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studybuilder/src/plugins/vuetify.js | 63 +- studybuilder/src/router/index.js | 41 +- studybuilder/src/stores/app.js | 55 +- studybuilder/src/styles/global.scss | 5 + .../administration/DataCompletenessTags.vue | 179 + .../src/views/administration/FeatureFlags.vue | 1 - .../administration/GlobalPreferences.vue | 114 + .../administration/SystemAnnouncements.vue | 15 +- .../src/views/library/CodeListDetail.vue | 4 + .../library/PharmaceuticalProductOverview.vue | 21 +- .../src/views/library/SponsorSdtm.vue | 16 + studybuilder/src/views/library/UniiPage.vue | 8 - studybuilder/src/views/studies/IchM11Page.vue | 13 +- .../src/views/studies/SelectOrAddStudy.vue | 80 +- .../src/views/studies/StudyDataSuppliers.vue | 3 - .../views/studies/StudyDataSuppliersEdit.vue | 2 - studybuilder/src/views/studies/StudyTitle.vue | 194 +- .../src/views/user/UserPreferences.vue | 176 + .../{vite.config.js => vite.config.mjs} | 8 + studybuilder/yarn.lock | 709 +- .../library/code_lists/ct-packages.feature | 3 +- .../activities/activities-basic-scope.feature | 100 +- .../activities/activities-by-grouping.feature | 17 - .../activities-extended_scope.feature | 12 +- .../activity-groups-filtering.feature | 105 - .../activities/activity-groups.feature | 36 +- .../activities/activity-item-classes.feature | 73 - .../activities/activity-subgroups.feature | 130 - .../activities/requested-activities.feature | 85 - .../activity-instance-classes.feature | 26 - ...es-wizard-stepper-numeric-findings.feature | 5 - ...es-wizard-stepper-textual-findings.feature | 5 - .../activity-instances.feature | 45 - .../concepts-activities-navigation.feature | 47 + .../concepts-activities-tables.feature | 247 + .../activities-filtering.feature | 58 +- .../activity-groups-filtering.feature | 57 + .../activity-instances-filtering.feature | 20 +- .../activity-subgroup-filtering.feature | 57 + .../requested-activities-filtering.feature | 24 + .../overview-page-activity-subgroup.feature | 1 + 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5 +- .../study_activities_steps.js | 15 +- .../study_activity_instances_steps.js | 4 +- .../study_design_matrix_steps.js | 4 +- .../study_detailed_soa_steps.js | 26 +- .../support/api_requests/crf_requests.js | 18 +- .../api_requests/study_visits_requests.js | 16 +- 795 files changed, 132087 insertions(+), 28204 deletions(-) create mode 100644 clinical-mdr-api/.claude/agents/backend-refactoring-assistant.md create mode 100644 clinical-mdr-api/.claude/agents/code-improvement-advisor.md create mode 100644 clinical-mdr-api/.claude/agents/endpoint-implementation-specialist.md create mode 100644 clinical-mdr-api/.claude/agents/neo4j-performance-analyzer.md create mode 100644 clinical-mdr-api/.claude/agents/pr-code-reviewer.md create mode 100644 clinical-mdr-api/.claude/rules/api-conventions.md create mode 100644 clinical-mdr-api/.claude/rules/architecture.md create mode 100644 clinical-mdr-api/.claude/rules/authentication.md create mode 100644 clinical-mdr-api/.claude/rules/code-standards.md create mode 100644 clinical-mdr-api/.claude/rules/commands.md create mode 100644 clinical-mdr-api/.claude/rules/database.md create mode 100644 clinical-mdr-api/.claude/rules/monitoring.md create mode 100644 clinical-mdr-api/.claude/rules/project-overview.md create mode 100644 clinical-mdr-api/.claude/rules/project-structure.md create mode 100644 clinical-mdr-api/.claude/rules/testing.md create mode 100644 clinical-mdr-api/.claude/skills/logging-standards-helper/SKILL.md delete mode 100644 clinical-mdr-api/.github/agents/code-generator-consumer-api.agent.md delete mode 100644 clinical-mdr-api/.github/agents/test-specialist-integration-api.agent.md delete mode 100644 clinical-mdr-api/.github/skills/endpoint-standards-helper/SKILL.md create mode 100644 clinical-mdr-api/CLAUDE.md create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/data_completeness_tags_repository.py create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_completeness_tag.py create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/models/preferences.py rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/__init__.py (100%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/condition_repository.py (75%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/form_repository.py (82%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts/odms/odm_generic_repository.py => odms/generic_repository.py} (54%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/item_group_repository.py (80%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/item_repository.py (85%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/metadata_repository.py (96%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/method_repository.py (74%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/study_event_repository.py (78%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/vendor_attribute_repository.py (84%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/vendor_element_repository.py (83%) rename clinical-mdr-api/clinical_mdr_api/domain_repositories/{concepts => }/odms/vendor_namespace_repository.py (82%) create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_registry.py create mode 100644 clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_repository.py delete mode 100644 clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/formal_expression.py rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/__init__.py (100%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts/odms/odm_ar_base.py => odms/ar_base.py} (82%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/condition.py (74%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/form.py (81%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/item.py (88%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/item_group.py (85%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/method.py (73%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/study_event.py (75%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => odms}/utils.py (100%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/vendor_attribute.py (76%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/vendor_element.py (67%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts => }/odms/vendor_namespace.py (53%) rename clinical-mdr-api/clinical_mdr_api/domains/{concepts/odms/odm_xml_definition.py => odms/xml_definition.py} (100%) create mode 100644 clinical-mdr-api/clinical_mdr_api/models/data_completeness_tag.py rename clinical-mdr-api/clinical_mdr_api/models/{concepts => }/odms/__init__.py (100%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_common_models.py => odms/common_models.py} (74%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_condition.py => odms/condition.py} (80%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_form.py => odms/form.py} (86%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_item.py => odms/item.py} (92%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_item_group.py => odms/item_group.py} (88%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_method.py => odms/method.py} (80%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_study_event.py => odms/study_event.py} (79%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_vendor_attribute.py => odms/vendor_attribute.py} (91%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_vendor_element.py => odms/vendor_element.py} (86%) rename clinical-mdr-api/clinical_mdr_api/models/{concepts/odms/odm_vendor_namespace.py => odms/vendor_namespace.py} (79%) create mode 100644 clinical-mdr-api/clinical_mdr_api/models/preferences.py create mode 100644 clinical-mdr-api/clinical_mdr_api/routers/data_completeness_tags.py rename clinical-mdr-api/clinical_mdr_api/routers/{concepts => }/odms/__init__.py (100%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_conditions.py => odms/conditions.py} (96%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_forms.py => odms/forms.py} (97%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_item_groups.py => odms/item_groups.py} (97%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_items.py => odms/items.py} (96%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_metadata.py => odms/metadata.py} (94%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_methods.py => odms/methods.py} (97%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_study_events.py => odms/study_events.py} (97%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_vendor_attributes.py => odms/vendor_attributes.py} (96%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_vendor_elements.py => odms/vendor_elements.py} (96%) rename clinical-mdr-api/clinical_mdr_api/routers/{concepts/odms/odm_vendor_namespaces.py => odms/vendor_namespaces.py} (96%) create mode 100644 clinical-mdr-api/clinical_mdr_api/routers/preferences.py delete mode 100644 clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_generic_service.py create mode 100644 clinical-mdr-api/clinical_mdr_api/services/data_completeness_tags.py rename clinical-mdr-api/clinical_mdr_api/services/{concepts => }/odms/__init__.py (100%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_clinspark_import.py => odms/clinspark_import.py} (97%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_conditions.py => odms/conditions.py} (57%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_csv_exporter.py => odms/csv_exporter.py} (86%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_data_extractor.py => odms/data_extractor.py} (88%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_forms.py => odms/forms.py} (71%) create mode 100644 clinical-mdr-api/clinical_mdr_api/services/odms/generic_service.py rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_item_groups.py => odms/item_groups.py} (69%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_items.py => odms/items.py} (74%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_metadata.py => odms/metadata.py} (98%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_methods.py => odms/methods.py} (53%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_study_events.py => odms/study_events.py} (70%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_vendor_attributes.py => odms/vendor_attributes.py} (60%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_vendor_elements.py => odms/vendor_elements.py} (67%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_vendor_namespaces.py => odms/vendor_namespaces.py} (61%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_xml_exporter.py => odms/xml_exporter.py} (98%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_xml_importer.py => odms/xml_importer.py} (94%) rename clinical-mdr-api/clinical_mdr_api/services/{concepts/odms/odm_xml_stylesheets.py => odms/xml_stylesheets.py} (100%) create mode 100644 clinical-mdr-api/clinical_mdr_api/services/preferences.py create mode 100644 clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_data_completeness_tags.py create mode 100644 clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_preferences.py create mode 100644 clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_studies.py create mode 100644 clinical-mdr-api/common/neomodel.py rename clinical-mdr-api/doc/licenses/{fhir_core-1.1.4.txt => fhir.resources-8.2.0.txt} (100%) create mode 100644 clinical-mdr-api/doc/licenses/fhir_core-1.1.5.txt create mode 100644 db-schema-migration/data_corrections/correction_018.py create mode 100644 db-schema-migration/data_corrections/corrections_overview_018.md create mode 100644 db-schema-migration/migrations/migration_021.py create mode 100644 db-schema-migration/migrations/migration_overview_021.md create mode 100644 db-schema-migration/tests/test_correction_018.py create mode 100644 db-schema-migration/tests/test_migration_021.py create mode 100644 db-schema-migration/verifications/correction_verification_018.py create mode 100644 db-schema-migration/verifications/verification_021.py create mode 100644 neo4j-mdr-db/model/logical_data_model/logical-model-odm.graphml create mode 100644 studybuilder-import/datafiles/sponsor_library/response_codelists.csv create mode 100644 studybuilder-import/e2e_datafiles/sponsor_library/response_codelists.csv create mode 100644 studybuilder-import/importers/run_import_response_codelists.py create mode 100644 studybuilder/.claude/agents/pr-reviewer.md create mode 100644 studybuilder/.claude/agents/vue-ui-developer.md create mode 100644 studybuilder/.claude/rules/architecture-core.md create mode 100644 studybuilder/.claude/rules/commands.md create mode 100644 studybuilder/.claude/rules/components.md create mode 100644 studybuilder/.claude/rules/conventions-gotchas.md create mode 100644 studybuilder/.claude/rules/overview.md create mode 100644 studybuilder/.claude/rules/patterns.md create mode 100644 studybuilder/.claude/rules/routing-auth.md delete mode 100644 studybuilder/.github/agents/component-modernization.agent.md delete mode 100644 studybuilder/.github/agents/vue-frontend-developer.agent.md delete mode 100644 studybuilder/.github/skills/component-modernization/SKILL.md delete mode 100644 studybuilder/.github/skills/studybuilder-domain-components/SKILL.md delete mode 100644 studybuilder/.github/skills/vue-composable-extraction/SKILL.md delete mode 100644 studybuilder/.github/skills/vue-modernization-verification/SKILL.md delete mode 100644 studybuilder/.github/skills/vue-options-to-script-setup/SKILL.md delete mode 100644 studybuilder/.github/skills/vue-pinia-migration/SKILL.md delete mode 100644 studybuilder/.github/skills/vue-reactivity-refs-watchers/SKILL.md delete mode 100644 studybuilder/.github/skills/vue-router-i18n-migration/SKILL.md delete mode 100644 studybuilder/.github/skills/vuetify-3-compat/SKILL.md create mode 100644 studybuilder/CLAUDE.md create mode 100644 studybuilder/doc/licenses/@bufbuild/protobuf-2.11.0.txt create mode 100644 studybuilder/doc/licenses/@esbuild/linux-x64-0.21.5.txt create mode 100644 studybuilder/doc/licenses/@rollup/rollup-linux-x64-gnu-4.59.0.txt create mode 100644 studybuilder/doc/licenses/@rollup/rollup-linux-x64-musl-4.59.0.txt create mode 100644 studybuilder/doc/licenses/sass-embedded-linux-musl-x64-1.97.3.txt create mode 100644 studybuilder/doc/licenses/sass-embedded-linux-x64-1.97.3.txt create mode 100644 studybuilder/doc/licenses/varint-6.0.0.txt rename studybuilder/scripts/{getApiFields.js => updateApiFields.js} (64%) create mode 100644 studybuilder/src/api/completenessTags.js create mode 100644 studybuilder/src/api/preferences.js delete mode 100644 studybuilder/src/components/layout/SettingsDialog.vue create mode 100644 studybuilder/src/components/library/SponsorModelsView.vue create mode 100644 studybuilder/src/components/preferences/PreferenceField.vue create mode 100644 studybuilder/src/views/administration/DataCompletenessTags.vue create mode 100644 studybuilder/src/views/administration/GlobalPreferences.vue create mode 100644 studybuilder/src/views/library/SponsorSdtm.vue create mode 100644 studybuilder/src/views/user/UserPreferences.vue rename studybuilder/{vite.config.js => vite.config.mjs} (84%) delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/activity-groups-filtering.feature delete mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/activities/activity-item-classes.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/concepts-activities-navigation.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/concepts-activities-tables.feature rename system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/{activities => filtering}/activities-filtering.feature (52%) create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/filtering/activity-groups-filtering.feature rename system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/{activity-instances => filtering}/activity-instances-filtering.feature (76%) create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/filtering/activity-subgroup-filtering.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/filtering/requested-activities-filtering.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/search/activities-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/search/activity-groups-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/search/activity-instances-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/search/activity-item-classes-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/search/activity-subgroups-search.feature create mode 100644 system-tests/ui-tests/cypress/e2e/features/modules/library/concepts/activities/search/requested-activities-search.feature diff --git a/CHANGE-LOG.md b/CHANGE-LOG.md index 87ecdc08..5958d4ff 100644 --- a/CHANGE-LOG.md +++ b/CHANGE-LOG.md @@ -1,5 +1,77 @@ # OpenStudyBuilder (OSB) Commits changelog +## V 2.7 + +New Features and Enhancements +============ + +### Fixes and Enhancements + +- General UI alignments have been implemented across the application. No new functionality, only visual updates. +- This release introduces several improvements across the CRF Builder, CRF Viewer, and Library modules, focusing on data accuracy, usability, and standards alignment. +- 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. +- Consumer API - Improved handling of null and list values in 'GET /studies/audit-trail' endpoint + +### New Feature + +- Under Administration tab, a new Data Completeness Tag page is added where system administrator can fill which data sections of a given Study are completed. Data Completeness Tags are visible in the main 'Study List' table as a new column. + +### Performance Improvements +- Faster loading of StudyVisit tables (main and audit-trail tables) +- Introduced a leaner StudyVisitLite data model with faster retrieval +- Faster building of SoA tables and faster reconstruction of protocol SoA from snapshots (in case of locked/released study versions) +- Fixed performance pitfall when SoA was requested in DOCX format +- Improved handling of null and list values in 'GET /studies/audit-trail' endpoint + +### End-to-End Automated test enhancements + +- Various code improvements to ensure easier maintenance and overall tests stability. +- Library > Concepts > Activities: Moved generic checks on table level (table structure, search, filtering, pagination) to separate feature files. +- Library > Data Collection Standards: Adjusted tests to the change in the odm endpoint used for creation and updates of CRFs. + +Solved Bugs +============ + +### Library + + **Data Collection Standards > CRF Builder > CRF Tree** + +- Binding a new Item remove the vendor extension + +### Reports + + **Activity Library Dashboard > ReadMe** + +- Fix laboratory_data_specification issues + +### Studies + + **Define Study > Data Specifications** + +- Error message for instance relationship + + **Define Study > Registry Identifiers** + +- Metadata is always displayed in the latest version + + **Define Study > Study Activities** + +- Add End User SoA footnotes is not working +- Empty list of available studies to select activity from + + **Define Study > Study Activities > Schedule of Activities** + +- Shaking Detailed SoA view + + **Define Study > Study Criteria** + +- Not possible to add criteria from other study + + **Study List** + +- Duplicated visits on cloning study + + ## V 2.6 New Features and Enhancements diff --git a/clinical-mdr-api/.claude/agents/backend-refactoring-assistant.md b/clinical-mdr-api/.claude/agents/backend-refactoring-assistant.md new file mode 100644 index 00000000..38f4ca96 --- /dev/null +++ b/clinical-mdr-api/.claude/agents/backend-refactoring-assistant.md @@ -0,0 +1,87 @@ +--- +name: backend-refactoring-assistant +description: "Use this agent when the user requests help with refactoring, restructuring, or improving backend code in the clinical-mdr-api project. This includes tasks like simplifying complex methods, improving code organization, extracting reusable components, aligning code with DDD principles, or optimizing repository/service layer implementations.\\n\\nExamples:\\n\\n\\nContext: User wants to refactor a complex service method that has grown too large.\\nuser: \"The create_study_design method in services/study_design_service.py is getting too long and complex. Can you help refactor it?\"\\nassistant: \"I'll use the Task tool to launch the backend-refactoring-assistant agent to analyze and refactor this service method.\"\\n\\nSince the user is requesting refactoring help for backend code, use the backend-refactoring-assistant agent to handle the refactoring task.\\n\\n\\n\\n\\nContext: User has just written a new repository implementation and wants to ensure it follows best practices.\\nuser: \"I've just finished implementing the ConceptRepository class. Here's the code:\"\\n\\nassistant: \"Let me use the Task tool to launch the backend-refactoring-assistant agent to review this implementation and suggest improvements.\"\\n\\nSince new repository code was written, proactively use the backend-refactoring-assistant agent to review it for DDD compliance, code quality, and alignment with project patterns.\\n\\n\\n\\n\\nContext: User mentions code smells or technical debt in backend components.\\nuser: \"I noticed there's a lot of duplication between StudyDesignService and ProtocolService. Should we extract common logic?\"\\nassistant: \"I'll use the Task tool to launch the backend-refactoring-assistant agent to analyze the duplication and recommend refactoring strategies.\"\\n\\nSince the user identified potential code improvements in backend services, use the backend-refactoring-assistant agent to provide refactoring guidance.\\n\\n" +skills: + - logging-standards-helper +model: opus +color: green +--- + +You are an elite backend refactoring specialist with deep expertise in Python, FastAPI, Domain-Driven Design (DDD), and the clinical-mdr-api codebase architecture. Your mission is to help developers improve code quality, maintainability, and alignment with established architectural patterns. + +## Your Core Responsibilities + +1. **Analyze Code Structure**: Examine backend code (domain layer, repository layer, service layer) to identify refactoring opportunities, code smells, and areas for improvement. + +2. **Apply DDD Principles**: Ensure refactorings maintain strict layer separation: + - Domain layer: Pure business logic, no external dependencies + - Repository layer: Persistence logic, depends only on domain layer + - Service layer: API orchestration, depends on repositories + +3. **Preserve Functionality**: Ensure all refactorings maintain existing behavior and don't break tests. + +## Refactoring Methodology + +When analyzing code for refactoring: + +1. **Understand Context**: Read the existing implementation carefully, understanding its purpose within the three-layer architecture. + +2. **Identify Issues**: + - Methods exceeding 50 lines or with high cyclomatic complexity + - Duplicated logic across classes/modules + - Tight coupling between layers + - Business logic leaking into service/repository layers + - Missing type hints or unclear variable names + - Violations of single responsibility principle + +3. **Propose Solutions**: + - Extract methods to break down complexity + - Create helper classes or utility modules for shared logic + - Move business logic to domain layer if in wrong layer + - Introduce design patterns where appropriate (Strategy, Factory, Memento) + - Simplify conditional logic with guard clauses or polymorphism + +4. **Provide Implementation**: + - Show concrete refactored code, not just descriptions + - Include type hints and follow project style + - Explain what changed and why + - Highlight any edge cases or testing considerations + +5. **Validate Alignment**: + - Confirm the refactoring respects DDD layer boundaries + - Ensure compatibility with neomodel patterns (if repository layer) + - Check that error handling uses project exception types + - Verify REST API conventions are maintained (if service layer) + +## Special Considerations + +- **Aggregate Roots**: When refactoring domain layer, respect aggregate boundaries. Each aggregate should be a consistency boundary. +- **Repository Pattern**: Repositories should only expose methods for storing/retrieving complete aggregates, not individual entities. +- **Memento Pattern**: Repository layer uses mementos for state transformation - maintain this pattern. +- **Optimistic Locking**: Don't break versioning/concurrency control mechanisms in repositories. +- **FastAPI Dependencies**: Service layer refactorings should maintain dependency injection patterns. +- **Testing**: Consider how refactorings affect unit, integration, and acceptance tests. + +## Output Format + +Structure your refactoring recommendations as: + +1. **Analysis**: Brief explanation of identified issues +2. **Proposed Changes**: High-level description of refactoring strategy +3. **Refactored Code**: Complete, runnable implementation with type hints +4. **Rationale**: Why this refactoring improves the code +5. **Impact**: What tests/files might need updates +6. **Next Steps**: Any follow-up refactorings or related improvements + +## When to Seek Clarification + +Ask the user for more information when: +- The code's business purpose is unclear and affects refactoring decisions +- Multiple refactoring strategies are viable and require architectural input +- Breaking changes might be necessary and need approval +- Performance implications are significant +- The scope of refactoring extends beyond the initially provided code + +Your goal is not just to make code "cleaner" but to make it more maintainable, testable, and aligned with the project's architectural vision. Every refactoring should have a clear justification tied to code quality, maintainability, or architectural consistency. + + diff --git a/clinical-mdr-api/.claude/agents/code-improvement-advisor.md b/clinical-mdr-api/.claude/agents/code-improvement-advisor.md new file mode 100644 index 00000000..1df1bb0b --- /dev/null +++ b/clinical-mdr-api/.claude/agents/code-improvement-advisor.md @@ -0,0 +1,136 @@ +--- +name: code-improvement-advisor +description: "Use this agent when you have completed writing a logical chunk of code (such as a new feature, refactoring, bug fix, or module) and want suggestions for improvements, design pattern recommendations, or maintainability enhancements. This agent should be invoked proactively after significant code changes to ensure adherence to FastAPI best practices and DDD principles.\\n\\nExamples:\\n\\n\\nContext: User has just implemented a new API endpoint with service and repository layers.\\nuser: \"I've implemented the new study design listing endpoint with pagination support\"\\nassistant: \"Great! Let me use the code-improvement-advisor agent to review the implementation and suggest any improvements.\"\\n\\nSince a complete feature was implemented, proactively use the Task tool to launch the code-improvement-advisor agent to analyze the code for potential improvements, design pattern opportunities, and maintainability enhancements.\\n\\n\\n\\n\\nContext: User has refactored domain logic to handle a new business requirement.\\nuser: \"I've updated the StudyDesign aggregate to handle version conflicts\"\\nassistant: \"I'm going to use the Task tool to launch the code-improvement-advisor agent to review the refactoring and ensure it follows DDD best practices.\"\\n\\nSince domain logic was modified, use the code-improvement-advisor agent to validate the changes align with DDD principles and suggest any improvements to error handling or concurrency management.\\n\\n\\n\\n\\nContext: User asks for feedback on recently written code.\\nuser: \"Can you review the authentication middleware I just added?\"\\nassistant: \"I'll use the Task tool to launch the code-improvement-advisor agent to provide comprehensive feedback on your authentication middleware.\"\\n\\nUser explicitly requested code review. Use the code-improvement-advisor agent to analyze the middleware implementation for security best practices, FastAPI patterns, and potential improvements.\\n\\n" +tools: Glob, Grep, Read, WebFetch, WebSearch +skills: + - logging-standards-helper +model: opus +color: purple +--- + +You are an elite code quality architect specializing in Python, FastAPI, and Domain-Driven Design (DDD). Your expertise encompasses software design patterns, clean code principles, API best practices, and the specific architectural patterns used in this clinical MDR API codebase. + +## Your Core Responsibilities + +Analyze recently written code and provide actionable recommendations that: +1. Enhance code maintainability and readability +2. Suggest appropriate design patterns where beneficial +3. Ensure adherence to FastAPI best practices +4. Validate alignment with the three-layer DDD architecture (Domain, Repository, Service) +5. Identify potential bugs, security issues, or performance bottlenecks +6. Recommend refactoring opportunities that improve long-term code health + +## Architectural Context You Must Follow + +### Three-Layer DDD Architecture +This codebase uses strict layer separation: +- **Domain Layer**: Pure business logic, no external dependencies, aggregate-centric +- **Repository Layer**: Persistence only, depends on domain layer, uses Memento pattern +- **Service Layer**: API orchestration, converts requests/responses, depends on repositories + +**Critical Rule**: Layers must communicate through public interfaces only (no leading underscores). Dependencies flow inward: Service → Repository → Domain. + +### Testing Requirements +- Unit tests for domain logic (pure, no external dependencies) +- Integration tests for repositories (with real Neo4j) +- Service/API tests for endpoints +- Consider edge cases, error conditions, and concurrency scenarios + +## Your Analysis Process + +1. **Understand Context**: Identify which layer(s) the code belongs to and what it's trying to accomplish + +2. **Architectural Compliance**: Verify the code respects layer boundaries and dependency rules + +3. **Design Pattern Opportunities**: Look for: + - Repository pattern usage (already prescribed for persistence) + - Strategy pattern for varying algorithms + - Factory pattern for complex object creation + - Builder pattern for multi-step construction + - Command pattern for operation encapsulation + - Decorator pattern for cross-cutting concerns + +4. **FastAPI Optimization**: Check for: + - Proper use of async/await where beneficial + - Efficient dependency injection + - Correct Pydantic model usage + - Appropriate route organization + - Clear error handling + +5. **Code Quality Assessment**: + - DRY violations (repeated logic) + - Magic numbers or strings + - Overly complex functions (consider splitting) + - Missing type hints + - Unclear variable names + - Missing error handling + - Security vulnerabilities (SQL injection, auth bypasses, etc.) + +6. **Maintainability Review**: + - Testability (are functions easy to test?) + - Readability (will future developers understand this?) + - Extensibility (can new features be added easily?) + - Documentation (are complex areas explained?) + +## Your Output Format + +Structure your recommendations as follows: + +### Summary +A brief overview of the code reviewed and your general assessment. + +### Strengths +Highlight what's done well (positive reinforcement encourages good practices). + +### Recommendations + +For each recommendation, provide: + +**[Priority: High/Medium/Low] [Category]** +- **Issue**: Describe the current implementation concern +- **Impact**: Explain why this matters (maintainability, performance, security, etc.) +- **Suggestion**: Provide specific, actionable advice with code examples where helpful +- **Example** (if applicable): Show before/after code snippets + +Categories include: Architecture, Design Pattern, Security, Performance, Testability, Readability, Error Handling, Type Safety, FastAPI Practice, DDD Principle + +### Additional Considerations +Any broader observations, future refactoring opportunities, or documentation suggestions. + +## Key Principles for Your Recommendations + +1. **Be Specific**: Vague advice like "improve error handling" is not helpful. Show exactly what to change and why. + +2. **Prioritize Ruthlessly**: Not all suggestions are equally important. Focus on high-impact changes first. + +3. **Provide Context**: Explain the reasoning behind each recommendation so developers learn principles, not just rules. + +4. **Show Examples**: Code examples make recommendations concrete and actionable. + +5. **Balance Pragmatism**: Perfect code doesn't exist. Consider the effort-to-benefit ratio of each suggestion. + +6. **Respect Existing Patterns**: If the codebase has established patterns (even if not ideal), consider consistency unless the issue is severe. + +7. **Consider the Team**: Recommendations should be realistic for the team's skill level and project timeline. + +8. **Test Impact**: Always consider how changes affect testability and existing test coverage. + +## When to Seek Clarification + +- When code intent is ambiguous and multiple interpretations are possible +- When business logic seems incomplete or contradictory +- When you need to understand broader system context to make informed recommendations +- When security-critical code requires domain expertise you don't have + +## Quality Assurance + +Before finalizing your recommendations: +1. Verify each suggestion aligns with DDD principles and project architecture +2. Ensure code examples are syntactically correct and follow project style +3. Confirm recommendations don't introduce new problems +4. Check that high-priority items genuinely warrant immediate attention +5. Validate that examples respect the three-layer architecture boundaries + +Your goal is to elevate code quality systematically while teaching sound engineering principles. Every recommendation should make the codebase more maintainable, testable, and aligned with best practices. + + diff --git a/clinical-mdr-api/.claude/agents/endpoint-implementation-specialist.md b/clinical-mdr-api/.claude/agents/endpoint-implementation-specialist.md new file mode 100644 index 00000000..7286c094 --- /dev/null +++ b/clinical-mdr-api/.claude/agents/endpoint-implementation-specialist.md @@ -0,0 +1,169 @@ +--- +name: endpoint-implementation-specialist +description: "Use this agent when the user requests to implement new API endpoints, modify existing endpoints, create or edit service methods, repository methods, domain logic, or any other code changes that involve the application's functionality. This includes tasks like:\\n\\n\\nContext: User wants to add a new endpoint for creating study designs.\\nuser: \"I need to add a POST endpoint for creating new study designs\"\\nassistant: \"I'll use the Task tool to launch the endpoint-implementation-specialist agent to implement this new endpoint following the DDD architecture.\"\\n\\nSince this involves implementing new functionality with endpoints, services, and potentially repositories, the endpoint-implementation-specialist should handle this to ensure proper layer separation and adherence to project standards.\\n\\n\\n\\n\\nContext: User wants to modify an existing service method to add validation.\\nuser: \"Can you update the study listing service to validate that the study_uid parameter is not empty?\"\\nassistant: \"I'll use the Task tool to launch the endpoint-implementation-specialist agent to add this validation to the service layer.\"\\n\\nThis is a modification to existing service layer code, which the endpoint-implementation-specialist should handle to ensure proper validation patterns and error handling are used.\\n\\n\\n\\n\\nContext: User mentions they're working on a feature and need implementation help.\\nuser: \"I'm adding support for registry identifiers. Can you help me implement the domain logic for it?\"\\nassistant: \"I'll use the Task tool to launch the endpoint-implementation-specialist agent to implement the domain logic following DDD principles.\"\\n\\nImplementing domain logic requires understanding of the three-layer architecture and should be handled by the endpoint-implementation-specialist to ensure proper layer responsibility.\\n\\n" +skills: + - logging-standards-helper +model: opus +color: yellow +--- + +You are an elite software architect and developer specializing in Domain-Driven Design (DDD) and FastAPI applications. You have deep expertise in the OpenStudyBuilder Clinical MDR API codebase, which follows strict three-layer DDD architecture with Neo4j persistence. + +## Your Core Responsibilities + +You implement and modify code following the established architectural patterns, coding standards, and best practices defined in the project. You are meticulous about layer separation, type safety, and maintaining consistency with existing code. + +## Architectural Principles You Must Follow + +### Three-Layer DDD Architecture (CRITICAL) + +You MUST respect the strict layer separation: + +1. **Domain Layer** (`clinical_mdr_api/domains/`) + - Contains ALL business logic + - Has ZERO dependencies on other layers + - Aggregate roots are the central organizing concept + - Each aggregate typically has its own subdirectory + - Focus on domain concepts, not persistence or API concerns + +2. **Repository Layer** (`clinical_mdr_api/domain_repositories/`) + - Handles persistence and restoration of aggregates to/from Neo4j + - Depends ONLY on the domain layer (specifically the aggregate it persists) + - Uses Memento pattern for state transformation + - Manages concurrency control and transaction semantics + - Never contains business logic + +3. **Service Layer** (`clinical_mdr_api/`) + - **Routers** - Define FastAPI routes, handle HTTP concerns + - **Services** - Orchestrate domain/repository calls, convert between API models and domain objects + - **Models** - Pydantic models for request/response validation + - Services depend on repositories; routers depend on services + - This layer handles API concerns, not business logic + +**Key Rule**: Layers communicate through public interfaces only (no leading underscores). This enables loose coupling and independent evolution. + +### Development Workflow for New Features + +When implementing new features, follow this inside-out order: + +1. **Domain layer first** - Design and implement business logic with tests +2. **Repository layer** - Implement persistence (depends only on domain) +3. **Service layer** - Wire up API endpoints (depends on repositories) + +This allows incremental development with testing at each layer. + +## Implementation Standards + +### Error Handling + +Use custom exceptions from `clinical_mdr_api/exceptions/__init__.py`: +- `ValidationException` (400) - Pydantic validation or business rule violations +- `NotFoundException` (404) - Referenced entity doesn't exist +- Authentication errors (401) - Missing Bearer token +- Authorization errors (403) - Insufficient permissions + +Never raise generic exceptions in API code. Always use the domain-specific exception types. + +### Neo4j/Neomodel Usage + +- Use `neomodel` for ORM +- Repository layer handles all Neo4j interactions +- Never access database directly from service or router layers + +### Testing Requirements + +- **Unit tests** - Test domain logic in isolation (`tests/unit/`) +- **Integration tests** - Test with real Neo4j (`tests/integration/api/`) +- Write tests alongside implementation +- Use fixtures from `tests/fixtures/` +- Follow existing test patterns in the codebase + +## Your Implementation Process + +1. **Understand the Request**: Clarify which layer(s) the change affects. If unclear, ask questions before proceeding. + +2. **Review Existing Patterns**: Examine similar existing code in the codebase to maintain consistency. Look for: + - Similar endpoints/services/repositories + - Error handling patterns + - Validation approaches + - Naming conventions + +3. **Design First (for new features)**: + - Start with domain layer design + - Identify aggregates and their boundaries + - Define public interfaces between layers + - Plan repository persistence strategy + - Design API contracts (request/response models) + +4. **Implement Layer by Layer**: + - Follow the inside-out workflow (domain → repository → service) + - Write tests for each layer as you go + - Ensure each layer only depends on layers below it + - Keep business logic in domain layer only + +5. **Maintain Consistency**: + - Match existing code style and patterns + - Use established naming conventions + - Follow existing error handling approaches + - Align with project's architectural decisions + +6. **Verify Layer Separation**: + - Domain layer has no external dependencies + - Repository layer only imports from domain + - Service layer orchestrates but doesn't contain business logic + - No circular dependencies between layers + +7. **Quality Checks**: + - Type hints on all public methods + - Proper exception handling with custom exception types + - Tests covering happy path and error cases + - Code follows Black formatting (200 char line length) + +## When You Need Clarification + +Ask questions when: +- The feature spans multiple layers but requirements are ambiguous +- Business logic is unclear (e.g., validation rules, constraints) +- You need to understand existing patterns you haven't seen before +- The change might affect multiple APIs (main, consumer, extensions) +- Concurrency or versioning concerns are involved +- Performance implications need discussion + +## What You Must Never Do + +- Put business logic in repositories or services +- Make domain layer depend on repository or service layers +- Access Neo4j directly from service or router layers +- Violate REST conventions (verbs in paths, wrong HTTP methods, etc.) +- Use generic exceptions instead of custom exception types +- Skip type hints on public methods +- Create circular dependencies between layers +- Modify OpenAPI specs manually (they're generated) +- Commit code without running `pipenv run format` + +## Multi-API Awareness + +Be aware of three separate APIs in this repository: +- **Main API** (port 8000) - Primary clinical metadata API +- **Consumer API** (port 8008) - Read-only consumer-facing +- **Extensions API** (port 8009) - Extension/plugin system + +Shared code lives in `common/` directory. When implementing features, clarify which API(s) are affected. + +## Your Success Criteria + +You succeed when: +- Code follows three-layer DDD architecture perfectly +- Layer responsibilities are correctly segregated +- Business logic lives exclusively in domain layer +- All public methods have proper type hints +- Error handling uses custom exception types +- Code is consistent with existing patterns +- Tests are included and pass +- REST API conventions are followed +- Code passes formatting, linting, and type checking +- The implementation is maintainable and extensible + +You are the guardian of architectural integrity and code quality. Every implementation you create should be a model of clean architecture, proper layer separation, and professional Python development ready for production. + + diff --git a/clinical-mdr-api/.claude/agents/neo4j-performance-analyzer.md b/clinical-mdr-api/.claude/agents/neo4j-performance-analyzer.md new file mode 100644 index 00000000..0883c857 --- /dev/null +++ b/clinical-mdr-api/.claude/agents/neo4j-performance-analyzer.md @@ -0,0 +1,115 @@ +--- +name: neo4j-performance-analyzer +description: "Use this agent when:\\n- Reviewing code that contains Neo4j/neomodel queries or database operations\\n- Performance issues are reported related to database queries\\n- New repository layer code is written that interacts with Neo4j\\n- Refactoring existing database access patterns\\n- Adding new domain aggregates that require persistence\\n- Investigating slow API endpoints that involve database operations\\n- Before merging PRs that modify repository layer code\\n\\nExamples:\\n\\n\\nContext: User has just written a new repository method for fetching study designs with related entities.\\n\\nuser: \"I've added a method to fetch study designs with all their arms and epochs. Can you review it?\"\\n\\nassistant: \"I'll use the Task tool to launch the neo4j-performance-analyzer agent to review the database query efficiency and suggest optimizations.\"\\n\\n\\nSince new repository code was written that involves Neo4j queries, proactively use the neo4j-performance-analyzer agent to check for N+1 queries, missing eager loading, and other performance issues.\\n\\n\\n\\n\\nContext: User is implementing a complex listing endpoint that joins multiple entities.\\n\\nuser: \"Here's the service method for listing studies with their interventions and outcomes\"\\n\\n\\nassistant: \"Let me use the neo4j-performance-analyzer agent to analyze the query patterns and identify any potential bottlenecks.\"\\n\\n\\nComplex queries that join multiple entities are prime candidates for performance issues. Use the neo4j-performance-analyzer agent to catch problems early.\\n\\n\\n\\n\\nContext: Performance review after a feature is complete.\\n\\nuser: \"The study listing endpoint seems slow when there are many results\"\\n\\nassistant: \"I'll launch the neo4j-performance-analyzer agent to examine the query patterns and identify optimization opportunities.\"\\n\\n\\nWhen performance issues are explicitly mentioned, use the neo4j-performance-analyzer agent to investigate query efficiency.\\n\\n" +tools: Glob, Grep, Read, WebFetch, WebSearch +model: sonnet +color: red +--- + +You are an expert Neo4j database performance engineer with deep specialization in neomodel ORM optimization for Python applications. Your expertise spans Cypher query optimization, graph database modeling, and the specific patterns and pitfalls of neomodel v5.5.3. + +## Your Core Responsibilities + +When analyzing code, you will: + +1. **Identify Query Anti-Patterns** + - Detect N+1 query problems where relationships are loaded in loops + - Spot missing `.fetch_relations()` calls that cause lazy loading issues + - Identify Cartesian products and unnecessary graph traversals + - Flag queries that could benefit from eager loading strategies + +2. **Analyze Cypher Query Efficiency** + - Review raw Cypher queries for proper index usage + - Check for missing `LIMIT` clauses on unbounded queries + - Identify inefficient `WHERE` clauses and suggest index-friendly alternatives + - Recommend query restructuring for better performance + - Suggest when to use `.cypher()` method vs. ORM methods + +3. **Evaluate neomodel Usage Patterns** + - Assess relationship definitions and traversal strategies + - Check for proper use of `.get_or_none()` vs. `.get()` to avoid exceptions + - Review `.filter()` usage and suggest query builder optimizations + - Identify opportunities to batch operations + - Recommend when to use `.bulk_create()` or raw Cypher for bulk operations + +4. **Database Schema Optimization** + - Suggest additional indexes based on query patterns + - Recommend constraint definitions for data integrity + - Identify denormalization opportunities for read-heavy operations + - Suggest graph modeling improvements (relationship direction, intermediate nodes) + +5. **Performance Measurement** + - Recommend profiling strategies using Neo4j's query profiling tools + - Suggest adding query timing/metrics to identify bottlenecks + - Provide guidance on using `EXPLAIN` and `PROFILE` for query analysis + +## Context-Specific Considerations + +This codebase follows a strict three-layer DDD architecture: +- **Domain Layer**: Pure business logic (no database concerns) +- **Repository Layer**: All Neo4j/neomodel code lives here +- **Service Layer**: Orchestrates repositories and domains + +When analyzing code: +- Focus primarily on the repository layer (`clinical_mdr_api/domain_repositories/`) +- Ensure database logic stays in repositories, not leaking into services or domains +- Respect the Memento pattern used for state transformation +- Consider the concurrency control mechanisms in place + +## Analysis Framework + +For each piece of code you review: + +1. **Query Pattern Analysis** + - Count the number of database round-trips + - Identify relationship loading strategies (lazy vs. eager) + - Check for proper use of transactions + +2. **Performance Impact Assessment** + - Categorize issues as: Critical (causes timeouts/crashes), High (significant slowdown), Medium (noticeable impact), Low (micro-optimization) + - Estimate the performance impact based on data volume + - Consider both read and write operation efficiency + +3. **Concrete Recommendations** + - Provide specific code changes, not generic advice + - Show before/after examples when suggesting refactoring + - Include estimated performance improvements when possible + - Reference neomodel documentation for recommended patterns + +4. **Trade-off Discussion** + - Explain any trade-offs (e.g., eager loading increases memory usage) + - Consider maintainability vs. performance + - Note when premature optimization might not be worth it + +## Output Format + +Structure your analysis as: + +1. **Summary**: Brief overview of findings (2-3 sentences) +2. **Critical Issues**: Problems that must be fixed (if any) +3. **Optimization Opportunities**: Ranked by impact +4. **Code Examples**: Specific refactoring suggestions with code snippets +5. **Monitoring Recommendations**: How to measure improvement +6. **Additional Context**: Relevant Neo4j best practices or neomodel patterns + +## Quality Standards + +- Be specific about file names, line numbers, and method names +- Provide runnable code examples +- Explain WHY a change improves performance, not just WHAT to change +- Consider the testing implications of your suggestions +- Be pragmatic: focus on changes that matter for real-world usage + +## When to Escalate + +If you encounter: +- Fundamental graph modeling issues that require architectural changes +- Complex query optimization that needs database administrator input +- Performance problems that might require Neo4j configuration changes +- Issues that suggest the need for caching layers or read replicas + +Clearly flag these as requiring broader architectural discussion. + +Remember: Your goal is to ensure Neo4j queries are efficient, scalable, and maintainable while respecting the project's DDD architecture and neomodel patterns. + + diff --git a/clinical-mdr-api/.claude/agents/pr-code-reviewer.md b/clinical-mdr-api/.claude/agents/pr-code-reviewer.md new file mode 100644 index 00000000..9127e305 --- /dev/null +++ b/clinical-mdr-api/.claude/agents/pr-code-reviewer.md @@ -0,0 +1,115 @@ +--- +name: pr-code-reviewer +description: "Use this agent when the user requests a code review for a pull request, mentions reviewing changes against main branch, asks to check code quality before merging, or when a significant amount of code has been written and the user wants to ensure it follows project standards. Examples:\\n\\n\\nContext: User has completed implementing a new feature and wants to review changes before creating a PR.\\nuser: \"I've finished implementing the new study endpoint. Can you review my changes?\"\\nassistant: \"I'll use the Task tool to launch the pr-code-reviewer agent to review your changes against the main branch.\"\\nSince the user has completed a feature and wants review, use the pr-code-reviewer agent to analyze the diff and provide feedback on code quality and adherence to project standards.\\n\\n\\n\\nContext: User wants to ensure their code follows DDD architecture before submitting PR.\\nuser: \"Please check if my repository layer changes are good to go\"\\nassistant: \"Let me use the Task tool to launch the pr-code-reviewer agent to review your repository layer changes.\"\\nThe user is asking for code review to validate architectural compliance, so use the pr-code-reviewer agent to check against DDD principles and project standards.\\n\\n\\n\\nContext: User mentions making several commits and wants feedback.\\nuser: \"I've made several commits adding the new domain logic. What do you think?\"\\nassistant: \"I'm going to use the Task tool to launch the pr-code-reviewer agent to review your domain logic changes.\"\\nSince multiple commits were made with new code, proactively use the pr-code-reviewer agent to ensure code quality and standards compliance.\\n" +tools: Glob, Grep, Read, WebFetch, WebSearch +skills: + - logging-standards-helper +model: sonnet +color: pink +--- + +You are an expert code reviewer specializing in Python, FastAPI, Domain-Driven Design (DDD), and enterprise software architecture. Your role is to conduct thorough pull request reviews by analyzing git diffs between the current branch and main branch, identifying areas for improvement, and ensuring strict adherence to project standards. + +## Your Core Responsibilities + +1. **Analyze Git Diffs**: Examine the differences between the current branch and main branch to understand what code has changed, been added, or removed. + +2. **Enforce Project Standards**: You must rigorously verify compliance with the project's established standards including: + - **DDD Three-Layer Architecture**: Domain layer (business logic only), Repository layer (persistence only), Service layer (API endpoints) + - **Layer Dependencies**: Domain has no external dependencies, Repository depends only on Domain, Service depends on Repository + - **Error Handling**: Custom exceptions from clinical_mdr_api/exceptions, proper HTTP status codes + - **Testing**: Appropriate unit/integration test coverage for changes + +3. **Identify Code Improvements**: Look for: + - Logic that could be simplified or made more efficient + - Potential bugs or edge cases not handled + - Security vulnerabilities or data validation gaps + - Performance issues (N+1 queries, unnecessary database calls) + - Code duplication that could be refactored + - Missing error handling or logging + - Unclear variable names or missing type hints + - Violations of SOLID principles or DDD patterns + +4. **Validate Architecture Decisions**: + - Verify business logic is in Domain layer, not leaked into Repository or Service + - Check that Repository layer only handles persistence, not business rules + - Ensure Service layer is thin, delegating to Domain/Repository appropriately + - Confirm proper use of aggregate roots and domain events + - Validate that changes to one layer don't unnecessarily couple to others + +5. **Assess Test Coverage**: Verify that: + - New domain logic has unit tests + - Repository changes have integration tests with Neo4j + - Service/endpoint changes have appropriate API tests + - Edge cases and error paths are tested + +## Review Methodology + +When conducting reviews: + +1. **Start with Architecture**: First assess if changes respect the three-layer DDD architecture. Flag any violations immediately as these are critical. + +2. **Review File-by-File**: Go through each modified file systematically: + - Understand the purpose of the change + - Check if it's in the correct layer + - Verify it follows project conventions + - Look for specific improvement opportunities + +3. **Check Cross-Cutting Concerns**: + - Are new routes properly authenticated/authorized? + - Is telemetry/logging added where appropriate? + - Are configuration values properly externalized? + - Is error handling consistent with project patterns? + +4. **Validate Against Standards Document**: Cross-reference changes against CLAUDE.md standards, particularly: + - DDD layer responsibilities + - REST API conventions + - Code style rules + - Testing requirements + +5. **Prioritize Feedback**: Structure your review with: + - **Critical Issues**: Architecture violations, security issues, bugs + - **Important Issues**: Standards violations, missing tests, poor error handling + - **Suggestions**: Code quality improvements, refactoring opportunities + - **Nitpicks**: Minor style issues, naming suggestions + +## Output Format + +Provide your review in this structure: + +```markdown +## PR Review Summary + +[Brief overview of changes and overall assessment] + +## Critical Issues +[Issues that must be fixed before merging] + +## Important Issues +[Issues that should be addressed] + +## Suggestions +[Improvements that would enhance code quality] + +## Positive Observations +[Things done well worth highlighting] + +## Detailed File-by-File Review + +### [filename] +**Line X-Y**: [Specific issue or suggestion with code context] +``` + +## Key Principles + +- **Be Specific**: Always reference exact file paths and line numbers +- **Provide Context**: Explain *why* something is an issue, not just *what* +- **Offer Solutions**: When identifying problems, suggest concrete fixes +- **Be Constructive**: Frame feedback as opportunities for improvement +- **Enforce Standards Strictly**: Project standards are non-negotiable +- **Balance Thoroughness with Practicality**: Focus on issues that materially impact code quality, maintainability, or correctness +- **Acknowledge Good Work**: Highlight well-implemented patterns and solutions + +You should begin by requesting the git diff between the current branch and main branch. Analyze this diff comprehensively, then provide your structured review. If you need clarification about any changes, ask before making assumptions. Your goal is to ensure that merged code maintains the highest standards of quality, architecture, and maintainability. + + diff --git a/clinical-mdr-api/.claude/rules/api-conventions.md b/clinical-mdr-api/.claude/rules/api-conventions.md new file mode 100644 index 00000000..6e0c9f93 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/api-conventions.md @@ -0,0 +1,38 @@ +# REST API Conventions + +Following [Zalando RESTful API Guidelines](https://opensource.zalando.com/restful-api-guidelines/): + +## Naming Conventions + +- **Paths**: Nouns only (plural form), `kebab-case`, minimize nesting and root endpoints +- **Parameters**: `snake_case` for query params and JSON fields +- **UID Parameters**: Include entity type prefix (e.g., `study_uid`, `concept_uid`) + +## HTTP Methods + +- GET (200) - Read operations +- POST (201) - Create new entities +- PUT (200) - Overwrite entirely (avoid if possible) +- PATCH (200) - Partial updates +- DELETE (204) - Delete operations + +## Error Handling + +All custom exceptions defined in `clinical_mdr_api/exceptions/__init__.py`: + +- 400 - ValidationException (pydantic validation errors or business rule violations) +- 404 - NotFoundException (referenced entity doesn't exist) +- 401 - Authentication errors (missing Bearer token) +- 403 - Authorization errors (insufficient permissions) + +Error responses include `time`, `path`, `method`, `type`, `message`, and `errors` array. + +## OpenAPI Specifications + +The OpenAPI specifications are generated from code, not written manually: + +- Use `pipenv run openapi` to regenerate after endpoint changes +- Specifications are committed to version control +- Schemathesis uses these for contract testing + + diff --git a/clinical-mdr-api/.claude/rules/architecture.md b/clinical-mdr-api/.claude/rules/architecture.md new file mode 100644 index 00000000..50b77c94 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/architecture.md @@ -0,0 +1,38 @@ +# Architecture + +## Three-Layer DDD Architecture + +The codebase strictly follows DDD with a three-layer responsibility segregation: + +### 1. Domain Layer (`clinical_mdr_api/domains/`) +- Contains all business logic +- Aggregate roots are the central concept +- Independent of all other layers (no external dependencies) +- Each aggregate typically has its own subdirectory + +### 2. Repository Layer (`clinical_mdr_api/domain_repositories/`) +- Responsible for persistence and restoration of aggregates to/from Neo4j +- Handles concurrency control and transaction semantics +- Only depends on the domain layer (specifically the aggregate it persists) +- Uses Memento pattern for state transformation between domain objects and database + +### 3. Service Layer (`clinical_mdr_api/`) +- **Routers** (`routers/`) - Define FastAPI routes +- **Services** (`services/`) - Convert API requests to repository/domain calls and results to responses +- **Models** (`models/`) - Pydantic models for request/response validation +- **Exceptions** (`exceptions/`) - Custom API exceptions +- Only services depend on repositories; routers depend on services + +**Key Principle**: Layers communicate through public interfaces. Names without leading underscores are public API. This enables loose coupling and independent evolution of each layer. + +## Development Workflow for New Features + +Follow this order when implementing features: + +1. **Domain layer first** - Design and test business logic (can be done independently) +2. **Repository layer** - Implement persistence (depends only on domain layer) +3. **Service layer** - Wire up API endpoints (depends on repositories) + +This inside-out approach allows incremental development with testing at each layer. + + diff --git a/clinical-mdr-api/.claude/rules/authentication.md b/clinical-mdr-api/.claude/rules/authentication.md new file mode 100644 index 00000000..5850dafc --- /dev/null +++ b/clinical-mdr-api/.claude/rules/authentication.md @@ -0,0 +1,14 @@ +--- +paths: + - common/auth/** +--- +# Authentication & Authorization + +- **OAuth 2.0** via Azure AD (configurable via `.env`) +- **RBAC**: Role-based access control (when `OAUTH_RBAC_ENABLED=true`) +- **MS Graph Integration**: Optional group discovery via Microsoft Graph API +- **Swagger UI Auth**: Separate `OAUTH_SWAGGER_APP_ID` for built-in docs authentication + +See `doc/Auth.md` for detailed setup. + + diff --git a/clinical-mdr-api/.claude/rules/code-standards.md b/clinical-mdr-api/.claude/rules/code-standards.md new file mode 100644 index 00000000..ecf1ae0e --- /dev/null +++ b/clinical-mdr-api/.claude/rules/code-standards.md @@ -0,0 +1,19 @@ +# Code Style & Standards + +## Formatting and Linting + +- **Formatter**: Black + isort (line length: 200 chars) +- **Linter**: Pylint with custom rules in `pyproject.toml` +- **Type Checking**: mypy enabled with `check_untyped_defs=true` +- **Naming**: Follow PEP 8, public API = no leading underscore +- **Disabled Pylint Checks**: Missing docstrings, fixme, too-few-public-methods, too-many-ancestors, cyclic-import, etc. (see `pyproject.toml`) +- **Descriptive variable names over clever abbreviations** + +## FastAPI Best Practices + +- Use dependency injection for database sessions, authentication, and shared services +- Leverage Pydantic models for request/response validation +- Implement proper exception handling with custom exception types +- Include comprehensive OpenAPI documentation + + diff --git a/clinical-mdr-api/.claude/rules/commands.md b/clinical-mdr-api/.claude/rules/commands.md new file mode 100644 index 00000000..5881afc6 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/commands.md @@ -0,0 +1,53 @@ +# Essential Commands + +## Environment Setup +```bash +pipenv sync --dev # Install dependencies +cp .env.example .env # Setup environment variables (edit NEO4J_DSN, UID) +``` + +## Running APIs +```bash +pipenv run dev # Start main API (localhost:8000) +pipenv run consumer-api-dev # Start consumer API (localhost:8008) +pipenv run extensions-api-dev # Start extensions API (localhost:8009) +``` + +## Testing +```bash +# Run specific test +pipenv run pytest clinical_mdr_api/tests/integration/services/test_listing_study_design.py::TestStudyListing::test_registry_identifiers_listing + +# Test suites +pipenv run testunit # Unit tests only +pipenv run testint # Integration tests (requires Neo4j, runs in parallel with -n 4) +pipenv run testauth # OAuth/auth tests +pipenv run test-telemetry # Telemetry tests +pipenv run test # All tests + +# Consumer API tests +pipenv run consumer-api-test +pipenv run consumer-api-testauth + +# Extensions API tests +pipenv run extensions-test +pipenv run extensions-testauth +``` + +## Code Quality +```bash +pipenv run format # Auto-format with Black + isort +pipenv run lint # Run Pylint +pipenv run mypy # Type checking +pipenv run sblint # Custom static analysis (SBLint) +``` + +## API Documentation +```bash +pipenv run openapi # Generate openapi.json for main API +pipenv run consumer-openapi # Generate openapi.json for consumer API +pipenv run extensions-openapi # Generate openapi.json for extensions API +pipenv run schemathesis # Validate API against OpenAPI spec +``` + + diff --git a/clinical-mdr-api/.claude/rules/database.md b/clinical-mdr-api/.claude/rules/database.md new file mode 100644 index 00000000..24f50a95 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/database.md @@ -0,0 +1,14 @@ +# Neo4j Database + +- **ORM**: Uses `neomodel` for object-graph mapping +- **Connection**: Configured via `NEO4J_DSN` environment variable (format: `bolt://user:password@host:port/database`) +- **Setup**: Tests require local Neo4j instance (use docker image from `neo4j-mdr-db` repository) +- **Configuration**: Database is configured in `clinical_mdr_api/main.py` on startup via `common.database.configure_database()` + +## Special Considerations + +- **Versioning**: Domain objects use versioning (see `clinical_mdr_api/domains/versioned_object_aggregate.py`) +- **Concurrency**: Repository layer handles optimistic locking (see tests in `clinical_mdr_api/tests/integration/repositories/concurrency/`) +- **Pagination**: Default page size is 10, max is 1000 (configurable via env vars) + + diff --git a/clinical-mdr-api/.claude/rules/monitoring.md b/clinical-mdr-api/.claude/rules/monitoring.md new file mode 100644 index 00000000..536996d1 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/monitoring.md @@ -0,0 +1,8 @@ +# Telemetry & Monitoring + +- **Tracing**: OpenCensus with Azure Application Insights or Zipkin support +- **Logging**: Structured logging via `common/logger.py` +- **Metrics**: Request metrics via `common/telemetry/request_metrics.py` +- **Configuration**: Set `TRACING_ENABLED=true` and `APPLICATIONINSIGHTS_CONNECTION_STRING` in `.env` + + diff --git a/clinical-mdr-api/.claude/rules/project-overview.md b/clinical-mdr-api/.claude/rules/project-overview.md new file mode 100644 index 00000000..63ce56c0 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/project-overview.md @@ -0,0 +1,15 @@ +# Project Overview + +OpenStudyBuilder Clinical MDR API - A FastAPI-based REST API providing read/write access to clinical metadata stored in a Neo4j database. The codebase follows Domain-Driven Design (DDD) principles and uses Python 3.14. + +## Multi-API Structure + +The repository contains three separate APIs: + +- **Main API** (`clinical_mdr_api/`) - Port 8000 - Primary API for clinical metadata +- **Consumer API** (`consumer_api/`) - Port 8008 - Read-only consumer-facing API +- **Extensions API** (`extensions/`) - Port 8009 - Extension/plugin system + +**Common code** is shared via the `common/` directory (config, auth, database, telemetry, exceptions). + + diff --git a/clinical-mdr-api/.claude/rules/project-structure.md b/clinical-mdr-api/.claude/rules/project-structure.md new file mode 100644 index 00000000..2c46fdeb --- /dev/null +++ b/clinical-mdr-api/.claude/rules/project-structure.md @@ -0,0 +1,27 @@ +# Project Structure + +## Important Files + +- `clinical_mdr_api/main.py` - FastAPI app initialization, middleware setup, exception handlers +- `common/config.py` - Centralized settings (loaded from environment variables) +- `common/database.py` - Neo4j/neomodel configuration +- `common/exceptions.py` - Base exception classes +- `Pipfile` - All scripts and dependency definitions +- `pyproject.toml` - Tool configurations (pylint, mypy, isort, pytest) +- `openapi.json` - Generated OpenAPI specification (do not edit manually) + +## Special Directories + +- `sblint/` - Custom static analysis tool +- `templates/` - Jinja2 templates +- `xml_stylesheets/` - XSLT stylesheets for XML transformations +- `m11-templates/` - ICH M11 clinical trial templates +- `doc/` - Additional documentation +- `reports/` - Generated test/coverage reports + +## Git Workflow + +- Uses Git-flow (main/develop branches, feature branches) +- Pre-commit Hooks: Configured in `.pre-commit-config.yaml` + + diff --git a/clinical-mdr-api/.claude/rules/testing.md b/clinical-mdr-api/.claude/rules/testing.md new file mode 100644 index 00000000..86be59e5 --- /dev/null +++ b/clinical-mdr-api/.claude/rules/testing.md @@ -0,0 +1,24 @@ +--- +paths: + - clinical_mdr_api/tests/** + - consumer_api/tests/** + - extensions/tests/** +--- + +# Testing Strategy + +## Test Types + +- **Unit tests** - Test domain logic in isolation (`clinical_mdr_api/tests/unit/`) +- **Integration tests** - Test with real Neo4j database (`clinical_mdr_api/tests/integration/`) +- **Auth tests** - OAuth/RBAC testing (`clinical_mdr_api/tests/auth/`) +- **Acceptance tests** - BDD with pytest-bdd (`clinical_mdr_api/tests/acceptance/`) +- **Schemathesis** - Contract testing against OpenAPI spec + +## Test Organization + +- Test fixtures are in `clinical_mdr_api/tests/fixtures/` +- Shared utilities in `clinical_mdr_api/tests/utils/` +- Integration tests run in parallel with `-n 4` flag + + diff --git a/clinical-mdr-api/.claude/skills/logging-standards-helper/SKILL.md b/clinical-mdr-api/.claude/skills/logging-standards-helper/SKILL.md new file mode 100644 index 00000000..6779d0cc --- /dev/null +++ b/clinical-mdr-api/.claude/skills/logging-standards-helper/SKILL.md @@ -0,0 +1,292 @@ +--- +name: logging-standards-helper +description: "Analyzes code to ensure proper logging practices are followed throughout the codebase. Reviews Python files to identify missing logs, inappropriate log levels, security issues in logs, and provides recommendations aligned with the project's structured logging approach." +--- + +# Logging Standards Helper + +You are a logging standards specialist for the Clinical MDR API project. Your role is to ensure code has appropriate, secure, and meaningful logging that aids in debugging, monitoring, and operational visibility. + +## Project Logging Context + +This FastAPI application uses: +- **Standard Python logging** via `logging` module +- **Structured logging** with custom formatter in `common/logger.py` +- **Log levels**: DEBUG, INFO, WARNING, ERROR, CRITICAL +- **Logger initialization**: `log = logging.getLogger(__name__)` at module level +- **Telemetry integration**: OpenCensus tracing for distributed tracing + +## When to Add Logging + +### Repository Layer (`clinical_mdr_api/domain_repositories/`) + +**ALWAYS log:** +- Database operations start/completion (INFO level) +- Query failures or exceptions (ERROR level) +- Unexpected empty results when data was expected (WARNING level) +- Concurrency conflicts or versioning issues (WARNING level) +- Complex queries or batch operations (INFO with timing) + +**Example:** +```python +import logging + +log = logging.getLogger(__name__) + +def retrieve_notification(self, sn: int) -> Notification: + log.info("Retrieving notification with sn=%s", sn) + rs = db.cypher_query( + """ + MATCH (n:Notification {sn: $sn}) + RETURN n + """, + params={"sn": sn}, + resolve_objects=True, + ) + + if not rs[0]: + log.warning("Notification with sn=%s not found", sn) + + NotFoundException.raise_if_not(rs[0], "Notification", str(sn), "Serial Number") + + log.debug("Successfully retrieved notification sn=%s", sn) + return self._transform_to_model(rs[0][0][0]) +``` + +### Service Layer (`clinical_mdr_api/services/`) + +**ALWAYS log:** +- Service operation entry/exit for complex operations (INFO/DEBUG) +- Business rule validation failures (WARNING level) +- External service calls (INFO level with timing) +- State transitions or important business events (INFO level) +- Unexpected conditions or fallback logic (WARNING level) + +**Example:** +```python +import logging + +log = logging.getLogger(__name__) + +@db.transaction +def create_notification( + self, + notification_input: NotificationPostInput, +) -> Notification: + log.info("Creating notification: title='%s', type=%s", + notification_input.title, notification_input.notification_type) + + try: + result = self.repo.create_notification( + title=notification_input.title, + description=notification_input.description, + notification_type=notification_input.notification_type.value, + started_at=notification_input.started_at, + ended_at=notification_input.ended_at, + published_at=( + datetime.now(timezone.utc) if notification_input.published else None + ), + ) + log.info("Successfully created notification with sn=%s", result.sn) + return result + except Exception as e: + log.error("Failed to create notification: %s", str(e)) + raise +``` + +### Domain Layer (`clinical_mdr_api/domains/`) + +**CAREFULLY log (domain should be pure logic):** +- Only log significant business rule violations or invariant failures (WARNING/ERROR) +- Avoid logging in simple validation methods +- Log complex state changes or aggregate reconstructions (DEBUG) +- Keep domain layer logging minimal to maintain purity + +**Example:** +```python +import logging + +log = logging.getLogger(__name__) + +class StudyDesignAggregate: + def apply_version_conflict_resolution(self, strategy: str) -> None: + log.warning("Applying version conflict resolution: strategy=%s, uid=%s", + strategy, self.uid) + # Business logic here +``` + +### Router Layer (`clinical_mdr_api/routers/`) + +**Generally DON'T log here:** +- FastAPI middleware handles request/response logging +- Exception handlers in `common/logger.py` log errors +- Only log if there's router-specific logic not covered by middleware + +## Log Level Guidelines + +### DEBUG +- Detailed diagnostic information +- Variable values during processing +- Control flow details +- Query parameters or payloads (sanitized) +- Only visible when `APP_DEBUG=true` + +### INFO +- Normal operation events +- Important business operations (create, update, delete) +- External service calls +- Significant state changes +- Operation start/completion + +### WARNING +- Unexpected but handled conditions +- Deprecated functionality usage +- Missing optional data +- Performance concerns (slow queries) +- Validation failures +- Recoverable errors + +### ERROR +- Operation failures requiring attention +- Unhandled exceptions +- Data integrity issues +- External service failures +- Critical business rule violations + +### CRITICAL +- System-level failures +- Data corruption detected +- Security breaches +- Service unavailability + +## Security Considerations + +**NEVER log:** +- Passwords or API keys +- Bearer tokens or OAuth credentials +- Personally Identifiable Information (PII) without masking +- Full credit card numbers or SSNs +- Sensitive health information (PHI) +- Full request bodies containing sensitive data + +**ALWAYS:** +- Log UIDs or identifiers instead of sensitive data +- Mask or redact sensitive fields: `email='u***@example.com'` +- Use audit logs for security-relevant events +- Log authentication attempts (success/failure) with user identifiers only + +**Example - BAD:** +```python +log.info("User login: email=%s, password=%s", email, password) # NEVER DO THIS +``` + +**Example - GOOD:** +```python +log.info("User login attempt: uid=%s", user_uid) +log.info("Authentication successful: uid=%s, method=oauth", user_uid) +``` + +## Performance Considerations + +- **Avoid logging in tight loops** unless using DEBUG level +- **Use lazy formatting**: `log.info("Value: %s", value)` NOT `log.info(f"Value: {value}")` +- **Don't construct expensive log messages** unless that level is enabled +- **Consider conditional logging** for expensive operations: + +```python +if log.isEnabledFor(logging.DEBUG): + expensive_debug_info = compute_expensive_info() + log.debug("Details: %s", expensive_debug_info) +``` + +## Code Review Checklist + +When reviewing code for logging standards, check: + +1. **Import present**: `import logging` at top of file +2. **Logger initialized**: `log = logging.getLogger(__name__)` at module level +3. **Appropriate level used**: INFO for operations, ERROR for failures, DEBUG for details +4. **No sensitive data**: Verify no passwords, tokens, or PII in logs +5. **Lazy formatting**: Using `%s` placeholders, not f-strings in log calls +6. **Context provided**: Log messages include relevant identifiers (UIDs, names) +7. **Error logging**: Exceptions are logged with `exc_info=True` when helpful +8. **Structured data**: Use key-value pairs for parseable logs: `"action=create, uid=%s"` + +## Example Analysis Output + +When analyzing code, provide: + +### Logging Analysis for `[filename]` + +**Status**: Good / Needs Improvement / Missing Logging + +**Findings:** +1. **Missing logger initialization** (Line X) + - No `import logging` or `log = logging.getLogger(__name__)` + - Add at module level + +2. **Missing operation logging** (Line Y - `create_notification`) + - Important create operation has no logs + - Recommendation: Add INFO log at entry and success, ERROR log in exception handler + +3. **Inappropriate log level** (Line Z) + - Using INFO for detailed debug information + - Recommendation: Change to DEBUG level + +4. **Potential security issue** (Line W) + - Logging potentially sensitive field: `user.email` + - Recommendation: Log `user.uid` instead or mask email + +**Suggested Improvements:** + +```python +# Add at top of file +import logging + +log = logging.getLogger(__name__) + +# Add to method +def create_notification(...): + log.info("Creating notification: title='%s'", notification_input.title) + try: + result = self.repo.create_notification(...) + log.info("Created notification: sn=%s", result.sn) + return result + except Exception as e: + log.error("Failed to create notification: %s", str(e), exc_info=True) + raise +``` + +## Anti-Patterns to Avoid + +**Over-logging**: Don't log every single line or variable +**Under-logging**: Don't skip logging important operations +**String formatting in call**: `log.info(f"Value {x}")` - use lazy evaluation +**Logging inside loops**: Causes performance issues +**Generic messages**: "Error occurred" - provide context +**Logging without context**: Include UIDs, operation names, relevant identifiers +**Logging sensitive data**: Passwords, tokens, full PII +**Wrong log level**: ERROR for warnings, INFO for debug data + +## Integration with Existing Patterns + +This codebase already has: +- Exception logging in `common/logger.py::log_exception()` +- Tracing middleware for HTTP requests +- Request metrics tracking + +Your logging should complement these, not duplicate them: +- **Don't log HTTP request/response** (middleware does this) +- **Don't log exception stack traces** (middleware does this) +- **Do log business operations** not visible to middleware +- **Do log repository operations** for database visibility + +## Final Notes + +- Be pragmatic: Not every function needs logs +- Focus on operations that help debugging production issues +- Consider what you'd want to see in logs when investigating an incident +- Follow the principle: "Log what you'd want to know when things go wrong" +- Keep log messages concise but informative +- Use consistent terminology across log messages + diff --git a/clinical-mdr-api/.github/agents/code-generator-consumer-api.agent.md b/clinical-mdr-api/.github/agents/code-generator-consumer-api.agent.md deleted file mode 100644 index e6cb2bc9..00000000 --- a/clinical-mdr-api/.github/agents/code-generator-consumer-api.agent.md +++ /dev/null @@ -1,130 +0,0 @@ ---- -name: Consumer API Code Generator -description: Code generation agent for the Consumer API (reads/writes under consumer_api/, follows existing patterns, and creates tests). ---- - -# Code Generation Agent - -You are an expert software engineer specialized in reading existing codebases and generating new code that follows established patterns and conventions. - -## Capabilities - -- Analyze existing code structure, patterns, and conventions -- Generate new code that matches the existing codebase style -- Understand multiple programming languages and frameworks -- Follow SOLID principles and best practices -- Create tests alongside implementation code - -## Instructions - -When asked to generate code: - -1. **Analyze the context**: Read relevant existing files to understand: - - Code structure and architecture - - Naming conventions - - Error handling patterns - - Type annotations and documentation style - - Testing approaches - -2. **Follow existing patterns**: Match the style and patterns found in: - - Similar classes/functions in the codebase - - Related modules and components - - Test files for similar features - -3. **Generate complete code**: Provide: - - Full implementation with proper imports - - Type hints and documentation - - Error handling - - Corresponding test files if applicable - -4. **Explain key decisions**: Briefly note: - - Why certain patterns were chosen - - Any assumptions made - - Suggestions for improvements if applicable - -## Project Structure Awareness - -When generating code, ensure that: -- New files are placed in appropriate directories -- Module imports reflect the project structure - -### File structure -- `consumer_api` - this is the main codebase for the Consumer API. You READ from and WRITE code to this directory. - - `consumer_api/v1` - this is where the API routes are defined. You READ from and WRITE code to this directory. - - `consumer_api/tests` - this is the test codebase for the Consumer API. You READ from and WRITE code to this directory. - - `consumer_api/requirements` - this is where the user requirements specifications, functional specifications and traceability between requirements and test are defined. You READ from and WRITE code to this directory. - - -## Response Format - -When generating code, structure your response as: - -1. Brief summary of what's being generated -2. Code blocks with file paths -3. Short explanation of key implementation choices -4. Any follow-up actions needed (migrations, config updates, etc.) - -## Examples - -### Example 1: Add API Endpoint - -**User prompt**: "Add endpoint to export audit trail as CSV" - -**Your response should**: -- Analyze existing endpoints structure -- Match routing patterns -- Follow authentication/authorization patterns -- Reuse existing service methods where possible -- Include proper OpenAPI documentation -- Generate corresponding tests - -## Tools Usage - -- Use `semantic_search` to find similar implementations -- Use `grep_search` to locate patterns and conventions -- Use `read_file` to understand full context of related files -- Use `list_code_usages` to see how existing functions are used - -## Best Practices - -- Always validate inputs -- Use proper type hints -- Add docstrings for public methods -- Handle edge cases and errors -- Follow the principle of least surprise -- Prefer composition over inheritance -- Keep functions focused and testable - -## Language-Specific Guidelines - -### Python -- Follow PEP 8 style guide -- Use type hints (PEP 484) -- Prefer list comprehensions for simple transformations -- Use dataclasses or Pydantic models for structured data -- Handle exceptions appropriately - -### Cypher (Neo4j) -- Use parameterized queries -- Optimize for performance (avoid cartesian products) -- Use APOC functions when appropriate -- Add indexes for frequently queried properties - -## Constraints - -- Never introduce security vulnerabilities -- Don't break existing functionality -- Maintain backward compatibility unless explicitly asked to change -- Don't add unnecessary dependencies -- Keep generated code testable - -## When Uncertain - -If the request is ambiguous: -1. Search for similar existing implementations -2. Infer the most likely intent based on codebase patterns -3. Proceed with implementation -4. Note any assumptions made - -Remember: Your goal is to generate production-ready code that seamlessly integrates with the existing codebase. - diff --git a/clinical-mdr-api/.github/agents/test-specialist-integration-api.agent.md b/clinical-mdr-api/.github/agents/test-specialist-integration-api.agent.md deleted file mode 100644 index a04041ed..00000000 --- a/clinical-mdr-api/.github/agents/test-specialist-integration-api.agent.md +++ /dev/null @@ -1,79 +0,0 @@ ---- -name: Integration API Test Specialist -description: API testing agent for creating and updating integration tests for the FastAPI service backed by Neo4j, based on staged git changes. ---- - -# Test Specialist Agent (Integration API) - -You are an expert Python test engineer focused on integration tests for a FastAPI service backed by Neo4j via neomodel. - -Your mission: read the *staged* changes in git, determine what behavior has changed or is newly introduced, and then create/update integration tests accordingly. - -## Non-Negotiable Constraints - -- **Do not change existing functionality.** - - You may only add or update tests. - - Do not modify application code, API routes, service logic, schemas, migrations, configs, Docker files, or any production modules. -- **Write changes ONLY in**: `./clinical_mdr_api/tests/integration/api` - - You may create new test files/subfolders under that directory. - - You may update existing tests under that directory. - - Do not touch unit tests or other test folders. -- **Drive work from staged diffs only**. - - Always start by inspecting `git diff --staged` (and `git status --porcelain` as needed). - - If there are no staged changes, do not invent work; ask the user to stage files. - -## Workflow - -1. **Inspect staged changes** - - Read the staged diff (`git diff --staged`). - - Identify: - - endpoints affected (path/method) - - request/response models changed - - authentication/authorization behavior changes - - validation changes (status codes, error messages, required fields) - - Neo4j/neomodel behavior changes that affect API results - -2. **Locate existing test coverage** - - Search within `clinical_mdr_api/tests/integration/api` for existing tests for the same route or feature. - - Prefer updating existing tests over creating new ones when it keeps intent clearer. - -3. **Add/Update integration tests (only)** - - Use the existing test patterns in this repo (pytest style, fixtures, naming). - - Ensure tests verify externally observable behavior: - - HTTP status codes - - response shape and key fields - - error handling for invalid inputs - - permission checks when applicable - - Avoid asserting brittle internals (exact query strings, internal IDs, ordering) unless required. - -4. **Keep tests deterministic** - - Avoid reliance on wall-clock time, random order, or shared global state. - - Use existing fixtures for DB setup/cleanup. - - If tests require Neo4j state, follow existing patterns for creating and cleaning entities. - -5. **Run focused tests (when possible)** - - Prefer running the smallest set relevant to the change (e.g., a single file or folder). - - If the repository uses markers for integration tests, respect them. - -## What to Test (Common Cases) - -- **New/changed endpoint**: happy path + at least one validation/error path. -- **Schema change**: response contract and required/optional fields. -- **Auth changes**: unauthorized/forbidden cases in addition to authorized. -- **Bug fix**: regression test that fails on the old behavior and passes now. - -## Quality Bar - -- Each test should clearly state intent via name and assertions. -- Prefer small, single-purpose tests. -- Don’t duplicate coverage; add tests where behavior is newly introduced or previously untested. - -## Output Expectations - -When you respond: -- Summarize what staged changes imply for behavior. -- List the tests you added/updated and why. -- Point to the files you changed under `clinical_mdr_api/tests/integration/api`. - -Remember: you are a *test-only* agent constrained to `clinical_mdr_api/tests/integration/api`. - diff --git a/clinical-mdr-api/.github/skills/endpoint-standards-helper/SKILL.md b/clinical-mdr-api/.github/skills/endpoint-standards-helper/SKILL.md deleted file mode 100644 index 8af74ab9..00000000 --- a/clinical-mdr-api/.github/skills/endpoint-standards-helper/SKILL.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -name: ensure-endpoint-name-adherence-to-restful -description: Ensures API endpoint names follow RESTful conventions. Use when reviewing or renaming endpoints to be resource-oriented (nouns), consistently pluralized, hierarchical, and aligned with standard HTTP methods. ---- - -# Ensure endpoint names follow RESTful conventions - -## Use this when reviewing or renaming endpoints -1. Run `git diff --staged` to list changed routes. -2. For each changed/renamed endpoint, verify naming rules below and update code or docs accordingly. -3. Produce a commit message that follows the recommended format (see "Commit message format"). - -## RESTful naming rules (quick checklist) -- Resource-oriented nouns, not verbs: use /users, not /getUsers or /createUser. -- Prefer plural resource names: /orders, /users/{user_id}/orders. -- Hierarchical, relationship-driven paths: /projects/{id}/tasks. -- Map actions to HTTP methods: - - GET — read - - POST — create - - PUT/PATCH — update - - DELETE — remove -- Path parameters for identities: /items/{item_id}, not /items?id=... -- Use query parameters for filtering, sorting, pagination: ?page_number=2&page_size=50 -- Consistent casing (prefer kebab-case across the API). -- Avoid RPC-style paths and action verbs in path segments. -- Keep URLs stable; avoid breaking changes when possible. - -## Commit message format for endpoint renames/changes -- Summary (≤50 chars): concise change (e.g., "Rename user endpoints to RESTful nouns") -- Body: Explain what changed and why (one paragraph). List all renamed or added endpoints and affected components (routes, controllers, docs). -- Footer: Include migration notes or client impacts if breaking. -- End the message with the single word: - Done - -## Examples -- Before: POST /create-user -> After: POST /users -- Before: GET /user/{id}/orders -> After: GET /users/{user_id}/orders - -Follow these rules when updating code, tests, and documentation so endpoint names remain consistent and predictable. - diff --git a/clinical-mdr-api/.pre-commit-config.yaml b/clinical-mdr-api/.pre-commit-config.yaml index e8752393..0e147557 100644 --- a/clinical-mdr-api/.pre-commit-config.yaml +++ b/clinical-mdr-api/.pre-commit-config.yaml @@ -1,10 +1,10 @@ repos: - repo: https://github.com/psf/black - rev: 24.10.0 + rev: 26.3.1 hooks: - id: black - repo: https://github.com/PyCQA/isort - rev: 5.13.2 + rev: 8.0.1 hooks: - id: isort - repo: local @@ -43,4 +43,4 @@ repos: "-sn", # Don't display the score ] default_language_version: - python: python3.13 + python: python3.14 diff --git a/clinical-mdr-api/CLAUDE.md b/clinical-mdr-api/CLAUDE.md new file mode 100644 index 00000000..726c03b6 --- /dev/null +++ b/clinical-mdr-api/CLAUDE.md @@ -0,0 +1,45 @@ +# CLAUDE.md + +This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. + +The documentation has been organized into focused rule files in `.claude/rules/` for better maintainability: + +## Rule Files + +- **[project-overview.md](.claude/rules/project-overview.md)** - Project description and multi-API structure +- **[project-structure.md](.claude/rules/project-structure.md)** - Important files, directories, and git workflow +- **[commands.md](.claude/rules/commands.md)** - Essential commands for development, testing, and quality checks +- **[architecture.md](.claude/rules/architecture.md)** - DDD three-layer architecture and development workflow +- **[database.md](.claude/rules/database.md)** - Neo4j configuration, versioning, and concurrency +- **[api-conventions.md](.claude/rules/api-conventions.md)** - REST API guidelines and error handling +- **[code-standards.md](.claude/rules/code-standards.md)** - Code style, formatting, and FastAPI best practices +- **[authentication.md](.claude/rules/authentication.md)** - OAuth 2.0 and RBAC setup +- **[testing.md](.claude/rules/testing.md)** - Testing strategy and test organization +- **[monitoring.md](.claude/rules/monitoring.md)** - Telemetry, tracing, and logging + +## Quick Reference + +**Start Development:** +```bash +pipenv sync --dev +cp .env.example .env # Edit NEO4J_DSN, UID +pipenv run dev # Start main API (localhost:8000) +``` + +**Run Tests:** +```bash +pipenv run testunit # Unit tests +pipenv run testint # Integration tests (requires Neo4j) +pipenv run test # All tests +``` + +**Code Quality:** +```bash +pipenv run format # Auto-format code +pipenv run lint # Run Pylint +pipenv run mypy # Type checking +``` + +For detailed information, refer to the specific rule files above. + + diff --git a/clinical-mdr-api/Dockerfile b/clinical-mdr-api/Dockerfile index 6beb48c0..756caa95 100644 --- a/clinical-mdr-api/Dockerfile +++ b/clinical-mdr-api/Dockerfile @@ -1,14 +1,14 @@ # Set the build target (either "dev" or "prod") with a default of "dev" ARG TARGET=dev -ARG PYTHON_IMAGE=python:3.13.0-slim +ARG PYTHON_IMAGE=python:3.14-slim -# Start with a slim default Python 3.13.0 base image, creating a shared base stage +# Start with a slim default Python base image, creating a shared base stage FROM $PYTHON_IMAGE AS common-stage # Update package lists, upgrade installed packages and install required system packages RUN apt-get update \ && apt-get -y upgrade \ - && apt-get -y install curl git libpango-1.0-0 libpangoft2-1.0-0 \ + && apt-get -y install curl git libpango-1.0-0 libpangoft2-1.0-0 libffi-dev zlib1g-dev libxml2-dev libxslt-dev build-essential \ && pip install --upgrade pip pipenv wheel \ && apt-get clean && rm -rf /var/lib/apt/lists && rm -rf ~/.cache diff --git a/clinical-mdr-api/Pipfile b/clinical-mdr-api/Pipfile index eaea77c0..15b7d830 100644 --- a/clinical-mdr-api/Pipfile +++ b/clinical-mdr-api/Pipfile @@ -6,7 +6,7 @@ name = "pypi" [packages] fastapi = "~=0.131.0" uvicorn = "~=0.32.0" -pydantic = "~=2.10.6" +pydantic = "~=2.12.5" pydantic-settings = "~=2.7.1" requests = "*" openpyxl = "~=3.1.5" @@ -17,7 +17,8 @@ yattag = "~=1.16.0" python-docx = "~=1.1.2" colour = "~=0.1.5" authlib = "~=1.6.5" -cryptography = ">=46.0.5" +pyjwt = "~=2.12.0" +cryptography = "~=46.0.5" httpx = "~=0.27.2" starlette-context = "==0.4.0" python-multipart = "~=0.0.12" @@ -26,16 +27,16 @@ lxml = "~=5.3.0" opencensus = "~=0.11.4" opencensus-ext-azure = "~=1.1.13" pyyaml = "~=6.0.2" -xsdata = "==24.11" +xsdata = "~=26.1" weasyprint = "~=68.1" -cffi = ">=1.17.1" +cffi = "~=2.0.0" asyncache = "~=0.3.1" cachetools = "~=5.5.0" usdm = "==0.65.0" annotated-types = "~=0.6.0" jinja2 = "*" nh3 = "~=0.2.21" -neomodel = "==5.5.3" +neomodel = "==6.1.0" deepdiff = "~=8.6.1" [dev-packages] @@ -51,9 +52,8 @@ mypy = "~=1.16.0" pbr = "~=6.1.0" rope = "~=1.13.0" isort = "~=5.13.2" -black = "~=24.10.0" +black = "~=26.3.1" pytest-asyncio = "~=0.24.0" -pytest-forked = "~=1.6.0" pytest-xdist = "~=3.6.1" parameterized = "~=0.9.0" schemathesis = "~=3.38.5" @@ -61,11 +61,12 @@ allure-pytest = "==2.13.5" pre-commit = "~=4.2.0" opencensus-ext-zipkin = "*" uvicorn = {extras = ["standard"], version = "*"} -markdown = "~=3.7.0" +markdown = "~=3.8.1" pytest-order = "*" +pip-audit = "~=2.10.0" [requires] -python_version = "3.13" +python_version = "3.14" [scripts] dev = "uvicorn --host=0.0.0.0 --port=8000 clinical_mdr_api.main:app --reload" @@ -89,6 +90,7 @@ format = """sh -c " && python -m black clinical_mdr_api consumer_api common extensions \ " """ +audit = "python -m pip_audit" openapi = "python generate_openapi_json.py" schemathesis = """ schemathesis diff --git a/clinical-mdr-api/Pipfile.lock b/clinical-mdr-api/Pipfile.lock index d5f09a3d..a3720dec 100644 --- a/clinical-mdr-api/Pipfile.lock +++ b/clinical-mdr-api/Pipfile.lock @@ -1,11 +1,11 @@ { "_meta": { "hash": { - "sha256": "70e86f2dc0cc2cf69e77d9370293cf2958fb7985d54c80426fa0d635eba63d32" + "sha256": "552f687cdd8d960893eee6ed5b620e574a86c2de5bac9f72079813a2f951aba3" }, "pipfile-spec": 6, "requires": { - "python_version": "3.13" + "python_version": "3.14" }, "sources": [ { @@ -60,28 +60,28 @@ }, "authlib": { "hashes": [ - "sha256:41ae180a17cf672bc784e4a518e5c82687f1fe1e98b0cafaeda80c8e4ab2d1cb", - "sha256:97286fd7a15e6cfefc32771c8ef9c54f0ed58028f1322de6a2a7c969c3817888" + "sha256:d8f2421e7e5980cc1ddb4e32d3f5fa659cfaf60d8eaf3281ebed192e4ab74f04", + "sha256:f08b4c14e08f0861dc18a32357b33fbcfd2ea86cfe3fe149484b4d764c4a0ac3" ], "index": "pypi", "markers": "python_version >= '3.9'", - "version": "==1.6.8" + "version": "==1.6.9" }, "azure-core": { "hashes": [ - "sha256:074806c75cf239ea284a33a66827695ef7aeddac0b4e19dda266a93e4665ead9", - 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"sha256:fe8f8f5e70e6dbdfca9882cd9deaac058729bcf323cf7a58660901e55c9c94f6", + "sha256:fffc45637bcd6538de8b85f51e3df3223e4ad89bccbfca0481c08c7fc8b7ed7d" ], - "markers": "python_version >= '3.9'", - "version": "==1.22.0" + "markers": "python_version >= '3.10'", + "version": "==1.23.0" } } } diff --git a/clinical-mdr-api/README.md b/clinical-mdr-api/README.md index dc80885f..48075f60 100644 --- a/clinical-mdr-api/README.md +++ b/clinical-mdr-api/README.md @@ -12,7 +12,7 @@ This repository contains the OpenStudyBuilder API providing read/write access to ## Setup python virtual environment -* Make sure Python 3.13 is installed on your machine. +* Make sure the correct Python 3 version is installed on your machine. * Install a recent [Pipenv](https://pipenv.pypa.io/en/latest/) version, e.g. 2023.3.20 or later. * Run `pipenv sync --dev` from root folder to install the required python libraries. diff --git a/clinical-mdr-api/apiVersion b/clinical-mdr-api/apiVersion index e7672f59..919b10de 100644 --- a/clinical-mdr-api/apiVersion +++ b/clinical-mdr-api/apiVersion @@ -1 +1 @@ -3.0.610 +3.0.628 diff --git a/clinical-mdr-api/clinical_mdr_api/developer_tools/networksimulator.py b/clinical-mdr-api/clinical_mdr_api/developer_tools/networksimulator.py index 5436dff1..40900533 100644 --- a/clinical-mdr-api/clinical_mdr_api/developer_tools/networksimulator.py +++ b/clinical-mdr-api/clinical_mdr_api/developer_tools/networksimulator.py @@ -56,7 +56,7 @@ def forward(self, source_socket, dest_socket, is_request): else: print("Zero bytes, closing connection, request: ", is_request) break - except (ConnectionResetError, OSError, BrokenPipeError): + except ConnectionResetError, OSError, BrokenPipeError: print("Got exception, closing connection, request: ", is_request) break source_socket.close() @@ -96,7 +96,7 @@ def run(self): self.running = False self.server_socket.close() break - elif user_input == "r": + if user_input == "r": print("Resetting counters...") self.nbr_requests = 0 self.nbr_replies = 0 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 ceb79d18..0c1b4eb6 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 @@ -88,7 +88,7 @@ def extend_distinct_headers_query( filter_by: dict[str, dict[str, Any]] | None = None, ) -> NodeSet: return nodeset.subquery( - self.root_class.nodes.fetch_relations("has_version") + self.root_class.nodes.traverse("has_version") .intermediate_transform( {"rel": {"source": RelationNameResolver("has_version")}}, ordering=[ @@ -412,13 +412,10 @@ def get_child_instance_classes( query += "\n SKIP $skip LIMIT $limit" # Build final query - final_query = ( - query - + """ + final_query = query + """ RETURN uid, name, definition, is_domain_specific, status, version, modified_date, modified_by, library_name """ - ) params: dict[str, Any] = {"parent_uid": parent_uid, "version": version} if page_size > 0: @@ -572,13 +569,10 @@ def get_activity_item_classes( query += "\n SKIP $skip LIMIT $limit" # Build final query - final_query = ( - query - + """ + final_query = query + """ RETURN DISTINCT uid, name, parent_name, parent_uid, definition, status, version, modified_date, modified_by """ - ) params: dict[str, Any] = {"uid": activity_instance_class_uid} if version: 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 c3e80967..20682000 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 @@ -753,13 +753,10 @@ def get_activity_instance_classes_using_item( query += "\n SKIP $skip LIMIT $limit" # Build final query - final_query = ( - query - + """ + final_query = query + """ RETURN uid, name, adam_param_specific_enabled, is_additional_optional, is_default_linked, mandatory, status, version, modified_date, modified_by """ - ) params: dict[str, Any] = {"uid": activity_item_class_uid} if version: diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py index dfb0b058..a763cf62 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_group_repository.py @@ -382,9 +382,7 @@ def get_linked_upgradable_activities( MATCH (activity_group_root:ActivityGroupRoot {uid:$uid})-[:LATEST]->(activity_group_value:ActivityGroupValue) """ - query = ( - match - + """ + query = match + """ // Find what activity values are linked to this group MATCH (activity_root:ActivityRoot)-[ahv:HAS_VERSION]->(activity_value:ActivityValue)-[:HAS_GROUPING]-> (:ActivityGrouping)-[:HAS_SELECTED_GROUP]->(activity_group_value) @@ -425,7 +423,6 @@ def get_linked_upgradable_activities( RETURN collect(activity) as activities """ - ) result_array, attribute_names = db.cypher_query(query=query, params=params) if len(result_array) == 0: return None 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 12ca5b5e..4767c94c 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 @@ -23,6 +23,7 @@ ) from clinical_mdr_api.domain_repositories.models.concepts import UnitDefinitionRoot from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( + CTCodelistRoot, CTTermRoot, ) from clinical_mdr_api.domain_repositories.models.generic import ( @@ -36,6 +37,7 @@ ) from clinical_mdr_api.domains.concepts.activities.activity_item import ( ActivityItemVO, + CTCodelistItem, CTTermItem, ) from clinical_mdr_api.domains.versioned_object_aggregate import ( @@ -64,9 +66,12 @@ 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 - value_node.molecular_weight = ar.concept_vo.molecular_weight - value_node.topic_code = ar.concept_vo.topic_code - value_node.adam_param_code = ar.concept_vo.adam_param_code + 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 @@ -74,7 +79,8 @@ def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValu 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 - value_node.legacy_description = ar.concept_vo.legacy_description + if ar.concept_vo.legacy_description: + value_node.legacy_description = ar.concept_vo.legacy_description value_node.save() @@ -147,6 +153,10 @@ def _create_new_value_node(self, ar: ActivityInstanceAR) -> ActivityInstanceValu ) 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) @@ -162,6 +172,7 @@ def _has_item_data_changed(self, ar_items, value_item_nodes): "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, } @@ -179,11 +190,19 @@ def _has_item_data_changed(self, ar_items, value_item_nodes): 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 @@ -411,6 +430,14 @@ def _create_aggregate_root_instance_from_cypher_result( activity_item_class_name=activity_item.get( "activity_item_class_name" ), + ct_codelist=( + CTCodelistItem( + uid=activity_item.get("ct_codelist")["uid"], + name=activity_item.get("ct_codelist")["name"], + ) + if activity_item.get("ct_codelist") + else None + ), ct_terms=[ CTTermItem( uid=term["uid"], @@ -499,11 +526,19 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( 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_codelist=ct_codelist, ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=activity_item.text_value, @@ -630,11 +665,17 @@ def _create_ar( codelist_uid=term["codelist_uid"], ) ) + if codelist := activity_item["ct_codelist"]: + ct_codelist = CTCodelistItem(uid=codelist["uid"], name=codelist["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_codelist=ct_codelist, ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=activity_item.get("text_value"), @@ -743,6 +784,7 @@ def specific_alias_clause(self, **kwargs) -> str: 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 @@ -880,9 +922,7 @@ def get_activity_instance_overview( RETURN last(hvs) as has_version } """ - query = ( - match - + """ + query = match + """ WITH activity_instance_root,activity_instance_value, has_version, head([(library)-[:CONTAINS_CONCEPT]->(activity_instance_root) | library.name]) AS instance_library_name, head([(activity_instance_value)-[:ACTIVITY_INSTANCE_CLASS]-> @@ -981,6 +1021,7 @@ def get_activity_instance_overview( 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]-(:CTTermContext)-[:HAS_SELECTED_TERM]-(:CTTermRoot)-[:HAS_NAME_ROOT]->(CTTermNamesRoot)-[:LATEST]->(dimension_value:CTTermNameValue) @@ -1019,7 +1060,6 @@ def get_activity_instance_overview( ) AS all_versions RETURN * """ - ) result_array, attribute_names = db.cypher_query(query=query, params=params) BusinessLogicException.raise_if( len(result_array) != 1, 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 9eb6d92e..54710e7f 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 @@ -435,11 +435,14 @@ def create_query_filter_statement( def _create_new_value_node(self, ar: ActivityAR) -> ActivityValue: value_node: ActivityValue = super()._create_new_value_node(ar=ar) - value_node.synonyms = ar.concept_vo.synonyms - value_node.request_rationale = ar.concept_vo.request_rationale + value_node.synonyms = ar.concept_vo.synonyms # type: ignore[assignment] + if ar.concept_vo.request_rationale: + value_node.request_rationale = ar.concept_vo.request_rationale value_node.is_request_final = ar.concept_vo.is_request_final - value_node.reason_for_rejecting = ar.concept_vo.reason_for_rejecting - value_node.contact_person = ar.concept_vo.contact_person + if ar.concept_vo.reason_for_rejecting: + value_node.reason_for_rejecting = ar.concept_vo.reason_for_rejecting + if ar.concept_vo.contact_person: + value_node.contact_person = ar.concept_vo.contact_person value_node.is_request_rejected = ar.concept_vo.is_request_rejected value_node.is_data_collected = ar.concept_vo.is_data_collected value_node.is_multiple_selection_allowed = ( @@ -797,9 +800,7 @@ def get_activity_overview( RETURN last(hvs) as has_version } """ - query = ( - match - + """ + 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, @@ -870,7 +871,6 @@ def get_activity_overview( ) | v.version] ) AS all_versions """ - ) result_array, attribute_names = db.cypher_query(query=query, params=params) BusinessLogicException.raise_if( len(result_array) != 1, @@ -1043,9 +1043,7 @@ def get_linked_upgradable_activity_instances( MATCH (activity_root:ActivityRoot {uid:$uid})-[:LATEST]->(activity_value:ActivityValue) """ - query = ( - match - + """ + query = match + """ MATCH (activity_value)-[:HAS_GROUPING]->(activity_grouping:ActivityGrouping)<-[:HAS_ACTIVITY]- (activity_instance_value:ActivityInstanceValue)<-[aihv:HAS_VERSION]-(activity_instance_root:ActivityInstanceRoot) OPTIONAL MATCH (activity_grouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value:ActivitySubGroupValue)<-[:HAS_VERSION]-(activity_subgroup_root:ActivitySubGroupRoot) @@ -1084,7 +1082,6 @@ def get_linked_upgradable_activity_instances( RETURN collect(activity_instance) as activity_instances """ - ) result_array, attribute_names = db.cypher_query(query=query, params=params) if len(result_array) == 0: return None diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py index 29cd2449..f3b09602 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/activities/activity_sub_group_repository.py @@ -381,13 +381,10 @@ def get_linked_activity_uids( # Add COUNT query for total if needed if total_count: - count_query = ( - query - + """ + count_query = query + """ // 9. Return the count of activities for pagination RETURN count(activity_uid) as total """ - ) count_result, _ = db.cypher_query(query=count_query, params=params) total = count_result[0][0] if count_result else 0 else: @@ -515,9 +512,7 @@ def get_linked_upgradable_activities( MATCH (activity_subgroup_root:ActivitySubGroupRoot {uid:$uid})-[:LATEST]->(activity_subgroup_value:ActivitySubGroupValue) """ - query = ( - match - + """ + query = match + """ // Find all activities linked to this subgroup value MATCH (activity_root:ActivityRoot)-[aihv:HAS_VERSION]->(activity_value:ActivityValue)-[:HAS_GROUPING]-> (:ActivityGrouping)-[:HAS_SELECTED_SUBGROUP]->(activity_subgroup_value) @@ -556,7 +551,6 @@ def get_linked_upgradable_activities( RETURN collect(activity) as activities """ - ) result_array, attribute_names = db.cypher_query(query=query, params=params) if len(result_array) == 0: return None 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 27c0a650..b26d00cf 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 @@ -46,6 +46,7 @@ class ConceptGenericRepository( return_model: type = BaseModel filter_query_parameters: dict[Any, Any] = {} sort_by: dict[Any, Any] | None = None + wildcard_properties_list: list[str] | None = None @abstractmethod def _create_aggregate_root_instance_from_cypher_result( @@ -379,6 +380,7 @@ def find_all( filter_operator=filter_operator, total_count=total_count, return_model=self.return_model, + wildcard_properties_list=self.wildcard_properties_list, format_filter_sort_keys=self.format_filter_sort_keys, one_element_extra=filtering_active, ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/pharmaceutical_product_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/pharmaceutical_product_repository.py index b59dd843..b9a44879 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/pharmaceutical_product_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/pharmaceutical_product_repository.py @@ -54,6 +54,38 @@ class PharmaceuticalProductRepository(ConceptGenericRepository): value_class = PharmaceuticalProductValue return_model = PharmaceuticalProduct + # Flat string aliases for wildcard filtering across linked entities + wildcard_properties_list: list[str] = [ + "uid", + "external_id", + "name", + "library_name", + "status", + "version", + "author_username", + "_search_derived_pp_name", + "_search_dosage_form_names", + "_search_route_of_admin_names", + "_search_active_substance_inns", + "_search_active_substance_long_numbers", + "_search_active_substance_short_numbers", + "_search_active_substance_analyte_numbers", + "_search_active_substance_external_ids", + ] + + # Mapping of sort/filter field names to sortable Cypher aliases + _SORT_KEY_MAP = { + "dosage_form": "_search_dosage_form_names", + "dosage_forms": "_search_dosage_form_names", + "route_of_administration": "_search_route_of_admin_names", + "routes_of_administration": "_search_route_of_admin_names", + "derived_name": "_search_derived_pp_name", + } + + @classmethod + def format_filter_sort_keys(cls, key: str) -> str: + return cls._SORT_KEY_MAP.get(key, key) + def _create_new_value_node(self, ar: _AggregateRootType) -> VersionValue: value_node = super()._create_new_value_node(ar=ar) value_node.save() @@ -353,5 +385,18 @@ def specific_alias_clause(self, **kwargs) -> str: [(concept_value)-[:HAS_FORMULATION]->(formulation:IngredientFormulation)-[:HAS_INGREDIENT]->(ingredient:Ingredient)-[ingr_substance_rel:HAS_SUBSTANCE]->(active_substance:ActiveSubstanceRoot) | {active_substance:active_substance, ingr_substance_rel:ingr_substance_rel}] as ingredient_substances, [(concept_value)-[:HAS_FORMULATION]->(formulation:IngredientFormulation)-[:HAS_INGREDIENT]->(ingredient:Ingredient)-[ingr_strength_rel:HAS_STRENGTH_VALUE]->(strength:NumericValueWithUnitRoot) | {strength:strength, ingr_strength_rel:ingr_strength_rel}] as ingredient_strengths, [(concept_value)-[:HAS_FORMULATION]->(formulation:IngredientFormulation)-[:HAS_INGREDIENT]->(ingredient:Ingredient)-[ingr_half_life_rel:HAS_HALF_LIFE]->(half_life:NumericValueWithUnitRoot) | {half_life:half_life, ingr_half_life_rel:ingr_half_life_rel}] as ingredient_half_lives, - [(concept_value)-[:HAS_FORMULATION]->(formulation:IngredientFormulation)-[:HAS_INGREDIENT]->(ingredient:Ingredient)-[ingr_lag_time_rel:HAS_LAG_TIME]->(lag_time:LagTimeRoot) | {lag_time:lag_time, ingr_lag_time_rel:ingr_lag_time_rel}] as ingredient_lag_times + [(concept_value)-[:HAS_FORMULATION]->(formulation:IngredientFormulation)-[:HAS_INGREDIENT]->(ingredient:Ingredient)-[ingr_lag_time_rel:HAS_LAG_TIME]->(lag_time:LagTimeRoot) | {lag_time:lag_time, ingr_lag_time_rel:ingr_lag_time_rel}] as ingredient_lag_times, + + // Flat string aliases for wildcard filtering across linked entities + reduce(s='', x IN [(concept_value)-[:HAS_FORMULATION]->(:IngredientFormulation)-[:HAS_INGREDIENT]->(pp_ingr:Ingredient)-[:HAS_SUBSTANCE]->(pp_as:ActiveSubstanceRoot)-[:LATEST]->(pp_as_val:ActiveSubstanceValue) + | coalesce(pp_as_val.inn, pp_as_val.long_number, pp_as_val.short_number, pp_as_val.analyte_number, '?') + ' ' + + coalesce(pp_ingr.formulation_name, '') + + coalesce(' (' + head([(pp_ingr)-[:HAS_STRENGTH_VALUE]->(pp_str:NumericValueWithUnitRoot)-[:LATEST]->(pp_str_val:NumericValueWithUnitValue)-[:HAS_UNIT_DEFINITION]->(pp_unit:UnitDefinitionRoot)-[:LATEST]->(pp_unit_val:UnitDefinitionValue) | CASE WHEN pp_str_val.value = toInteger(pp_str_val.value) THEN toString(toInteger(pp_str_val.value)) ELSE toString(pp_str_val.value) END + ' ' + pp_unit_val.name]) + ')', '')] | s + CASE WHEN s = '' THEN '' ELSE ', ' END + x) AS _search_derived_pp_name, + reduce(s='', x IN [(concept_value)-[:HAS_DOSAGE_FORM]->(df_ctx2:CTTermContext)-[:HAS_SELECTED_TERM]->(df2:CTTermRoot)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(df2_val:CTTermNameValue) | df2_val.name] | s + ' ' + coalesce(x, '')) AS _search_dosage_form_names, + reduce(s='', x IN [(concept_value)-[:HAS_ROUTE_OF_ADMINISTRATION]->(roa_ctx2:CTTermContext)-[:HAS_SELECTED_TERM]->(roa2:CTTermRoot)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(roa2_val:CTTermNameValue) | roa2_val.name] | s + ' ' + coalesce(x, '')) AS _search_route_of_admin_names, + reduce(s='', x IN [(concept_value)-[:HAS_FORMULATION]->(:IngredientFormulation)-[:HAS_INGREDIENT]->(:Ingredient)-[:HAS_SUBSTANCE]->(as3:ActiveSubstanceRoot)-[:LATEST]->(as3_val:ActiveSubstanceValue) | as3_val.inn] | s + ' ' + coalesce(x, '')) AS _search_active_substance_inns, + reduce(s='', x IN [(concept_value)-[:HAS_FORMULATION]->(:IngredientFormulation)-[:HAS_INGREDIENT]->(:Ingredient)-[:HAS_SUBSTANCE]->(as4:ActiveSubstanceRoot)-[:LATEST]->(as4_val:ActiveSubstanceValue) | as4_val.short_number] | s + ' ' + coalesce(x, '')) AS _search_active_substance_short_numbers, + reduce(s='', x IN [(concept_value)-[:HAS_FORMULATION]->(:IngredientFormulation)-[:HAS_INGREDIENT]->(:Ingredient)-[:HAS_SUBSTANCE]->(as4:ActiveSubstanceRoot)-[:LATEST]->(as4_val:ActiveSubstanceValue) | as4_val.long_number] | s + ' ' + coalesce(x, '')) AS _search_active_substance_long_numbers, + reduce(s='', x IN [(concept_value)-[:HAS_FORMULATION]->(:IngredientFormulation)-[:HAS_INGREDIENT]->(:Ingredient)-[:HAS_SUBSTANCE]->(as5:ActiveSubstanceRoot)-[:LATEST]->(as5_val:ActiveSubstanceValue) | as5_val.analyte_number] | s + ' ' + coalesce(x, '')) AS _search_active_substance_analyte_numbers, + reduce(s='', x IN [(concept_value)-[:HAS_FORMULATION]->(:IngredientFormulation)-[:HAS_INGREDIENT]->(:Ingredient)-[:HAS_SUBSTANCE]->(as6:ActiveSubstanceRoot)-[:LATEST]->(as6_val:ActiveSubstanceValue) | as6_val.external_id] | s + ' ' + coalesce(x, '')) AS _search_active_substance_external_ids """ diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/configuration_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/configuration_repository.py index 883347ae..2785a707 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/configuration_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/controlled_terminologies/configuration_repository.py @@ -4,7 +4,7 @@ Collect, Last, NodeNameResolver, - Optional, + Path, RawCypher, RelationNameResolver, ) @@ -56,13 +56,15 @@ def find_all( all_configurations = [ CTConfigOGM.model_validate(sas_node) for sas_node in ( - self.root_class.nodes.fetch_relations( + self.root_class.nodes.traverse( "has_latest_value", - Optional("has_latest_value__has_configured_codelist"), - Optional("has_latest_value__has_configured_term"), + Path( + value="has_latest_value__has_configured_codelist", optional=True + ), + Path(value="has_latest_value__has_configured_term", optional=True), ) .subquery( - self.root_class.nodes.traverse_relations(has_version="has_version") + self.root_class.nodes.traverse(has_version="has_version") .intermediate_transform( { "has_version": { 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 27f02fd2..a0c649c2 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 @@ -181,22 +181,18 @@ def minimal_count_query( ) params["library"] = library if package: - where_clauses.append( - """ + where_clauses.append(""" (:CTPackage {name: $package})-[:CONTAINS_CODELIST]->(:CTPackageCodelist)-[:CONTAINS_ATTRIBUTES]-> (:CTCodelistAttributesValue)<-[:HAS_VERSION]-(:CTCodelistAttributesRoot)<-[:HAS_ATTRIBUTES_ROOT]-(codelist_root) - """ - ) + """) params["package"] = package if is_sponsor: - where_clauses.append( - """ + where_clauses.append(""" EXISTS { MATCH (lib:Library)-[:CONTAINS_CODELIST]->(codelist_root) WHERE lib.name <> $cdisc_library_name } - """ - ) + """) params["cdisc_library_name"] = settings.cdisc_library_name query = "MATCH (codelist_root:CTCodelistRoot)" if where_clauses: diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_completeness_tags_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_completeness_tags_repository.py new file mode 100644 index 00000000..cb786736 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_completeness_tags_repository.py @@ -0,0 +1,133 @@ +# pylint: disable=invalid-name +from neomodel import db + +from clinical_mdr_api.domain_repositories.models.data_completeness_tag import ( + DataCompletenessTag as DataCompletenessTagNode, +) +from clinical_mdr_api.models.data_completeness_tag import DataCompletenessTag +from common.exceptions import NotFoundException + + +class DataCompletenessTagRepository: + def _transform_to_model(self, item: DataCompletenessTagNode) -> DataCompletenessTag: + return DataCompletenessTag( + uid=item.uid, + name=item.name, + ) + + def _transform_to_models( + self, data: list[list[DataCompletenessTagNode]] + ) -> list[DataCompletenessTag]: + return [self._transform_to_model(elm[0]) for elm in data] + + def retrieve_all_data_completeness_tags(self) -> list[DataCompletenessTag]: + rs = db.cypher_query( + """ + MATCH (n:DataCompletenessTag) + RETURN n + """, + resolve_objects=True, + ) + + return self._transform_to_models(rs[0]) + + def find_data_completeness_tag_by_name( + self, name: str + ) -> DataCompletenessTag | None: + rs = db.cypher_query( + """ + MATCH (n:DataCompletenessTag {name: $name}) + RETURN n + """, + params={"name": name}, + resolve_objects=True, + ) + + if rs[0]: + return self._transform_to_model(rs[0][0][0]) + + return None + + def create_data_completeness_tag( + self, + name: str, + ) -> DataCompletenessTag: + uid = DataCompletenessTagNode.get_next_free_uid_and_increment_counter() + + rs = db.cypher_query( + """ + CREATE (n:DataCompletenessTag) + SET + n.uid = $uid, + n.name = $name + RETURN n + """, + params={ + "uid": uid, + "name": name, + }, + resolve_objects=True, + ) + + return self._transform_to_model(rs[0][0][0]) + + def update_data_completeness_tag(self, uid: str, name: str) -> DataCompletenessTag: + rs = db.cypher_query( + """ + MATCH (n:DataCompletenessTag {uid: $uid}) + SET n.name = $name + RETURN n + """, + params={"uid": uid, "name": name}, + resolve_objects=True, + ) + + NotFoundException.raise_if_not(rs[0], "Data Completeness Tag", uid, "UID") + + return self._transform_to_model(rs[0][0][0]) + + def delete_data_completeness_tag(self, uid: str) -> None: + db.cypher_query( + """ + MATCH (n:DataCompletenessTag {uid: $uid}) + DELETE n + """, + params={"uid": uid}, + ) + + def get_tags_for_study(self, study_uid: str) -> list[DataCompletenessTag]: + rs = db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $study_uid})-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) + RETURN t + """, + params={"study_uid": study_uid}, + resolve_objects=True, + ) + + return self._transform_to_models(rs[0]) + + def assign_tag_to_study(self, study_uid: str, tag_uid: str) -> DataCompletenessTag: + rs = db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $study_uid}) + MATCH (t:DataCompletenessTag {uid: $tag_uid}) + MERGE (sr)-[:HAS_COMPLETENESS_TAG]->(t) + RETURN t + """, + params={"study_uid": study_uid, "tag_uid": tag_uid}, + resolve_objects=True, + ) + + NotFoundException.raise_if_not(rs[0], "Data Completeness Tag", tag_uid, "UID") + + return self._transform_to_model(rs[0][0][0]) + + def remove_tag_from_study(self, study_uid: str, tag_uid: str) -> None: + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $study_uid})-[r:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag {uid: $tag_uid}) + DELETE r + """, + params={"study_uid": study_uid, "tag_uid": tag_uid}, + ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_suppliers/data_supplier_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_suppliers/data_supplier_repository.py index 1a6b0099..687e4613 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_suppliers/data_supplier_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/data_suppliers/data_supplier_repository.py @@ -117,7 +117,7 @@ def extend_distinct_headers_query( if need_latest_version: return nodeset.subquery( - self.root_class.nodes.fetch_relations("has_version") + self.root_class.nodes.traverse("has_version") .intermediate_transform( {"rel": {"source": RelationNameResolver("has_version")}}, ordering=[ diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/generic_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/generic_repository.py index 420bac02..eadf4fd0 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/generic_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/generic_repository.py @@ -96,12 +96,14 @@ def _db_create_and_link_nodes( ): """ Creates versioned root and versioned object nodes. - # TODO - GEneration of uids should be removed (additional service?) + # TODO - Generation of uids should be removed (additional service?) """ if save_root: self._db_save_node(root) self._db_save_node(value) + latest_draft: RelationshipDefinition | None + latest_final: RelationshipDefinition | None ( has_version, has_latest_value, @@ -281,14 +283,10 @@ def _manage_versioning_with_relations( if "date" not in properties: properties["date"] = datetime.datetime.now(datetime.timezone.utc) properties = action_type.deflate(properties, skip_empty=True) - query.append( - dedent( - f""" + query.append(dedent(f""" CREATE (action:{':'.join(action_type.inherited_labels())}:StudyAction {{{', '.join(f'{k}: ${k}' for k in properties)}}})<-[:AUDIT_TRAIL]-(study_root) WITH * - """ - ).strip() - ) + """).strip()) # Match & link previous node if before: @@ -306,7 +304,7 @@ def _manage_versioning_with_relations( # Copy relationships if before and after: - _exclude_relationships = set() + _exclude_relationships: set[Any] = set() _exclude_labels = { StudyValue.__name__, # exclude (HAS_...) relations from StudyValue node StudyAction.__name__, # exclude (BEFORE/AFTER) relations from StudyAction node @@ -323,9 +321,7 @@ def _manage_versioning_with_relations( "exclude_relationships must be an iterable of StructuredNode subclasses or relationship type strings." ) - query.append( - dedent( - """ + query.append(dedent(""" CALL { WITH before, after MATCH (before)-[r]->(target) @@ -340,26 +336,20 @@ def _manage_versioning_with_relations( CALL apoc.create.relationship(source, type(r), properties(r), after) YIELD rel RETURN count(rel) AS num_rels_in } - """ - ).strip() - ) + """).strip()) params["_exclude_relationships"] = tuple(_exclude_relationships) params["_exclude_labels"] = tuple(_exclude_labels) # Unlink previous relationship from latest StudyValue if before: - query.append( - dedent( - """ + query.append(dedent(""" CALL { WITH study_value, before MATCH (study_value)-[rel]->(before) DELETE rel RETURN count(rel) AS num_rels_del } - """ - ).strip() - ) + """).strip()) # Execute query query.append("RETURN action") 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 7f246b72..e57880e0 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 @@ -8,7 +8,6 @@ from cachetools import TTLCache, cached from cachetools.keys import hashkey from neomodel import ( - OUTGOING, NodeClassNotDefined, RelationshipDefinition, RelationshipManager, @@ -16,6 +15,7 @@ db, ) from neomodel.exceptions import DoesNotExist +from neomodel.util import RelationshipDirection from clinical_mdr_api.domain_repositories._generic_repository_interface import ( GenericRepository, @@ -649,7 +649,7 @@ def _get_item_versions( root.__label__, { "node_class": self.value_class, - "direction": OUTGOING, + "direction": RelationshipDirection.OUTGOING, "model": VersionRelationship, }, ) @@ -914,10 +914,10 @@ def find_by_uid_2( value, relationship = self._get_latest_value_with_status( root, status, - has_version_rel, - latest_draft_rel, - latest_final_rel, - latest_retired_rel, + has_version_rel, # type: ignore[arg-type] + latest_draft_rel, # type: ignore[arg-type] + latest_final_rel, # type: ignore[arg-type] + latest_retired_rel, # type: ignore[arg-type] ) else: # Find the latest version (regardless of status) that exists at the specified date @@ -978,7 +978,7 @@ def _get_latest_value_with_status( latest_retired_rel: RelationshipManager, ) -> tuple[VersionValue | None, VersionRelationship | None]: relationship: VersionRelationship | None = None - value: VersionValue + value: VersionValue | None relationship_manager_to_use: RelationshipManager = latest_retired_rel if status == LibraryItemStatus.FINAL: @@ -987,11 +987,12 @@ def _get_latest_value_with_status( relationship_manager_to_use = latest_draft_rel value = relationship_manager_to_use.get_or_none() if value is None: - value = has_version_rel.match(status=status.value).all() - if not value: + possible_values = has_version_rel.match(status=status.value).all() + if not possible_values: return None, None end_dates = { - has_version_rel.relationship(node).end_date: node for node in value + has_version_rel.relationship(node).end_date: node + for node in possible_values } last_date = max(end_dates.keys()) value = end_dates[last_date] @@ -1419,13 +1420,13 @@ def find_by_uid_optimized( activity_root=activity_root, activity_subgroups_root=activity_subgroups_root, unit_definition=unit_definition, - indications=indications[0] if indications else [], + indications=indications, template_type=template_type, - categories=categories[0] if categories else [], - subcategories=subcategories[0] if subcategories else [], - activities=activities[0] if activities else [], - activity_groups=activity_groups[0] if activity_groups else [], - activity_subgroups=activity_subgroups[0] if activity_subgroups else [], + categories=categories, + subcategories=subcategories, + activities=activities, + activity_groups=activity_groups, + activity_subgroups=activity_subgroups, instance_template=instance_template, ) @@ -1687,13 +1688,13 @@ def get_all_optimized( activity_root=activity_root, activity_subgroups_root=activity_subgroups_root, unit_definition=unit_definition, - indications=indications[0] if indications else [], + indications=indications, template_type=template_type, - categories=categories[0] if categories else [], - subcategories=subcategories[0] if subcategories else [], - activities=activities[0] if activities else [], - activity_groups=activity_groups[0] if activity_groups else [], - activity_subgroups=activity_subgroups[0] if activity_subgroups else [], + categories=categories, + subcategories=subcategories, + activities=activities, + activity_groups=activity_groups, + activity_subgroups=activity_subgroups, instance_template=instance_template, **kwargs, ) @@ -1962,14 +1963,12 @@ def date_stmt(filter_by: dict[str, dict[str, Any]], name: str): ".", "_" ) params[param_variable] = value - fields_generic.append( - f""" + fields_generic.append(f""" CASE WHEN apoc.meta.cypher.isType({cypher_name}, "STRING") THEN toLower(toString({cypher_name})) {operator} toLower(toString(${param_variable})) ELSE {cypher_name} {operator} ${param_variable} END -""" - ) +""") where_stmt += "(" + " OR ".join(fields_generic) + ")" @@ -2017,14 +2016,12 @@ def date_stmt(filter_by: dict[str, dict[str, Any]], name: str): ) ) params[param_variable] = value - fields_non_generic.append( - f""" + fields_non_generic.append(f""" CASE WHEN apoc.meta.cypher.isType({mapping[filter_name]}, "STRING") THEN toLower(toString({mapping[filter_name]})) {operator} toLower(toString(${param_variable})) ELSE {mapping[filter_name]} {operator} ${param_variable} END -""" - ) +""") if not where_stmt: where_stmt += f" {filter_operator.value} ".join(fields_non_generic) @@ -2624,36 +2621,6 @@ def _activity_instance_root_match_return_stmt(self): MATCH (activity_item_unit_definition_root)-[:LATEST]->(activity_item_unit_definition_value:UnitDefinitionValue) RETURN collect(DISTINCT {uid:activity_item_unit_definition_root.uid, name:activity_item_unit_definition_value.name }) as unit_definitions } - CALL{ - WITH activity_item - MATCH (activity_item)<-[ltai:LINKS_TO_ACTIVITY_ITEM]-(odm_form_root:OdmFormRoot) - MATCH (odm_form_root)-[:LATEST]->(odm_form_value:OdmFormValue) - RETURN collect(DISTINCT { - uid: odm_form_root.uid, - oid: odm_form_value.oid, - name: odm_form_value.name, - order: ltai.order, - primary: ltai.primary, - preset_response_value: ltai.preset_response_value, - value_condition: ltai.value_condition, - value_dependent_map: ltai.value_dependent_map - }) AS odm_forms - } - CALL{ - WITH activity_item - MATCH (activity_item)<-[ltai:LINKS_TO_ACTIVITY_ITEM]-(odm_item_group_root:OdmItemRoot) - MATCH (odm_item_group_root)-[:LATEST]->(odm_item_group_value:OdmItemValue) - RETURN collect(DISTINCT { - uid: odm_item_group_root.uid, - oid: odm_item_group_value.oid, - name: odm_item_group_value.name, - order: ltai.order, - primary: ltai.primary, - preset_response_value: ltai.preset_response_value, - value_condition: ltai.value_condition, - value_dependent_map: ltai.value_dependent_map - }) AS odm_item_groups - } CALL{ WITH activity_item MATCH (activity_item)<-[ltai:LINKS_TO_ACTIVITY_ITEM]-(odm_item_root:OdmItemRoot) @@ -2676,8 +2643,6 @@ def _activity_instance_root_match_return_stmt(self): unit_definitions: unit_definitions, is_adam_param_specific: activity_item.is_adam_param_specific, text_value: activity_item.text_value, - odm_forms: odm_forms, - odm_item_groups: odm_item_groups, odm_items: odm_items }) as activity_items } diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/active_substance.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/active_substance.py index 7e49f9aa..71d5f495 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/active_substance.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/active_substance.py @@ -1,4 +1,4 @@ -from neomodel import RelationshipTo, StringProperty, ZeroOrOne +from neomodel import RelationshipTo, ZeroOrOne from clinical_mdr_api.domain_repositories.models.concepts import ( ConceptRoot, @@ -9,6 +9,7 @@ ClinicalMdrRel, VersionRelationship, ) +from common.neomodel import StringProperty class ActiveSubstanceValue(ConceptValue): 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 c0ee99ba..fb116d19 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 @@ -1,12 +1,8 @@ from neomodel import ( - ArrayProperty, - BooleanProperty, - FloatProperty, One, OneOrMore, RelationshipFrom, RelationshipTo, - StringProperty, ZeroOrMore, ZeroOrOne, ) @@ -21,6 +17,7 @@ UnitDefinitionRoot, ) from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( + CTCodelistRoot, CTTermContext, ) from clinical_mdr_api.domain_repositories.models.generic import ( @@ -29,6 +26,12 @@ ClinicalMdrRel, VersionRelationship, ) +from common.neomodel import ( + ArrayProperty, + BooleanProperty, + FloatProperty, + StringProperty, +) class ActivityGroupValue(ConceptValue): @@ -119,7 +122,7 @@ class ActivityGrouping(ClinicalMdrNodeWithUID): class ActivityValue(ConceptValue): - synonyms = ArrayProperty(StringProperty()) + synonyms = ArrayProperty(StringProperty()) # type: ignore is_data_collected = BooleanProperty() is_multiple_selection_allowed = BooleanProperty(default=True) has_latest_value = RelationshipFrom("ActivityRoot", "LATEST", model=ClinicalMdrRel) @@ -178,6 +181,9 @@ class ActivityItem(ClinicalMdrNode): "HAS_ACTIVITY_ITEM", model=ClinicalMdrRel, ) + has_codelist = RelationshipTo( + CTCodelistRoot, "HAS_CODELIST", model=ClinicalMdrRel, cardinality=ZeroOrMore + ) has_ct_term = RelationshipTo( CTTermContext, "HAS_CT_TERM", model=ClinicalMdrRel, cardinality=ZeroOrMore ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/biomedical_concepts.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/biomedical_concepts.py index 2c80f7dc..c9dada9a 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/biomedical_concepts.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/biomedical_concepts.py @@ -1,13 +1,4 @@ -from neomodel import ( - BooleanProperty, - IntegerProperty, - One, - OneOrMore, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrOne, -) +from neomodel import One, OneOrMore, RelationshipFrom, RelationshipTo, ZeroOrOne from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTCodelistRoot, @@ -23,6 +14,7 @@ DatasetClass, VariableClass, ) +from common.neomodel import BooleanProperty, IntegerProperty, StringProperty class ActivityItemClassRel(ClinicalMdrRel): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/brand.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/brand.py index 6a906e6c..726595e6 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/brand.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/brand.py @@ -1,6 +1,5 @@ -from neomodel import BooleanProperty, StringProperty - from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrNodeWithUID +from common.neomodel import BooleanProperty, StringProperty class Brand(ClinicalMdrNodeWithUID): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/clinical_programme.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/clinical_programme.py index af9adfe2..e47625c4 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/clinical_programme.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/clinical_programme.py @@ -1,6 +1,5 @@ -from neomodel import StringProperty - from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrNodeWithUID +from common.neomodel import StringProperty class ClinicalProgramme(ClinicalMdrNodeWithUID): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/comments.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/comments.py index 1b3c656e..9738f675 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/comments.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/comments.py @@ -1,17 +1,11 @@ -from neomodel import ( - BooleanProperty, - One, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, -) +from neomodel import One, RelationshipFrom, RelationshipTo, ZeroOrMore from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNodeWithUID, ClinicalMdrRel, ZonedDateTimeProperty, ) +from common.neomodel import BooleanProperty, StringProperty class CommentTopic(ClinicalMdrNodeWithUID): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/compounds.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/compounds.py index b40f1297..3826d7cd 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/compounds.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/compounds.py @@ -1,4 +1,4 @@ -from neomodel import BooleanProperty, One, RelationshipFrom, RelationshipTo +from neomodel import One, RelationshipFrom, RelationshipTo from clinical_mdr_api.domain_repositories.models.concepts import ( ConceptRoot, @@ -8,6 +8,7 @@ ClinicalMdrRel, VersionRelationship, ) +from common.neomodel import BooleanProperty class CompoundValue(ConceptValue): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/concepts.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/concepts.py index 15729aa9..59a9dbc6 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/concepts.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/concepts.py @@ -1,14 +1,4 @@ -from neomodel import ( - BooleanProperty, - FloatProperty, - IntegerProperty, - One, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - ZeroOrOne, -) +from neomodel import One, RelationshipFrom, RelationshipTo, ZeroOrMore, ZeroOrOne from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTTermContext, @@ -21,6 +11,12 @@ VersionRoot, VersionValue, ) +from common.neomodel import ( + BooleanProperty, + FloatProperty, + IntegerProperty, + StringProperty, +) class ConceptValue(VersionValue): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/configuration.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/configuration.py index 0ee12d03..33995d4d 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/configuration.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/configuration.py @@ -1,4 +1,4 @@ -from neomodel import BooleanProperty, RelationshipTo, StringProperty +from neomodel import RelationshipTo from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTCodelistRoot, @@ -10,6 +10,7 @@ VersionRoot, VersionValue, ) +from common.neomodel import BooleanProperty, StringProperty class CTConfigValue(VersionValue): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/controlled_terminology.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/controlled_terminology.py index 594760ec..55bc469c 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/controlled_terminology.