status_filter = f"WHERE {name_status_filter}" - params = { - "codelist_submission_value": codelist_submission_value, + params: dict[str, Any] = { "status_attributes": attributes_status.value if attributes_status else None, "status_name": name_status.value if name_status else None, } + # Build the codelist match clause depending on which filters are provided + codelist_match_lines = [ + "MATCH (codelist_root:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)-[:LATEST]->(clav:CTCodelistAttributesValue)" + ] + codelist_where_parts = [] + + if codelist_submission_value is not None: + codelist_where_parts.append( + "clav.submission_value = $codelist_submission_value" + ) + params["codelist_submission_value"] = codelist_submission_value + + if codelist_uid is not None: + codelist_where_parts.append("codelist_root.uid = $codelist_uid") + params["codelist_uid"] = codelist_uid + + if codelist_where_parts: + codelist_match_lines.append("WHERE " + " AND ".join(codelist_where_parts)) + + codelist_match = "\n ".join(codelist_match_lines) + base_query = f""" - MATCH (codelist_root:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]-> - (:CTCodelistAttributesRoot)-[:LATEST]->(:CTCodelistAttributesValue {{submission_value: $codelist_submission_value}}) + {codelist_match} MATCH (codelist_root)-[ht:HAS_TERM]->(ct_cl_term:CTCodelistTerm)-[:HAS_TERM_ROOT]->(ct_term_root:CTTermRoot)<-[:CONTAINS_TERM]-(library:Library) WHERE ht.end_date IS NULL @@ -1112,13 +1193,17 @@ def get_codelist_terms( RETURN last(hvs) AS last_version_rel_name }} - WITH ct_term_root, ct_cl_term, tnv, tav, library, + WITH codelist_root, ct_term_root, ct_cl_term, ht, tnv, tav, library, last_version_rel_attributes, last_version_rel_name {status_filter} WITH - ct_term_root.uid AS uid, + codelist_root.uid as codelist_uid, + ct_term_root.uid AS term_uid, + codelist_root.uid + '_' + ct_term_root.uid AS sort_field, + ht.order AS order, + ht.ordinal AS ordinal, ct_cl_term.submission_value AS submission_value, tav.concept_id AS concept_id, tav.preferred_term AS nci_preferred_name, @@ -1135,7 +1220,7 @@ def get_codelist_terms( full_query = " ".join( [ base_query, - db_sort_clause("sponsor_preferred_name", "ASC"), + db_sort_clause("sort_field", "ASC", secondary_sort_fields="sort_field"), db_pagination_clause(page_size, page_number), ] ) diff --git a/clinical-mdr-api/consumer_api/v1/main.py b/clinical-mdr-api/consumer_api/v1/main.py index 09eb1cb9..8209848a 100644 --- a/clinical-mdr-api/consumer_api/v1/main.py +++ b/clinical-mdr-api/consumer_api/v1/main.py @@ -51,6 +51,10 @@ def get_studies( Returned `version_number` value can be used in other endpoints to retrieve study entities (e.g. visits, activities, etc.) associated with a specific study version. + + Codelist details can be retrieved from the `GET /v1/library/ct/codelists` endpoint. + + Details related to the Data Supplier type can be retrieved from the `GET /v1/library/ct/codelist-terms?codelist_submission_value=DATA_SUPPLIER_TYPE` endpoint. """ studies = DB.get_studies( sort_by=sort_by, @@ -714,7 +718,7 @@ def get_codelists( ) -# GET endpoint /library/ct/codelist-terms?codelist_submission_value=XYZ that returns list of codelist terms for the specified codelist submission value +# GET endpoint /library/ct/codelist-terms that returns list of codelist terms, optionally filtered by codelist submission value and/or codelist UID @router.get( "/library/ct/codelist-terms", tags=["[V1] Library"], @@ -730,11 +734,15 @@ def get_codelists( def get_codelist_terms( request: Request, codelist_submission_value: Annotated[ - str, + str | None, Query( description="Codelist submission value to filter by, for example `TIMELB`, `TIMEREF`, `VISCNTMD`, `FLWCRTGRP`, `EPOCHSTP` etc." ), - ], + ] = None, + codelist_uid: Annotated[ + str | None, + Query(description="Codelist UID to filter by."), + ] = None, page_size: Annotated[int, PAGE_SIZE_QUERY] = settings.page_size_100, page_number: Annotated[ int, PAGE_NUMBER_QUERY @@ -743,13 +751,16 @@ def get_codelist_terms( attributes_status: models.LibraryItemStatus | None = models.LibraryItemStatus.FINAL, ) -> PaginatedResponse[models.CodelistTerm]: """ - Returns a paginated list of CT codelist terms for the specified codelist submission value, - sorted by ascending sponsor preferred name. + Returns a paginated list of CT codelist terms, sorted by ascending by codelist UID, then term UID. + + If neither `codelist_submission_value` nor `codelist_uid` is provided, all terms are returned. + If either is provided, terms are filtered accordingly. - Terms can be filtered by `name_status` and `attributes_status` (_Final, Draft, Retired_). Both default to _Final_. + Terms can also be filtered by `name_status` and `attributes_status` (_Final, Draft, Retired_). Both default to _Final_. """ codelist_terms = DB.get_codelist_terms( codelist_submission_value=codelist_submission_value, + codelist_uid=codelist_uid, page_size=page_size, page_number=page_number, name_status=name_status, @@ -768,6 +779,7 @@ def get_codelist_terms( ], query_param_names=[ "codelist_submission_value", + "codelist_uid", "name_status", "attributes_status", ], diff --git a/clinical-mdr-api/consumer_api/v1/models.py b/clinical-mdr-api/consumer_api/v1/models.py index 18a47ef0..7e098ade 100644 --- a/clinical-mdr-api/consumer_api/v1/models.py +++ b/clinical-mdr-api/consumer_api/v1/models.py @@ -112,6 +112,12 @@ def from_input(cls, val: dict[str, Any]): version_description=val.get("version_description", None), ) + class StudyDataSupplier(BaseModel): + uid: Annotated[str, Field()] + name: Annotated[str, Field()] + type: Annotated["SimpleCodelistTerm", Field()] + order: Annotated[int | None, Field(json_schema_extra={"nullable": True})] = None + uid: Annotated[str, Field(description="Study UID")] id: Annotated[str, Field(description="Study ID")] id_prefix: Annotated[str, Field(description="Study ID prefix")] @@ -128,6 +134,10 @@ def from_input(cls, val: dict[str, Any]): description="List of data completeness tag names assigned to the study.", default_factory=list, ) + data_suppliers: list[StudyDataSupplier] = Field( + description="List of data suppliers of the study.", + default_factory=list, + ) @classmethod def from_input(cls, val: dict[str, Any]): @@ -143,6 +153,21 @@ def from_input(cls, val: dict[str, Any]): for version in val.get("versions", []) ], data_completeness_tags=val.get("data_completeness_tags", []), + data_suppliers=sorted( + [ + Study.StudyDataSupplier( + uid=study_data_supplier["uid"], + name=study_data_supplier["name"], + type=SimpleCodelistTerm( + codelist_uid=study_data_supplier["type_codelist_uid"], + term_uid=study_data_supplier["type_uid"], + ), + order=study_data_supplier.get("order", None), + ) + for study_data_supplier in val.get("study_data_suppliers", []) + ], + key=lambda x: x.order if x.order is not None else float("inf"), + ), ) @@ -803,6 +828,64 @@ def from_input(cls, val: dict[str, Any]): ) +class LibraryActivityItemUnitDefinition(BaseModel): + uid: Annotated[str, Field(description="Unit Definition UID")] + + +class LibraryActivityItemClass(BaseModel): + uid: Annotated[str, Field(description="Activity Item Class UID")] + name: Annotated[str, Field(description="Activity Item Class Name")] + + +class LibraryActivityItemCTCodelist(BaseModel): + uid: Annotated[str, Field(description="CT Codelist UID")] + submission_value: Annotated[str, Field(description="CT Codelist Submission Value")] + + +class LibraryActivityItem(BaseModel): + activity_item_class: Annotated[ + LibraryActivityItemClass, + Field(description="Activity Item Class"), + ] + data_type: Annotated[ + str, + Field(description="Data type of the activity item"), + ] + ct_codelist: Annotated[ + LibraryActivityItemCTCodelist | None, + Field(description="CT Codelist", json_schema_extra={"nullable": True}), + ] = None + ct_terms: Annotated[ + list[SimpleCodelistTerm], + Field(description="CT Terms"), + ] = [] + unit_definitions: Annotated[ + list[LibraryActivityItemUnitDefinition], + Field(description="Unit Definitions"), + ] = [] + text_value: Annotated[ + str | None, + Field(description="Text Value", json_schema_extra={"nullable": True}), + ] = None + is_adam_param_specific: Annotated[ + bool, Field(description="Is ADaM Parameter Specific") + ] = False + is_activity_instance_id_specific: Annotated[ + bool | None, Field(description="Is Activity Instance ID Specific") + ] = None + + +class LibraryActivityInstanceClass(BaseModel): + uid: Annotated[str, Field(description="Activity Instance Class UID")] + name: Annotated[ + str | None, + Field( + description="Activity Instance Class Name", + json_schema_extra={"nullable": True}, + ), + ] = None + + class LibraryActivityInstance(BaseModel): uid: Annotated[str, Field(description="Activity UID")] library: Annotated[str, Field(description="Library Name")] @@ -829,13 +912,29 @@ class LibraryActivityInstance(BaseModel): ] = None status: Annotated[LibraryItemStatus, Field(description="Activity Status")] version: Annotated[str, Field(description="Activity Version")] + activity_instance_class: Annotated[ + LibraryActivityInstanceClass | None, + Field( + description="Activity Instance Class", json_schema_extra={"nullable": True} + ), + ] = None groupings: Annotated[ list[LibraryActivityGroupingWithActivity], Field(description="Activity Groups/Subgroups"), ] = [] + groupings_status: Annotated[ + LibraryItemStatus, Field(description="Activity Groupings Status") + ] + groupings_version: Annotated[str, Field(description="Activity Groupings Version")] + activity_items: Annotated[ + list[LibraryActivityItem], + Field(description="Activity Items"), + ] = [] @classmethod def from_input(cls, val: dict[str, Any]): + aic_uid = val.get("activity_instance_class_uid") + aic_name = val.get("activity_instance_class_name") return cls( uid=val["uid"], library=val["library_name"], @@ -847,6 +946,11 @@ def from_input(cls, val: dict[str, Any]): param_code=val.get("param_code", None), status=LibraryItemStatus(val["status"]), version=val["version"], + activity_instance_class=( + LibraryActivityInstanceClass(uid=aic_uid, name=aic_name) + if aic_uid + else None + ), groupings=[ LibraryActivityGroupingWithActivity( activity_uid=grouping["activity"]["uid"], @@ -858,6 +962,50 @@ def from_input(cls, val: dict[str, Any]): ) for grouping in val.get("activity_groupings", []) ], + groupings_status=LibraryItemStatus(val["groupings_status"]), + groupings_version=val["groupings_version"], + activity_items=[ + LibraryActivityItem( + activity_item_class=LibraryActivityItemClass( + uid=item.get("activity_item_class_uid", ""), + name=item.get("activity_item_class_name", ""), + ), + data_type=item["data_type"], + ct_codelist=( + LibraryActivityItemCTCodelist( + uid=item["ct_codelist"]["uid"], + submission_value=item["ct_codelist"]["submission_value"], + ) + if item.get("ct_codelist") + else None + ), + ct_terms=sorted( + [ + SimpleCodelistTerm( + term_uid=t["uid"], + codelist_uid=t["codelist_uid"], + ) + for t in item.get("ct_terms", []) + ], + key=lambda x: x.term_uid or "", + ), + unit_definitions=sorted( + [ + LibraryActivityItemUnitDefinition( + uid=u.get("uid", ""), + ) + for u in item.get("unit_definitions", []) + ], + key=lambda x: x.uid or "", + ), + text_value=item.get("text_value"), + is_adam_param_specific=item.get("is_adam_param_specific", False), + is_activity_instance_id_specific=item.get( + "is_activity_instance_id_specific" + ), + ) + for item in val.get("activity_items", []) + ], ) @@ -1015,8 +1163,28 @@ class SoACreateResponse(BaseModel): ] +class SimpleCodelistTerm(BaseModel): + codelist_uid: Annotated[str, Field(description="Codelist Term UID")] + term_uid: Annotated[str, Field(description="Codelist Term UID")] + + class CodelistTerm(BaseModel): - uid: Annotated[str, Field(description="Codelist Term UID")] + codelist_uid: Annotated[str, Field(description="Codelist UID")] + term_uid: Annotated[str, Field(description="Codelist Term UID")] + order: Annotated[ + int | None, + Field( + description="Term order within the codelist", + json_schema_extra={"nullable": True}, + ), + ] = None + ordinal: Annotated[ + float | None, + Field( + description="Term ordinal value (only for ordinal codelists)", + json_schema_extra={"nullable": True}, + ), + ] = None submission_value: Annotated[str, Field(description="Submission Value")] sponsor_preferred_name: Annotated[ str, @@ -1046,7 +1214,10 @@ class CodelistTerm(BaseModel): @classmethod def from_input(cls, val: dict[str, Any]): return cls( - uid=val["uid"], + term_uid=val["term_uid"], + codelist_uid=val["codelist_uid"], + order=val.get("order"), + ordinal=val.get("ordinal"), submission_value=val["submission_value"], sponsor_preferred_name=val["sponsor_preferred_name"], concept_id=val.get("concept_id", None), diff --git a/clinical-mdr-api/openapi.json b/clinical-mdr-api/openapi.json index c054dbe4..53a2fe3e 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": "3.0.628" + "version": "3.0.642" }, "paths": { "/": { @@ -2561,11 +2561,11 @@ "required": false, "schema": { "type": "boolean", - "description": "If true, all existing form relationships will be replaced with the provided form relationships.", + "description": "\nWhen true, replaces all existing item relationships with the provided ones.\nWhen false, appends the provided item relationships to existing ones, continuing the order sequence.\n ", "default": false, "title": "Override" }, - "description": "If true, all existing form relationships will be replaced with the provided form relationships." + "description": "\nWhen true, replaces all existing item relationships with the provided ones.\nWhen false, appends the provided item relationships to existing ones, continuing the order sequence.\n " } ], "requestBody": { @@ -3845,11 +3845,11 @@ "required": false, "schema": { "type": "boolean", - "description": "If true, all existing item group relationships will be replaced with the provided item group relationships.", + "description": "\nWhen true, replaces all existing item relationships with the provided ones. \nWhen false, appends the provided item relationships to existing ones, continuing the order sequence.\n ", "default": false, "title": "Override" }, - "description": "If true, all existing item group relationships will be replaced with the provided item group relationships." + "description": "\nWhen true, replaces all existing item relationships with the provided ones. \nWhen false, appends the provided item relationships to existing ones, continuing the order sequence.\n " } ], "requestBody": { @@ -5129,11 +5129,11 @@ "required": false, "schema": { "type": "boolean", - "description": "If true, all existing item relationships will be replaced with the provided item relationships.", + "description": "\nWhen true, replaces all existing item relationships with the provided ones. \nWhen false, appends the provided item relationships to existing ones, continuing the order sequence.\n ", "default": false, "title": "Override" }, - "description": "If true, all existing item relationships will be replaced with the provided item relationships." + "description": "\nWhen true, replaces all existing item relationships with the provided ones. \nWhen false, appends the provided item relationships to existing ones, continuing the order sequence.\n " } ], "requestBody": { @@ -38439,6 +38439,190 @@ } } }, + "/ct/paired-codelists/{codelist_uid}/terms": { + "get": { + "tags": [ + "CT Codelists" + ], + "summary": "Returns terms from the paired codelists identified by the given codelist UID.", + "description": "Returns the list of all terms coming from the codelist specified by the given UID and its paired codelist. Each term includes both the code_submission_value (from the codes codelist) and the name_submission_value (from the names codelist).", + "operationId": "get_paired_codelist_terms_ct_paired_codelists__codelist_uid__terms_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "codelist_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the CTCodelistRoot", + "title": "Codelist Uid" + }, + "description": "The unique id of the CTCodelistRoot" + }, + { + "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": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "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_CTPairedCodelistTerm_" + } + } + } + }, + "400": { + "description": "Bad Request - The codelist does not have a paired codelist.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, "/ct/codelists/headers": { "get": { "tags": [ @@ -47272,6 +47456,24 @@ }, "description": "A list of activity_instance_class names to use as a specific filter" }, + { + "name": "status", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Filter by status, matching either activity instance status or groupings status", + "title": "Status" + }, + "description": "Filter by status, matching either activity instance status or groupings status" + }, { "name": "sort_by", "in": "query", @@ -47489,14 +47691,14 @@ } } }, - "/concepts/activities/activity-instances/versions": { + "/concepts/activities/activity-instances/attributes/versions": { "get": { "tags": [ "Activity Instances" ], "summary": "List all versions of all activity instances (for a given library)", "description": "State before:\n - The library must exist (if specified)\n \nBusiness logic:\n - List version history of all activity instances\n - The returned versions are ordered by version start_date descending (newest entries first).\n\nState after:\n - No change\n \nPossible errors:\n - Invalid library name specified.\n\n\n\nResponse format:\n\n- In addition to retrieving data in JSON format (default behaviour), \nit is possible to request data to be returned in CSV, XML or Excel formats \nby sending the `Accept` http request header with one of the following values:\n - `text/csv`\n\n - `text/xml`\n\n - `application/vnd.openxmlformats-officedocument.spreadsheetml.sheet`", - "operationId": "get_activity_instances_versions_concepts_activities_activity_instances_versions_get", + "operationId": "get_activity_instances_versions_concepts_activities_activity_instances_attributes_versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -47665,7 +47867,7 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/CustomPage_ActivityInstance_" + "$ref": "#/components/schemas/CustomPage_ActivityInstanceAttributes_" } } } @@ -47956,87 +48158,6 @@ } } }, - "patch": { - "tags": [ - "Activity Instances" - ], - "summary": "Update activity instance", - "description": "State before:\n - uid must exist and activity instance must exist in status draft.\n - The activity instance must belongs to a library that allows deleting (the 'is_editable' property of the library needs to be true).\n\nBusiness logic:\n - If activity instance exist in status draft then attributes are updated.\n- If the linked activity instance is updated, the relationships are updated to point to the activity instance value node.\n\nState after:\n - attributes are updated for the activity instance.\n - Audit trail entry must be made with update of attributes.\n\nPossible errors:\n - Invalid uid.", - "operationId": "edit_concepts_activities_activity_instances__activity_instance_uid__patch", - "security": [ - { - "OAuth2AuthorizationCodeBearer": [] - }, - { - "BearerJwtAuth": [] - } - ], - "parameters": [ - { - "name": "activity_instance_uid", - "in": "path", - "required": true, - "schema": { - "type": "string", - "description": "The unique id of the ActivityInstance", - "title": "Activity Instance Uid" - }, - "description": "The unique id of the ActivityInstance" - } - ], - "requestBody": { - "required": true, - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ActivityInstanceEditInput" - } - } - } - }, - "responses": { - "200": { - "description": "OK.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ActivityInstance" - } - } - } - }, - "403": { - "description": "Forbidden", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "400": { - "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in draft status.\n- The activity instance had been in 'Final' status before.\n- The library doesn't allow to edit draft versions.\n", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "404": { - "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - } - } - }, "delete": { "tags": [ "Activity Instances" @@ -48193,14 +48314,14 @@ } } }, - "/concepts/activities/activity-instances/{activity_instance_uid}/activity-groupings": { + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes": { "get": { "tags": [ "Activity Instances" ], - "summary": "Get activity groupings for a specific activity instance", - "description": "Returns activity groupings (hierarchy) for an activity instance, including:\n - Activity information with version and library details\n - Activity groups with name and definition\n - Activity subgroups with name and definition\n\nState before:\n - an activity instance with uid must exist.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.\n\n{_generic_descriptions.DATA_EXPORTS_HEADER}", - "operationId": "get_activity_instance_groupings_concepts_activities_activity_instances__activity_instance_uid__activity_groupings_get", + "summary": "Get details on a specific activity instance attributes (in a specific version)", + "description": "State before:\n - a activity instance with uid must exist.\n\nBusiness logic:\n - If parameter at_specified_date_time is specified then the latest/newest representation of the concept at this point in time is returned. The point in time needs to be specified in ISO 8601 format including the timezone, e.g.: '2020-10-31T16:00:00+02:00' for October 31, 2020 at 4pm in UTC+2 timezone. If the timezone is ommitted, UTC\ufffd0 is assumed.\n - If parameter status is specified then the representation of the concept in that status is returned (if existent). This is useful if the concept has a status 'Draft' and a status 'Final'.\n - If parameter version is specified then the latest/newest representation of the concept in that version is returned. Only exact matches are considered. The version is specified in the following format: . where and are digits. E.g. '0.1', '0.2', '1.0', ...\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid, at_specified_date_time, status or version.", + "operationId": "get_activity_instance_attributes_concepts_activities_activity_instances__activity_instance_uid__attributes_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48220,22 +48341,6 @@ "title": "Activity Instance Uid" }, "description": "The unique id of the ActivityInstance" - }, - { - "name": "version", - "in": "query", - "required": false, - "schema": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Version" - } } ], "responses": { @@ -48244,11 +48349,7 @@ "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SimpleActivityInstanceGrouping" - }, - "title": "Response 200 Get Activity Instance Groupings Concepts Activities Activity Instances Activity Instance Uid Activity Groupings Get" + "$ref": "#/components/schemas/ActivityInstanceAttributes" } } } @@ -48284,16 +48385,14 @@ } } } - } - }, - "/concepts/activities/activity-instances/{activity_instance_uid}/activity-items": { - "get": { + }, + "patch": { "tags": [ "Activity Instances" ], - "summary": "Get activity items for a specific activity instance", - "description": "Returns activity items for an activity instance, including:\n - Activity item class information (name, role, data type)\n - CT terms (controlled terminology terms)\n - Unit definitions with dimension names\n - ODM forms, item groups, and items\n - ADaM parameter specificity flags\n\nState before:\n - an activity instance with uid must exist.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.\n\n{_generic_descriptions.DATA_EXPORTS_HEADER}", - "operationId": "get_activity_instance_items_concepts_activities_activity_instances__activity_instance_uid__activity_items_get", + "summary": "Update activity instance attributes", + "description": "State before:\n - uid must exist and activity instance attributes must exist in status draft.\n - The activity instance must belongs to a library that allows deleting (the 'is_editable' property of the library needs to be true).\n\nBusiness logic:\n - If activity instance exist in status draft then attributes are updated.\n- If the linked activity instance is updated, the relationships are updated to point to the activity instance value node.\n\nState after:\n - attributes are updated for the activity instance.\n - Audit trail entry must be made with update of attributes.\n\nPossible errors:\n - Invalid uid.", + "operationId": "edit_concepts_activities_activity_instances__activity_instance_uid__attributes_patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48313,35 +48412,25 @@ "title": "Activity Instance Uid" }, "description": "The unique id of the ActivityInstance" - }, - { - "name": "version", - "in": "query", - "required": false, - "schema": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Version" - } } ], + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceAttributesEditInput" + } + } + } + }, "responses": { "200": { - "description": "Successful Response", + "description": "OK.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SimplifiedActivityItem" - }, - "title": "Response 200 Get Activity Instance Items Concepts Activities Activity Instances Activity Instance Uid Activity Items Get" + "$ref": "#/components/schemas/ActivityInstanceAttributes" } } } @@ -48356,8 +48445,8 @@ } } }, - "404": { - "description": "Entity not found", + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in draft status.\n- The activity instance had been in 'Final' status before.\n- The library doesn't allow to edit draft versions.\n", "content": { "application/json": { "schema": { @@ -48366,8 +48455,8 @@ } } }, - "400": { - "description": "Bad Request", + "404": { + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", "content": { "application/json": { "schema": { @@ -48379,14 +48468,14 @@ } } }, - "/concepts/activities/activity-instances/{activity_instance_uid}/overview.cosmos": { + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings": { "get": { "tags": [ "Activity Instances" ], - "summary": "Get a COSMoS compatible representation of a specific activity instance", - "description": "Returns detailed description about activity instance, including information about:\n - Activity subgroups\n - Activity groups\n - Activity instance\n - Activity instance class\n\nState before:\n - an activity instance with uid must exist.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.", - "operationId": "get_cosmos_activity_instance_overview_concepts_activities_activity_instances__activity_instance_uid__overview_cosmos_get", + "summary": "Get details on a specific activity instance groupings (in a specific version)", + "description": "State before:\n - a activity instance with uid must exist.\n\nBusiness logic:\n - If parameter at_specified_date_time is specified then the latest/newest representation of the concept at this point in time is returned. The point in time needs to be specified in ISO 8601 format including the timezone, e.g.: '2020-10-31T16:00:00+02:00' for October 31, 2020 at 4pm in UTC+2 timezone. If the timezone is ommitted, UTC\ufffd0 is assumed.\n - If parameter status is specified then the representation of the concept in that status is returned (if existent). This is useful if the concept has a status 'Draft' and a status 'Final'.\n - If parameter version is specified then the latest/newest representation of the concept in that version is returned. Only exact matches are considered. The version is specified in the following format: . where and are digits. E.g. '0.1', '0.2', '1.0', ...\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid, at_specified_date_time, status or version.", + "operationId": "get_activity_instance_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48406,6 +48495,22 @@ "title": "Activity Instance Uid" }, "description": "The unique id of the ActivityInstance" + }, + { + "name": "version", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Version" + } } ], "responses": { @@ -48413,9 +48518,10 @@ "description": "Successful Response", "content": { "application/json": { - "schema": {} - }, - "application/x-yaml": {} + "schema": { + "$ref": "#/components/schemas/ActivityInstanceGroupings" + } + } } }, "403": { @@ -48449,16 +48555,14 @@ } } } - } - }, - "/concepts/activities/activity-instances/{activity_instance_uid}/versions": { - "get": { + }, + "patch": { "tags": [ "Activity Instances" ], - "summary": "List version history for activity instance", - "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for activity instance.\n - The returned versions are ordered by start_date descending (newest entries first).\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.", - "operationId": "get_versions_concepts_activities_activity_instances__activity_instance_uid__versions_get", + "summary": "Update activity instance groupings", + "description": "State before:\n - uid must exist and activity instance groupings must exist in status draft.\n - The activity instance must belongs to a library that allows deleting (the 'is_editable' property of the library needs to be true).\n\nBusiness logic:\n - If activity instance exist in status draft then groupings are updated.\n- If the linked activity instance is updated, the relationships are updated to point to the activity instance value node.\n\nState after:\n - groupings are updated for the activity instance.\n - Audit trail entry must be made with update of groupings.\n\nPossible errors:\n - Invalid uid.", + "operationId": "edit_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48480,17 +48584,23 @@ "description": "The unique id of the ActivityInstance" } ], + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceGroupingsEditInput" + } + } + } + }, "responses": { "200": { - "description": "Successful Response", + "description": "OK.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/ActivityInstance" - }, - "title": "Response Get Versions Concepts Activities Activity Instances Activity Instance Uid Versions Get" + "$ref": "#/components/schemas/ActivityInstanceGroupings" } } } @@ -48505,8 +48615,8 @@ } } }, - "404": { - "description": "Not Found - The activity isntance with the specified 'activity_instance_uid' wasn't found.", + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in draft status.\n- The activity instance had been in 'Final' status before.\n- The library doesn't allow to edit draft versions.\n", "content": { "application/json": { "schema": { @@ -48515,8 +48625,8 @@ } } }, - "400": { - "description": "Bad Request", + "404": { + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", "content": { "application/json": { "schema": { @@ -48526,14 +48636,16 @@ } } } - }, - "post": { + } + }, + "/concepts/activities/activity-instances/{activity_instance_uid}/activity-items": { + "get": { "tags": [ "Activity Instances" ], - "summary": " Create a new version of an activity instance", - "description": "State before:\n - uid must exist and the activity instance must be in status Final.\n \nBusiness logic:\n- The activity instance is changed to a draft state.\n\nState after:\n - Activity instance changed status to Draft and assigned a new minor version number.\n - Audit trail entry must be made with action of creating a new draft version.\n \nPossible errors:\n - Invalid uid or status not Final.", - "operationId": "create_new_version_concepts_activities_activity_instances__activity_instance_uid__versions_post", + "summary": "Get activity items for a specific activity instance", + "description": "Returns activity items for an activity instance, including:\n - Activity item class information (name, role, data type)\n - CT terms (controlled terminology terms)\n - Unit definitions with dimension names\n - ODM forms, item groups, and items\n - ADaM parameter specificity flags\n\nState before:\n - an activity instance with uid must exist.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.\n\n{_generic_descriptions.DATA_EXPORTS_HEADER}", + "operationId": "get_activity_instance_items_concepts_activities_activity_instances__activity_instance_uid__activity_items_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48553,15 +48665,35 @@ "title": "Activity Instance Uid" }, "description": "The unique id of the ActivityInstance" + }, + { + "name": "version", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Version" + } } ], "responses": { - "201": { - "description": "OK.", + "200": { + "description": "Successful Response", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ActivityInstance" + "type": "array", + "items": { + "$ref": "#/components/schemas/SimplifiedActivityItem" + }, + "title": "Response 200 Get Activity Instance Items Concepts Activities Activity Instances Activity Instance Uid Activity Items Get" } } } @@ -48576,8 +48708,8 @@ } } }, - "400": { - "description": "Forbidden - Reasons include e.g.: \n- The library doesn't allow to create activity instances.\n", + "404": { + "description": "Entity not found", "content": { "application/json": { "schema": { @@ -48586,8 +48718,8 @@ } } }, - "404": { - "description": "Not Found - Reasons include e.g.: \n- The activity instance is not in final status.\n- The activity instance with the specified 'activity_instance_uid' could not be found.", + "400": { + "description": "Bad Request", "content": { "application/json": { "schema": { @@ -48599,34 +48731,43 @@ } } }, - "/concepts/activities/activity-instances/preview": { - "post": { + "/concepts/activities/activity-instances/{activity_instance_uid}/overview.cosmos": { + "get": { "tags": [ "Activity Instances" ], - "summary": "Previews the creation of a new activity instance.", - "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 with the set properties.\n - relationships to specified activity parent are created (as in the model)\n - relationships to specified activity instance class is 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 - activity instance 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": "preview_concepts_activities_activity_instances_preview_post", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ActivityInstancePreviewInput", - "description": "Related parameters of the objective that shall be previewed." - } - } + "summary": "Get a COSMoS compatible representation of a specific activity instance", + "description": "Returns detailed description about activity instance, including information about:\n - Activity subgroups\n - Activity groups\n - Activity instance\n - Activity instance class\n\nState before:\n - an activity instance with uid must exist.\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.", + "operationId": "get_cosmos_activity_instance_overview_concepts_activities_activity_instances__activity_instance_uid__overview_cosmos_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] }, - "required": true - }, + { + "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" + } + ], "responses": { - "201": { - "description": "Created - The activity instance was successfully previewed.", + "200": { + "description": "Successful Response", "content": { "application/json": { - "schema": { - "$ref": "#/components/schemas/ActivityInstance" - } - } + "schema": {} + }, + "application/x-yaml": {} } }, "403": { @@ -48639,8 +48780,8 @@ } } }, - "400": { - "description": "Forbidden - Reasons include e.g.: \n- The library doesn't exist.\n- The library doesn't allow to add new items.\n", + "404": { + "description": "Entity not found", "content": { "application/json": { "schema": { @@ -48649,8 +48790,8 @@ } } }, - "404": { - "description": "Entity not found", + "400": { + "description": "Bad Request", "content": { "application/json": { "schema": { @@ -48659,25 +48800,17 @@ } } } - }, - "security": [ - { - "OAuth2AuthorizationCodeBearer": [] - }, - { - "BearerJwtAuth": [] - } - ] + } } }, - "/concepts/activities/activity-instances/{activity_instance_uid}/approvals": { - "post": { + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/versions": { + "get": { "tags": [ "Activity Instances" ], - "summary": "Approve draft version of an activity instance", - "description": "State before:\n - uid must exist and activity instance must be in status Draft.\n \nBusiness logic:\n - The latest 'Draft' version will remain the same as before.\n - The status of the new approved version will be automatically set to 'Final'.\n - The 'version' property of the new version will be automatically set to the version of the latest 'Final' version increased by +1.0.\n - The 'change_description' property will be set automatically 'Approved version'.\n \nState after:\n - Activity instance changed status to Final and assigned a new major version number.\n - Audit trail entry must be made with action of approving to new Final version.\n \nPossible errors:\n - Invalid uid or status not Draft.", - "operationId": "approve_concepts_activities_activity_instances__activity_instance_uid__approvals_post", + "summary": "List version history for activity instance attributes", + "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for activity instance.\n - The returned versions are ordered by start_date descending (newest entries first).\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.", + "operationId": "get_versions_concepts_activities_activity_instances__activity_instance_uid__attributes_versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48700,12 +48833,16 @@ } ], "responses": { - "201": { - "description": "OK.", + "200": { + "description": "Successful Response", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ActivityInstance" + "type": "array", + "items": { + "$ref": "#/components/schemas/ActivityInstanceAttributes" + }, + "title": "Response Get Versions Concepts Activities Activity Instances Activity Instance Uid Attributes Versions Get" } } } @@ -48720,8 +48857,8 @@ } } }, - "400": { - "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in draft status.\n- The library doesn't allow to approve activity instance.\n", + "404": { + "description": "Not Found - The activity isntance with the specified 'activity_instance_uid' wasn't found.", "content": { "application/json": { "schema": { @@ -48730,8 +48867,8 @@ } } }, - "404": { - "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", + "400": { + "description": "Bad Request", "content": { "application/json": { "schema": { @@ -48741,16 +48878,14 @@ } } } - } - }, - "/concepts/activities/activity-instances/{activity_instance_uid}/activations": { - "delete": { + }, + "post": { "tags": [ "Activity Instances" ], - "summary": " Inactivate final version of an activity instance", - "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__activations_delete", + "summary": " Create a new version of an activity instance attributes", + "description": "State before:\n - uid must exist and the activity instance must be in status Final.\n \nBusiness logic:\n- The activity instance is changed to a draft state.\n\nState after:\n - Activity instance changed status to Draft and assigned a new minor version number.\n - Audit trail entry must be made with action of creating a new draft version.\n \nPossible errors:\n - Invalid uid or status not Final.", + "operationId": "create_new_version_concepts_activities_activity_instances__activity_instance_uid__attributes_versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48773,8 +48908,71 @@ } ], "responses": { - "200": { + "201": { "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceAttributes" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The library doesn't allow to create activity instances.\n", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - Reasons include e.g.: \n- The activity instance is not in final status.\n- The activity instance with the specified 'activity_instance_uid' could not be found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/concepts/activities/activity-instances/preview": { + "post": { + "tags": [ + "Activity Instances" + ], + "summary": "Previews the creation of a new activity instance.", + "description": "State before:\n - The specified library allows creation of concepts (the 'is_editable' property of the library needs to be true).\n\nBusiness logic:\n - New node is created for the activity instance with the set properties.\n - relationships to specified activity parent are created (as in the model)\n - relationships to specified activity instance class is created (as in the model)\n - The status of the new created version will be automatically set to 'Draft'.\n - The 'version' property of the new version will be automatically set to 0.1.\n - The 'change_description' property will be set automatically to 'Initial version'.\n\nState after:\n - activity instance is created in status Draft and assigned an initial minor version number as 0.1.\n - Audit trail entry must be made with action of creating new Draft version.\n\nPossible errors:\n - Invalid library or control terminology uid's specified.", + "operationId": "preview_concepts_activities_activity_instances_preview_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstancePreviewInput", + "description": "Related parameters of the objective that shall be previewed." + } + } + }, + "required": true + }, + "responses": { + "201": { + "description": "Created - The activity instance was successfully previewed.", "content": { "application/json": { "schema": { @@ -48793,6 +48991,160 @@ } } }, + "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": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + } + }, + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/approvals": { + "post": { + "tags": [ + "Activity Instances" + ], + "summary": "Approve draft version of an activity instance attributes", + "description": "State before:\n - uid must exist and activity instance must be in status Draft.\n \nBusiness logic:\n - The latest 'Draft' version will remain the same as before.\n - The status of the new approved version will be automatically set to 'Final'.\n - The 'version' property of the new version will be automatically set to the version of the latest 'Final' version increased by +1.0.\n - The 'change_description' property will be set automatically 'Approved version'.\n \nState after:\n - Activity instance changed status to Final and assigned a new major version number.\n - Audit trail entry must be made with action of approving to new Final version.\n \nPossible errors:\n - Invalid uid or status not Draft.", + "operationId": "approve_concepts_activities_activity_instances__activity_instance_uid__attributes_approvals_post", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "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" + } + ], + "responses": { + "201": { + "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceAttributes" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in draft status.\n- The library doesn't allow to approve activity instance.\n", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/concepts/activities/activity-instances/{activity_instance_uid}/attributes/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", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "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" + } + ], + "responses": { + "200": { + "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceAttributes" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, "400": { "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in final status.", "content": { @@ -48819,9 +49171,9 @@ "tags": [ "Activity Instances" ], - "summary": "Reactivate retired version of an activity instance", + "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__activations_post", + "operationId": "reactivate_concepts_activities_activity_instances__activity_instance_uid__attributes_activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -48849,7 +49201,372 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ActivityInstance" + "$ref": "#/components/schemas/ActivityInstanceAttributes" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in retired status.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' could not be found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/versions": { + "get": { + "tags": [ + "Activity Instances" + ], + "summary": "List version history for activity instance groupings", + "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for activity instance groupings.\n - The returned versions are ordered by start_date descending (newest entries first).\n\nState after:\n - No change\n\nPossible errors:\n - Invalid uid.", + "operationId": "get_groupings_versions_concepts_activities_activity_instances__activity_instance_uid__groupings_versions_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "activity_instance_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the ActivityInstance", + "title": "Activity Instance Uid" + }, + "description": "The unique id of the ActivityInstance" + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/ActivityInstanceGroupings" + }, + "title": "Response Get Groupings Versions Concepts Activities Activity Instances Activity Instance Uid Groupings Versions Get" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - The activity isntance with the specified 'activity_instance_uid' wasn't found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + }, + "post": { + "tags": [ + "Activity Instances" + ], + "summary": " Create a new version of an activity instance groupings", + "description": "State before:\n - uid must exist and the activity instance must be in status Final.\n \nBusiness logic:\n- The activity instance is changed to a draft state.\n\nState after:\n - Activity instance changed status to Draft and assigned a new minor version number.\n - Audit trail entry must be made with action of creating a new draft version.\n \nPossible errors:\n - Invalid uid or status not Final.", + "operationId": "create_new_groupings_version_concepts_activities_activity_instances__activity_instance_uid__groupings_versions_post", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "activity_instance_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the ActivityInstance", + "title": "Activity Instance Uid" + }, + "description": "The unique id of the ActivityInstance" + } + ], + "responses": { + "201": { + "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceGroupings" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The library doesn't allow to create activity instances.\n", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - Reasons include e.g.: \n- The activity instance is not in final status.\n- The activity instance with the specified 'activity_instance_uid' could not be found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/approvals": { + "post": { + "tags": [ + "Activity Instances" + ], + "summary": "Approve draft version of an activity instance groupings", + "description": "State before:\n - uid must exist and activity instance must be in status Draft.\n \nBusiness logic:\n - The latest 'Draft' version will remain the same as before.\n - The status of the new approved version will be automatically set to 'Final'.\n - The 'version' property of the new version will be automatically set to the version of the latest 'Final' version increased by +1.0.\n - The 'change_description' property will be set automatically 'Approved version'.\n \nState after:\n - Activity instance changed status to Final and assigned a new major version number.\n - Audit trail entry must be made with action of approving to new Final version.\n \nPossible errors:\n - Invalid uid or status not Draft.", + "operationId": "approve_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_approvals_post", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "activity_instance_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the ActivityInstance", + "title": "Activity Instance Uid" + }, + "description": "The unique id of the ActivityInstance" + } + ], + "responses": { + "201": { + "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceGroupings" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in draft status.\n- The library doesn't allow to approve activity instance.\n", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' wasn't found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, + "/concepts/activities/activity-instances/{activity_instance_uid}/groupings/activations": { + "delete": { + "tags": [ + "Activity Instances" + ], + "summary": " Inactivate final version of an activity instance groupings", + "description": "State before:\n - uid must exist and activity instance must be in status Final.\n \nBusiness logic:\n - The latest 'Final' version will remain the same as before.\n - The status will be automatically set to 'Retired'.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n \nState after:\n - Activity instance changed status to Retired.\n - Audit trail entry must be made with action of inactivating to retired version.\n \nPossible errors:\n - Invalid uid or status not Final.", + "operationId": "inactivate_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_activations_delete", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "activity_instance_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the ActivityInstance", + "title": "Activity Instance Uid" + }, + "description": "The unique id of the ActivityInstance" + } + ], + "responses": { + "200": { + "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceGroupings" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Forbidden - Reasons include e.g.: \n- The activity instance is not in final status.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Not Found - The activity instance with the specified 'activity_instance_uid' could not be found.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + }, + "post": { + "tags": [ + "Activity Instances" + ], + "summary": "Reactivate retired version of an activity instance groupings", + "description": "State before:\n - uid must exist and activity instance must be in status Retired.\n \nBusiness logic:\n - The latest 'Retired' version will remain the same as before.\n - The status will be automatically set to 'Final'.\n - The 'change_description' property will be set automatically.\n - The 'version' property will remain the same as before.\n\nState after:\n - Activity instance changed status to Final.\n - An audit trail entry must be made with action of reactivating to final version.\n \nPossible errors:\n - Invalid uid or status not Retired.", + "operationId": "reactivate_groupings_concepts_activities_activity_instances__activity_instance_uid__groupings_activations_post", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "activity_instance_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the ActivityInstance", + "title": "Activity Instance Uid" + }, + "description": "The unique id of the ActivityInstance" + } + ], + "responses": { + "200": { + "description": "OK.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ActivityInstanceGroupings" } } } @@ -49111,6 +49828,108 @@ } } }, + "/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", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "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": "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" + } + } + } + } + } + } + }, "/activity-instance-classes/headers": { "get": { "tags": [ @@ -50826,6 +51645,108 @@ } } }, + "/activity-item-classes/versions": { + "get": { + "tags": [ + "Activity Item Classes" + ], + "summary": "List all versions of activity item classes", + "description": "State before:\n - The library must exist (if specified)\n\nBusiness logic:\n - List version history of activity item 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_item_classes_versions_activity_item_classes_versions_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "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": "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": { + "$ref": "#/components/schemas/CustomPage_ActivityItemClass_" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$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" + } + } + } + } + } + } + }, "/activity-item-classes/headers": { "get": { "tags": [ @@ -75124,6 +76045,18 @@ "title": "Debug Propagation" }, "description": "Debug propagations without hiding rows" + }, + { + "name": "include_uids", + "in": "query", + "required": false, + "schema": { + "type": "boolean", + "description": "Include uids in the HTML as data attributes", + "default": false, + "title": "Include Uids" + }, + "description": "Include uids in the HTML as data attributes" } ], "responses": { @@ -76198,6 +77131,18 @@ "title": "Study Value Version" }, "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": "protocol_lab_table", + "in": "query", + "required": false, + "schema": { + "type": "boolean", + "description": "Whether to export Protocol Lab table SoA", + "default": false, + "title": "Protocol Lab Table" + }, + "description": "Whether to export Protocol Lab table SoA" } ], "responses": { @@ -116815,140 +117760,8 @@ ], "title": "Possible Actions", "description": "Holds those actions that can be performed on the ActivityInstances. Actions are: 'approve', 'edit', 'new_version'." - } - }, - "type": "object", - "required": [ - "uid", - "library_name" - ], - "title": "ActivityGroup" - }, - "ActivityGroupCreateInput": { - "properties": { - "name": { - "type": "string", - "minLength": 1, - "title": "Name", - "description": "The name or the actual value. E.g. 'Systolic Blood Pressure', 'Body Temperature', 'Metformin', ..." }, - "name_sentence_case": { - "type": "string", - "minLength": 1, - "title": "Name Sentence Case" - }, - "definition": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Definition" - }, - "abbreviation": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Abbreviation" - }, - "library_name": { - "type": "string", - "minLength": 1, - "title": "Library Name" - } - }, - "type": "object", - "required": [ - "name", - "name_sentence_case", - "library_name" - ], - "title": "ActivityGroupCreateInput" - }, - "ActivityGroupDetail": { - "properties": { - "name": { - "type": "string", - "title": "Name" - }, - "name_sentence_case": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Name Sentence Case" - }, - "library_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Library Name" - }, - "start_date": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Start Date" - }, - "end_date": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "End Date" - }, - "status": { - "type": "string", - "title": "Status" - }, - "version": { - "type": "string", - "title": "Version" - }, - "possible_actions": { - "items": { - "type": "string" - }, - "type": "array", - "title": "Possible Actions" - }, - "change_description": { - "type": "string", - "title": "Change Description" - }, - "author_username": { - "type": "string", - "title": "Author Username" - }, - "definition": { + "nci_concept_id": { "anyOf": [ { "type": "string" @@ -116957,9 +117770,10 @@ "type": "null" } ], - "title": "Definition" + "title": "Nci Concept Id", + "nullable": true }, - "abbreviation": { + "nci_concept_name": { "anyOf": [ { "type": "string" @@ -116968,35 +117782,236 @@ "type": "null" } ], - "title": "Abbreviation" - }, - "all_versions": { - "items": { - "type": "string" - }, - "type": "array", - "title": "All Versions" + "title": "Nci Concept Name", + "nullable": true } }, "type": "object", "required": [ - "name", - "status", - "version", - "possible_actions", - "change_description", - "author_username" + "uid", + "library_name" ], - "title": "ActivityGroupDetail", - "description": "Detailed view of an Activity Group for the overview endpoint" + "title": "ActivityGroup" }, - "ActivityGroupEditInput": { + "ActivityGroupCreateInput": { "properties": { - "change_description": { - "type": "string", - "minLength": 1, - "title": "Change Description" - }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name", + "description": "The name or the actual value. E.g. 'Systolic Blood Pressure', 'Body Temperature', 'Metformin', ..." + }, + "name_sentence_case": { + "type": "string", + "minLength": 1, + "title": "Name Sentence Case" + }, + "definition": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Definition" + }, + "abbreviation": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Abbreviation" + }, + "library_name": { + "type": "string", + "minLength": 1, + "title": "Library Name" + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" + } + }, + "type": "object", + "required": [ + "name", + "name_sentence_case", + "library_name" + ], + "title": "ActivityGroupCreateInput" + }, + "ActivityGroupDetail": { + "properties": { + "name": { + "type": "string", + "title": "Name" + }, + "name_sentence_case": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name Sentence Case" + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" + }, + "library_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Library Name" + }, + "start_date": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Start Date" + }, + "end_date": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "End Date" + }, + "status": { + "type": "string", + "title": "Status" + }, + "version": { + "type": "string", + "title": "Version" + }, + "possible_actions": { + "items": { + "type": "string" + }, + "type": "array", + "title": "Possible Actions" + }, + "change_description": { + "type": "string", + "title": "Change Description" + }, + "author_username": { + "type": "string", + "title": "Author Username" + }, + "definition": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Definition" + }, + "abbreviation": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Abbreviation" + }, + "all_versions": { + "items": { + "type": "string" + }, + "type": "array", + "title": "All Versions" + } + }, + "type": "object", + "required": [ + "name", + "status", + "version", + "possible_actions", + "change_description", + "author_username" + ], + "title": "ActivityGroupDetail", + "description": "Detailed view of an Activity Group for the overview endpoint" + }, + "ActivityGroupEditInput": { + "properties": { + "change_description": { + "type": "string", + "minLength": 1, + "title": "Change Description" + }, "name": { "type": "string", "minLength": 1, @@ -117037,6 +118052,30 @@ "minLength": 1, "title": "Library Name", "default": "Sponsor" + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" } }, "type": "object", @@ -117468,6 +118507,25 @@ "title": "Legacy Description", "nullable": true }, + "activity_instance_class": { + "$ref": "#/components/schemas/CompactActivityInstanceClass", + "description": "The uid and the name of the linked activity instance class" + }, + "activity_items": { + "anyOf": [ + { + "items": { + "$ref": "#/components/schemas/ActivityItem" + }, + "type": "array" + }, + { + "type": "null" + } + ], + "title": "Activity Items", + "description": "List of activity items" + }, "activity_groupings": { "anyOf": [ { @@ -117494,6 +118552,345 @@ "title": "Activity Name", "nullable": true }, + "groupings_status": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Groupings Status" + }, + "groupings_version": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Groupings Version" + }, + "groupings_start_date": { + "anyOf": [ + { + "type": "string", + "format": "date-time" + }, + { + "type": "null" + } + ], + "title": "Groupings Start Date" + }, + "groupings_end_date": { + "anyOf": [ + { + "type": "string", + "format": "date-time" + }, + { + "type": "null" + } + ], + "title": "Groupings End Date", + "nullable": true + }, + "groupings_change_description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Groupings Change Description" + }, + "groupings_author_username": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Groupings Author Username", + "nullable": true + }, + "groupings_possible_actions": { + "anyOf": [ + { + "items": { + "type": "string" + }, + "type": "array" + }, + { + "type": "null" + } + ], + "title": "Groupings Possible Actions", + "description": "Holds those actions that can be performed on the ActivityInstance groupings. Actions are: 'approve', 'edit', 'new_version'." + } + }, + "type": "object", + "required": [ + "uid", + "library_name", + "activity_instance_class" + ], + "title": "ActivityInstance" + }, + "ActivityInstanceAttributes": { + "properties": { + "start_date": { + "anyOf": [ + { + "type": "string", + "format": "date-time" + }, + { + "type": "null" + } + ], + "title": "Start Date" + }, + "end_date": { + "anyOf": [ + { + "type": "string", + "format": "date-time" + }, + { + "type": "null" + } + ], + "title": "End Date", + "nullable": true + }, + "status": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Status" + }, + "version": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Version" + }, + "change_description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Change Description" + }, + "author_username": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Author Username", + "nullable": true + }, + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name", + "description": "The name or the actual value. E.g. 'Systolic Blood Pressure', 'Body Temperature', 'Metformin', ..." + }, + "name_sentence_case": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name Sentence Case", + "nullable": true + }, + "definition": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Definition", + "nullable": true + }, + "abbreviation": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Abbreviation", + "nullable": true + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, + "possible_actions": { + "anyOf": [ + { + "items": { + "type": "string" + }, + "type": "array" + }, + { + "type": "null" + } + ], + "title": "Possible Actions", + "description": "Holds those actions that can be performed on the ActivityInstances. Actions are: 'approve', 'edit', 'new_version'." + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id", + "nullable": true + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name", + "nullable": true + }, + "topic_code": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Topic Code", + "nullable": true + }, + "adam_param_code": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Adam Param Code", + "nullable": true + }, + "is_research_lab": { + "type": "boolean", + "title": "Is Research Lab", + "default": false + }, + "molecular_weight": { + "anyOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Molecular Weight", + "nullable": true + }, + "is_required_for_activity": { + "type": "boolean", + "title": "Is Required For Activity", + "default": false + }, + "is_default_selected_for_activity": { + "type": "boolean", + "title": "Is Default Selected For Activity", + "default": false + }, + "is_data_sharing": { + "type": "boolean", + "title": "Is Data Sharing", + "default": false + }, + "is_legacy_usage": { + "type": "boolean", + "title": "Is Legacy Usage", + "default": false + }, + "is_derived": { + "type": "boolean", + "title": "Is Derived", + "default": false + }, + "legacy_description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Legacy Description", + "nullable": true + }, "activity_instance_class": { "$ref": "#/components/schemas/CompactActivityInstanceClass", "description": "The uid and the name of the linked activity instance class" @@ -117520,7 +118917,251 @@ "library_name", "activity_instance_class" ], - "title": "ActivityInstance" + "title": "ActivityInstanceAttributes" + }, + "ActivityInstanceAttributesEditInput": { + "properties": { + "name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Name", + "description": "The name or the actual value. E.g. 'Systolic Blood Pressure', 'Body Temperature', 'Metformin', ..." + }, + "name_sentence_case": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Name Sentence Case" + }, + "definition": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Definition" + }, + "abbreviation": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Abbreviation" + }, + "library_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Library Name" + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" + }, + "topic_code": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Topic Code" + }, + "is_research_lab": { + "type": "boolean", + "title": "Is Research Lab", + "default": false + }, + "molecular_weight": { + "anyOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Molecular Weight" + }, + "adam_param_code": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Adam Param Code" + }, + "is_required_for_activity": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Required For Activity" + }, + "is_default_selected_for_activity": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Default Selected For Activity" + }, + "is_data_sharing": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Data Sharing" + }, + "is_legacy_usage": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Legacy Usage" + }, + "is_derived": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Derived" + }, + "legacy_description": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Legacy Description" + }, + "activity_instance_class_uid": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Activity Instance Class Uid" + }, + "activity_items": { + "anyOf": [ + { + "items": { + "$ref": "#/components/schemas/ActivityItemCreateInput" + }, + "type": "array" + }, + { + "type": "null" + } + ], + "title": "Activity Items" + }, + "strict_mode": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Strict Mode", + "description": "If True, enforces strict validation for parent mandatory activity item classes. Defaults to False (relaxed mode) when not provided." + }, + "change_description": { + "type": "string", + "minLength": 1, + "title": "Change Description" + } + }, + "type": "object", + "required": [ + "change_description" + ], + "title": "ActivityInstanceAttributesEditInput" }, "ActivityInstanceClass": { "properties": { @@ -118466,212 +120107,148 @@ "title": "ActivityInstanceDetail", "description": "Model for activity instance detail information with pagination support." }, - "ActivityInstanceEditInput": { + "ActivityInstanceGrouping": { "properties": { - "name": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Name", - "description": "The name or the actual value. E.g. 'Systolic Blood Pressure', 'Body Temperature', 'Metformin', ..." - }, - "name_sentence_case": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Name Sentence Case" - }, - "definition": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Definition" - }, - "abbreviation": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Abbreviation" - }, - "library_name": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Library Name" - }, - "nci_concept_id": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Nci Concept Id" + "activity_group_uid": { + "type": "string", + "title": "Activity Group Uid" }, - "nci_concept_name": { - "anyOf": [ - { - "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Nci Concept Name" + "activity_subgroup_uid": { + "type": "string", + "title": "Activity Subgroup Uid" }, - "topic_code": { + "activity_uid": { + "type": "string", + "title": "Activity Uid" + } + }, + "type": "object", + "required": [ + "activity_group_uid", + "activity_subgroup_uid", + "activity_uid" + ], + "title": "ActivityInstanceGrouping" + }, + "ActivityInstanceGroupings": { + "properties": { + "start_date": { "anyOf": [ { "type": "string", - "minLength": 1 - }, - { - "type": "null" - } - ], - "title": "Topic Code" - }, - "is_research_lab": { - "type": "boolean", - "title": "Is Research Lab", - "default": false - }, - "molecular_weight": { - "anyOf": [ - { - "type": "number" + "format": "date-time" }, { "type": "null" } ], - "title": "Molecular Weight" + "title": "Start Date" }, - "adam_param_code": { + "end_date": { "anyOf": [ { "type": "string", - "minLength": 1 + "format": "date-time" }, { "type": "null" } ], - "title": "Adam Param Code" + "title": "End Date", + "nullable": true }, - "is_required_for_activity": { + "status": { "anyOf": [ { - "type": "boolean" + "type": "string" }, { "type": "null" } ], - "title": "Is Required For Activity" + "title": "Status" }, - "is_default_selected_for_activity": { + "version": { "anyOf": [ { - "type": "boolean" + "type": "string" }, { "type": "null" } ], - "title": "Is Default Selected For Activity" + "title": "Version" }, - "is_data_sharing": { + "change_description": { "anyOf": [ { - "type": "boolean" + "type": "string" }, { "type": "null" } ], - "title": "Is Data Sharing" + "title": "Change Description" }, - "is_legacy_usage": { + "author_username": { "anyOf": [ { - "type": "boolean" + "type": "string" }, { "type": "null" } ], - "title": "Is Legacy Usage" + "title": "Author Username", + "nullable": true }, - "is_derived": { + "possible_actions": { "anyOf": [ { - "type": "boolean" + "items": { + "type": "string" + }, + "type": "array" }, { "type": "null" } ], - "title": "Is Derived" + "title": "Possible Actions", + "description": "Holds those actions that can be performed on the ActivityInstances. Actions are: 'approve', 'edit', 'new_version'." }, - "legacy_description": { + "activity_groupings": { "anyOf": [ { - "type": "string", - "minLength": 1 + "items": { + "$ref": "#/components/schemas/ActivityInstanceHierarchySimpleModel" + }, + "type": "array" }, { "type": "null" } ], - "title": "Legacy Description" + "title": "Activity Groupings" }, - "activity_instance_class_uid": { + "activity_name": { "anyOf": [ { - "type": "string", - "minLength": 1 + "type": "string" }, { "type": "null" } ], - "title": "Activity Instance Class Uid" - }, + "title": "Activity Name", + "nullable": true + } + }, + "type": "object", + "title": "ActivityInstanceGroupings" + }, + "ActivityInstanceGroupingsEditInput": { + "properties": { "activity_groupings": { "anyOf": [ { @@ -118686,32 +120263,6 @@ ], "title": "Activity Groupings" }, - "activity_items": { - "anyOf": [ - { - "items": { - "$ref": "#/components/schemas/ActivityItemCreateInput" - }, - "type": "array" - }, - { - "type": "null" - } - ], - "title": "Activity Items" - }, - "strict_mode": { - "anyOf": [ - { - "type": "boolean" - }, - { - "type": "null" - } - ], - "title": "Strict Mode", - "description": "If True, enforces strict validation for parent mandatory activity item classes. Defaults to False (relaxed mode) when not provided." - }, "change_description": { "type": "string", "minLength": 1, @@ -118722,30 +120273,7 @@ "required": [ "change_description" ], - "title": "ActivityInstanceEditInput" - }, - "ActivityInstanceGrouping": { - "properties": { - "activity_group_uid": { - "type": "string", - "title": "Activity Group Uid" - }, - "activity_subgroup_uid": { - "type": "string", - "title": "Activity Subgroup Uid" - }, - "activity_uid": { - "type": "string", - "title": "Activity Uid" - } - }, - "type": "object", - "required": [ - "activity_group_uid", - "activity_subgroup_uid", - "activity_uid" - ], - "title": "ActivityInstanceGrouping" + "title": "ActivityInstanceGroupingsEditInput" }, "ActivityInstanceHierarchySimpleModel": { "properties": { @@ -118769,12 +120297,12 @@ }, "ActivityInstanceOverview": { "properties": { - "activity_groupings": { + "activity_groupings_versions": { "items": { - "$ref": "#/components/schemas/SimpleActivityInstanceGrouping" + "type": "string" }, "type": "array", - "title": "Activity Groupings" + "title": "Activity Groupings Versions" }, "activity_instance": { "$ref": "#/components/schemas/SimpleActivityInstance" @@ -118796,7 +120324,7 @@ }, "type": "object", "required": [ - "activity_groupings", + "activity_groupings_versions", "activity_instance", "activity_items", "all_versions" @@ -121063,6 +122591,17 @@ "type": "boolean", "title": "Is Adam Param Specific" }, + "is_activity_instance_id_specific": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Activity Instance Id Specific" + }, "text_value": { "anyOf": [ { @@ -121778,6 +123317,17 @@ "type": "boolean", "title": "Is Adam Param Specific" }, + "is_activity_instance_id_specific": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Activity Instance Id Specific" + }, "text_value": { "anyOf": [ { @@ -122003,6 +123553,30 @@ ], "title": "Possible Actions", "description": "Holds those actions that can be performed on the ActivityInstances. Actions are: 'approve', 'edit', 'new_version'." + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id", + "nullable": true + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name", + "nullable": true } }, "type": "object", @@ -122053,6 +123627,30 @@ "type": "string", "minLength": 1, "title": "Library Name" + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" } }, "type": "object", @@ -122087,6 +123685,28 @@ ], "title": "Name Sentence Case" }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" + }, "library_name": { "anyOf": [ { @@ -122237,6 +123857,30 @@ "type": "string", "minLength": 1, "title": "Library Name" + }, + "nci_concept_id": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Id" + }, + "nci_concept_name": { + "anyOf": [ + { + "type": "string", + "minLength": 1 + }, + { + "type": "null" + } + ], + "title": "Nci Concept Name" } }, "type": "object", @@ -124376,10 +126020,6 @@ "type": "string", "title": "Term Uid" }, - "submission_value": { - "type": "string", - "title": "Submission Value" - }, "order": { "anyOf": [ { @@ -124486,12 +126126,15 @@ ], "title": "End Date", "nullable": true + }, + "submission_value": { + "type": "string", + "title": "Submission Value" } }, "type": "object", "required": [ "term_uid", - "submission_value", "order", "library_name", "sponsor_preferred_name", @@ -124504,7 +126147,8 @@ "attributes_date", "attributes_status", "start_date", - "end_date" + "end_date", + "submission_value" ], "title": "CTCodelistTerm" }, @@ -125308,6 +126952,165 @@ ], "title": "CTPackageDates" }, + "CTPairedCodelistTerm": { + "properties": { + "term_uid": { + "type": "string", + "title": "Term Uid" + }, + "order": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Order", + "nullable": true + }, + "ordinal": { + "anyOf": [ + { + "type": "number" + }, + { + "type": "null" + } + ], + "title": "Ordinal", + "nullable": true + }, + "library_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Library Name" + }, + "sponsor_preferred_name": { + "type": "string", + "title": "Sponsor Preferred Name" + }, + "sponsor_preferred_name_sentence_case": { + "type": "string", + "title": "Sponsor Preferred Name Sentence Case" + }, + "concept_id": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Concept Id", + "nullable": true + }, + "nci_preferred_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Nci Preferred Name", + "nullable": true + }, + "definition": { + "type": "string", + "title": "Definition" + }, + "name_date": { + "type": "string", + "format": "date-time", + "title": "Name Date" + }, + "name_status": { + "type": "string", + "title": "Name Status" + }, + "attributes_date": { + "type": "string", + "format": "date-time", + "title": "Attributes Date" + }, + "attributes_status": { + "type": "string", + "title": "Attributes Status" + }, + "start_date": { + "type": "string", + "format": "date-time", + "title": "Start Date" + }, + "end_date": { + "anyOf": [ + { + "type": "string", + "format": "date-time" + }, + { + "type": "null" + } + ], + "title": "End Date", + "nullable": true + }, + "code_submission_value": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Code Submission Value", + "nullable": true + }, + "name_submission_value": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name Submission Value", + "nullable": true + } + }, + "type": "object", + "required": [ + "term_uid", + "order", + "library_name", + "sponsor_preferred_name", + "sponsor_preferred_name_sentence_case", + "concept_id", + "nci_preferred_name", + "definition", + "name_date", + "name_status", + "attributes_date", + "attributes_status", + "start_date", + "end_date", + "code_submission_value", + "name_submission_value" + ], + "title": "CTPairedCodelistTerm" + }, "CTStats": { "properties": { "catalogues": { @@ -126473,6 +128276,8 @@ }, "order": { "type": "integer", + "maximum": 9.223372036854776e+18, + "minimum": 0.0, "title": "Order" }, "submission_value": { @@ -127344,6 +129149,30 @@ "title": "Is Default Linked", "default": false, "nullable": true + }, + "data_type_uid": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Data Type Uid", + "nullable": true + }, + "data_type_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Data Type Name", + "nullable": true } }, "type": "object", @@ -131245,6 +133074,40 @@ ], "title": "CustomPage[ActivityGroup]" }, + "CustomPage_ActivityInstanceAttributes_": { + "properties": { + "items": { + "items": { + "$ref": "#/components/schemas/ActivityInstanceAttributes" + }, + "type": "array", + "title": "Items" + }, + "total": { + "type": "integer", + "minimum": -1.0, + "title": "Total" + }, + "page": { + "type": "integer", + "minimum": 0.0, + "title": "Page" + }, + "size": { + "type": "integer", + "minimum": 0.0, + "title": "Size" + } + }, + "type": "object", + "required": [ + "items", + "total", + "page", + "size" + ], + "title": "CustomPage[ActivityInstanceAttributes]" + }, "CustomPage_ActivityInstanceClass_": { "properties": { "items": { @@ -131925,6 +133788,40 @@ ], "title": "CustomPage[CTCodelistTerm]" }, + "CustomPage_CTPairedCodelistTerm_": { + "properties": { + "items": { + "items": { + "$ref": "#/components/schemas/CTPairedCodelistTerm" + }, + "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[CTPairedCodelistTerm]" + }, "CustomPage_CTTermAttributes_": { "properties": { "items": { @@ -151617,123 +153514,6 @@ ], "title": "SimpleActivity" }, - "SimpleActivityForActivityInstance": { - "properties": { - "uid": { - "type": "string", - "title": "Uid" - }, - "nci_concept_id": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Nci Concept Id", - "nullable": true - }, - "nci_concept_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Nci Concept Name", - "nullable": true - }, - "name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Name", - "nullable": true - }, - "definition": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Definition", - "nullable": true - }, - "synonyms": { - "items": { - "type": "string" - }, - "type": "array", - "title": "Synonyms" - }, - "is_data_collected": { - "type": "boolean", - "title": "Is Data Collected", - "description": "Boolean flag indicating whether data is collected for this activity", - "default": false - }, - "is_multiple_selection_allowed": { - "type": "boolean", - "title": "Is Multiple Selection Allowed", - "description": "Boolean flag indicating whether multiple selections are allowed for this activity", - "default": true - }, - "library_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Library Name", - "nullable": true - }, - "version": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Version", - "nullable": true - }, - "status": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Status", - "nullable": true - } - }, - "type": "object", - "required": [ - "uid", - "synonyms" - ], - "title": "SimpleActivityForActivityInstance" - }, "SimpleActivityGroup": { "properties": { "uid": { @@ -152216,26 +153996,6 @@ "title": "SimpleActivityInstanceClassForItem", "description": "Simple representation of an Activity Instance Class that uses an Activity Item Class" }, - "SimpleActivityInstanceGrouping": { - "properties": { - "activity_group": { - "$ref": "#/components/schemas/SimpleActivityGroup" - }, - "activity_subgroup": { - "$ref": "#/components/schemas/SimpleActivitySubGroup" - }, - "activity": { - "$ref": "#/components/schemas/SimpleActivityForActivityInstance" - } - }, - "type": "object", - "required": [ - "activity_group", - "activity_subgroup", - "activity" - ], - "title": "SimpleActivityInstanceGrouping" - }, "SimpleActivityItemClass": { "properties": { "uid": { @@ -153642,6 +155402,17 @@ "type": "boolean", "title": "Is Adam Param Specific" }, + "is_activity_instance_id_specific": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Is Activity Instance Id Specific" + }, "text_value": { "anyOf": [ { @@ -153680,6 +155451,7 @@ "type": "string", "enum": [ "protocol", + "protocol_lab_table", "detailed", "operational" ], @@ -160229,6 +162001,18 @@ ], "title": "Acronym", "nullable": true + }, + "subpart_acronym": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Subpart Acronym", + "nullable": true } }, "type": "object", @@ -169242,7 +171026,7 @@ "title": "Acronym", "nullable": true }, - "number": { + "subpart_acronym": { "anyOf": [ { "type": "string" @@ -169251,10 +171035,10 @@ "type": "null" } ], - "title": "Number", + "title": "Subpart Acronym", "nullable": true }, - "title": { + "main_id": { "anyOf": [ { "type": "string" @@ -169263,10 +171047,11 @@ "type": "null" } ], - "title": "Title", + "title": "Main Id", + "description": "Main ID of the study, e.g. 'NN1234-56789'", "nullable": true }, - "subpart_id": { + "number": { "anyOf": [ { "type": "string" @@ -169275,10 +171060,10 @@ "type": "null" } ], - "title": "Subpart Id", + "title": "Number", "nullable": true }, - "subpart_acronym": { + "title": { "anyOf": [ { "type": "string" @@ -169287,7 +171072,19 @@ "type": "null" } ], - "title": "Subpart Acronym", + "title": "Title", + "nullable": true + }, + "subpart_id": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Subpart Id", "nullable": true }, "clinical_programme_name": { @@ -170018,6 +171815,12 @@ "description": "Show the baseline visit as time 0 in all SoA layouts", "default": false }, + "soa_show_all_visits_lab_table": { + "type": "boolean", + "title": "Soa Show All Visits Lab Table", + "description": "Show all visits in protocol lab table SoA (incl. those without lab assessments)", + "default": false + }, "study_uid": { "type": "string", "title": "Study Uid", @@ -170049,6 +171852,12 @@ "title": "Baseline As Time Zero", "description": "Show the baseline visit as time 0 in all SoA layouts", "default": false + }, + "soa_show_all_visits_lab_table": { + "type": "boolean", + "title": "Soa Show All Visits Lab Table", + "description": "Show all visits in protocol lab table SoA (incl. those without lab assessments)", + "default": false } }, "type": "object", @@ -170717,7 +172526,9 @@ "properties": { "study_subpart_acronym": { "type": "string", + "maxLength": 10, "minLength": 1, + "pattern": "^[A-Za-z0-9]+$", "title": "Study Subpart Acronym" }, "description": { diff --git a/clinical-mdr-api/sbom.md b/clinical-mdr-api/sbom.md index f1abf6e2..87b0b8fa 100644 --- a/clinical-mdr-api/sbom.md +++ b/clinical-mdr-api/sbom.md @@ -5,11 +5,11 @@ |--------------------------|--------------|--------------------------------------------------------------| | annotated-doc | 0.0.4 | [MIT](#annotated-doc) | | annotated-types | 0.6.0 | [see below](#annotated-types) | -| anyio | 4.12.1 | [MIT](#anyio) | +| anyio | 4.13.0 | [MIT](#anyio) | | asyncache | 0.3.1 | [MIT](#asyncache) | -| attrs | 25.4.0 | [MIT](#attrs) | +| attrs | 26.1.0 | [MIT](#attrs) | | Authlib | 1.6.9 | [BSD-3-Clause](#authlib) | -| azure-core | 1.38.3 | [MIT](#azure-core) | +| azure-core | 1.39.0 | [MIT](#azure-core) | | azure-identity | 1.25.3 | [MIT](#azure-identity) | | beautifulsoup4 | 4.12.3 | [MIT License](#beautifulsoup4) | | brotli | 1.2.0 | [MIT](#brotli) | @@ -19,14 +19,14 @@ | charset-normalizer | 3.4.6 | [MIT](#charset-normalizer) | | click | 8.3.1 | [BSD-3-Clause](#click) | | colour | 0.1.5 | [BSD 3-Clause License](#colour) | -| cryptography | 46.0.5 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | +| cryptography | 46.0.6 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | | cssselect2 | 0.9.0 | [see below](#cssselect2) | -| deepdiff | 8.6.1 | [see below](#deepdiff) | +| deepdiff | 8.6.2 | [see below](#deepdiff) | | dict2xml | 1.7.8 | [MIT](#dict2xml) | | docraptor | 3.1.0 | [MIT](#docraptor) | | et_xmlfile | 2.0.0 | [MIT](#et_xmlfile) | | fastapi | 0.131.0 | [MIT](#fastapi) | -| fhir_core | 1.1.5 | [BSD license](#fhir_core) | +| 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) | @@ -54,9 +54,9 @@ | 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 | 6.33.5 | [3-Clause BSD License](#protobuf) | +| protobuf | 6.33.6 | [3-Clause BSD License](#protobuf) | | psutil | 7.2.2 | [BSD-3-Clause](#psutil) | -| pyasn1 | 0.6.2 | [BSD-2-Clause](#pyasn1) | +| pyasn1 | 0.6.3 | [BSD-2-Clause](#pyasn1) | | pyasn1_modules | 0.4.2 | [BSD](#pyasn1_modules) | | pycparser | 3.0 | [BSD-3-Clause](#pycparser) | | pydantic | 2.12.5 | [MIT](#pydantic) | @@ -71,7 +71,7 @@ | python-multipart | 0.0.22 | [Apache-2.0](#python-multipart) | | pytz | 2026.1.post1 | [MIT](#pytz) | | PyYAML | 6.0.3 | [MIT](#pyyaml) | -| requests | 2.32.5 | [Apache-2.0](#requests) | +| requests | 2.33.0 | [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) | @@ -9330,6 +9330,9 @@ incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. + Requests + Copyright 2019 Kenneth Reitz + --- ### six diff --git a/clinical-mdr-api/templates/odm/crf.html b/clinical-mdr-api/templates/odm/crf.html index 5959c1e3..17042c57 100644 --- a/clinical-mdr-api/templates/odm/crf.html +++ b/clinical-mdr-api/templates/odm/crf.html @@ -822,13 +822,13 @@