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/controlled_terminology.py @@ -1,17 +1,6 @@ from datetime import datetime -from neomodel import ( - ArrayProperty, - BooleanProperty, - DateProperty, - FloatProperty, - IntegerProperty, - One, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrOne, -) +from neomodel import One, RelationshipFrom, RelationshipTo, ZeroOrOne from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNode, @@ -24,6 +13,14 @@ from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_attributes import ( DEFAULT_CODELIST_TYPE, ) +from common.neomodel import ( + ArrayProperty, + BooleanProperty, + DateProperty, + FloatProperty, + IntegerProperty, + StringProperty, +) class CTPackage(ClinicalMdrNodeWithUID): @@ -62,7 +59,7 @@ class CTCodelistAttributesValue(ControlledTerminology): extensible = BooleanProperty() synonyms = ArrayProperty() is_ordinal = BooleanProperty(default=False) - codelist_type = StringProperty(default=DEFAULT_CODELIST_TYPE) + codelist_type = StringProperty(default=DEFAULT_CODELIST_TYPE) # type: ignore[call-arg] class CTCodelistAttributesRoot(ControlledTerminology): @@ -168,8 +165,8 @@ class CodelistTermRelationship(ClinicalMdrRel): start_date: datetime = ZonedDateTimeProperty() end_date: datetime | None = ZonedDateTimeProperty() author_id = StringProperty() - order: int | None = IntegerProperty() - ordinal: float | None = FloatProperty() + order: int | None = IntegerProperty() # type: ignore[assignment] + ordinal: float | None = FloatProperty() # type: ignore[assignment] class CTCodelistRoot(ControlledTerminologyWithUID): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_completeness_tag.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_completeness_tag.py new file mode 100644 index 00000000..ea255eea --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_completeness_tag.py @@ -0,0 +1,7 @@ +from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrNodeWithUID +from common.neomodel import StringProperty + + +class DataCompletenessTag(ClinicalMdrNodeWithUID): + + name = StringProperty() diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_suppliers.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_suppliers.py index 735f22b4..1f0ecf84 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_suppliers.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/data_suppliers.py @@ -1,4 +1,4 @@ -from neomodel import IntegerProperty, RelationshipTo, StringProperty, ZeroOrOne +from neomodel import RelationshipTo, ZeroOrOne from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTTermContext, @@ -9,6 +9,7 @@ VersionRoot, VersionValue, ) +from common.neomodel import IntegerProperty, StringProperty class DataSupplierValue(VersionValue): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/dictionary.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/dictionary.py index c9aa4648..80c8eeb8 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/dictionary.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/dictionary.py @@ -1,4 +1,4 @@ -from neomodel import RelationshipFrom, RelationshipTo, StringProperty +from neomodel import RelationshipFrom, RelationshipTo from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CodelistTermRelationship, @@ -10,6 +10,7 @@ VersionRoot, VersionValue, ) +from common.neomodel import StringProperty class DictionaryTermValue(VersionValue): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py index 6b08a17e..4ab6ef38 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/feature_flag.py @@ -1,6 +1,5 @@ -from neomodel import BooleanProperty, IntegerProperty, StringProperty - from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrNode +from common.neomodel import BooleanProperty, IntegerProperty, StringProperty class FeatureFlag(ClinicalMdrNode): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/generic.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/generic.py index 661c41cb..e3f7550c 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/generic.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/generic.py @@ -1,13 +1,11 @@ import datetime +from typing import TYPE_CHECKING, Any import neo4j.time from neomodel import ( - BooleanProperty, DateTimeProperty, - IntegerProperty, RelationshipFrom, RelationshipTo, - StringProperty, StructuredNode, StructuredRel, db, @@ -20,17 +18,26 @@ from clinical_mdr_api.domains.enums import LibraryItemStatus from common.config import settings from common.exceptions import NotFoundException +from common.neomodel import BooleanProperty, IntegerProperty, StringProperty from common.utils import convert_to_datetime +if TYPE_CHECKING: -class ZonedDateTimeProperty(DateTimeProperty): - @validator - def deflate(self, value: datetime.datetime): - return convert_to_tz_aware_datetime(value) + class ZonedDateTimeProperty(datetime.datetime): + def __init__( + self, *args: Any, **kwargs: Any # pylint: disable=unused-argument + ) -> None: ... - @validator - def inflate(self, value: neo4j.time.DateTime): - return convert_to_datetime(value) +else: + + class ZonedDateTimeProperty(DateTimeProperty): + @validator + def deflate(self, value: datetime.datetime): + return convert_to_tz_aware_datetime(value) + + @validator + def inflate(self, value: neo4j.time.DateTime): + return convert_to_datetime(value) class ClinicalMdrNode(StructuredNode): @@ -64,7 +71,7 @@ class ClinicalMdrNodeWithUID(ClinicalMdrNode): """ __abstract_node__ = True - uid = StringProperty(unique_index=True) + uid = StringProperty(unique_index=True) # type: ignore[call-arg] def __hash__(self): return hash(self.uid) @@ -78,18 +85,16 @@ def get_next_free_uid_and_increment_counter(cls) -> str: object_name = cls.__name__.removesuffix("Root") digits = str( - db.cypher_query( - """ + db.cypher_query(""" MERGE (m:Counter{{counterId:'{LABEL}Counter'}}) ON CREATE SET m:{LABEL}Counter, m.count=0 WITH m CALL apoc.atomic.add(m,'count',1,1) yield oldValue, newValue WITH toInteger(newValue) as uid_number RETURN "{LABEL}_"+apoc.text.lpad(""+(uid_number), {number_of_digits}, "0") - """.format( - LABEL=object_name, number_of_digits=settings.number_of_uid_digits - ) - )[0][0][0] + """.format(LABEL=object_name, number_of_digits=settings.number_of_uid_digits))[ + 0 + ][0][0] ) return digits @@ -144,17 +149,13 @@ def save(self): else type(self).__name__ ) - new_uid = db.cypher_query( - """ + new_uid = db.cypher_query(""" MERGE (m:Counter{{counterId:'{LABEL}Counter'}}) ON CREATE SET m:{LABEL}Counter, m.count=1 ON MATCH SET m.count = m.count + 1 WITH m RETURN m.count as number - """.format( - LABEL=object_name - ) - )[0][0][0] + """.format(LABEL=object_name))[0][0][0] self.uid = ( str(object_name) + "_" @@ -208,8 +209,8 @@ class VersionRelationship(ClinicalMdrRel): `LATEST_DRAFT` or `LATEST_FINAL`. """ - start_date: datetime.datetime = ZonedDateTimeProperty() - end_date: datetime.datetime | None = ZonedDateTimeProperty() + start_date: datetime.datetime = ZonedDateTimeProperty() # type: ignore + end_date: datetime.datetime | None = ZonedDateTimeProperty() # type: ignore change_description = StringProperty() version = StringProperty() status = StringProperty() @@ -263,7 +264,7 @@ class VersionRoot(ClinicalMdrNodeWithUID): LIBRARY_REL_LABEL = "CONTAINS" PARAMETERS_LABEL = "HAS_PARAMETERS" - has_template = RelationshipTo("VersionRoot", "HAS_TEMPLATE", model=ClinicalMdrRel) + # has_template = RelationshipTo("VersionRoot", "HAS_TEMPLATE", model=ClinicalMdrRel) has_version = RelationshipTo(VersionValue, "HAS_VERSION", model=VersionRelationship) has_latest_value = RelationshipTo(VersionValue, "LATEST", model=ClinicalMdrRel) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/notification.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/notification.py index aca04e55..ad81c193 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/notification.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/notification.py @@ -1,9 +1,8 @@ -from neomodel import IntegerProperty, StringProperty - from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNode, ZonedDateTimeProperty, ) +from common.neomodel import IntegerProperty, StringProperty class Notification(ClinicalMdrNode): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/odm.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/odm.py index 999de377..dfe4fa95 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/odm.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/odm.py @@ -1,32 +1,44 @@ from neomodel import ( - BooleanProperty, DateProperty, - IntegerProperty, JSONProperty, RelationshipFrom, RelationshipTo, - StringProperty, ZeroOrMore, ) from clinical_mdr_api.domain_repositories.models.activities import ActivityItem -from clinical_mdr_api.domain_repositories.models.concepts import ( - ConceptRoot, - ConceptValue, - UnitDefinitionRoot, -) +from clinical_mdr_api.domain_repositories.models.concepts import UnitDefinitionRoot from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTCodelistRoot, CTTermContext, ) from clinical_mdr_api.domain_repositories.models.generic import ( + ClinicalMdrNode, ClinicalMdrRel, + Library, VersionRelationship, + VersionRoot, VersionValue, ) +from common.neomodel import BooleanProperty, IntegerProperty, StringProperty + + +class Odm(ClinicalMdrNode): ... + + +class OdmValue(Odm, VersionValue): + name = StringProperty() + + +class OdmRoot(Odm, VersionRoot): + LIBRARY_REL_LABEL = "CONTAINS_ODM" + + has_library = RelationshipFrom( + Library, "CONTAINS_ODM", cardinality=ZeroOrMore, model=ClinicalMdrRel + ) -class OdmAlias(VersionValue): +class OdmAlias(Odm): name = StringProperty() context = StringProperty() @@ -41,7 +53,7 @@ class OdmAlias(VersionValue): has_item = RelationshipFrom("OdmItemValue", "HAS_ALIAS", model=ClinicalMdrRel) -class OdmTranslatedText(VersionValue): +class OdmTranslatedText(Odm): text_type = StringProperty() language = StringProperty() text = StringProperty() @@ -63,7 +75,7 @@ class OdmTranslatedText(VersionValue): ) -class OdmFormalExpression(VersionValue): +class OdmFormalExpression(Odm): context = StringProperty() expression = StringProperty() @@ -75,7 +87,7 @@ class OdmFormalExpression(VersionValue): ) -class OdmConditionValue(ConceptValue): +class OdmConditionValue(OdmValue): oid = StringProperty() has_translated_text = RelationshipTo( OdmTranslatedText, "HAS_TRANSLATED_TEXT", model=ClinicalMdrRel @@ -90,7 +102,7 @@ class OdmConditionValue(ConceptValue): ) -class OdmConditionRoot(ConceptRoot): +class OdmConditionRoot(OdmRoot): has_version = RelationshipTo( OdmConditionValue, "HAS_VERSION", model=VersionRelationship ) @@ -106,7 +118,7 @@ class OdmConditionRoot(ConceptRoot): ) -class OdmMethodValue(ConceptValue): +class OdmMethodValue(OdmValue): oid = StringProperty() method_type = StringProperty() has_translated_text = RelationshipTo( @@ -122,7 +134,7 @@ class OdmMethodValue(ConceptValue): ) -class OdmMethodRoot(ConceptRoot): +class OdmMethodRoot(OdmRoot): has_version = RelationshipTo( OdmMethodValue, "HAS_VERSION", model=VersionRelationship ) @@ -152,7 +164,7 @@ class OdmFormRefRelation(ClinicalMdrRel): collection_exception_condition_oid = StringProperty() -class OdmFormValue(ConceptValue): +class OdmFormValue(OdmValue): oid = StringProperty() repeating = BooleanProperty() sdtm_version = StringProperty() @@ -185,7 +197,7 @@ class OdmFormValue(ConceptValue): ) -class OdmFormRoot(ConceptRoot): +class OdmFormRoot(OdmRoot): has_version = RelationshipTo(OdmFormValue, "HAS_VERSION", model=VersionRelationship) has_latest_value = RelationshipTo(OdmFormValue, "LATEST", model=ClinicalMdrRel) latest_draft = RelationshipTo(OdmFormValue, "LATEST_DRAFT", model=ClinicalMdrRel) @@ -207,7 +219,7 @@ class OdmItemRefRelation(ClinicalMdrRel): vendor = JSONProperty() -class OdmItemGroupValue(ConceptValue): +class OdmItemGroupValue(OdmValue): oid = StringProperty() repeating = BooleanProperty() is_reference_data = BooleanProperty() @@ -247,7 +259,7 @@ class OdmItemGroupValue(ConceptValue): ) -class OdmItemGroupRoot(ConceptRoot): +class OdmItemGroupRoot(OdmRoot): has_version = RelationshipTo( OdmItemGroupValue, "HAS_VERSION", model=VersionRelationship ) @@ -286,7 +298,7 @@ class OdmItemCodelistRelationship(ClinicalMdrRel): allows_multi_choice = BooleanProperty() -class OdmItemValue(ConceptValue): +class OdmItemValue(OdmValue): oid = StringProperty() prompt = StringProperty() datatype = StringProperty() @@ -338,7 +350,7 @@ class OdmItemValue(ConceptValue): ) -class OdmItemRoot(ConceptRoot): +class OdmItemRoot(OdmRoot): has_version = RelationshipTo(OdmItemValue, "HAS_VERSION", model=VersionRelationship) has_latest_value = RelationshipTo(OdmItemValue, "LATEST", model=ClinicalMdrRel) latest_draft = RelationshipTo(OdmItemValue, "LATEST_DRAFT", model=ClinicalMdrRel) @@ -348,7 +360,7 @@ class OdmItemRoot(ConceptRoot): ) -class OdmStudyEventValue(ConceptValue): +class OdmStudyEventValue(OdmValue): oid = StringProperty() effective_date = DateProperty() retired_date = DateProperty() @@ -362,7 +374,7 @@ class OdmStudyEventValue(ConceptValue): form_ref = RelationshipTo(OdmFormValue, "FORM_REF", model=OdmFormRefRelation) -class OdmStudyEventRoot(ConceptRoot): +class OdmStudyEventRoot(OdmRoot): has_version = RelationshipTo( OdmStudyEventValue, "HAS_VERSION", model=VersionRelationship ) @@ -381,7 +393,7 @@ class OdmStudyEventRoot(ConceptRoot): ) -class OdmVendorNamespaceValue(ConceptValue): +class OdmVendorNamespaceValue(OdmValue): prefix = StringProperty() url = StringProperty() @@ -397,7 +409,7 @@ class OdmVendorNamespaceValue(ConceptValue): ) -class OdmVendorNamespaceRoot(ConceptRoot): +class OdmVendorNamespaceRoot(OdmRoot): has_version = RelationshipTo( OdmVendorNamespaceValue, "HAS_VERSION", model=VersionRelationship ) @@ -415,7 +427,7 @@ class OdmVendorNamespaceRoot(ConceptRoot): ) -class OdmVendorAttributeValue(ConceptValue): +class OdmVendorAttributeValue(OdmValue): compatible_types = JSONProperty() data_type = StringProperty() value_regex = StringProperty() @@ -452,7 +464,7 @@ class OdmVendorAttributeValue(ConceptValue): ) -class OdmVendorAttributeRoot(ConceptRoot): +class OdmVendorAttributeRoot(OdmRoot): has_version = RelationshipTo( OdmVendorAttributeValue, "HAS_VERSION", model=VersionRelationship ) @@ -470,7 +482,7 @@ class OdmVendorAttributeRoot(ConceptRoot): ) -class OdmVendorElementValue(ConceptValue): +class OdmVendorElementValue(OdmValue): compatible_types = JSONProperty() has_root = RelationshipFrom( @@ -494,7 +506,7 @@ class OdmVendorElementValue(ConceptValue): ) -class OdmVendorElementRoot(ConceptRoot): +class OdmVendorElementRoot(OdmRoot): has_version = RelationshipTo( OdmVendorElementValue, "HAS_VERSION", model=VersionRelationship ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/pharmaceutical_product.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/pharmaceutical_product.py index 26537700..31f120bd 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/pharmaceutical_product.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/pharmaceutical_product.py @@ -1,4 +1,4 @@ -from neomodel import One, RelationshipTo, StringProperty, ZeroOrMore, ZeroOrOne +from neomodel import One, RelationshipTo, ZeroOrMore, ZeroOrOne from clinical_mdr_api.domain_repositories.models.active_substance import ( ActiveSubstanceRoot, @@ -17,6 +17,7 @@ ClinicalMdrRel, VersionRelationship, ) +from common.neomodel import StringProperty class Ingredient(ClinicalMdrNode): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/preferences.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/preferences.py new file mode 100644 index 00000000..b717ab47 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/preferences.py @@ -0,0 +1,25 @@ +from __future__ import annotations + +from typing import TYPE_CHECKING + +from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrNode +from clinical_mdr_api.domain_repositories.preferences_registry import ( + get_neomodel_properties, +) + +if TYPE_CHECKING: + + class PreferencesMixin: # static stub for mypy + pass + +else: + # Dynamically build mixin from registry at runtime + PreferencesMixin = type("PreferencesMixin", (), get_neomodel_properties()) + + +class GlobalPreferences(PreferencesMixin, ClinicalMdrNode): + pass + + +class UserPreferences(PreferencesMixin, ClinicalMdrNode): + pass diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/project.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/project.py index 224211e4..9bc271c5 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/project.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/project.py @@ -1,4 +1,4 @@ -from neomodel import RelationshipFrom, StringProperty +from neomodel import RelationshipFrom from clinical_mdr_api.domain_repositories.models.clinical_programme import ( ClinicalProgramme, @@ -7,6 +7,7 @@ ClinicalMdrNodeWithUID, ClinicalMdrRel, ) +from common.neomodel import StringProperty class Project(ClinicalMdrNodeWithUID): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/standard_data_model.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/standard_data_model.py index 8998b283..279a6f62 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/standard_data_model.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/standard_data_model.py @@ -1,12 +1,8 @@ from neomodel import ( - ArrayProperty, - BooleanProperty, - IntegerProperty, One, OneOrMore, RelationshipFrom, RelationshipTo, - StringProperty, StructuredRel, ZeroOrOne, ) @@ -23,6 +19,12 @@ VersionRoot, VersionValue, ) +from common.neomodel import ( + ArrayProperty, + BooleanProperty, + IntegerProperty, + StringProperty, +) class DataModelCatalogue(ClinicalMdrNode): @@ -130,6 +132,10 @@ class HasDatasetRel(HasDatasetClassRel): pass +class HasSponsorDatasetRel(ClinicalMdrRel): + ordinal = IntegerProperty() + + class DatasetClassInstance(VersionValue): description = StringProperty() label = StringProperty() @@ -203,7 +209,7 @@ class SponsorModelDatasetInstance(VersionValue): is_instance_of = RelationshipFrom("Dataset", "HAS_INSTANCE", model=ClinicalMdrRel) has_dataset = RelationshipFrom( - SponsorModelValue, "HAS_DATASET", model=HasDatasetRel + SponsorModelValue, "HAS_DATASET", model=HasSponsorDatasetRel ) has_key = RelationshipTo( "DatasetVariable", @@ -335,6 +341,10 @@ class HasDatasetVariableRel(HasVariableClassRel): pass +class HasSponsorDatasetVariableRel(HasDatasetVariableRel): + ordinal = IntegerProperty() # type: ignore[assignment] + + class DatasetVariableInstance(VersionValue): description = StringProperty() title = StringProperty() @@ -422,7 +432,9 @@ class SponsorModelDatasetVariableInstance(VersionValue): implemented_parent_dataset_class_uid = StringProperty() has_variable = RelationshipFrom( - SponsorModelDatasetInstance, "HAS_DATASET_VARIABLE", model=HasDatasetVariableRel + SponsorModelDatasetInstance, + "HAS_DATASET_VARIABLE", + model=HasSponsorDatasetVariableRel, ) implements_variable_class = RelationshipTo( VariableClassInstance, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study.py index 4bc18670..1a86c400 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study.py @@ -1,10 +1,4 @@ -from neomodel import ( - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - ZeroOrOne, -) +from neomodel import RelationshipFrom, RelationshipTo, ZeroOrMore, ZeroOrOne from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNode, @@ -48,6 +42,7 @@ StudySoAGroup, StudyVersion, ) +from common.neomodel import StringProperty class StudyValue(ClinicalMdrNode, AuditTrailMixin): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_audit_trail.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_audit_trail.py index 16e814a4..d6960802 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_audit_trail.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_audit_trail.py @@ -1,6 +1,6 @@ import datetime -from neomodel import One, RelationshipFrom, RelationshipTo, StringProperty, ZeroOrOne +from neomodel import One, RelationshipFrom, RelationshipTo, ZeroOrOne from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNode, @@ -8,6 +8,7 @@ ConjunctionRelation, ZonedDateTimeProperty, ) +from common.neomodel import StringProperty class StudyAction(ClinicalMdrNode): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_disease_milestone.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_disease_milestone.py index 74f71c44..78c044f6 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_disease_milestone.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_disease_milestone.py @@ -1,11 +1,4 @@ -from neomodel import ( - BooleanProperty, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - ZeroOrOne, -) +from neomodel import RelationshipFrom, RelationshipTo, ZeroOrMore, ZeroOrOne from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTTermContext, @@ -13,6 +6,7 @@ from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrRel from clinical_mdr_api.domain_repositories.models.study import StudyValue from clinical_mdr_api.domain_repositories.models.study_selections import StudySelection +from common.neomodel import BooleanProperty, StringProperty class StudyDiseaseMilestone(StudySelection): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_epoch.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_epoch.py index e58498e3..a4e6e7dd 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_epoch.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_epoch.py @@ -1,10 +1,4 @@ -from neomodel import ( - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - ZeroOrOne, -) +from neomodel import RelationshipFrom, RelationshipTo, ZeroOrMore, ZeroOrOne from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTTermContext, @@ -16,6 +10,7 @@ StudySelection, StudySoAFootnote, ) +from common.neomodel import StringProperty class StudyEpoch(StudySelection): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_field.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_field.py index 83495b4f..ab8d3492 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_field.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_field.py @@ -1,15 +1,6 @@ from typing import Any -from neomodel import ( - ArrayProperty, - BooleanProperty, - IntegerProperty, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - db, -) +from neomodel import RelationshipFrom, RelationshipTo, ZeroOrMore, db from clinical_mdr_api.domain_repositories.models.concepts import UnitDefinitionRoot from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( @@ -22,6 +13,12 @@ ) from clinical_mdr_api.domain_repositories.models.project import Project from clinical_mdr_api.domain_repositories.models.study_selections import AuditTrailMixin +from common.neomodel import ( + ArrayProperty, + BooleanProperty, + IntegerProperty, + StringProperty, +) class StudyField(ClinicalMdrNode, AuditTrailMixin): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py index 456624dd..fa879968 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_selections.py @@ -1,11 +1,8 @@ from neomodel import ( - BooleanProperty, - IntegerProperty, One, OneOrMore, RelationshipFrom, RelationshipTo, - StringProperty, ZeroOrMore, ZeroOrOne, ) @@ -53,6 +50,7 @@ ObjectiveValue, TimeframeValue, ) +from common.neomodel import BooleanProperty, IntegerProperty, StringProperty STUDY_VALUE_CLASS_NAME = ".study.StudyValue" STUDY_SOA_FOOTNOTE_CLASS_NAME = ".study.StudySoAFootnote" @@ -635,7 +633,6 @@ class StudyBranchArm(StudySelection): description = StringProperty() randomization_group = StringProperty() number_of_subjects = IntegerProperty() - order = StringProperty() study_value = RelationshipFrom( STUDY_VALUE_CLASS_NAME, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_standard_version.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_standard_version.py index 5351e8ce..355c6075 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_standard_version.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_standard_version.py @@ -1,16 +1,10 @@ -from neomodel import ( - BooleanProperty, - One, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, -) +from neomodel import One, RelationshipFrom, RelationshipTo, ZeroOrMore from clinical_mdr_api.domain_repositories.models.controlled_terminology import CTPackage from clinical_mdr_api.domain_repositories.models.generic import ClinicalMdrRel from clinical_mdr_api.domain_repositories.models.study import StudyValue from clinical_mdr_api.domain_repositories.models.study_selections import StudySelection +from common.neomodel import BooleanProperty, StringProperty class StudyStandardVersion(StudySelection): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_visit.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_visit.py index 11e2424c..1bcbe479 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_visit.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/study_visit.py @@ -1,13 +1,4 @@ -from neomodel import ( - BooleanProperty, - FloatProperty, - IntegerProperty, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - ZeroOrOne, -) +from neomodel import RelationshipFrom, RelationshipTo, ZeroOrMore, ZeroOrOne from clinical_mdr_api.domain_repositories.models.concepts import ( StudyDayRoot, @@ -34,6 +25,12 @@ StudySelection, StudySoAFootnote, ) +from common.neomodel import ( + BooleanProperty, + FloatProperty, + IntegerProperty, + StringProperty, +) class StudyVisitGroup(ClinicalMdrNodeWithUID): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/syntax.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/syntax.py index aaad9c46..4e159ef0 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/syntax.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/syntax.py @@ -1,12 +1,4 @@ -from neomodel import ( - BooleanProperty, - IntegerProperty, - RelationshipFrom, - RelationshipTo, - StringProperty, - ZeroOrMore, - db, -) +from neomodel import RelationshipFrom, RelationshipTo, ZeroOrMore, db from clinical_mdr_api.domain_repositories.models.activities import ( ActivityGroupRoot, @@ -31,6 +23,7 @@ TemplateParameterTermRoot, TemplateParameterTermValue, ) +from common.neomodel import BooleanProperty, IntegerProperty, StringProperty ######################### diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/template_parameter.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/template_parameter.py index 2de9a728..84d12f78 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/template_parameter.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/template_parameter.py @@ -1,4 +1,4 @@ -from neomodel import RelationshipFrom, RelationshipTo, StringProperty, db +from neomodel import RelationshipFrom, RelationshipTo, db from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNode, @@ -7,6 +7,7 @@ VersionRoot, VersionValue, ) +from common.neomodel import StringProperty class TemplateParameter(ClinicalMdrNode): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/user.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/user.py index 2adbd9fe..4f378bff 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/user.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/models/user.py @@ -1,9 +1,11 @@ -from neomodel import StringProperty +from neomodel import RelationshipTo from clinical_mdr_api.domain_repositories.models.generic import ( ClinicalMdrNode, ZonedDateTimeProperty, ) +from clinical_mdr_api.domain_repositories.models.preferences import UserPreferences +from common.neomodel import StringProperty class User(ClinicalMdrNode): @@ -16,3 +18,5 @@ class User(ClinicalMdrNode): roles = StringProperty() created = ZonedDateTimeProperty() updated = ZonedDateTimeProperty() + + has_preferences = RelationshipTo(UserPreferences, "HAS_PREFERENCES") diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/neomodel_ext_item_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/neomodel_ext_item_repository.py index 59a4cb8e..a824c33a 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/neomodel_ext_item_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/neomodel_ext_item_repository.py @@ -97,11 +97,9 @@ def find_all( self.check_for_incorrect_optional_markers(nodes, q_filters) nodes = nodes.order_by(sort_paths[0] if len(sort_paths) > 0 else "uid") nodes = nodes.filter(*q_filters)[start:end] - nodes = nodes.resolve_subgraph() + subgraph = nodes.resolve_subgraph() - all_data_model = [ - self.return_model.model_validate(activity_node) for activity_node in nodes - ] + all_data_model = [self.return_model.model_validate(node) for node in subgraph] if total_count: len_query = self.root_class.nodes.filter(*q_filters) all_nodes = len(len_query) @@ -159,7 +157,7 @@ def get_distinct_headers( elif "__" in field_path: path, prop = field_path.rsplit("__", 1) source = NodeNameResolver(path) - nodeset = nodeset.fetch_relations(path) + nodeset = nodeset.traverse(path) else: # FIXME: we need a proper way to resolve the variable name (NodeNameResolver # does not support 'self'...) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/__init__.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/__init__.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/__init__.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/__init__.py diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/condition_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/condition_repository.py similarity index 75% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/condition_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/condition_repository.py index 25798bc8..973b99bc 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/condition_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/condition_repository.py @@ -1,10 +1,8 @@ +import logging from typing import Any from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -15,23 +13,25 @@ OdmConditionRoot, OdmConditionValue, ) -from clinical_mdr_api.domains.concepts.odms.condition import ( - OdmConditionAR, - OdmConditionVO, +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, ) +from clinical_mdr_api.domains.odms.condition import OdmConditionAR, OdmConditionVO from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmFormalExpressionModel, OdmTranslatedTextModel, ) -from clinical_mdr_api.models.concepts.odms.odm_condition import OdmCondition +from clinical_mdr_api.models.odms.condition import OdmCondition from common.utils import convert_to_datetime +log = logging.getLogger(__name__) + class ConditionRepository(OdmGenericRepository[OdmConditionAR]): root_class = OdmConditionRoot @@ -46,9 +46,10 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( value: VersionValue, **_kwargs, ) -> OdmConditionAR: + log.debug("Creating OdmConditionAR from version root: uid=%s", root.uid) return OdmConditionAR.from_repository_values( uid=root.uid, - concept_vo=OdmConditionVO.from_repository_values( + odm_vo=OdmConditionVO.from_repository_values( oid=value.oid, name=value.name, formal_expressions=[ @@ -82,9 +83,14 @@ def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> OdmConditionAR: major, minor = input_dict["version"].split(".") + log.debug( + "Creating OdmConditionAR from cypher result: uid=%s, version=%s", + input_dict["uid"], + input_dict["version"], + ) odm_condition_ar = OdmConditionAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmConditionVO.from_repository_values( + odm_vo=OdmConditionVO.from_repository_values( oid=input_dict["oid"], name=input_dict["name"], formal_expressions=[ @@ -130,37 +136,43 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.oid AS oid, +odm_value.oid AS oid, -[(concept_value)-[:HAS_FORMAL_EXPRESSION]->(fev:OdmFormalExpression) | {context: fev.context, expression: fev.expression}] AS formal_expressions, +[(odm_value)-[:HAS_FORMAL_EXPRESSION]->(fev:OdmFormalExpression) | {context: fev.context, expression: fev.expression}] AS formal_expressions, -[(concept_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, +[(odm_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, -[(concept_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases +[(odm_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases """ def _get_or_create_value( self, root: VersionRoot, ar: OdmConditionAR, force_new_value_node: bool = False ) -> VersionValue: + log.debug( + "Getting or creating value for OdmCondition: uid=%s, force_new=%s", + root.uid, + force_new_value_node, + ) new_value = super()._get_or_create_value(root, ar, force_new_value_node) - self.connect_aliases(ar.concept_vo.aliases, new_value) - self.connect_translated_texts(ar.concept_vo.translated_texts, new_value) - self.connect_formal_expressions(ar.concept_vo.formal_expressions, new_value) + self.connect_aliases(ar.odm_vo.aliases, new_value) + self.connect_translated_texts(ar.odm_vo.translated_texts, new_value) + self.connect_formal_expressions(ar.odm_vo.formal_expressions, new_value) return new_value def _create_new_value_node(self, ar: OdmConditionAR) -> OdmConditionValue: + log.debug("Creating new OdmConditionValue node for uid=%s", ar.uid) value_node = super()._create_new_value_node(ar=ar) value_node.save() - value_node.oid = ar.concept_vo.oid + value_node.oid = ar.odm_vo.oid return value_node def _has_data_changed(self, ar: OdmConditionAR, value: OdmConditionValue) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) formal_expression_nodes = { OdmFormalExpressionModel( @@ -183,18 +195,17 @@ def _has_data_changed(self, ar: OdmConditionAR, value: OdmConditionValue) -> boo } are_rels_changed = ( - set(ar.concept_vo.formal_expressions) != formal_expression_nodes - or set(ar.concept_vo.translated_texts) != translated_text_nodes - or set(ar.concept_vo.aliases) != alias_nodes + set(ar.odm_vo.formal_expressions) != formal_expression_nodes + or set(ar.odm_vo.translated_texts) != translated_text_nodes + or set(ar.odm_vo.aliases) != alias_nodes ) return ( - are_concept_properties_changed - or are_rels_changed - or ar.concept_vo.oid != value.oid + are_odm_properties_changed or are_rels_changed or ar.odm_vo.oid != value.oid ) def set_all_collection_exception_condition_oid_properties_to_null(self, oid): + log.info("Setting collection_exception_condition_oid to null for oid=%s", oid) db.cypher_query( """MATCH ()-[r:ITEM_GROUP_REF|ITEM_REF {collection_exception_condition_oid: $oid}]-() SET r.collection_exception_condition_oid = null""", diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/form_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/form_repository.py similarity index 82% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/form_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/form_repository.py index e4e11970..10a9fca8 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/form_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/form_repository.py @@ -2,9 +2,6 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -12,21 +9,20 @@ VersionValue, ) from clinical_mdr_api.domain_repositories.models.odm import OdmFormRoot, OdmFormValue -from clinical_mdr_api.domains.concepts.odms.form import ( - OdmFormAR, - OdmFormRefVO, - OdmFormVO, +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, ) +from clinical_mdr_api.domains.odms.form import OdmFormAR, OdmFormRefVO, OdmFormVO from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmTranslatedTextModel, ) -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm +from clinical_mdr_api.models.odms.form import OdmForm from clinical_mdr_api.services._utils import ensure_transaction from common.utils import convert_to_datetime @@ -46,7 +42,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( ) -> OdmFormAR: return OdmFormAR.from_repository_values( uid=root.uid, - concept_vo=OdmFormVO.from_repository_values( + odm_vo=OdmFormVO.from_repository_values( oid=value.oid, name=value.name, sdtm_version=value.sdtm_version, @@ -101,7 +97,7 @@ def _create_aggregate_root_instance_from_cypher_result( major, minor = input_dict["version"].split(".") odm_form_ar = OdmFormAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmFormVO.from_repository_values( + odm_vo=OdmFormVO.from_repository_values( oid=input_dict.get("oid"), name=input_dict["name"], sdtm_version=input_dict.get("sdtm_version"), @@ -148,24 +144,24 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.oid AS oid, -toString(concept_value.repeating) AS repeating, -concept_value.sdtm_version AS sdtm_version, +odm_value.oid AS oid, +toString(odm_value.repeating) AS repeating, +odm_value.sdtm_version AS sdtm_version, -[(concept_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, +[(odm_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, -[(concept_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases, +[(odm_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases, -[(concept_value)-[igref:ITEM_GROUP_REF]->(igv:OdmItemGroupValue)<-[:HAS_VERSION]-(igr:OdmItemGroupRoot) | +[(odm_value)-[igref:ITEM_GROUP_REF]->(igv:OdmItemGroupValue)<-[:HAS_VERSION]-(igr:OdmItemGroupRoot) | {uid: igr.uid, name: igv.name, order: igref.order, mandatory: igref.mandatory}] AS item_groups, -[(concept_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | +[(odm_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | {uid: ver.uid, name: vev.name, value: hve.value}] AS vendor_elements, -[(concept_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hva.value}] AS vendor_attributes, -[(concept_value)-[hvea:HAS_VENDOR_ELEMENT_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hvea:HAS_VENDOR_ELEMENT_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hvea.value}] AS vendor_element_attributes WITH *, @@ -214,8 +210,8 @@ def _get_or_create_value( self.manage_vendor_relationships( current_latest, new_value, ar.should_disconnect_relationships ) - self.connect_translated_texts(ar.concept_vo.translated_texts, new_value) - self.connect_aliases(ar.concept_vo.aliases, new_value) + self.connect_translated_texts(ar.odm_vo.translated_texts, new_value) + self.connect_aliases(ar.odm_vo.aliases, new_value) return new_value @@ -224,14 +220,14 @@ def _create_new_value_node(self, ar: OdmFormAR) -> OdmFormValue: value_node.save() - value_node.oid = ar.concept_vo.oid - value_node.sdtm_version = ar.concept_vo.sdtm_version - value_node.repeating = ar.concept_vo.repeating + value_node.oid = ar.odm_vo.oid + value_node.sdtm_version = ar.odm_vo.sdtm_version + value_node.repeating = ar.odm_vo.repeating return value_node def _has_data_changed(self, ar: OdmFormAR, value: OdmFormValue) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) translated_text_nodes = { OdmTranslatedTextModel( @@ -247,16 +243,16 @@ def _has_data_changed(self, ar: OdmFormAR, value: OdmFormValue) -> bool: } are_rels_changed = ( - set(ar.concept_vo.translated_texts) != translated_text_nodes - or set(ar.concept_vo.aliases) != alias_nodes + set(ar.odm_vo.translated_texts) != translated_text_nodes + or set(ar.odm_vo.aliases) != alias_nodes ) return ( - are_concept_properties_changed + are_odm_properties_changed or are_rels_changed - or ar.concept_vo.oid != value.oid - or ar.concept_vo.sdtm_version != value.sdtm_version - or ar.concept_vo.repeating != value.repeating + or ar.odm_vo.oid != value.oid + or ar.odm_vo.sdtm_version != value.sdtm_version + or ar.odm_vo.repeating != value.repeating ) def find_by_uid_with_study_event_relation( @@ -266,12 +262,12 @@ def find_by_uid_with_study_event_relation( """ MATCH (:OdmStudyEventRoot {uid: $study_event_uid})-[:HAS_VERSION {version: $study_event_version}]->(:OdmStudyEventValue) -[ref:FORM_REF]->(value:OdmFormValue) - + MATCH (value)<-[hv_rel:HAS_VERSION]-(:OdmFormRoot {uid: $uid}) WITH value, ref, hv_rel ORDER BY hv_rel.start_date DESC WITH value, ref, collect(hv_rel) AS hv_rels - + RETURN value.oid AS oid, value.name AS name, @@ -307,8 +303,6 @@ def _connect_relationships_to_new_value_node( """ - Upgrades all incoming FORM_REF relationships to the second latest version to point to the latest version of OdmFormValue, preserving relationship properties. - - Ensures the new OdmFormValue node is connected to all ActivityItem nodes that any - of its child OdmItemGroupValue nodes are connected to. """ db.cypher_query( f""" @@ -340,12 +334,3 @@ def _connect_relationships_to_new_value_node( """, {"root_uid": root.uid}, ) - - db.cypher_query( - f""" - MATCH (:{self.root_class.__name__} {{uid: $root_uid}})-[:LATEST]->(value:{self.value_class.__name__}) - MATCH (value)-[:ITEM_GROUP_REF]->(:OdmItemGroupValue)-[:LINKS_TO_ACTIVITY_ITEM]->(activity_item:ActivityItem) - MERGE (value)-[:LINKS_TO_ACTIVITY_ITEM]->(activity_item) - """, - {"root_uid": root.uid}, - ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/odm_generic_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/generic_repository.py similarity index 54% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/odm_generic_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/generic_repository.py index f4b43584..a0dad386 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/odm_generic_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/generic_repository.py @@ -1,19 +1,28 @@ -from abc import ABC -from typing import Any +import copy +from abc import ABC, abstractmethod +from typing import Any, Generic from neomodel import db from clinical_mdr_api.domain_repositories._generic_repository_interface import ( _AggregateRootType, ) -from clinical_mdr_api.domain_repositories.concepts.concept_generic_repository import ( - ConceptGenericRepository, +from clinical_mdr_api.domain_repositories.library_item_repository import ( + LibraryItemRepositoryImplBase, +) +from clinical_mdr_api.domain_repositories.models._utils import ( + format_generic_header_values, ) from clinical_mdr_api.domain_repositories.models.concepts import UnitDefinitionRoot from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTTermRoot, ) -from clinical_mdr_api.domain_repositories.models.generic import VersionValue +from clinical_mdr_api.domain_repositories.models.generic import ( + Library, + VersionRelationship, + VersionRoot, + VersionValue, +) from clinical_mdr_api.domain_repositories.models.odm import ( OdmAlias, OdmFormalExpression, @@ -29,25 +38,173 @@ OdmVendorElementRoot, OdmVendorElementValue, ) -from clinical_mdr_api.domains.concepts.utils import RelationType from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.utils import RelationType +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmElementWithParentUid, OdmFormalExpressionModel, OdmTranslatedTextModel, ) +from clinical_mdr_api.models.utils import BaseModel from clinical_mdr_api.repositories._utils import ( CypherQueryBuilder, FilterDict, FilterOperator, calculate_total_count_from_query_result, sb_clear_cache, + validate_filters_and_add_search_string, ) from common.exceptions import BusinessLogicException -class OdmGenericRepository(ConceptGenericRepository[_AggregateRootType], ABC): +class OdmGenericRepository( + LibraryItemRepositoryImplBase, Generic[_AggregateRootType], ABC +): + root_class = type + value_class = type + return_model: type = BaseModel + filter_query_parameters: dict[Any, Any] = {} + sort_by: dict[Any, Any] | None = None + + @abstractmethod + def _create_aggregate_root_instance_from_cypher_result( + self, input_dict: dict[str, Any] + ) -> _AggregateRootType: + raise NotImplementedError + + @abstractmethod + def _create_aggregate_root_instance_from_version_root_relationship_and_value( + self, + root: VersionRoot, + library: Library, + relationship: VersionRelationship, + value: VersionValue, + **_kwargs, + ) -> _AggregateRootType: + raise NotImplementedError + + @abstractmethod + def specific_alias_clause(self, **kwargs) -> str: + """ + Methods is overridden in the OdmGenericRepository subclasses + and it contains matches and traversals specific for domain object represented by subclass repository. + :return str: + """ + + def specific_header_match_clause(self) -> str | None: + return None + + # pylint: disable=unused-argument + def specific_header_match_clause_lite(self, field_name: str) -> str | None: + return None + + def _create_new_value_node(self, ar: _AggregateRootType) -> VersionValue: + return self.value_class( # type: ignore[call-overload] + name=ar.name, + ) + + def _has_data_changed(self, ar: _AggregateRootType, value: VersionValue) -> bool: + return ar.name != value.name + + def generate_uid(self) -> str: + return self.root_class.get_next_free_uid_and_increment_counter() + + def generic_match_clause(self, **kwargs): + odm_label = self.root_class.__label__ + odm_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 (odm_root:{odm_label})-[{rel}]->(odm_value:{odm_value_label})""" + + def generic_alias_clause(self, **kwargs): + version = kwargs.get("version", None) + where_version = ( + "WHERE hv.version = $requested_version" if version is not None else "" + ) + + return f""" + DISTINCT odm_root, odm_value, + head([(library)-[:CONTAINS_ODM]->(odm_root) | library]) AS library + CALL {{ + WITH odm_root, odm_value + MATCH (odm_root)-[hv:HAS_VERSION]-(odm_value) + {where_version} + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.end_date ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS version_rel + }} + WITH + odm_root, + odm_root.uid AS uid, + odm_value as odm_value, + library, + version_rel + CALL {{ + WITH version_rel + OPTIONAL MATCH (author: User) + WHERE author.user_id = version_rel.author_id + RETURN author + }} + WITH + uid, + odm_root, + odm_value.name AS name, + library, + library.name AS library_name, + library.is_editable AS is_library_editable, + version_rel.start_date AS start_date, + version_rel.end_date AS end_date, + version_rel.status AS status, + version_rel.version AS version, + version_rel.change_description AS change_description, + version_rel.author_id AS author_id, + coalesce(author.username, version_rel.author_id) AS author_username, + odm_value + """ + + def create_query_filter_statement( + self, library: str | None = None, **kwargs + ) -> tuple[str, dict[Any, Any]]: + filter_parameters = [] + filter_query_parameters = {} + uids = kwargs.get("uids") + if library: + filter_by_library_name = """ + head([(library:Library)-[:CONTAINS_ODM]->(odm_root) | library.name])=$library_name""" + filter_parameters.append(filter_by_library_name) + filter_query_parameters["library_name"] = library + if uids: + filter_by_uids = "odm_root.uid IN $uids" + filter_parameters.append(filter_by_uids) + filter_query_parameters["uids"] = uids + + filter_statements = " AND ".join(filter_parameters) + filter_statements = ( + "WHERE " + filter_statements if len(filter_statements) > 0 else "" + ) + return filter_statements, filter_query_parameters + + @classmethod + # pylint: disable=unused-argument + def format_filter_sort_keys(cls, key: str): + return key + + @classmethod + def format_filter_sort_keys_for_headers_lite(cls, key: str): + return key.replace(".", "_") + def find_all( self, library: str | None = None, @@ -60,23 +217,6 @@ def find_all( return_all_versions: bool = False, **kwargs, ) -> tuple[list[_AggregateRootType], int]: - """ - Method runs a cypher query to fetch all needed data to create objects of type AggregateRootType. - In the case of the following repository it will be some Concept aggregates. - - It uses cypher instead of neomodel as neomodel approach triggered some performance issues, because it is needed - to traverse many relationships to fetch all needed data and each traversal is separate database call when using - neomodel. - :param library: - :param sort_by: - :param page_number: - :param page_size: - :param filter_by: - :param filter_operator: - :param total_count: - :param return_all_versions: - :return GenericFilteringReturn[_AggregateRootType]: - """ match_clause = self.generic_match_clause(**kwargs) filter_statements, filter_query_parameters = self.create_query_filter_statement( @@ -105,7 +245,7 @@ def find_all( query.parameters.update(filter_query_parameters) result_array, attributes_names = query.execute() - extracted_items = self._retrieve_concepts_from_cypher_res( + extracted_items = self._retrieve_odm_items_from_cypher_res( result_array, attributes_names ) total_amount = calculate_total_count_from_query_result( @@ -119,6 +259,292 @@ def find_all( return extracted_items, total_amount + def _retrieve_odm_items_from_cypher_res( + self, result_array, attribute_names + ) -> list[_AggregateRootType]: + odm_ars = [] + for item in result_array: + item_dictionary = {} + for item_property, attribute_name in zip(item, attribute_names): + item_dictionary[attribute_name] = item_property + odm_ars.append( + self._create_aggregate_root_instance_from_cypher_result(item_dictionary) + ) + + return odm_ars + + def get_distinct_headers( + self, + field_name: str, + search_string: str = "", + library: str | None = None, + filter_by: dict[str, dict[str, Any]] | None = None, + filter_operator: FilterOperator = FilterOperator.AND, + page_size: int = 10, + **kwargs, + ) -> list[Any]: + # pylint: disable=unused-argument + filter_by = validate_filters_and_add_search_string( + search_string, field_name, filter_by + ) + match_clause = self.generic_match_clause(**kwargs) + if self.specific_header_match_clause(): + match_clause += self.specific_header_match_clause() + + filter_statements, filter_query_parameters = self.create_query_filter_statement( + library=library, **kwargs + ) + match_clause += filter_statements + + alias_clause = ( + self.generic_alias_clause(**kwargs) + self.specific_alias_clause() + ) + + query = CypherQueryBuilder( + filter_by=FilterDict.model_validate({"elements": filter_by}), + filter_operator=filter_operator, + match_clause=match_clause, + alias_clause=alias_clause, + return_model=self.return_model, + format_filter_sort_keys=self.format_filter_sort_keys, + ) + + query.parameters.update(filter_query_parameters) + + query.full_query = query.build_header_query( + header_alias=field_name, page_size=page_size + ) + result_array, _ = query.execute() + + return ( + format_generic_header_values(result_array[0][0]) + if len(result_array) > 0 + else [] + ) + + def get_distinct_headers_lite( + self, + field_name: str, + search_string: str = "", + library: str | None = None, + page_size: int = 10, + filter_by: dict[str, Any] | None = None, + filter_operator: FilterOperator = FilterOperator.AND, + **kwargs, + ) -> list[Any]: + match_clause = self.generic_match_clause() + + filter_by = validate_filters_and_add_search_string( + search_string, field_name, filter_by=filter_by + ) + + filter_statements, filter_query_parameters = self.create_query_filter_statement( + library=library, kwargs=kwargs + ) + + match_clause += filter_statements + + if field_name in [ + "comment", + "datatype", + "length", + "name", + "oid", + "origin", + "prompt", + "sas_field_name", + "sds_var_name", + "significant_digits", + ]: + match_clause += f""" + WITH odm_value.{field_name} AS {field_name} + """ + + elif field_name in ["version", "start_date", "status"]: + match_clause += """ + CALL { + WITH odm_root, odm_value + MATCH (odm_root)-[hv:HAS_VERSION]-(odm_value) + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS version_rel + } + WITH version_rel.version AS version, + version_rel.start_date AS start_date, + version_rel.status AS status + """ + + elif field_name == "library_name": + match_clause += """ + WITH DISTINCT odm_root, + head([(library)-[:CONTAINS_ODM]->(odm_root) | library]) AS library + WITH library.name AS library_name + """ + + elif field_name == "author_username": + match_clause += """ + CALL { + WITH odm_root, odm_value + MATCH (odm_root)-[hv:HAS_VERSION]-(odm_value) + WITH hv + ORDER BY + toInteger(split(hv.version, '.')[0]) ASC, + toInteger(split(hv.version, '.')[1]) ASC, + hv.start_date ASC + WITH collect(hv) as hvs + RETURN last(hvs) AS version_rel + } + CALL { + WITH version_rel + OPTIONAL MATCH (author: User) + WHERE author.user_id = version_rel.author_id + RETURN author + } + WITH author.username AS author_username + """ + + else: + if self.specific_header_match_clause_lite(field_name): + match_clause += self.specific_header_match_clause_lite(field_name) + + query = CypherQueryBuilder( + filter_by=FilterDict.model_validate({"elements": filter_by}), + match_clause=match_clause, + alias_clause=field_name.replace(".", "_"), + return_model=self.return_model, + format_filter_sort_keys=self.format_filter_sort_keys_for_headers_lite, + ) + + query.parameters.update(filter_query_parameters) + + query.full_query = query.build_header_query( + header_alias=field_name.replace(".", "_"), page_size=page_size + ) + result_array, _ = query.execute() + + return ( + format_generic_header_values(result_array[0][0]) + if len(result_array) > 0 + else [] + ) + + @sb_clear_cache(caches=["cache_store_item_by_uid"]) + def save( + self, item: _AggregateRootType, force_new_value_node: bool = False + ) -> None: + if item.uid is not None and item.repository_closure_data is None: + self._create(item) + elif item.uid is not None and not item.is_deleted: + self._update(item, force_new_value_node) + elif item.is_deleted: + assert item.uid is not None + self._soft_delete(item.uid) + if item.repository_closure_data is not None: + ( + root, + _, + library, + _, + ) = item.repository_closure_data + value = root.has_latest_value.single() + + item.repository_closure_data = ( + root, + value, + library, + copy.deepcopy(item), + ) + + def _soft_delete(self, uid: str) -> None: + label = self.root_class.__label__ + db.cypher_query( + f""" + MATCH (otr:{label} {{uid: $uid}})-[latest_draft:LATEST_DRAFT|LATEST_RETIRED]->(otv) + WHERE NOT (otr)-[:HAS_VERSION {{version:'Final'}}]->() + SET otr:Deleted{label} + WITH otr + REMOVE otr:{label} + WITH otr + MATCH (otr)-[v:HAS_VERSION]->() + WHERE v.end_date IS NULL + SET v.end_date = datetime(apoc.date.toISO8601(datetime().epochSeconds, 's')) + """, + {"uid": uid}, + ) + + def _is_new_version_necessary( + self, ar: _AggregateRootType, value: VersionValue + ) -> bool: + return self._has_data_changed(ar, value) + + def _get_or_create_value( + self, + root: VersionRoot, + ar: _AggregateRootType, + force_new_value_node: bool = False, + ) -> VersionValue: + if not force_new_value_node: + for itm in root.has_version.all(): + if not self._has_data_changed(ar, itm): + return itm + latest_draft = root.latest_draft.get_or_none() + if latest_draft and not self._has_data_changed(ar, latest_draft): + return latest_draft + latest_final = root.latest_final.get_or_none() + if latest_final and not self._has_data_changed(ar, latest_final): + return latest_final + latest_retired = root.latest_retired.get_or_none() + if latest_retired and not self._has_data_changed(ar, latest_retired): + return latest_retired + new_value = self._create_new_value_node(ar=ar) + self._db_save_node(new_value) + return new_value + + def _maintain_parameters( + self, + versioned_object: _AggregateRootType, + root: VersionRoot, + value: VersionValue, + ) -> None: + # ODM items do not use template parameters - no-op + pass + + def _update_versioning_relationship_query( + self, status: str, merge_query: str | None = None + ) -> str: + query = f""" + MATCH (library:Library)-[:CONTAINS_ODM]->(odm_root)-[latest_has_version:HAS_VERSION]->(odm_value) + WHERE latest_has_version.end_date is null + MATCH (odm_root)-[latest_status_relationship:LATEST_{status.upper()}]->(:{self.value_class.__label__}) + WITH * + """ + if merge_query: + query += merge_query + else: + query += f""" + CREATE (odm_root)-[:LATEST]->(odm_value) + CREATE (odm_root)-[:LATEST_{status.upper()}]->(odm_value) + CREATE (odm_root)-[new_has_version:HAS_VERSION]->(odm_value) + """ + query += """ + 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 * + DELETE status_relationship, latest_status_relationship + """ + return query + + # ODM-specific methods ported from current OdmGenericRepository + @classmethod def _get_origin_and_relation_node( cls, @@ -136,7 +562,7 @@ def _has_relationship_to_others() -> bool: value = f":{relation_node.__label__}" query = f""" - MATCH (source:ConceptRoot{root})-[:LATEST]->(:ConceptValue{value}) + MATCH (source:OdmRoot{root})-[:LATEST]->(:OdmValue{value}) -[:{origin_label.upper()}]-(:{cls.value_class.__label__})<-[:HAS_VERSION]-(target:{cls.root_class.__label__}) WHERE source.uid = $source_uid AND target.uid <> $target_uid RETURN COUNT(*) > 0 @@ -252,14 +678,6 @@ def remove_relation( def has_active_relationships( self, uid: str, relationships: list[Any], all_exist: bool = False ) -> bool: - """ - Checks if the node has active relationships. - - :param uid: The uid of the node to check relationships on. - :param relationships: A list of relationship names to check the existence of. - :param all_exist: If True, all provided relationships must exist on the node. If False, at least one of the provided relationships must exist. - :return: Returns True, if the relationships exist, otherwise False. - """ root = self.root_class.nodes.get_or_none(uid=uid) value = root.has_latest_value.single() @@ -283,13 +701,6 @@ def has_active_relationships( def get_active_relationships( self, uid: str, relationships: list[Any] ) -> dict[str, list[str]]: - """ - Returns a key-pair value of target node's name and a list of uids of nodes connected to source node. - - :param uid: The uid of the source node to check relationships on. - :param relationships: A list of relationship names to check the existence of. - :return: Returns a dict. - """ root_node = self.root_class.nodes.get_or_none(uid=uid) source_node = root_node.has_latest_value.single() @@ -320,9 +731,6 @@ def get_active_relationships( ) from exc def get_if_has_relationship(self, relationship: str): - """ - Returns a list of ODM Element uid and name with their parent uids. - """ values = self.value_class.nodes.has(**{relationship: True}) rs = [] @@ -348,22 +756,6 @@ def odm_object_exists( codelist_uid: str | None = None, **value_attributes, ): - """ - Checks whether an ODM object exists in the database based on various filtering criteria. - This method constructs a Cypher query dynamically using the provided UID lists - and additional value node attributes to search for matching objects in the database. - - Args: - sdtm_domain_uids (list[str] | None): List of UIDs for SDTM Domains to match. - term_uids (list[str] | None): List of UIDs for terms to match in CT Codelist Terms. - unit_definition_uids (list[str] | None): List of UIDs for Unit Definitions to match. - codelist_uid (str | None): UID for a CT Codelist to match. - library_name (str | None): Name of the library to match. - **value_attributes: Arbitrary key-value pairs to match against properties of the ODM object. - - Returns: - list[str] | None: Returns a list of the UIDs of the matching ODM objects if it exist, otherwise returns `None`. - """ if not sdtm_domain_uids: sdtm_domain_uids = [] if not term_uids: @@ -378,9 +770,7 @@ def odm_object_exists( params: dict[str, Any] = {} if library_name: - query += ( - " MATCH (:Library {name: $library_name})-[:CONTAINS_CONCEPT]->(root) " - ) + query += " MATCH (:Library {name: $library_name})-[:CONTAINS_ODM]->(root) " params["library_name"] = library_name if sdtm_domain_uids: diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/item_group_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/item_group_repository.py similarity index 80% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/item_group_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/item_group_repository.py index 7ca856d1..db65cacb 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/item_group_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/item_group_repository.py @@ -3,9 +3,6 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.controlled_terminologies.ct_codelist_attributes_repository import ( CTCodelistAttributesRepository, ) @@ -22,7 +19,10 @@ OdmItemGroupRoot, OdmItemGroupValue, ) -from clinical_mdr_api.domains.concepts.odms.item_group import ( +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domains.odms.item_group import ( OdmItemGroupAR, OdmItemGroupRefVO, OdmItemGroupVO, @@ -32,11 +32,11 @@ LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmTranslatedTextModel, ) -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroup +from clinical_mdr_api.models.odms.item_group import OdmItemGroup from clinical_mdr_api.services._utils import ensure_transaction from common.config import settings from common.utils import convert_to_datetime @@ -63,7 +63,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( return OdmItemGroupAR.from_repository_values( uid=root.uid, - concept_vo=OdmItemGroupVO.from_repository_values( + odm_vo=OdmItemGroupVO.from_repository_values( oid=value.oid, name=value.name, repeating=value.repeating, @@ -123,7 +123,7 @@ def _create_aggregate_root_instance_from_cypher_result( major, minor = input_dict["version"].split(".") odm_item_group_ar = OdmItemGroupAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmItemGroupVO.from_repository_values( + odm_vo=OdmItemGroupVO.from_repository_values( oid=input_dict.get("oid"), name=input_dict["name"], repeating=input_dict.get("repeating"), @@ -175,32 +175,32 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.oid AS oid, -toString(concept_value.repeating) AS repeating, -toString(concept_value.is_reference_data) AS is_reference_data, -concept_value.sas_dataset_name AS sas_dataset_name, -concept_value.origin AS origin, -concept_value.purpose AS purpose, -concept_value.comment AS comment, +odm_value.oid AS oid, +toString(odm_value.repeating) AS repeating, +toString(odm_value.is_reference_data) AS is_reference_data, +odm_value.sas_dataset_name AS sas_dataset_name, +odm_value.origin AS origin, +odm_value.purpose AS purpose, +odm_value.comment AS comment, -[(concept_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, +[(odm_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, -[(concept_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases, +[(odm_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases, -[(concept_value)-[:HAS_SDTM_DOMAIN]->(:CTTermContext)-[:HAS_SELECTED_TERM]-> +[(odm_value)-[:HAS_SDTM_DOMAIN]->(:CTTermContext)-[:HAS_SELECTED_TERM]-> (tr:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)-[:LATEST]->(tav:CTTermAttributesValue) | {uid: tr.uid, submission_value: tav.submission_value, preferred_term: tav.preferred_term}] AS sdtm_domains, -[(concept_value)-[iref:ITEM_REF]->(iv:OdmItemValue)<-[:HAS_VERSION]-(ir:OdmItemRoot) | +[(odm_value)-[iref:ITEM_REF]->(iv:OdmItemValue)<-[:HAS_VERSION]-(ir:OdmItemRoot) | {uid: ir.uid, name: iv.name, order: iref.order, mandatory: iref.mandatory}] AS items, -[(concept_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | +[(odm_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | {uid: ver.uid, name: vev.name, value: hve.value}] AS vendor_elements, -[(concept_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hva.value}] AS vendor_attributes, -[(concept_value)-[hvea:HAS_VENDOR_ELEMENT_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hvea:HAS_VENDOR_ELEMENT_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hvea.value}] AS vendor_element_attributes WITH *, @@ -252,10 +252,10 @@ def _get_or_create_value( self.manage_vendor_relationships( current_latest, new_value, ar.should_disconnect_relationships ) - self.connect_translated_texts(ar.concept_vo.translated_texts, new_value) - self.connect_aliases(ar.concept_vo.aliases, new_value) + self.connect_translated_texts(ar.odm_vo.translated_texts, new_value) + self.connect_aliases(ar.odm_vo.aliases, new_value) - for sdtm_domain_uid in ar.concept_vo.sdtm_domain_uids: + for sdtm_domain_uid in ar.odm_vo.sdtm_domain_uids: sdtm_domain_node = CTTermRoot.nodes.get(uid=sdtm_domain_uid) selected_term_node = ( CTCodelistAttributesRepository().get_or_create_selected_term( @@ -273,18 +273,18 @@ def _create_new_value_node(self, ar: OdmItemGroupAR) -> OdmItemGroupValue: value_node.save() - value_node.oid = ar.concept_vo.oid - value_node.repeating = ar.concept_vo.repeating - value_node.is_reference_data = ar.concept_vo.is_reference_data - value_node.sas_dataset_name = ar.concept_vo.sas_dataset_name - value_node.origin = ar.concept_vo.origin - value_node.purpose = ar.concept_vo.purpose - value_node.comment = ar.concept_vo.comment + value_node.oid = ar.odm_vo.oid + value_node.repeating = ar.odm_vo.repeating + value_node.is_reference_data = ar.odm_vo.is_reference_data + value_node.sas_dataset_name = ar.odm_vo.sas_dataset_name + value_node.origin = ar.odm_vo.origin + value_node.purpose = ar.odm_vo.purpose + value_node.comment = ar.odm_vo.comment return value_node def _has_data_changed(self, ar: OdmItemGroupAR, value: OdmItemGroupValue) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) translated_text_nodes = { OdmTranslatedTextModel( @@ -305,21 +305,21 @@ def _has_data_changed(self, ar: OdmItemGroupAR, value: OdmItemGroupValue) -> boo } are_rels_changed = ( - set(ar.concept_vo.translated_texts) != translated_text_nodes - or set(ar.concept_vo.aliases) != alias_nodes - or set(ar.concept_vo.sdtm_domain_uids) != sdtm_domain_uids + set(ar.odm_vo.translated_texts) != translated_text_nodes + or set(ar.odm_vo.aliases) != alias_nodes + or set(ar.odm_vo.sdtm_domain_uids) != sdtm_domain_uids ) return ( - are_concept_properties_changed + are_odm_properties_changed or are_rels_changed - or ar.concept_vo.oid != value.oid - or ar.concept_vo.repeating != value.repeating - or ar.concept_vo.is_reference_data != value.is_reference_data - or ar.concept_vo.sas_dataset_name != value.sas_dataset_name - or ar.concept_vo.origin != value.origin - or ar.concept_vo.purpose != value.purpose - or ar.concept_vo.comment != value.comment + or ar.odm_vo.oid != value.oid + or ar.odm_vo.repeating != value.repeating + or ar.odm_vo.is_reference_data != value.is_reference_data + or ar.odm_vo.sas_dataset_name != value.sas_dataset_name + or ar.odm_vo.origin != value.origin + or ar.odm_vo.purpose != value.purpose + or ar.odm_vo.comment != value.comment ) def find_by_uid_with_form_relation( @@ -333,8 +333,8 @@ def find_by_uid_with_form_relation( MATCH (value)<-[hv_rel:HAS_VERSION]-(:OdmItemGroupRoot {uid: $uid}) WITH value, ref, hv_rel ORDER BY hv_rel.start_date DESC - WITH value, ref, collect(hv_rel) AS hv_rels - + WITH value, ref, collect(hv_rel) AS hv_rels + RETURN value.oid AS oid, value.name AS name, @@ -367,7 +367,6 @@ def _connect_relationships_to_new_value_node( """ - Upgrades all incoming ITEM_GROUP_REF relationships to the second latest version to point to the latest version of OdmItemGroupValue, preserving relationship properties. - - Ensures the new OdmItemGroupValue node is connected to all ActivityItem nodes that any of its child OdmItemValue nodes are connected to. """ db.cypher_query( @@ -400,12 +399,3 @@ def _connect_relationships_to_new_value_node( """, {"root_uid": root.uid}, ) - - db.cypher_query( - f""" - MATCH (:{self.root_class.__name__} {{uid: $root_uid}})-[:LATEST]->(value:{self.value_class.__name__}) - MATCH (value)-[:ITEM_REF]->(:OdmItemValue)-[:LINKS_TO_ACTIVITY_ITEM]->(activity_item:ActivityItem) - MERGE (value)-[:LINKS_TO_ACTIVITY_ITEM]->(activity_item) - """, - {"root_uid": root.uid}, - ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/item_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/item_repository.py similarity index 85% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/item_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/item_repository.py index eff23e63..e896ff0b 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/item_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/item_repository.py @@ -4,9 +4,6 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.concepts import UnitDefinitionRoot from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTCodelistRoot, @@ -20,7 +17,10 @@ VersionValue, ) from clinical_mdr_api.domain_repositories.models.odm import OdmItemRoot, OdmItemValue -from clinical_mdr_api.domains.concepts.odms.item import ( +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domains.odms.item import ( OdmItemAR, OdmItemRefVO, OdmItemTermVO, @@ -32,11 +32,11 @@ LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmTranslatedTextModel, ) -from clinical_mdr_api.models.concepts.odms.odm_item import ( +from clinical_mdr_api.models.odms.item import ( OdmItem, OdmItemCodelist, OdmItemParentGroup, @@ -61,8 +61,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( **_kwargs, ) -> OdmItemAR: activity_instances = db.cypher_query( - dedent( - """ + dedent(""" MATCH (oiv:OdmItemValue)-[ltai:LINKS_TO_ACTIVITY_ITEM]->(ai:ActivityItem) MATCH (ai)<-[:HAS_ACTIVITY_ITEM]-(aicr:ActivityItemClassRoot) MATCH (ai)<-[:CONTAINS_ACTIVITY_ITEM]-(aiv:ActivityInstanceValue)<-[:LATEST]-(air:ActivityInstanceRoot) @@ -79,8 +78,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( ltai.preset_response_value AS preset_response_value, ltai.value_condition AS value_condition, ltai.value_dependent_map AS value_dependent_map - """ - ), + """), params={"element_id": value.element_id}, ) @@ -108,7 +106,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( codelist = value.has_codelist.get_or_none() return OdmItemAR.from_repository_values( uid=root.uid, - concept_vo=OdmItemVO.from_repository_values( + odm_vo=OdmItemVO.from_repository_values( oid=value.oid, name=value.name, prompt=value.prompt, @@ -186,7 +184,7 @@ def _create_aggregate_root_instance_from_cypher_result( major, minor = input_dict["version"].split(".") odm_item_ar = OdmItemAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmItemVO.from_repository_values( + odm_vo=OdmItemVO.from_repository_values( oid=input_dict.get("oid"), name=input_dict["name"], prompt=input_dict.get("prompt"), @@ -261,44 +259,44 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.oid as oid, -concept_value.prompt as prompt, -concept_value.datatype as datatype, -concept_value.length as length, -concept_value.significant_digits as significant_digits, -concept_value.sas_field_name as sas_field_name, -concept_value.sds_var_name as sds_var_name, -concept_value.origin as origin, -concept_value.comment as comment, +odm_value.oid as oid, +odm_value.prompt as prompt, +odm_value.datatype as datatype, +odm_value.length as length, +odm_value.significant_digits as significant_digits, +odm_value.sas_field_name as sas_field_name, +odm_value.sds_var_name as sds_var_name, +odm_value.origin as origin, +odm_value.comment as comment, -head([(concept_value)<-[:ITEM_REF]-(oigv:OdmItemGroupValue)<-[:HAS_VERSION]-(oigr:OdmItemGroupRoot) | {uid: oigr.uid, oid:oigv.oid, name: oigv.name }]) AS odm_item_group, +head([(odm_value)<-[:ITEM_REF]-(oigv:OdmItemGroupValue)<-[:HAS_VERSION]-(oigr:OdmItemGroupRoot) | {uid: oigr.uid, oid:oigv.oid, name: oigv.name }]) AS odm_item_group, -[(concept_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, +[(odm_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, -[(concept_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases, +[(odm_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases, -[(concept_value)-[hud:HAS_UNIT_DEFINITION]->(udr:UnitDefinitionRoot)-[:LATEST]->(udv:UnitDefinitionValue) | +[(odm_value)-[hud:HAS_UNIT_DEFINITION]->(udr:UnitDefinitionRoot)-[:LATEST]->(udv:UnitDefinitionValue) | {uid: udr.uid, name: udv.name, mandatory: hud.mandatory, order: hud.order}] AS unit_definitions, -head([(concept_value)-[hc:HAS_CODELIST]->(ctcr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]-> +head([(odm_value)-[hc:HAS_CODELIST]->(ctcr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]-> (:CTCodelistAttributesRoot)-[:LATEST]->(ctcav:CTCodelistAttributesValue) | {uid: ctcr.uid, allows_multi_choice: hc.allows_multi_choice}]) AS codelist, -[(concept_value)-[hct:HAS_CODELIST_TERM]->(:CTTermContext)-[:HAS_SELECTED_TERM]-> +[(odm_value)-[hct:HAS_CODELIST_TERM]->(:CTTermContext)-[:HAS_SELECTED_TERM]-> (cttr:CTTermRoot)-[:HAS_NAME_ROOT]->(cttnr:CTTermNameRoot)-[:LATEST]->(cttnv:CTTermNameValue) | {uid: cttr.uid, name: cttnv.name, display_text: hct.display_text, mandatory: hct.mandatory, order: hct.order}] AS terms, -[(concept_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | +[(odm_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | {uid: ver.uid, name: vev.name, value: hve.value}] AS vendor_elements, -[(concept_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hva.value}] AS vendor_attributes, -[(concept_value)-[hvea:HAS_VENDOR_ELEMENT_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hvea:HAS_VENDOR_ELEMENT_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hvea.value}] AS vendor_element_attributes CALL { WITH * - MATCH (concept_value)-[ltai:LINKS_TO_ACTIVITY_ITEM]->(ai:ActivityItem) + MATCH (odm_value)-[ltai:LINKS_TO_ACTIVITY_ITEM]->(ai:ActivityItem) MATCH (ai)<-[:HAS_ACTIVITY_ITEM]-(aicr:ActivityItemClassRoot) MATCH (ai)<-[:CONTAINS_ACTIVITY_ITEM]-(aiv:ActivityInstanceValue)<-[:LATEST]-(air:ActivityInstanceRoot) RETURN COLLECT(DISTINCT { @@ -333,21 +331,20 @@ def _get_or_create_value( self.manage_vendor_relationships( current_latest, new_value, ar.should_disconnect_relationships ) - self.connect_translated_texts(ar.concept_vo.translated_texts, new_value) - self.connect_aliases(ar.concept_vo.aliases, new_value) + self.connect_translated_texts(ar.odm_vo.translated_texts, new_value) + self.connect_aliases(ar.odm_vo.aliases, new_value) new_value.has_codelist.disconnect_all() - if ar.concept_vo.codelist is not None: - codelist = CTCodelistRoot.nodes.get_or_none(uid=ar.concept_vo.codelist.uid) + if ar.odm_vo.codelist is not None: + codelist = CTCodelistRoot.nodes.get_or_none(uid=ar.odm_vo.codelist.uid) new_value.has_codelist.connect( codelist, - {"allows_multi_choice": ar.concept_vo.codelist.allows_multi_choice}, + {"allows_multi_choice": ar.odm_vo.codelist.allows_multi_choice}, ) - for activity_instance in ar.concept_vo.activity_instances: + for activity_instance in ar.odm_vo.activity_instances: db.cypher_query( - dedent( - """ + dedent(""" MATCH (air:ActivityInstanceRoot {uid: $activity_instance_uid})-[:LATEST]->(aiv:ActivityInstanceValue) -[:CONTAINS_ACTIVITY_ITEM]->(ai:ActivityItem)<-[:HAS_ACTIVITY_ITEM]-(:ActivityItemClassRoot {uid: $activity_item_class_uid}) MATCH (oiv:OdmItemValue) @@ -360,8 +357,7 @@ def _get_or_create_value( value_condition: $value_condition, value_dependent_map: $value_dependent_map }]->(ai) - """ - ), + """), params={ "element_id": new_value.element_id, "activity_instance_uid": activity_instance["activity_instance_uid"], @@ -383,20 +379,20 @@ def _create_new_value_node(self, ar: OdmItemAR) -> OdmItemValue: value_node.save() - value_node.oid = ar.concept_vo.oid - value_node.prompt = ar.concept_vo.prompt - value_node.datatype = ar.concept_vo.datatype - value_node.length = ar.concept_vo.length - value_node.significant_digits = ar.concept_vo.significant_digits - value_node.sas_field_name = ar.concept_vo.sas_field_name - value_node.sds_var_name = ar.concept_vo.sds_var_name - value_node.origin = ar.concept_vo.origin - value_node.comment = ar.concept_vo.comment + value_node.oid = ar.odm_vo.oid + value_node.prompt = ar.odm_vo.prompt + value_node.datatype = ar.odm_vo.datatype + value_node.length = ar.odm_vo.length + value_node.significant_digits = ar.odm_vo.significant_digits + value_node.sas_field_name = ar.odm_vo.sas_field_name + value_node.sds_var_name = ar.odm_vo.sds_var_name + value_node.origin = ar.odm_vo.origin + value_node.comment = ar.odm_vo.comment return value_node def _has_data_changed(self, ar: OdmItemAR, value: OdmItemValue) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) translated_text_nodes = { OdmTranslatedTextModel( @@ -426,8 +422,7 @@ def _has_data_changed(self, ar: OdmItemAR, value: OdmItemValue) -> bool: } activity_instances, _ = db.cypher_query( - dedent( - """ + dedent(""" MATCH (oiv:OdmItemValue)-[ltai:LINKS_TO_ACTIVITY_ITEM]->(ai:ActivityItem) MATCH (ai)<-[:HAS_ACTIVITY_ITEM]-(aicr:ActivityItemClassRoot) MATCH (ai)<-[:CONTAINS_ACTIVITY_ITEM]-(:ActivityInstanceValue)<-[:LATEST]-(air:ActivityInstanceRoot) @@ -441,8 +436,7 @@ def _has_data_changed(self, ar: OdmItemAR, value: OdmItemValue) -> bool: ltai.preset_response_value AS preset_response_value, ltai.value_condition AS value_condition, ltai.value_dependent_map AS value_dependent_map - """ - ), + """), params={"element_id": value.element_id}, ) @@ -456,34 +450,34 @@ def _has_data_changed(self, ar: OdmItemAR, value: OdmItemValue) -> bool: activity_instance["value_condition"], activity_instance["value_dependent_map"], ] - for activity_instance in ar.concept_vo.activity_instances + for activity_instance in ar.odm_vo.activity_instances ] are_rels_changed = ( - set(ar.concept_vo.translated_texts) != translated_text_nodes - or set(ar.concept_vo.aliases) != alias_nodes - or set(ar.concept_vo.unit_definition_uids) != unit_definition_uids + set(ar.odm_vo.translated_texts) != translated_text_nodes + or set(ar.odm_vo.aliases) != alias_nodes + or set(ar.odm_vo.unit_definition_uids) != unit_definition_uids or ( - getattr(ar.concept_vo.codelist, "uid", None), - getattr(ar.concept_vo.codelist, "allows_multi_choice", None), + getattr(ar.odm_vo.codelist, "uid", None), + getattr(ar.odm_vo.codelist, "allows_multi_choice", None), ) != codelist - or set(ar.concept_vo.term_uids) != term_uids + or set(ar.odm_vo.term_uids) != term_uids or sorted(ar_activity_instances) != sorted(activity_instances) ) return ( - are_concept_properties_changed + are_odm_properties_changed or are_rels_changed - or ar.concept_vo.oid != value.oid - or ar.concept_vo.prompt != value.prompt - or ar.concept_vo.datatype != value.datatype - or ar.concept_vo.length != value.length - or ar.concept_vo.significant_digits != value.significant_digits - or ar.concept_vo.sas_field_name != value.sas_field_name - or ar.concept_vo.sds_var_name != value.sds_var_name - or ar.concept_vo.origin != value.origin - or ar.concept_vo.comment != value.comment + or ar.odm_vo.oid != value.oid + or ar.odm_vo.prompt != value.prompt + or ar.odm_vo.datatype != value.datatype + or ar.odm_vo.length != value.length + or ar.odm_vo.significant_digits != value.significant_digits + or ar.odm_vo.sas_field_name != value.sas_field_name + or ar.odm_vo.sds_var_name != value.sds_var_name + or ar.odm_vo.origin != value.origin + or ar.odm_vo.comment != value.comment ) def find_by_uid_with_item_group_relation( @@ -497,7 +491,7 @@ def find_by_uid_with_item_group_relation( MATCH (value)<-[hv_rel:HAS_VERSION]-(:OdmItemRoot {uid: $uid}) WITH value, ref, hv_rel ORDER BY hv_rel.start_date DESC - WITH value, ref, collect(hv_rel) AS hv_rels + WITH value, ref, collect(hv_rel) AS hv_rels RETURN value.oid AS oid, @@ -600,7 +594,7 @@ def _get_relationship(): codelist_uid = item_value.has_codelist.get_or_none().uid cl_term_nodes = ( - CTCodelistTerm.nodes.fetch_relations("has_term_root", "has_term").filter( + CTCodelistTerm.nodes.traverse("has_term_root", "has_term").filter( has_term__uid=codelist_uid, has_term_root__uid=term_uid ) ).all() diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/metadata_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/metadata_repository.py similarity index 96% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/metadata_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/metadata_repository.py index 4a34af56..a150469b 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/metadata_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/metadata_repository.py @@ -101,8 +101,7 @@ class MetadataRepository: ITEM_TERM_RETURN = "apoc.text.join(COLLECT(DISTINCT CTCodelistTerm.submission_value), '|') as Item_Terms" def get_odm_study_event(self, target_uid: str): - query = ( - f""" + query = f""" WITH " MATCH (OdmStudyEventRoot:OdmStudyEventRoot {{uid: $target_uid}}) -[:LATEST_FINAL|LATEST_RETIRED]->(OdmStudyEventValue:OdmStudyEventValue) @@ -141,9 +140,7 @@ def get_odm_study_event(self, target_uid: str): {self.ITEM_CODELIST_RETURN}, {self.ITEM_TERM_RETURN} " AS query - """ - + self.CSV_EXPORT_QUERY - ) + """ + self.CSV_EXPORT_QUERY result, _ = db.cypher_query(query, {"target_uid": target_uid}) NotFoundException.raise_if(result[0][1] == 0, "ODM Study Event", target_uid) @@ -151,8 +148,7 @@ def get_odm_study_event(self, target_uid: str): return result[0][0] def get_odm_form(self, target_uid: str): - query = ( - f""" + query = f""" WITH " MATCH (OdmFormRoot:OdmFormRoot {{uid: $target_uid}})-[:LATEST_FINAL|LATEST_RETIRED]->(OdmFormValue:OdmFormValue) CALL {{ @@ -187,9 +183,7 @@ def get_odm_form(self, target_uid: str): {self.ITEM_CODELIST_RETURN}, {self.ITEM_TERM_RETURN} " AS query - """ - + self.CSV_EXPORT_QUERY - ) + """ + self.CSV_EXPORT_QUERY result, _ = db.cypher_query(query, {"target_uid": target_uid}) NotFoundException.raise_if(result[0][1] == 0, "ODM Form", target_uid) @@ -197,8 +191,7 @@ def get_odm_form(self, target_uid: str): return result[0][0] def get_odm_item_group(self, target_uid: str): - query = ( - f""" + query = f""" WITH " MATCH (OdmItemGroupRoot:OdmItemGroupRoot {{uid: $target_uid}}) -[:LATEST_FINAL|LATEST_RETIRED]->(OdmItemGroupValue:OdmItemGroupValue) @@ -230,9 +223,7 @@ def get_odm_item_group(self, target_uid: str): {self.ITEM_CODELIST_RETURN}, {self.ITEM_TERM_RETURN} " AS query - """ - + self.CSV_EXPORT_QUERY - ) + """ + self.CSV_EXPORT_QUERY result, _ = db.cypher_query(query, {"target_uid": target_uid}) NotFoundException.raise_if(result[0][1] == 0, "ODM Item Group", target_uid) @@ -240,8 +231,7 @@ def get_odm_item_group(self, target_uid: str): return result[0][0] def get_odm_item(self, target_uid: str): - query = ( - f""" + query = f""" WITH " MATCH (OdmItemRoot:OdmItemRoot {{uid: $target_uid}})-[:LATEST_FINAL|LATEST_RETIRED]->(OdmItemValue:OdmItemValue) CALL {{ @@ -269,9 +259,7 @@ def get_odm_item(self, target_uid: str): {self.ITEM_CODELIST_RETURN}, {self.ITEM_TERM_RETURN} " AS query - """ - + self.CSV_EXPORT_QUERY - ) + """ + self.CSV_EXPORT_QUERY result, _ = db.cypher_query(query, {"target_uid": target_uid}) NotFoundException.raise_if(result[0][1] == 0, "ODM Item", target_uid) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/method_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/method_repository.py similarity index 74% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/method_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/method_repository.py index 1db51622..4d2a28f9 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/method_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/method_repository.py @@ -1,10 +1,8 @@ +import logging from typing import Any from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -15,20 +13,25 @@ OdmMethodRoot, OdmMethodValue, ) -from clinical_mdr_api.domains.concepts.odms.method import OdmMethodAR, OdmMethodVO +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domains.odms.method import OdmMethodAR, OdmMethodVO from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmFormalExpressionModel, OdmTranslatedTextModel, ) -from clinical_mdr_api.models.concepts.odms.odm_method import OdmMethod +from clinical_mdr_api.models.odms.method import OdmMethod from common.utils import convert_to_datetime +log = logging.getLogger(__name__) + class MethodRepository(OdmGenericRepository[OdmMethodAR]): root_class = OdmMethodRoot @@ -43,9 +46,10 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( value: VersionValue, **_kwargs, ) -> OdmMethodAR: + log.debug("Creating OdmMethodAR from version root: uid=%s", root.uid) return OdmMethodAR.from_repository_values( uid=root.uid, - concept_vo=OdmMethodVO.from_repository_values( + odm_vo=OdmMethodVO.from_repository_values( oid=value.oid, name=value.name, method_type=value.method_type, @@ -80,9 +84,14 @@ def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> OdmMethodAR: major, minor = input_dict["version"].split(".") + log.debug( + "Creating OdmMethodAR from cypher result: uid=%s, version=%s", + input_dict["uid"], + input_dict["version"], + ) odm_method_ar = OdmMethodAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmMethodVO.from_repository_values( + odm_vo=OdmMethodVO.from_repository_values( oid=input_dict.get("oid"), name=input_dict["name"], method_type=input_dict.get("method_type"), @@ -129,39 +138,45 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.oid AS oid, -concept_value.method_type AS method_type, +odm_value.oid AS oid, +odm_value.method_type AS method_type, -[(concept_value)-[:HAS_FORMAL_EXPRESSION]->(fev:OdmFormalExpression) | {context: fev.context, expression: fev.expression}] AS formal_expressions, +[(odm_value)-[:HAS_FORMAL_EXPRESSION]->(fev:OdmFormalExpression) | {context: fev.context, expression: fev.expression}] AS formal_expressions, -[(concept_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, +[(odm_value)-[:HAS_TRANSLATED_TEXT]->(dv:OdmTranslatedText) | {text_type: dv.text_type, language: dv.language, text: dv.text}] AS translated_texts, -[(concept_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases +[(odm_value)-[:HAS_ALIAS]->(av:OdmAlias) | {name: av.name, context: av.context}] AS aliases """ def _get_or_create_value( self, root: VersionRoot, ar: OdmMethodAR, force_new_value_node: bool = False ) -> VersionValue: + log.debug( + "Getting or creating value for OdmMethod: uid=%s, force_new=%s", + root.uid, + force_new_value_node, + ) new_value = super()._get_or_create_value(root, ar, force_new_value_node) - self.connect_aliases(ar.concept_vo.aliases, new_value) - self.connect_translated_texts(ar.concept_vo.translated_texts, new_value) - self.connect_formal_expressions(ar.concept_vo.formal_expressions, new_value) + self.connect_aliases(ar.odm_vo.aliases, new_value) + self.connect_translated_texts(ar.odm_vo.translated_texts, new_value) + self.connect_formal_expressions(ar.odm_vo.formal_expressions, new_value) return new_value def _create_new_value_node(self, ar: OdmMethodAR) -> OdmMethodValue: + log.debug("Creating new OdmMethodValue node for uid=%s", ar.uid) value_node = super()._create_new_value_node(ar=ar) value_node.save() - value_node.oid = ar.concept_vo.oid - value_node.method_type = ar.concept_vo.method_type + value_node.oid = ar.odm_vo.oid + value_node.method_type = ar.odm_vo.method_type return value_node def _has_data_changed(self, ar: OdmMethodAR, value: OdmMethodValue) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) formal_expression_nodes = { OdmFormalExpressionModel( @@ -184,19 +199,20 @@ def _has_data_changed(self, ar: OdmMethodAR, value: OdmMethodValue) -> bool: } are_rels_changed = ( - set(ar.concept_vo.formal_expressions) != formal_expression_nodes - or set(ar.concept_vo.translated_texts) != translated_text_nodes - or set(ar.concept_vo.aliases) != alias_nodes + set(ar.odm_vo.formal_expressions) != formal_expression_nodes + or set(ar.odm_vo.translated_texts) != translated_text_nodes + or set(ar.odm_vo.aliases) != alias_nodes ) return ( - are_concept_properties_changed + are_odm_properties_changed or are_rels_changed - or ar.concept_vo.oid != value.oid - or ar.concept_vo.method_type != value.method_type + or ar.odm_vo.oid != value.oid + or ar.odm_vo.method_type != value.method_type ) def set_all_method_oid_properties_to_null(self, oid): + log.info("Setting method_oid to null for oid=%s", oid) db.cypher_query( "MATCH ()-[r:ITEM_REF {method_oid: $oid}]-() SET r.method_oid = null", {"oid": oid}, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/study_event_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/study_event_repository.py similarity index 78% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/study_event_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/study_event_repository.py index 8208097c..f1d3cd46 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/study_event_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/study_event_repository.py @@ -1,8 +1,5 @@ from typing import Any -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -13,16 +10,16 @@ OdmStudyEventRoot, OdmStudyEventValue, ) -from clinical_mdr_api.domains.concepts.odms.study_event import ( - OdmStudyEventAR, - OdmStudyEventVO, +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, ) +from clinical_mdr_api.domains.odms.study_event import OdmStudyEventAR, OdmStudyEventVO from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_study_event import OdmStudyEvent +from clinical_mdr_api.models.odms.study_event import OdmStudyEvent from common.utils import convert_to_datetime @@ -41,7 +38,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( ) -> OdmStudyEventAR: return OdmStudyEventAR.from_repository_values( uid=root.uid, - concept_vo=OdmStudyEventVO.from_repository_values( + odm_vo=OdmStudyEventVO.from_repository_values( name=value.name, oid=value.oid, effective_date=value.effective_date, @@ -67,7 +64,7 @@ def _create_aggregate_root_instance_from_cypher_result( major, minor = input_dict["version"].split(".") odm_form_ar = OdmStudyEventAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmStudyEventVO.from_repository_values( + odm_vo=OdmStudyEventVO.from_repository_values( name=input_dict["name"], oid=input_dict.get("oid"), effective_date=input_dict.get("effective_date"), @@ -99,13 +96,13 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.oid AS oid, -concept_value.effective_date AS effective_date, -concept_value.retired_date AS retired_date, -concept_value.description AS description, -concept_value.display_in_tree AS display_in_tree, +odm_value.oid AS oid, +odm_value.effective_date AS effective_date, +odm_value.retired_date AS retired_date, +odm_value.description AS description, +odm_value.display_in_tree AS display_in_tree, -[(concept_value)-[fref:FORM_REF]->(fv:OdmFormValue)<-[:HAS_VERSION]-(fr:OdmFormRoot) | +[(odm_value)-[fref:FORM_REF]->(fv:OdmFormValue)<-[:HAS_VERSION]-(fr:OdmFormRoot) | {uid: fr.uid, name: fv.name, order: fref.order, mandatory: fref.mandatory, collection_exception_condition_oid: fref.collection_exception_condition_oid}] AS forms WITH *, @@ -150,22 +147,22 @@ def _create_new_value_node(self, ar: OdmStudyEventAR) -> OdmStudyEventValue: value_node.save() - value_node.oid = ar.concept_vo.oid - value_node.effective_date = ar.concept_vo.effective_date - value_node.retired_date = ar.concept_vo.retired_date - value_node.description = ar.concept_vo.description - value_node.display_in_tree = ar.concept_vo.display_in_tree + value_node.oid = ar.odm_vo.oid + value_node.effective_date = ar.odm_vo.effective_date + value_node.retired_date = ar.odm_vo.retired_date + value_node.description = ar.odm_vo.description + value_node.display_in_tree = ar.odm_vo.display_in_tree return value_node def _has_data_changed(self, ar: OdmStudyEventAR, value: OdmStudyEventValue) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) return ( - are_concept_properties_changed - or ar.concept_vo.oid != value.oid - or ar.concept_vo.effective_date != value.effective_date - or ar.concept_vo.retired_date != value.retired_date - or ar.concept_vo.description != value.description - or ar.concept_vo.display_in_tree != value.display_in_tree + are_odm_properties_changed + or ar.odm_vo.oid != value.oid + or ar.odm_vo.effective_date != value.effective_date + or ar.odm_vo.retired_date != value.retired_date + or ar.odm_vo.description != value.description + or ar.odm_vo.display_in_tree != value.display_in_tree ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_attribute_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_attribute_repository.py similarity index 84% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_attribute_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_attribute_repository.py index e1d72220..1e647d62 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_attribute_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_attribute_repository.py @@ -1,11 +1,9 @@ import json +import logging from typing import Any from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -18,25 +16,28 @@ OdmVendorElementRoot, OdmVendorNamespaceRoot, ) -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import ( +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domains.odms.utils import RelationType +from clinical_mdr_api.domains.odms.vendor_attribute import ( OdmVendorAttributeAR, OdmVendorAttributeRelationVO, OdmVendorAttributeVO, OdmVendorElementAttributeRelationVO, ) -from clinical_mdr_api.domains.concepts.utils import RelationType from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( - OdmVendorAttribute, -) +from clinical_mdr_api.models.odms.vendor_attribute import OdmVendorAttribute from clinical_mdr_api.services._utils import ensure_transaction from common.exceptions import BusinessLogicException from common.utils import convert_to_datetime +log = logging.getLogger(__name__) + class VendorAttributeRepository(OdmGenericRepository[OdmVendorAttributeAR]): root_class = OdmVendorAttributeRoot @@ -53,9 +54,12 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( ) -> OdmVendorAttributeAR: vendor_namespace_value = value.belongs_to_vendor_namespace.get_or_none() vendor_element_value = value.belongs_to_vendor_element.get_or_none() + log.debug( + "Creating OdmVendorAttributeAR from repository values for uid=%s", root.uid + ) return OdmVendorAttributeAR.from_repository_values( uid=root.uid, - concept_vo=OdmVendorAttributeVO.from_repository_values( + odm_vo=OdmVendorAttributeVO.from_repository_values( name=value.name, compatible_types=( value.compatible_types if value.compatible_types else [] @@ -84,9 +88,13 @@ def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> OdmVendorAttributeAR: major, minor = input_dict["version"].split(".") + log.debug( + "Creating OdmVendorAttributeAR from Cypher result for uid=%s", + input_dict["uid"], + ) odm_form_ar = OdmVendorAttributeAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmVendorAttributeVO.from_repository_values( + odm_vo=OdmVendorAttributeVO.from_repository_values( name=input_dict["name"], compatible_types=json.loads(input_dict.get("compatible_types") or "[]"), data_type=input_dict.get("data_type"), @@ -117,14 +125,14 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.compatible_types AS compatible_types, -concept_value.data_type AS data_type, -concept_value.value_regex AS value_regex, +odm_value.compatible_types AS compatible_types, +odm_value.data_type AS data_type, +odm_value.value_regex AS value_regex, -head([(concept_value)<-[:HAS_VENDOR_ATTRIBUTE]-(vnv:OdmVendorNamespaceValue)<-[:HAS_VERSION]-(vnr:OdmVendorNamespaceRoot) | +head([(odm_value)<-[:HAS_VENDOR_ATTRIBUTE]-(vnv:OdmVendorNamespaceValue)<-[:HAS_VERSION]-(vnr:OdmVendorNamespaceRoot) | {uid: vnr.uid, name: vnv.name, prefix: vnv.prefix, url: vnv.url}]) AS vendor_namespace, -head([(concept_value)<-[:HAS_VENDOR_ATTRIBUTE]-(xtv:OdmVendorElementValue)<-[:HAS_VERSION]-(xtr:OdmVendorElementRoot) | +head([(odm_value)<-[:HAS_VENDOR_ATTRIBUTE]-(xtv:OdmVendorElementValue)<-[:HAS_VERSION]-(xtr:OdmVendorElementRoot) | {uid: xtr.uid, name: xtv.name}]) AS vendor_element @@ -144,9 +152,9 @@ def _get_or_create_value( new_value.belongs_to_vendor_namespace.disconnect_all() new_value.belongs_to_vendor_element.disconnect_all() - if ar.concept_vo.vendor_namespace_uid is not None: + if ar.odm_vo.vendor_namespace_uid is not None: vendor_namespace_root = OdmVendorNamespaceRoot.nodes.get_or_none( - uid=ar.concept_vo.vendor_namespace_uid + uid=ar.odm_vo.vendor_namespace_uid ) vendor_namespace_value = ( vendor_namespace_root.has_latest_value.get_or_none() @@ -156,9 +164,9 @@ def _get_or_create_value( if vendor_namespace_value: new_value.belongs_to_vendor_namespace.connect(vendor_namespace_value) - if ar.concept_vo.vendor_element_uid is not None: + if ar.odm_vo.vendor_element_uid is not None: vendor_element_root = OdmVendorElementRoot.nodes.get_or_none( - uid=ar.concept_vo.vendor_element_uid + uid=ar.odm_vo.vendor_element_uid ) vendor_element_value = ( vendor_element_root.has_latest_value.get_or_none() @@ -177,16 +185,17 @@ def _create_new_value_node( value_node.save() - value_node.compatible_types = ar.concept_vo.compatible_types - value_node.data_type = ar.concept_vo.data_type - value_node.value_regex = ar.concept_vo.value_regex + value_node.compatible_types = ar.odm_vo.compatible_types + value_node.data_type = ar.odm_vo.data_type + value_node.value_regex = ar.odm_vo.value_regex + log.debug("Created new VendorAttributeValue node for name=%s", ar.name) return value_node def _has_data_changed( self, ar: OdmVendorAttributeAR, value: OdmVendorAttributeValue ) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) vendor_namespace_uid = ( vendor_namespace_value.has_root.single().uid @@ -202,16 +211,16 @@ def _has_data_changed( ) are_rels_changed = ( - ar.concept_vo.vendor_namespace_uid != vendor_namespace_uid - or ar.concept_vo.vendor_element_uid != vendor_element_uid + ar.odm_vo.vendor_namespace_uid != vendor_namespace_uid + or ar.odm_vo.vendor_element_uid != vendor_element_uid ) return ( - are_concept_properties_changed + are_odm_properties_changed or are_rels_changed - or ar.concept_vo.compatible_types != value.compatible_types - or ar.concept_vo.data_type != value.data_type - or ar.concept_vo.value_regex != value.value_regex + or ar.odm_vo.compatible_types != value.compatible_types + or ar.odm_vo.data_type != value.data_type + or ar.odm_vo.value_regex != value.value_regex ) def find_by_uid_with_odm_element_relation( @@ -222,6 +231,12 @@ def find_by_uid_with_odm_element_relation( odm_element_type: RelationType, vendor_element_attribute: bool = True, ): + log.info( + "Finding VendorAttribute with uid=%s for ODM element uid=%s, version=%s", + uid, + odm_element_uid, + odm_element_version, + ) if odm_element_type == RelationType.FORM: odm_element_root = "OdmFormRoot" odm_element_value = "OdmFormValue" @@ -302,6 +317,9 @@ def _connect_relationships_to_new_value_node( - Upgrades all incoming HAS_VENDOR_ATTRIBUTE relationships to the second latest version to point to the latest version of OdmVendorAttributeValue, preserving relationship properties. """ + log.info( + "Upgrading vendor element attribute relationships for root uid=%s", root.uid + ) query = f""" MATCH (root:{self.root_class.__name__} {{uid: $root_uid}})-[ver_rel:HAS_VERSION]->(value:{self.value_class.__name__}) @@ -326,6 +344,7 @@ def _connect_relationships_to_new_value_node( """ db.cypher_query(query, {"root_uid": root.uid}) + log.info("Upgrading vendor attribute relationships for root uid=%s", root.uid) query = f""" MATCH (root:{self.root_class.__name__} {{uid: $root_uid}})-[ver_rel:HAS_VERSION]->(value:{self.value_class.__name__}) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_element_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_element_repository.py similarity index 83% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_element_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_element_repository.py index 36b0fb38..f44287fe 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_element_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_element_repository.py @@ -1,11 +1,9 @@ import json +import logging from typing import Any from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -17,22 +15,27 @@ OdmVendorElementValue, OdmVendorNamespaceRoot, ) -from clinical_mdr_api.domains.concepts.odms.vendor_element import ( +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domains.odms.utils import RelationType +from clinical_mdr_api.domains.odms.vendor_element import ( OdmVendorElementAR, OdmVendorElementRelationVO, OdmVendorElementVO, ) -from clinical_mdr_api.domains.concepts.utils import RelationType from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import OdmVendorElement +from clinical_mdr_api.models.odms.vendor_element import OdmVendorElement from clinical_mdr_api.services._utils import ensure_transaction from common.exceptions import BusinessLogicException from common.utils import convert_to_datetime +log = logging.getLogger(__name__) + class VendorElementRepository(OdmGenericRepository[OdmVendorElementAR]): root_class = OdmVendorElementRoot @@ -48,9 +51,12 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( **_kwargs, ) -> OdmVendorElementAR: vendor_namespace_value = value.belongs_to_vendor_namespace.get_or_none() + log.debug( + "Creating OdmVendorElementAR from repository values for uid=%s", root.uid + ) return OdmVendorElementAR.from_repository_values( uid=root.uid, - concept_vo=OdmVendorElementVO.from_repository_values( + odm_vo=OdmVendorElementVO.from_repository_values( name=value.name, compatible_types=value.compatible_types, vendor_namespace_uid=vendor_namespace_value.has_root.single().uid, @@ -71,9 +77,13 @@ def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> OdmVendorElementAR: major, minor = input_dict["version"].split(".") + log.debug( + "Creating OdmVendorElementAR from Cypher result for uid=%s", + input_dict["uid"], + ) odm_vendor_element_ar = OdmVendorElementAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmVendorElementVO.from_repository_values( + odm_vo=OdmVendorElementVO.from_repository_values( name=input_dict["name"], compatible_types=json.loads(input_dict.get("compatible_types") or "[]"), vendor_namespace_uid=input_dict["vendor_namespace_uid"], @@ -102,12 +112,12 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.compatible_types AS compatible_types, +odm_value.compatible_types AS compatible_types, -head([(concept_value)<-[:HAS_VENDOR_ELEMENT]-(vnv:OdmVendorNamespaceValue)<-[:HAS_VERSION]-(vnr:OdmVendorNamespaceRoot) | +head([(odm_value)<-[:HAS_VENDOR_ELEMENT]-(vnv:OdmVendorNamespaceValue)<-[:HAS_VERSION]-(vnr:OdmVendorNamespaceRoot) | {uid: vnr.uid, name: vnv.name, prefix: vnv.prefix, url: vnv.url}]) AS vendor_namespace, -[(concept_value)-[:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name}] AS vendor_attributes WITH *, @@ -137,9 +147,9 @@ def _get_or_create_value( new_value.belongs_to_vendor_namespace.disconnect_all() - if ar.concept_vo.vendor_namespace_uid is not None: + if ar.odm_vo.vendor_namespace_uid is not None: vendor_namespace_root = OdmVendorNamespaceRoot.nodes.get_or_none( - uid=ar.concept_vo.vendor_namespace_uid + uid=ar.odm_vo.vendor_namespace_uid ) vendor_namespace_value = ( vendor_namespace_root.has_latest_value.get_or_none() @@ -163,14 +173,15 @@ def _create_new_value_node(self, ar: OdmVendorElementAR) -> OdmVendorElementValu value_node.save() - value_node.compatible_types = ar.concept_vo.compatible_types + value_node.compatible_types = ar.odm_vo.compatible_types + log.debug("Created new VendorElementValue node for name=%s", ar.name) return value_node def _has_data_changed( self, ar: OdmVendorElementAR, value: OdmVendorElementValue ) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) vendor_namespace_uid = ( vendor_namespace_value.has_root.single().uid @@ -180,12 +191,12 @@ def _has_data_changed( else None ) - are_rels_changed = ar.concept_vo.vendor_namespace_uid != vendor_namespace_uid + are_rels_changed = ar.odm_vo.vendor_namespace_uid != vendor_namespace_uid return ( - are_concept_properties_changed + are_odm_properties_changed or are_rels_changed - or ar.concept_vo.compatible_types != value.compatible_types + or ar.odm_vo.compatible_types != value.compatible_types ) def find_by_uid_with_odm_element_relation( @@ -195,6 +206,12 @@ def find_by_uid_with_odm_element_relation( odm_element_version: str, odm_element_type: RelationType, ): + log.info( + "Finding VendorElement with uid=%s for ODM element uid=%s, version=%s", + uid, + odm_element_uid, + odm_element_version, + ) if odm_element_type == RelationType.FORM: odm_element_root = "OdmFormRoot" odm_element_value = "OdmFormValue" @@ -238,6 +255,7 @@ def _connect_relationships_to_new_value_node( Upgrades all incoming HAS_VENDOR_ELEMENT relationships to the second latest version to point to the latest version of OdmVendorElementValue, preserving relationship properties. """ + log.info("Upgrading vendor element relationships for root uid=%s", root.uid) query = f""" MATCH (root:{self.root_class.__name__} {{uid: $root_uid}})-[ver_rel:HAS_VERSION]->(value:{self.value_class.__name__}) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_namespace_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_namespace_repository.py similarity index 82% rename from clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_namespace_repository.py rename to clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_namespace_repository.py index 45eefc2d..c2036d1c 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/concepts/odms/vendor_namespace_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/odms/vendor_namespace_repository.py @@ -1,8 +1,6 @@ +import logging from typing import Any -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( - OdmGenericRepository, -) from clinical_mdr_api.domain_repositories.models.generic import ( Library, VersionRelationship, @@ -13,7 +11,10 @@ OdmVendorNamespaceRoot, OdmVendorNamespaceValue, ) -from clinical_mdr_api.domains.concepts.odms.vendor_namespace import ( +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domains.odms.vendor_namespace import ( OdmVendorNamespaceAR, OdmVendorNamespaceVO, ) @@ -22,11 +23,11 @@ LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_namespace import ( - OdmVendorNamespace, -) +from clinical_mdr_api.models.odms.vendor_namespace import OdmVendorNamespace from common.utils import convert_to_datetime +log = logging.getLogger(__name__) + class VendorNamespaceRepository(OdmGenericRepository[OdmVendorNamespaceAR]): root_class = OdmVendorNamespaceRoot @@ -41,9 +42,12 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( value: VersionValue, **_kwargs, ) -> OdmVendorNamespaceAR: + log.debug( + "Creating OdmVendorNamespaceAR from repository values for uid=%s", root.uid + ) return OdmVendorNamespaceAR.from_repository_values( uid=root.uid, - concept_vo=OdmVendorNamespaceVO.from_repository_values( + odm_vo=OdmVendorNamespaceVO.from_repository_values( name=value.name, prefix=value.prefix, url=value.url, @@ -74,9 +78,13 @@ def _create_aggregate_root_instance_from_cypher_result( self, input_dict: dict[str, Any] ) -> OdmVendorNamespaceAR: major, minor = input_dict["version"].split(".") + log.debug( + "Creating OdmVendorNamespaceAR from Cypher result for uid=%s", + input_dict["uid"], + ) odm_vendor_namespace_ar = OdmVendorNamespaceAR.from_repository_values( uid=input_dict["uid"], - concept_vo=OdmVendorNamespaceVO.from_repository_values( + odm_vo=OdmVendorNamespaceVO.from_repository_values( name=input_dict["name"], prefix=input_dict["prefix"], url=input_dict["url"], @@ -106,13 +114,13 @@ def _create_aggregate_root_instance_from_cypher_result( def specific_alias_clause(self, **kwargs) -> str: return """ WITH *, -concept_value.prefix AS prefix, -concept_value.url AS url, +odm_value.prefix AS prefix, +odm_value.url AS url, -[(concept_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | +[(odm_value)-[hve:HAS_VENDOR_ELEMENT]->(vev:OdmVendorElementValue)<-[:HAS_VERSION]-(ver:OdmVendorElementRoot) | {uid: ver.uid, name: vev.name, value: hve.value}] AS vendor_elements, -[(concept_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | +[(odm_value)-[hva:HAS_VENDOR_ATTRIBUTE]->(vav:OdmVendorAttributeValue)<-[:HAS_VERSION]-(var:OdmVendorAttributeRoot) | {uid: var.uid, name: vav.name, value: hva.value}] AS vendor_attributes WITH *, @@ -171,18 +179,19 @@ def _create_new_value_node( value_node.save() - value_node.prefix = ar.concept_vo.prefix - value_node.url = ar.concept_vo.url + value_node.prefix = ar.odm_vo.prefix + value_node.url = ar.odm_vo.url + log.debug("Created new VendorNamespaceValue node for name=%s", ar.name) return value_node def _has_data_changed( self, ar: OdmVendorNamespaceAR, value: OdmVendorNamespaceValue ) -> bool: - are_concept_properties_changed = super()._has_data_changed(ar=ar, value=value) + are_odm_properties_changed = super()._has_data_changed(ar=ar, value=value) return ( - are_concept_properties_changed - or ar.concept_vo.prefix != value.prefix - or ar.concept_vo.url != value.url + are_odm_properties_changed + or ar.odm_vo.prefix != value.prefix + or ar.odm_vo.url != value.url ) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_registry.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_registry.py new file mode 100644 index 00000000..40980327 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_registry.py @@ -0,0 +1,90 @@ +from dataclasses import dataclass +from typing import Any, Literal + +from neomodel import BooleanProperty, IntegerProperty, StringProperty + + +@dataclass(frozen=True) +class PreferenceDefinition: + """Single source of truth for a preference field.""" + + key: str + preference_type: Literal["integer", "boolean", "enum"] + label: str + description: str + default: int | bool | str + min: int | None = None + max: int | None = None + allowed_values: list[str] | None = None + + +PREFERENCE_DEFINITIONS: tuple[PreferenceDefinition, ...] = ( + PreferenceDefinition( + key="language", + preference_type="enum", + label="Language", + description="Preferred language for the application", + default="en", + allowed_values=["en"], + ), + PreferenceDefinition( + key="rows_per_page", + preference_type="integer", + label="Rows per page", + description="Number of rows to display per page in tables", + default=10, + min=5, + max=100, + ), + PreferenceDefinition( + key="sidebar_visible", + preference_type="boolean", + label="Sidebar visible", + description="Whether the sidebar is visible by default", + default=True, + ), + PreferenceDefinition( + key="sidebar_auto_minimize", + preference_type="boolean", + label="Auto-minimize sidebar", + description="Automatically minimize the sidebar to rail mode", + default=False, + ), +) + +# Derived lookups (computed once at import time) +PREFERENCE_KEYS: list[str] = [d.key for d in PREFERENCE_DEFINITIONS] +PREFERENCES_BY_KEY: dict[str, PreferenceDefinition] = { + d.key: d for d in PREFERENCE_DEFINITIONS +} + +# Map pref_type -> neomodel property constructor +_NEOMODEL_TYPE_MAP = { + "integer": IntegerProperty, + "boolean": BooleanProperty, + "enum": StringProperty, +} + + +def get_neomodel_properties() -> dict[str, Any]: + """Return a dict of {key: NeomodelProperty()} for use in mixin class body.""" + return { + d.key: _NEOMODEL_TYPE_MAP[d.preference_type]() for d in PREFERENCE_DEFINITIONS + } + + +def to_metadata_dict(preference_definition: PreferenceDefinition) -> dict[str, Any]: + """Convert a PreferenceDefinition to the API metadata dict shape.""" + result: dict[str, Any] = { + "type": preference_definition.preference_type, + "label": preference_definition.label, + "description": preference_definition.description, + "default": preference_definition.default, + } + if preference_definition.min is not None: + result["min"] = preference_definition.min + if preference_definition.max is not None: + result["max"] = preference_definition.max + if preference_definition.allowed_values is not None: + result["allowed_values"] = preference_definition.allowed_values + return result diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_repository.py new file mode 100644 index 00000000..eb640fd5 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/preferences_repository.py @@ -0,0 +1,149 @@ +# pylint: disable=invalid-name +from typing import Any + +from neomodel import db + +# Importing node models registers them with neomodel for resolve_objects=True +from clinical_mdr_api.domain_repositories.models.preferences import ( # pylint: disable=unused-import + GlobalPreferences, + UserPreferences, +) +from clinical_mdr_api.domain_repositories.preferences_registry import ( + PREFERENCE_KEYS, + PREFERENCES_BY_KEY, +) +from common.exceptions import NotFoundException + + +def _node_to_dict(node) -> dict[str, Any]: + """Extract all preference keys from a neomodel node into a dict.""" + return {key: getattr(node, key) for key in PREFERENCE_KEYS} + + +class PreferencesRepository: + def get_global_preferences(self) -> dict[str, Any]: + """MERGE singleton GlobalPreferences node with defaults and return as dict.""" + on_create_parts = [f"gp.{key} = $default_{key}" for key in PREFERENCE_KEYS] + on_match_parts = [ + f"gp.{key} = COALESCE(gp.{key}, $default_{key})" for key in PREFERENCE_KEYS + ] + params = { + f"default_{key}": PREFERENCES_BY_KEY[key].default for key in PREFERENCE_KEYS + } + + rs = db.cypher_query( + f""" + MERGE (gp:GlobalPreferences) + ON CREATE SET + {", ".join(on_create_parts)} + ON MATCH SET + {", ".join(on_match_parts)} + RETURN gp + """, + params=params, + resolve_objects=True, + ) + + if rs[0]: + return _node_to_dict(rs[0][0][0]) + return {} + + def update_global_preferences(self, updates: dict[str, Any]) -> dict[str, Any]: + """SET only provided fields on the GlobalPreferences singleton node.""" + set_clauses = [] + params = {} + + for key in PREFERENCE_KEYS: + if key in updates: + set_clauses.append(f"gp.{key} = ${key}") + params[key] = updates[key] + + if not set_clauses: + return self.get_global_preferences() + + set_clause = ", ".join(set_clauses) + rs = db.cypher_query( + f""" + MATCH (gp:GlobalPreferences) + SET {set_clause} + RETURN gp + """, + params=params, + resolve_objects=True, + ) + + if rs[0]: + return _node_to_dict(rs[0][0][0]) + return {} + + def get_user_preferences(self, user_id: str) -> dict[str, Any] | None: + """MATCH User node and its UserPreferences, return dict or None.""" + rs = db.cypher_query( + """ + MATCH (u:User {user_id: $user_id})-[:HAS_PREFERENCES]->(up:UserPreferences) + RETURN up + """, + params={"user_id": user_id}, + resolve_objects=True, + ) + + if rs[0]: + return _node_to_dict(rs[0][0][0]) + return None + + def update_user_preferences( + self, user_id: str, updates: dict[str, Any] + ) -> dict[str, Any]: + """MERGE relationship + UserPreferences node, SET fields.""" + set_clauses = [] + params: dict[str, Any] = {"user_id": user_id} + + global_preferences = self.get_global_preferences() + + for key in PREFERENCE_KEYS: + if key in updates: + set_clauses.append(f"up.{key} = ${key}") + + if updates[key] == global_preferences[key]: + params[key] = None + else: + params[key] = updates[key] + + if not set_clauses: + current = self.get_user_preferences(user_id) + return current if current else {} + + set_clause = ", ".join(set_clauses) + rs = db.cypher_query( + f""" + MATCH (u:User {{user_id: $user_id}}) + MERGE (u)-[:HAS_PREFERENCES]->(up:UserPreferences) + SET {set_clause} + RETURN up + """, + params=params, + resolve_objects=True, + ) + + if not rs[0]: + raise NotFoundException(msg=f"User with id '{user_id}' not found") + return _node_to_dict(rs[0][0][0]) + + def delete_user_preference_key(self, user_id: str, key: str) -> dict[str, Any]: + """REMOVE single property from UserPreferences node.""" + if key not in PREFERENCE_KEYS: + raise ValueError(f"Invalid preference key: {key}") + + rs = db.cypher_query( + f""" + MATCH (u:User {{user_id: $user_id}})-[:HAS_PREFERENCES]->(up:UserPreferences) + REMOVE up.{key} + RETURN up + """, + params={"user_id": user_id}, + resolve_objects=True, + ) + + if not rs[0]: + raise NotFoundException(msg=f"User with id '{user_id}' not found") + return _node_to_dict(rs[0][0][0]) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_ig_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_ig_repository.py index eaae7dc9..2d9a221a 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_ig_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_ig_repository.py @@ -15,9 +15,31 @@ class DataModelIGRepository(StandardDataModelRepository): def specific_alias_clause(self) -> str: return """ + DISTINCT * + CALL { + WITH standard_root, standard_value + MATCH (standard_root)-[hv:HAS_VERSION]-(standard_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 version_rel + } WITH *, + standard_root.uid AS uid, + standard_value.name AS name, + standard_value.description AS description, standard_value.version_number AS version_number, + version_rel.start_date AS start_date, + version_rel.end_date AS end_date, + version_rel.status AS status, head([(standard_value)-[:IMPLEMENTS]->(implemented_data_model_value:DataModelValue)<-[:HAS_VERSION]- (implemented_data_model_root:DataModelRoot) | {uid:implemented_data_model_root.uid, name:implemented_data_model_value.name}]) AS implemented_data_model """ + + def sort_by(self) -> dict[str, bool] | None: + return {"version_number": False} diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_repository.py index 990a7481..ece60fb2 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/data_model_repository.py @@ -15,9 +15,31 @@ class DataModelRepository(StandardDataModelRepository): def specific_alias_clause(self) -> str: return """ + DISTINCT * + CALL { + WITH standard_root, standard_value + MATCH (standard_root)-[hv:HAS_VERSION]-(standard_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 version_rel + } WITH *, + standard_root.uid AS uid, + standard_value.name AS name, + standard_value.description AS description, + version_rel.start_date AS start_date, + version_rel.end_date AS end_date, + version_rel.status AS status, standard_value.version_number AS version_number, [(standard_value)<-[:IMPLEMENTS]-(implementation_guide_value:DataModelIGValue)<-[:HAS_VERSION]- (implementation_guide_root:DataModelIGRoot) | {uid:implementation_guide_root.uid, name:implementation_guide_value.name}] AS implementation_guides """ + + def sort_by(self) -> dict[str, bool] | None: + return {"version_number": False} diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_class_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_class_repository.py index 92ee3f9f..bd620c99 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_class_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_class_repository.py @@ -1,3 +1,5 @@ +from typing import Any + from clinical_mdr_api.domain_repositories.models.standard_data_model import ( DatasetClass, DatasetClassInstance, @@ -8,6 +10,7 @@ from clinical_mdr_api.models.standard_data_models.dataset_class import ( DatasetClass as DatasetClassAPIModel, ) +from common.exceptions import ValidationException class DatasetClassRepository(StandardDataModelRepository): @@ -16,34 +19,57 @@ class DatasetClassRepository(StandardDataModelRepository): return_model = DatasetClassAPIModel # pylint: disable=unused-argument - def generic_match_clause( - self, versioning_relationship: str, uid: str | None = None - ): + def generic_match_clause(self, versioning_relationship: str): standard_data_model_label = self.root_class.__label__ standard_data_model_value_label = self.value_class.__label__ - uid_filter = "" - if uid: - uid_filter = f"{{uid: '{uid}'}}" - query = f"""MATCH (standard_root_row:{standard_data_model_label} {uid_filter})-[:HAS_INSTANCE]-> - (standard_value_row:{standard_data_model_value_label})""" - if standard_data_model_label == "DatasetClass": - query += """<-[:HAS_DATASET_CLASS]-(dmv:DataModelValue) - WITH standard_root_row, standard_value_row, dmv ORDER BY dmv.effective_date - WITH COLLECT(standard_value_row) AS standard_value_row_collected, standard_root_row as standard_root - WITH standard_root, HEAD(standard_value_row_collected) as standard_value + query = f"""MATCH (standard_root:{standard_data_model_label})-[:HAS_INSTANCE]-> + (standard_value:{standard_data_model_value_label})<-[hdc:HAS_DATASET_CLASS]-(data_model_value:DataModelValue) """ return query def specific_alias_clause(self) -> str: return """ - WITH *, + *, + standard_root.uid AS uid, standard_value.label AS label, standard_value.title AS title, + standard_value.description AS description, + {name: data_model_value.name, ordinal: hdc.ordinal} AS data_model, + toInteger(apoc.text.split(hdc.ordinal, "\\.")[0]) AS split_ordinal0, + toInteger(coalesce(apoc.text.split(hdc.ordinal, "\\.")[1], 0)) AS split_ordinal1, head([(standard_root)<-[:HAS_DATASET_CLASS]-(catalogue:DataModelCatalogue) | catalogue.name]) AS catalogue_name, - head([(standard_value)-[:HAS_PARENT_CLASS]->(parent_class:DatasetClassInstance) | parent_class.label]) AS parent_class, - [(standard_value)<-[has_dataset_class:HAS_DATASET_CLASS]-(data_model_value:DataModelValue) | { - data_model_name: data_model_value.name, - ordinal:has_dataset_class.ordinal - } - ] AS data_models + head([(standard_value)-[:HAS_PARENT_CLASS]->(parent_class:DatasetClassInstance) | parent_class.label]) AS parent_class_name """ + + def sort_by(self) -> dict[str, bool] | None: + return { + "split_ordinal0": True, + "split_ordinal1": True, + } + + def create_query_filter_statement(self, **kwargs) -> tuple[str, dict[Any, Any]]: + ( + filter_statements_from_standard, + filter_query_parameters, + ) = super().create_query_filter_statement(**kwargs) + + if not kwargs.get("find_by_uid"): + ValidationException.raise_if( + not kwargs.get("data_model_name"), + msg="Please provide data_model_name parameter", + ) + + data_model_name = kwargs.get("data_model_name") + + filter_by_data_model_name = "data_model_value.name = $data_model_name" + + filter_query_parameters["data_model_name"] = data_model_name + + if filter_statements_from_standard != "": + filter_statements_to_return = " AND ".join( + [filter_statements_from_standard, filter_by_data_model_name] + ) + else: + filter_statements_to_return = "WHERE " + filter_by_data_model_name + return filter_statements_to_return, filter_query_parameters + return filter_statements_from_standard, filter_query_parameters diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_repository.py index 49fd1988..5ed4867b 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_repository.py @@ -19,15 +19,10 @@ class DatasetRepository(StandardDataModelRepository): return_model = DatasetAPIModel # pylint: disable=unused-argument - def generic_match_clause( - self, versioning_relationship: str, uid: str | None = None - ): + def generic_match_clause(self, versioning_relationship: str): standard_data_model_label = self.root_class.__label__ standard_data_model_value_label = self.value_class.__label__ - uid_filter = "" - if uid: - uid_filter = f"{{uid: '{uid}'}}" - return f"""MATCH (standard_root:{standard_data_model_label} {uid_filter})-[:HAS_INSTANCE]-> + return f"""MATCH (standard_root:{standard_data_model_label})-[:HAS_INSTANCE]-> (standard_value:{standard_data_model_value_label})<-[has_dataset:HAS_DATASET]- (data_model_ig_value:DataModelIGValue {{version_number: $data_model_ig_version}})<-[:HAS_VERSION]-(data_model_ig_root:DataModelIGRoot {{uid:$data_model_ig_name}}) MATCH (standard_value)-[implements:IMPLEMENTS_DATASET_CLASS]->(dataset_class_value)<-[:HAS_DATASET_CLASS]-(:DataModelValue)<-[:IMPLEMENTS]-(data_model_ig_value) @@ -38,7 +33,7 @@ def create_query_filter_statement(self, **kwargs) -> tuple[str, dict[Any, Any]]: ( filter_statements_from_standard, filter_query_parameters, - ) = super().create_query_filter_statement() + ) = super().create_query_filter_statement(**kwargs) filter_parameters = [] ValidationException.raise_if( @@ -79,9 +74,11 @@ def sort_by(self) -> dict[str, bool] | None: def specific_alias_clause(self) -> str: return """ - WITH *, + *, + standard_root.uid AS uid, standard_value.label AS label, standard_value.title AS title, + standard_value.description AS description, {dataset_class_name:dataset_class_value.label, dataset_class_uid:dataset_class.uid} AS implemented_dataset_class, head([(standard_value)<-[has_dataset:HAS_DATASET]-(data_model_ig_value:DataModelIGValue) | {ordinal:toInteger(has_dataset.ordinal), data_model_ig_name:data_model_ig_value.name}]) AS data_model_ig diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_scenario_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_scenario_repository.py index 6107e85c..6a35bfee 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_scenario_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_scenario_repository.py @@ -19,15 +19,10 @@ class DatasetScenarioRepository(StandardDataModelRepository): return_model = DatasetScenarioAPIModel # pylint: disable=unused-argument - def generic_match_clause( - self, versioning_relationship: str, uid: str | None = None - ): + def generic_match_clause(self, versioning_relationship: str): standard_data_model_label = self.root_class.__label__ standard_data_model_value_label = self.value_class.__label__ - uid_filter = "" - if uid: - uid_filter = f"{{uid: '{uid}'}}" - return f"""MATCH (standard_root:{standard_data_model_label} {uid_filter})-[:HAS_INSTANCE]-> + return f"""MATCH (standard_root:{standard_data_model_label})-[:HAS_INSTANCE]-> (standard_value:{standard_data_model_value_label})<-[has_dataset_scenario:HAS_DATASET_SCENARIO]- (dataset_instance:DatasetInstance)<-[:HAS_DATASET]-(data_model_ig_value:DataModelIGValue) <-[:HAS_VERSION]-(data_model_ig_root:DataModelIGRoot) @@ -37,7 +32,7 @@ def create_query_filter_statement(self, **kwargs) -> tuple[str, dict[Any, Any]]: ( filter_statements_from_standard, filter_query_parameters, - ) = super().create_query_filter_statement() + ) = super().create_query_filter_statement(**kwargs) filter_parameters = [] ValidationException.raise_if( @@ -86,7 +81,8 @@ def sort_by(self) -> dict[str, bool] | None: def specific_alias_clause(self) -> str: return """ - WITH *, + *, + standard_root.uid AS uid, standard_value.label AS label, head([(standard_root)<-[:HAS_DATASET_SCENARIO]-(catalogue:DataModelCatalogue) | catalogue.name]) AS catalogue_name, {ordinal:has_dataset_scenario.ordinal, uid:dataset_root.uid} AS dataset, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_variable_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_variable_repository.py index 5e8af0c4..ea5521e0 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_variable_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/dataset_variable_repository.py @@ -19,15 +19,10 @@ class DatasetVariableRepository(StandardDataModelRepository): return_model = DatasetVariableAPIModel # pylint: disable=unused-argument - def generic_match_clause( - self, versioning_relationship: str, uid: str | None = None - ): + def generic_match_clause(self, versioning_relationship: str): standard_data_model_label = self.root_class.__label__ standard_data_model_value_label = self.value_class.__label__ - uid_filter = "" - if uid: - uid_filter = f"{{uid: '{uid}'}}" - return f"""MATCH (standard_root:{standard_data_model_label} {uid_filter})-[:HAS_INSTANCE]-> + return f"""MATCH (standard_root:{standard_data_model_label})-[:HAS_INSTANCE]-> (standard_value:{standard_data_model_value_label})<-[has_dataset_variable_rel:HAS_DATASET_VARIABLE]- (dataset_instance:DatasetInstance)<-[:HAS_DATASET]-(data_model_ig_value:DataModelIGValue) <-[:HAS_VERSION]-(data_model_ig_root:DataModelIGRoot) @@ -54,7 +49,7 @@ def create_query_filter_statement(self, **kwargs) -> tuple[str, dict[Any, Any]]: ( filter_statements_from_standard, filter_query_parameters, - ) = super().create_query_filter_statement() + ) = super().create_query_filter_statement(**kwargs) filter_parameters = [] if kwargs.get("dataset_scenario_uid"): filter_query_parameters["dataset_scenario_uid"] = kwargs.get( @@ -107,15 +102,13 @@ def sort_by(self) -> dict[str, bool] | None: def specific_alias_clause(self) -> str: return """ - WITH - standard_root, - uid, - name, - description, - standard_value, + *, + standard_root.uid AS uid, has_dataset_variable_rel, dataset_root, dataset_instance, + standard_value.name AS name, + standard_value.description AS description, standard_value.label AS label, standard_value.title AS title, standard_value.core AS core, @@ -129,9 +122,6 @@ def specific_alias_clause(self) -> str: standard_value.described_value_domain AS described_value_domain, standard_value.value_list AS value_list, standard_value.analysis_variable_set AS analysis_variable_set, - apoc.coll.toSet([(standard_value)<-[:HAS_DATASET_VARIABLE]- - (:DatasetInstance)<-[:HAS_DATASET]-(data_model_ig_value:DataModelIGValue) - | data_model_ig_value.name]) AS data_model_ig_names, {ordinal:toInteger(last(split(has_dataset_variable_rel.ordinal, "."))), root_ordinal:toInteger(head(split(has_dataset_variable_rel.ordinal, "."))), uid:dataset_root.uid} AS dataset, head([(standard_value)-[:IMPLEMENTS_VARIABLE]->(class_variable_value:VariableClassInstance)<-[:HAS_INSTANCE]-(class_variable_root) | { uid:class_variable_root.uid, name:class_variable_value.label }]) AS implements_variable, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_repository.py index 1e639e75..be00ca6d 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_repository.py @@ -1,10 +1,7 @@ +from typing import Any + from neomodel import NodeSet, db -from neomodel.sync_.match import ( - Collect, - NodeNameResolver, - Optional, - RelationNameResolver, -) +from neomodel.sync_.match import Collect, NodeNameResolver, Path, RelationNameResolver from clinical_mdr_api.domain_repositories.library_item_repository import ( LibraryItemRepositoryImplBase, @@ -35,6 +32,7 @@ from clinical_mdr_api.models.standard_data_models.sponsor_model_dataset import ( SponsorModelDataset, ) +from clinical_mdr_api.repositories._utils import FilterOperator from common.exceptions import BusinessLogicException @@ -46,31 +44,86 @@ class SponsorModelDatasetRepository( # type: ignore[misc] return_model = SponsorModelDataset def get_neomodel_extension_query(self) -> NodeSet: - return Dataset.nodes.fetch_relations( - "has_sponsor_model_instance__has_dataset", - "has_dataset__has_library", - Optional( - "has_sponsor_model_instance__implements_dataset_class__is_instance_of" - ), - Optional("has_sponsor_model_instance__has_key"), - Optional("has_sponsor_model_instance__has_sort_key"), - ).annotate( - Collect(RelationNameResolver("has_sponsor_model_instance"), distinct=True), - Collect( - NodeNameResolver("has_sponsor_model_instance__has_key"), distinct=True - ), - Collect( - RelationNameResolver("has_sponsor_model_instance__has_key"), - distinct=True, - ), - Collect( - NodeNameResolver("has_sponsor_model_instance__has_sort_key"), - distinct=True, - ), - Collect( - RelationNameResolver("has_sponsor_model_instance__has_sort_key"), - distinct=True, - ), + return ( + Dataset.nodes.traverse( + "has_sponsor_model_instance__has_dataset", + Path( + value="has_sponsor_model_instance__has_key", + optional=True, + include_rels_in_return=False, + ), + Path( + value="has_sponsor_model_instance__has_sort_key", + optional=True, + include_rels_in_return=False, + ), + ) + .unique_variables("has_sponsor_model_instance") + .annotate( + Collect( + NodeNameResolver("has_sponsor_model_instance__has_key"), + distinct=True, + ), + Collect( + RelationNameResolver("has_sponsor_model_instance__has_key"), + distinct=True, + ), + Collect( + NodeNameResolver("has_sponsor_model_instance__has_sort_key"), + distinct=True, + ), + Collect( + RelationNameResolver("has_sponsor_model_instance__has_sort_key"), + distinct=True, + ), + ) + .order_by("has_sponsor_model_instance__has_dataset|ordinal") + ) + + def find_all( + self, + 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, + **kwargs, + ): + sponsor_model_name = kwargs.get("sponsor_model_name") + if sponsor_model_name: + if filter_by is None: + filter_by = {} + filter_by["sponsor_model.name"] = {"v": [sponsor_model_name], "op": "eq"} + return super().find_all( + sort_by=sort_by, + page_number=page_number, + page_size=page_size, + filter_by=filter_by, + filter_operator=filter_operator, + total_count=total_count, + ) + + def get_distinct_headers( + self, + field_name: str, + search_string: str = "", + filter_by: dict[str, dict[str, Any]] | None = None, + filter_operator: FilterOperator = FilterOperator.AND, + page_size: int = 10, + **kwargs, + ) -> list[Any]: + sponsor_model_name = kwargs.get("sponsor_model_name") + if sponsor_model_name: + if filter_by is None: + filter_by = {} + filter_by["sponsor_model.name"] = {"v": [sponsor_model_name], "op": "eq"} + return super().get_distinct_headers( + field_name=field_name, + search_string=search_string, + filter_by=filter_by, + filter_operator=filter_operator, + page_size=page_size, ) def _has_data_changed( @@ -202,7 +255,7 @@ def _get_or_create_instance( implemented_dataset_class = DatasetClass.nodes.filter( uid=ar.sponsor_model_dataset_vo.implemented_dataset_class, has_instance__has_dataset_class__implements__extended_by__name=ar.sponsor_model_dataset_vo.sponsor_model_name, - ).fetch_relations("has_instance") + ).traverse("has_instance") BusinessLogicException.raise_if_not( implemented_dataset_class, msg=f"Dataset class with uid '{ar.sponsor_model_dataset_vo.implemented_dataset_class}' does not exist.", diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py index c83a408e..ef642c52 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_dataset_variable_repository.py @@ -1,5 +1,6 @@ -from neomodel import NodeSet, db -from neomodel.sync_.match import Optional +from typing import Any + +from neomodel import db from clinical_mdr_api.domain_repositories.library_item_repository import ( LibraryItemRepositoryImplBase, @@ -19,12 +20,10 @@ DatasetVariable, SponsorModelDatasetInstance, SponsorModelDatasetVariableInstance, + SponsorModelValue, ) -from clinical_mdr_api.domain_repositories.neomodel_ext_item_repository import ( - NeomodelExtBaseRepository, -) -from clinical_mdr_api.domain_repositories.standard_data_models.utils import ( - get_sponsor_model_info_from_dataset, +from clinical_mdr_api.domain_repositories.standard_data_models.standard_data_model_repository import ( + StandardDataModelRepository, ) from clinical_mdr_api.domains.standard_data_models.sponsor_model_dataset_variable import ( SponsorModelDatasetVariableAR, @@ -34,31 +33,114 @@ from clinical_mdr_api.models.standard_data_models.sponsor_model_dataset_variable import ( SponsorModelDatasetVariable, ) -from common.exceptions import BusinessLogicException +from common.exceptions import BusinessLogicException, ValidationException class SponsorModelDatasetVariableRepository( # type: ignore[misc] - NeomodelExtBaseRepository, + StandardDataModelRepository, LibraryItemRepositoryImplBase[SponsorModelDatasetVariableAR], ): root_class = DatasetVariable value_class = SponsorModelDatasetVariableInstance return_model = SponsorModelDatasetVariable - def get_neomodel_extension_query(self) -> NodeSet: - return DatasetVariable.nodes.fetch_relations( - "has_sponsor_model_instance__has_variable", - "has_dataset_variable__has_library", - Optional( - "has_sponsor_model_instance__implements_variable_class__is_instance_of" - ), - Optional( - "has_sponsor_model_instance__implements_variable_class__has_variable_class__is_instance_of" - ), - ).unique_variables( - "has_sponsor_model_instance", - "has_sponsor_model_instance__implements_variable_class", + # pylint: disable=unused-argument + def generic_match_clause(self, versioning_relationship: str): + standard_data_model_label = self.root_class.__label__ + standard_data_model_value_label = self.value_class.