{% set border_style = 'border-dashed' if 'note:' in alias.name|lower or 'not submitted' in alias.name|lower else '' %} {% if ':' in alias.name %} - {% set sub_val, _ = alias.name.rsplit(':', maxsplit=1) %} + {% set sub_val, _ = alias.name.split(':', maxsplit=1) %} {% set group_domain = group_domains.get(sub_val, none) %} {% set name = group_domain[0] %} {% set color = group_domain[1] %} - {{ alias.name.rsplit(':', maxsplit=1) | last }} + {{ alias.name.split(':', maxsplit=1) | last }} {% else %} @@ -1036,13 +1036,13 @@

{% set border_style = 'border-dashed' if 'note:' in alias.name|lower or 'not submitted' in alias.name|lower else '' %} {% if ':' in alias.name %} - {% set sub_val, _ = alias.name.rsplit(':', maxsplit=1) %} + {% set sub_val, _ = alias.name.split(':', maxsplit=1) %} {% set group_domain = group_domains.get(sub_val, none) %} {% set name = group_domain[0] %} {% set color = group_domain[1] %} - {{ alias.name.rsplit(':', maxsplit=1) | last }} + {{ alias.name.split(':', maxsplit=1) | last }} {% else %} @@ -1077,7 +1077,8 @@

first | default(none) if item_group_in.vendor else none %}

- diff --git a/db-schema-migration/Pipfile b/db-schema-migration/Pipfile index a6c09d31..24efb7cf 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_021.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_021.py" -migrate = "python -m migrations.migration_021" -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_018.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_018.py" -apply_corrections = "python -m data_corrections.correction_018" +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" 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/correction_019.py b/db-schema-migration/data_corrections/correction_019.py new file mode 100644 index 00000000..5be6d4fb --- /dev/null +++ b/db-schema-migration/data_corrections/correction_019.py @@ -0,0 +1,208 @@ +"""PRD Data Corrections: Remove Veeva-imported codelists and terms""" + +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_019 + +LOGGER = get_logger(os.path.basename(__file__)) +DB_DRIVER = get_db_driver() +CORRECTION_DESC = "data-correction-remove-veeva-imports" + +VEEVA_DEFINITIONS = [ + "Created by Library Importer", + "Created by Veeva Library Importer", +] + + +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) + + remove_veeva_terms(DB_DRIVER, LOGGER, run_label) + remove_veeva_codelists(DB_DRIVER, LOGGER, run_label) + + +@capture_changes(verify_func=correction_verification_019.test_no_veeva_codelists_remain) +def remove_veeva_codelists(db_driver, log, run_label): + """ + ### Problem description + The initial import of ODM data from Veeva created 301 codelists in the library. + When the ODM data was wiped, these codelists were left behind and need to be removed. + Some Veeva codelists contain non-Veeva terms that must be unlinked before deletion. + Runs after term deletion so codelists with remaining protected terms are preserved. + ### Change description + - Phase A: Unlink non-Veeva terms from Veeva codelists (remove CTCodelistTerm junctions) + - Phase B: Delete Veeva codelists that have no remaining terms + ### Nodes and relationships affected + - `CTCodelistRoot`, `CTCodelistNameRoot`, `CTCodelistNameValue` + - `CTCodelistAttributesRoot`, `CTCodelistAttributesValue` + - `CTCodelistTerm` (junction nodes) + ### Expected changes: Veeva codelists with no remaining terms deleted + """ + contains_updates = [] + + # Phase A: Unlink non-Veeva terms from Veeva codelists + log.info(f"Run: {run_label}, Unlinking non-Veeva terms from Veeva codelists") + query_unlink = """ + MATCH (clr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot) + -[:HAS_VERSION]->(clav:CTCodelistAttributesValue) + WHERE clav.definition IN $definitions + WITH DISTINCT clr + MATCH (clr)-[:HAS_TERM]->(clt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(tr:CTTermRoot) + WHERE NOT EXISTS { + MATCH (tr)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot) + -[:HAS_VERSION]->(tav:CTTermAttributesValue) + WHERE tav.definition IN $definitions + } + DETACH DELETE clt + """ + _, summary = run_cypher_query( + db_driver, + query_unlink, + params={"definitions": VEEVA_DEFINITIONS}, + ) + counters = summary.counters + print_counters_table(counters) + contains_updates.append(counters.contains_updates) + + # Phase B: Delete Veeva codelists that have no remaining terms + log.info(f"Run: {run_label}, Deleting Veeva codelists with no remaining terms") + query_delete = """ + MATCH (clr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot) + -[:HAS_VERSION]->(clav:CTCodelistAttributesValue) + WHERE clav.definition IN $definitions + WITH DISTINCT clr + WHERE NOT EXISTS { MATCH (clr)-[:HAS_TERM]->(:CTCodelistTerm) } + CALL { + WITH clr + OPTIONAL MATCH (clr)-[:HAS_NAME_ROOT]->(clnr:CTCodelistNameRoot) + OPTIONAL MATCH (clnr)-[]->(clnv:CTCodelistNameValue) + DETACH DELETE clnv, clnr + } + CALL { + WITH clr + OPTIONAL MATCH (clr)-[:HAS_ATTRIBUTES_ROOT]->(clar:CTCodelistAttributesRoot) + OPTIONAL MATCH (clar)-[]->(clav2:CTCodelistAttributesValue) + DETACH DELETE clav2, clar + } + CALL { + WITH clr + OPTIONAL MATCH (clr)-[:HAS_TERM]->(clt:CTCodelistTerm) + DETACH DELETE clt + } + DETACH DELETE clr + """ + _, summary = run_cypher_query( + db_driver, + query_delete, + params={"definitions": VEEVA_DEFINITIONS}, + ) + counters = summary.counters + print_counters_table(counters) + contains_updates.append(counters.contains_updates) + + return any(contains_updates) + + +@capture_changes(verify_func=correction_verification_019.test_no_veeva_terms_remain) +def remove_veeva_terms(db_driver, log, run_label): + """ + ### Problem description + The initial import of ODM data from Veeva created 652 terms in the library. + When the ODM data was wiped, these terms were left behind and need to be removed. + 6 terms have active CTTermContext references (UnitDefinitionValue/ActivityItem) and must + be preserved. + ### Change description + - Step 1: Identify protected terms (those referenced by CTTermContext nodes that + themselves have incoming relationships, i.e. are actually used by studies/concepts) + - Step 2: Delete all unprotected Veeva terms (CTTermRoot + name/attributes sub-trees + + CTCodelistTerm junctions + orphaned CTTermContext nodes) + ### Nodes and relationships affected + - `CTTermRoot`, `CTTermNameRoot`, `CTTermNameValue` + - `CTTermAttributesRoot`, `CTTermAttributesValue` + - `CTCodelistTerm` (junction nodes linking terms to non-Veeva codelists) + - `CTTermContext` (orphaned nodes with no incoming relationships) + ### Expected changes: 646 terms deleted, 6 terms preserved + """ + # Step 1: Find protected terms (those with CTTermContext references) + log.info( + f"Run: {run_label}, Finding protected Veeva terms with CTTermContext references" + ) + query_protected = """ + MATCH (tr:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot) + -[:HAS_VERSION]->(tav:CTTermAttributesValue) + WHERE tav.definition IN $definitions + WITH DISTINCT tr + WHERE EXISTS { + MATCH (ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(tr) + WHERE EXISTS { MATCH ()-[]->(ctx) } + } + RETURN tr.uid AS term_uid + """ + protected_records, _ = run_cypher_query( + db_driver, + query_protected, + params={"definitions": VEEVA_DEFINITIONS}, + ) + protected_uids = [record["term_uid"] for record in protected_records] + log.info( + f"Run: {run_label}, Found {len(protected_uids)} protected terms: {protected_uids}" + ) + + # Step 2: Delete unprotected Veeva terms + log.info(f"Run: {run_label}, Deleting unprotected Veeva terms") + query_delete = """ + MATCH (tr:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot) + -[:HAS_VERSION]->(tav:CTTermAttributesValue) + WHERE tav.definition IN $definitions + WITH DISTINCT tr + WHERE NOT tr.uid IN $protected_uids + CALL { + WITH tr + OPTIONAL MATCH (tr)-[:HAS_NAME_ROOT]->(tnr:CTTermNameRoot) + OPTIONAL MATCH (tnr)-[]->(tnv:CTTermNameValue) + DETACH DELETE tnv, tnr + } + CALL { + WITH tr + OPTIONAL MATCH (tr)-[:HAS_ATTRIBUTES_ROOT]->(tar:CTTermAttributesRoot) + OPTIONAL MATCH (tar)-[]->(tav2:CTTermAttributesValue) + DETACH DELETE tav2, tar + } + CALL { + WITH tr + OPTIONAL MATCH (clt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(tr) + DETACH DELETE clt + } + CALL { + WITH tr + OPTIONAL MATCH (ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(tr) + WHERE NOT EXISTS { MATCH ()-[]->(ctx) } + DETACH DELETE ctx + } + DETACH DELETE tr + """ + _, summary = run_cypher_query( + db_driver, + query_delete, + params={ + "definitions": VEEVA_DEFINITIONS, + "protected_uids": protected_uids, + }, + ) + counters = summary.counters + print_counters_table(counters) + return counters.contains_updates + + +if __name__ == "__main__": + main() diff --git a/db-schema-migration/data_corrections/correction_019_overview.md b/db-schema-migration/data_corrections/correction_019_overview.md new file mode 100644 index 00000000..646e17e4 --- /dev/null +++ b/db-schema-migration/data_corrections/correction_019_overview.md @@ -0,0 +1,43 @@ +## Data corrections: overview of data_corrections.correction_019 + +PRD Data Corrections: Remove Veeva-imported codelists and terms + + + +## 1. Correction: remove_veeva_codelists + +#### Problem description +The initial import of ODM data from Veeva created 301 codelists in the library. +When the ODM data was wiped, these codelists were left behind and need to be removed. +Some Veeva codelists contain non-Veeva terms that must be unlinked before deletion. +Runs after term deletion so codelists with remaining protected terms are preserved. +#### Change description +- Phase A: Unlink non-Veeva terms from Veeva codelists (remove CTCodelistTerm junctions) +- Phase B: Delete Veeva codelists that have no remaining terms +#### Nodes and relationships affected +- `CTCodelistRoot`, `CTCodelistNameRoot`, `CTCodelistNameValue` +- `CTCodelistAttributesRoot`, `CTCodelistAttributesValue` +- `CTCodelistTerm` (junction nodes) +#### Expected changes: Veeva codelists with no remaining terms deleted + + +## 2. Correction: remove_veeva_terms + +#### Problem description +The initial import of ODM data from Veeva created 652 terms in the library. +When the ODM data was wiped, these terms were left behind and need to be removed. +6 terms have active CTTermContext references (UnitDefinitionValue/ActivityItem) and must +be preserved. +#### Change description +- Step 1: Identify protected terms (those referenced by CTTermContext nodes that + themselves have incoming relationships, i.e. are actually used by studies/concepts) +- Step 2: Delete all unprotected Veeva terms (CTTermRoot + name/attributes sub-trees + + CTCodelistTerm junctions + orphaned CTTermContext nodes) +#### Nodes and relationships affected +- `CTTermRoot`, `CTTermNameRoot`, `CTTermNameValue` +- `CTTermAttributesRoot`, `CTTermAttributesValue` +- `CTCodelistTerm` (junction nodes linking terms to non-Veeva codelists) +- `CTTermContext` (orphaned nodes with no incoming relationships) +#### Expected changes: 646 terms deleted, 6 terms preserved + + diff --git a/db-schema-migration/migrations/migration_022.py b/db-schema-migration/migrations/migration_022.py new file mode 100644 index 00000000..c9770379 --- /dev/null +++ b/db-schema-migration/migrations/migration_022.py @@ -0,0 +1,104 @@ +"""Schema migrations needed to release 2.8 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-2.8" + + +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 migrate_instance_split(db_driver, log) -> bool: + """ + Split ActivityInstance data into the grouping model. + + For each ActivityInstanceRoot -> ActivityInstanceValue pair that has + direct HAS_ACTIVITY links and no HAS_GROUPING_ROOT, this migration creates + an ActivityInstanceGroupingRoot and a corresponding + ActivityInstanceGroupingValue. It then recreates the existing + ActivityInstanceRoot -> ActivityInstanceValue relationship types/properties + between the new grouping nodes and moves HAS_ACTIVITY relationships from + ActivityInstanceValue to ActivityInstanceGroupingValue. + """ + + log.info("Running instance split migration query") + + _, summary = run_cypher_query( + db_driver, + """ + MATCH (air:ActivityInstanceRoot)-[rel]->(aiv:ActivityInstanceValue)-[:HAS_ACTIVITY]->(activity:ActivityGrouping) + WHERE NOT (air)-[:HAS_GROUPING_ROOT]->(:ActivityInstanceGroupingRoot) + WITH DISTINCT air, aiv, collect(rel) AS rels, collect(activity) AS activities + MERGE (air)-[:HAS_GROUPING_ROOT]->(gr:ActivityInstanceGroupingRoot) + WITH air, aiv, gr, rels, activities + CALL { + WITH air, aiv, gr, rels + CREATE (gv:ActivityInstanceGroupingValue) + WITH gr, gv, rels + UNWIND rels AS rel + CALL apoc.create.relationship(gr,type(rel),properties(rel), gv) YIELD rel AS new_rel + RETURN gv + } + CALL { + with air, aiv, gr, gv, activities + UNWIND activities as activity + MATCH (aiv)-[ha:HAS_ACTIVITY]->(activity) + MERGE (gv)-[:HAS_ACTIVITY]->(activity) + DELETE ha + } + RETURN count(aiv) + """, + ) + print_counters_table(summary.counters) + return summary.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) + + ### Release migrations + migrate_feature_flags(DB_DRIVER, logger) + migrate_instance_split(DB_DRIVER, logger) + + +if __name__ == "__main__": + main() diff --git a/db-schema-migration/migrations/migration_overview_022.md b/db-schema-migration/migrations/migration_overview_022.md new file mode 100644 index 00000000..d6be3a66 --- /dev/null +++ b/db-schema-migration/migrations/migration_overview_022.md @@ -0,0 +1,58 @@ +# Release 2.8 (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 + +### 2. Split ActivityInstance data into grouping model +------------------------------------- +#### Change Description +- For each `ActivityInstanceRoot` -> `ActivityInstanceValue` pair with direct + `HAS_ACTIVITY` links and no `HAS_GROUPING_ROOT`, + create a new `ActivityInstanceGroupingRoot` and `ActivityInstanceGroupingValue`. +- Copy existing direct relationships (type and properties) from + `ActivityInstanceRoot` -> `ActivityInstanceValue` + to `ActivityInstanceGroupingRoot` -> `ActivityInstanceGroupingValue`. +- Move all `HAS_ACTIVITY` relationships from `ActivityInstanceValue` to `ActivityInstanceGroupingValue`. + +#### Nodes Affected +- `ActivityInstanceRoot` +- `ActivityInstanceValue` +- `ActivityInstanceGroupingRoot` +- `ActivityInstanceGroupingValue` +- `ActivityGrouping` + +#### Relationships affected +- `HAS_GROUPING_ROOT` +- `HAS_ACTIVITY` +- Dynamic relationship types copied from `(:ActivityInstanceRoot)-[rel]->(:ActivityInstanceValue)` to + `(:ActivityInstanceGroupingRoot)-[rel]->(:ActivityInstanceGroupingValue)` with relationship properties preserved. + + diff --git a/db-schema-migration/tests/test_correction_019.py b/db-schema-migration/tests/test_correction_019.py new file mode 100644 index 00000000..22eacebf --- /dev/null +++ b/db-schema-migration/tests/test_correction_019.py @@ -0,0 +1,168 @@ +"""Data corrections for PROD: Test removal of Veeva-imported codelists and terms.""" + +import os + +import pytest + +from data_corrections import correction_019 +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_019 import TEST_DATA_REMOVE_VEEVA_IMPORTS +from tests.utils.utils import clear_db +from verifications import correction_verification_019 + +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_019.__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_remove_veeva_codelists_and_terms(): + """Test removal of Veeva-imported codelists and terms""" + # Setup test data + _setup_test_data(TEST_DATA_REMOVE_VEEVA_IMPORTS) + + # Verify initial state (should fail — unprotected Veeva terms exist) + with pytest.raises(AssertionError): + correction_verification_019.test_no_veeva_terms_remain() + + # Run corrections (terms first, then codelists) + correction_019.remove_veeva_terms(*CORRECTION_ARGS) + correction_019.remove_veeva_codelists(*CORRECTION_ARGS) + + # Verify corrections worked + correction_verification_019.test_no_veeva_codelists_remain() + correction_verification_019.test_no_veeva_terms_remain() + + # Assert non-Veeva codelist C is preserved + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (clr:CTCodelistRoot {uid: 'CTCodelistRoot_cdisc_c'}) RETURN clr", + ) + assert len(res) == 1, "Non-Veeva codelist C should be preserved" + + # Assert CDISC term from mixed codelist B is preserved (unlinked, not deleted) + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (tr:CTTermRoot {uid: 'CTTermRoot_cdisc_in_veeva'}) RETURN tr", + ) + assert len(res) == 1, "CDISC term from mixed codelist B should be preserved" + + # Assert CDISC term is no longer linked to deleted Veeva codelist B + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'CTCodelistRoot_veeva_b'}) + -[:HAS_TERM]->(clt:CTCodelistTerm)-[:HAS_TERM_ROOT]-> + (tr:CTTermRoot {uid: 'CTTermRoot_cdisc_in_veeva'}) + RETURN clt + """, + ) + assert len(res) == 0, "CDISC term should be unlinked from deleted Veeva codelist B" + + # Assert protected term D with CTTermContext is preserved + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (tr:CTTermRoot {uid: 'CTTermRoot_veeva_protected_d'}) RETURN tr", + ) + assert len(res) == 1, "Protected Veeva term D should be preserved" + + # Assert CTTermContext reference is intact + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (ctx:CTTermContext)-[:HAS_SELECTED_TERM]-> + (tr:CTTermRoot {uid: 'CTTermRoot_veeva_protected_d'}) + RETURN ctx + """, + ) + assert len(res) == 1, "CTTermContext reference to protected term should be intact" + + # Assert Veeva term E with orphaned CTTermContext is deleted + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (tr:CTTermRoot {uid: 'CTTermRoot_veeva_orphaned_e'}) RETURN tr", + ) + assert len(res) == 0, "Veeva term E with orphaned CTTermContext should be deleted" + + # Assert orphaned CTTermContext is also deleted + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (ctx:CTTermContext {uid: 'CTTermContext_orphaned_e'}) RETURN ctx", + ) + assert len(res) == 0, "Orphaned CTTermContext should be deleted" + + # Assert unprotected Veeva terms are deleted + for term_uid in [ + "CTTermRoot_veeva_a1", + "CTTermRoot_veeva_a2", + "CTTermRoot_veeva_b1", + ]: + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (tr:CTTermRoot {uid: $uid}) RETURN tr", + params={"uid": term_uid}, + ) + assert len(res) == 0, f"Veeva term {term_uid} should be deleted" + + # Assert empty Veeva codelists are deleted + for cl_uid in ["CTCodelistRoot_veeva_a", "CTCodelistRoot_veeva_b"]: + res, _ = run_cypher_query( + DB_DRIVER, + "MATCH (clr:CTCodelistRoot {uid: $uid}) RETURN clr", + params={"uid": cl_uid}, + ) + assert len(res) == 0, f"Veeva codelist {cl_uid} should be deleted" + + # Assert Veeva codelist F is preserved (still has protected term D) + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'CTCodelistRoot_veeva_f'}) + -[:HAS_TERM]->(clt:CTCodelistTerm)-[:HAS_TERM_ROOT]-> + (tr:CTTermRoot {uid: 'CTTermRoot_veeva_protected_d'}) + RETURN clr + """, + ) + assert ( + len(res) == 1 + ), "Veeva codelist F should be preserved (contains protected term D)" + + # Assert non-Veeva CDISC term C1 is untouched + res, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (clr:CTCodelistRoot {uid: 'CTCodelistRoot_cdisc_c'}) + -[:HAS_TERM]->(clt:CTCodelistTerm)-[:HAS_TERM_ROOT]-> + (tr:CTTermRoot {uid: 'CTTermRoot_cdisc_c1'}) + RETURN tr + """, + ) + assert len(res) == 1, "CDISC term C1 should still be linked to CDISC codelist C" + + +@pytest.mark.order(after="test_remove_veeva_codelists_and_terms") +def test_repeat_remove_veeva_codelists(): + """Test that codelist removal is idempotent""" + assert not correction_019.remove_veeva_codelists(*CORRECTION_ARGS) + + +@pytest.mark.order(after="test_remove_veeva_codelists_and_terms") +def test_repeat_remove_veeva_terms(): + """Test that term removal is idempotent""" + assert not correction_019.remove_veeva_terms(*CORRECTION_ARGS) diff --git a/db-schema-migration/tests/test_migration_022.py b/db-schema-migration/tests/test_migration_022.py new file mode 100644 index 00000000..3eb6a9bb --- /dev/null +++ b/db-schema-migration/tests/test_migration_022.py @@ -0,0 +1,131 @@ +import os + +import pytest + +from migrations import migration_022 +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_022 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_022.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_022.migrate_feature_flags(DB_DRIVER, logger) + + +def test_migrate_instance_split(migration): + logger.info("Verify instance split migration results") + + records, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (air:ActivityInstanceRoot)-[rel]->(aiv:ActivityInstanceValue)-[:HAS_ACTIVITY]->(:ActivityGrouping) + RETURN count(DISTINCT aiv) AS unmigrated_count + """, + ) + + assert ( + records[0]["unmigrated_count"] == 0 + ), "There are still ActivityInstanceValue nodes linked to ActivityGrouping nodes after migration" + + records, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (air:ActivityInstanceRoot) + WHERE NOT (air)-[:HAS_GROUPING_ROOT]-(:ActivityInstanceGroupingRoot) + RETURN count(DISTINCT air) AS unmigrated_count + """, + ) + assert ( + records[0]["unmigrated_count"] == 0 + ), "There are still ActivityInstanceRoot nodes not linked to an ActivityInstanceGroupingRoot node after migration" + + records, _ = run_cypher_query( + DB_DRIVER, + """ + MATCH (gr:ActivityInstanceGroupingRoot) + WHERE NOT (gr)-[:HAS_VERSION]->(:ActivityInstanceGroupingValue) + OR NOT (gr)-[:LATEST]->(:ActivityInstanceGroupingValue) + RETURN count(DISTINCT gr) AS unmigrated_count + """, + ) + assert ( + records[0]["unmigrated_count"] == 0 + ), "There are ActivityInstanceGroupingRoot nodes not linked to a ActivityInstanceGroupingValue node with HAS_VERSION and LATEST relationships after migration" + + +@pytest.mark.order(after="test_migrate_instance_split") +def test_repeat_migrate_instance_split(migration): + assert not migration_022.migrate_instance_split(DB_DRIVER, logger) diff --git a/db-schema-migration/verifications/correction_verification_019.py b/db-schema-migration/verifications/correction_verification_019.py new file mode 100644 index 00000000..de1abd2b --- /dev/null +++ b/db-schema-migration/verifications/correction_verification_019.py @@ -0,0 +1,69 @@ +""" +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() + +VEEVA_DEFINITIONS = [ + "Created by Library Importer", + "Created by Veeva Library Importer", +] + + +def test_no_veeva_codelists_remain(): + """Verify that no empty Veeva-imported codelists remain in the database. + + Veeva codelists that still contain protected terms (terms with active + CTTermContext references) are expected to be preserved. + """ + LOGGER.info("Checking for remaining empty Veeva-imported codelists") + query = """ + MATCH (clr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot) + -[:HAS_VERSION]->(clav:CTCodelistAttributesValue) + WHERE clav.definition IN $definitions + WITH DISTINCT clr + WHERE NOT EXISTS { MATCH (clr)-[:HAS_TERM]->(:CTCodelistTerm) } + RETURN count(clr) AS count + """ + res, _ = run_cypher_query( + DB_DRIVER, query, params={"definitions": VEEVA_DEFINITIONS} + ) + count = res[0]["count"] + assert count == 0, f"Found {count} empty Veeva codelists still in the database" + + +def test_no_veeva_terms_remain(): + """Verify that no unprotected Veeva-imported terms remain in the database. + + Terms with active CTTermContext references (i.e. the CTTermContext has incoming + relationships from UnitDefinitionValue, ActivityItem, etc.) are expected to be + preserved and are excluded from this check. + """ + LOGGER.info("Checking for remaining unprotected Veeva-imported terms") + query = """ + MATCH (tr:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot) + -[:HAS_VERSION]->(tav:CTTermAttributesValue) + WHERE tav.definition IN $definitions + WITH DISTINCT tr + WHERE NOT EXISTS { + MATCH (ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(tr) + WHERE EXISTS { MATCH ()-[]->(ctx) } + } + RETURN count(tr) AS count + """ + res, _ = run_cypher_query( + DB_DRIVER, query, params={"definitions": VEEVA_DEFINITIONS} + ) + count = res[0]["count"] + assert ( + count == 0 + ), f"Found {count} unprotected Veeva-imported terms still in the database" diff --git a/db-schema-migration/verifications/verification_022.py b/db-schema-migration/verifications/verification_022.py new file mode 100644 index 00000000..4bac8278 --- /dev/null +++ b/db-schema-migration/verifications/verification_022.py @@ -0,0 +1,34 @@ +""" +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_022 + + +@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_022.test_ct_config_values(migration) + + +def test_indexes_and_constraints(): + test_migration_022.test_indexes_and_constraints(migration) + + +def test_migrate_featureflag_nodes(): + test_migration_022.test_migrate_featureflag_nodes(migration) + + +def test_migrate_instance_split(): + test_migration_022.test_migrate_instance_split(migration) diff --git a/documentation-portal/docs/guides/userguide/studies/manage_studies.md b/documentation-portal/docs/guides/userguide/studies/manage_studies.md index 810470be..148b4a96 100644 --- a/documentation-portal/docs/guides/userguide/studies/manage_studies.md +++ b/documentation-portal/docs/guides/userguide/studies/manage_studies.md @@ -154,7 +154,7 @@ This option is to create a new study as a subpart. Make sure to have the study s 1. Select ‘Create new study to be study subpart’ 1. Select ‘continue’ -1. Write study subpart acronym (could be Multi Dose, or part 2 or something else, this field is required) +1. Write study subpart acronym (could be MULTIDOSE, or PART2 or something else, this field is required) 1. Write study acronym (this is the basic acronym for the study similar to the acronym for normal studies, the field is optional) 1. Write a description (optional) 1. Press ‘Save’ @@ -189,7 +189,7 @@ Only studies within same project ID can be add as subpart to the ‘main’ stud 1. Select ‘Add existing study as study subpart’ 1. Select ‘continue’ 1. Select existing study by using the copy button ![Copy](~@source/images/user_guides/copy_button.png) -1. Write study subpart acronym (could be Multi Dose, or part 2 or something else, this field is required) +1. Write study subpart acronym (could be MULTIDOSE, or PART2 or something else, this field is required) 1. Write a description (optional) or reuse any existing description 1. Press ‘Save’ @@ -218,10 +218,10 @@ Then go to Manage study/Study/Study Subparts to get the overview – see Figure | Column | Explanation | Example | | --- | --------- | --- | -| Study ID | The study ID number including project ID | CDISC DEV-5555 | +| Study ID | The study ID number including project ID and subpart acronym | CDISC DEV-5555-SINGLEDOSE | | Study Acronym | The acronym for the whole study | DEFINE6 | | Subpart ID | The unique ID for the subpart | a | -| Subpart acronym | An acronym that describes the subpart | SD/Single Dose | +| Subpart acronym | An acronym that describes the subpart | SINGLEDOSE | | Description | Free text description as needed | Lorem ipsum etc | @@ -231,3 +231,4 @@ A study subpart cannot be released or locked individually - a subpart can only b See more on [study versioning](#maintain-study-status-and-versioning). + diff --git a/mdr-standards-import/mdr_standards_import/container_booting/packages/cdisc_ct/ddfct-2024-09-27.json b/mdr-standards-import/mdr_standards_import/container_booting/packages/cdisc_ct/ddfct-2024-09-27.json new file mode 100644 index 00000000..2cbca163 --- /dev/null +++ b/mdr-standards-import/mdr_standards_import/container_booting/packages/cdisc_ct/ddfct-2024-09-27.json @@ -0,0 +1,3528 @@ +{ + "_links": + { + "priorVersion": + { + "href": "/mdr/ct/packages/ddfct-2024-03-29", + "title": "DDF Controlled Terminology Package 57 Effective 2024-03-29", + "type": "Terminology" + }, + "self": + { + "href": "/mdr/ct/packages/ddfct-2024-09-27", + "title": "DDF Controlled Terminology Package 58 Effective 2024-09-27", + "type": "Terminology" + } + }, + "codelists": + [ + { + "conceptId": "C188714", + "definition": "A terminology value set relevant to the attributes of the activity.", + "extensible": "false", + "name": "DDF Activity Attribute Terminology", + "preferredTerm": "CDISC DDF Activity Attribute Terminology", + "submissionValue": "DDF Activity Attribute Terminology", + "synonyms": + [ + "DDF Activity Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C70960", + "definition": "The textual representation of the study activity.", + "preferredTerm": "Clinical Study Activity Description", + "submissionValue": "Clinical Study Activity Description" + }, + { + "conceptId": "C207458", + "definition": "The short descriptive designation for the study activity.", + "preferredTerm": "Study Activity Label", + "submissionValue": "Clinical Study Activity Label" + }, + { + "conceptId": "C188842", + "definition": "The literal identifier (i.e., distinctive designation) of the clinical study activity.", + "preferredTerm": "Clinical Study Activity Name", + "submissionValue": "Clinical Study Activity Name" + } + ] + }, + { + "conceptId": "C201253", + "definition": "A terminology value set relevant to the attributes of the address.", + "extensible": "false", + "name": "DDF Address Attribute Terminology", + "preferredTerm": "CDISC DDF Address Attribute Terminology", + "submissionValue": "DDF Address Attribute Terminology", + "synonyms": + [ + "DDF Address Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C201311", + "definition": "A standardized representation of the complete set of components denoting the physical address of the person, business, building, or organization.", + "preferredTerm": "Address Full Text", + "submissionValue": "Address Full Text" + }, + { + "conceptId": "C25690", + "definition": "The street name and number, building number, apartment or unit number, or post office box number where an entity is physically located.", + "preferredTerm": "Street Address", + "submissionValue": "Address Line" + }, + { + "conceptId": "C25160", + "definition": "A relatively large and/or densely populated area of human habitation with administrative or legal status that may be specified as a component of a postal address.", + "preferredTerm": "City", + "submissionValue": "City" + }, + { + "conceptId": "C25464", + "definition": "A sovereign nation occupying a distinct territory and ruled by an autonomous government.", + "preferredTerm": "Country", + "submissionValue": "Country" + }, + { + "conceptId": "C176229", + "definition": "An administrative or territorial division of a city, town, county, parish, state, country, or other locality based on a shared characteristic.", + "preferredTerm": "District", + "submissionValue": "District" + }, + { + "conceptId": "C25621", + "definition": "An alphanumeric code assigned to a mail delivery area.", + "preferredTerm": "Postal Code", + "submissionValue": "Postal Code" + }, + { + "conceptId": "C87194", + "definition": "A sub-division of a country that forms part of a federal union. States are usually, but not always, more autonomous than provinces and may have different laws from the central government.", + "preferredTerm": "State", + "submissionValue": "State" + } + ] + }, + { + "conceptId": "C207420", + "definition": "A terminology value set relevant to the attributes of the administration duration.", + "extensible": "false", + "name": "DDF Administration Duration Attribute Terminology", + "preferredTerm": "CDISC DDF Administration Duration Attribute Terminology", + "submissionValue": "DDF Administration Duration Attribute Terminology", + "synonyms": + [ + "DDF Administration Duration Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207459", + "definition": "A narrative representation of the agent administration duration.", + "preferredTerm": "Administration Duration Description", + "submissionValue": "Administration Duration Description" + }, + { + "conceptId": "C207460", + "definition": "The value representing the amount of time over which the administration of an agent occurs.", + "preferredTerm": "Administration Duration Quantity Value", + "submissionValue": "Administration Duration Quantity Value" + }, + { + "conceptId": "C207462", + "definition": "The explanation for why the agent administration duration will vary within and/or across subjects.", + "preferredTerm": "Reason Administration Duration Will Vary", + "submissionValue": "Administration Duration Reason Duration Will Vary", + "synonyms": + [ + "Reason Administration Duration Will Vary" + ] + }, + { + "conceptId": "C207461", + "definition": "An indication as to whether the agent administration duration is planned to vary within and/or across subjects.", + "preferredTerm": "Administration Duration Will Vary Indicator", + "submissionValue": "Administration Duration Will Vary Indicator" + } + ] + }, + { + "conceptId": "C207421", + "definition": "A terminology value set relevant to the attributes of the agent administration.", + "extensible": "false", + "name": "DDF Agent Administration Attribute Terminology", + "preferredTerm": "CDISC DDF Agent Administration Attribute Terminology", + "submissionValue": "DDF Agent Administration Attribute Terminology", + "synonyms": + [ + "DDF Agent Administration Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207463", + "definition": "A narrative representation of the agent administration.", + "preferredTerm": "Agent Administration Description", + "submissionValue": "Agent Administration Description" + }, + { + "conceptId": "C167190", + "definition": "The value representing the amount of an agent given to an individual at one time.", + "preferredTerm": "Dose Administered", + "submissionValue": "Agent Administration Dose" + }, + { + "conceptId": "C207464", + "definition": "The short descriptive designation for the agent administration.", + "preferredTerm": "Agent Administration Label", + "submissionValue": "Agent Administration Label" + }, + { + "conceptId": "C207465", + "definition": "The literal identifier (i.e., distinctive designation) of the agent administration.", + "preferredTerm": "Agent Administration Name", + "submissionValue": "Agent Administration Name" + }, + { + "conceptId": "C89081", + "definition": "The number of doses administered per a specific interval.", + "preferredTerm": "Dose Frequency", + "submissionValue": "Dosing Frequency", + "synonyms": + [ + "Dosing Frequency" + ] + }, + { + "conceptId": "C38114", + "definition": "The way in which a pharmaceutical product is taken into, or makes contact with, the body. (CDISC Glossary)", + "preferredTerm": "Route of Administration", + "submissionValue": "Route of Administration", + "synonyms": + [ + "Route of Administration" + ] + } + ] + }, + { + "conceptId": "C188720", + "definition": "A terminology value set relevant to the attributes of the analysis population.", + "extensible": "false", + "name": "DDF Analysis Population Attribute Terminology", + "preferredTerm": "CDISC DDF Analysis Population Attribute Terminology", + "submissionValue": "DDF Analysis Population Attribute Terminology", + "synonyms": + [ + "DDF Analysis Population Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188854", + "definition": "The textual representation of the study population for analysis.", + "preferredTerm": "Analysis Population Description", + "submissionValue": "Analysis Population Description" + }, + { + "conceptId": "C207466", + "definition": "The short descriptive designation for the analysis population.", + "preferredTerm": "Analysis Population Label", + "submissionValue": "Analysis Population Label" + }, + { + "conceptId": "C207467", + "definition": "The literal identifier (i.e., distinctive designation) of the analysis population.", + "preferredTerm": "Analysis Population Name", + "submissionValue": "Analysis Population Name" + }, + { + "conceptId": "C207468", + "definition": "An instance of unstructured text that represents the analysis population.", + "preferredTerm": "Analysis Population Text", + "submissionValue": "Analysis Population Text" + } + ] + }, + { + "conceptId": "C201254", + "definition": "A terminology value set relevant to the attributes of the biomedical concept.", + "extensible": "false", + "name": "DDF Biomedical Concept Attribute Terminology", + "preferredTerm": "CDISC DDF Biomedical Concept Attribute Terminology", + "submissionValue": "DDF Biomedical Concept Attribute Terminology", + "synonyms": + [ + "DDF Biomedical Concept Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207469", + "definition": "A concept unique identifier assigned to a biomedical concept that points to the meaning of that biomedical concept.", + "preferredTerm": "Biomedical Concept Code", + "submissionValue": "Biomedical Concept Concept Code" + }, + { + "conceptId": "C207470", + "definition": "The short descriptive designation for the biomedical concept.", + "preferredTerm": "Biomedical Concept Label", + "submissionValue": "Biomedical Concept Label" + }, + { + "conceptId": "C201312", + "definition": "The literal identifier (i.e., distinctive designation) of the biomedical concept.", + "preferredTerm": "Biomedical Concept Name", + "submissionValue": "Biomedical Concept Name" + }, + { + "conceptId": "C201313", + "definition": "A citation to an authoritative source for a biomedical concept.", + "preferredTerm": "Biomedical Concept Reference", + "submissionValue": "Biomedical Concept Reference" + }, + { + "conceptId": "C201314", + "definition": "A word or an expression that serves as a figurative, symbolic, or exact substitute for a biomedical concept, and which has the same meaning.", + "preferredTerm": "Biomedical Concept Synonym", + "submissionValue": "Biomedical Concept Synonym" + } + ] + }, + { + "conceptId": "C201255", + "definition": "A terminology value set relevant to the attributes of the biomedical concept category.", + "extensible": "false", + "name": "DDF Biomedical Concept Category Attribute Terminology", + "preferredTerm": "CDISC DDF Biomedical Concept Category Attribute Terminology", + "submissionValue": "DDF Biomedical Concept Category Attribute Terminology", + "synonyms": + [ + "DDF Biomedical Concept Category Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C201315", + "definition": "A symbol or combination of symbols which is assigned to the biomedical concept category.", + "preferredTerm": "Biomedical Concept Category Code", + "submissionValue": "Biomedical Concept Category Code" + }, + { + "conceptId": "C201316", + "definition": "A narrative representation of the biomedical concept category.", + "preferredTerm": "Biomedical Concept Category Description", + "submissionValue": "Biomedical Concept Category Description" + }, + { + "conceptId": "C207471", + "definition": "The short descriptive designation for the biomedical concept category.", + "preferredTerm": "Biomedical Concept Category Label", + "submissionValue": "Biomedical Concept Category Label" + }, + { + "conceptId": "C201317", + "definition": "The literal identifier (i.e., distinctive designation) of the biomedical concept category.", + "preferredTerm": "Biomedical Concept Category Name", + "submissionValue": "Biomedical Concept Category Name" + } + ] + }, + { + "conceptId": "C201256", + "definition": "A terminology value set relevant to the attributes of the biomedical concept property.", + "extensible": "false", + "name": "DDF Biomedical Concept Property Attribute Terminology", + "preferredTerm": "CDISC DDF Biomedical Concept Property Attribute Terminology", + "submissionValue": "DDF Biomedical Concept Property Attribute Terminology", + "synonyms": + [ + "DDF Biomedical Concept Property Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C201318", + "definition": "A concept unique identifier assigned to a biomedical concept property that points to the meaning of that biomedical concept property.", + "preferredTerm": "Biomedical Concept Property Concept Code", + "submissionValue": "Biomedical Concept Property Concept Code" + }, + { + "conceptId": "C202496", + "definition": "An indication as to whether the biomedical concept property is activated for use within a given usage context for a biomedical concept.", + "preferredTerm": "Biomedical Concept Property Enabled Indicator", + "submissionValue": "Biomedical Concept Property Enabled Indicator" + }, + { + "conceptId": "C207472", + "definition": "The short descriptive designation for the biomedical concept property.", + "preferredTerm": "Biomedical Concept Property