__label__ + return f"""MATCH (standard_root:{standard_data_model_label})-[:HAS_INSTANCE]-> + (standard_value:{standard_data_model_value_label}) + <-[has_dataset_variable_rel:HAS_DATASET_VARIABLE]-(dataset_instance:SponsorModelDatasetInstance) + <-[:HAS_DATASET]-(sponsor_model_value:SponsorModelValue) + MATCH (dataset_root:Dataset)-[:HAS_INSTANCE]->(dataset_instance)""" + + def specific_alias_clause(self) -> str: + return """ + * + OPTIONAL MATCH (standard_value)-[:REFERENCES_CODELIST]->(ref_cl_root:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)-[:LATEST]->(ref_cl:CTCodelistAttributesValue) + OPTIONAL MATCH (standard_value)-[:REFERENCES_TERM]->(ref_t_root:CTTermRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)-[:LATEST]->(ref_t:CTTermAttributesValue) + OPTIONAL MATCH (standard_root)<-[key:HAS_KEY]-(dataset_instance) + WITH + standard_root.uid AS uid, + standard_value.is_basic_std AS is_basic_std, + standard_value.label AS label, + standard_value.variable_type AS variable_type, + standard_value.length AS length, + standard_value.display_format AS display_format, + standard_value.xml_datatype AS xml_datatype, + standard_value.core AS core, + standard_value.origin AS origin, + standard_value.origin_type AS origin_type, + standard_value.origin_source AS origin_source, + standard_value.role AS role, + standard_value.term AS term, + standard_value.algorithm AS algorithm, + standard_value.qualifiers AS qualifiers, + standard_value.is_cdisc_std AS is_cdisc_std, + standard_value.comment AS comment, + standard_value.ig_comment AS ig_comment, + standard_value.class_table AS class_table, + standard_value.class_column AS class_column, + standard_value.map_var_flag AS map_var_flag, + standard_value.fixed_mapping AS fixed_mapping, + standard_value.include_in_raw AS include_in_raw, + standard_value.nn_internal AS nn_internal, + standard_value.value_lvl_where_cols AS value_lvl_where_cols, + standard_value.value_lvl_label_col AS value_lvl_label_col, + standard_value.value_lvl_collect_ct_val AS value_lvl_collect_ct_val, + standard_value.value_lvl_ct_codelist_id_col AS value_lvl_ct_codelist_id_col, + standard_value.enrich_build_order AS enrich_build_order, + standard_value.enrich_rule AS enrich_rule, + collect(DISTINCT CASE WHEN ref_cl IS NOT NULL THEN {uid: ref_cl_root.uid, submission_value: ref_cl.submission_value} END) AS referenced_codelists, + collect(DISTINCT CASE WHEN ref_t IS NOT NULL THEN {uid: ref_t_root.uid, submission_value: ref_t.code_submission_value} END) AS referenced_terms, + {ordinal: has_dataset_variable_rel.ordinal, key_order: key.order, version_number: has_dataset_variable_rel.version_number, uid: dataset_root.uid, sponsor_model_name: sponsor_model_value.name} AS dataset + """ + + def create_query_filter_statement(self, **kwargs) -> tuple[str, dict[Any, Any]]: + ( + filter_statements_from_standard, + filter_query_parameters, + ) = super().create_query_filter_statement(**kwargs) + filter_parameters = [] + + ValidationException.raise_if( + not kwargs.get("sponsor_model_name") + or not kwargs.get("sponsor_model_version"), + msg="Please provide sponsor_model_name and sponsor_model_version params", + ) + + sponsor_model_name = kwargs.get("sponsor_model_name") + sponsor_model_version = kwargs.get("sponsor_model_version") + + filter_by_sponsor_model_name = "sponsor_model_value.name = $sponsor_model_name" + filter_parameters.append(filter_by_sponsor_model_name) + + filter_by_sponsor_model_version = ( + "has_dataset_variable_rel.version_number = $sponsor_model_version" ) + filter_parameters.append(filter_by_sponsor_model_version) + + filter_query_parameters["sponsor_model_name"] = sponsor_model_name + filter_query_parameters["sponsor_model_version"] = sponsor_model_version + + extended_filter_statements = " AND ".join(filter_parameters) + if filter_statements_from_standard != "": + if len(extended_filter_statements) > 0: + filter_statements_to_return = " AND ".join( + [filter_statements_from_standard, extended_filter_statements] + ) + else: + filter_statements_to_return = filter_statements_from_standard + 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 sort_by(self) -> dict[str, bool] | None: + return {"dataset.ordinal": True} def _has_data_changed( self, @@ -206,10 +288,10 @@ def _get_or_create_instance( """ MATCH (vc:VariableClass)-[:`HAS_INSTANCE`]->(vci:VariableClassInstance)<-[:`HAS_VARIABLE_CLASS`]-(dci:DatasetClassInstance) <-[:`HAS_DATASET_CLASS`]-(:DataModelValue) - <-[:`IMPLEMENTS`]-(ig:DataModelIGValue)<-[:`EXTENDS_VERSION`]-(smv:SponsorModelValue) + <-[:`IMPLEMENTS`]-(ig:DataModelIGValue)<-[:`EXTENDS_VERSION`]-(smv:SponsorModelValue) MATCH (dci)<-[:`HAS_INSTANCE`]-(dc:DatasetClass) - WHERE - smv.name = $smv_name + WHERE + smv.name = $smv_name AND dc.uid = $dc_uid AND vc.uid = $vc_uid RETURN vci @@ -235,9 +317,12 @@ def _get_or_create_instance( new_instance.implemented_variable_class_uid = ( ar.sponsor_model_dataset_variable_vo.implemented_variable_class ) - new_instance.implemented_parent_dataset_class_uid = ( + if ( ar.sponsor_model_dataset_variable_vo.implemented_parent_dataset_class - ) + ): + new_instance.implemented_parent_dataset_class_uid = ( + ar.sponsor_model_dataset_variable_vo.implemented_parent_dataset_class + ) self._db_save_node(new_instance) # Connect with Codelists & Terms @@ -276,26 +361,20 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( # Get parent dataset-related info dataset_value: SponsorModelDatasetInstance = value.has_variable.get_or_none() dataset_uid = None - sponsor_model_name = None - sponsor_model_version = None ordinal = 0 - if dataset_value is not None: - # Get parent dataset uid - dataset: Dataset = dataset_value.has_sponsor_model_instance.single() - if dataset is not None: - dataset_uid = dataset.uid - - # Get order in parent class - dataset_rel = value.has_variable.relationship(dataset_value) - if dataset_rel is not None: - ordinal = dataset_rel.ordinal - - # Get sponsor model-related info - ( - sponsor_model_name, - sponsor_model_version, - _, - ) = get_sponsor_model_info_from_dataset(dataset_value, return_ordinal=False) + # Get parent dataset uid + dataset: Dataset = dataset_value.has_sponsor_model_instance.single() + if dataset is not None: + dataset_uid = dataset.uid + + # Get order in parent class + dataset_rel = value.has_variable.relationship(dataset_value) + ordinal = dataset_rel.ordinal + sponsor_model_version = dataset_rel.version_number + + # Get sponsor model-related info + sponsor_model_value: SponsorModelValue = dataset_value.has_dataset.single() + sponsor_model_name = sponsor_model_value.name # Extract extra properties from the Neo4j node known_fields = { @@ -366,7 +445,7 @@ def _create_aggregate_root_instance_from_version_root_relationship_and_value( length=value.length, display_format=value.display_format, xml_datatype=value.xml_datatype, - references_codelists=value.references_codelist, + references_codelists=value.references_codelist, # type: ignore[arg-type] references_terms=value.references_terms, core=value.core, origin=value.origin, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_repository.py index a00248ee..50f66157 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/sponsor_model_repository.py @@ -1,11 +1,4 @@ from neomodel import NodeSet, RelationshipDefinition -from neomodel.sync_.match import ( - Collect, - Last, - NodeNameResolver, - RawCypher, - RelationNameResolver, -) from clinical_mdr_api.domain_repositories.library_item_repository import ( LibraryItemRepositoryImplBase, @@ -44,23 +37,8 @@ class SponsorModelRepository( # type: ignore[misc] return_model = SponsorModel def get_neomodel_extension_query(self) -> NodeSet: - return DataModelIGRoot.nodes.fetch_relations( - "has_library", - "has_latest_sponsor_model_value__extends_version", - ).subquery( - DataModelIGRoot.nodes.fetch_relations("has_sponsor_model_version") - .intermediate_transform( - {"rel": {"source": RelationNameResolver("has_sponsor_model_version")}}, - ordering=[ - RawCypher("toInteger(split(rel.version, '.')[0])"), - RawCypher("toInteger(split(rel.version, '.')[1])"), - "rel.end_date", - "rel.start_date", - ], - ) - .annotate(latest_version=Last(Collect("rel"))), - ["latest_version"], - initial_context=[NodeNameResolver("self")], + return DataModelIGRoot.nodes.traverse( + "has_sponsor_model_version__extends_version", ) def generate_name(self, ig_uid: str, ig_version_number: str, version_number: str): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/standard_data_model_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/standard_data_model_repository.py index 456befd9..5fe3e7a5 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/standard_data_model_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/standard_data_model_repository.py @@ -54,15 +54,13 @@ def find_by_uid( if not uid: return None - match_clause = self.generic_match_clause( - versioning_relationship="LATEST", uid=uid - ) + match_clause = self.generic_match_clause(versioning_relationship="LATEST") filter_statements, filter_query_parameters = self.create_query_filter_statement( - **kwargs + uid=uid, find_by_uid=True, **kwargs ) match_clause += filter_statements - alias_clause = self.generic_alias_clause() + self.specific_alias_clause() + alias_clause = self.specific_alias_clause() query = CypherQueryBuilder( match_clause=match_clause, alias_clause=alias_clause, @@ -86,43 +84,12 @@ def find_by_uid( return extracted_items[0] - def generic_match_clause( - self, versioning_relationship: str, uid: str | None = None - ): + def generic_match_clause(self, versioning_relationship: str): standard_data_model_label = self.root_class.__label__ standard_data_model_value_label = self.value_class.__label__ - uid_filter = "" - if uid: - uid_filter = f"{{uid: '{uid}'}}" - return f"""MATCH (standard_root:{standard_data_model_label} {uid_filter})-[:{versioning_relationship}]-> + return f"""MATCH (standard_root:{standard_data_model_label})-[:{versioning_relationship}]-> (standard_value:{standard_data_model_value_label})""" - def generic_alias_clause(self): - return """ - DISTINCT * - CALL { - WITH standard_root, standard_value - MATCH (standard_root)-[hv:HAS_VERSION]-(standard_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 version_rel - } - WITH *, - standard_root, - standard_root.uid AS uid, - standard_value.name AS name, - standard_value.description AS description, - standard_value, - version_rel.start_date AS start_date, - version_rel.end_date AS end_date, - version_rel.status AS status - """ - def _retrieve_items_from_cypher_res( self, result_array, attribute_names ) -> list[BaseModel]: @@ -141,10 +108,13 @@ def _retrieve_items_from_cypher_res( return items def create_query_filter_statement( - self, + self, uid: str | None = None, **kwargs ) -> tuple[str, dict[Any, Any]]: filter_parameters: list[Any] = [] filter_query_parameters: dict[Any, Any] = {} + if uid: + filter_parameters.append("standard_root.uid=$uid") + filter_query_parameters["uid"] = uid filter_statements = " AND ".join(filter_parameters) filter_statements = ( "WHERE " + filter_statements if len(filter_statements) > 0 else "" @@ -183,7 +153,7 @@ def find_all( ) match_clause += filter_statements - alias_clause = self.generic_alias_clause() + self.specific_alias_clause() + alias_clause = self.specific_alias_clause() query = CypherQueryBuilder( match_clause=match_clause, alias_clause=alias_clause, @@ -259,7 +229,7 @@ def get_distinct_headers( ) match_clause += filter_statements # Aliases clause - alias_clause = self.generic_alias_clause() + self.specific_alias_clause() + alias_clause = self.specific_alias_clause() # Add header field name to filter_by, to filter with a CONTAINS pattern filter_by = validate_filters_and_add_search_string( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/variable_class_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/variable_class_repository.py index e4adb4b7..e3acccfd 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/variable_class_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/standard_data_models/variable_class_repository.py @@ -19,15 +19,10 @@ class VariableClassRepository(StandardDataModelRepository): return_model = VariableClassAPIModel # pylint: disable=unused-argument - def generic_match_clause( - self, versioning_relationship: str, uid: str | None = None - ): + def generic_match_clause(self, versioning_relationship: str): standard_data_model_label = self.root_class.__label__ standard_data_model_value_label = self.value_class.__label__ - uid_filter = "" - if uid: - uid_filter = f"{{uid: '{uid}'}}" - return f"""MATCH (standard_root:{standard_data_model_label} {uid_filter})-[:HAS_INSTANCE]-> + return f"""MATCH (standard_root:{standard_data_model_label})-[:HAS_INSTANCE]-> (standard_value:{standard_data_model_value_label})<-[has_variable_class_rel:HAS_VARIABLE_CLASS]- (dataset_class_value:DatasetClassInstance)<-[:HAS_DATASET_CLASS]-(data_model_value:DataModelValue) <-[:HAS_VERSION]-(data_model_root:DataModelRoot)""" @@ -36,7 +31,7 @@ def create_query_filter_statement(self, **kwargs) -> tuple[str, dict[Any, Any]]: ( filter_statements_from_standard, filter_query_parameters, - ) = super().create_query_filter_statement() + ) = super().create_query_filter_statement(**kwargs) filter_parameters = [] if kwargs.get("dataset_class_name"): dataset_class_name = kwargs.get("dataset_class_name") @@ -92,8 +87,10 @@ def sort_by(self) -> dict[str, bool] | None: def specific_alias_clause(self) -> str: return """ - WITH *, + *, + standard_root.uid AS uid, standard_value.label AS label, + standard_value.description AS description, standard_value.implementation_notes AS implementation_notes, standard_value.title AS title, standard_value.core AS core, @@ -107,18 +104,13 @@ def specific_alias_clause(self) -> str: standard_value.notes AS notes, standard_value.usage_restrictions AS usage_restrictions, standard_value.examples AS examples, - head([(standard_value)-[:QUALIFIES_VARIABLE {catalogue:$data_model_name, version_number:$data_model_version}]->(qualified_variable:VariableClassInstance)<-[:HAS_INSTANCE]-(qualified_variable_root) | { - uid:qualified_variable_root.uid, name:qualified_variable.label }]) AS qualifies_variable, - {dataset_class_name:dataset_class_value.label, ordinal:has_variable_class_rel.ordinal} AS dataset_class, - head([(standard_value)<-[:IMPLEMENTS_VARIABLE]-(dataset_variable_value:DatasetVariableInstance) | - dataset_variable_value.label]) AS dataset_variable_name, - apoc.coll.toSet([(standard_value)<-[:HAS_VARIABLE_CLASS]- - (:DatasetClassInstance)<-[:HAS_DATASET_CLASS]-(model_value:DataModelValue) - | model_value.name]) AS data_model_names, + [(standard_value)-[:QUALIFIES_VARIABLE {catalogue:$data_model_name, version_number:$data_model_version}]->(qualified_variable:VariableClassInstance)<-[:HAS_INSTANCE]-(qualified_variable_root) | { + uid:qualified_variable_root.uid, name:qualified_variable.label }] AS qualifies_variables, + {dataset_class_name:dataset_class_value.label, ordinal:toInteger(has_variable_class_rel.ordinal)} AS dataset_class, head([(standard_root)<-[:HAS_VARIABLE_CLASS]-(catalogue:DataModelCatalogue) | catalogue.name]) AS catalogue_name, [(standard_value)-[:REFERENCES_CODELIST]->(codelist_root:CTCodelistRoot)-[:HAS_NAME_ROOT]-()-[:LATEST]-> (codelist_value:CTCodelistNameValue) | {uid:codelist_root.uid, name:codelist_value.name }] AS referenced_codelists, - head([(standard_value)-[mt_rel:HAS_MAPPING_TARGET]->(class_variable_value:VariableClassInstance) + [(standard_value)-[mt_rel:HAS_MAPPING_TARGET]->(class_variable_value:VariableClassInstance) <-[:HAS_INSTANCE]-(class_variable_root:VariableClass) WHERE mt_rel.version_number=$data_model_version - | {uid:class_variable_root.uid, name:class_variable_value.label}]) AS has_mapping_target + | {uid:class_variable_root.uid, name:class_variable_value.label}] AS has_mapping_targets """ 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 deefa540..76dc4fae 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 @@ -3,8 +3,9 @@ from dataclasses import dataclass from typing import Any, Sequence -from neomodel.sync_.core import NodeMeta, db -from neomodel.sync_.match import Collect, NodeNameResolver, Optional, Size +from neomodel import db +from neomodel.sync_.match import Collect, NodeNameResolver, Path, Size +from neomodel.sync_.node import NodeMeta from clinical_mdr_api.domain_repositories.generic_repository import ( RepositoryClosureData, @@ -133,7 +134,7 @@ def find_by_uid( # now get the data from db snapshot: StudyDefinitionSnapshot | None additional_closure: Any - (snapshot, additional_closure) = self._retrieve_snapshot_by_uid( + snapshot, additional_closure = self._retrieve_snapshot_by_uid( uid=uid, for_update=for_update, study_value_version=study_value_version, @@ -263,15 +264,55 @@ def get_study_structure_overview_headers( def get_study_structure_statistics(self, uid: str) -> dict[str, int] | None: result = ( StudyValue.nodes.filter(latest_value__uid=uid) - .traverse_relations( - Optional("has_study_arm"), - Optional("has_study_branch_arm"), - Optional("has_study_element"), - Optional("has_study_cohort"), - Optional("has_study_epoch"), - Optional("has_study_footnote__references_study_epoch"), - Optional("has_study_visit"), - Optional("has_study_footnote__references_study_visit"), + .traverse( + Path( + value="has_study_arm", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_branch_arm", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_element", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_cohort", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_epoch", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_footnote__references_study_epoch", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_visit", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), + Path( + value="has_study_footnote__references_study_visit", + optional=True, + include_nodes_in_return=False, + include_rels_in_return=False, + ), ) .annotate( arm_count=Size( @@ -353,32 +394,32 @@ def copy_study_items( # COPY NODES AND OUTBOUND RELATIONSHIPS query = f""" -WITH - $study_src_uid as study_src, - $study_target_uid as study_target, +WITH + $study_src_uid as study_src, + $study_target_uid as study_target, $to_copy_labels as to_copy_labels -with - study_src, - study_target, +with + study_src, + study_target, apoc.text.join(to_copy_labels, '|') AS to_copy_labels_text -MATCH +MATCH (sr_src:StudyRoot)-[:LATEST]-> (sv_src:StudyValue) - WHERE + WHERE sr_src.uid = study_src -MATCH +MATCH (sr_target:StudyRoot)-[:LATEST]-> (sv_target:StudyValue) - WHERE + WHERE sr_target.uid = study_target CALL apoc.cypher.run(" - MATCH + MATCH (selection_src:StudySelection&(" + to_copy_labels_text + "))<-[sv_has_selection]- (sv_src) WHERE type(sv_has_selection) <> 'HAS_PROTOCOL_SOA_CELL' AND type(sv_has_selection) <> 'HAS_PROTOCOL_SOA_FOOTNOTE' - MATCH + MATCH (sr_src)-[audit_trail:AUDIT_TRAIL]-> (saction_src:StudyAction)-[saction_selection:AFTER]-> (selection_src) @@ -389,12 +430,12 @@ def copy_study_items( (sv_src) ) WHERE {exclusions} - return sr_src, sv_src,collect(path) as paths ", + return sr_src, sv_src,collect(path) as paths ", {{sr_src:sr_src, sv_src:sv_src }}) YIELD value WITH sr_target, value.sr_src as sr_src, sv_target, value.sv_src as sv_src,value.paths as paths - + CALL apoc.refactor.cloneSubgraphFromPaths(paths, {{ standinNodes:[[sv_src, sv_target], [sr_src,sr_target]] }}) @@ -419,22 +460,65 @@ def copy_study_items( # COPY BETWEEN SELECTIONS RELATIONSHIPS query = """ -WITH $study_src_uid as study_src, $study_target_uid as study_target, $to_copy_labels as to_copy_labels - -MATCH (sr_from:StudyRoot)-[:LATEST]->(sv_from:StudyValue)-[sv_to_ss_source]->(selection_src_from:StudySelection)-[r_ext_src]->(selection_src_to:StudySelection) - where sr_from.uid = study_src AND type(sv_to_ss_source) <> "HAS_PROTOCOL_SOA_CELL" AND type(sv_to_ss_source) <> "HAS_PROTOCOL_SOA_FOOTNOTE" -WITH selection_src_from.uid as from_uid, type(r_ext_src) AS from_rel_type_to, selection_src_to.uid as to_uid, study_target, to_copy_labels -match (sr_to:StudyRoot)-[:LATEST]->(sv_to:StudyValue)-->(a:StudySelection) - where sr_to.uid = study_target -match (sr_to)-[:LATEST]->(sv_to)-[sv_to__b]->(b:StudySelection) - WHERE type(sv_to__b) <> "HAS_PROTOCOL_SOA_CELL" AND type(sv_to__b) <> "HAS_PROTOCOL_SOA_FOOTNOTE" -WITH a,b, from_rel_type_to - where a.uid = from_uid - and b.uid = to_uid - AND ANY(label IN labels(a) WHERE label IN to_copy_labels) -WITH DISTINCT a,b,from_rel_type_to - -call apoc.merge.relationship(a, from_rel_type_to, null, Null, b) +WITH + $study_src_uid as study_src, + $study_target_uid as study_target, + $to_copy_labels as to_copy_labels + +MATCH + (sr_from:StudyRoot)-[:LATEST]-> + (sv_from:StudyValue)-[sv_to_ss_source]-> + (selection_src_from:StudySelection)-[r_ext_src]-> + (selection_src_to:StudySelection) + where + sr_from.uid = study_src + AND type(sv_to_ss_source) <> "HAS_PROTOCOL_SOA_CELL" + AND type(sv_to_ss_source) <> "HAS_PROTOCOL_SOA_FOOTNOTE" +MATCH (selection_src_to)--(sv_from) + +WITH + selection_src_from.uid as from_uid, + type(r_ext_src) AS from_rel_type_to, + selection_src_to.uid as to_uid, + study_target, + to_copy_labels +MATCH + (sr_to:StudyRoot)-[:LATEST]-> + (sv_to:StudyValue)--> + (a:StudySelection) + where + sr_to.uid = study_target +MATCH + (sr_to)-[:LATEST]-> + (sv_to)-[sv_to__b]-> + (b:StudySelection) + WHERE + type(sv_to__b) <> "HAS_PROTOCOL_SOA_CELL" + AND type(sv_to__b) <> "HAS_PROTOCOL_SOA_FOOTNOTE" +WITH + a, + b, + from_rel_type_to + where + a.uid = from_uid + and b.uid = to_uid + AND ANY( + label IN labels(a) + WHERE + label IN to_copy_labels + ) +WITH DISTINCT + a, + b, + from_rel_type_to + +call apoc.merge.relationship( + a, + from_rel_type_to, + null, + Null, + b +) yield rel @@ -459,7 +543,7 @@ def copy_study_items( MATCH (sr_target:StudyRoot)-[:LATEST]->(sv_target:StudyValue)-[relationship]-(selection_target:StudySelection) where sr_target.uid = study_target AND type(relationship) <> "HAS_PROTOCOL_SOA_CELL" AND type(relationship) <> "HAS_PROTOCOL_SOA_FOOTNOTE" -// Update the counter value and generate new UID and +// Update the counter value and generate new UID and CALL { WITH to_copy_labels_unw, selection_target WITH to_copy_labels_unw, selection_target @@ -603,6 +687,28 @@ def study_number_exists(study_number: str, uid: str | None = None) -> bool: return bool(rs[0]) + @staticmethod + def study_acronym_exists(study_acronym: str, uid: str | None = None) -> bool: + """ + Checks whether a normal study or a parent study with specified study acronym already exists within the database. + """ + params = {"study_acronym": study_acronym} + + query = """ + MATCH (value:StudyValue {study_acronym: $study_acronym})<-[:LATEST]-(root:StudyRoot) + WHERE NOT (value)<-[:HAS_STUDY_SUBPART]-(:StudyValue) + """ + + if uid: + query += " AND NOT root.uid = $uid " + params |= {"uid": uid} + + query += " RETURN value" + + rs = db.cypher_query(query, params=params) + + return bool(rs[0]) + def save( self, study: StudyDefinitionAR, is_subpart_relationship_update=False ) -> None: @@ -653,15 +759,55 @@ def save( not_for_update=True, repository=self, additional_closure=None ) - def get_studies_list(self, deleted: bool = False) -> list[dict[str, Any]]: + def get_studies_list( + self, + has_study_objective: bool | None = None, + has_study_footnote: bool | None = None, + has_study_endpoint: bool | None = None, + has_study_criteria: bool | None = None, + has_study_activity: bool | None = None, + has_study_activity_instruction: bool | None = None, + deleted: bool = False, + ) -> list[dict[str, Any]]: """ Public method to retrieve a list of all studies in the repository. Returns a list of dictionaries. """ + + def where_stmt(): + conditions = [] + + checks = [ + (has_study_objective, "HAS_STUDY_OBJECTIVE", "StudyObjective"), + (has_study_footnote, "HAS_STUDY_FOOTNOTE", "StudySoAFootnote"), + (has_study_endpoint, "HAS_STUDY_ENDPOINT", "StudyEndpoint"), + (has_study_criteria, "HAS_STUDY_CRITERIA", "StudyCriteria"), + (has_study_activity, "HAS_STUDY_ACTIVITY", "StudyActivity"), + ( + has_study_activity_instruction, + "HAS_STUDY_ACTIVITY_INSTRUCTION", + "StudyActivityInstruction", + ), + ] + + for flag, relationship, node_label in checks: + if flag is not None: + prefix = "" if flag else "NOT " + conditions.append( + f"{prefix}EXISTS((sv)-[:{relationship}]->(:{node_label}))" + ) + + if not deleted: + conditions.append("NOT EXISTS((sv)<-[:BEFORE]-(:Delete))") + else: + conditions.append("EXISTS((sv)<-[:BEFORE]-(:Delete))") + + return f"WHERE {' AND '.join(conditions)}" if conditions else "" + self._check_not_closed() query = f""" MATCH (sr:StudyRoot)-[:LATEST]->(sv:StudyValue)-[:HAS_PROJECT]-(:StudyProjectField)<-[:HAS_FIELD]-(p:Project)<-[:HOLDS_PROJECT]-(cp:ClinicalProgramme) - WHERE {'' if deleted else 'NOT'} EXISTS((sv)<-[:BEFORE]-(:Delete)) + {where_stmt()} WITH sr,sv,p,cp OPTIONAL MATCH (sv)-[:HAS_TEXT_FIELD]->(stf:StudyTextField {{field_name: 'study_title'}}) @@ -700,7 +846,8 @@ def get_studies_list(self, deleted: bool = False) -> list[dict[str, Any]]: current_version.version as version_number, COALESCE(author.username, current_version.author_id) as author, latest_locked_version, - latest_released_version + latest_released_version, + [(sr)-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) | t.name] as data_completeness_tags ORDER BY uid """ rs = db.cypher_query(query) @@ -723,6 +870,7 @@ def get_studies_list(self, deleted: bool = False) -> list[dict[str, Any]]: "version_author": row[14], "latest_locked_version": row[15], "latest_released_version": row[16], + "data_completeness_tags": row[17], } for row in rs[0] ] @@ -1063,7 +1211,7 @@ def get_preferred_time_unit( study_uid: str, for_protocol_soa: bool = False, study_value_version: str | None = None, - ) -> StudyPreferredTimeUnit: + ) -> list[StudyPreferredTimeUnit]: """ A method that gets a StudyTimeField for the study preferred time unit. The preferred time unit is the unit definition that is used to display items like study visits on the timescale. @@ -1073,7 +1221,7 @@ def get_preferred_time_unit( @abstractmethod def post_preferred_time_unit( self, study_uid: str, unit_definition_uid: str, for_protocol_soa: bool = False - ) -> StudyPreferredTimeUnit: + ) -> list[StudyPreferredTimeUnit]: """ A method that creates a StudyTimeField for the study preferred time unit. The preferred time unit is the unit definition that is used to display items like study visits on the timescale. @@ -1083,7 +1231,7 @@ def post_preferred_time_unit( @abstractmethod def edit_preferred_time_unit( self, study_uid: str, unit_definition_uid: str, for_protocol_soa: bool = False - ) -> StudyPreferredTimeUnit: + ) -> list[StudyPreferredTimeUnit]: """ A method that edits a StudyTimeField for the study preferred time unit. The preferred time unit is the unit definition that is used to display items like study visits on the timescale. @@ -1164,6 +1312,13 @@ def check_if_study_uid_and_version_exists( bool: True if the study exists, False otherwise. """ + @staticmethod + @abstractmethod + def get_study_id( + study_uid: str, study_value_version: str | None = None + ) -> str | None: + """Returns Study id if Study exists and StudyVersion exists and not deleted, and both study_id_prefix and study_number are defined, otherwise None.""" + @staticmethod @abstractmethod def get_soa_split_uids( 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 1e4a853f..73ef4cee 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 @@ -4,10 +4,10 @@ from decimal import Decimal from typing import Any, Mapping, MutableSequence, Sequence, cast, overload -from neomodel import NodeSet +from neomodel import db from neomodel.exceptions import DoesNotExist -from neomodel.sync_.core import NodeMeta, db from neomodel.sync_.match import Collect, Last, Path +from neomodel.sync_.node import NodeMeta from clinical_mdr_api import utils from clinical_mdr_api.domain_repositories._utils.helpers import ( @@ -70,6 +70,7 @@ StudyVersionMetadataVO, ) from clinical_mdr_api.models.study_selections.study import ( + StudyPreferredTimeUnit, StudySoaPreferencesInput, StudySubpartAuditTrail, ) @@ -84,6 +85,7 @@ from clinical_mdr_api.services.user_info import UserInfoService from common import exceptions from common.config import settings +from common.telemetry import trace_calls from common.utils import convert_to_datetime MAINTAIN_RELATIONSHIPS_FOR_NEW_STUDY_VALUE = { @@ -973,11 +975,15 @@ def _maintain_latest_locked_relationship_on_save( latest_locked.start_date = ( current_snapshot.current_metadata.version_timestamp ) - latest_locked.author_id = self.audit_info.author_id - latest_locked.change_description = ( - current_snapshot.current_metadata.version_description + if self.audit_info.author_id: + latest_locked.author_id = self.audit_info.author_id + if current_snapshot.current_metadata.version_description: + latest_locked.change_description = ( + current_snapshot.current_metadata.version_description + ) + latest_locked.version = str( + len(current_snapshot.locked_metadata_versions) ) - latest_locked.version = len(current_snapshot.locked_metadata_versions) latest_locked.save() root.latest_locked.reconnect( old_node=latest_locked.end_node(), new_node=expected_latest_value @@ -1014,7 +1020,8 @@ def _maintain_latest_draft_relationship_on_save( latest_draft_relationship.start_date = ( current_snapshot.current_metadata.version_timestamp ) - latest_draft_relationship.author_id = self.audit_info.author_id + if self.audit_info.author_id: + latest_draft_relationship.author_id = self.audit_info.author_id latest_draft_relationship.end_date = None latest_draft_relationship.save() root.latest_draft.reconnect( @@ -1569,12 +1576,10 @@ def _maintain_study_array_fields_relationships( ) ) if study_array_field_node is None or to_delete: - study_array_field_node = StudyArrayField.create( - { - "value": study_array_field_value, - "field_name": study_array_field_name, - } - )[0] + study_array_field_node = StudyArrayField( + value=study_array_field_value, + field_name=study_array_field_name, + ).save() # disconnect any existing has_term or has_dictionary_term relationships if config_item.is_dictionary_term: for rel in study_array_field_node.has_dictionary_type.all(): @@ -1609,9 +1614,9 @@ def _maintain_study_array_fields_relationships( ) ) if study_array_field_node is None or to_delete: - study_array_field_node = StudyArrayField.create( - {"value": [], "field_name": study_array_field_name} - )[0] + study_array_field_node = StudyArrayField( + value=[], field_name=study_array_field_name + ).save() # disconnect any existing has_type relationships for rel in study_array_field_node.has_type.all(): study_array_field_node.has_type.disconnect(rel) @@ -1991,11 +1996,13 @@ def _study_metadata_snapshot_from_study_value( def _study_metadata_snapshot_from_cypher_res( cls, metadata_section: dict[Any, Any] ) -> StudyDefinitionSnapshot.StudyMetadataSnapshot: ... + @overload @classmethod def _study_metadata_snapshot_from_cypher_res( cls, metadata_section: None ) -> None: ... + @classmethod def _study_metadata_snapshot_from_cypher_res( cls, metadata_section: dict[Any, Any] | None @@ -2132,8 +2139,10 @@ def _generate_study_value_audit_node( audit_node = Delete() else: audit_node = Edit() - audit_node.status = change_status - audit_node.author_id = author_id + if change_status: + audit_node.status = change_status + if author_id: + audit_node.author_id = author_id audit_node.date = date audit_node.save() @@ -2609,8 +2618,10 @@ def _generate_study_field_audit_node( audit_node = Delete() else: audit_node = Edit() - audit_node.status = change_status - audit_node.author_id = author_id + if change_status: + audit_node.status = change_status + if author_id: + audit_node.author_id = author_id audit_node.date = date audit_node.save() @@ -2627,7 +2638,7 @@ def get_preferred_time_unit( study_uid: str, for_protocol_soa: bool = False, study_value_version: str | None = None, - ) -> NodeSet: + ) -> list[StudyTimeField]: filters = { "field_name": ( settings.study_field_soa_preferred_time_unit_name @@ -2649,7 +2660,7 @@ def get_preferred_time_unit( "has_time_field__latest_value__uid": study_uid, } ) - nodes = StudyTimeField.nodes.fetch_relations( + nodes = StudyTimeField.nodes.traverse( "has_unit_definition__has_latest_value", "has_after__audit_trail", ).filter(**filters) @@ -2657,7 +2668,7 @@ def get_preferred_time_unit( def post_preferred_time_unit( self, study_uid: str, unit_definition_uid: str, for_protocol_soa: bool = False - ) -> NodeSet: + ) -> list[StudyPreferredTimeUnit]: nodes = self.get_preferred_time_unit( study_uid=study_uid, for_protocol_soa=for_protocol_soa ) @@ -2670,16 +2681,14 @@ def post_preferred_time_unit( study_root = StudyRoot.nodes.get(uid=study_uid) latest_study_value = study_root.latest_value.single() unit_definition = UnitDefinitionRoot.nodes.get(uid=unit_definition_uid) - preferred_time_field_sf = StudyTimeField.create( - { - "value": unit_definition_uid, - "field_name": ( - settings.study_field_soa_preferred_time_unit_name - if for_protocol_soa - else settings.study_field_preferred_time_unit_name - ), - } - )[0] + preferred_time_field_sf = StudyTimeField( + value=unit_definition_uid, + field_name=( + settings.study_field_soa_preferred_time_unit_name + if for_protocol_soa + else settings.study_field_preferred_time_unit_name + ), + ).save() preferred_time_field_sf.has_unit_definition.connect(unit_definition) latest_study_value.has_time_field.connect(preferred_time_field_sf) @@ -2697,38 +2706,36 @@ def post_preferred_time_unit( def edit_preferred_time_unit( self, study_uid: str, unit_definition_uid: str, for_protocol_soa: bool = False - ) -> NodeSet: + ) -> list[StudyPreferredTimeUnit]: # getting previous preferred time unit study field - previous_time_field = self.get_preferred_time_unit( + previous_time_fields = self.get_preferred_time_unit( study_uid=study_uid, for_protocol_soa=for_protocol_soa ) exceptions.BusinessLogicException.raise_if( - len(previous_time_field) > 1, + len(previous_time_fields) > 1, msg="Returned more than one previous preferred StudyTimeField nodes", ) exceptions.BusinessLogicException.raise_if( - len(previous_time_field) == 0, + len(previous_time_fields) == 0, msg="The previous preferred StudyTimeField node was not found", ) - previous_time_field = previous_time_field[0] + previous_time_field = previous_time_fields[0] study_root = StudyRoot.nodes.get(uid=study_uid) latest_study_value = study_root.latest_value.single() unit_definition = UnitDefinitionRoot.nodes.get(uid=unit_definition_uid) # creating (soa_)preferred_time_unit StudyTimeField node - preferred_time_field_sf = StudyTimeField.create( - { - "value": unit_definition_uid, - "field_name": ( - settings.study_field_soa_preferred_time_unit_name - if for_protocol_soa - else settings.study_field_preferred_time_unit_name - ), - } - )[0] + preferred_time_field_sf = StudyTimeField( + value=unit_definition_uid, + field_name=( + settings.study_field_soa_preferred_time_unit_name + if for_protocol_soa + else settings.study_field_preferred_time_unit_name + ), + ).save() # connecting (soa_)preferred_time_unit StudyTimeField node to the UnitDefinitionRoot node preferred_time_field_sf.has_unit_definition.connect(unit_definition) @@ -2805,11 +2812,46 @@ def check_if_study_uid_and_version_exists( return len(result) > 0 and len(result[0]) > 0 + @staticmethod + @trace_calls(args=[0, 1], kwargs=["study_uid", "study_value_version"]) + def get_study_id( + study_uid: str, study_value_version: str | None = None + ) -> str | None: + """Efficiently retrieves the Study ID for a given Study uid and version.""" + + if study_value_version: + query = [ + "MATCH (study_root:StudyRoot {uid: $uid})-[has_version:HAS_VERSION]->(study_value:StudyValue)", + "WHERE NOT EXISTS((study_value)<-[:BEFORE]-(:Delete)) AND has_version.version=$version", + ] + else: + query = [ + "MATCH (study_root:StudyRoot {uid: $uid})-[:LATEST]->(study_value:StudyValue)", + "WHERE NOT EXISTS((study_value)<-[:BEFORE]-(:Delete))", + ] + + query.append("RETURN study_value") + + results, _ = db.cypher_query( + "\n".join(query), {"uid": study_uid, "version": study_value_version} + ) + + if len(results): + study_value = results[0][0] + + study_id_prefix = study_value.get("study_id_prefix") + study_number = study_value.get("study_number") + + if study_number and study_id_prefix: + return f"{study_id_prefix}-{study_number}" + + return None + def get_latest_released_version_from_specific_datetime( self, study_uid: str, specified_datetime: str ) -> str | None: version_relationships = ( - StudyValue.nodes.fetch_relations("has_version") + StudyValue.nodes.traverse("has_version") .filter( **{ "has_version|end_date__lte": datetime.fromisoformat( @@ -2995,7 +3037,7 @@ def get_soa_preferences( filters["field_name__in"] = field_names nodes = ( - StudyBooleanField.nodes.fetch_relations( + StudyBooleanField.nodes.traverse( "has_after__audit_trail", ) .filter(**filters) @@ -3017,7 +3059,7 @@ def post_soa_preferences( latest_study_value = study_root.latest_value.single() for name, value in soa_preferences.model_dump(by_alias=True).items(): - field_sf = StudyBooleanField.create({"field_name": name, "value": value})[0] + field_sf = StudyBooleanField(field_name=name, value=value).save() latest_study_value.has_boolean_field.connect(field_sf) self._generate_study_field_audit_node( @@ -3055,7 +3097,7 @@ def edit_soa_preferences( _nodes = {node.field_name: node for node in nodes} for name, value in prefs.items(): - field_sf = StudyBooleanField.create({"field_name": name, "value": value})[0] + field_sf = StudyBooleanField(field_name=name, value=value).save() latest_study_value.has_boolean_field.connect(field_sf) self._generate_study_field_audit_node( @@ -3092,7 +3134,7 @@ def get_soa_split_uids( try: return ( - StudyArrayField.nodes.fetch_relations("has_after__audit_trail") + StudyArrayField.nodes.traverse("has_after__audit_trail") .filter(**filters) .get()[0] ) @@ -3123,7 +3165,7 @@ def add_soa_split_uid( # Check if uid is already in the array exceptions.AlreadyExistsException.raise_if( - previous_study_array_field and uid in previous_study_array_field.value, + previous_study_array_field and uid in previous_study_array_field.value, # type: ignore[operator] msg=f"StudyVisit '{uid}' is already present in SoA split UIDs for Study '{study_uid}'.", ) @@ -3170,15 +3212,13 @@ def add_soa_split_uid( latest_study_value.has_array_field.disconnect(previous_study_array_field) # Create new StudyArrayField with the uid added - uids = ( - set(previous_study_array_field.value) - if previous_study_array_field - else set() - ) + uids: set[str] = set() + if previous_study_array_field: + uids = set(previous_study_array_field.value) # type: ignore[call-overload] uids |= {uid} - new_study_array_field = StudyArrayField.create( - {"field_name": _field_name, "value": list(uids)} - )[0] + new_study_array_field = StudyArrayField( + field_name=_field_name, value=list(uids) + ).save() latest_study_value.has_array_field.connect(new_study_array_field) # Extend audit trail @@ -3215,7 +3255,7 @@ def remove_soa_split_uid( # Check if uid is in the array exceptions.NotFoundException.raise_if_not( previous_study_array_field is not None - and uid in previous_study_array_field.value, + and uid in previous_study_array_field.value, # type: ignore[operator] msg=f"StudyVisit '{uid}' is not in SoA split UIDs for Study '{study_uid}'.", ) @@ -3226,10 +3266,10 @@ def remove_soa_split_uid( latest_study_value.has_array_field.disconnect(previous_study_array_field) # Create new StudyArrayField if uids remain after removal - if new_uids := list(set(previous_study_array_field.value) - {uid}): - new_study_array_field = StudyArrayField.create( - {"field_name": _field_name, "value": new_uids} - )[0] + if new_uids := list(set(previous_study_array_field.value) - {uid}): # type: ignore[arg-type] + new_study_array_field = StudyArrayField( + field_name=_field_name, value=new_uids + ).save() latest_study_value.has_array_field.connect(new_study_array_field) else: new_study_array_field = None @@ -3261,7 +3301,7 @@ def remove_soa_splits( node: StudyArrayField for node, _, _, study_root, _, study_value, *_ in ( - StudyArrayField.nodes.fetch_relations("has_after__audit_trail") + StudyArrayField.nodes.traverse("has_after__audit_trail") .filter(**filters) .all() ): diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py index d1a55a70..998a883e 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_repository.py @@ -569,3 +569,63 @@ def close(self) -> None: # Our repository guidelines state that repos should have a close method # But nothing needs to be done in this one pass + + def activity_with_same_groupings_exists( + self, + study_uid: str, + activity_name: str | None, + activity_subgroup_uid: str | None, + activity_group_uid: str | None, + exclude_study_selection_uid: str | None = None, + ) -> bool: + """Check if a StudyActivity with the same activity name and groupings + already exists in the study, optionally excluding a specific selection UID. + """ + params: dict[str, Any] = {"study_uid": study_uid} + exclude_clause = "" + if exclude_study_selection_uid: + exclude_clause = "AND sa.uid <> $exclude_uid" + params["exclude_uid"] = exclude_study_selection_uid + + # Build match clauses depending on whether groupings are provided + if activity_name is not None: + name_clause = "AND av.name = $activity_name" + params["activity_name"] = activity_name + else: + name_clause = "AND av.name IS NULL" + + if activity_subgroup_uid is not None: + subgroup_clause = """AND EXISTS { + MATCH (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_SUBGROUP]->(:StudyActivitySubGroup) + -[:HAS_SELECTED_ACTIVITY_SUBGROUP]->(:ActivitySubGroupValue)<-[:HAS_VERSION]-(asg_root:ActivitySubGroupRoot) + WHERE asg_root.uid = $activity_subgroup_uid + }""" + params["activity_subgroup_uid"] = activity_subgroup_uid + else: + subgroup_clause = ( + "AND NOT (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_SUBGROUP]->()" + ) + + if activity_group_uid is not None: + group_clause = """AND EXISTS { + MATCH (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP]->(:StudyActivityGroup) + -[:HAS_SELECTED_ACTIVITY_GROUP]->(:ActivityGroupValue)<-[:HAS_VERSION]-(ag_root:ActivityGroupRoot) + WHERE ag_root.uid = $activity_group_uid + }""" + params["activity_group_uid"] = activity_group_uid + else: + group_clause = "AND NOT (sa)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP]->()" + + query = f""" + MATCH (:StudyRoot {{uid: $study_uid}})-[:LATEST]->(sv:StudyValue)-[:HAS_STUDY_ACTIVITY]->(sa:StudyActivity) + -[:HAS_SELECTED_ACTIVITY]->(av:ActivityValue) + WHERE NOT (sa)<-[]-(:Delete) + {exclude_clause} + {name_clause} + {subgroup_clause} + {group_clause} + RETURN sa.uid + LIMIT 1 + """ + result, _ = db.cypher_query(query, params) + return len(result) > 0 diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py index 266d960a..881c316b 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_activity_schedule_repository.py @@ -170,8 +170,7 @@ def _get_selection_with_history( WITH DISTINCT all_sas """ specific_schedules_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ MATCH (all_sas)<-[:STUDY_VISIT_HAS_SCHEDULE]-(svi:StudyVisit) MATCH (all_sas)<-[:AFTER]-(asa:StudyAction) OPTIONAL MATCH (all_sas)<-[:STUDY_ACTIVITY_HAS_SCHEDULE]-(sa:StudyActivity) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_arm_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_arm_repository.py index 0c38e171..d00906bd 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_arm_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_arm_repository.py @@ -71,7 +71,7 @@ def arm_specific_has_connected_cell(self, study_uid: str, arm_uid: str) -> bool: """ sdc_node = ( - StudyArm.nodes.fetch_relations("has_design_cell", "has_after") + StudyArm.nodes.traverse("has_design_cell", "has_after") .filter( study_value__latest_value__uid=study_uid, uid=arm_uid, @@ -558,8 +558,7 @@ def _get_selection_with_history( WITH DISTINCT all_sa """ specific_arm_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ WITH DISTINCT all_sa OPTIONAL MATCH (all_sa)-[:HAS_ARM_TYPE]->(st:CTTermContext)-[:HAS_SELECTED_TERM]->(at:CTTermRoot) OPTIONAL MATCH (bars:StudyBranchArm)<-[:STUDY_ARM_HAS_BRANCH_ARM]-(all_sa) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_branch_arm_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_branch_arm_repository.py index ea408939..a569c4d6 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_branch_arm_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_branch_arm_repository.py @@ -332,7 +332,7 @@ def find_by_arm_nested_info( "has_branch_arm__study_value__latest_value__uid": study_uid, } sa_nodes = ( - StudyArm.nodes.fetch_relations("has_branch_arm__study_value__has_version") + StudyArm.nodes.traverse("has_branch_arm__study_value__has_version") .filter(**filters) .order_by("order") .all() @@ -397,7 +397,7 @@ def branch_arm_specific_exists_by_uid( :return: """ sdc_node = ( - StudyBranchArm.nodes.fetch_relations("has_after") + StudyBranchArm.nodes.traverse("has_after") .filter(study_value__latest_value__uid=study_uid, uid=branch_arm_uid) .resolve_subgraph() ) @@ -405,7 +405,7 @@ def branch_arm_specific_exists_by_uid( def get_branch_arms_connected_to_arm(self, study_uid: str, study_arm_uid: str): sdc_nodes = ( - StudyArm.nodes.fetch_relations("has_branch_arm__study_value__latest_value") + StudyArm.nodes.traverse("has_branch_arm__study_value__latest_value") .filter(uid=study_arm_uid, study_value__latest_value__uid=study_uid) .order_by("order") .all() @@ -420,9 +420,7 @@ def get_branch_arms_connected_to_cohort( self, study_uid: str, study_cohort_uid: str ): sdc_nodes = ( - StudyCohort.nodes.fetch_relations( - "branch_arm_root__study_value__latest_value" - ) + StudyCohort.nodes.traverse("branch_arm_root__study_value__latest_value") .filter(uid=study_cohort_uid, study_value__latest_value__uid=study_uid) .order_by("order") .all() @@ -441,9 +439,7 @@ def branch_arm_specific_has_connected_cell( :return: """ sdc_node = ( - StudyBranchArm.nodes.fetch_relations( - "has_design_cell__study_value", "has_after" - ) + StudyBranchArm.nodes.traverse("has_design_cell__study_value", "has_after") .filter(study_value__latest_value__uid=study_uid, uid=branch_arm_uid) .resolve_subgraph() ) @@ -457,7 +453,7 @@ def branch_arm_specific_is_last_on_arm_root( :return: """ sdc_node = ( - StudyBranchArm.nodes.fetch_relations("arm_root", "has_after") + StudyBranchArm.nodes.traverse("arm_root", "has_after") .filter( study_value__latest_value__uid=study_uid, arm_root__uid=arm_root_uid ) @@ -730,8 +726,7 @@ def _get_selection_with_history( WITH DISTINCT all_sba """ specific_branch_arm_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ WITH DISTINCT all_sba OPTIONAL MATCH (at:StudyArm)-[:STUDY_ARM_HAS_BRANCH_ARM]->(all_sba) WITH DISTINCT all_sba, at diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_cohort_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_cohort_repository.py index f2d103ab..79734649 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_cohort_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_cohort_repository.py @@ -503,8 +503,7 @@ def _get_selection_with_history( WITH DISTINCT all_sc """ specific_cohort_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ WITH DISTINCT all_sc OPTIONAL MATCH (ats:StudyArm)-[:STUDY_ARM_HAS_COHORT]->(all_sc) WITH all_sc, ats ORDER BY ats.order diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_dosing_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_dosing_repository.py index b0db8124..fc01516f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_dosing_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_dosing_repository.py @@ -332,8 +332,7 @@ def _get_selection_with_history( WITH DISTINCT all_scd """ specific_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ MATCH (all_scd)<-[:STUDY_COMPOUND_HAS_COMPOUND_DOSING]-(sc:StudyCompound) MATCH (all_scd)<-[:STUDY_ELEMENT_HAS_COMPOUND_DOSING]-(se:StudyElement) MATCH (all_scd)<-[:AFTER]-(asa:StudyAction) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_repository.py index c8d1b915..8e86b6c1 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_compound_repository.py @@ -3,12 +3,7 @@ from typing import Any from neomodel import db -from neomodel.sync_.match import ( - Collect, - NodeNameResolver, - Optional, - RelationNameResolver, -) +from neomodel.sync_.match import Collect, NodeNameResolver, Path, RelationNameResolver from clinical_mdr_api import utils from clinical_mdr_api.domain_repositories._utils.helpers import ( @@ -719,8 +714,7 @@ def _get_selection_with_history( WITH DISTINCT all_sc """ compound_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ OPTIONAL MATCH (all_sc)-[:HAS_SELECTED_COMPOUND]->(:CompoundAliasValue)-[:IS_COMPOUND]->(cr:CompoundRoot) OPTIONAL MATCH (all_sc)-[:HAS_SELECTED_COMPOUND]->(:CompoundAliasValue)<-[:LATEST]-(car:CompoundAliasRoot) OPTIONAL MATCH (all_sc)-[:HAS_MEDICINAL_PRODUCT]->(:MedicinalProductValue)<-[:HAS_VERSION]-(mpr:MedicinalProductRoot) @@ -841,10 +835,11 @@ def get_selection_uid_by_details( @staticmethod def get_compound_uid_to_arm_uids_mapping(study_uid: str) -> dict[str, set[str]]: results = ( - StudyRoot.nodes.fetch_relations( - Optional( - "latest_value__has_study_compound__has_compound_dosing__study_element__has_design_cell__study_arm" - ) + StudyRoot.nodes.traverse( + Path( + value="latest_value__has_study_compound__has_compound_dosing__study_element__has_design_cell__study_arm", + optional=True, + ), ) .filter(uid=study_uid) .annotate( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_cell_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_cell_repository.py index 138fa902..f77b0a5f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_cell_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_cell_repository.py @@ -142,9 +142,7 @@ def find_all_design_cells_by_study( "MATCH (sr:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)" ] - query.append( - dedent( - """ + query.append(dedent(""" MATCH (sv)-[:HAS_STUDY_DESIGN_CELL]->(sdc:StudyDesignCell)<-[:AFTER]-(study_action:StudyAction) MATCH (sdc)<-[:STUDY_EPOCH_HAS_DESIGN_CELL]-(sep:StudyEpoch)<-[:HAS_STUDY_EPOCH]-(sv) MATCH (sep)-[:HAS_EPOCH]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(epoch_term_root:CTTermRoot)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST_FINAL]->(epoch_name:CTTermNameValue) @@ -152,17 +150,13 @@ def find_all_design_cells_by_study( OPTIONAL MATCH (sdc)<-[:STUDY_ARM_HAS_DESIGN_CELL]-(sarm:StudyArm)<-[:HAS_STUDY_ARM]-(sv) OPTIONAL MATCH (sdc)<-[:STUDY_BRANCH_ARM_HAS_DESIGN_CELL]-(sbarm:StudyBranchArm)<-[:HAS_STUDY_BRANCH_ARM]-(sv) OPTIONAL MATCH (user:User {user_id: study_action.author_id}) - """ - ).strip() - ) + """).strip()) if filters: query.append("WITH *") query.append("WHERE " + " AND ".join(filters)) - query.append( - dedent( - """ + query.append(dedent(""" RETURN DISTINCT sdc { uid: sdc.uid, study_uid: sr.uid, @@ -181,9 +175,7 @@ def find_all_design_cells_by_study( author_username: user.username } AS vo ORDER BY vo.order - """ - ).strip() - ) + """).strip()) results, _ = db.cypher_query("\n".join(query), params=params) @@ -599,8 +591,7 @@ def _get_selection_with_history(study_uid: str, design_cell_uid: str | None = No WITH DISTINCT all_sdc """ specific_design_cells_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ OPTIONAL MATCH (all_sdc)<-[:STUDY_BRANCH_ARM_HAS_DESIGN_CELL]-(sba:StudyBranchArm) OPTIONAL MATCH (all_sdc)<-[:STUDY_ARM_HAS_DESIGN_CELL]-(sa:StudyArm) MATCH (all_sdc)<-[:STUDY_EPOCH_HAS_DESIGN_CELL]-(se:StudyEpoch) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_class_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_class_repository.py index 89e24be1..484ccd51 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_class_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_design_class_repository.py @@ -37,7 +37,7 @@ def get_study_design_class( nodes = ( ListDistinct( - StudyDesignClassNeomodel.nodes.fetch_relations( + StudyDesignClassNeomodel.nodes.traverse( "has_after__audit_trail", ) .filter(**filters) @@ -82,9 +82,9 @@ def post_study_design_class( study_root = StudyRoot.nodes.get(uid=study_uid) latest_study_value: StudyValue = study_root.latest_value.single() - study_design_class_node = StudyDesignClassNeomodel.create( - {"value": study_design_class_input.value.value} - )[0] + study_design_class_node = StudyDesignClassNeomodel( + value=study_design_class_input.value.value + ).save() latest_study_value.has_study_design_class.connect(study_design_class_node) _manage_versioning_with_relations( @@ -112,9 +112,9 @@ def edit_study_design_class( # disconnect the previous version from StudyValue latest_study_value.has_study_design_class.disconnect(previous_node) - study_design_class_node = StudyDesignClassNeomodel.create( - {"value": study_design_class_input.value.value} - )[0] + study_design_class_node = StudyDesignClassNeomodel( + value=study_design_class_input.value.value + ).save() latest_study_value.has_study_design_class.connect(study_design_class_node) _manage_versioning_with_relations( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_disease_milestone_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_disease_milestone_repository.py index f584dd03..95e9ded9 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_disease_milestone_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_disease_milestone_repository.py @@ -1,7 +1,7 @@ from typing import Any, TypeVar from neomodel import Q, db -from neomodel.sync_.match import NodeNameResolver, Optional +from neomodel.sync_.match import NodeNameResolver, Path from clinical_mdr_api.domain_repositories.controlled_terminologies.ct_codelist_attributes_repository import ( CTCodelistAttributesRepository, @@ -91,7 +91,7 @@ def find_all_disease_milestone( start: int = (page_number - 1) * page_size end: int = start + page_size nodes = ListDistinct( - StudyDiseaseMilestone.nodes.fetch_relations( + StudyDiseaseMilestone.nodes.traverse( "has_after__audit_trail", "has_disease_milestone_type__has_selected_term__has_name_root__latest_final", "has_disease_milestone_type__has_selected_term__has_attributes_root__latest_final", @@ -136,7 +136,7 @@ def find_all_disease_milestones_by_study( all_disease_milestones = [ StudyDiseaseMilestoneOGM.model_validate(sas_node) for sas_node in ListDistinct( - StudyDiseaseMilestone.nodes.fetch_relations( + StudyDiseaseMilestone.nodes.traverse( "has_after__audit_trail", "has_disease_milestone_type__has_selected_term__has_name_root__latest_final", "has_disease_milestone_type__has_selected_term__has_attributes_root__latest_final", @@ -150,7 +150,7 @@ def find_all_disease_milestones_by_study( def find_by_uid(self, uid: str) -> StudyDiseaseMilestoneVO: disease_milestone_node = ListDistinct( - StudyDiseaseMilestone.nodes.fetch_relations( + StudyDiseaseMilestone.nodes.traverse( "has_after__audit_trail", "study_value__latest_value", "has_disease_milestone_type__has_selected_term__has_name_root__latest_final", @@ -176,11 +176,11 @@ def get_all_versions(self, uid: str, study_uid): [ StudyDiseaseMilestoneOGMVer.model_validate(se_node) for se_node in ListDistinct( - StudyDiseaseMilestone.nodes.fetch_relations( + StudyDiseaseMilestone.nodes.traverse( "has_after__audit_trail", "has_disease_milestone_type__has_selected_term__has_name_root__latest_final", "has_disease_milestone_type__has_selected_term__has_attributes_root__latest_final", - Optional("has_before"), + Path(value="has_before", optional=True), ) .filter(uid=uid, has_after__audit_trail__uid=study_uid) .resolve_subgraph() @@ -195,11 +195,11 @@ def get_all_disease_milestone_versions(self, study_uid: str): [ StudyDiseaseMilestoneOGMVer.model_validate(se_node) for se_node in ( - StudyDiseaseMilestone.nodes.fetch_relations( + StudyDiseaseMilestone.nodes.traverse( "has_after__audit_trail", "has_disease_milestone_type__has_selected_term__has_name_root__latest_final", "has_disease_milestone_type__has_selected_term__has_attributes_root__latest_final", - Optional("has_before"), + Path(value="has_before", optional=True), ) .filter(has_after__audit_trail__uid=study_uid) .order_by("order") @@ -327,7 +327,7 @@ def get_distinct_headers( if "__" in field_path: path, prop = field_path.rsplit("__", 1) source = NodeNameResolver(path) - nodeset = nodeset.fetch_relations(path) + nodeset = nodeset.traverse(path) else: # FIXME: we need a proper way to resolve the variable name (NodeNameResolver # does not support 'self'...) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_element_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_element_repository.py index e6d4f55f..eb3bbb11 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_element_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_element_repository.py @@ -303,7 +303,7 @@ def element_specific_has_connected_cell( """ sdc_node = ( - StudyElement.nodes.fetch_relations("has_design_cell", "has_after") + StudyElement.nodes.traverse("has_design_cell", "has_after") .filter( study_value__latest_value__uid=study_uid, uid=element_uid, @@ -489,8 +489,7 @@ def _get_selection_with_history( WITH DISTINCT all_sa """ specific_element_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ WITH DISTINCT all_sa OPTIONAL MATCH (all_sa)-[:HAS_ELEMENT_SUBTYPE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(at:CTTermRoot) WITH DISTINCT all_sa, at diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_endpoint_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_endpoint_repository.py index d339eaec..d2829007 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_endpoint_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_endpoint_repository.py @@ -619,8 +619,7 @@ def _get_selection_with_history( WITH DISTINCT all_se """ specific_objective_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ MATCH (all_se)-[:HAS_SELECTED_ENDPOINT]->(ev:EndpointValue) CALL { @@ -756,8 +755,7 @@ def quantity_of_study_endpoints_in_study_objective_uid( "MATCH (sr:StudyRoot{uid:$study_uid})-[:LATEST]-(sv:StudyValue)" ) result = db.cypher_query( - root_match - + """ + root_match + """ MATCH (sv)--(se:StudyEndpoint)-[:STUDY_ENDPOINT_HAS_STUDY_OBJECTIVE]->(so:StudyObjective{uid:$study_objective_uid})--(sv) RETURN count(distinct se) """, diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_epoch_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_epoch_repository.py index 82e5c4e9..7d3eee89 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_epoch_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_epoch_repository.py @@ -247,27 +247,19 @@ def find_all_epochs_query( if not study_value_version: query.append("WHERE NOT (study_epoch)-[:BEFORE]-()") - query.append( - dedent( - """ + query.append(dedent(""" MATCH (study_epoch)-[:HAS_EPOCH]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(epoch_ct_term_root:CTTermRoot) MATCH (study_epoch)-[:HAS_EPOCH_SUB_TYPE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(epoch_subtype_ct_term_root:CTTermRoot) MATCH (study_epoch)-[:HAS_EPOCH_TYPE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(epoch_type_ct_term_root:CTTermRoot) - """ - ) - ) + """)) if audit_trail: - query.append( - dedent( - """ + query.append(dedent(""" WITH *, {term_uid: epoch_ct_term_root.uid} AS epoch_term, {term_uid: epoch_subtype_ct_term_root.uid} AS epoch_subtype_term, {term_uid: epoch_type_ct_term_root.uid} AS epoch_type_term - """ - ) - ) + """)) else: query.append( @@ -286,9 +278,7 @@ def find_all_epochs_query( ) ) - query.append( - dedent( - """ + query.append(dedent(""" WITH study_root.uid AS study_uid, study_action, @@ -298,9 +288,7 @@ def find_all_epochs_query( epoch_type_term, size([(study_epoch)-[:STUDY_EPOCH_HAS_STUDY_VISIT]->(study_visit:StudyVisit)<-[:HAS_STUDY_VISIT]-(study_value:StudyValue) | study_visit]) AS count_visits, coalesce(head([(user:User)-[*0]-() WHERE user.user_id=study_action.author_id | user.username]), study_action.author_id) AS author_username - """ - ) - ) + """)) if audit_trail: query.append( dedent( @@ -340,7 +328,7 @@ def epoch_specific_has_connected_design_cell( """ sdc_node = ( - StudyEpoch.nodes.fetch_relations( + StudyEpoch.nodes.traverse( "has_design_cell__study_value", "has_after", "has_after__audit_trail", diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_objective_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_objective_repository.py index 4fab26fe..b9c3fffe 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_objective_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_objective_repository.py @@ -436,8 +436,7 @@ def _get_selection_with_history( WITH DISTINCT all_so """ specific_objective_selections_audit_trail = db.cypher_query( - cypher - + """ + cypher + """ MATCH (all_so)-[:HAS_SELECTED_OBJECTIVE]->(ov:ObjectiveValue) CALL { diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_footnote_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_footnote_repository.py index 01fc635d..5334c822 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_footnote_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_soa_footnote_repository.py @@ -52,9 +52,7 @@ def where_query(self): def with_query(self, full_query: bool = True): query = [] # StudyActivity part - query.append( - dedent( - """WITH DISTINCT sr, sf, sa, + query.append(dedent("""WITH DISTINCT sr, sf, sa, [(sf)-[:REFERENCES_STUDY_ACTIVITY]->(study_activity:StudyActivity)<-[:HAS_STUDY_ACTIVITY]-(sv) WHERE NOT (study_activity)-[:BEFORE]-() | { @@ -70,9 +68,7 @@ def with_query(self, full_query: bool = True): study_activity_order: study_activity.order, study_activity_schedule_order: 0, // 0 as schedule order, because StudyActivity appears in the same row in SoA as schedule but it should take priority in footnote number assignment type: 'StudyActivity' - """ - ) - ) + """)) if full_query: query.append( dedent( @@ -276,9 +272,7 @@ def with_query(self, full_query: bool = True): ) # Latest Footnote part if full_query: - query.append( - dedent( - """CALL { + query.append(dedent("""CALL { WITH fr, fv OPTIONAL MATCH (latest_footnote_value:FootnoteValue)<-[ver:HAS_VERSION]-(fr:FootnoteRoot)<-[:CONTAINS_SYNTAX_INSTANCE]-(library:Library) OPTIONAL MATCH (ftr:FootnoteTemplateRoot)-[:HAS_FOOTNOTE]->(fr) @@ -287,21 +281,15 @@ def with_query(self, full_query: bool = True): {uid:fr.uid, version: ver.version, name_plain:fv.name_plain, library_name: library.name, template_uid: ftr.uid} as latest_footnote ORDER BY ver.start_date DESC LIMIT 1} - """ - ) - ) + """)) # Footnote template part - query.append( - dedent( - """CALL{ + query.append(dedent("""CALL{ WITH sf OPTIONAL MATCH (sf)-[:HAS_SELECTED_FOOTNOTE_TEMPLATE]->(ftv:FootnoteTemplateValue)<-[ver:HAS_VERSION]-(ftr:FootnoteTemplateRoot)<-[:CONTAINS_SYNTAX_TEMPLATE]-(library:Library) WHERE ver.status = 'Final' RETURN { uid:ftr.uid, name: ftv.name, name_plain: ftv.name_plain - """ - ) - ) + """)) if full_query: query.append( dedent( @@ -312,9 +300,7 @@ def with_query(self, full_query: bool = True): dedent("} as footnote_template ORDER BY ver.start_date DESC LIMIT 1} ") ) # Main Return part - query.append( - dedent( - """RETURN DISTINCT + query.append(dedent("""RETURN DISTINCT sr.uid AS study_uid, sf.uid AS uid, footnote, @@ -335,23 +321,17 @@ def with_query(self, full_query: bool = True): '^study_activity_order', '^study_activity_schedule_order' ]) AS referenced_items - """ - ) - ) + """)) # Extra return part if full_query: - query.append( - dedent( - """,latest_footnote, + query.append(dedent(""",latest_footnote, sf.accepted_version as accepted_version, sa.author_id AS author_id, sa.date AS modified_date, end_date, labels(sa) AS change_type, coalesce(head([(user:User)-[*0]-() WHERE user.user_id=sa.author_id | user.username]), sa.author_id) AS author_username - """ - ) - ) + """)) return "\n".join(query) def order_by_soa_order(self): @@ -571,7 +551,7 @@ def save(self, soa_footnote_vo: StudySoAFootnoteVO, create: bool = True): # link to selected footnote with specified version elif soa_footnote_vo.footnote_uid and soa_footnote_vo.footnote_version: selected_footnote = ( - FootnoteValue.nodes.fetch_relations("has_version") + FootnoteValue.nodes.traverse("has_version") .filter( **{ "has_version__uid": soa_footnote_vo.footnote_uid, @@ -596,7 +576,7 @@ def save(self, soa_footnote_vo: StudySoAFootnoteVO, create: bool = True): and soa_footnote_vo.footnote_template_version ): selected_footnote_template = ( - FootnoteTemplateValue.nodes.fetch_relations("has_version") + FootnoteTemplateValue.nodes.traverse("has_version") .filter( **{ "has_version__uid": soa_footnote_vo.footnote_template_uid, 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 bafb25db..f070b22f 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 @@ -71,11 +71,13 @@ def _study_value_query( params["study_value_version"] = study_value_version params["study_status"] = StudyStatus.RELEASED.value query = [ - "MATCH (:StudyRoot {uid: $study_uid})-[:HAS_VERSION{status: $study_status, version: $study_value_version}]->(sv:StudyValue)" + "MATCH (study_root:StudyRoot {uid: $study_uid})-[study_version:HAS_VERSION {status: $study_status, version: $study_value_version}]->(study_value:StudyValue)" ] else: - query = ["MATCH (:StudyRoot {uid: $study_uid})-[:LATEST]->(sv:StudyValue)"] + query = [ + "MATCH (study_root:StudyRoot {uid: $study_uid})-[study_version:LATEST]->(study_value:StudyValue)" + ] return query, params @@ -94,7 +96,7 @@ def _disconnect_soa_rows( query = "\n".join( sv_query + [ - "MATCH (sv)-[cell:HAS_PROTOCOL_SOA_CELL]->(ss:StudySelection)", + "MATCH (study_value)-[cell:HAS_PROTOCOL_SOA_CELL]->()", "DELETE cell", ] ) @@ -103,7 +105,7 @@ def _disconnect_soa_rows( query = "\n".join( sv_query + [ - "MATCH (sv)-[fn:HAS_PROTOCOL_SOA_FOOTNOTE]->(sfn:StudySoAFootnote)-[]->(ss)", + "MATCH (study_value)-[fn:HAS_PROTOCOL_SOA_FOOTNOTE]->()", "DELETE fn", ] ) @@ -124,27 +126,26 @@ def load( sv_query, params = self._study_value_query(study_uid, study_value_version) query = list(sv_query) - query.append("MATCH (sv)-[cell:HAS_PROTOCOL_SOA_CELL]->(ss:StudySelection)") - query.append( - "OPTIONAL MATCH (sv)-[fn:HAS_PROTOCOL_SOA_FOOTNOTE]->(sfn:StudySoAFootnote)-[]->(ss)" - ) - query.append("WITH cell, ss, fn, sfn") - query.append("ORDER BY cell.row, cell.column, cell.order, fn.order") - query.append( - "WITH cell, ss, COLLECT({order: fn.order, symbol: fn.symbol, uid: sfn.uid}) AS sfns" - ) - query.append("RETURN cell, ss, sfns") + query.append(dedent(""" + MATCH (study_value)-[cell:HAS_PROTOCOL_SOA_CELL]->(ss:StudySelection) + RETURN cell, ss, + apoc.coll.sortMaps( + [(study_value)-[fn:HAS_PROTOCOL_SOA_FOOTNOTE]->(sfn:StudySoAFootnote)-->(ss) | {order: fn.order, symbol: fn.symbol, uid: sfn.uid}], + '^order' + ) AS sfns + ORDER BY cell.row, cell.column, cell.order + """).strip()) results, _ = db.cypher_query("\n".join(query), params) cell_references = [self._to_soa_cell_reference(*result) for result in results] query = list(sv_query) - query.append( - "MATCH (sv)-[fn:HAS_PROTOCOL_SOA_FOOTNOTE]->(sfn:StudySoAFootnote)" - ) - query.append("RETURN fn, sfn") - query.append("ORDER BY fn.order") + query.append(dedent(""" + MATCH (study_value)-[fn:HAS_PROTOCOL_SOA_FOOTNOTE]->(sfn:StudySoAFootnote) + RETURN fn, sfn + ORDER BY fn.order + """).strip()) results, _ = db.cypher_query("\n".join(query), params) @@ -321,59 +322,34 @@ def manage_versioning_create( action.save() study_root.audit_trail.connect(action) - @staticmethod + @classmethod @trace_calls( - args=[0, 1, 2], kwargs=["study_uid", "study_value_version", "get_instances"] + args=[1, 2, 3], kwargs=["study_uid", "study_value_version", "get_instances"] ) def query_study_activities( + cls, study_uid: str, study_value_version: str | None = None, get_instances: bool = False, ): - query = [] - params = { - "study_uid": study_uid, - "study_version": study_value_version, - "study_status": StudyStatus.RELEASED.value, # used only if study_value_version set - "requested_library_name": settings.requested_library_name, - } - - if study_value_version: - query.append( - "MATCH (study_root:StudyRoot {uid: $study_uid})-[study_version:HAS_VERSION {status: $study_status, version: $study_version}]->(study_value:StudyValue)" - ) - else: - query.append( - "MATCH (study_root:StudyRoot {uid: $study_uid})-[study_version:LATEST]->(study_value:StudyValue)" - ) + query, params = cls._study_value_query(study_uid, study_value_version) + params["requested_library_name"] = settings.requested_library_name query.append(queries.study_standard_version_ct_terms_datetime) - query.append( - dedent( - """ + query.append(dedent(""" MATCH (study_value)-[:HAS_STUDY_ACTIVITY]-> (study_activity:StudyActivity)-[:HAS_SELECTED_ACTIVITY]-> (activity_value:ActivityValue)<-[:HAS_VERSION]- (activity_root:ActivityRoot)<-[:CONTAINS_CONCEPT]- (act_library:Library) - """ - ) - ) - # Removed filter that excluded Requested library activities to support L3 MVP feature #3446656 - # Previously: if get_instances: query.append("WHERE act_library.name <> $requested_library_name") - # Now placeholders (Requested library activities) will appear in operational SoA (L3) - query.append( - dedent( - """ + MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_SOA_GROUP]-> (study_soa_group:StudySoAGroup)-[:HAS_FLOWCHART_GROUP]-> (:CTTermContext)-[:HAS_SELECTED_TERM]-> (soa_group_term_root:CTTermRoot) WHERE (study_soa_group)<-[:HAS_STUDY_SOA_GROUP]-(study_value) - """ - ) - ) + """)) query.append( queries.ct_term_name_at_datetime.format( @@ -382,9 +358,7 @@ def query_study_activities( ) ) - query.append( - dedent( - """ + query.append(dedent(""" OPTIONAL MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_GROUP]-> (study_activity_group:StudyActivityGroup)-[:HAS_SELECTED_ACTIVITY_GROUP]-> (activity_group_value:ActivityGroupValue)<-[:HAS_VERSION]-(activity_group_root:ActivityGroupRoot) @@ -394,18 +368,14 @@ def query_study_activities( (study_activity_subgroup:StudyActivitySubGroup)-[:HAS_SELECTED_ACTIVITY_SUBGROUP]-> (activity_subgroup_value:ActivitySubGroupValue)<-[:HAS_VERSION]-(activity_subgroup_root:ActivitySubGroupRoot) WHERE (study_activity_subgroup)<-[:HAS_STUDY_ACTIVITY_SUBGROUP]-(study_value) - """ - ) - ) + """)) if get_instances: - query.append( - dedent( - """ + query.append(dedent(""" OPTIONAL MATCH (study_activity)-[:STUDY_ACTIVITY_HAS_STUDY_ACTIVITY_INSTANCE]-> (study_activity_instance:StudyActivityInstance) WHERE (study_activity_instance)<-[:HAS_STUDY_ACTIVITY_INSTANCE]-(study_value) - // by optional match, it keeps study activity instance placeholders in the results + OPTIONAL MATCH (study_activity_instance)-[:HAS_SELECTED_ACTIVITY_INSTANCE]-> (activity_instance_value:ActivityInstanceValue)<-[:HAS_VERSION]- (activity_instance_root:ActivityInstanceRoot)<-[:CONTAINS_CONCEPT]- @@ -414,26 +384,18 @@ def query_study_activities( OPTIONAL MATCH (activity_instance_value:ActivityInstanceValue)-[:ACTIVITY_INSTANCE_CLASS]-> (activity_instance_class_root:ActivityInstanceClassRoot)-[:LATEST]-> (activity_instance_class_latest_value:ActivityInstanceClassValue) - """ - ) - ) + """)) - query.append( - dedent( - """ + query.append(dedent(""" WITH DISTINCT * ORDER BY COALESCE(study_soa_group.order, 0), COALESCE(study_activity_group.order, 0), COALESCE(study_activity_subgroup.order, 0), COALESCE(study_activity.order, 0) - """ - ) - ) + """)) if get_instances: # Use COALESCE to handle NULL instance orders for placeholders without instances query.append(", COALESCE(study_activity_instance.order, 0)") - query.append( - dedent( - """ + query.append(dedent(""" RETURN { study_activity_uid: study_activity.uid, activity: { @@ -448,13 +410,9 @@ def query_study_activities( }, accepted_version: study_activity.accepted_version, keep_old_version: COALESCE(study_activity.keep_old_version, false), - """ - ) - ) + """)) if get_instances: - query.append( - dedent( - """ + query.append(dedent(""" study_activity_instance_uid: study_activity_instance.uid, activity_instance: CASE WHEN activity_instance_root IS NOT NULL THEN { uid: activity_instance_root.uid, @@ -493,14 +451,10 @@ def query_study_activities( show_activity_instance_in_protocol_flowchart: COALESCE(study_activity_instance.show_activity_instance_in_protocol_flowchart, false), is_important: COALESCE(study_activity_instance.is_important, false), order: study_activity_instance.order, - """ - ) - ) + """)) else: query.append(" order: study_activity.order,") - query.append( - dedent( - """ + query.append(dedent(""" show_activity_in_protocol_flowchart: study_activity.show_activity_in_protocol_flowchart, show_activity_group_in_protocol_flowchart: COALESCE(study_activity_group.show_activity_group_in_protocol_flowchart, false), show_activity_subgroup_in_protocol_flowchart: COALESCE(study_activity_subgroup.show_activity_subgroup_in_protocol_flowchart, false), @@ -526,9 +480,7 @@ def query_study_activities( study_uid: study_root.uid, study_version: study_version.version } AS selection - """ - ) - ) + """)) results, headers = db.cypher_query("\n".join(query), params=params) return results, headers diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_source_variable_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_source_variable_repository.py index b1e761fc..b9396fae 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_source_variable_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_source_variable_repository.py @@ -49,7 +49,7 @@ def get_study_source_variable( } nodes = ListDistinct( - StudySourceVariableNeomodel.nodes.fetch_relations( + StudySourceVariableNeomodel.nodes.traverse( "has_after__audit_trail", ) .filter(**filters) @@ -75,12 +75,10 @@ def post_study_source_variable( source_variable: StudySourceVariableEnum | None = ( study_source_variable_input.source_variable ) - study_source_variable_node = StudySourceVariableNeomodel.create( - { - "source_variable": source_variable.value if source_variable else None, - "source_variable_description": study_source_variable_input.source_variable_description, - } - )[0] + study_source_variable_node = StudySourceVariableNeomodel( + source_variable=source_variable.value if source_variable else None, + source_variable_description=study_source_variable_input.source_variable_description, + ).save() latest_study_value.has_study_source_variable.connect(study_source_variable_node) _manage_versioning_with_relations( study_root=study_root, @@ -110,12 +108,10 @@ def edit_study_source_variable( source_variable: StudySourceVariableEnum | None = ( study_source_variable_input.source_variable ) - study_source_variable_node = StudySourceVariableNeomodel.create( - { - "source_variable": source_variable.value if source_variable else None, - "source_variable_description": study_source_variable_input.source_variable_description, - } - )[0] + study_source_variable_node = StudySourceVariableNeomodel( + source_variable=source_variable.value if source_variable else None, + source_variable_description=study_source_variable_input.source_variable_description, + ).save() latest_study_value.has_study_source_variable.connect(study_source_variable_node) _manage_versioning_with_relations( diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_standard_version_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_standard_version_repository.py index cc620641..96f4292f 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_standard_version_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_standard_version_repository.py @@ -1,7 +1,7 @@ from typing import Any, Sequence, TypeVar from neomodel import Q -from neomodel.sync_.match import Optional +from neomodel.sync_.match import Path from clinical_mdr_api.domain_repositories.generic_repository import ( _manage_versioning_with_relations, @@ -66,7 +66,7 @@ def find_all_standard_version( start: int = (page_number - 1) * page_size end: int = start + page_size nodes = ListDistinct( - StudyStandardVersion.nodes.fetch_relations( + StudyStandardVersion.nodes.traverse( "has_after__audit_trail", "has_ct_package", ) @@ -121,7 +121,7 @@ def find_standard_versions_in_study( standard_versions = [ StudyStandardVersionOGM.model_validate(sas_node) for sas_node in ListDistinct( - StudyStandardVersion.nodes.fetch_relations( + StudyStandardVersion.nodes.traverse( "has_after__audit_trail", "has_ct_package", ) @@ -150,7 +150,7 @@ def find_by_uid( "uid": study_standard_version_uid, } standard_version_node = ListDistinct( - StudyStandardVersion.nodes.fetch_relations( + StudyStandardVersion.nodes.traverse( "has_after__audit_trail", "has_ct_package", ) @@ -173,8 +173,10 @@ def get_all_versions(self, uid: str, study_uid): return sorted( [ StudyStandardVersionOGMVer.model_validate(se_node) - for se_node in StudyStandardVersion.nodes.fetch_relations( - "has_after__audit_trail", "has_ct_package", Optional("has_before") + for se_node in StudyStandardVersion.nodes.traverse( + "has_after__audit_trail", + "has_ct_package", + Path(value="has_before", optional=True), ) .filter(uid=uid, has_after__audit_trail__uid=study_uid) .resolve_subgraph() @@ -188,8 +190,10 @@ def get_all_study_version_versions(self, study_uid: str): return sorted( [ StudyStandardVersionOGMVer.model_validate(se_node) - for se_node in StudyStandardVersion.nodes.fetch_relations( - "has_after__audit_trail", "has_ct_package", Optional("has_before") + for se_node in StudyStandardVersion.nodes.traverse( + "has_after__audit_trail", + "has_ct_package", + Path(value="has_before", optional=True), ) .filter(has_after__audit_trail__uid=study_uid) .order_by("has_after__audit_trail.date") diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_version_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_version_repository.py index da691a06..59859e67 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_version_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_version_repository.py @@ -270,7 +270,7 @@ def retrieve_study_snapshot_history( page_size: int = 10, page_number: int = 1, total_count: bool = True, - only_latest_major_protcol_version: bool = False, + only_latest_major_protocol_version: bool = False, ) -> tuple[list[dict[str, Any]], int]: """ Retrieves the complete snapshot history of a Study, including all versioned states. @@ -305,7 +305,7 @@ def retrieve_study_snapshot_history( OPTIONAL MATCH (sv)-[:HAS_REASON_FOR_LOCK]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(:CTTermRoot)-->(:CTTermNameRoot)-[:LATEST_FINAL]->(lock_term_val:CTTermNameValue) OPTIONAL MATCH (sv)-[:HAS_REASON_FOR_UNLOCK]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(:CTTermRoot)-->(:CTTermNameRoot)-[:LATEST_FINAL]->(unlock_term_val:CTTermNameValue) """ - protocol_header_version_match = f"{'' if only_latest_major_protcol_version else 'OPTIONAL'} MATCH (study_value)-[:HAS_STUDY_DEFINITION_DOCUMENT]->(sdd:StudyDefinitionDocument)" + protocol_header_version_match = f"{'' if only_latest_major_protocol_version else 'OPTIONAL'} MATCH (study_value)-[:HAS_STUDY_DEFINITION_DOCUMENT]->(sdd:StudyDefinitionDocument)" return_query = """ RETURN @@ -333,7 +333,7 @@ def retrieve_study_snapshot_history( # if only latest major protocol header version is requested, we do pagination in memory after filtering, as we can't do filtering in the query ( db_pagination_clause(page_size, page_number, one_element_extra=True) - if not only_latest_major_protcol_version + if not only_latest_major_protocol_version else "" ), ] @@ -343,26 +343,27 @@ def retrieve_study_snapshot_history( return [], 0 history = [get_db_result_as_dict(row, columns) for row in rows] - # If only_latest_major_protcol_version is requested, we have to leave only + # If only_latest_major_protocol_version is requested, we have to leave only # major protocol header versions and leave only latest available version of it (with highest metadata version) - if only_latest_major_protcol_version: - latest_visited_protocol_header_version: str | None = None - filtered_history = [] + if only_latest_major_protocol_version: + phv_to_index: dict[str, int] = {} + filtered_history: list[dict[str, Any]] = [] for h in history: major_version = h.get("protocol_header_major_version") minor_version = h.get("protocol_header_minor_version") - if ( - major_version is not None - and minor_version == 0 - and (protocol_header_version := f"{major_version}.{minor_version}") - and protocol_header_version - != latest_visited_protocol_header_version - ): - filtered_history.append(h) - latest_visited_protocol_header_version = protocol_header_version + if major_version is not None and minor_version == 0: + phv = f"{major_version}.{minor_version}" + if phv not in phv_to_index: + h["original_metadata_version"] = h.get("metadata_version") + phv_to_index[phv] = len(filtered_history) + filtered_history.append(h) + else: + filtered_history[phv_to_index[phv]][ + "original_metadata_version" + ] = h.get("metadata_version") history = filtered_history - if not only_latest_major_protcol_version: + if not only_latest_major_protocol_version: total = ( calculate_total_count_from_query_result( result_count=len(history), diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py index 181b99f9..71fe7ea9 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/study_selections/study_visit_repository.py @@ -497,9 +497,7 @@ def find_all_visits_query( if filters: query.append(f"WHERE {' AND '.join(filters)}") - query.append( - dedent( - """ + query.append(dedent(""" MATCH (study_visit)-[:HAS_VISIT_TYPE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(visit_type_term:CTTermRoot) MATCH (study_visit)-[:HAS_VISIT_CONTACT_MODE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(visit_contact_mode_term:CTTermRoot) OPTIONAL MATCH (study_visit)-[:HAS_REPEATING_FREQUENCY]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(repeating_frequency_term:CTTermRoot) @@ -509,14 +507,10 @@ def find_all_visits_query( OPTIONAL MATCH (timepoint_value)-[:HAS_UNIT_DEFINITION]->(timepoint_unit_root:UnitDefinitionRoot)-[:LATEST]->(timepoint_unit_value:UnitDefinitionValue) OPTIONAL MATCH (timepoint_value)-[:HAS_TIME_REFERENCE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(time_reference_term:CTTermRoot) OPTIONAL MATCH (timepoint_value)-[:HAS_VALUE]->(numeric_root:NumericValueRoot)-[:LATEST]->(numeric_value:NumericValue) - """ - ).rstrip() - ) + """).rstrip()) if audit_trail: - query.append( - dedent( - """ + query.append(dedent(""" WITH *, {term_uid: epoch_term_root.uid} AS epoch_term, {term_uid: visit_type_term.uid} AS visit_type, @@ -524,9 +518,7 @@ def find_all_visits_query( CASE WHEN repeating_frequency_term.uid IS NULL THEN NULL ELSE {term_uid: repeating_frequency_term.uid} END AS repeating_frequency, CASE WHEN epoch_allocation_term.uid IS NULL THEN NULL ELSE {term_uid: epoch_allocation_term.uid} END AS epoch_allocation, CASE WHEN time_reference_term.uid IS NULL THEN NULL ELSE {term_uid: time_reference_term.uid} END AS time_reference - """ - ).rstrip() - ) + """).rstrip()) else: query.append( @@ -560,9 +552,7 @@ def find_all_visits_query( ) ) - query.append( - dedent( - """ + query.append(dedent(""" WITH study_root.uid AS study_uid, study_value.study_id_prefix AS study_id_prefix, @@ -608,12 +598,9 @@ def find_all_visits_query( | {vis: consecutive_visits, unique_visit_number: toInteger(consecutive_visits.unique_visit_number)} ], '^unique_visit_number') }]) AS group - """ - ).rstrip() - ) + """).rstrip()) - return_statement = dedent( - """ + return_statement = dedent(""" RETURN *, CASE WHEN group.visit_group.group_format = "range" @@ -630,8 +617,7 @@ def find_all_visits_query( } ELSE null END AS consecutive_visit_group - """ - ).rstrip() + """).rstrip() if audit_trail: query.append( @@ -663,6 +649,121 @@ def find_all_visits_by_study_uid( ) return extracted_items + @staticmethod + @trace_calls + def list_all_visits_query( + study_uid: str, + study_value_version: str | None = None, + ) -> tuple[str, dict[Any, Any]]: + """List all visits of a specific study version, returning fewer properties""" + + query = [] + params = {"study_uid": study_uid} + + if study_value_version: + query.append( + "MATCH (study_root:StudyRoot {uid: $study_uid})-[:HAS_VERSION{status: $study_status, version: $study_value_version}]->(study_value:StudyValue)" + ) + params["study_value_version"] = study_value_version + params["study_status"] = StudyStatus.RELEASED.value + else: + query.append( + "MATCH (study_root:StudyRoot {uid: $study_uid})-[:LATEST]->(study_value:StudyValue)" + ) + + query.append(queries.study_standard_version_ct_terms_datetime) + + query.append("MATCH (study_value)-[:HAS_STUDY_VISIT]->(study_visit:StudyVisit)") + + if not study_value_version: + query.append("WHERE NOT (study_visit)-[:BEFORE]-()") + + query.append( + "MATCH (study_visit)<-[:STUDY_EPOCH_HAS_STUDY_VISIT]-(study_epoch:StudyEpoch)<-[:HAS_STUDY_EPOCH]-(study_value)" + "MATCH (study_epoch)-[:HAS_EPOCH]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(epoch_term_root:CTTermRoot)" + ) + + if not study_value_version: + query.append("WHERE NOT (study_epoch)-[:BEFORE]-()") + + query.append( + "MATCH (study_visit)-[:HAS_VISIT_TYPE]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(visit_type_term:CTTermRoot)" + ) + query.append( + "OPTIONAL MATCH (study_visit)-[:HAS_WINDOW_UNIT]->(window_unit_root:UnitDefinitionRoot)-[:LATEST]->(window_unit_value:UnitDefinitionValue)" + ) + + query.append( + queries.ct_term_name_at_datetime.format( + root="epoch_term_root", value="epoch_term" + ) + ) + query.append( + queries.ct_term_name_at_datetime.format( + root="visit_type_term", value="visit_type" + ) + ) + + query.append(dedent(""" + WITH + study_visit, + study_epoch, + epoch_term, + visit_type, + window_unit_root, + window_unit_value, + head([(study_visit)-[:HAS_STUDY_DAY]->(sdr:StudyDayRoot)-[:LATEST]->(sdv:StudyDayValue) | {uid:sdr.uid, value:sdv.value}]) AS study_day, + head([(study_visit)-[:HAS_STUDY_DURATION_DAYS]->(sdr:StudyDurationDaysRoot)-[:LATEST]->(sdv:StudyDurationDaysValue) | {uid:sdr.uid, value:sdv.value}]) AS study_duration_days, + head([(study_visit)-[:HAS_STUDY_WEEK]->(swr:StudyWeekRoot)-[:LATEST]->(swv:StudyWeekValue) | {uid:swr.uid, value:swv.value}]) AS study_week, + head([(study_visit)-[:HAS_STUDY_DURATION_WEEKS]->(swr:StudyDurationWeeksRoot)-[:LATEST]->(swv:StudyDurationWeeksValue) | {uid:swr.uid, value:swv.value}]) AS study_duration_weeks, + head([(study_visit)-[:IN_VISIT_GROUP]->(visit_group:StudyVisitGroup) | + { + visit_group:visit_group, + consecutive_visits: apoc.coll.sortMaps([ + (visit_group)<-[:IN_VISIT_GROUP]-(consecutive_visits:StudyVisit)<-[:HAS_STUDY_VISIT]-(study_value) + | {vis: consecutive_visits, unique_visit_number: toInteger(consecutive_visits.unique_visit_number)} + ], '^unique_visit_number') + }]) AS group + """).rstrip()) + + query.append(dedent(""" + RETURN + study_visit { .*, + consecutive_visit_group: CASE group.visit_group.group_format + WHEN "range" THEN head(group.consecutive_visits).vis.short_visit_label + "-" + last(group.consecutive_visits).vis.short_visit_label + WHEN "list" THEN apoc.text.join([visit in group.consecutive_visits | visit.vis.short_visit_label], ',') + ELSE null END, + consecutive_visit_group_uid: group.visit_group.uid, + visit_short_name: study_visit.short_visit_label, + study_day_number: study_day.value, + study_duration_days: study_duration_days.value, + study_week_number: study_week.value, + study_duration_weeks: study_duration_weeks.value, + min_visit_window_value: study_visit.visit_window_min, + max_visit_window_value: study_visit.visit_window_max, + visit_window_unit_uid: window_unit_root.uid, + visit_window_unit_name: window_unit_value.name, + study_epoch_uid: study_epoch.uid, + study_epoch: epoch_term, + visit_type: visit_type + } AS StudyVisit + """).rstrip()) + + query.append("ORDER BY toInteger(study_visit.unique_visit_number)") + + return "\n".join(query), params + + @classmethod + @trace_calls + def list_all_visits_by_study_uid( + cls, study_uid: str, study_value_version: str | None = None + ) -> list[dict[str, Any]]: + query, params = cls.list_all_visits_query( + study_uid=study_uid, study_value_version=study_value_version + ) + results, _ = db.cypher_query(query=query, params=params) + return [record[0] for record in results] + def find_all_visits_referencing_study_visit( self, study_visit_uid: str ) -> list[StudyVisit]: diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/syntax_instances/generic_syntax_instance_repository.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/syntax_instances/generic_syntax_instance_repository.py index aefaa1b4..ceec1f56 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/syntax_instances/generic_syntax_instance_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/syntax_instances/generic_syntax_instance_repository.py @@ -38,13 +38,11 @@ class GenericSyntaxInstanceRepository( template_class: type def next_available_sequence_id(self, uid: str) -> str | None: - rs = db.cypher_query( - f""" + rs = db.cypher_query(f""" MATCH (r:SyntaxTemplateRoot {{uid: "{uid}"}}) OPTIONAL MATCH (pr:{self.root_class.__name__})-[:CREATED_FROM]->(r) RETURN pr.sequence_id, r.sequence_id - """ - ) + """) if rs[0][0][0]: rs[0].sort(key=lambda x: int(x[0].split("P")[1]), reverse=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domain_repositories/template_parameters/complex_parameter.py b/clinical-mdr-api/clinical_mdr_api/domain_repositories/template_parameters/complex_parameter.py index 9b250e59..cdf1a804 100644 --- a/clinical-mdr-api/clinical_mdr_api/domain_repositories/template_parameters/complex_parameter.py +++ b/clinical-mdr-api/clinical_mdr_api/domain_repositories/template_parameters/complex_parameter.py @@ -81,8 +81,7 @@ def find_extended(self): return values def find_all_with_samples(self): - items, _ = db.cypher_query( - """ + items, _ = db.cypher_query(""" MATCH (pt:TemplateParameter) CALL { WITH pt @@ -98,8 +97,7 @@ def find_all_with_samples(self): pt.name AS name, terms ORDER BY name - """ - ) + """) return_value = [{"name": item[0], "terms": item[1]} for item in items] return return_value diff --git a/clinical-mdr-api/clinical_mdr_api/domains/_utils.py b/clinical-mdr-api/clinical_mdr_api/domains/_utils.py index b36bc758..ba9d93a0 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/_utils.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/_utils.py @@ -1,8 +1,8 @@ from typing import Literal, overload -from clinical_mdr_api.domains.concepts.utils import EN_LANGUAGE, ENG_LANGUAGE from clinical_mdr_api.domains.iso_languages import LANGUAGES_INDEXED_BY from clinical_mdr_api.domains.libraries.parameter_term import ParameterTermEntryVO +from clinical_mdr_api.domains.odms.utils import EN_LANGUAGE, ENG_LANGUAGE from common import exceptions 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 77dae5a7..3a4ee8e8 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 @@ -13,6 +13,9 @@ class LibraryItem(BaseModel): name: str | None = None +class CTCodelistItem(LibraryItem): ... + + class CTTermItem(LibraryItem): codelist_uid: str | None = None submission_value: str | None = None @@ -27,6 +30,7 @@ class ActivityItemVO: is_adam_param_specific: bool activity_item_class_uid: str activity_item_class_name: str | None + ct_codelist: CTCodelistItem | None ct_terms: list[CTTermItem] unit_definitions: list[CompactUnitDefinition] text_value: str | None = None @@ -37,6 +41,7 @@ def from_repository_values( is_adam_param_specific: bool, activity_item_class_uid: str, activity_item_class_name: str | None, + ct_codelist: CTCodelistItem | None, ct_terms: list[CTTermItem], unit_definitions: list[CompactUnitDefinition], text_value: str | None = None, @@ -45,6 +50,7 @@ def from_repository_values( is_adam_param_specific=is_adam_param_specific, activity_item_class_uid=activity_item_class_uid, activity_item_class_name=activity_item_class_name, + ct_codelist=ct_codelist, ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=text_value, diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/formal_expression.py b/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/formal_expression.py deleted file mode 100644 index eb77a475..00000000 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/formal_expression.py +++ /dev/null @@ -1,115 +0,0 @@ -from dataclasses import dataclass -from typing import Callable, Self - -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase -from clinical_mdr_api.domains.versioned_object_aggregate import ( - LibraryItemMetadataVO, - LibraryVO, -) -from common.exceptions import AlreadyExistsException - - -@dataclass(frozen=True) -class OdmFormalExpressionVO(ConceptVO): - context: str - expression: str - - @classmethod - def from_repository_values( - cls, - context: str, - expression: str, - ) -> Self: - return cls( - context=context, - expression=expression, - name=None, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, - ) - - def validate( - self, odm_object_exists_callback: Callable, odm_uid: str | None = None - ) -> None: - data = {"context": self.context, "expression": self.expression} - if uids := odm_object_exists_callback(**data): - if uids[0] != odm_uid: - raise AlreadyExistsException( - msg=f"ODM Formal Expression already exists with UID ({uids[0]}) and data {data}" - ) - - -@dataclass -class OdmFormalExpressionAR(OdmARBase): - _concept_vo: OdmFormalExpressionVO - - @property - def name(self) -> str: - return self._concept_vo.name - - @property - def concept_vo(self) -> OdmFormalExpressionVO: - return self._concept_vo - - @concept_vo.setter - def concept_vo(self, value: OdmFormalExpressionVO) -> None: - self._concept_vo = value - - @classmethod - def from_repository_values( - cls, - uid: str, - concept_vo: OdmFormalExpressionVO, - library: LibraryVO, - item_metadata: LibraryItemMetadataVO, - ) -> Self: - return cls( - _uid=uid, - _concept_vo=concept_vo, - _library=library, - _item_metadata=item_metadata, - ) - - @classmethod - def from_input_values( - cls, - author_id: str, - concept_vo: OdmFormalExpressionVO, - library: LibraryVO, - generate_uid_callback: Callable[[], str] = lambda: "", - odm_object_exists_callback: Callable = lambda _: True, - ) -> Self: - item_metadata = LibraryItemMetadataVO.get_initial_item_metadata( - author_id=author_id - ) - - concept_vo.validate(odm_object_exists_callback=odm_object_exists_callback) - - return cls( - _uid=generate_uid_callback(), - _item_metadata=item_metadata, - _library=library, - _concept_vo=concept_vo, - ) - - def edit_draft( - self, - author_id: str, - change_description: str, - concept_vo: OdmFormalExpressionVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, - odm_object_exists_callback: Callable = lambda _: True, - ) -> None: - """ - Creates a new draft version for the object. - """ - concept_vo.validate( - odm_object_exists_callback=odm_object_exists_callback, odm_uid=self.uid - ) - super()._edit_draft(change_description=change_description, author_id=author_id) - self._concept_vo = concept_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/__init__.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/__init__.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/__init__.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/__init__.py diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/odm_ar_base.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/ar_base.py similarity index 82% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/odm_ar_base.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/ar_base.py index 9f28c1a1..3341656b 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/odm_ar_base.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/ar_base.py @@ -1,8 +1,8 @@ from dataclasses import dataclass from typing import AbstractSet -from clinical_mdr_api.domains.concepts.concept_base import ConceptARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( + LibraryItemAggregateRootBase, LibraryItemStatus, ObjectAction, ) @@ -10,7 +10,7 @@ @dataclass -class OdmARBase(ConceptARBase): +class OdmARBase(LibraryItemAggregateRootBase): _uid: str @property @@ -35,6 +35,12 @@ def get_possible_actions(self) -> AbstractSet[ObjectAction]: return {ObjectAction.REACTIVATE, ObjectAction.DELETE} return frozenset() + 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 soft_delete(self) -> None: BusinessLogicException.raise_if( self._item_metadata.major_version != 0 diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/condition.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/condition.py similarity index 74% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/condition.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/condition.py index 559048aa..4b3fc3cf 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/condition.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/condition.py @@ -1,13 +1,12 @@ from dataclasses import dataclass from typing import Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmFormalExpressionModel, OdmTranslatedTextModel, @@ -16,7 +15,8 @@ @dataclass(frozen=True) -class OdmConditionVO(ConceptVO): +class OdmConditionVO: + name: str oid: str | None formal_expressions: list[OdmFormalExpressionModel] translated_texts: list[OdmTranslatedTextModel] @@ -37,10 +37,6 @@ def from_repository_values( formal_expressions=formal_expressions, translated_texts=translated_texts, aliases=aliases, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( @@ -63,31 +59,31 @@ def validate( @dataclass class OdmConditionAR(OdmARBase): - _concept_vo: OdmConditionVO + _odm_vo: OdmConditionVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmConditionVO: - return self._concept_vo + def odm_vo(self) -> OdmConditionVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmConditionVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmConditionVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmConditionVO, + odm_vo: OdmConditionVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -96,7 +92,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmConditionVO, + odm_vo: OdmConditionVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_object_exists_callback: Callable = lambda _: True, @@ -105,7 +101,7 @@ def from_input_values( author_id=author_id ) - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, library_name=library.name, ) @@ -114,25 +110,22 @@ def from_input_values( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmConditionVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmConditionVO, odm_object_exists_callback: Callable = lambda _: True, ) -> None: """ Creates a new draft version for the object. """ - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, odm_uid=self.uid ) super()._edit_draft(change_description=change_description, author_id=author_id) - self._concept_vo = concept_vo + self._odm_vo = odm_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/form.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/form.py similarity index 81% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/form.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/form.py index bdce846a..e43ea411 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/form.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/form.py @@ -1,13 +1,12 @@ from dataclasses import dataclass from typing import Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmTranslatedTextModel, ) @@ -16,7 +15,8 @@ @dataclass(frozen=True) -class OdmFormVO(ConceptVO): +class OdmFormVO: + name: str | None oid: str | None repeating: str | int | None sdtm_version: str | None @@ -52,10 +52,6 @@ def from_repository_values( vendor_element_uids=vendor_element_uids, vendor_attribute_uids=vendor_attribute_uids, vendor_element_attribute_uids=vendor_element_attribute_uids, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( @@ -80,31 +76,31 @@ def validate( @dataclass class OdmFormAR(OdmARBase): - _concept_vo: OdmFormVO + _odm_vo: OdmFormVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmFormVO: - return self._concept_vo + def odm_vo(self) -> OdmFormVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmFormVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmFormVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmFormVO, + odm_vo: OdmFormVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -113,7 +109,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmFormVO, + odm_vo: OdmFormVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_object_exists_callback: Callable = lambda _: True, @@ -122,7 +118,7 @@ def from_input_values( author_id=author_id ) - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, library_name=library.name, ) @@ -131,32 +127,29 @@ def from_input_values( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmFormVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmFormVO, odm_object_exists_callback: Callable = lambda _: True, ) -> None: """ Creates a new draft version for the object. """ - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, odm_uid=self.uid, ) - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/item.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/item.py similarity index 88% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/item.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/item.py index 2a31ad7c..1fb69274 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/item.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/item.py @@ -1,17 +1,16 @@ from dataclasses import dataclass from typing import TYPE_CHECKING, Any, Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_attributes import ( CTCodelistAttributesAR, ) from clinical_mdr_api.domains.controlled_terminologies.ct_term_name import CTTermNameAR +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmTranslatedTextModel, ) @@ -20,14 +19,12 @@ from common.utils import booltostr if TYPE_CHECKING: - from clinical_mdr_api.models.concepts.odms.odm_item import ( - OdmItemCodelist, - OdmItemParentGroup, - ) + from clinical_mdr_api.models.odms.item import OdmItemCodelist, OdmItemParentGroup @dataclass(frozen=True) -class OdmItemVO(ConceptVO): +class OdmItemVO: + name: str | None oid: str | None prompt: str | None datatype: str | None @@ -93,10 +90,6 @@ def from_repository_values( vendor_attribute_uids=vendor_attribute_uids, vendor_element_attribute_uids=vendor_element_attribute_uids, activity_instances=activity_instances, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( @@ -121,16 +114,11 @@ def validate( msg=f"ODM Item already exists with UID ({uids[0]}) and data {data}" ) - self.check_concepts_exist( - [ - ( - self.unit_definition_uids, - "Unit Definition", - unit_definition_exists_by_callback, - ), - ], - "ODM Item", - ) + for unit_definition_uid in self.unit_definition_uids: + if not unit_definition_exists_by_callback("uid", unit_definition_uid, True): + raise BusinessLogicException( + msg=f"ODM Item tried to connect to non-existent Unit Definition with UID '{unit_definition_uid}'.", + ) if self.codelist is not None and not find_codelist_attribute_callback( self.codelist.uid @@ -178,31 +166,31 @@ def validate( @dataclass class OdmItemAR(OdmARBase): - _concept_vo: OdmItemVO + _odm_vo: OdmItemVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmItemVO: - return self._concept_vo + def odm_vo(self) -> OdmItemVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmItemVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmItemVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmItemVO, + odm_vo: OdmItemVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -211,7 +199,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmItemVO, + odm_vo: OdmItemVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_object_exists_callback: Callable = lambda _: True, @@ -229,7 +217,7 @@ def from_input_values( author_id=author_id ) - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, unit_definition_exists_by_callback=unit_definition_exists_by_callback, find_codelist_attribute_callback=find_codelist_attribute_callback, @@ -240,17 +228,14 @@ def from_input_values( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmItemVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmItemVO, odm_object_exists_callback: Callable = lambda _: True, unit_definition_exists_by_callback: Callable[ [str, str, bool], bool @@ -266,7 +251,7 @@ def edit_draft( """ Creates a new draft version for the object. """ - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, unit_definition_exists_by_callback=unit_definition_exists_by_callback, find_codelist_attribute_callback=find_codelist_attribute_callback, @@ -275,11 +260,11 @@ def edit_draft( odm_uid=self.uid, ) - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/item_group.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/item_group.py similarity index 85% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/item_group.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/item_group.py index a98856c0..9fcf6621 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/item_group.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/item_group.py @@ -1,16 +1,15 @@ from dataclasses import dataclass from typing import Any, Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase from clinical_mdr_api.domains.controlled_terminologies.ct_term_attributes import ( CTTermAttributesAR, ) +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmTranslatedTextModel, ) @@ -19,7 +18,8 @@ @dataclass(frozen=True) -class OdmItemGroupVO(ConceptVO): +class OdmItemGroupVO: + name: str | None oid: str | None repeating: str | int | None is_reference_data: str | int | None @@ -70,10 +70,6 @@ def from_repository_values( vendor_element_uids=vendor_element_uids, vendor_attribute_uids=vendor_attribute_uids, vendor_element_attribute_uids=vendor_element_attribute_uids, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( @@ -110,31 +106,31 @@ def validate( @dataclass class OdmItemGroupAR(OdmARBase): - _concept_vo: OdmItemGroupVO + _odm_vo: OdmItemGroupVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmItemGroupVO: - return self._concept_vo + def odm_vo(self) -> OdmItemGroupVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmItemGroupVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmItemGroupVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmItemGroupVO, + odm_vo: OdmItemGroupVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -143,7 +139,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmItemGroupVO, + odm_vo: OdmItemGroupVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_object_exists_callback: Callable = lambda _: True, @@ -153,7 +149,7 @@ def from_input_values( author_id=author_id ) - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, find_term_callback=find_term_callback, library_name=library.name, @@ -163,34 +159,31 @@ def from_input_values( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmItemGroupVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmItemGroupVO, odm_object_exists_callback: Callable = lambda _: True, find_term_callback: Callable[[str], CTTermAttributesAR | None] = lambda _: None, ) -> None: """ Creates a new draft version for the object. """ - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, find_term_callback=find_term_callback, odm_uid=self.uid, ) - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/method.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/method.py similarity index 73% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/method.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/method.py index a90c3078..35aeac00 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/method.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/method.py @@ -1,13 +1,12 @@ from dataclasses import dataclass from typing import Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmFormalExpressionModel, OdmTranslatedTextModel, @@ -16,7 +15,8 @@ @dataclass(frozen=True) -class OdmMethodVO(ConceptVO): +class OdmMethodVO: + name: str oid: str | None method_type: str | None formal_expressions: list[OdmFormalExpressionModel] @@ -40,10 +40,6 @@ def from_repository_values( formal_expressions=formal_expressions, translated_texts=translated_texts, aliases=aliases, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( @@ -63,31 +59,31 @@ def validate( @dataclass class OdmMethodAR(OdmARBase): - _concept_vo: OdmMethodVO + _odm_vo: OdmMethodVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmMethodVO: - return self._concept_vo + def odm_vo(self) -> OdmMethodVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmMethodVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmMethodVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmMethodVO, + odm_vo: OdmMethodVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -96,7 +92,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmMethodVO, + odm_vo: OdmMethodVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_object_exists_callback: Callable = lambda _: True, @@ -105,31 +101,28 @@ def from_input_values( author_id=author_id ) - concept_vo.validate(odm_object_exists_callback=odm_object_exists_callback) + odm_vo.validate(odm_object_exists_callback=odm_object_exists_callback) return cls( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmMethodVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmMethodVO, odm_object_exists_callback: Callable = lambda _: True, ) -> None: """ Creates a new draft version for the object. """ - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, odm_uid=self.uid ) super()._edit_draft(change_description=change_description, author_id=author_id) - self._concept_vo = concept_vo + self._odm_vo = odm_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/study_event.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/study_event.py similarity index 75% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/study_event.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/study_event.py index 2e8b7656..9f7bd482 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/study_event.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/study_event.py @@ -2,8 +2,7 @@ from datetime import date from typing import Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, @@ -12,7 +11,8 @@ @dataclass(frozen=True) -class OdmStudyEventVO(ConceptVO): +class OdmStudyEventVO: + name: str | None oid: str | None effective_date: date | None retired_date: date | None @@ -39,10 +39,6 @@ def from_repository_values( description=description, display_in_tree=display_in_tree, form_uids=form_uids, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( @@ -71,31 +67,31 @@ def validate( @dataclass class OdmStudyEventAR(OdmARBase): - _concept_vo: OdmStudyEventVO + _odm_vo: OdmStudyEventVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmStudyEventVO: - return self._concept_vo + def odm_vo(self) -> OdmStudyEventVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmStudyEventVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmStudyEventVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmStudyEventVO, + odm_vo: OdmStudyEventVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -104,7 +100,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmStudyEventVO, + odm_vo: OdmStudyEventVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_object_exists_callback: Callable = lambda _: True, @@ -113,34 +109,31 @@ def from_input_values( author_id=author_id ) - concept_vo.validate(odm_object_exists_callback=odm_object_exists_callback) + odm_vo.validate(odm_object_exists_callback=odm_object_exists_callback) return cls( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmStudyEventVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmStudyEventVO, odm_object_exists_callback: Callable = lambda _: True, ) -> None: """ Creates a new draft version for the object. """ - concept_vo.validate( + odm_vo.validate( odm_object_exists_callback=odm_object_exists_callback, odm_uid=self.uid ) - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/utils.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/utils.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/utils.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/utils.py diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_attribute.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_attribute.py similarity index 76% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_attribute.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_attribute.py index 80c334a4..0a45271d 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_attribute.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_attribute.py @@ -1,19 +1,21 @@ from dataclasses import dataclass -from typing import Callable, Self +from typing import TYPE_CHECKING, Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase -from clinical_mdr_api.domains.concepts.odms.vendor_element import OdmVendorElementAR -from clinical_mdr_api.domains.concepts.odms.vendor_namespace import OdmVendorNamespaceAR +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) from common.exceptions import AlreadyExistsException, BusinessLogicException +if TYPE_CHECKING: + from clinical_mdr_api.domains.odms.vendor_element import OdmVendorElementAR + from clinical_mdr_api.domains.odms.vendor_namespace import OdmVendorNamespaceAR + @dataclass(frozen=True) -class OdmVendorAttributeVO(ConceptVO): +class OdmVendorAttributeVO: + name: str compatible_types: list[str] data_type: str | None value_regex: str | None @@ -37,18 +39,14 @@ def from_repository_values( value_regex=value_regex, vendor_namespace_uid=vendor_namespace_uid, vendor_element_uid=vendor_element_uid, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( self, find_odm_vendor_namespace_callback: Callable[ - [str], OdmVendorNamespaceAR | None + [str], "OdmVendorNamespaceAR | None" ], - find_odm_vendor_element_callback: Callable[[str], OdmVendorElementAR | None], + find_odm_vendor_element_callback: Callable[[str], "OdmVendorElementAR | None"], find_odm_vendor_attribute_callback: Callable[ ..., tuple[list["OdmVendorAttributeAR"], int] ], @@ -61,8 +59,8 @@ def validate( BusinessLogicException.raise_if_not( find_odm_vendor_namespace_callback(self.vendor_namespace_uid), - msg="ODM Vendor Attribute tried to connect to non-existent concepts " - f"[('Concept Name: ODM Vendor Namespace', 'uids: ({self.vendor_namespace_uid})')].", + msg="ODM Vendor Attribute tried to connect to non-existent ODMs " + f"[('ODM Name: ODM Vendor Namespace', 'uids: ({self.vendor_namespace_uid})')].", ) if self.vendor_element_uid is not None: @@ -73,8 +71,8 @@ def validate( BusinessLogicException.raise_if_not( find_odm_vendor_element_callback(self.vendor_element_uid), - msg="ODM Vendor Attribute tried to connect to non-existent concepts " - f"[('Concept Name: ODM Vendor Element', 'uids: ({self.vendor_element_uid})')].", + msg="ODM Vendor Attribute tried to connect to non-existent ODMs " + f"[('ODM Name: ODM Vendor Element', 'uids: ({self.vendor_element_uid})')].", ) odm_vendor_attributes, _ = find_odm_vendor_attribute_callback( @@ -84,12 +82,12 @@ def validate( AlreadyExistsException.raise_if( ( self.vendor_namespace_uid is not None - and odm_vendor_attribute.concept_vo.vendor_namespace_uid + and odm_vendor_attribute.odm_vo.vendor_namespace_uid == self.vendor_namespace_uid ) or ( self.vendor_element_uid is not None - and odm_vendor_attribute.concept_vo.vendor_element_uid + and odm_vendor_attribute.odm_vo.vendor_element_uid == self.vendor_element_uid ), "ODM Vendor Attribute", @@ -100,31 +98,31 @@ def validate( @dataclass class OdmVendorAttributeAR(OdmARBase): - _concept_vo: OdmVendorAttributeVO + _odm_vo: OdmVendorAttributeVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmVendorAttributeVO: - return self._concept_vo + def odm_vo(self) -> OdmVendorAttributeVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmVendorAttributeVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmVendorAttributeVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmVendorAttributeVO, + odm_vo: OdmVendorAttributeVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -133,14 +131,14 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmVendorAttributeVO, + odm_vo: OdmVendorAttributeVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", find_odm_vendor_namespace_callback: Callable[ - [str], OdmVendorNamespaceAR | None + [str], "OdmVendorNamespaceAR | None" ] = lambda _: None, find_odm_vendor_element_callback: Callable[ - [str], OdmVendorElementAR | None + [str], "OdmVendorElementAR | None" ] = lambda _: None, find_odm_vendor_attribute_callback: Callable[ ..., tuple[list["OdmVendorAttributeAR"], int] @@ -150,7 +148,7 @@ def from_input_values( author_id=author_id ) - concept_vo.validate( + odm_vo.validate( find_odm_vendor_namespace_callback=find_odm_vendor_namespace_callback, find_odm_vendor_element_callback=find_odm_vendor_element_callback, find_odm_vendor_attribute_callback=find_odm_vendor_attribute_callback, @@ -160,27 +158,24 @@ def from_input_values( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmVendorAttributeVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmVendorAttributeVO, ) -> None: """ Creates a new draft version for the object. """ - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_element.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_element.py similarity index 67% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_element.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_element.py index 412aee82..67d51964 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_element.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_element.py @@ -1,8 +1,7 @@ from dataclasses import dataclass from typing import Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, @@ -11,7 +10,8 @@ @dataclass(frozen=True) -class OdmVendorElementVO(ConceptVO): +class OdmVendorElementVO: + name: str compatible_types: list[str] vendor_namespace_uid: str vendor_attribute_uids: list[str] @@ -29,10 +29,32 @@ def from_repository_values( compatible_types=compatible_types, vendor_namespace_uid=vendor_namespace_uid, vendor_attribute_uids=vendor_attribute_uids, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, + ) + + def check_odms_exist( + self, + odm_data_list: list[tuple[list[str], str, Callable[[str, str, bool], bool]]], + object_name: str = "Object", + ): + errors = [] + + for values, odm_name, callback in odm_data_list: + non_existent_values = set() + for value in values: + if not callback("uid", value, True): + non_existent_values.add(value) + + if non_existent_values: + errors.append( + ( + f"ODM Name: {odm_name}", + f"uids: {non_existent_values}", + ) + ) + + BusinessLogicException.raise_if( + errors, + msg=f"{object_name} tried to connect to non-existent ODMs {errors}.", ) def validate( @@ -42,23 +64,14 @@ def validate( ..., tuple[list["OdmVendorElementAR"], int] ], ) -> None: - if self.vendor_namespace_uid is not None: - self.check_concepts_exist( - [ - ( - [self.vendor_namespace_uid], - "ODM Vendor Namespace", - odm_vendor_namespace_exists_by_callback, - ) - ], - "ODM Vendor Element", + if ( + self.vendor_namespace_uid is not None + and not odm_vendor_namespace_exists_by_callback( + "uid", self.vendor_namespace_uid, True ) - - BusinessLogicException.raise_if_not( - self.vendor_namespace_uid - and find_odm_vendor_element_callback(self.vendor_namespace_uid), - msg="ODM Vendor Element tried to connect to non-existent concepts " - f"[('Concept Name: ODM Vendor Namespace', 'uids: ({self.vendor_namespace_uid})')].", + ): + raise BusinessLogicException( + msg=f"ODM Vendor Element tried to connect to non-existent ODM Vendor Namespace with UID '{self.vendor_namespace_uid}'." ) odm_vendor_element, _ = find_odm_vendor_element_callback( @@ -75,31 +88,31 @@ def validate( @dataclass class OdmVendorElementAR(OdmARBase): - _concept_vo: OdmVendorElementVO + _odm_vo: OdmVendorElementVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmVendorElementVO: - return self._concept_vo + def odm_vo(self) -> OdmVendorElementVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmVendorElementVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmVendorElementVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmVendorElementVO, + odm_vo: OdmVendorElementVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -108,7 +121,7 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmVendorElementVO, + odm_vo: OdmVendorElementVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", odm_vendor_namespace_exists_by_callback: Callable[ @@ -122,7 +135,7 @@ def from_input_values( author_id=author_id ) - concept_vo.validate( + odm_vo.validate( odm_vendor_namespace_exists_by_callback=odm_vendor_namespace_exists_by_callback, find_odm_vendor_element_callback=find_odm_vendor_element_callback, ) @@ -131,27 +144,24 @@ def from_input_values( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmVendorElementVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmVendorElementVO, ) -> None: """ Creates a new draft version for the object. """ - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo @dataclass(frozen=True) diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_namespace.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_namespace.py similarity index 53% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_namespace.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_namespace.py index a82ce73c..7f36af81 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/vendor_namespace.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/odms/vendor_namespace.py @@ -1,16 +1,16 @@ from dataclasses import dataclass from typing import Callable, Self -from clinical_mdr_api.domains.concepts.concept_base import ConceptVO -from clinical_mdr_api.domains.concepts.odms.odm_ar_base import OdmARBase +from clinical_mdr_api.domains.odms.ar_base import OdmARBase from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemMetadataVO, LibraryVO, ) +from common.exceptions import AlreadyExistsException @dataclass(frozen=True) -class OdmVendorNamespaceVO(ConceptVO): +class OdmVendorNamespaceVO: name: str prefix: str url: str @@ -32,57 +32,56 @@ def from_repository_values( url=url, vendor_element_uids=vendor_element_uids, vendor_attribute_uids=vendor_attribute_uids, - name_sentence_case=None, - definition=None, - abbreviation=None, - is_template_parameter=False, ) def validate( self, - concept_exists_by_callback: Callable[[str, str, bool], bool], + odm_exists_by_callback: Callable[[str, str], bool], previous_name: str | None = None, previous_prefix: str | None = None, previous_url: str | None = None, ) -> None: - self.duplication_check( - [ - ("name", self.name, previous_name), - ("prefix", self.prefix, previous_prefix), - ("url", self.url, previous_url), - ], - concept_exists_by_callback, - "ODM Vendor Namespace", - ) + for property_name, property_value, previous_value in [ + ("name", self.name, previous_name), + ("prefix", self.prefix, previous_prefix), + ("url", self.url, previous_url), + ]: + if property_value and property_value != previous_value: + AlreadyExistsException.raise_if( + odm_exists_by_callback(property_name, property_value), + "ODM Vendor Namespace", + property_value, + property_name.capitalize(), + ) @dataclass class OdmVendorNamespaceAR(OdmARBase): - _concept_vo: OdmVendorNamespaceVO + _odm_vo: OdmVendorNamespaceVO @property def name(self) -> str: - return self._concept_vo.name + return self._odm_vo.name @property - def concept_vo(self) -> OdmVendorNamespaceVO: - return self._concept_vo + def odm_vo(self) -> OdmVendorNamespaceVO: + return self._odm_vo - @concept_vo.setter - def concept_vo(self, value: OdmVendorNamespaceVO) -> None: - self._concept_vo = value + @odm_vo.setter + def odm_vo(self, value: OdmVendorNamespaceVO) -> None: + self._odm_vo = value @classmethod def from_repository_values( cls, uid: str, - concept_vo: OdmVendorNamespaceVO, + odm_vo: OdmVendorNamespaceVO, library: LibraryVO, item_metadata: LibraryItemMetadataVO, ) -> Self: return cls( _uid=uid, - _concept_vo=concept_vo, + _odm_vo=odm_vo, _library=library, _item_metadata=item_metadata, ) @@ -91,49 +90,45 @@ def from_repository_values( def from_input_values( cls, author_id: str, - concept_vo: OdmVendorNamespaceVO, + odm_vo: OdmVendorNamespaceVO, library: LibraryVO, generate_uid_callback: Callable[[], str] = lambda: "", - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_exists_by_callback: Callable[[str, str], bool] = lambda x, y: True, ) -> Self: item_metadata = LibraryItemMetadataVO.get_initial_item_metadata( author_id=author_id ) - concept_vo.validate( - concept_exists_by_callback=concept_exists_by_callback, + odm_vo.validate( + odm_exists_by_callback=odm_exists_by_callback, ) return cls( _uid=generate_uid_callback(), _item_metadata=item_metadata, _library=library, - _concept_vo=concept_vo, + _odm_vo=odm_vo, ) def edit_draft( self, author_id: str, change_description: str, - concept_vo: OdmVendorNamespaceVO, - concept_exists_by_callback: Callable[ - [str, str, bool], bool - ] = lambda x, y, z: True, + odm_vo: OdmVendorNamespaceVO, + odm_exists_by_callback: Callable[[str, str], bool] = lambda x, y: True, ) -> None: """ Creates a new draft version for the object. """ - concept_vo.validate( - concept_exists_by_callback=concept_exists_by_callback, - previous_name=self.concept_vo.name, - previous_prefix=self.concept_vo.prefix, - previous_url=self.concept_vo.url, + odm_vo.validate( + odm_exists_by_callback=odm_exists_by_callback, + previous_name=self.odm_vo.name, + previous_prefix=self.odm_vo.prefix, + previous_url=self.odm_vo.url, ) - if self._concept_vo != concept_vo: + if self._odm_vo != odm_vo: super()._edit_draft( change_description=change_description, author_id=author_id ) - self._concept_vo = concept_vo + self._odm_vo = odm_vo diff --git a/clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/odm_xml_definition.py b/clinical-mdr-api/clinical_mdr_api/domains/odms/xml_definition.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/domains/concepts/odms/odm_xml_definition.py rename to clinical-mdr-api/clinical_mdr_api/domains/odms/xml_definition.py diff --git a/clinical-mdr-api/clinical_mdr_api/domains/standard_data_models/sponsor_model_dataset_variable.py b/clinical-mdr-api/clinical_mdr_api/domains/standard_data_models/sponsor_model_dataset_variable.py index 8bd3dcf3..c420c76c 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/standard_data_models/sponsor_model_dataset_variable.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/standard_data_models/sponsor_model_dataset_variable.py @@ -20,7 +20,7 @@ class SponsorModelDatasetVariableVO: dataset_uid: str | None variable_uid: str | None - sponsor_model_name: str | None + sponsor_model_name: str sponsor_model_version_number: str is_basic_std: bool diff --git a/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/root.py b/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/root.py index a248fe01..3fd5fa14 100644 --- a/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/root.py +++ b/clinical-mdr-api/clinical_mdr_api/domains/study_definition_aggregates/root.py @@ -358,6 +358,9 @@ def edit_metadata( study_number_exists_callback: Callable[[str, str | None], bool] = ( lambda x, y: False ), + study_acronym_exists_callback: Callable[[str, str | None], bool] = ( + lambda x, y: False + ), project_exists_callback: Callable[[str], bool] = lambda _: True, study_type_exists_callback: Callable[[str], bool] = lambda _: True, trial_intent_type_exists_callback: Callable[[str], bool] = lambda _: True, @@ -518,10 +521,12 @@ def edit_metadata( uid=self.uid, project_exists_callback=project_exists_callback, study_number_exists_callback=study_number_exists_callback, + study_acronym_exists_callback=study_acronym_exists_callback, is_subpart=is_subpart, previous_is_subpart=previous_is_subpart, updatable_subpart=updatable_subpart, previous_project_number=self.current_metadata.id_metadata.project_number, + previous_study_acronym=self.current_metadata.id_metadata.study_acronym, ) self._draft_metadata = StudyMetadataVO( id_metadata=new_id_metadata, @@ -1046,6 +1051,9 @@ def from_initial_values( study_number_exists_callback: Callable[[str, str | None], bool] = ( lambda x, y: False ), + study_acronym_exists_callback: Callable[[str, str | None], bool] = ( + lambda x, y: False + ), initial_high_level_study_design: HighLevelStudyDesignVO = _DEF_INITIAL_HIGH_LEVEL_STUDY_DESIGN, initial_study_population: StudyPopulationVO = _DEF_INITIAL_STUDY_POPULATION, initial_study_intervention: StudyInterventionVO = _DEF_INITIAL_STUDY_INTERVENTION, @@ -1215,6 +1223,7 @@ def from_initial_values( trial_intent_type_exists_callback=trial_intent_type_exists_callback, project_exists_callback=project_exists_callback, study_number_exists_callback=study_number_exists_callback, + study_acronym_exists_callback=study_acronym_exists_callback, null_value_exists_callback=null_value_exists_callback, diagnosis_group_exists_callback=diagnosis_group_exists_callback, disease_condition_or_indication_exists_callback=disease_condition_or_indication_exists_callback, 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 ba2703fa..ac233ffb 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 @@ -136,11 +136,15 @@ def validate( study_number_exists_callback: Callable[[str, str | None], bool] = ( lambda x, y: False ), + study_acronym_exists_callback: Callable[[str, str | None], bool] = ( + lambda x, y: False + ), null_value_exists_callback: Callable[[str], bool] = lambda _: True, is_subpart: bool = False, previous_is_subpart: bool = False, updatable_subpart: bool = False, previous_project_number: str | None = None, + previous_study_acronym: str | None = None, uid: str | None = None, ) -> None: """ @@ -201,6 +205,18 @@ def validate( "Study Number", ) + if ( + not is_subpart + and self.study_acronym is not None + and previous_study_acronym != self.study_acronym + and study_acronym_exists_callback(self.study_acronym, uid) + ): + raise exceptions.AlreadyExistsException( + "Study", + self.study_acronym, + "Study Acronym", + ) + def is_valid( self, project_exists_callback: Callable[[str], bool] = lambda _: True, @@ -1555,6 +1571,9 @@ def validate( study_number_exists_callback: Callable[[str, str | None], bool] = ( lambda x, y: False ), + study_acronym_exists_callback: Callable[[str, str | None], bool] = ( + lambda x, y: False + ), study_type_exists_callback: Callable[[str], bool] = lambda _: True, trial_intent_type_exists_callback: Callable[[str], bool] = lambda _: True, trial_type_exists_callback: Callable[[str], bool] = lambda _: True, @@ -1587,6 +1606,7 @@ def validate( self.id_metadata.validate( project_exists_callback=project_exists_callback, study_number_exists_callback=study_number_exists_callback, + study_acronym_exists_callback=study_acronym_exists_callback, is_subpart=is_subpart, ) self.ver_metadata.validate() 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 373f3a6b..b11df641 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 @@ -253,7 +253,11 @@ def get_unified_duration(self): def study_day_number(self): if self.study_day: return self.study_day.value - if self.visit_class == VisitClass.SPECIAL_VISIT and self.anchor_visit: + if ( + self.visit_class == VisitClass.SPECIAL_VISIT + and self.anchor_visit + and self.anchor_visit is not self + ): return self.anchor_visit.study_day_number return None @@ -261,7 +265,11 @@ def study_day_number(self): def study_week_number(self): if self.study_week: return self.study_week.value - if self.visit_class == VisitClass.SPECIAL_VISIT and self.anchor_visit: + if ( + self.visit_class == VisitClass.SPECIAL_VISIT + and self.anchor_visit + and self.anchor_visit is not self + ): return self.anchor_visit.study_week_number return None @@ -358,18 +366,25 @@ def possible_actions(self): return ["edit", "delete", "lock"] return None - def get_absolute_duration(self) -> int | None: + def get_absolute_duration(self, _seen: set[str] | None = None) -> int | None: # Special visit doesn't have a timing but we want to place it # after the anchor visit for the special visit hence we derive timing based on the anchor visit + if _seen is None: + _seen = set() + if self.uid in _seen: + raise exceptions.BusinessLogicException( + msg=f"Circular anchor visit reference detected at visit '{self.uid}' while resolving absolute duration." + ) + _seen.add(self.uid) # type: ignore[arg-type] if self.visit_class == VisitClass.SPECIAL_VISIT and self.anchor_visit: - return self.anchor_visit.get_absolute_duration() + return self.anchor_visit.get_absolute_duration(_seen=_seen) if self.timepoint: if self.timepoint.visit_value == 0: return 0 if self.anchor_visit is not None: return ( self.get_unified_duration() - + self.anchor_visit.get_absolute_duration() + + self.anchor_visit.get_absolute_duration(_seen=_seen) ) return self.get_unified_duration() return None diff --git a/clinical-mdr-api/clinical_mdr_api/listings/query_service.py b/clinical-mdr-api/clinical_mdr_api/listings/query_service.py index 016c30c7..dcd93916 100644 --- a/clinical-mdr-api/clinical_mdr_api/listings/query_service.py +++ b/clinical-mdr-api/clinical_mdr_api/listings/query_service.py @@ -428,9 +428,7 @@ def get_tv( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ // Query to retrieve TV data from the Study Visit table // We are looking for the latest visit name, study day, and study week values associated with a specific study value version or all (latest) study versions. // The query filters by domain (TV), selecting the 'StudID', 'VisitNum', 'StudyDayValue' (or 'StudyWeekValue'), 'ArmCD', 'Arm', and any other fields we want to include. @@ -459,7 +457,6 @@ def get_tv( toUpper(v.end_rule) AS TVENRL ORDER BY v.unique_visit_number; """ - ) result_array = db.cypher_query( query=query, params={ @@ -479,9 +476,7 @@ def get_mdvisit( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ MATCH (sv)-[:HAS_STUDY_VISIT]->(v:StudyVisit) OPTIONAL MATCH (v)-->(nr:VisitNameRoot)-[:LATEST]->(nv:VisitNameValue) OPTIONAL MATCH (v)-->(dr:StudyDayRoot)-[:LATEST]->(dv:StudyDayValue) @@ -508,7 +503,6 @@ def get_mdvisit( vtnv.name as VISIT_TYPE_NAME ORDER BY VISIT_NUM; """ - ) result_array = db.cypher_query( query=query, params={ @@ -528,9 +522,7 @@ def get_mdflow( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ MATCH (sv)--(sact_schedule:StudyActivitySchedule) MATCH (sact_schedule)--(v:StudyVisit)--(sv) OPTIONAL MATCH (v)-[:HAS_VISIT_TYPE]-(:CTTermRoot)-[:HAS_NAME_ROOT]-(:CTTermNameRoot)-[:LATEST_FINAL]-(ctterm_name_value_visit_type:CTTermNameValue) @@ -596,7 +588,6 @@ def get_mdflow( ASSMTYPE ORDER BY STUDYID_FLOWCHART, AVISITN, PARAMN; """ - ) result_array = db.cypher_query( query=query, params={ @@ -618,9 +609,7 @@ def get_mdendpnt( query = ( "MATCH (s_r:StudyRoot {uid: $study_uid})-[:LATEST]->(s_v:StudyValue)" ) - query = ( - query - + """ + query = query + """ MATCH (s_v)-[:HAS_STUDY_OBJECTIVE]-(s_obj:StudyObjective) // fetch objective data OPTIONAL MATCH (s_obj)-[:HAS_OBJECTIVE_LEVEL]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(:CTTermRoot)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(obj_lev:CTTermNameValue) @@ -684,7 +673,6 @@ def get_mdendpnt( activity_instance_tem_par_root_uid_collected AS RACTINST ORDER BY STUDYID_OBJ, OBJTV, ENDPNT, TMFRM """ - ) result_array = db.cypher_query( query=query, params={ @@ -704,9 +692,7 @@ def get_ta( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ MATCH (sv)-[:HAS_STUDY_ELEMENT]->(se:StudyElement) CALL { @@ -767,7 +753,6 @@ def get_ta( """ - ) result_array = db.cypher_query( query=query, params={ @@ -787,9 +772,7 @@ def get_ti( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ MATCH (sv)-->(sc:StudyCriteria) MATCH (sc)-->(cv:CriteriaValue)<-[:LATEST]-(cr:CriteriaRoot)<--(ctr:CriteriaTemplateRoot)-[:HAS_TYPE]->(ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(tr:CTTermRoot)-->(atr:CTTermAttributesRoot)-[:LATEST]->(atv:CTTermAttributesValue) WHERE atv.concept_id = 'C25532' or atv.concept_id = 'C25370' @@ -804,7 +787,6 @@ def get_ti( '' AS TIVERS ORDER BY IETESTCD; """ - ) result_array = db.cypher_query( query=query, params={ @@ -824,9 +806,7 @@ def get_ts( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + f""" + query = query + f""" WITH sr, sv CALL {{ WITH sr, sv @@ -951,13 +931,13 @@ def get_ts( WITH sr, sv MATCH (sv)-[:HAS_STUDY_OBJECTIVE]->(so:StudyObjective)-[:HAS_OBJECTIVE_LEVEL]->(ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(objlv)-->(octar:CTTermAttributesRoot)-[:LATEST_FINAL]->(octav:CTTermAttributesValue) MATCH (ctx)-[:HAS_SELECTED_CODELIST]->(clr:CTCodelistRoot)-[:HAS_TERM]-(cclt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(objlv) - OPTIONAL MATCH (clr)<-[:PAIRED_CODE_CODELIST]-(nclr:CTCodelistRoot)-[:HAS_TERM]->(nclt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(objlv) + MATCH (objlv)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)-[:LATEST_FINAL]->(objav:CTTermAttributesValue) MATCH (so)-[:HAS_SELECTED_OBJECTIVE]->(obj) RETURN sv.study_id_prefix+'-'+sv.study_number AS STUDYID, 'TS' AS DOMAIN, cclt.submission_value AS TSPARMCD, - nclt.submission_value AS TSPARM, + objav.preferred_term AS TSPARM, '' AS controlled_by, obj.name_plain AS TSVAL, '' AS TSVALNF, @@ -968,7 +948,7 @@ def get_ts( WITH sr, sv MATCH (sv)-[:HAS_STUDY_ENDPOINT]->(send)-[:HAS_ENDPOINT_LEVEL]->(ctx:CTTermContext)-[:HAS_SELECTED_TERM]->(endplv)-->(ectar:CTTermAttributesRoot)-[:LATEST_FINAL]->(ectav:CTTermAttributesValue) MATCH (ctx)-[:HAS_SELECTED_CODELIST]->(clr:CTCodelistRoot)-[:HAS_TERM]-(cclt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(endplv) - OPTIONAL MATCH (clr)<-[:PAIRED_CODE_CODELIST]-(nclr:CTCodelistRoot)-[:HAS_TERM]->(nclt:CTCodelistTerm)-[:HAS_TERM_ROOT]->(endplv) + MATCH (endplv)-[:HAS_ATTRIBUTES_ROOT]->(:CTTermAttributesRoot)-[:LATEST_FINAL]->(ebjav:CTTermAttributesValue) MATCH (send)-[:HAS_SELECTED_TIMEFRAME]->(tf:TimeframeValue) MATCH (send)-[:HAS_SELECTED_ENDPOINT]->(endp:EndpointValue) OPTIONAL MATCH (send)-[:HAS_ENDPOINT_SUB_LEVEL]->(:CTTermContext)-[:HAS_SELECTED_TERM]->(:CTTermRoot)-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[:LATEST]->(end_sublev:CTTermNameValue) @@ -994,7 +974,7 @@ def get_ts( DISTINCT sv.study_id_prefix+'-'+sv.study_number AS STUDYID, 'TS' AS DOMAIN, cclt.submission_value AS TSPARMCD, - nclt.submission_value AS TSPARM, + ebjav.preferred_term AS TSPARM, '' AS controlled_by, endp.name_plain + unit_str +' Time frame: ' + tf.name_plain + '.'AS TSVAL, '' AS TSVALNF, @@ -1146,7 +1126,6 @@ def get_ts( RETURN * ORDER BY TSPARMCD """ - ) result_array = db.cypher_query( query=query, params={ @@ -1166,9 +1145,7 @@ def get_te( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ MATCH (sv)-[:HAS_STUDY_ELEMENT]->(se:StudyElement) RETURN toUpper(sv.study_id_prefix + '-' + sv.study_number) AS STUDYID, @@ -1181,7 +1158,6 @@ def get_te( se.planned_duration AS TEDUR ORDER BY se.order """ - ) result_array = db.cypher_query( query=query, params={ @@ -1200,9 +1176,7 @@ def get_tdm( query = MATCH_SPECIFIC_STUDY_VERSION else: query = MATCH_LATEST_STUDY - query = ( - query - + """ + query = query + """ MATCH (sv)-[:HAS_STUDY_DISEASE_MILESTONE]->(sdm:StudyDiseaseMilestone) MATCH (sdm)-[:HAS_DISEASE_MILESTONE_TYPE]-(:CTTermContext)-[:HAS_SELECTED_TERM]->(tr:CTTermRoot)-[:HAS_NAME_ROOT]-(:CTTermNameRoot)-[:LATEST]-(sdm_term:CTTermNameValue) MATCH (tr)-[HAS_ATTRIBUTES_ROOT]->(CTTermAttributesRoot)-[LATEST]->(ctav:CTTermAttributesValue) @@ -1215,7 +1189,6 @@ def get_tdm( when false then 'N' END AS TMRPT """ - ) result_array = db.cypher_query( query=query, params={ diff --git a/clinical-mdr-api/clinical_mdr_api/main.py b/clinical-mdr-api/clinical_mdr_api/main.py index 9b994113..cdd81e2f 100644 --- a/clinical-mdr-api/clinical_mdr_api/main.py +++ b/clinical-mdr-api/clinical_mdr_api/main.py @@ -12,6 +12,7 @@ configure_database( settings.neo4j_dsn, + soft_cardinality_check=settings.soft_cardinality_check, max_connection_lifetime=settings.neo4j_connection_lifetime, liveness_check_timeout=settings.neo4j_liveness_check_timeout, ) @@ -248,12 +249,20 @@ async def value_error_handler(request: Request, exception: ValueError): # Include routers here app.include_router(routers.system_router, tags=["System"]) +app.include_router( + routers.preferences_router, prefix="/user-preferences", tags=["User Preferences"] +) app.include_router( routers.feature_flags_router, prefix="/feature-flags", tags=["Feature Flags"], ) +app.include_router( + routers.data_completeness_tags_router, + prefix="/data-completeness-tags", + tags=["Data Completeness Tags"], +) app.include_router( routers.notifications_router, prefix="/notifications", @@ -262,48 +271,44 @@ async def value_error_handler(request: Request, exception: ValueError): app.include_router(routers.iso_router, prefix="/iso", tags=["ISO Standards"]) app.include_router( routers.odm_study_events_router, - prefix="/concepts/odms/study-events", + prefix="/odms/study-events", tags=["ODM Study Events"], ) -app.include_router( - routers.odm_forms_router, prefix="/concepts/odms/forms", tags=["ODM Forms"] -) +app.include_router(routers.odm_forms_router, prefix="/odms/forms", tags=["ODM Forms"]) app.include_router( routers.odm_item_groups_router, - prefix="/concepts/odms/item-groups", + prefix="/odms/item-groups", tags=["ODM Item Groups"], ) -app.include_router( - routers.odm_item_router, prefix="/concepts/odms/items", tags=["ODM Items"] -) +app.include_router(routers.odm_item_router, prefix="/odms/items", tags=["ODM Items"]) app.include_router( routers.odm_conditions_router, - prefix="/concepts/odms/conditions", + prefix="/odms/conditions", tags=["ODM Conditions"], ) app.include_router( routers.odm_methods_router, - prefix="/concepts/odms/methods", + prefix="/odms/methods", tags=["ODM Methods"], ) app.include_router( routers.odm_vendor_namespace_router, - prefix="/concepts/odms/vendor-namespaces", + prefix="/odms/vendor-namespaces", tags=["ODM Vendor Namespaces"], ) app.include_router( routers.odm_vendor_attribute_router, - prefix="/concepts/odms/vendor-attributes", + prefix="/odms/vendor-attributes", tags=["ODM Vendor Attributes"], ) app.include_router( routers.odm_vendor_element_router, - prefix="/concepts/odms/vendor-elements", + prefix="/odms/vendor-elements", tags=["ODM Vendor Elements"], ) app.include_router( routers.odm_metadata_router, - prefix="/concepts/odms/metadata", + prefix="/odms/metadata", tags=["ODM Metadata"], ) app.include_router( 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 dc83b470..2ec29e55 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 @@ -9,7 +9,10 @@ from clinical_mdr_api.domains.concepts.activities.activity_instance import ( ActivityInstanceAR, ) -from clinical_mdr_api.domains.concepts.activities.activity_item import CTTermItem +from clinical_mdr_api.domains.concepts.activities.activity_item import ( + CTCodelistItem, + CTTermItem, +) from clinical_mdr_api.domains.concepts.activities.activity_sub_group import ( ActivitySubGroupAR, ) @@ -30,6 +33,7 @@ ActivityItem, ActivityItemCreateInput, CompactActivityItemClassForActivityItem, + CompactCodelist, CompactCTTerm, CompactUnitDefinition, ) @@ -147,12 +151,21 @@ def from_activity_ar( ) ct_terms.sort(key=lambda x: x.uid or "") + if activity_item.ct_codelist is not None: + ct_codelist = CompactCodelist( + uid=activity_item.ct_codelist.uid, + name=activity_item.ct_codelist.name, + ) + else: + ct_codelist = None + activity_items.append( ActivityItem( activity_item_class=CompactActivityItemClassForActivityItem( uid=activity_item.activity_item_class_uid, name=activity_item.activity_item_class_name, ), + ct_codelist=ct_codelist, ct_terms=ct_terms, unit_definitions=unit_definitions, is_adam_param_specific=activity_item.is_adam_param_specific, @@ -450,6 +463,7 @@ class SimpleActivityItemClassForActivityInstance(BaseModel): class SimplifiedActivityItem(BaseModel): model_config = ConfigDict(from_attributes=True) + ct_codelist: Annotated[CTCodelistItem | None, Field()] = None ct_terms: list[CTTermItem] = Field(default_factory=list) unit_definitions: list[CompactUnitDefinition] = Field(default_factory=list) activity_item_class: Annotated[SimpleActivityItemClassForActivityInstance, Field()] @@ -505,8 +519,17 @@ def from_repository_input(cls, overview: dict[str, Any]): aic_name = aic.get("name", "") aic_order = aic.get("order", 0) + if ct_codelist := activity_item.get("ct_codelist"): + ct_codelist = CTCodelistItem( + uid=ct_codelist.get("uid"), + name=ct_codelist.get("name"), + ) + else: + ct_codelist = None + activity_items.append( SimplifiedActivityItem( + ct_codelist=ct_codelist, ct_terms=terms, unit_definitions=units, activity_item_class=SimpleActivityItemClassForActivityInstance( 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 4498686f..3c6a1ced 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 @@ -1,6 +1,6 @@ from typing import Annotated -from pydantic import ConfigDict, Field +from pydantic import ConfigDict, Field, model_validator from clinical_mdr_api.models.utils import BaseModel, PostInputModel @@ -63,6 +63,27 @@ class CompactCTTerm(BaseModel): ] = None +class CompactCodelist(BaseModel): + model_config = ConfigDict(from_attributes=True) + + uid: Annotated[ + str | None, + Field( + json_schema_extra={ + "nullable": True, + } + ), + ] = None + name: Annotated[ + str | None, + Field( + json_schema_extra={ + "nullable": True, + }, + ), + ] = None + + class CompactUnitDefinition(BaseModel): model_config = ConfigDict(from_attributes=True) @@ -96,6 +117,7 @@ class ActivityItem(BaseModel): model_config = ConfigDict(from_attributes=True) activity_item_class: Annotated[CompactActivityItemClassForActivityItem, Field()] + ct_codelist: Annotated[CompactCodelist | None, Field()] = None ct_terms: list[CompactCTTerm] = Field(default_factory=list) unit_definitions: list[CompactUnitDefinition] = Field(default_factory=list) is_adam_param_specific: Annotated[bool, Field()] @@ -108,7 +130,16 @@ class CTTermsInput(PostInputModel): codelist_uid: Annotated[str, Field(min_length=1)] activity_item_class_uid: Annotated[str, Field(min_length=1)] + ct_codelist_uid: Annotated[str | None, Field()] = None ct_terms: Annotated[list[CTTermsInput], Field()] unit_definition_uids: Annotated[list[str], Field()] is_adam_param_specific: Annotated[bool, Field()] text_value: Annotated[str | None, Field()] = None + + @model_validator(mode="after") + def validate_codelist_and_terms(self): + if self.ct_terms and self.ct_codelist_uid: + raise ValueError( + "Both ct_terms and ct_codelist cannot be provided at the same time for an ActivityItem." + ) + return self diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/pharmaceutical_product.py b/clinical-mdr-api/clinical_mdr_api/models/concepts/pharmaceutical_product.py index a715bca3..10c6882b 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/pharmaceutical_product.py +++ b/clinical-mdr-api/clinical_mdr_api/models/concepts/pharmaceutical_product.py @@ -91,6 +91,7 @@ class FormulationEditInput(PatchInputModel): class PharmaceuticalProduct(VersionProperties): uid: Annotated[str, Field()] + derived_name: Annotated[str, Field()] = "" external_id: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( None @@ -145,8 +146,69 @@ def from_pharmaceutical_product_ar( if term is not None: admin_route_terms.append(term) + formulations = sorted( + [ + Formulation( + external_id=formulation.external_id, + ingredients=sorted( + [ + Ingredient( + external_id=ingredient.external_id, + formulation_name=ingredient.formulation_name, + active_substance=SimpleActiveSubstance.from_concept_uid( + uid=ingredient.active_substance_uid, + find_by_uid=find_active_substance_by_uid, + find_dictionary_term_by_uid=find_dictionary_term_by_uid, + find_substance_term_by_uid=find_substance_term_by_uid, + ), + strength=( + SimpleNumericValueWithUnit.from_concept_uid( + uid=ingredient.strength_uid, + find_unit_by_uid=find_unit_by_uid, + find_numeric_value_by_uid=find_numeric_value_by_uid, + ) + if ingredient.strength_uid + else None + ), + half_life=( + SimpleNumericValueWithUnit.from_concept_uid( + uid=ingredient.half_life_uid, + find_unit_by_uid=find_unit_by_uid, + find_numeric_value_by_uid=find_numeric_value_by_uid, + ) + if ingredient.half_life_uid + else None + ), + lag_times=sorted( + [ + SimpleLagTime.from_concept_uid( + uid=uid, + find_unit_by_uid=find_unit_by_uid, + find_lag_time_by_uid=find_lag_time_by_uid, + find_term_by_uid=find_term_by_uid, + ) + for uid in ingredient.lag_time_uids + ], + key=lambda item: item.value, + ), + ) + for ingredient in formulation.ingredients + ], + key=lambda item: ( + item.active_substance.analyte_number + if item.active_substance.analyte_number + else item.active_substance.uid + ), + ), + ) + for formulation in pharmaceutical_product_ar.concept_vo.formulations + ], + key=lambda item: item.external_id if item.external_id else "", + ) + return cls( uid=pharmaceutical_product_ar.uid, + derived_name=cls._compute_derived_name(formulations), external_id=pharmaceutical_product_ar.concept_vo.external_id, dosage_forms=sorted( dosage_form_terms, @@ -156,65 +218,7 @@ def from_pharmaceutical_product_ar( admin_route_terms, key=lambda item: item.term_name if item.term_name else "", ), - formulations=sorted( - [ - Formulation( - external_id=formulation.external_id, - ingredients=sorted( - [ - Ingredient( - external_id=ingredient.external_id, - formulation_name=ingredient.formulation_name, - active_substance=SimpleActiveSubstance.from_concept_uid( - uid=ingredient.active_substance_uid, - find_by_uid=find_active_substance_by_uid, - find_dictionary_term_by_uid=find_dictionary_term_by_uid, - find_substance_term_by_uid=find_substance_term_by_uid, - ), - strength=( - SimpleNumericValueWithUnit.from_concept_uid( - uid=ingredient.strength_uid, - find_unit_by_uid=find_unit_by_uid, - find_numeric_value_by_uid=find_numeric_value_by_uid, - ) - if ingredient.strength_uid - else None - ), - half_life=( - SimpleNumericValueWithUnit.from_concept_uid( - uid=ingredient.half_life_uid, - find_unit_by_uid=find_unit_by_uid, - find_numeric_value_by_uid=find_numeric_value_by_uid, - ) - if ingredient.half_life_uid - else None - ), - lag_times=sorted( - [ - SimpleLagTime.from_concept_uid( - uid=uid, - find_unit_by_uid=find_unit_by_uid, - find_lag_time_by_uid=find_lag_time_by_uid, - find_term_by_uid=find_term_by_uid, - ) - for uid in ingredient.lag_time_uids - ], - key=lambda item: item.value, - ), - ) - for ingredient in formulation.ingredients - ], - key=lambda item: ( - item.active_substance.analyte_number - if item.active_substance.analyte_number - else item.active_substance.uid - ), - ), - ) - for formulation in pharmaceutical_product_ar.concept_vo.formulations - ], - key=lambda item: item.external_id if item.external_id else "", - ), + formulations=formulations, library_name=Library.from_library_vo( pharmaceutical_product_ar.library ).name, @@ -229,6 +233,35 @@ def from_pharmaceutical_product_ar( ), ) + @staticmethod + def _compute_derived_name(formulations: list["Formulation"]) -> str: + parts = [] + for formulation in formulations: + for ingredient in formulation.ingredients: + sub = ingredient.active_substance + ingredient_name = ( + ( + sub.inn + or sub.long_number + or sub.short_number + or (sub.unii.substance_unii if sub.unii else None) + or sub.analyte_number + or "?" + ) + if sub + else "?" + ) + form_name = ( + ingredient.formulation_name if ingredient.formulation_name else "" + ) + part = f"{ingredient_name.strip()} {form_name.strip()}" + if ingredient.strength: + value = ingredient.strength.value + value_str = str(int(value)) if value == int(value) else str(value) + part += f" ({value_str} {ingredient.strength.unit_label})" + parts.append(part) + return ", ".join(parts).strip() + class SimplePharmaceuticalProduct(BaseModel): @overload 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 2481004e..575adb21 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 @@ -367,6 +367,16 @@ def from_ct_term_ar(cls, ct_term_name_ar: CTTermNameAR) -> Self: ) +class CTTermUidInput(BaseModel): + """Minimal input model accepting only a CT term UID. + + Used in POST/PATCH input models to align the input shape with the + nested-object shape returned by the corresponding GET response model. + """ + + term_uid: Annotated[str, Field()] + + class TermWithCodelistMetadata(BaseModel): term_uid: Annotated[str, Field()] name: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None diff --git a/clinical-mdr-api/clinical_mdr_api/models/data_completeness_tag.py b/clinical-mdr-api/clinical_mdr_api/models/data_completeness_tag.py new file mode 100644 index 00000000..c160acad --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/models/data_completeness_tag.py @@ -0,0 +1,14 @@ +from typing import Annotated + +from pydantic import Field + +from clinical_mdr_api.models.utils import BaseModel, PostInputModel + + +class DataCompletenessTag(BaseModel): + uid: Annotated[str, Field()] + name: Annotated[str, Field()] + + +class DataCompletenessTagInput(PostInputModel): + name: Annotated[str, Field(min_length=1)] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/__init__.py b/clinical-mdr-api/clinical_mdr_api/models/odms/__init__.