Label", + "submissionValue": "Biomedical Concept Property Label" + }, + { + "conceptId": "C202494", + "definition": "The literal identifier (i.e., distinctive designation) of the biomedical concept property.", + "preferredTerm": "Biomedical Concept Property Name", + "submissionValue": "Biomedical Concept Property Name" + }, + { + "conceptId": "C202495", + "definition": "An indication as to whether the biomedical concept property is required.", + "preferredTerm": "Biomedical Concept Property Required Indicator", + "submissionValue": "Biomedical Concept Property Required Indicator" + }, + { + "conceptId": "C201319", + "definition": "The structural format of the biomedical concept property response value. The datatype is carried in the attribute and influences the set of allowable values the attribute may assume. (After HL7)", + "preferredTerm": "Biomedical Concept Property Response Data Type", + "submissionValue": "Biomedical Concept Property Response Data Type" + } + ] + }, + { + "conceptId": "C201257", + "definition": "A terminology value set relevant to the attributes of the biomedical concept surrogate.", + "extensible": "false", + "name": "DDF Biomedical Concept Surrogate Attribute Terminology", + "preferredTerm": "CDISC DDF Biomedical Concept Surrogate Attribute Terminology", + "submissionValue": "DDF Biomedical Concept Surrogate Attribute Terminology", + "synonyms": + [ + "DDF Biomedical Concept Surrogate Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C201320", + "definition": "A narrative representation of the biomedical concept surrogate.", + "preferredTerm": "Biomedical Concept Surrogate Description", + "submissionValue": "Biomedical Concept Surrogate Description" + }, + { + "conceptId": "C207473", + "definition": "The short descriptive designation for the biomedical concept surrogate.", + "preferredTerm": "Biomedical Concept Surrogate Label", + "submissionValue": "Biomedical Concept Surrogate Label" + }, + { + "conceptId": "C207474", + "definition": "The literal identifier (i.e., distinctive designation) of the biomedical concept surrogate.", + "preferredTerm": "Biomedical Concept Surrogate Name", + "submissionValue": "Biomedical Concept Surrogate Name" + }, + { + "conceptId": "C201321", + "definition": "A citation to an authoritative source for a biomedical concept surrogate.", + "preferredTerm": "Biomedical Concept Surrogate Reference", + "submissionValue": "Biomedical Concept Surrogate Reference" + } + ] + }, + { + "conceptId": "C207422", + "definition": "A terminology value set relevant to the attributes of the characteristic.", + "extensible": "false", + "name": "DDF Characteristic Attribute Terminology", + "preferredTerm": "CDISC DDF Characteristic Attribute Terminology", + "submissionValue": "DDF Characteristic Attribute Terminology", + "synonyms": + [ + "DDF Characteristic Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207475", + "definition": "A narrative representation of the characteristic.", + "preferredTerm": "Characteristic Description", + "submissionValue": "Characteristic Description" + }, + { + "conceptId": "C207476", + "definition": "The short descriptive designation for the characteristic.", + "preferredTerm": "Characteristic Label", + "submissionValue": "Characteristic Label" + }, + { + "conceptId": "C207477", + "definition": "The literal identifier (i.e., distinctive designation) of the characteristic.", + "preferredTerm": "Characteristic Name", + "submissionValue": "Characteristic Name" + }, + { + "conceptId": "C207478", + "definition": "An instance of structured text that represents the characteristic.", + "preferredTerm": "Characteristic Text", + "submissionValue": "Characteristic Text" + } + ] + }, + { + "conceptId": "C188699", + "definition": "A terminology value set relevant to the attributes of the clinical study.", + "extensible": "false", + "name": "DDF Clinical Study Attribute Terminology", + "preferredTerm": "CDISC DDF Clinical Study Attribute Terminology", + "submissionValue": "DDF Clinical Study Attribute Terminology", + "synonyms": + [ + "DDF Clinical Study Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207479", + "definition": "The short descriptive designation for the clinical study.", + "preferredTerm": "Clinical Study Label", + "submissionValue": "Clinical Study Label" + }, + { + "conceptId": "C142704", + "definition": "A narrative representation of the study.", + "preferredTerm": "Study Description", + "submissionValue": "Study Description" + }, + { + "conceptId": "C68631", + "definition": "The literal identifier (i.e., distinctive designation) of the study.", + "preferredTerm": "Study Name", + "submissionValue": "Study Name" + } + ] + }, + { + "conceptId": "C188722", + "definition": "A terminology value set relevant to the attributes of the code.", + "extensible": "false", + "name": "DDF Code Attribute Terminology", + "preferredTerm": "CDISC DDF Code Attribute Terminology", + "submissionValue": "DDF Code Attribute Terminology", + "synonyms": + [ + "DDF Code Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188859", + "definition": "The literal identifier (i.e., distinctive designation) of the system used to assign and/or manage codes.", + "preferredTerm": "Code System Name", + "submissionValue": "Code System Name" + }, + { + "conceptId": "C188868", + "definition": "The version of the code system.", + "preferredTerm": "Coding System Version", + "submissionValue": "Code System Version" + }, + { + "conceptId": "C188858", + "definition": "The literal value of a code.", + "preferredTerm": "Code Value", + "submissionValue": "Code Value" + }, + { + "conceptId": "C188861", + "definition": "Standardized or dictionary-derived human readable text associated with a code.", + "preferredTerm": "Decode Text", + "submissionValue": "Decode" + } + ] + }, + { + "conceptId": "C207425", + "definition": "A terminology value set relevant to the attributes of the condition assignment.", + "extensible": "false", + "name": "DDF Condition Assignment Attribute Terminology", + "preferredTerm": "CDISC DDF Condition Assignment Attribute Terminology", + "submissionValue": "DDF Condition Assignment Attribute Terminology", + "synonyms": + [ + "DDF Condition Assignment Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C47953", + "definition": "An assumption on which rests the validity or effect of something else.", + "preferredTerm": "Logical Condition", + "submissionValue": "Logical Condition" + } + ] + }, + { + "conceptId": "C207424", + "definition": "A terminology value set relevant to the attributes of the condition.", + "extensible": "false", + "name": "DDF Condition Attribute Terminology", + "preferredTerm": "CDISC DDF Condition Attribute Terminology", + "submissionValue": "DDF Condition Attribute Terminology", + "synonyms": + [ + "DDF Condition Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207481", + "definition": "A narrative representation of the condition.", + "preferredTerm": "Condition Description", + "submissionValue": "Condition Description" + }, + { + "conceptId": "C207482", + "definition": "The short descriptive designation for the condition.", + "preferredTerm": "Condition Label", + "submissionValue": "Condition Label" + }, + { + "conceptId": "C207483", + "definition": "The literal identifier (i.e., distinctive designation) of the condition.", + "preferredTerm": "Condition Name", + "submissionValue": "Condition Name" + }, + { + "conceptId": "C207484", + "definition": "An instance of structured text that represents the condition.", + "preferredTerm": "Condition Text", + "submissionValue": "Condition Text" + } + ] + }, + { + "conceptId": "C207427", + "definition": "A terminology value set relevant to the attributes of the eligibility criteria.", + "extensible": "false", + "name": "DDF Eligibility Criteria Attribute Terminology", + "preferredTerm": "CDISC DDF Eligibility Criteria Attribute Terminology", + "submissionValue": "DDF Eligibility Criteria Attribute Terminology", + "synonyms": + [ + "DDF Eligibility Criteria Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C83016", + "definition": "A classification of the inclusion exclusion criterion.", + "preferredTerm": "Inclusion Exclusion Criterion Category", + "submissionValue": "Study Eligibility Criteria Category" + }, + { + "conceptId": "C207486", + "definition": "A narrative representation of the study eligibility criterion.", + "preferredTerm": "Study Eligibility Criteria Description", + "submissionValue": "Study Eligibility Criterion Description" + }, + { + "conceptId": "C207489", + "definition": "A sequence of characters used to identify, name, or characterize the inclusion or exclusion criterion.", + "preferredTerm": "Study Eligibility Criterion Identifier", + "submissionValue": "Study Eligibility Criterion Identifier" + }, + { + "conceptId": "C207487", + "definition": "The short descriptive designation for the study eligibility criterion.", + "preferredTerm": "Study Eligibility Criteria Label", + "submissionValue": "Study Eligibility Criterion Label" + }, + { + "conceptId": "C207488", + "definition": "The literal identifier (i.e., distinctive designation) of the study eligibility criterion.", + "preferredTerm": "Study Eligibility Criteria Name", + "submissionValue": "Study Eligibility Criterion Name" + }, + { + "conceptId": "C207485", + "definition": "An instance of structured text that represents the study eligibility criterion.", + "preferredTerm": "Study Eligibility Criteria Text", + "submissionValue": "Study Eligibility Criterion Text" + } + ] + }, + { + "conceptId": "C188713", + "definition": "A terminology value set relevant to the attributes of the encounter.", + "extensible": "false", + "name": "DDF Encounter Attribute Terminology", + "preferredTerm": "CDISC DDF Encounter Attribute Terminology", + "submissionValue": "DDF Encounter Attribute Terminology", + "synonyms": + [ + "DDF Encounter Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188836", + "definition": "A narrative representation of the protocol-defined clinical encounter.", + "preferredTerm": "Clinical Encounter Description", + "submissionValue": "Clinical Encounter Description" + }, + { + "conceptId": "C171010", + "definition": "The literal identifier (i.e., distinctive designation) for a protocol-defined clinical encounter.", + "preferredTerm": "Clinical Encounter Name", + "submissionValue": "Clinical Encounter Name" + }, + { + "conceptId": "C188839", + "definition": "A characterization or classification of contact between subject/patient and healthcare practitioner/researcher, during which an assessment or activity is performed.", + "preferredTerm": "Clinical Encounter Type", + "submissionValue": "Clinical Encounter Type" + }, + { + "conceptId": "C188841", + "definition": "The means by which an interaction occurs between the subject/participant and person or entity (e.g., a device).", + "preferredTerm": "Contact Mode", + "submissionValue": "Contact Mode" + }, + { + "conceptId": "C188840", + "definition": "The environment/setting where the event, intervention, or finding occurred.", + "preferredTerm": "Environmental Setting", + "submissionValue": "Environmental Setting" + }, + { + "conceptId": "C207490", + "definition": "The short descriptive designation for the study encounter.", + "preferredTerm": "Study Encounter Label", + "submissionValue": "Study Encounter Label" + } + ] + }, + { + "conceptId": "C188708", + "definition": "A terminology value set relevant to the attributes of the endpoint.", + "extensible": "false", + "name": "DDF Endpoint Attribute Terminology", + "preferredTerm": "CDISC DDF Endpoint Attribute Terminology", + "submissionValue": "DDF Endpoint Attribute Terminology", + "synonyms": + [ + "DDF Endpoint Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188824", + "definition": "A narrative representation of the study endpoint.", + "preferredTerm": "Study Endpoint Description", + "submissionValue": "Study Endpoint Description" + }, + { + "conceptId": "C207491", + "definition": "The short descriptive designation for the study endpoint.", + "preferredTerm": "Study Endpoint Label", + "submissionValue": "Study Endpoint Label" + }, + { + "conceptId": "C188826", + "definition": "A characterization or classification of the study endpoint that determines its category of importance relative to other study endpoints.", + "preferredTerm": "Study Endpoint Level", + "submissionValue": "Study Endpoint Level" + }, + { + "conceptId": "C207492", + "definition": "The literal identifier (i.e., distinctive designation) of the study endpoint.", + "preferredTerm": "Study Endpoint Name", + "submissionValue": "Study Endpoint Name" + }, + { + "conceptId": "C188825", + "definition": "The reason or intention for the study endpoint.", + "preferredTerm": "Study Endpoint Purpose", + "submissionValue": "Study Endpoint Purpose" + }, + { + "conceptId": "C207493", + "definition": "An instance of structured text that represents the study endpoint.", + "preferredTerm": "Study Endpoint Text", + "submissionValue": "Study Endpoint Text" + } + ] + }, + { + "conceptId": "C188698", + "definition": "A terminology value set relevant to the entities within the CDISC digital data flow (DDF) model.", + "extensible": "false", + "name": "DDF Entity Terminology", + "preferredTerm": "CDISC DDF Entities Terminology", + "submissionValue": "DDF Entity Terminology", + "synonyms": + [ + "DDF Entity Terminology" + ], + "terms": + [ + { + "conceptId": "C25407", + "definition": "A standardized representation of the location of a person, business, building, or organization. (NCI)", + "preferredTerm": "Address", + "submissionValue": "Address" + }, + { + "conceptId": "C69282", + "definition": "The amount of time elapsed during the administration of an agent.", + "preferredTerm": "Duration of Administration", + "submissionValue": "Administration Duration" + }, + { + "conceptId": "C70962", + "definition": "The act of the dispensing, applying, or tendering a medical product or other agent.", + "preferredTerm": "Agent Administration", + "submissionValue": "Agent Administration" + }, + { + "conceptId": "C201344", + "definition": "An alternative symbol or combination of symbols which is assigned to the members of a collection.", + "preferredTerm": "Alias Code", + "submissionValue": "Alias Code" + }, + { + "conceptId": "C201346", + "definition": "A grouping of biomedical concepts based on some commonality or by user defined characteristics.", + "preferredTerm": "Biomedical Concept Category", + "submissionValue": "Biomedical Concept Category" + }, + { + "conceptId": "C202493", + "definition": "A characteristic from a set of characteristics used to define a biomedical concept.", + "preferredTerm": "Biomedical Concept Property", + "submissionValue": "Biomedical Concept Property" + }, + { + "conceptId": "C207590", + "definition": "A concept that substitutes for a standard biomedical concept from the designated source.", + "preferredTerm": "Biomedical Concept Surrogate", + "submissionValue": "Biomedical Concept Surrogate" + }, + { + "conceptId": "C201345", + "definition": "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.", + "preferredTerm": "Biomedical Concept", + "submissionValue": "Biomedical Concept" + }, + { + "conceptId": "C25447", + "definition": "The distinguishing qualities or prominent aspects of an entity.", + "preferredTerm": "Characteristic", + "submissionValue": "Characteristic" + }, + { + "conceptId": "C142427", + "definition": "Contact between subject/patient and healthcare practitioner/researcher, during which an assessment or activity is performed. Contact may be physical or virtual.", + "preferredTerm": "Clinical Encounter", + "submissionValue": "Clinical Encounter" + }, + { + "conceptId": "C15206", + "definition": "A clinical study involves research using human volunteers (also called participants) that is intended to add to medical knowledge. There are two main types of clinical studies: clinical trials (also called interventional studies) and observational studies. [ClinicalTrials.gov] See also clinical trial. (CDISC Glossary)", + "preferredTerm": "Clinical Study", + "submissionValue": "Clinical Study" + }, + { + "conceptId": "C25162", + "definition": "A symbol or combination of symbols which is assigned to the members of a collection.", + "preferredTerm": "Code", + "submissionValue": "Code" + }, + { + "conceptId": "C201335", + "definition": "An allotting or appointment to a set of conditions that are to be met in order to make a logical decision.", + "preferredTerm": "Condition Assignment", + "submissionValue": "Condition Assignments" + }, + { + "conceptId": "C25457", + "definition": "A state of being.", + "preferredTerm": "Condition", + "submissionValue": "Condition" + }, + { + "conceptId": "C41184", + "definition": "A health problem or disease that is identified as likely to be benefited by a therapy being studied in clinical trials.", + "preferredTerm": "Indication", + "submissionValue": "Disease/Condition Indication" + }, + { + "conceptId": "C188813", + "definition": "A precise description of the treatment effect reflecting the clinical question posed by a given clinical trial objective. It summarises at a population level what the outcomes would be in the same patients under different treatment conditions being compared. (ICH E9 R1 Addendum)", + "preferredTerm": "Estimand", + "submissionValue": "Estimand" + }, + { + "conceptId": "C207591", + "definition": "The extent or range related to the physical location of an entity.", + "preferredTerm": "Geographic Scope", + "submissionValue": "Geographic Scope" + }, + { + "conceptId": "C188815", + "definition": "An event(s) occurring after treatment initiation that affects either the interpretation or the existence of the measurements associated with the clinical question of interest. (ICH E9 Addendum on Estimands)", + "preferredTerm": "Intercurrent Event", + "submissionValue": "Intercurrent Event" + }, + { + "conceptId": "C191278", + "definition": "The mechanism used to obscure the distinctive characteristics of the study intervention or procedure to make it indistinguishable from the comparator. NOTE: Blinding refers to study participants while masking refers to the study intervention. (CDISC Glossary)", + "preferredTerm": "Masking", + "submissionValue": "Masking" + }, + { + "conceptId": "C207592", + "definition": "The container that holds an instance of unstructured text and which may include objects such as tables, figures, and images.", + "preferredTerm": "Narrative Content", + "submissionValue": "Narrative Content" + }, + { + "conceptId": "C19711", + "definition": "A formalized group of persons or other organizations collected together for a common purpose (such as administrative, legal, political) and the infrastructure to carry out that purpose. (BRIDG)", + "preferredTerm": "Professional Organization or Group", + "submissionValue": "Organization" + }, + { + "conceptId": "C207456", + "definition": "The paired name and value for a given parameter.", + "preferredTerm": "Parameter Map", + "submissionValue": "Parameter Map" + }, + { + "conceptId": "C207593", + "definition": "A concise explanation of the meaning of a population.", + "preferredTerm": "Population Definition", + "submissionValue": "Population Definition" + }, + { + "conceptId": "C98769", + "definition": "Any activity performed by manual and/or instrumental means for the purpose of diagnosis, assessment, therapy, prevention, or palliative care.", + "preferredTerm": "Physical Medical Procedure", + "submissionValue": "Procedure", + "synonyms": + [ + "Medical Procedure" + ] + }, + { + "conceptId": "C25256", + "definition": "How much there is of something that can be measured; the total amount or number.", + "preferredTerm": "Quantity", + "submissionValue": "Quantity" + }, + { + "conceptId": "C38013", + "definition": "The difference between the lowest and highest numerical values; the limits or scale of variation.", + "preferredTerm": "Range", + "submissionValue": "Range" + }, + { + "conceptId": "C93448", + "definition": "An organization that undertakes systematic investigation within a field of study in order to discover facts, establish or revise a theory, test a hypothesis, or develop a plan of action based on the facts discovered.", + "preferredTerm": "Research Organization", + "submissionValue": "Research Organization" + }, + { + "conceptId": "C201347", + "definition": "A symbol or combination of symbols representing the response to the question.", + "preferredTerm": "Response Code", + "submissionValue": "Response Code" + }, + { + "conceptId": "C201349", + "definition": "To go out of or leave the schedule timeline.", + "preferredTerm": "Schedule Timeline Exit", + "submissionValue": "Schedule Timeline Exit" + }, + { + "conceptId": "C201348", + "definition": "A chronological schedule of planned temporal events.", + "preferredTerm": "Schedule Timeline", + "submissionValue": "Schedule Timeline" + }, + { + "conceptId": "C201350", + "definition": "A scheduled occurrence of an activity event.", + "preferredTerm": "Scheduled Activity Instance", + "submissionValue": "Scheduled Activity Instance" + }, + { + "conceptId": "C201351", + "definition": "A scheduled occurrence of a decision event.", + "preferredTerm": "Scheduled Decision Instance", + "submissionValue": "Scheduled Decision Instance" + }, + { + "conceptId": "C201299", + "definition": "A scheduled occurrence of a temporal event.", + "preferredTerm": "Scheduled Instance", + "submissionValue": "Scheduled Instance" + }, + { + "conceptId": "C71473", + "definition": "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.", + "preferredTerm": "Study Activity", + "submissionValue": "Study Activity" + }, + { + "conceptId": "C207457", + "definition": "The rationale for the change(s) to, or formal clarification of, a protocol.", + "preferredTerm": "Study Amendment Reason", + "submissionValue": "Study Amendment Reason", + "synonyms": + [ + "Reason(s) for Amendment" + ] + }, + { + "conceptId": "C207594", + "definition": "A written description of a change(s) to, or formal clarification of, a study.", + "preferredTerm": "Study Amendment", + "submissionValue": "Study Amendment" + }, + { + "conceptId": "C174447", + "definition": "A planned pathway assigned to the subject as they progress through the study, usually referred to by a name that reflects one or more treatments, exposures, and/or controls included in the path.", + "preferredTerm": "Study Arm", + "submissionValue": "Study Arm", + "synonyms": + [ + "Arm" + ] + }, + { + "conceptId": "C61512", + "definition": "A group of individuals who share a set of characteristics (e.g., exposures, experiences, attributes), which logically defines a population under study.", + "preferredTerm": "Cohort", + "submissionValue": "Study Cohort" + }, + { + "conceptId": "C188810", + "definition": "A partitioning of a study arm into individual pieces, which are associated with an epoch and any number of sequential elements within that epoch.", + "preferredTerm": "Study Design Cell", + "submissionValue": "Study Design Cell" + }, + { + "conceptId": "C142735", + "definition": "A basic building block for time within a clinical study comprising the following characteristics: a description of what happens to the subject during the element; a definition of the start of the element; a rule for ending the element.", + "preferredTerm": "Trial Design Element", + "submissionValue": "Study Design Element" + }, + { + "conceptId": "C15320", + "definition": "A strategy that specifies the structure of a study in terms of the planned activities (including timing) and statistical analysis approach intended to meet the objectives of the study.", + "preferredTerm": "Study Design", + "submissionValue": "Study Design" + }, + { + "conceptId": "C16112", + "definition": "Characteristics which are necessary to allow a subject to participate in a clinical study, as outlined in the study protocol. The concept covers inclusion and exclusion criteria.", + "preferredTerm": "Clinical Trial Eligibility Criteria", + "submissionValue": "Study Eligibility Criteria", + "synonyms": + [ + "Trial Eligibility Criteria" + ] + }, + { + "conceptId": "C25212", + "definition": "A defined variable intended to reflect an outcome of interest that is statistically analyzed to address a particular research question. NOTE: A precise definition of an endpoint typically specifies the type of assessments made, the timing of those assessments, the assessment tools used, and possibly other details, as applicable, such as how multiple assessments within an individual are to be combined. [After BEST Resource] (CDISC Glossary)", + "preferredTerm": "End Point", + "submissionValue": "Study Endpoint" + }, + { + "conceptId": "C71738", + "definition": "A named time period defined in the protocol, wherein a study activity is specified and unchanging throughout the interval, to support a study-specific purpose.", + "preferredTerm": "Clinical Trial Epoch", + "submissionValue": "Study Epoch" + }, + { + "conceptId": "C207595", + "definition": "Any of the dates associated with event milestones within a clinical study's oversight and management framework.", + "preferredTerm": "Study Governance Date", + "submissionValue": "Study Governance Date" + }, + { + "conceptId": "C83082", + "definition": "A sequence of characters used to identify, name, or characterize the study.", + "preferredTerm": "Study Identifier", + "submissionValue": "Study Identifier" + }, + { + "conceptId": "C142450", + "definition": "The reason for performing a study in terms of the scientific questions to be answered by the analysis of data collected during the study.", + "preferredTerm": "Clinical Trial Objective", + "submissionValue": "Study Objective" + }, + { + "conceptId": "C93381", + "definition": "A representation of the study protocol (that persists over time) in document form.", + "preferredTerm": "Study Protocol Document", + "submissionValue": "Study Protocol Document" + }, + { + "conceptId": "C93490", + "definition": "A plan at a particular point in time for a formal investigation to assess the utility, impact, pharmacological, physiological, and/or psychological effects of a particular treatment, procedure, drug, device, biologic, food product, cosmetic, care plan, or subject characteristic. (BRIDG)", + "preferredTerm": "Study Protocol Version", + "submissionValue": "Study Protocol Version" + }, + { + "conceptId": "C80403", + "definition": "The location at which a study investigator conducts study activities.", + "preferredTerm": "Study Site", + "submissionValue": "Study Site" + }, + { + "conceptId": "C49802", + "definition": "The sponsor-defined name of the clinical study.", + "preferredTerm": "Trial Title", + "submissionValue": "Study Title", + "synonyms": + [ + "Official Study Title", + "Study Title", + "Trial Title" + ] + }, + { + "conceptId": "C188816", + "definition": "A plan at a particular point in time for a study.", + "preferredTerm": "Study Version", + "submissionValue": "Study Version" + }, + { + "conceptId": "C37948", + "definition": "The act of enrolling subjects into a study. The subject will have met the inclusion/exclusion criteria to participate in the trial and will have signed an informed consent form. (CDISC Glossary)", + "preferredTerm": "Enrollment", + "submissionValue": "Subject Enrollment" + }, + { + "conceptId": "C207597", + "definition": "A reference source that provides a listing of valid parameter names and values used in syntax template text strings.", + "preferredTerm": "Syntax Template Dictionary", + "submissionValue": "Syntax Template Dictionary" + }, + { + "conceptId": "C207596", + "definition": "A standardized pattern used for the arrangement of words and phrases to create well-formed, structured sentences.", + "preferredTerm": "Syntax Template", + "submissionValue": "Syntax Template" + }, + { + "conceptId": "C188814", + "definition": "A target study population on which an analysis is performed. These may be represented by the entire study population, a subgroup defined by a particular characteristic measured at baseline, or a principal stratum defined by the occurrence (or non-occurrence, depending on context) of a specific intercurrent event. (ICH E9 R1 Addendum)", + "preferredTerm": "Target Study Population for Analysis", + "submissionValue": "Target Study Population for Analysis" + }, + { + "conceptId": "C142728", + "definition": "The group of people in the general population to which the study results can be generalized.", + "preferredTerm": "Target Study Population", + "submissionValue": "Target Study Population", + "synonyms": + [ + "Target Population" + ] + }, + { + "conceptId": "C80484", + "definition": "The chronological relationship between temporal events.", + "preferredTerm": "Timing", + "submissionValue": "Timing" + }, + { + "conceptId": "C82567", + "definition": "A guide that governs the allocation of subjects to operational options at a discrete decision point or branch (e.g., assignment to a particular arm, discontinuation) within a clinical trial plan.", + "preferredTerm": "Transition Rule", + "submissionValue": "Transition Rule" + } + ] + }, + { + "conceptId": "C188719", + "definition": "A terminology value set relevant to the attributes of the estimand.", + "extensible": "false", + "name": "DDF Estimand Attribute Terminology", + "preferredTerm": "CDISC DDF Estimand Attribute Terminology", + "submissionValue": "DDF Estimand Attribute Terminology", + "synonyms": + [ + "DDF Estimand Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188853", + "definition": "A synopsis of the clinical endpoint of interest within the analysis target study population.", + "preferredTerm": "Population-Level Summary", + "submissionValue": "Population-Level Summary" + } + ] + }, + { + "conceptId": "C207428", + "definition": "A terminology value set relevant to the attributes of the geographic scope.", + "extensible": "false", + "name": "DDF Geographic Scope Attribute Terminology", + "preferredTerm": "CDISC DDF Geographic Scope Attribute Terminology", + "submissionValue": "DDF Geographic Scope Attribute Terminology", + "synonyms": + [ + "DDF Geographic Scope Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207494", + "definition": "A symbol or combination of symbols which is assigned to the geographic scope.", + "preferredTerm": "Geographic Scope Code", + "submissionValue": "Geographic Scope Code" + }, + { + "conceptId": "C207495", + "definition": "A characterization or classification of the geographic scope.", + "preferredTerm": "Geographic Scope Type", + "submissionValue": "Geographic Scope Type" + } + ] + }, + { + "conceptId": "C207429", + "definition": "A terminology value set relevant to the attributes of the governance date.", + "extensible": "false", + "name": "DDF Governance Date Attribute Terminology", + "preferredTerm": "CDISC DDF Governance Date Attribute Terminology", + "submissionValue": "DDF Governance Date Attribute Terminology", + "synonyms": + [ + "DDF Governance Date Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207496", + "definition": "A characterization or classification of the protocol approval date.", + "preferredTerm": "Protocol Approval Date Type", + "submissionValue": "Protocol Approval Date Type" + }, + { + "conceptId": "C207497", + "definition": "A narrative representation of the study governance date.", + "preferredTerm": "Study Governance Date Description", + "submissionValue": "Study Governance Date Description" + }, + { + "conceptId": "C207498", + "definition": "The short descriptive designation for the study governance date.", + "preferredTerm": "Study Governance Date Label", + "submissionValue": "Study Governance Date Label" + }, + { + "conceptId": "C207499", + "definition": "The literal identifier (i.e., distinctive designation) of the study governance date", + "preferredTerm": "Study Governance Date Name", + "submissionValue": "Study Governance Date Name" + }, + { + "conceptId": "C207500", + "definition": "The information contained in the date field.", + "preferredTerm": "Study Governance Date Value", + "submissionValue": "Study Governance Date Value" + } + ] + }, + { + "conceptId": "C188705", + "definition": "A terminology value set relevant to the attributes of the disease indication.", + "extensible": "false", + "name": "DDF Indication Attribute Terminology", + "preferredTerm": "CDISC DDF Indication Attribute Terminology", + "submissionValue": "DDF Indication Attribute Terminology", + "synonyms": + [ + "DDF Indication Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188822", + "definition": "A short sequence of characters that represents the disease indication.", + "preferredTerm": "Disease Indication Code", + "submissionValue": "Disease Indication Code" + }, + { + "conceptId": "C112038", + "definition": "A narrative representation of the condition, disease or disorder that the clinical trial is intended to investigate or address.", + "preferredTerm": "Trial Indication", + "submissionValue": "Disease/Condition Indication Description", + "synonyms": + [ + "Indication for Use", + "Trial Disease/Condition Indication", + "Trial Disease/Condition Indication Description" + ] + }, + { + "conceptId": "C207501", + "definition": "An indication as to whether the disease/condition indication under study is considered a rare disease.", + "preferredTerm": "Disease Indication Is Rare Disease Indicator", + "submissionValue": "Disease/Condition Indication Is Rare Disease Indicator" + }, + { + "conceptId": "C207502", + "definition": "The short descriptive designation for the disease/condition indication.", + "preferredTerm": "Disease Indication Label", + "submissionValue": "Disease/Condition Indication Label" + }, + { + "conceptId": "C207503", + "definition": "The literal identifier (i.e., distinctive designation) of the disease/condition indication.", + "preferredTerm": "Disease Indication Name", + "submissionValue": "Disease/Condition Indication Name" + } + ] + }, + { + "conceptId": "C188721", + "definition": "A terminology value set relevant to the attributes of the intercurrent event.", + "extensible": "false", + "name": "DDF Intercurrent Event Attribute Terminology", + "preferredTerm": "CDISC DDF Intercurrent Event Attribute Terminology", + "submissionValue": "DDF Intercurrent Event Attribute Terminology", + "synonyms": + [ + "DDF Intercurrent Event Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188856", + "definition": "A narrative representation of the intercurrent event.", + "preferredTerm": "Intercurrent Event Description", + "submissionValue": "Intercurrent Event Description" + }, + { + "conceptId": "C207504", + "definition": "The short descriptive designation for the intercurrent event.", + "preferredTerm": "Intercurrent Event Label", + "submissionValue": "Intercurrent Event Label" + }, + { + "conceptId": "C188855", + "definition": "The literal identifier (i.e., distinctive designation) of the intercurrent event.", + "preferredTerm": "Intercurrent Event Name", + "submissionValue": "Intercurrent Event Name" + }, + { + "conceptId": "C188857", + "definition": "A textual description of the planned strategy to manage and/or mitigate intercurrent events.", + "preferredTerm": "Intercurrent Event Strategy", + "submissionValue": "Intercurrent Event Strategy" + } + ] + }, + { + "conceptId": "C207430", + "definition": "A terminology value set relevant to the attributes of the masking.", + "extensible": "false", + "name": "DDF Masking Attribute Terminology", + "preferredTerm": "CDISC DDF Masking Attribute Terminology", + "submissionValue": "DDF Masking Attribute Terminology", + "synonyms": + [ + "DDF Masking Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207505", + "definition": "A narrative representation of the study masking strategy, based on a person's role within the study.", + "preferredTerm": "Study Masking Description", + "submissionValue": "Masking Description" + }, + { + "conceptId": "C207506", + "definition": "An identifying designation assigned to a masked individual within a study that corresponds with their function.", + "preferredTerm": "Study Masking Role", + "submissionValue": "Masking Role", + "synonyms": + [ + "Blinded Roles", + "Blinding Roles" + ] + } + ] + }, + { + "conceptId": "C207426", + "definition": "A terminology value set relevant to the attributes of the narrative content.", + "extensible": "false", + "name": "DDF Narrative Content Attribute Terminology", + "preferredTerm": "CDISC DDF Narrative Content Attribute Terminology", + "submissionValue": "DDF Narrative Content Attribute Terminology", + "synonyms": + [ + "DDF Narrative Content Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207507", + "definition": "The literal identifier (i.e., distinctive designation) of the narrative content.", + "preferredTerm": "Narrative Content Name", + "submissionValue": "Narrative Content Name" + }, + { + "conceptId": "C207509", + "definition": "The numeric identifier assigned to a particular document section containing narrative content.", + "preferredTerm": "Narrative Content Section Number", + "submissionValue": "Narrative Content Section Number" + }, + { + "conceptId": "C207510", + "definition": "An identifying designation for the document section containing narrative content.", + "preferredTerm": "Narrative Content Section Title", + "submissionValue": "Narrative Content Section Title" + }, + { + "conceptId": "C207508", + "definition": "A textual representation of the narrative content.", + "preferredTerm": "Narrative Content Text", + "submissionValue": "Narrative Content Text" + } + ] + }, + { + "conceptId": "C188707", + "definition": "A terminology value set relevant to the attributes of the objective.", + "extensible": "false", + "name": "DDF Objective Attribute Terminology", + "preferredTerm": "CDISC DDF Objective Attribute Terminology", + "submissionValue": "DDF Objective Attribute Terminology", + "synonyms": + [ + "DDF Objective Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C94090", + "definition": "A narrative representation of the study objective.", + "preferredTerm": "Study Objective Description", + "submissionValue": "Study Objective Description" + }, + { + "conceptId": "C207511", + "definition": "The short descriptive designation for the study objective.", + "preferredTerm": "Study Objective Label", + "submissionValue": "Study Objective Label" + }, + { + "conceptId": "C188823", + "definition": "A characterization or classification of the study objective that determines its category of importance relative to other study objectives.", + "preferredTerm": "Study Objective Level", + "submissionValue": "Study Objective Level" + }, + { + "conceptId": "C207512", + "definition": "The literal identifier (i.e., distinctive designation) of the study objective.", + "preferredTerm": "Study Objective Name", + "submissionValue": "Study Objective Name" + }, + { + "conceptId": "C207513", + "definition": "An instance of structured text that represents the study objective.", + "preferredTerm": "Study Objective Text", + "submissionValue": "Study Objective Text" + } + ] + }, + { + "conceptId": "C188702", + "definition": "A terminology value set relevant to the attributes of the organization.", + "extensible": "false", + "name": "DDF Organization Attribute Terminology", + "preferredTerm": "CDISC DDF Organization Attribute Terminology", + "submissionValue": "DDF Organization Attribute Terminology", + "synonyms": + [ + "DDF Organization Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188819", + "definition": "The name of the organization that provides the identifier for the entity.", + "preferredTerm": "Identifier Provider Organization Name", + "submissionValue": "Identifier Provider Organization Name" + }, + { + "conceptId": "C93401", + "definition": "A unique symbol that establishes identity of the organization. (BRIDG)", + "preferredTerm": "Organization Identifier", + "submissionValue": "Organization Identifier" + }, + { + "conceptId": "C207514", + "definition": "The short descriptive designation for the organization.", + "preferredTerm": "Organization Label", + "submissionValue": "Organization Label" + }, + { + "conceptId": "C93874", + "definition": "A non-unique textual identifier for the organization. (BRIDG)", + "preferredTerm": "Organization Name", + "submissionValue": "Organization Name" + }, + { + "conceptId": "C188820", + "definition": "A characterization or classification of the formalized group of persons or other organizations collected together for a common purpose (such as administrative, legal, political) and the infrastructure to carry out that purpose.", + "preferredTerm": "Organization Type", + "submissionValue": "Organization Type" + } + ] + }, + { + "conceptId": "C207431", + "definition": "A terminology value set relevant to the attributes of the parameter map.", + "extensible": "false", + "name": "DDF Parameter Map Attribute Terminology", + "preferredTerm": "CDISC DDF Parameter Map Attribute Terminology", + "submissionValue": "DDF Parameter Map Attribute Terminology", + "synonyms": + [ + "DDF Parameter Map Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207516", + "definition": "The reference for a tag used in programming languages, such as a markup language (e.g., HTML, XML), to store attributes and elements.", + "preferredTerm": "Programming Tag Reference", + "submissionValue": "Programming Tag Reference" + }, + { + "conceptId": "C207515", + "definition": "Character strings bounded by angle brackets that act as containers for programming language elements.", + "preferredTerm": "Programming Tag", + "submissionValue": "Programming Tag" + } + ] + }, + { + "conceptId": "C207432", + "definition": "A terminology value set relevant to the attributes of the population definition.", + "extensible": "false", + "name": "DDF Population Definition Attribute Terminology", + "preferredTerm": "CDISC DDF Population Definition Attribute Terminology", + "submissionValue": "DDF Population Definition Attribute Terminology", + "synonyms": + [ + "DDF Population Definition Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207517", + "definition": "A narrative representation of the population definition.", + "preferredTerm": "Population Definition Description", + "submissionValue": "Population Definition Description" + }, + { + "conceptId": "C207518", + "definition": "An indication as to whether the population definition includes healthy subjects, that is, subjects without the disease or condition under study.", + "preferredTerm": "Population Definition Includes Healthy Subjects Indicator", + "submissionValue": "Population Definition Includes Healthy Subjects Indicator" + }, + { + "conceptId": "C207519", + "definition": "The short descriptive designation for the population definition.", + "preferredTerm": "Population Definition Label", + "submissionValue": "Population Definition Label" + }, + { + "conceptId": "C207520", + "definition": "The literal identifier (i.e., distinctive designation) of the population definition.", + "preferredTerm": "Population Definition Name", + "submissionValue": "Population Definition Name" + }, + { + "conceptId": "C207701", + "definition": "The anticipated age of subjects within the population definition.", + "preferredTerm": "Population Definition Planned Age", + "submissionValue": "Population Definition Planned Age" + }, + { + "conceptId": "C207521", + "definition": "The value representing the planned number of subjects that must complete the study in order to meet the objectives and endpoints of the study, within the population definition.", + "preferredTerm": "Population Definition Planned Completion Number", + "submissionValue": "Population Definition Planned Completion Number" + }, + { + "conceptId": "C207522", + "definition": "The value representing the planned number of subjects to be entered in a clinical trial, within the population definition.", + "preferredTerm": "Population Definition Planned Enrollment Number", + "submissionValue": "Population Definition Planned Enrollment Number" + }, + { + "conceptId": "C207523", + "definition": "The protocol-defined sex within the population definition.", + "preferredTerm": "Population Definition Planned Sex", + "submissionValue": "Population Definition Planned Sex" + } + ] + }, + { + "conceptId": "C188716", + "definition": "A terminology value set relevant to the attributes of the procedure.", + "extensible": "false", + "name": "DDF Procedure Attribute Terminology", + "preferredTerm": "CDISC DDF Procedure Attribute Terminology", + "submissionValue": "DDF Procedure Attribute Terminology", + "synonyms": + [ + "DDF Procedure Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C154626", + "definition": "A symbol or combination of symbols which is assigned to medical procedure.", + "preferredTerm": "Procedure Code", + "submissionValue": "Procedure Code" + }, + { + "conceptId": "C201324", + "definition": "A narrative representation of the procedure.", + "preferredTerm": "Procedure Description", + "submissionValue": "Procedure Description" + }, + { + "conceptId": "C207524", + "definition": "The short descriptive designation for the procedure.", + "preferredTerm": "Procedure Label", + "submissionValue": "Procedure Label" + }, + { + "conceptId": "C201325", + "definition": "The literal identifier (i.e., distinctive designation) of the procedure.", + "preferredTerm": "Procedure Name", + "submissionValue": "Procedure Name" + }, + { + "conceptId": "C188848", + "definition": "A characterization or classification of the study procedure.", + "preferredTerm": "Study Procedure Type", + "submissionValue": "Procedure Type" + } + ] + }, + { + "conceptId": "C207433", + "definition": "A terminology value set relevant to the attributes of the quantity.", + "extensible": "false", + "name": "DDF Quantity Attribute Terminology", + "preferredTerm": "CDISC DDF Quantity Attribute Terminology", + "submissionValue": "DDF Quantity Attribute Terminology", + "synonyms": + [ + "DDF Quantity Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C44258", + "definition": "The type of unit of measure being used to express a quantity.", + "preferredTerm": "Unit of Quantity", + "submissionValue": "Quantity Unit" + }, + { + "conceptId": "C25712", + "definition": "A numerical quantity measured or assigned or computed.", + "preferredTerm": "Value", + "submissionValue": "Quantity Value" + } + ] + }, + { + "conceptId": "C207434", + "definition": "A terminology value set relevant to the attributes of the range.", + "extensible": "false", + "name": "DDF Range Attribute Terminology", + "preferredTerm": "CDISC DDF Range Attribute Terminology", + "submissionValue": "DDF Range Attribute Terminology", + "synonyms": + [ + "DDF Range Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C25564", + "definition": "The largest value in quantity or degree in a set of values.", + "preferredTerm": "Maximum", + "submissionValue": "Maximum Value" + }, + { + "conceptId": "C25570", + "definition": "The smallest value in quantity or degree in a set of values.", + "preferredTerm": "Minimum", + "submissionValue": "Minimum Value" + }, + { + "conceptId": "C25709", + "definition": "A named quantity in terms of which other quantities are measured or specified, used as a standard measurement of like kinds.", + "preferredTerm": "Unit of Measure", + "submissionValue": "Unit of Measure" + }, + { + "conceptId": "C207525", + "definition": "An indication as to whether the value range is almost, but not quite, exact.", + "preferredTerm": "Value Range is Approximate Indicator", + "submissionValue": "Value Range is Approximate Indicator" + } + ] + }, + { + "conceptId": "C207435", + "definition": "A terminology value set relevant to the attributes of the research organization.", + "extensible": "false", + "name": "DDF Research Organization Attribute Terminology", + "preferredTerm": "CDISC DDF Research Organization Attribute Terminology", + "submissionValue": "DDF Research Organization Attribute Terminology", + "synonyms": + [ + "DDF Research Organization Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207526", + "definition": "The name of the research organization that provides the identifier for the entity.", + "preferredTerm": "Identifier Provider Research Organization Name", + "submissionValue": "Identifier Provider Research Organization Name" + }, + { + "conceptId": "C188820", + "definition": "A characterization or classification of the formalized group of persons or other organizations collected together for a common purpose (such as administrative, legal, political) and the infrastructure to carry out that purpose.", + "preferredTerm": "Organization Type", + "submissionValue": "Organization Type" + }, + { + "conceptId": "C207527", + "definition": "A sequence of characters used to identify, name, or characterize the research organization.", + "preferredTerm": "Research Organization Identifier", + "submissionValue": "Research Organization Identifier" + }, + { + "conceptId": "C207528", + "definition": "The short descriptive designation for the research organization.", + "preferredTerm": "Research Organization Label", + "submissionValue": "Research Organization Label" + }, + { + "conceptId": "C207529", + "definition": "The literal identifier (i.e., distinctive designation) of the research organization.", + "preferredTerm": "Research Organization Name", + "submissionValue": "Research Organization Name" + } + ] + }, + { + "conceptId": "C201258", + "definition": "A terminology value set relevant to the attributes of the response code.", + "extensible": "false", + "name": "DDF Response Code Attribute Terminology", + "preferredTerm": "CDISC DDF Response Code Attribute Terminology", + "submissionValue": "DDF Response Code Attribute Terminology", + "synonyms": + [ + "DDF Response Code Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C25162", + "definition": "A symbol or combination of symbols which is assigned to the members of a collection.", + "preferredTerm": "Code", + "submissionValue": "Code" + }, + { + "conceptId": "C201330", + "definition": "An indication as to whether the response code is activated for use within a given usage context.", + "preferredTerm": "Response Code Enabled Indicator", + "submissionValue": "Response Code Enabled Indicator" + } + ] + }, + { + "conceptId": "C201259", + "definition": "A terminology value set relevant to the attributes of the schedule timeline.", + "extensible": "false", + "name": "DDF Schedule Timeline Attribute Terminology", + "preferredTerm": "CDISC DDF Schedule Timeline Attribute Terminology", + "submissionValue": "DDF Schedule Timeline Attribute Terminology", + "synonyms": + [ + "DDF Schedule Timeline Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C201331", + "definition": "An indication as to whether the timeline or timeline component is part of the central or principal timeline.", + "preferredTerm": "Main Timeline Indicator", + "submissionValue": "Main Timeline Indicator" + }, + { + "conceptId": "C201332", + "definition": "A narrative representation of the schedule timeline.", + "preferredTerm": "Schedule Timeline Description", + "submissionValue": "Schedule Timeline Description" + }, + { + "conceptId": "C201333", + "definition": "A logical evaluation on which rests the validity of entry into a schedule timeline.", + "preferredTerm": "Schedule Timeline Entry Condition", + "submissionValue": "Schedule Timeline Entry Condition" + }, + { + "conceptId": "C207530", + "definition": "The short descriptive designation for the schedule timeline.", + "preferredTerm": "Schedule Timeline Label", + "submissionValue": "Schedule Timeline Label" + }, + { + "conceptId": "C201334", + "definition": "The literal identifier (i.e., distinctive designation) of the schedule timeline.", + "preferredTerm": "Schedule Timeline Name", + "submissionValue": "Schedule Timeline Name" + } + ] + }, + { + "conceptId": "C207436", + "definition": "A terminology value set relevant to the attributes of the scheduled activity instance.", + "extensible": "false", + "name": "DDF Scheduled Activity Instance Attribute Terminology", + "preferredTerm": "CDISC DDF Scheduled Activity Instance Attribute Terminology", + "submissionValue": "DDF Scheduled Activity Instance Attribute Terminology", + "synonyms": + [ + "DDF Scheduled Activity Instance Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207531", + "definition": "A narrative representation of the scheduled activity instance.", + "preferredTerm": "Scheduled Activity Instance Description", + "submissionValue": "Scheduled Activity Instance Description" + }, + { + "conceptId": "C207532", + "definition": "The short descriptive designation for the scheduled activity instance.", + "preferredTerm": "Scheduled Activity Instance Label", + "submissionValue": "Scheduled Activity Instance Label" + }, + { + "conceptId": "C207533", + "definition": "The literal identifier (i.e., distinctive designation) of the scheduled activity instance.", + "preferredTerm": "Scheduled Activity Instance Name", + "submissionValue": "Scheduled Activity Instance Name" + } + ] + }, + { + "conceptId": "C201260", + "definition": "A terminology value set relevant to the attributes of the scheduled decision instance.", + "extensible": "false", + "name": "DDF Scheduled Decision Instance Attribute Terminology", + "preferredTerm": "CDISC DDF Scheduled Decision Instance Attribute Terminology", + "submissionValue": "DDF Scheduled Decision Instance Attribute Terminology", + "synonyms": + [ + "DDF Scheduled Decision Instance Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207534", + "definition": "A narrative representation of the scheduled Decision instance.", + "preferredTerm": "Scheduled Decision Instance Description", + "submissionValue": "Scheduled Decision Instance Description" + }, + { + "conceptId": "C207535", + "definition": "The short descriptive designation for the scheduled Decision instance.", + "preferredTerm": "Scheduled Decision Instance Label", + "submissionValue": "Scheduled Decision Instance Label" + }, + { + "conceptId": "C207536", + "definition": "The literal identifier (i.e., distinctive designation) of the scheduled Decision instance.", + "preferredTerm": "Scheduled Decision Instance Name", + "submissionValue": "Scheduled Decision Instance Name" + } + ] + }, + { + "conceptId": "C201261", + "definition": "A terminology value set relevant to the attributes of the scheduled instance.", + "extensible": "false", + "name": "DDF Scheduled Instance Attribute Terminology", + "preferredTerm": "CDISC DDF Scheduled Instance Attribute Terminology", + "submissionValue": "DDF Scheduled Instance Attribute Terminology", + "synonyms": + [ + "DDF Scheduled Instance Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207453", + "definition": "A narrative representation of the scheduled instance.", + "preferredTerm": "Scheduled Instance Description", + "submissionValue": "Scheduled Instance Description" + }, + { + "conceptId": "C207454", + "definition": "The short descriptive designation for the scheduled instance.", + "preferredTerm": "Scheduled Instance Label", + "submissionValue": "Scheduled Instance Label" + }, + { + "conceptId": "C207455", + "definition": "The literal identifier (i.e., distinctive designation) of the scheduled instance.", + "preferredTerm": "Scheduled Instance Name", + "submissionValue": "Scheduled Instance Name" + } + ] + }, + { + "conceptId": "C207437", + "definition": "A terminology value set relevant to the attributes of the study amendment.", + "extensible": "false", + "name": "DDF Study Amendment Attribute Terminology", + "preferredTerm": "CDISC DDF Study Amendment Attribute Terminology", + "submissionValue": "DDF Study Amendment Attribute Terminology", + "synonyms": + [ + "DDF Study Amendment Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207537", + "definition": "A string of numerals that uniquely identifies a protocol amendment.", + "preferredTerm": "Study Amendment Number", + "submissionValue": "Study Amendment Number", + "synonyms": + [ + "Amendment Identifier" + ] + }, + { + "conceptId": "C207538", + "definition": "An indication as to whether the amendment is likely to have a substantial impact on the safety or rights of study subjects/participants.", + "preferredTerm": "Study Amendment Substantial Impact Indicator", + "submissionValue": "Study Amendment Substantial Impact Indicator" + }, + { + "conceptId": "C115627", + "definition": "A short narrative representation describing the changes introduced in the current version of the protocol.", + "preferredTerm": "Clinical Trial Protocol Amendment Summary", + "submissionValue": "Study Amendment Summary" + } + ] + }, + { + "conceptId": "C207438", + "definition": "A terminology value set relevant to the attributes of the study amendment reason.", + "extensible": "false", + "name": "DDF Study Amendment Reason Attribute Terminology", + "preferredTerm": "CDISC DDF Study Amendment Reason Attribute Terminology", + "submissionValue": "DDF Study Amendment Reason Attribute Terminology", + "synonyms": + [ + "DDF Study Amendment Reason Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207539", + "definition": "The rationale for the change(s) to, or formal clarification of, a protocol that is not otherwise specified.", + "preferredTerm": "Other Reason for Study Amendment", + "submissionValue": "Other Reason for Study Amendment" + }, + { + "conceptId": "C207540", + "definition": "A symbol or combination of symbols which is assigned to the study amendment reason.", + "preferredTerm": "Study Amendment Reason Code", + "submissionValue": "Study Amendment Reason Code", + "synonyms": + [ + "Study Amendment Reason Code" + ] + } + ] + }, + { + "conceptId": "C188709", + "definition": "A terminology value set relevant to the attributes of the study Arm.", + "extensible": "false", + "name": "DDF Study Arm Attribute Terminology", + "preferredTerm": "CDISC DDF Study Arm Attribute Terminology", + "submissionValue": "DDF Study Arm Attribute Terminology", + "synonyms": + [ + "DDF Study Arm Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188828", + "definition": "The textual representation of the study arm data origin.", + "preferredTerm": "Study Arm Data Origin Description", + "submissionValue": "Study Arm Data Origin Description" + }, + { + "conceptId": "C188829", + "definition": "A characterization or classification of the study arm with respect to where the study arm data originates.", + "preferredTerm": "Study Arm Data Origin Type", + "submissionValue": "Study Arm Data Origin Type" + }, + { + "conceptId": "C93728", + "definition": "A narrative representation of the study arm.", + "preferredTerm": "Arm Description", + "submissionValue": "Study Arm Description", + "synonyms": + [ + "Arm Description" + ] + }, + { + "conceptId": "C172456", + "definition": "The short descriptive designation for the study arm.", + "preferredTerm": "Study Arm Label", + "submissionValue": "Study Arm Label", + "synonyms": + [ + "Arm Label" + ] + }, + { + "conceptId": "C170984", + "definition": "The literal identifier (i.e., distinctive designation) of the study arm.", + "preferredTerm": "Planned Study Arm Name", + "submissionValue": "Study Arm Name" + }, + { + "conceptId": "C172457", + "definition": "A characterization or classification of the study arm.", + "preferredTerm": "Study Arm Type", + "submissionValue": "Study Arm Type", + "synonyms": + [ + "Arm Type" + ] + } + ] + }, + { + "conceptId": "C207439", + "definition": "A terminology value set relevant to the attributes of the study cohort.", + "extensible": "false", + "name": "DDF Study Cohort Attribute Terminology", + "preferredTerm": "CDISC DDF Study Cohort Attribute Terminology", + "submissionValue": "DDF Study Cohort Attribute Terminology", + "synonyms": + [ + "DDF Study Cohort Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207542", + "definition": "A narrative representation of the study cohort.", + "preferredTerm": "Study Cohort Description", + "submissionValue": "Study Cohort Description" + }, + { + "conceptId": "C207480", + "definition": "An indication as to whether the study cohort includes healthy subjects, that is, subjects without the disease or condition under study.", + "preferredTerm": "Study Cohort Includes Healthy Subjects Indicator", + "submissionValue": "Study Cohort Includes Healthy Subjects Indicator" + }, + { + "conceptId": "C207543", + "definition": "The short descriptive designation for the study cohort.", + "preferredTerm": "Study Cohort Label", + "submissionValue": "Study Cohort Label" + }, + { + "conceptId": "C207544", + "definition": "The literal identifier (i.e., distinctive designation) of the study cohort.", + "preferredTerm": "Study Cohort Name", + "submissionValue": "Study Cohort Name" + }, + { + "conceptId": "C207545", + "definition": "The anticipated age of subjects within the study cohort.", + "preferredTerm": "Study Cohort Planned Age", + "submissionValue": "Study Cohort Planned Age" + }, + { + "conceptId": "C207546", + "definition": "The value representing the planned number of subjects that must complete the study in order to meet the objectives and endpoints of the study, within the study cohort.", + "preferredTerm": "Study Cohort Planned Completion Number", + "submissionValue": "Study Cohort Planned Completion Number" + }, + { + "conceptId": "C207702", + "definition": "The value representing the planned number of subjects to be entered in a clinical trial, within the study cohort.", + "preferredTerm": "Study Cohort Planned Enrollment Number", + "submissionValue": "Study Cohort Planned Enrollment Number" + }, + { + "conceptId": "C207541", + "definition": "The protocol-defined sex within the study cohort.", + "preferredTerm": "Planned Sex of Study Cohort Participants", + "submissionValue": "Study Cohort Planned Sex" + } + ] + }, + { + "conceptId": "C188703", + "definition": "A terminology value set relevant to the attributes of the study design.", + "extensible": "false", + "name": "DDF Study Design Attribute Terminology", + "preferredTerm": "CDISC DDF Study Design Attribute Terminology", + "submissionValue": "DDF Study Design Attribute Terminology", + "synonyms": + [ + "DDF Study Design Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C98746", + "definition": "The general design of the strategy for assigning interventions to participants in a clinical study. (clinicaltrials.gov)", + "preferredTerm": "Intervention Model", + "submissionValue": "Intervention Model Type", + "synonyms": + [ + "Intervention Model" + ] + }, + { + "conceptId": "C207547", + "definition": "The distinguishing qualities or prominent aspect of a study design.", + "preferredTerm": "Study Design Characteristic", + "submissionValue": "Study Design Characteristic" + }, + { + "conceptId": "C147139", + "definition": "A narrative representation of the study design.", + "preferredTerm": "Study Design Description", + "submissionValue": "Study Design Description", + "synonyms": + [ + "Overall Design", + "Study Design Description", + "Study Design Overview", + "Summary of Study Design" + ] + }, + { + "conceptId": "C207548", + "definition": "The short descriptive designation for the study design.", + "preferredTerm": "Study Design Label", + "submissionValue": "Study Design Label" + }, + { + "conceptId": "C201338", + "definition": "The literal identifier (i.e., distinctive designation) of the study design.", + "preferredTerm": "Study Design Name", + "submissionValue": "Study Design Name" + }, + { + "conceptId": "C70834", + "definition": "A narrative representation of the study design population.", + "preferredTerm": "Study Population Description", + "submissionValue": "Study Design Population Description" + }, + { + "conceptId": "C142705", + "definition": "Reason(s) for choosing the study design. This may include reasons for the choice of control or comparator, as well as the scientific rationale for the study design.", + "preferredTerm": "Study Design Rationale", + "submissionValue": "Study Design Rationale" + }, + { + "conceptId": "C101302", + "definition": "A categorization of a disease, disorder, or other condition based on common characteristics and often associated with a medical specialty focusing on research and development of specific therapeutic interventions for the purpose of treatment and prevention.", + "preferredTerm": "Therapeutic Area", + "submissionValue": "Therapeutic Areas", + "synonyms": + [ + "Therapeutic Area" + ] + }, + { + "conceptId": "C49658", + "definition": "The type of experimental design used to describe the level of awareness of the study subjects and/ or study personnel as it relates to the respective intervention(s) or assessments being observed, received or administered.", + "preferredTerm": "Trial Blinding Schema", + "submissionValue": "Trial Blinding Schema", + "synonyms": + [ + "Study Blinding Design", + "Study Blinding Schema", + "Study Masking Design", + "Trial Blinding Design", + "Trial Blinding Schema", + "Trial Masking Design" + ] + }, + { + "conceptId": "C49652", + "definition": "The planned purpose of the therapy, device, or agent under study in the clinical trial.", + "preferredTerm": "Clinical Study by Intent", + "submissionValue": "Trial Intent Type", + "synonyms": + [ + "Trial Intent Type" + ] + }, + { + "conceptId": "C49660", + "definition": "The nature of the interventional study for which information is being collected.", + "preferredTerm": "Trial Type", + "submissionValue": "Trial Type", + "synonyms": + [ + "Trial Scope", + "Trial Type" + ] + } + ] + }, + { + "conceptId": "C188706", + "definition": "A terminology value set relevant to the attributes of the study design population.", + "extensible": "false", + "name": "DDF Study Design Population Attribute Terminology", + "preferredTerm": "CDISC DDF Study Design Population Attribute Terminology", + "submissionValue": "DDF Study Design Population Attribute Terminology", + "synonyms": + [ + "DDF Study Design Population Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207549", + "definition": "An indication as to whether the study design population includes healthy subjects, that is, subjects without the disease or condition under study.", + "preferredTerm": "Study Design Population Includes Healthy Subjects Indicator", + "submissionValue": "Study Design Population Includes Healthy Subjects Indicator" + }, + { + "conceptId": "C207550", + "definition": "The short descriptive designation for the study design population.", + "preferredTerm": "Study Design Population Label", + "submissionValue": "Study Design Population Label" + }, + { + "conceptId": "C207553", + "definition": "The literal identifier (i.e., distinctive designation) of the study design population.", + "preferredTerm": "Study Design Population Name", + "submissionValue": "Study Design Population Name" + }, + { + "conceptId": "C207450", + "definition": "The anticipated age of subjects within the study design population.", + "preferredTerm": "Study Design Population Planned Age", + "submissionValue": "Study Design Population Planned Age" + }, + { + "conceptId": "C207451", + "definition": "The value representing the planned number of subjects that must complete the study in order to meet the objectives and endpoints of the study, within the study design population.", + "preferredTerm": "Study Design Population Planned Completion Number", + "submissionValue": "Study Design Population Planned Completion Number" + }, + { + "conceptId": "C207452", + "definition": "The value representing the planned number of subjects to be entered in a clinical trial, within the study design population.", + "preferredTerm": "Study Design Population Planned Enrollment Number", + "submissionValue": "Study Design Population Planned Enrollment Number" + }, + { + "conceptId": "C207551", + "definition": "The protocol-defined sex within the study design population.", + "preferredTerm": "Study Design Population Planned Sex", + "submissionValue": "Study Design Population Planned Sex" + } + ] + }, + { + "conceptId": "C188711", + "definition": "A terminology value set relevant to the attributes of the study element.", + "extensible": "false", + "name": "DDF Study Element Attribute Terminology", + "preferredTerm": "CDISC DDF Study Element Attribute Terminology", + "submissionValue": "DDF Study Element Attribute Terminology", + "synonyms": + [ + "DDF Study Element Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188834", + "definition": "A narrative representation of the study design element.", + "preferredTerm": "Study Design Element Description", + "submissionValue": "Study Design Element Description" + }, + { + "conceptId": "C207554", + "definition": "The short descriptive designation for the study design element.", + "preferredTerm": "Study Design Element Label", + "submissionValue": "Study Design Element Label" + }, + { + "conceptId": "C188833", + "definition": "The literal identifier (i.e., distinctive designation) of the study design element.", + "preferredTerm": "Study Design Element Name", + "submissionValue": "Study Design Element Name" + } + ] + }, + { + "conceptId": "C188710", + "definition": "A terminology value set relevant to the attributes of the study epoch.", + "extensible": "false", + "name": "DDF Study Epoch Attribute Terminology", + "preferredTerm": "CDISC DDF Study Epoch Attribute Terminology", + "submissionValue": "DDF Study Epoch Attribute Terminology", + "synonyms": + [ + "DDF Study Epoch Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C93824", + "definition": "A narrative representation of the study epoch.", + "preferredTerm": "Epoch Description", + "submissionValue": "Study Epoch Description" + }, + { + "conceptId": "C207555", + "definition": "The short descriptive designation for the study epoch.", + "preferredTerm": "Study Epoch Label", + "submissionValue": "Study Epoch Label" + }, + { + "conceptId": "C93825", + "definition": "The literal identifier (i.e., distinctive designation) of the study epoch, i.e., the named time period defined in the protocol, wherein a study activity is specified and unchanging throughout the interval, to support a study-specific purpose.", + "preferredTerm": "Epoch Name", + "submissionValue": "Study Epoch Name" + }, + { + "conceptId": "C188830", + "definition": "A characterization or classification of the study epoch, i.e., the named time period defined in the protocol, wherein a study activity is specified and unchanging throughout the interval, to support a study-specific purpose.", + "preferredTerm": "Study Epoch Type", + "submissionValue": "Study Epoch Type" + } + ] + }, + { + "conceptId": "C188701", + "definition": "A terminology value set relevant to the attributes of the study identifier.", + "extensible": "false", + "name": "DDF Study Identifier Attribute Terminology", + "preferredTerm": "CDISC DDF Study Identifier Attribute Terminology", + "submissionValue": "DDF Study Identifier Attribute Terminology", + "synonyms": + [ + "DDF Study Identifier Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C83082", + "definition": "A sequence of characters used to identify, name, or characterize the study.", + "preferredTerm": "Study Identifier", + "submissionValue": "Study Identifier" + } + ] + }, + { + "conceptId": "C188704", + "definition": "A terminology value set relevant to the attributes of the study interventions.", + "extensible": "false", + "name": "DDF Study Intervention Attribute Terminology", + "preferredTerm": "CDISC DDF Study Intervention Attribute Terminology", + "submissionValue": "DDF Study Intervention Attribute Terminology", + "synonyms": + [ + "DDF Study Intervention Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C98768", + "definition": "The pharmacological class of the investigational product.", + "preferredTerm": "Pharmacological Class of Investigational Therapy", + "submissionValue": "Pharmacologic Class", + "synonyms": + [ + "Pharmacologic Class" + ] + }, + { + "conceptId": "C207648", + "definition": "A symbol or combination of symbols which is assigned to the study intervention.", + "preferredTerm": "Study Intervention Code", + "submissionValue": "Study Intervention Code" + }, + { + "conceptId": "C207647", + "definition": "A narrative representation of the study intervention.", + "preferredTerm": "Study Intervention Description", + "submissionValue": "Study Intervention Description" + }, + { + "conceptId": "C207556", + "definition": "The short descriptive designation for the study intervention.", + "preferredTerm": "Study Intervention Label", + "submissionValue": "Study Intervention Label" + }, + { + "conceptId": "C207557", + "definition": "The value representing the minimum amount of time required to meet the criteria for response to study intervention.", + "preferredTerm": "Study Intervention Minimum Response Duration", + "submissionValue": "Study Intervention Minimum Response Duration" + }, + { + "conceptId": "C207558", + "definition": "The literal identifier (i.e., distinctive designation) of the study intervention.", + "preferredTerm": "Study Intervention Name", + "submissionValue": "Study Intervention Name" + }, + { + "conceptId": "C207559", + "definition": "An indication as to whether the investigational intervention is an investigational medicinal product or an auxiliary medicinal product.", + "preferredTerm": "Study Intervention Product Type", + "submissionValue": "Study Intervention Product Designation" + }, + { + "conceptId": "C207560", + "definition": "The intended use of the trial intervention within the context of the study design.", + "preferredTerm": "Study Intervention Role", + "submissionValue": "Study Intervention Role", + "synonyms": + [ + "Study Intervention Use" + ] + }, + { + "conceptId": "C98747", + "definition": "The kind of product or procedure studied in a trial.", + "preferredTerm": "Intervention Type", + "submissionValue": "Study Intervention Type", + "synonyms": + [ + "Intervention Type" + ] + } + ] + }, + { + "conceptId": "C207440", + "definition": "A terminology value set relevant to the attributes of the study protocol document.", + "extensible": "false", + "name": "DDF Study Protocol Document Attribute Terminology", + "preferredTerm": "CDISC DDF Study Protocol Document Attribute Terminology", + "submissionValue": "DDF Study Protocol Document Attribute Terminology", + "synonyms": + [ + "DDF Study Protocol Document Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207561", + "definition": "A narrative representation of the study protocol document.", + "preferredTerm": "Study Protocol Document Description", + "submissionValue": "Study Protocol Document Description" + }, + { + "conceptId": "C207562", + "definition": "The short descriptive designation for the study protocol document.", + "preferredTerm": "Study Protocol Document Label", + "submissionValue": "Study Protocol Document Label" + }, + { + "conceptId": "C207563", + "definition": "The literal identifier (i.e., distinctive designation) of the study protocol document.", + "preferredTerm": "Study Protocol Document Name", + "submissionValue": "Study Protocol Document Name" + } + ] + }, + { + "conceptId": "C207441", + "definition": "A terminology value set relevant to the attributes of the study site.", + "extensible": "false", + "name": "DDF Study Site Attribute Terminology", + "preferredTerm": "CDISC DDF Study Site Attribute Terminology", + "submissionValue": "DDF Study Site Attribute Terminology", + "synonyms": + [ + "DDF Study Site Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207564", + "definition": "A narrative representation of the study site.", + "preferredTerm": "Study Site Description", + "submissionValue": "Study Site Description" + }, + { + "conceptId": "C207565", + "definition": "The short descriptive designation for the study site.", + "preferredTerm": "Study Site Label", + "submissionValue": "Study Site Label" + }, + { + "conceptId": "C207566", + "definition": "The literal identifier (i.e., distinctive designation) of the study site.", + "preferredTerm": "Study Site Name", + "submissionValue": "Study Site Name" + } + ] + }, + { + "conceptId": "C207442", + "definition": "A terminology value set relevant to the attributes of the study title.", + "extensible": "false", + "name": "DDF Study Title Attribute Terminology", + "preferredTerm": "CDISC DDF Study Title Attribute Terminology", + "submissionValue": "DDF Study Title Attribute Terminology", + "synonyms": + [ + "DDF Study Title Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207567", + "definition": "An instance of unstructured text that represents the study title.", + "preferredTerm": "Study Title Text", + "submissionValue": "Study Title Text" + }, + { + "conceptId": "C207568", + "definition": "A characterization or classification of the study title.", + "preferredTerm": "Study Title Type", + "submissionValue": "Study Title Type" + } + ] + }, + { + "conceptId": "C207443", + "definition": "A terminology value set relevant to the attributes of the study version.", + "extensible": "false", + "name": "DDF Study Version Attribute Terminology", + "preferredTerm": "CDISC DDF Study Version Attribute Terminology", + "submissionValue": "DDF Study Version Attribute Terminology", + "synonyms": + [ + "DDF Study Version Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C201322", + "definition": "A therapeutic area classification based on the structure and operations of the business unit.", + "preferredTerm": "Business Therapeutic Area", + "submissionValue": "Business Therapeutic Areas" + }, + { + "conceptId": "C94122", + "definition": "A statement describing the overall rationale of the study. This field describes the contribution of this study to product development, i.e., what knowledge is being contributed from the conduct of this study.", + "preferredTerm": "Study Protocol Version Purpose Statement", + "submissionValue": "Study Rationale", + "synonyms": + [ + "Study Purpose" + ] + }, + { + "conceptId": "C142175", + "definition": "The nature of the investigation for which study information is being collected. (After clinicaltrials.gov)", + "preferredTerm": "Study Type", + "submissionValue": "Study Type Classification", + "synonyms": + [ + "Study Type", + "Study Type Classification" + ] + }, + { + "conceptId": "C207570", + "definition": "A sequence of characters used to identify, name, or characterize the study version.", + "preferredTerm": "Study Version Identifier", + "submissionValue": "Study Version Identifier" + }, + { + "conceptId": "C48281", + "definition": "A step in the clinical research and development of a therapy from initial clinical trials to post-approval studies. NOTE: Clinical trials are generally categorized into four (sometimes