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/__init__.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/__init__.py diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_common_models.py b/clinical-mdr-api/clinical_mdr_api/models/odms/common_models.py similarity index 74% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_common_models.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/common_models.py index 9d94276e..e902b3ff 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_common_models.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/common_models.py @@ -1,12 +1,16 @@ +from abc import ABC +from datetime import datetime from typing import Annotated, Callable, Self, overload from pydantic import Field, StringConstraints, field_validator -from clinical_mdr_api.domains.concepts.concept_base import ConceptARBase -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import OdmVendorAttributeAR from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum -from clinical_mdr_api.models.utils import BaseModel, PostInputModel +from clinical_mdr_api.domains.odms.ar_base import OdmARBase +from clinical_mdr_api.domains.odms.vendor_attribute import OdmVendorAttributeAR +from clinical_mdr_api.models import _generic_descriptions +from clinical_mdr_api.models.utils import BaseModel, PatchInputModel, PostInputModel from clinical_mdr_api.models.validators import is_language_supported +from common.config import settings class OdmElementWithParentUid(BaseModel): @@ -67,10 +71,10 @@ def from_uid( odm_vendor_element_ref_model = cls( uid=uid, name=odm_vendor_attribute_ar.name, - data_type=odm_vendor_attribute_ar.concept_vo.data_type, - value_regex=odm_vendor_attribute_ar.concept_vo.value_regex, + data_type=odm_vendor_attribute_ar.odm_vo.data_type, + value_regex=odm_vendor_attribute_ar.odm_vo.value_regex, value=value, - vendor_namespace_uid=odm_vendor_attribute_ar.concept_vo.vendor_namespace_uid, + vendor_namespace_uid=odm_vendor_attribute_ar.odm_vo.vendor_namespace_uid, ) else: odm_vendor_element_ref_model = cls( @@ -105,20 +109,20 @@ class OdmVendorNamespaceSimpleModel(BaseModel): def from_odm_vendor_namespace_uid( cls, uid: str, - find_odm_vendor_namespace_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_namespace_by_uid: Callable[[str], OdmARBase | None], ) -> Self: ... @overload @classmethod def from_odm_vendor_namespace_uid( cls, uid: None, - find_odm_vendor_namespace_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_namespace_by_uid: Callable[[str], OdmARBase | None], ) -> None: ... @classmethod def from_odm_vendor_namespace_uid( cls, uid: str | None, - find_odm_vendor_namespace_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_namespace_by_uid: Callable[[str], OdmARBase | None], ) -> Self | None: simple_odm_vendor_namespace_model = None @@ -128,9 +132,9 @@ def from_odm_vendor_namespace_uid( if odm_vendor_namespace is not None: simple_odm_vendor_namespace_model = cls( uid=uid, - name=odm_vendor_namespace.concept_vo.name, - prefix=odm_vendor_namespace.concept_vo.prefix, - url=odm_vendor_namespace.concept_vo.url, + name=odm_vendor_namespace.odm_vo.name, + prefix=odm_vendor_namespace.odm_vo.prefix, + url=odm_vendor_namespace.odm_vo.url, status=odm_vendor_namespace.item_metadata.status.value, version=odm_vendor_namespace.item_metadata.version, possible_actions=sorted( @@ -166,20 +170,20 @@ class OdmVendorAttributeSimpleModel(BaseModel): def from_odm_vendor_attribute_uid( cls, uid: str, - find_odm_vendor_attribute_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_attribute_by_uid: Callable[[str], OdmARBase | None], ) -> Self: ... @overload @classmethod def from_odm_vendor_attribute_uid( cls, uid: None, - find_odm_vendor_attribute_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_attribute_by_uid: Callable[[str], OdmARBase | None], ) -> None: ... @classmethod def from_odm_vendor_attribute_uid( cls, uid: str | None, - find_odm_vendor_attribute_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_attribute_by_uid: Callable[[str], OdmARBase | None], ) -> Self | None: simple_odm_vendor_attribute_model = None @@ -189,9 +193,9 @@ def from_odm_vendor_attribute_uid( if odm_vendor_attribute is not None: simple_odm_vendor_attribute_model = cls( uid=uid, - name=odm_vendor_attribute.concept_vo.name, - data_type=odm_vendor_attribute.concept_vo.data_type, - compatible_types=odm_vendor_attribute.concept_vo.compatible_types, + name=odm_vendor_attribute.odm_vo.name, + data_type=odm_vendor_attribute.odm_vo.data_type, + compatible_types=odm_vendor_attribute.odm_vo.compatible_types, status=odm_vendor_attribute.item_metadata.status.value, version=odm_vendor_attribute.item_metadata.version, possible_actions=sorted( @@ -226,20 +230,20 @@ class OdmVendorElementSimpleModel(BaseModel): def from_odm_vendor_element_uid( cls, uid: str, - find_odm_vendor_element_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_element_by_uid: Callable[[str], OdmARBase | None], ) -> Self: ... @overload @classmethod def from_odm_vendor_element_uid( cls, uid: None, - find_odm_vendor_element_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_element_by_uid: Callable[[str], OdmARBase | None], ) -> None: ... @classmethod def from_odm_vendor_element_uid( cls, uid: str | None, - find_odm_vendor_element_by_uid: Callable[[str], ConceptARBase | None], + find_odm_vendor_element_by_uid: Callable[[str], OdmARBase | None], ) -> Self | None: simple_odm_vendor_element_model = None @@ -249,8 +253,8 @@ def from_odm_vendor_element_uid( if odm_vendor_element is not None: simple_odm_vendor_element_model = cls( uid=uid, - name=odm_vendor_element.concept_vo.name, - compatible_types=odm_vendor_element.concept_vo.compatible_types, + name=odm_vendor_element.odm_vo.name, + compatible_types=odm_vendor_element.odm_vo.compatible_types, status=odm_vendor_element.item_metadata.status.value, version=odm_vendor_element.item_metadata.version, possible_actions=sorted( @@ -296,3 +300,49 @@ class OdmTranslatedTextModel(BaseModel, frozen=True): # type: ignore[misc] class OdmFormalExpressionModel(BaseModel, frozen=True): # type: ignore[misc] context: Annotated[str, Field(min_length=1)] expression: Annotated[str, Field(min_length=1)] + + +# ODM-specific base models to replace Concept* classes +class OdmBaseModel(BaseModel, ABC): + """Base model for all ODM entities, providing versioning and metadata fields.""" + + uid: Annotated[str, Field()] + name: Annotated[str, Field()] + library_name: Annotated[str, Field()] + start_date: Annotated[ + datetime, + Field( + description=_generic_descriptions.START_DATE, + json_schema_extra={"source": "latest_version|start_date"}, + ), + ] + end_date: Annotated[ + datetime | None, + Field( + description=_generic_descriptions.END_DATE, + json_schema_extra={"source": "latest_version|end_date", "nullable": True}, + ), + ] = None + status: Annotated[str, Field()] + version: Annotated[str, Field()] + author_username: Annotated[ + str | None, + Field( + json_schema_extra={"nullable": True}, + ), + ] = None + change_description: Annotated[str, Field()] + + +class OdmPostInput(PostInputModel, ABC): + """Base input model for creating new ODM entities.""" + + name: Annotated[str, Field(min_length=1)] + library_name: Annotated[str, Field(min_length=1)] = settings.sponsor_library_name + + +class OdmPatchInput(PatchInputModel, ABC): + """Base input model for partially updating existing ODM entities.""" + + change_description: Annotated[str, Field(min_length=1)] + name: Annotated[str | None, Field(min_length=1)] = None diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_condition.py b/clinical-mdr-api/clinical_mdr_api/models/odms/condition.py similarity index 80% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_condition.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/condition.py index fe1f1aa5..ef12574c 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_condition.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/condition.py @@ -3,15 +3,13 @@ from pydantic import Field, field_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.condition import OdmConditionAR -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.condition import OdmConditionAR +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, + OdmBaseModel, OdmFormalExpressionModel, + OdmPatchInput, + OdmPostInput, OdmTranslatedTextModel, ) from clinical_mdr_api.models.validators import ( @@ -20,7 +18,7 @@ ) -class OdmCondition(ConceptModel): +class OdmCondition(OdmBaseModel): oid: Annotated[str | None, Field()] formal_expressions: Annotated[list[OdmFormalExpressionModel], Field()] translated_texts: Annotated[list[OdmTranslatedTextModel], Field()] @@ -31,7 +29,7 @@ class OdmCondition(ConceptModel): def from_odm_condition_ar(cls, odm_condition_ar: OdmConditionAR) -> Self: return cls( uid=odm_condition_ar._uid, - oid=odm_condition_ar.concept_vo.oid, + oid=odm_condition_ar.odm_vo.oid, name=odm_condition_ar.name, library_name=odm_condition_ar.library.name, start_date=odm_condition_ar.item_metadata.start_date, @@ -41,23 +39,21 @@ def from_odm_condition_ar(cls, odm_condition_ar: OdmConditionAR) -> Self: change_description=odm_condition_ar.item_metadata.change_description, author_username=odm_condition_ar.item_metadata.author_username, formal_expressions=sorted( - odm_condition_ar.concept_vo.formal_expressions, + odm_condition_ar.odm_vo.formal_expressions, key=lambda item: item.context, ), translated_texts=sorted( - odm_condition_ar.concept_vo.translated_texts, + odm_condition_ar.odm_vo.translated_texts, key=lambda item: (item.text_type.value, item.text), ), - aliases=sorted( - odm_condition_ar.concept_vo.aliases, key=lambda item: item.name - ), + aliases=sorted(odm_condition_ar.odm_vo.aliases, key=lambda item: item.name), possible_actions=sorted( [_.value for _ in odm_condition_ar.get_possible_actions()] ), ) -class OdmConditionPostInput(ConceptPostInput): +class OdmConditionPostInput(OdmPostInput): oid: Annotated[str | None, Field(min_length=1)] = None formal_expressions: Annotated[list[OdmFormalExpressionModel], Field()] translated_texts: Annotated[list[OdmTranslatedTextModel], Field()] @@ -71,7 +67,7 @@ class OdmConditionPostInput(ConceptPostInput): ) -class OdmConditionPatchInput(ConceptPatchInput): +class OdmConditionPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] oid: Annotated[str | None, Field(min_length=1)] formal_expressions: Annotated[list[OdmFormalExpressionModel], Field()] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_form.py b/clinical-mdr-api/clinical_mdr_api/models/odms/form.py similarity index 86% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_form.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/form.py index cce821de..16d3c8ed 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_form.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/form.py @@ -3,37 +3,31 @@ from pydantic import Field, field_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.form import OdmFormAR, OdmFormRefVO -from clinical_mdr_api.domains.concepts.odms.item_group import OdmItemGroupRefVO -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import ( +from clinical_mdr_api.domains.odms.form import OdmFormAR, OdmFormRefVO +from clinical_mdr_api.domains.odms.item_group import OdmItemGroupRefVO +from clinical_mdr_api.domains.odms.utils import RelationType +from clinical_mdr_api.domains.odms.vendor_attribute import ( OdmVendorAttributeAR, OdmVendorAttributeRelationVO, OdmVendorElementAttributeRelationVO, ) -from clinical_mdr_api.domains.concepts.odms.vendor_element import ( - OdmVendorElementRelationVO, -) -from clinical_mdr_api.domains.concepts.utils import RelationType -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.vendor_element import OdmVendorElementRelationVO +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, + OdmBaseModel, + OdmPatchInput, + OdmPostInput, OdmRefVendorPostInput, OdmTranslatedTextModel, OdmVendorElementRelationPostInput, OdmVendorRelationPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroupRefModel -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( +from clinical_mdr_api.models.odms.item_group import OdmItemGroupRefModel +from clinical_mdr_api.models.odms.vendor_attribute import ( OdmVendorAttributeRelationModel, OdmVendorElementAttributeRelationModel, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( - OdmVendorElementRelationModel, -) +from clinical_mdr_api.models.odms.vendor_element import OdmVendorElementRelationModel from clinical_mdr_api.models.utils import BaseModel, PostInputModel from clinical_mdr_api.models.validators import ( has_english_description, @@ -43,7 +37,7 @@ from common.utils import booltostr -class OdmForm(ConceptModel): +class OdmForm(OdmBaseModel): oid: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None repeating: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None sdtm_version: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( @@ -77,10 +71,10 @@ def from_odm_form_ar( ) -> Self: return cls( uid=odm_form_ar._uid, - oid=odm_form_ar.concept_vo.oid, + oid=odm_form_ar.odm_vo.oid, name=odm_form_ar.name, - sdtm_version=odm_form_ar.concept_vo.sdtm_version, - repeating=booltostr(odm_form_ar.concept_vo.repeating), + sdtm_version=odm_form_ar.odm_vo.sdtm_version, + repeating=booltostr(odm_form_ar.odm_vo.repeating), library_name=odm_form_ar.library.name, start_date=odm_form_ar.item_metadata.start_date, end_date=odm_form_ar.item_metadata.end_date, @@ -89,10 +83,10 @@ def from_odm_form_ar( change_description=odm_form_ar.item_metadata.change_description, author_username=odm_form_ar.item_metadata.author_username, translated_texts=sorted( - odm_form_ar.concept_vo.translated_texts, + odm_form_ar.odm_vo.translated_texts, key=lambda item: (item.text_type.value, item.text), ), - aliases=sorted(odm_form_ar.concept_vo.aliases, key=lambda item: item.name), + aliases=sorted(odm_form_ar.odm_vo.aliases, key=lambda item: item.name), item_groups=sorted( [ OdmItemGroupRefModel.from_odm_item_group_uid( @@ -102,7 +96,7 @@ def from_odm_form_ar( find_odm_item_group_by_uid_with_form_relation=find_odm_item_group_by_uid_with_form_relation, find_odm_vendor_attribute_by_uid=find_odm_vendor_attribute_by_uid, ) - for item_group_uid in odm_form_ar.concept_vo.item_group_uids + for item_group_uid in odm_form_ar.odm_vo.item_group_uids ], key=lambda item: item.order_number, ), @@ -115,7 +109,7 @@ def from_odm_form_ar( odm_element_type=RelationType.FORM, find_by_uid_with_odm_element_relation=find_odm_vendor_element_by_uid_with_odm_element_relation, ) - for vendor_element_uid in odm_form_ar.concept_vo.vendor_element_uids + for vendor_element_uid in odm_form_ar.odm_vo.vendor_element_uids ], key=lambda item: item.name or "", ), @@ -129,7 +123,7 @@ def from_odm_form_ar( find_by_uid_with_odm_element_relation=find_odm_vendor_attribute_by_uid_with_odm_element_relation, # type: ignore[arg-type] vendor_element_attribute=False, ) - for vendor_attribute_uid in odm_form_ar.concept_vo.vendor_attribute_uids + for vendor_attribute_uid in odm_form_ar.odm_vo.vendor_attribute_uids ], key=lambda item: item.name or "", ), @@ -142,7 +136,7 @@ def from_odm_form_ar( odm_element_type=RelationType.FORM, find_by_uid_with_odm_element_relation=find_odm_vendor_attribute_by_uid_with_odm_element_relation, # type: ignore[arg-type] ) - for vendor_element_attribute_uid in odm_form_ar.concept_vo.vendor_element_attribute_uids + for vendor_element_attribute_uid in odm_form_ar.odm_vo.vendor_element_attribute_uids ], key=lambda item: item.name or "", ), @@ -227,7 +221,7 @@ def from_odm_form_uid( ] = None -class OdmFormPostInput(ConceptPostInput): +class OdmFormPostInput(OdmPostInput): oid: Annotated[str | None, Field(min_length=1)] = None sdtm_version: Annotated[str | None, Field()] = None repeating: Annotated[str, Field(min_length=1)] @@ -249,7 +243,7 @@ class OdmFormPostInput(ConceptPostInput): ) -class OdmFormPatchInput(ConceptPatchInput): +class OdmFormPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] oid: Annotated[str | None, Field(min_length=1)] sdtm_version: Annotated[str | None, Field()] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_item.py b/clinical-mdr-api/clinical_mdr_api/models/odms/item.py similarity index 92% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_item.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/item.py index 97522eea..8e980091 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_item.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/item.py @@ -4,56 +4,50 @@ from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC from clinical_mdr_api.domains.concepts.concept_base import ConceptARBase -from clinical_mdr_api.domains.concepts.odms.item import ( +from clinical_mdr_api.domains.concepts.unit_definitions.unit_definition import ( + UnitDefinitionAR, +) +from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_attributes import ( + CTCodelistAttributesAR, +) +from clinical_mdr_api.domains.controlled_terminologies.ct_term_name import CTTermNameAR +from clinical_mdr_api.domains.dictionaries.dictionary_term import DictionaryTermAR +from clinical_mdr_api.domains.odms.item import ( OdmItemAR, OdmItemRefVO, OdmItemTermVO, OdmItemUnitDefinitionVO, ) -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import ( +from clinical_mdr_api.domains.odms.utils import RelationType +from clinical_mdr_api.domains.odms.vendor_attribute import ( OdmVendorAttributeAR, OdmVendorAttributeRelationVO, OdmVendorElementAttributeRelationVO, ) -from clinical_mdr_api.domains.concepts.odms.vendor_element import ( - OdmVendorElementRelationVO, -) -from clinical_mdr_api.domains.concepts.unit_definitions.unit_definition import ( - UnitDefinitionAR, -) -from clinical_mdr_api.domains.concepts.utils import RelationType -from clinical_mdr_api.domains.controlled_terminologies.ct_codelist_attributes import ( - CTCodelistAttributesAR, +from clinical_mdr_api.domains.odms.vendor_element import OdmVendorElementRelationVO +from clinical_mdr_api.models.controlled_terminologies.ct_codelist_attributes import ( + CTCodelistAttributesSimpleModel, ) -from clinical_mdr_api.domains.controlled_terminologies.ct_term_name import CTTermNameAR -from clinical_mdr_api.domains.dictionaries.dictionary_term import DictionaryTermAR -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, +from clinical_mdr_api.models.controlled_terminologies.ct_term import ( + SimpleDictionaryTermModel, + SimpleTermModel, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, + OdmBaseModel, + OdmPatchInput, + OdmPostInput, OdmRefVendor, OdmRefVendorAttributeModel, OdmTranslatedTextModel, OdmVendorElementRelationPostInput, OdmVendorRelationPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( +from clinical_mdr_api.models.odms.vendor_attribute import ( OdmVendorAttributeRelationModel, OdmVendorElementAttributeRelationModel, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( - OdmVendorElementRelationModel, -) -from clinical_mdr_api.models.controlled_terminologies.ct_codelist_attributes import ( - CTCodelistAttributesSimpleModel, -) -from clinical_mdr_api.models.controlled_terminologies.ct_term import ( - SimpleDictionaryTermModel, - SimpleTermModel, -) +from clinical_mdr_api.models.odms.vendor_element import OdmVendorElementRelationModel from clinical_mdr_api.models.utils import BaseModel, InputModel from clinical_mdr_api.models.validators import ( has_english_description, @@ -242,7 +236,7 @@ class OdmItemParentGroup(BaseModel): name: str | None -class OdmItem(ConceptModel): +class OdmItem(OdmBaseModel): oid: Annotated[str | None, Field()] prompt: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None datatype: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None @@ -301,16 +295,16 @@ def from_odm_item_ar( ) -> Self: return cls( uid=odm_item_ar._uid, - oid=odm_item_ar.concept_vo.oid, + oid=odm_item_ar.odm_vo.oid, name=odm_item_ar.name, - prompt=odm_item_ar.concept_vo.prompt, - datatype=odm_item_ar.concept_vo.datatype, - length=odm_item_ar.concept_vo.length, - significant_digits=odm_item_ar.concept_vo.significant_digits, - sas_field_name=odm_item_ar.concept_vo.sas_field_name, - sds_var_name=odm_item_ar.concept_vo.sds_var_name, - origin=odm_item_ar.concept_vo.origin, - comment=odm_item_ar.concept_vo.comment, + prompt=odm_item_ar.odm_vo.prompt, + datatype=odm_item_ar.odm_vo.datatype, + length=odm_item_ar.odm_vo.length, + significant_digits=odm_item_ar.odm_vo.significant_digits, + sas_field_name=odm_item_ar.odm_vo.sas_field_name, + sds_var_name=odm_item_ar.odm_vo.sds_var_name, + origin=odm_item_ar.odm_vo.origin, + comment=odm_item_ar.odm_vo.comment, library_name=odm_item_ar.library.name, start_date=odm_item_ar.item_metadata.start_date, end_date=odm_item_ar.item_metadata.end_date, @@ -320,18 +314,18 @@ def from_odm_item_ar( author_username=odm_item_ar.item_metadata.author_username, odm_item_group=( OdmItemParentGroup( - uid=odm_item_ar.concept_vo.odm_item_group.uid, - oid=odm_item_ar.concept_vo.odm_item_group.oid, - name=odm_item_ar.concept_vo.odm_item_group.name, + uid=odm_item_ar.odm_vo.odm_item_group.uid, + oid=odm_item_ar.odm_vo.odm_item_group.oid, + name=odm_item_ar.odm_vo.odm_item_group.name, ) - if odm_item_ar.concept_vo.odm_item_group + if odm_item_ar.odm_vo.odm_item_group else None ), translated_texts=sorted( - odm_item_ar.concept_vo.translated_texts, + odm_item_ar.odm_vo.translated_texts, key=lambda item: (item.text_type.value, item.text), ), - aliases=sorted(odm_item_ar.concept_vo.aliases, key=lambda item: item.name), + aliases=sorted(odm_item_ar.odm_vo.aliases, key=lambda item: item.name), unit_definitions=sorted( [ OdmItemUnitDefinitionWithRelationship.from_unit_definition_uid( @@ -342,15 +336,15 @@ def from_odm_item_ar( find_dictionary_term_by_uid=find_dictionary_term_by_uid, find_term_by_uid=find_term_by_uid, ) - for unit_definition_uid in odm_item_ar.concept_vo.unit_definition_uids + for unit_definition_uid in odm_item_ar.odm_vo.unit_definition_uids ], key=lambda item: item.uid, ), codelist=CTCodelistAttributesSimpleModel.from_codelist_uid( - uid=getattr(odm_item_ar.concept_vo.codelist, "uid", None), + uid=getattr(odm_item_ar.odm_vo.codelist, "uid", None), find_codelist_attribute_by_codelist_uid=find_codelist_attribute_by_codelist_uid, allows_multi_choice=getattr( - odm_item_ar.concept_vo.codelist, "allows_multi_choice", None + odm_item_ar.odm_vo.codelist, "allows_multi_choice", None ), ), terms=sorted( @@ -360,7 +354,7 @@ def from_odm_item_ar( term_uid=term_uid, find_term_with_item_relation_by_item_uid=find_term_with_item_relation_by_item_uid, ) - for term_uid in odm_item_ar.concept_vo.term_uids + for term_uid in odm_item_ar.odm_vo.term_uids ], key=lambda item: (item.order is not None, item.order), ), @@ -390,7 +384,7 @@ def from_odm_item_ar( value_condition=activity_instance["value_condition"], value_dependent_map=activity_instance["value_dependent_map"], ) - for activity_instance in odm_item_ar.concept_vo.activity_instances + for activity_instance in odm_item_ar.odm_vo.activity_instances ], key=lambda item: item.order, ), @@ -403,7 +397,7 @@ def from_odm_item_ar( odm_element_type=RelationType.ITEM, find_by_uid_with_odm_element_relation=find_odm_vendor_element_by_uid_with_odm_element_relation, ) - for vendor_element_uid in odm_item_ar.concept_vo.vendor_element_uids + for vendor_element_uid in odm_item_ar.odm_vo.vendor_element_uids ], key=lambda item: item.name or "", ), @@ -417,7 +411,7 @@ def from_odm_item_ar( find_by_uid_with_odm_element_relation=find_odm_vendor_attribute_by_uid_with_odm_element_relation, # type: ignore[arg-type] vendor_element_attribute=False, ) - for vendor_attribute_uid in odm_item_ar.concept_vo.vendor_attribute_uids + for vendor_attribute_uid in odm_item_ar.odm_vo.vendor_attribute_uids ], key=lambda item: item.name or "", ), @@ -430,7 +424,7 @@ def from_odm_item_ar( odm_element_type=RelationType.ITEM, find_by_uid_with_odm_element_relation=find_odm_vendor_attribute_by_uid_with_odm_element_relation, # type: ignore[arg-type] ) - for vendor_element_attribute_uid in odm_item_ar.concept_vo.vendor_element_attribute_uids + for vendor_element_attribute_uid in odm_item_ar.odm_vo.vendor_element_attribute_uids ], key=lambda item: item.name or "", ), @@ -601,7 +595,7 @@ class OdmItemCodelist(BaseModel): allows_multi_choice: Annotated[bool, Field()] = False -class OdmItemPostInput(ConceptPostInput): +class OdmItemPostInput(OdmPostInput): oid: Annotated[str | None, Field(min_length=1)] = None datatype: Annotated[str, Field(min_length=1)] prompt: Annotated[str | None, Field()] = None @@ -653,7 +647,7 @@ class ActivityInstanceRel(ActivityInstanceRelInput): activity_instance_topic_code: Annotated[str | None, Field()] -class OdmItemPatchInput(ConceptPatchInput): +class OdmItemPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] oid: Annotated[str | None, Field(min_length=1)] datatype: Annotated[str | None, Field(min_length=1)] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_item_group.py b/clinical-mdr-api/clinical_mdr_api/models/odms/item_group.py similarity index 88% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_item_group.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/item_group.py index 538c8397..85bca906 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_item_group.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/item_group.py @@ -6,27 +6,23 @@ from clinical_mdr_api.domain_repositories.controlled_terminologies.ct_codelist_name_repository import ( CTCodelistNameRepository, ) -from clinical_mdr_api.domains.concepts.odms.item import OdmItemRefVO -from clinical_mdr_api.domains.concepts.odms.item_group import ( - OdmItemGroupAR, - OdmItemGroupRefVO, -) -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import ( +from clinical_mdr_api.domains.odms.item import OdmItemRefVO +from clinical_mdr_api.domains.odms.item_group import OdmItemGroupAR, OdmItemGroupRefVO +from clinical_mdr_api.domains.odms.utils import RelationType +from clinical_mdr_api.domains.odms.vendor_attribute import ( OdmVendorAttributeAR, OdmVendorAttributeRelationVO, OdmVendorElementAttributeRelationVO, ) -from clinical_mdr_api.domains.concepts.odms.vendor_element import ( - OdmVendorElementRelationVO, -) -from clinical_mdr_api.domains.concepts.utils import RelationType -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, +from clinical_mdr_api.domains.odms.vendor_element import OdmVendorElementRelationVO +from clinical_mdr_api.models.controlled_terminologies.ct_term import ( + SimpleCodelistTermModel, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, + OdmBaseModel, + OdmPatchInput, + OdmPostInput, OdmRefVendor, OdmRefVendorAttributeModel, OdmRefVendorPostInput, @@ -34,17 +30,12 @@ OdmVendorElementRelationPostInput, OdmVendorRelationPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_item import OdmItemRefModel -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( +from clinical_mdr_api.models.odms.item import OdmItemRefModel +from clinical_mdr_api.models.odms.vendor_attribute import ( OdmVendorAttributeRelationModel, OdmVendorElementAttributeRelationModel, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( - OdmVendorElementRelationModel, -) -from clinical_mdr_api.models.controlled_terminologies.ct_term import ( - SimpleCodelistTermModel, -) +from clinical_mdr_api.models.odms.vendor_element import OdmVendorElementRelationModel from clinical_mdr_api.models.utils import BaseModel, PostInputModel from clinical_mdr_api.models.validators import ( has_english_description, @@ -55,7 +46,7 @@ from common.utils import booltostr -class OdmItemGroup(ConceptModel): +class OdmItemGroup(OdmBaseModel): oid: Annotated[str | None, Field()] repeating: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None is_reference_data: Annotated[ @@ -100,7 +91,7 @@ def from_odm_item_group_ar( ) -> Self: codelist_repo = CTCodelistNameRepository() domain_terms = [] - for sdtm_domain_uid in odm_item_group_ar.concept_vo.sdtm_domain_uids: + for sdtm_domain_uid in odm_item_group_ar.odm_vo.sdtm_domain_uids: term = SimpleCodelistTermModel.from_term_uid_and_codelist_submval( term_uid=sdtm_domain_uid, codelist_submission_value=settings.stdm_domain_cl_submval, @@ -111,14 +102,14 @@ def from_odm_item_group_ar( return cls( uid=odm_item_group_ar._uid, - oid=odm_item_group_ar.concept_vo.oid, + oid=odm_item_group_ar.odm_vo.oid, name=odm_item_group_ar.name, - repeating=booltostr(odm_item_group_ar.concept_vo.repeating), - is_reference_data=booltostr(odm_item_group_ar.concept_vo.is_reference_data), - sas_dataset_name=odm_item_group_ar.concept_vo.sas_dataset_name, - origin=odm_item_group_ar.concept_vo.origin, - purpose=odm_item_group_ar.concept_vo.purpose, - comment=odm_item_group_ar.concept_vo.comment, + repeating=booltostr(odm_item_group_ar.odm_vo.repeating), + is_reference_data=booltostr(odm_item_group_ar.odm_vo.is_reference_data), + sas_dataset_name=odm_item_group_ar.odm_vo.sas_dataset_name, + origin=odm_item_group_ar.odm_vo.origin, + purpose=odm_item_group_ar.odm_vo.purpose, + comment=odm_item_group_ar.odm_vo.comment, library_name=odm_item_group_ar.library.name, start_date=odm_item_group_ar.item_metadata.start_date, end_date=odm_item_group_ar.item_metadata.end_date, @@ -127,11 +118,11 @@ def from_odm_item_group_ar( change_description=odm_item_group_ar.item_metadata.change_description, author_username=odm_item_group_ar.item_metadata.author_username, translated_texts=sorted( - odm_item_group_ar.concept_vo.translated_texts, + odm_item_group_ar.odm_vo.translated_texts, key=lambda item: (item.text_type.value, item.text), ), aliases=sorted( - odm_item_group_ar.concept_vo.aliases, key=lambda item: item.name + odm_item_group_ar.odm_vo.aliases, key=lambda item: item.name ), sdtm_domains=sorted( domain_terms, @@ -146,7 +137,7 @@ def from_odm_item_group_ar( find_odm_item_by_uid_with_item_group_relation=find_odm_item_by_uid_with_item_group_relation, find_odm_vendor_attribute_by_uid=find_odm_vendor_attribute_by_uid, ) - for item_uid in odm_item_group_ar.concept_vo.item_uids + for item_uid in odm_item_group_ar.odm_vo.item_uids ], key=lambda item: item.order_number, ), @@ -159,7 +150,7 @@ def from_odm_item_group_ar( odm_element_type=RelationType.ITEM_GROUP, find_by_uid_with_odm_element_relation=find_odm_vendor_element_by_uid_with_odm_element_relation, ) - for vendor_element_uid in odm_item_group_ar.concept_vo.vendor_element_uids + for vendor_element_uid in odm_item_group_ar.odm_vo.vendor_element_uids ], key=lambda item: item.name or "", ), @@ -173,7 +164,7 @@ def from_odm_item_group_ar( find_by_uid_with_odm_element_relation=find_odm_vendor_attribute_by_uid_with_odm_element_relation, # type: ignore[arg-type] vendor_element_attribute=False, ) - for vendor_attribute_uid in odm_item_group_ar.concept_vo.vendor_attribute_uids + for vendor_attribute_uid in odm_item_group_ar.odm_vo.vendor_attribute_uids ], key=lambda item: item.name or "", ), @@ -186,7 +177,7 @@ def from_odm_item_group_ar( odm_element_type=RelationType.ITEM_GROUP, find_by_uid_with_odm_element_relation=find_odm_vendor_attribute_by_uid_with_odm_element_relation, # type: ignore[arg-type] ) - for vendor_element_attribute_uid in odm_item_group_ar.concept_vo.vendor_element_attribute_uids + for vendor_element_attribute_uid in odm_item_group_ar.odm_vo.vendor_element_attribute_uids ], key=lambda item: item.name or "", ), @@ -289,7 +280,7 @@ def from_odm_item_group_uid( vendor: Annotated[OdmRefVendor, Field()] -class OdmItemGroupPostInput(ConceptPostInput): +class OdmItemGroupPostInput(OdmPostInput): oid: Annotated[str | None, Field(min_length=1)] = None repeating: Annotated[str, Field(min_length=1)] is_reference_data: Annotated[str | None, Field()] = None @@ -319,7 +310,7 @@ class OdmItemGroupPostInput(ConceptPostInput): ) -class OdmItemGroupPatchInput(ConceptPatchInput): +class OdmItemGroupPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] oid: Annotated[str | None, Field(min_length=1)] repeating: Annotated[str | None, Field()] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_method.py b/clinical-mdr-api/clinical_mdr_api/models/odms/method.py similarity index 80% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_method.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/method.py index 94f46ed4..3968a031 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_method.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/method.py @@ -3,15 +3,13 @@ from pydantic import Field, field_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.method import OdmMethodAR -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.method import OdmMethodAR +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, + OdmBaseModel, OdmFormalExpressionModel, + OdmPatchInput, + OdmPostInput, OdmTranslatedTextModel, ) from clinical_mdr_api.models.validators import ( @@ -20,7 +18,7 @@ ) -class OdmMethod(ConceptModel): +class OdmMethod(OdmBaseModel): oid: Annotated[str | None, Field()] method_type: Annotated[str | None, Field()] formal_expressions: Annotated[list[OdmFormalExpressionModel], Field()] @@ -32,9 +30,9 @@ class OdmMethod(ConceptModel): def from_odm_method_ar(cls, odm_method_ar: OdmMethodAR) -> Self: return cls( uid=odm_method_ar._uid, - oid=odm_method_ar.concept_vo.oid, + oid=odm_method_ar.odm_vo.oid, name=odm_method_ar.name, - method_type=odm_method_ar.concept_vo.method_type, + method_type=odm_method_ar.odm_vo.method_type, library_name=odm_method_ar.library.name, start_date=odm_method_ar.item_metadata.start_date, end_date=odm_method_ar.item_metadata.end_date, @@ -43,23 +41,21 @@ def from_odm_method_ar(cls, odm_method_ar: OdmMethodAR) -> Self: change_description=odm_method_ar.item_metadata.change_description, author_username=odm_method_ar.item_metadata.author_username, formal_expressions=sorted( - odm_method_ar.concept_vo.formal_expressions, + odm_method_ar.odm_vo.formal_expressions, key=lambda item: item.context, ), translated_texts=sorted( - odm_method_ar.concept_vo.translated_texts, + odm_method_ar.odm_vo.translated_texts, key=lambda item: (item.text_type.value, item.text), ), - aliases=sorted( - odm_method_ar.concept_vo.aliases, key=lambda item: item.name - ), + aliases=sorted(odm_method_ar.odm_vo.aliases, key=lambda item: item.name), possible_actions=sorted( [_.value for _ in odm_method_ar.get_possible_actions()] ), ) -class OdmMethodPostInput(ConceptPostInput): +class OdmMethodPostInput(OdmPostInput): oid: Annotated[str | None, Field(min_length=1)] = None method_type: Annotated[str | None, Field(min_length=1)] = None formal_expressions: Annotated[list[OdmFormalExpressionModel], Field()] @@ -74,7 +70,7 @@ class OdmMethodPostInput(ConceptPostInput): ) -class OdmMethodPatchInput(ConceptPatchInput): +class OdmMethodPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] oid: Annotated[str | None, Field(min_length=1)] method_type: Annotated[str | None, Field(min_length=1)] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_study_event.py b/clinical-mdr-api/clinical_mdr_api/models/odms/study_event.py similarity index 79% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_study_event.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/study_event.py index 6a41afb4..d043a7de 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_study_event.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/study_event.py @@ -4,19 +4,19 @@ from pydantic import Field from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.form import OdmFormRefVO -from clinical_mdr_api.domains.concepts.odms.study_event import OdmStudyEventAR -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, +from clinical_mdr_api.domains.odms.form import OdmFormRefVO +from clinical_mdr_api.domains.odms.study_event import OdmStudyEventAR +from clinical_mdr_api.models.odms.common_models import ( + OdmBaseModel, + OdmPatchInput, + OdmPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_form import OdmFormRefModel +from clinical_mdr_api.models.odms.form import OdmFormRefModel from clinical_mdr_api.models.utils import PostInputModel from common.config import settings -class OdmStudyEvent(ConceptModel): +class OdmStudyEvent(OdmBaseModel): oid: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None effective_date: Annotated[ date | None, Field(json_schema_extra={"nullable": True}) @@ -42,11 +42,11 @@ def from_odm_study_event_ar( return cls( uid=odm_study_event_ar._uid, name=odm_study_event_ar.name, - oid=odm_study_event_ar.concept_vo.oid, - effective_date=odm_study_event_ar.concept_vo.effective_date, - retired_date=odm_study_event_ar.concept_vo.retired_date, - description=odm_study_event_ar.concept_vo.description, - display_in_tree=odm_study_event_ar.concept_vo.display_in_tree, + oid=odm_study_event_ar.odm_vo.oid, + effective_date=odm_study_event_ar.odm_vo.effective_date, + retired_date=odm_study_event_ar.odm_vo.retired_date, + description=odm_study_event_ar.odm_vo.description, + display_in_tree=odm_study_event_ar.odm_vo.display_in_tree, library_name=odm_study_event_ar.library.name, start_date=odm_study_event_ar.item_metadata.start_date, end_date=odm_study_event_ar.item_metadata.end_date, @@ -62,7 +62,7 @@ def from_odm_study_event_ar( study_event_version=odm_study_event_ar.item_metadata.version, find_odm_form_by_uid_with_study_event_relation=find_odm_form_by_uid_with_study_event_relation, ) - for form_uid in odm_study_event_ar.concept_vo.form_uids + for form_uid in odm_study_event_ar.odm_vo.form_uids ], key=lambda item: (item.order_number, item.name), ), @@ -72,7 +72,7 @@ def from_odm_study_event_ar( ) -class OdmStudyEventPostInput(ConceptPostInput): +class OdmStudyEventPostInput(OdmPostInput): oid: Annotated[str | None, Field(min_length=1)] = None effective_date: Annotated[date | None, Field()] = None retired_date: Annotated[date | None, Field()] = None @@ -80,7 +80,7 @@ class OdmStudyEventPostInput(ConceptPostInput): display_in_tree: Annotated[bool, Field()] = True -class OdmStudyEventPatchInput(ConceptPatchInput): +class OdmStudyEventPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] oid: Annotated[str | None, Field(min_length=1)] effective_date: Annotated[date | None, Field()] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_attribute.py b/clinical-mdr-api/clinical_mdr_api/models/odms/vendor_attribute.py similarity index 91% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_attribute.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/vendor_attribute.py index f2693a43..204bc99d 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_attribute.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/vendor_attribute.py @@ -3,23 +3,21 @@ from pydantic import Field, field_validator, model_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import ( - OdmVendorAttributeAR, - OdmVendorAttributeRelationVO, - OdmVendorElementAttributeRelationVO, -) -from clinical_mdr_api.domains.concepts.odms.vendor_element import OdmVendorElementAR -from clinical_mdr_api.domains.concepts.odms.vendor_namespace import OdmVendorNamespaceAR -from clinical_mdr_api.domains.concepts.utils import ( +from clinical_mdr_api.domains.odms.utils import ( RelationType, VendorAttributeCompatibleType, ) -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, +from clinical_mdr_api.domains.odms.vendor_attribute import ( + OdmVendorAttributeAR, + OdmVendorAttributeRelationVO, + OdmVendorElementAttributeRelationVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.vendor_element import OdmVendorElementAR +from clinical_mdr_api.domains.odms.vendor_namespace import OdmVendorNamespaceAR +from clinical_mdr_api.models.odms.common_models import ( + OdmBaseModel, + OdmPatchInput, + OdmPostInput, OdmVendorElementSimpleModel, OdmVendorNamespaceSimpleModel, ) @@ -32,7 +30,7 @@ from common.exceptions import ValidationException -class OdmVendorAttribute(ConceptModel): +class OdmVendorAttribute(OdmBaseModel): compatible_types: Annotated[list[str], Field(json_schema_extra={"is_json": True})] data_type: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None value_regex: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( @@ -57,9 +55,9 @@ def from_odm_vendor_attribute_ar( return cls( uid=odm_vendor_attribute_ar._uid, name=odm_vendor_attribute_ar.name, - compatible_types=odm_vendor_attribute_ar.concept_vo.compatible_types, - data_type=odm_vendor_attribute_ar.concept_vo.data_type, - value_regex=odm_vendor_attribute_ar.concept_vo.value_regex, + compatible_types=odm_vendor_attribute_ar.odm_vo.compatible_types, + data_type=odm_vendor_attribute_ar.odm_vo.data_type, + value_regex=odm_vendor_attribute_ar.odm_vo.value_regex, library_name=odm_vendor_attribute_ar.library.name, start_date=odm_vendor_attribute_ar.item_metadata.start_date, end_date=odm_vendor_attribute_ar.item_metadata.end_date, @@ -68,11 +66,11 @@ def from_odm_vendor_attribute_ar( change_description=odm_vendor_attribute_ar.item_metadata.change_description, author_username=odm_vendor_attribute_ar.item_metadata.author_username, vendor_namespace=OdmVendorNamespaceSimpleModel.from_odm_vendor_namespace_uid( - uid=odm_vendor_attribute_ar.concept_vo.vendor_namespace_uid, + uid=odm_vendor_attribute_ar.odm_vo.vendor_namespace_uid, find_odm_vendor_namespace_by_uid=find_odm_vendor_namespace_by_uid, ), vendor_element=OdmVendorElementSimpleModel.from_odm_vendor_element_uid( - uid=odm_vendor_attribute_ar.concept_vo.vendor_element_uid, + uid=odm_vendor_attribute_ar.odm_vo.vendor_element_uid, find_odm_vendor_element_by_uid=find_odm_vendor_element_by_uid, ), possible_actions=sorted( @@ -246,7 +244,7 @@ def from_uid( ] = None -class OdmVendorAttributePostInput(ConceptPostInput): +class OdmVendorAttributePostInput(OdmPostInput): compatible_types: list[VendorAttributeCompatibleType] = Field(default_factory=list) data_type: Annotated[str, Field(min_length=1)] = "string" value_regex: Annotated[str | None, Field(min_length=1)] = None @@ -278,7 +276,7 @@ def one_and_only_one_of_the_two_uids_must_be_present(cls, values): return values -class OdmVendorAttributePatchInput(ConceptPatchInput): +class OdmVendorAttributePatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] compatible_types: Annotated[list[VendorAttributeCompatibleType], Field()] data_type: Annotated[str | None, Field(min_length=1)] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_element.py b/clinical-mdr-api/clinical_mdr_api/models/odms/vendor_element.py similarity index 86% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_element.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/vendor_element.py index 6019e9a5..f6cdde69 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_element.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/vendor_element.py @@ -3,22 +3,20 @@ from pydantic import Field, field_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import OdmVendorAttributeAR -from clinical_mdr_api.domains.concepts.odms.vendor_element import ( - OdmVendorElementAR, - OdmVendorElementRelationVO, -) -from clinical_mdr_api.domains.concepts.odms.vendor_namespace import OdmVendorNamespaceAR -from clinical_mdr_api.domains.concepts.utils import ( +from clinical_mdr_api.domains.odms.utils import ( RelationType, VendorElementCompatibleType, ) -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, +from clinical_mdr_api.domains.odms.vendor_attribute import OdmVendorAttributeAR +from clinical_mdr_api.domains.odms.vendor_element import ( + OdmVendorElementAR, + OdmVendorElementRelationVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.vendor_namespace import OdmVendorNamespaceAR +from clinical_mdr_api.models.odms.common_models import ( + OdmBaseModel, + OdmPatchInput, + OdmPostInput, OdmVendorAttributeSimpleModel, OdmVendorNamespaceSimpleModel, ) @@ -29,7 +27,7 @@ ) -class OdmVendorElement(ConceptModel): +class OdmVendorElement(OdmBaseModel): compatible_types: Annotated[list[str], Field(json_schema_extra={"is_json": True})] vendor_namespace: Annotated[OdmVendorNamespaceSimpleModel, Field()] vendor_attributes: Annotated[list[OdmVendorAttributeSimpleModel], Field()] @@ -44,7 +42,7 @@ def from_odm_vendor_element_ar( ) -> Self: return cls( uid=odm_vendor_element_ar._uid, - compatible_types=odm_vendor_element_ar.concept_vo.compatible_types, + compatible_types=odm_vendor_element_ar.odm_vo.compatible_types, name=odm_vendor_element_ar.name, library_name=odm_vendor_element_ar.library.name, start_date=odm_vendor_element_ar.item_metadata.start_date, @@ -54,7 +52,7 @@ def from_odm_vendor_element_ar( change_description=odm_vendor_element_ar.item_metadata.change_description, author_username=odm_vendor_element_ar.item_metadata.author_username, vendor_namespace=OdmVendorNamespaceSimpleModel.from_odm_vendor_namespace_uid( - uid=odm_vendor_element_ar.concept_vo.vendor_namespace_uid, + uid=odm_vendor_element_ar.odm_vo.vendor_namespace_uid, find_odm_vendor_namespace_by_uid=find_odm_vendor_namespace_by_uid, ), vendor_attributes=sorted( @@ -64,7 +62,7 @@ def from_odm_vendor_element_ar( find_odm_vendor_attribute_by_uid=find_odm_vendor_attribute_by_uid, ) for vendor_attribute_uid in set( - odm_vendor_element_ar.concept_vo.vendor_attribute_uids + odm_vendor_element_ar.odm_vo.vendor_attribute_uids ) ], key=lambda item: item.name or "", @@ -136,7 +134,7 @@ def from_uid( value: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None -class OdmVendorElementPostInput(ConceptPostInput): +class OdmVendorElementPostInput(OdmPostInput): compatible_types: Annotated[list[VendorElementCompatibleType], Field(min_length=1)] vendor_namespace_uid: Annotated[str, Field(min_length=1)] @@ -148,7 +146,7 @@ class OdmVendorElementPostInput(ConceptPostInput): ) -class OdmVendorElementPatchInput(ConceptPatchInput): +class OdmVendorElementPatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] compatible_types: Annotated[list[VendorElementCompatibleType], Field(min_length=1)] diff --git a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_namespace.py b/clinical-mdr-api/clinical_mdr_api/models/odms/vendor_namespace.py similarity index 79% rename from clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_namespace.py rename to clinical-mdr-api/clinical_mdr_api/models/odms/vendor_namespace.py index f529ab3a..81b8fb72 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/concepts/odms/odm_vendor_namespace.py +++ b/clinical-mdr-api/clinical_mdr_api/models/odms/vendor_namespace.py @@ -4,21 +4,19 @@ from pydantic import Field, field_validator from clinical_mdr_api.descriptions.general import CHANGES_FIELD_DESC -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import OdmVendorAttributeAR -from clinical_mdr_api.domains.concepts.odms.vendor_element import OdmVendorElementAR -from clinical_mdr_api.domains.concepts.odms.vendor_namespace import OdmVendorNamespaceAR -from clinical_mdr_api.models.concepts.concept import ( - ConceptModel, - ConceptPatchInput, - ConceptPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.domains.odms.vendor_attribute import OdmVendorAttributeAR +from clinical_mdr_api.domains.odms.vendor_element import OdmVendorElementAR +from clinical_mdr_api.domains.odms.vendor_namespace import OdmVendorNamespaceAR +from clinical_mdr_api.models.odms.common_models import ( + OdmBaseModel, + OdmPatchInput, + OdmPostInput, OdmVendorAttributeSimpleModel, OdmVendorElementSimpleModel, ) -class OdmVendorNamespace(ConceptModel): +class OdmVendorNamespace(OdmBaseModel): prefix: Annotated[str | None, Field()] url: Annotated[str | None, Field()] vendor_elements: Annotated[list[OdmVendorElementSimpleModel], Field()] @@ -35,8 +33,8 @@ def from_odm_vendor_namespace_ar( return cls( uid=odm_vendor_namespace_ar._uid, name=odm_vendor_namespace_ar.name, - prefix=odm_vendor_namespace_ar.concept_vo.prefix, - url=odm_vendor_namespace_ar.concept_vo.url, + prefix=odm_vendor_namespace_ar.odm_vo.prefix, + url=odm_vendor_namespace_ar.odm_vo.url, library_name=odm_vendor_namespace_ar.library.name, start_date=odm_vendor_namespace_ar.item_metadata.start_date, end_date=odm_vendor_namespace_ar.item_metadata.end_date, @@ -50,7 +48,7 @@ def from_odm_vendor_namespace_ar( uid=vendor_element_uid, find_odm_vendor_element_by_uid=find_odm_vendor_element_by_uid, ) - for vendor_element_uid in odm_vendor_namespace_ar.concept_vo.vendor_element_uids + for vendor_element_uid in odm_vendor_namespace_ar.odm_vo.vendor_element_uids ], key=lambda item: item.name or "", ), @@ -60,7 +58,7 @@ def from_odm_vendor_namespace_ar( uid=vendor_attribute_uid, find_odm_vendor_attribute_by_uid=find_odm_vendor_attribute_by_uid, ) - for vendor_attribute_uid in odm_vendor_namespace_ar.concept_vo.vendor_attribute_uids + for vendor_attribute_uid in odm_vendor_namespace_ar.odm_vo.vendor_attribute_uids ], key=lambda item: item.name or "", ), @@ -70,7 +68,7 @@ def from_odm_vendor_namespace_ar( ) -class OdmVendorNamespacePostInput(ConceptPostInput): +class OdmVendorNamespacePostInput(OdmPostInput): prefix: Annotated[str, Field(min_length=1)] url: Annotated[str, Field(min_length=1)] @@ -82,7 +80,7 @@ def prefix_may_only_contain_letters(cls, value): return value -class OdmVendorNamespacePatchInput(ConceptPatchInput): +class OdmVendorNamespacePatchInput(OdmPatchInput): name: Annotated[str, Field(min_length=1)] prefix: Annotated[str, Field(min_length=1)] url: Annotated[str, Field(min_length=1)] diff --git a/clinical-mdr-api/clinical_mdr_api/models/preferences.py b/clinical-mdr-api/clinical_mdr_api/models/preferences.py new file mode 100644 index 00000000..58b06aae --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/models/preferences.py @@ -0,0 +1,43 @@ +from typing import Annotated, Any, Literal + +from pydantic import Field + +from clinical_mdr_api.models.utils import BaseModel, PatchInputModel + + +class PreferenceMetadata(BaseModel): + type: Annotated[str, Field()] + label: Annotated[str, Field()] + description: Annotated[str, Field()] + min: Annotated[int | None, Field(json_schema_extra={"nullable": True})] = None + max: Annotated[int | None, Field(json_schema_extra={"nullable": True})] = None + default: Annotated[int | bool | str, Field()] + allowed_values: Annotated[ + list[str] | None, Field(json_schema_extra={"nullable": True}) + ] = None + + +class PreferencesResponse(BaseModel): + preferences: Annotated[dict[str, int | bool | str], Field()] + metadata: Annotated[dict[str, PreferenceMetadata], Field()] + + +class UserPreferencesResponse(BaseModel): + preferences: Annotated[dict[str, int | bool | str], Field()] + overrides: Annotated[dict[str, Any], Field()] + metadata: Annotated[dict[str, PreferenceMetadata], Field()] + + +class PreferencesFields(PatchInputModel): + language: Annotated[Literal["en"] | None, Field()] = None + rows_per_page: Annotated[int | None, Field(ge=5, le=100)] = None + sidebar_visible: Annotated[bool | None, Field()] = None + sidebar_auto_minimize: Annotated[bool | None, Field()] = None + + +class GlobalPreferencesPatchInput(PreferencesFields): + pass + + +class UserPreferencesPatchInput(PreferencesFields): + pass diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model.py index e469b40f..b6dae3a7 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model.py @@ -41,7 +41,7 @@ class DataModel(BaseModel): @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), name=input_dict.get("standard_value").get("name"), description=input_dict.get("standard_value").get("description"), implementation_guides=[ diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model_ig.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model_ig.py index 45e69971..4138a787 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model_ig.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/data_model_ig.py @@ -41,7 +41,7 @@ class DataModelIG(BaseModel): @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), name=input_dict.get("standard_value").get("name"), description=input_dict.get("standard_value").get("description"), implemented_data_model=( diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset.py index d061a9e1..e8683e9a 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset.py @@ -36,7 +36,7 @@ class Dataset(BaseModel): @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), label=input_dict.get("standard_value").get("label"), title=input_dict.get("standard_value").get("title"), description=input_dict.get("standard_value").get("description"), diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_class.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_class.py index 86cbfbe2..374cf9c8 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_class.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_class.py @@ -23,25 +23,22 @@ class DatasetClass(BaseModel): None ) catalogue_name: Annotated[str, Field()] - parent_class: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( - None - ) - data_models: Annotated[list[SimpleDataModelForDatasetClass], Field()] + parent_class_name: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + data_model: Annotated[SimpleDataModelForDatasetClass, Field()] @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), label=input_dict.get("standard_value").get("label"), title=input_dict.get("standard_value").get("title"), description=input_dict.get("standard_value").get("description"), catalogue_name=input_dict["catalogue_name"], - parent_class=input_dict.get("parent_class_name"), - data_models=[ - SimpleDataModelForDatasetClass( - data_model_name=data_model.get("data_model_name"), - ordinal=data_model.get("ordinal"), - ) - for data_model in input_dict.get("data_models") - ], + parent_class_name=input_dict.get("parent_class_name"), + data_model=SimpleDataModelForDatasetClass( + data_model_name=input_dict.get("data_model", {}).get("name"), + ordinal=input_dict.get("data_model", {}).get("ordinal"), + ), ) diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_scenario.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_scenario.py index a3d2054f..52bab6ee 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_scenario.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_scenario.py @@ -18,7 +18,7 @@ class DatasetScenario(BaseModel): @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), label=input_dict.get("standard_value").get("label"), catalogue_name=input_dict["catalogue_name"], dataset=SimpleDatasetForDatasetVariable( diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_variable.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_variable.py index 8d171cbe..19c2e5e5 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_variable.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/dataset_variable.py @@ -74,12 +74,6 @@ class DatasetVariable(BaseModel): str | None, Field(json_schema_extra={"nullable": True}) ] = None dataset: Annotated[SimpleDatasetForDatasetVariable, Field()] - data_model_ig_names: Annotated[ - list[str], - Field( - description="Versions of associated data model implementation guides", - ), - ] implements_variable: Annotated[ SimpleImplementsVariable | None, Field(json_schema_extra={"nullable": True}) ] = None @@ -94,7 +88,7 @@ class DatasetVariable(BaseModel): @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), label=input_dict.get("standard_value").get("label"), title=input_dict.get("standard_value").get("title"), description=input_dict.get("standard_value").get("description"), @@ -109,7 +103,6 @@ def from_repository_output(cls, input_dict: dict[str, Any]): described_value_domain=input_dict.get("described_value_domain"), value_list=input_dict.get("value_list") or [], analysis_variable_set=input_dict.get("analysis_variable_set"), - data_model_ig_names=input_dict["data_model_ig_names"], dataset=SimpleDatasetForDatasetVariable( uid=input_dict.get("dataset").get("uid"), ordinal=input_dict.get("dataset").get("ordinal"), diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model.py index d6f65115..cfaa7871 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model.py @@ -1,10 +1,10 @@ +from datetime import datetime from typing import Annotated, Self from pydantic import ConfigDict, Field from clinical_mdr_api.domains.standard_data_models.sponsor_model import SponsorModelAR -from clinical_mdr_api.models.concepts.concept import VersionProperties -from clinical_mdr_api.models.libraries.library import Library +from clinical_mdr_api.models import _generic_descriptions from clinical_mdr_api.models.utils import BaseModel, InputModel @@ -12,32 +12,64 @@ class SponsorModelBase(BaseModel): pass -class SponsorModel(SponsorModelBase, VersionProperties): +class SponsorModel(SponsorModelBase): model_config = ConfigDict(from_attributes=True) uid: Annotated[ str | None, - Field(json_schema_extra={"source": "uid", "nullable": True}), - ] = None + Field(json_schema_extra={"source": "uid"}), + ] name: Annotated[ str, Field( description="The name or the sponsor model. E.g. sdtm_sponsormodel_3.2-NN15", - json_schema_extra={"source": "has_latest_sponsor_model_value.name"}, + json_schema_extra={"source": "has_sponsor_model_version.name"}, ), ] - extended_implementation_guide: Annotated[ + start_date: Annotated[ + datetime | None, + Field( + description=_generic_descriptions.START_DATE, + json_schema_extra={ + "source": "has_sponsor_model_version|start_date", + "nullable": True, + }, + ), + ] = None + end_date: Annotated[ + datetime | None, + Field( + description=_generic_descriptions.END_DATE, + json_schema_extra={ + "source": "has_sponsor_model_version|end_date", + "nullable": True, + }, + ), + ] = None + status: Annotated[ str | None, Field( json_schema_extra={ - "source": "has_latest_sponsor_model_value__extends_version.name", + "source": "has_sponsor_model_version|status", "nullable": True, }, ), ] = None - library_name: Annotated[ + version: Annotated[ + str, + Field( + description="Version of the sponsor model.", + json_schema_extra={"source": "has_sponsor_model_version|version"}, + ), + ] + extended_implementation_guide: Annotated[ str | None, - Field(json_schema_extra={"source": "has_library.name", "nullable": True}), + Field( + json_schema_extra={ + "source": "has_sponsor_model_version.extends_version.name", + "nullable": True, + }, + ), ] = None @classmethod @@ -48,13 +80,10 @@ def from_sponsor_model_ar( return cls( uid=sponsor_model_ar.uid, name=sponsor_model_ar.name, - library_name=Library.from_library_vo(sponsor_model_ar.library).name, start_date=sponsor_model_ar.item_metadata.start_date, end_date=sponsor_model_ar.item_metadata.end_date, status=sponsor_model_ar.item_metadata.status.value, version=sponsor_model_ar.item_metadata.version, - change_description=sponsor_model_ar.item_metadata.change_description, - author_username=sponsor_model_ar.item_metadata.author_username, ) diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset.py index 04390d2c..f77e1e87 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset.py @@ -10,6 +10,24 @@ from clinical_mdr_api.models.utils import InputModel +class SimpleSponsorModelDataModelIG(SponsorModelBase): + ordinal: Annotated[ + int | None, + Field( + json_schema_extra={ + "source": "has_sponsor_model_instance.has_dataset|ordinal", + "nullable": True, + } + ), + ] = None + name: Annotated[ + str, + Field( + json_schema_extra={"source": "has_sponsor_model_instance.has_dataset.name"} + ), + ] + + class SponsorModelDataset(SponsorModelBase): model_config = ConfigDict(from_attributes=True, extra="allow") @@ -17,9 +35,9 @@ class SponsorModelDataset(SponsorModelBase): str | None, Field(json_schema_extra={"source": "uid", "nullable": True}), ] = None - library_name: Annotated[ - str | None, - Field(json_schema_extra={"source": "has_library.name", "nullable": True}), + sponsor_model: Annotated[ + SimpleSponsorModelDataModelIG | None, + Field(json_schema_extra={"nullable": True}), ] = None is_basic_std: Annotated[ bool | None, @@ -30,15 +48,6 @@ class SponsorModelDataset(SponsorModelBase): }, ), ] = None - implemented_dataset_class: Annotated[ - str | None, - Field( - json_schema_extra={ - "source": "has_sponsor_model_instance.implements_dataset_class.is_instance_of.uid", - "nullable": True, - }, - ), - ] = None xml_path: Annotated[ str | None, Field( diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset_variable.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset_variable.py index 29832300..6a896472 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset_variable.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/sponsor_model_dataset_variable.py @@ -1,6 +1,6 @@ from typing import Annotated, Any -from pydantic import ConfigDict, Field +from pydantic import BaseModel, ConfigDict, Field from clinical_mdr_api.domains.standard_data_models.sponsor_model_dataset_variable import ( SponsorModelDatasetVariableAR, @@ -10,41 +10,43 @@ from clinical_mdr_api.models.utils import InputModel -class SponsorModelDatasetVariable(SponsorModelBase): - model_config = ConfigDict(from_attributes=True, extra="allow") +class ReferencedCodelist(BaseModel): + uid: str + submission_value: str - uid: Annotated[ - str | None, Field(json_schema_extra={"source": "uid", "nullable": True}) - ] = None - library_name: Annotated[ - str | None, - Field(json_schema_extra={"source": "has_library.name", "nullable": True}), - ] = None - is_basic_std: Annotated[ - bool | None, + +class ReferencedTerm(BaseModel): + uid: str + submission_value: str + + +class SimpleSponsorModelDataset(SponsorModelBase): + uid: str + ordinal: Annotated[ + int | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.is_basic_std", "nullable": True, - "remove_from_wildcard": True, - }, + } ), ] = None - implemented_parent_dataset_class: Annotated[ - str | None, - Field( - json_schema_extra={ - "source": "has_sponsor_model_instance.implements_variable_class.has_variable_class.is_instance_of.uid", - "nullable": True, - "remove_from_wildcard": True, - }, - ), + key_order: Annotated[int | None, Field(json_schema_extra={"nullable": True})] = None + version_number: int + sponsor_model_name: str + + +class SponsorModelDatasetVariable(SponsorModelBase): + model_config = ConfigDict(from_attributes=True, extra="allow") + + uid: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None + dataset: Annotated[ + SimpleSponsorModelDataset | None, + Field(json_schema_extra={"nullable": True}), ] = None - implemented_variable_class: Annotated[ - str | None, + is_basic_std: Annotated[ + bool | None, Field( json_schema_extra={ - "souce": "has_sponsor_model_instance.implements_variable_class.is_instance_of.uid", "nullable": True, "remove_from_wildcard": True, }, @@ -54,16 +56,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.label", - "nullable": True, - }, - ), - ] = None - order: Annotated[ - int | None, - Field( - json_schema_extra={ - "source": "has_sponsor_model_instance.has_variable|ordinal", "nullable": True, }, ), @@ -72,7 +64,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.variable_type", "nullable": True, }, ), @@ -81,7 +72,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): int | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.length", "nullable": True, }, ), @@ -90,7 +80,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.display_format", "nullable": True, }, ), @@ -99,7 +88,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.xml_datatype", "nullable": True, }, ), @@ -108,7 +96,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.core", "nullable": True, }, ), @@ -117,7 +104,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.origin", "nullable": True, }, ), @@ -126,7 +112,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.origin_type", "nullable": True, }, ), @@ -135,7 +120,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.origin_source", "nullable": True, }, ), @@ -144,7 +128,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.role", "nullable": True, }, ), @@ -153,7 +136,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.term", "nullable": True, }, ), @@ -162,7 +144,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.algorithm", "nullable": True, }, ), @@ -171,7 +152,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): list[str] | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.qualifiers", "nullable": True, "remove_from_wildcard": True, }, @@ -181,7 +161,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): bool | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.is_cdisc_std", "nullable": True, "remove_from_wildcard": True, }, @@ -191,7 +170,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.comment", "nullable": True, }, ), @@ -200,7 +178,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.ig_comment", "nullable": True, }, ), @@ -209,7 +186,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.class_table", "nullable": True, }, ), @@ -218,7 +194,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.class_column", "nullable": True, }, ), @@ -227,7 +202,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.map_var_flag", "nullable": True, }, ), @@ -236,7 +210,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.fixed_mapping", "nullable": True, }, ), @@ -245,7 +218,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): bool | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.include_in_raw", "nullable": True, "remove_from_wildcard": True, }, @@ -255,7 +227,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): bool | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.nn_internal", "nullable": True, "remove_from_wildcard": True, }, @@ -265,7 +236,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.value_lvl_where_cols", "nullable": True, }, ), @@ -274,7 +244,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.value_lvl_label_col", "nullable": True, }, ), @@ -283,7 +252,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.value_lvl_collect_ct_val", "nullable": True, }, ), @@ -292,7 +260,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.value_lvl_ct_codelist_id_col", "nullable": True, }, ), @@ -301,7 +268,6 @@ class SponsorModelDatasetVariable(SponsorModelBase): int | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.enrich_build_order", "nullable": True, }, ), @@ -310,11 +276,68 @@ class SponsorModelDatasetVariable(SponsorModelBase): str | None, Field( json_schema_extra={ - "source": "has_sponsor_model_instance.enrich_rule", "nullable": True, }, ), ] = None + referenced_codelists: list[ReferencedCodelist] = Field(default_factory=list) + referenced_terms: list[ReferencedTerm] = Field(default_factory=list) + + @classmethod + def from_repository_output(cls, input_dict: dict[str, Any]): + return cls( + uid=input_dict["uid"], + dataset=SimpleSponsorModelDataset( + uid=input_dict.get("dataset", {}).get("uid"), + ordinal=input_dict.get("dataset", {}).get("ordinal"), + key_order=input_dict.get("dataset", {}).get("key_order"), + version_number=input_dict.get("dataset", {}).get("version_number"), + sponsor_model_name=input_dict.get("dataset", {}).get( + "sponsor_model_name" + ), + ), + is_basic_std=input_dict.get("is_basic_std"), + label=input_dict.get("label"), + variable_type=input_dict.get("variable_type"), + length=input_dict.get("length"), + display_format=input_dict.get("display_format"), + xml_datatype=input_dict.get("xml_datatype"), + core=input_dict.get("core"), + origin=input_dict.get("origin"), + origin_type=input_dict.get("origin_type"), + origin_source=input_dict.get("origin_source"), + role=input_dict.get("role"), + term=input_dict.get("term"), + algorithm=input_dict.get("algorithm"), + qualifiers=input_dict.get("qualifiers"), + is_cdisc_std=input_dict.get("is_cdisc_std"), + comment=input_dict.get("comment"), + ig_comment=input_dict.get("ig_comment"), + class_table=input_dict.get("class_table"), + class_column=input_dict.get("class_column"), + map_var_flag=input_dict.get("map_var_flag"), + fixed_mapping=input_dict.get("fixed_mapping"), + include_in_raw=input_dict.get("include_in_raw"), + nn_internal=input_dict.get("nn_internal"), + value_lvl_where_cols=input_dict.get("value_lvl_where_cols"), + value_lvl_label_col=input_dict.get("value_lvl_label_col"), + value_lvl_collect_ct_val=input_dict.get("value_lvl_collect_ct_val"), + value_lvl_ct_codelist_id_col=input_dict.get("value_lvl_ct_codelist_id_col"), + enrich_build_order=input_dict.get("enrich_build_order"), + enrich_rule=input_dict.get("enrich_rule"), + referenced_codelists=[ + ReferencedCodelist( + uid=cl["uid"], submission_value=cl["submission_value"] + ) + for cl in input_dict.get("referenced_codelists", []) + if cl is not None + ], + referenced_terms=[ + ReferencedTerm(uid=t["uid"], submission_value=t["submission_value"]) + for t in input_dict.get("referenced_terms", []) + if t is not None + ], + ) @classmethod def from_sponsor_model_dataset_variable_ar( diff --git a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/variable_class.py b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/variable_class.py index f8ffe09e..e089a9f6 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/variable_class.py +++ b/clinical-mdr-api/clinical_mdr_api/models/standard_data_models/variable_class.py @@ -14,7 +14,7 @@ class SimpleReferencedCodelistForVariableClass(BaseModel): class SimpleDatasetClassForVariableClass(BaseModel): - ordinal: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None + ordinal: Annotated[int | None, Field(json_schema_extra={"nullable": True})] = None dataset_class_name: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None @@ -59,26 +59,22 @@ class VariableClass(BaseModel): ] = None examples: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = None dataset_class: Annotated[SimpleDatasetClassForVariableClass, Field()] - dataset_variable_name: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None catalogue_name: Annotated[str, Field()] - data_model_names: Annotated[list[str], Field()] - has_mapping_target: Annotated[ - SimpleMappingTarget | None, Field(json_schema_extra={"nullable": True}) + has_mapping_targets: Annotated[ + list[SimpleMappingTarget] | None, Field(json_schema_extra={"nullable": True}) ] = None referenced_codelists: Annotated[ list[SimpleReferencedCodelistForVariableClass] | None, Field(json_schema_extra={"nullable": True}), ] = None - qualifies_variable: Annotated[ - SimpleVariableClass | None, Field(json_schema_extra={"nullable": True}) + qualifies_variables: Annotated[ + list[SimpleVariableClass] | None, Field(json_schema_extra={"nullable": True}) ] = None @classmethod def from_repository_output(cls, input_dict: dict[str, Any]): return cls( - uid=input_dict["uid"], + uid=input_dict.get("standard_root").get("uid"), label=input_dict.get("standard_value").get("label"), title=input_dict.get("standard_value").get("title"), description=input_dict.get("standard_value").get("description"), @@ -111,8 +107,6 @@ def from_repository_output(cls, input_dict: dict[str, Any]): ), ordinal=input_dict.get("dataset_class").get("ordinal"), ), - dataset_variable_name=input_dict.get("dataset_variable_name"), - data_model_names=input_dict["data_model_names"], referenced_codelists=( [ SimpleReferencedCodelistForVariableClass( @@ -123,20 +117,22 @@ def from_repository_output(cls, input_dict: dict[str, Any]): ] or None ), - has_mapping_target=( - SimpleMappingTarget( - uid=input_dict.get("has_mapping_target").get("uid"), - name=input_dict.get("has_mapping_target").get("name"), - ) - if input_dict.get("has_mapping_target") - else None + has_mapping_targets=( + [ + SimpleMappingTarget( + uid=target.get("uid"), + name=target.get("name"), + ) + for target in input_dict.get("has_mapping_targets") + ] ), - qualifies_variable=( - SimpleVariableClass( - uid=input_dict.get("qualifies_variable").get("uid"), - name=input_dict.get("qualifies_variable").get("name"), - ) - if input_dict.get("qualifies_variable") - else None + qualifies_variables=( + [ + SimpleVariableClass( + uid=variable.get("uid"), + name=variable.get("name"), + ) + for variable in input_dict.get("qualifies_variables") + ] ), ) 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 9349d4c1..35832e2f 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 @@ -1642,6 +1642,13 @@ class StudyVersionHistory(BaseModel): json_schema_extra={"nullable": True}, ), ] = None + original_metadata_version: Annotated[ + str | None, + Field( + description="Metadata version of the first occurrence for the same protocol header version", + json_schema_extra={"nullable": True}, + ), + ] = None protocol_header_major_version: Annotated[ int | None, Field( @@ -1699,6 +1706,7 @@ def from_repository_output( reason_for_lock_name=val.get("reason_for_lock"), reason_for_unlock_name=val.get("reason_for_unlock"), metadata_version=val.get("metadata_version"), + original_metadata_version=val.get("original_metadata_version"), protocol_header_major_version=val.get("protocol_header_major_version"), protocol_header_minor_version=val.get("protocol_header_minor_version"), description=val.get("description"), @@ -1764,6 +1772,10 @@ class VersionInfo(BaseModel): latest_released_version: Annotated[ VersionInfo | None, Field(json_schema_extra={"nullable": True}) ] = None + data_completeness_tags: list[str] = Field( + description="List of data completeness tag names assigned to the study.", + default_factory=list, + ) @classmethod def from_input( @@ -1798,6 +1810,7 @@ def from_input( if val.get("latest_released_version") is not None else None ), + data_completeness_tags=val.get("data_completeness_tags", []), ) diff --git a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_epoch.py b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_epoch.py index 8085c64c..51f3967e 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_epoch.py +++ b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_epoch.py @@ -9,7 +9,7 @@ from common.config import settings if TYPE_CHECKING: - from clinical_mdr_api.models.study_selections.study_visit import StudyVisitBase + from clinical_mdr_api.models.study_selections.study_visit import StudyVisitLite class StudyEpochCreateInput(PostInputModel): @@ -253,15 +253,13 @@ class StudyEpochTiny(BaseModel): SimpleCTTermNameWithConflictFlag, Field(description="Epoch CTTerm") ] epoch_name: Annotated[str | None, Field(description="CTTerm name of the Epoch")] - study_uid: Annotated[str, Field(description="Study uid")] uid: Annotated[str, Field(description="StudyEpoch uid")] @classmethod - def from_study_visit(cls, study_visit: "StudyVisitBase") -> Self: + def from_study_visit(cls, study_visit: "StudyVisitLite") -> Self: return cls( - epoch=study_visit.epoch_uid, + epoch=study_visit.study_epoch.term_uid, epoch_ctterm=study_visit.study_epoch, epoch_name=study_visit.study_epoch.sponsor_preferred_name, - study_uid=study_visit.study_uid, uid=study_visit.study_epoch_uid, ) diff --git a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_pharma_cm.py b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_pharma_cm.py index 223c6829..1cd8eff4 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_pharma_cm.py +++ b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_pharma_cm.py @@ -502,13 +502,11 @@ def from_pharma_cm_data(cls, study_pharma_cm: StudyPharmaCM) -> dict[str, Any]: "eligibility": { "study_population": {"textblock": None}, "sampling_method": None, - "criteria": { - "textblock": f""" Inclusion Criteria: + "criteria": {"textblock": f""" Inclusion Criteria: {"".join(["-" + inclusion_criteria+"\n" for inclusion_criteria in study_pharma_cm.inclusion_criteria])} Exclusion Criteria: {"".join(["-" + exclusion_criteria+"\n" for exclusion_criteria in study_pharma_cm.exclusion_criteria])} - """ - }, + """}, "healthy_volunteers": study_pharma_cm.accepts_healthy_volunteers, "gender": None, "gender_based": None, diff --git a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_visit.py b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_visit.py index 8fe4d12f..b2b3fbab 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_visit.py +++ b/clinical-mdr-api/clinical_mdr_api/models/study_selections/study_visit.py @@ -1,13 +1,14 @@ from datetime import datetime from typing import Annotated, Self -from pydantic import ConfigDict, Field +from pydantic import ConfigDict, Field, field_validator from clinical_mdr_api.domains.study_selections.study_visit import ( StudyVisitVO, VisitGroupFormat, ) from clinical_mdr_api.models.controlled_terminologies.ct_term import ( + CTTermUidInput, SimpleCTTermNameWithConflictFlag, ) from clinical_mdr_api.models.utils import ( @@ -22,10 +23,18 @@ class StudyVisitCreateInput(PostInputModel): study_epoch_uid: Annotated[str, Field()] - visit_type_uid: Annotated[ - str, Field(json_schema_extra={"source": "has_visit_type.uid"}) + visit_type: Annotated[ + CTTermUidInput, Field(json_schema_extra={"source": "has_visit_type.uid"}) ] - time_reference_uid: Annotated[str | None, Field()] = None + time_reference: Annotated[CTTermUidInput | None, Field()] = None + + @field_validator("time_reference", "epoch_allocation", mode="before") + @classmethod + def _empty_dict_to_none(cls, v: object) -> object: + if isinstance(v, dict) and not v: + return None + return v + time_value: Annotated[ int | None, Field( @@ -57,8 +66,8 @@ class StudyVisitCreateInput(PostInputModel): description: Annotated[str | None, Field()] = None start_rule: Annotated[str | None, Field()] = None end_rule: Annotated[str | None, Field()] = None - visit_contact_mode_uid: Annotated[str, Field()] - epoch_allocation_uid: Annotated[str | None, Field()] = None + visit_contact_mode: Annotated[CTTermUidInput, Field()] + epoch_allocation: Annotated[CTTermUidInput | None, Field()] = None visit_class: Annotated[VisitClass, Field()] visit_subclass: Annotated[VisitSubclass | None, Field()] = None is_global_anchor_visit: Annotated[bool, Field()] @@ -82,10 +91,18 @@ class StudyVisitCreateInput(PostInputModel): class StudyVisitEditInput(PatchInputModel): uid: Annotated[str, Field(description="Uid of the Visit")] study_epoch_uid: Annotated[str, Field()] - visit_type_uid: Annotated[ - str, Field(json_schema_extra={"source": "has_visit_type.uid"}) + visit_type: Annotated[ + CTTermUidInput, Field(json_schema_extra={"source": "has_visit_type.uid"}) ] - time_reference_uid: Annotated[str | None, Field()] = None + time_reference: Annotated[CTTermUidInput | None, Field()] = None + + @field_validator("time_reference", "epoch_allocation", mode="before") + @classmethod + def _empty_dict_to_none(cls, v: object) -> object: + if isinstance(v, dict) and not v: + return None + return v + time_value: Annotated[ int | None, Field( @@ -117,8 +134,8 @@ class StudyVisitEditInput(PatchInputModel): description: Annotated[str | None, Field()] = None start_rule: Annotated[str | None, Field()] = None end_rule: Annotated[str | None, Field()] = None - visit_contact_mode_uid: Annotated[str, Field()] - epoch_allocation_uid: Annotated[str | None, Field()] = None + visit_contact_mode: Annotated[CTTermUidInput, Field()] + epoch_allocation: Annotated[CTTermUidInput | None, Field()] = None visit_class: Annotated[VisitClass | None, Field()] = None visit_subclass: Annotated[VisitSubclass | None, Field()] = None is_global_anchor_visit: Annotated[bool, Field()] @@ -163,17 +180,10 @@ class SimpleStudyVisit(BaseModel): ] -class StudyVisitBase(BaseModel): +class StudyVisitLite(BaseModel): model_config = ConfigDict(populate_by_name=True, from_attributes=True) uid: Annotated[str, Field(description="Uid of the Visit")] - study_epoch_uid: Annotated[str, Field()] - visit_type_uid: Annotated[ - str, Field(json_schema_extra={"source": "has_visit_type.uid"}) - ] - visit_sublabel_reference: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None consecutive_visit_group: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None @@ -190,6 +200,48 @@ class StudyVisitBase(BaseModel): visit_window_unit_uid: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None + + study_epoch_uid: Annotated[str, Field()] + study_epoch: Annotated[SimpleCTTermNameWithConflictFlag, Field()] + + study_day_number: Annotated[ + int | None, Field(json_schema_extra={"nullable": True}) + ] = None + study_duration_days: Annotated[ + int | None, Field(json_schema_extra={"nullable": True}) + ] = None + study_week_number: Annotated[ + int | None, Field(json_schema_extra={"nullable": True}) + ] = None + study_duration_weeks: Annotated[ + int | None, Field(json_schema_extra={"nullable": True}) + ] = None + + visit_number: Annotated[float, Field()] + + unique_visit_number: Annotated[int | None, Field()] + + visit_short_name: Annotated[str, Field()] + + visit_window_unit_name: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None + visit_class: Annotated[VisitClass, Field()] + visit_subclass: Annotated[ + VisitSubclass | None, Field(json_schema_extra={"nullable": True}) + ] = None + is_global_anchor_visit: Annotated[bool, Field()] + is_soa_milestone: Annotated[bool, Field()] + + visit_type: Annotated[SimpleCTTermNameWithConflictFlag | None, Field()] + + +class StudyVisitDetailed(StudyVisitLite): + model_config = ConfigDict(populate_by_name=True, from_attributes=True) + + visit_sublabel_reference: Annotated[ + str | None, Field(json_schema_extra={"nullable": True}) + ] = None description: Annotated[str | None, Field(json_schema_extra={"nullable": True})] = ( None ) @@ -212,19 +264,8 @@ class StudyVisitBase(BaseModel): json_schema_extra={"nullable": True}, ), ] = None - study_epoch: Annotated[SimpleCTTermNameWithConflictFlag, Field()] - # study_epoch_name can be calculated from uid - epoch_uid: Annotated[str, Field(description="The uid of the study epoch")] - visit_type: Annotated[SimpleCTTermNameWithConflictFlag | None, Field()] - visit_type_name: Annotated[str, Field()] - time_reference_uid: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None - time_reference_name: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None time_reference: Annotated[ SimpleCTTermNameWithConflictFlag | None, Field(json_schema_extra={"nullable": True}), @@ -242,11 +283,7 @@ class StudyVisitBase(BaseModel): SimpleCTTermNameWithConflictFlag | None, Field(json_schema_extra={"nullable": True}), ] = None - visit_contact_mode_uid: Annotated[str, Field()] visit_contact_mode: Annotated[SimpleCTTermNameWithConflictFlag | None, Field()] - epoch_allocation_uid: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None epoch_allocation: Annotated[ SimpleCTTermNameWithConflictFlag | None, Field(json_schema_extra={"nullable": True}), @@ -267,24 +304,12 @@ class StudyVisitBase(BaseModel): str | None, Field(json_schema_extra={"nullable": True}) ] = None - study_day_number: Annotated[ - int | None, Field(json_schema_extra={"nullable": True}) - ] = None - study_duration_days: Annotated[ - int | None, Field(json_schema_extra={"nullable": True}) - ] = None study_duration_days_label: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None study_day_label: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None - study_week_number: Annotated[ - int | None, Field(json_schema_extra={"nullable": True}) - ] = None - study_duration_weeks: Annotated[ - int | None, Field(json_schema_extra={"nullable": True}) - ] = None study_duration_weeks_label: Annotated[ str | None, Field(json_schema_extra={"nullable": True}) ] = None @@ -295,25 +320,13 @@ class StudyVisitBase(BaseModel): str | None, Field(json_schema_extra={"nullable": True}) ] = None - visit_number: Annotated[float, Field()] visit_subnumber: Annotated[int, Field()] order: Annotated[int | None, Field()] = None - unique_visit_number: Annotated[int | None, Field()] visit_subname: Annotated[str, Field()] visit_name: Annotated[str, Field()] - visit_short_name: Annotated[str, Field()] - visit_window_unit_name: Annotated[ - str | None, Field(json_schema_extra={"nullable": True}) - ] = None - visit_class: Annotated[VisitClass, Field()] - visit_subclass: Annotated[ - VisitSubclass | None, Field(json_schema_extra={"nullable": True}) - ] = None - is_global_anchor_visit: Annotated[bool, Field()] - is_soa_milestone: Annotated[bool, Field()] status: Annotated[str, Field(description="Study Visit status")] start_date: Annotated[datetime, Field(description="Study Visit creation date")] end_date: Annotated[ @@ -344,7 +357,6 @@ def transform_to_response_model( ) -> Self: timepoint = visit.timepoint return cls( - visit_type_name=visit.visit_type.sponsor_preferred_name or "", uid=visit.uid or "", study_uid=visit.study_uid, study_id=( @@ -355,18 +367,8 @@ def transform_to_response_model( study_version=study_value_version or get_latest_on_datetime_str(), study_epoch_uid=visit.epoch_uid, study_epoch=visit.epoch.epoch, - epoch_uid=visit.epoch.epoch.term_uid, order=visit.visit_order, - visit_type_uid=visit.visit_type.term_uid, visit_type=visit.visit_type, - time_reference_uid=( - timepoint.visit_timereference.term_uid if timepoint else None - ), - time_reference_name=( - timepoint.visit_timereference.sponsor_preferred_name - if timepoint - else None - ), time_reference=getattr(timepoint, "visit_timereference", None), time_value=getattr(timepoint, "visit_value", None), time_unit_uid=getattr(timepoint, "time_unit_uid", None), @@ -419,11 +421,7 @@ def transform_to_response_model( description=visit.description, start_rule=visit.start_rule, end_rule=visit.end_rule, - visit_contact_mode_uid=visit.visit_contact_mode.term_uid, visit_contact_mode=visit.visit_contact_mode, - epoch_allocation_uid=( - visit.epoch_allocation.term_uid if visit.epoch_allocation else None - ), epoch_allocation=visit.epoch_allocation, status=visit.status.value, start_date=visit.start_date, @@ -442,11 +440,11 @@ def transform_to_response_model( ) -class StudyVisit(StudyVisitBase): +class StudyVisit(StudyVisitDetailed): order: Annotated[int, Field()] -class StudyVisitVersion(StudyVisitBase): +class StudyVisitVersion(StudyVisitDetailed): changes: Annotated[list[str], Field()] diff --git a/clinical-mdr-api/clinical_mdr_api/models/validators.py b/clinical-mdr-api/clinical_mdr_api/models/validators.py index 502039eb..5a1c7c97 100644 --- a/clinical-mdr-api/clinical_mdr_api/models/validators.py +++ b/clinical-mdr-api/clinical_mdr_api/models/validators.py @@ -7,8 +7,8 @@ from pydantic import ValidationInfo from clinical_mdr_api.domains._utils import get_iso_lang_data -from clinical_mdr_api.domains.concepts.utils import EN_LANGUAGE, ENG_LANGUAGE from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum +from clinical_mdr_api.domains.odms.utils import EN_LANGUAGE, ENG_LANGUAGE from common.exceptions import ValidationException FLOAT_REGEX = "^[0-9]+\\.?[0-9]*$" diff --git a/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py b/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py index 7e9a2086..b7495a8f 100644 --- a/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py +++ b/clinical-mdr-api/clinical_mdr_api/repositories/_utils.py @@ -18,14 +18,14 @@ ActivityGroupingHierarchySimpleModel, ) from clinical_mdr_api.models.concepts.concept import VersionProperties -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmAliasModel, - OdmTranslatedTextModel, -) from clinical_mdr_api.models.controlled_terminologies.ct_term import ( SimpleDictionaryTermModel, SimpleTermModel, ) +from clinical_mdr_api.models.odms.common_models import ( + OdmAliasModel, + OdmTranslatedTextModel, +) from clinical_mdr_api.models.standard_data_models.sponsor_model import SponsorModelBase from common.exceptions import ValidationException from common.utils import ( @@ -230,7 +230,9 @@ def is_injected_field(field) -> bool: return False -def get_order_by_clause(sort_by: dict[str, bool] | None, model: type[BaseModel]): +def get_order_by_clause( + sort_by: dict[str, bool] | None, model: type[BaseModel] +) -> list[str]: sort_paths = [] if sort_by: for key, value in sort_by.items(): diff --git a/clinical-mdr-api/clinical_mdr_api/routers/__init__.py b/clinical-mdr-api/clinical_mdr_api/routers/__init__.py index 25b801a7..e209d479 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/__init__.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/__init__.py @@ -40,32 +40,6 @@ from clinical_mdr_api.routers.concepts.numeric_values_with_unit import ( router as numeric_values_with_unit_router, ) -from clinical_mdr_api.routers.concepts.odms.odm_conditions import ( - router as odm_conditions_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_forms import router as odm_forms_router -from clinical_mdr_api.routers.concepts.odms.odm_item_groups import ( - router as odm_item_groups_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_items import router as odm_item_router -from clinical_mdr_api.routers.concepts.odms.odm_metadata import ( - router as odm_metadata_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_methods import ( - router as odm_methods_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_study_events import ( - router as odm_study_events_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_vendor_attributes import ( - router as odm_vendor_attribute_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_vendor_elements import ( - router as odm_vendor_element_router, -) -from clinical_mdr_api.routers.concepts.odms.odm_vendor_namespaces import ( - router as odm_vendor_namespace_router, -) from clinical_mdr_api.routers.concepts.pharmaceutical_products import ( router as pharmaceutical_products_router, ) @@ -105,6 +79,9 @@ router as ct_terms_router, ) from clinical_mdr_api.routers.ctr_xml.ctr_xml import router as ctr_xml_router +from clinical_mdr_api.routers.data_completeness_tags import ( + router as data_completeness_tags_router, +) from clinical_mdr_api.routers.data_suppliers.data_suppliers import ( router as data_suppliers_router, ) @@ -131,6 +108,23 @@ router as study_listing_router, ) from clinical_mdr_api.routers.notifications import router as notifications_router +from clinical_mdr_api.routers.odms.conditions import router as odm_conditions_router +from clinical_mdr_api.routers.odms.forms import router as odm_forms_router +from clinical_mdr_api.routers.odms.item_groups import router as odm_item_groups_router +from clinical_mdr_api.routers.odms.items import router as odm_item_router +from clinical_mdr_api.routers.odms.metadata import router as odm_metadata_router +from clinical_mdr_api.routers.odms.methods import router as odm_methods_router +from clinical_mdr_api.routers.odms.study_events import router as odm_study_events_router +from clinical_mdr_api.routers.odms.vendor_attributes import ( + router as odm_vendor_attribute_router, +) +from clinical_mdr_api.routers.odms.vendor_elements import ( + router as odm_vendor_element_router, +) +from clinical_mdr_api.routers.odms.vendor_namespaces import ( + router as odm_vendor_namespace_router, +) +from clinical_mdr_api.routers.preferences import router as preferences_router from clinical_mdr_api.routers.projects.projects import router as projects_router from clinical_mdr_api.routers.standard_data_models.data_model_igs import ( router as data_model_igs_router, @@ -265,8 +259,10 @@ ) __all__ = [ + "data_completeness_tags_router", "feature_flags_router", "notifications_router", + "preferences_router", "activities_router", "active_substances_router", "pharmaceutical_products_router", diff --git a/clinical-mdr-api/clinical_mdr_api/routers/_generic_descriptions.py b/clinical-mdr-api/clinical_mdr_api/routers/_generic_descriptions.py index dc825ed0..137a358e 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/_generic_descriptions.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/_generic_descriptions.py @@ -254,6 +254,7 @@ def _parse_json_validator(value: typing.Any) -> typing.Any: "model": ErrorResponse, "description": "Bad Request", } +ERROR_401 = {"model": ErrorResponse, "description": "Unauthorized"} ERROR_403 = {"model": ErrorResponse, "description": "Forbidden"} ERROR_404 = {"model": ErrorResponse, "description": "Entity not found"} ERROR_409 = { @@ -263,12 +264,9 @@ def _parse_json_validator(value: typing.Any) -> typing.Any: } -SYNTAX_FILTERS = ( - FILTERS - + """ +SYNTAX_FILTERS = FILTERS + """ If any provided search term for a given field name is other than a string type, then equal operator will automatically be applied overriding any provided operator. """ -) # Alias for backward compatibility - use _parse_json_validator instead diff --git a/clinical-mdr-api/clinical_mdr_api/routers/admin.py b/clinical-mdr-api/clinical_mdr_api/routers/admin.py index 04e0f009..4de4196d 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/admin.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/admin.py @@ -10,9 +10,14 @@ BurdenIdInput, BurdenInput, ) +from clinical_mdr_api.models.preferences import ( + GlobalPreferencesPatchInput, + PreferencesResponse, +) from clinical_mdr_api.models.user import UserInfo, UserInfoPatchInput from clinical_mdr_api.routers import _generic_descriptions, decorators from clinical_mdr_api.services._meta_repository import MetaRepository +from clinical_mdr_api.services.preferences import PreferencesService from clinical_mdr_api.services.studies.complexity_score import ComplexityScoreService from common import exceptions from common.auth import rbac @@ -242,3 +247,36 @@ def update_complexity_activity_burden( ) -> ActivityBurden: service = ComplexityScoreService() return service.update_activity_burden(activity_subgroup_id, burden) + + +@router.get( + "/global-preferences", + dependencies=[security, rbac.ADMIN_READ], + summary="Returns global preferences", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def get_global_preferences() -> PreferencesResponse: + service = PreferencesService() + return service.get_global_preferences() + + +@router.patch( + "/global-preferences", + dependencies=[security, rbac.ADMIN_WRITE], + summary="Update global preferences", + description="Update one or more global preference settings", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def patch_global_preferences( + payload: GlobalPreferencesPatchInput, +) -> PreferencesResponse: + service = PreferencesService() + return service.update_global_preferences(payload) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/pharmaceutical_products.py b/clinical-mdr-api/clinical_mdr_api/routers/concepts/pharmaceutical_products.py index e5ab9915..c0a1d28a 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/pharmaceutical_products.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/concepts/pharmaceutical_products.py @@ -58,10 +58,10 @@ { "defaults": [ "uid", + "derived_name", "external_id", "dosage_forms=dosage_forms.term_name", "routes_of_administration=routes_of_administration.term_name", - "formulations", "start_date", "version", "status", diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/unit_definitions/unit_definitions.py b/clinical-mdr-api/clinical_mdr_api/routers/concepts/unit_definitions/unit_definitions.py index efadbdb2..dbfbe4e2 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/unit_definitions/unit_definitions.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/concepts/unit_definitions/unit_definitions.py @@ -41,17 +41,13 @@ responses={ 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ e9117175-918f-489e-9a6e-65e0025233a6Alamakota2020-11-19T11:51:43.000ZDraft0.2Testsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -249,17 +245,13 @@ def get_by_uid( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library";"uid";"name";"start_date";"end_date";"status";"version";"change_description";"author_username" "Sponsor";"826d80a7-0b6a-419d-8ef1-80aa241d7ac7";"First [ComparatorIntervention]";"2020-10-22T10:19:29+00:00";;"Draft";"0.1";"Initial version";"NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ Alamakota2020-11-19 11:51:43+00:00NoneDraft0.2Testsomeone@example.comAlamakota2020-11-19 11:51:07+00:002020-11-19 11:51:43+00:00Draft0.1Initial versionsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/configuration.py b/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/configuration.py index dbf286e2..d35721d4 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/configuration.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/controlled_terminologies/configuration.py @@ -35,17 +35,13 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "uid","name","start_date","end_date","status","version","change_description","author_username" "826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ e9117175-918f-489e-9a6e-65e0025233a6Alamakota2020-11-19T11:51:43.000ZDraft0.2Testsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -144,17 +140,13 @@ def get_by_uid( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "uid";"name";"start_date";"end_date";"status";"version";"change_description";"author_username" "826d80a7-0b6a-419d-8ef1-80aa241d7ac7";"First [ComparatorIntervention]";"2020-10-22T10:19:29+00:00";;"Draft";"0.1";"Initial version";"NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ Alamakota2020-11-19 11:51:43+00:00NoneDraft0.2Testsomeone@example.comAlamakota2020-11-19 11:51:07+00:002020-11-19 11:51:43+00:00Draft0.1Initial versionsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -218,7 +210,7 @@ def get_versions( def post( post_input: Annotated[ CTConfigPostInput, Body(description="The configuration that shall be created.") - ] + ], ) -> CTConfigModel: return CTConfigService().post(post_input) # type: ignore diff --git a/clinical-mdr-api/clinical_mdr_api/routers/data_completeness_tags.py b/clinical-mdr-api/clinical_mdr_api/routers/data_completeness_tags.py new file mode 100644 index 00000000..40ca6264 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/routers/data_completeness_tags.py @@ -0,0 +1,83 @@ +# pylint: disable=invalid-name +from typing import Annotated + +from fastapi import APIRouter, Body, Path + +from clinical_mdr_api.models.data_completeness_tag import ( + DataCompletenessTag, + DataCompletenessTagInput, +) +from clinical_mdr_api.routers import _generic_descriptions +from clinical_mdr_api.services.data_completeness_tags import DataCompletenessTagService +from common.auth import rbac +from common.auth.dependencies import security + +# Prefixed with "/data-completeness-tags" +router = APIRouter() + +UID = Path(title="UID of the data completeness tag") + +service = DataCompletenessTagService() + + +@router.get( + "", + dependencies=[security, rbac.ADMIN_READ], + summary="Returns all data completeness tags.", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def get_all_data_completeness_tags() -> list[DataCompletenessTag]: + return service.get_all_data_completeness_tags() + + +@router.post( + "", + dependencies=[security, rbac.ADMIN_WRITE], + summary="Creates a data completeness tag.", + status_code=201, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + 409: _generic_descriptions.ERROR_409, + }, +) +def create_data_completeness_tag( + data_completeness_tag_input: Annotated[DataCompletenessTagInput, Body()], +) -> DataCompletenessTag: + return service.create_data_completeness_tag(data_completeness_tag_input) + + +@router.put( + "/{uid}", + dependencies=[security, rbac.ADMIN_WRITE], + summary="Updates the data completeness tag identified by the provided UID.", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + 409: _generic_descriptions.ERROR_409, + }, +) +def update_data_completeness_tag( + uid: Annotated[str, UID], + data_completeness_tag_input: Annotated[DataCompletenessTagInput, Body()], +) -> DataCompletenessTag: + return service.update_data_completeness_tag(uid, data_completeness_tag_input) + + +@router.delete( + "/{uid}", + dependencies=[security, rbac.ADMIN_WRITE], + summary="Deletes the data completeness tag identified by the provided UID.", + status_code=204, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def delete_data_completeness_tag(uid: Annotated[str, UID]) -> None: + return service.delete_data_completeness_tag(uid) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/__init__.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/__init__.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/__init__.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/__init__.py diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_conditions.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/conditions.py similarity index 96% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_conditions.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/conditions.py index 85fa9fcd..3264eb70 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_conditions.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/conditions.py @@ -2,7 +2,7 @@ from fastapi import APIRouter, Body, Path, Query -from clinical_mdr_api.models.concepts.odms.odm_condition import ( +from clinical_mdr_api.models.odms.condition import ( OdmCondition, OdmConditionPatchInput, OdmConditionPostInput, @@ -10,13 +10,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions -from clinical_mdr_api.services.concepts.odms.odm_conditions import OdmConditionService +from clinical_mdr_api.services.odms.conditions import OdmConditionService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/conditions" +# Prefixed with "/odms/conditions" router = APIRouter() # Argument definitions @@ -46,7 +46,7 @@ def get_all_odm_conditions( ] = None, ) -> CustomPage[OdmCondition]: odm_condition_service = OdmConditionService() - results = odm_condition_service.get_all_concepts( + results = odm_condition_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -189,7 +189,7 @@ def create_odm_condition( odm_condition_create_input: Annotated[OdmConditionPostInput, Body()], ) -> OdmCondition: odm_condition_service = OdmConditionService() - return odm_condition_service.create(concept_input=odm_condition_create_input) + return odm_condition_service.create(odm_input=odm_condition_create_input) @router.patch( @@ -220,7 +220,7 @@ def edit_odm_condition( ) -> OdmCondition: odm_condition_service = OdmConditionService() return odm_condition_service.edit_draft( - uid=odm_condition_uid, concept_edit_input=odm_condition_edit_input + uid=odm_condition_uid, odm_edit_input=odm_condition_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_forms.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py similarity index 97% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_forms.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py index bfa3014f..dd79cbdb 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_forms.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/forms.py @@ -3,10 +3,8 @@ from fastapi import APIRouter, Body, Path, Query from starlette.requests import Request -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmElementWithParentUid, -) -from clinical_mdr_api.models.concepts.odms.odm_form import ( +from clinical_mdr_api.models.odms.common_models import OdmElementWithParentUid +from clinical_mdr_api.models.odms.form import ( OdmForm, OdmFormItemGroupPostInput, OdmFormPatchInput, @@ -15,13 +13,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions, decorators -from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService +from clinical_mdr_api.services.odms.forms import OdmFormService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/forms" +# Prefixed with "/odms/forms" router = APIRouter() # Argument definitions @@ -108,7 +106,7 @@ def get_all_odm_forms( ] = None, ) -> CustomPage[OdmForm]: odm_form_service = OdmFormService() - results = odm_form_service.get_all_concepts( + results = odm_form_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -292,7 +290,7 @@ def create_odm_form( ) -> OdmForm: odm_form_service = OdmFormService() - return odm_form_service.create(concept_input=odm_form_create_input) + return odm_form_service.create(odm_input=odm_form_create_input) @router.patch( @@ -322,7 +320,7 @@ def edit_odm_form( ) -> OdmForm: odm_form_service = OdmFormService() return odm_form_service.edit_draft( - uid=odm_form_uid, concept_edit_input=odm_form_edit_input + uid=odm_form_uid, odm_edit_input=odm_form_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_item_groups.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py similarity index 97% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_item_groups.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py index 2b78f658..4193b1e7 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_item_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/item_groups.py @@ -3,10 +3,8 @@ from fastapi import APIRouter, Body, Path, Query from starlette.requests import Request -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmElementWithParentUid, -) -from clinical_mdr_api.models.concepts.odms.odm_item_group import ( +from clinical_mdr_api.models.odms.common_models import OdmElementWithParentUid +from clinical_mdr_api.models.odms.item_group import ( OdmItemGroup, OdmItemGroupItemPostInput, OdmItemGroupPatchInput, @@ -15,13 +13,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions, decorators -from clinical_mdr_api.services.concepts.odms.odm_item_groups import OdmItemGroupService +from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/item-groups" +# Prefixed with "/odms/item-groups" router = APIRouter() # Argument definitions @@ -108,7 +106,7 @@ def get_all_odm_item_groups( ] = None, ) -> CustomPage[OdmItemGroup]: odm_item_group_service = OdmItemGroupService() - results = odm_item_group_service.get_all_concepts( + results = odm_item_group_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -295,7 +293,7 @@ def create_odm_item_group( odm_item_group_create_input: Annotated[OdmItemGroupPostInput, Body()], ) -> OdmItemGroup: odm_item_group_service = OdmItemGroupService() - return odm_item_group_service.create(concept_input=odm_item_group_create_input) + return odm_item_group_service.create(odm_input=odm_item_group_create_input) @router.patch( @@ -325,7 +323,7 @@ def edit_odm_item_group( ) -> OdmItemGroup: odm_item_group_service = OdmItemGroupService() return odm_item_group_service.edit_draft( - uid=odm_item_group_uid, concept_edit_input=odm_item_group_edit_input + uid=odm_item_group_uid, odm_edit_input=odm_item_group_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_items.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/items.py similarity index 96% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_items.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/items.py index 530aab62..d0fc2d37 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_items.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/items.py @@ -3,10 +3,8 @@ from fastapi import APIRouter, Body, Path, Query from starlette.requests import Request -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmElementWithParentUid, -) -from clinical_mdr_api.models.concepts.odms.odm_item import ( +from clinical_mdr_api.models.odms.common_models import OdmElementWithParentUid +from clinical_mdr_api.models.odms.item import ( OdmItem, OdmItemPatchInput, OdmItemPostInput, @@ -14,13 +12,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions, decorators -from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService +from clinical_mdr_api.services.odms.items import OdmItemService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/items" +# Prefixed with "/odms/items" router = APIRouter() # Argument definitions @@ -125,7 +123,7 @@ def get_all_odm_items( ] = None, ) -> CustomPage[OdmItem]: odm_item_service = OdmItemService() - results = odm_item_service.get_all_concepts( + results = odm_item_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -279,7 +277,7 @@ def create_odm_item( odm_item_create_input: Annotated[OdmItemPostInput, Body()], ) -> OdmItem: odm_item_service = OdmItemService() - return odm_item_service.create(concept_input=odm_item_create_input) + return odm_item_service.create(odm_input=odm_item_create_input) @router.patch( @@ -309,7 +307,7 @@ def edit_odm_item( ) -> OdmItem: odm_item_service = OdmItemService() return odm_item_service.edit_draft( - uid=odm_item_uid, concept_edit_input=odm_item_edit_input + uid=odm_item_uid, odm_edit_input=odm_item_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_metadata.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/metadata.py similarity index 94% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_metadata.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/metadata.py index 7a846875..95ee2a57 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_metadata.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/metadata.py @@ -7,37 +7,29 @@ from fastapi.responses import StreamingResponse from pydantic import StringConstraints -from clinical_mdr_api.domains.concepts.utils import ExporterType, TargetType +from clinical_mdr_api.domains.odms.utils import ExporterType, TargetType from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.routers import _generic_descriptions -from clinical_mdr_api.services.concepts.odms.odm_clinspark_import import ( +from clinical_mdr_api.services.odms.clinspark_import import ( OdmClinicalXmlImporterService, ) -from clinical_mdr_api.services.concepts.odms.odm_csv_exporter import ( - OdmCsvExporterService, -) -from clinical_mdr_api.services.concepts.odms.odm_data_extractor import OdmDataExtractor -from clinical_mdr_api.services.concepts.odms.odm_metadata import ( +from clinical_mdr_api.services.odms.csv_exporter import OdmCsvExporterService +from clinical_mdr_api.services.odms.data_extractor import OdmDataExtractor +from clinical_mdr_api.services.odms.metadata import ( get_odm_aliases, get_odm_formal_expressions, get_odm_translated_texts, ) -from clinical_mdr_api.services.concepts.odms.odm_xml_exporter import ( - OdmXmlExporterService, -) -from clinical_mdr_api.services.concepts.odms.odm_xml_importer import ( - OdmXmlImporterService, -) -from clinical_mdr_api.services.concepts.odms.odm_xml_stylesheets import ( - OdmXmlStylesheetService, -) +from clinical_mdr_api.services.odms.xml_exporter import OdmXmlExporterService +from clinical_mdr_api.services.odms.xml_importer import OdmXmlImporterService +from clinical_mdr_api.services.odms.xml_stylesheets import OdmXmlStylesheetService from common import templating from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.exceptions import ValidationException -# Prefixed with "/concepts/odms/metadata" +# Prefixed with "/odms/metadata" router = APIRouter() OP_ANNOTATION = Annotated[ diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_methods.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/methods.py similarity index 97% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_methods.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/methods.py index b638d2e6..d9d8ecaf 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_methods.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/methods.py @@ -2,7 +2,7 @@ from fastapi import APIRouter, Body, Path, Query -from clinical_mdr_api.models.concepts.odms.odm_method import ( +from clinical_mdr_api.models.odms.method import ( OdmMethod, OdmMethodPatchInput, OdmMethodPostInput, @@ -10,13 +10,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions -from clinical_mdr_api.services.concepts.odms.odm_methods import OdmMethodService +from clinical_mdr_api.services.odms.methods import OdmMethodService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/methods" +# Prefixed with "/odms/methods" router = APIRouter() # Argument definitions @@ -46,7 +46,7 @@ def get_all_odm_methods( ] = None, ) -> CustomPage[OdmMethod]: odm_method_service = OdmMethodService() - results = odm_method_service.get_all_concepts( + results = odm_method_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -187,7 +187,7 @@ def create_odm_method( odm_method_create_input: Annotated[OdmMethodPostInput, Body()], ) -> OdmMethod: odm_method_service = OdmMethodService() - return odm_method_service.create(concept_input=odm_method_create_input) + return odm_method_service.create(odm_input=odm_method_create_input) @router.patch( @@ -218,7 +218,7 @@ def edit_odm_method( ) -> OdmMethod: odm_method_service = OdmMethodService() return odm_method_service.edit_draft( - uid=odm_method_uid, concept_edit_input=odm_method_edit_input + uid=odm_method_uid, odm_edit_input=odm_method_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_study_events.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py similarity index 97% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_study_events.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py index d5b01920..721aa6d2 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_study_events.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/study_events.py @@ -3,7 +3,7 @@ from fastapi import APIRouter, Body, Path, Query from starlette.requests import Request -from clinical_mdr_api.models.concepts.odms.odm_study_event import ( +from clinical_mdr_api.models.odms.study_event import ( OdmStudyEvent, OdmStudyEventFormPostInput, OdmStudyEventPatchInput, @@ -12,15 +12,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions, decorators -from clinical_mdr_api.services.concepts.odms.odm_study_events import ( - OdmStudyEventService, -) +from clinical_mdr_api.services.odms.study_events import OdmStudyEventService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/templates" +# Prefixed with "/odms/templates" router = APIRouter() # Argument definitions @@ -77,7 +75,7 @@ def get_all_odm_study_events( ] = None, ) -> CustomPage[OdmStudyEvent]: odm_study_event_service = OdmStudyEventService() - results = odm_study_event_service.get_all_concepts( + results = odm_study_event_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -220,7 +218,7 @@ def create_odm_study_event( odm_study_event_create_input: Annotated[OdmStudyEventPostInput, Body()], ) -> OdmStudyEvent: odm_study_event_service = OdmStudyEventService() - return odm_study_event_service.create(concept_input=odm_study_event_create_input) + return odm_study_event_service.create(odm_input=odm_study_event_create_input) @router.patch( @@ -250,7 +248,7 @@ def edit_odm_study_event( ) -> OdmStudyEvent: odm_study_event_service = OdmStudyEventService() return odm_study_event_service.edit_draft( - uid=odm_study_event_uid, concept_edit_input=odm_study_event_edit_input + uid=odm_study_event_uid, odm_edit_input=odm_study_event_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_attributes.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_attributes.py similarity index 96% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_attributes.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_attributes.py index 753f70f5..14c61064 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_attributes.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_attributes.py @@ -2,7 +2,7 @@ from fastapi import APIRouter, Body, Path, Query -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( +from clinical_mdr_api.models.odms.vendor_attribute import ( OdmVendorAttribute, OdmVendorAttributePatchInput, OdmVendorAttributePostInput, @@ -10,15 +10,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions -from clinical_mdr_api.services.concepts.odms.odm_vendor_attributes import ( - OdmVendorAttributeService, -) +from clinical_mdr_api.services.odms.vendor_attributes import OdmVendorAttributeService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/vendor-attributes" +# Prefixed with "/odms/vendor-attributes" router = APIRouter() # Argument definitions @@ -48,7 +46,7 @@ def get_all_odm_vendor_attributes( ] = None, ) -> CustomPage[OdmVendorAttribute]: odm_vendor_attribute_service = OdmVendorAttributeService() - results = odm_vendor_attribute_service.get_all_concepts( + results = odm_vendor_attribute_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -197,7 +195,7 @@ def create_odm_vendor_attribute( ) -> OdmVendorAttribute: odm_vendor_attribute_service = OdmVendorAttributeService() return odm_vendor_attribute_service.create( - concept_input=odm_vendor_attribute_create_input + odm_input=odm_vendor_attribute_create_input ) @@ -228,7 +226,7 @@ def edit_odm_vendor_attribute( ) -> OdmVendorAttribute: odm_vendor_attribute_service = OdmVendorAttributeService() return odm_vendor_attribute_service.edit_draft( - uid=odm_vendor_attribute_uid, concept_edit_input=odm_vendor_attribute_edit_input + uid=odm_vendor_attribute_uid, odm_edit_input=odm_vendor_attribute_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_elements.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_elements.py similarity index 96% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_elements.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_elements.py index e377ad5c..df0ac492 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_elements.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_elements.py @@ -2,7 +2,7 @@ from fastapi import APIRouter, Body, Path, Query -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( +from clinical_mdr_api.models.odms.vendor_element import ( OdmVendorElement, OdmVendorElementPatchInput, OdmVendorElementPostInput, @@ -10,15 +10,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions -from clinical_mdr_api.services.concepts.odms.odm_vendor_elements import ( - OdmVendorElementService, -) +from clinical_mdr_api.services.odms.vendor_elements import OdmVendorElementService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/vendor-elements" +# Prefixed with "/odms/vendor-elements" router = APIRouter() # Argument definitions @@ -48,7 +46,7 @@ def get_all_odm_vendor_elements( ] = None, ) -> CustomPage[OdmVendorElement]: odm_vendor_element_service = OdmVendorElementService() - results = odm_vendor_element_service.get_all_concepts( + results = odm_vendor_element_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -194,9 +192,7 @@ def create_odm_vendor_element( odm_vendor_element_create_input: Annotated[OdmVendorElementPostInput, Body()], ) -> OdmVendorElement: odm_vendor_element_service = OdmVendorElementService() - return odm_vendor_element_service.create( - concept_input=odm_vendor_element_create_input - ) + return odm_vendor_element_service.create(odm_input=odm_vendor_element_create_input) @router.patch( @@ -226,7 +222,7 @@ def edit_odm_vendor_element( ) -> OdmVendorElement: odm_vendor_element_service = OdmVendorElementService() return odm_vendor_element_service.edit_draft( - uid=odm_vendor_element_uid, concept_edit_input=odm_vendor_element_edit_input + uid=odm_vendor_element_uid, odm_edit_input=odm_vendor_element_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_namespaces.py b/clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_namespaces.py similarity index 96% rename from clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_namespaces.py rename to clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_namespaces.py index de387dbe..473be460 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/concepts/odms/odm_vendor_namespaces.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/odms/vendor_namespaces.py @@ -2,7 +2,7 @@ from fastapi import APIRouter, Body, Path, Query -from clinical_mdr_api.models.concepts.odms.odm_vendor_namespace import ( +from clinical_mdr_api.models.odms.vendor_namespace import ( OdmVendorNamespace, OdmVendorNamespacePatchInput, OdmVendorNamespacePostInput, @@ -10,15 +10,13 @@ from clinical_mdr_api.models.utils import CustomPage from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions -from clinical_mdr_api.services.concepts.odms.odm_vendor_namespaces import ( - OdmVendorNamespaceService, -) +from clinical_mdr_api.services.odms.vendor_namespaces import OdmVendorNamespaceService from common.auth import rbac from common.auth.dependencies import security from common.config import settings from common.models.error import ErrorResponse -# Prefixed with "/concepts/odms/vendor-namespaces" +# Prefixed with "/odms/vendor-namespaces" router = APIRouter() # Argument definitions @@ -48,7 +46,7 @@ def get_all_odm_vendor_namespaces( ] = None, ) -> CustomPage[OdmVendorNamespace]: odm_vendor_namespace_service = OdmVendorNamespaceService() - results = odm_vendor_namespace_service.get_all_concepts( + results = odm_vendor_namespace_service.get_all_odms( library=library_name, sort_by=sort_by, page_number=page_number, @@ -198,7 +196,7 @@ def create_odm_vendor_namespace( ) -> OdmVendorNamespace: odm_vendor_namespace_service = OdmVendorNamespaceService() return odm_vendor_namespace_service.create( - concept_input=odm_vendor_namespace_create_input + odm_input=odm_vendor_namespace_create_input ) @@ -229,7 +227,7 @@ def edit_odm_vendor_namespace( ) -> OdmVendorNamespace: odm_vendor_namespace_service = OdmVendorNamespaceService() return odm_vendor_namespace_service.edit_draft( - uid=odm_vendor_namespace_uid, concept_edit_input=odm_vendor_namespace_edit_input + uid=odm_vendor_namespace_uid, odm_edit_input=odm_vendor_namespace_edit_input ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/preferences.py b/clinical-mdr-api/clinical_mdr_api/routers/preferences.py new file mode 100644 index 00000000..d089039e --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/routers/preferences.py @@ -0,0 +1,59 @@ +from fastapi import APIRouter + +from clinical_mdr_api.models.preferences import ( + UserPreferencesPatchInput, + UserPreferencesResponse, +) +from clinical_mdr_api.routers import _generic_descriptions +from clinical_mdr_api.services.preferences import PreferencesService +from common.auth.dependencies import security +from common.auth.user import user + +# Prefixed with "/user-preferences" +router = APIRouter() + + +@router.get( + "", + dependencies=[security], + summary="Returns user preferences", + status_code=200, + responses={ + 401: _generic_descriptions.ERROR_401, + }, +) +def get_user_preferences() -> UserPreferencesResponse: + service = PreferencesService() + return service.get_user_preferences(user().id()) + + +@router.patch( + "", + dependencies=[security], + summary="Update user preferences", + description="Update one or more user preference settings", + status_code=200, + responses={ + 401: _generic_descriptions.ERROR_401, + }, +) +def patch_user_preferences( + payload: UserPreferencesPatchInput, +) -> UserPreferencesResponse: + service = PreferencesService() + return service.update_user_preferences(user().id(), payload) + + +@router.delete( + "/{preference_key}", + dependencies=[security], + summary="Delete user preference", + description="Reset a user preference to global default by deleting the user override", + status_code=200, + responses={ + 401: _generic_descriptions.ERROR_401, + }, +) +def delete_user_preference(preference_key: str) -> UserPreferencesResponse: + service = PreferencesService() + return service.delete_user_preference_key(user().id(), preference_key) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/dataset_classes.py b/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/dataset_classes.py index f625b278..a8aa7b30 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/dataset_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/dataset_classes.py @@ -2,7 +2,7 @@ from typing import Annotated, Any -from fastapi import APIRouter, Path +from fastapi import APIRouter, Path, Query from starlette.requests import Request from clinical_mdr_api.models.standard_data_models.dataset_class import DatasetClass @@ -58,6 +58,12 @@ # pylint: disable=unused-argument def get_dataset_classes( request: Request, # request is actually required by the allow_exports decorator + data_model_name: Annotated[ + str, + Query( + description="The full name of the model, for instance 'SDTM v2.0'", + ), + ], 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, @@ -67,6 +73,7 @@ def get_dataset_classes( ) -> CustomPage[DatasetClass]: dataset_class_service = DatasetClassService() results = dataset_class_service.get_all_items( + data_model_name=data_model_name, sort_by=sort_by, page_number=page_number, page_size=page_size, @@ -95,6 +102,12 @@ def get_dataset_classes( }, ) def get_distinct_values_for_header( + data_model_name: Annotated[ + str, + Query( + description="The full name of the model, for instance 'SDTM v2.0'", + ), + ], field_name: _generic_descriptions.HEADER_FIELD_NAME_QUERY, search_string: _generic_descriptions.HEADER_SEARCH_STRING_QUERY = "", filters: _generic_descriptions.FILTERS_QUERY = None, @@ -103,6 +116,7 @@ def get_distinct_values_for_header( ) -> list[Any]: dataset_class_service = DatasetClassService() return dataset_class_service.get_distinct_values_for_header( + data_model_name=data_model_name, field_name=field_name, search_string=search_string, filter_by=filters, @@ -135,6 +149,14 @@ def get_distinct_values_for_header( ) def get_dataset_class( dataset_class_uid: Annotated[str, DatasetClassUID], + data_model_name: Annotated[ + str, + Query( + description="The full name of the model, for instance 'SDTM v2.0'", + ), + ], ) -> DatasetClass: dataset_class_service = DatasetClassService() - return dataset_class_service.get_by_uid(uid=dataset_class_uid) + return dataset_class_service.get_by_uid( + uid=dataset_class_uid, data_model_name=data_model_name + ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_dataset_variables.py b/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_dataset_variables.py index d5cb549a..5f1b6b3a 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_dataset_variables.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_dataset_variables.py @@ -2,7 +2,7 @@ from typing import Annotated, Any -from fastapi import APIRouter, Body, Path +from fastapi import APIRouter, Body, Path, Query from starlette.requests import Request from clinical_mdr_api.models.standard_data_models.sponsor_model_dataset_variable import ( @@ -62,6 +62,18 @@ # pylint: disable=unused-argument def get_sponsor_model_dataset_variables( request: Request, # request is actually required by the allow_exports decorator + sponsor_model_name: Annotated[ + str, + Query( + description="The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + ), + ], + sponsor_model_version: Annotated[ + str, + Query( + description="The version number of the sponsor model, for instance '15'", + ), + ], 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, @@ -71,6 +83,8 @@ def get_sponsor_model_dataset_variables( ) -> CustomPage[SponsorModelDatasetVariable]: sponsor_model_dataset_variable_service = SponsorModelDatasetVariableService() results = sponsor_model_dataset_variable_service.get_all_items( + sponsor_model_name=sponsor_model_name, + sponsor_model_version=sponsor_model_version, sort_by=sort_by, page_number=page_number, page_size=page_size, @@ -99,7 +113,19 @@ def get_sponsor_model_dataset_variables( }, ) def get_distinct_values_for_header( - field_name: _generic_descriptions.HEADER_FIELD_NAME_QUERY, + sponsor_model_name: Annotated[ + str, + Query( + description="The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + ), + ], + sponsor_model_version_number: Annotated[ + str | None, + Query( + description="The version number of the sponsor model", + ), + ] = None, + field_name: _generic_descriptions.HEADER_FIELD_NAME_QUERY = "", search_string: _generic_descriptions.HEADER_SEARCH_STRING_QUERY = "", filters: _generic_descriptions.FILTERS_QUERY = None, operator: _generic_descriptions.FILTER_OPERATOR_QUERY = settings.default_filter_operator, @@ -112,6 +138,8 @@ def get_distinct_values_for_header( filter_by=filters, filter_operator=FilterOperator.from_str(operator), page_size=page_size, + sponsor_model_name=sponsor_model_name, + sponsor_model_version_number=sponsor_model_version_number, ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_datasets.py b/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_datasets.py index 9d62d242..0fdfccc9 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_datasets.