five) phases. A therapeutic intervention may be evaluated in two or more phases simultaneously in different trials, and some trials may overlap two different phases. [21 CFR section 312.21; After ICH Topic E8 NOTE FOR GUIDANCE ON GENERAL CONSIDERATIONS FOR CLINICAL TRIALS, CPMP/ICH/291/95 March 1998]", + "preferredTerm": "Trial Phase", + "submissionValue": "Trial Phase", + "synonyms": + [ + "Trial Phase", + "Trial Phase Classification" + ] + } + ] + }, + { + "conceptId": "C207444", + "definition": "A terminology value set relevant to the attributes of the subject enrollment.", + "extensible": "false", + "name": "DDF Subject Enrollment Attribute Terminology", + "preferredTerm": "CDISC DDF Subject Enrollment Attribute Terminology", + "submissionValue": "DDF Subject Enrollment Attribute Terminology", + "synonyms": + [ + "DDF Subject Enrollment Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207571", + "definition": "A symbol or combination of symbols which is assigned to the subject enrollment.", + "preferredTerm": "Subject Enrollment Code", + "submissionValue": "Subject Enrollment Code" + }, + { + "conceptId": "C207573", + "definition": "The value representing the number of individuals enrolled in a study.", + "preferredTerm": "Subject Enrollment Quantity Value", + "submissionValue": "Subject Enrollment Quantity Value" + }, + { + "conceptId": "C207574", + "definition": "A characterization or classification of the subject enrollment.", + "preferredTerm": "Subject Enrollment Type", + "submissionValue": "Subject Enrollment Type" + } + ] + }, + { + "conceptId": "C207445", + "definition": "A terminology value set relevant to the attributes of the syntax template.", + "extensible": "false", + "name": "DDF Syntax Template Attribute Terminology", + "preferredTerm": "CDISC DDF Syntax Template Attribute Terminology", + "submissionValue": "DDF Syntax Template Attribute Terminology", + "synonyms": + [ + "DDF Syntax Template Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207575", + "definition": "A narrative representation of the syntax template.", + "preferredTerm": "Syntax Template Description", + "submissionValue": "Syntax Template Description" + }, + { + "conceptId": "C207576", + "definition": "The short descriptive designation for the syntax template.", + "preferredTerm": "Syntax Template Label", + "submissionValue": "Syntax Template Label" + }, + { + "conceptId": "C207577", + "definition": "The literal identifier (i.e., distinctive designation) of the syntax template.", + "preferredTerm": "Syntax Template Name", + "submissionValue": "Syntax Template Name" + }, + { + "conceptId": "C207578", + "definition": "A structured text string containing prescribed text interspersed with user-defined parameter values.", + "preferredTerm": "Syntax Template Text", + "submissionValue": "Syntax Template Text" + } + ] + }, + { + "conceptId": "C207446", + "definition": "A terminology value set relevant to the attributes of the syntax template dictionary.", + "extensible": "false", + "name": "DDF Syntax Template Dictionary Attribute Terminology", + "preferredTerm": "CDISC DDF Syntax Template Dictionary Attribute Terminology", + "submissionValue": "DDF Syntax Template Dictionary Attribute Terminology", + "synonyms": + [ + "DDF Syntax Template Dictionary Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C207579", + "definition": "A narrative representation of the syntax template dictionary.", + "preferredTerm": "Syntax Template Dictionary Description", + "submissionValue": "Syntax Template Dictionary Description" + }, + { + "conceptId": "C207580", + "definition": "The short descriptive designation for the syntax template dictionary.", + "preferredTerm": "Syntax Template Dictionary Label", + "submissionValue": "Syntax Template Dictionary Label" + }, + { + "conceptId": "C207581", + "definition": "The literal identifier (i.e., distinctive designation) of the syntax template dictionary.", + "preferredTerm": "Syntax Template Dictionary Name", + "submissionValue": "Syntax Template Dictionary Name" + } + ] + }, + { + "conceptId": "C201262", + "definition": "A terminology value set relevant to the attributes of the timing.", + "extensible": "false", + "name": "DDF Timing Attribute Terminology", + "preferredTerm": "CDISC DDF Timing Attribute Terminology", + "submissionValue": "DDF Timing Attribute Terminology", + "synonyms": + [ + "DDF Timing Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C164648", + "definition": "A narrative representation of the biomedical concept category.", + "preferredTerm": "Timing Description", + "submissionValue": "Timing Description" + }, + { + "conceptId": "C207583", + "definition": "The short descriptive designation for the timing.", + "preferredTerm": "Timing Label", + "submissionValue": "Timing Label" + }, + { + "conceptId": "C207584", + "definition": "The literal identifier (i.e., distinctive designation) of the timing.", + "preferredTerm": "Timing Name", + "submissionValue": "Timing Name" + }, + { + "conceptId": "C201297", + "definition": "The name of the reference event used to define the temporal relationship with another event.", + "preferredTerm": "Timing Relative To From Name", + "submissionValue": "Timing Relative To From" + }, + { + "conceptId": "C201298", + "definition": "A characterization or classification of the chronological relationship between temporal events.", + "preferredTerm": "Timing Type", + "submissionValue": "Timing Type" + }, + { + "conceptId": "C207585", + "definition": "The short descriptive designation for the timing value.", + "preferredTerm": "Timing Value Label", + "submissionValue": "Timing Value Label" + }, + { + "conceptId": "C201341", + "definition": "The temporal value of the chronological relationship between temporal events.", + "preferredTerm": "Timing Value", + "submissionValue": "Timing Value" + }, + { + "conceptId": "C207586", + "definition": "The short descriptive designation for a time period, or other type of interval, during which a temporal event may be achieved, obtained, or observed.", + "preferredTerm": "Timing Window Label", + "submissionValue": "Timing Window Label" + }, + { + "conceptId": "C201342", + "definition": "The earliest chronological value of an allowable period of time during which a temporal event takes place.", + "preferredTerm": "Lower Timing Window", + "submissionValue": "Timing Window, Lower" + }, + { + "conceptId": "C201343", + "definition": "The latest chronological value of an allowable period of time during which a temporal event takes place.", + "preferredTerm": "Upper Timing Window", + "submissionValue": "Timing Window, Upper" + } + ] + }, + { + "conceptId": "C188712", + "definition": "A terminology value set relevant to the attributes of the transition rule.", + "extensible": "false", + "name": "DDF Transition Rule Attribute Terminology", + "preferredTerm": "CDISC DDF Transition Rule Attribute Terminology", + "submissionValue": "DDF Transition Rule Attribute Terminology", + "synonyms": + [ + "DDF Transition Rule Attribute Terminology" + ], + "terms": + [ + { + "conceptId": "C188835", + "definition": "A narrative representation of the transition rule.", + "preferredTerm": "Transition Rule Description", + "submissionValue": "Transition Rule Description" + }, + { + "conceptId": "C207587", + "definition": "The short descriptive designation for the transition rule.", + "preferredTerm": "Transition Rule Label", + "submissionValue": "Transition Rule Label" + }, + { + "conceptId": "C207588", + "definition": "The literal identifier (i.e., distinctive designation) of the transition rule.", + "preferredTerm": "Transition Rule Name", + "submissionValue": "Transition Rule Name" + }, + { + "conceptId": "C207589", + "definition": "An instance of unstructured text that represents the transition rule.", + "preferredTerm": "Transition Rule Text", + "submissionValue": "Transition Rule Text" + } + ] + }, + { + "conceptId": "C188728", + "definition": "The terminology relevant to the encounter type.", + "extensible": "true", + "name": "Encounter Type Value Set Terminology", + "preferredTerm": "CDISC DDF Encounter Type Value Set Terminology", + "submissionValue": "Encounter Type Value Set Terminology", + "synonyms": + [ + "Encounter Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C25716", + "definition": "The act of going to see some person or place or thing; it can cover a short or long period but refers to a non-permanent arrangement.", + "preferredTerm": "Visit", + "submissionValue": "Visit" + } + ] + }, + { + "conceptId": "C188726", + "definition": "The terminology relevant to the endpoint level.", + "extensible": "false", + "name": "Endpoint Level Value Set Terminology", + "preferredTerm": "CDISC DDF Endpoint Level Value Set Terminology", + "submissionValue": "Endpoint Level Value Set Terminology", + "synonyms": + [ + "Endpoint Level Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C170559", + "definition": "Endpoint(s) that may include clinically important events that are expected to occur too infrequently to show a treatment effect or endpoints that for other reasons are thought to be less likely to show an effect but are included to explore new hypotheses. (After FDA-NIH Protocol Template)", + "preferredTerm": "Exploratory Endpoint", + "submissionValue": "Exploratory Endpoint" + }, + { + "conceptId": "C94496", + "definition": "Endpoint(s) of greatest importance that is the basis for concluding whether the study met its objective(s) and provides a clinically relevant, valid, and reliable measure of the primary objective(s). (After FDA-NIH Protocol Template)", + "preferredTerm": "Primary Endpoint", + "submissionValue": "Primary Endpoint" + }, + { + "conceptId": "C139173", + "definition": "Endpoint(s) that may provide supportive information about the effect of the study intervention(s) on the primary endpoint or demonstrate additional effects on the disease or condition. (After FDA-NIH Protocol Template)", + "preferredTerm": "Secondary Endpoint", + "submissionValue": "Secondary Endpoint" + } + ] + }, + { + "conceptId": "C207412", + "definition": "The terminology relevant to the geographic scope type value set.", + "extensible": "false", + "name": "Geographic Scope Type Value Set Terminology", + "preferredTerm": "CDISC DDF Geographic Scope Type Value Set Terminology", + "submissionValue": "Geographic Scope Type Value Set Terminology", + "synonyms": + [ + "Geographic Scope Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C25464", + "definition": "A sovereign nation occupying a distinct territory and ruled by an autonomous government.", + "preferredTerm": "Country", + "submissionValue": "Country" + }, + { + "conceptId": "C68846", + "definition": "Covering or affecting the whole of a system.", + "preferredTerm": "Global", + "submissionValue": "Global" + }, + { + "conceptId": "C41129", + "definition": "An area or portion of something with more or less definite boundaries designed or specified according to some established criteria.", + "preferredTerm": "Region", + "submissionValue": "Region" + } + ] + }, + { + "conceptId": "C207413", + "definition": "The terminology relevant to the governance date type value set.", + "extensible": "true", + "name": "Governance Date Type Value Set Terminology", + "preferredTerm": "CDISC DDF Governance Date Type Value Set Terminology", + "submissionValue": "Governance Date Type Value Set Terminology", + "synonyms": + [ + "Governance Date Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C207598", + "definition": "The date and time specifying when the protocol takes effect or becomes operative.", + "preferredTerm": "Protocol Effective Date", + "submissionValue": "Protocol Effective Date" + }, + { + "conceptId": "C132352", + "definition": "The date on which a version of the protocol was finalized or approved by the sponsor.", + "preferredTerm": "Protocol Approval by Sponsor Date", + "submissionValue": "Sponsor Approval Date", + "synonyms": + [ + "Protocol Amendment Approval by Sponsor Date", + "Study Protocol Version Approval Date" + ] + } + ] + }, + { + "conceptId": "C207414", + "definition": "The terminology relevant to the masking role value set.", + "extensible": "true", + "name": "Masking Role Value Set Terminology", + "preferredTerm": "CDISC DDF Masking Role Value Set Terminology", + "submissionValue": "Masking Role Value Set Terminology", + "synonyms": + [ + "Masking Role Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C17445", + "definition": "The primary person in charge of the care of a patient, usually a family member or a designated health care professional. (NCI)", + "preferredTerm": "Caregiver", + "submissionValue": "Care Provider", + "synonyms": + [ + "Caregiver", + "Carer", + "Caretaker" + ] + }, + { + "conceptId": "C25936", + "definition": "A person responsible for the conduct of the study, ensuring adherence to the protocol and good clinical practices. (CDISC Glossary)", + "preferredTerm": "Investigator", + "submissionValue": "Investigator" + }, + { + "conceptId": "C207599", + "definition": "The individual who evaluates the outcome(s) of interest. (Clinicaltrials.gov)", + "preferredTerm": "Outcomes Assessor", + "submissionValue": "Outcomes Assessor" + }, + { + "conceptId": "C70793", + "definition": "An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical study. [After ICH E6, WHO, 21 CFR 50.3 (e), and after IDMP]", + "preferredTerm": "Clinical Study Sponsor", + "submissionValue": "Sponsor", + "synonyms": + [ + "Clinical Study Sponsor", + "Sponsor", + "Study Sponsor" + ] + }, + { + "conceptId": "C41189", + "definition": "An individual who is observed, analyzed, examined, investigated, experimented upon, or/and treated in the course of a particular study.", + "preferredTerm": "Study Subject", + "submissionValue": "Study Subject" + } + ] + }, + { + "conceptId": "C188725", + "definition": "The terminology relevant to the objective level.", + "extensible": "false", + "name": "Objective Level Value Set Terminology", + "preferredTerm": "CDISC DDF Objective Level Value Set Terminology", + "submissionValue": "Objective Level Value Set Terminology", + "synonyms": + [ + "Objective Level Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C163559", + "definition": "Additional scientific question(s) within the study that enable further discovery research, beyond the primary and secondary objectives.", + "preferredTerm": "Trial Exploratory Objective", + "submissionValue": "Exploratory Objective", + "synonyms": + [ + "Study Exploratory Objective", + "Trial Exploratory Objective" + ] + }, + { + "conceptId": "C85826", + "definition": "The main scientific question(s) the study is designed to answer. (CDISC Glossary)", + "preferredTerm": "Trial Primary Objective", + "submissionValue": "Study Primary Objective", + "synonyms": + [ + "Study Primary Objective", + "Trial Primary Objective" + ] + }, + { + "conceptId": "C85827", + "definition": "The supportive or ancillary scientific question(s) the study is designed to answer. (CDISC Glossary)", + "preferredTerm": "Trial Secondary Objective", + "submissionValue": "Study Secondary Objective", + "synonyms": + [ + "Study Secondary Objective", + "Trial Secondary Objective" + ] + } + ] + }, + { + "conceptId": "C188724", + "definition": "The terminology relevant to the organization type.", + "extensible": "true", + "name": "Organization Type Value Set Terminology", + "preferredTerm": "CDISC DDF Organization Type Value Set Terminology", + "submissionValue": "Organization Type Value Set Terminology", + "synonyms": + [ + "Organization Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C93453", + "definition": "An organization (typically a government agency) that administers the registration of studies. (BRIDG)", + "preferredTerm": "Study Registry", + "submissionValue": "Clinical Study Registry" + }, + { + "conceptId": "C70793", + "definition": "An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical study. [After ICH E6, WHO, 21 CFR 50.3 (e), and after IDMP]", + "preferredTerm": "Clinical Study Sponsor", + "submissionValue": "Clinical Study Sponsor", + "synonyms": + [ + "Clinical Study Sponsor", + "Sponsor", + "Study Sponsor" + ] + }, + { + "conceptId": "C188863", + "definition": "An organization (typically a government agency) that is responsible for implementing and enforcing laws, licensing and regulating products and services, promoting the use of standards, and ensuring safety and consumer protections.", + "preferredTerm": "Regulatory Agency", + "submissionValue": "Regulatory Agency", + "synonyms": + [ + "Regulator", + "Regulatory Body" + ] + } + ] + }, + { + "conceptId": "C188723", + "definition": "The terminology relevant to the protocol status.", + "extensible": "false", + "name": "Protocol Status Value Set Terminology", + "preferredTerm": "CDISC DDF Protocol Status Value Set Terminology", + "submissionValue": "Protocol Status Value Set Terminology", + "synonyms": + [ + "Protocol Status Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C25425", + "definition": "Acceptance as satisfactory by an authoritative body; established by authority; given authoritative approval.", + "preferredTerm": "Approval", + "submissionValue": "Approved" + }, + { + "conceptId": "C85255", + "definition": "A preliminary version of a written work, design, or picture.", + "preferredTerm": "Draft", + "submissionValue": "Draft" + }, + { + "conceptId": "C25508", + "definition": "Conclusive in a process or progression.", + "preferredTerm": "Final", + "submissionValue": "Final" + }, + { + "conceptId": "C63553", + "definition": "No longer in use or valid; old.", + "preferredTerm": "Obsolete", + "submissionValue": "Obsolete" + }, + { + "conceptId": "C188862", + "definition": "A preliminary version of a written work, design, or picture that is awaiting review.", + "preferredTerm": "Pending Review", + "submissionValue": "Pending Review", + "synonyms": + [ + "Draft Pending Review" + ] + } + ] + }, + { + "conceptId": "C207415", + "definition": "The terminology relevant to the study amendment reason code value set.", + "extensible": "false", + "name": "Study Amendment Reason Code Value Set Terminology", + "preferredTerm": "CDISC DDF Study Amendment Reason Code Value Set Terminology", + "submissionValue": "Study Amendment Reason Code Value Set Terminology", + "synonyms": + [ + "Study Amendment Reason Code Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C207600", + "definition": "A change in the standard of care necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Change In Standard Of Care", + "submissionValue": "Change In Standard Of Care" + }, + { + "conceptId": "C207601", + "definition": "A change in the study purpose or intent of the scientific plan necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Change In Strategy", + "submissionValue": "Change In Strategy" + }, + { + "conceptId": "C207602", + "definition": "The addition of an investigational medicinal product to a clinical trial design necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "IMP Addition", + "submissionValue": "IMP Addition" + }, + { + "conceptId": "C207603", + "definition": "An error or inconsistency in the protocol necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Inconsistency and/or Error In The Protocol", + "submissionValue": "Inconsistency And/or Error In The Protocol" + }, + { + "conceptId": "C207604", + "definition": "Feedback from the investigator or study site necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Investigator/Site Feedback", + "submissionValue": "Investigator/Site Feedback" + }, + { + "conceptId": "C207605", + "definition": "Feedback from the institutional review board or independent ethics committee necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "IRB/IEC Feedback", + "submissionValue": "IRB/IEC Feedback" + }, + { + "conceptId": "C207606", + "definition": "A change to manufacturing processes of the study agents necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Manufacturing Change", + "submissionValue": "Manufacturing Change" + }, + { + "conceptId": "C207607", + "definition": "Previously unavailable data (other than safety data) becomes available, which necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "New Data Available (Other Than Safety Data)", + "submissionValue": "New Data Available (Other Than Safety Data)" + }, + { + "conceptId": "C207608", + "definition": "A regulatory agency has published a guidance document that necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "New Regulatory Guidance", + "submissionValue": "New Regulatory Guidance" + }, + { + "conceptId": "C207609", + "definition": "Previously unavailable safety data becomes available, which necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "New Safety Information Available", + "submissionValue": "New Safety Information Available" + }, + { + "conceptId": "C207610", + "definition": "A protocol design error necessitates a change(s) to, or formal clarification of, a document. (ICH M11)", + "preferredTerm": "Protocol Design Error", + "submissionValue": "Protocol Design Error" + }, + { + "conceptId": "C207611", + "definition": "Challenges with participant recruitment necessitates a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Recruitment Difficulty", + "submissionValue": "Recruitment Difficulty" + }, + { + "conceptId": "C207612", + "definition": "A regulatory agency has expressed a need for a change(s) to, or formal clarification of, the protocol. (ICH M11)", + "preferredTerm": "Regulatory Agency Request To Amend", + "submissionValue": "Regulatory Agency Request To Amend" + } + ] + }, + { + "conceptId": "C188727", + "definition": "The terminology relevant to the study arm data origin type.", + "extensible": "true", + "name": "Study Arm Data Origin Type Value Set Terminology", + "preferredTerm": "CDISC DDF Study Arm Data Origin Type Value Set Terminology", + "submissionValue": "Study Arm Data Origin Type Value Set Terminology", + "synonyms": + [ + "Study Arm Data Origin Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C188866", + "definition": "Data that are generated from the current study.", + "preferredTerm": "Data Generated Within Study", + "submissionValue": "Data Generated Within Study" + }, + { + "conceptId": "C188864", + "definition": "Data from studies that have occurred in the past.", + "preferredTerm": "Historical Data", + "submissionValue": "Historical Data" + }, + { + "conceptId": "C165830", + "definition": "Data relating to patient health status and/or the delivery of health care routinely collected from sources other than traditional clinical trials. NOTE: Examples of sources include data derived from electronic health records (EHRs); medical claims and billing data; data from product and disease registries; patient-generated data, including from in-home-use settings; and data gathered from other sources that can inform on health status, such as mobile devices. [After 21 U.S.C. 355g(b)).5 and Framework for FDA's Real-World Evidence Program December 2018] See also Real-World Evidence (RWE)", + "preferredTerm": "Real-world Data", + "submissionValue": "Real World Data" + }, + { + "conceptId": "C176263", + "definition": "Data that are artificially created rather than being generated by actual events. NOTE: Data are often created with the help of algorithms and used for a wide range of activities, including as test data for new products and tools, for model validation, and in AI optimization. [After The Ultimate Guide to Synthetic Data in 2020, August 29, 2020]. See also artificial intelligence.", + "preferredTerm": "Synthetic Data", + "submissionValue": "Synthetic Data" + }, + { + "conceptId": "C188865", + "definition": "Data that are generated from virtual encounters between investigators and subjects.", + "preferredTerm": "Virtual Data", + "submissionValue": "Virtual Data" + } + ] + }, + { + "conceptId": "C207416", + "definition": "The terminology relevant to the study design characteristics value set.", + "extensible": "true", + "name": "Study Design Characteristics Value Set Terminology", + "preferredTerm": "CDISC DDF Study Design Characteristics Value Set Terminology", + "submissionValue": "Study Design Characteristics Value Set Terminology", + "synonyms": + [ + "Study Design Characteristics Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C98704", + "definition": "A study design that allows for prospectively planned modifications to one or more aspects of the design based on accumulating data from subjects in the trial. (FDA)", + "preferredTerm": "Adaptive Design", + "submissionValue": "Adaptive" + }, + { + "conceptId": "C207613", + "definition": "A study design in which subjects enrolled in one study are subsequently continued into a related study for longer term safety, tolerability, and/or effectiveness monitoring.", + "preferredTerm": "Extension Study Design", + "submissionValue": "Extension", + "synonyms": + [ + "Roll-over Study" + ] + }, + { + "conceptId": "C46079", + "definition": "A study design in which interventions are assigned to subjects according to randomization principles.", + "preferredTerm": "Randomized Controlled Clinical Trial", + "submissionValue": "Randomized" + } + ] + }, + { + "conceptId": "C207418", + "definition": "The terminology relevant to the study intervention product designation value set.", + "extensible": "false", + "name": "Study Intervention Product Designation Value Set Terminology", + "preferredTerm": "CDISC DDF Study Intervention Product Designation Value Set Terminology", + "submissionValue": "Study Intervention Product Designation Value Set Terminology", + "synonyms": + [ + "Study Intervention Product Designation Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C202579", + "definition": "A medicinal product which is being tested or used as a reference, including as a placebo, in a clinical trial. (Regulation (EU) No 536/2014 Article 2 (5))", + "preferredTerm": "Investigational Medicinal Product", + "submissionValue": "IMP" + }, + { + "conceptId": "C156473", + "definition": "A medicinal product that is related to the specific needs of the clinical trial as described in the protocol, but not as an investigational medicinal product. NOTE: Auxiliary medicinal products may be authorised for marketing in a country or region or non-authorised. (CDISC Glossary)", + "preferredTerm": "Auxiliary Medicinal Product", + "submissionValue": "NIMP (AxMP)" + } + ] + }, + { + "conceptId": "C207417", + "definition": "The terminology relevant to the study intervention role value set.", + "extensible": "false", + "name": "Study Intervention Role Value Set Terminology", + "preferredTerm": "CDISC DDF Study Intervention Role Value Set Terminology", + "submissionValue": "Study Intervention Role Value Set Terminology", + "synonyms": + [ + "Study Intervention Role Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C207614", + "definition": "A medicinal product that must be administered along with the experimental treatment (e.g., drug studies wherein opioid blockers are administered to prevent overdose).", + "preferredTerm": "Additional Required Medicinal Product", + "submissionValue": "Additional Required Treatment" + }, + { + "conceptId": "C165822", + "definition": "Medicinal products that are administered to each clinical trial subject, regardless of randomization group, a) to treat the indication which is the object of the study, or b) required in the protocol as part of standard care for a condition that is not the indication under investigation, and is relevant for the clinical trial design. [After Recommendations from the expert group on clinical trials for the implementation of Regulation (EU) No 536/2014' dd 28 June 2017]", + "preferredTerm": "Background Treatment", + "submissionValue": "Background Treatment" + }, + { + "conceptId": "C158128", + "definition": "A non-investigational medicinal product (NIMP) given to trial subjects to produce a physiological response that is necessary before the pharmacological action of the investigational medicinal product can be assessed. [After Recommendations from the expert group on clinical trials for the implementation of Regulation (EU) No 536/2014' dd 28 June 2017]", + "preferredTerm": "Challenge Agent", + "submissionValue": "Challenge Agent" + }, + { + "conceptId": "C18020", + "definition": "Any procedure or test used to diagnose a disease or disorder.", + "preferredTerm": "Diagnostic Procedure", + "submissionValue": "Diagnostic" + }, + { + "conceptId": "C41161", + "definition": "The drug, device, therapy, procedure, or process under investigation in a clinical study that is believed to have an effect on outcomes of interest in a study (e.g., health-related quality of life, efficacy, safety, pharmacoeconomics). [After https://grants.nih.gov/grants/policy/faq_clinical_trial_definition.htm#5224; https://grants.nih.gov/policy/clinical-trials/protocol-template.htm] See also test articles, devices, drug product, combination product, treatment, diagnosis. Contrast with investigational medicinal product.", + "preferredTerm": "Protocol Agent", + "submissionValue": "Experimental Intervention", + "synonyms": + [ + "Investigational Interventional", + "Investigational Therapy or Treatment" + ] + }, + { + "conceptId": "C753", + "definition": "A pharmaceutical preparation that does not contain the investigational agent and is generally prepared to be physically indistinguishable from the preparation containing the investigational product.", + "preferredTerm": "Placebo", + "submissionValue": "Placebo" + }, + { + "conceptId": "C165835", + "definition": "Medicinal products identified in the protocol as those that may be administered to subjects when the efficacy of the investigational medicinal product (IMP) is not satisfactory, the effect of the IMP is too great and is likely to cause a hazard to the patient, or to manage an emergency situation. [After EU-CTR Recommendations from the expert group on clinical trials for the implementation of Regulation (EU) No 536/2014' dd 28 June 2017]", + "preferredTerm": "Rescue Medications", + "submissionValue": "Rescue Medicine" + } + ] + }, + { + "conceptId": "C207419", + "definition": "The terminology relevant to the study title type value set.", + "extensible": "false", + "name": "Study Title Type Value Set Terminology", + "preferredTerm": "CDISC DDF Study Title Type Value Set Terminology", + "submissionValue": "Study Title Type Value Set Terminology", + "synonyms": + [ + "Study Title Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C207615", + "definition": "The short descriptive name for the study.", + "preferredTerm": "Brief Study Title", + "submissionValue": "Brief Study Title", + "synonyms": + [ + "Abbreviated Protocol Title" + ] + }, + { + "conceptId": "C207616", + "definition": "The formal descriptive name for the study.", + "preferredTerm": "Official Study Title", + "submissionValue": "Official Study Title" + }, + { + "conceptId": "C207617", + "definition": "The descriptive name of the study that is intended for the lay public, written in easily understood language.", + "preferredTerm": "Public Study Title", + "submissionValue": "Public Study Title" + }, + { + "conceptId": "C207618", + "definition": "A more extensive descriptive name of the study that is intended for medical professionals, written using medical and scientific language.", + "preferredTerm": "Scientific Study Title", + "submissionValue": "Scientific Study Title" + }, + { + "conceptId": "C207646", + "definition": "A word or words formed from the beginning letters or a combination of syllables and letters of a compound term, which identifies a clinical study.", + "preferredTerm": "Study Acronym", + "submissionValue": "Study Acronym", + "synonyms": + [ + "Trial Acronym" + ] + } + ] + }, + { + "conceptId": "C201265", + "definition": "The terminology relevant to the timing relative to from value set.", + "extensible": "false", + "name": "Timing Relative To From Value Set Terminology", + "preferredTerm": "CDISC DDF Timing Relative To From Value Set Terminology", + "submissionValue": "Timing Relative To From Value Set Terminology", + "synonyms": + [ + "Timing Relative To From Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C201352", + "definition": "A timing relationship defined as the end of one event to the end of another event.", + "preferredTerm": "End to End", + "submissionValue": "End to End" + }, + { + "conceptId": "C201353", + "definition": "A timing relationship defined as the end of one event to the start of another event.", + "preferredTerm": "End to Start", + "submissionValue": "End to Start" + }, + { + "conceptId": "C201354", + "definition": "A timing relationship defined as the start of one event to the end of another event.", + "preferredTerm": "Start to End", + "submissionValue": "Start to End" + }, + { + "conceptId": "C201355", + "definition": "A timing relationship defined as the start of one event to the start of another event.", + "preferredTerm": "Start to Start", + "submissionValue": "Start to Start" + } + ] + }, + { + "conceptId": "C201264", + "definition": "The terminology relevant to the timing type value set.", + "extensible": "false", + "name": "Timing Type Value Set Terminology", + "preferredTerm": "CDISC DDF Timing Type Value Set Terminology", + "submissionValue": "Timing Type Value Set Terminology", + "synonyms": + [ + "Timing Type Value Set Terminology" + ], + "terms": + [ + { + "conceptId": "C201356", + "definition": "A type of time point relationship that follows a point or period of time within a timeline.", + "preferredTerm": "After Timing Type", + "submissionValue": "After" + }, + { + "conceptId": "C201357", + "definition": "A type of time point relationship that comes before a point or period of time within a timeline.", + "preferredTerm": "Before Timing Type", + "submissionValue": "Before" + }, + { + "conceptId": "C201358", + "definition": "A type of time point relationship that is fixed with respect to a timeline.", + "preferredTerm": "Fixed Reference Timing Type", + "submissionValue": "Fixed Reference" + } + ] + } + ], + "description": "CDISC Controlled Terminology for DDF is the set of CDISC-developed or CDISC-adopted standard expressions (values) used with data items within CDISC-defined DDF datasets.", + "effectiveDate": "2024-09-27", + "label": "DDF Controlled Terminology Package 58 Effective 2024-09-27", + "name": "DDF CT 2024-09-27", + "registrationStatus": "Final", + "source": "DDF Controlled Terminology developed by the CDISC Terminology Team in collaboration with the National Cancer Institute's Enterprise Vocabulary Services (EVS)", + "version": "2024-09-27" +} \ No newline at end of file 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 b5351926..7767d3eb 100644 --- a/neo4j-mdr-db/model/physical_data_model/neo4j-model.graphml +++ b/neo4j-mdr-db/model/physical_data_model/neo4j-model.graphml @@ -1,6 +1,6 @@ - + @@ -3803,11 +3803,12 @@ title: String - + - ActivityItem - is_adam_param_specific: Boolean + ActivityItem + is_adam_param_specific: Boolean +is_activity_instance_id_specific: Boolean @@ -4655,7 +4656,7 @@ external_id: String - + ActiveSubstanceRoot @@ -4718,7 +4719,7 @@ external_id: String - + Ingredient @@ -4733,7 +4734,7 @@ formulation_name: String - + IngredientFormulation @@ -5053,6 +5054,48 @@ median_cost_usd: Float + + + + + + + ActivityInstanceGroupingRoot + + + + + + + + + + + + + + + + + + + + + ActivityInstanceGroupingValue + + + + + + + + + + + + + + @@ -7075,7 +7118,7 @@ COMPOUND_PARAMETER 1 - HAS_UNIT_DEFINITION + HAS_UNIT_DEFINITION 0..* @@ -8011,9 +8054,9 @@ COMPOUND_PARAMETER - HAS_HALF_LIFE - 0..* - 0..1 + HAS_HALF_LIFE + 0..* + 0..1 @@ -8028,8 +8071,8 @@ COMPOUND_PARAMETER - HAS_STRENGTH_VALUE - 0..* + HAS_STRENGTH_VALUE + 0..* @@ -8098,9 +8141,9 @@ COMPOUND_PARAMETER - HAS_LAG_TIME - 0..* - 0..* + HAS_LAG_TIME + 0..* + 0..* @@ -8590,12 +8633,12 @@ COMPOUND_PARAMETER - + - HAS_ACTIVITY_ITEM - 0..1 - 1 + HAS_ACTIVITY_ITEM + 0..1 + 1 @@ -8603,14 +8646,14 @@ COMPOUND_PARAMETER - + - 0..* - 0..* - HAS_UNIT_DEFINITION + 0..* + 0..* + HAS_UNIT_DEFINITION @@ -8618,14 +8661,14 @@ COMPOUND_PARAMETER - + - 0..* - 0..* - HAS_CT_TERM + 0..* + 0..* + HAS_CT_TERM @@ -8633,7 +8676,7 @@ COMPOUND_PARAMETER - + @@ -9153,7 +9196,7 @@ is_default_linked: Boolean - IMPLEMENTS_VARIABLE + IMPLEMENTS_VARIABLE 0..* 0..* @@ -9738,7 +9781,7 @@ is_default_linked: Boolean - + @@ -9747,22 +9790,23 @@ is_default_linked: Boolean CONTAINS_ACTIVITY_ITEM 0..* - 0..* + 0..* - + - - + + + - HAS_ACTIVITY - 1..* - 0..* + HAS_ACTIVITY + 1..* + 0..* @@ -10214,9 +10258,7 @@ is_default_linked: Boolean - - - + @@ -10227,12 +10269,14 @@ is_default_linked: Boolean - + + + - 1 - 0..* - HAS_SUBSTANCE + 1 + 0..* + HAS_SUBSTANCE @@ -10244,9 +10288,9 @@ is_default_linked: Boolean - HAS_INGREDIENT - 0..* - 0..* + HAS_INGREDIENT + 0..* + 0..* @@ -10257,12 +10301,13 @@ is_default_linked: Boolean + - HAS_FORMULATION - 0..* - 0..* + HAS_FORMULATION + 0..* + 0..