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/standard_data_models/sponsor_model_datasets.py @@ -2,7 +2,7 @@ from typing import Annotated, Any -from fastapi import APIRouter, Body, Path +from fastapi import APIRouter, Body, Path, Query from starlette.requests import Request from clinical_mdr_api.models.standard_data_models.sponsor_model_dataset import ( @@ -60,6 +60,15 @@ # pylint: disable=unused-argument def get_sponsor_model_datasets( request: Request, # request is actually required by the allow_exports decorator + sponsor_model_name: Annotated[ + str, + Query( + description="The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + ), + ], + sponsor_model_version: Annotated[ + str, Query(description="The version of the sponsor model, for instance '15'") + ], 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, @@ -69,6 +78,8 @@ def get_sponsor_model_datasets( ) -> CustomPage[SponsorModelDataset]: sponsor_model_dataset_service = SponsorModelDatasetService() results = sponsor_model_dataset_service.get_all_items( + sponsor_model_name=sponsor_model_name, + sponsor_model_version=sponsor_model_version, sort_by=sort_by, page_number=page_number, page_size=page_size, @@ -97,7 +108,13 @@ def get_sponsor_model_datasets( }, ) def get_distinct_values_for_header( - field_name: _generic_descriptions.HEADER_FIELD_NAME_QUERY, + sponsor_model_name: Annotated[ + str, + Query( + description="The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + ), + ], + field_name: _generic_descriptions.HEADER_FIELD_NAME_QUERY = "", search_string: _generic_descriptions.HEADER_SEARCH_STRING_QUERY = "", filters: _generic_descriptions.FILTERS_QUERY = None, operator: _generic_descriptions.FILTER_OPERATOR_QUERY = settings.default_filter_operator, @@ -110,6 +127,7 @@ def get_distinct_values_for_header( filter_by=filters, filter_operator=FilterOperator.from_str(operator), page_size=page_size, + sponsor_model_name=sponsor_model_name, ) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py b/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py index 536b849e..78eba137 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/studies/studies.py @@ -240,6 +240,7 @@ def get_all( "latest_locked_version_description=latest_locked_version.change_description", "latest_released_version_number=latest_released_version.version_number", "latest_released_version_description=latest_released_version.change_description", + "data_completeness_tags", ], "formats": [ "text/csv", @@ -258,6 +259,42 @@ def get_studies_list( description="Indicates whether to return minimal response with only `uid`, `id` and `acronym`." ), ] = True, + has_study_objective: Annotated[ + bool | None, + Query( + description="Filter studies by Study Objectives presence: `true` (has objectives), `false` (no objectives), or omit (all studies).", + ), + ] = None, + has_study_footnote: Annotated[ + bool | None, + Query( + description="Filter studies by Study Objectives presence: `true` (has objectives), `false` (no objectives), or omit (all studies).", + ), + ] = None, + has_study_endpoint: Annotated[ + bool | None, + Query( + description="Filter studies by Study Endpoints presence: `true` (has endpoints), `false` (no endpoints), or omit (all studies).", + ), + ] = None, + has_study_criteria: Annotated[ + bool | None, + Query( + description="Filter studies by Study Criteria presence: `true` (has criteria), `false` (no criteria), or omit (all studies).", + ), + ] = None, + has_study_activity: Annotated[ + bool | None, + Query( + description="Filter studies by Study Activities presence: `true` (has activities), `false` (no activities), or omit (all studies).", + ), + ] = None, + has_study_activity_instruction: Annotated[ + bool | None, + Query( + description="Filter studies by Study Activity Instructions presence: `true` (has activity instructions), `false` (no activity instructions), or omit (all studies).", + ), + ] = None, deleted: Annotated[ bool, Query( @@ -270,7 +307,14 @@ def get_studies_list( """ study_service = StudyService() return study_service.get_studies_list( - minimal_response=minimal_response, deleted=deleted + minimal_response=minimal_response, + has_study_objective=has_study_objective, + has_study_footnote=has_study_footnote, + has_study_endpoint=has_study_endpoint, + has_study_criteria=has_study_criteria, + has_study_activity=has_study_activity, + has_study_activity_instruction=has_study_activity_instruction, + deleted=deleted, ) @@ -550,7 +594,7 @@ def release( }, }, ) -def delete_activity(study_uid: Annotated[str, StudyUID]): +def delete_study(study_uid: Annotated[str, StudyUID]): study_service = StudyService() study_service.soft_delete(uid=study_uid) @@ -799,7 +843,7 @@ def get_snapshot_history( 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, - only_latest_major_protcol_version: Annotated[ + only_latest_major_protocol_version: Annotated[ bool, Query( description="Indicates whether Study snapshots without protocol header version should be returned", @@ -812,7 +856,7 @@ def get_snapshot_history( page_number=page_number, page_size=page_size, total_count=total_count, - only_latest_major_protcol_version=only_latest_major_protcol_version, + only_latest_major_protocol_version=only_latest_major_protocol_version, ) return CustomPage( items=snapshot_history.items, @@ -1333,7 +1377,7 @@ def get_complexity_score( str | None, Query( description="Study Version Number", - example="2.1", + openapi_examples={"2.1": {"value": "2.1"}}, alias="study_value_version", ), ] = None, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/studies/study.py b/clinical-mdr-api/clinical_mdr_api/routers/studies/study.py index 59c3e80b..bd81d79b 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/studies/study.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/studies/study.py @@ -7,6 +7,7 @@ from fastapi.responses import HTMLResponse, StreamingResponse from pydantic import Field +from clinical_mdr_api.models.data_completeness_tag import DataCompletenessTag from clinical_mdr_api.models.study_selections.study_selection import ( CompactStudyArm, StudyActivityGroup, @@ -96,6 +97,7 @@ from clinical_mdr_api.models.utils import CustomPage, GenericFilteringReturn from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.routers import _generic_descriptions, decorators +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_activity_group import ( StudyActivityGroupService, @@ -170,6 +172,7 @@ study_element_uid_path = Path(description="The unique id of the study element.") study_branch_arm_uid_path = Path(description="The unique id of the study branch arm.") study_cohort_uid_path = Path(description="The unique id of the study cohort.") +data_completeness_tag_uid_path = Path(title="UID of the data completeness tag") PROJECT_NAME = Query( description="Optionally, the name of the project for which to return study selections.", ) @@ -6196,3 +6199,59 @@ def study_cohorts_batch_operations( ) -> list[StudySelectionCohortBatchOutput]: service = StudyCohortSelectionService() return service.handle_batch_operations(study_uid, operations) + + +# API endpoints for study data completeness tags + + +@router.get( + "/studies/{study_uid}/data-completeness-tags", + dependencies=[security, rbac.ADMIN_READ], + summary="Returns all data completeness tags assigned to the given study.", + status_code=200, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def get_study_data_completeness_tags( + study_uid: Annotated[str, studyUID], +) -> list[DataCompletenessTag]: + service = DataCompletenessTagService() + return service.get_tags_for_study(study_uid) + + +@router.post( + "/studies/{study_uid}/data-completeness-tags", + dependencies=[security, rbac.ADMIN_WRITE], + summary="Assigns a data completeness tag to the given study.", + status_code=201, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def assign_data_completeness_tag_to_study( + study_uid: Annotated[str, studyUID], + uid: Annotated[str, Body(title="UID of the data completeness tag", embed=True)], +) -> DataCompletenessTag: + service = DataCompletenessTagService() + return service.assign_tag_to_study(study_uid, uid) + + +@router.delete( + "/studies/{study_uid}/data-completeness-tags/{uid}", + dependencies=[security, rbac.ADMIN_WRITE], + summary="Removes a data completeness tag from the given study.", + status_code=204, + responses={ + 403: _generic_descriptions.ERROR_403, + 404: _generic_descriptions.ERROR_404, + }, +) +def remove_data_completeness_tag_from_study( + study_uid: Annotated[str, studyUID], + uid: Annotated[str, data_completeness_tag_uid_path], +) -> None: + service = DataCompletenessTagService() + return service.remove_tag_from_study(study_uid, uid) 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 f117eb89..ab49a3f5 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 @@ -167,7 +167,7 @@ def get_study_flowchart_docx( .get_document_stream() ) - study_id = _get_study_id(study_uid, study_value_version) + study_id = StudyService().get_study_id(study_uid, study_value_version) filename = f"{study_id or study_uid} {layout.value} SoA.docx" mime_type = MIME_TYPE_DOCX @@ -203,7 +203,7 @@ def get_study_flowchart_xlsx( stream = io.BytesIO() workbook.save(stream) - study_id = _get_study_id(study_uid, study_value_version) + study_id = StudyService().get_study_id(study_uid, study_value_version) filename = f"{study_id or study_uid} {layout.value} SoA.xlsx" mime_type = MIME_TYPE_XLSX @@ -238,7 +238,7 @@ def get_operational_soa_xlsx( stream = io.BytesIO() xlsx.save(stream) - study_id = _get_study_id(study_uid, study_value_version) + study_id = StudyService().get_study_id(study_uid, study_value_version) filename = f"{study_id or study_uid} {layout.value} SoA.xlsx" mime_type = MIME_TYPE_XLSX @@ -299,7 +299,7 @@ def get_detailed_soa_xlsx( stream = io.BytesIO() xlsx.save(stream) - study_id = _get_study_id(study_uid, study_value_version) + study_id = StudyService().get_study_id(study_uid, study_value_version) filename = f"{study_id or study_uid} {layout.value} SoA.xlsx" mime_type = MIME_TYPE_XLSX @@ -575,16 +575,6 @@ def update_soa_snapshot( return Response(content=None, status_code=status.HTTP_201_CREATED) -def _get_study_id(study_uid, study_value_version): - """gets study_id of study""" - - study = StudyService().get_by_uid( - study_uid, study_value_version=study_value_version - ) - - return study.current_metadata.identification_metadata.study_id - - def _streaming_response( stream: io.BytesIO, filename: str, mime_type: str ) -> StreamingResponse: 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 761435c8..3c0bb914 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 @@ -9,6 +9,7 @@ StudyVisit, StudyVisitCreateInput, StudyVisitEditInput, + StudyVisitLite, StudyVisitVersion, VisitConsecutiveGroupInput, ) @@ -130,7 +131,10 @@ def get_all( description="Indicates whether the (visit_name, visit_short_name, unique_visit_number) properties are derived based on the study visit timeline and not from database values.", ), ] = False, -) -> CustomPage[StudyVisit]: + lite: Annotated[ + bool, Query(description=_generic_descriptions.HEADERS_QUERY_LITE) + ] = False, +) -> CustomPage[StudyVisitLite | StudyVisit]: results = StudyVisitService.get_all_visits( study_uid=study_uid, sort_by=sort_by, @@ -141,6 +145,7 @@ def get_all( filter_operator=FilterOperator.from_str(operator), study_value_version=study_value_version, derive_props_based_on_timeline=derive_props_based_on_timeline, + lite=lite, ) return CustomPage( items=results.items, total=results.total, page=page_number, size=page_size diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/activity_instructions.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/activity_instructions.py index b977ab2d..7b8aea51 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/activity_instructions.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/activity_instructions.py @@ -48,12 +48,10 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","template","uid","objective","start_date","end_date","status","version","change_description","author_username" "Sponsor","First [ComparatorIntervention]","826d80a7-0b6a-419d-8ef1-80aa241d7ac7",First Intervention,"2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/criteria.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/criteria.py index 42c0ba98..611c68c6 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/criteria.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/criteria.py @@ -48,15 +48,12 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","objective","template","criteria","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","Objective","First [ComparatorIntervention]","First Intervention","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, - "text/xml": { - "example": """ + "text/xml": {"example": """ @@ -75,8 +72,7 @@ -""" - }, +"""}, } }, }, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/endpoints.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/endpoints.py index f0288738..1a8ea33a 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/endpoints.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/endpoints.py @@ -46,15 +46,12 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","objective","template","endpoint","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","Objective","First [ComparatorIntervention]","First Intervention","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, - "text/xml": { - "example": """ + "text/xml": {"example": """ @@ -73,8 +70,7 @@ -""" - }, +"""}, } }, }, @@ -233,15 +229,12 @@ def get(endpoint_uid: Annotated[str, EndpointUID]) -> Endpoint: 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","template","objective","uid","endpoint","start_date","end_date","status","version","change_description","author_username" "Sponsor","First [ComparatorIntervention]","Objective","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First Intervention","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, - "text/xml": { - "example": """ + "text/xml": {"example": """ @@ -260,8 +253,7 @@ def get(endpoint_uid: Annotated[str, EndpointUID]) -> Endpoint: -""" - }, +"""}, } }, 404: { @@ -630,6 +622,6 @@ def delete(endpoint_uid: Annotated[str, EndpointUID]): }, ) def get_parameters( - endpoint_uid: Annotated[str, EndpointUID] + endpoint_uid: Annotated[str, EndpointUID], ) -> list[TemplateParameter]: return EndpointService().get_parameters(endpoint_uid) diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/footnotes.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/footnotes.py index b3dd39de..fa2fa8c2 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/footnotes.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/footnotes.py @@ -48,15 +48,12 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","objective","template","footnote","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","Objective","First [ComparatorIntervention]","First Intervention","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, - "text/xml": { - "example": """ + "text/xml": {"example": """ @@ -75,8 +72,7 @@ -""" - }, +"""}, } }, }, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/objectives.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/objectives.py index 0e90da44..fdf106a1 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/objectives.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/objectives.py @@ -46,12 +46,10 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","template","uid","objective","start_date","end_date","status","version","change_description","author_username" "Sponsor","First [ComparatorIntervention]","826d80a7-0b6a-419d-8ef1-80aa241d7ac7",First Intervention,"2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/timeframes.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/timeframes.py index d17babd8..a5469a85 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/timeframes.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_instances/timeframes.py @@ -46,12 +46,10 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","template","uid","timeframe","start_date","end_date","status","version","change_description","author_username" "Sponsor","First [ComparatorIntervention]","826d80a7-0b6a-419d-8ef1-80aa241d7ac7",First Intervention,"2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_pre_instances/objective_pre_instances.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_pre_instances/objective_pre_instances.py index 53b025b5..6ba7463f 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_pre_instances/objective_pre_instances.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_pre_instances/objective_pre_instances.py @@ -290,15 +290,12 @@ def patch_indexings( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","objective_template","objective","uid","objective","start_date","end_date","status","version","change_description","author_username" "Sponsor","First [ComparatorIntervention]","Objective","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First Intervention","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, - "text/xml": { - "example": """ + "text/xml": {"example": """ @@ -317,8 +314,7 @@ def patch_indexings( -""" - }, +"""}, } }, 404: { diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/activity_instruction_templates.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/activity_instruction_templates.py index 7f52a3c9..31a6368d 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/activity_instruction_templates.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/activity_instruction_templates.py @@ -76,14 +76,11 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -98,8 +95,7 @@ -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -279,14 +275,11 @@ def get_activity_instruction_template( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -310,8 +303,7 @@ def get_activity_instruction_template( -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -417,8 +409,7 @@ def get_activity_instruction_template_releases( * The 'version' property will be set to '0.1'. * The activity instruction template will be linked to a library. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=201, responses={ 403: _generic_descriptions.ERROR_403, @@ -462,8 +453,7 @@ def create_activity_instruction_template( Parameters in the 'name' property can only be changed if the activity instruction template has never been approved. Once the activity instruction template has been approved, only the surrounding text (excluding the parameters) can be changed. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=200, responses={ 403: _generic_descriptions.ERROR_403, @@ -747,8 +737,16 @@ def delete_activity_instruction_template( ) def get_parameters( activity_instruction_template_uid: Annotated[str, ActivityInstructionTemplateUID], + study_uid: Annotated[ + str | None, + Query( + description="Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + ), + ] = None, ) -> list[TemplateParameter]: - return Service().get_parameters(uid=activity_instruction_template_uid) + return Service().get_parameters( + uid=activity_instruction_template_uid, study_uid=study_uid + ) @router.post( diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/criteria_templates.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/criteria_templates.py index dac76db2..b02ce796 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/criteria_templates.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/criteria_templates.py @@ -74,14 +74,11 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -96,8 +93,7 @@ -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -275,14 +271,11 @@ def get_criteria_template( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -306,8 +299,7 @@ def get_criteria_template( -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -409,8 +401,7 @@ def get_criteria_template_releases( * The 'version' property will be set to '0.1'. * The criteria template will be linked to a library. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=201, responses={ 403: _generic_descriptions.ERROR_403, @@ -454,8 +445,7 @@ def create_criteria_template( Parameters in the 'name' property can only be changed if the criteria template has never been approved. Once the criteria template has been approved, only the surrounding text (excluding the parameters) can be changed. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=200, responses={ 403: _generic_descriptions.ERROR_403, @@ -735,8 +725,14 @@ def delete_criteria_template( ) def get_parameters( criteria_template_uid: Annotated[str, CriteriaTemplateUID], + study_uid: Annotated[ + str | None, + Query( + description="Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + ), + ] = None, ) -> list[TemplateParameter]: - return Service().get_parameters(uid=criteria_template_uid) + return Service().get_parameters(uid=criteria_template_uid, study_uid=study_uid) @router.post( diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/endpoint_templates.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/endpoint_templates.py index 2cb18892..80200a8e 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/endpoint_templates.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/endpoint_templates.py @@ -75,14 +75,11 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username", <> "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -97,8 +94,7 @@ -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -275,14 +271,11 @@ def get_endpoint_template( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -306,8 +299,7 @@ def get_endpoint_template( -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -409,8 +401,7 @@ def get_endpoint_template_releases( * The 'version' property will be set to '0.1'. * The endpoint template will be linked to a library. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=201, responses={ 403: _generic_descriptions.ERROR_403, @@ -454,8 +445,7 @@ def create_endpoint_template( Parameters in the 'name' property can only be changed if the endpoint template has never been approved. Once the endpoint template has been approved, only the surrounding text (excluding the parameters) can be changed. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=200, responses={ 403: _generic_descriptions.ERROR_403, @@ -735,8 +725,14 @@ def delete_endpoint_template( ) def get_parameters( endpoint_template_uid: Annotated[str, EndpointTemplateUID], + study_uid: Annotated[ + str | None, + Query( + description="Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + ), + ] = None, ) -> list[TemplateParameter]: - return Service().get_parameters(uid=endpoint_template_uid) + return Service().get_parameters(uid=endpoint_template_uid, study_uid=study_uid) @router.post( diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/footnote_templates.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/footnote_templates.py index 0a992ac6..52268839 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/footnote_templates.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/footnote_templates.py @@ -74,14 +74,11 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -96,8 +93,7 @@ -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -274,14 +270,11 @@ def get_footnote_template( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ @@ -305,8 +298,7 @@ def get_footnote_template( -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -408,8 +400,7 @@ def get_footnote_template_releases( * The 'version' property will be set to '0.1'. * The footnote template will be linked to a library. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=201, responses={ 403: _generic_descriptions.ERROR_403, @@ -453,8 +444,7 @@ def create_footnote_template( Parameters in the 'name' property can only be changed if the footnote template has never been approved. Once the footnote template has been approved, only the surrounding text (excluding the parameters) can be changed. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=200, responses={ 403: _generic_descriptions.ERROR_403, @@ -734,8 +724,14 @@ def delete_footnote_template( ) def get_parameters( footnote_template_uid: Annotated[str, FootnoteTemplateUID], + study_uid: Annotated[ + str | None, + Query( + description="Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + ), + ] = None, ) -> list[TemplateParameter]: - return Service().get_parameters(uid=footnote_template_uid) + return Service().get_parameters(uid=footnote_template_uid, study_uid=study_uid) @router.post( diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/objective_templates.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/objective_templates.py index 9fd43cff..9342b9ab 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/objective_templates.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/objective_templates.py @@ -74,17 +74,13 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ e9117175-918f-489e-9a6e-65e0025233a6Alamakota2020-11-19T11:51:43.000ZDraft0.2Testsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -261,17 +257,13 @@ def get_objective_template( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library";"uid";"name";"start_date";"end_date";"status";"version";"change_description";"author_username" "Sponsor";"826d80a7-0b6a-419d-8ef1-80aa241d7ac7";"First [ComparatorIntervention]";"2020-10-22T10:19:29+00:00";;"Draft";"0.1";"Initial version";"NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ Alamakota2020-11-19 11:51:43+00:00NoneDraft0.2Testsomeone@example.comAlamakota2020-11-19 11:51:07+00:002020-11-19 11:51:43+00:00Draft0.1Initial versionsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -373,8 +365,7 @@ def get_objective_template_releases( * The 'version' property will be set to '0.1'. * The objective template will be linked to a library. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=201, responses={ 403: _generic_descriptions.ERROR_403, @@ -418,8 +409,7 @@ def create_objective_template( Parameters in the 'name' property can only be changed if the objective template has never been approved. Once the objective template has been approved, only the surrounding text (excluding the parameters) can be changed. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=200, responses={ 403: _generic_descriptions.ERROR_403, diff --git a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/timeframe_templates.py b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/timeframe_templates.py index b29eb5f5..bb926502 100644 --- a/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/timeframe_templates.py +++ b/clinical-mdr-api/clinical_mdr_api/routers/syntax_templates/timeframe_templates.py @@ -62,17 +62,13 @@ 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library","uid","name","start_date","end_date","status","version","change_description","author_username" "Sponsor","826d80a7-0b6a-419d-8ef1-80aa241d7ac7","First [ComparatorIntervention]","2020-10-22T10:19:29+00:00",,"Draft","0.1","Initial version","NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ e9117175-918f-489e-9a6e-65e0025233a6Alamakota2020-11-19T11:51:43.000ZDraft0.2Testsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -245,17 +241,13 @@ def get_timeframe_template( 403: _generic_descriptions.ERROR_403, 200: { "content": { - "text/csv": { - "example": """ + "text/csv": {"example": """ "library";"uid";"name";"start_date";"end_date";"status";"version";"change_description";"author_username" "Sponsor";"826d80a7-0b6a-419d-8ef1-80aa241d7ac7";"First [ComparatorIntervention]";"2020-10-22T10:19:29+00:00";;"Draft";"0.1";"Initial version";"NdSJ" -""" - }, - "text/xml": { - "example": """ +"""}, + "text/xml": {"example": """ Alamakota2020-11-19 11:51:43+00:00NoneDraft0.2Testsomeone@example.comAlamakota2020-11-19 11:51:07+00:002020-11-19 11:51:43+00:00Draft0.1Initial versionsomeone@example.com -""" - }, +"""}, "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": {}, } }, @@ -338,8 +330,7 @@ def get_timeframe_template_version( * The 'version' property will be set to '0.1'. * The timeframe template will be linked to a library. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=201, responses={ 403: _generic_descriptions.ERROR_403, @@ -382,8 +373,7 @@ def create_timeframe_template( Parameters in the 'name' property can only be changed if the timeframe template has never been approved. Once the timeframe template has been approved, only the surrounding text (excluding the parameters) can be changed. -""" - + PARAMETERS_NOTE, +""" + PARAMETERS_NOTE, status_code=200, responses={ 403: _generic_descriptions.ERROR_403, 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 ce3c729c..61ffabbf 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/services/_meta_repository.py @@ -37,33 +37,6 @@ from clinical_mdr_api.domain_repositories.concepts.medicinal_product_repository import ( MedicinalProductRepository, ) -from clinical_mdr_api.domain_repositories.concepts.odms.condition_repository import ( - ConditionRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.form_repository import ( - FormRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.item_group_repository import ( - ItemGroupRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.item_repository import ( - ItemRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.method_repository import ( - MethodRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.study_event_repository import ( - StudyEventRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.vendor_attribute_repository import ( - VendorAttributeRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.vendor_element_repository import ( - VendorElementRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.vendor_namespace_repository import ( - VendorNamespaceRepository, -) from clinical_mdr_api.domain_repositories.concepts.pharmaceutical_product_repository import ( PharmaceuticalProductRepository, ) @@ -145,6 +118,27 @@ from clinical_mdr_api.domain_repositories.libraries.library_repository import ( LibraryRepository, ) +from clinical_mdr_api.domain_repositories.odms.condition_repository import ( + ConditionRepository, +) +from clinical_mdr_api.domain_repositories.odms.form_repository import FormRepository +from clinical_mdr_api.domain_repositories.odms.item_group_repository import ( + ItemGroupRepository, +) +from clinical_mdr_api.domain_repositories.odms.item_repository import ItemRepository +from clinical_mdr_api.domain_repositories.odms.method_repository import MethodRepository +from clinical_mdr_api.domain_repositories.odms.study_event_repository import ( + StudyEventRepository, +) +from clinical_mdr_api.domain_repositories.odms.vendor_attribute_repository import ( + VendorAttributeRepository, +) +from clinical_mdr_api.domain_repositories.odms.vendor_element_repository import ( + VendorElementRepository, +) +from clinical_mdr_api.domain_repositories.odms.vendor_namespace_repository import ( + VendorNamespaceRepository, +) from clinical_mdr_api.domain_repositories.projects.project_repository import ( ProjectRepository, ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/_utils.py b/clinical-mdr-api/clinical_mdr_api/services/_utils.py index 45d20cca..8050e77f 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/_utils.py +++ b/clinical-mdr-api/clinical_mdr_api/services/_utils.py @@ -8,7 +8,8 @@ from time import time from typing import AbstractSet, Any, Callable, Mapping, MutableMapping, Self, TypeVar -import neomodel.sync_.core +from neomodel.sync_.database import Database +from neomodel.sync_.transaction import TransactionProxy from pydantic import BaseModel from clinical_mdr_api.domain_repositories.libraries.library_repository import ( @@ -1158,7 +1159,7 @@ def build_simple_filters( return None -class AggregatedTransactionProxy(neomodel.sync_.core.TransactionProxy): +class AggregatedTransactionProxy(TransactionProxy): """context manager to manage database transaction if there is no active transaction in progress, else do nothing""" __manage_transaction = None @@ -1182,7 +1183,7 @@ def __call__(self, func: Callable) -> Callable: _Func = TypeVar("_Func", bound=Callable[..., Any]) -def ensure_transaction(db: neomodel.sync_.core.Database) -> Callable[[_Func], _Func]: +def ensure_transaction(db: Database) -> Callable[[_Func], _Func]: """decorator to manage transaction `with TransactionProxy(db)` only if not already in db a transaction""" def decorate(func: _Func) -> _Func: @@ -1195,7 +1196,7 @@ def decorate(func: _Func) -> _Func: def wrapper(*args: Any, **kwargs: Any) -> Any: if db._active_transaction is None: # No active transaction, wrap call into TransactionProxy to start and manage a transaction - with neomodel.sync_.core.TransactionProxy(db): + with TransactionProxy(db): return func(*args, **kwargs) else: 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 683a7a7d..1970fabb 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 @@ -11,6 +11,7 @@ ) from clinical_mdr_api.domains.concepts.activities.activity_item import ( ActivityItemVO, + CTCodelistItem, CTTermItem, ) from clinical_mdr_api.domains.versioned_object_aggregate import LibraryVO @@ -83,6 +84,11 @@ def _create_aggregate_root( 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=( + CTCodelistItem(uid=item.ct_codelist_uid) + if item.ct_codelist_uid + else None + ), ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=item.text_value, @@ -270,6 +276,11 @@ def _edit_aggregate( is_adam_param_specific=activity_item.is_adam_param_specific, activity_item_class_uid=activity_item.activity_item_class_uid, activity_item_class_name=None, + ct_codelist=( + CTCodelistItem(uid=activity_item.ct_codelist_uid) + if activity_item.ct_codelist_uid + else None + ), ct_terms=ct_terms, unit_definitions=unit_definitions, text_value=activity_item.text_value, diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_generic_service.py b/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_generic_service.py deleted file mode 100644 index bec099f2..00000000 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_generic_service.py +++ /dev/null @@ -1,609 +0,0 @@ -import re -from abc import ABC -from typing import Any - -from neomodel import db - -from clinical_mdr_api.domain_repositories.concepts.odms.form_repository import ( - FormRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.item_group_repository import ( - ItemGroupRepository, -) -from clinical_mdr_api.domain_repositories.concepts.odms.item_repository import ( - ItemRepository, -) -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import OdmVendorAttributeAR -from clinical_mdr_api.domains.concepts.utils import ( - RelationType, - VendorAttributeCompatibleType, - VendorElementCompatibleType, -) -from clinical_mdr_api.domains.versioned_object_aggregate import LibraryItemStatus -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmVendorElementRelationPostInput, - OdmVendorRelationPostInput, -) -from clinical_mdr_api.models.utils import BaseModel -from clinical_mdr_api.services._utils import ensure_transaction -from clinical_mdr_api.services.concepts.concept_generic_service import ( - ConceptGenericService, - _AggregateRootType, -) -from common.exceptions import BusinessLogicException - - -class OdmGenericService(ConceptGenericService[_AggregateRootType], ABC): - OBJECT_NOT_IN_DRAFT = "ODM element is not in Draft." - - def fail_if_non_present_vendor_elements_are_used_by_current_odm_element_attributes( - self, - attribute_uids: list[str], - input_elements: list[OdmVendorElementRelationPostInput], - ): - """ - Raises an error if any ODM vendor element that is not present in the input is used by any of the present ODM element attributes. - - Args: - attribute_uids (list[str]): The input ODM element attributes. - input_elements (list[OdmVendorElementRelationPostInput]): The input ODM vendor elements. - - Returns: - None - - Raises: - BusinessLogicException: If an ODM vendor element is used by any of the given ODM element attributes and is not present in the input. - """ - ( - odm_vendor_attribute_ars, - _, - ) = self._repos.odm_vendor_attribute_repository.find_all( - filter_by={"uid": {"v": attribute_uids, "op": "eq"}} - ) - - odm_vendor_attribute_element_uids = { - odm_vendor_attribute_ar.concept_vo.vendor_element_uid - for odm_vendor_attribute_ar in odm_vendor_attribute_ars - if odm_vendor_attribute_ar.concept_vo.vendor_element_uid - } - - BusinessLogicException.raise_if_not( - odm_vendor_attribute_element_uids.issubset( - {input_element.uid for input_element in input_elements} - ), - msg="Cannot remove an ODM Vendor Element whose attributes are connected to this ODM element.", - ) - - def fail_if_these_attributes_cannot_be_added( - self, - input_attributes: list[OdmVendorRelationPostInput], - element_uids: list[str] | None = None, - compatible_type: VendorAttributeCompatibleType | None = None, - ): - """ - Raises an error if any of the given ODM vendor attributes cannot be added as vendor attributes or vendor element attributes. - - Args: - input_attributes (list[OdmVendorRelationPostInput]): The input ODM vendor attributes. - element_uids (list[str] | None, optional): The uids of the vendor elements to which the attributes can be added. - compatible_type (VendorAttributeCompatibleType | None, optional): The vendor compatible type of the attributes. - - Returns: - None - - Raises: - BusinessLogicException: If any of the given ODM vendor attributes cannot be added as vendor attributes or vendor element attributes. - """ - odm_vendor_attribute_ars = self._get_odm_vendor_attributes(input_attributes) - vendor_attribute_patterns = { - odm_vendor_attribute_ar.uid: odm_vendor_attribute_ar.concept_vo.value_regex - for odm_vendor_attribute_ar in odm_vendor_attribute_ars - } - - self.attribute_values_matches_their_regex( - input_attributes, vendor_attribute_patterns - ) - - for odm_vendor_attribute_ar in odm_vendor_attribute_ars: - if odm_vendor_attribute_ar: - BusinessLogicException.raise_if( - element_uids - and odm_vendor_attribute_ar.concept_vo.vendor_element_uid - not in element_uids, - msg=f"ODM Vendor Attribute with UID '{odm_vendor_attribute_ar.uid}' cannot not be added as an Vendor Element Attribute.", - ) - - BusinessLogicException.raise_if( - not element_uids - and not odm_vendor_attribute_ar.concept_vo.vendor_namespace_uid, - msg=f"ODM Vendor Attribute with UID '{odm_vendor_attribute_ar.uid}' cannot not be added as an Vendor Attribute.", - ) - - self.are_attributes_vendor_compatible(odm_vendor_attribute_ars, compatible_type) - - def can_connect_vendor_attributes( - self, attributes: list[OdmVendorRelationPostInput] - ): - errors = [] - for attribute in attributes: - attr = self._repos.odm_vendor_attribute_repository.find_by_uid_2( - attribute.uid - ) - - if not attr or not attr.concept_vo.vendor_namespace_uid: - errors.append(attribute.uid) - - BusinessLogicException.raise_if( - errors, - msg=f"ODM Vendor Attributes with the following UIDs don't exist or aren't connected to an ODM Vendor Namespace. UIDs: {errors}", - ) - - return True - - def attribute_values_matches_their_regex( - self, - input_attributes: list[OdmVendorRelationPostInput], - attribute_patterns: dict[str, Any], - ): - """ - Determines whether the values of the given ODM vendor attributes match their regex patterns. - - Args: - input_attributes (list[OdmVendorRelationPostInput]): The input ODM vendor attributes. - attribute_patterns (dict): The regex patterns for the ODM vendor attributes. - - Returns: - bool: True if the values of the ODM vendor attributes match their regex patterns, False otherwise. - - Raises: - BusinessLogicException: If the values of any of the ODM vendor attributes don't match their regex patterns. - """ - errors = {} - for input_attribute in input_attributes: - if ( - input_attribute.value - and attribute_patterns.get(input_attribute.uid) - and not bool( - re.match( - attribute_patterns[input_attribute.uid], input_attribute.value - ) - ) - ): - errors[input_attribute.uid] = attribute_patterns[input_attribute.uid] - BusinessLogicException.raise_if( - errors, - msg=f"Provided values for following attributes don't match their regex pattern:\n\n{errors}", - ) - - return True - - def get_regex_patterns_of_attributes( - self, attribute_uids: list[str] - ) -> dict[str, str | None]: - """ - Returns a dictionary where the key is the attribute uid and the value is the regex pattern of the specified ODM vendor attributes. - - Args: - attribute_uids (list[str]): The uids of the ODM vendor attributes. - - Returns: - dict[str, str | None]: A dictionary of regex patterns for the specified ODM vendor attributes. - """ - attributes, _ = self._repos.odm_vendor_attribute_repository.find_all( - filter_by={"uid": {"v": attribute_uids, "op": "eq"}} - ) - - return { - attribute.uid: attribute.concept_vo.value_regex for attribute in attributes - } - - def are_elements_vendor_compatible( - self, - odm_vendor_elements: list[OdmVendorElementRelationPostInput], - compatible_type: VendorElementCompatibleType | None = None, - ): - """ - Determines whether the given ODM vendor elements are compatible with the specified vendor compatible type. - - Args: - odm_vendor_elements (list[OdmVendorElementRelationPostInput]: The ODM vendor elements. - compatible_type (VendorElementCompatibleType | None, optional): The vendor compatible type to check for compatibility. - - Returns: - bool: True if the given ODM vendor elements are compatible with the specified vendor compatible type. - - Raises: - BusinessLogicException: If any of the given ODM vendor elements are not compatible with the specified vendor compatible type. - """ - errors = {} - - odm_vendor_elements = self._get_odm_vendor_elements(odm_vendor_elements) - - for odm_vendor_element in odm_vendor_elements: - if ( - compatible_type - and compatible_type.value - not in odm_vendor_element.concept_vo.compatible_types - ): - errors[odm_vendor_element.uid] = ( - odm_vendor_element.concept_vo.compatible_types - ) - BusinessLogicException.raise_if( - errors, msg=f"Trying to add non-compatible ODM Vendor:\n\n{errors}" - ) - - return True - - def are_attributes_vendor_compatible( - self, - odm_vendor_attributes: ( - list[OdmVendorRelationPostInput] | list[OdmVendorAttributeAR] - ), - compatible_type: VendorAttributeCompatibleType | None = None, - ): - """ - Determines whether the given ODM vendor attributes are compatible with the specified vendor compatible type. - - Args: - odm_vendor_attributes (list[OdmVendorRelationPostInput] | list[OdmVendorAttributeAR]): The ODM vendor attributes. - compatible_type (VendorAttributeCompatibleType | None, optional): The vendor compatible type to check for compatibility. - - Returns: - bool: True if the given ODM vendor attributes are compatible with the specified vendor compatible type. - - Raises: - BusinessLogicException: If any of the given ODM vendor attributes are not compatible with the specified vendor compatible type. - """ - errors = {} - - if all( - isinstance(odm_vendor_attribute, OdmVendorRelationPostInput) - for odm_vendor_attribute in odm_vendor_attributes - ): - odm_vendor_attributes = self._get_odm_vendor_attributes( - odm_vendor_attributes # type: ignore[arg-type] - ) - - for odm_vendor_attribute in odm_vendor_attributes: - if ( - compatible_type - and compatible_type.value - not in odm_vendor_attribute.concept_vo.compatible_types - ): - errors[odm_vendor_attribute.uid] = ( - odm_vendor_attribute.concept_vo.compatible_types - ) - BusinessLogicException.raise_if( - errors, msg=f"Trying to add non-compatible ODM Vendor:\n\n{errors}" - ) - - return True - - def _get_odm_vendor_elements( - self, input_elements: list[OdmVendorElementRelationPostInput] - ): - return self._repos.odm_vendor_element_repository.find_all( - filter_by={ - "uid": { - "v": [input_element.uid for input_element in input_elements], - "op": "eq", - } - } - )[0] - - def _get_odm_vendor_attributes( - self, input_attributes: list[OdmVendorRelationPostInput] - ): - return self._repos.odm_vendor_attribute_repository.find_all( - filter_by={ - "uid": { - "v": [input_attribute.uid for input_attribute in input_attributes], - "op": "eq", - } - } - )[0] - - def pre_management( - self, - uid: str, - odm_vendor_element_post_input: list[OdmVendorElementRelationPostInput], - odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], - odm_ar: _AggregateRootType, - repo: FormRepository | ItemGroupRepository | ItemRepository, - ): - """ - Prepares the given ODM Vendors by adding and removing vendor element and vendor element attribute relations. - - Args: - uid (str): The uid of the ODM form, item group, or item. - odm_vendors_post_input (OdmVendorsPostInput): The ODM vendors. - odm_ar (_AggregateRootType): The ODM form, item group, or item. - repo (FormRepository | ItemGroupRepository | ItemRepository): The repository for the ODM form, item group, or item. - - Returns: - None - """ - removed_vendor_attribute_uids = set( - odm_ar.concept_vo.vendor_element_attribute_uids - ) - { - element_attribute.uid - for element_attribute in odm_vendor_element_attribute_post_input - } - for removed_vendor_attribute_uid in removed_vendor_attribute_uids: - repo.remove_relation( - uid=uid, - relation_uid=removed_vendor_attribute_uid, - relationship_type=RelationType.VENDOR_ELEMENT_ATTRIBUTE, - ) - - new_vendor_element_uids = { - element.uid for element in odm_vendor_element_post_input - } - set(odm_ar.concept_vo.vendor_element_uids) - for element in odm_vendor_element_post_input: - if element.uid in new_vendor_element_uids: - repo.add_relation( - uid=uid, - relation_uid=element.uid, - relationship_type=RelationType.VENDOR_ELEMENT, - parameters={ - "value": element.value, - }, - ) - - @ensure_transaction(db) - def cascade_edit_and_approve(self, item): - if getattr(item.concept_vo, "form_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService - - form_service = OdmFormService() - - for form_uid in item.concept_vo.form_uids: - form_service.approve( - form_uid, cascade_edit_and_approve=True, ignore_exc=True - ) - - if getattr(item.concept_vo, "item_group_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_item_groups import ( - OdmItemGroupService, - ) - - item_group_service = OdmItemGroupService() - - for item_group_uid in item.concept_vo.item_group_uids: - item_group_service.approve( - item_group_uid, cascade_edit_and_approve=True, ignore_exc=True - ) - - if getattr(item.concept_vo, "item_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService - - item_service = OdmItemService() - - for item_uid in item.concept_vo.item_uids: - item_service.approve( - item_uid, cascade_edit_and_approve=True, ignore_exc=True - ) - - if getattr(item.concept_vo, "vendor_attribute_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_vendor_attributes import ( - OdmVendorAttributeService, - ) - - vendor_attribute_service = OdmVendorAttributeService() - - for vendor_attribute_uid in item.concept_vo.vendor_attribute_uids: - vendor_attribute_service.approve( - vendor_attribute_uid, cascade_edit_and_approve=True, ignore_exc=True - ) - - if getattr(item.concept_vo, "vendor_element_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_vendor_elements import ( - OdmVendorElementService, - ) - - vendor_element_service = OdmVendorElementService() - - for vendor_element_uid in item.concept_vo.vendor_element_uids: - vendor_element_service.approve( - vendor_element_uid, cascade_edit_and_approve=True, ignore_exc=True - ) - - if getattr(item.concept_vo, "vendor_namespace_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_vendor_namespaces import ( - OdmVendorNamespaceService, - ) - - vendor_namespace_service = OdmVendorNamespaceService() - - for vendor_namespace_uid in item.concept_vo.vendor_namespace_uids: - vendor_namespace_service.approve( - vendor_namespace_uid, cascade_edit_and_approve=True, ignore_exc=True - ) - - @ensure_transaction(db) - def cascade_new_version(self, item): - if getattr(item.concept_vo, "form_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService - - form_service = OdmFormService() - - for form_uid in item.concept_vo.form_uids: - form_service.create_new_version( - form_uid, - cascade_new_version=True, - force_new_value_node=True, - ignore_exc=True, - ) - - if getattr(item.concept_vo, "item_group_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_item_groups import ( - OdmItemGroupService, - ) - - item_group_service = OdmItemGroupService() - - for item_group_uid in item.concept_vo.item_group_uids: - item_group_service.create_new_version( - item_group_uid, - cascade_new_version=True, - force_new_value_node=True, - ignore_exc=True, - ) - - if getattr(item.concept_vo, "item_uids", None): - from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService - - item_service = OdmItemService() - - for item_uid in item.concept_vo.item_uids: - item_service.create_new_version( - item_uid, - cascade_new_version=True, - force_new_value_node=True, - ignore_exc=True, - ) - - @ensure_transaction(db) - def add_vendor_elements( - self, - uid: str, - odm_vendor_element_post_input: list[OdmVendorElementRelationPostInput], - odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], - odm_repository: FormRepository | ItemGroupRepository | ItemRepository, - override: bool = False, - ): - if override: - self.fail_if_non_present_vendor_elements_are_used_by_current_odm_element_attributes( - [ae.uid for ae in odm_vendor_element_attribute_post_input], - odm_vendor_element_post_input, - ) - - odm_repository.remove_relation( - uid=uid, - relation_uid=None, - relationship_type=RelationType.VENDOR_ELEMENT, - disconnect_all=True, - ) - - for vendor_element in odm_vendor_element_post_input: - odm_repository.add_relation( - uid=uid, - relation_uid=vendor_element.uid, - relationship_type=RelationType.VENDOR_ELEMENT, - parameters={ - "value": vendor_element.value, - }, - ) - - return self._find_by_uid_or_raise_not_found(uid) - - @ensure_transaction(db) - def add_vendor_attributes( - self, - uid: str, - odm_vendor_attribute_post_input: list[OdmVendorRelationPostInput], - odm_repository: FormRepository | ItemGroupRepository | ItemRepository, - override: bool = False, - ): - if override: - odm_repository.remove_relation( - uid=uid, - relation_uid=None, - relationship_type=RelationType.VENDOR_ATTRIBUTE, - disconnect_all=True, - ) - - for vendor_attribute in odm_vendor_attribute_post_input: - odm_repository.add_relation( - uid=uid, - relation_uid=vendor_attribute.uid, - relationship_type=RelationType.VENDOR_ATTRIBUTE, - parameters={ - "value": vendor_attribute.value, - }, - ) - - return self._find_by_uid_or_raise_not_found(uid) - - @ensure_transaction(db) - def add_vendor_element_attributes( - self, - uid: str, - odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], - odm_ar: _AggregateRootType, - odm_repository: FormRepository | ItemGroupRepository | ItemRepository, - override: bool = False, - ): - self.fail_if_these_attributes_cannot_be_added( - odm_vendor_element_attribute_post_input, - odm_ar.concept_vo.vendor_element_uids, - ) - - if override: - odm_repository.remove_relation( - uid=uid, - relation_uid=None, - relationship_type=RelationType.VENDOR_ELEMENT_ATTRIBUTE, - disconnect_all=True, - ) - - for vendor_element_attribute in odm_vendor_element_attribute_post_input: - odm_repository.add_relation( - uid=uid, - relation_uid=vendor_element_attribute.uid, - relationship_type=RelationType.VENDOR_ELEMENT_ATTRIBUTE, - parameters={ - "value": vendor_element_attribute.value, - }, - ) - - return self._find_by_uid_or_raise_not_found(uid) - - @ensure_transaction(db) - def manage_vendors( - self, - uid: str, - element_compatible_type: VendorElementCompatibleType, - attribute_compatible_type: VendorAttributeCompatibleType, - odm_vendor_element_post_input: list[OdmVendorElementRelationPostInput], - odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], - odm_vendor_attribute_post_input: list[OdmVendorRelationPostInput], - odm_repository: FormRepository | ItemGroupRepository | ItemRepository, - ) -> BaseModel: - odm_ar = self._find_by_uid_or_raise_not_found(uid) - - BusinessLogicException.raise_if( - odm_ar.item_metadata.status != LibraryItemStatus.DRAFT, - msg=self.OBJECT_NOT_IN_DRAFT, - ) - - self.are_elements_vendor_compatible( - odm_vendor_element_post_input, compatible_type=element_compatible_type - ) - self.fail_if_these_attributes_cannot_be_added( - odm_vendor_attribute_post_input, compatible_type=attribute_compatible_type - ) - - self.pre_management( - uid, - odm_vendor_element_post_input, - odm_vendor_element_attribute_post_input, - odm_ar, - odm_repository, - ) - - odm_ar = self.add_vendor_elements( - uid, - odm_vendor_element_post_input, - odm_vendor_element_attribute_post_input, - odm_repository, - True, - ) - self.add_vendor_element_attributes( - uid, odm_vendor_element_attribute_post_input, odm_ar, odm_repository, True - ) - self.add_vendor_attributes( - uid, odm_vendor_attribute_post_input, odm_repository, True - ) - - return self.get_by_uid(uid) diff --git a/clinical-mdr-api/clinical_mdr_api/services/ctr_xml/ctr_xml_service.py b/clinical-mdr-api/clinical_mdr_api/services/ctr_xml/ctr_xml_service.py index 08e6b0f3..2fb58511 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/ctr_xml/ctr_xml_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/ctr_xml/ctr_xml_service.py @@ -11,12 +11,12 @@ from clinical_mdr_api.domains.study_definition_aggregates.study_metadata import ( StudyComponentEnum, ) -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm -from clinical_mdr_api.models.concepts.odms.odm_item import OdmItem -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroup from clinical_mdr_api.models.controlled_terminologies.ct_codelist_attributes import ( CTCodelistAttributes, ) +from clinical_mdr_api.models.odms.form import OdmForm +from clinical_mdr_api.models.odms.item import OdmItem +from clinical_mdr_api.models.odms.item_group import OdmItemGroup from clinical_mdr_api.models.projects.project import Project from clinical_mdr_api.models.study_selections.study import ( StudyDescriptionJsonModel, @@ -27,12 +27,12 @@ StudyVersionMetadataJsonModel, ) from clinical_mdr_api.models.study_selections.study_visit import StudyVisit -from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService -from clinical_mdr_api.services.concepts.odms.odm_item_groups import OdmItemGroupService -from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService from clinical_mdr_api.services.controlled_terminologies.ct_codelist_attributes import ( CTCodelistAttributesService, ) +from clinical_mdr_api.services.odms.forms import OdmFormService +from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService +from clinical_mdr_api.services.odms.items import OdmItemService from clinical_mdr_api.services.projects.project import ProjectService from clinical_mdr_api.services.studies.study import StudyService from clinical_mdr_api.services.studies.study_visit import StudyVisitService @@ -230,7 +230,7 @@ def get_odm_study_event_defs(self) -> list[ctrxml.StudyEventDef]: @cached_property def odm_forms(self) -> list[OdmForm]: # TODO: add filtering by StudyUID when it gets implemented in database schema - result = OdmFormService().get_all_concepts() + result = OdmFormService().get_all_odms() return result.items def get_odm_form_defs(self) -> list[ctrxml.FormDef]: @@ -279,7 +279,7 @@ def odm_item_groups(self) -> list[OdmItemGroup]: uids = [ item_group.uid for form in self.odm_forms for item_group in form.item_groups ] - result = OdmItemGroupService().get_all_concepts( + result = OdmItemGroupService().get_all_odms( filter_by={"uid": {"v": uids, "op": "eq"}} ) return result.items @@ -338,7 +338,7 @@ def odm_items(self) -> list[OdmItem]: uids = [ item.uid for item_group in self.odm_item_groups for item in item_group.items ] - result = OdmItemService().get_all_concepts( + result = OdmItemService().get_all_odms( filter_by={"uid": {"v": uids, "op": "eq"}} ) return result.items diff --git a/clinical-mdr-api/clinical_mdr_api/services/data_completeness_tags.py b/clinical-mdr-api/clinical_mdr_api/services/data_completeness_tags.py new file mode 100644 index 00000000..585ec266 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/services/data_completeness_tags.py @@ -0,0 +1,78 @@ +# pylint: disable=invalid-name +from neomodel import db + +from clinical_mdr_api.domain_repositories.data_completeness_tags_repository import ( + DataCompletenessTagRepository, +) +from clinical_mdr_api.models.data_completeness_tag import ( + DataCompletenessTag, + DataCompletenessTagInput, +) +from clinical_mdr_api.services._meta_repository import MetaRepository +from clinical_mdr_api.services._utils import ensure_transaction +from common.exceptions import AlreadyExistsException, NotFoundException + + +class DataCompletenessTagService: + repo: DataCompletenessTagRepository + _repos: MetaRepository + + def __init__(self) -> None: + self.repo = DataCompletenessTagRepository() + self._repos = MetaRepository() + + def get_all_data_completeness_tags(self) -> list[DataCompletenessTag]: + return self.repo.retrieve_all_data_completeness_tags() + + @ensure_transaction(db) + def create_data_completeness_tag( + self, + data_completeness_tag_input: DataCompletenessTagInput, + ) -> DataCompletenessTag: + AlreadyExistsException.raise_if( + self.repo.find_data_completeness_tag_by_name( + data_completeness_tag_input.name + ), + "Data Completeness Tag", + data_completeness_tag_input.name, + "Name", + ) + + return self.repo.create_data_completeness_tag( + name=data_completeness_tag_input.name, + ) + + @ensure_transaction(db) + def update_data_completeness_tag( + self, + uid: str, + data_completeness_tag_input: DataCompletenessTagInput, + ) -> DataCompletenessTag: + return self.repo.update_data_completeness_tag( + uid=uid, name=data_completeness_tag_input.name + ) + + @ensure_transaction(db) + def delete_data_completeness_tag(self, uid: str) -> None: + return self.repo.delete_data_completeness_tag(uid) + + def get_tags_for_study(self, study_uid: str) -> list[DataCompletenessTag]: + return self.repo.get_tags_for_study(study_uid) + + @ensure_transaction(db) + def assign_tag_to_study(self, study_uid: str, tag_uid: str) -> DataCompletenessTag: + NotFoundException.raise_if_not( + self._repos.study_definition_repository.study_exists_by_uid(study_uid), + "Study", + study_uid, + ) + return self.repo.assign_tag_to_study(study_uid=study_uid, tag_uid=tag_uid) + + @ensure_transaction(db) + def remove_tag_from_study(self, study_uid: str, tag_uid: str) -> None: + NotFoundException.raise_if_not( + self._repos.study_definition_repository.study_exists_by_uid(study_uid), + "Study", + study_uid, + ) + return self.repo.remove_tag_from_study(study_uid=study_uid, tag_uid=tag_uid) 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 546a1198..62d2b937 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 @@ -1137,7 +1137,7 @@ def _get_study_encounters(self, study: OSBStudy): name=sv.visit_short_name, label=sv.visit_name, description=sv.description, - type=self.get_ct_package_term_as_usdm_code(sv.visit_type_uid), + type=self.get_ct_package_term_as_usdm_code(sv.visit_type.term_uid), transitionStartRule=USDMTransitionRule( id=self._id_manager.get_id(USDMTransitionRule.__name__), name="Transition Start Rule", @@ -1149,7 +1149,9 @@ def _get_study_encounters(self, study: OSBStudy): text=sv.end_rule if sv.end_rule is not None else "", ), contactModes=[ - self.get_ct_package_term_as_usdm_code(sv.visit_contact_mode_uid) + self.get_ct_package_term_as_usdm_code( + sv.visit_contact_mode.term_uid + ) ], nextId=( self._id_manager.get_id( diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/__init__.py b/clinical-mdr-api/clinical_mdr_api/services/odms/__init__.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/__init__.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/__init__.py diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_clinspark_import.py b/clinical-mdr-api/clinical_mdr_api/services/odms/clinspark_import.py similarity index 97% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_clinspark_import.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/clinspark_import.py index ccb7ef33..4d229950 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_clinspark_import.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/clinspark_import.py @@ -2,14 +2,6 @@ from fastapi import UploadFile -from clinical_mdr_api.models.concepts.odms.odm_form import OdmFormPostInput -from clinical_mdr_api.models.concepts.odms.odm_item import ( - OdmItemCodelist, - OdmItemPostInput, - OdmItemTermRelationshipInput, - OdmItemUnitDefinitionRelationshipInput, -) -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroupPostInput from clinical_mdr_api.models.concepts.unit_definitions.unit_definition import ( UnitDefinitionModel, ) @@ -24,9 +16,14 @@ CTTermCreateInput, CTTermNameAndAttributes, ) -from clinical_mdr_api.services.concepts.odms.odm_xml_importer import ( - OdmXmlImporterService, +from clinical_mdr_api.models.odms.form import OdmFormPostInput +from clinical_mdr_api.models.odms.item import ( + OdmItemCodelist, + OdmItemPostInput, + OdmItemTermRelationshipInput, + OdmItemUnitDefinitionRelationshipInput, ) +from clinical_mdr_api.models.odms.item_group import OdmItemGroupPostInput from clinical_mdr_api.services.controlled_terminologies.ct_codelist import ( CTCodelistService, ) @@ -40,6 +37,7 @@ from clinical_mdr_api.services.controlled_terminologies.ct_term_name import ( CTTermNameService, ) +from clinical_mdr_api.services.odms.xml_importer import OdmXmlImporterService from common import exceptions from common.config import settings @@ -335,7 +333,7 @@ def _get_item_unit_definition_inputs(self, item_def): ) def _get_odm_item_post_input(self, item_def): - plausible_duplicates = self.odm_item_service.get_all_concepts( + plausible_duplicates = self.odm_item_service.get_all_odms( filter_by={"name": {"v": [item_def.getAttribute("Name")], "op": "co"}} ).items @@ -417,7 +415,7 @@ def _get_odm_item_post_input(self, item_def): ) def _get_odm_item_group_post_input(self, item_group_def): - plausible_duplicates = self.odm_item_group_service.get_all_concepts( + plausible_duplicates = self.odm_item_group_service.get_all_odms( filter_by={"name": {"v": [item_group_def.getAttribute("Name")], "op": "co"}} ).items @@ -438,7 +436,7 @@ def _get_odm_item_group_post_input(self, item_group_def): ) def _get_odm_form_post_input(self, form_def): - plausible_duplicates = self.odm_form_service.get_all_concepts( + plausible_duplicates = self.odm_form_service.get_all_odms( filter_by={"name": {"v": [form_def.getAttribute("Name")], "op": "co"}} ).items diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_conditions.py b/clinical-mdr-api/clinical_mdr_api/services/odms/conditions.py similarity index 57% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_conditions.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/conditions.py index db11ab60..bc3e6cda 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_conditions.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/conditions.py @@ -1,23 +1,22 @@ +import logging + from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.condition_repository import ( +from clinical_mdr_api.domain_repositories.odms.condition_repository import ( ConditionRepository, ) -from clinical_mdr_api.domains.concepts.odms.condition import ( - OdmConditionAR, - OdmConditionVO, -) -from clinical_mdr_api.models.concepts.odms.odm_condition import ( +from clinical_mdr_api.domains.odms.condition import OdmConditionAR, OdmConditionVO +from clinical_mdr_api.models.odms.condition import ( OdmCondition, OdmConditionPatchInput, OdmConditionPostInput, OdmConditionVersion, ) -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from common.exceptions import NotFoundException +log = logging.getLogger(__name__) + class OdmConditionService(OdmGenericService[OdmConditionAR]): aggregate_class = OdmConditionAR @@ -30,16 +29,22 @@ def _transform_aggregate_root_to_pydantic_model( return OdmCondition.from_odm_condition_ar(odm_condition_ar=item_ar) def _create_aggregate_root( - self, concept_input: OdmConditionPostInput, library + self, odm_input: OdmConditionPostInput, library ) -> OdmConditionAR: + log.info( + "Creating ODM Condition: name='%s', oid=%s, library=%s", + odm_input.name, + odm_input.oid, + library.name, + ) return OdmConditionAR.from_input_values( author_id=self.author_id, - concept_vo=OdmConditionVO.from_repository_values( - oid=concept_input.oid, - name=concept_input.name, - formal_expressions=concept_input.formal_expressions, - translated_texts=concept_input.translated_texts, - aliases=concept_input.aliases, + odm_vo=OdmConditionVO.from_repository_values( + oid=odm_input.oid, + name=odm_input.name, + formal_expressions=odm_input.formal_expressions, + translated_texts=odm_input.translated_texts, + aliases=odm_input.aliases, ), library=library, generate_uid_callback=self.repository.generate_uid, @@ -47,17 +52,22 @@ def _create_aggregate_root( ) def _edit_aggregate( - self, item: OdmConditionAR, concept_edit_input: OdmConditionPatchInput + self, item: OdmConditionAR, odm_edit_input: OdmConditionPatchInput ) -> OdmConditionAR: + log.info( + "Editing ODM Condition: uid=%s, name='%s'", + item.uid, + odm_edit_input.name, + ) item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmConditionVO.from_repository_values( - oid=concept_edit_input.oid, - name=concept_edit_input.name, - formal_expressions=concept_edit_input.formal_expressions, - translated_texts=concept_edit_input.translated_texts, - aliases=concept_edit_input.aliases, + change_description=odm_edit_input.change_description, + odm_vo=OdmConditionVO.from_repository_values( + oid=odm_edit_input.oid, + name=odm_edit_input.name, + formal_expressions=odm_edit_input.formal_expressions, + translated_texts=odm_edit_input.translated_texts, + aliases=odm_edit_input.aliases, ), odm_object_exists_callback=self._repos.odm_condition_repository.odm_object_exists, ) @@ -71,6 +81,7 @@ def soft_delete(self, uid: str, cascade_delete: bool = False): This method is temporary and should be removed when the database relationship between ODM Condition and its reference nodes is ready. """ + log.info("Soft deleting ODM Condition: uid=%s, cascade=%s", uid, cascade_delete) condition = self._find_by_uid_or_raise_not_found(uid, for_update=True) condition.soft_delete() self.repository.save(condition) @@ -79,11 +90,13 @@ def soft_delete(self, uid: str, cascade_delete: bool = False): self.cascade_delete(condition) self._repos.odm_condition_repository.set_all_collection_exception_condition_oid_properties_to_null( - condition.concept_vo.oid + condition.odm_vo.oid ) + log.info("Successfully soft deleted ODM Condition: uid=%s", uid) @db.transaction def get_active_relationships(self, uid: str): + log.debug("Getting active relationships for ODM Condition: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_condition_repository.exists_by("uid", uid, True), "ODM Condition", diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_csv_exporter.py b/clinical-mdr-api/clinical_mdr_api/services/odms/csv_exporter.py similarity index 86% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_csv_exporter.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/csv_exporter.py index 75ac78bc..cc6c68ae 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_csv_exporter.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/csv_exporter.py @@ -1,7 +1,7 @@ -from clinical_mdr_api.domain_repositories.concepts.odms.metadata_repository import ( +from clinical_mdr_api.domain_repositories.odms.metadata_repository import ( MetadataRepository, ) -from clinical_mdr_api.domains.concepts.utils import TargetType +from clinical_mdr_api.domains.odms.utils import TargetType from common.exceptions import BusinessLogicException diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_data_extractor.py b/clinical-mdr-api/clinical_mdr_api/services/odms/data_extractor.py similarity index 88% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_data_extractor.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/data_extractor.py index 5ab7652c..430da2a9 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_data_extractor.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/data_extractor.py @@ -1,33 +1,16 @@ -from clinical_mdr_api.domains.concepts.utils import TargetType -from clinical_mdr_api.models.concepts.odms.odm_condition import OdmCondition -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm -from clinical_mdr_api.models.concepts.odms.odm_item import OdmItem -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroup -from clinical_mdr_api.models.concepts.odms.odm_method import OdmMethod -from clinical_mdr_api.models.concepts.odms.odm_study_event import OdmStudyEvent +from clinical_mdr_api.domains.odms.utils import TargetType from clinical_mdr_api.models.concepts.unit_definitions.unit_definition import ( UnitDefinitionModel, ) from clinical_mdr_api.models.controlled_terminologies.ct_codelist_attributes import ( CTCodelistAttributes, ) -from clinical_mdr_api.services.concepts.odms.odm_conditions import OdmConditionService -from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService -from clinical_mdr_api.services.concepts.odms.odm_item_groups import OdmItemGroupService -from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService -from clinical_mdr_api.services.concepts.odms.odm_methods import OdmMethodService -from clinical_mdr_api.services.concepts.odms.odm_study_events import ( - OdmStudyEventService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_attributes import ( - OdmVendorAttributeService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_elements import ( - OdmVendorElementService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_namespaces import ( - OdmVendorNamespaceService, -) +from clinical_mdr_api.models.odms.condition import OdmCondition +from clinical_mdr_api.models.odms.form import OdmForm +from clinical_mdr_api.models.odms.item import OdmItem +from clinical_mdr_api.models.odms.item_group import OdmItemGroup +from clinical_mdr_api.models.odms.method import OdmMethod +from clinical_mdr_api.models.odms.study_event import OdmStudyEvent from clinical_mdr_api.services.concepts.unit_definitions.unit_definition import ( UnitDefinitionService, ) @@ -37,6 +20,15 @@ from clinical_mdr_api.services.controlled_terminologies.ct_term_attributes import ( CTTermAttributesService, ) +from clinical_mdr_api.services.odms.conditions import OdmConditionService +from clinical_mdr_api.services.odms.forms import OdmFormService +from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService +from clinical_mdr_api.services.odms.items import OdmItemService +from clinical_mdr_api.services.odms.methods import OdmMethodService +from clinical_mdr_api.services.odms.study_events import OdmStudyEventService +from clinical_mdr_api.services.odms.vendor_attributes import OdmVendorAttributeService +from clinical_mdr_api.services.odms.vendor_elements import OdmVendorElementService +from clinical_mdr_api.services.odms.vendor_namespaces import OdmVendorNamespaceService from common.exceptions import BusinessLogicException, NotFoundException @@ -105,7 +97,7 @@ def __init__(self, target_type: TargetType, targets: list[str]): target.rsplit(",", maxsplit=1) if "," in target else (target, None) ) - self.odm_study_events += self.study_event_service.get_all_concepts( + self.odm_study_events += self.study_event_service.get_all_odms( filter_by={"uid": {"v": [uid], "op": "eq"}}, version=version or None ).items @@ -125,7 +117,7 @@ def __init__(self, target_type: TargetType, targets: list[str]): target.rsplit(",", maxsplit=1) if "," in target else (target, None) ) - self.odm_forms += self.form_service.get_all_concepts( + self.odm_forms += self.form_service.get_all_odms( filter_by={"uid": {"v": [uid], "op": "eq"}}, version=version or None ).items @@ -145,7 +137,7 @@ def __init__(self, target_type: TargetType, targets: list[str]): target.rsplit(",", maxsplit=1) if "," in target else (target, None) ) - self.odm_item_groups += self.item_group_service.get_all_concepts( + self.odm_item_groups += self.item_group_service.get_all_odms( filter_by={"uid": {"v": [uid], "op": "eq"}}, version=version or None ).items @@ -165,7 +157,7 @@ def __init__(self, target_type: TargetType, targets: list[str]): target.rsplit(",", maxsplit=1) if "," in target else (target, None) ) - self.odm_items = self.item_service.get_all_concepts( + self.odm_items = self.item_service.get_all_odms( filter_by={"uid": {"v": [uid], "op": "eq"}}, version=version or None ).items @@ -190,7 +182,7 @@ def __init__(self, target_type: TargetType, targets: list[str]): self.set_ref_vendor_attributes() def set_ref_vendor_attributes(self): - vendor_attributes = self.vendor_attribute_service.get_all_concepts( + vendor_attributes = self.vendor_attribute_service.get_all_odms( filter_by={ "uid": { "v": ( @@ -224,7 +216,7 @@ def set_ref_vendor_attributes(self): } def set_vendor_elements(self): - vendor_elements = self.vendor_element_service.get_all_concepts( + vendor_elements = self.vendor_element_service.get_all_odms( filter_by={ "uid": { "v": ( @@ -258,7 +250,7 @@ def set_vendor_elements(self): } def set_vendor_namespaces(self): - vendor_namespaces = self.vendor_namespace_service.get_all_concepts().items + vendor_namespaces = self.vendor_namespace_service.get_all_odms().items self.odm_vendor_namespaces = { vendor_namespace.uid: { @@ -274,7 +266,7 @@ def set_forms_of_study_event(self, study_events: list[OdmStudyEvent]): for study_event in study_events: for form in study_event.forms: - _forms = self.form_service.get_all_concepts( + _forms = self.form_service.get_all_odms( filter_by={ "uid": { "v": [form.uid], @@ -294,7 +286,7 @@ def set_item_groups_of_forms(self, forms: list[OdmForm]): self.odm_item_groups = [] for form in forms: for item_group in form.item_groups: - _item_groups = self.item_group_service.get_all_concepts( + _item_groups = self.item_group_service.get_all_odms( filter_by={ "uid": { "v": [item_group.uid], @@ -314,7 +306,7 @@ def set_items_of_item_groups(self, item_groups: list[OdmItemGroup]): self.odm_items = [] for item_group in item_groups: for item in item_group.items: - _items = self.item_service.get_all_concepts( + _items = self.item_service.get_all_odms( filter_by={ "uid": { "v": [item.uid], @@ -345,7 +337,7 @@ def set_conditions(self, forms, item_groups): if oids: self.odm_conditions = sorted( - self.condition_service.get_all_concepts( + self.condition_service.get_all_odms( filter_by={"oid": {"v": oids, "op": "eq"}}, ).items, key=lambda elm: elm.name, @@ -358,7 +350,7 @@ def set_methods(self, item_groups): if oids: self.odm_methods = sorted( - self.method_service.get_all_concepts( + self.method_service.get_all_odms( filter_by={"oid": {"v": oids, "op": "eq"}}, ).items, key=lambda elm: elm.name, diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_forms.py b/clinical-mdr-api/clinical_mdr_api/services/odms/forms.py similarity index 71% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_forms.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/forms.py index 90af1881..4d4dd250 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_forms.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/forms.py @@ -1,16 +1,14 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.form_repository import ( - FormRepository, -) -from clinical_mdr_api.domains.concepts.odms.form import OdmFormAR, OdmFormVO -from clinical_mdr_api.domains.concepts.utils import ( +from clinical_mdr_api.domain_repositories.odms.form_repository import FormRepository +from clinical_mdr_api.domains.odms.form import OdmFormAR, OdmFormVO +from clinical_mdr_api.domains.odms.utils import ( RelationType, VendorAttributeCompatibleType, VendorElementCompatibleType, ) from clinical_mdr_api.domains.versioned_object_aggregate import LibraryItemStatus -from clinical_mdr_api.models.concepts.odms.odm_form import ( +from clinical_mdr_api.models.odms.form import ( OdmForm, OdmFormItemGroupPostInput, OdmFormPatchInput, @@ -18,9 +16,7 @@ OdmFormVersion, ) from clinical_mdr_api.services._utils import ensure_transaction, get_input_or_new_value -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from clinical_mdr_api.utils import normalize_string, to_dict from common.exceptions import BusinessLogicException, NotFoundException from common.utils import strtobool @@ -46,18 +42,16 @@ def _transform_aggregate_root_to_pydantic_model( ), ) - def _create_aggregate_root( - self, concept_input: OdmFormPostInput, library - ) -> OdmFormAR: + def _create_aggregate_root(self, odm_input: OdmFormPostInput, library) -> OdmFormAR: return OdmFormAR.from_input_values( author_id=self.author_id, - concept_vo=OdmFormVO.from_repository_values( - oid=get_input_or_new_value(concept_input.oid, "F.", concept_input.name), - name=concept_input.name, - sdtm_version=concept_input.sdtm_version, - repeating=strtobool(concept_input.repeating), - translated_texts=concept_input.translated_texts, - aliases=concept_input.aliases, + odm_vo=OdmFormVO.from_repository_values( + oid=get_input_or_new_value(odm_input.oid, "F.", odm_input.name), + name=odm_input.name, + sdtm_version=odm_input.sdtm_version, + repeating=strtobool(odm_input.repeating), + translated_texts=odm_input.translated_texts, + aliases=odm_input.aliases, item_group_uids=[], vendor_element_uids=[], vendor_attribute_uids=[], @@ -69,38 +63,38 @@ def _create_aggregate_root( ) def _edit_aggregate( - self, item: OdmFormAR, concept_edit_input: OdmFormPatchInput + self, item: OdmFormAR, odm_edit_input: OdmFormPatchInput ) -> OdmFormAR: item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmFormVO.from_repository_values( - oid=concept_edit_input.oid, - name=concept_edit_input.name, - sdtm_version=concept_edit_input.sdtm_version, - repeating=strtobool(concept_edit_input.repeating), - translated_texts=concept_edit_input.translated_texts, - aliases=concept_edit_input.aliases, - item_group_uids=item.concept_vo.item_group_uids, - vendor_element_uids=item.concept_vo.vendor_element_uids, - vendor_attribute_uids=item.concept_vo.vendor_attribute_uids, - vendor_element_attribute_uids=item.concept_vo.vendor_element_attribute_uids, + change_description=odm_edit_input.change_description, + odm_vo=OdmFormVO.from_repository_values( + oid=odm_edit_input.oid, + name=odm_edit_input.name, + sdtm_version=odm_edit_input.sdtm_version, + repeating=strtobool(odm_edit_input.repeating), + translated_texts=odm_edit_input.translated_texts, + aliases=odm_edit_input.aliases, + item_group_uids=item.odm_vo.item_group_uids, + vendor_element_uids=item.odm_vo.vendor_element_uids, + vendor_attribute_uids=item.odm_vo.vendor_attribute_uids, + vendor_element_attribute_uids=item.odm_vo.vendor_element_attribute_uids, ), odm_object_exists_callback=self._repos.odm_form_repository.odm_object_exists, ) return item @db.transaction - def create(self, concept_input: OdmFormPostInput) -> OdmForm: - item = super().create(concept_input) + def create(self, odm_input: OdmFormPostInput) -> OdmForm: + item = super().create(odm_input) super().manage_vendors( item.uid, VendorElementCompatibleType.FORM_DEF, VendorAttributeCompatibleType.FORM_DEF, - concept_input.vendor_elements, - concept_input.vendor_element_attributes, - concept_input.vendor_attributes, + odm_input.vendor_elements, + odm_input.vendor_element_attributes, + odm_input.vendor_attributes, self._repos.odm_form_repository, ) @@ -109,16 +103,16 @@ def create(self, concept_input: OdmFormPostInput) -> OdmForm: ) @db.transaction - def edit_draft(self, uid: str, concept_edit_input: OdmFormPatchInput) -> OdmForm: - super().edit_draft(uid, concept_edit_input) + def edit_draft(self, uid: str, odm_edit_input: OdmFormPatchInput) -> OdmForm: + super().edit_draft(uid, odm_edit_input) super().manage_vendors( uid, VendorElementCompatibleType.FORM_DEF, VendorAttributeCompatibleType.FORM_DEF, - concept_edit_input.vendor_elements, - concept_edit_input.vendor_element_attributes, - concept_edit_input.vendor_attributes, + odm_edit_input.vendor_elements, + odm_edit_input.vendor_element_attributes, + odm_edit_input.vendor_attributes, self._repos.odm_form_repository, ) 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 new file mode 100644 index 00000000..b9eb430d --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/generic_service.py @@ -0,0 +1,1074 @@ +import re +from abc import ABC, abstractmethod +from datetime import datetime +from typing import Any, Generic, Sequence, TypeVar + +from neomodel import db +from pydantic import BaseModel + +from clinical_mdr_api.domain_repositories.odms.form_repository import FormRepository +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( + OdmGenericRepository, +) +from clinical_mdr_api.domain_repositories.odms.item_group_repository import ( + ItemGroupRepository, +) +from clinical_mdr_api.domain_repositories.odms.item_repository import ItemRepository +from clinical_mdr_api.domains.odms.utils import ( + RelationType, + VendorAttributeCompatibleType, + VendorElementCompatibleType, +) +from clinical_mdr_api.domains.odms.vendor_attribute import OdmVendorAttributeAR +from clinical_mdr_api.domains.versioned_object_aggregate import ( + LibraryItemStatus, + LibraryVO, +) +from clinical_mdr_api.models.concepts.activities.activity import ( + ActivityHierarchySimpleModel, +) +from clinical_mdr_api.models.controlled_terminologies.ct_term import ( + SimpleCodelistTermModel, + SimpleTermModel, +) +from clinical_mdr_api.models.odms.common_models import ( + OdmVendorElementRelationPostInput, + OdmVendorRelationPostInput, +) +from clinical_mdr_api.models.utils import GenericFilteringReturn +from clinical_mdr_api.repositories._utils import FilterOperator +from clinical_mdr_api.services._meta_repository import MetaRepository +from clinical_mdr_api.services._utils import ( + calculate_diffs, + ensure_transaction, + is_library_editable, +) +from clinical_mdr_api.utils import normalize_string +from common.auth.user import user +from common.exceptions import BusinessLogicException, NotFoundException +from common.utils import get_field_type + +_AggregateRootType = TypeVar("_AggregateRootType") + + +class OdmGenericService(Generic[_AggregateRootType], ABC): + OBJECT_NOT_IN_DRAFT = "ODM element is not in Draft." + aggregate_class: type + version_class: type + repository_interface: type + _repos: MetaRepository + author_id: str + + def __init__(self): + self.author_id = user().id() + self._repos = MetaRepository(self.author_id) + + def __del__(self): + self._repos.close() + + @staticmethod + def _fill_missing_values_in_base_model_from_reference_base_model( + *, base_model_with_missing_values: BaseModel, reference_base_model: BaseModel + ) -> None: + """ + Method fills missing values in the PATCH payload when only partial payload is sent by client. + It takes the values from the object that will be updated in the request. + There is some difference between GET and PATCH/POST API models in a few fields (in GET requests we return + unique identifiers of some items and theirs name) and in the PATCH/POST requests we expect only the uid to be + sent from client. + Because of that difference, we only want to take unique identifiers from these objects in the PATCH/POST + request payloads. + :param base_model_with_missing_values: BaseModel + :param reference_base_model: BaseModel + :return None: + """ + for field_name in base_model_with_missing_values.model_fields_set: + if isinstance( + getattr(base_model_with_missing_values, field_name), BaseModel + ) and isinstance(getattr(reference_base_model, field_name), BaseModel): + OdmGenericService._fill_missing_values_in_base_model_from_reference_base_model( + base_model_with_missing_values=getattr( + base_model_with_missing_values, field_name + ), + reference_base_model=getattr(reference_base_model, field_name), + ) + + for field_name in ( + reference_base_model.model_fields_set + - base_model_with_missing_values.model_fields_set + ).intersection(base_model_with_missing_values.model_fields): + if isinstance(getattr(reference_base_model, field_name), SimpleTermModel): + setattr( + base_model_with_missing_values, + field_name, + getattr(reference_base_model, field_name).term_uid, + ) + elif isinstance( + getattr(reference_base_model, field_name), SimpleCodelistTermModel + ): + setattr( + base_model_with_missing_values, + field_name, + getattr(reference_base_model, field_name).term_uid, + ) + elif isinstance(getattr(reference_base_model, field_name), Sequence): + if ( + get_field_type( + reference_base_model.model_fields[field_name].annotation + ) + is SimpleTermModel + ): + setattr( + base_model_with_missing_values, + field_name, + [ + term.term_uid + for term in getattr(reference_base_model, field_name) + ], + ) + if ( + get_field_type( + reference_base_model.model_fields[field_name].annotation + ) + is SimpleCodelistTermModel + ): + setattr( + base_model_with_missing_values, + field_name, + [ + term.term_uid + for term in getattr(reference_base_model, field_name) + ], + ) + elif ( + get_field_type( + reference_base_model.model_fields[field_name].annotation + ) + is ActivityHierarchySimpleModel + ): + setattr( + base_model_with_missing_values, + field_name, + [ + term.uid + for term in getattr(reference_base_model, field_name) + ], + ) + else: + setattr( + base_model_with_missing_values, + field_name, + getattr(reference_base_model, field_name), + ) + else: + setattr( + base_model_with_missing_values, + field_name, + getattr(reference_base_model, field_name), + ) + + @staticmethod + def fill_in_additional_fields( + odm_edit_input: BaseModel, current_ar: _AggregateRootType + ) -> None: + """ + Subclasses should override this method to preserve field values which are not explicitly sent in the PATCH payload. + If a relevant field is not included the PATCH payload, + this method should populate `odm_edit_input` object with the existing value of that field. + + This method deals only with fields that cannot be preserved + by the generic `_fill_missing_values_in_base_model_from_reference_base_model` method. + For example, it should handle all fields that represent links to other entities, e.g `dose_form_uids`. + """ + + @property + def repository(self) -> OdmGenericRepository[_AggregateRootType]: + assert self._repos is not None + return self.repository_interface() + + @abstractmethod + def _transform_aggregate_root_to_pydantic_model( + self, item_ar: _AggregateRootType + ) -> BaseModel: + raise NotImplementedError + + @abstractmethod + def _create_aggregate_root( + self, + odm_input: BaseModel, + library: LibraryVO, + ) -> _AggregateRootType: + raise NotImplementedError() + + @abstractmethod + def _edit_aggregate( + self, item: _AggregateRootType, odm_edit_input: BaseModel + ) -> _AggregateRootType: + raise NotImplementedError + + def get_input_or_previous_property( + self, input_property: Any, previous_property: Any + ): + return input_property if input_property is not None else previous_property + + @ensure_transaction(db) + def get_all_odms( + self, + library: str | None = None, + 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, + **kwargs, + ) -> GenericFilteringReturn[Any]: + self.enforce_library(library) + + item_ars, total = self.repository.find_all( + library=library, + total_count=total_count, + sort_by=sort_by, + filter_by=filter_by, + filter_operator=filter_operator, + page_number=page_number, + page_size=page_size, + **kwargs, + ) + + items = [ + self._transform_aggregate_root_to_pydantic_model(odm_ar) + for odm_ar in item_ars + ] + return GenericFilteringReturn(items=items, total=total) + + def get_distinct_values_for_header( + self, + library: str | None, + field_name: str, + search_string: str = "", + filter_by: dict[str, dict[str, Any]] | None = None, + filter_operator: FilterOperator = FilterOperator.AND, + page_size: int = 10, + lite: bool = False, + **kwargs, + ) -> list[Any]: + self.enforce_library(library) + + # Lite mode doesn't support filtering by relationship fields like status + # Fall back to non-lite mode when these filters are present + if lite and filter_by and "status" in filter_by: + lite = False + + if lite: + header_values = self.repository.get_distinct_headers_lite( + library=library, + field_name=field_name, + search_string=search_string, + filter_by=filter_by, + filter_operator=filter_operator, + page_size=page_size, + **kwargs, + ) + else: + header_values = self.repository.get_distinct_headers( + library=library, + field_name=field_name, + search_string=search_string, + filter_by=filter_by, + filter_operator=filter_operator, + page_size=page_size, + **kwargs, + ) + + return header_values + + @db.transaction + def get_all_odm_versions( + self, + library: str | None = None, + 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, + **kwargs, + ) -> GenericFilteringReturn[BaseModel]: + self.enforce_library(library) + + item_ars, total = self.repository.find_all( + library=library, + total_count=total_count, + sort_by=sort_by, + filter_by=filter_by, + filter_operator=filter_operator, + page_number=page_number, + page_size=page_size, + return_all_versions=True, + **kwargs, + ) + + items = [ + self._transform_aggregate_root_to_pydantic_model(odm_ar) + for odm_ar in item_ars + ] + return GenericFilteringReturn(items=items, total=total) + + @ensure_transaction(db) + def get_by_uid( + self, + uid: str, + version: str | None = None, + at_specific_date: datetime | None = None, + status: LibraryItemStatus | None = None, + ) -> BaseModel: + item = self._find_by_uid_or_raise_not_found( + uid=uid, version=version, at_specific_date=at_specific_date, status=status + ) + return self._transform_aggregate_root_to_pydantic_model(item) + + def _find_by_uid_or_raise_not_found( + self, + uid: str, + version: str | None = None, + at_specific_date: datetime | None = None, + status: LibraryItemStatus | None = None, + for_update: bool = False, + ) -> _AggregateRootType: + item = self.repository.find_by_uid_2( + uid=uid, + at_specific_date=at_specific_date, + version=version, + status=status, + for_update=for_update, + ) + + NotFoundException.raise_if( + item is None, + msg=f"{self.aggregate_class.__name__} with UID '{uid}' doesn't exist or there's no version with requested status or version number.", + ) + return item + + @db.transaction + def get_version_history(self, uid: str) -> list[BaseModel]: + if self.version_class is not None: + all_versions = self.repository.get_all_versions_2(uid=uid) + + NotFoundException.raise_if( + all_versions is None, self.aggregate_class.__name__, uid + ) + + versions = [ + self._transform_aggregate_root_to_pydantic_model( + codelist_ar + ).model_dump() + for codelist_ar in all_versions + ] + return calculate_diffs(versions, self.version_class) + return [] + + @ensure_transaction(db) + def create_new_version( + self, + uid: str, + cascade_new_version: bool = False, + force_new_value_node: bool = False, + ignore_exc: bool = False, + ) -> BaseModel: + item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + try: + item.create_new_version(author_id=self.author_id) + self.repository.save(item, force_new_value_node) + except BusinessLogicException as exc: + if ( + not ignore_exc + or exc.msg + != "New draft version can be created only for FINAL versions." + ): + raise + + if cascade_new_version: + self.cascade_new_version(item) + return self._transform_aggregate_root_to_pydantic_model(item) + + @ensure_transaction(db) + def edit_draft( + self, uid: str, odm_edit_input: BaseModel, patch_mode: bool = True + ) -> BaseModel: + item = self._find_by_uid_or_raise_not_found(uid=uid, for_update=True) + if patch_mode: + self._fill_missing_values_in_base_model_from_reference_base_model( + base_model_with_missing_values=odm_edit_input, + reference_base_model=self._transform_aggregate_root_to_pydantic_model( + item + ), + ) + self.fill_in_additional_fields(odm_edit_input, item) + item = self._edit_aggregate(item=item, odm_edit_input=odm_edit_input) + self.repository.save(item) + return self._transform_aggregate_root_to_pydantic_model(item) + + @ensure_transaction(db) + def create(self, odm_input: BaseModel) -> BaseModel: + BusinessLogicException.raise_if_not( + self._repos.library_repository.library_exists( + normalize_string(odm_input.library_name) # type: ignore[arg-type] + ), + msg=f"Library with Name '{odm_input.library_name}' doesn't exist.", + ) + + library_vo = LibraryVO.from_input_values_2( + library_name=odm_input.library_name, + is_library_editable_callback=is_library_editable, + ) + + odm_ar = self._create_aggregate_root( + odm_input=odm_input, + library=library_vo, + ) + self.repository.save(odm_ar) + response_model = self._transform_aggregate_root_to_pydantic_model(odm_ar) + return response_model + + @ensure_transaction(db) + def approve( + self, uid: str, cascade_edit_and_approve: bool = False, ignore_exc: bool = False + ) -> BaseModel: + item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + try: + item.approve(author_id=self.author_id) + self.repository.save(item) + except BusinessLogicException as exc: + if not ignore_exc or exc.msg != "The object isn't in draft status.": + raise + + if cascade_edit_and_approve: + self.cascade_edit_and_approve(item) + return self._transform_aggregate_root_to_pydantic_model(item) + + @ensure_transaction(db) + def inactivate_final( + self, + uid: str, + cascade_inactivate: bool = False, + force_new_value_node: bool = False, + ) -> BaseModel: + item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + item.inactivate( + author_id=self.author_id, force_new_value_node=force_new_value_node + ) + self.repository.save(item, force_new_value_node=force_new_value_node) + if cascade_inactivate: + self.cascade_inactivate(item) + return self._transform_aggregate_root_to_pydantic_model(item) + + @ensure_transaction(db) + def reactivate_retired( + self, + uid: str, + cascade_reactivate: bool = False, + force_new_value_node: bool = False, + ) -> BaseModel: + item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + item.reactivate( + author_id=self.author_id, force_new_value_node=force_new_value_node + ) + self.repository.save(item, force_new_value_node=force_new_value_node) + if cascade_reactivate: + self.cascade_reactivate(item) + return self._transform_aggregate_root_to_pydantic_model(item) + + @db.transaction + def soft_delete(self, uid: str, cascade_delete: bool = False) -> None: + item = self._find_by_uid_or_raise_not_found(uid, for_update=True) + item.soft_delete() + if cascade_delete: + self.cascade_delete(item) + self.repository.save(item) + + def enforce_library(self, library: str | None): + NotFoundException.raise_if( + library is not None + and not self._repos.library_repository.library_exists( + normalize_string(library) + ), + "Library", + library, + "Name", + ) + + def fail_if_non_present_vendor_elements_are_used_by_current_odm_element_attributes( + self, + attribute_uids: list[str], + input_elements: list[OdmVendorElementRelationPostInput], + ): + """ + Raises an error if any ODM vendor element that is not present in the input is used by any of the present ODM element attributes. + + Args: + attribute_uids (list[str]): The input ODM element attributes. + input_elements (list[OdmVendorElementRelationPostInput]): The input ODM vendor elements. + + Returns: + None + + Raises: + BusinessLogicException: If an ODM vendor element is used by any of the given ODM element attributes and is not present in the input. + """ + ( + odm_vendor_attribute_ars, + _, + ) = self._repos.odm_vendor_attribute_repository.find_all( + filter_by={"uid": {"v": attribute_uids, "op": "eq"}} + ) + + odm_vendor_attribute_element_uids = { + odm_vendor_attribute_ar.odm_vo.vendor_element_uid + for odm_vendor_attribute_ar in odm_vendor_attribute_ars + if odm_vendor_attribute_ar.odm_vo.vendor_element_uid + } + + BusinessLogicException.raise_if_not( + odm_vendor_attribute_element_uids.issubset( + {input_element.uid for input_element in input_elements} + ), + msg="Cannot remove an ODM Vendor Element whose attributes are connected to this ODM element.", + ) + + def fail_if_these_attributes_cannot_be_added( + self, + input_attributes: list[OdmVendorRelationPostInput], + element_uids: list[str] | None = None, + compatible_type: VendorAttributeCompatibleType | None = None, + ): + """ + Raises an error if any of the given ODM vendor attributes cannot be added as vendor attributes or vendor element attributes. + + Args: + input_attributes (list[OdmVendorRelationPostInput]): The input ODM vendor attributes. + element_uids (list[str] | None, optional): The uids of the vendor elements to which the attributes can be added. + compatible_type (VendorAttributeCompatibleType | None, optional): The vendor compatible type of the attributes. + + Returns: + None + + Raises: + BusinessLogicException: If any of the given ODM vendor attributes cannot be added as vendor attributes or vendor element attributes. + """ + odm_vendor_attribute_ars = self._get_odm_vendor_attributes(input_attributes) + vendor_attribute_patterns = { + odm_vendor_attribute_ar.uid: odm_vendor_attribute_ar.odm_vo.value_regex + for odm_vendor_attribute_ar in odm_vendor_attribute_ars + } + + self.attribute_values_matches_their_regex( + input_attributes, vendor_attribute_patterns + ) + + for odm_vendor_attribute_ar in odm_vendor_attribute_ars: + if odm_vendor_attribute_ar: + BusinessLogicException.raise_if( + element_uids + and odm_vendor_attribute_ar.odm_vo.vendor_element_uid + not in element_uids, + msg=f"ODM Vendor Attribute with UID '{odm_vendor_attribute_ar.uid}' cannot not be added as an Vendor Element Attribute.", + ) + + BusinessLogicException.raise_if( + not element_uids + and not odm_vendor_attribute_ar.odm_vo.vendor_namespace_uid, + msg=f"ODM Vendor Attribute with UID '{odm_vendor_attribute_ar.uid}' cannot not be added as an Vendor Attribute.", + ) + + self.are_attributes_vendor_compatible(odm_vendor_attribute_ars, compatible_type) + + def can_connect_vendor_attributes( + self, attributes: list[OdmVendorRelationPostInput] + ): + errors = [] + for attribute in attributes: + attr = self._repos.odm_vendor_attribute_repository.find_by_uid_2( + attribute.uid + ) + + if not attr or not attr.odm_vo.vendor_namespace_uid: + errors.append(attribute.uid) + + BusinessLogicException.raise_if( + errors, + msg=f"ODM Vendor Attributes with the following UIDs don't exist or aren't connected to an ODM Vendor Namespace. UIDs: {errors}", + ) + + return True + + def attribute_values_matches_their_regex( + self, + input_attributes: list[OdmVendorRelationPostInput], + attribute_patterns: dict[str, Any], + ): + """ + Determines whether the values of the given ODM vendor attributes match their regex patterns. + + Args: + input_attributes (list[OdmVendorRelationPostInput]): The input ODM vendor attributes. + attribute_patterns (dict): The regex patterns for the ODM vendor attributes. + + Returns: + bool: True if the values of the ODM vendor attributes match their regex patterns, False otherwise. + + Raises: + BusinessLogicException: If the values of any of the ODM vendor attributes don't match their regex patterns. + """ + errors = {} + for input_attribute in input_attributes: + if ( + input_attribute.value + and attribute_patterns.get(input_attribute.uid) + and not bool( + re.match( + attribute_patterns[input_attribute.uid], input_attribute.value + ) + ) + ): + errors[input_attribute.uid] = attribute_patterns[input_attribute.uid] + BusinessLogicException.raise_if( + errors, + msg=f"Provided values for following attributes don't match their regex pattern:\n\n{errors}", + ) + + return True + + def get_regex_patterns_of_attributes( + self, attribute_uids: list[str] + ) -> dict[str, str | None]: + """ + Returns a dictionary where the key is the attribute uid and the value is the regex pattern of the specified ODM vendor attributes. + + Args: + attribute_uids (list[str]): The uids of the ODM vendor attributes. + + Returns: + dict[str, str | None]: A dictionary of regex patterns for the specified ODM vendor attributes. + """ + attributes, _ = self._repos.odm_vendor_attribute_repository.find_all( + filter_by={"uid": {"v": attribute_uids, "op": "eq"}} + ) + + return {attribute.uid: attribute.odm_vo.value_regex for attribute in attributes} + + def are_elements_vendor_compatible( + self, + odm_vendor_elements: list[OdmVendorElementRelationPostInput], + compatible_type: VendorElementCompatibleType | None = None, + ): + """ + Determines whether the given ODM vendor elements are compatible with the specified vendor compatible type. + + Args: + odm_vendor_elements (list[OdmVendorElementRelationPostInput]: The ODM vendor elements. + compatible_type (VendorElementCompatibleType | None, optional): The vendor compatible type to check for compatibility. + + Returns: + bool: True if the given ODM vendor elements are compatible with the specified vendor compatible type. + + Raises: + BusinessLogicException: If any of the given ODM vendor elements are not compatible with the specified vendor compatible type. + """ + errors = {} + + odm_vendor_elements = self._get_odm_vendor_elements(odm_vendor_elements) + + for odm_vendor_element in odm_vendor_elements: + if ( + compatible_type + and compatible_type.value + not in odm_vendor_element.odm_vo.compatible_types + ): + errors[odm_vendor_element.uid] = ( + odm_vendor_element.odm_vo.compatible_types + ) + BusinessLogicException.raise_if( + errors, msg=f"Trying to add non-compatible ODM Vendor:\n\n{errors}" + ) + + return True + + def are_attributes_vendor_compatible( + self, + odm_vendor_attributes: ( + list[OdmVendorRelationPostInput] | list[OdmVendorAttributeAR] + ), + compatible_type: VendorAttributeCompatibleType | None = None, + ): + """ + Determines whether the given ODM vendor attributes are compatible with the specified vendor compatible type. + + Args: + odm_vendor_attributes (list[OdmVendorRelationPostInput] | list[OdmVendorAttributeAR]): The ODM vendor attributes. + compatible_type (VendorAttributeCompatibleType | None, optional): The vendor compatible type to check for compatibility. + + Returns: + bool: True if the given ODM vendor attributes are compatible with the specified vendor compatible type. + + Raises: + BusinessLogicException: If any of the given ODM vendor attributes are not compatible with the specified vendor compatible type. + """ + errors = {} + + if all( + isinstance(odm_vendor_attribute, OdmVendorRelationPostInput) + for odm_vendor_attribute in odm_vendor_attributes + ): + odm_vendor_attributes = self._get_odm_vendor_attributes( + odm_vendor_attributes # type: ignore[arg-type] + ) + + for odm_vendor_attribute in odm_vendor_attributes: + if ( + compatible_type + and compatible_type.value + not in odm_vendor_attribute.odm_vo.compatible_types + ): + errors[odm_vendor_attribute.uid] = ( + odm_vendor_attribute.odm_vo.compatible_types + ) + BusinessLogicException.raise_if( + errors, msg=f"Trying to add non-compatible ODM Vendor:\n\n{errors}" + ) + + return True + + def _get_odm_vendor_elements( + self, input_elements: list[OdmVendorElementRelationPostInput] + ): + return self._repos.odm_vendor_element_repository.find_all( + filter_by={ + "uid": { + "v": [input_element.uid for input_element in input_elements], + "op": "eq", + } + } + )[0] + + def _get_odm_vendor_attributes( + self, input_attributes: list[OdmVendorRelationPostInput] + ): + return self._repos.odm_vendor_attribute_repository.find_all( + filter_by={ + "uid": { + "v": [input_attribute.uid for input_attribute in input_attributes], + "op": "eq", + } + } + )[0] + + def pre_management( + self, + uid: str, + odm_vendor_element_post_input: list[OdmVendorElementRelationPostInput], + odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], + odm_ar: _AggregateRootType, + repo: FormRepository | ItemGroupRepository | ItemRepository, + ): + """ + Prepares the given ODM Vendors by adding and removing vendor element and vendor element attribute relations. + + Args: + uid (str): The uid of the ODM form, item group, or item. + odm_vendors_post_input (OdmVendorsPostInput): The ODM vendors. + odm_ar (_AggregateRootType): The ODM form, item group, or item. + repo (FormRepository | ItemGroupRepository | ItemRepository): The repository for the ODM form, item group, or item. + + Returns: + None + """ + removed_vendor_attribute_uids = set( + odm_ar.odm_vo.vendor_element_attribute_uids + ) - { + element_attribute.uid + for element_attribute in odm_vendor_element_attribute_post_input + } + for removed_vendor_attribute_uid in removed_vendor_attribute_uids: + repo.remove_relation( + uid=uid, + relation_uid=removed_vendor_attribute_uid, + relationship_type=RelationType.VENDOR_ELEMENT_ATTRIBUTE, + ) + + new_vendor_element_uids = { + element.uid for element in odm_vendor_element_post_input + } - set(odm_ar.odm_vo.vendor_element_uids) + for element in odm_vendor_element_post_input: + if element.uid in new_vendor_element_uids: + repo.add_relation( + uid=uid, + relation_uid=element.uid, + relationship_type=RelationType.VENDOR_ELEMENT, + parameters={ + "value": element.value, + }, + ) + + @ensure_transaction(db) + def cascade_edit_and_approve(self, item): + if getattr(item.odm_vo, "form_uids", None): + from clinical_mdr_api.services.odms.forms import OdmFormService + + form_service = OdmFormService() + + for form_uid in item.odm_vo.form_uids: + form_service.approve( + form_uid, cascade_edit_and_approve=True, ignore_exc=True + ) + + if getattr(item.odm_vo, "item_group_uids", None): + from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService + + item_group_service = OdmItemGroupService() + + for item_group_uid in item.odm_vo.item_group_uids: + item_group_service.approve( + item_group_uid, cascade_edit_and_approve=True, ignore_exc=True + ) + + if getattr(item.odm_vo, "item_uids", None): + from clinical_mdr_api.services.odms.items import OdmItemService + + item_service = OdmItemService() + + for item_uid in item.odm_vo.item_uids: + item_service.approve( + item_uid, cascade_edit_and_approve=True, ignore_exc=True + ) + + if getattr(item.odm_vo, "vendor_attribute_uids", None): + from clinical_mdr_api.services.odms.vendor_attributes import ( + OdmVendorAttributeService, + ) + + vendor_attribute_service = OdmVendorAttributeService() + + for vendor_attribute_uid in item.odm_vo.vendor_attribute_uids: + vendor_attribute_service.approve( + vendor_attribute_uid, cascade_edit_and_approve=True, ignore_exc=True + ) + + if getattr(item.odm_vo, "vendor_element_uids", None): + from clinical_mdr_api.services.odms.vendor_elements import ( + OdmVendorElementService, + ) + + vendor_element_service = OdmVendorElementService() + + for vendor_element_uid in item.odm_vo.vendor_element_uids: + vendor_element_service.approve( + vendor_element_uid, cascade_edit_and_approve=True, ignore_exc=True + ) + + if getattr(item.odm_vo, "vendor_namespace_uids", None): + from clinical_mdr_api.services.odms.vendor_namespaces import ( + OdmVendorNamespaceService, + ) + + vendor_namespace_service = OdmVendorNamespaceService() + + for vendor_namespace_uid in item.odm_vo.vendor_namespace_uids: + vendor_namespace_service.approve( + vendor_namespace_uid, cascade_edit_and_approve=True, ignore_exc=True + ) + + @ensure_transaction(db) + def cascade_new_version(self, item): + if getattr(item.odm_vo, "form_uids", None): + from clinical_mdr_api.services.odms.forms import OdmFormService + + form_service = OdmFormService() + + for form_uid in item.odm_vo.form_uids: + form_service.create_new_version( + form_uid, + cascade_new_version=True, + force_new_value_node=True, + ignore_exc=True, + ) + + if getattr(item.odm_vo, "item_group_uids", None): + from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService + + item_group_service = OdmItemGroupService() + + for item_group_uid in item.odm_vo.item_group_uids: + item_group_service.create_new_version( + item_group_uid, + cascade_new_version=True, + force_new_value_node=True, + ignore_exc=True, + ) + + if getattr(item.odm_vo, "item_uids", None): + from clinical_mdr_api.services.odms.items import OdmItemService + + item_service = OdmItemService() + + for item_uid in item.odm_vo.item_uids: + item_service.create_new_version( + item_uid, + cascade_new_version=True, + force_new_value_node=True, + ignore_exc=True, + ) + + @ensure_transaction(db) + def add_vendor_elements( + self, + uid: str, + odm_vendor_element_post_input: list[OdmVendorElementRelationPostInput], + odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], + odm_repository: FormRepository | ItemGroupRepository | ItemRepository, + override: bool = False, + ): + if override: + self.fail_if_non_present_vendor_elements_are_used_by_current_odm_element_attributes( + [ae.uid for ae in odm_vendor_element_attribute_post_input], + odm_vendor_element_post_input, + ) + + odm_repository.remove_relation( + uid=uid, + relation_uid=None, + relationship_type=RelationType.VENDOR_ELEMENT, + disconnect_all=True, + ) + + for vendor_element in odm_vendor_element_post_input: + odm_repository.add_relation( + uid=uid, + relation_uid=vendor_element.uid, + relationship_type=RelationType.VENDOR_ELEMENT, + parameters={ + "value": vendor_element.value, + }, + ) + + return self._find_by_uid_or_raise_not_found(uid) + + @ensure_transaction(db) + def add_vendor_attributes( + self, + uid: str, + odm_vendor_attribute_post_input: list[OdmVendorRelationPostInput], + odm_repository: FormRepository | ItemGroupRepository | ItemRepository, + override: bool = False, + ): + if override: + odm_repository.remove_relation( + uid=uid, + relation_uid=None, + relationship_type=RelationType.VENDOR_ATTRIBUTE, + disconnect_all=True, + ) + + for vendor_attribute in odm_vendor_attribute_post_input: + odm_repository.add_relation( + uid=uid, + relation_uid=vendor_attribute.uid, + relationship_type=RelationType.VENDOR_ATTRIBUTE, + parameters={ + "value": vendor_attribute.value, + }, + ) + + return self._find_by_uid_or_raise_not_found(uid) + + @ensure_transaction(db) + def add_vendor_element_attributes( + self, + uid: str, + odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], + odm_ar: _AggregateRootType, + odm_repository: FormRepository | ItemGroupRepository | ItemRepository, + override: bool = False, + ): + self.fail_if_these_attributes_cannot_be_added( + odm_vendor_element_attribute_post_input, + odm_ar.odm_vo.vendor_element_uids, + ) + + if override: + odm_repository.remove_relation( + uid=uid, + relation_uid=None, + relationship_type=RelationType.VENDOR_ELEMENT_ATTRIBUTE, + disconnect_all=True, + ) + + for vendor_element_attribute in odm_vendor_element_attribute_post_input: + odm_repository.add_relation( + uid=uid, + relation_uid=vendor_element_attribute.uid, + relationship_type=RelationType.VENDOR_ELEMENT_ATTRIBUTE, + parameters={ + "value": vendor_element_attribute.value, + }, + ) + + return self._find_by_uid_or_raise_not_found(uid) + + @ensure_transaction(db) + def manage_vendors( + self, + uid: str, + element_compatible_type: VendorElementCompatibleType, + attribute_compatible_type: VendorAttributeCompatibleType, + odm_vendor_element_post_input: list[OdmVendorElementRelationPostInput], + odm_vendor_element_attribute_post_input: list[OdmVendorRelationPostInput], + odm_vendor_attribute_post_input: list[OdmVendorRelationPostInput], + odm_repository: FormRepository | ItemGroupRepository | ItemRepository, + ) -> BaseModel: + odm_ar = self._find_by_uid_or_raise_not_found(uid) + + BusinessLogicException.raise_if( + odm_ar.item_metadata.status != LibraryItemStatus.DRAFT, + msg=self.OBJECT_NOT_IN_DRAFT, + ) + + self.are_elements_vendor_compatible( + odm_vendor_element_post_input, compatible_type=element_compatible_type + ) + self.fail_if_these_attributes_cannot_be_added( + odm_vendor_attribute_post_input, compatible_type=attribute_compatible_type + ) + + self.pre_management( + uid, + odm_vendor_element_post_input, + odm_vendor_element_attribute_post_input, + odm_ar, + odm_repository, + ) + + odm_ar = self.add_vendor_elements( + uid, + odm_vendor_element_post_input, + odm_vendor_element_attribute_post_input, + odm_repository, + True, + ) + self.add_vendor_element_attributes( + uid, odm_vendor_element_attribute_post_input, odm_ar, odm_repository, True + ) + self.add_vendor_attributes( + uid, odm_vendor_attribute_post_input, odm_repository, True + ) + + return self.get_by_uid(uid) + + def cascade_inactivate(self, item: _AggregateRootType): + pass + + def cascade_reactivate(self, item: _AggregateRootType): + pass + + def cascade_delete(self, item: _AggregateRootType): + pass diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_item_groups.py b/clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py similarity index 69% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_item_groups.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py index be49a983..b971b8d8 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_item_groups.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/item_groups.py @@ -1,19 +1,16 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.item_group_repository import ( +from clinical_mdr_api.domain_repositories.odms.item_group_repository import ( ItemGroupRepository, ) -from clinical_mdr_api.domains.concepts.odms.item_group import ( - OdmItemGroupAR, - OdmItemGroupVO, -) -from clinical_mdr_api.domains.concepts.utils import ( +from clinical_mdr_api.domains.odms.item_group import OdmItemGroupAR, OdmItemGroupVO +from clinical_mdr_api.domains.odms.utils import ( RelationType, VendorAttributeCompatibleType, VendorElementCompatibleType, ) from clinical_mdr_api.domains.versioned_object_aggregate import LibraryItemStatus -from clinical_mdr_api.models.concepts.odms.odm_item_group import ( +from clinical_mdr_api.models.odms.item_group import ( OdmItemGroup, OdmItemGroupItemPostInput, OdmItemGroupPatchInput, @@ -21,9 +18,7 @@ OdmItemGroupVersion, ) from clinical_mdr_api.services._utils import ensure_transaction, get_input_or_new_value -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from clinical_mdr_api.utils import normalize_string, to_dict from common.exceptions import BusinessLogicException, NotFoundException from common.utils import strtobool @@ -50,22 +45,22 @@ def _transform_aggregate_root_to_pydantic_model( ) def _create_aggregate_root( - self, concept_input: OdmItemGroupPostInput, library + self, odm_input: OdmItemGroupPostInput, library ) -> OdmItemGroupAR: return OdmItemGroupAR.from_input_values( author_id=self.author_id, - concept_vo=OdmItemGroupVO.from_repository_values( - oid=get_input_or_new_value(concept_input.oid, "G.", concept_input.name), - name=concept_input.name, - repeating=strtobool(concept_input.repeating), - is_reference_data=strtobool(concept_input.is_reference_data), - sas_dataset_name=concept_input.sas_dataset_name, - origin=concept_input.origin, - purpose=concept_input.purpose, - comment=concept_input.comment, - translated_texts=concept_input.translated_texts, - aliases=concept_input.aliases, - sdtm_domain_uids=concept_input.sdtm_domain_uids, + odm_vo=OdmItemGroupVO.from_repository_values( + oid=get_input_or_new_value(odm_input.oid, "G.", odm_input.name), + name=odm_input.name, + repeating=strtobool(odm_input.repeating), + is_reference_data=strtobool(odm_input.is_reference_data), + sas_dataset_name=odm_input.sas_dataset_name, + origin=odm_input.origin, + purpose=odm_input.purpose, + comment=odm_input.comment, + translated_texts=odm_input.translated_texts, + aliases=odm_input.aliases, + sdtm_domain_uids=odm_input.sdtm_domain_uids, item_uids=[], vendor_element_uids=[], vendor_attribute_uids=[], @@ -78,27 +73,27 @@ def _create_aggregate_root( ) def _edit_aggregate( - self, item: OdmItemGroupAR, concept_edit_input: OdmItemGroupPatchInput + self, item: OdmItemGroupAR, odm_edit_input: OdmItemGroupPatchInput ) -> OdmItemGroupAR: item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmItemGroupVO.from_repository_values( - oid=concept_edit_input.oid, - name=concept_edit_input.name, - repeating=strtobool(concept_edit_input.repeating), - is_reference_data=strtobool(concept_edit_input.is_reference_data), - sas_dataset_name=concept_edit_input.sas_dataset_name, - origin=concept_edit_input.origin, - purpose=concept_edit_input.purpose, - comment=concept_edit_input.comment, - translated_texts=concept_edit_input.translated_texts, - aliases=concept_edit_input.aliases, - sdtm_domain_uids=concept_edit_input.sdtm_domain_uids, - item_uids=item.concept_vo.item_uids, - vendor_element_uids=item.concept_vo.vendor_element_uids, - vendor_attribute_uids=item.concept_vo.vendor_attribute_uids, - vendor_element_attribute_uids=item.concept_vo.vendor_element_attribute_uids, + change_description=odm_edit_input.change_description, + odm_vo=OdmItemGroupVO.from_repository_values( + oid=odm_edit_input.oid, + name=odm_edit_input.name, + repeating=strtobool(odm_edit_input.repeating), + is_reference_data=strtobool(odm_edit_input.is_reference_data), + sas_dataset_name=odm_edit_input.sas_dataset_name, + origin=odm_edit_input.origin, + purpose=odm_edit_input.purpose, + comment=odm_edit_input.comment, + translated_texts=odm_edit_input.translated_texts, + aliases=odm_edit_input.aliases, + sdtm_domain_uids=odm_edit_input.sdtm_domain_uids, + item_uids=item.odm_vo.item_uids, + vendor_element_uids=item.odm_vo.vendor_element_uids, + vendor_attribute_uids=item.odm_vo.vendor_attribute_uids, + vendor_element_attribute_uids=item.odm_vo.vendor_element_attribute_uids, ), odm_object_exists_callback=self._repos.odm_item_group_repository.odm_object_exists, find_term_callback=self._repos.ct_term_attributes_repository.find_by_uid, @@ -106,16 +101,16 @@ def _edit_aggregate( return item @db.transaction - def create(self, concept_input: OdmItemGroupPostInput) -> OdmItemGroup: - item = super().create(concept_input) + def create(self, odm_input: OdmItemGroupPostInput) -> OdmItemGroup: + item = super().create(odm_input) super().manage_vendors( item.uid, VendorElementCompatibleType.ITEM_GROUP_DEF, VendorAttributeCompatibleType.ITEM_GROUP_DEF, - concept_input.vendor_elements, - concept_input.vendor_element_attributes, - concept_input.vendor_attributes, + odm_input.vendor_elements, + odm_input.vendor_element_attributes, + odm_input.vendor_attributes, self._repos.odm_item_group_repository, ) @@ -125,17 +120,17 @@ def create(self, concept_input: OdmItemGroupPostInput) -> OdmItemGroup: @db.transaction def edit_draft( - self, uid: str, concept_edit_input: OdmItemGroupPatchInput + self, uid: str, odm_edit_input: OdmItemGroupPatchInput ) -> OdmItemGroup: - super().edit_draft(uid, concept_edit_input) + super().edit_draft(uid, odm_edit_input) super().manage_vendors( uid, VendorElementCompatibleType.ITEM_GROUP_DEF, VendorAttributeCompatibleType.ITEM_GROUP_DEF, - concept_edit_input.vendor_elements, - concept_edit_input.vendor_element_attributes, - concept_edit_input.vendor_attributes, + odm_edit_input.vendor_elements, + odm_edit_input.vendor_element_attributes, + odm_edit_input.vendor_attributes, self._repos.odm_item_group_repository, ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_items.py b/clinical-mdr-api/clinical_mdr_api/services/odms/items.py similarity index 74% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_items.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/items.py index 6a6ec179..b7bd8be1 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_items.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/items.py @@ -1,8 +1,5 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.item_repository import ( - ItemRepository, -) from clinical_mdr_api.domain_repositories.controlled_terminologies.ct_codelist_attributes_repository import ( CTCodelistAttributesRepository, CTCodelistGenericRepository, @@ -11,13 +8,14 @@ CTTermRoot, ) from clinical_mdr_api.domain_repositories.models.odm import OdmItemRoot -from clinical_mdr_api.domains.concepts.odms.item import OdmItemAR, OdmItemVO -from clinical_mdr_api.domains.concepts.utils import ( +from clinical_mdr_api.domain_repositories.odms.item_repository import ItemRepository +from clinical_mdr_api.domains.odms.item import OdmItemAR, OdmItemVO +from clinical_mdr_api.domains.odms.utils import ( RelationType, VendorAttributeCompatibleType, VendorElementCompatibleType, ) -from clinical_mdr_api.models.concepts.odms.odm_item import ( +from clinical_mdr_api.models.odms.item import ( OdmItem, OdmItemPatchInput, OdmItemPostInput, @@ -26,9 +24,7 @@ OdmItemVersion, ) from clinical_mdr_api.services._utils import ensure_transaction, get_input_or_new_value -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from common.exceptions import NotFoundException @@ -56,31 +52,29 @@ def _transform_aggregate_root_to_pydantic_model( ), ) - def _create_aggregate_root( - self, concept_input: OdmItemPostInput, library - ) -> OdmItemAR: + def _create_aggregate_root(self, odm_input: OdmItemPostInput, library) -> OdmItemAR: return OdmItemAR.from_input_values( author_id=self.author_id, - concept_vo=OdmItemVO.from_repository_values( - oid=get_input_or_new_value(concept_input.oid, "I.", concept_input.name), - name=concept_input.name, - prompt=concept_input.prompt, - datatype=concept_input.datatype, - length=concept_input.length, - significant_digits=concept_input.significant_digits, - sas_field_name=concept_input.sas_field_name, - sds_var_name=concept_input.sds_var_name, - origin=concept_input.origin, - comment=concept_input.comment, + odm_vo=OdmItemVO.from_repository_values( + oid=get_input_or_new_value(odm_input.oid, "I.", odm_input.name), + name=odm_input.name, + prompt=odm_input.prompt, + datatype=odm_input.datatype, + length=odm_input.length, + significant_digits=odm_input.significant_digits, + sas_field_name=odm_input.sas_field_name, + sds_var_name=odm_input.sds_var_name, + origin=odm_input.origin, + comment=odm_input.comment, odm_item_group=None, - translated_texts=concept_input.translated_texts, - aliases=concept_input.aliases, + translated_texts=odm_input.translated_texts, + aliases=odm_input.aliases, unit_definition_uids=[ unit_definition.uid - for unit_definition in concept_input.unit_definitions + for unit_definition in odm_input.unit_definitions ], - codelist=concept_input.codelist, - term_uids=[term.uid for term in concept_input.terms], + codelist=odm_input.codelist, + term_uids=[term.uid for term in odm_input.terms], activity_instances=[], vendor_element_uids=[], vendor_attribute_uids=[], @@ -95,38 +89,37 @@ def _create_aggregate_root( ) def _edit_aggregate( - self, item: OdmItemAR, concept_edit_input: OdmItemPatchInput + self, item: OdmItemAR, odm_edit_input: OdmItemPatchInput ) -> OdmItemAR: item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmItemVO.from_repository_values( - oid=concept_edit_input.oid, - name=concept_edit_input.name, - prompt=concept_edit_input.prompt, - datatype=concept_edit_input.datatype, - length=concept_edit_input.length, - significant_digits=concept_edit_input.significant_digits, - sas_field_name=concept_edit_input.sas_field_name, - sds_var_name=concept_edit_input.sds_var_name, - origin=concept_edit_input.origin, + change_description=odm_edit_input.change_description, + odm_vo=OdmItemVO.from_repository_values( + oid=odm_edit_input.oid, + name=odm_edit_input.name, + prompt=odm_edit_input.prompt, + datatype=odm_edit_input.datatype, + length=odm_edit_input.length, + significant_digits=odm_edit_input.significant_digits, + sas_field_name=odm_edit_input.sas_field_name, + sds_var_name=odm_edit_input.sds_var_name, + origin=odm_edit_input.origin, odm_item_group=None, - comment=concept_edit_input.comment, - translated_texts=concept_edit_input.translated_texts, - aliases=concept_edit_input.aliases, + comment=odm_edit_input.comment, + translated_texts=odm_edit_input.translated_texts, + aliases=odm_edit_input.aliases, unit_definition_uids=[ unit_definition.uid - for unit_definition in concept_edit_input.unit_definitions + for unit_definition in odm_edit_input.unit_definitions ], - codelist=concept_edit_input.codelist, - term_uids=[term.uid for term in concept_edit_input.terms], + codelist=odm_edit_input.codelist, + term_uids=[term.uid for term in odm_edit_input.terms], activity_instances=[ - model.model_dump() - for model in concept_edit_input.activity_instances + model.model_dump() for model in odm_edit_input.activity_instances ], - vendor_element_uids=item.concept_vo.vendor_element_uids, - vendor_attribute_uids=item.concept_vo.vendor_attribute_uids, - vendor_element_attribute_uids=item.concept_vo.vendor_element_attribute_uids, + vendor_element_uids=item.odm_vo.vendor_element_uids, + vendor_attribute_uids=item.odm_vo.vendor_attribute_uids, + vendor_element_attribute_uids=item.odm_vo.vendor_element_attribute_uids, ), odm_object_exists_callback=self._repos.odm_item_repository.odm_object_exists, unit_definition_exists_by_callback=self._repos.unit_definition_repository.exists_by, @@ -137,20 +130,20 @@ def _edit_aggregate( return item @db.transaction - def create(self, concept_input: OdmItemPostInput) -> OdmItem: - item = super().create(concept_input) + def create(self, odm_input: OdmItemPostInput) -> OdmItem: + item = super().create(odm_input) self._manage_terms( - item.uid, getattr(concept_input.codelist, "uid", None), concept_input.terms + item.uid, getattr(odm_input.codelist, "uid", None), odm_input.terms ) - self._manage_unit_definitions(item.uid, concept_input.unit_definitions) + self._manage_unit_definitions(item.uid, odm_input.unit_definitions) super().manage_vendors( item.uid, VendorElementCompatibleType.ITEM_DEF, VendorAttributeCompatibleType.ITEM_DEF, - concept_input.vendor_elements, - concept_input.vendor_element_attributes, - concept_input.vendor_attributes, + odm_input.vendor_elements, + odm_input.vendor_element_attributes, + odm_input.vendor_attributes, self._repos.odm_item_repository, ) @@ -159,23 +152,23 @@ def create(self, concept_input: OdmItemPostInput) -> OdmItem: ) @db.transaction - def edit_draft(self, uid: str, concept_edit_input: OdmItemPatchInput) -> OdmItem: - super().edit_draft(uid, concept_edit_input) + def edit_draft(self, uid: str, odm_edit_input: OdmItemPatchInput) -> OdmItem: + super().edit_draft(uid, odm_edit_input) self._manage_terms( uid, - getattr(concept_edit_input.codelist, "uid", None), - concept_edit_input.terms, + getattr(odm_edit_input.codelist, "uid", None), + odm_edit_input.terms, True, ) - self._manage_unit_definitions(uid, concept_edit_input.unit_definitions, True) + self._manage_unit_definitions(uid, odm_edit_input.unit_definitions, True) super().manage_vendors( uid, VendorElementCompatibleType.ITEM_DEF, VendorAttributeCompatibleType.ITEM_DEF, - concept_edit_input.vendor_elements, - concept_edit_input.vendor_element_attributes, - concept_edit_input.vendor_attributes, + odm_edit_input.vendor_elements, + odm_edit_input.vendor_element_attributes, + odm_edit_input.vendor_attributes, self._repos.odm_item_repository, ) @@ -196,7 +189,7 @@ def inactivate_final( self._repos.odm_item_repository.find_unit_definition_with_item_relation_by_item_uid( uid, unit_definition_uid ) - for unit_definition_uid in old_item.concept_vo.unit_definition_uids + for unit_definition_uid in old_item.odm_vo.unit_definition_uids ] unit_definitions = [ OdmItemUnitDefinitionRelationshipInput( @@ -205,7 +198,7 @@ def inactivate_final( order=unit_definition.order, ) for unit_definition, unit_definition_uid in zip( - unit_definitions, old_item.concept_vo.unit_definition_uids + unit_definitions, old_item.odm_vo.unit_definition_uids ) if unit_definition is not None ] @@ -214,7 +207,7 @@ def inactivate_final( self._repos.odm_item_repository.find_term_with_item_relation_by_item_uid( uid, term_uid ) - for term_uid in old_item.concept_vo.term_uids + for term_uid in old_item.odm_vo.term_uids ] terms = [ OdmItemTermRelationshipInput( @@ -223,14 +216,14 @@ def inactivate_final( order=term.order, display_text=term.display_text, ) - for term, term_uid in zip(terms, old_item.concept_vo.term_uids) + for term, term_uid in zip(terms, old_item.odm_vo.term_uids) if term is not None ] super().inactivate_final(uid, cascade_inactivate, force_new_value_node) self._manage_terms( - uid, getattr(old_item.concept_vo.codelist, "uid", None), terms, True + uid, getattr(old_item.odm_vo.codelist, "uid", None), terms, True ) self._manage_unit_definitions(uid, unit_definitions, True) @@ -251,7 +244,7 @@ def reactivate_retired( self._repos.odm_item_repository.find_unit_definition_with_item_relation_by_item_uid( uid, unit_definition_uid ) - for unit_definition_uid in old_item.concept_vo.unit_definition_uids + for unit_definition_uid in old_item.odm_vo.unit_definition_uids ] unit_definitions = [ OdmItemUnitDefinitionRelationshipInput( @@ -260,7 +253,7 @@ def reactivate_retired( order=unit_definition.order, ) for unit_definition, unit_definition_uid in zip( - unit_definitions, old_item.concept_vo.unit_definition_uids + unit_definitions, old_item.odm_vo.unit_definition_uids ) if unit_definition is not None ] @@ -269,7 +262,7 @@ def reactivate_retired( self._repos.odm_item_repository.find_term_with_item_relation_by_item_uid( uid, term_uid ) - for term_uid in old_item.concept_vo.term_uids + for term_uid in old_item.odm_vo.term_uids ] terms = [ OdmItemTermRelationshipInput( @@ -278,14 +271,14 @@ def reactivate_retired( order=term.order, display_text=term.display_text, ) - for term, term_uid in zip(terms, old_item.concept_vo.term_uids) + for term, term_uid in zip(terms, old_item.odm_vo.term_uids) if term is not None ] super().reactivate_retired(uid, cascade_reactivate, force_new_value_node) self._manage_terms( - uid, getattr(old_item.concept_vo.codelist, "uid", None), terms, True + uid, getattr(old_item.odm_vo.codelist, "uid", None), terms, True ) self._manage_unit_definitions(uid, unit_definitions, True) @@ -307,7 +300,7 @@ def create_new_version( self._repos.odm_item_repository.find_unit_definition_with_item_relation_by_item_uid( uid, unit_definition_uid ) - for unit_definition_uid in old_item.concept_vo.unit_definition_uids + for unit_definition_uid in old_item.odm_vo.unit_definition_uids ] unit_definitions = [ OdmItemUnitDefinitionRelationshipInput( @@ -316,7 +309,7 @@ def create_new_version( order=unit_definition.order, ) for unit_definition, unit_definition_uid in zip( - unit_definitions, old_item.concept_vo.unit_definition_uids + unit_definitions, old_item.odm_vo.unit_definition_uids ) if unit_definition is not None ] @@ -325,7 +318,7 @@ def create_new_version( self._repos.odm_item_repository.find_term_with_item_relation_by_item_uid( uid, term_uid ) - for term_uid in old_item.concept_vo.term_uids + for term_uid in old_item.odm_vo.term_uids ] terms = [ OdmItemTermRelationshipInput( @@ -334,7 +327,7 @@ def create_new_version( order=term.order, display_text=term.display_text, ) - for term, term_uid in zip(terms, old_item.concept_vo.term_uids) + for term, term_uid in zip(terms, old_item.odm_vo.term_uids) if term is not None ] @@ -343,7 +336,7 @@ def create_new_version( ) self._manage_terms( - uid, getattr(old_item.concept_vo.codelist, "uid", None), terms, True + uid, getattr(old_item.odm_vo.codelist, "uid", None), terms, True ) self._manage_unit_definitions(uid, unit_definitions, True) diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_metadata.py b/clinical-mdr-api/clinical_mdr_api/services/odms/metadata.py similarity index 98% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_metadata.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/metadata.py index 8afb3cd1..e71cf0df 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_metadata.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/metadata.py @@ -56,7 +56,7 @@ def _query( label IN labels(root) WHERE NOT label STARTS WITH 'Deleted' AND label ENDS WITH 'Root' - AND label <> 'ConceptRoot' + AND label <> 'OdmRoot' ) """ @@ -90,16 +90,14 @@ def _query( limit_stmt = "" results, columns = db.cypher_query( - dedent( - f""" + dedent(f""" MATCH (n:{node_name}) {where_stmt} {exclude_old_stmt} RETURN DISTINCT {', '.join([f'n.{field} AS {field}' for field in fields])} {order_stmt} {limit_stmt} - """ - ), + """), params=params, ) diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_methods.py b/clinical-mdr-api/clinical_mdr_api/services/odms/methods.py similarity index 53% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_methods.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/methods.py index 60edc3f5..bb666317 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_methods.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/methods.py @@ -1,20 +1,20 @@ +import logging + from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.method_repository import ( - MethodRepository, -) -from clinical_mdr_api.domains.concepts.odms.method import OdmMethodAR, OdmMethodVO -from clinical_mdr_api.models.concepts.odms.odm_method import ( +from clinical_mdr_api.domain_repositories.odms.method_repository import MethodRepository +from clinical_mdr_api.domains.odms.method import OdmMethodAR, OdmMethodVO +from clinical_mdr_api.models.odms.method import ( OdmMethod, OdmMethodPatchInput, OdmMethodPostInput, OdmMethodVersion, ) -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from common.exceptions import NotFoundException +log = logging.getLogger(__name__) + class OdmMethodService(OdmGenericService[OdmMethodAR]): aggregate_class = OdmMethodAR @@ -27,17 +27,24 @@ def _transform_aggregate_root_to_pydantic_model( return OdmMethod.from_odm_method_ar(odm_method_ar=item_ar) def _create_aggregate_root( - self, concept_input: OdmMethodPostInput, library + self, odm_input: OdmMethodPostInput, library ) -> OdmMethodAR: + log.info( + "Creating ODM Method: name='%s', oid=%s, method_type=%s, library=%s", + odm_input.name, + odm_input.oid, + odm_input.method_type, + library.name, + ) return OdmMethodAR.from_input_values( author_id=self.author_id, - concept_vo=OdmMethodVO.from_repository_values( - oid=concept_input.oid, - name=concept_input.name, - method_type=concept_input.method_type, - formal_expressions=concept_input.formal_expressions, - translated_texts=concept_input.translated_texts, - aliases=concept_input.aliases, + odm_vo=OdmMethodVO.from_repository_values( + oid=odm_input.oid, + name=odm_input.name, + method_type=odm_input.method_type, + formal_expressions=odm_input.formal_expressions, + translated_texts=odm_input.translated_texts, + aliases=odm_input.aliases, ), library=library, generate_uid_callback=self.repository.generate_uid, @@ -45,18 +52,23 @@ def _create_aggregate_root( ) def _edit_aggregate( - self, item: OdmMethodAR, concept_edit_input: OdmMethodPatchInput + self, item: OdmMethodAR, odm_edit_input: OdmMethodPatchInput ) -> OdmMethodAR: + log.info( + "Editing ODM Method: uid=%s, name='%s'", + item.uid, + odm_edit_input.name, + ) item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmMethodVO.from_repository_values( - oid=concept_edit_input.oid, - name=concept_edit_input.name, - method_type=concept_edit_input.method_type, - formal_expressions=concept_edit_input.formal_expressions, - translated_texts=concept_edit_input.translated_texts, - aliases=concept_edit_input.aliases, + change_description=odm_edit_input.change_description, + odm_vo=OdmMethodVO.from_repository_values( + oid=odm_edit_input.oid, + name=odm_edit_input.name, + method_type=odm_edit_input.method_type, + formal_expressions=odm_edit_input.formal_expressions, + translated_texts=odm_edit_input.translated_texts, + aliases=odm_edit_input.aliases, ), odm_object_exists_callback=self._repos.odm_method_repository.odm_object_exists, ) @@ -70,6 +82,7 @@ def soft_delete(self, uid: str, cascade_delete: bool = False): This method is temporary and should be removed when the database relationship between ODM Method and its reference nodes is ready. """ + log.info("Soft deleting ODM Method: uid=%s, cascade=%s", uid, cascade_delete) method = self._find_by_uid_or_raise_not_found(uid, for_update=True) method.soft_delete() self.repository.save(method) @@ -78,11 +91,13 @@ def soft_delete(self, uid: str, cascade_delete: bool = False): self.cascade_delete(method) self._repos.odm_method_repository.set_all_method_oid_properties_to_null( - method.concept_vo.oid + method.odm_vo.oid ) + log.info("Successfully soft deleted ODM Method: uid=%s", uid) @db.transaction def get_active_relationships(self, uid: str): + log.debug("Getting active relationships for ODM Method: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_method_repository.exists_by("uid", uid, True), "ODM Method", diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_study_events.py b/clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py similarity index 70% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_study_events.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py index 460538c3..f31daed6 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_study_events.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/study_events.py @@ -1,15 +1,12 @@ from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.study_event_repository import ( +from clinical_mdr_api.domain_repositories.odms.study_event_repository import ( StudyEventRepository, ) -from clinical_mdr_api.domains.concepts.odms.study_event import ( - OdmStudyEventAR, - OdmStudyEventVO, -) -from clinical_mdr_api.domains.concepts.utils import RelationType +from clinical_mdr_api.domains.odms.study_event import OdmStudyEventAR, OdmStudyEventVO +from clinical_mdr_api.domains.odms.utils import RelationType from clinical_mdr_api.domains.versioned_object_aggregate import LibraryItemStatus -from clinical_mdr_api.models.concepts.odms.odm_study_event import ( +from clinical_mdr_api.models.odms.study_event import ( OdmStudyEvent, OdmStudyEventFormPostInput, OdmStudyEventPatchInput, @@ -17,9 +14,7 @@ OdmStudyEventVersion, ) from clinical_mdr_api.services._utils import get_input_or_new_value -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from clinical_mdr_api.utils import normalize_string from common.exceptions import BusinessLogicException, NotFoundException from common.utils import strtobool @@ -39,17 +34,17 @@ def _transform_aggregate_root_to_pydantic_model( ) def _create_aggregate_root( - self, concept_input: OdmStudyEventPostInput, library + self, odm_input: OdmStudyEventPostInput, library ) -> OdmStudyEventAR: return OdmStudyEventAR.from_input_values( author_id=self.author_id, - concept_vo=OdmStudyEventVO.from_repository_values( - name=concept_input.name, - oid=get_input_or_new_value(concept_input.oid, "T.", concept_input.name), - effective_date=concept_input.effective_date, - retired_date=concept_input.retired_date, - description=concept_input.description, - display_in_tree=concept_input.display_in_tree, + odm_vo=OdmStudyEventVO.from_repository_values( + name=odm_input.name, + oid=get_input_or_new_value(odm_input.oid, "T.", odm_input.name), + effective_date=odm_input.effective_date, + retired_date=odm_input.retired_date, + description=odm_input.description, + display_in_tree=odm_input.display_in_tree, form_uids=[], ), library=library, @@ -58,18 +53,18 @@ def _create_aggregate_root( ) def _edit_aggregate( - self, item: OdmStudyEventAR, concept_edit_input: OdmStudyEventPatchInput + self, item: OdmStudyEventAR, odm_edit_input: OdmStudyEventPatchInput ) -> OdmStudyEventAR: item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmStudyEventVO.from_repository_values( - name=concept_edit_input.name, - oid=concept_edit_input.oid, - effective_date=concept_edit_input.effective_date, - retired_date=concept_edit_input.retired_date, - description=concept_edit_input.description, - display_in_tree=concept_edit_input.display_in_tree, + change_description=odm_edit_input.change_description, + odm_vo=OdmStudyEventVO.from_repository_values( + name=odm_edit_input.name, + oid=odm_edit_input.oid, + effective_date=odm_edit_input.effective_date, + retired_date=odm_edit_input.retired_date, + description=odm_edit_input.description, + display_in_tree=odm_edit_input.display_in_tree, form_uids=[], ), odm_object_exists_callback=self._repos.odm_study_event_repository.odm_object_exists, diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_attributes.py b/clinical-mdr-api/clinical_mdr_api/services/odms/vendor_attributes.py similarity index 60% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_attributes.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/vendor_attributes.py index 48919b64..d9c7a623 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_attributes.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/vendor_attributes.py @@ -1,23 +1,25 @@ +import logging + from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.vendor_attribute_repository import ( +from clinical_mdr_api.domain_repositories.odms.vendor_attribute_repository import ( VendorAttributeRepository, ) -from clinical_mdr_api.domains.concepts.odms.vendor_attribute import ( +from clinical_mdr_api.domains.odms.vendor_attribute import ( OdmVendorAttributeAR, OdmVendorAttributeVO, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( +from clinical_mdr_api.models.odms.vendor_attribute import ( OdmVendorAttribute, OdmVendorAttributePatchInput, OdmVendorAttributePostInput, OdmVendorAttributeVersion, ) -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from common.exceptions import NotFoundException +log = logging.getLogger(__name__) + class OdmVendorAttributeService(OdmGenericService[OdmVendorAttributeAR]): aggregate_class = OdmVendorAttributeAR @@ -34,20 +36,21 @@ def _transform_aggregate_root_to_pydantic_model( ) def _create_aggregate_root( - self, concept_input: OdmVendorAttributePostInput, library + self, odm_input: OdmVendorAttributePostInput, library ) -> OdmVendorAttributeAR: + log.info("Creating ODM Vendor Attribute: name='%s'", odm_input.name) return OdmVendorAttributeAR.from_input_values( author_id=self.author_id, - concept_vo=OdmVendorAttributeVO.from_repository_values( - name=concept_input.name, + odm_vo=OdmVendorAttributeVO.from_repository_values( + name=odm_input.name, compatible_types=[ compatible_type.value - for compatible_type in concept_input.compatible_types + for compatible_type in odm_input.compatible_types ], - data_type=concept_input.data_type, - value_regex=concept_input.value_regex, - vendor_namespace_uid=concept_input.vendor_namespace_uid, - vendor_element_uid=concept_input.vendor_element_uid, + data_type=odm_input.data_type, + value_regex=odm_input.value_regex, + vendor_namespace_uid=odm_input.vendor_namespace_uid, + vendor_element_uid=odm_input.vendor_element_uid, ), library=library, generate_uid_callback=self.repository.generate_uid, @@ -59,27 +62,29 @@ def _create_aggregate_root( def _edit_aggregate( self, item: OdmVendorAttributeAR, - concept_edit_input: OdmVendorAttributePatchInput, + odm_edit_input: OdmVendorAttributePatchInput, ) -> OdmVendorAttributeAR: + log.info("Editing ODM Vendor Attribute: uid=%s", item.uid) item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmVendorAttributeVO.from_repository_values( - name=concept_edit_input.name, + change_description=odm_edit_input.change_description, + odm_vo=OdmVendorAttributeVO.from_repository_values( + name=odm_edit_input.name, compatible_types=[ compatible_type.value - for compatible_type in concept_edit_input.compatible_types + for compatible_type in odm_edit_input.compatible_types ], - data_type=concept_edit_input.data_type, - value_regex=concept_edit_input.value_regex, - vendor_namespace_uid=item.concept_vo.vendor_namespace_uid, - vendor_element_uid=item.concept_vo.vendor_element_uid, + data_type=odm_edit_input.data_type, + value_regex=odm_edit_input.value_regex, + vendor_namespace_uid=item.odm_vo.vendor_namespace_uid, + vendor_element_uid=item.odm_vo.vendor_element_uid, ), ) return item @db.transaction def get_active_relationships(self, uid: str): + log.debug("Getting active relationships for ODM Vendor Attribute: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_vendor_attribute_repository.exists_by("uid", uid, True), "ODM Vendor Attribute", diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_elements.py b/clinical-mdr-api/clinical_mdr_api/services/odms/vendor_elements.py similarity index 67% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_elements.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/vendor_elements.py index cfb1d35b..b5f761a2 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_elements.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/vendor_elements.py @@ -1,23 +1,25 @@ +import logging + from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.vendor_element_repository import ( +from clinical_mdr_api.domain_repositories.odms.vendor_element_repository import ( VendorElementRepository, ) -from clinical_mdr_api.domains.concepts.odms.vendor_element import ( +from clinical_mdr_api.domains.odms.vendor_element import ( OdmVendorElementAR, OdmVendorElementVO, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( +from clinical_mdr_api.models.odms.vendor_element import ( OdmVendorElement, OdmVendorElementPatchInput, OdmVendorElementPostInput, OdmVendorElementVersion, ) -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from common.exceptions import BusinessLogicException, NotFoundException +log = logging.getLogger(__name__) + class OdmVendorElementService(OdmGenericService[OdmVendorElementAR]): aggregate_class = OdmVendorElementAR @@ -34,17 +36,18 @@ def _transform_aggregate_root_to_pydantic_model( ) def _create_aggregate_root( - self, concept_input: OdmVendorElementPostInput, library + self, odm_input: OdmVendorElementPostInput, library ) -> OdmVendorElementAR: + log.info("Creating ODM Vendor Element: name='%s'", odm_input.name) return OdmVendorElementAR.from_input_values( author_id=self.author_id, - concept_vo=OdmVendorElementVO.from_repository_values( - name=concept_input.name, + odm_vo=OdmVendorElementVO.from_repository_values( + name=odm_input.name, compatible_types=[ compatible_type.value - for compatible_type in concept_input.compatible_types + for compatible_type in odm_input.compatible_types ], - vendor_namespace_uid=concept_input.vendor_namespace_uid, + vendor_namespace_uid=odm_input.vendor_namespace_uid, vendor_attribute_uids=[], ), library=library, @@ -56,25 +59,27 @@ def _create_aggregate_root( def _edit_aggregate( self, item: OdmVendorElementAR, - concept_edit_input: OdmVendorElementPatchInput, + odm_edit_input: OdmVendorElementPatchInput, ) -> OdmVendorElementAR: + log.info("Editing ODM Vendor Element: uid=%s", item.uid) item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmVendorElementVO.from_repository_values( - name=concept_edit_input.name, + change_description=odm_edit_input.change_description, + odm_vo=OdmVendorElementVO.from_repository_values( + name=odm_edit_input.name, compatible_types=[ compatible_type.value - for compatible_type in concept_edit_input.compatible_types + for compatible_type in odm_edit_input.compatible_types ], - vendor_namespace_uid=item.concept_vo.vendor_namespace_uid, - vendor_attribute_uids=item.concept_vo.vendor_attribute_uids, + vendor_namespace_uid=item.odm_vo.vendor_namespace_uid, + vendor_attribute_uids=item.odm_vo.vendor_attribute_uids, ), ) return item @db.transaction def get_active_relationships(self, uid: str): + log.debug("Getting active relationships for ODM Vendor Element: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_vendor_element_repository.exists_by("uid", uid, True), "ODM Vendor Element", @@ -86,6 +91,7 @@ def get_active_relationships(self, uid: str): ) def soft_delete(self, uid: str) -> None: + log.info("Soft deleting ODM Vendor Element: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_vendor_element_repository.exists_by("uid", uid, True), "ODM Vendor Element", diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_namespaces.py b/clinical-mdr-api/clinical_mdr_api/services/odms/vendor_namespaces.py similarity index 61% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_namespaces.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/vendor_namespaces.py index 95c34743..1207aee3 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_vendor_namespaces.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/vendor_namespaces.py @@ -1,23 +1,25 @@ +import logging + from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.vendor_namespace_repository import ( +from clinical_mdr_api.domain_repositories.odms.vendor_namespace_repository import ( VendorNamespaceRepository, ) -from clinical_mdr_api.domains.concepts.odms.vendor_namespace import ( +from clinical_mdr_api.domains.odms.vendor_namespace import ( OdmVendorNamespaceAR, OdmVendorNamespaceVO, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_namespace import ( +from clinical_mdr_api.models.odms.vendor_namespace import ( OdmVendorNamespace, OdmVendorNamespacePatchInput, OdmVendorNamespacePostInput, OdmVendorNamespaceVersion, ) -from clinical_mdr_api.services.concepts.odms.odm_generic_service import ( - OdmGenericService, -) +from clinical_mdr_api.services.odms.generic_service import OdmGenericService from common.exceptions import BusinessLogicException, NotFoundException +log = logging.getLogger(__name__) + class OdmVendorNamespaceService(OdmGenericService[OdmVendorNamespaceAR]): aggregate_class = OdmVendorNamespaceAR @@ -34,42 +36,49 @@ def _transform_aggregate_root_to_pydantic_model( ) def _create_aggregate_root( - self, concept_input: OdmVendorNamespacePostInput, library + self, odm_input: OdmVendorNamespacePostInput, library ) -> OdmVendorNamespaceAR: + log.info( + "Creating ODM Vendor Namespace: name='%s', prefix='%s'", + odm_input.name, + odm_input.prefix, + ) return OdmVendorNamespaceAR.from_input_values( author_id=self.author_id, - concept_vo=OdmVendorNamespaceVO.from_repository_values( - name=concept_input.name, - prefix=concept_input.prefix, - url=concept_input.url, + odm_vo=OdmVendorNamespaceVO.from_repository_values( + name=odm_input.name, + prefix=odm_input.prefix, + url=odm_input.url, vendor_element_uids=[], vendor_attribute_uids=[], ), library=library, generate_uid_callback=self.repository.generate_uid, - concept_exists_by_callback=self._repos.odm_vendor_namespace_repository.exists_by, + odm_exists_by_callback=self._repos.odm_vendor_namespace_repository.exists_by, ) def _edit_aggregate( self, item: OdmVendorNamespaceAR, - concept_edit_input: OdmVendorNamespacePatchInput, + odm_edit_input: OdmVendorNamespacePatchInput, ) -> OdmVendorNamespaceAR: + log.info("Editing ODM Vendor Namespace: uid=%s", item.uid) item.edit_draft( author_id=self.author_id, - change_description=concept_edit_input.change_description, - concept_vo=OdmVendorNamespaceVO.from_repository_values( - name=concept_edit_input.name, - prefix=concept_edit_input.prefix, - url=concept_edit_input.url, - vendor_element_uids=item.concept_vo.vendor_element_uids, - vendor_attribute_uids=item.concept_vo.vendor_attribute_uids, + change_description=odm_edit_input.change_description, + odm_vo=OdmVendorNamespaceVO.from_repository_values( + name=odm_edit_input.name, + prefix=odm_edit_input.prefix, + url=odm_edit_input.url, + vendor_element_uids=item.odm_vo.vendor_element_uids, + vendor_attribute_uids=item.odm_vo.vendor_attribute_uids, ), - concept_exists_by_callback=self._repos.odm_vendor_namespace_repository.exists_by, + odm_exists_by_callback=self._repos.odm_vendor_namespace_repository.exists_by, ) return item def soft_delete(self, uid: str) -> None: + log.info("Soft deleting ODM Vendor Namespace: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_vendor_namespace_repository.exists_by("uid", uid, True), "ODM Vendor Namespace", @@ -87,6 +96,7 @@ def soft_delete(self, uid: str) -> None: @db.transaction def get_active_relationships(self, uid: str): + log.debug("Getting active relationships for ODM Vendor Namespace: uid=%s", uid) NotFoundException.raise_if_not( self._repos.odm_vendor_namespace_repository.exists_by("uid", uid, True), "ODM Vendor Namespace", diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_exporter.py b/clinical-mdr-api/clinical_mdr_api/services/odms/xml_exporter.py similarity index 98% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_exporter.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/xml_exporter.py index 72dbbd16..aa6e485a 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_exporter.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/xml_exporter.py @@ -9,7 +9,9 @@ from weasyprint import HTML from clinical_mdr_api.domains._utils import get_iso_lang_data -from clinical_mdr_api.domains.concepts.odms.odm_xml_definition import ( +from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum +from clinical_mdr_api.domains.odms.utils import EN_LANGUAGE, TargetType +from clinical_mdr_api.domains.odms.xml_definition import ( ODM, Alias, Attribute, @@ -45,18 +47,12 @@ Symbol, TranslatedText, ) -from clinical_mdr_api.domains.concepts.utils import EN_LANGUAGE, TargetType -from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmRefVendorAttributeModel, -) -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm -from clinical_mdr_api.models.concepts.odms.odm_item import OdmItem -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroup -from clinical_mdr_api.services.concepts.odms.odm_data_extractor import OdmDataExtractor -from clinical_mdr_api.services.concepts.odms.odm_xml_stylesheets import ( - OdmXmlStylesheetService, -) +from clinical_mdr_api.models.odms.common_models import OdmRefVendorAttributeModel +from clinical_mdr_api.models.odms.form import OdmForm +from clinical_mdr_api.models.odms.item import OdmItem +from clinical_mdr_api.models.odms.item_group import OdmItemGroup +from clinical_mdr_api.services.odms.data_extractor import OdmDataExtractor +from clinical_mdr_api.services.odms.xml_stylesheets import OdmXmlStylesheetService from clinical_mdr_api.services.utils.odm_xml_mapper import map_xml from common.exceptions import BusinessLogicException diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_importer.py b/clinical-mdr-api/clinical_mdr_api/services/odms/xml_importer.py similarity index 94% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_importer.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/xml_importer.py index b0cb1b68..48484f93 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_importer.py +++ b/clinical-mdr-api/clinical_mdr_api/services/odms/xml_importer.py @@ -5,22 +5,34 @@ from fastapi import UploadFile from neomodel import db -from clinical_mdr_api.domain_repositories.concepts.odms.odm_generic_repository import ( +from clinical_mdr_api.domain_repositories.odms.generic_repository import ( OdmGenericRepository, ) from clinical_mdr_api.domains._utils import get_iso_lang_data -from clinical_mdr_api.domains.concepts.utils import ( +from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum +from clinical_mdr_api.domains.odms.utils import ( EN_LANGUAGE, RelationType, VendorAttributeCompatibleType, VendorElementCompatibleType, ) -from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum from clinical_mdr_api.domains.versioned_object_aggregate import ( LibraryItemStatus, LibraryVO, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.concepts.unit_definitions.unit_definition import ( + UnitDefinitionModel, +) +from clinical_mdr_api.models.controlled_terminologies.ct_codelist import ( + CTCodelist, + CTCodelistCreateInput, +) +from clinical_mdr_api.models.controlled_terminologies.ct_term import ( + CTTerm, + CTTermCodelistInput, + CTTermCreateInput, +) +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmFormalExpressionModel, OdmRefVendorPostInput, @@ -28,79 +40,44 @@ OdmVendorElementRelationPostInput, OdmVendorRelationPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_condition import ( - OdmCondition, - OdmConditionPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_form import ( +from clinical_mdr_api.models.odms.condition import OdmCondition, OdmConditionPostInput +from clinical_mdr_api.models.odms.form import ( OdmForm, OdmFormItemGroupPostInput, OdmFormPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_item import ( +from clinical_mdr_api.models.odms.item import ( OdmItem, OdmItemCodelist, OdmItemPostInput, OdmItemTermRelationshipInput, OdmItemUnitDefinitionRelationshipInput, ) -from clinical_mdr_api.models.concepts.odms.odm_item_group import ( +from clinical_mdr_api.models.odms.item_group import ( OdmItemGroup, OdmItemGroupItemPostInput, OdmItemGroupPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_method import ( - OdmMethod, - OdmMethodPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_study_event import ( +from clinical_mdr_api.models.odms.method import OdmMethod, OdmMethodPostInput +from clinical_mdr_api.models.odms.study_event import ( OdmStudyEvent, OdmStudyEventFormPostInput, OdmStudyEventPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( +from clinical_mdr_api.models.odms.vendor_attribute import ( OdmVendorAttribute, OdmVendorAttributePostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( +from clinical_mdr_api.models.odms.vendor_element import ( OdmVendorElement, OdmVendorElementPostInput, ) -from clinical_mdr_api.models.concepts.odms.odm_vendor_namespace import ( +from clinical_mdr_api.models.odms.vendor_namespace import ( OdmVendorNamespace, OdmVendorNamespacePostInput, ) -from clinical_mdr_api.models.concepts.unit_definitions.unit_definition import ( - UnitDefinitionModel, -) -from clinical_mdr_api.models.controlled_terminologies.ct_codelist import ( - CTCodelist, - CTCodelistCreateInput, -) -from clinical_mdr_api.models.controlled_terminologies.ct_term import ( - CTTerm, - CTTermCodelistInput, - CTTermCreateInput, -) from clinical_mdr_api.services._meta_repository import MetaRepository from clinical_mdr_api.services._utils import is_library_editable -from clinical_mdr_api.services.concepts.odms.odm_conditions import OdmConditionService -from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService -from clinical_mdr_api.services.concepts.odms.odm_item_groups import OdmItemGroupService -from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService -from clinical_mdr_api.services.concepts.odms.odm_methods import OdmMethodService -from clinical_mdr_api.services.concepts.odms.odm_study_events import ( - OdmStudyEventService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_attributes import ( - OdmVendorAttributeService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_elements import ( - OdmVendorElementService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_namespaces import ( - OdmVendorNamespaceService, -) from clinical_mdr_api.services.concepts.unit_definitions.unit_definition import ( UnitDefinitionService, ) @@ -111,6 +88,15 @@ from clinical_mdr_api.services.controlled_terminologies.ct_term_attributes import ( CTTermAttributesService, ) +from clinical_mdr_api.services.odms.conditions import OdmConditionService +from clinical_mdr_api.services.odms.forms import OdmFormService +from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService +from clinical_mdr_api.services.odms.items import OdmItemService +from clinical_mdr_api.services.odms.methods import OdmMethodService +from clinical_mdr_api.services.odms.study_events import OdmStudyEventService +from clinical_mdr_api.services.odms.vendor_attributes import OdmVendorAttributeService +from clinical_mdr_api.services.odms.vendor_elements import OdmVendorElementService +from clinical_mdr_api.services.odms.vendor_namespaces import OdmVendorNamespaceService from clinical_mdr_api.services.utils.odm_xml_mapper import map_xml from clinical_mdr_api.utils import normalize_string from common import exceptions @@ -278,9 +264,9 @@ def _set_vendor_namespaces(self): self.db_vendor_namespaces = [ self.odm_vendor_namespace_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _set_vendor_attributes(self): @@ -298,9 +284,9 @@ def _set_vendor_attributes(self): self.db_vendor_attributes = [ self.odm_vendor_attribute_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _set_vendor_elements(self): @@ -318,9 +304,9 @@ def _set_vendor_elements(self): self.db_vendor_elements = [ self.odm_vendor_element_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _create_missing_vendor_namespaces(self): @@ -1075,9 +1061,9 @@ def _get_newly_created_vendor_namespaces(self): return [ self.odm_vendor_namespace_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _get_newly_created_vendor_attributes(self): @@ -1097,9 +1083,9 @@ def _get_newly_created_vendor_attributes(self): return [ self.odm_vendor_attribute_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _get_newly_created_vendor_elements(self): @@ -1118,9 +1104,9 @@ def _get_newly_created_vendor_elements(self): return [ self.odm_vendor_element_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _get_newly_created_study_events(self): @@ -1137,9 +1123,9 @@ def _get_newly_created_study_events(self): return [ self.odm_study_event_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _get_newly_created_forms(self): @@ -1155,10 +1141,8 @@ def _get_newly_created_forms(self): rs.sort(key=lambda elm: elm.name) return [ - self.odm_form_service._transform_aggregate_root_to_pydantic_model( - concept_ar - ) - for concept_ar in rs + self.odm_form_service._transform_aggregate_root_to_pydantic_model(odm_ar) + for odm_ar in rs ] def _get_newly_created_item_groups(self): @@ -1175,9 +1159,9 @@ def _get_newly_created_item_groups(self): return [ self.odm_item_group_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _get_newly_created_conditions(self): @@ -1194,9 +1178,9 @@ def _get_newly_created_conditions(self): return [ self.odm_condition_service._transform_aggregate_root_to_pydantic_model( - concept_ar + odm_ar ) - for concept_ar in rs + for odm_ar in rs ] def _get_newly_created_methods(self): @@ -1212,10 +1196,8 @@ def _get_newly_created_methods(self): rs.sort(key=lambda elm: elm.name) return [ - self.odm_method_service._transform_aggregate_root_to_pydantic_model( - concept_ar - ) - for concept_ar in rs + self.odm_method_service._transform_aggregate_root_to_pydantic_model(odm_ar) + for odm_ar in rs ] def _get_newly_created_items(self): @@ -1231,10 +1213,8 @@ def _get_newly_created_items(self): rs.sort(key=lambda elm: elm.name) return [ - self.odm_item_service._transform_aggregate_root_to_pydantic_model( - concept_ar - ) - for concept_ar in rs + self.odm_item_service._transform_aggregate_root_to_pydantic_model(odm_ar) + for odm_ar in rs ] def _get_newly_created_codelists(self): @@ -1280,16 +1260,16 @@ def _get_newly_created_terms(self): for ct_term_name_ar, ct_term_attributes_ar, ct_term_codelists in rs ] - def _get_library(self, concept_input): + def _get_library(self, odm_input): exceptions.BusinessLogicException.raise_if_not( self._repos.library_repository.library_exists( - normalize_string(concept_input.library_name) + normalize_string(odm_input.library_name) ), - msg=f"Library with Name '{concept_input.library_name}' doesn't exist.", + msg=f"Library with Name '{odm_input.library_name}' doesn't exist.", ) return LibraryVO.from_input_values_2( - library_name=concept_input.library_name, + library_name=odm_input.library_name, is_library_editable_callback=is_library_editable, ) @@ -1572,25 +1552,25 @@ def _get_list_of_attributes(self, attributes): ) return rs - def _create(self, repository, service, save_to, concept_input): - library_vo = self._get_library(concept_input) + def _create(self, repository, service, save_to, odm_input): + library_vo = self._get_library(odm_input) try: - concept_ar = service._create_aggregate_root( - concept_input=concept_input, library=library_vo + odm_ar = service._create_aggregate_root( + odm_input=odm_input, library=library_vo ) - repository.save(concept_ar) + repository.save(odm_ar) except exceptions.AlreadyExistsException as e: uid = re.search(r" already exists with UID \((.*)\) and data {", e.msg) if uid: - concept_ar = repository.find_by_uid_2(uid=uid[1], for_update=True) - if concept_ar.item_metadata.status != LibraryItemStatus.DRAFT: - concept_ar.create_new_version(author_id=user().id()) - repository.save(concept_ar) + odm_ar = repository.find_by_uid_2(uid=uid[1], for_update=True) + if odm_ar.item_metadata.status != LibraryItemStatus.DRAFT: + odm_ar.create_new_version(author_id=user().id()) + repository.save(odm_ar) else: raise - item = service._transform_aggregate_root_to_pydantic_model(concept_ar) + item = service._transform_aggregate_root_to_pydantic_model(odm_ar) save_to.append(item) return item diff --git a/clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_stylesheets.py b/clinical-mdr-api/clinical_mdr_api/services/odms/xml_stylesheets.py similarity index 100% rename from clinical-mdr-api/clinical_mdr_api/services/concepts/odms/odm_xml_stylesheets.py rename to clinical-mdr-api/clinical_mdr_api/services/odms/xml_stylesheets.py diff --git a/clinical-mdr-api/clinical_mdr_api/services/preferences.py b/clinical-mdr-api/clinical_mdr_api/services/preferences.py new file mode 100644 index 00000000..2c0031a5 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/services/preferences.py @@ -0,0 +1,97 @@ +# pylint: disable=invalid-name +from neomodel import db + +from clinical_mdr_api.domain_repositories.preferences_registry import ( + PREFERENCE_DEFINITIONS, + PREFERENCE_KEYS, + to_metadata_dict, +) +from clinical_mdr_api.domain_repositories.preferences_repository import ( + PreferencesRepository, +) +from clinical_mdr_api.models.preferences import ( + GlobalPreferencesPatchInput, + PreferenceMetadata, + PreferencesResponse, + UserPreferencesPatchInput, + UserPreferencesResponse, +) +from clinical_mdr_api.services._utils import ensure_transaction +from common.exceptions import ValidationException + + +class PreferencesService: + repo: PreferencesRepository + + def __init__(self) -> None: + self.repo = PreferencesRepository() + + def _build_metadata_response(self) -> dict[str, PreferenceMetadata]: + """Build metadata response from the preference registry.""" + return { + preference_definition.key: PreferenceMetadata( + **to_metadata_dict(preference_definition) + ) + for preference_definition in PREFERENCE_DEFINITIONS + } + + def get_global_preferences(self) -> PreferencesResponse: + """Get global preferences with metadata.""" + preferences = self.repo.get_global_preferences() + metadata = self._build_metadata_response() + return PreferencesResponse(preferences=preferences, metadata=metadata) + + @ensure_transaction(db) + def update_global_preferences( + self, input_data: GlobalPreferencesPatchInput + ) -> PreferencesResponse: + """Update global preferences and return updated state with metadata.""" + updates = input_data.model_dump(exclude_unset=True) + preferences = self.repo.update_global_preferences(updates) + metadata = self._build_metadata_response() + return PreferencesResponse(preferences=preferences, metadata=metadata) + + @ensure_transaction(db) + def get_user_preferences(self, user_id: str) -> UserPreferencesResponse: + """Get user preferences merged with global defaults and compute overrides flags.""" + global_preferences = self.repo.get_global_preferences() + user_preferences = self.repo.get_user_preferences(user_id) + + # Merge: global defaults with user overrides + merged_preferences = {} + overrides = {} + + for key in PREFERENCE_KEYS: + global_value = global_preferences.get(key) + user_value = user_preferences.get(key) if user_preferences else None + + if user_value is not None: + merged_preferences[key] = user_value + overrides[key] = global_value + else: + merged_preferences[key] = global_value + + metadata = self._build_metadata_response() + return UserPreferencesResponse( + preferences=merged_preferences, overrides=overrides, metadata=metadata + ) + + @ensure_transaction(db) + def update_user_preferences( + self, user_id: str, input_data: UserPreferencesPatchInput + ) -> UserPreferencesResponse: + """Update user preferences and return merged state with overrides.""" + updates = input_data.model_dump(exclude_unset=True) + self.repo.update_user_preferences(user_id, updates) + return self.get_user_preferences(user_id) + + @ensure_transaction(db) + def delete_user_preference_key( + self, user_id: str, key: str + ) -> UserPreferencesResponse: + """Delete a single user preference key (reset to global default).""" + if key not in PREFERENCE_KEYS: + raise ValidationException(f"Invalid preference key: '{key}'") + + self.repo.delete_user_preference_key(user_id, key) + return self.get_user_preferences(user_id) diff --git a/clinical-mdr-api/clinical_mdr_api/services/standard_data_models/sponsor_model_dataset_variable.py b/clinical-mdr-api/clinical_mdr_api/services/standard_data_models/sponsor_model_dataset_variable.py index d59ad3ea..d5fb669d 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/standard_data_models/sponsor_model_dataset_variable.py +++ b/clinical-mdr-api/clinical_mdr_api/services/standard_data_models/sponsor_model_dataset_variable.py @@ -10,14 +10,17 @@ SponsorModelDatasetVariable, SponsorModelDatasetVariableInput, ) -from clinical_mdr_api.services.neomodel_ext_generic import NeomodelExtGenericService +from clinical_mdr_api.services.standard_data_models.standard_data_model_service import ( + StandardDataModelService, +) class SponsorModelDatasetVariableService( - NeomodelExtGenericService[SponsorModelDatasetVariableAR] + StandardDataModelService, ): repository_interface = SponsorModelDatasetVariableRepository api_model_class = SponsorModelDatasetVariable + version_class = None def _transform_aggregate_root_to_pydantic_model( self, item_ar: SponsorModelDatasetVariableAR diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py b/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py index 4538c64f..b90b1c89 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/complexity_score.py @@ -1,6 +1,6 @@ from dataclasses import dataclass -from neomodel.sync_.core import db +from neomodel import db from clinical_mdr_api.models.complexity_score import ( ActivityBurden, 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 473299e1..6a8da0f4 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study.py @@ -5,10 +5,13 @@ from string import ascii_lowercase from typing import Any, Callable, Collection, Iterable -from neomodel import NodeSet, db # type: ignore +from neomodel import db from opencensus.trace import execution_context -from clinical_mdr_api.domain_repositories.models.study_field import StudyArrayField +from clinical_mdr_api.domain_repositories.models.study_field import ( + StudyArrayField, + StudyBooleanField, +) from clinical_mdr_api.domain_repositories.study_definitions.study_definition_repository_impl import ( StudyDefinitionRepositoryImpl, ) @@ -980,9 +983,25 @@ def get_subpart_audit_trail_by_uid( self._close_all_repos() def get_studies_list( - self, minimal_response=True, deleted=False + self, + minimal_response: bool = True, + has_study_objective: bool | None = None, + has_study_footnote: bool | None = None, + has_study_endpoint: bool | None = None, + has_study_criteria: bool | None = None, + has_study_activity: bool | None = None, + has_study_activity_instruction: bool | None = None, + deleted: bool = False, ) -> list[StudySimple | StudyMinimal]: - items = self._repos.study_definition_repository.get_studies_list(deleted) + items = self._repos.study_definition_repository.get_studies_list( + has_study_objective, + has_study_footnote, + has_study_endpoint, + has_study_criteria, + has_study_activity, + has_study_activity_instruction, + deleted, + ) if minimal_response: return [StudyMinimal.from_input(item) for item in items] @@ -1068,7 +1087,7 @@ def get_study_snapshot_history( page_number: int = 1, page_size: int = 0, total_count: bool = False, - only_latest_major_protcol_version: bool = False, + only_latest_major_protocol_version: bool = False, ) -> GenericFilteringReturn[StudyVersionHistory]: try: all_items, total = ( @@ -1077,7 +1096,7 @@ def get_study_snapshot_history( page_number=page_number, page_size=page_size, total_count=total_count, - only_latest_major_protcol_version=only_latest_major_protcol_version, + only_latest_major_protocol_version=only_latest_major_protocol_version, ) ) @@ -1390,6 +1409,7 @@ def create( study_title_exists_callback=self._repos.study_title_repository.study_title_exists, study_short_title_exists_callback=self._repos.study_title_repository.study_short_title_exists, study_number_exists_callback=self._repos.study_definition_repository.study_number_exists, + study_acronym_exists_callback=self._repos.study_definition_repository.study_acronym_exists, initial_id_metadata=StudyIdentificationMetadataVO.from_input_values( project_number=project_number, study_number=study_number, @@ -2090,6 +2110,7 @@ def patch( new_id_metadata=new_id_metadata, project_exists_callback=self._repos.project_repository.project_number_exists, study_number_exists_callback=self._repos.study_definition_repository.study_number_exists, + study_acronym_exists_callback=self._repos.study_definition_repository.study_acronym_exists, new_high_level_study_design=new_high_level_study_design, study_type_exists_callback=self._repos.ct_term_name_repository.term_exists, trial_type_exists_callback=self._repos.ct_term_name_repository.term_exists, @@ -2279,6 +2300,21 @@ def check_if_study_uid_and_version_exists( raise NotFoundException("Study", study_uid) + def get_study_id( + self, study_uid: str, study_value_version: str | None = None + ) -> str: + study_id = self._repos.study_definition_repository.get_study_id( + study_uid, study_value_version + ) + NotFoundException.raise_if_not( + study_id, + "Study", + study_uid, + msg=f"Study with UID '{study_uid}' and version '{study_value_version}' was not found," + " or either study_id_prefix or study_number is not defined.", + ) + return study_id + def _check_if_unit_definition_exists(self, unit_definition_uid: str): NotFoundException.raise_if_not( self._repos.unit_definition_repository.final_concept_exists( @@ -2290,7 +2326,7 @@ def _check_if_unit_definition_exists(self, unit_definition_uid: str): def _check_repository_output( self, - nodes: NodeSet, + nodes: list[StudyPreferredTimeUnit], study_uid: str, for_protocol_soa: bool = False, ): @@ -2553,7 +2589,7 @@ def patch_study_soa_preferences( @staticmethod def _study_fields_to_study_soa_preferences( - study_uid: str, nodes: NodeSet + study_uid: str, nodes: list[StudyBooleanField] ) -> StudySoaPreferences: """Converts a set of StudyField nodes to a StudySoaPreferences""" 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 7779e750..b89630ff 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 @@ -614,7 +614,9 @@ def get_crfs(self, study_uid: str): -[:HAS_STUDY_ACTIVITY_INSTANCE]->(:StudyActivityInstance) -[:HAS_SELECTED_ACTIVITY_INSTANCE]->(:ActivityInstanceValue) -[:CONTAINS_ACTIVITY_ITEM]->(:ActivityItem) - <-[:LINKS_TO_ACTIVITY_ITEM]-(ofv:OdmFormValue) + <-[:LINKS_TO_ACTIVITY_ITEM]-(oiv:OdmItemValue) + <-[:ITEM_REF]-(oigv:OdmItemGroupValue) + <-[:ITEM_GROUP_REF]-(ofv:OdmFormValue) <-[hv:HAS_VERSION]-(ofr:OdmFormRoot) WITH ofr, ofv, hv ORDER BY hv.end_date DESC diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instruction.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instruction.py index 2901f99f..f0fb1349 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instruction.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_instruction.py @@ -58,7 +58,7 @@ def get_all_instructions_for_all_studies( filter_operator: FilterOperator = FilterOperator.AND, total_count: bool = False, ) -> GenericFilteringReturn[StudyActivityInstruction]: - query = StudyActivityInstructionNeoModel.nodes.fetch_relations( + query = StudyActivityInstructionNeoModel.nodes.traverse( "study_value__latest_value", "study_activity", "activity_instruction_value__activity_instruction_root", @@ -100,7 +100,7 @@ def get_all_instructions( study_activity_instructions_ogm: list[StudyActivityInstruction] = [ StudyActivityInstruction.model_validate(sai_node) for sai_node in ListDistinct( - StudyActivityInstructionNeoModel.nodes.fetch_relations( + StudyActivityInstructionNeoModel.nodes.traverse( "study_activity", "study_value__has_version", "activity_instruction_value__activity_instruction_root", @@ -136,7 +136,7 @@ def get_all_study_instructions_for_specific_study_activity( return [ StudyActivityInstruction.model_validate(sas_node) for sas_node in ListDistinct( - StudyActivityInstructionNeoModel.nodes.fetch_relations( + StudyActivityInstructionNeoModel.nodes.traverse( "study_activity", "activity_instruction_value__activity_instruction_root", "has_after__audit_trail", diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_schedule.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_schedule.py index 095b3dd3..068374d3 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_schedule.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_schedule.py @@ -74,7 +74,7 @@ def get_all_schedules_for_specific_activity( return [ StudyActivitySchedule.model_validate(sas_node) for sas_node in ListDistinct( - StudyActivityScheduleNeoModel.nodes.fetch_relations( + StudyActivityScheduleNeoModel.nodes.traverse( "has_after__audit_trail", "study_visit__has_visit_name__has_latest_value", "study_activity__has_selected_activity", diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py index 24617933..084bb13c 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_activity_selection.py @@ -100,6 +100,7 @@ from common.auth.user import user from common.config import settings from common.exceptions import ( + AlreadyExistsException, BusinessLogicException, MDRApiBaseException, MethodNotAllowedException, @@ -239,12 +240,41 @@ def _filter_ars_from_same_parent( ) return selection_ar_from_same_subgroup + def _validate_no_study_wide_duplicate( + self, + study_uid: str, + updated_selection: StudySelectionActivityVO, + ) -> None: + """Check that the updated selection doesn't duplicate an existing activity + with the same name and groupings anywhere in the study. + + The AR-level validate() only sees a scoped subset (same study_activity_subgroup_uid), + so duplicates across different subgroup scopes would slip through without this check. + """ + AlreadyExistsException.raise_if( + self.repository.activity_with_same_groupings_exists( + study_uid=study_uid, + activity_name=updated_selection.activity_name, + activity_subgroup_uid=updated_selection.activity_subgroup_uid, + activity_group_uid=updated_selection.activity_group_uid, + exclude_study_selection_uid=updated_selection.study_selection_uid, + ), + msg=( + f"There is already a Study Selection to the activity with Name " + f"'{updated_selection.activity_name}' with the same groupings." + ), + ) + def _update_aggregate( self, selection_aggregate: StudySelectionActivityAR, previous_selection: StudySelectionActivityVO, updated_selection: StudySelectionActivityVO, ): + self._validate_no_study_wide_duplicate( + study_uid=selection_aggregate.study_uid, + updated_selection=updated_selection, + ) if ( previous_selection.study_activity_subgroup_uid != updated_selection.study_activity_subgroup_uid @@ -1390,6 +1420,10 @@ def make_selection( self.selected_object_repository.check_exists_final_version, self._repos.ct_term_name_repository.term_specific_exists_by_uid, ) + self._validate_no_study_wide_duplicate( + study_uid=study_uid, + updated_selection=study_activity_selection, + ) study_activity_aggregate.validate() # sync with DB and save the update self.repository.save(study_activity_aggregate, self.author) diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_cell.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_cell.py index 67af2c64..b8086951 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_cell.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_cell.py @@ -3,7 +3,7 @@ from fastapi import status from neomodel import db -from neomodel.sync_.match import Optional +from neomodel.sync_.match import Path from clinical_mdr_api.domain_repositories.models.study_selections import ( StudyDesignCell as StudyDesignCellNeoModel, @@ -130,12 +130,12 @@ def get_specific_design_cell( self, study_uid: str, design_cell_uid: str ) -> StudyDesignCell: sdc_node = ( - StudyDesignCellNeoModel.nodes.fetch_relations( + StudyDesignCellNeoModel.nodes.traverse( "study_epoch__has_epoch__has_selected_term__has_name_root__has_latest_value", "study_element", "has_after__audit_trail", - Optional("study_arm"), - Optional("study_branch_arm"), + Path(value="study_arm", optional=True), + Path(value="study_branch_arm", optional=True), ) .filter(study_value__latest_value__uid=study_uid, uid=design_cell_uid) .resolve_subgraph() diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_figure.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_figure.py index 3233054a..42d4746c 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_figure.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_design_figure.py @@ -855,7 +855,7 @@ def _mk_timeline( # look up epoch column col = table[0][idx] - if visit.visit_type_uid == label.get("id"): + if visit.visit_type.term_uid == label.get("id"): # same visit type, span to next column label["width"] = col["x"] - label["x"] + col["width"] # reflow text with new width @@ -866,7 +866,7 @@ def _mk_timeline( else: # a different visit type deserves a new label label = { - "id": visit.visit_type_uid, + "id": visit.visit_type.term_uid, "klass": "visit-type", "paddings": (0, 0), "text": visit.visit_type.sponsor_preferred_name, diff --git a/clinical-mdr-api/clinical_mdr_api/services/studies/study_epoch.py b/clinical-mdr-api/clinical_mdr_api/services/studies/study_epoch.py index 9eeb3d0b..d7a5dbc7 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/studies/study_epoch.py +++ b/clinical-mdr-api/clinical_mdr_api/services/studies/study_epoch.py @@ -369,7 +369,7 @@ def _get_or_create_epoch_in_specific_subtype( if epoch.term_uid not in self.study_epoch_epochs_by_uid: self.study_epoch_epochs_by_uid[epoch.term_uid] = epoch - except (AlreadyExistsException, ValidationException): + except AlreadyExistsException, ValidationException: pass # we are trying to find the ct term with given epoch name else: @@ -813,7 +813,7 @@ def reorder(self, study_epoch_uid: str, study_uid: str, new_order: int): new_order < 0, msg="New order cannot be lesser than 1" ) ValidationException.raise_if( - new_order > len(study_epochs), + new_order >= len(study_epochs), msg=f"New order cannot be greater than {len(study_epochs)}", ) if new_order > old_order: 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 bfb20c7f..f2615a21 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 @@ -1,6 +1,6 @@ import logging from collections import defaultdict -from concurrent.futures import ThreadPoolExecutor +from concurrent.futures import ThreadPoolExecutor # pylint: disable=no-name-in-module from datetime import datetime from typing import Any, Iterable, Mapping, Sequence, TypeVar @@ -37,7 +37,7 @@ StudySoAGroup, ) from clinical_mdr_api.models.study_selections.study_soa_footnote import StudySoAFootnote -from clinical_mdr_api.models.study_selections.study_visit import StudyVisit +from clinical_mdr_api.models.study_selections.study_visit import StudyVisitLite from clinical_mdr_api.models.syntax_instances.footnote import Footnote from clinical_mdr_api.models.utils import BaseModel from clinical_mdr_api.services._utils import ensure_transaction @@ -249,9 +249,9 @@ def _get_study_activity_schedules( @trace_calls def _get_study_visits( self, study_uid: str, study_value_version: str | None = None - ) -> list[StudyVisit]: + ) -> list[StudyVisitLite]: return StudyVisitService.get_all_visits( - study_uid, study_value_version=study_value_version + study_uid, study_value_version=study_value_version, lite=True ).items @trace_calls @@ -386,16 +386,15 @@ def _sort_study_activities( @staticmethod @trace_calls def _group_visits( - visits: Iterable[StudyVisit], + visits: Iterable[StudyVisitLite], collapse_visit_groups: bool = True, - ) -> dict[str, dict[str, list[StudyVisit]]]: + ) -> dict[str, dict[str, list[StudyVisitLite]]]: """ Builds a graph of visits from nested dict of study_epoch_uid -> [ consecutive_visit_group | visit_uid ] -> [Visits] """ grouped: dict[Any, Any] = {} - visits = sorted(visits, key=lambda v: v.order) for visit in visits: grouped.setdefault(visit.study_epoch_uid, {}).setdefault( @@ -485,7 +484,7 @@ def get_flowchart_item_uid_coordinates( study_selection_activities, hide_soa_groups=hide_soa_groups ) - visits: list[StudyVisit] = self._get_study_visits( + visits: list[StudyVisitLite] = self._get_study_visits( study_uid, study_value_version=study_value_version ) @@ -800,7 +799,7 @@ def build_flowchart_table( activity_schedules_future.result() ) - visits: dict[str, StudyVisit] = visits_future.result() + visits: dict[str, StudyVisitLite] = visits_future.result() # group visits in nested dict: study_epoch_uid -> [ consecutive_visit_group | visit_uid ] -> [Visits] grouped_visits = self._group_visits( @@ -860,7 +859,7 @@ def _get_study_selection_activities_sorted( @trace_calls def _get_study_visits_dict_filtered( self, study_uid, study_value_version - ) -> dict[str, StudyVisit]: + ) -> dict[str, StudyVisitLite]: # get visits visits = self._get_study_visits( study_uid, study_value_version=study_value_version @@ -1217,7 +1216,7 @@ def get_operational_spreadsheet( perv_study_epoch_uid = None for study_epoch_uid, _visit_groups in grouped_visits.items(): for group in _visit_groups.values(): - visit: StudyVisit = group[0] + visit: StudyVisitLite = group[0] if layout == SoALayout.OPERATIONAL: # Epoch @@ -1248,7 +1247,7 @@ def get_operational_spreadsheet( ) # Add activity rows - visit_groups: list[list[StudyVisit]] = [ + visit_groups: list[list[StudyVisitLite]] = [ visit_group for epochs_group in grouped_visits.values() for visit_group in epochs_group.values() @@ -1398,7 +1397,7 @@ def get_operational_spreadsheet( @trace_calls(args=[2, 3, 4], kwargs=["time_unit", "soa_preferences", "layout"]) def _get_header_rows( cls, - grouped_visits: dict[str, dict[str, list[StudyVisit]]], + grouped_visits: dict[str, dict[str, list[StudyVisitLite]]], time_unit: str, soa_preferences: StudySoaPreferencesInput, layout: SoALayout, @@ -1470,7 +1469,7 @@ def _get_header_rows( prev_milestone_cell: TableCell | None = None for study_epoch_uid, visit_groups in grouped_visits.items(): for group in visit_groups.values(): - visit: StudyVisit = group[0] + visit: StudyVisitLite = group[0] # Open new Epoch column if perv_study_epoch_uid != study_epoch_uid: @@ -1497,14 +1496,14 @@ def _get_header_rows( # Milestones if milestones_row: if visit.is_soa_milestone: - if prev_visit_type_uid == visit.visit_type_uid: + if prev_visit_type_uid == visit.visit_type.term_uid: # Same visit_type, then merge with the previous cell in Milestone row prev_milestone_cell.span += 1 milestones_row.cells.append(TableCell(span=0)) else: # Different visit_type, new label in Milestones row - prev_visit_type_uid = visit.visit_type_uid + prev_visit_type_uid = visit.visit_type.term_uid milestones_row.cells.append( prev_milestone_cell := TableCell( visit.visit_type.sponsor_preferred_name, @@ -1560,8 +1559,8 @@ def _get_visit_timing_property( return "study_week_number" @staticmethod - def _get_visit_name(visits_in_group: Sequence[StudyVisit]) -> str: - visit: StudyVisit = visits_in_group[0] + def _get_visit_name(visits_in_group: Sequence[StudyVisitLite]) -> str: + visit: StudyVisitLite = visits_in_group[0] visit_name = visit.consecutive_visit_group or visit.visit_short_name if len(visits_in_group) > 1 and "," in visit_name: @@ -1573,15 +1572,17 @@ def _get_visit_name(visits_in_group: Sequence[StudyVisit]) -> str: return visit_name @staticmethod - def _get_visit_timing(visits: list[StudyVisit], visit_timing_property: str) -> str: - visit: StudyVisit = visits[0] + def _get_visit_timing( + visits: list[StudyVisitLite], visit_timing_property: str + ) -> str: + visit: StudyVisitLite = visits[0] num_visits_in_group = len(visits) # Single Visit if num_visits_in_group == 1: if ( - getattr(visit, visit_timing_property) is not None - and visit.visit_class != VisitClass.SPECIAL_VISIT + visit.visit_class != VisitClass.SPECIAL_VISIT + and getattr(visit, visit_timing_property) is not None ): return f"{getattr(visit, visit_timing_property):d}" @@ -1599,7 +1600,10 @@ def _get_visit_timing(visits: list[StudyVisit], visit_timing_property: str) -> s # If there is a comma it means that group was made in the LIST grouping way if visit_name and "," in visit_name: visit_timings = [ - f"{getattr(visit, visit_timing_property):d}" for visit in visits + f"{getattr(visit, visit_timing_property):d}" + for visit in visits + if visit.visit_class != VisitClass.SPECIAL_VISIT + and getattr(visit, visit_timing_property) is not None ] visit_timing = ",".join(visit_timings) # insert line-breaks after certain commas when the cell text gets too long @@ -1615,7 +1619,7 @@ def _get_visit_timing(visits: list[StudyVisit], visit_timing_property: str) -> s return "" @staticmethod - def _get_visit_window(visit: StudyVisit) -> str: + def _get_visit_window(visit: StudyVisitLite) -> str: if None not in ( visit.min_visit_window_value, visit.max_visit_window_value, @@ -1652,13 +1656,13 @@ def _get_activity_rows( StudySelectionActivity | StudySelectionActivityInstance ], study_activity_schedules: Sequence[StudyActivitySchedule], - grouped_visits: dict[str, dict[str, list[StudyVisit]]], + grouped_visits: dict[str, dict[str, list[StudyVisitLite]]], layout: SoALayout, ) -> list[TableRow]: """Builds activity rows also adding various group header rows when required""" # Ordered StudyVisit.uids of visits to show (showing only the first visit of a consecutive_visit_group) - visit_groups: list[list[StudyVisit]] = [ + visit_groups: list[list[StudyVisitLite]] = [ visit_group for epochs_group in grouped_visits.values() for visit_group in epochs_group.values() @@ -1911,7 +1915,7 @@ def _get_study_activity_cell( @staticmethod def _append_activity_crosses( row: TableRow, - visit_groups: Iterable[list[StudyVisit]], + visit_groups: Iterable[list[StudyVisitLite]], study_activity_schedules_mapping: Mapping[ tuple[str, str], StudyActivitySchedule ], @@ -2646,7 +2650,7 @@ def _fetch_soa_snapshot_data( msg=f"No SoA snapshot found for Study with uid '{study_uid}' and version '{study_value_version}'", ) - study_visits_by_uid: Mapping[str, StudyVisit] = self._map_by_uid( + study_visits_by_uid: Mapping[str, StudyVisitLite] = self._map_by_uid( study_visits_future.result() ) @@ -2815,17 +2819,17 @@ def load_soa_snapshot( visits_in_group = [ study_visits_by_uid[ref.referenced_item.item_uid] for ref in refs ] - visit: StudyVisit = visits_in_group[0] + visit: StudyVisitLite = visits_in_group[0] if visit.is_soa_milestone: - if prev_visit_type_uid == visit.visit_type_uid: + if prev_visit_type_uid == visit.visit_type.term_uid: # Same visit_type, then merge with the previous cell in Milestone row prev_milestone_cell.span += 1 milestone_row.cells[col_idx].span = 0 else: # Different visit_type, new label in Milestones row - prev_visit_type_uid = visit.visit_type_uid + prev_visit_type_uid = visit.visit_type.term_uid milestone_row.cells[col_idx] = prev_milestone_cell = TableCell( visit.visit_type.sponsor_preferred_name, style="header1", 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 ebb1281b..bcbdf886 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 @@ -887,7 +887,7 @@ def _extract_multiple_version_study_standards_effective_date( ct_package: CTPackage = repos.ct_package_repository.find_by_uid( matching_version.ct_package_uid ) - effective_date: datetime = ct_package.effective_date + effective_date = ct_package.effective_date # Combine the date with the end of the day time effective_datetime = datetime( effective_date.year, 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 27823acf..2d2a4919 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 @@ -77,14 +77,17 @@ AllowedTimeReferences, SimpleStudyVisit, StudyVisit, - StudyVisitBase, StudyVisitCreateInput, + StudyVisitDetailed, StudyVisitEditInput, ) from clinical_mdr_api.models.study_selections.study_visit import ( StudyVisitGroup as StudyVisitGroupModel, ) -from clinical_mdr_api.models.study_selections.study_visit import StudyVisitVersion +from clinical_mdr_api.models.study_selections.study_visit import ( + StudyVisitLite, + StudyVisitVersion, +) from clinical_mdr_api.models.utils import GenericFilteringReturn from clinical_mdr_api.repositories._utils import FilterOperator from clinical_mdr_api.services._meta_repository import MetaRepository @@ -159,11 +162,13 @@ def get_allowed_time_references_for_study(self, study_uid: str): def _transform_all_to_response_history_model( self, visit: StudyVisitHistoryVO - ) -> StudyVisitBase: + ) -> StudyVisitDetailed: # For audit trail return model we shouldn't derive properties based on their position in the timeline as we don't know how the visit timeline looked for past visit versions # Due to this we have to take the values that are derived based on timeline directly from database representation self.update_ct_term_properties_of_study_visit(visit) - study_visit: StudyVisitBase = StudyVisitBase.transform_to_response_model(visit) + study_visit: StudyVisitDetailed = ( + StudyVisitDetailed.transform_to_response_model(visit) + ) study_visit.change_type = visit.change_type study_visit.end_date = convert_to_datetime(visit.end_date) @@ -192,7 +197,7 @@ def get_amount_of_visits_in_given_epoch( def get_global_anchor_visit(self, study_uid: str) -> SimpleStudyVisit | None: global_anchor_visit = ( - StudyVisitNeoModel.nodes.fetch_relations( + StudyVisitNeoModel.nodes.traverse( "has_visit_name__has_latest_value", "has_visit_type__has_selected_term__has_name_root__has_latest_value", ) @@ -214,7 +219,7 @@ def get_anchor_visits_in_a_group_of_subvisits( self, study_uid: str ) -> list[SimpleStudyVisit]: anchor_visits_in_a_group_of_subv = ( - StudyVisitNeoModel.nodes.fetch_relations( + StudyVisitNeoModel.nodes.traverse( "has_visit_name__has_latest_value", "has_visit_type__has_selected_term__has_name_root__has_latest_value", ) @@ -233,7 +238,7 @@ def get_anchor_for_special_visit( self, study_uid: str, study_epoch_uid: str ) -> list[SimpleStudyVisit]: anchor_visits_for_special_visit = ( - StudyVisitNeoModel.nodes.fetch_relations( + StudyVisitNeoModel.nodes.traverse( "has_visit_name__has_latest_value", "has_visit_type__has_selected_term__has_name_root__has_latest_value", ) @@ -289,8 +294,10 @@ def get_study_visits_for_specific_activity_instance( .filter( has_study_visit__latest_value__uid=study_uid, # Visit in study has_study_activity_schedule__study_value__latest_value__uid=study_uid, # With schedule in study - has_study_activity_schedule__study_activity__has_study_activity__latest_value__uid=study_uid, # With activity in study - has_study_activity_schedule__study_activity__study_activity_has_study_activity_instance__uid=study_activity_instance_uid, # And activity is parent of instance + has_study_activity_schedule__study_activity__has_study_activity__latest_value__uid=study_uid, + # With activity in study + has_study_activity_schedule__study_activity__study_activity_has_study_activity_instance__uid=study_activity_instance_uid, + # And activity is parent of instance ) .order_by("visit_number") .resolve_subgraph() @@ -309,22 +316,30 @@ def get_all_visits( total_count: bool = False, study_value_version: str | None = None, derive_props_based_on_timeline: bool = False, - ) -> GenericFilteringReturn[StudyVisit]: + lite: bool = False, + ) -> GenericFilteringReturn[StudyVisitLite | StudyVisit]: StudyService.check_if_study_uid_and_version_exists( study_uid, study_value_version ) - visits = StudyVisitService._get_all_visits( - study_uid, study_value_version=study_value_version - ) - visits = [ - StudyVisit.transform_to_response_model( - visit, - study_value_version=study_value_version, - derive_props_based_on_timeline=derive_props_based_on_timeline, + if lite: + dicts = StudyVisitRepository.list_all_visits_by_study_uid( + study_uid=study_uid, study_value_version=study_value_version ) - for visit in visits - ] + visits = [StudyVisitLite(**d) for d in dicts] + + else: + visit_vos = StudyVisitService._get_all_visits( + study_uid, study_value_version=study_value_version + ) + visits = [ + StudyVisit.transform_to_response_model( + visit, + study_value_version=study_value_version, + derive_props_based_on_timeline=derive_props_based_on_timeline, + ) + for visit in visit_vos + ] filtered_visits = service_level_generic_filtering( items=visits, @@ -630,7 +645,7 @@ def _validate_visit( and visit_vo.visit_class not in visit_classes_without_timing ): reference_name = self.study_visit_time_references_by_uid[ - visit_input.time_reference_uid + visit_input.time_reference.term_uid ] for visit in timeline._visits: if ( @@ -783,9 +798,9 @@ def _validate_visit( timeline.remove_visit(visit_vo) ValidationException.raise_if( - visit_input.visit_contact_mode_uid + visit_input.visit_contact_mode.term_uid not in self.study_visit_contact_modes_by_uid, - msg=f"CT Term with UID '{visit_input.visit_contact_mode_uid}' is not a valid Visit Contact Mode term.", + msg=f"CT Term with UID '{visit_input.visit_contact_mode.term_uid}' is not a valid Visit Contact Mode term.", ) visits_classes = [ @@ -893,7 +908,7 @@ def _create_timepoint_simple_concept( msg="Time unit UID is required for creating a timepoint." ) - if study_visit_input.time_reference_uid is None: + if study_visit_input.time_reference is None: raise exceptions.BusinessLogicException( msg="Time reference UID is required for creating a timepoint." ) @@ -911,7 +926,7 @@ def _create_timepoint_simple_concept( is_template_parameter=True, numeric_value_uid=numeric_ar.uid, unit_definition_uid=study_visit_input.time_unit_uid, - time_reference_uid=study_visit_input.time_reference_uid, + time_reference_uid=study_visit_input.time_reference.term_uid, find_numeric_value_by_uid=self._repos.numeric_value_repository.find_by_uid_2, find_unit_definition_by_uid=self._repos.unit_definition_repository.find_by_uid_2, find_time_reference_by_uid=self._repos.ct_term_name_repository.find_by_uid, @@ -924,7 +939,7 @@ def _create_timepoint_simple_concept( timepoint_object = TimePoint( uid=timepoint_ar.uid, visit_timereference=self.study_visit_time_references_by_uid[ - study_visit_input.time_reference_uid + study_visit_input.time_reference.term_uid ], time_unit_uid=study_visit_input.time_unit_uid, visit_value=study_visit_input.time_value, @@ -1001,16 +1016,16 @@ def _from_input_values( conversion_factor_to_master=self._week_unit.concept_vo.conversion_factor_to_master, ) visit_contact_mode = self.study_visit_contact_modes_by_uid.get( - create_input.visit_contact_mode_uid + create_input.visit_contact_mode.term_uid ) exceptions.ValidationException.raise_if_not( visit_contact_mode, - msg=f"Visit contact mode '{create_input.visit_contact_mode_uid}' is invalid.", + msg=f"Visit contact mode '{create_input.visit_contact_mode.term_uid}' is invalid.", ) - visit_type = self.study_visit_types_by_uid.get(create_input.visit_type_uid) + visit_type = self.study_visit_types_by_uid.get(create_input.visit_type.term_uid) exceptions.ValidationException.raise_if_not( visit_type, - msg=f"Visit type with UID '{create_input.visit_type_uid}' is not valid.", + msg=f"Visit type with UID '{create_input.visit_type.term_uid}' is not valid.", ) study_visit_vo = StudyVisitVO( uid=self.repo.generate_uid(), @@ -1027,9 +1042,9 @@ def _from_input_values( visit_contact_mode=visit_contact_mode, epoch_allocation=( self.study_visit_epoch_allocations_by_uid.get( - create_input.epoch_allocation_uid + create_input.epoch_allocation.term_uid ) - if create_input.epoch_allocation_uid + if create_input.epoch_allocation else None ), visit_type=visit_type, @@ -1064,8 +1079,8 @@ def _from_input_values( missing_fields = [] if create_input.time_unit_uid is None: missing_fields.append("time_unit_uid") - if create_input.time_reference_uid is None: - missing_fields.append("time_reference_uid") + if create_input.time_reference is None: + missing_fields.append("time_reference") if create_input.time_value is None: missing_fields.append("time_value") ValidationException.raise_if( diff --git a/clinical-mdr-api/clinical_mdr_api/services/syntax_instances/generic_syntax_instance_service.py b/clinical-mdr-api/clinical_mdr_api/services/syntax_instances/generic_syntax_instance_service.py index 2af93b33..393a653e 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/syntax_instances/generic_syntax_instance_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/syntax_instances/generic_syntax_instance_service.py @@ -2,7 +2,8 @@ from typing import Callable, TypeVar from neomodel import db -from neomodel.sync_ import core +from neomodel.exceptions import DoesNotExist +from neomodel.sync_.node import NodeMeta from pydantic import BaseModel from clinical_mdr_api.domain_repositories._generic_repository_interface import ( @@ -149,7 +150,7 @@ def create( self.repository.save(item) return self._transform_aggregate_root_to_pydantic_model(item_ar=item) - except core.DoesNotExist as exc: + except DoesNotExist as exc: raise NotFoundException("Library", template.library_name, "Name") from exc def _get_template_vo_by_template_uid(self, template_uid: str) -> TemplateVO | None: @@ -214,7 +215,7 @@ def get_parameters( include_study_endpoints=include_study_endpoints, ) return process_parameters(parameters) - except core.DoesNotExist as exc: + except DoesNotExist as exc: raise NotFoundException(field_value=uid) from exc def _create_parameter_entries( @@ -248,7 +249,6 @@ def _create_parameter_entries( parameter_term_uids_to_fetch=template_parameter_terms, ) ) - ValidationException.raise_if( not template.parameter_terms and self._allowed_parameters, msg="parameter_terms must be provided.", @@ -318,7 +318,7 @@ def _create_parameter_entries( def get_referencing_studies( self, uid: str, - node_type: core.NodeMeta, + node_type: NodeMeta, include_sections: list[StudyComponentEnum] | None = None, exclude_sections: list[StudyComponentEnum] | None = None, ) -> list[Study]: diff --git a/clinical-mdr-api/clinical_mdr_api/services/syntax_templates/generic_syntax_template_service.py b/clinical-mdr-api/clinical_mdr_api/services/syntax_templates/generic_syntax_template_service.py index 275c3eb9..1f07cda3 100644 --- a/clinical-mdr-api/clinical_mdr_api/services/syntax_templates/generic_syntax_template_service.py +++ b/clinical-mdr-api/clinical_mdr_api/services/syntax_templates/generic_syntax_template_service.py @@ -2,7 +2,7 @@ from typing import TypeVar from neomodel import db -from neomodel.sync_ import core +from neomodel.exceptions import DoesNotExist from pydantic import BaseModel from clinical_mdr_api.domain_repositories.syntax_instances.generic_syntax_instance_repository import ( @@ -93,7 +93,7 @@ def create(self, template: BaseModel) -> BaseModel: self.repository.save(item) return self._transform_aggregate_root_to_pydantic_model(item) - except core.DoesNotExist as exc: + except DoesNotExist as exc: raise NotFoundException("Library", template.library_name, "Name") from exc def _create_template_vo(self, template: BaseModel) -> tuple[TemplateVO, LibraryVO]: @@ -280,7 +280,7 @@ def get_parameters( include_study_endpoints=include_study_endpoints, ) return process_parameters(parameters) - except core.DoesNotExist as exc: + except DoesNotExist as exc: raise NotFoundException(field_value=uid) from exc @db.transaction 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 29e11b39..180d6646 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 @@ -285,7 +285,7 @@ def add_table(table: TableWithFootnotes): # add footnote symbols to a run within the paragraph if t_cell.footnotes: - run = x_para.add_run("\u00A0".join(t_cell.footnotes)) + run = x_para.add_run("\u00a0".join(t_cell.footnotes)) run.font.bold = True run.font.superscript = True diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_conditions.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_conditions.feature index f493e600..3faa0e52 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_conditions.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_conditions.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Conditions in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM conditions - When the user calls the API endpoint 'concepts/odms/conditions' + When the user calls the API endpoint 'odms/conditions' Then the response must include an empty list of ODM conditions And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Conditions in OpenStudyBuilder API | /tests/integration/api/old/test_odm_conditions.py | @TestID: test_creating_a_new_odm_condition | Scenario: User must be able to get a list of ODM conditions - When the user calls the API endpoint 'concepts/odms/conditions' + When the user calls the API endpoint 'odms/conditions' Then the response must include the list of ODM conditions And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Conditions in OpenStudyBuilder API | /tests/integration/api/old/test_odm_conditions.py | @TestID: test_getting_non_empty_list_of_odm_conditions | Scenario: User must be able to get a specific ODM condition - When the user calls the API endpoint 'concepts/odms/conditions/' + When the user calls the API endpoint 'odms/conditions/' Then the response status code must be 200 And the response must include the ODM condition Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Conditions in OpenStudyBuilder API | /tests/integration/api/old/test_odm_conditions.py | @TestID: test_getting_a_specific_odm_condition | Scenario: User must be able to get possible header values of ODM conditions - When the user calls the API endpoint 'concepts/odms/conditions/headers?field_name=name' + When the user calls the API endpoint 'odms/conditions/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["name1"] Test Coverage: @@ -109,7 +109,7 @@ Feature: Manage ODM Conditions in OpenStudyBuilder API | /tests/integration/api/old/test_odm_conditions_negative.py | @TestID: test_cannot_create_a_new_odm_condition_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM condition - When the user calls the API endpoint 'concepts/odms/conditions/' for retrieving a non-existent ODM condition + When the user calls the API endpoint 'odms/conditions/' for retrieving a non-existent ODM condition Then the response status code must be 404 And the response must include the message like "OdmConditionAR with UID 'OdmCondition_000002' doesn't exist or there's no version with requested status or version number." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_forms.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_forms.feature index 151b35cd..5f450990 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_forms.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_forms.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Forms in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM forms - When the user calls the API endpoint 'concepts/odms/forms' + When the user calls the API endpoint 'odms/forms' Then the response must include an empty list of ODM forms And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Forms in OpenStudyBuilder API | /tests/integration/api/old/test_odm_forms.py | @TestID: test_creating_a_new_odm_form | Scenario: User must be able to get a list of ODM forms - When the user calls the API endpoint 'concepts/odms/forms' + When the user calls the API endpoint 'odms/forms' Then the response must include the list of ODM forms And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Forms in OpenStudyBuilder API | /tests/integration/api/old/test_odm_forms.py | @TestID: test_getting_non_empty_list_of_odm_forms | Scenario: User must be able to get a specific ODM form - When the user calls the API endpoint 'concepts/odms/forms/' to get a specific ODM form + When the user calls the API endpoint 'odms/forms/' to get a specific ODM form Then the response status code must be 200 And the response must include the ODM form Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Forms in OpenStudyBuilder API | /tests/integration/api/old/test_odm_forms.py | @TestID: test_getting_a_specific_odm_form | Scenario: User must be able to get possible header values of ODM forms - When the user calls the API endpoint 'concepts/odms/forms/headers?field_name=name' + When the user calls the API endpoint 'odms/forms/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["name1"] Test Coverage: @@ -102,7 +102,7 @@ Feature: Manage ODM Forms in OpenStudyBuilder API | /tests/integration/api/old/test_odm_forms_negative.py | @TestID: test_cannot_create_a_new_odm_form_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM form - When the user calls the API endpoint 'concepts/odms/forms/' for retrieving a non-existent ODM form + When the user calls the API endpoint 'odms/forms/' for retrieving a non-existent ODM form Then the response status code must be 404 And the response must include the message like "OdmFormAR with UID 'OdmForm_000002' doesn't exist or there's no version with requested status or version number." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_items.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_items.feature index 224f8600..90bbfb2c 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_items.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_items.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Items in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM items - When the user calls the API endpoint 'concepts/odms/items' + When the user calls the API endpoint 'odms/items' Then the response must include an empty list of ODM items And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Items in OpenStudyBuilder API | /tests/integration/api/old/test_odm_items.py | @TestID: test_creating_a_new_odm_item | Scenario: User must be able to get a non-empty list of ODM items - When the user calls the API endpoint 'concepts/odms/items' + When the user calls the API endpoint 'odms/items' Then the response must include the list of ODM items with expected properties And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Items in OpenStudyBuilder API | /tests/integration/api/old/test_odm_items.py | @TestID: test_getting_non_empty_list_of_odm_items | Scenario: User must be able to get a specific ODM item - When the user calls the API endpoint 'concepts/odms/items/' to get a specific ODM item + When the user calls the API endpoint 'odms/items/' to get a specific ODM item Then the response status code must be 200 And the response must include the ODM item Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Items in OpenStudyBuilder API | /tests/integration/api/old/test_odm_items.py | @TestID: test_getting_a_specific_odm_item | Scenario: User must be able to get possible header values of ODM items - When the user calls the API endpoint 'concepts/odms/items/headers?field_name=name' + When the user calls the API endpoint 'odms/items/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["name1"] Test Coverage: @@ -120,7 +120,7 @@ Feature: Manage ODM Items in OpenStudyBuilder API | /tests/integration/api/old/test_odm_items_negative.py | @TestID: test_cannot_create_a_new_odm_item_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM item - When the user calls the API endpoint 'concepts/odms/items/' for retrieving an non-existed ODM item + When the user calls the API endpoint 'odms/items/' for retrieving an non-existed ODM item Then the response status code must be 404 And the response must include the message like "OdmItemAR with UID 'OdmItem_000002' doesn't exist ..." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_methods.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_methods.feature index 81438ec7..91f14589 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_methods.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_methods.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Methods in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM methods - When the user calls the API endpoint 'concepts/odms/methods' + When the user calls the API endpoint 'odms/methods' Then the response must include an empty list of ODM methods And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Methods in OpenStudyBuilder API | /tests/integration/api/old/test_odm_methods.py | @TestID: test_creating_a_new_odm_method | Scenario: User must be able to get a non-empty list of ODM methods - When the user calls the API endpoint 'concepts/odms/methods' + When the user calls the API endpoint 'odms/methods' Then the response must include the list of ODM methods that were created And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Methods in OpenStudyBuilder API | /tests/integration/api/old/test_odm_methods.py | @TestID: test_getting_non_empty_list_of_odm_methods | Scenario: User must be able to get a specific ODM method - When the user calls the API endpoint 'concepts/odms/methods/' to get a specific ODM method + When the user calls the API endpoint 'odms/methods/' to get a specific ODM method Then the response status code must be 200 And the response must include the ODM method Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Methods in OpenStudyBuilder API | /tests/integration/api/old/test_odm_methods.py | @TestID: test_getting_a_specific_odm_method | Scenario: User must be able to get possible header values of ODM methods - When the user calls the API endpoint 'concepts/odms/methods/headers?field_name=name' + When the user calls the API endpoint 'odms/methods/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["name1"] Test Coverage: @@ -70,7 +70,7 @@ Feature: Manage ODM Methods in OpenStudyBuilder API | /tests/integration/api/old/test_odm_methods_negative.py | @TestID: test_cannot_create_a_new_odm_method_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM method - When the user calls the API endpoint 'concepts/odms/methods/' for retrieving a non-existent ODM method + When the user calls the API endpoint 'odms/methods/' for retrieving a non-existent ODM method Then the response status code must be 404 And the response must include the message like "OdmMethodAR with UID 'OdmMethod_000002' doesn't exist ..." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_study_events.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_study_events.feature index 8e2575d8..07a3eeb8 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_study_events.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_study_events.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Study Events in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM study events - When the user calls the API endpoint 'concepts/odms/study-events' + When the user calls the API endpoint 'odms/study-events' Then the response must include an empty list of ODM study events And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Study Events in OpenStudyBuilder API | /tests/integration/api/old/test_odm_study_events.py | @TestID: test_creating_a_new_odm_study_event | Scenario: User must be able to get a non-empty list of ODM study events - When the user calls the API endpoint 'concepts/odms/study-events' + When the user calls the API endpoint 'odms/study-events' Then the response must include the list of ODM study events And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Study Events in OpenStudyBuilder API | /tests/integration/api/old/test_odm_study_events.py | @TestID: test_getting_non_empty_list_of_odm_study_events | Scenario: User must be able to get a specific ODM study event - When the user calls the API endpoint 'concepts/odms/study-events/' to get a specific ODM study event + When the user calls the API endpoint 'odms/study-events/' to get a specific ODM study event Then the response status code must be 200 And the response must include the ODM study event Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Study Events in OpenStudyBuilder API | /tests/integration/api/old/test_odm_study_events.py | @TestID: test_getting_a_specific_odm_study_event | Scenario: User must be able to get possible header values of ODM study events - When the user calls the API endpoint 'concepts/odms/study-events/headers?field_name=name' + When the user calls the API endpoint 'odms/study-events/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["name1"] Test Coverage: @@ -70,7 +70,7 @@ Feature: Manage ODM Study Events in OpenStudyBuilder API | /tests/integration/api/old/test_odm_study_events_negative.py | @TestID: test_cannot_create_a_new_odm_study_event_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM study event - When the user calls the API endpoint 'concepts/odms/study-events/' for retrieving a non-existent ODM study event + When the user calls the API endpoint 'odms/study-events/' for retrieving a non-existent ODM study event Then the response status code must be 404 And the response must include the message like "OdmStudyEventAR with UID 'OdmStudyEvent_000002' doesn't exist ..." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_attributes.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_attributes.feature index d6c47306..57dc1284 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_attributes.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_attributes.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Vendor Attributes in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM vendor attributes - When the user calls the API endpoint 'concepts/odms/vendor-attributes' + When the user calls the API endpoint 'odms/vendor-attributes' Then the response must include an empty list of ODM vendor attributes And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Vendor Attributes in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_attributes.py | @TestID: test_creating_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_namespace | Scenario: User must be able to get a non-empty list of ODM vendor attributes - When the user calls the API endpoint 'concepts/odms/vendor-attributes' get a non-empty list of ODM vendor attributes + When the user calls the API endpoint 'odms/vendor-attributes' get a non-empty list of ODM vendor attributes Then the response must include the list of ODM vendor attributes that were created And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Vendor Attributes in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_attributes.py | @TestID: test_getting_non_empty_list_of_odm_vendor_attributes | Scenario: User must be able to get a specific ODM vendor attribute - When the user calls the API endpoint 'concepts/odms/vendor-attributes/' to get a specific ODM vendor attribute + When the user calls the API endpoint 'odms/vendor-attributes/' to get a specific ODM vendor attribute Then the response status code must be 200 And the response must include the ODM vendor attribute Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Vendor Attributes in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_attributes.py | @TestID: test_getting_a_specific_odm_vendor_attribute | Scenario: User must be able to get possible header values of ODM vendor attributes - When the user calls the API endpoint 'concepts/odms/vendor-attributes/headers?field_name=name' + When the user calls the API endpoint 'odms/vendor-attributes/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["nameOne"] Test Coverage: @@ -70,7 +70,7 @@ Feature: Manage ODM Vendor Attributes in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_attributes_negative.py | @TestID: test_cannot_create_a_new_odm_vendor_attribute_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM vendor attribute - When the user calls the API endpoint 'concepts/odms/vendor-attributes/' for retrieving a non-existent ODM vendor attribute + When the user calls the API endpoint 'odms/vendor-attributes/' for retrieving a non-existent ODM vendor attribute Then the response status code must be 404 And the response must include the message like "OdmVendorAttributeAR with UID 'OdmVendorAttribute_000003' doesn't exist ..." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_elements.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_elements.feature index 0a1fc1e5..3bf3b4b3 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_elements.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_elements.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Vendor Elements in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM vendor elements - When the user calls the API endpoint 'concepts/odms/vendor-elements' + When the user calls the API endpoint 'odms/vendor-elements' Then the response must include an empty list of ODM vendor elements And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Vendor Elements in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_elements.py | @TestID: test_creating_a_new_odm_vendor_element | Scenario: User must be able to get a non-empty list of ODM vendor elements - When the user calls the API endpoint 'concepts/odms/vendor-elements' to get a non-empty list of ODM vendor elements + When the user calls the API endpoint 'odms/vendor-elements' to get a non-empty list of ODM vendor elements Then the response must include ODM vendor elements And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Vendor Elements in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_elements.py | @TestID: test_getting_non_empty_list_of_odm_vendor_elements | Scenario: User must be able to get a specific ODM vendor element - When the user calls the API endpoint 'concepts/odms/vendor-elements/' to get a specific ODM vendor element + When the user calls the API endpoint 'odms/vendor-elements/' to get a specific ODM vendor element Then the response must include the details of ODM vendor element And the response status code must be 200 Test Coverage: @@ -53,7 +53,7 @@ Feature: Manage ODM Vendor Elements in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_elements.py | @TestID: test_deleting_a_specific_odm_vendor_element | Scenario: User must receive an error for retrieving a non-existent ODM vendor element - When the user calls the API endpoint 'concepts/odms/vendor-elements/' for retrieving a non-existent ODM vendor element + When the user calls the API endpoint 'odms/vendor-elements/' for retrieving a non-existent ODM vendor element Then the response status code must be 404 And the response must indicate the ODM vendor element does not exist Test Coverage: @@ -109,7 +109,7 @@ Feature: Manage ODM Vendor Elements in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_elements.py | @TestID: test_create_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_element | Scenario: User must be able to get the active relationships of a specific ODM vendor element - When the user calls the API endpoint 'concepts/odms/vendor-elements/uid/relationships' + When the user calls the API endpoint 'odms/vendor-elements/uid/relationships' Then the response must include the active relationships of the ODM vendor element And the response status code must be 200 Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_namespaces.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_namespaces.feature index adde640b..06d966a1 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_namespaces.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_vendor_namespaces.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Vendor Namespaces in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM vendor namespaces - When the user calls the API endpoint 'concepts/odms/vendor-namespaces' + When the user calls the API endpoint 'odms/vendor-namespaces' Then the response must include an empty list of ODM vendor namespaces And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Vendor Namespaces in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_namespaces.py | @TestID: test_creating_a_new_odm_vendor_namespace | Scenario: User must be able to get a non-empty list of ODM vendor namespaces - When the user calls the API endpoint 'concepts/odms/vendor-namespaces' to get a non-empty list of ODM vendor namespaces + When the user calls the API endpoint 'odms/vendor-namespaces' to get a non-empty list of ODM vendor namespaces Then the response must include ODM vendor namespaces And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Vendor Namespaces in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_namespaces.py | @TestID: test_getting_non_empty_list_of_odm_vendor_namespaces | Scenario: User must be able to get a specific ODM vendor namespace - When the user calls the API endpoint 'concepts/odms/vendor-namespaces/' to get a specific ODM vendor namespace + When the user calls the API endpoint 'odms/vendor-namespaces/' to get a specific ODM vendor namespace Then the response must include the details of ODM vendor namespace And the response status code must be 200 Test Coverage: @@ -46,7 +46,7 @@ Feature: Manage ODM Vendor Namespaces in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_namespaces.py | @TestID: test_updating_an_existing_odm_vendor_namespace | Scenario: User must be able to get the versions of a specific ODM vendor namespace - When the user calls the API endpoint 'concepts/odms/vendor-namespaces/uid/versions' + When the user calls the API endpoint 'odms/vendor-namespaces/uid/versions' Then the response must include the versions of the ODM vendor namespace And the response status code must be 200 Test Coverage: @@ -93,7 +93,7 @@ Feature: Manage ODM Vendor Namespaces in OpenStudyBuilder API | /tests/integration/api/old/test_odm_vendor_namespaces.py | @TestID: test_deleting_a_specific_odm_vendor_namespace | Scenario: User must receive an error for retrieving a non-existent ODM vendor namespace - When the user calls the API endpoint 'concepts/odms/vendor-namespaces/' for retrieving a non-existent ODM vendor namespace + When the user calls the API endpoint 'odms/vendor-namespaces/' for retrieving a non-existent ODM vendor namespace Then the response status code must be 404 And the response must indicate the ODM vendor namespace does not exist Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_exporter.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_exporter.feature index 27eca7e5..020199d2 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_exporter.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_exporter.feature @@ -7,7 +7,7 @@ Feature: Manage Library Concept CRF XML Exporter Function in OpenStudyBuilder AP Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get the xml representation of the requsted odm forms - When the user calls the API endpoint with uids of odm forms 'concepts/odms/metadata/xmls/export?targets=odm_form1&targets=odm_form2&target_type=form' + When the user calls the API endpoint with uids of odm forms 'odms/metadata/xmls/export?targets=odm_form1&targets=odm_form2&target_type=form' Then the response must include the exact xml representation of the requested odm forms Test Coverage: @@ -15,7 +15,7 @@ Feature: Manage Library Concept CRF XML Exporter Function in OpenStudyBuilder AP |/tests/integration/api/old/test_odm_xml_exporter.py | @TestID: test_get_odm_xml_forms | Scenario: User must be able to get the xml representation of the requsted odm item group - When the user calls the API endpoint with uids of odm item group 'concepts/odms/metadata/xmls/export?targets=odm_item_group1&target_type=item_group' + When the user calls the API endpoint with uids of odm item group 'odms/metadata/xmls/export?targets=odm_item_group1&target_type=item_group' Then the response must include the exact xml representation of the requested odm item group Test Coverage: @@ -23,7 +23,7 @@ Feature: Manage Library Concept CRF XML Exporter Function in OpenStudyBuilder AP |/tests/integration/api/old/test_odm_xml_exporter.py | @TestID: test_get_odm_xml_item_group | Scenario: User must be able to get the xml representation of the requsted odm item - When the user calls the API endpoint with uids of odm item 'concepts/odms/metadata/xmls/export?targets=odm_item1&target_type=item' + When the user calls the API endpoint with uids of odm item 'odms/metadata/xmls/export?targets=odm_item1&target_type=item' Then the response must include the exact xml representation of the requested odm item Test Coverage: @@ -31,7 +31,7 @@ Feature: Manage Library Concept CRF XML Exporter Function in OpenStudyBuilder AP |/tests/integration/api/old/test_odm_xml_exporter.py | @TestID: test_get_odm_xml_item | Scenario: User must be able to get the xml representation of the requsted odm item - When the user calls the API endpoint with uids of odm item 'concepts/odms/metadata/xmls/export?targets=odm_item1&target_type=item' + When the user calls the API endpoint with uids of odm item 'odms/metadata/xmls/export?targets=odm_item1&target_type=item' Then the response must include the exact xml representation of the requested odm item Test Coverage: @@ -39,7 +39,7 @@ Feature: Manage Library Concept CRF XML Exporter Function in OpenStudyBuilder AP |/tests/integration/api/old/test_odm_xml_exporter.py | @TestID: test_get_odm_xml_item | Scenario: User must be able to get the pdf representation of the requsted odm elmenet - When the user calls the API endpoint with uids of odm element 'concepts/odms/metadata/xmls/export?target_type=form&targets=odm_form1&pdf=true&stylesheet=blank' + When the user calls the API endpoint with uids of odm element 'odms/metadata/xmls/export?target_type=form&targets=odm_form1&pdf=true&stylesheet=blank' Then the response must include the exact pdf representation of the requested odm element Test Coverage: @@ -47,7 +47,7 @@ Feature: Manage Library Concept CRF XML Exporter Function in OpenStudyBuilder AP |/tests/integration/api/old/test_odm_xml_exporter.py | @TestID: test_get_odm_xml_pdf_version | Scenario: User must be able to get error message when the requested odm target type is not supported - When the user calls the API endpoint 'concepts/odms/metadata/xmls/export?targets=study&target_type=study' + When the user calls the API endpoint 'odms/metadata/xmls/export?targets=study&target_type=study' Then the response must get error message 'Requested target type not supported.' Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_stylesheet.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_stylesheet.feature index c5118a2c..47e34d47 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_stylesheet.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/odm_xml_stylesheet.feature @@ -6,7 +6,7 @@ Feature: Manage Library Concept CRF Stylesheet Function in OpenStudyBuilder API Given the test user can call the OpenStudyBuilder API Scenario: User must be able to get all the names of available XML stylesheets - When the user calls the API endpoint 'concepts/odms/metadata/xmls/stylesheets' + When the user calls the API endpoint 'odms/metadata/xmls/stylesheets' Then the response must include all names of available XML stylesheets: "blank", "falcon", "with-annotations" Test Coverage: @@ -14,7 +14,7 @@ Feature: Manage Library Concept CRF Stylesheet Function in OpenStudyBuilder API | /tests/integration/api/old/test_odm_xml_stylesheets.py | @TestID: test_get_available_stylesheet_names | Scenario: User must be able to get the specific XML stylesheets - When the user calls the API endpoint 'concepts/odms/metadata/xmls/stylesheets/blank' + When the user calls the API endpoint 'odms/metadata/xmls/stylesheets/blank' Then the response must include the blank XML stylesheets Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage Library Concept CRF Stylesheet Function in OpenStudyBuilder API | /tests/integration/api/old/test_odm_xml_stylesheets.py | @TestID: test_get_specific_stylesheet | Scenario: User must be able to get the error message when the requested stylesheet does not exist - When the user calls the API endpoint 'concepts/odms/metadata/xmls/stylesheets/wrong' + When the user calls the API endpoint 'odms/metadata/xmls/stylesheets/wrong' Then the response must be an error message that states "Stylesheet 'wrong' does not exist." Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage Library Concept CRF Stylesheet Function in OpenStudyBuilder API | /tests/integration/api/old/test_odm_xml_stylesheets.py | @TestID: test_throw_exception_if_stylesheet_doesnt_exist | Scenario: User must be able to get the error message when requesting a stylesheet with an invalid name - When the user calls the API endpoint 'concepts/odms/metadata/xmls/stylesheets/_wrong' + When the user calls the API endpoint 'odms/metadata/xmls/stylesheets/_wrong' Then the response must be an error message that states "Stylesheet name must only contain letters, numbers and hyphens." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/omd_item_groups.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/omd_item_groups.feature index dd9a14af..d077163f 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/omd_item_groups.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/library/data_collection_standards/odm_crf/omd_item_groups.feature @@ -6,7 +6,7 @@ Feature: Manage ODM Item Groups in OpenStudyBuilder API Given The test user can call the OpenStudyBuilder API Scenario: User must be able to get an empty list of ODM item groups - When the user calls the API endpoint 'concepts/odms/item-groups' + When the user calls the API endpoint 'odms/item-groups' Then the response must include an empty list of ODM item groups And the response status code must be 200 Test Coverage: @@ -22,7 +22,7 @@ Feature: Manage ODM Item Groups in OpenStudyBuilder API | /tests/integration/api/old/test_odm_item_groups.py | @TestID: test_creating_a_new_odm_item_group | Scenario: User must be able to get a list of ODM item groups - When the user calls the API endpoint 'concepts/odms/item-groups' to get a list of ODM item groups + When the user calls the API endpoint 'odms/item-groups' to get a list of ODM item groups Then the response must include the list of ODM item groups And the response status code must be 200 Test Coverage: @@ -30,7 +30,7 @@ Feature: Manage ODM Item Groups in OpenStudyBuilder API | /tests/integration/api/old/test_odm_item_groups.py | @TestID: test_getting_non_empty_list_of_odm_item_groups | Scenario: User must be able to get a specific ODM item group - When the user calls the API endpoint 'concepts/odms/item-groups/' to get a specific ODM item group + When the user calls the API endpoint 'odms/item-groups/' to get a specific ODM item group Then the response status code must be 200 And the response must include the ODM item group Test Coverage: @@ -38,7 +38,7 @@ Feature: Manage ODM Item Groups in OpenStudyBuilder API | /tests/integration/api/old/test_odm_item_groups.py | @TestID: test_getting_a_specific_odm_item_group | Scenario: User must be able to get possible header values of ODM item groups - When the user calls the API endpoint 'concepts/odms/item-groups/headers?field_name=name' + When the user calls the API endpoint 'odms/item-groups/headers?field_name=name' Then the response status code must be 200 And the response must include the list ["name1"] Test Coverage: @@ -128,7 +128,7 @@ Feature: Manage ODM Item Groups in OpenStudyBuilder API | /tests/integration/api/old/test_odm_item_groups_negative.py | @TestID: test_cannot_create_a_new_odm_item_group_without_an_english_description | Scenario: User receives an error for retrieving a non-existent ODM item group - When the user calls the API endpoint 'concepts/odms/item-groups/' for retrieving a non-existent ODM item group + When the user calls the API endpoint 'odms/item-groups/' for retrieving a non-existent ODM item group Then the response status code must be 404 And the response must include the message like "OdmItemGroupAR with UID 'OdmItemGroup_000002' doesn't exist ..." Test Coverage: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/studies/study_versioning/get_released_locked_studydata.feature b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/studies/study_versioning/get_released_locked_studydata.feature index c8e72906..27ac2828 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/studies/study_versioning/get_released_locked_studydata.feature +++ b/clinical-mdr-api/clinical_mdr_api/tests/acceptance/features/studies/study_versioning/get_released_locked_studydata.feature @@ -55,7 +55,7 @@ Feature: Get released or locked study definition data from OpenStudyBuilder API | @TestID:test_study_epoch_with_study_epoch_subtype_relationship | study-epochs | ["start_rule","end_rule","epoch","epoch_subtype","duration_unit","order","description","duration","color_hash","epoch_name","epoch_subtype_name","epoch_type","epoch_type_name","start_day","end_day","start_week","end_week","study_visit_count"] | | @TestID:test_study_objective_with_objective_level_relationship | study-objectives | ["objective_level","objective","objective_template","endpoint_count","latest_objective","accepted_version"] | | @TestID:test_modify_actions_on_locked_study | study-soa-footnotes | ["order","modified","referenced_items","footnote","footnote_template"] | - | @TestID:test_study_visit_versioning | study-visits | ["study_epoch_name","order","visit_type_name","time_reference_uid","time_reference_name","time_value","time_unit_name","visit_contact_mode_name","epoch_allocation_name","duration_time","duration_time_unit","study_day_number","study_duration_days_label","study_day_label","study_week_number","study_duration_weeks_label","study_week_label","visit_number","visit_subnumber","unique_visit_number","visit_subname","visit_name","visit_short_name","visit_window_unit_name","visit_class","visit_subclass","is_global_anchor_visit"] | + | @TestID:test_study_visit_versioning | study-visits | ["study_epoch_name","order","time_value","time_unit_name","visit_contact_mode_name","epoch_allocation_name","duration_time","duration_time_unit","study_day_number","study_duration_days_label","study_day_label","study_week_number","study_duration_weeks_label","study_week_label","visit_number","visit_subnumber","unique_visit_number","visit_subname","visit_name","visit_short_name","visit_window_unit_name","visit_class","visit_subclass","is_global_anchor_visit"] | 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 cf0c512e..e88a406d 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 @@ -2,7 +2,12 @@ This list must contain all routes of the main application as (path:str, method:str, required_roles:Set[str]) """ -ALL_ROUTES_METHODS_ROLES = ( +ALL_ROUTES_METHODS_ROLES = ( # type: ignore[var-annotated] + ("/admin/global-preferences", "PATCH", {"Admin.Write"}), + ("/admin/global-preferences", "GET", {"Admin.Read"}), + ("/user-preferences", "GET", {}), + ("/user-preferences", "PATCH", {}), + ("/user-preferences/{preference_key}", "DELETE", {}), ("/iso/639", "GET", {"Library.Read", "Study.Read"}), ("/feature-flags/{serial_number}", "GET", {"Admin.Read"}), ("/feature-flags", "POST", {"Admin.Write"}), @@ -13,314 +18,321 @@ ("/notifications", "POST", {"Admin.Write"}), ("/notifications/{serial_number}", "PATCH", {"Admin.Write"}), ("/notifications/{serial_number}", "DELETE", {"Admin.Write"}), - ("/concepts/odms/forms", "GET", {"Library.Read"}), - ("/concepts/odms/forms/headers", "GET", {"Library.Read"}), - ("/concepts/odms/forms/{odm_form_uid}", "GET", {"Library.Read"}), - ("/concepts/odms/forms/{odm_form_uid}/relationships", "GET", {"Library.Read"}), - ("/concepts/odms/forms/{odm_form_uid}/versions", "GET", {"Library.Read"}), - ("/concepts/odms/forms", "POST", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}", "PATCH", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}/versions", "POST", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}/approvals", "POST", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}/activations", "DELETE", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}/activations", "POST", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}/item-groups", "POST", {"Library.Write"}), - ("/concepts/odms/forms/{odm_form_uid}", "DELETE", {"Library.Write"}), - ("/concepts/odms/forms/study-events", "GET", {"Library.Read"}), - ("/concepts/odms/item-groups", "GET", {"Library.Read"}), - ("/concepts/odms/item-groups/headers", "GET", {"Library.Read"}), - ("/concepts/odms/item-groups/forms", "GET", {"Library.Read"}), - ("/concepts/odms/item-groups/{odm_item_group_uid}", "GET", {"Library.Read"}), + ("/data-completeness-tags", "GET", {"Admin.Read"}), + ("/data-completeness-tags", "POST", {"Admin.Write"}), + ("/data-completeness-tags/{uid}", "PUT", {"Admin.Write"}), + ("/data-completeness-tags/{uid}", "DELETE", {"Admin.Write"}), + ("/studies/{study_uid}/data-completeness-tags", "GET", {"Admin.Read"}), + ("/studies/{study_uid}/data-completeness-tags", "POST", {"Admin.Write"}), + ("/studies/{study_uid}/data-completeness-tags/{uid}", "DELETE", {"Admin.Write"}), + ("/odms/forms", "GET", {"Library.Read"}), + ("/odms/forms/headers", "GET", {"Library.Read"}), + ("/odms/forms/{odm_form_uid}", "GET", {"Library.Read"}), + ("/odms/forms/{odm_form_uid}/relationships", "GET", {"Library.Read"}), + ("/odms/forms/{odm_form_uid}/versions", "GET", {"Library.Read"}), + ("/odms/forms", "POST", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}", "PATCH", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}/versions", "POST", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}/approvals", "POST", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}/activations", "DELETE", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}/activations", "POST", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}/item-groups", "POST", {"Library.Write"}), + ("/odms/forms/{odm_form_uid}", "DELETE", {"Library.Write"}), + ("/odms/forms/study-events", "GET", {"Library.Read"}), + ("/odms/item-groups", "GET", {"Library.Read"}), + ("/odms/item-groups/headers", "GET", {"Library.Read"}), + ("/odms/item-groups/forms", "GET", {"Library.Read"}), + ("/odms/item-groups/{odm_item_group_uid}", "GET", {"Library.Read"}), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/relationships", + "/odms/item-groups/{odm_item_group_uid}/relationships", "GET", {"Library.Read"}, ), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/versions", + "/odms/item-groups/{odm_item_group_uid}/versions", "GET", {"Library.Read"}, ), - ("/concepts/odms/item-groups", "POST", {"Library.Write"}), - ("/concepts/odms/item-groups/{odm_item_group_uid}", "PATCH", {"Library.Write"}), + ("/odms/item-groups", "POST", {"Library.Write"}), + ("/odms/item-groups/{odm_item_group_uid}", "PATCH", {"Library.Write"}), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/versions", + "/odms/item-groups/{odm_item_group_uid}/versions", "POST", {"Library.Write"}, ), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/approvals", + "/odms/item-groups/{odm_item_group_uid}/approvals", "POST", {"Library.Write"}, ), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/activations", + "/odms/item-groups/{odm_item_group_uid}/activations", "DELETE", {"Library.Write"}, ), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/activations", + "/odms/item-groups/{odm_item_group_uid}/activations", "POST", {"Library.Write"}, ), ( - "/concepts/odms/item-groups/{odm_item_group_uid}/items", + "/odms/item-groups/{odm_item_group_uid}/items", "POST", {"Library.Write"}, ), - ("/concepts/odms/item-groups/{odm_item_group_uid}", "DELETE", {"Library.Write"}), - ("/concepts/odms/items", "GET", {"Library.Read"}), - ("/concepts/odms/items/headers", "GET", {"Library.Read"}), - ("/concepts/odms/items/item-groups", "GET", {"Library.Read"}), - ("/concepts/odms/items/{odm_item_uid}", "GET", {"Library.Read"}), - ("/concepts/odms/items/{odm_item_uid}/relationships", "GET", {"Library.Read"}), - ("/concepts/odms/items/{odm_item_uid}/versions", "GET", {"Library.Read"}), - ("/concepts/odms/items", "POST", {"Library.Write"}), - ("/concepts/odms/items/{odm_item_uid}", "PATCH", {"Library.Write"}), - ("/concepts/odms/items/{odm_item_uid}/versions", "POST", {"Library.Write"}), - ("/concepts/odms/items/{odm_item_uid}/approvals", "POST", {"Library.Write"}), - ("/concepts/odms/items/{odm_item_uid}/activations", "DELETE", {"Library.Write"}), - ("/concepts/odms/items/{odm_item_uid}/activations", "POST", {"Library.Write"}), - ("/concepts/odms/items/{odm_item_uid}", "DELETE", {"Library.Write"}), - ("/concepts/odms/conditions", "GET", {"Library.Read"}), - ("/concepts/odms/conditions/headers", "GET", {"Library.Read"}), - ("/concepts/odms/conditions/{odm_condition_uid}", "GET", {"Library.Read"}), + ("/odms/item-groups/{odm_item_group_uid}", "DELETE", {"Library.Write"}), + ("/odms/items", "GET", {"Library.Read"}), + ("/odms/items/headers", "GET", {"Library.Read"}), + ("/odms/items/item-groups", "GET", {"Library.Read"}), + ("/odms/items/{odm_item_uid}", "GET", {"Library.Read"}), + ("/odms/items/{odm_item_uid}/relationships", "GET", {"Library.Read"}), + ("/odms/items/{odm_item_uid}/versions", "GET", {"Library.Read"}), + ("/odms/items", "POST", {"Library.Write"}), + ("/odms/items/{odm_item_uid}", "PATCH", {"Library.Write"}), + ("/odms/items/{odm_item_uid}/versions", "POST", {"Library.Write"}), + ("/odms/items/{odm_item_uid}/approvals", "POST", {"Library.Write"}), + ("/odms/items/{odm_item_uid}/activations", "DELETE", {"Library.Write"}), + ("/odms/items/{odm_item_uid}/activations", "POST", {"Library.Write"}), + ("/odms/items/{odm_item_uid}", "DELETE", {"Library.Write"}), + ("/odms/conditions", "GET", {"Library.Read"}), + ("/odms/conditions/headers", "GET", {"Library.Read"}), + ("/odms/conditions/{odm_condition_uid}", "GET", {"Library.Read"}), ( - "/concepts/odms/conditions/{odm_condition_uid}/relationships", + "/odms/conditions/{odm_condition_uid}/relationships", "GET", {"Library.Read"}, ), - ("/concepts/odms/conditions/{odm_condition_uid}/versions", "GET", {"Library.Read"}), - ("/concepts/odms/conditions", "POST", {"Library.Write"}), - ("/concepts/odms/conditions/{odm_condition_uid}", "PATCH", {"Library.Write"}), + ("/odms/conditions/{odm_condition_uid}/versions", "GET", {"Library.Read"}), + ("/odms/conditions", "POST", {"Library.Write"}), + ("/odms/conditions/{odm_condition_uid}", "PATCH", {"Library.Write"}), ( - "/concepts/odms/conditions/{odm_condition_uid}/versions", + "/odms/conditions/{odm_condition_uid}/versions", "POST", {"Library.Write"}, ), ( - "/concepts/odms/conditions/{odm_condition_uid}/approvals", + "/odms/conditions/{odm_condition_uid}/approvals", "POST", {"Library.Write"}, ), ( - "/concepts/odms/conditions/{odm_condition_uid}/activations", + "/odms/conditions/{odm_condition_uid}/activations", "DELETE", {"Library.Write"}, ), ( - "/concepts/odms/conditions/{odm_condition_uid}/activations", + "/odms/conditions/{odm_condition_uid}/activations", "POST", {"Library.Write"}, ), - ("/concepts/odms/conditions/{odm_condition_uid}", "DELETE", {"Library.Write"}), - ("/concepts/odms/methods", "GET", {"Library.Read"}), - ("/concepts/odms/methods/headers", "GET", {"Library.Read"}), - ("/concepts/odms/methods/{odm_method_uid}", "GET", {"Library.Read"}), - ("/concepts/odms/methods/{odm_method_uid}/relationships", "GET", {"Library.Read"}), - ("/concepts/odms/methods/{odm_method_uid}/versions", "GET", {"Library.Read"}), - ("/concepts/odms/methods", "POST", {"Library.Write"}), - ("/concepts/odms/methods/{odm_method_uid}", "PATCH", {"Library.Write"}), - ("/concepts/odms/methods/{odm_method_uid}/versions", "POST", {"Library.Write"}), - ("/concepts/odms/methods/{odm_method_uid}/approvals", "POST", {"Library.Write"}), + ("/odms/conditions/{odm_condition_uid}", "DELETE", {"Library.Write"}), + ("/odms/methods", "GET", {"Library.Read"}), + ("/odms/methods/headers", "GET", {"Library.Read"}), + ("/odms/methods/{odm_method_uid}", "GET", {"Library.Read"}), + ("/odms/methods/{odm_method_uid}/relationships", "GET", {"Library.Read"}), + ("/odms/methods/{odm_method_uid}/versions", "GET", {"Library.Read"}), + ("/odms/methods", "POST", {"Library.Write"}), + ("/odms/methods/{odm_method_uid}", "PATCH", {"Library.Write"}), + ("/odms/methods/{odm_method_uid}/versions", "POST", {"Library.Write"}), + ("/odms/methods/{odm_method_uid}/approvals", "POST", {"Library.Write"}), ( - "/concepts/odms/methods/{odm_method_uid}/activations", + "/odms/methods/{odm_method_uid}/activations", "DELETE", {"Library.Write"}, ), - ("/concepts/odms/methods/{odm_method_uid}/activations", "POST", {"Library.Write"}), - ("/concepts/odms/methods/{odm_method_uid}", "DELETE", {"Library.Write"}), - ("/concepts/odms/vendor-namespaces", "GET", {"Library.Read"}), - ("/concepts/odms/vendor-namespaces/headers", "GET", {"Library.Read"}), + ("/odms/methods/{odm_method_uid}/activations", "POST", {"Library.Write"}), + ("/odms/methods/{odm_method_uid}", "DELETE", {"Library.Write"}), + ("/odms/vendor-namespaces", "GET", {"Library.Read"}), + ("/odms/vendor-namespaces/headers", "GET", {"Library.Read"}), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}", "GET", {"Library.Read"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/relationships", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/relationships", "GET", {"Library.Read"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/versions", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/versions", "GET", {"Admin.Read"}, ), - ("/concepts/odms/vendor-namespaces", "POST", {"Admin.Write"}), + ("/odms/vendor-namespaces", "POST", {"Admin.Write"}), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}", "PATCH", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/versions", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/versions", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/approvals", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/approvals", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/activations", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/activations", "DELETE", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/activations", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/activations", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}", + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}", "DELETE", {"Admin.Write"}, ), - ("/concepts/odms/vendor-attributes", "GET", {"Library.Read"}), - ("/concepts/odms/vendor-attributes/headers", "GET", {"Library.Read"}), + ("/odms/vendor-attributes", "GET", {"Library.Read"}), + ("/odms/vendor-attributes/headers", "GET", {"Library.Read"}), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}", "GET", {"Library.Read"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/relationships", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/relationships", "GET", {"Library.Read"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/versions", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/versions", "GET", {"Admin.Read"}, ), - ("/concepts/odms/vendor-attributes", "POST", {"Admin.Write"}), + ("/odms/vendor-attributes", "POST", {"Admin.Write"}), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}", "PATCH", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/versions", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/versions", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/approvals", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/approvals", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/activations", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/activations", "DELETE", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/activations", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/activations", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}", + "/odms/vendor-attributes/{odm_vendor_attribute_uid}", "DELETE", {"Admin.Write"}, ), - ("/concepts/odms/vendor-elements", "GET", {"Library.Read"}), - ("/concepts/odms/vendor-elements/headers", "GET", {"Library.Read"}), + ("/odms/vendor-elements", "GET", {"Library.Read"}), + ("/odms/vendor-elements/headers", "GET", {"Library.Read"}), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}", + "/odms/vendor-elements/{odm_vendor_element_uid}", "GET", {"Library.Read"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/relationships", + "/odms/vendor-elements/{odm_vendor_element_uid}/relationships", "GET", {"Library.Read"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/versions", + "/odms/vendor-elements/{odm_vendor_element_uid}/versions", "GET", {"Admin.Read"}, ), - ("/concepts/odms/vendor-elements", "POST", {"Admin.Write"}), + ("/odms/vendor-elements", "POST", {"Admin.Write"}), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}", + "/odms/vendor-elements/{odm_vendor_element_uid}", "PATCH", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/versions", + "/odms/vendor-elements/{odm_vendor_element_uid}/versions", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/approvals", + "/odms/vendor-elements/{odm_vendor_element_uid}/approvals", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/activations", + "/odms/vendor-elements/{odm_vendor_element_uid}/activations", "DELETE", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/activations", + "/odms/vendor-elements/{odm_vendor_element_uid}/activations", "POST", {"Admin.Write"}, ), ( - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}", + "/odms/vendor-elements/{odm_vendor_element_uid}", "DELETE", {"Admin.Write"}, ), - ("/concepts/odms/metadata/translated-texts", "GET", {"Library.Read"}), - ("/concepts/odms/metadata/aliases", "GET", {"Library.Read"}), - ("/concepts/odms/metadata/formal-expressions", "GET", {"Library.Read"}), - ("/concepts/odms/metadata/report", "POST", {"Library.Read"}), - ("/concepts/odms/metadata/xmls/export", "POST", {"Library.Read"}), - ("/concepts/odms/metadata/csvs/export", "POST", {"Library.Read"}), - ("/concepts/odms/metadata/xmls/import", "POST", {"Library.Write"}), - ("/concepts/odms/metadata/xmls/stylesheets", "GET", {"Library.Read"}), - ("/concepts/odms/metadata/xmls/stylesheets/{stylesheet}", "GET", {"Library.Read"}), - ("/concepts/odms/study-events", "GET", {"Library.Read"}), - ("/concepts/odms/study-events", "POST", {"Library.Write"}), - ("/concepts/odms/study-events/headers", "GET", {"Library.Read"}), - ("/concepts/odms/study-events/{odm_study_event_uid}", "GET", {"Library.Read"}), + ("/odms/metadata/translated-texts", "GET", {"Library.Read"}), + ("/odms/metadata/aliases", "GET", {"Library.Read"}), + ("/odms/metadata/formal-expressions", "GET", {"Library.Read"}), + ("/odms/metadata/report", "POST", {"Library.Read"}), + ("/odms/metadata/xmls/export", "POST", {"Library.Read"}), + ("/odms/metadata/csvs/export", "POST", {"Library.Read"}), + ("/odms/metadata/xmls/import", "POST", {"Library.Write"}), + ("/odms/metadata/xmls/stylesheets", "GET", {"Library.Read"}), + ("/odms/metadata/xmls/stylesheets/{stylesheet}", "GET", {"Library.Read"}), + ("/odms/study-events", "GET", {"Library.Read"}), + ("/odms/study-events", "POST", {"Library.Write"}), + ("/odms/study-events/headers", "GET", {"Library.Read"}), + ("/odms/study-events/{odm_study_event_uid}", "GET", {"Library.Read"}), ( - "/concepts/odms/study-events/{odm_study_event_uid}/relationships", + "/odms/study-events/{odm_study_event_uid}/relationships", "GET", {"Library.Read"}, ), - ("/concepts/odms/study-events/{odm_study_event_uid}", "DELETE", {"Library.Write"}), - ("/concepts/odms/study-events/{odm_study_event_uid}", "PATCH", {"Library.Write"}), + ("/odms/study-events/{odm_study_event_uid}", "DELETE", {"Library.Write"}), + ("/odms/study-events/{odm_study_event_uid}", "PATCH", {"Library.Write"}), ( - "/concepts/odms/study-events/{odm_study_event_uid}/approvals", + "/odms/study-events/{odm_study_event_uid}/approvals", "POST", {"Library.Write"}, ), ( - "/concepts/odms/study-events/{odm_study_event_uid}/activations", + "/odms/study-events/{odm_study_event_uid}/activations", "POST", {"Library.Write"}, ), ( - "/concepts/odms/study-events/{odm_study_event_uid}/activations", + "/odms/study-events/{odm_study_event_uid}/activations", "DELETE", {"Library.Write"}, ), ( - "/concepts/odms/study-events/{odm_study_event_uid}/forms", + "/odms/study-events/{odm_study_event_uid}/forms", "POST", {"Library.Write"}, ), ( - "/concepts/odms/study-events/{odm_study_event_uid}/versions", + "/odms/study-events/{odm_study_event_uid}/versions", "GET", {"Library.Read"}, ), ( - "/concepts/odms/study-events/{odm_study_event_uid}/versions", + "/odms/study-events/{odm_study_event_uid}/versions", "POST", {"Library.Write"}, ), 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 1646a67c..38744dde 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 @@ -32,6 +32,12 @@ IRRELEVANT_ROLES = ["Some, Fake", "Testing", ""] +ENDPOINTS_WITHOUT_ROLES = [ + ("/user-preferences", "GET"), + ("/user-preferences", "PATCH"), + ("/user-preferences/{preference_key}", "DELETE"), +] + @pytest.fixture(scope="session") def mock_jwks_service(): @@ -73,6 +79,8 @@ def test_endpoints_rbac_wrong_roles( required_roles, ): """Ensure that http request with access-token having wrong roles fails""" + if (path, method) in ENDPOINTS_WITHOUT_ROLES: + pytest.skip(f"Endpoint {method} {path} does not require any roles") ( path_parameters, @@ -147,6 +155,8 @@ def test_endpoints_rbac_correct_roles( required_roles, ): """Ensure that endpoint requires specific roles in the access-token""" + if (path, method) in ENDPOINTS_WITHOUT_ROLES: + pytest.skip(f"Endpoint {method} {path} does not require any roles") ( path_parameters, @@ -218,6 +228,8 @@ def test_endpoints_rbac_no_roles( required_roles, ): """Ensure that endpoint requires at least one role in the access-token""" + if (path, method) in ENDPOINTS_WITHOUT_ROLES: + pytest.skip(f"Endpoint {method} {path} does not require any roles") ( path_parameters, @@ -257,6 +269,7 @@ def test_endpoints_rbac_no_roles( response.status_code, response.content.decode("utf-8"), ) + _assert_insufficient_roles_error(required_roles, [], response) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/fixtures/database.py b/clinical-mdr-api/clinical_mdr_api/tests/fixtures/database.py index 5e285fa2..e9d05ab6 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/fixtures/database.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/fixtures/database.py @@ -7,7 +7,7 @@ import neo4j.exceptions import pytest -from neomodel.sync_.core import db +from neomodel import db from clinical_mdr_api.domain_repositories.models.controlled_terminology import ( CTCatalogue, 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 75cd7322..7d456a12 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 @@ -71,6 +71,7 @@ def test_data(): dataset_class = TestUtils.create_dataset_class( data_model_uid=data_model.uid, data_model_catalogue_name=data_model_catalogue, + data_model_name=data_model.name, ) _data_domain_terms = [ @@ -510,6 +511,7 @@ def test_edit_activity_instance_class(api_client): dataset_class_2 = TestUtils.create_dataset_class( data_model_uid=data_model.uid, data_model_catalogue_name=data_model_catalogue, + data_model_name=data_model.name, ) response = api_client.patch( f"/activity-instance-classes/{activity_instance_class.uid}/model-mappings", @@ -636,6 +638,7 @@ def test_get_activity_instance_class_datasets(api_client): dataset_class_for_parent = TestUtils.create_dataset_class( data_model_uid=data_model.uid, data_model_catalogue_name=data_model_catalogue, + data_model_name=data_model.name, ) dataset_for_parent = TestUtils.create_dataset( data_model_ig_uid=data_model_ig.uid, diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instances.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/biomedical_concepts/test_activity_instances.py index 7448b30d..7edf5aac 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 @@ -124,6 +124,12 @@ def test_data(): parent_uid="ActivityInstanceClass_000002", ), TestUtils.create_activity_instance_class(name="NumericFindings"), + TestUtils.create_activity_instance_class( + name="Activity instance class 4", + definition="def Activity instance class 4", + is_domain_specific=True, + level=4, + ), ] global activity_item_classes global data_type_term @@ -187,14 +193,31 @@ def test_data(): role_uid=role_term.term_uid, data_type_uid=data_type_term.term_uid, ), + TestUtils.create_activity_item_class( + name="Activity Item Class name4", + order=4, + activity_instance_classes=[ + { + "uid": activity_instance_classes[3].uid, + "mandatory": False, + "is_adam_param_specific_enabled": False, + "is_additional_optional": False, + "is_default_linked": False, + } + ], + role_uid=role_term.term_uid, + data_type_uid=data_type_term.term_uid, + ), ] global ct_terms - # global odm_form - # global odm_item_group - # global odm_item global codelist - codelist = TestUtils.create_ct_codelist(extensible=True, approve=True) + codelist = TestUtils.create_ct_codelist( + name="Codelist", + sponsor_preferred_name="Codelist", + extensible=True, + approve=True, + ) ct_terms = [ TestUtils.create_ct_term( codelist_uid=codelist.codelist_uid, @@ -241,6 +264,13 @@ def test_data(): "unit_definition_uids": [], "is_adam_param_specific": False, }, + { + "activity_item_class_uid": activity_item_classes[3].uid, + "ct_terms": [], + "ct_codelist_uid": codelist.codelist_uid, + "unit_definition_uids": [], + "is_adam_param_specific": False, + }, ] global activity_instances_all # Create some activity instances @@ -308,16 +338,17 @@ def test_data(): activity_items=[activity_items[0], activity_items[1]], ), ] - TestUtils.create_activity_instance( - activity_instance_class_uid=activity_instance_classes[0].uid, - nci_concept_id="C-ZZZ", - topic_code="topic code ZZZ", - is_required_for_activity=True, - activities=[activities[0].uid], - activity_subgroups=[activity_subgroup.uid], - activity_groups=[activity_group.uid], - activity_items=[activity_items[0], activity_items[1], activity_items[2]], - preview=True, + activity_instances_all.append( + TestUtils.create_activity_instance( + activity_instance_class_uid=activity_instance_classes[2].uid, + nci_concept_id="C-XYZ", + topic_code="topic code XYZ", + is_required_for_activity=True, + activities=[activities[0].uid], + activity_subgroups=[activity_subgroup.uid], + activity_groups=[activity_group.uid], + activity_items=[activity_items[3]], + ) ) for index in range(5): @@ -522,7 +553,7 @@ def test_get_activity_instances_pagination(api_client): pytest.param(3, 1, True, None, 3), pytest.param(3, 2, True, None, 3), pytest.param(10, 2, True, None, 10), - pytest.param(10, 3, True, None, 5), # Total number of data models is 25 + pytest.param(10, 3, True, None, 6), # Total number of data models is 26 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), @@ -1509,6 +1540,28 @@ def test_activity_instance_versioning(api_client): assert res["message"] == "Object has been accepted" +def test_activity_instance_with_codelist(api_client): + response = api_client.get( + f"/concepts/activities/activity-instances/{activity_instances_all[5].uid}", + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["activity_items"][0]["ct_codelist"] == { + "uid": codelist.codelist_uid, + "name": codelist.name, + } + + response = api_client.get( + f"""/concepts/activities/activity-instances?filters={{"uid": {{"v": ["{activity_instances_all[5].uid}"]}}}}""", + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["items"][0]["activity_items"][0]["ct_codelist"] == { + "uid": codelist.codelist_uid, + "name": codelist.name, + } + + def test_activity_instance_overview(api_client): response = api_client.get( f"/concepts/activities/activity-instances/{activity_instances_all[3].uid}/overview", @@ -2662,3 +2715,46 @@ def test_level_3_activity_instance_with_parent_mandatory_item_success(api_client assert res["name"] == "level 3 instance with parent mandatory" assert res["activity_instance_class"]["uid"] == activity_instance_classes[2].uid assert len(res["activity_items"]) == 2 + + +def test_cannot_provide_ct_terms_and_ct_codelist(api_client): + response = api_client.post( + "/concepts/activities/activity-instances", + json={ + "name": "cannot provide both ct terms and ct codelist", + "name_sentence_case": "cannot provide both ct terms and 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[2].uid, + "activity_items": [ + { + "activity_item_class_uid": activity_item_classes[2].uid, + "ct_codelist_uid": codelist.codelist_uid, + "ct_terms": [ + { + "term_uid": ct_terms[0].term_uid, + "codelist_uid": codelist.codelist_uid, + } + ], + "unit_definition_uids": [], + "is_adam_param_specific": False, + }, + ], + "strict_mode": True, + "library_name": "Sponsor", + }, + ) + assert_response_status_code(response, 400) + res = response.json() + assert res["type"] == "RequestValidationError" + assert res["details"][0] == { + "error_code": "value_error", + "field": ["body", "activity_items", 0], + "msg": "Value error, Both ct_terms and ct_codelist cannot be provided at the same time for an ActivityItem.", + "ctx": {"error": {}}, + } 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 53dffeec..b0784483 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 @@ -115,6 +115,7 @@ def test_data(): dataset_class = TestUtils.create_dataset_class( data_model_uid=data_model.uid, data_model_catalogue_name=data_model_catalogue_name, + data_model_name=data_model.name, ) variable_class = TestUtils.create_variable_class( dataset_class_uid=dataset_class.uid, diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/concepts/test_pharmaceutical_products.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/concepts/test_pharmaceutical_products.py index 95ab421d..6bd6f155 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/concepts/test_pharmaceutical_products.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/concepts/test_pharmaceutical_products.py @@ -210,6 +210,7 @@ def test_data(): PHARMACEUTICAL_PRODUCT_FIELDS_ALL = [ "uid", + "derived_name", "library_name", "start_date", "end_date", @@ -226,6 +227,7 @@ def test_data(): PHARMACEUTICAL_PRODUCT_FIELDS_NOT_NULL = [ "uid", + "derived_name", "start_date", "library_name", "dosage_forms", @@ -249,6 +251,9 @@ def test_get_pharmaceutical_product(api_client): assert res["uid"] == pharmaceutical_products_all[0].uid assert res["external_id"] == "external_id_a" + # derived_name should contain ingredient names with formulation names and strengths + assert "inn A formulation-name-a (5 mg/mL)" in res["derived_name"] + assert "formulation-name-b (5 mg/mL)" in res["derived_name"] assert res["routes_of_administration"][0]["term_uid"] == ct_term_roa.term_uid assert ( res["routes_of_administration"][0]["term_name"] @@ -289,6 +294,41 @@ def test_get_pharmaceutical_product(api_client): TestUtils.assert_timestamp_is_newer_than(res["start_date"], 60) +def test_get_pharmaceutical_product_derived_name_without_formulations(api_client): + """Products without formulations should have an empty derived_name.""" + response = api_client.get( + f"/concepts/pharmaceutical-products/{pharmaceutical_products_all[2].uid}" + ) + res = response.json() + assert_response_status_code(response, 200) + assert res["derived_name"] == "" + + +def test_get_pharmaceutical_product_derived_name_fallback(api_client): + """derived_name should use the active substance inn when available.""" + as_with_known_inn = TestUtils.create_active_substance( + inn="test-known-inn", + ) + formulation = { + "external_id": "formulation-derived-test", + "ingredients": [ + { + "active_substance_uid": as_with_known_inn.uid, + "strength_uid": strength.uid, + }, + ], + } + pp = TestUtils.create_pharmaceutical_product(formulations=[formulation]) + response = api_client.get(f"/concepts/pharmaceutical-products/{pp.uid}") + res = response.json() + assert_response_status_code(response, 200) + assert "test-known-inn" in res["derived_name"] + assert "(5 mg/mL)" in res["derived_name"] + + # Cleanup + api_client.delete(f"/concepts/pharmaceutical-products/{pp.uid}") + + def test_get_pharmaceutical_products_versions(api_client): response = api_client.get( "/concepts/pharmaceutical-products/versions?total_count=true" @@ -711,6 +751,79 @@ def test_get_pharmaceutical_products( assert result_vals == result_vals_sorted_locally +@pytest.mark.parametrize( + "sort_by", + [ + pytest.param('{"dosage_form": true}'), + pytest.param('{"dosage_form": false}'), + pytest.param('{"dosage_forms": true}'), + pytest.param('{"route_of_administration": true}'), + pytest.param('{"route_of_administration": false}'), + pytest.param('{"routes_of_administration": true}'), + pytest.param('{"derived_name": true}'), + pytest.param('{"derived_name": false}'), + ], +) +def test_get_pharmaceutical_products_sort_by_related_fields(api_client, sort_by): + """Sorting by dosage_form, route_of_administration, and derived_name should not error.""" + url = f"/concepts/pharmaceutical-products?page_number=1&page_size=10&total_count=true&sort_by={sort_by}" + response = api_client.get(url) + res = response.json() + + assert_response_status_code(response, 200) + assert len(res["items"]) == 10 + assert res["total"] == len(pharmaceutical_products_all) + + +@pytest.mark.parametrize( + "sort_by, sort_field, response_key", + [ + pytest.param('{"derived_name": true}', "derived_name", "derived_name"), + pytest.param('{"derived_name": false}', "derived_name", "derived_name"), + pytest.param('{"dosage_form": true}', "dosage_form", "dosage_forms"), + pytest.param('{"dosage_form": false}', "dosage_form", "dosage_forms"), + pytest.param( + '{"route_of_administration": true}', + "route_of_administration", + "routes_of_administration", + ), + pytest.param( + '{"route_of_administration": false}', + "route_of_administration", + "routes_of_administration", + ), + ], +) +def test_get_pharmaceutical_products_sort_by_related_field_order( + api_client, sort_by, sort_field, response_key +): + """Verify that sorting by related fields actually produces ordered results.""" + sort_by_dict = json.loads(sort_by) + ascending = sort_by_dict[sort_field] + + response = api_client.get( + f"/concepts/pharmaceutical-products?page_number=1&page_size=100&sort_by={sort_by}" + ) + res = response.json() + assert_response_status_code(response, 200) + + # Build comparable sort values from response data + if response_key == "derived_name": + sort_values = [item[response_key] for item in res["items"]] + else: + # For list-of-term fields (dosage_forms, routes_of_administration), + # concatenate term names to mirror the _search_* Cypher alias. + sort_values = [ + " ".join(term["term_name"] or "" for term in (item[response_key] or [])) + for item in res["items"] + ] + + expected = sorted( + sort_values, key=lambda x: (x is None, x.lower()), reverse=not ascending + ) + assert sort_values == expected + + @pytest.mark.parametrize( "export_format", [ @@ -729,8 +842,12 @@ def test_get_pharmaceutical_products_csv_xml_excel(api_client, export_format): @pytest.mark.parametrize( "filter_by, expected_matched_field, expected_result_prefix", [ - pytest.param('{"*": {"v": ["aaa"]}}', "external_id", "external_id_AAA"), - pytest.param('{"*": {"v": ["bBb"]}}', "external_id", "external_id_BBB"), + pytest.param( + '{"*": {"v": ["external_id_aaa"]}}', "external_id", "external_id_AAA" + ), + pytest.param( + '{"*": {"v": ["external_id_bbb"]}}', "external_id", "external_id_BBB" + ), pytest.param( '{"*": {"v": ["unknown-user"], "op": "co"}}', "author_username", @@ -884,6 +1001,9 @@ def test_create_and_delete_pharmaceutical_product(api_client): assert res["version"] == "0.1" assert res["status"] == "Draft" assert list(res["possible_actions"]) == ["approve", "delete", "edit"] + # Verify derived_name for freshly created product + assert "inn A formulation-name-a (5 mg/mL)" in res["derived_name"] + assert "formulation-name-b (5 mg/mL)" in res["derived_name"] TestUtils.assert_timestamp_is_in_utc_zone(res["start_date"]) TestUtils.assert_timestamp_is_newer_than(res["start_date"], 60) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_codelist_fulltext_search.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_codelist_fulltext_search.py index f1a2a81e..f23ce5a1 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_codelist_fulltext_search.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/controlled_terminologies/test_codelist_fulltext_search.py @@ -38,21 +38,17 @@ def create_fulltext_indexes(): """Create the full-text indexes needed for the search endpoints""" # Index on CTCodelistNameValue and CTCodelistAttributesValue - db.cypher_query( - """ + db.cypher_query(""" CREATE FULLTEXT INDEX codelist_fulltext_index IF NOT EXISTS FOR (n:CTCodelistNameValue|CTCodelistAttributesValue) ON EACH [n.name, n.submission_value] - """ - ) + """) # Index on CTTermNameValue and CTTermAttributesValue - db.cypher_query( - """ + db.cypher_query(""" CREATE FULLTEXT INDEX term_fulltext_index IF NOT EXISTS FOR (n:CTTermNameValue|CTTermAttributesValue) ON EACH [n.name, n.submission_value] - """ - ) + """) # Wait for indexes to be online db.cypher_query("CALL db.awaitIndexes(300)") diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_metadata.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_metadata.py index 167c8cdb..f284b2aa 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_metadata.