* @@ -10846,7 +10891,7 @@ is_default_linked: Boolean - + @@ -10856,7 +10901,7 @@ is_default_linked: Boolean - LINKS_TO_ACTIVITY_ITEM + LINKS_TO_ACTIVITY_ITEM @@ -11616,12 +11661,41 @@ value: String + + + + + + + + + + + HAS_GROUPING_ROOT + 1 + 1 + + + + + + + + + + + + HAS_VERSION* + + + + - - <svg xmlns="http://www.w3.org/2000/svg" version="1.0" width="30" height="30"> + + <svg xmlns="http://www.w3.org/2000/svg" version="1.0" width="30" height="30"> <g> <path d="M30,15A15,15,0,1,1,0,15A15,15,0,1,1,30,15Z" fill="#0055d4"/> <path d="M25.9545,15A10.9545,10.9545,0,1,1,4.0455,15A10.9545,10.9545,0,1,1,25.9545,15Z" fill="#ffffff"/> diff --git a/studybuilder-import/datafiles/configuration/feature_flags.csv b/studybuilder-import/datafiles/configuration/feature_flags.csv index e4e7368f..cfb3cb38 100644 --- a/studybuilder-import/datafiles/configuration/feature_flags.csv +++ b/studybuilder-import/datafiles/configuration/feature_flags.csv @@ -1,15 +1,17 @@ -name,enabled,description -studies_view_listings_analysis_study_metadata_new,1,"This flag toggles on/off the whole subpage found at Studies/View Listings/Analysis Study Metadata (New)" -new_activity_instance_wizard_stepper,1,"This flag toggles on/off the new wizard stepper to create/edit Activity Instances (Library/Concepts/Activities/Activity Instances)" -activity_instance_wizard_stepper_categoric_findings,0,"This flag toggles on/off the Categoric Findings use case in the new wizard stepper for activity instances" -activity_instance_wizard_stepper_events,0,"This flag toggles on/off the Events use case in the new wizard stepper for activity instances" -activity_instance_wizard_stepper_textual_findings,0,"This flag toggles on/off the Textual Findings use case in the new wizard stepper for activity instances" -activity_instance_wizard_stepper_edit_mode,0,"This flag toggles on/off the edit mode of the new wizard stepper for activity instances" -compounds_library,0,"This flag toggles on/off the whole subpage found at Library/Concepts/Compounds" -compounds_studies,0,"This flag toggles on/off the whole subpage found at Studies/Define Study/Study Interventions" -complexity_score_calculation,1,"Enables complexity score calculation on the Detailed SoA page" -study_data_suppliers,0,"This flag toggles on/off the Study Data Suppliers page found at Studies/Manage/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)" -prodex_extension,1,"Show/hide admin menu for managing extracts and loads of ProdEx data into OSB" -meddra_dictionary,0,"This flag toggles on/off the MedDRA dictionary page found at Library/Dictionaries/MedDRA" -loinc_dictionary,0,"This flag toggles on/off the LOINC dictionary page found at Library/Dictionaries/LOINC" \ No newline at end of file +section,feature,name,enabled,description +studies,Analysis Study Metadata,studies_view_listings_analysis_study_metadata_new,1,This flag toggles on/off the whole subpage found at Studies/View Listings/Analysis Study Metadata (New) +library,Wizard Stepper,new_activity_instance_wizard_stepper,1,This flag toggles on/off the new wizard stepper to create/edit Activity Instances (Library/Concepts/Activities/Activity Instances) +library,Wizard Stepper,activity_instance_wizard_stepper_categoric_findings,0,This flag toggles on/off the Categoric Findings use case in the new wizard stepper for activity instances +library,Wizard Stepper,activity_instance_wizard_stepper_events,0,This flag toggles on/off the Events use case in the new wizard stepper for activity instances +library,Wizard Stepper,activity_instance_wizard_stepper_textual_findings,0,This flag toggles on/off the Textual Findings use case in the new wizard stepper for activity instances +library,Wizard Stepper,activity_instance_wizard_stepper_edit_mode,0,This flag toggles on/off the edit mode of the new wizard stepper for activity instances +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,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 diff --git a/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv b/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv index fa1bd1ac..cfb3cb38 100644 --- a/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv +++ b/studybuilder-import/e2e_datafiles/configuration/feature_flags.csv @@ -1,15 +1,17 @@ -name,enabled,description -studies_view_listings_analysis_study_metadata_new,1,"This flag toggles on/off the whole subpage found at Studies/View Listings/Analysis Study Metadata (New)" -new_activity_instance_wizard_stepper,1,"This flag toggles on/off the new wizard stepper to create/edit Activity Instances (Library/Concepts/Activities/Activity Instances)" -activity_instance_wizard_stepper_categoric_findings,0,"This flag toggles on/off the Categoric Findings use case in the new wizard stepper for activity instances" -activity_instance_wizard_stepper_events,0,"This flag toggles on/off the Events use case in the new wizard stepper for activity instances" -activity_instance_wizard_stepper_textual_findings,0,"This flag toggles on/off the Textual Findings use case in the new wizard stepper for activity instances" -activity_instance_wizard_stepper_edit_mode,0,"This flag toggles on/off the edit mode of the new wizard stepper for activity instances" -compounds_library,0,"This flag toggles on/off the whole subpage found at Library/Concepts/Compounds" -compounds_studies,0,"This flag toggles on/off the whole subpage found at Studies/Define Study/Study Interventions" -complexity_score_calculation,1,"Enables complexity score calculation on the Detailed SoA page" -study_data_suppliers,1,"This flag toggles on/off the Study Data Suppliers page found at Studies/Manage/Study Data Suppliers" -study_data_suppliers_create_from_study,1,"This flag toggles on/off the ability to create a user-defined data supplier from study level (Add a user defined data supplier button)" -prodex_extension,1,"Show/hide admin menu for managing extracts and loads of ProdEx data into OSB" -meddra_dictionary,0,"This flag toggles on/off the MedDRA dictionary page found at Library/Dictionaries/MedDRA" -loinc_dictionary,0,"This flag toggles on/off the LOINC dictionary page found at Library/Dictionaries/LOINC" \ No newline at end of file +section,feature,name,enabled,description +studies,Analysis Study Metadata,studies_view_listings_analysis_study_metadata_new,1,This flag toggles on/off the whole subpage found at Studies/View Listings/Analysis Study Metadata (New) +library,Wizard Stepper,new_activity_instance_wizard_stepper,1,This flag toggles on/off the new wizard stepper to create/edit Activity Instances (Library/Concepts/Activities/Activity Instances) +library,Wizard Stepper,activity_instance_wizard_stepper_categoric_findings,0,This flag toggles on/off the Categoric Findings use case in the new wizard stepper for activity instances +library,Wizard Stepper,activity_instance_wizard_stepper_events,0,This flag toggles on/off the Events use case in the new wizard stepper for activity instances +library,Wizard Stepper,activity_instance_wizard_stepper_textual_findings,0,This flag toggles on/off the Textual Findings use case in the new wizard stepper for activity instances +library,Wizard Stepper,activity_instance_wizard_stepper_edit_mode,0,This flag toggles on/off the edit mode of the new wizard stepper for activity instances +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,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 diff --git a/studybuilder-import/importers/run_import_activities.py b/studybuilder-import/importers/run_import_activities.py index 2b75250c..9f3a4cf2 100644 --- a/studybuilder-import/importers/run_import_activities.py +++ b/studybuilder-import/importers/run_import_activities.py @@ -939,47 +939,53 @@ async def handle_activity_item_classes(self, csvfile, session): await asyncio.gather(*api_tasks) # await session.close() - def compare_instance_items(self, old, new): - new_items = set( - ( - item.get("activity_item_class_uid"), - frozenset(item.get("ct_term_uids", [])), - frozenset(item.get("unit_definition_uids", [])), - ) - for item in new - ) - old_items = set( - ( - item.get("activity_item_class", {}).get("uid"), - frozenset(term["uid"] for term in item.get("ct_terms", [])), - frozenset(unit["uid"] for unit in item.get("unit_definitions", [])), - ) - for item in old + def _normalize_instance_item(self, item): + activity_item_class_uid = item.get("activity_item_class_uid") or ( + item.get("activity_item_class") or {} + ).get("uid") + + unit_definition_uids = item.get("unit_definition_uids") + if unit_definition_uids is None: + unit_definition_uids = [ + unit.get("uid") for unit in item.get("unit_definitions", []) + ] + + term_uids = item.get("ct_term_uids") + if term_uids is None: + term_uids = [] + for term in item.get("ct_terms", []): + term_uid = term.get("term_uid") or term.get("uid") + if term_uid: + term_uids.append(term_uid) + + return ( + activity_item_class_uid, + frozenset(term_uids), + frozenset(uid for uid in unit_definition_uids if uid is not None), ) + + def compare_instance_items(self, old, new): + new_items = {self._normalize_instance_item(item) for item in new} + old_items = {self._normalize_instance_item(item) for item in old} return new_items == old_items + def _normalize_instance_grouping(self, item): + return ( + item.get("activity_uid") or (item.get("activity") or {}).get("uid"), + item.get("activity_group_uid") + or (item.get("activity_group") or {}).get("uid"), + item.get("activity_subgroup_uid") + or (item.get("activity_subgroup") or {}).get("uid"), + ) + def compare_instance_groupings(self, old, new): # Convert both old and new to lists of tuples, (activity_uid, group_uid, subgroup_uid) # These are hashable so the lists can be made into sets for easy comparison - new_groupings = set( - ( - item["activity_uid"], - item["activity_group_uid"], - item["activity_subgroup_uid"], - ) - for item in new - ) - old_groupings = set( - ( - item.get("activity", {}).get("uid"), - item.get("activity_group", {}).get("uid"), - item.get("activity_subgroup", {}).get("uid"), - ) - for item in old - ) + new_groupings = {self._normalize_instance_grouping(item) for item in new} + old_groupings = {self._normalize_instance_grouping(item) for item in old} return new_groupings == old_groupings - def are_instances_equal(self, new, existing): + def are_instance_attributes_equal(self, new, existing): # Define properties to compare directly properties_to_compare = [ "activity_instance_class_uid", @@ -1003,19 +1009,128 @@ def are_instances_equal(self, new, existing): # Compare complex structures if not self.compare_instance_items( - existing["activity_items"], new["activity_items"] + existing.get("activity_items", []), new.get("activity_items", []) ): self.log.debug("Difference found in activity_items") return False + return True + + def are_instance_groupings_equal(self, new, existing): if not self.compare_instance_groupings( - existing["activity_groupings"], new["activity_groupings"] + existing.get("activity_groupings", []), new.get("activity_groupings", []) ): self.log.debug("Difference found in activity_groupings") return False return True + def are_instances_equal(self, new, existing): + return self.are_instance_attributes_equal( + new, existing + ) and self.are_instance_groupings_equal(new, existing) + + def _split_activity_instance_payload(self, body): + attributes_payload = { + key: value for key, value in body.items() if key != "activity_groupings" + } + groupings_payload = {"activity_groupings": body.get("activity_groupings", [])} + return attributes_payload, groupings_payload + + async def _patch_activity_instance_part( + self, + activity_instance_name, + activity_instance_uid, + part, + payload, + session, + ): + part_path = path_join(ACTIVITY_INSTANCES_PATH, activity_instance_uid, part) + body = dict(payload) + body["change_description"] = "Migration modification" + + status, response = await self.api.new_version_to_api_async( + path=path_join(part_path, "versions"), + session=session, + ) + if status >= 400: + error_message = ( + response.get("message") or response.get("detail") or str(response) + ) + if "New draft version can be created only for FINAL versions" in str( + error_message + ): + self.log.warning( + f"Skipping new {part} version for '{activity_instance_name}' because it is already in draft" + ) + else: + self.log.error( + f"Failed to create new {part} version for activity instance '{activity_instance_name}': {error_message}" + ) + return + + status, response = await self.api.patch_to_api_async( + path=part_path, + body=body, + session=session, + ) + if status >= 400: + error_message = ( + response.get("message") or response.get("detail") or str(response) + ) + self.log.error( + f"Failed to patch activity instance '{activity_instance_name}' ({part}): {error_message}" + ) + return + + status, _ = await self.api.approve_async( + path_join(part_path, "approvals"), session=session + ) + if status >= 400: + self.log.error( + f"Failed to approve activity instance '{activity_instance_name}' ({part})" + ) + + async def _patch_activity_instance_parts( + self, + activity_instance_name, + activity_instance_uid, + attributes_payload, + groupings_payload, + patch_attributes, + patch_groupings, + session, + ): + if not patch_attributes and not patch_groupings: + self.log.info( + f"Identical activity instance '{activity_instance_name}' already exists" + ) + return + + if patch_attributes: + self.log.info( + f"Patch activity instance attributes '{activity_instance_name}'" + ) + await self._patch_activity_instance_part( + activity_instance_name=activity_instance_name, + activity_instance_uid=activity_instance_uid, + part="attributes", + payload=attributes_payload, + session=session, + ) + + if patch_groupings: + self.log.info( + f"Patch activity instance groupings '{activity_instance_name}'" + ) + await self._patch_activity_instance_part( + activity_instance_name=activity_instance_name, + activity_instance_uid=activity_instance_uid, + part="groupings", + payload=groupings_payload, + session=session, + ) + @open_file_async() async def handle_activity_instances(self, csvfile, session): readCSV = csv.DictReader(csvfile, delimiter=",") @@ -1273,31 +1388,43 @@ async def handle_activity_instances(self, csvfile, session): f" since instance with name {activity_instance_name} already exists" f" with different topic code {existing_rows_by_name[activity_instance_name]['topic_code']}" ) - elif not self.are_instances_equal( - activity_instance_data["body"], existing_rows_by_tc[topic_code] - ): - self.log.info(f"Patch activity instance '{activity_instance_name}'") - activity_instance_data["patch_path"] = path_join( - ACTIVITY_INSTANCES_PATH, - existing_rows_by_tc[topic_code].get("uid"), - ) - activity_instance_data["new_path"] = path_join( - ACTIVITY_INSTANCES_PATH, - existing_rows_by_tc[topic_code].get("uid"), - "versions", - ) - activity_instance_data["body"][ - "change_description" - ] = "Migration modification" - api_tasks.append( - self.api.new_version_patch_then_approve( - data=activity_instance_data, session=session, approve=True + else: + existing_instance = existing_rows_by_tc.get(topic_code) + if existing_instance is None: + self.log.warning( + f"Cannot patch activity instance '{activity_instance_name}' because no existing instance was found for topic code '{topic_code}'" ) + continue + existing_uid = existing_instance.get("uid") + + patch_attributes = not self.are_instance_attributes_equal( + activity_instance_data["body"], existing_instance ) - else: - self.log.info( - f"Identical activity instance '{activity_instance_name}' already exists" + patch_groupings = not self.are_instance_groupings_equal( + activity_instance_data["body"], existing_instance ) + + if patch_attributes or patch_groupings: + attributes_payload, groupings_payload = ( + self._split_activity_instance_payload( + activity_instance_data["body"] + ) + ) + api_tasks.append( + self._patch_activity_instance_parts( + activity_instance_name=activity_instance_name, + activity_instance_uid=existing_uid, + attributes_payload=attributes_payload, + groupings_payload=groupings_payload, + patch_attributes=patch_attributes, + patch_groupings=patch_groupings, + session=session, + ) + ) + else: + self.log.info( + f"Identical activity instance '{activity_instance_name}' already exists" + ) await asyncio.gather(*api_tasks) # Get the item class for combination of column name and domain diff --git a/studybuilder-import/importers/run_import_feature_flags.py b/studybuilder-import/importers/run_import_feature_flags.py index 74028185..c554ac06 100644 --- a/studybuilder-import/importers/run_import_feature_flags.py +++ b/studybuilder-import/importers/run_import_feature_flags.py @@ -36,6 +36,8 @@ def handle_feature_flags(self, csvfile, update: bool = False): for feature_flag_name, feature_flag_data in feature_flags_in_csv.items(): body = { + "section": feature_flag_data["section"], + "feature": feature_flag_data["feature"], "name": feature_flag_data["name"], "enabled": map_boolean(feature_flag_data["enabled"]), "description": feature_flag_data["description"] or None, diff --git a/studybuilder-import/importers/run_import_mockdatajson.py b/studybuilder-import/importers/run_import_mockdatajson.py index 3a5445e5..fe3f40f4 100644 --- a/studybuilder-import/importers/run_import_mockdatajson.py +++ b/studybuilder-import/importers/run_import_mockdatajson.py @@ -46,6 +46,7 @@ ) from .utils.importer import BaseImporter, open_file from .utils.metrics import Metrics +from .utils.path_join import path_join metrics = Metrics() @@ -125,6 +126,8 @@ CONCEPT_VALUES = "ConceptValues" DICTIONARIES = "Dictionaries" +ACTIVITY_INSTANCES_PATH = "/concepts/activities/activity-instances" + DEFINITION_PLACEHOLDER = None @@ -3168,6 +3171,503 @@ def handle_activities(self, jsonfile): else: self.log.warning(f"Failed to add activity '{data['name']}'") + def _normalize_instance_item(self, item): + activity_item_class_uid = item.get("activity_item_class_uid") or ( + item.get("activity_item_class") or {} + ).get("uid") + + unit_definition_uids = item.get("unit_definition_uids") + if unit_definition_uids is None: + unit_definition_uids = [ + unit.get("uid") for unit in item.get("unit_definitions", []) + ] + + term_uids = item.get("ct_term_uids") + if term_uids is None: + term_uids = [] + for term in item.get("ct_terms", []): + term_uid = term.get("term_uid") or term.get("uid") + if term_uid: + term_uids.append(term_uid) + + return ( + activity_item_class_uid, + frozenset(term_uids), + frozenset(uid for uid in unit_definition_uids if uid is not None), + ) + + def _normalize_instance_grouping(self, grouping): + return ( + grouping.get("activity_uid") or (grouping.get("activity") or {}).get("uid"), + grouping.get("activity_group_uid") + or (grouping.get("activity_group") or {}).get("uid"), + grouping.get("activity_subgroup_uid") + or (grouping.get("activity_subgroup") or {}).get("uid"), + ) + + def compare_instance_items(self, old, new): + new_items = {self._normalize_instance_item(item) for item in new} + old_items = {self._normalize_instance_item(item) for item in old} + return new_items == old_items + + def compare_instance_groupings(self, old, new): + new_groupings = {self._normalize_instance_grouping(item) for item in new} + old_groupings = {self._normalize_instance_grouping(item) for item in old} + return new_groupings == old_groupings + + def are_instance_attributes_equal(self, new, existing): + properties_to_compare = [ + "activity_instance_class_uid", + "library_name", + "name_sentence_case", + "definition", + "adam_param_code", + "legacy_description", + "topic_code", + "nci_concept_id", + "is_required_for_activity", + "is_default_selected_for_activity", + "is_data_sharing", + "is_legacy_usage", + ] + + for prop_name in properties_to_compare: + new_value = new.get(prop_name) + existing_value = existing.get(prop_name) + if prop_name == "definition": + if new_value == "": + new_value = None + if existing_value == "": + existing_value = None + if new_value != existing_value: + self.log.debug( + "Difference found in property '%s': existing='%s', new='%s'", + prop_name, + existing_value, + new_value, + ) + return False + + if not self.compare_instance_items( + existing.get("activity_items", []), new.get("activity_items", []) + ): + self.log.debug("Difference found in activity_items") + return False + return True + + def are_instance_groupings_equal(self, new, existing): + if not self.compare_instance_groupings( + existing.get("activity_groupings", []), new.get("activity_groupings", []) + ): + self.log.debug("Difference found in activity_groupings") + return False + return True + + def _split_activity_instance_payload(self, body): + attributes_payload = { + key: value for key, value in body.items() if key != "activity_groupings" + } + groupings_payload = {"activity_groupings": body.get("activity_groupings", [])} + return attributes_payload, groupings_payload + + def _resolve_activity_instance_groupings( + self, instance, all_activities, all_groups, all_subgroups + ): + groupings = [] + for grouping in instance.get("activity_groupings") or []: + if MDR_MIGRATION_FROM_SAME_ENV: + activity_uid = grouping.get("activity_uid") or ( + grouping.get("activity") or {} + ).get("uid") + group_uid = grouping.get("activity_group_uid") or ( + grouping.get("activity_group") or {} + ).get("uid") + subgroup_uid = grouping.get("activity_subgroup_uid") or ( + grouping.get("activity_subgroup") or {} + ).get("uid") + else: + activity_name = grouping.get("activity_name") or ( + grouping.get("activity") or {} + ).get("name") + group_name = grouping.get("activity_group_name") or ( + grouping.get("activity_group") or {} + ).get("name") + subgroup_name = grouping.get("activity_subgroup_name") or ( + grouping.get("activity_subgroup") or {} + ).get("name") + activity_uid = all_activities.get(activity_name) + group_uid = all_groups.get(group_name) + subgroup_uid = all_subgroups.get(subgroup_name) + + if not activity_uid or not group_uid or not subgroup_uid: + self.log.warning( + "Skipping incomplete grouping for instance '%s': activity_uid=%s, group_uid=%s, subgroup_uid=%s", + instance.get("name"), + activity_uid, + group_uid, + subgroup_uid, + ) + continue + + resolved = { + "activity_uid": activity_uid, + "activity_group_uid": group_uid, + "activity_subgroup_uid": subgroup_uid, + } + if resolved not in groupings: + groupings.append(resolved) + return groupings + + def _build_activity_items_payload(self, instance, all_item_classes, all_units): + grouped_items = {} + for item in instance.get("activity_items") or []: + if MDR_MIGRATION_FROM_SAME_ENV: + class_uid = item.get("activity_item_class_uid") or ( + item.get("activity_item_class") or {} + ).get("uid") + else: + class_name = (item.get("activity_item_class") or {}).get("name") + class_uid = all_item_classes.get(class_name) + + if class_uid is None: + self.log.warning( + "Skipping activity item with unknown class for instance '%s': %s", + instance.get("name"), + item.get("activity_item_class"), + ) + continue + + if class_uid not in grouped_items: + grouped_items[class_uid] = { + "activity_item_class_uid": class_uid, + "ct_term_uids": set(), + "unit_definition_uids": set(), + "is_adam_param_specific": item.get("is_adam_param_specific", False), + "odm_form_uid": item.get("odm_form_uid"), + "odm_item_group_uid": item.get("odm_item_group_uid"), + "odm_item_uid": item.get("odm_item_uid"), + } + + for term in item.get("ct_terms") or []: + term_uid = term.get("term_uid") or term.get("uid") + if term_uid: + grouped_items[class_uid]["ct_term_uids"].add(term_uid) + + for term_uid in item.get("ct_term_uids") or []: + if term_uid: + grouped_items[class_uid]["ct_term_uids"].add(term_uid) + + for unit_uid in item.get("unit_definition_uids") or []: + if unit_uid: + grouped_items[class_uid]["unit_definition_uids"].add(unit_uid) + + for unit in item.get("unit_definitions") or []: + if MDR_MIGRATION_FROM_SAME_ENV: + unit_uid = unit.get("uid") + else: + unit_name = unit.get("name") + unit_uid = all_units.get(unit_name) or unit.get("uid") + if unit_uid: + grouped_items[class_uid]["unit_definition_uids"].add(unit_uid) + + items = [] + for item in grouped_items.values(): + if item["ct_term_uids"] and item["unit_definition_uids"]: + self.log.warning( + "Activity item class '%s' links to both terms and units, dropping units", + item["activity_item_class_uid"], + ) + item["unit_definition_uids"] = set() + item["ct_term_uids"] = sorted(item["ct_term_uids"]) + item["unit_definition_uids"] = sorted(item["unit_definition_uids"]) + items.append(item) + return items + + def _build_activity_instance_payload( + self, + instance, + all_activities, + all_groups, + all_subgroups, + all_instance_classes, + all_item_classes, + all_units, + ): + name = instance.get("name") + if not name: + self.log.warning("Skipping activity instance with missing name") + return None + + if MDR_MIGRATION_FROM_SAME_ENV: + activity_instance_class_uid = instance.get( + "activity_instance_class_uid" + ) or (instance.get("activity_instance_class") or {}).get("uid") + else: + instance_class_name = (instance.get("activity_instance_class") or {}).get( + "name" + ) + activity_instance_class_uid = all_instance_classes.get(instance_class_name) + + if not activity_instance_class_uid: + self.log.warning( + "Skipping activity instance '%s' with unknown activity instance class", + name, + ) + return None + + activity_groupings = self._resolve_activity_instance_groupings( + instance, all_activities, all_groups, all_subgroups + ) + if len(activity_groupings) == 0: + self.log.warning( + "Skipping activity instance '%s' because it lacks valid groupings", + name, + ) + return None + + activity_items = self._build_activity_items_payload( + instance, all_item_classes, all_units + ) + + body = { + "activity_instance_class_uid": activity_instance_class_uid, + "name": name, + "name_sentence_case": instance.get("name_sentence_case") or name.lower(), + "definition": instance.get("definition") or None, + "adam_param_code": instance.get("adam_param_code") or None, + "activity_groupings": activity_groupings, + "activity_items": activity_items, + "legacy_description": instance.get("legacy_description") or None, + "topic_code": instance.get("topic_code") or None, + "library_name": instance.get("library_name") or "Sponsor", + "nci_concept_id": instance.get("nci_concept_id") or None, + "is_required_for_activity": instance.get("is_required_for_activity", False), + "is_default_selected_for_activity": instance.get( + "is_default_selected_for_activity", False + ), + "is_data_sharing": instance.get("is_data_sharing", True), + "is_legacy_usage": instance.get("is_legacy_usage", False), + } + return { + "path": ACTIVITY_INSTANCES_PATH, + "approve_path": ACTIVITY_INSTANCES_PATH, + "body": body, + } + + def _patch_activity_instance_part( + self, + activity_instance_name, + activity_instance_uid, + part, + payload, + ): + part_path = path_join(ACTIVITY_INSTANCES_PATH, activity_instance_uid, part) + body = dict(payload) + body["change_description"] = "Migration modification" + + version_path = path_join(part_path, "versions") + version_response = self.api.simple_post_to_api( + version_path, + {}, + simple_path=ACTIVITY_INSTANCES_PATH, + ) + if version_response is None: + self.log.warning( + "Could not create new %s version for activity instance '%s', attempting to patch current draft", + part, + activity_instance_name, + ) + + response = self.api.simple_patch( + body=body, + url=part_path, + path=ACTIVITY_INSTANCES_PATH, + ) + if response is None: + response = self.api.simple_put( + body=body, + url=part_path, + path=ACTIVITY_INSTANCES_PATH, + ) + if response is None: + self.log.error( + "Failed to patch activity instance '%s' (%s)", + activity_instance_name, + part, + ) + return + + if not self.api.simple_approve(path_join(part_path, "approvals")): + self.log.error( + "Failed to approve activity instance '%s' (%s)", + activity_instance_name, + part, + ) + + def _patch_activity_instance_parts( + self, + activity_instance_name, + activity_instance_uid, + attributes_payload, + groupings_payload, + patch_attributes, + patch_groupings, + ): + if not patch_attributes and not patch_groupings: + self.log.info( + f"Identical activity instance '{activity_instance_name}' already exists" + ) + return + + if patch_attributes: + self.log.info( + f"Patch activity instance attributes '{activity_instance_name}'" + ) + self._patch_activity_instance_part( + activity_instance_name=activity_instance_name, + activity_instance_uid=activity_instance_uid, + part="attributes", + payload=attributes_payload, + ) + + if patch_groupings: + self.log.info( + f"Patch activity instance groupings '{activity_instance_name}'" + ) + self._patch_activity_instance_part( + activity_instance_name=activity_instance_name, + activity_instance_uid=activity_instance_uid, + part="groupings", + payload=groupings_payload, + ) + + @open_file() + def handle_activity_instances(self, jsonfile): + self.log.info("======== Activity instances ========") + imported = json.load(jsonfile) + + all_activities = self.fetch_all_activities() + all_groups = self.fetch_all_activity_groups() + all_subgroups = self.fetch_all_activity_subgroups() + all_instance_classes = self.api.get_all_identifiers( + self.api.get_all_from_api("/activity-instance-classes"), + identifier="name", + value="uid", + ) + all_item_classes = self.api.get_all_identifiers( + self.api.get_all_from_api("/activity-item-classes"), + identifier="name", + value="uid", + ) + all_units = self.api.get_all_identifiers( + self.api.get_all_from_api("/concepts/unit-definitions"), + identifier="name", + value="uid", + ) + + existing_instances = self.api.get_all_from_api(ACTIVITY_INSTANCES_PATH) + existing_rows_by_name = self.api.response_to_dict(existing_instances, "name") + existing_rows_by_tc = {} + for item in existing_instances: + topic_code = item.get("topic_code") + if topic_code: + existing_rows_by_tc[topic_code] = item + + for instance in imported: + activity_instance_data = self._build_activity_instance_payload( + instance, + all_activities, + all_groups, + all_subgroups, + all_instance_classes, + all_item_classes, + all_units, + ) + if activity_instance_data is None: + continue + + activity_instance_name = activity_instance_data["body"]["name"] + topic_code = activity_instance_data["body"]["topic_code"] + existing_by_name = existing_rows_by_name.get(activity_instance_name) + existing_by_topic = ( + existing_rows_by_tc.get(topic_code) if topic_code else None + ) + + if existing_by_name is None and ( + topic_code is None or existing_by_topic is None + ): + self.log.info(f"Adding activity instance '{activity_instance_name}'") + response = self.api.simple_post_to_api( + ACTIVITY_INSTANCES_PATH, + 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" + ) + else: + self.log.warning( + "Failed to add activity instance '%s'", + activity_instance_name, + ) + if response is not None: + existing_rows_by_name[activity_instance_name] = response + if topic_code: + existing_rows_by_tc[topic_code] = response + continue + + if ( + existing_by_name is not None + and topic_code is not None + and existing_by_name.get("topic_code") != topic_code + ): + self.log.warning( + "Not patching activity instance '%s' because topic code '%s' conflicts with existing '%s'", + activity_instance_name, + topic_code, + existing_by_name.get("topic_code"), + ) + continue + + existing_instance = existing_by_topic or existing_by_name + if existing_instance is None: + self.log.warning( + "Cannot patch activity instance '%s' because no existing instance was found", + activity_instance_name, + ) + continue + + patch_attributes = not self.are_instance_attributes_equal( + activity_instance_data["body"], existing_instance + ) + patch_groupings = not self.are_instance_groupings_equal( + activity_instance_data["body"], existing_instance + ) + + if patch_attributes or patch_groupings: + attributes_payload, groupings_payload = ( + self._split_activity_instance_payload( + activity_instance_data["body"] + ) + ) + self._patch_activity_instance_parts( + activity_instance_name=activity_instance_name, + activity_instance_uid=existing_instance.get("uid"), + attributes_payload=attributes_payload, + groupings_payload=groupings_payload, + patch_attributes=patch_attributes, + patch_groupings=patch_groupings, + ) + else: + self.log.info( + f"Identical activity instance '{activity_instance_name}' already exists" + ) + def run(self): self.log.info("Migrating json mock data") @@ -3231,7 +3731,14 @@ def run(self): else: self.log.info("Skipping activities") - # TODO Activity instances + # Activity instances + if MDR_MIGRATION_EXPORTED_ACTIVITY_INSTANCES: + act_inst_json = os.path.join( + self.import_dir, "concepts.activities.activity-instances.json" + ) + self.handle_activity_instances(act_inst_json) + else: + self.log.info("Skipping activity instances") # Compounds and compound aliases if MDR_MIGRATION_EXPORTED_COMPOUNDS: diff --git a/studybuilder/config/config.json b/studybuilder/config/config.json index 00d56e10..de92775b 100644 --- a/studybuilder/config/config.json +++ b/studybuilder/config/config.json @@ -25,15 +25,15 @@ "AUTH_CLIENT_ID": "", "AUTH_ENABLED": "", - "API_BUILD_NUMBER" : "OSB v2.7.0", + "API_BUILD_NUMBER" : "OSB v2.8.0", "DATA_IMPORT_BUILD_NUMBER": "N/A", - "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.7.0", - "FRONTEND_BUILD_NUMBER" : "OSB v2.7.0", + "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.8.0", + "FRONTEND_BUILD_NUMBER" : "OSB v2.8.0", "NEO4J_MDR_BUILD_NUMBER": "N/A", "NEODASH_BUILD_NUMBER": "N/A", - "RELEASE_VERSION_NUMBER" : "OSB v2.7.0", + "RELEASE_VERSION_NUMBER" : "OSB v2.8.0", "STANDARDS_IMPORT_BUILD_NUMBER": "N/A", "STUDYBUILDER_EXPORT_BUILD_NUMBER": "N/A", - "STUDYBUILDER_VERSION" : "OSB v2.7.0" + "STUDYBUILDER_VERSION" : "OSB v2.8.0" } diff --git a/studybuilder/package.json b/studybuilder/package.json index cf33b191..dae10707 100644 --- a/studybuilder/package.json +++ b/studybuilder/package.json @@ -38,7 +38,7 @@ "vue-chartjs": "^5.2.0", "vue-i18n": "11.1.10", "vue-router": "^4.2.5", - "vuetify": "3.12.2", + "vuetify": "4.0.2", "yaml": "^2.3.4" }, "devDependencies": { diff --git a/studybuilder/public/config.json b/studybuilder/public/config.json index 00d56e10..de92775b 100644 --- a/studybuilder/public/config.json +++ b/studybuilder/public/config.json @@ -25,15 +25,15 @@ "AUTH_CLIENT_ID": "", "AUTH_ENABLED": "", - "API_BUILD_NUMBER" : "OSB v2.7.0", + "API_BUILD_NUMBER" : "OSB v2.8.0", "DATA_IMPORT_BUILD_NUMBER": "N/A", - "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.7.0", - "FRONTEND_BUILD_NUMBER" : "OSB v2.7.0", + "DOCUMENTATION_PORTAL_BUILD_NUMBER" : "OSB v2.8.0", + "FRONTEND_BUILD_NUMBER" : "OSB v2.8.0", "NEO4J_MDR_BUILD_NUMBER": "N/A", "NEODASH_BUILD_NUMBER": "N/A", - "RELEASE_VERSION_NUMBER" : "OSB v2.7.0", + "RELEASE_VERSION_NUMBER" : "OSB v2.8.0", "STANDARDS_IMPORT_BUILD_NUMBER": "N/A", "STUDYBUILDER_EXPORT_BUILD_NUMBER": "N/A", - "STUDYBUILDER_VERSION" : "OSB v2.7.0" + "STUDYBUILDER_VERSION" : "OSB v2.8.0" } diff --git a/studybuilder/public/sbom-clinical-mdr-api.md b/studybuilder/public/sbom-clinical-mdr-api.md index 71665f70..87b0b8fa 100644 --- a/studybuilder/public/sbom-clinical-mdr-api.md +++ b/studybuilder/public/sbom-clinical-mdr-api.md @@ -5,33 +5,33 @@ |--------------------------|--------------|--------------------------------------------------------------| | annotated-doc | 0.0.4 | [MIT](#annotated-doc) | | annotated-types | 0.6.0 | [see below](#annotated-types) | -| anyio | 4.12.1 | [MIT](#anyio) | +| anyio | 4.13.0 | [MIT](#anyio) | | asyncache | 0.3.1 | [MIT](#asyncache) | -| attrs | 25.4.0 | [MIT](#attrs) | +| attrs | 26.1.0 | [MIT](#attrs) | | Authlib | 1.6.9 | [BSD-3-Clause](#authlib) | -| azure-core | 1.38.2 | [MIT License](#azure-core) | -| azure-identity | 1.25.2 | [MIT](#azure-identity) | +| azure-core | 1.39.0 | [MIT](#azure-core) | +| azure-identity | 1.25.3 | [MIT](#azure-identity) | | beautifulsoup4 | 4.12.3 | [MIT License](#beautifulsoup4) | | brotli | 1.2.0 | [MIT](#brotli) | | cachetools | 5.5.2 | [MIT](#cachetools) | | certifi | 2026.2.25 | [MPL-2.0](#certifi) | | cffi | 2.0.0 | [MIT](#cffi) | -| charset-normalizer | 3.4.5 | [MIT](#charset-normalizer) | +| charset-normalizer | 3.4.6 | [MIT](#charset-normalizer) | | click | 8.3.1 | [BSD-3-Clause](#click) | | colour | 0.1.5 | [BSD 3-Clause License](#colour) | -| cryptography | 46.0.5 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | +| cryptography | 46.0.6 | [Apache-2.0 OR BSD-3-Clause](#cryptography) | | cssselect2 | 0.9.0 | [see below](#cssselect2) | -| deepdiff | 8.6.1 | [see below](#deepdiff) | +| deepdiff | 8.6.2 | [see below](#deepdiff) | | dict2xml | 1.7.8 | [MIT](#dict2xml) | | docraptor | 3.1.0 | [MIT](#docraptor) | | et_xmlfile | 2.0.0 | [MIT](#et_xmlfile) | | fastapi | 0.131.0 | [MIT](#fastapi) | -| fhir_core | 1.1.5 | [BSD license](#fhir_core) | +| fhir_core | 1.1.7 | [BSD license](#fhir_core) | | fhir.resources | 8.2.0 | [BSD license](#fhirresources) | -| fonttools | 4.61.1 | [MIT](#fonttools) | +| fonttools | 4.62.1 | [MIT](#fonttools) | | google-api-core | 2.30.0 | [Apache 2.0](#google-api-core) | -| google-auth | 2.48.0 | [Apache 2.0](#google-auth) | -| googleapis-common-protos | 1.72.0 | [Apache 2.0](#googleapis-common-protos) | +| google-auth | 2.49.1 | [Apache 2.0](#google-auth) | +| googleapis-common-protos | 1.73.0 | [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) | @@ -42,10 +42,10 @@ | MarkupSafe | 3.0.3 | [BSD-3-Clause](#markupsafe) | | msal | 1.35.1 | [MIT](#msal) | | msal-extensions | 1.3.1 | [MIT License](#msal-extensions) | -| neo4j | 5.28.3 | [Apache License, Version 2.0](#neo4j) | -| neomodel | 5.5.3 | [MIT](#neomodel) | +| 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 | 2.4.2 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | +| numpy | 2.4.3 | [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) | @@ -54,16 +54,16 @@ | 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 | 6.33.5 | [3-Clause BSD License](#protobuf) | +| protobuf | 6.33.6 | [3-Clause BSD License](#protobuf) | | psutil | 7.2.2 | [BSD-3-Clause](#psutil) | -| pyasn1 | 0.6.2 | [BSD-2-Clause](#pyasn1) | +| pyasn1 | 0.6.3 | [BSD-2-Clause](#pyasn1) | | pyasn1_modules | 0.4.2 | [BSD](#pyasn1_modules) | | pycparser | 3.0 | [BSD-3-Clause](#pycparser) | | pydantic | 2.12.5 | [MIT](#pydantic) | | pydantic_core | 2.41.5 | [MIT](#pydantic_core) | | pydantic-settings | 2.7.1 | [MIT](#pydantic-settings) | | pydyf | 0.12.1 | [see below](#pydyf) | -| PyJWT | 2.11.0 | [MIT](#pyjwt) | +| PyJWT | 2.12.1 | [MIT](#pyjwt) | | pyphen | 0.17.2 | [see below](#pyphen) | | python-dateutil | 2.9.0.post0 | [Dual License](#python-dateutil) | | python-docx | 1.1.2 | [MIT](#python-docx) | @@ -71,8 +71,7 @@ | python-multipart | 0.0.22 | [Apache-2.0](#python-multipart) | | pytz | 2026.1.post1 | [MIT](#pytz) | | PyYAML | 6.0.3 | [MIT](#pyyaml) | -| requests | 2.32.5 | [Apache-2.0](#requests) | -| rsa | 4.9.1 | [Apache-2.0](#rsa) | +| requests | 2.33.0 | [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) | @@ -9331,22 +9330,8 @@ incurred by, or claims asserted against, such Contributor by reason of your accepting any such warranty or additional liability. ---- -### rsa - - Copyright 2011 Sybren A. Stüvel - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - https://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. + Requests + Copyright 2019 Kenneth Reitz --- ### six diff --git a/studybuilder/public/sbom-studybuilder.md b/studybuilder/public/sbom-studybuilder.md index 19b30790..da5aca4b 100644 --- a/studybuilder/public/sbom-studybuilder.md +++ b/studybuilder/public/sbom-studybuilder.md @@ -240,7 +240,7 @@ | vue-i18n | 11.1.10 | [MIT](#vue-i18n) | | vue-router | 4.6.4 | [MIT](#vue-router) | | vue | 3.5.29 | [MIT](#vue) | -| vuetify | 3.12.2 | [MIT](#vuetify) | +| vuetify | 4.0.2 | [MIT](#vuetify) | | webpack-merge | 5.10.0 | [MIT](#webpack-merge) | | which | 2.0.2 | [ISC](#which) | | wildcard | 2.0.1 | [MIT](#wildcard) | diff --git a/studybuilder/sbom.md b/studybuilder/sbom.md index 19b30790..da5aca4b 100644 --- a/studybuilder/sbom.md +++ b/studybuilder/sbom.md @@ -240,7 +240,7 @@ | vue-i18n | 11.1.10 | [MIT](#vue-i18n) | | vue-router | 4.6.4 | [MIT](#vue-router) | | vue | 3.5.29 | [MIT](#vue) | -| vuetify | 3.12.2 | [MIT](#vuetify) | +| vuetify | 4.0.2 | [MIT](#vuetify) | | webpack-merge | 5.10.0 | [MIT](#webpack-merge) | | which | 2.0.2 | [ISC](#which) | | wildcard | 2.0.1 | [MIT](#wildcard) | diff --git a/studybuilder/src/App.vue b/studybuilder/src/App.vue index 097ce003..9ff94cea 100644 --- a/studybuilder/src/App.vue +++ b/studybuilder/src/App.vue @@ -116,6 +116,7 @@ function navigateToRoot() { diff --git a/studybuilder/src/components/library/ActivitiesTable.vue b/studybuilder/src/components/library/ActivitiesTable.vue index 982ba784..fe3ed3c6 100644 --- a/studybuilder/src/components/library/ActivitiesTable.vue +++ b/studybuilder/src/components/library/ActivitiesTable.vue @@ -95,7 +95,11 @@ + + @@ -538,14 +555,17 @@ fullscreen content-class="fullscreen-dialog" > - diff --git a/studybuilder/src/components/library/ActivityGroupingsSummary.vue b/studybuilder/src/components/library/ActivityGroupingsSummary.vue new file mode 100644 index 00000000..fba40d88 --- /dev/null +++ b/studybuilder/src/components/library/ActivityGroupingsSummary.vue @@ -0,0 +1,185 @@ + + + + + diff --git a/studybuilder/src/components/library/ActivityInstanceClassOverview.vue b/studybuilder/src/components/library/ActivityInstanceClassOverview.vue index 342eba90..38ff7b8a 100644 --- a/studybuilder/src/components/library/ActivityInstanceClassOverview.vue +++ b/studybuilder/src/components/library/ActivityInstanceClassOverview.vue @@ -19,7 +19,7 @@
-