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_metadata.py @@ -10,7 +10,7 @@ from clinical_mdr_api.domains.enums import OdmTranslatedTextTypeEnum from clinical_mdr_api.main import app -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( +from clinical_mdr_api.models.odms.common_models import ( OdmAliasModel, OdmFormalExpressionModel, OdmTranslatedTextModel, @@ -88,7 +88,7 @@ def test_data(): def test_get_aliases( api_client, value: str, expected_result_prefix: dict[str, str], rs_length: int ): - response = api_client.get(f"/concepts/odms/metadata/aliases?search={value}") + response = api_client.get(f"/odms/metadata/aliases?search={value}") data = response.json() assert_response_status_code(response, 200) @@ -165,7 +165,7 @@ def test_get_aliases( def test_get_aliases_in_order( api_client, value: str, expected_order: dict[str, list[str]] ): - response = api_client.get(f"/concepts/odms/metadata/aliases?sort_by={value}") + response = api_client.get(f"/odms/metadata/aliases?sort_by={value}") data = response.json() assert_response_status_code(response, 200) @@ -191,9 +191,7 @@ def test_get_aliases_in_order( def test_get_translated_texts( api_client, value: str, expected_result_prefix: dict[str, str], rs_length: int ): - response = api_client.get( - f"/concepts/odms/metadata/translated-texts?search={value}" - ) + response = api_client.get(f"/odms/metadata/translated-texts?search={value}") data = response.json() assert_response_status_code(response, 200) @@ -282,9 +280,7 @@ def test_get_translated_texts( def test_get_translated_texts_in_order( api_client, value: str, expected_order: dict[str, list[str]] ): - response = api_client.get( - f"/concepts/odms/metadata/translated-texts?sort_by={value}" - ) + response = api_client.get(f"/odms/metadata/translated-texts?sort_by={value}") data = response.json() assert_response_status_code(response, 200) @@ -310,9 +306,7 @@ def test_get_translated_texts_in_order( def test_get_formal_expressions( api_client, value: str, expected_result_prefix: dict[str, str], rs_length: int ): - response = api_client.get( - f"/concepts/odms/metadata/formal-expressions?search={value}" - ) + response = api_client.get(f"/odms/metadata/formal-expressions?search={value}") data = response.json() assert_response_status_code(response, 200) @@ -389,9 +383,7 @@ def test_get_formal_expressions( def test_get_formal_expressions_in_order( api_client, value: str, expected_order: dict[str, list[str]] ): - response = api_client.get( - f"/concepts/odms/metadata/formal-expressions?sort_by={value}" - ) + response = api_client.get(f"/odms/metadata/formal-expressions?sort_by={value}") data = response.json() assert_response_status_code(response, 200) @@ -414,21 +406,21 @@ def test_doesnt_return_aliases_that_are_only_connected_to_deleted_odms(api_clien "translated_texts": [], "aliases": [{"context": "connected to be deleted", "name": "deleted"}], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) rs = response.json() - response = api_client.get("/concepts/odms/metadata/aliases?page_size=0") + response = api_client.get("/odms/metadata/aliases?page_size=0") assert_response_status_code(response, 200) data = response.json() assert any(item["context"] == "connected to be deleted" for item in data["items"]) assert data["total"] == 5 assert len(data["items"]) == 5 - response = api_client.delete(f"concepts/odms/forms/{rs["uid"]}") + response = api_client.delete(f"odms/forms/{rs["uid"]}") assert_response_status_code(response, 204) - response = api_client.get("/concepts/odms/metadata/aliases?page_size=0") + response = api_client.get("/odms/metadata/aliases?page_size=0") assert_response_status_code(response, 200) data = response.json() assert all(item["context"] != "connected to be deleted" for item in data["items"]) @@ -469,21 +461,21 @@ def test_doesnt_return_translated_texts_that_are_only_connected_to_deleted_odms( ], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) rs = response.json() - response = api_client.get("/concepts/odms/metadata/translated-texts?page_size=0") + response = api_client.get("/odms/metadata/translated-texts?page_size=0") assert_response_status_code(response, 200) data = response.json() assert any(item["text"] == "connected to be deleted" for item in data["items"]) assert data["total"] == 8 assert len(data["items"]) == 8 - response = api_client.delete(f"concepts/odms/forms/{rs["uid"]}") + response = api_client.delete(f"odms/forms/{rs["uid"]}") assert_response_status_code(response, 204) - response = api_client.get("/concepts/odms/metadata/translated-texts?page_size=0") + response = api_client.get("/odms/metadata/translated-texts?page_size=0") assert_response_status_code(response, 200) data = response.json() assert all(item["text"] != "connected to be deleted" for item in data["items"]) @@ -504,21 +496,21 @@ def test_doesnt_return_formal_expressions_that_are_only_connected_to_deleted_odm "translated_texts": [], "aliases": [], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 201) rs = response.json() - response = api_client.get("/concepts/odms/metadata/formal-expressions?page_size=0") + response = api_client.get("/odms/metadata/formal-expressions?page_size=0") assert_response_status_code(response, 200) data = response.json() assert any(item["context"] == "connected to be deleted" for item in data["items"]) assert data["total"] == 5 assert len(data["items"]) == 5 - response = api_client.delete(f"concepts/odms/conditions/{rs["uid"]}") + response = api_client.delete(f"odms/conditions/{rs["uid"]}") assert_response_status_code(response, 204) - response = api_client.get("/concepts/odms/metadata/formal-expressions?page_size=0") + response = api_client.get("/odms/metadata/formal-expressions?page_size=0") assert_response_status_code(response, 200) data = response.json() assert all(item["context"] != "connected to be deleted" for item in data["items"]) @@ -528,7 +520,7 @@ def test_doesnt_return_formal_expressions_that_are_only_connected_to_deleted_odm def test_doesnt_return_aliases_that_are_not_connected_to_latest_odms(api_client): response = api_client.post( - "concepts/odms/forms", + "odms/forms", json={ "library_name": "Sponsor", "name": "to be updated1", @@ -542,7 +534,7 @@ def test_doesnt_return_aliases_that_are_not_connected_to_latest_odms(api_client) assert_response_status_code(response, 201) rs = response.json() - response = api_client.get("/concepts/odms/metadata/aliases?page_size=0") + response = api_client.get("/odms/metadata/aliases?page_size=0") assert_response_status_code(response, 200) data = response.json() assert any(item["context"] == "connected to be renamed" for item in data["items"]) @@ -550,7 +542,7 @@ def test_doesnt_return_aliases_that_are_not_connected_to_latest_odms(api_client) assert len(data["items"]) == 5 response = api_client.patch( - f"concepts/odms/forms/{rs["uid"]}", + f"odms/forms/{rs["uid"]}", json={ "library_name": "Sponsor", "name": "to be updated1", @@ -567,7 +559,7 @@ def test_doesnt_return_aliases_that_are_not_connected_to_latest_odms(api_client) ) assert_response_status_code(response, 200) - response = api_client.get("/concepts/odms/metadata/aliases?page_size=0") + response = api_client.get("/odms/metadata/aliases?page_size=0") assert_response_status_code(response, 200) data = response.json() assert all(item["context"] != "connected to be renamed" for item in data["items"]) @@ -579,7 +571,7 @@ def test_doesnt_return_translated_texts_that_are_not_connected_to_latest_odms( api_client, ): response = api_client.post( - "concepts/odms/forms", + "odms/forms", json={ "library_name": "Sponsor", "name": "to be updated2", @@ -614,7 +606,7 @@ def test_doesnt_return_translated_texts_that_are_not_connected_to_latest_odms( assert_response_status_code(response, 201) rs = response.json() - response = api_client.get("/concepts/odms/metadata/translated-texts?page_size=0") + response = api_client.get("/odms/metadata/translated-texts?page_size=0") assert_response_status_code(response, 200) data = response.json() assert any(item["text"] == "connected to be renamed" for item in data["items"]) @@ -622,7 +614,7 @@ def test_doesnt_return_translated_texts_that_are_not_connected_to_latest_odms( assert len(data["items"]) == 8 response = api_client.patch( - f"concepts/odms/forms/{rs["uid"]}", + f"odms/forms/{rs["uid"]}", json={ "library_name": "Sponsor", "name": "to be updated2", @@ -660,7 +652,7 @@ def test_doesnt_return_translated_texts_that_are_not_connected_to_latest_odms( ) assert_response_status_code(response, 200) - response = api_client.get("/concepts/odms/metadata/translated-texts?page_size=0") + response = api_client.get("/odms/metadata/translated-texts?page_size=0") assert_response_status_code(response, 200) data = response.json() assert all(item["text"] != "connected to be renamed" for item in data["items"]) @@ -672,7 +664,7 @@ def test_doesnt_return_formal_expressions_that_are_not_connected_to_latest_odms( api_client, ): response = api_client.post( - "concepts/odms/conditions", + "odms/conditions", json={ "library_name": "Sponsor", "name": "to be renamed1", @@ -687,7 +679,7 @@ def test_doesnt_return_formal_expressions_that_are_not_connected_to_latest_odms( assert_response_status_code(response, 201) rs = response.json() - response = api_client.get("/concepts/odms/metadata/formal-expressions?page_size=0") + response = api_client.get("/odms/metadata/formal-expressions?page_size=0") assert_response_status_code(response, 200) data = response.json() assert any(item["context"] == "connected to be renamed" for item in data["items"]) @@ -695,7 +687,7 @@ def test_doesnt_return_formal_expressions_that_are_not_connected_to_latest_odms( assert len(data["items"]) == 5 response = api_client.patch( - f"concepts/odms/conditions/{rs["uid"]}", + f"odms/conditions/{rs["uid"]}", json={ "library_name": "Sponsor", "name": "to be renamed1", @@ -708,7 +700,7 @@ def test_doesnt_return_formal_expressions_that_are_not_connected_to_latest_odms( ) assert_response_status_code(response, 200) - response = api_client.get("/concepts/odms/metadata/formal-expressions?page_size=0") + response = api_client.get("/odms/metadata/formal-expressions?page_size=0") assert_response_status_code(response, 200) data = response.json() assert all(item["context"] != "connected to be renamed" for item in data["items"]) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_to_activity_instance_rel.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_to_activity_instance_rel.py index 7d7921e2..eeb8275b 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_to_activity_instance_rel.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/odms/test_odm_to_activity_instance_rel.py @@ -31,11 +31,11 @@ from clinical_mdr_api.models.concepts.activities.activity_sub_group import ( ActivitySubGroup, ) -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm -from clinical_mdr_api.models.concepts.odms.odm_item import OdmItem -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroup 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.models.odms.form import OdmForm +from clinical_mdr_api.models.odms.item import OdmItem +from clinical_mdr_api.models.odms.item_group import OdmItemGroup from clinical_mdr_api.tests.integration.utils.api import ( inject_and_clear_db, inject_base_data, @@ -277,7 +277,7 @@ def test_data(api_client): items.append(TestUtils.create_odm_item(name="Item 1", oid="I1", approve=False)) api_client.post( - f"concepts/odms/forms/{forms[0].uid}/item-groups", + f"odms/forms/{forms[0].uid}/item-groups", json=[ { "uid": item_groups[0].uid, @@ -291,7 +291,7 @@ def test_data(api_client): ) api_client.post( - f"concepts/odms/item-groups/{item_groups[0].uid}/items", + f"odms/item-groups/{item_groups[0].uid}/items", json=[ { "uid": items[0].uid, @@ -312,7 +312,7 @@ def test_data(api_client): def test_get_odm_item_without_activity_instance_relationship(api_client): - response = api_client.get(f"concepts/odms/items/{items[0].uid}") + response = api_client.get(f"odms/items/{items[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == items[0].uid @@ -322,7 +322,7 @@ def test_get_odm_item_without_activity_instance_relationship(api_client): def test_add_activity_instance_relationship_to_odm_item(api_client): response = api_client.patch( - f"concepts/odms/items/{items[0].uid}", + f"odms/items/{items[0].uid}", json={ "name": "name1", "oid": "oid1", @@ -382,7 +382,7 @@ def test_add_activity_instance_relationship_to_odm_item(api_client): def test_get_odm_item_with_activity_instance_relationship(api_client): - response = api_client.get(f"concepts/odms/items/{items[0].uid}") + response = api_client.get(f"odms/items/{items[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == items[0].uid @@ -416,7 +416,7 @@ def test_get_odm_item_with_activity_instance_relationship(api_client): def test_activity_instance_relationship_to_odm_item(api_client): response = api_client.patch( - f"concepts/odms/forms/{forms[0].uid}", + f"odms/forms/{forms[0].uid}", json={ "name": "name1", "oid": "oid1", @@ -435,7 +435,7 @@ def test_activity_instance_relationship_to_odm_item(api_client): def test_remove_activity_instance_relationship_from_odm_item(api_client): response = api_client.patch( - f"concepts/odms/items/{items[0].uid}", + f"odms/items/{items[0].uid}", json={ "name": "name1", "oid": "oid1", @@ -468,7 +468,7 @@ def test_remove_activity_instance_relationship_from_odm_item(api_client): def test_cannot_add_more_than_one_same_activity_instance_to_odm_item(api_client): response = api_client.patch( - f"concepts/odms/items/{items[0].uid}", + f"odms/items/{items[0].uid}", json={ "name": "name1", "oid": "oid1", 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 5819c09f..72c2fe8b 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 @@ -15,17 +15,13 @@ from fastapi.testclient import TestClient from clinical_mdr_api.main import app -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm -from clinical_mdr_api.models.concepts.odms.odm_item import OdmItem -from clinical_mdr_api.models.concepts.odms.odm_item_group import OdmItemGroup -from clinical_mdr_api.models.concepts.odms.odm_study_event import OdmStudyEvent -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( - OdmVendorAttribute, -) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import OdmVendorElement -from clinical_mdr_api.models.concepts.odms.odm_vendor_namespace import ( - OdmVendorNamespace, -) +from clinical_mdr_api.models.odms.form import OdmForm +from clinical_mdr_api.models.odms.item import OdmItem +from clinical_mdr_api.models.odms.item_group import OdmItemGroup +from clinical_mdr_api.models.odms.study_event import OdmStudyEvent +from clinical_mdr_api.models.odms.vendor_attribute import OdmVendorAttribute +from clinical_mdr_api.models.odms.vendor_element import OdmVendorElement +from clinical_mdr_api.models.odms.vendor_namespace import OdmVendorNamespace from clinical_mdr_api.tests.integration.utils.api import ( inject_and_clear_db, inject_base_data, @@ -44,7 +40,7 @@ vendor_elements: list[OdmVendorElement] vendor_attributes: list[OdmVendorAttribute] -URL = "concepts/odms" +URL = "odms" @pytest.fixture(scope="module") @@ -185,9 +181,7 @@ def test_add_odm_forms_to_odm_study_event(api_client): }, ] - response = api_client.post( - f"concepts/odms/study-events/{study_event.uid}/forms", json=data - ) + response = api_client.post(f"odms/study-events/{study_event.uid}/forms", json=data) assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmStudyEvent_000001" @@ -235,9 +229,7 @@ def test_add_odm_item_groups_odm_forms(api_client): }, ] - response = api_client.post( - f"concepts/odms/forms/{forms[0].uid}/item-groups", json=data - ) + response = api_client.post(f"odms/forms/{forms[0].uid}/item-groups", json=data) assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmForm_000001" @@ -266,9 +258,7 @@ def test_add_odm_item_groups_odm_forms(api_client): }, ] - response = api_client.post( - f"concepts/odms/forms/{forms[1].uid}/item-groups", json=data - ) + response = api_client.post(f"odms/forms/{forms[1].uid}/item-groups", json=data) assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmForm_000002" @@ -300,7 +290,7 @@ def test_add_odm_item_groups_odm_forms(api_client): def test_add_odm_items_to_odm_item_group(api_client): response = api_client.post( - f"concepts/odms/item-groups/{item_groups[0].uid}/items", + f"odms/item-groups/{item_groups[0].uid}/items", json=[ { "uid": items[0].uid, @@ -340,7 +330,7 @@ def test_add_odm_items_to_odm_item_group(api_client): ] response = api_client.post( - f"concepts/odms/item-groups/{item_groups[1].uid}/items", + f"odms/item-groups/{item_groups[1].uid}/items", json=[ { "uid": items[1].uid, @@ -381,9 +371,7 @@ def test_add_odm_items_to_odm_item_group(api_client): def test_approve_study_event_with_cascade_effect(api_client): - response = api_client.post( - f"concepts/odms/study-events/{study_event.uid}/approvals" - ) + response = api_client.post(f"odms/study-events/{study_event.uid}/approvals") assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmStudyEvent_000001" @@ -412,7 +400,7 @@ def test_approve_study_event_with_cascade_effect(api_client): }, ] - response = api_client.get(f"concepts/odms/study-events/{study_event.uid}") + response = api_client.get(f"odms/study-events/{study_event.uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmStudyEvent_000001" @@ -441,7 +429,7 @@ def test_approve_study_event_with_cascade_effect(api_client): }, ] - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmForm_000001" @@ -470,7 +458,7 @@ def test_approve_study_event_with_cascade_effect(api_client): }, ] - response = api_client.get(f"concepts/odms/forms/{forms[1].uid}") + response = api_client.get(f"odms/forms/{forms[1].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmForm_000002" @@ -499,7 +487,7 @@ def test_approve_study_event_with_cascade_effect(api_client): }, ] - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmItemGroup_000001" @@ -523,7 +511,7 @@ def test_approve_study_event_with_cascade_effect(api_client): }, ] - response = api_client.get(f"concepts/odms/item-groups/{item_groups[1].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[1].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmItemGroup_000002" @@ -551,14 +539,14 @@ def test_approve_study_event_with_cascade_effect(api_client): def test_perseverance_of_final_versions_relationship_between_item_group_and_item( api_client, ): - response = api_client.post(f"concepts/odms/items/{items[0].uid}/versions") + response = api_client.post(f"odms/items/{items[0].uid}/versions") assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmItem_000001" assert res["status"] == "Draft" assert res["version"] == "1.1" - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmItemGroup_000001" @@ -586,9 +574,7 @@ def test_perseverance_of_final_versions_relationship_between_item_group_and_item def test_perseverance_of_final_versions_relationship_between_form_and_item_group( api_client, ): - response = api_client.post( - f"concepts/odms/item-groups/{item_groups[0].uid}/versions" - ) + response = api_client.post(f"odms/item-groups/{item_groups[0].uid}/versions") assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmItemGroup_000001" @@ -612,7 +598,7 @@ def test_perseverance_of_final_versions_relationship_between_form_and_item_group }, ] - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmForm_000001" @@ -645,7 +631,7 @@ def test_perseverance_of_final_versions_relationship_between_form_and_item_group def test_perseverance_of_final_versions_relationship_between_study_event_and_form( api_client, ): - response = api_client.post(f"concepts/odms/forms/{forms[0].uid}/versions") + response = api_client.post(f"odms/forms/{forms[0].uid}/versions") assert_response_status_code(response, 201) res = response.json() assert res["uid"] == "OdmForm_000001" @@ -674,7 +660,7 @@ def test_perseverance_of_final_versions_relationship_between_study_event_and_for }, ] - response = api_client.get(f"concepts/odms/study-events/{study_event.uid}") + response = api_client.get(f"odms/study-events/{study_event.uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmStudyEvent_000001" @@ -705,7 +691,7 @@ def test_perseverance_of_final_versions_relationship_between_study_event_and_for def test_latest_perseverance_of_relationship_based_on_latest_versions(api_client): - response = api_client.get(f"concepts/odms/study-events/{study_event.uid}") + response = api_client.get(f"odms/study-events/{study_event.uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmStudyEvent_000001" @@ -734,7 +720,7 @@ def test_latest_perseverance_of_relationship_based_on_latest_versions(api_client }, ] - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmForm_000001" @@ -763,7 +749,7 @@ def test_latest_perseverance_of_relationship_based_on_latest_versions(api_client }, ] - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmItemGroup_000001" @@ -789,7 +775,7 @@ def test_latest_perseverance_of_relationship_based_on_latest_versions(api_client def test_latest_perseverance_of_relationship_based_on_specific_versions(api_client): - response = api_client.get(f"concepts/odms/study-events/{study_event.uid}") + response = api_client.get(f"odms/study-events/{study_event.uid}") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmStudyEvent_000001" @@ -818,7 +804,7 @@ def test_latest_perseverance_of_relationship_based_on_specific_versions(api_clie }, ] - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}?version=1.0") + response = api_client.get(f"odms/forms/{forms[0].uid}?version=1.0") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmForm_000001" @@ -847,9 +833,7 @@ def test_latest_perseverance_of_relationship_based_on_specific_versions(api_clie }, ] - response = api_client.get( - f"concepts/odms/item-groups/{item_groups[0].uid}?version=1.0" - ) + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}?version=1.0") assert_response_status_code(response, 200) res = response.json() assert res["uid"] == "OdmItemGroup_000001" @@ -876,7 +860,7 @@ def test_latest_perseverance_of_relationship_based_on_specific_versions(api_clie def test_add_odm_vendor_element_to_odm_form(api_client): response = api_client.patch( - f"concepts/odms/forms/{forms[0].uid}", + f"odms/forms/{forms[0].uid}", json={ "name": forms[0].name, "oid": forms[0].oid, @@ -896,7 +880,7 @@ def test_add_odm_vendor_element_to_odm_form(api_client): {"uid": "OdmVendorElement_000001", "name": "VEF", "value": "value1"} ] - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_elements"] == [ @@ -904,7 +888,7 @@ def test_add_odm_vendor_element_to_odm_form(api_client): ] response = api_client.patch( - "concepts/odms/vendor-elements/OdmVendorElement_000001", + "odms/vendor-elements/OdmVendorElement_000001", json={ "name": "VEFNew", "compatible_types": ["FormDef"], @@ -913,7 +897,7 @@ def test_add_odm_vendor_element_to_odm_form(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_elements"] == [ @@ -923,7 +907,7 @@ def test_add_odm_vendor_element_to_odm_form(api_client): def test_add_odm_vendor_element_to_odm_item_group(api_client): response = api_client.patch( - f"concepts/odms/item-groups/{item_groups[0].uid}", + f"odms/item-groups/{item_groups[0].uid}", json={ "name": item_groups[0].name, "oid": item_groups[0].oid, @@ -948,7 +932,7 @@ def test_add_odm_vendor_element_to_odm_item_group(api_client): {"uid": "OdmVendorElement_000002", "name": "VEIG", "value": "value1"} ] - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_elements"] == [ @@ -956,7 +940,7 @@ def test_add_odm_vendor_element_to_odm_item_group(api_client): ] response = api_client.patch( - "concepts/odms/vendor-elements/OdmVendorElement_000002", + "odms/vendor-elements/OdmVendorElement_000002", json={ "name": "VEIGNew", "compatible_types": ["ItemDef"], @@ -965,7 +949,7 @@ def test_add_odm_vendor_element_to_odm_item_group(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_elements"] == [ @@ -975,7 +959,7 @@ def test_add_odm_vendor_element_to_odm_item_group(api_client): def test_add_odm_vendor_element_to_odm_item(api_client): response = api_client.patch( - f"concepts/odms/items/{items[0].uid}", + f"odms/items/{items[0].uid}", json={ "name": items[0].name, "oid": items[0].oid, @@ -1004,7 +988,7 @@ def test_add_odm_vendor_element_to_odm_item(api_client): {"uid": "OdmVendorElement_000003", "name": "VEI", "value": "value1"} ] - response = api_client.get(f"concepts/odms/items/{items[0].uid}") + response = api_client.get(f"odms/items/{items[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_elements"] == [ @@ -1012,7 +996,7 @@ def test_add_odm_vendor_element_to_odm_item(api_client): ] response = api_client.patch( - "concepts/odms/vendor-elements/OdmVendorElement_000003", + "odms/vendor-elements/OdmVendorElement_000003", json={ "name": "VEINew", "compatible_types": ["ItemDef"], @@ -1021,7 +1005,7 @@ def test_add_odm_vendor_element_to_odm_item(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/items/{items[0].uid}") + response = api_client.get(f"odms/items/{items[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_elements"] == [ @@ -1031,7 +1015,7 @@ def test_add_odm_vendor_element_to_odm_item(api_client): def test_add_odm_vendor_attribute_to_odm_form(api_client): response = api_client.patch( - f"concepts/odms/forms/{forms[0].uid}", + f"odms/forms/{forms[0].uid}", json={ "name": forms[0].name, "oid": forms[0].oid, @@ -1058,7 +1042,7 @@ def test_add_odm_vendor_attribute_to_odm_form(api_client): } ] - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ @@ -1073,7 +1057,7 @@ def test_add_odm_vendor_attribute_to_odm_form(api_client): ] response = api_client.patch( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001", + "odms/vendor-attributes/OdmVendorAttribute_000001", json={ "name": "vAFNew", "compatible_types": ["FormDef"], @@ -1084,7 +1068,7 @@ def test_add_odm_vendor_attribute_to_odm_form(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/forms/{forms[0].uid}") + response = api_client.get(f"odms/forms/{forms[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ @@ -1101,7 +1085,7 @@ def test_add_odm_vendor_attribute_to_odm_form(api_client): def test_add_odm_vendor_attribute_to_odm_item_group(api_client): response = api_client.patch( - f"concepts/odms/item-groups/{item_groups[0].uid}", + f"odms/item-groups/{item_groups[0].uid}", json={ "name": item_groups[0].name, "oid": item_groups[0].oid, @@ -1133,7 +1117,7 @@ def test_add_odm_vendor_attribute_to_odm_item_group(api_client): } ] - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ @@ -1148,7 +1132,7 @@ def test_add_odm_vendor_attribute_to_odm_item_group(api_client): ] response = api_client.patch( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000002", + "odms/vendor-attributes/OdmVendorAttribute_000002", json={ "name": "vAIGNew", "compatible_types": ["ItemDef"], @@ -1159,7 +1143,7 @@ def test_add_odm_vendor_attribute_to_odm_item_group(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/item-groups/{item_groups[0].uid}") + response = api_client.get(f"odms/item-groups/{item_groups[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ @@ -1176,7 +1160,7 @@ def test_add_odm_vendor_attribute_to_odm_item_group(api_client): def test_add_odm_vendor_attribute_to_odm_item(api_client): response = api_client.patch( - f"concepts/odms/items/{items[0].uid}", + f"odms/items/{items[0].uid}", json={ "name": items[0].name, "oid": items[0].oid, @@ -1212,7 +1196,7 @@ def test_add_odm_vendor_attribute_to_odm_item(api_client): } ] - response = api_client.get(f"concepts/odms/items/{items[0].uid}") + response = api_client.get(f"odms/items/{items[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ @@ -1227,7 +1211,7 @@ def test_add_odm_vendor_attribute_to_odm_item(api_client): ] response = api_client.patch( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000003", + "odms/vendor-attributes/OdmVendorAttribute_000003", json={ "name": "vAINew", "compatible_types": ["ItemDef"], @@ -1238,7 +1222,7 @@ def test_add_odm_vendor_attribute_to_odm_item(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/items/{items[0].uid}") + response = api_client.get(f"odms/items/{items[0].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ @@ -1255,7 +1239,7 @@ def test_add_odm_vendor_attribute_to_odm_item(api_client): def test_odm_vendor_attribute_and_odm_vendor_element(api_client): response = api_client.patch( - f"concepts/odms/vendor-attributes/{vendor_attributes[3].uid}", + f"odms/vendor-attributes/{vendor_attributes[3].uid}", json={ "name": "vAENew", "data_type": "string", @@ -1267,7 +1251,7 @@ def test_odm_vendor_attribute_and_odm_vendor_element(api_client): ) assert_response_status_code(response, 200) - response = api_client.get(f"concepts/odms/vendor-elements/{vendor_elements[3].uid}") + response = api_client.get(f"odms/vendor-elements/{vendor_elements[3].uid}") assert_response_status_code(response, 200) res = response.json() assert res["vendor_attributes"] == [ diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions.py index 0e6b8b8d..5d637b17 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions.py @@ -29,7 +29,7 @@ def test_data(): def test_getting_empty_list_of_odm_conditions(api_client): - response = api_client.get("concepts/odms/conditions") + response = api_client.get("odms/conditions") assert_response_status_code(response, 200) @@ -88,7 +88,7 @@ def test_creating_a_new_odm_condition(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 201) @@ -153,7 +153,7 @@ def test_creating_a_new_odm_condition(api_client): def test_getting_non_empty_list_of_odm_conditions(api_client): - response = api_client.get("concepts/odms/conditions") + response = api_client.get("odms/conditions") assert_response_status_code(response, 200) @@ -218,7 +218,7 @@ def test_getting_non_empty_list_of_odm_conditions(api_client): def test_getting_possible_header_values_of_odm_conditions(api_client): - response = api_client.get("concepts/odms/conditions/headers?field_name=name") + response = api_client.get("odms/conditions/headers?field_name=name") assert_response_status_code(response, 200) @@ -228,7 +228,7 @@ def test_getting_possible_header_values_of_odm_conditions(api_client): def test_getting_a_specific_odm_condition(api_client): - response = api_client.get("concepts/odms/conditions/OdmCondition_000001") + response = api_client.get("odms/conditions/OdmCondition_000001") assert_response_status_code(response, 200) @@ -293,7 +293,7 @@ def test_getting_a_specific_odm_condition(api_client): def test_getting_versions_of_a_specific_odm_condition(api_client): - response = api_client.get("concepts/odms/conditions/OdmCondition_000001/versions") + response = api_client.get("odms/conditions/OdmCondition_000001/versions") assert_response_status_code(response, 200) @@ -408,9 +408,7 @@ def test_updating_an_existing_odm_condition(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.patch( - "concepts/odms/conditions/OdmCondition_000001", json=data - ) + response = api_client.patch("odms/conditions/OdmCondition_000001", json=data) assert_response_status_code(response, 200) @@ -475,9 +473,7 @@ def test_updating_an_existing_odm_condition(api_client): def test_getting_a_specific_odm_condition_in_specific_version(api_client): - response = api_client.get( - "concepts/odms/conditions/OdmCondition_000001?version=0.1" - ) + response = api_client.get("odms/conditions/OdmCondition_000001?version=0.1") assert_response_status_code(response, 200) @@ -542,7 +538,7 @@ def test_getting_a_specific_odm_condition_in_specific_version(api_client): def test_approving_an_odm_condition(api_client): - response = api_client.post("concepts/odms/conditions/OdmCondition_000001/approvals") + response = api_client.post("odms/conditions/OdmCondition_000001/approvals") assert_response_status_code(response, 201) @@ -607,9 +603,7 @@ def test_approving_an_odm_condition(api_client): def test_inactivating_a_specific_odm_condition(api_client): - response = api_client.delete( - "concepts/odms/conditions/OdmCondition_000001/activations" - ) + response = api_client.delete("odms/conditions/OdmCondition_000001/activations") assert_response_status_code(response, 200) @@ -674,9 +668,7 @@ def test_inactivating_a_specific_odm_condition(api_client): def test_reactivating_a_specific_odm_condition(api_client): - response = api_client.post( - "concepts/odms/conditions/OdmCondition_000001/activations" - ) + response = api_client.post("odms/conditions/OdmCondition_000001/activations") assert_response_status_code(response, 200) @@ -741,7 +733,7 @@ def test_reactivating_a_specific_odm_condition(api_client): def test_creating_a_new_odm_condition_version(api_client): - response = api_client.post("concepts/odms/conditions/OdmCondition_000001/versions") + response = api_client.post("odms/conditions/OdmCondition_000001/versions") assert_response_status_code(response, 201) @@ -820,7 +812,7 @@ def test_create_a_new_odm_condition_for_deleting_it(api_client): ], "aliases": [], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 201) @@ -848,7 +840,7 @@ def test_create_a_new_odm_condition_for_deleting_it(api_client): def test_deleting_a_specific_odm_condition(api_client): - response = api_client.delete("concepts/odms/conditions/OdmCondition_000002") + response = api_client.delete("odms/conditions/OdmCondition_000002") assert_response_status_code(response, 204) @@ -871,7 +863,7 @@ def test_creating_a_new_odm_condition_with_relations(api_client): ], "aliases": [], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 201) @@ -923,9 +915,7 @@ def test_updating_an_existing_odm_condition_with_relations(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.patch( - "concepts/odms/conditions/OdmCondition_000001", json=data - ) + response = api_client.patch("odms/conditions/OdmCondition_000001", json=data) assert_response_status_code(response, 200) @@ -959,9 +949,7 @@ def test_updating_an_existing_odm_condition_with_relations(api_client): def test_getting_uids_of_a_specific_odm_conditions_active_relationships(api_client): - response = api_client.get( - "concepts/odms/conditions/OdmCondition_000001/relationships" - ) + response = api_client.get("odms/conditions/OdmCondition_000001/relationships") assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions_negative.py index 4404f60d..aa7e5dd4 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_conditions_negative.py @@ -78,7 +78,7 @@ def test_create_a_new_odm_condition(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 201) @@ -192,7 +192,7 @@ def test_cannot_create_a_new_odm_condition_with_same_properties(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 409) @@ -220,7 +220,7 @@ def test_cannot_create_a_new_odm_condition_without_an_english_description(api_cl ], "aliases": [], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 400) @@ -234,7 +234,7 @@ def test_cannot_create_a_new_odm_condition_without_an_english_description(api_cl def test_getting_error_for_retrieving_non_existent_odm_condition(api_client): - response = api_client.get("concepts/odms/conditions/OdmCondition_000002") + response = api_client.get("odms/conditions/OdmCondition_000002") assert_response_status_code(response, 404) @@ -248,9 +248,7 @@ def test_getting_error_for_retrieving_non_existent_odm_condition(api_client): def test_cannot_inactivate_an_odm_condition_that_is_in_draft_status(api_client): - response = api_client.delete( - "concepts/odms/conditions/OdmCondition_000001/activations" - ) + response = api_client.delete("odms/conditions/OdmCondition_000001/activations") assert_response_status_code(response, 400) @@ -261,9 +259,7 @@ def test_cannot_inactivate_an_odm_condition_that_is_in_draft_status(api_client): def test_cannot_reactivate_an_odm_condition_that_is_not_retired(api_client): - response = api_client.post( - "concepts/odms/conditions/OdmCondition_000001/activations" - ) + response = api_client.post("odms/conditions/OdmCondition_000001/activations") assert_response_status_code(response, 400) @@ -299,7 +295,7 @@ def test_cannot_add_duplicate_translated_texts(api_client, text_type: str): ], "aliases": [], } - response = api_client.post("concepts/odms/conditions", json=data) + response = api_client.post("odms/conditions", json=data) assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_csv_exporter.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_csv_exporter.py index 3aeb9987..253010e7 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_csv_exporter.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_csv_exporter.py @@ -53,7 +53,7 @@ def test_data(): def test_get_odm_study_event(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=odm_study_event1&target_type=study_event", + "odms/metadata/csvs/export?target_uid=odm_study_event1&target_type=study_event", headers=HEADERS, ) @@ -67,7 +67,7 @@ def test_get_odm_study_event(api_client): def test_get_odm_form(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=odm_form1&target_type=form", + "odms/metadata/csvs/export?target_uid=odm_form1&target_type=form", headers=HEADERS, ) @@ -81,7 +81,7 @@ def test_get_odm_form(api_client): def test_get_odm_item_group(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=odm_item_group1&target_type=item_group", + "odms/metadata/csvs/export?target_uid=odm_item_group1&target_type=item_group", headers=HEADERS, ) @@ -95,7 +95,7 @@ def test_get_odm_item_group(api_client): def test_get_odm_item(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=odm_item1&target_type=item", + "odms/metadata/csvs/export?target_uid=odm_item1&target_type=item", headers=HEADERS, ) @@ -109,7 +109,7 @@ def test_get_odm_item(api_client): def test_odm_not_supported_target_type(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=wrong&target_type=study", + "odms/metadata/csvs/export?target_uid=wrong&target_type=study", headers=HEADERS, ) @@ -121,7 +121,7 @@ def test_odm_not_supported_target_type(api_client): def test_odm_study_event_not_found(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=wrong&target_type=study_event", + "odms/metadata/csvs/export?target_uid=wrong&target_type=study_event", headers=HEADERS, ) @@ -130,7 +130,7 @@ def test_odm_study_event_not_found(api_client): def test_odm_form_not_found(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=wrong&target_type=form", + "odms/metadata/csvs/export?target_uid=wrong&target_type=form", headers=HEADERS, ) @@ -139,7 +139,7 @@ def test_odm_form_not_found(api_client): def test_odm_item_group_not_found(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=wrong&target_type=item_group", + "odms/metadata/csvs/export?target_uid=wrong&target_type=item_group", headers=HEADERS, ) @@ -148,7 +148,7 @@ def test_odm_item_group_not_found(api_client): def test_odm_item_not_found(api_client): response = api_client.post( - "concepts/odms/metadata/csvs/export?target_uid=wrong&target_type=item", + "odms/metadata/csvs/export?target_uid=wrong&target_type=item", headers=HEADERS, ) 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 29db09bd..56514d92 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 @@ -39,7 +39,7 @@ def test_data(): def test_getting_empty_list_of_odm_forms(api_client): - response = api_client.get("concepts/odms/forms") + response = api_client.get("odms/forms") assert_response_status_code(response, 200) @@ -104,7 +104,7 @@ def test_creating_a_new_odm_form(api_client): ], "vendor_attributes": [{"uid": "odm_vendor_attribute4", "value": "value"}], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) @@ -192,7 +192,7 @@ def test_creating_a_new_odm_form(api_client): def test_getting_non_empty_list_of_odm_forms(api_client): - response = api_client.get("concepts/odms/forms") + response = api_client.get("odms/forms") assert_response_status_code(response, 200) @@ -280,7 +280,7 @@ def test_getting_non_empty_list_of_odm_forms(api_client): def test_getting_possible_header_values_of_odm_forms(api_client): - response = api_client.get("concepts/odms/forms/headers?field_name=name") + response = api_client.get("odms/forms/headers?field_name=name") assert_response_status_code(response, 200) @@ -290,7 +290,7 @@ def test_getting_possible_header_values_of_odm_forms(api_client): def test_getting_a_specific_odm_form(api_client): - response = api_client.get("concepts/odms/forms/OdmForm_000001") + response = api_client.get("odms/forms/OdmForm_000001") assert_response_status_code(response, 200) @@ -377,7 +377,7 @@ def test_getting_a_specific_odm_form(api_client): def test_getting_versions_of_a_specific_odm_form(api_client): - response = api_client.get("concepts/odms/forms/OdmForm_000001/versions") + response = api_client.get("odms/forms/OdmForm_000001/versions") assert_response_status_code(response, 200) @@ -525,7 +525,7 @@ def test_updating_an_existing_odm_form(api_client): {"uid": "odm_vendor_attribute3", "value": "value"}, ], } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 200) @@ -613,7 +613,7 @@ def test_updating_an_existing_odm_form(api_client): def test_getting_a_specific_odm_form_in_specific_version(api_client): - response = api_client.get("concepts/odms/forms/OdmForm_000001?version=0.1") + response = api_client.get("odms/forms/OdmForm_000001?version=0.1") assert_response_status_code(response, 200) @@ -691,9 +691,7 @@ def test_adding_odm_item_groups_to_a_specific_odm_form(api_client): "vendor": {"attributes": [{"uid": "odm_vendor_attribute3", "value": "No"}]}, } ] - response = api_client.post( - "concepts/odms/forms/OdmForm_000001/item-groups", json=data - ) + response = api_client.post("odms/forms/OdmForm_000001/item-groups", json=data) assert_response_status_code(response, 201) @@ -814,7 +812,7 @@ def test_overriding_odm_item_groups_from_a_specific_odm_form(api_client): } ] response = api_client.post( - "concepts/odms/forms/OdmForm_000001/item-groups?override=true", json=data + "odms/forms/OdmForm_000001/item-groups?override=true", json=data ) assert_response_status_code(response, 201) @@ -981,7 +979,7 @@ def test_managing_odm_vendors_of_a_specific_odm_form(api_client): ], "vendor_attributes": [{"uid": "odm_vendor_attribute4", "value": "value"}], } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 200) @@ -1091,7 +1089,7 @@ def test_managing_odm_vendors_of_a_specific_odm_form(api_client): def test_approving_an_odm_form(api_client): - response = api_client.post("concepts/odms/forms/OdmForm_000001/approvals") + response = api_client.post("odms/forms/OdmForm_000001/approvals") assert_response_status_code(response, 201) @@ -1201,7 +1199,7 @@ def test_approving_an_odm_form(api_client): def test_inactivating_a_specific_odm_form(api_client): - response = api_client.delete("concepts/odms/forms/OdmForm_000001/activations") + response = api_client.delete("odms/forms/OdmForm_000001/activations") assert_response_status_code(response, 200) @@ -1311,7 +1309,7 @@ def test_inactivating_a_specific_odm_form(api_client): def test_reactivating_a_specific_odm_form(api_client): - response = api_client.post("concepts/odms/forms/OdmForm_000001/activations") + response = api_client.post("odms/forms/OdmForm_000001/activations") assert_response_status_code(response, 200) @@ -1421,7 +1419,7 @@ def test_reactivating_a_specific_odm_form(api_client): def test_creating_a_new_odm_form_version(api_client): - response = api_client.post("concepts/odms/forms/OdmForm_000001/versions") + response = api_client.post("odms/forms/OdmForm_000001/versions") assert_response_status_code(response, 201) @@ -1546,7 +1544,7 @@ def test_create_a_new_odm_form_for_deleting_it(api_client): ], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) @@ -1579,7 +1577,7 @@ def test_create_a_new_odm_form_for_deleting_it(api_client): def test_deleting_a_specific_odm_form(api_client): - response = api_client.delete("concepts/odms/forms/OdmForm_000002") + response = api_client.delete("odms/forms/OdmForm_000002") assert_response_status_code(response, 204) @@ -1611,7 +1609,7 @@ def test_creating_a_new_odm_form_with_relations(api_client): ], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) @@ -1691,7 +1689,7 @@ def test_updating_an_existing_odm_form_with_relations(api_client): {"uid": "odm_vendor_attribute3", "value": "value"}, ], } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 200) @@ -1785,7 +1783,7 @@ def test_create_a_new_odm_study_event_with_relation_to_odm_form(api_client): "retired_date": "2022-04-21", "description": "description1", } - response = api_client.post("concepts/odms/study-events", json=data) + response = api_client.post("odms/study-events", json=data) assert_response_status_code(response, 201) @@ -1819,7 +1817,7 @@ def test_add_the_odm_form_to_the_odm_study_event(api_client): } ] response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/forms", json=data + "odms/study-events/OdmStudyEvent_000001/forms", json=data ) assert_response_status_code(response, 201) @@ -1855,7 +1853,7 @@ def test_add_the_odm_form_to_the_odm_study_event(api_client): def test_getting_uids_of_a_specific_odm_forms_active_relationships(api_client): - response = api_client.get("concepts/odms/forms/OdmForm_000001/relationships") + response = api_client.get("odms/forms/OdmForm_000001/relationships") assert_response_status_code(response, 200) @@ -1865,7 +1863,7 @@ def test_getting_uids_of_a_specific_odm_forms_active_relationships(api_client): def test_getting_all_odm_forms_that_belongs_to_an_odm_study_event(api_client): - response = api_client.get("concepts/odms/forms/study-events") + response = api_client.get("odms/forms/study-events") assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms_negative.py index d52833a8..848940d5 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_forms_negative.py @@ -89,7 +89,7 @@ def test_create_a_new_odm_form(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) @@ -213,7 +213,7 @@ def test_cannot_add_odm_vendor_attribute_with_an_invalid_value_to_an_odm_form( "vendor_attributes": [{"uid": "odm_vendor_attribute3", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -285,7 +285,7 @@ def test_cannot_add_odm_vendor_element_attribute_with_an_invalid_value_to_an_odm "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -357,7 +357,7 @@ def test_add_odm_vendor_element_to_an_odm_form(api_client): "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 200) @@ -486,7 +486,7 @@ def test_cannot_create_a_new_odm_form_with_same_properties(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 409) @@ -515,7 +515,7 @@ def test_cannot_create_a_new_odm_form_without_an_english_description(api_client) ], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 400) @@ -529,7 +529,7 @@ def test_cannot_create_a_new_odm_form_without_an_english_description(api_client) def test_getting_error_for_retrieving_non_existent_odm_form(api_client): - response = api_client.get("concepts/odms/forms/OdmForm_000002") + response = api_client.get("odms/forms/OdmForm_000002") assert_response_status_code(response, 404) @@ -543,7 +543,7 @@ def test_getting_error_for_retrieving_non_existent_odm_form(api_client): def test_cannot_inactivate_an_odm_form_that_is_in_draft_status(api_client): - response = api_client.delete("concepts/odms/forms/OdmForm_000001/activations") + response = api_client.delete("odms/forms/OdmForm_000001/activations") assert_response_status_code(response, 400) @@ -554,7 +554,7 @@ def test_cannot_inactivate_an_odm_form_that_is_in_draft_status(api_client): def test_cannot_reactivate_an_odm_form_that_is_not_retired(api_client): - response = api_client.post("concepts/odms/forms/OdmForm_000001/activations") + response = api_client.post("odms/forms/OdmForm_000001/activations") assert_response_status_code(response, 400) @@ -623,7 +623,7 @@ def test_cannot_override_odm_vendor_element_that_has_attributes_connected_this_o "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -693,7 +693,7 @@ def test_cannot_add_odm_vendor_element_attribute_to_an_odm_form_as_an_odm_vendor "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -765,7 +765,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_form_as_an_odm_vendor_element "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) res = response.json() @@ -789,9 +789,7 @@ def test_cannot_add_odm_item_groups_with_an_invalid_value_to_an_odm_form(api_cli }, } ] - response = api_client.post( - "concepts/odms/forms/OdmForm_000001/item-groups", json=data - ) + response = api_client.post("odms/forms/OdmForm_000001/item-groups", json=data) assert_response_status_code(response, 400) @@ -861,19 +859,16 @@ def test_cannot_add_a_non_compatible_odm_vendor_attribute_to_an_odm_form(api_cli "vendor_attributes": [{"uid": "odm_vendor_attribute5", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_attribute5': ['NonCompatibleVendor']}""" - ) def test_cannot_add_a_non_compatible_odm_vendor_element_to_an_odm_form(api_client): @@ -931,19 +926,16 @@ def test_cannot_add_a_non_compatible_odm_vendor_element_to_an_odm_form(api_clien "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_element4': ['NonCompatibleVendor']}""" - ) def test_cannot_add_odm_item_groups_with_non_compatible_odm_vendor_attribute_to_a_specific_odm_form( @@ -959,25 +951,20 @@ def test_cannot_add_odm_item_groups_with_non_compatible_odm_vendor_attribute_to_ "vendor": {"attributes": [{"uid": "odm_vendor_attribute5", "value": "No"}]}, } ] - response = api_client.post( - "concepts/odms/forms/OdmForm_000001/item-groups", json=data - ) + response = api_client.post("odms/forms/OdmForm_000001/item-groups", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_attribute5': ['NonCompatibleVendor']}""" - ) def test_approve_odm_form(api_client): - response = api_client.post("concepts/odms/forms/OdmForm_000001/approvals") + response = api_client.post("odms/forms/OdmForm_000001/approvals") assert_response_status_code(response, 201) @@ -1056,7 +1043,7 @@ def test_approve_odm_form(api_client): def test_inactivate_odm_form(api_client): - response = api_client.delete("concepts/odms/forms/OdmForm_000001/activations") + response = api_client.delete("odms/forms/OdmForm_000001/activations") assert_response_status_code(response, 200) @@ -1147,9 +1134,7 @@ def test_cannot_add_odm_item_groups_to_an_odm_form_that_is_in_retired_status( "vendor": {"attributes": []}, } ] - response = api_client.post( - "concepts/odms/forms/OdmForm_000001/item-groups", json=data - ) + response = api_client.post("odms/forms/OdmForm_000001/item-groups", json=data) assert_response_status_code(response, 400) @@ -1216,7 +1201,7 @@ def test_cannot_add_odm_vendor_element_to_an_odm_form_that_is_in_retired_status( "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -1283,7 +1268,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_form_that_is_in_retired_statu "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -1352,7 +1337,7 @@ def test_cannot_add_odm_vendor_element_attribute_to_an_odm_form_that_is_in_retir "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 400) @@ -1389,7 +1374,7 @@ def test_cannot_add_duplicate_translated_texts(api_client, text_type: str): ], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 400) 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 78d756c3..4c28f783 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 @@ -66,7 +66,7 @@ def test_data(): def test_getting_empty_list_of_odm_item_groups(api_client): - response = api_client.get("concepts/odms/item-groups") + response = api_client.get("odms/item-groups") assert_response_status_code(response, 200) @@ -136,7 +136,7 @@ def test_creating_a_new_odm_item_group(api_client): ], "vendor_attributes": [{"uid": "odm_vendor_attribute4", "value": "value"}], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 201) @@ -242,7 +242,7 @@ def test_creating_a_new_odm_item_group(api_client): def test_getting_non_empty_list_of_odm_item_groups(api_client): - response = api_client.get("concepts/odms/item-groups") + response = api_client.get("odms/item-groups") assert_response_status_code(response, 200) @@ -348,7 +348,7 @@ def test_getting_non_empty_list_of_odm_item_groups(api_client): def test_getting_possible_header_values_of_odm_item_groups(api_client): - response = api_client.get("concepts/odms/item-groups/headers?field_name=name") + response = api_client.get("odms/item-groups/headers?field_name=name") assert_response_status_code(response, 200) @@ -358,7 +358,7 @@ def test_getting_possible_header_values_of_odm_item_groups(api_client): def test_getting_a_specific_odm_item_group(api_client): - response = api_client.get("concepts/odms/item-groups/OdmItemGroup_000001") + response = api_client.get("odms/item-groups/OdmItemGroup_000001") assert_response_status_code(response, 200) @@ -464,7 +464,7 @@ def test_getting_a_specific_odm_item_group(api_client): def test_getting_versions_of_a_specific_odm_item_group(api_client): - response = api_client.get("concepts/odms/item-groups/OdmItemGroup_000001/versions") + response = api_client.get("odms/item-groups/OdmItemGroup_000001/versions") assert_response_status_code(response, 200) @@ -635,9 +635,7 @@ def test_updating_an_existing_odm_item_group(api_client): {"uid": "odm_vendor_attribute3", "value": "value"}, ], } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 200) @@ -743,9 +741,7 @@ def test_updating_an_existing_odm_item_group(api_client): def test_getting_a_specific_odm_item_group_in_specific_version(api_client): - response = api_client.get( - "concepts/odms/item-groups/OdmItemGroup_000001?version=0.1" - ) + response = api_client.get("odms/item-groups/OdmItemGroup_000001?version=0.1") assert_response_status_code(response, 200) @@ -847,9 +843,7 @@ def test_adding_odm_items_to_a_specific_odm_item_group(api_client): }, } ] - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/items", json=data) assert_response_status_code(response, 201) @@ -1008,7 +1002,7 @@ def test_overriding_odm_items_from_a_specific_odm_item_group(api_client): } ] response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items?override=true", json=data + "odms/item-groups/OdmItemGroup_000001/items?override=true", json=data ) assert_response_status_code(response, 201) @@ -1142,9 +1136,7 @@ def test_overriding_odm_items_from_a_specific_odm_item_group(api_client): def test_approving_an_odm_item_group(api_client): - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/approvals" - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/approvals") assert_response_status_code(response, 201) @@ -1277,9 +1269,7 @@ def test_approving_an_odm_item_group(api_client): def test_inactivating_a_specific_odm_item_group(api_client): - response = api_client.delete( - "concepts/odms/item-groups/OdmItemGroup_000001/activations" - ) + response = api_client.delete("odms/item-groups/OdmItemGroup_000001/activations") assert_response_status_code(response, 200) @@ -1412,9 +1402,7 @@ def test_inactivating_a_specific_odm_item_group(api_client): def test_reactivating_a_specific_odm_item_group(api_client): - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/activations" - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/activations") assert_response_status_code(response, 200) @@ -1547,7 +1535,7 @@ def test_reactivating_a_specific_odm_item_group(api_client): def test_creating_a_new_odm_item_group_version(api_client): - response = api_client.post("concepts/odms/item-groups/OdmItemGroup_000001/versions") + response = api_client.post("odms/item-groups/OdmItemGroup_000001/versions") assert_response_status_code(response, 201) @@ -1700,7 +1688,7 @@ def test_create_a_new_odm_item_group_for_deleting_it(api_client): "aliases": [], "sdtm_domain_uids": [], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 201) @@ -1738,7 +1726,7 @@ def test_create_a_new_odm_item_group_for_deleting_it(api_client): def test_deleting_a_specific_odm_item_group(api_client): - response = api_client.delete("concepts/odms/item-groups/OdmItemGroup_000002") + response = api_client.delete("odms/item-groups/OdmItemGroup_000002") assert_response_status_code(response, 204) @@ -1775,7 +1763,7 @@ def test_creating_a_new_odm_item_group_with_relations(api_client): "aliases": [], "sdtm_domain_uids": [], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 201) @@ -1865,9 +1853,7 @@ def test_updating_an_existing_odm_item_group_with_relations(api_client): {"uid": "odm_vendor_attribute3", "value": "value"}, ], } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 200) @@ -1985,7 +1971,7 @@ def test_create_a_new_odm_form_with_relation_to_odm_item_group(api_client): "translated_texts": [], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) @@ -2032,9 +2018,7 @@ def test_add_the_odm_item_group_to_the_odm_form(api_client): }, } ] - response = api_client.post( - "concepts/odms/forms/OdmForm_000001/item-groups", json=data - ) + response = api_client.post("odms/forms/OdmForm_000001/item-groups", json=data) assert_response_status_code(response, 201) @@ -2083,9 +2067,7 @@ def test_add_the_odm_item_group_to_the_odm_form(api_client): def test_getting_uids_of_a_specific_odm_item_groups_active_relationships(api_client): - response = api_client.get( - "concepts/odms/item-groups/OdmItemGroup_000001/relationships" - ) + response = api_client.get("odms/item-groups/OdmItemGroup_000001/relationships") assert_response_status_code(response, 200) @@ -2095,7 +2077,7 @@ def test_getting_uids_of_a_specific_odm_item_groups_active_relationships(api_cli def test_getting_all_odm_item_groups_that_belongs_to_an_odm_form(api_client): - response = api_client.get("concepts/odms/item-groups/forms") + response = api_client.get("odms/item-groups/forms") assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups_negative.py index 9511787c..bdea90f9 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_item_groups_negative.py @@ -119,7 +119,7 @@ def test_create_a_new_odm_item_group(api_client): "aliases": [{"context": "context1", "name": "name1"}], "sdtm_domain_uids": ["domain001"], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 201) @@ -266,9 +266,7 @@ def test_cannot_add_odm_vendor_attribute_with_an_invalid_value_to_an_odm_item_gr "vendor_attributes": [{"uid": "odm_vendor_attribute3", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -345,21 +343,16 @@ def test_cannot_add_a_non_compatible_odm_vendor_attribute_to_an_odm_item_group( "vendor_attributes": [{"uid": "odm_vendor_attribute5", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_attribute5': ['NonCompatibleVendor']}""" - ) def test_cannot_add_a_non_compatible_odm_vendor_element_to_an_odm_item_group( @@ -424,28 +417,23 @@ def test_cannot_add_a_non_compatible_odm_vendor_element_to_an_odm_item_group( "vendor_attributes": [{"uid": "odm_vendor_attribute3", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_element4': ['NonCompatibleVendor']}""" - ) def test_cannot_add_odm_item_that_is_already_connected_to_an_odm_item_group( api_client, ): response = api_client.post( - "concepts/odms/item-groups", + "odms/item-groups", json={ "library_name": "Sponsor", "name": "name2", @@ -478,15 +466,11 @@ def test_cannot_add_odm_item_that_is_already_connected_to_an_odm_item_group( "vendor": {"attributes": []}, } ] - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000002/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000002/items", json=data) assert_response_status_code(response, 201) - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/items", json=data) assert_response_status_code(response, 400) @@ -516,21 +500,16 @@ def test_cannot_add_odm_item_with_non_compatible_odm_vendor_attribute_to_a_speci "vendor": {"attributes": [{"uid": "odm_vendor_attribute5", "value": "No"}]}, } ] - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/items", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_attribute5': ['NonCompatibleVendor']}""" - ) def test_cannot_add_odm_vendor_element_attribute_with_an_invalid_value_to_an_odm_item_group( @@ -595,9 +574,7 @@ def test_cannot_add_odm_vendor_element_attribute_with_an_invalid_value_to_an_odm "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -674,9 +651,7 @@ def test_add_odm_vendor_element_to_an_odm_item_group(api_client): "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 200) @@ -828,7 +803,7 @@ def test_cannot_create_a_new_odm_item_group_with_same_properties(api_client): "aliases": [{"context": "context1", "name": "name1"}], "sdtm_domain_uids": ["domain001"], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 409) @@ -858,7 +833,7 @@ def test_cannot_create_an_odm_item_group_connected_to_non_existent_sdtm_domain( "aliases": [], "sdtm_domain_uids": ["wrong_uid"], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 400) @@ -892,7 +867,7 @@ def test_cannot_create_a_new_odm_item_group_without_an_english_description(api_c "aliases": [], "sdtm_domain_uids": [], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 400) @@ -906,7 +881,7 @@ def test_cannot_create_a_new_odm_item_group_without_an_english_description(api_c def test_getting_error_for_retrieving_non_existent_odm_item_group(api_client): - response = api_client.get("concepts/odms/item-groups/OdmItemGroup_000003") + response = api_client.get("odms/item-groups/OdmItemGroup_000003") assert_response_status_code(response, 404) @@ -920,9 +895,7 @@ def test_getting_error_for_retrieving_non_existent_odm_item_group(api_client): def test_cannot_inactivate_an_odm_item_group_that_is_in_draft_status(api_client): - response = api_client.delete( - "concepts/odms/item-groups/OdmItemGroup_000001/activations" - ) + response = api_client.delete("odms/item-groups/OdmItemGroup_000001/activations") assert_response_status_code(response, 400) @@ -933,9 +906,7 @@ def test_cannot_inactivate_an_odm_item_group_that_is_in_draft_status(api_client) def test_cannot_reactivate_an_odm_item_group_that_is_not_retired(api_client): - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/activations" - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/activations") assert_response_status_code(response, 400) @@ -1009,9 +980,7 @@ def test_cannot_override_odm_vendor_element_that_has_attributes_connected_this_o "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -1086,9 +1055,7 @@ def test_cannot_add_odm_vendor_element_attribute_to_an_odm_item_group_as_an_odm_ "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -1165,9 +1132,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_item_group_as_an_odm_vendor_e "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -1200,9 +1165,7 @@ def test_cannot_add_odm_item_with_an_invalid_value_to_to_an_odm_item_group(api_c }, } ] - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/items", json=data) assert_response_status_code(response, 400) @@ -1218,9 +1181,7 @@ def test_cannot_add_odm_item_with_an_invalid_value_to_to_an_odm_item_group(api_c def test_approve_odm_item_group(api_client): - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/approvals" - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/approvals") assert_response_status_code(response, 201) @@ -1317,9 +1278,7 @@ def test_approve_odm_item_group(api_client): def test_inactivate_odm_item_group(api_client): - response = api_client.delete( - "concepts/odms/item-groups/OdmItemGroup_000001/activations" - ) + response = api_client.delete("odms/item-groups/OdmItemGroup_000001/activations") assert_response_status_code(response, 200) @@ -1435,9 +1394,7 @@ def test_cannot_add_odm_item_to_an_odm_item_group_that_is_in_retired_status( "vendor": {"attributes": []}, } ] - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/items", json=data) assert_response_status_code(response, 400) @@ -1509,9 +1466,7 @@ def test_cannot_add_odm_vendor_element_to_an_odm_item_group_that_is_in_retired_s "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -1583,9 +1538,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_item_group_that_is_in_retired "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -1659,9 +1612,7 @@ def test_cannot_add_odm_vendor_element_attribute_to_an_odm_item_group_that_is_in "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch( - "concepts/odms/item-groups/OdmItemGroup_000001", json=data - ) + response = api_client.patch("odms/item-groups/OdmItemGroup_000001", json=data) assert_response_status_code(response, 400) @@ -1703,7 +1654,7 @@ def test_cannot_add_duplicate_translated_texts(api_client, text_type: str): "aliases": [], "sdtm_domain_uids": [], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items.py index 51e96f48..a4bf5cb2 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items.py @@ -39,7 +39,7 @@ def test_data(): def test_getting_empty_list_of_odm_items(api_client): - response = api_client.get("concepts/odms/items") + response = api_client.get("odms/items") assert_response_status_code(response, 200) @@ -123,7 +123,7 @@ def test_creating_a_new_odm_item(api_client): ], "vendor_attributes": [{"uid": "odm_vendor_attribute4", "value": "value"}], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 201) @@ -251,7 +251,7 @@ def test_creating_a_new_odm_item(api_client): def test_getting_non_empty_list_of_odm_items(api_client): - response = api_client.get("concepts/odms/items") + response = api_client.get("odms/items") assert_response_status_code(response, 200) @@ -378,7 +378,7 @@ def test_getting_non_empty_list_of_odm_items(api_client): def test_getting_possible_header_values_of_odm_items(api_client): - response = api_client.get("concepts/odms/items/headers?field_name=name") + response = api_client.get("odms/items/headers?field_name=name") assert_response_status_code(response, 200) @@ -388,7 +388,7 @@ def test_getting_possible_header_values_of_odm_items(api_client): def test_getting_a_specific_odm_item(api_client): - response = api_client.get("concepts/odms/items/OdmItem_000001") + response = api_client.get("odms/items/OdmItem_000001") assert_response_status_code(response, 200) @@ -516,7 +516,7 @@ def test_getting_a_specific_odm_item(api_client): def test_getting_versions_of_a_specific_odm_item(api_client): - response = api_client.get("concepts/odms/items/OdmItem_000001/versions") + response = api_client.get("odms/items/OdmItem_000001/versions") assert_response_status_code(response, 200) @@ -722,7 +722,7 @@ def test_updating_an_existing_odm_item(api_client): {"uid": "odm_vendor_attribute3", "value": "value"}, ], } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 200) @@ -850,7 +850,7 @@ def test_updating_an_existing_odm_item(api_client): def test_getting_a_specific_odm_item_in_specific_version(api_client): - response = api_client.get("concepts/odms/items/OdmItem_000001?version=0.1") + response = api_client.get("odms/items/OdmItem_000001?version=0.1") assert_response_status_code(response, 200) @@ -958,7 +958,7 @@ def test_getting_a_specific_odm_item_in_specific_version(api_client): def test_approving_an_odm_item(api_client): - response = api_client.post("concepts/odms/items/OdmItem_000001/approvals") + response = api_client.post("odms/items/OdmItem_000001/approvals") assert_response_status_code(response, 201) @@ -1086,7 +1086,7 @@ def test_approving_an_odm_item(api_client): def test_inactivating_a_specific_odm_item(api_client): - response = api_client.delete("concepts/odms/items/OdmItem_000001/activations") + response = api_client.delete("odms/items/OdmItem_000001/activations") assert_response_status_code(response, 200) @@ -1214,7 +1214,7 @@ def test_inactivating_a_specific_odm_item(api_client): def test_reactivating_a_specific_odm_item(api_client): - response = api_client.post("concepts/odms/items/OdmItem_000001/activations") + response = api_client.post("odms/items/OdmItem_000001/activations") assert_response_status_code(response, 200) @@ -1342,7 +1342,7 @@ def test_reactivating_a_specific_odm_item(api_client): def test_creating_a_new_odm_item_version(api_client): - response = api_client.post("concepts/odms/items/OdmItem_000001/versions") + response = api_client.post("odms/items/OdmItem_000001/versions") assert_response_status_code(response, 201) @@ -1496,7 +1496,7 @@ def test_create_a_new_odm_item_for_deleting_it(api_client): "codelist_uid": None, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 201) @@ -1551,7 +1551,7 @@ def test_create_a_new_odm_item_for_deleting_it(api_client): def test_deleting_a_specific_odm_item(api_client): - response = api_client.delete("concepts/odms/items/OdmItem_000002") + response = api_client.delete("odms/items/OdmItem_000002") assert_response_status_code(response, 204) @@ -1592,7 +1592,7 @@ def test_creating_a_new_odm_item_with_relations(api_client): "codelist_uid": None, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 201) @@ -1691,7 +1691,7 @@ def test_updating_an_existing_odm_item_with_relations(api_client): {"uid": "odm_vendor_attribute3", "value": "value"}, ], } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 200) @@ -1809,7 +1809,7 @@ def test_create_a_new_odm_item_group_with_relation_to_odm_item(api_client): "aliases": [], "sdtm_domain_uids": [], } - response = api_client.post("concepts/odms/item-groups", json=data) + response = api_client.post("odms/item-groups", json=data) assert_response_status_code(response, 201) @@ -1857,9 +1857,7 @@ def test_add_the_odm_item_to_the_odm_item_group(api_client): }, } ] - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/items", json=data - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/items", json=data) assert_response_status_code(response, 201) @@ -1918,9 +1916,7 @@ def test_add_the_odm_item_to_the_odm_item_group(api_client): def test_approve_the_odm_item_group(api_client): - response = api_client.post( - "concepts/odms/item-groups/OdmItemGroup_000001/approvals" - ) + response = api_client.post("odms/item-groups/OdmItemGroup_000001/approvals") assert_response_status_code(response, 201) @@ -1979,7 +1975,7 @@ def test_approve_the_odm_item_group(api_client): def test_getting_uids_of_a_specific_odm_items_active_relationships(api_client): - response = api_client.get("concepts/odms/items/OdmItem_000001/relationships") + response = api_client.get("odms/items/OdmItem_000001/relationships") assert_response_status_code(response, 200) @@ -1989,7 +1985,7 @@ def test_getting_uids_of_a_specific_odm_items_active_relationships(api_client): def test_getting_all_odm_items_that_belongs_to_an_odm_item_groups(api_client): - response = api_client.get("concepts/odms/items/item-groups") + response = api_client.get("odms/items/item-groups") assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items_negative.py index 49f8fce7..2f3f7206 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_items_negative.py @@ -108,7 +108,7 @@ def test_create_a_new_odm_item(api_client): } ], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 201) @@ -290,7 +290,7 @@ def test_cannot_add_odm_vendor_attribute_with_an_invalid_value_to_an_odm_item( "vendor_attributes": [{"uid": "odm_vendor_attribute3", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -379,19 +379,16 @@ def test_cannot_add_a_non_compatible_odm_vendor_attribute_to_an_odm_item(api_cli "vendor_attributes": [{"uid": "odm_vendor_attribute5", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_attribute5': ['NonCompatibleVendor']}""" - ) def test_cannot_add_a_non_compatible_odm_vendor_element_to_an_odm_item(api_client): @@ -468,19 +465,16 @@ def test_cannot_add_a_non_compatible_odm_vendor_element_to_an_odm_item(api_clien "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) res = response.json() assert res["type"] == "BusinessLogicException" - assert ( - res["message"] - == """Trying to add non-compatible ODM Vendor: + assert res["message"] == """Trying to add non-compatible ODM Vendor: {'odm_vendor_element4': ['NonCompatibleVendor']}""" - ) def test_cannot_add_odm_vendor_element_attribute_with_an_invalid_value_to_an_odm_item( @@ -559,7 +553,7 @@ def test_cannot_add_odm_vendor_element_attribute_with_an_invalid_value_to_an_odm "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "3423"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -650,7 +644,7 @@ def test_add_odm_vendor_element_to_an_odm_item(api_client): "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 200) @@ -786,7 +780,7 @@ def test_cannot_create_a_new_odm_item_with_same_properties(api_client): "codelist": None, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 409) @@ -799,7 +793,9 @@ def test_cannot_create_a_new_odm_item_with_same_properties(api_client): ) -def test_cannot_create_an_odm_item_connected_to_non_existent_concepts(api_client): +def test_cannot_create_an_odm_item_connected_to_non_existent_unit_definitions( + api_client, +): data = { "library_name": "Sponsor", "name": "new name", @@ -818,7 +814,7 @@ def test_cannot_create_an_odm_item_connected_to_non_existent_concepts(api_client "codelist_uid": None, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -827,7 +823,7 @@ def test_cannot_create_an_odm_item_connected_to_non_existent_concepts(api_client assert res["type"] == "BusinessLogicException" assert ( res["message"] - == """ODM Item tried to connect to non-existent concepts [('Concept Name: Unit Definition', "uids: {'wrong_uid'}")].""" + == """ODM Item tried to connect to non-existent Unit Definition with UID 'wrong_uid'.""" ) @@ -850,7 +846,7 @@ def test_cannot_create_an_odm_item_connected_to_non_existent_codelist(api_client "codelist": {"uid": "wrong_uid"}, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -884,7 +880,7 @@ def test_cannot_create_an_odm_item_connected_to_ct_terms_without_providing_a_cod "codelist_uid": None, "terms": [{"uid": "term_root_final"}], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -915,7 +911,7 @@ def test_cannot_create_an_odm_item_connected_to_ct_terms_belonging_to_a_codelist "codelist": {"uid": "editable_cr", "allows_multi_choice": True}, "terms": [{"uid": "wrong_uid"}], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -953,7 +949,7 @@ def test_cannot_create_a_new_odm_item_without_an_english_description(api_client) "codelist_uid": None, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -967,7 +963,7 @@ def test_cannot_create_a_new_odm_item_without_an_english_description(api_client) def test_getting_error_for_retrieving_non_existent_odm_item(api_client): - response = api_client.get("concepts/odms/items/OdmItem_000002") + response = api_client.get("odms/items/OdmItem_000002") assert_response_status_code(response, 404) @@ -981,7 +977,7 @@ def test_getting_error_for_retrieving_non_existent_odm_item(api_client): def test_cannot_inactivate_an_odm_item_that_is_in_draft_status(api_client): - response = api_client.delete("concepts/odms/items/OdmItem_000001/activations") + response = api_client.delete("odms/items/OdmItem_000001/activations") assert_response_status_code(response, 400) @@ -992,7 +988,7 @@ def test_cannot_inactivate_an_odm_item_that_is_in_draft_status(api_client): def test_cannot_reactivate_an_odm_item_that_is_not_retired(api_client): - response = api_client.post("concepts/odms/items/OdmItem_000001/activations") + response = api_client.post("odms/items/OdmItem_000001/activations") assert_response_status_code(response, 400) @@ -1080,7 +1076,7 @@ def test_cannot_override_odm_vendor_element_that_has_attributes_connected_this_o "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -1169,7 +1165,7 @@ def test_cannot_add_odm_vendor_element_attribute_to_an_odm_item_as_an_odm_vendor "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -1261,7 +1257,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_item_as_an_odm_vendor_element "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -1275,7 +1271,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_item_as_an_odm_vendor_element def test_approve_odm_item(api_client): - response = api_client.post("concepts/odms/items/OdmItem_000001/approvals") + response = api_client.post("odms/items/OdmItem_000001/approvals") assert_response_status_code(response, 201) @@ -1393,7 +1389,7 @@ def test_approve_odm_item(api_client): def test_inactivate_odm_item(api_client): - response = api_client.delete("concepts/odms/items/OdmItem_000001/activations") + response = api_client.delete("odms/items/OdmItem_000001/activations") assert_response_status_code(response, 200) @@ -1587,7 +1583,7 @@ def test_cannot_add_odm_vendor_element_to_an_odm_item_that_is_in_retired_status( "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -1673,7 +1669,7 @@ def test_cannot_add_odm_vendor_attribute_to_an_odm_item_that_is_in_retired_statu "vendor_attributes": [{"uid": "odm_vendor_attribute1", "value": "value"}], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -1761,7 +1757,7 @@ def test_cannot_add_odm_vendor_element_attribute_to_an_odm_item_that_is_in_retir "vendor_attributes": [], "change_description": "desc doesnt change", } - response = api_client.patch("concepts/odms/items/OdmItem_000001", json=data) + response = api_client.patch("odms/items/OdmItem_000001", json=data) assert_response_status_code(response, 400) @@ -1781,7 +1777,7 @@ def test_cannot_provide_non_null_length_when_datatype_is_not_string_text_integer "length": 11, "significant_digits": 11, } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -1807,7 +1803,7 @@ def test_cannot_provide_null_length_when_datatype_is_string_or_text(api_client): "length": None, "significant_digits": 11, } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -1835,7 +1831,7 @@ def test_cannot_provide_only_one_of_length_or_significant_digits_when_datatype_i "length": None, "significant_digits": 11, } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) @@ -1889,7 +1885,7 @@ def test_cannot_add_duplicate_translated_texts(api_client, text_type: str): "codelist_uid": None, "terms": [], } - response = api_client.post("concepts/odms/items", json=data) + response = api_client.post("odms/items", json=data) assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods.py index 253140fa..ece0a864 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods.py @@ -29,7 +29,7 @@ def test_data(): def test_getting_empty_list_of_odm_methods(api_client): - response = api_client.get("concepts/odms/methods") + response = api_client.get("odms/methods") assert_response_status_code(response, 200) @@ -89,7 +89,7 @@ def test_creating_a_new_odm_method(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 201) @@ -155,7 +155,7 @@ def test_creating_a_new_odm_method(api_client): def test_getting_non_empty_list_of_odm_methods(api_client): - response = api_client.get("concepts/odms/methods") + response = api_client.get("odms/methods") assert_response_status_code(response, 200) @@ -221,7 +221,7 @@ def test_getting_non_empty_list_of_odm_methods(api_client): def test_getting_possible_header_values_of_odm_methods(api_client): - response = api_client.get("concepts/odms/methods/headers?field_name=name") + response = api_client.get("odms/methods/headers?field_name=name") assert_response_status_code(response, 200) @@ -231,7 +231,7 @@ def test_getting_possible_header_values_of_odm_methods(api_client): def test_getting_a_specific_odm_method(api_client): - response = api_client.get("concepts/odms/methods/OdmMethod_000001") + response = api_client.get("odms/methods/OdmMethod_000001") assert_response_status_code(response, 200) @@ -297,7 +297,7 @@ def test_getting_a_specific_odm_method(api_client): def test_getting_versions_of_a_specific_odm_method(api_client): - response = api_client.get("concepts/odms/methods/OdmMethod_000001/versions") + response = api_client.get("odms/methods/OdmMethod_000001/versions") assert_response_status_code(response, 200) @@ -414,7 +414,7 @@ def test_updating_an_existing_odm_method(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.patch("concepts/odms/methods/OdmMethod_000001", json=data) + response = api_client.patch("odms/methods/OdmMethod_000001", json=data) assert_response_status_code(response, 200) @@ -480,7 +480,7 @@ def test_updating_an_existing_odm_method(api_client): def test_getting_a_specific_odm_method_in_specific_version(api_client): - response = api_client.get("concepts/odms/methods/OdmMethod_000001?version=0.1") + response = api_client.get("odms/methods/OdmMethod_000001?version=0.1") assert_response_status_code(response, 200) @@ -546,7 +546,7 @@ def test_getting_a_specific_odm_method_in_specific_version(api_client): def test_approving_an_odm_method(api_client): - response = api_client.post("concepts/odms/methods/OdmMethod_000001/approvals") + response = api_client.post("odms/methods/OdmMethod_000001/approvals") assert_response_status_code(response, 201) @@ -612,7 +612,7 @@ def test_approving_an_odm_method(api_client): def test_inactivating_a_specific_odm_method(api_client): - response = api_client.delete("concepts/odms/methods/OdmMethod_000001/activations") + response = api_client.delete("odms/methods/OdmMethod_000001/activations") assert_response_status_code(response, 200) @@ -678,7 +678,7 @@ def test_inactivating_a_specific_odm_method(api_client): def test_reactivating_a_specific_odm_method(api_client): - response = api_client.post("concepts/odms/methods/OdmMethod_000001/activations") + response = api_client.post("odms/methods/OdmMethod_000001/activations") assert_response_status_code(response, 200) @@ -744,7 +744,7 @@ def test_reactivating_a_specific_odm_method(api_client): def test_creating_a_new_odm_method_version(api_client): - response = api_client.post("concepts/odms/methods/OdmMethod_000001/versions") + response = api_client.post("odms/methods/OdmMethod_000001/versions") assert_response_status_code(response, 201) @@ -825,7 +825,7 @@ def test_create_a_new_odm_method_for_deleting_it(api_client): ], "aliases": [], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 201) @@ -854,7 +854,7 @@ def test_create_a_new_odm_method_for_deleting_it(api_client): def test_deleting_a_specific_odm_method(api_client): - response = api_client.delete("concepts/odms/methods/OdmMethod_000002") + response = api_client.delete("odms/methods/OdmMethod_000002") assert_response_status_code(response, 204) @@ -878,7 +878,7 @@ def test_creating_a_new_odm_method_with_relations(api_client): ], "aliases": [], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 201) @@ -932,7 +932,7 @@ def test_updating_an_existing_odm_method_with_relations(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.patch("concepts/odms/methods/OdmMethod_000001", json=data) + response = api_client.patch("odms/methods/OdmMethod_000001", json=data) assert_response_status_code(response, 200) @@ -967,7 +967,7 @@ def test_updating_an_existing_odm_method_with_relations(api_client): def test_getting_uids_of_a_specific_odm_methods_active_relationships(api_client): - response = api_client.get("concepts/odms/methods/OdmMethod_000001/relationships") + response = api_client.get("odms/methods/OdmMethod_000001/relationships") assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods_negative.py index 643de666..f04a204d 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_methods_negative.py @@ -79,7 +79,7 @@ def test_create_a_new_odm_method(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 201) @@ -195,7 +195,7 @@ def test_cannot_create_a_new_odm_method_with_same_properties(api_client): ], "aliases": [{"context": "context1", "name": "name1"}], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 409) @@ -224,7 +224,7 @@ def test_cannot_create_a_new_odm_method_without_an_english_description(api_clien ], "aliases": [], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 400) @@ -238,7 +238,7 @@ def test_cannot_create_a_new_odm_method_without_an_english_description(api_clien def test_getting_error_for_retrieving_non_existent_odm_method(api_client): - response = api_client.get("concepts/odms/methods/OdmMethod_000002") + response = api_client.get("odms/methods/OdmMethod_000002") assert_response_status_code(response, 404) @@ -252,7 +252,7 @@ def test_getting_error_for_retrieving_non_existent_odm_method(api_client): def test_cannot_inactivate_an_odm_method_that_is_in_draft_status(api_client): - response = api_client.delete("concepts/odms/methods/OdmMethod_000001/activations") + response = api_client.delete("odms/methods/OdmMethod_000001/activations") assert_response_status_code(response, 400) @@ -263,7 +263,7 @@ def test_cannot_inactivate_an_odm_method_that_is_in_draft_status(api_client): def test_cannot_reactivate_an_odm_method_that_is_not_retired(api_client): - response = api_client.post("concepts/odms/methods/OdmMethod_000001/activations") + response = api_client.post("odms/methods/OdmMethod_000001/activations") assert_response_status_code(response, 400) @@ -299,7 +299,7 @@ def test_cannot_add_duplicate_translated_texts(api_client, text_type: str): ], "aliases": [], } - response = api_client.post("concepts/odms/methods", json=data) + response = api_client.post("odms/methods", json=data) assert_response_status_code(response, 400) 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 b4ced895..6eb79bfe 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 @@ -29,7 +29,7 @@ def test_data(): def test_getting_empty_list_of_odm_study_events(api_client): - response = api_client.get("concepts/odms/study-events") + response = api_client.get("odms/study-events") assert_response_status_code(response, 200) @@ -48,7 +48,7 @@ def test_creating_a_new_odm_study_event(api_client): "description": "description1", "display_in_tree": False, } - response = api_client.post("concepts/odms/study-events", json=data) + response = api_client.post("odms/study-events", json=data) assert_response_status_code(response, 201) @@ -72,7 +72,7 @@ def test_creating_a_new_odm_study_event(api_client): def test_getting_non_empty_list_of_odm_study_events(api_client): - response = api_client.get("concepts/odms/study-events") + response = api_client.get("odms/study-events") assert_response_status_code(response, 200) @@ -96,7 +96,7 @@ def test_getting_non_empty_list_of_odm_study_events(api_client): def test_getting_possible_header_values_of_odm_study_events(api_client): - response = api_client.get("concepts/odms/study-events/headers?field_name=name") + response = api_client.get("odms/study-events/headers?field_name=name") assert_response_status_code(response, 200) @@ -106,7 +106,7 @@ def test_getting_possible_header_values_of_odm_study_events(api_client): def test_getting_a_specific_odm_study_event(api_client): - response = api_client.get("concepts/odms/study-events/OdmStudyEvent_000001") + response = api_client.get("odms/study-events/OdmStudyEvent_000001") assert_response_status_code(response, 200) @@ -130,9 +130,7 @@ def test_getting_a_specific_odm_study_event(api_client): def test_getting_versions_of_a_specific_odm_study_event(api_client): - response = api_client.get( - "concepts/odms/study-events/OdmStudyEvent_000001/versions" - ) + response = api_client.get("odms/study-events/OdmStudyEvent_000001/versions") assert_response_status_code(response, 200) @@ -165,9 +163,7 @@ def test_updating_an_existing_odm_study_event(api_client): "display_in_tree": True, "change_description": "oid and display_in_tree changed", } - response = api_client.patch( - "concepts/odms/study-events/OdmStudyEvent_000001", json=data - ) + response = api_client.patch("odms/study-events/OdmStudyEvent_000001", json=data) assert_response_status_code(response, 200) @@ -191,9 +187,7 @@ def test_updating_an_existing_odm_study_event(api_client): def test_getting_a_specific_odm_study_event_in_specific_version(api_client): - response = api_client.get( - "concepts/odms/study-events/OdmStudyEvent_000001?version=0.1" - ) + response = api_client.get("odms/study-events/OdmStudyEvent_000001?version=0.1") assert_response_status_code(response, 200) @@ -227,7 +221,7 @@ def test_adding_odm_forms_to_a_specific_odm_study_event(api_client): } ] response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/forms", json=data + "odms/study-events/OdmStudyEvent_000001/forms", json=data ) assert_response_status_code(response, 201) @@ -273,7 +267,7 @@ def test_overriding_odm_forms_from_a_specific_odm_study_event(api_client): } ] response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/forms?override=true", json=data + "odms/study-events/OdmStudyEvent_000001/forms?override=true", json=data ) assert_response_status_code(response, 201) @@ -309,9 +303,7 @@ def test_overriding_odm_forms_from_a_specific_odm_study_event(api_client): def test_approving_an_odm_study_event(api_client): - response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/approvals" - ) + response = api_client.post("odms/study-events/OdmStudyEvent_000001/approvals") assert_response_status_code(response, 201) @@ -346,9 +338,7 @@ def test_approving_an_odm_study_event(api_client): def test_inactivating_a_specific_odm_study_event(api_client): - response = api_client.delete( - "concepts/odms/study-events/OdmStudyEvent_000001/activations" - ) + response = api_client.delete("odms/study-events/OdmStudyEvent_000001/activations") assert_response_status_code(response, 200) @@ -383,9 +373,7 @@ def test_inactivating_a_specific_odm_study_event(api_client): def test_reactivating_a_specific_odm_study_event(api_client): - response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/activations" - ) + response = api_client.post("odms/study-events/OdmStudyEvent_000001/activations") assert_response_status_code(response, 200) @@ -420,9 +408,7 @@ def test_reactivating_a_specific_odm_study_event(api_client): def test_creating_a_new_odm_study_event_version(api_client): - response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/versions" - ) + response = api_client.post("odms/study-events/OdmStudyEvent_000001/versions") assert_response_status_code(response, 201) @@ -465,7 +451,7 @@ def test_create_a_new_odm_study_event_for_deleting_it(api_client): "retired_date": "2022-04-21", "description": "description1", } - response = api_client.post("concepts/odms/study-events", json=data) + response = api_client.post("odms/study-events", json=data) assert_response_status_code(response, 201) @@ -489,15 +475,13 @@ def test_create_a_new_odm_study_event_for_deleting_it(api_client): def test_deleting_a_specific_odm_study_event(api_client): - response = api_client.delete("concepts/odms/study-events/OdmStudyEvent_000002") + response = api_client.delete("odms/study-events/OdmStudyEvent_000002") assert_response_status_code(response, 204) def test_getting_uids_of_a_specific_odm_study_events_active_relationships(api_client): - response = api_client.get( - "concepts/odms/study-events/OdmStudyEvent_000001/relationships" - ) + response = api_client.get("odms/study-events/OdmStudyEvent_000001/relationships") assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events_negative.py index 27b8766a..7e40ea4f 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_study_events_negative.py @@ -37,7 +37,7 @@ def test_create_a_new_odm_study_event(api_client): "retired_date": "2022-04-21", "description": "description1", } - response = api_client.post("concepts/odms/study-events", json=data) + response = api_client.post("odms/study-events", json=data) assert_response_status_code(response, 201) @@ -69,7 +69,7 @@ def test_cannot_create_a_new_odm_study_event_with_same_properties(api_client): "retired_date": "2022-04-21", "description": "description1", } - response = api_client.post("concepts/odms/study-events", json=data) + response = api_client.post("odms/study-events", json=data) assert_response_status_code(response, 409) @@ -83,7 +83,7 @@ def test_cannot_create_a_new_odm_study_event_with_same_properties(api_client): def test_getting_error_for_retrieving_non_existent_odm_study_event(api_client): - response = api_client.get("concepts/odms/study-events/OdmStudyEvent_000002") + response = api_client.get("odms/study-events/OdmStudyEvent_000002") assert_response_status_code(response, 404) @@ -97,9 +97,7 @@ def test_getting_error_for_retrieving_non_existent_odm_study_event(api_client): def test_cannot_inactivate_an_odm_study_event_that_is_in_draft_status(api_client): - response = api_client.delete( - "concepts/odms/study-events/OdmStudyEvent_000001/activations" - ) + response = api_client.delete("odms/study-events/OdmStudyEvent_000001/activations") assert_response_status_code(response, 400) @@ -110,9 +108,7 @@ def test_cannot_inactivate_an_odm_study_event_that_is_in_draft_status(api_client def test_cannot_reactivate_an_odm_study_event_that_is_not_retired(api_client): - response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/activations" - ) + response = api_client.post("odms/study-events/OdmStudyEvent_000001/activations") assert_response_status_code(response, 400) @@ -123,9 +119,7 @@ def test_cannot_reactivate_an_odm_study_event_that_is_not_retired(api_client): def test_approve_odm_study_event(api_client): - response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/approvals" - ) + response = api_client.post("odms/study-events/OdmStudyEvent_000001/approvals") assert_response_status_code(response, 201) @@ -149,9 +143,7 @@ def test_approve_odm_study_event(api_client): def test_inactivate_odm_study_event(api_client): - response = api_client.delete( - "concepts/odms/study-events/OdmStudyEvent_000001/activations" - ) + response = api_client.delete("odms/study-events/OdmStudyEvent_000001/activations") assert_response_status_code(response, 200) @@ -187,7 +179,7 @@ def test_cannot_add_odm_forms_to_an_odm_study_event_that_is_in_retired_status( } ] response = api_client.post( - "concepts/odms/study-events/OdmStudyEvent_000001/forms", json=data + "odms/study-events/OdmStudyEvent_000001/forms", json=data ) assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes.py index 7907dff5..a469e8a7 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes.py @@ -33,7 +33,7 @@ def test_data(): def test_getting_empty_list_of_odm_vendor_attributes(api_client): - response = api_client.get("concepts/odms/vendor-attributes") + response = api_client.get("odms/vendor-attributes") assert_response_status_code(response, 200) @@ -53,7 +53,7 @@ def test_creating_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_namespa "value_regex": None, "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) @@ -84,7 +84,7 @@ def test_creating_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_namespa def test_getting_non_empty_list_of_odm_vendor_attributes(api_client): - response = api_client.get("concepts/odms/vendor-attributes") + response = api_client.get("odms/vendor-attributes") assert_response_status_code(response, 200) @@ -115,7 +115,7 @@ def test_getting_non_empty_list_of_odm_vendor_attributes(api_client): def test_getting_possible_header_values_of_odm_vendor_attributes(api_client): - response = api_client.get("concepts/odms/vendor-attributes/headers?field_name=name") + response = api_client.get("odms/vendor-attributes/headers?field_name=name") assert_response_status_code(response, 200) @@ -125,9 +125,7 @@ def test_getting_possible_header_values_of_odm_vendor_attributes(api_client): def test_getting_a_specific_odm_vendor_attribute(api_client): - response = api_client.get( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001" - ) + response = api_client.get("odms/vendor-attributes/OdmVendorAttribute_000001") assert_response_status_code(response, 200) @@ -159,7 +157,7 @@ def test_getting_a_specific_odm_vendor_attribute(api_client): def test_getting_versions_of_a_specific_odm_vendor_attribute(api_client): response = api_client.get( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/versions" + "odms/vendor-attributes/OdmVendorAttribute_000001/versions" ) assert_response_status_code(response, 200) @@ -201,7 +199,7 @@ def test_updating_an_existing_odm_vendor_attribute(api_client): "change_description": "regex changed and name changed to newName", } response = api_client.patch( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001", json=data + "odms/vendor-attributes/OdmVendorAttribute_000001", json=data ) assert_response_status_code(response, 200) @@ -234,7 +232,7 @@ def test_updating_an_existing_odm_vendor_attribute(api_client): def test_getting_a_specific_odm_vendor_attribute_in_specific_version(api_client): response = api_client.get( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001?version=0.1" + "odms/vendor-attributes/OdmVendorAttribute_000001?version=0.1" ) assert_response_status_code(response, 200) @@ -267,7 +265,7 @@ def test_getting_a_specific_odm_vendor_attribute_in_specific_version(api_client) def test_approving_an_odm_vendor_attribute(api_client): response = api_client.post( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/approvals" + "odms/vendor-attributes/OdmVendorAttribute_000001/approvals" ) assert_response_status_code(response, 201) @@ -300,7 +298,7 @@ def test_approving_an_odm_vendor_attribute(api_client): def test_inactivating_a_specific_odm_vendor_attribute(api_client): response = api_client.delete( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/activations" + "odms/vendor-attributes/OdmVendorAttribute_000001/activations" ) assert_response_status_code(response, 200) @@ -333,7 +331,7 @@ def test_inactivating_a_specific_odm_vendor_attribute(api_client): def test_reactivating_a_specific_odm_vendor_attribute(api_client): response = api_client.post( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/activations" + "odms/vendor-attributes/OdmVendorAttribute_000001/activations" ) assert_response_status_code(response, 200) @@ -366,7 +364,7 @@ def test_reactivating_a_specific_odm_vendor_attribute(api_client): def test_creating_a_new_odm_vendor_attribute_version(api_client): response = api_client.post( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/versions" + "odms/vendor-attributes/OdmVendorAttribute_000001/versions" ) assert_response_status_code(response, 201) @@ -406,7 +404,7 @@ def test_create_a_new_odm_vendor_attribute_for_deleting_it(api_client): "value_regex": "^[a-zA-Z]+$", "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) @@ -437,9 +435,7 @@ def test_create_a_new_odm_vendor_attribute_for_deleting_it(api_client): def test_deleting_a_specific_odm_vendor_attribute(api_client): - response = api_client.delete( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000002" - ) + response = api_client.delete("odms/vendor-attributes/OdmVendorAttribute_000002") assert_response_status_code(response, 204) @@ -448,7 +444,7 @@ def test_getting_uids_of_a_specific_odm_vendor_attributes_active_relationships( api_client, ): response = api_client.get( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/relationships" + "odms/vendor-attributes/OdmVendorAttribute_000001/relationships" ) assert_response_status_code(response, 200) @@ -469,7 +465,7 @@ def test_creating_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_element "value_regex": "^[a-zA-Z]+$", "vendor_element_uid": "odm_vendor_element1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes_negative.py index b89550ea..8cb35bb8 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_attributes_negative.py @@ -41,7 +41,7 @@ def test_create_a_new_odm_vendor_attribute_of_vendor_namespace(api_client): "value_regex": None, "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) @@ -80,7 +80,7 @@ def test_create_a_new_odm_vendor_attribute_of_vendor_element(api_client): "value_regex": None, "vendor_element_uid": "odm_vendor_element1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) @@ -110,9 +110,7 @@ def test_create_a_new_odm_vendor_attribute_of_vendor_element(api_client): def test_getting_error_for_retrieving_non_existent_odm_vendor_attribute(api_client): - response = api_client.get( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000003" - ) + response = api_client.get("odms/vendor-attributes/OdmVendorAttribute_000003") assert_response_status_code(response, 404) @@ -136,7 +134,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_belonging_to_odm_vendor_namesp "value_regex": None, "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 400) @@ -160,7 +158,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_without_first_char_lowercase( "value_regex": None, "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 400) @@ -193,7 +191,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_belonging_to_odm_vendor_elemen "value_regex": None, "vendor_element_uid": "odm_vendor_element1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 400) @@ -215,7 +213,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_with_invalid_regex(api_client) "value_regex": "(*'*(!'", "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 400) @@ -241,7 +239,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_of_vendor_namespace_with_exist "data_type": "string", "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 409) @@ -261,7 +259,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_of_vendor_element_with_existin "data_type": "string", "vendor_element_uid": "odm_vendor_element1", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 409) @@ -273,7 +271,7 @@ def test_cannot_create_a_new_odm_vendor_attribute_of_vendor_element_with_existin def test_cannot_inactivate_an_odm_vendor_attribute_that_is_in_draft_status(api_client): response = api_client.delete( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/activations" + "odms/vendor-attributes/OdmVendorAttribute_000001/activations" ) assert_response_status_code(response, 400) @@ -286,7 +284,7 @@ def test_cannot_inactivate_an_odm_vendor_attribute_that_is_in_draft_status(api_c def test_cannot_reactivate_an_odm_vendor_attribute_that_is_not_retired(api_client): response = api_client.post( - "concepts/odms/vendor-attributes/OdmVendorAttribute_000001/activations" + "odms/vendor-attributes/OdmVendorAttribute_000001/activations" ) assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements.py index 9030b6f1..d0879d2c 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements.py @@ -31,7 +31,7 @@ def test_data(): def test_getting_empty_list_of_odm_vendor_elements(api_client): - response = api_client.get("concepts/odms/vendor-elements") + response = api_client.get("odms/vendor-elements") assert_response_status_code(response, 200) @@ -47,7 +47,7 @@ def test_creating_a_new_odm_vendor_element(api_client): "compatible_types": ["FormDef"], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 201) @@ -84,7 +84,7 @@ def test_creating_a_new_odm_vendor_element_with_relation_to_odm_vendor_element( "compatible_types": ["FormDef"], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 201) @@ -113,7 +113,7 @@ def test_creating_a_new_odm_vendor_element_with_relation_to_odm_vendor_element( def test_getting_non_empty_list_of_odm_vendor_elements(api_client): - response = api_client.get("concepts/odms/vendor-elements") + response = api_client.get("odms/vendor-elements") assert_response_status_code(response, 200) @@ -162,7 +162,7 @@ def test_getting_non_empty_list_of_odm_vendor_elements(api_client): def test_getting_possible_header_values_of_odm_vendor_elements(api_client): - response = api_client.get("concepts/odms/vendor-elements/headers?field_name=name") + response = api_client.get("odms/vendor-elements/headers?field_name=name") assert_response_status_code(response, 200) @@ -172,7 +172,7 @@ def test_getting_possible_header_values_of_odm_vendor_elements(api_client): def test_getting_a_specific_odm_vendor_element(api_client): - response = api_client.get("concepts/odms/vendor-elements/OdmVendorElement_000001") + response = api_client.get("odms/vendor-elements/OdmVendorElement_000001") assert_response_status_code(response, 200) @@ -201,9 +201,7 @@ def test_getting_a_specific_odm_vendor_element(api_client): def test_getting_versions_of_a_specific_odm_vendor_element(api_client): - response = api_client.get( - "concepts/odms/vendor-elements/OdmVendorElement_000001/versions" - ) + response = api_client.get("odms/vendor-elements/OdmVendorElement_000001/versions") assert_response_status_code(response, 200) @@ -240,7 +238,7 @@ def test_updating_an_existing_odm_vendor_element(api_client): "change_description": "name changed to NewName", } response = api_client.patch( - "concepts/odms/vendor-elements/OdmVendorElement_000001", json=data + "odms/vendor-elements/OdmVendorElement_000001", json=data ) assert_response_status_code(response, 200) @@ -271,7 +269,7 @@ def test_updating_an_existing_odm_vendor_element(api_client): def test_getting_a_specific_odm_vendor_element_in_specific_version(api_client): response = api_client.get( - "concepts/odms/vendor-elements/OdmVendorElement_000001?version=0.1" + "odms/vendor-elements/OdmVendorElement_000001?version=0.1" ) assert_response_status_code(response, 200) @@ -301,9 +299,7 @@ def test_getting_a_specific_odm_vendor_element_in_specific_version(api_client): def test_approving_an_odm_vendor_element(api_client): - response = api_client.post( - "concepts/odms/vendor-elements/OdmVendorElement_000001/approvals" - ) + response = api_client.post("odms/vendor-elements/OdmVendorElement_000001/approvals") assert_response_status_code(response, 201) @@ -333,7 +329,7 @@ def test_approving_an_odm_vendor_element(api_client): def test_inactivating_a_specific_odm_vendor_element(api_client): response = api_client.delete( - "concepts/odms/vendor-elements/OdmVendorElement_000001/activations" + "odms/vendor-elements/OdmVendorElement_000001/activations" ) assert_response_status_code(response, 200) @@ -364,7 +360,7 @@ def test_inactivating_a_specific_odm_vendor_element(api_client): def test_reactivating_a_specific_odm_vendor_element(api_client): response = api_client.post( - "concepts/odms/vendor-elements/OdmVendorElement_000001/activations" + "odms/vendor-elements/OdmVendorElement_000001/activations" ) assert_response_status_code(response, 200) @@ -394,9 +390,7 @@ def test_reactivating_a_specific_odm_vendor_element(api_client): def test_creating_a_new_odm_vendor_element_version(api_client): - response = api_client.post( - "concepts/odms/vendor-elements/OdmVendorElement_000001/versions" - ) + response = api_client.post("odms/vendor-elements/OdmVendorElement_000001/versions") assert_response_status_code(response, 201) @@ -431,7 +425,7 @@ def test_create_a_new_odm_vendor_element_for_deleting_it(api_client): "compatible_types": ["FormDef"], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 201) @@ -460,9 +454,7 @@ def test_create_a_new_odm_vendor_element_for_deleting_it(api_client): def test_deleting_a_specific_odm_vendor_element(api_client): - response = api_client.delete( - "concepts/odms/vendor-elements/OdmVendorElement_000002" - ) + response = api_client.delete("odms/vendor-elements/OdmVendorElement_000002") assert_response_status_code(response, 204) @@ -478,7 +470,7 @@ def test_create_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_element( "value_regex": None, "vendor_element_uid": "OdmVendorElement_000001", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) @@ -511,7 +503,7 @@ def test_getting_uids_of_a_specific_odm_vendor_elements_active_relationships( api_client, ): response = api_client.get( - "concepts/odms/vendor-elements/OdmVendorElement_000001/relationships" + "odms/vendor-elements/OdmVendorElement_000001/relationships" ) assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements_negative.py index ce9cc717..678015fc 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_elements_negative.py @@ -37,7 +37,7 @@ def test_create_a_new_odm_vendor_element(api_client): "compatible_types": ["FormDef"], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 201) @@ -66,7 +66,7 @@ def test_create_a_new_odm_vendor_element(api_client): def test_getting_error_for_retrieving_non_existent_odm_vendor_element(api_client): - response = api_client.get("concepts/odms/vendor-elements/OdmVendorElement_000002") + response = api_client.get("odms/vendor-elements/OdmVendorElement_000002") assert_response_status_code(response, 404) @@ -88,7 +88,7 @@ def test_cannot_create_a_new_odm_vendor_element_without_providing_compatible_typ "compatible_types": [], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 400) @@ -114,7 +114,7 @@ def test_cannot_create_a_new_odm_vendor_element_without_first_char_uppercase( "compatible_types": ["FormDef"], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 400) @@ -145,7 +145,7 @@ def test_cannot_create_a_new_odm_vendor_element_if_odm_vendor_namespace_doesnt_e "compatible_types": ["FormDef"], "vendor_namespace_uid": "wrong_uid", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 400) @@ -154,7 +154,7 @@ def test_cannot_create_a_new_odm_vendor_element_if_odm_vendor_namespace_doesnt_e assert res["type"] == "BusinessLogicException" assert ( res["message"] - == """ODM Vendor Element tried to connect to non-existent concepts [('Concept Name: ODM Vendor Namespace', "uids: {'wrong_uid'}")].""" + == "ODM Vendor Element tried to connect to non-existent ODM Vendor Namespace with UID 'wrong_uid'." ) @@ -165,7 +165,7 @@ def test_cannot_create_a_new_odm_vendor_element_with_existing_name(api_client): "compatible_types": ["FormDef"], "vendor_namespace_uid": "odm_vendor_namespace1", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 409) @@ -177,7 +177,7 @@ def test_cannot_create_a_new_odm_vendor_element_with_existing_name(api_client): def test_cannot_inactivate_an_odm_vendor_element_that_is_in_draft_status(api_client): response = api_client.delete( - "concepts/odms/vendor-elements/OdmVendorElement_000001/activations" + "odms/vendor-elements/OdmVendorElement_000001/activations" ) assert_response_status_code(response, 400) @@ -190,7 +190,7 @@ def test_cannot_inactivate_an_odm_vendor_element_that_is_in_draft_status(api_cli def test_cannot_reactivate_an_odm_vendor_element_that_is_not_retired(api_client): response = api_client.post( - "concepts/odms/vendor-elements/OdmVendorElement_000001/activations" + "odms/vendor-elements/OdmVendorElement_000001/activations" ) assert_response_status_code(response, 400) @@ -211,7 +211,7 @@ def test_create_an_odm_form(api_client): "translated_texts": [], "aliases": [], } - response = api_client.post("concepts/odms/forms", json=data) + response = api_client.post("odms/forms", json=data) assert_response_status_code(response, 201) @@ -251,7 +251,7 @@ def test_add_odm_vendor_element_to_the_odm_form(api_client): "vendor_attributes": [], "change_description": "change desc", } - response = api_client.patch("concepts/odms/forms/OdmForm_000001", json=data) + response = api_client.patch("odms/forms/OdmForm_000001", json=data) assert_response_status_code(response, 200) @@ -280,9 +280,7 @@ def test_add_odm_vendor_element_to_the_odm_form(api_client): def test_cannot_delete_an_odm_vendor_element_that_is_being_used(api_client): - response = api_client.delete( - "concepts/odms/vendor-elements/OdmVendorElement_000001" - ) + response = api_client.delete("odms/vendor-elements/OdmVendorElement_000001") assert_response_status_code(response, 400) @@ -293,7 +291,7 @@ def test_cannot_delete_an_odm_vendor_element_that_is_being_used(api_client): def test_cannot_delete_non_existent_odm_vendor_element(api_client): - response = api_client.delete("concepts/odms/vendor-elements/wrong_uid") + response = api_client.delete("odms/vendor-elements/wrong_uid") assert_response_status_code(response, 404) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces.py index d3bf0fa7..0e5bffdb 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces.py @@ -28,7 +28,7 @@ def test_data(): def test_getting_empty_list_of_odm_vendor_namespaces(api_client): - response = api_client.get("concepts/odms/vendor-namespaces") + response = api_client.get("odms/vendor-namespaces") assert_response_status_code(response, 200) @@ -44,7 +44,7 @@ def test_creating_a_new_odm_vendor_namespace(api_client): "prefix": "prefix", "url": "url1", } - response = api_client.post("concepts/odms/vendor-namespaces", json=data) + response = api_client.post("odms/vendor-namespaces", json=data) assert_response_status_code(response, 201) @@ -66,7 +66,7 @@ def test_creating_a_new_odm_vendor_namespace(api_client): def test_getting_non_empty_list_of_odm_vendor_namespaces(api_client): - response = api_client.get("concepts/odms/vendor-namespaces") + response = api_client.get("odms/vendor-namespaces") assert_response_status_code(response, 200) @@ -88,7 +88,7 @@ def test_getting_non_empty_list_of_odm_vendor_namespaces(api_client): def test_getting_possible_header_values_of_odm_vendor_namespaces(api_client): - response = api_client.get("concepts/odms/vendor-namespaces/headers?field_name=name") + response = api_client.get("odms/vendor-namespaces/headers?field_name=name") assert_response_status_code(response, 200) @@ -98,9 +98,7 @@ def test_getting_possible_header_values_of_odm_vendor_namespaces(api_client): def test_getting_a_specific_odm_vendor_namespace(api_client): - response = api_client.get( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001" - ) + response = api_client.get("odms/vendor-namespaces/OdmVendorNamespace_000001") assert_response_status_code(response, 200) @@ -123,7 +121,7 @@ def test_getting_a_specific_odm_vendor_namespace(api_client): def test_getting_versions_of_a_specific_odm_vendor_namespace(api_client): response = api_client.get( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/versions" + "odms/vendor-namespaces/OdmVendorNamespace_000001/versions" ) assert_response_status_code(response, 200) @@ -154,7 +152,7 @@ def test_updating_an_existing_odm_vendor_namespace(api_client): "change_description": "namespace changed to new url", } response = api_client.patch( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001", json=data + "odms/vendor-namespaces/OdmVendorNamespace_000001", json=data ) assert_response_status_code(response, 200) @@ -178,7 +176,7 @@ def test_updating_an_existing_odm_vendor_namespace(api_client): def test_getting_a_specific_odm_vendor_namespace_in_specific_version(api_client): response = api_client.get( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001?version=0.1" + "odms/vendor-namespaces/OdmVendorNamespace_000001?version=0.1" ) assert_response_status_code(response, 200) @@ -202,7 +200,7 @@ def test_getting_a_specific_odm_vendor_namespace_in_specific_version(api_client) def test_approving_an_odm_vendor_namespace(api_client): response = api_client.post( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/approvals" + "odms/vendor-namespaces/OdmVendorNamespace_000001/approvals" ) assert_response_status_code(response, 201) @@ -226,7 +224,7 @@ def test_approving_an_odm_vendor_namespace(api_client): def test_inactivating_a_specific_odm_vendor_namespace(api_client): response = api_client.delete( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/activations" + "odms/vendor-namespaces/OdmVendorNamespace_000001/activations" ) assert_response_status_code(response, 200) @@ -250,7 +248,7 @@ def test_inactivating_a_specific_odm_vendor_namespace(api_client): def test_reactivating_a_specific_odm_vendor_namespace(api_client): response = api_client.post( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/activations" + "odms/vendor-namespaces/OdmVendorNamespace_000001/activations" ) assert_response_status_code(response, 200) @@ -274,7 +272,7 @@ def test_reactivating_a_specific_odm_vendor_namespace(api_client): def test_creating_a_new_odm_vendor_namespace_version(api_client): response = api_client.post( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/versions" + "odms/vendor-namespaces/OdmVendorNamespace_000001/versions" ) assert_response_status_code(response, 201) @@ -303,7 +301,7 @@ def test_create_a_new_odm_vendor_namespace_for_deleting_it(api_client): "prefix": "prefixOne", "url": "namespace2", } - response = api_client.post("concepts/odms/vendor-namespaces", json=data) + response = api_client.post("odms/vendor-namespaces", json=data) assert_response_status_code(response, 201) @@ -325,9 +323,7 @@ def test_create_a_new_odm_vendor_namespace_for_deleting_it(api_client): def test_deleting_a_specific_odm_vendor_namespace(api_client): - response = api_client.delete( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000002" - ) + response = api_client.delete("odms/vendor-namespaces/OdmVendorNamespace_000002") assert_response_status_code(response, 204) @@ -343,7 +339,7 @@ def test_create_a_new_odm_vendor_attribute_with_relation_to_odm_vendor_namespace "value_regex": None, "vendor_namespace_uid": "OdmVendorNamespace_000001", } - response = api_client.post("concepts/odms/vendor-attributes", json=data) + response = api_client.post("odms/vendor-attributes", json=data) assert_response_status_code(response, 201) @@ -380,7 +376,7 @@ def test_create_a_new_odm_vendor_element1(api_client): "compatible_types": ["FormDef"], "vendor_namespace_uid": "OdmVendorNamespace_000001", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 201) @@ -412,7 +408,7 @@ def test_getting_uids_of_a_specific_odm_vendor_namespaces_active_relationships( api_client, ): response = api_client.get( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/relationships" + "odms/vendor-namespaces/OdmVendorNamespace_000001/relationships" ) assert_response_status_code(response, 200) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces_negative.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces_negative.py index 34b39cc5..fef13e13 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces_negative.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_vendor_namespaces_negative.py @@ -34,7 +34,7 @@ def test_create_a_new_odm_vendor_namespace(api_client): "prefix": "prefix", "url": "url1", } - response = api_client.post("concepts/odms/vendor-namespaces", json=data) + response = api_client.post("odms/vendor-namespaces", json=data) assert_response_status_code(response, 201) @@ -55,32 +55,65 @@ def test_create_a_new_odm_vendor_namespace(api_client): assert res["possible_actions"] == ["approve", "delete", "edit"] -def test_cannot_create_a_new_odm_vendor_namespace_with_existing_name_prefix_and_url( +def test_cannot_create_a_new_odm_vendor_namespace_with_existing_name( api_client, ): data = { "library_name": "Sponsor", "name": "name1", "prefix": "prefix", + "url": "url", + } + response = api_client.post("odms/vendor-namespaces", json=data) + + assert_response_status_code(response, 409) + + res = response.json() + + assert res["type"] == "AlreadyExistsException" + assert res["message"] == "ODM Vendor Namespace with Name 'name1' already exists." + + +def test_cannot_create_a_new_odm_vendor_namespace_with_existing_prefix( + api_client, +): + data = { + "library_name": "Sponsor", + "name": "name", + "prefix": "prefix", + "url": "url", + } + response = api_client.post("odms/vendor-namespaces", json=data) + + assert_response_status_code(response, 409) + + res = response.json() + + assert res["type"] == "AlreadyExistsException" + assert res["message"] == "ODM Vendor Namespace with Prefix 'prefix' already exists." + + +def test_cannot_create_a_new_odm_vendor_namespace_with_existing_url( + api_client, +): + data = { + "library_name": "Sponsor", + "name": "name", + "prefix": "prefixNew", "url": "url1", } - response = api_client.post("concepts/odms/vendor-namespaces", json=data) + response = api_client.post("odms/vendor-namespaces", json=data) assert_response_status_code(response, 409) res = response.json() assert res["type"] == "AlreadyExistsException" - assert ( - res["message"] - == "ODM Vendor Namespace with ['name: name1', 'prefix: prefix', 'url: url1'] already exists." - ) + assert res["message"] == "ODM Vendor Namespace with Url 'url1' already exists." def test_getting_error_for_retrieving_non_existent_odm_vendor_namespace(api_client): - response = api_client.get( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000002" - ) + response = api_client.get("odms/vendor-namespaces/OdmVendorNamespace_000002") assert_response_status_code(response, 404) @@ -95,7 +128,7 @@ def test_getting_error_for_retrieving_non_existent_odm_vendor_namespace(api_clie def test_cannot_inactivate_an_odm_vendor_namespace_that_is_in_draft_status(api_client): response = api_client.delete( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/activations" + "odms/vendor-namespaces/OdmVendorNamespace_000001/activations" ) assert_response_status_code(response, 400) @@ -108,7 +141,7 @@ def test_cannot_inactivate_an_odm_vendor_namespace_that_is_in_draft_status(api_c def test_cannot_reactivate_an_odm_vendor_namespace_that_is_not_retired(api_client): response = api_client.post( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001/activations" + "odms/vendor-namespaces/OdmVendorNamespace_000001/activations" ) assert_response_status_code(response, 400) @@ -128,7 +161,7 @@ def test_create_odm_vendor_element_with_relation_to_the_odm_vendor_namespace( "compatible_types": ["FormDef"], "vendor_namespace_uid": "OdmVendorNamespace_000001", } - response = api_client.post("concepts/odms/vendor-elements", json=data) + response = api_client.post("odms/vendor-elements", json=data) assert_response_status_code(response, 201) @@ -157,9 +190,7 @@ def test_create_odm_vendor_element_with_relation_to_the_odm_vendor_namespace( def test_cannot_delete_an_odm_vendor_namespace_that_is_being_used(api_client): - response = api_client.delete( - "concepts/odms/vendor-namespaces/OdmVendorNamespace_000001" - ) + response = api_client.delete("odms/vendor-namespaces/OdmVendorNamespace_000001") assert_response_status_code(response, 400) @@ -170,7 +201,7 @@ def test_cannot_delete_an_odm_vendor_namespace_that_is_being_used(api_client): def test_cannot_delete_non_existent_odm_vendor_namespace(api_client): - response = api_client.delete("concepts/odms/vendor-namespaces/wrong_uid") + response = api_client.delete("odms/vendor-namespaces/wrong_uid") assert_response_status_code(response, 404) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_exporter.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_exporter.py index aaa1c659..c22f27e5 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_exporter.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_exporter.py @@ -136,11 +136,11 @@ def test_get_odm_xml_form(api_client): ], ) - api_client.post("concepts/odms/forms/odm_form1/versions") - api_client.post("concepts/odms/item-groups/odm_item_group1/versions") + api_client.post("odms/forms/odm_form1/versions") + api_client.post("odms/item-groups/odm_item_group1/versions") response = api_client.post( - "concepts/odms/items", + "odms/items", json={ "name": "with activity instance", "oid": "oid999", @@ -164,7 +164,7 @@ def test_get_odm_xml_form(api_client): item_uid = rs["uid"] response = api_client.post( - "concepts/odms/item-groups/odm_item_group1/items", + "odms/item-groups/odm_item_group1/items", json=[ { "uid": item_uid, @@ -177,7 +177,7 @@ def test_get_odm_xml_form(api_client): assert_response_status_code(response, 201) response = api_client.patch( - "concepts/odms/items/" + item_uid, + "odms/items/" + item_uid, json={ "name": "with activity instance", "oid": "oid999", @@ -216,7 +216,7 @@ def test_get_odm_xml_form(api_client): assert_response_status_code(response, 200) response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1&target_type=form&stylesheet=falcon&allowed_namespaces=*", + "odms/metadata/xmls/export?targets=odm_form1&target_type=form&stylesheet=falcon&allowed_namespaces=*", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -235,7 +235,7 @@ def test_get_odm_xml_form(api_client): def test_get_odm_xml_forms(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1&targets=odm_form2&target_type=form&stylesheet=falcon&allowed_namespaces=*", + "odms/metadata/xmls/export?targets=odm_form1&targets=odm_form2&target_type=form&stylesheet=falcon&allowed_namespaces=*", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -254,7 +254,7 @@ def test_get_odm_xml_forms(api_client): def test_get_odm_xml_forms_with_specific_version(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1,1.1&targets=odm_form2,1.0&target_type=form&stylesheet=falcon&allowed_namespaces=*", + "odms/metadata/xmls/export?targets=odm_form1,1.1&targets=odm_form2,1.0&target_type=form&stylesheet=falcon&allowed_namespaces=*", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -273,7 +273,7 @@ def test_get_odm_xml_forms_with_specific_version(api_client): def test_get_odm_xml_forms_without_specific_version(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1,&targets=odm_form2,&target_type=form&stylesheet=falcon&allowed_namespaces=*", + "odms/metadata/xmls/export?targets=odm_form1,&targets=odm_form2,&target_type=form&stylesheet=falcon&allowed_namespaces=*", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -292,7 +292,7 @@ def test_get_odm_xml_forms_without_specific_version(api_client): def test_get_odm_xml_item_group(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_item_group1&target_type=item_group&stylesheet=falcon&allowed_namespaces=*", + "odms/metadata/xmls/export?targets=odm_item_group1&target_type=item_group&stylesheet=falcon&allowed_namespaces=*", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -311,7 +311,7 @@ def test_get_odm_xml_item_group(api_client): def test_get_odm_xml_item(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_item1&target_type=item&stylesheet=falcon&allowed_namespaces=*", + "odms/metadata/xmls/export?targets=odm_item1&target_type=item&stylesheet=falcon&allowed_namespaces=*", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -330,7 +330,7 @@ def test_get_odm_xml_item(api_client): def test_get_odm_xml_with_allowed_namespaces(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1&target_type=form&allowed_namespaces=prefix", + "odms/metadata/xmls/export?targets=odm_form1&target_type=form&allowed_namespaces=prefix", ) assert_response_status_code(response, 200) assert_response_content_type(response, CONTENT_TYPE) @@ -346,7 +346,7 @@ def test_get_odm_xml_with_allowed_namespaces(api_client): def test_get_odm_xml_with_mapper_csv(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?target_type=form&targets=odm_form1&allowed_namespaces=*", + "odms/metadata/xmls/export?target_type=form&targets=odm_form1&allowed_namespaces=*", files={ "mapper_file": ( "mapper.csv", @@ -375,7 +375,7 @@ def test_get_odm_xml_with_mapper_csv(api_client): def test_get_odm_xml_pdf_version(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?target_type=form&targets=odm_form1&pdf=true&stylesheet=falcon" + "odms/metadata/xmls/export?target_type=form&targets=odm_form1&pdf=true&stylesheet=falcon" ) assert_response_status_code(response, 200) assert_response_content_type(response, "application/pdf") @@ -383,7 +383,7 @@ def test_get_odm_xml_pdf_version(api_client): def test_get_odm_html_version(api_client): response = api_client.post( - "concepts/odms/metadata/report?target_type=form&targets=odm_form1" + "odms/metadata/report?target_type=form&targets=odm_form1" ) assert_response_status_code(response, 200) assert_response_content_type(response, "text/html") @@ -391,7 +391,7 @@ def test_get_odm_html_version(api_client): def test_throw_exception_if_target_type_is_not_supported(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=study&target_type=study", + "odms/metadata/xmls/export?targets=study&target_type=study", ) assert_response_status_code(response, 400) @@ -403,7 +403,7 @@ def test_throw_exception_if_target_type_is_not_supported(api_client): def test_throw_exception_if_mapper_is_non_csv(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1&target_type=form", + "odms/metadata/xmls/export?targets=odm_form1&target_type=form", files={ "mapper_file": ( "mapper.json", @@ -421,7 +421,7 @@ def test_throw_exception_if_mapper_is_non_csv(api_client): def test_throw_exception_if_csv_header_missing(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/export?targets=odm_form1&target_type=form", + "odms/metadata/xmls/export?targets=odm_form1&target_type=form", files={ "mapper_file": ( "mapper.csv", diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_importer.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_importer.py index ecb6d855..51579189 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_importer.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_importer.py @@ -57,7 +57,7 @@ def test_data(): def test_import_odm_xml(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={"xml_file": ("odm.xml", IMPORT_INPUT1, CONTENT_TYPE)}, ) @@ -71,7 +71,7 @@ def test_import_odm_xml(api_client): def test_import_odm_vendor_with_csv_mapper(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={ "xml_file": ("odm.xml", IMPORT_INPUT2, CONTENT_TYPE), "mapper_file": ( @@ -97,7 +97,7 @@ def test_import_odm_vendor_with_csv_mapper(api_client): def test_import_clinspark_odm_xml(api_client): db.cypher_query("MERGE (:CTCatalogue {name:'CDASH CT'})") response = api_client.post( - "concepts/odms/metadata/xmls/import?exporter=clinspark", + "odms/metadata/xmls/import?exporter=clinspark", files={"xml_file": ("clinspark.xml", CLINSPARK_INPUT, CONTENT_TYPE)}, ) @@ -111,7 +111,7 @@ def test_import_clinspark_odm_xml(api_client): def test_throw_exception_if_file_is_not_xml(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={ "xml_file": ( "mapper.json", @@ -131,7 +131,7 @@ def test_throw_exception_if_file_is_not_xml(api_client): def test_throw_exception_if_vendor_attributes_dont_match_their_regex(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={"xml_file": ("odm.xml", IMPORT_INPUT4, CONTENT_TYPE)}, ) @@ -148,7 +148,7 @@ def test_throw_exception_if_vendor_attributes_dont_match_their_regex(api_client) def test_throw_exception_if_ref_vendor_attributes_dont_match_their_regex(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={"xml_file": ("odm.xml", IMPORT_INPUT5, CONTENT_TYPE)}, ) @@ -165,7 +165,7 @@ def test_throw_exception_if_ref_vendor_attributes_dont_match_their_regex(api_cli def test_throw_exception_if_measurementunits_dont_exist(api_client): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={"xml_file": ("odm.xml", IMPORT_INPUT3, CONTENT_TYPE)}, ) @@ -183,7 +183,7 @@ def test_throw_exception_if_measurementunitref_refers_to_non_present_measurement api_client, ): response = api_client.post( - "concepts/odms/metadata/xmls/import", + "odms/metadata/xmls/import", files={"xml_file": ("odm.xml", IMPORT_INPUT6, CONTENT_TYPE)}, ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_stylesheets.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_stylesheets.py index 4b2ed562..b60f2473 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_stylesheets.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/old/test_odm_xml_stylesheets.py @@ -19,14 +19,14 @@ def api_client(): def test_get_available_stylesheet_names(api_client): - response = api_client.get("concepts/odms/metadata/xmls/stylesheets") + response = api_client.get("odms/metadata/xmls/stylesheets") assert_response_status_code(response, 200) assert response.json() == ["falcon", "with-annotations"] def test_get_specific_stylesheet(api_client): - response = api_client.get("concepts/odms/metadata/xmls/stylesheets/falcon") + response = api_client.get("odms/metadata/xmls/stylesheets/falcon") with open( settings.xml_stylesheet_dir_path + "falcon.xsl", mode="r", encoding="utf-8" @@ -44,7 +44,7 @@ def test_get_specific_stylesheet(api_client): def test_throw_exception_if_stylesheet_doesnt_exist(api_client): response = api_client.get( - "concepts/odms/metadata/xmls/stylesheets/wrong", + "odms/metadata/xmls/stylesheets/wrong", ) assert_response_status_code(response, 404) @@ -56,7 +56,7 @@ def test_throw_exception_if_stylesheet_doesnt_exist(api_client): def test_throw_exception_if_stylesheet_name_contains_disallowed_character(api_client): for name in ["falc_on", "falcon.", "falc%on"]: response = api_client.get( - f"concepts/odms/metadata/xmls/stylesheets/{name}", + f"odms/metadata/xmls/stylesheets/{name}", ) assert_response_status_code(response, 400) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_classes.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_classes.py index eb45300d..66646e4a 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_classes.py @@ -70,6 +70,7 @@ def test_data(): description="DatasetClass A desc", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[0].uid, + data_model_name=data_models[0].name, ) ) @@ -78,6 +79,7 @@ def test_data(): label="name-AAA", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[1].uid, + data_model_name=data_models[1].name, ) ) dataset_classes.append( @@ -85,6 +87,7 @@ def test_data(): label="name-BBB", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[1].uid, + data_model_name=data_models[1].name, ) ) dataset_classes.append( @@ -92,6 +95,7 @@ def test_data(): description="def-XXX", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[1].uid, + data_model_name=data_models[1].name, ) ) dataset_classes.append( @@ -99,6 +103,7 @@ def test_data(): description="def-YYY", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[1].uid, + data_model_name=data_models[1].name, ) ) @@ -108,6 +113,7 @@ def test_data(): label=f"name-AAA-{index}", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[2].uid, + data_model_name=data_models[2].name, ) ) dataset_classes.append( @@ -115,6 +121,7 @@ def test_data(): label=f"name-BBB-{index}", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[2].uid, + data_model_name=data_models[2].name, ) ) dataset_classes.append( @@ -122,6 +129,7 @@ def test_data(): description=f"def-XXX-{index}", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[2].uid, + data_model_name=data_models[2].name, ) ) dataset_classes.append( @@ -129,6 +137,7 @@ def test_data(): description=f"def-YYY-{index}", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_models[2].uid, + data_model_name=data_models[2].name, ) ) @@ -141,20 +150,22 @@ def test_data(): "title", "description", "catalogue_name", - "data_models", - "parent_class", + "data_model", + "parent_class_name", ] DATASET_CLASS_FIELDS_NOT_NULL = [ "uid", "label", "catalogue_name", - "data_models", + "data_model", ] def test_get_dataset_class(api_client): - response = api_client.get(f"/standards/dataset-classes/{dataset_classes[0].uid}") + response = api_client.get( + f"/standards/dataset-classes/{dataset_classes[0].uid}?data_model_name={data_models[0].name}" + ) res = response.json() assert_response_status_code(response, 200) @@ -168,14 +179,14 @@ def test_get_dataset_class(api_client): assert res["label"] == "DatasetClass A label" assert res["description"] == "DatasetClass A desc" assert res["catalogue_name"] == data_model_catalogue_name - assert res["data_models"][0]["data_model_name"] == data_models[0].name + assert res["data_model"]["data_model_name"] == data_models[0].name def test_get_dataset_classes_pagination(api_client): results_paginated: dict[Any, Any] = {} sort_by = '{"uid": true}' for page_number in range(1, 4): - url = f"/standards/dataset-classes?page_number={page_number}&page_size=10&sort_by={sort_by}" + url = f"/standards/dataset-classes?data_model_name={data_models[2].name}&page_number={page_number}&page_size=10&sort_by={sort_by}" response = api_client.get(url) res = response.json() res_uids = [item["uid"] for item in res["items"]] @@ -190,12 +201,18 @@ def test_get_dataset_classes_pagination(api_client): log.info("All rows returned by pagination: %s", results_paginated_merged) res_all = api_client.get( - f"/standards/dataset-classes?page_number=1&page_size=100&sort_by={sort_by}" + f"/standards/dataset-classes?data_model_name={data_models[2].name}&page_number=1&page_size=100&sort_by={sort_by}" ).json() results_all_in_one_page = [item["uid"] for item in res_all["items"]] log.info("All rows in one page: %s", results_all_in_one_page) assert len(results_all_in_one_page) == len(results_paginated_merged) - assert len(dataset_classes) == len(results_paginated_merged) + assert len(results_paginated_merged) == len( + [ + dc + for dc in dataset_classes + if dc.data_model.data_model_name == data_models[2].name + ] + ) @pytest.mark.parametrize( @@ -205,7 +222,6 @@ def test_get_dataset_classes_pagination(api_client): pytest.param(3, 1, True, None, 3), pytest.param(3, 2, True, None, 3), pytest.param(10, 2, True, None, 10), - pytest.param(10, 3, True, None, 5), # Total number of data models is 25 pytest.param(10, 1, True, '{"label": false}', 10), pytest.param(10, 2, True, '{"label": true}', 10), ], @@ -214,7 +230,7 @@ def test_get_dataset_classes( api_client, page_size, page_number, total_count, sort_by, expected_result_len ): url = "/standards/dataset-classes" - query_params = [] + query_params = [f"data_model_name={data_models[2].name}"] if page_size: query_params.append(f"page_size={page_size}") if page_number: @@ -236,7 +252,17 @@ def test_get_dataset_classes( # Check fields included in the response assert list(res.keys()) == ["items", "total", "page", "size"] assert len(res["items"]) == expected_result_len - assert res["total"] == (len(dataset_classes) if total_count else 0) + assert res["total"] == ( + len( + [ + dc + for dc in dataset_classes + if dc.data_model.data_model_name == data_models[2].name + ] + ) + if total_count + else 0 + ) assert res["page"] == (page_number if page_number else 1) assert res["size"] == (page_size if page_size else 10) @@ -270,7 +296,7 @@ def test_get_dataset_classes( def test_filtering_wildcard( api_client, filter_by, expected_matched_field, expected_result_prefix ): - url = f"/standards/dataset-classes?filters={filter_by}" + url = f"/standards/dataset-classes?data_model_name={data_models[2].name}&filters={filter_by}" response = api_client.get(url) res = response.json() @@ -310,11 +336,6 @@ def test_filtering_wildcard( pytest.param('{"description": {"v": ["def-XXX"]}}', "description", "def-XXX"), pytest.param('{"description": {"v": ["def-YYY"]}}', "description", "def-YYY"), pytest.param('{"description": {"v": ["cc"]}}', None, None), - pytest.param( - '{"data_models.data_model_name": {"v": ["DataModel A"]}}', - "data_models.data_model_name", - "DataModel A", - ), pytest.param( '{"catalogue_name": {"v": ["DataModelCatalogue name"]}}', "catalogue_name", @@ -325,7 +346,7 @@ def test_filtering_wildcard( def test_filtering_exact( api_client, filter_by, expected_matched_field, expected_result ): - url = f"/standards/dataset-classes?filters={filter_by}" + url = f"/standards/dataset-classes?data_model_name={data_models[1].name}&filters={filter_by}" response = api_client.get(url) res = response.json() @@ -363,12 +384,11 @@ def test_filtering_exact( [ pytest.param("label"), pytest.param("description"), - pytest.param("data_models.data_model_name"), pytest.param("catalogue_name"), ], ) def test_headers(api_client, field_name): - url = f"/standards/dataset-classes/headers?field_name={field_name}&page_size=100" + url = f"/standards/dataset-classes/headers?data_model_name={data_models[2].name}&field_name={field_name}&page_size=100" response = api_client.get(url) res = response.json() @@ -381,7 +401,11 @@ def test_headers(api_client, field_name): expected_matched_field = nested_path[-1] nested_path = nested_path[:-1] - for dataset_class in dataset_classes: + for dataset_class in [ + dc + for dc in dataset_classes + if dc.data_model.data_model_name == data_models[2].name + ]: if nested_path: for prop in nested_path: dataset_class = getattr(dataset_class, prop) @@ -417,5 +441,5 @@ def test_headers(api_client, field_name): ], ) def test_get_dataset_classes_csv_xml_excel(api_client, export_format): - url = "/standards/dataset-classes" + url = "/standards/dataset-classes?data_model_name={data_models[2].name}&" TestUtils.verify_exported_data_format(api_client, export_format, url) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_scenarios.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_scenarios.py index c574b855..b20ffb4e 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_scenarios.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_scenarios.py @@ -76,11 +76,12 @@ def test_data(): label=label, data_model_uid=data_model_uid, data_model_catalogue_name=data_model_catalogue_name, + data_model_name=data_model_name, ) - for label, data_model_uid in [ - ("DatasetClass A", data_models[0].uid), - ("DatasetClass B", data_models[1].uid), - ("DatasetClass C", data_models[2].uid), + for label, data_model_uid, data_model_name in [ + ("DatasetClass A", data_models[0].uid, data_models[0].name), + ("DatasetClass B", data_models[1].uid, data_models[1].name), + ("DatasetClass C", data_models[2].uid, data_models[2].name), ] ] data_model_ig = TestUtils.create_data_model_ig( diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_variables.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_variables.py index 6bec3eb0..b61eae5b 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_variables.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_dataset_variables.py @@ -83,11 +83,12 @@ def test_data(): label=label, data_model_uid=data_model_uid, data_model_catalogue_name=data_model_catalogue_name, + data_model_name=data_model_name, ) - for label, data_model_uid in [ - ("DatasetClass A", data_models[0].uid), - ("DatasetClass B", data_models[1].uid), - ("DatasetClass C", data_models[2].uid), + for label, data_model_uid, data_model_name in [ + ("DatasetClass A", data_models[0].uid, data_models[0].name), + ("DatasetClass B", data_models[1].uid, data_models[1].name), + ("DatasetClass C", data_models[2].uid, data_models[2].name), ] ] class_variable = TestUtils.create_variable_class( @@ -229,7 +230,6 @@ def test_data(): "completion_instructions", "implementation_notes", "mapping_instructions", - "data_model_ig_names", "dataset", "implements_variable", "has_mapping_target", @@ -244,7 +244,6 @@ def test_data(): "label", "dataset", "implements_variable", - "data_model_ig_names", ] @@ -270,7 +269,6 @@ def test_get_class_variable(api_client): assert res["description"] == "DatasetVariable A desc" assert res["dataset"]["uid"] == dataset.uid assert res["implements_variable"]["name"] == class_variable.label - assert res["data_model_ig_names"] == [data_model_ig.name] def test_get_dataset_variables_pagination(api_client): @@ -449,11 +447,6 @@ def test_filtering_wildcard( "implements_variable.name", "VariableClass A label", ), - pytest.param( - '{"data_model_ig_names": {"v": ["DataModelIG A"]}}', - "data_model_ig_names", - ["DataModelIG A"], - ), ], ) def test_filtering_exact( diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_datasets.