+

{{ $t('ActivityInstanceClassOverview.activity_item_classes') }}

diff --git a/studybuilder/src/components/library/ActivityInstanceClassTable.vue b/studybuilder/src/components/library/ActivityInstanceClassTable.vue index 2ffccc92..4fbe79f4 100644 --- a/studybuilder/src/components/library/ActivityInstanceClassTable.vue +++ b/studybuilder/src/components/library/ActivityInstanceClassTable.vue @@ -302,7 +302,12 @@ const headers = [ ] const fetchAuditTrail = async (options) => { - const resp = await api.getVersions(options) + const data = { + page_number: options.page, + page_size: options.itemsPerPage, + total_count: true, + } + const resp = await api.getVersions(data) return resp.data } diff --git a/studybuilder/src/components/library/ActivityInstanceForm.vue b/studybuilder/src/components/library/ActivityInstanceForm.vue index cb748d63..4bbe246c 100644 --- a/studybuilder/src/components/library/ActivityInstanceForm.vue +++ b/studybuilder/src/components/library/ActivityInstanceForm.vue @@ -11,14 +11,84 @@ @save="submit" > + @@ -558,6 +924,27 @@ onMounted(() => { padding-left: 0; } +.section-header--with-actions { + display: flex; + align-items: center; + justify-content: space-between; + gap: 12px; +} + +.activity-instance-attributes-section { + margin-bottom: 8px; +} + +.section-divider { + margin-top: 20px; + margin-bottom: 20px; +} + +.groupings-action-buttons { + display: flex; + align-items: center; +} + /* Tables styling */ .groupings-table { margin-top: 8px; diff --git a/studybuilder/src/components/library/ActivityInstanceParentClassOverview.vue b/studybuilder/src/components/library/ActivityInstanceParentClassOverview.vue index d89c7f05..eaf139ec 100644 --- a/studybuilder/src/components/library/ActivityInstanceParentClassOverview.vue +++ b/studybuilder/src/components/library/ActivityInstanceParentClassOverview.vue @@ -21,7 +21,7 @@
-

+

{{ $t('ActivityInstanceClassOverview.activity_instance_classes') }} @@ -90,7 +90,7 @@
-

+

{{ $t('ActivityInstanceClassOverview.activity_item_classes') }}

diff --git a/studybuilder/src/components/library/ActivityItemClassField.vue b/studybuilder/src/components/library/ActivityItemClassField.vue index a35ec03d..dd14f0b1 100644 --- a/studybuilder/src/components/library/ActivityItemClassField.vue +++ b/studybuilder/src/components/library/ActivityItemClassField.vue @@ -12,14 +12,12 @@ item-value="uid" return-object :disabled="selectValueOnly || props.disabled" + :rules="[formRules.required]" class="w-50" @update:model-value="resetAndUpdate" /> diff --git a/studybuilder/src/components/library/ActivityItemClassOverview.vue b/studybuilder/src/components/library/ActivityItemClassOverview.vue index 232c0913..b2746225 100644 --- a/studybuilder/src/components/library/ActivityItemClassOverview.vue +++ b/studybuilder/src/components/library/ActivityItemClassOverview.vue @@ -19,7 +19,7 @@
-

+

{{ $t('ActivityItemClassOverview.activity_instance_classes') }}

@@ -88,7 +88,7 @@
-

+

{{ $t('ActivityItemClassOverview.applicable_codelists') }}

diff --git a/studybuilder/src/components/library/ActivityItemClassTable.vue b/studybuilder/src/components/library/ActivityItemClassTable.vue index 22302454..2b92debf 100644 --- a/studybuilder/src/components/library/ActivityItemClassTable.vue +++ b/studybuilder/src/components/library/ActivityItemClassTable.vue @@ -76,7 +76,12 @@ const fetchItems = (filters, options, filtersUpdated) => { } const fetchAuditTrail = async (options) => { - const resp = await api.getVersions(options) + const data = { + page_number: options.page, + page_size: options.itemsPerPage, + total_count: true, + } + const resp = await api.getVersions(data) return resp.data } diff --git a/studybuilder/src/components/library/ActivityItemsTable.vue b/studybuilder/src/components/library/ActivityItemsTable.vue index d86c885d..8689c53d 100644 --- a/studybuilder/src/components/library/ActivityItemsTable.vue +++ b/studybuilder/src/components/library/ActivityItemsTable.vue @@ -3,7 +3,7 @@
-

+

{{ $t('ActivityOverview.activity_items') }}

@@ -38,6 +38,13 @@ .join(', ') }} + + {{ + $t('ActivityInstanceForm.all_terms_in_codelist_named', { + name: item.ct_codelist.name, + }) + }} + 0"> {{ item.ct_terms.map((term) => term.name).join(', ') }} - * + + {{ + $t('ActivityInstanceForm.all_terms_in_codelist_named', { + name: item.ct_codelist.name, + }) + }} + -
@@ -81,7 +94,13 @@ .join(', ') }} - * + + {{ + $t('ActivityInstanceForm.all_terms_in_codelist_named', { + name: item.ct_codelist.name, + }) + }} + -
diff --git a/studybuilder/src/components/library/ActivityOverview.vue b/studybuilder/src/components/library/ActivityOverview.vue index 54cb85aa..73ea1fca 100644 --- a/studybuilder/src/components/library/ActivityOverview.vue +++ b/studybuilder/src/components/library/ActivityOverview.vue @@ -18,15 +18,16 @@ :show-author="true" class="activity-summary" @version-change="(value) => manualChangeVersion(value)" - /> - - - + > + +
-

+

{{ $t('ActivityOverview.instances') }}

diff --git a/studybuilder/src/components/library/ActivitySummary.vue b/studybuilder/src/components/library/ActivitySummary.vue index 4b07f642..17a471e4 100644 --- a/studybuilder/src/components/library/ActivitySummary.vue +++ b/studybuilder/src/components/library/ActivitySummary.vue @@ -89,6 +89,11 @@

+

@@ -1109,6 +1110,29 @@

{% endfor %} + + {% for alias in item_group.aliases %} + + {% endfor %}

Integration
+
+ + + +
@@ -207,7 +212,6 @@ const organizedRows = computed(() => { label: t('_global.version'), value: props.activity.version || '-', }) - // Definition is always shown fields.push({ key: 'definition', @@ -247,7 +251,7 @@ const organizedRows = computed(() => { if (props.showNciConceptId) { fields.push({ key: 'nci_concept_id', - label: t('ActivityForms.nci_concept_id') || 'NCI Concept ID', + label: t('ActivityForms.nci_concept_id'), value: props.activity.nci_concept_id || '-', }) } @@ -255,7 +259,7 @@ const organizedRows = computed(() => { if (props.showNciConceptId) { fields.push({ key: 'nci_concept_name', - label: t('ActivityForms.nci_concept_name') || 'NCI Concept Name', + label: t('ActivityForms.nci_concept_name'), value: props.activity.nci_concept_name || '-', }) } @@ -278,7 +282,7 @@ const organizedRows = computed(() => { if (props.activity.is_legacy_usage !== undefined) { fields.push({ key: 'legacy_usage', - label: t('ActivityInstanceOverview.is_legacy_usage') || 'Legacy usage', + label: t('ActivityInstanceOverview.is_legacy_usage'), value: $filters.yesno(props.activity.is_legacy_usage), }) } @@ -286,7 +290,7 @@ const organizedRows = computed(() => { if (props.activity.adam_param_code !== undefined) { fields.push({ key: 'adam_param_code', - label: t('ActivityInstanceOverview.adam_code') || 'ADoM parameter code', + label: t('ActivityInstanceOverview.adam_code'), value: props.activity.adam_param_code || '-', }) } @@ -294,9 +298,7 @@ const organizedRows = computed(() => { if (props.activity.activity_instance_class !== undefined) { fields.push({ key: 'activity_instance_class', - label: - t('ActivityInstanceOverview.activity_instance_class') || - 'Activity instance class', + label: t('ActivityInstanceOverview.activity_instance_class'), value: props.activity.activity_instance_class || '-', }) } @@ -304,9 +306,7 @@ const organizedRows = computed(() => { if (props.activity.is_required_for_activity !== undefined) { fields.push({ key: 'required_for_activity', - label: - t('ActivityInstanceOverview.is_required_for_activity') || - 'Required for activity', + label: t('ActivityInstanceOverview.is_required_for_activity'), value: $filters.yesno(props.activity.is_required_for_activity), }) } @@ -314,9 +314,7 @@ const organizedRows = computed(() => { if (props.activity.is_default_selected_for_activity !== undefined) { fields.push({ key: 'default_selected_for_activity', - label: - t('ActivityInstanceOverview.is_default_selected_for_activity') || - 'Default selected for activity', + label: t('ActivityInstanceOverview.is_default_selected_for_activity'), value: $filters.yesno(props.activity.is_default_selected_for_activity), }) } @@ -324,7 +322,7 @@ const organizedRows = computed(() => { if (props.activity.topic_code !== undefined) { fields.push({ key: 'topic_code', - label: t('ActivityInstanceOverview.topic_code') || 'Topic code', + label: t('ActivityInstanceOverview.topic_code'), value: props.activity.topic_code || '-', }) } @@ -332,15 +330,26 @@ const organizedRows = computed(() => { if (props.activity.is_data_sharing !== undefined) { fields.push({ key: 'data_sharing', - label: t('ActivityInstanceOverview.is_data_sharing') || 'Data sharing', + label: t('ActivityInstanceOverview.is_data_sharing'), value: $filters.yesno(props.activity.is_data_sharing), }) } + if ( + props.activity.molecular_weight !== undefined && + props.activity.molecular_weight !== null + ) { + fields.push({ + key: 'molecular_weight', + label: t('ActivityInstanceOverview.molecular_weight'), + value: `${props.activity.molecular_weight} g/mol`, + }) + } + if (props.activity.activity_name !== undefined) { fields.push({ key: 'activity_name', - label: t('ActivityInstanceOverview.activity_name') || 'Activity', + label: t('ActivityInstanceOverview.activity_name'), value: props.activity.activity_name || '-', }) } @@ -357,8 +366,7 @@ const organizedRows = computed(() => { if (props.activity.domain_specific !== undefined) { fields.push({ key: 'domain_specific', - label: - t('ActivityInstanceClassOverview.domain_specific') || 'Domain specific', + label: t('ActivityInstanceClassOverview.domain_specific'), value: props.activity.domain_specific || '-', }) } @@ -367,7 +375,7 @@ const organizedRows = computed(() => { if (props.activity.hierarchy_label !== undefined) { fields.push({ key: 'hierarchy', - label: t('ActivityInstanceClassOverview.hierarchy') || 'Hierarchy', + label: t('ActivityInstanceClassOverview.hierarchy'), value: props.activity.hierarchy_label || '-', }) } @@ -376,7 +384,7 @@ const organizedRows = computed(() => { if (props.activity.modified_by !== undefined) { fields.push({ key: 'modified_by', - label: t('_global.modified_by') || 'Modified by', + label: t('_global.modified_by'), value: props.activity.modified_by || '-', }) } @@ -427,6 +435,11 @@ const organizedRows = computed(() => { background: transparent; } +.summary-content { + border-top: 1px solid #e0e0e0; + padding: 0 16px 16px; +} + .summary-label { font-size: 14px; color: var(--semantic-system-brand, #001965); diff --git a/studybuilder/src/components/library/BaseActivityOverview.vue b/studybuilder/src/components/library/BaseActivityOverview.vue index f95352b7..e75692e0 100644 --- a/studybuilder/src/components/library/BaseActivityOverview.vue +++ b/studybuilder/src/components/library/BaseActivityOverview.vue @@ -108,6 +108,8 @@ name="itemForm" :show="showForm" :item="item" + :action-source="source" + :action-subitem="resolveActionSubitem('edit')" :close="closeForm" /> ({}), + }, }, emits: ['closePage', 'refresh'], setup() { @@ -299,6 +305,9 @@ export default { this.fetchItem() }, methods: { + resolveActionSubitem(actionName) { + return this.actionSubitemMap?.[actionName] || null + }, async closeForm() { this.showForm = false this.navigateToVersion(this.item, null) @@ -321,7 +330,11 @@ export default { this.showForm = true }, async inactivateItem() { - await activities.inactivate(this.itemUid, this.source) + await activities.inactivate( + this.itemUid, + this.source, + this.resolveActionSubitem('inactivate') + ) this.notificationHub.add({ msg: this.$t(`ActivitiesTable.inactivate_${this.source}_success`), type: 'success', @@ -330,7 +343,11 @@ export default { await this.fetchItem() }, async reactivateItem() { - await activities.reactivate(this.itemUid, this.source) + await activities.reactivate( + this.itemUid, + this.source, + this.resolveActionSubitem('reactivate') + ) this.notificationHub.add({ msg: this.$t(`ActivitiesTable.reactivate_${this.source}_success`), type: 'success', @@ -356,8 +373,10 @@ export default { ) { options.cascade_edit_and_approve = true } + const approveSource = this.source + const approveSubitem = this.resolveActionSubitem('approve') activities - .approve(this.itemUid, this.source, options) + .approve(this.itemUid, approveSource, options, approveSubitem) .then(async (resp) => { if (this.source === 'activity-sub-groups') { if (resp.data.was_cascade_update_performed) { @@ -386,7 +405,11 @@ export default { }) }, async newItemVersion() { - await activities.newVersion(this.itemUid, this.source) + await activities.newVersion( + this.itemUid, + this.source, + this.resolveActionSubitem('newVersion') + ) this.notificationHub.add({ msg: this.$t('_global.new_version_success'), type: 'success', diff --git a/studybuilder/src/components/library/BaseTemplateForm.vue b/studybuilder/src/components/library/BaseTemplateForm.vue index 239ab4dc..e672fca0 100644 --- a/studybuilder/src/components/library/BaseTemplateForm.vue +++ b/studybuilder/src/components/library/BaseTemplateForm.vue @@ -27,7 +27,7 @@ -

+

{{ $t('_global.plain_text_version') }}

@@ -43,7 +43,7 @@ data-cy="verify-syntax-button" color="white" variant="outlined" - elevation="2" + elevation="1" rounded="xl" @click="verifySyntax" > diff --git a/studybuilder/src/components/library/CodelistSummary.vue b/studybuilder/src/components/library/CodelistSummary.vue index 40ffb320..b185817a 100644 --- a/studybuilder/src/components/library/CodelistSummary.vue +++ b/studybuilder/src/components/library/CodelistSummary.vue @@ -3,7 +3,7 @@ {{ $t('CodelistSummary.title') }} diff --git a/studybuilder/src/components/library/CodelistTable.vue b/studybuilder/src/components/library/CodelistTable.vue index c29c15b2..20ee032d 100644 --- a/studybuilder/src/components/library/CodelistTable.vue +++ b/studybuilder/src/components/library/CodelistTable.vue @@ -71,26 +71,21 @@ {{ termslabel }}
- + (+{{ selectedTerms.length - 1 }}) -