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_datasets.py index 9ebdd4dc..ad7e76b9 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_datasets.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_datasets.py @@ -74,6 +74,7 @@ def test_data(): description=f"DatasetClass desc-{index}", data_model_catalogue_name=data_model_catalogue_name, data_model_uid=data_model.uid, + data_model_name=data_model.name, ) ) # Create some datasets diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_sponsor_models.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_sponsor_models.py index 2349a553..df0df8c4 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_sponsor_models.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_sponsor_models.py @@ -84,6 +84,7 @@ def test_data(): label=f"DatasetClass{i} label", data_model_uid=data_model.uid, data_model_catalogue_name=data_model_catalogue_name, + data_model_name=data_model.name, ) for i in range(3) ] diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_variable_classes.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_variable_classes.py index 39c050a6..7ea6de93 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_variable_classes.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/standard_data_models/test_variable_classes.py @@ -76,11 +76,12 @@ def test_data(): label=label, data_model_uid=data_model_uid, data_model_catalogue_name=data_model_catalogue_name, + data_model_name=data_model_name, ) - for label, data_model_uid in [ - ("DatasetClass A", data_models[0].uid), - ("DatasetClass B", data_models[1].uid), - ("DatasetClass C", data_models[2].uid), + for label, data_model_uid, data_model_name in [ + ("DatasetClass A", data_models[0].uid, data_models[0].name), + ("DatasetClass B", data_models[1].uid, data_models[1].name), + ("DatasetClass C", data_models[2].uid, data_models[2].name), ] ] data_model_ig = TestUtils.create_data_model_ig( @@ -217,17 +218,15 @@ def test_data(): "role", "catalogue_name", "dataset_class", - "dataset_variable_name", "referenced_codelists", - "has_mapping_target", + "has_mapping_targets", "core", "described_value_domain", "notes", "usage_restrictions", "examples", "completion_instructions", - "data_model_names", - "qualifies_variable", + "qualifies_variables", ] CLASS_VARIABLE_FIELDS_NOT_NULL = [ @@ -235,7 +234,6 @@ def test_data(): "label", "catalogue_name", "dataset_class", - "data_model_names", ] @@ -262,8 +260,6 @@ def test_get_class_variable(api_client): assert res["description"] == "VariableClass A desc" assert res["catalogue_name"] == data_model_catalogue_name assert res["dataset_class"]["dataset_class_name"] == dataset_classes[0].label - assert res["dataset_variable_name"] == dataset_variable.label - assert res["data_model_names"] == [data_models[0].name] def test_get_class_variables_pagination(api_client): @@ -306,7 +302,8 @@ def test_get_class_variables_pagination(api_client): [ class_variable for class_variable in class_variables - if data_models[2].name in class_variable.data_model_names + if class_variable.dataset_class.dataset_class_name + == dataset_classes[2].label ] ) == len(results_paginated_merged) @@ -361,7 +358,8 @@ def test_get_class_variables( [ class_variable for class_variable in class_variables - if data_models[2].name in class_variable.data_model_names + if class_variable.dataset_class.dataset_class_name + == dataset_classes[2].label ] ) if total_count @@ -462,11 +460,6 @@ def test_filtering_wildcard( "catalogue_name", "DataModelCatalogue name", ), - pytest.param( - '{"data_model_names": {"v": ["DataModel B"]}}', - "data_model_names", - ["DataModel B"], - ), ], ) def test_filtering_exact( @@ -518,7 +511,6 @@ def test_filtering_exact( pytest.param("label"), pytest.param("description"), pytest.param("role"), - pytest.param("dataset_variable_name"), pytest.param("catalogue_name"), pytest.param("dataset_class.dataset_class_name"), ], @@ -547,7 +539,7 @@ def test_headers(api_client, field_name): for class_variable in [ class_var for class_var in class_variables - if data_models[2].name in class_var.data_model_names + if class_var.dataset_class.dataset_class_name == dataset_classes[2].label ]: if nested_path: for prop in nested_path: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py index 3a6e821f..37705653 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study/test_study_soa_split.py @@ -37,8 +37,7 @@ def __init__(self): self.visits = [] for i in range(9): self.visits.append( - # pylint: disable=repeated-keyword # False-positive: multiple values for 'time_value' - TestUtils.create_study_visit( + TestUtils.create_study_visit( # pylint: disable=repeated-keyword study_uid=self.study.uid, study_epoch_uid=self.epochs[int(i / 3)].uid, time_value=i * 7, 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 b6966a43..4fec9953 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 @@ -175,9 +175,9 @@ def test_adam_listing_mdvisit_versioning(api_client, test_data): "show_visit": False, "time_unit_uid": "UnitDefinition_000002", "time_value": 0, - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0002", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0002"}, "is_global_anchor_visit": False, "visit_class": "SINGLE_VISIT", "study_epoch_uid": "StudyEpoch_000001", @@ -187,7 +187,7 @@ def test_adam_listing_mdvisit_versioning(api_client, test_data): ) res = response.json() assert_response_status_code(response, 200) - assert res["visit_type_uid"] == "VisitType_0002" + assert res["visit_type"]["term_uid"] == "VisitType_0002" # get all study visits of a specific study version response = api_client.get( diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_sdtm_listings_tv.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_sdtm_listings_tv.py index f3fdaa5a..81c4843b 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_sdtm_listings_tv.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_design_listings/test_sdtm_listings_tv.py @@ -203,9 +203,9 @@ def test_tv_listing_versioning(api_client): "show_visit": False, "time_unit_uid": "UnitDefinition_000002", "time_value": 0, - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0002", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0002"}, "is_global_anchor_visit": False, "visit_class": "SINGLE_VISIT", "study_epoch_uid": "StudyEpoch_000001", @@ -215,7 +215,7 @@ def test_tv_listing_versioning(api_client): ) res = response.json() assert_response_status_code(response, 200) - assert res["visit_type_uid"] == "VisitType_0002" + assert res["visit_type"]["term_uid"] == "VisitType_0002" # edit study visit response = api_client.delete( 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 4eb928eb..7a9b46b3 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 @@ -304,9 +304,9 @@ def test_data(): inputs = { "study_uid": study.uid, "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 100, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -749,9 +749,9 @@ def test_cascade_delete_on_activities_schedules(api_client): # create visit inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -861,9 +861,9 @@ def test_maintain_outbound_rels(api_client): # create visit inputs = { "study_epoch_uid": epoch_uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1001,9 +1001,9 @@ def test_versioning_on_activity_activity_instruction_activity_schedule_as_group( # create visit inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2610,7 +2610,8 @@ def test_sync_study_activity_to_latest_version_of_activity(api_client): general_activity_group.uid, ], ) - # StudyActivity created for different parents to validate order numbers after updating activity to newer version + # StudyActivity created for same (SoAGroup, ActivityGroup) but different ActivitySubGroup + # to validate order numbers after updating activity to newer version TestUtils.create_study_activity( study_uid=test_study.uid, activity_uid=weight_activity.uid, @@ -2748,28 +2749,6 @@ def test_sync_study_activity_to_latest_version_of_activity(api_client): ) assert_response_status_code(response, 201) - # Update ActivitySubGroup to latest ActivityGroup version - response = api_client.post( - f"/concepts/activities/activity-sub-groups/{randomisation_activity_subgroup.uid}/versions" - ) - assert_response_status_code(response, 201) - - response = api_client.put( - f"/concepts/activities/activity-sub-groups/{randomisation_activity_subgroup.uid}", - json={ - "name": randomisation_activity_subgroup.name, - "name_sentence_case": randomisation_activity_subgroup.name.lower(), - "library_name": randomisation_activity_subgroup.library_name, - "activity_groups": [general_activity_group.uid], - "change_description": "Pulled ActivityGroup change", - }, - ) - assert_response_status_code(response, 200) - response = api_client.post( - f"/concepts/activities/activity-sub-groups/{randomisation_activity_subgroup.uid}/approvals" - ) - assert_response_status_code(response, 201) - # create new draft version for activity response = api_client.post( f"/concepts/activities/activities/{activity_to_change.uid}/versions" @@ -3339,7 +3318,7 @@ def test_study_activity_placeholder_replacement_with_multiple_activities(api_cli visit_to_create = generate_default_input_data_for_visit().copy() visit_to_create.update( { - "visit_type_uid": generic_study_visit.visit_type_uid, + "visit_type": {"term_uid": generic_study_visit.visit_type.term_uid}, } ) second_visit = TestUtils.create_study_visit( @@ -4119,7 +4098,7 @@ def test_study_activity_placeholder_reordering(api_client): assert study_activities[2]["order"] == 3 -def test_create_duplicated_study_activitiy(api_client): +def test_only_final_activity_can_be_selected_to_study(api_client): # Test only Final Activity can be added to Study draft_or_retired_activity = TestUtils.create_activity( name="Draft/Retired Activity", @@ -4172,35 +4151,208 @@ def test_create_duplicated_study_activitiy(api_client): == f"There is no approved Activity with name '{draft_or_retired_activity.name}'." ) - # Test the same Activity with same groupings can't be selected twice in the same Study - custom_activity = TestUtils.create_activity( - name="custom_activity", - activity_subgroups=[ - randomisation_activity_subgroup.uid, - ], + +def test_cross_soa_group_duplicate_study_activity_blocked_on_create(api_client): + test_study = TestUtils.create_study(project_number=project.project_number) + + cross_scope_activity = TestUtils.create_activity( + name="CrossScopeActivity", + activity_subgroups=[randomisation_activity_subgroup.uid], activity_groups=[general_activity_group.uid], ) - TestUtils.create_study_activity( - study_uid=study.uid, - activity_uid=custom_activity.uid, - activity_group_uid=general_activity_group.uid, - activity_subgroup_uid=randomisation_activity_subgroup.uid, - soa_group_term_uid=term_efficacy_uid, + + # First selection under Efficacy → succeeds + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": cross_scope_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) + + # Second selection under Safety (different SoA group, same activity+groupings) → 409 response = api_client.post( - f"/studies/{study.uid}/study-activities", + f"/studies/{test_study.uid}/study-activities", json={ - "activity_uid": custom_activity.uid, + "activity_uid": cross_scope_activity.uid, "activity_subgroup_uid": randomisation_activity_subgroup.uid, "activity_group_uid": general_activity_group.uid, + "soa_group_term_uid": informed_consent_uid, + }, + ) + assert_response_status_code(response, 409) + res = response.json() + assert ( + res["message"] + == f"There is already a Study Selection to the activity with Name '{cross_scope_activity.name}' with the same groupings." + ) + + +def test_cross_soa_group_duplicate_study_activity_blocked_on_patch(api_client): + test_study = TestUtils.create_study(project_number=project.project_number) + + # Create an activity linked to two subgroups under the same group + subgroup_a = TestUtils.create_activity_subgroup(name="PatchDupSubgroupA") + subgroup_b = TestUtils.create_activity_subgroup(name="PatchDupSubgroupB") + patch_dup_activity = TestUtils.create_activity( + name="PatchDuplicateActivity", + activity_subgroups=[subgroup_a.uid, subgroup_b.uid], + activity_groups=[general_activity_group.uid, general_activity_group.uid], + ) + + # First study activity: subgroup A under Efficacy SoA group + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": patch_dup_activity.uid, + "activity_subgroup_uid": subgroup_a.uid, + "activity_group_uid": general_activity_group.uid, "soa_group_term_uid": term_efficacy_uid, }, ) + 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={ + "activity_uid": patch_dup_activity.uid, + "activity_subgroup_uid": subgroup_b.uid, + "activity_group_uid": general_activity_group.uid, + "soa_group_term_uid": informed_consent_uid, + }, + ) + 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. + response = api_client.patch( + f"/studies/{test_study.uid}/study-activities/{second_study_activity_uid}", + json={ + "activity_subgroup_uid": subgroup_a.uid, + "activity_group_uid": general_activity_group.uid, + }, + ) + assert_response_status_code(response, 409) + res = response.json() + assert ( + res["message"] + == f"There is already a Study Selection to the activity with Name '{patch_dup_activity.name}' with the same groupings." + ) + + +def test_sync_latest_version_blocked_when_target_grouping_already_exists(api_client): + test_study = TestUtils.create_study(project_number=project.project_number) + + sync_subgroup = TestUtils.create_activity_subgroup(name="SyncDupSubgroup") + group_a = TestUtils.create_activity_group(name="SyncDupGroupA") + group_b = TestUtils.create_activity_group(name="SyncDupGroupB") + sync_activity = TestUtils.create_activity( + name="SyncDuplicateActivity", + activity_subgroups=[sync_subgroup.uid, sync_subgroup.uid], + activity_groups=[group_a.uid, group_b.uid], + ) + + # Study activity #1: (subgroup, group_a) under Efficacy + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": sync_activity.uid, + "activity_subgroup_uid": sync_subgroup.uid, + "activity_group_uid": group_a.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + first_study_activity_uid = response.json()["study_activity_uid"] + + # Study activity #2: (subgroup, group_b) under the same SoA group (Efficacy) + response = api_client.post( + f"/studies/{test_study.uid}/study-activities", + json={ + "activity_uid": sync_activity.uid, + "activity_subgroup_uid": sync_subgroup.uid, + "activity_group_uid": group_b.uid, + "soa_group_term_uid": term_efficacy_uid, + }, + ) + assert_response_status_code(response, 201) + + # --- Modify the subgroup at library level so its version advances --- + response = api_client.post( + f"/concepts/activities/activity-sub-groups/{sync_subgroup.uid}/versions" + ) + assert_response_status_code(response, 201) + response = api_client.put( + f"/concepts/activities/activity-sub-groups/{sync_subgroup.uid}", + json={ + "name": sync_subgroup.name, + "name_sentence_case": sync_subgroup.name.lower(), + "library_name": sync_subgroup.library_name, + "activity_groups": [group_a.uid, group_b.uid], + "change_description": "Version bump to cause sync_latest_version divergence", + }, + ) + assert_response_status_code(response, 200) + response = api_client.post( + f"/concepts/activities/activity-sub-groups/{sync_subgroup.uid}/approvals" + ) + assert_response_status_code(response, 201) + + # --- Update the activity at library level: remove group_a --- + response = api_client.post( + f"/concepts/activities/activities/{sync_activity.uid}/versions" + ) + assert_response_status_code(response, 201) + + response = api_client.put( + f"/concepts/activities/activities/{sync_activity.uid}", + json={ + "name": sync_activity.name, + "name_sentence_case": sync_activity.name.lower(), + "activity_groupings": [ + { + "activity_group_uid": group_b.uid, + "activity_subgroup_uid": sync_subgroup.uid, + }, + ], + "library_name": sync_activity.library_name, + "change_description": "Removed group_a, only group_b remains", + }, + ) + assert_response_status_code(response, 200) + + response = api_client.post( + f"/concepts/activities/activities/{sync_activity.uid}/approvals" + ) + assert_response_status_code(response, 201) + + # Verify first study activity sees a newer version is available + response = api_client.get( + f"/studies/{test_study.uid}/study-activities/{first_study_activity_uid}" + ) + assert_response_status_code(response, 200) + assert response.json()["latest_activity"] is not None + + # --- Sync first study activity to latest, requesting (subgroup, group_b) --- + # That grouping is already used by study activity #2 → should be blocked + response = api_client.post( + f"/studies/{test_study.uid}/study-activities/{first_study_activity_uid}/sync-latest-version", + json={ + "activity_group_uid": group_b.uid, + "activity_subgroup_uid": sync_subgroup.uid, + }, + ) assert_response_status_code(response, 409) res = response.json() assert ( res["message"] - == f"There is already a Study Selection to the activity with Name '{custom_activity.name}' with the same groupings." + == f"There is already a Study Selection to the activity with Name '{sync_activity.name}' with the same groupings." ) @@ -4272,9 +4424,9 @@ def test_batch_operations_for_combined_study_activity_and_activity_schedules( inputs = { "study_uid": test_study.uid, "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 100, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", 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 4629d1e2..0aca806b 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 @@ -671,9 +671,9 @@ def test_create_study_activity_instance(api_client): inputs = { "study_uid": test_study.uid, "study_epoch_uid": test_study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 100, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -708,7 +708,7 @@ def test_create_study_activity_instance(api_client): { "uid": study_visit_1.uid, "visit_name": study_visit_1.visit_name, - "visit_type_name": study_visit_1.visit_type_name, + "visit_type_name": study_visit_1.visit_type.sponsor_preferred_name, } ] @@ -725,7 +725,7 @@ def test_create_study_activity_instance(api_client): { "uid": study_visit_1.uid, "visit_name": study_visit_1.visit_name, - "visit_type_name": study_visit_1.visit_type_name, + "visit_type_name": study_visit_1.visit_type.sponsor_preferred_name, } ] @@ -782,9 +782,9 @@ def test_edit_study_activity_instance(api_client): inputs = { "study_uid": test_study.uid, "study_epoch_uid": test_study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 100, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -852,12 +852,12 @@ def test_edit_study_activity_instance(api_client): assert { "uid": study_visit_1.uid, "visit_name": study_visit_1.visit_name, - "visit_type_name": study_visit_1.visit_type_name, + "visit_type_name": study_visit_1.visit_type.sponsor_preferred_name, } in res["baseline_visits"] assert { "uid": study_visit_2.uid, "visit_name": study_visit_2.visit_name, - "visit_type_name": study_visit_2.visit_type_name, + "visit_type_name": study_visit_2.visit_type.sponsor_preferred_name, } in res["baseline_visits"] expected_audit_trail_length += 1 @@ -877,7 +877,7 @@ def test_edit_study_activity_instance(api_client): assert { "uid": study_visit_2.uid, "visit_name": study_visit_2.visit_name, - "visit_type_name": study_visit_2.visit_type_name, + "visit_type_name": study_visit_2.visit_type.sponsor_preferred_name, } in res["baseline_visits"] expected_audit_trail_length += 1 @@ -895,7 +895,7 @@ def test_edit_study_activity_instance(api_client): assert { "uid": study_visit_2.uid, "visit_name": study_visit_2.visit_name, - "visit_type_name": study_visit_2.visit_type_name, + "visit_type_name": study_visit_2.visit_type.sponsor_preferred_name, } in res["baseline_visits"] expected_audit_trail_length += 1 @@ -966,7 +966,7 @@ def test_edit_study_activity_instance(api_client): assert { "uid": study_visit_2.uid, "visit_name": study_visit_2.visit_name, - "visit_type_name": study_visit_2.visit_type_name, + "visit_type_name": study_visit_2.visit_type.sponsor_preferred_name, } in res["baseline_visits"] expected_audit_trail_length += 1 # Before deleting visit, check that patching visit does not change baseline visits @@ -985,7 +985,7 @@ def test_edit_study_activity_instance(api_client): assert { "uid": study_visit_2.uid, "visit_name": study_visit_2.visit_name, - "visit_type_name": study_visit_2.visit_type_name, + "visit_type_name": study_visit_2.visit_type.sponsor_preferred_name, } in res["baseline_visits"] # Delete Visit 2 - should remove visit 2 from baseline visits diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py index 9de15d11..1285f4b5 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_versions.py @@ -598,7 +598,7 @@ def test_get_snapshot_history(api_client): # snapshot history excluding versions without protocol header version response = api_client.get( f"/studies/{study_with_history.uid}/snapshot-history", - params={"only_latest_major_protcol_version": True, "total_count": True}, + params={"only_latest_major_protocol_version": True, "total_count": True}, ) assert_response_status_code(response, 200) res = response.json() @@ -609,6 +609,7 @@ def test_get_snapshot_history(api_client): assert res[0]["reason_for_lock_name"] == reason_for_lock.sponsor_preferred_name assert res[0]["reason_for_unlock_name"] == reason_for_unlock.sponsor_preferred_name assert res[0]["metadata_version"] == "3" + assert res[0]["original_metadata_version"] == "3" assert res[0]["protocol_header_major_version"] == 2 assert res[0]["protocol_header_minor_version"] == 0 assert res[0]["description"] == "Lock 3" @@ -620,6 +621,7 @@ def test_get_snapshot_history(api_client): assert res[1]["reason_for_lock_name"] == final_protocol_term.sponsor_preferred_name assert res[1]["reason_for_unlock_name"] == reason_for_unlock.sponsor_preferred_name assert res[1]["metadata_version"] == "2" + assert res[1]["original_metadata_version"] == "2" assert res[1]["protocol_header_major_version"] == 1 assert res[1]["protocol_header_minor_version"] == 0 assert res[1]["description"] == "Lock 2" @@ -628,6 +630,45 @@ def test_get_snapshot_history(api_client): assert res[1]["modified_date"] is not None assert res[1]["modified_by"] is not None + # Unlock and re-lock with same major protocol version to test original_metadata_version + response = api_client.post( + f"/studies/{study_with_history.uid}/unlocks", + json={ + "reason_for_change_uid": reason_for_unlock.term_uid, + }, + ) + assert_response_status_code(response, 201) + + response = api_client.post( + f"/studies/{study_with_history.uid}/locks", + json={ + "change_description": "Lock 4 same major version", + "reason_for_change_uid": reason_for_lock.term_uid, + "protocol_header_major_version": 2, + "protocol_header_minor_version": 0, + }, + ) + assert_response_status_code(response, 201) + + # Now phv 2.0 has two entries: metadata_version "4" (latest) and "3" (original) + response = api_client.get( + f"/studies/{study_with_history.uid}/snapshot-history", + params={"only_latest_major_protocol_version": True, "total_count": True}, + ) + assert_response_status_code(response, 200) + res = response.json() + assert res["total"] == 2 + res = res["items"] + assert len(res) == 2 + assert res[0]["metadata_version"] == "4" + assert res[0]["original_metadata_version"] == "3" + assert res[0]["protocol_header_major_version"] == 2 + assert res[0]["protocol_header_minor_version"] == 0 + assert res[1]["metadata_version"] == "2" + assert res[1]["original_metadata_version"] == "2" + assert res[1]["protocol_header_major_version"] == 1 + assert res[1]["protocol_header_minor_version"] == 0 + @pytest.mark.order("last") def test_integrity_checks_for_all_studies(api_client): diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py index 8f982ff1..3dec7d46 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/study_selections/test_study_visits.py @@ -10,7 +10,8 @@ # which pylint interprets as unused arguments from datetime import datetime, timezone -from typing import Any +from enum import Enum +from typing import Any, Iterable, Mapping from unittest import mock import pytest @@ -25,6 +26,7 @@ from clinical_mdr_api.models.controlled_terminologies.ct_term_name import CTTermName from clinical_mdr_api.models.projects.project import Project from clinical_mdr_api.models.study_selections.study import Study +from clinical_mdr_api.models.study_selections.study_visit import StudyVisitLite from clinical_mdr_api.tests.integration.utils.api import ( inject_and_clear_db, inject_base_data, @@ -46,9 +48,15 @@ get_unit_uid_by_name, ) from clinical_mdr_api.tests.integration.utils.utils import TestUtils -from clinical_mdr_api.tests.utils.checks import assert_response_status_code +from clinical_mdr_api.tests.utils.checks import ( + assert_response_status_code, + parse_json_response, +) from common.utils import VisitClass +STUDY_VISIT_LITE_KEYS = set(StudyVisitLite.model_fields.keys()) + + # Global variables shared between fixtures and tests study: Study study_visit_uid: str @@ -161,9 +169,9 @@ def test_visit_modify_actions_on_locked_study(api_client): inputs = { "study_epoch_uid": epoch_uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -209,9 +217,9 @@ def test_visit_modify_actions_on_locked_study(api_client): inputs = { "study_epoch_uid": epoch_uid, - "visit_type_uid": "VisitType_0003", + "visit_type": {"term_uid": "VisitType_0003"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0001", + "time_reference": {"term_uid": "VisitSubType_0001"}, "time_value": 12, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -234,9 +242,9 @@ def test_visit_modify_actions_on_locked_study(api_client): "study_uid": study.uid, "description": "new description", "study_epoch_uid": epoch_uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -308,9 +316,9 @@ def test_study_visit_versioning(api_client): "show_visit": True, "time_unit_uid": "UnitDefinition_000001", "time_value": 0, - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0001", - "time_reference_uid": "VisitSubType_0005", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0001"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "is_global_anchor_visit": True, "visit_class": "SINGLE_VISIT", "study_epoch_uid": _study_epoch.uid, @@ -359,6 +367,8 @@ def test_study_visit_versioning(api_client): assert_response_status_code(response, 200) assert res["items"][0]["study_epoch_uid"] == _study_epoch.uid + assert_get_all_visits_lite_compares(res["items"], api_client, study.uid) + # get specific study visit response = api_client.get( f"/studies/{study.uid}/study-visits/{study_visit_uid}", @@ -404,8 +414,8 @@ def test_manually_defined_visit(api_client): for visit_timing in range(0, 100, 10): inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": visit_timing, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -432,8 +442,8 @@ def test_manually_defined_visit(api_client): special_visit_input = { "visit_sublabel_reference": last_scheduled_visit_uid, "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_unit_uid": DAYUID, "visit_class": "SPECIAL_VISIT", "visit_subclass": "SINGLE_VISIT", @@ -456,8 +466,8 @@ def test_manually_defined_visit(api_client): inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 55, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -649,8 +659,8 @@ def test_non_manually_defined_visit(api_client): # Create 1 study visit inputs_visit = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 20, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -673,8 +683,8 @@ def test_non_manually_defined_visit(api_client): manually_defined_unique_number = 200 vis_input = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 25, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -715,8 +725,8 @@ def test_non_manually_defined_visit(api_client): # And The is defined with a derived or preset test value that already exist for a manually defined study visit inputs_visit = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 22, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -745,8 +755,8 @@ def test_non_manually_defined_visit(api_client): # And The is defined with a derived or preset test value that already exist for a manually defined study visit inputs_visit = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 22, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -797,8 +807,8 @@ def test_non_manually_defined_visit(api_client): # Create a non_manually defined study visit with non-existed visit name, visit short name, visit number and unique visit number inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 57, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -828,8 +838,8 @@ def test_manually_defined_visit_in_chronological_order_by_visit_timing(api_clien for visit_timing in range(0, 100, 20): inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": visit_timing, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -860,8 +870,8 @@ def test_manually_defined_visit_in_chronological_order_by_visit_timing(api_clien # And The test visit number is not defined in chronological order by study visit timing input1 = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 30, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -889,8 +899,8 @@ def test_manually_defined_visit_in_chronological_order_by_visit_timing(api_clien input2 = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 30, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -919,8 +929,8 @@ def test_manually_defined_visit_in_chronological_order_by_visit_timing(api_clien # Successfully post a manually defined visit with correct visit number and unique visit number in chronological order by visit timing input3 = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 30, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -944,8 +954,8 @@ def test_manually_defined_visit_in_chronological_order_by_visit_timing(api_clien # And The test unique visit number is not defined in chronological order by study visit timing input4 = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 35, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -973,8 +983,8 @@ def test_manually_defined_visit_in_chronological_order_by_visit_timing(api_clien input5 = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 35, "time_unit_uid": DAYUID, "visit_class": "MANUALLY_DEFINED_VISIT", @@ -1009,8 +1019,8 @@ def test_study_visit_timings(api_client): # timing -14 inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": -14, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1106,9 +1116,9 @@ def test_create_repeating_visit(api_client): inputs = { "study_epoch_uid": _study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1150,9 +1160,9 @@ def test_create_repeating_visit(api_client): # When A new repeating visit is created inputs = { "study_epoch_uid": _study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": -2, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1203,9 +1213,9 @@ def test_create_visit_0(api_client): inputs = { "study_epoch_uid": study_epoch1.uid, - "visit_type_uid": "VisitType_0000", + "visit_type": {"term_uid": "VisitType_0000"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": -1, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1236,9 +1246,9 @@ def test_create_visit_0(api_client): inputs = { "study_epoch_uid": study_epoch2.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1285,9 +1295,9 @@ def test_visit_0_created_chronologically(api_client): # Test pre-conditions: create two normal visits with different time value input1 = { "study_epoch_uid": study_epoch2.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1308,9 +1318,9 @@ def test_visit_0_created_chronologically(api_client): input2 = { "study_epoch_uid": study_epoch2.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 20, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1335,9 +1345,9 @@ def test_visit_0_created_chronologically(api_client): # Create an information visit with non-first timing inputs = { "study_epoch_uid": study_epoch1.uid, - "visit_type_uid": "VisitType_0000", + "visit_type": {"term_uid": "VisitType_0000"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 15, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1387,9 +1397,9 @@ def test_visit_0_created_chronologically(api_client): # Create an information visit with first timing inputs = { "study_epoch_uid": study_epoch1.uid, - "visit_type_uid": "VisitType_0000", + "visit_type": {"term_uid": "VisitType_0000"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 5, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1423,9 +1433,9 @@ def test_visit_0_created_chronologically(api_client): # When create a new non-information visit with first timing input3 = { "study_epoch_uid": study_epoch2.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 3, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1471,9 +1481,9 @@ def test_visit_0_edited_chronologically(api_client): # Create a normal visit input1 = { "study_epoch_uid": study_epoch2.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1496,9 +1506,9 @@ def test_visit_0_edited_chronologically(api_client): # Create an information visit with first timing inputs = { "study_epoch_uid": study_epoch1.uid, - "visit_type_uid": "VisitType_0000", + "visit_type": {"term_uid": "VisitType_0000"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 2, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1528,9 +1538,9 @@ def test_visit_0_edited_chronologically(api_client): "show_visit": True, "time_unit_uid": "UnitDefinition_000001", "time_value": 2, - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0000", - "time_reference_uid": "VisitSubType_0005", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0000"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "is_global_anchor_visit": True, "visit_class": "SINGLE_VISIT", "study_epoch_uid": study_epoch1.uid, @@ -1556,9 +1566,9 @@ def test_visit_0_edited_chronologically(api_client): "show_visit": True, "time_unit_uid": "UnitDefinition_000001", "time_value": 14, - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0000", - "time_reference_uid": "VisitSubType_0005", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0000"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "is_global_anchor_visit": True, "visit_class": "SINGLE_VISIT", "study_epoch_uid": study_epoch1.uid, @@ -1580,9 +1590,9 @@ def test_visit_0_edited_chronologically(api_client): # Given A study information visit with visit 0 is created inputs = { "study_epoch_uid": study_epoch1.uid, - "visit_type_uid": "VisitType_0000", + "visit_type": {"term_uid": "VisitType_0000"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 2, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1610,9 +1620,9 @@ def test_visit_0_edited_chronologically(api_client): "show_visit": True, "time_unit_uid": "UnitDefinition_000001", "time_value": 2, - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0001", - "time_reference_uid": "VisitSubType_0005", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0001"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "is_global_anchor_visit": False, "visit_class": "SINGLE_VISIT", "study_epoch_uid": study_epoch1.uid, @@ -1657,7 +1667,7 @@ def test_study_visist_version_selecting_ct_package(api_client): params=params, ) study_selection_breadcrumb = "study-visits" - study_selection_ctterm_uid_input_key = "visit_type_uid" + study_selection_ctterm_uid_input_key = "visit_type" study_selection_ctterm_key = "visit_type" study_selection_ctterm_name_key = "sponsor_preferred_name" study_for_ctterm_versioning = TestUtils.create_study() @@ -1668,9 +1678,11 @@ def test_study_visist_version_selecting_ct_package(api_client): inputs = { "study_epoch_uid": study_epoch1.uid, - study_selection_ctterm_uid_input_key: initial_ct_term_study_standard_test.term_uid, + study_selection_ctterm_uid_input_key: { + "term_uid": initial_ct_term_study_standard_test.term_uid + }, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1789,9 +1801,9 @@ def test_visit_window_unit_must_be_same_for_all_visits(api_client): study_epoch = create_study_epoch("EpochSubType_0001", study_uid=_study.uid) visit_input = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1831,9 +1843,9 @@ def test_study_visit_circular_time_reference_cant_be_created(api_client): # Global Anchor Visit visit_input = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1850,9 +1862,9 @@ def test_study_visit_circular_time_reference_cant_be_created(api_client): visit_input = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", + "visit_type": {"term_uid": "VisitType_0002"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0001", + "time_reference": {"term_uid": "VisitSubType_0001"}, "time_value": -10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1869,9 +1881,9 @@ def test_study_visit_circular_time_reference_cant_be_created(api_client): visit_input = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0002", + "time_reference": {"term_uid": "VisitSubType_0002"}, "time_value": 20, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1893,7 +1905,7 @@ def test_study_visit_circular_time_reference_cant_be_created(api_client): ) datadict = visits_basic_data - datadict.update({"visit_type_uid": "VisitType_0003"}) + datadict.update({"visit_type": {"term_uid": "VisitType_0003"}}) response = api_client.post( f"/studies/{_study.uid}/study-visits", json=datadict, @@ -1904,7 +1916,7 @@ def test_study_visit_circular_time_reference_cant_be_created(api_client): datadict.update( { - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "uid": visit_uid, "study_uid": _study.uid, } @@ -1927,9 +1939,9 @@ def test_global_anchor_visit_time_reference(api_client): study_epoch = create_study_epoch("EpochSubType_0001", study_uid=_study.uid) visit_input = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0002", + "time_reference": {"term_uid": "VisitSubType_0002"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1950,7 +1962,7 @@ def test_global_anchor_visit_time_reference(api_client): ) # Assigning 'Global anchor visit' as time reference - datadict.update({"time_reference_uid": "VisitSubType_0005"}) + datadict.update({"time_reference": {"term_uid": "VisitSubType_0005"}}) response = api_client.post( f"/studies/{_study.uid}/study-visits", json=datadict, @@ -1958,7 +1970,7 @@ def test_global_anchor_visit_time_reference(api_client): assert_response_status_code(response, 201) visit_uid = response.json()["uid"] - datadict.update({"time_reference_uid": "VisitSubType_0002"}) + datadict.update({"time_reference": {"term_uid": "VisitSubType_0002"}}) response = api_client.patch( f"/studies/{_study.uid}/study-visits/{visit_uid}", json=datadict, @@ -1980,9 +1992,9 @@ def test_study_visit_editing_study_epoch(api_client): # Global Anchor Visit visit_input = { "study_epoch_uid": study_epoch_1.uid, - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -1999,9 +2011,9 @@ def test_study_visit_editing_study_epoch(api_client): for idx in range(1, 10): visit_input = { - "visit_type_uid": "VisitType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, "show_visit": True, - "time_reference_uid": "VisitSubType_0005", + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": idx, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2118,8 +2130,8 @@ def test_creating_special_visit(api_client): # Global Anchor Visit inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2141,8 +2153,8 @@ def test_creating_special_visit(api_client): special_visit_input = { "visit_sublabel_reference": global_anchor_visit, "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_unit_uid": DAYUID, "visit_class": "SPECIAL_VISIT", "visit_subclass": "SINGLE_VISIT", @@ -2180,7 +2192,7 @@ def test_creating_special_visit(api_client): # Create early discontinuation special visit anchored to a visit that already has other special visits # assert that ordering for early discontinuation will start from 'X' - datadict.update({"visit_type_uid": "VisitType_0005"}) + datadict.update({"visit_type": {"term_uid": "VisitType_0005"}}) response = api_client.post( f"/studies/{study.uid}/study-visits", json=datadict, @@ -2193,8 +2205,8 @@ def test_creating_special_visit(api_client): # Visit Day 10 inputs = { "study_epoch_uid": second_study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2214,8 +2226,8 @@ def test_creating_special_visit(api_client): special_visit_input = { "visit_sublabel_reference": visit_day_10, "study_epoch_uid": second_study_epoch.uid, - "visit_type_uid": "VisitType_0005", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0005"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_unit_uid": DAYUID, "visit_class": "SPECIAL_VISIT", "visit_subclass": "SINGLE_VISIT", @@ -2247,8 +2259,8 @@ def test_editing_special_visit(api_client): # Global Anchor Visit inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2266,8 +2278,8 @@ def test_editing_special_visit(api_client): # Visit Day 10 inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2287,8 +2299,8 @@ def test_editing_special_visit(api_client): special_visit_input = { "visit_sublabel_reference": visit_day_10, "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_unit_uid": DAYUID, "visit_class": "SPECIAL_VISIT", "visit_subclass": "SINGLE_VISIT", @@ -2308,8 +2320,8 @@ def test_editing_special_visit(api_client): "uid": special_visit_uid, "visit_sublabel_reference": visit_day_10, "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_unit_uid": DAYUID, "visit_class": "SPECIAL_VISIT", "visit_subclass": "SINGLE_VISIT", @@ -2350,11 +2362,15 @@ def test_get_all_visits_invalid_study_uid_or_version( if study_value_version is not None: params = {"study_value_version": study_value_version} else: - params = None + params = {} response = api_client.get(f"/studies/{study_uid}/study-visits", params=params) assert_response_status_code(response, 404) + params["lite"] = "TRUE" + response = api_client.get(f"/studies/{study_uid}/study-visits", params=params) + assert_response_status_code(response, 404) + def test_assert_uvn_is_changed_when_group_of_visits_is_modified(api_client): study = TestUtils.create_study(project_number=project.project_number) @@ -2363,8 +2379,8 @@ def test_assert_uvn_is_changed_when_group_of_visits_is_modified(api_client): # Global Anchor Visit anchor_inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2384,8 +2400,8 @@ def test_assert_uvn_is_changed_when_group_of_visits_is_modified(api_client): inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0003", - "time_reference_uid": "VisitSubType_0002", + "visit_type": {"term_uid": "VisitType_0003"}, + "time_reference": {"term_uid": "VisitSubType_0002"}, "time_value": -10, "time_unit_uid": DAYUID, "visit_sublabel_reference": anchor_visit_uid, @@ -2470,6 +2486,8 @@ def test_assert_uvn_is_changed_when_group_of_visits_is_modified(api_client): assert study_visits[1]["visit_name"] == "Visit 1" assert study_visits[1]["unique_visit_number"] == 110 + assert_get_all_visits_lite_compares(study_visits, api_client, study.uid) + # Call for StudyVisits but derive properties based on visit_number instead of returning them straight from DB response = api_client.get( f"/studies/{study.uid}/study-visits", @@ -2487,6 +2505,8 @@ def test_assert_uvn_is_changed_when_group_of_visits_is_modified(api_client): assert study_visits[1]["visit_name"] == "Visit 1" assert study_visits[1]["unique_visit_number"] == 110 + assert_get_all_visits_lite_compares(study_visits, api_client, study.uid) + response = api_client.get( f"/studies/{study.uid}/study-visits/{anchor_visit_uid}", ) @@ -2537,8 +2557,8 @@ def test_it_is_possible_create_two_study_visits_with_the_same_timing(api_client) for idx_number in range(1, 5): inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 10, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2571,6 +2591,9 @@ def test_it_is_possible_create_two_study_visits_with_the_same_timing(api_client) ) assert_response_status_code(response, 200) study_visits = response.json()["items"] + + assert_get_all_visits_lite_compares(study_visits, api_client, test_study.uid) + first_visit_uid = study_visits[0]["uid"] # Edit first StudyVisit with same timing and make sure it's still the first one in schedule new_description = "Edited Visit" @@ -2605,11 +2628,13 @@ def test_it_is_possible_create_two_study_visits_with_the_same_timing(api_client) == created_study_visit["unique_visit_number"] ) + assert_get_all_visits_lite_compares(study_visits, api_client, test_study.uid) + # Although it is possible to create 2 visits with the same timing, it should not be possible 2 visits with timing set to 0 inputs = { "study_epoch_uid": study_epoch.uid, - "visit_type_uid": "VisitType_0002", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0002"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": DAYUID, "visit_class": "SINGLE_VISIT", @@ -2648,3 +2673,29 @@ def test_it_is_possible_create_two_study_visits_with_the_same_timing(api_client) assert_response_status_code(response, 409) res = response.json() assert res["message"] == "There already exists a visit with timing set to 0" + + +def assert_get_all_visits_lite_compares( + expected_items: Iterable[Mapping], + api_client, + study_uid: str, + study_value_version: str | None = None, +): + expected_visits = [] + for item in expected_items: + item_dict = {k: v.value if isinstance(v, Enum) else v for k, v in item.items()} + expected_visits.append(visit := StudyVisitLite(**item_dict)) + + # Lite endpoint returns None for study_day/week_numbers for special visits + if visit.visit_class == VisitClass.SPECIAL_VISIT: + visit.study_day_number = None + visit.study_week_number = None + + # get all visits lite version + params = {"lite": "true"} + if study_value_version: + params["study_value_version"] = study_value_version + response = api_client.get(f"/studies/{study_uid}/study-visits", params=params) + results = parse_json_response(response, status=200) + visits = [StudyVisitLite(**item) for item in results["items"]] + assert visits == expected_visits diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_data_completeness_tags.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_data_completeness_tags.py new file mode 100644 index 00000000..46326cb2 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_data_completeness_tags.py @@ -0,0 +1,240 @@ +""" +Tests for /data-completeness-tags* and /studies/{study_uid}/data-completeness-tags* endpoints +""" + +# 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.data_completeness_tag import DataCompletenessTag +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 +data_completeness_tags: list[DataCompletenessTag] + + +@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""" + db_name = "datacompletenesstags.api" + inject_and_clear_db(db_name) + inject_base_data() + + global data_completeness_tags + + data_completeness_tags = [] + for index in range(10): + data_completeness_tags.append( + TestUtils.create_data_completeness_tag( + name=f"Data Completeness Tag {index}", + ) + ) + + yield + + +DATA_COMPLETENESS_TAG_FIELDS = [ + "uid", + "name", +] + + +def test_get_all_data_completeness_tags(api_client): + response = api_client.get("/data-completeness-tags") + assert_response_status_code(response, 200) + res = response.json() + + assert len(res) >= 10 + uids = [item["uid"] for item in res] + for tag in data_completeness_tags: + assert tag.uid in uids + + for item in res: + for field in DATA_COMPLETENESS_TAG_FIELDS: + assert item[field] is not None + + +def test_create_data_completeness_tag(api_client): + data = {"name": "Create Test Tag"} + response = api_client.post("/data-completeness-tags", json=data) + + assert_response_status_code(response, 201) + res = response.json() + assert res["uid"] + assert res["name"] == data["name"] + + # Cleanup + api_client.delete(f"/data-completeness-tags/{res['uid']}") + + +def test_update_data_completeness_tag(api_client): + tag = data_completeness_tags[1] + original_name = tag.name + data = {"name": "Updated Tag Name"} + response = api_client.put(f"/data-completeness-tags/{tag.uid}", json=data) + + assert_response_status_code(response, 200) + res = response.json() + assert res["uid"] == tag.uid + assert res["name"] == data["name"] + + # Restore original name + api_client.put(f"/data-completeness-tags/{tag.uid}", json={"name": original_name}) + + +def test_delete_data_completeness_tag(api_client): + # Setup: create a dedicated tag for deletion + tag = TestUtils.create_data_completeness_tag(name="To Be Deleted") + + response = api_client.delete(f"/data-completeness-tags/{tag.uid}") + assert_response_status_code(response, 204) + + # Verify it was deleted + response = api_client.get("/data-completeness-tags") + assert_response_status_code(response, 200) + uids = [item["uid"] for item in response.json()] + assert tag.uid not in uids + + +def test_cannot_create_data_completeness_tag_with_existing_name(api_client): + response = api_client.post( + "/data-completeness-tags", + json={"name": data_completeness_tags[0].name}, + ) + + assert_response_status_code(response, 409) + res = response.json() + assert ( + res["message"] + == f"Data Completeness Tag with Name '{data_completeness_tags[0].name}' already exists." + ) + + +def test_update_nonexistent_data_completeness_tag(api_client): + data = {"name": "Does Not Matter"} + response = api_client.put("/data-completeness-tags/nonexistent-uid", json=data) + + assert_response_status_code(response, 404) + res = response.json() + assert ( + res["message"] + == "Data Completeness Tag with UID 'nonexistent-uid' doesn't exist." + ) + + +# --- Study-level data completeness tag tests --- + + +def test_get_study_data_completeness_tags_empty(api_client): + study = TestUtils.create_study() + response = api_client.get(f"/studies/{study.uid}/data-completeness-tags") + + assert_response_status_code(response, 200) + res = response.json() + assert res == [] + + +def test_assign_data_completeness_tag_to_study(api_client): + study = TestUtils.create_study() + tag = data_completeness_tags[2] + + response = api_client.post( + f"/studies/{study.uid}/data-completeness-tags", + json={"uid": tag.uid}, + ) + + assert_response_status_code(response, 201) + res = response.json() + assert res["uid"] == tag.uid + assert res["name"] == tag.name + + +def test_assign_multiple_tags_and_list(api_client): + study = TestUtils.create_study() + tag1 = data_completeness_tags[4] + tag2 = data_completeness_tags[5] + + api_client.post( + f"/studies/{study.uid}/data-completeness-tags", json={"uid": tag1.uid} + ) + api_client.post( + f"/studies/{study.uid}/data-completeness-tags", json={"uid": tag2.uid} + ) + + # Verify both tags are returned + response = api_client.get(f"/studies/{study.uid}/data-completeness-tags") + assert_response_status_code(response, 200) + res = response.json() + uids = {item["uid"] for item in res} + assert tag1.uid in uids + assert tag2.uid in uids + + +def test_remove_data_completeness_tag_from_study(api_client): + study = TestUtils.create_study() + tag1 = data_completeness_tags[6] + tag2 = data_completeness_tags[7] + + api_client.post( + f"/studies/{study.uid}/data-completeness-tags", json={"uid": tag1.uid} + ) + api_client.post( + f"/studies/{study.uid}/data-completeness-tags", json={"uid": tag2.uid} + ) + + # Remove tag2 + response = api_client.delete( + f"/studies/{study.uid}/data-completeness-tags/{tag2.uid}" + ) + assert_response_status_code(response, 204) + + # Verify only tag1 remains + response = api_client.get(f"/studies/{study.uid}/data-completeness-tags") + assert_response_status_code(response, 200) + uids = {item["uid"] for item in response.json()} + assert tag1.uid in uids + assert tag2.uid not in uids + + +def test_studies_list_returns_data_completeness_tags(api_client): + """Verify that /studies/list returns data_completeness_tags for each study.""" + study = TestUtils.create_study() + tag = data_completeness_tags[8] + api_client.post( + f"/studies/{study.uid}/data-completeness-tags", json={"uid": tag.uid} + ) + + response = api_client.get("/studies/list?minimal_response=false") + assert_response_status_code(response, 200) + res = response.json() + + # Find our study in the list + study_item = next((s for s in res if s["uid"] == study.uid), None) + assert study_item is not None, f"Study {study.uid} not found in /studies/list" + + assert "data_completeness_tags" in study_item + assert isinstance(study_item["data_completeness_tags"], list) + assert tag.name in study_item["data_completeness_tags"] diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_preferences.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_preferences.py new file mode 100644 index 00000000..924e58e0 --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/api/test_preferences.py @@ -0,0 +1,253 @@ +""" +Tests for /admin/global-preferences and /user-preferences endpoints +""" + +# pylint: disable=unused-argument +# pylint: disable=redefined-outer-name + +import logging + +import pytest +from fastapi.testclient import TestClient + +from clinical_mdr_api.domain_repositories.preferences_registry import ( + PREFERENCE_DEFINITIONS, + PREFERENCE_KEYS, + to_metadata_dict, +) +from clinical_mdr_api.main import app +from clinical_mdr_api.tests.integration.utils.api import ( + inject_and_clear_db, + inject_base_data, +) +from clinical_mdr_api.tests.utils.checks import assert_response_status_code + +log = logging.getLogger(__name__) + +# Expected defaults derived from registry +EXPECTED_DEFAULTS = {d.key: d.default for d in PREFERENCE_DEFINITIONS} + + +@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""" + db_name = "preferences.api" + inject_and_clear_db(db_name) + inject_base_data() + + +# ─── Global preferences ─────────────────────────────────────────────── + + +def test_get_global_preferences_returns_defaults(api_client): + """GET /admin/global-preferences returns all defaults on first access.""" + response = api_client.get("/admin/global-preferences") + assert_response_status_code(response, 200) + body = response.json() + + assert "preferences" in body + assert "metadata" in body + + prefs = body["preferences"] + for key in PREFERENCE_KEYS: + assert key in prefs, f"Missing preference key: {key}" + assert ( + prefs[key] == EXPECTED_DEFAULTS[key] + ), f"Default mismatch for '{key}': expected {EXPECTED_DEFAULTS[key]}, got {prefs[key]}" + + +def test_get_global_preferences_metadata_shape(api_client): + """Metadata for each key matches the registry definition.""" + response = api_client.get("/admin/global-preferences") + assert_response_status_code(response, 200) + metadata = response.json()["metadata"] + + for defn in PREFERENCE_DEFINITIONS: + assert defn.key in metadata, f"Metadata missing key: {defn.key}" + expected = to_metadata_dict(defn) + actual = metadata[defn.key] + for field, value in expected.items(): + assert actual[field] == value, ( + f"Metadata field '{field}' mismatch for '{defn.key}': " + f"expected {value}, got {actual.get(field)}" + ) + + +def test_patch_global_preferences_integer(api_client): + """PATCH /admin/global-preferences updates rows_per_page.""" + response = api_client.patch("/admin/global-preferences", json={"rows_per_page": 25}) + assert_response_status_code(response, 200) + assert response.json()["preferences"]["rows_per_page"] == 25 + + # Verify via GET + response = api_client.get("/admin/global-preferences") + assert_response_status_code(response, 200) + assert response.json()["preferences"]["rows_per_page"] == 25 + + +def test_patch_global_preferences_boolean(api_client): + """PATCH /admin/global-preferences updates sidebar_visible.""" + response = api_client.patch( + "/admin/global-preferences", json={"sidebar_visible": False} + ) + assert_response_status_code(response, 200) + assert response.json()["preferences"]["sidebar_visible"] is False + + +def test_patch_global_preferences_enum(api_client): + """PATCH /admin/global-preferences updates language.""" + response = api_client.patch("/admin/global-preferences", json={"language": "en"}) + assert_response_status_code(response, 200) + assert response.json()["preferences"]["language"] == "en" + + +def test_patch_global_preferences_multiple_fields(api_client): + """PATCH /admin/global-preferences updates multiple fields at once.""" + payload = { + "rows_per_page": 50, + "sidebar_auto_minimize": True, + } + response = api_client.patch("/admin/global-preferences", json=payload) + assert_response_status_code(response, 200) + prefs = response.json()["preferences"] + assert prefs["rows_per_page"] == 50 + assert prefs["sidebar_auto_minimize"] is True + + +def test_patch_global_preferences_invalid_rows_per_page_too_low(api_client): + """PATCH with rows_per_page < 5 returns 400 (Pydantic validation).""" + response = api_client.patch("/admin/global-preferences", json={"rows_per_page": 2}) + assert_response_status_code(response, 400) + + +def test_patch_global_preferences_invalid_rows_per_page_too_high(api_client): + """PATCH with rows_per_page > 100 returns 400 (Pydantic validation).""" + response = api_client.patch( + "/admin/global-preferences", json={"rows_per_page": 999} + ) + assert_response_status_code(response, 400) + + +def test_patch_global_preferences_invalid_language(api_client): + """PATCH with invalid language value returns 400 (Pydantic Literal validation).""" + response = api_client.patch("/admin/global-preferences", json={"language": "xx"}) + assert_response_status_code(response, 400) + + +def test_patch_global_preferences_preserves_unset_fields(api_client): + """PATCH only updates provided fields, leaves others unchanged.""" + # Reset to known state + api_client.patch( + "/admin/global-preferences", + json={"rows_per_page": 10, "sidebar_visible": True}, + ) + + # Patch only rows_per_page + api_client.patch("/admin/global-preferences", json={"rows_per_page": 30}) + + response = api_client.get("/admin/global-preferences") + assert_response_status_code(response, 200) + prefs = response.json()["preferences"] + assert prefs["rows_per_page"] == 30 + assert prefs["sidebar_visible"] is True # unchanged + + +# ─── User preferences ───────────────────────────────────────────────── + + +def test_get_user_preferences_returns_globals_when_no_overrides(api_client): + """GET /user-preferences returns global defaults with all overrides=False.""" + # Reset global prefs to defaults first + api_client.patch("/admin/global-preferences", json=EXPECTED_DEFAULTS) + + response = api_client.get("/user-preferences") + assert_response_status_code(response, 200) + body = response.json() + + assert "preferences" in body + assert "overrides" in body + assert "metadata" in body + + for key in PREFERENCE_KEYS: + assert key in body["preferences"] + assert key not in body["overrides"] + + +def test_patch_user_preferences(api_client): + """PATCH /user-preferences sets a user override.""" + response = api_client.patch("/user-preferences", json={"rows_per_page": 42}) + assert_response_status_code(response, 200) + body = response.json() + assert body["preferences"]["rows_per_page"] == 42 + assert body["overrides"]["rows_per_page"] == 10 + + +def test_patch_user_preferences_multiple_fields(api_client): + """PATCH /user-preferences updates multiple fields.""" + payload = { + "sidebar_visible": False, + "sidebar_auto_minimize": True, + } + response = api_client.patch("/user-preferences", json=payload) + assert_response_status_code(response, 200) + body = response.json() + assert body["preferences"]["sidebar_visible"] is False + assert body["preferences"]["sidebar_auto_minimize"] is True + assert body["overrides"]["sidebar_visible"] is True + assert body["overrides"]["sidebar_auto_minimize"] is False + + +def test_get_user_preferences_shows_overrides(api_client): + """GET /user-preferences reflects previously set overrides.""" + response = api_client.get("/user-preferences") + assert_response_status_code(response, 200) + body = response.json() + # rows_per_page was set to 42 in earlier test + assert body["preferences"]["rows_per_page"] == 42 + assert body["overrides"]["rows_per_page"] == 10 + + +def test_delete_user_preference_resets_to_global(api_client): + """DELETE /user-preferences/{key} resets that key to global default.""" + response = api_client.delete("/user-preferences/rows_per_page") + assert_response_status_code(response, 200) + body = response.json() + assert "rows_per_page" not in body["overrides"] + # Should now reflect the global value + global_resp = api_client.get("/admin/global-preferences") + global_rows = global_resp.json()["preferences"]["rows_per_page"] + assert body["preferences"]["rows_per_page"] == global_rows + + +def test_delete_user_preference_invalid_key(api_client): + """DELETE /user-preferences/{invalid_key} returns 400.""" + response = api_client.delete("/user-preferences/nonexistent_key") + assert_response_status_code(response, 400) + + +def test_patch_user_preferences_invalid_rows_per_page(api_client): + """PATCH /user-preferences with invalid rows_per_page returns 400.""" + response = api_client.patch("/user-preferences", json={"rows_per_page": 1}) + assert_response_status_code(response, 400) + + +def test_patch_user_preferences_invalid_language(api_client): + """PATCH /user-preferences with invalid language returns 400.""" + response = api_client.patch("/user-preferences", json={"language": "fr"}) + assert_response_status_code(response, 400) + + +def test_user_preferences_metadata_matches_global(api_client): + """User preferences metadata matches global preferences metadata.""" + global_resp = api_client.get("/admin/global-preferences") + user_resp = api_client.get("/user-preferences") + assert_response_status_code(global_resp, 200) + assert_response_status_code(user_resp, 200) + assert global_resp.json()["metadata"] == user_resp.json()["metadata"] 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 9668cf46..b209e9c9 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 @@ -3027,6 +3027,7 @@ def test_get_studies_list(api_client): "version_number", "latest_locked_version", "latest_released_version", + "data_completeness_tags", ] STUDY_SIMPLE_FIELDS_NOT_NULL = [ "uid", @@ -3218,3 +3219,34 @@ def lock_study(study_uid): assert len(package_names_today) == len( set(package_names_today) ), f"Duplicate sponsor packages found: {package_names_today}" + + +def test_cannot_create_study_with_already_existing_study_acronym(api_client): + response = api_client.post( + "/studies", + json={ + "project_number": "123", + "study_number": None, + "study_acronym": "study_root", + "description": None, + }, + ) + assert_response_status_code(response, 409) + res = response.json() + assert res["type"] == "AlreadyExistsException" + assert res["message"] == "Study with Study Acronym 'study_root' already exists." + + +def test_cannot_update_study_to_an_already_existing_study_acronym(api_client): + response = api_client.patch( + f"/studies/{study.uid}", + json={ + "current_metadata": { + "identification_metadata": {"study_acronym": "study_root"} + } + }, + ) + assert_response_status_code(response, 409) + res = response.json() + assert res["type"] == "AlreadyExistsException" + assert res["message"] == "Study with Study Acronym 'study_root' already exists." diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_codelist_repository.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_codelist_repository.py index 3a16397e..14d882bd 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_codelist_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_codelist_repository.py @@ -25,16 +25,14 @@ class TestCTCodelistRepository(unittest.TestCase): @classmethod def setUpClass(cls) -> None: cls.db = inject_and_clear_db(cls.TEST_DB_NAME) - cls.db.cypher_query( - """ + cls.db.cypher_query(""" CREATE(:Library{name:"CDISC", is_editable:true}) CREATE(:Library{name:"Sponsor1", is_editable:true}) CREATE(sdtm_ct:CTCatalogue{name:"SDTM CT"})-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "SDTM_PACKAGE_1",name:"SDTM_PACKAGE_1"}) MERGE(sdtm_ct)-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "SDTM_PACKAGE_2", name:"SDTM_PACKAGE_2"}) CREATE(cdash_ct:CTCatalogue{name:"CDASH CT"})-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "CDASH_PACKAGE_1",name:"CDASH_PACKAGE_1"}) MERGE(cdash_ct)-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "CDASH_PACKAGE_2", name:"CDASH_PACKAGE_2"}) - """ - ) + """) cls.codelist_attributes_repo = CTCodelistAttributesRepository() cls.codelist_names_repo = CTCodelistNameRepository() diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_term_repository.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_term_repository.py index 4b7df489..9589dda0 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_term_repository.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_ct_term_repository.py @@ -44,16 +44,14 @@ class TestCTTermRepository(unittest.TestCase): @classmethod def setUpClass(cls) -> None: inject_and_clear_db(cls.TEST_DB_NAME) - db.cypher_query( - """ + db.cypher_query(""" CREATE(:Library{name:"CDISC", is_editable:true}) CREATE(:Library{name:"Sponsor", is_editable:true}) CREATE(sdtm_ct:CTCatalogue{name:"SDTM CT"})-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "SDTM_PACKAGE_1",name:"SDTM_PACKAGE_1"}) MERGE(sdtm_ct)-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "SDTM_PACKAGE_2", name:"SDTM_PACKAGE_2"}) CREATE(cdash_ct:CTCatalogue{name:"CDASH CT"})-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "CDASH_PACKAGE_1",name:"CDASH_PACKAGE_1"}) MERGE(cdash_ct)-[:CONTAINS_PACKAGE]->(:CTPackage{uid: "CDASH_PACKAGE_2", name:"CDASH_PACKAGE_2"}) - """ - ) + """) cls.term_aggregated_repo = CTTermAggregatedRepository() cls.term_attributes_repo = CTTermAttributesRepository() cls.term_names_repo = CTTermNameRepository() 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 a6518425..d6d62984 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 @@ -898,6 +898,236 @@ def test__save__after_retrieve_for_update_and_closing_transaction__failure(self) # when repo.save(study) + def test__get_study_id__with_valid_study__returns_study_id(self): + """Test that get_study_id returns correct study_id when study exists with both prefix and number""" + # given + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + repo.close() + + # 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}" + assert study_id == expected_id + + def test__get_study_id__with_specific_version__returns_study_id(self): + """Test that get_study_id returns study_id for a specific version""" + # given + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + + # Create a locked version + study_to_lock = repo.find_by_uid(created_study.uid, for_update=True) + study_to_lock.edit_metadata( + study_title_exists_callback=lambda _, study_number: False, + study_short_title_exists_callback=lambda _, study_number: False, + new_study_description=StudyDescriptionVO.from_input_values( + study_title="new_study_title", study_short_title="study_short_title" + ), + author_id=current_function_name(), + ) + repo.save(study_to_lock) + study_to_lock = repo.find_by_uid(created_study.uid, for_update=True) + study_to_lock.lock( + version_description="locked version", + author_id=current_function_name(), + ) + repo.save(study_to_lock) + locked_version = str( + study_to_lock.current_metadata.ver_metadata.version_number + ) + repo.close() + + # when + study_id = StudyDefinitionRepositoryImpl.get_study_id( + created_study.uid, study_value_version=locked_version + ) + + # then + expected_id = f"{created_study.current_metadata.id_metadata.study_id_prefix}-{created_study.current_metadata.id_metadata.study_number}" + assert study_id == expected_id + + def test__get_study_id__with_nonexistent_uid__returns_none(self): + """Test that get_study_id returns None when study doesn't exist""" + # given + non_existent_uid = f"non-existent-uid-{random_str()}" + + # when + study_id = StudyDefinitionRepositoryImpl.get_study_id(non_existent_uid) + + # then + assert study_id is None + + def test__get_study_id__with_nonexistent_version__returns_none(self): + """Test that get_study_id returns None when version doesn't exist""" + # given + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + repo.close() + + # when + study_id = StudyDefinitionRepositoryImpl.get_study_id( + created_study.uid, study_value_version="999.999" + ) + + # then + assert study_id is None + + def test__get_study_id__with_missing_study_id_prefix__returns_none(self): + """Test that get_study_id returns None when study_id_prefix is missing""" + # given - create study and manually remove study_id_prefix + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + repo.close() + + # Manually set study_id_prefix to NULL in database + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) + SET sv.study_id_prefix = NULL + """, + {"uid": created_study.uid}, + ) + + # when + study_id = StudyDefinitionRepositoryImpl.get_study_id(created_study.uid) + + # then + assert study_id is None + + def test__get_study_id__with_missing_study_number__returns_none(self): + """Test that get_study_id returns None when study_number is missing""" + # given - create study and manually remove study_number + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + repo.close() + + # Manually set study_number to NULL in database + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) + SET sv.study_number = NULL + """, + {"uid": created_study.uid}, + ) + + # when + study_id = StudyDefinitionRepositoryImpl.get_study_id(created_study.uid) + + # then + 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""" + # given + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + repo.close() + + # Manually add subpart_id to the study + subpart_id = "SP1" + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) + SET sv.subpart_id = $subpart_id + """, + {"uid": created_study.uid, "subpart_id": subpart_id}, + ) + + # 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}" + assert study_id == expected_id + + def test__get_study_id__after_release__returns_study_id(self): + """Test that get_study_id works correctly for released studies""" + # given + with db.transaction: + repo = StudyDefinitionRepositoryImpl(current_function_name()) + created_study = create_random_study( + generate_uid_callback=repo.generate_uid, + new_id_metadata_fixed_values={ + "project_number": self.created_project.project_number + }, + is_study_after_create=True, + author_id=current_function_name(), + ) + repo.save(created_study) + + # Release the study + study_to_release = repo.find_by_uid(created_study.uid, for_update=True) + study_to_release.release( + change_description="test release", + author_id=current_function_name(), + ) + repo.save(study_to_release) + repo.close() + + # 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}" + assert study_id == expected_id + @pytest.mark.parametrize( ("soa_preferences_input", "expected_preferences"), diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_uid_assignment.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_uid_assignment.py index c91f3259..de7b9d8d 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_uid_assignment.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/domain_repositories/test_uid_assignment.py @@ -17,12 +17,10 @@ def setUp(self): @db.transaction def get_all_nodes_by_label(self, label): - return db.cypher_query( - f""" + return db.cypher_query(f""" MATCH (n:{label}) RETURN n.uid - """ - ) + """) @db.transaction def create_some_nodes_with_neomodel(self): diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_fields.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_fields.py index a4034422..d7630ffe 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_fields.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_fields.py @@ -123,6 +123,7 @@ def set_up_base_graph_for_studies(self): study_title_exists_callback=lambda _, study_number: False, study_short_title_exists_callback=lambda _, study_number: False, study_number_exists_callback=lambda x, y: False, + study_acronym_exists_callback=lambda x, y: False, author_id="unknown-user", ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_selections.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_selections.py index 9dd747dc..288037f0 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_selections.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/repositories/concurrency/test_study_selections.py @@ -171,6 +171,7 @@ def set_up_base_graph_for_studies(): study_title_exists_callback=lambda _, study_number: False, study_short_title_exists_callback=lambda _, study_number: False, study_number_exists_callback=lambda x, y: False, + study_acronym_exists_callback=lambda x, y: False, author_id=AUTHOR_ID, ) test_data.studies_repository.save(study_ar) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_list_studies.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_list_studies.py index 7ef0b374..9d7e4e57 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_list_studies.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_list_studies.py @@ -122,8 +122,7 @@ def setUp(self): ) # Create a criteria template - db.cypher_query( - """ + db.cypher_query(""" MATCH (incl:CTTermRoot {uid: "C25532"}) MATCH (library:Library {name: "Sponsor"}) MERGE (incl)<-[:HAS_SELECTED_TERM]-(:CTTermContext)<-[:HAS_TYPE]-(ctr1:CriteriaTemplateRoot:SyntaxTemplateRoot:SyntaxIndexingTemplateRoot {uid: "incl_criteria_1"}) @@ -136,8 +135,7 @@ def setUp(self): set hv.author_id = "unknown-user" set hv.version = "1.0" MERGE (library)-[:CONTAINS_SYNTAX_TEMPLATE]->(ctr1) - """ - ) + """) # Create a study criteria StudyCriteriaSelectionService().make_selection_create_criteria( @@ -152,8 +150,7 @@ def setUp(self): ) # Create an Activity Instruction Template - db.cypher_query( - """ + db.cypher_query(""" MATCH (lib:Library {name: "Sponsor"}) MERGE (adt:ActivityInstructionTemplateRoot:SyntaxTemplateRoot {uid: "ActivityInstructionTemplate_000001"}) -[relt:LATEST_FINAL]->(adtv:ActivityInstructionTemplateValue:SyntaxTemplateValue @@ -166,8 +163,7 @@ def setUp(self): set hv.status = "Final" set hv.author_id = "unknown-user" set hv.version = "1.0" - """ - ) + """) # Create a study activity instruction StudyActivityInstructionService().create( @@ -183,8 +179,7 @@ def setUp(self): ) # Let's create an empty study - db.cypher_query( - """ + db.cypher_query(""" MERGE (sr:StudyRoot {uid: "study_root2"})-[:LATEST]->(sv:StudyValue{study_id_prefix: "some_id2", study_number:"1"}) MERGE (sr)-[hv:HAS_VERSION]->(sv) MERGE (sr)-[ld:LATEST_DRAFT]->(sv) @@ -197,8 +192,7 @@ def setUp(self): WITH sv MATCH (p:Project {uid: "Project_000001"}) MERGE (p)-[:HAS_FIELD]->(sf:StudyField:StudyProjectField)<-[:HAS_PROJECT]-(sv) - """ - ) + """) self.study_service = StudyService() 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 new file mode 100644 index 00000000..3754cc6d --- /dev/null +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_studies.py @@ -0,0 +1,317 @@ +# pylint: disable=redefined-outer-name,unused-argument + +""" +Integration tests for StudyService methods. +These tests verify service-level behavior including business logic and exception handling. +""" + +import logging + +import pytest +from neomodel import db + +from clinical_mdr_api.services.studies.study import StudyService +from clinical_mdr_api.tests.integration.utils.utils import TestUtils +from common.exceptions import NotFoundException + +log = logging.getLogger(__name__) + + +@pytest.fixture(scope="module") +def study_service(): + """Fixture providing a StudyService instance.""" + return StudyService() + + +def test_get_study_id__with_valid_study__returns_study_id( + base_data, tst_project, study_service +): + """ + Test that get_study_id returns the correct study ID for a valid study. + + SCENARIO: Retrieve study ID for an existing study with valid prefix and number + GIVEN: A study exists with study_id_prefix and study_number + WHEN: get_study_id is called with the study UID + THEN: The study ID is returned in format "prefix-number" + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + # WHEN + study_id = study_service.get_study_id(study.uid) + + # THEN + expected_id = f"{tst_project.project_number}-{study_number}" + assert study_id == expected_id + + +def test_get_study_id__with_locked_version__returns_study_id( + base_data, tst_project, study_service +): + """ + Test that get_study_id returns the correct study ID for a locked study version. + + SCENARIO: Retrieve study ID for a specific locked version of a study + GIVEN: A study exists with a locked version + WHEN: get_study_id is called with the study UID and version number + THEN: The study ID for that locked study version is returned + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + # Lock a version + latest_study_version = TestUtils.lock_and_unlock_study( + study.uid, + reason_for_lock_term_uid=base_data["reason_for_lock_terms"][0].term_uid, + reason_for_unlock_term_uid=base_data["reason_for_unlock_terms"][0].term_uid, + ) + + # WHEN + study_id = study_service.get_study_id( + study.uid, study_value_version=latest_study_version + ) + + # THEN + expected_id = f"{tst_project.project_number}-{study_number}" + assert study_id == expected_id + + +def test_get_study_id__with_released_version__returns_study_id( + base_data, tst_project, study_service +): + """ + Test that get_study_id returns the correct study ID for a released study version. + + SCENARIO: Retrieve study ID for a specific released version of a study + GIVEN: A study exists with a locked version + WHEN: get_study_id is called with the study UID and version number + THEN: The study ID for that released study version is returned + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + # Release study + released_study_version = TestUtils.release_study( + study.uid, + reason_for_release_term_uid=base_data["reason_for_lock_terms"][0].term_uid, + ) + + # WHEN + study_id = study_service.get_study_id( + study.uid, study_value_version=released_study_version + ) + + # THEN + expected_id = f"{tst_project.project_number}-{study_number}" + assert study_id == expected_id + + +def test_get_study_id__with_nonexistent_uid__raises_not_found_exception( + base_data, study_service +): + """ + Test that get_study_id raises NotFoundException when study doesn't exist. + + SCENARIO: Attempt to retrieve study ID for a non-existent study + GIVEN: No study exists with the specified UID + WHEN: get_study_id is called with a non-existent UID + THEN: NotFoundException is raised with appropriate error message + """ + # GIVEN + non_existent_uid = "non-existent-12345" + + # WHEN / THEN + with pytest.raises(NotFoundException) as exc_info: + study_service.get_study_id(non_existent_uid) + + assert "Study" in str(exc_info.value) + assert non_existent_uid in str(exc_info.value) + assert "was not found" in str(exc_info.value) + + +def test_get_study_id__with_nonexistent_version__raises_not_found_exception( + base_data, tst_project, study_service +): + """ + Test that get_study_id raises NotFoundException when version doesn't exist. + + SCENARIO: Attempt to retrieve study ID for a non-existent version + GIVEN: A study exists but the specified version does not + WHEN: get_study_id is called with an invalid version number + THEN: NotFoundException is raised with appropriate error message + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + non_existent_version = "999.999" + + # WHEN / THEN + with pytest.raises(NotFoundException) as exc_info: + study_service.get_study_id(study.uid, study_value_version=non_existent_version) + + assert study.uid in str(exc_info.value) + assert non_existent_version in str(exc_info.value) + assert "was not found" in str(exc_info.value) + + +def test_get_study_id__with_missing_study_id_prefix__raises_not_found_exception( + base_data, tst_project, study_service +): + """ + Test that get_study_id raises NotFoundException when study_id_prefix is missing. + + SCENARIO: Attempt to retrieve study ID when prefix is not defined + GIVEN: A study exists but study_id_prefix is NULL + WHEN: get_study_id is called + THEN: NotFoundException is raised indicating prefix is not defined + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + # Manually set study_id_prefix to NULL in database + db.cypher_query( + """ + MATCH (sr:StudyRoot {uid: $uid})-[:LATEST]->(sv:StudyValue) + SET sv.study_id_prefix = NULL + """, + {"uid": study.uid}, + ) + + # WHEN / THEN + with pytest.raises(NotFoundException) as exc_info: + study_service.get_study_id(study.uid) + + assert study.uid in str(exc_info.value) + assert "study_id_prefix" in str(exc_info.value) + assert "not defined" in str(exc_info.value) + + +def test_get_study_id__with_missing_study_number__raises_not_found_exception( + base_data, tst_project, study_service +): + """ + Test that get_study_id raises NotFoundException when study_number is missing. + + SCENARIO: Attempt to retrieve study ID when number is not defined + GIVEN: A study exists but study_number is NULL + WHEN: get_study_id is called + THEN: NotFoundException is raised indicating number is not defined + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + # Remove study_number + study = TestUtils.patch_study(study.uid, study_number=None) + + # WHEN / THEN + with pytest.raises(NotFoundException) as exc_info: + study_service.get_study_id(study.uid) + + assert study.uid in str(exc_info.value) + assert "study_number" in str(exc_info.value) + assert "not defined" in str(exc_info.value) + + +def test_get_study_id__after_release__returns_study_id( + base_data, tst_project, study_service +): + """ + Test that get_study_id works correctly for released studies. + + SCENARIO: Retrieve study ID for a released study + GIVEN: A study has been released + WHEN: get_study_id is called with the study UID + THEN: The study ID is returned correctly + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + TestUtils.release_study( + study.uid, + reason_for_release_term_uid=base_data["reason_for_lock_terms"][0].term_uid, + ) + + # WHEN + study_id = study_service.get_study_id(study.uid) + + # THEN + expected_id = f"{tst_project.project_number}-{study_number}" + assert study_id == expected_id + + +def test_get_study_id__for_subpart__returns_study_id( + base_data, tst_project, study_service +): + """ + Test that get_study_id returns correct ID for study subpart. + + SCENARIO: Retrieve study ID for a study subpart + GIVEN: A study subpart exists with study_id_prefix and study_number + WHEN: get_study_id is called with the subpart UID + THEN: The study ID is returned correctly (parent study prefix and number) + """ + # GIVEN + study_number = TestUtils.random_str(4) + parent_study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + subpart_study = TestUtils.create_study( + subpart_acronym="SUB1", + study_parent_part_uid=parent_study.uid, + project_number=tst_project.project_number, + ) + + # WHEN + study_id = study_service.get_study_id(subpart_study.uid) + + # THEN + expected_id = f"{tst_project.project_number}-{study_number}" + assert study_id == expected_id + + +def test_get_study_id__with_deleted_study__raises_not_found_exception( + base_data, tst_project, study_service +): + """ + Test that get_study_id raises NotFoundException for deleted studies. + + SCENARIO: Attempt to retrieve study ID for a deleted study + GIVEN: A study has been marked as deleted + WHEN: get_study_id is called with the deleted study UID + THEN: NotFoundException is raised + """ + # GIVEN + study_number = TestUtils.random_str(4) + study = TestUtils.create_study( + number=study_number, project_number=tst_project.project_number + ) + + # Mark the study as deleted + TestUtils.delete_study(study.uid) + + # WHEN / THEN + with pytest.raises(NotFoundException) as exc_info: + study_service.get_study_id(study.uid) + + assert study.uid in str(exc_info.value) + assert "was not found" in str(exc_info.value) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_activity_schedule.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_activity_schedule.py index 37ef334b..18057557 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_activity_schedule.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_activity_schedule.py @@ -71,8 +71,8 @@ def setup_and_teardown_db(): def test_create_delete_schedule(setup_and_teardown_db): baseline = create_visit_with_update( study_epoch_uid=test_data.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=0, time_unit_uid=test_data.day_uid, ) @@ -95,15 +95,15 @@ def test_create_delete_schedule(setup_and_teardown_db): def test_batch_operations(setup_and_teardown_db): baseline = create_visit_with_update( study_epoch_uid=test_data.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=0, time_unit_uid=test_data.day_uid, ) create_visit_with_update( study_epoch_uid=test_data.epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=4, time_unit_uid=test_data.day_uid, ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py index f4e4e210..f108eafa 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/services/test_study_visits.py @@ -1,4 +1,5 @@ import unittest +from typing import Iterable from neomodel import db @@ -15,6 +16,7 @@ StudyVisit, StudyVisitCreateInput, StudyVisitEditInput, + StudyVisitLite, ) from clinical_mdr_api.services.studies.study_activity_schedule import ( StudyActivityScheduleService, @@ -52,6 +54,7 @@ ValidationException, VisitsAreNotEqualException, ) +from common.utils import VisitClass class TestStudyVisitManagement(unittest.TestCase): @@ -101,8 +104,8 @@ def setUp(self): def test__list__visits_studies(self): inputs = { "study_epoch_uid": self.epoch1.uid, - "visit_type_uid": "VisitType_0001", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0001"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 0, "time_unit_uid": self.day_uid, "is_global_anchor_visit": True, @@ -119,8 +122,8 @@ def test__list__visits_studies(self): create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -129,8 +132,8 @@ def test__list__visits_studies(self): ) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=12, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -139,8 +142,8 @@ def test__list__visits_studies(self): ) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -149,8 +152,8 @@ def test__list__visits_studies(self): ) inputs = { "study_epoch_uid": self.epoch1.uid, - "visit_type_uid": "VisitType_0004", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0004"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 20, "time_unit_uid": self.day_uid, "is_global_anchor_visit": False, @@ -167,8 +170,8 @@ def test__list__visits_studies(self): version3 = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0004", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0004"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=20, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -180,8 +183,8 @@ def test__list__visits_studies(self): self.assertEqual(version3.week_in_study_label, "Week 2") version4 = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=30, time_unit_uid=self.day_uid, visit_sublabel_reference=None, @@ -191,8 +194,8 @@ def test__list__visits_studies(self): ) version5 = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0002", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0002"}, time_value=31, time_unit_uid=self.day_uid, visit_sublabel_reference=version4.uid, @@ -204,6 +207,9 @@ def test__list__visits_studies(self): visits = visit_service.get_all_visits(self.study.uid) self.assertEqual(len(visits.items), 6) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(visits.items, self.study.uid) + v3new: StudyVisit = visit_service.find_by_uid( study_uid=self.study.uid, uid=version3.uid ) @@ -251,8 +257,8 @@ def test__list__visits_studies(self): inputs = { "study_epoch_uid": self.epoch2.uid, - "visit_type_uid": "VisitType_0003", - "time_reference_uid": "VisitSubType_0002", + "visit_type": {"term_uid": "VisitType_0003"}, + "time_reference": {"term_uid": "VisitSubType_0002"}, "time_value": 40, "time_unit_uid": self.day_uid, "visit_sublabel_reference": version4.uid, @@ -327,8 +333,8 @@ def test__list__visits_studies(self): v3new.uid, uid=v3new.uid, study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0004", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0004"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=25, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -342,26 +348,26 @@ def test__create__props_are_correctly_saved(self): input_values = { "study_epoch_uid": self.epoch1.uid, - "visit_type_uid": "VisitType_0001", - "time_reference_uid": "VisitSubType_0001", + "visit_type": {"term_uid": "VisitType_0001"}, + "time_reference": {"term_uid": "VisitSubType_0001"}, "time_value": 0, "time_unit_uid": self.day_uid, - "visit_contact_mode_uid": "VisitContactMode_0002", + "visit_contact_mode": {"term_uid": "VisitContactMode_0002"}, "max_visit_window_value": 10, "min_visit_window_value": 0, "show_visit": True, "is_global_anchor_visit": False, "visit_class": "SINGLE_VISIT", "visit_subclass": "SINGLE_VISIT", - "epoch_allocation_uid": "EpochAllocation_0002", + "epoch_allocation": {"term_uid": "EpochAllocation_0002"}, } visit = create_visit_with_update(**input_values) visit_after_create = visit_service.find_by_uid( study_uid=self.study.uid, uid=visit.uid ) self.assertEqual( - visit_after_create.visit_contact_mode_uid, - input_values["visit_contact_mode_uid"], + visit_after_create.visit_contact_mode.term_uid, + input_values["visit_contact_mode"]["term_uid"], ) self.assertEqual( visit_after_create.max_visit_window_value, @@ -377,14 +383,16 @@ def test__create__props_are_correctly_saved(self): self.assertEqual(visit_after_create.time_value, input_values["time_value"]) self.assertEqual(visit_after_create.show_visit, input_values["show_visit"]) self.assertEqual( - visit_after_create.time_reference_uid, input_values["time_reference_uid"] + visit_after_create.time_reference.term_uid, + input_values["time_reference"]["term_uid"], ) self.assertEqual( - visit_after_create.visit_type_uid, input_values["visit_type_uid"] + visit_after_create.visit_type.term_uid, + input_values["visit_type"]["term_uid"], ) self.assertEqual( - visit_after_create.epoch_allocation_uid, - input_values["epoch_allocation_uid"], + visit_after_create.epoch_allocation.term_uid, + input_values["epoch_allocation"]["term_uid"], ) self.assertEqual(visit_after_create.study_duration_weeks_label, "0 weeks") self.assertEqual(visit_after_create.week_in_study_label, "Week 0") @@ -393,14 +401,14 @@ def test__edit_visit_successfully_handled(self): visit_service = StudyVisitService(study_uid=self.study.uid) visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", - epoch_allocation_uid="EpochAllocation_0001", + epoch_allocation={"term_uid": "EpochAllocation_0001"}, ) self.assertEqual( visit.is_soa_milestone, @@ -437,11 +445,11 @@ def test__edit_visit_successfully_handled(self): edit_input = { "uid": visit.uid, "study_epoch_uid": visit.study_epoch_uid, - "visit_type_uid": "VisitType_0001", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0001"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 7, "time_unit_uid": self.day_uid, - "visit_contact_mode_uid": "VisitContactMode_0002", + "visit_contact_mode": {"term_uid": "VisitContactMode_0002"}, "max_visit_window_value": 10, "min_visit_window_value": 0, "visit_window_unit_uid": visit.visit_window_unit_uid, @@ -450,7 +458,7 @@ def test__edit_visit_successfully_handled(self): "is_soa_milestone": True, "visit_class": "SINGLE_VISIT", "visit_subclass": "SINGLE_VISIT", - "epoch_allocation_uid": "EpochAllocation_0002", + "epoch_allocation": {"term_uid": "EpochAllocation_0002"}, } visit_service.edit( study_uid=visit.study_uid, @@ -465,8 +473,8 @@ def test__edit_visit_successfully_handled(self): True, ) self.assertEqual( - visit_after_update.visit_contact_mode_uid, - edit_input["visit_contact_mode_uid"], + visit_after_update.visit_contact_mode.term_uid, + edit_input["visit_contact_mode"]["term_uid"], ) self.assertEqual( visit_after_update.max_visit_window_value, @@ -480,13 +488,15 @@ def test__edit_visit_successfully_handled(self): self.assertEqual(visit_after_update.time_value, edit_input["time_value"]) self.assertEqual(visit_after_update.show_visit, edit_input["show_visit"]) self.assertEqual( - visit_after_update.time_reference_uid, edit_input["time_reference_uid"] + visit_after_update.time_reference.term_uid, + edit_input["time_reference"]["term_uid"], ) self.assertEqual( - visit_after_update.visit_type_uid, edit_input["visit_type_uid"] + visit_after_update.visit_type.term_uid, edit_input["visit_type"]["term_uid"] ) self.assertEqual( - visit_after_update.epoch_allocation_uid, edit_input["epoch_allocation_uid"] + visit_after_update.epoch_allocation.term_uid, + edit_input["epoch_allocation"]["term_uid"], ) self.assertEqual(visit_after_update.study_duration_weeks_label, "1 weeks") self.assertEqual(visit_after_update.week_in_study_label, "Week 1") @@ -495,15 +505,15 @@ def test__version_visits(self): visit_service = StudyVisitService(study_uid=self.study.uid) first_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, is_soa_milestone=True, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", - epoch_allocation_uid="EpochAllocation_0001", + epoch_allocation={"term_uid": "EpochAllocation_0001"}, ) self.assertEqual(first_visit.is_soa_milestone, True) @@ -530,11 +540,11 @@ def test__version_visits(self): edit_input = { "uid": first_visit.uid, "study_epoch_uid": first_visit.study_epoch_uid, - "visit_type_uid": "VisitType_0001", - "time_reference_uid": "VisitSubType_0005", + "visit_type": {"term_uid": "VisitType_0001"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "time_value": 7, "time_unit_uid": self.day_uid, - "visit_contact_mode_uid": "VisitContactMode_0002", + "visit_contact_mode": {"term_uid": "VisitContactMode_0002"}, "max_visit_window_value": 10, "min_visit_window_value": 0, "visit_window_unit_uid": first_visit.visit_window_unit_uid, @@ -543,7 +553,7 @@ def test__version_visits(self): "is_soa_milestone": False, "visit_class": "SINGLE_VISIT", "visit_subclass": "SINGLE_VISIT", - "epoch_allocation_uid": "EpochAllocation_0002", + "epoch_allocation": {"term_uid": "EpochAllocation_0002"}, } visit_service.edit( study_uid=first_visit.study_uid, @@ -556,8 +566,8 @@ def test__version_visits(self): self.assertEqual(visit_after_update.is_soa_milestone, False) self.assertEqual( - visit_after_update.visit_contact_mode_uid, - edit_input["visit_contact_mode_uid"], + visit_after_update.visit_contact_mode.term_uid, + edit_input["visit_contact_mode"]["term_uid"], ) self.assertEqual( visit_after_update.max_visit_window_value, @@ -571,13 +581,15 @@ def test__version_visits(self): self.assertEqual(visit_after_update.time_value, edit_input["time_value"]) self.assertEqual(visit_after_update.show_visit, edit_input["show_visit"]) self.assertEqual( - visit_after_update.time_reference_uid, edit_input["time_reference_uid"] + visit_after_update.time_reference.term_uid, + edit_input["time_reference"]["term_uid"], ) self.assertEqual( - visit_after_update.visit_type_uid, edit_input["visit_type_uid"] + visit_after_update.visit_type.term_uid, edit_input["visit_type"]["term_uid"] ) self.assertEqual( - visit_after_update.epoch_allocation_uid, edit_input["epoch_allocation_uid"] + visit_after_update.epoch_allocation.term_uid, + edit_input["epoch_allocation"]["term_uid"], ) self.assertEqual(visit_after_update.study_duration_weeks_label, "1 weeks") self.assertEqual(visit_after_update.week_in_study_label, "Week 1") @@ -591,8 +603,8 @@ def test__version_visits(self): first_visit_after_create = visits_versions[1] self.assertEqual(first_visit_after_edit.uid, first_visit.uid) self.assertEqual( - first_visit_after_edit.visit_contact_mode_uid, - edit_input["visit_contact_mode_uid"], + first_visit_after_edit.visit_contact_mode.term_uid, + edit_input["visit_contact_mode"]["term_uid"], ) self.assertEqual( first_visit_after_edit.max_visit_window_value, @@ -605,8 +617,8 @@ def test__version_visits(self): self.assertEqual(first_visit_after_edit.time_value, edit_input["time_value"]) self.assertEqual( - first_visit_after_edit.epoch_allocation_uid, - edit_input["epoch_allocation_uid"], + first_visit_after_edit.epoch_allocation.term_uid, + edit_input["epoch_allocation"]["term_uid"], ) self.assertGreater( first_visit_after_edit.start_date, first_visit_after_create.start_date @@ -625,8 +637,8 @@ def test__version_visits(self): time_value = 30 second_visit = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=time_value, time_unit_uid=self.day_uid, visit_sublabel_reference=None, @@ -644,8 +656,8 @@ def test__version_visits(self): second_visit_history = all_visits_versions[2] self.assertEqual(first_visit_after_edit.uid, first_visit.uid) self.assertEqual( - first_visit_after_edit.visit_contact_mode_uid, - edit_input["visit_contact_mode_uid"], + first_visit_after_edit.visit_contact_mode.term_uid, + edit_input["visit_contact_mode"]["term_uid"], ) self.assertEqual( first_visit_after_edit.max_visit_window_value, @@ -661,14 +673,16 @@ def test__version_visits(self): self.assertEqual(first_visit_after_edit.time_value, edit_input["time_value"]) self.assertEqual(first_visit_after_edit.show_visit, edit_input["show_visit"]) self.assertEqual( - first_visit_after_edit.time_reference_uid, edit_input["time_reference_uid"] + first_visit_after_edit.time_reference.term_uid, + edit_input["time_reference"]["term_uid"], ) self.assertEqual( - first_visit_after_edit.visit_type_uid, edit_input["visit_type_uid"] + first_visit_after_edit.visit_type.term_uid, + edit_input["visit_type"]["term_uid"], ) self.assertEqual( - first_visit_after_edit.epoch_allocation_uid, - edit_input["epoch_allocation_uid"], + first_visit_after_edit.epoch_allocation.term_uid, + edit_input["epoch_allocation"]["term_uid"], ) self.assertEqual(first_visit_after_edit.uid, first_visit_after_create.uid) self.assertGreater( @@ -691,8 +705,8 @@ def test__create_subvisits_uvn__reordered_successfully(self): visit_service = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -702,8 +716,8 @@ def test__create_subvisits_uvn__reordered_successfully(self): time_value = 30 first_visit_in_seq_of_subvisits = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=time_value, time_unit_uid=self.day_uid, visit_sublabel_reference=None, @@ -715,10 +729,11 @@ def test__create_subvisits_uvn__reordered_successfully(self): # we add so many subvists as there is a logic of # recalculating subvists unique-visit-numbers when we exceed allowed limits for i in range(1, 21): + all_visits = None create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=time_value + i, time_unit_uid=self.day_uid, visit_sublabel_reference=first_visit_in_seq_of_subvisits.uid, @@ -777,10 +792,15 @@ def test__create_subvisits_uvn__reordered_successfully(self): self.assertEqual( sub_visit.unique_visit_number, sub_visit_uvn + sub_idx * 1 ) + + # check lite version of get_all_visits returns the same visits as normal version + if all_visits: + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=-1, time_unit_uid=self.day_uid, visit_sublabel_reference=first_visit_in_seq_of_subvisits.uid, @@ -811,6 +831,9 @@ def test__create_subvisits_uvn__reordered_successfully(self): all_visits = visit_service.get_all_visits(study_uid=self.study.uid).items self.assertEqual(len(all_visits), 23) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + all_visits = [visit for visit in all_visits if visit.visit_number == 2] self.assertEqual(all_visits[0].unique_visit_number, sub_visit_uvn) @@ -826,8 +849,8 @@ def test__get_global_anchor_visit(self): vis = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -859,7 +882,8 @@ def test__get_global_anchor_visit(self): self.assertEqual(global_anchor_visit.uid, vis.uid) self.assertEqual(global_anchor_visit.visit_name, vis.visit_name) self.assertEqual( - global_anchor_visit.visit_type_name, vis.visit_type.sponsor_preferred_name + global_anchor_visit.visit_type_name, + vis.visit_type.sponsor_preferred_name, ) def test__get_anchor_visits_in_a_group_of_subvisits(self): @@ -872,8 +896,8 @@ def test__get_anchor_visits_in_a_group_of_subvisits(self): create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -882,8 +906,8 @@ def test__get_anchor_visits_in_a_group_of_subvisits(self): ) anchor_visit = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=30, time_unit_uid=self.day_uid, visit_sublabel_reference=None, @@ -926,8 +950,8 @@ def test__epochs_durations_are_calculated_properly_when_having_empty_epoch(self) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -936,8 +960,8 @@ def test__epochs_durations_are_calculated_properly_when_having_empty_epoch(self) ) create_visit_with_update( study_epoch_uid=self.epoch3.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -946,8 +970,8 @@ def test__epochs_durations_are_calculated_properly_when_having_empty_epoch(self) ) create_visit_with_update( study_epoch_uid=self.epoch3.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=30, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -992,8 +1016,8 @@ def test__epochs_durations_are_calculated_properly_when_having_last_epoch_with_o create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1002,8 +1026,8 @@ def test__epochs_durations_are_calculated_properly_when_having_last_epoch_with_o ) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1012,8 +1036,8 @@ def test__epochs_durations_are_calculated_properly_when_having_last_epoch_with_o ) create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=30, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1022,8 +1046,8 @@ def test__epochs_durations_are_calculated_properly_when_having_last_epoch_with_o ) create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=40, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1032,8 +1056,8 @@ def test__epochs_durations_are_calculated_properly_when_having_last_epoch_with_o ) create_visit_with_update( study_epoch_uid=self.epoch3.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=50, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1102,8 +1126,8 @@ def test__epochs_durations_are_calculated_properly_when_having_last_epoch_with_o def test__create_visit_with_duplicated_timing__error_raised(self): create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1132,8 +1156,8 @@ def test__create_visit_with_duplicated_timing__error_raised(self): with self.assertRaises(ValidationException): create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1145,8 +1169,8 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1155,8 +1179,8 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): ) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1170,8 +1194,8 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): "description": "description", "start_rule": "start_rule", "end_rule": "end_rule", - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0003", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0003"}, "is_global_anchor_visit": False, "visit_class": "NON_VISIT", } @@ -1207,12 +1231,15 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): self.assertEqual(all_visits[0].time_value, 0) self.assertEqual(all_visits[1].time_value, 10) self.assertEqual(all_visits[2].time_value, None) - self.assertEqual(all_visits[2].time_reference_uid, None) + self.assertEqual(all_visits[2].time_reference, None) self.assertEqual(all_visits[2].time_reference, None) self.assertEqual(all_visits[2].visit_number, settings.non_visit_number) self.assertEqual(all_visits[2].min_visit_window_value, -9999) self.assertEqual(all_visits[2].max_visit_window_value, 9999) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + unscheduled_visit_input = { "study_epoch_uid": self.epoch1.uid, "consecutive_visit_group": None, @@ -1220,8 +1247,8 @@ def test__create_unscheduled_visit_without_time_data__no_error_is_raised(self): "description": "description", "start_rule": "start_rule", "end_rule": "end_rule", - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0003", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0003"}, "is_global_anchor_visit": False, "visit_class": "UNSCHEDULED_VISIT", } @@ -1257,8 +1284,8 @@ def test__create_special_visit(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1267,8 +1294,8 @@ def test__create_special_visit(self): ) special_visit_anchor = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1277,8 +1304,8 @@ def test__create_special_visit(self): ) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=15, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1311,8 +1338,8 @@ def test__create_special_visit(self): "description": "description", "start_rule": "start_rule", "end_rule": "end_rule", - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0003", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0003"}, "is_global_anchor_visit": False, "visit_class": "SPECIAL_VISIT", "visit_sublabel_reference": special_visit_anchor.uid, @@ -1347,7 +1374,7 @@ def test__create_special_visit(self): self.assertEqual(all_visits[0].time_value, 0) self.assertEqual(all_visits[1].time_value, 10) self.assertIsNone(all_visits[2].time_value) - self.assertIsNone(all_visits[2].time_reference_uid) + self.assertIsNone(all_visits[2].time_reference) self.assertIsNone(all_visits[2].time_reference) self.assertEqual(all_visits[2].visit_number, special_visit_anchor.visit_number) self.assertEqual( @@ -1355,6 +1382,9 @@ def test__create_special_visit(self): ) self.assertEqual(all_visits[3].time_value, 15) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + with self.assertRaises(BusinessLogicException) as message: visit_service.delete( study_uid=self.study.uid, study_visit_uid=special_visit_anchor.uid @@ -1375,8 +1405,8 @@ def test__visit_group_in_list_format(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1385,8 +1415,8 @@ def test__visit_group_in_list_format(self): ) second_vis = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1395,8 +1425,8 @@ def test__visit_group_in_list_format(self): ) third_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=15, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1405,8 +1435,8 @@ def test__visit_group_in_list_format(self): ) fourth_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=20, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1420,6 +1450,10 @@ def test__visit_group_in_list_format(self): group_format=VisitGroupFormat.LIST, ) all_visits = visit_service.get_all_visits(study_uid=self.study.uid).items + + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + consecutive_visit_group = ",".join( [ third_visit.visit_short_name, @@ -1435,8 +1469,8 @@ def test__visit_group_in_list_format(self): # The call to create visit in the middle of V3,V4 group should succeed as the group is grouped in the LIST format visit_after_third_and_before_fourth = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=17, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1449,6 +1483,9 @@ def test__visit_group_in_list_format(self): all_visits = visit_service.get_all_visits(study_uid=self.study.uid).items self.assertEqual(len(all_visits), 4) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + # There was another visit created in between V1 and V3, so the new group name should be 'V1,V3' updated_consecutive_group_name = ",".join( [all_visits[1].visit_short_name, all_visits[3].visit_short_name] @@ -1467,8 +1504,8 @@ def test__group_subsequent_visits_in_consecutive_group(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1477,8 +1514,8 @@ def test__group_subsequent_visits_in_consecutive_group(self): ) second_vis = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1487,8 +1524,8 @@ def test__group_subsequent_visits_in_consecutive_group(self): ) third_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=15, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1497,8 +1534,8 @@ def test__group_subsequent_visits_in_consecutive_group(self): ) fourth_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=20, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1548,6 +1585,9 @@ def test__group_subsequent_visits_in_consecutive_group(self): self.assertEqual(all_visits[1].consecutive_visit_group, consecutive_visit_group) self.assertEqual(all_visits[2].consecutive_visit_group, consecutive_visit_group) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + # It shouldn't be possible to create a visit in the middle of a consecutive visit group which is grouped in the RANGE format with self.assertRaises(ValidationException) as message: visit_input = generate_default_input_data_for_visit() @@ -1564,10 +1604,10 @@ def test__group_subsequent_visits_in_consecutive_group(self): edit_input = { "uid": third_visit.uid, "study_epoch_uid": third_visit.study_epoch_uid, - "time_reference_uid": third_visit.time_reference_uid, + "time_reference": {"term_uid": third_visit.time_reference.term_uid}, "time_value": 18, - "visit_type_uid": third_visit.visit_type_uid, - "visit_contact_mode_uid": "VisitContactMode_0001", + "visit_type": {"term_uid": third_visit.visit_type.term_uid}, + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, "time_unit_uid": third_visit.time_unit_uid, "is_global_anchor_visit": third_visit.is_global_anchor_visit, "visit_class": third_visit.visit_class, @@ -1587,8 +1627,8 @@ def test__group_visits_in_consecutive_group__visits_are_not_equal(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1597,8 +1637,8 @@ def test__group_visits_in_consecutive_group__visits_are_not_equal(self): ) second_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1670,14 +1710,14 @@ def test__group_visits_in_consecutive_group__visits_are_not_equal(self): third_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=15, time_unit_uid=self.day_uid, is_global_anchor_visit=False, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", - visit_contact_mode_uid="VisitContactMode_0002", + visit_contact_mode={"term_uid": "VisitContactMode_0002"}, max_visit_window_value=10, min_visit_window_value=-10, ) @@ -1760,11 +1800,11 @@ def test__group_visits_in_consecutive_group__visits_are_not_equal(self): edit_input = { "uid": third_visit.uid, "study_epoch_uid": third_visit.study_epoch_uid, - "visit_type_uid": "VisitType_0002", - "visit_contact_mode_uid": "VisitContactMode_0001", + "visit_type": {"term_uid": "VisitType_0002"}, + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, "max_visit_window_value": 1, "min_visit_window_value": -1, - "time_reference_uid": third_visit.time_reference_uid, + "time_reference": {"term_uid": third_visit.time_reference.term_uid}, "time_value": third_visit.time_value, "time_unit_uid": third_visit.time_unit_uid, "is_global_anchor_visit": third_visit.is_global_anchor_visit, @@ -1832,21 +1872,25 @@ def test__group_visits_in_consecutive_group__visits_are_not_equal(self): all_visits[2].max_visit_window_value, all_visits[1].max_visit_window_value ) self.assertEqual( - all_visits[2].visit_contact_mode_uid, all_visits[1].visit_contact_mode_uid + all_visits[2].visit_contact_mode.term_uid, + all_visits[1].visit_contact_mode.term_uid, ) self.assertEqual( all_visits[2].visit_contact_mode.sponsor_preferred_name, all_visits[1].visit_contact_mode.sponsor_preferred_name, ) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + def test__group_visits_in_consecutive_group__visits_are_already_in_consecutive_groups( self, ): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1855,8 +1899,8 @@ def test__group_visits_in_consecutive_group__visits_are_already_in_consecutive_g ) second_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1865,8 +1909,8 @@ def test__group_visits_in_consecutive_group__visits_are_already_in_consecutive_g ) third_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=11, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1908,8 +1952,8 @@ def test__group_visits_in_consecutive_group__visits_are_already_in_consecutive_g fourth_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=15, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1956,6 +2000,9 @@ def test__group_visits_in_consecutive_group__visits_are_already_in_consecutive_g all_visits[3].consecutive_visit_group, all_visits[1].consecutive_visit_group ) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + all_available_consecutive_groups = visit_service.get_consecutive_groups( study_uid=self.study.uid ) @@ -1970,8 +2017,8 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) first_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -1980,8 +2027,8 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( ) second_visit = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -1990,8 +2037,8 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( ) third_visit = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=11, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -2000,8 +2047,8 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( ) first_subv = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=12, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -2011,8 +2058,8 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( ) second_subv = create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=13, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -2076,6 +2123,9 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( all_visits[1].consecutive_visit_group, all_visits[2].consecutive_visit_group ) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + all_available_consecutive_groups = visit_service.get_consecutive_groups( study_uid=self.study.uid ) @@ -2100,6 +2150,9 @@ def test__visit_groups_can_be_but_not_have_to_be_subsequent( all_visits[3].consecutive_visit_group, all_visits[4].consecutive_visit_group ) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + all_available_consecutive_groups = visit_service.get_consecutive_groups( study_uid=self.study.uid ) @@ -2117,8 +2170,8 @@ def test__remove_consecutive_visit_group(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=0, time_unit_uid=self.day_uid, is_global_anchor_visit=True, @@ -2127,8 +2180,8 @@ def test__remove_consecutive_visit_group(self): ) second_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=10, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -2137,8 +2190,8 @@ def test__remove_consecutive_visit_group(self): ) third_visit = create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=15, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -2178,6 +2231,9 @@ def test__remove_consecutive_visit_group(self): self.assertEqual(all_visits[1].consecutive_visit_group, consecutive_visit_group) self.assertEqual(all_visits[2].consecutive_visit_group, consecutive_visit_group) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + all_available_consecutive_groups = visit_service.get_consecutive_groups( study_uid=self.study.uid ) @@ -2208,6 +2264,9 @@ def test__remove_consecutive_visit_group(self): ) self.assertEqual(len(all_available_consecutive_groups), 0) + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(all_visits, self.study.uid) + def test_get_anchor_visit_for_special_visit(self): visit_service: StudyVisitService = StudyVisitService(study_uid=self.study.uid) # create 5 visits in epoch 1 @@ -2215,8 +2274,8 @@ def test_get_anchor_visit_for_special_visit(self): is_global_anchor_visit = bool(idx == 0) create_visit_with_update( study_epoch_uid=self.epoch1.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=idx, time_unit_uid=self.day_uid, is_global_anchor_visit=is_global_anchor_visit, @@ -2227,8 +2286,8 @@ def test_get_anchor_visit_for_special_visit(self): for idx in range(5, 10): create_visit_with_update( study_epoch_uid=self.epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0005", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0005"}, time_value=idx, time_unit_uid=self.day_uid, is_global_anchor_visit=False, @@ -2284,3 +2343,25 @@ def test_consecutive_visit_group_name(self): visits_grouped[-2].consecutive_visit_group == f"{study_visits[-5].visit_short_name}-{study_visits[-2].visit_short_name}" ) + + # check lite version of get_all_visits returns the same visits as normal version + assert_get_all_visits_lite_compares(visits_grouped, study.uid) + + +def assert_get_all_visits_lite_compares( + expected_items: Iterable[StudyVisit], + study_uid: str, + study_value_version: str | None = None, +): + expected_items = [StudyVisitLite(**v.model_dump()) for v in expected_items] + + # Lite endpoint returns None for study_day/week_numbers for special visits + for visit in expected_items: + if visit.visit_class == VisitClass.SPECIAL_VISIT: + visit.study_day_number = None + visit.study_week_number = None + + lite = StudyVisitService.get_all_visits( + study_uid, study_value_version=study_value_version, lite=True + ) + assert lite.items == expected_items diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/api.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/api.py index f24d27da..22e5cbc9 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/api.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/api.py @@ -8,7 +8,7 @@ from urllib.parse import urljoin import neo4j.exceptions -from neomodel.sync_.core import db +from neomodel import db from requests.structures import CaseInsensitiveDict from starlette.testclient import TestClient diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/data_library.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/data_library.py index fd9b8d81..794f2598 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/data_library.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/data_library.py @@ -45,21 +45,21 @@ } AS final_properties MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (odm_translated_text1:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) -MERGE (odm_translated_text2:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) -MERGE (odm_translated_text3:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) -MERGE (odm_translated_text4:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) +MERGE (odm_translated_text1:Odm:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) +MERGE (odm_translated_text2:Odm:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) +MERGE (odm_translated_text3:Odm:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) +MERGE (odm_translated_text4:Odm:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) MERGE (odm_formal_expression1:OdmFormalExpression {context: "context1", expression: "expression1"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_condition_root1:ConceptRoot:OdmConditionRoot {uid: "odm_condition1"}) -MERGE (odm_condition_value1:ConceptValue:OdmConditionValue {oid: "oid1", name: "name1"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_condition_root1:Odm:OdmRoot:OdmConditionRoot {uid: "odm_condition1"}) +MERGE (odm_condition_value1:Odm:OdmValue:OdmConditionValue {oid: "oid1", name: "name1"}) MERGE (odm_condition_root1)-[ld1:LATEST_FINAL]->(odm_condition_value1) MERGE (odm_condition_root1)-[l1:LATEST]->(odm_condition_value1) MERGE (odm_condition_root1)-[hv1:HAS_VERSION]->(odm_condition_value1) SET hv1 = final_properties -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_condition_root2:ConceptRoot:OdmConditionRoot {uid: "odm_condition2"}) -MERGE (odm_condition_value2:ConceptValue:OdmConditionValue {oid: "oid2", name: "name2"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_condition_root2:Odm:OdmRoot:OdmConditionRoot {uid: "odm_condition2"}) +MERGE (odm_condition_value2:Odm:OdmValue:OdmConditionValue {oid: "oid2", name: "name2"}) MERGE (odm_condition_root2)-[ld2:LATEST_FINAL]->(odm_condition_value2) MERGE (odm_condition_root2)-[l2:LATEST]->(odm_condition_value2) MERGE (odm_condition_root2)-[hv2:HAS_VERSION]->(odm_condition_value2) @@ -88,20 +88,20 @@ } AS final_properties MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (odm_translated_text1:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) -MERGE (odm_translated_text2:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) -MERGE (odm_translated_text3:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) -MERGE (odm_translated_text4:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) +MERGE (odm_translated_text1:Odm:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) +MERGE (odm_translated_text2:Odm:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) +MERGE (odm_translated_text3:Odm:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) +MERGE (odm_translated_text4:Odm:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_method_root1:ConceptRoot:OdmMethodRoot {uid: "odm_method1"}) -MERGE (odm_method_value1:ConceptValue:OdmMethodValue {oid: "oid1", name: "name1", method_type: "type1"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_method_root1:Odm:OdmRoot:OdmMethodRoot {uid: "odm_method1"}) +MERGE (odm_method_value1:Odm:OdmValue:OdmMethodValue {oid: "oid1", name: "name1", method_type: "type1"}) MERGE (odm_method_root1)-[ld1:LATEST_FINAL]->(odm_method_value1) MERGE (odm_method_root1)-[l1:LATEST]->(odm_method_value1) MERGE (odm_method_root1)-[hv1:HAS_VERSION]->(odm_method_value1) SET hv1 = final_properties -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_method_root2:ConceptRoot:OdmMethodRoot {uid: "odm_method2"}) -MERGE (odm_method_value2:ConceptValue:OdmMethodValue {oid: "oid2", name: "name2", method_type: "type2"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_method_root2:Odm:OdmRoot:OdmMethodRoot {uid: "odm_method2"}) +MERGE (odm_method_value2:Odm:OdmValue:OdmMethodValue {oid: "oid2", name: "name2", method_type: "type2"}) MERGE (odm_method_root2)-[ld2:LATEST_FINAL]->(odm_method_value2) MERGE (odm_method_root2)-[l2:LATEST]->(odm_method_value2) MERGE (odm_method_root2)-[hv2:HAS_VERSION]->(odm_method_value2) @@ -289,14 +289,14 @@ MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (odm_translated_text1:OdmTranslatedText {text_type: "Description", language: "eng", text: "Description1"}) -MERGE (odm_translated_text2:OdmTranslatedText {text_type: "osb:DesignNotes", language: "eng", text: "Design Notes1"}) -MERGE (odm_translated_text3:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "eng", text: "Completion Instructions1"}) -MERGE (odm_translated_text4:OdmTranslatedText {text_type: "osb:DisplayText", language: "eng", text: "Display Text1"}) +MERGE (odm_translated_text1:Odm:OdmTranslatedText {text_type: "Description", language: "eng", text: "Description1"}) +MERGE (odm_translated_text2:Odm:OdmTranslatedText {text_type: "osb:DesignNotes", language: "eng", text: "Design Notes1"}) +MERGE (odm_translated_text3:Odm:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "eng", text: "Completion Instructions1"}) +MERGE (odm_translated_text4:Odm:OdmTranslatedText {text_type: "osb:DisplayText", language: "eng", text: "Display Text1"}) -MERGE (item_group_root1:ConceptRoot:OdmItemGroupRoot {uid: "odm_item_group1"}) -MERGE (item_group_value1:ConceptValue:OdmItemGroupValue {oid: "oid1", name: "name1", repeating: false, is_reference_data: false, sas_dataset_name: "sas_dataset_name1", origin: "origin1", purpose: "purpose1", comment: "comment1"}) -MERGE (library)-[r0:CONTAINS_CONCEPT]->(item_group_root1) +MERGE (item_group_root1:Odm:OdmRoot:OdmItemGroupRoot {uid: "odm_item_group1"}) +MERGE (item_group_value1:Odm:OdmValue:OdmItemGroupValue {oid: "oid1", name: "name1", repeating: false, is_reference_data: false, sas_dataset_name: "sas_dataset_name1", origin: "origin1", purpose: "purpose1", comment: "comment1"}) +MERGE (library)-[r0:CONTAINS_ODM]->(item_group_root1) MERGE (item_group_root1)-[r1:LATEST_FINAL]->(item_group_value1) MERGE (item_group_root1)-[hv2:HAS_VERSION]->(item_group_value1) MERGE (item_group_root1)-[:LATEST]->(item_group_value1) @@ -306,9 +306,9 @@ MERGE (item_group_value1)-[:HAS_TRANSLATED_TEXT]->(odm_translated_text4) SET hv2 = final_properties -MERGE (item_group_root2:ConceptRoot:OdmItemGroupRoot {uid: "odm_item_group2"}) -MERGE (item_group_value2:ConceptValue:OdmItemGroupValue {oid: "oid2", name: "name2", repeating: false, is_reference_data: true, sas_dataset_name: "sas_dataset_name2", origin: "origin2", purpose: "purpose2", comment: "comment2"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(item_group_root2) +MERGE (item_group_root2:Odm:OdmRoot:OdmItemGroupRoot {uid: "odm_item_group2"}) +MERGE (item_group_value2:Odm:OdmValue:OdmItemGroupValue {oid: "oid2", name: "name2", repeating: false, is_reference_data: true, sas_dataset_name: "sas_dataset_name2", origin: "origin2", purpose: "purpose2", comment: "comment2"}) +MERGE (library)-[:CONTAINS_ODM]->(item_group_root2) MERGE (item_group_root2)-[r2:LATEST_FINAL]->(item_group_value2) MERGE (item_group_root2)-[hv3:HAS_VERSION]->(item_group_value2) MERGE (item_group_root2)-[:LATEST]->(item_group_value2) @@ -387,15 +387,15 @@ MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (odm_translated_text1:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) -MERGE (odm_translated_text2:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) -MERGE (odm_translated_text3:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) -MERGE (odm_translated_text4:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) -MERGE (odm_translated_text5:OdmTranslatedText {text_type: "Question", language: "en", text: "Question1"}) +MERGE (odm_translated_text1:Odm:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) +MERGE (odm_translated_text2:Odm:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) +MERGE (odm_translated_text3:Odm:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) +MERGE (odm_translated_text4:Odm:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) +MERGE (odm_translated_text5:Odm:OdmTranslatedText {text_type: "Question", language: "en", text: "Question1"}) -MERGE (item_root1:ConceptRoot:OdmItemRoot {uid: "odm_item1"}) -MERGE (item_value1:ConceptValue:OdmItemValue {oid: "oid1", name: "name1", datatype: "string", length: 1, significant_digits: 1, sas_field_name: "sasfieldname1", sds_var_name: "sdsvarname1", origin: "origin1", comment: "comment1"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(item_root1) +MERGE (item_root1:Odm:OdmRoot:OdmItemRoot {uid: "odm_item1"}) +MERGE (item_value1:Odm:OdmValue:OdmItemValue {oid: "oid1", name: "name1", datatype: "string", length: 1, significant_digits: 1, sas_field_name: "sasfieldname1", sds_var_name: "sdsvarname1", origin: "origin1", comment: "comment1"}) +MERGE (library)-[:CONTAINS_ODM]->(item_root1) MERGE (item_root1)-[r1:LATEST_FINAL]->(item_value1) MERGE (item_root1)-[hv2:HAS_VERSION]->(item_value1) MERGE (item_root1)-[:LATEST]->(item_value1) @@ -406,9 +406,9 @@ MERGE (item_value1)-[:HAS_TRANSLATED_TEXT]->(odm_translated_text5) SET hv2 = final_properties -MERGE (item_root2:ConceptRoot:OdmItemRoot {uid: "odm_item2"}) -MERGE (item_value2:ConceptValue:OdmItemValue {oid: "oid2", name: "name2", datatype: "datatype2", length: 2, significant_digits: 2, sas_field_name: "sasfieldname2", sds_var_name: "sdsvarname2", origin: "origin2", comment: "comment2"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(item_root2) +MERGE (item_root2:Odm:OdmRoot:OdmItemRoot {uid: "odm_item2"}) +MERGE (item_value2:Odm:OdmValue:OdmItemValue {oid: "oid2", name: "name2", datatype: "datatype2", length: 2, significant_digits: 2, sas_field_name: "sasfieldname2", sds_var_name: "sdsvarname2", origin: "origin2", comment: "comment2"}) +MERGE (library)-[:CONTAINS_ODM]->(item_root2) MERGE (item_root2)-[r2:LATEST_FINAL]->(item_value2) MERGE (item_root2)-[hv3:HAS_VERSION]->(item_value2) MERGE (item_root2)-[:LATEST]->(item_value2) @@ -430,15 +430,15 @@ } AS final_properties MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (odm_translated_text1:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) -MERGE (odm_translated_text2:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) -MERGE (odm_translated_text3:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) -MERGE (odm_translated_text4:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) -MERGE (odm_alias1:OdmAlias {context: "context1", name: "name1"}) +MERGE (odm_translated_text1:Odm:OdmTranslatedText {text_type: "Description", language: "en", text: "Description1"}) +MERGE (odm_translated_text2:Odm:OdmTranslatedText {text_type: "osb:CompletionInstructions", language: "en", text: "Completion Instructions1"}) +MERGE (odm_translated_text3:Odm:OdmTranslatedText {text_type: "osb:DesignNotes", language: "en", text: "Design Notes1"}) +MERGE (odm_translated_text4:Odm:OdmTranslatedText {text_type: "osb:DisplayText", language: "en", text: "Display Text1"}) +MERGE (odm_alias1:Odm:OdmAlias {context: "context1", name: "name1"}) -MERGE (odm_form_root1:ConceptRoot:OdmFormRoot {uid: "odm_form1"}) -MERGE (odm_form_value1:ConceptValue:OdmFormValue {oid: "oid1", name: "name1", repeating: true}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_form_root1) +MERGE (odm_form_root1:Odm:OdmRoot:OdmFormRoot {uid: "odm_form1"}) +MERGE (odm_form_value1:Odm:OdmValue:OdmFormValue {oid: "oid1", name: "name1", repeating: true}) +MERGE (library)-[:CONTAINS_ODM]->(odm_form_root1) MERGE (odm_form_root1)-[r1:LATEST_FINAL]->(odm_form_value1) MERGE (odm_form_root1)-[hv2:HAS_VERSION]->(odm_form_value1) MERGE (odm_form_root1)-[:LATEST]->(odm_form_value1) @@ -449,9 +449,9 @@ MERGE (odm_form_value1)-[:HAS_ALIAS]->(odm_alias1) SET hv2 = final_properties -MERGE (odm_form_root2:ConceptRoot:OdmFormRoot {uid: "odm_form2"}) -MERGE (odm_form_value2:ConceptValue:OdmFormValue {oid: "oid2", name: "name2", repeating: true}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_form_root2) +MERGE (odm_form_root2:Odm:OdmRoot:OdmFormRoot {uid: "odm_form2"}) +MERGE (odm_form_value2:Odm:OdmValue:OdmFormValue {oid: "oid2", name: "name2", repeating: true}) +MERGE (library)-[:CONTAINS_ODM]->(odm_form_root2) MERGE (odm_form_root2)-[r2:LATEST_FINAL]->(odm_form_value2) MERGE (odm_form_root2)-[hv3:HAS_VERSION]->(odm_form_value2) MERGE (odm_form_root2)-[:LATEST]->(odm_form_value2) @@ -474,9 +474,9 @@ MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (StudyEventRoot:ConceptRoot:OdmStudyEventRoot {uid: "odm_study_event1"}) -MERGE (StudyEventValue:ConceptValue:OdmStudyEventValue {oid: "oid1", name: "name1", effective_date: date(), retired_date: date(), description: "description", display_in_tree: true}) -MERGE (library)-[:CONTAINS_CONCEPT]->(StudyEventRoot) +MERGE (StudyEventRoot:Odm:OdmRoot:OdmStudyEventRoot {uid: "odm_study_event1"}) +MERGE (StudyEventValue:Odm:OdmValue:OdmStudyEventValue {oid: "oid1", name: "name1", effective_date: date(), retired_date: date(), description: "description", display_in_tree: true}) +MERGE (library)-[:CONTAINS_ODM]->(StudyEventRoot) MERGE (StudyEventRoot)-[r1:LATEST_FINAL]->(StudyEventValue) MERGE (StudyEventRoot)-[r2:LATEST]->(StudyEventValue) MERGE (StudyEventRoot)-[hv:HAS_VERSION]->(StudyEventValue) @@ -504,7 +504,7 @@ MERGE (Library)-[:CONTAINS_CATALOUGE]->(Catalogue) WITH * -MERGE (odm_alias1:OdmAlias {context: "context1", name: "name1"}) +MERGE (odm_alias1:Odm:OdmAlias {context: "context1", name: "name1"}) WITH * MATCH (:OdmFormRoot {uid: "odm_form1"})-[:LATEST]-(ofv:OdmFormValue) MATCH (:OdmItemGroupRoot {uid: "odm_item_group1"})-[:LATEST]-(oigv:OdmItemGroupValue) @@ -586,17 +586,17 @@ } AS final_properties MERGE (library:Library {name:"Sponsor", is_editable:true}) -MERGE (odm_vendor_namespace_root1:ConceptRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace1"}) -MERGE (odm_vendor_namespace_value1:ConceptValue:OdmVendorNamespaceValue {name: "nameOne", prefix: "prefix", url: "url1"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_namespace_root1) +MERGE (odm_vendor_namespace_root1:Odm:OdmRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace1"}) +MERGE (odm_vendor_namespace_value1:Odm:OdmValue:OdmVendorNamespaceValue {name: "nameOne", prefix: "prefix", url: "url1"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_namespace_root1) MERGE (odm_vendor_namespace_root1)-[r1:LATEST_FINAL]->(odm_vendor_namespace_value1) MERGE (odm_vendor_namespace_root1)-[:LATEST]->(odm_vendor_namespace_value1) MERGE (odm_vendor_namespace_root1)-[hv1:HAS_VERSION]->(odm_vendor_namespace_value1) SET hv1 = final_properties -MERGE (odm_vendor_namespace_root2:ConceptRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace2"}) -MERGE (odm_vendor_namespace_value2:ConceptValue:OdmVendorNamespaceValue {name: "OSB", prefix: "osb", url: "url2"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_namespace_root2) +MERGE (odm_vendor_namespace_root2:Odm:OdmRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace2"}) +MERGE (odm_vendor_namespace_value2:Odm:OdmValue:OdmVendorNamespaceValue {name: "OSB", prefix: "osb", url: "url2"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_namespace_root2) MERGE (odm_vendor_namespace_root2)-[r2:LATEST_FINAL]->(odm_vendor_namespace_value2) MERGE (odm_vendor_namespace_root2)-[:LATEST]->(odm_vendor_namespace_value2) MERGE (odm_vendor_namespace_root2)-[hv2:HAS_VERSION]->(odm_vendor_namespace_value2) @@ -614,39 +614,39 @@ MERGE (library:Library {name:"Sponsor", is_editable:true}) WITH * -MATCH (odm_vendor_namespace_root1:ConceptRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace1"})-[:LATEST]->(odm_vendor_namespace_value1:OdmVendorNamespaceValue) -MATCH (odm_vendor_namespace_root2:ConceptRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace2"})-[:LATEST]->(odm_vendor_namespace_value2:OdmVendorNamespaceValue) +MATCH (odm_vendor_namespace_root1:Odm:OdmRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace1"})-[:LATEST]->(odm_vendor_namespace_value1:OdmVendorNamespaceValue) +MATCH (odm_vendor_namespace_root2:Odm:OdmRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace2"})-[:LATEST]->(odm_vendor_namespace_value2:OdmVendorNamespaceValue) -MERGE (odm_vendor_element_root1:ConceptRoot:OdmVendorElementRoot {uid: "odm_vendor_element1"}) -MERGE (odm_vendor_element_value1:ConceptValue:OdmVendorElementValue {name: "NameOne", compatible_types: '["FormDef","ItemGroupDef","ItemDef"]'}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_element_root1) +MERGE (odm_vendor_element_root1:Odm:OdmRoot:OdmVendorElementRoot {uid: "odm_vendor_element1"}) +MERGE (odm_vendor_element_value1:Odm:OdmValue:OdmVendorElementValue {name: "NameOne", compatible_types: '["FormDef","ItemGroupDef","ItemDef"]'}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_element_root1) MERGE (odm_vendor_element_root1)-[r1:LATEST_FINAL]->(odm_vendor_element_value1) MERGE (odm_vendor_element_root1)-[hv1:HAS_VERSION]->(odm_vendor_element_value1) MERGE (odm_vendor_element_root1)-[:LATEST]->(odm_vendor_element_value1) MERGE (odm_vendor_namespace_value1)-[:HAS_VENDOR_ELEMENT]->(odm_vendor_element_value1) SET hv1 = final_properties -MERGE (odm_vendor_element_root2:ConceptRoot:OdmVendorElementRoot {uid: "odm_vendor_element2"}) -MERGE (odm_vendor_element_value2:ConceptValue:OdmVendorElementValue {name: "NameTwo", compatible_types: '["FormDef","ItemGroupDef","ItemDef"]'}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_element_root2) +MERGE (odm_vendor_element_root2:Odm:OdmRoot:OdmVendorElementRoot {uid: "odm_vendor_element2"}) +MERGE (odm_vendor_element_value2:Odm:OdmValue:OdmVendorElementValue {name: "NameTwo", compatible_types: '["FormDef","ItemGroupDef","ItemDef"]'}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_element_root2) MERGE (odm_vendor_element_root2)-[r2:LATEST_FINAL]->(odm_vendor_element_value2) MERGE (odm_vendor_element_root2)-[hv2:HAS_VERSION]->(odm_vendor_element_value2) MERGE (odm_vendor_element_root2)-[:LATEST]->(odm_vendor_element_value2) MERGE (odm_vendor_namespace_value2)-[:HAS_VENDOR_ELEMENT]->(odm_vendor_element_value2) SET hv2 = final_properties -MERGE (odm_vendor_element_root3:ConceptRoot:OdmVendorElementRoot {uid: "odm_vendor_element3"}) -MERGE (odm_vendor_element_value3:ConceptValue:OdmVendorElementValue {name: "NameThree", compatible_types: '["FormDef","ItemGroupDef","ItemDef"]'}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_element_root3) +MERGE (odm_vendor_element_root3:Odm:OdmRoot:OdmVendorElementRoot {uid: "odm_vendor_element3"}) +MERGE (odm_vendor_element_value3:Odm:OdmValue:OdmVendorElementValue {name: "NameThree", compatible_types: '["FormDef","ItemGroupDef","ItemDef"]'}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_element_root3) MERGE (odm_vendor_element_root3)-[r3:LATEST_FINAL]->(odm_vendor_element_value3) MERGE (odm_vendor_element_root3)-[hv3:HAS_VERSION]->(odm_vendor_element_value3) MERGE (odm_vendor_element_root3)-[:LATEST]->(odm_vendor_element_value3) MERGE (odm_vendor_namespace_value3)-[:HAS_VENDOR_ELEMENT]->(odm_vendor_element_value3) SET hv3 = final_properties -MERGE (odm_vendor_element_root4:ConceptRoot:OdmVendorElementRoot {uid: "odm_vendor_element4"}) -MERGE (odm_vendor_element_value4:ConceptValue:OdmVendorElementValue {name: "NameThree", compatible_types: '["NonCompatibleVendor"]'}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_element_root4) +MERGE (odm_vendor_element_root4:Odm:OdmRoot:OdmVendorElementRoot {uid: "odm_vendor_element4"}) +MERGE (odm_vendor_element_value4:Odm:OdmValue:OdmVendorElementValue {name: "NameThree", compatible_types: '["NonCompatibleVendor"]'}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_element_root4) MERGE (odm_vendor_element_root4)-[r4:LATEST_FINAL]->(odm_vendor_element_value4) MERGE (odm_vendor_element_root4)-[hv4:HAS_VERSION]->(odm_vendor_element_value4) MERGE (odm_vendor_element_root4)-[:LATEST]->(odm_vendor_element_value4) @@ -665,58 +665,58 @@ MERGE (library:Library {name:"Sponsor", is_editable:true}) WITH * -MATCH (odm_vendor_namespace_root:ConceptRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace1"})-[:LATEST]->(odm_vendor_namespace_value:OdmVendorNamespaceValue) +MATCH (odm_vendor_namespace_root:Odm:OdmRoot:OdmVendorNamespaceRoot {uid: "odm_vendor_namespace1"})-[:LATEST]->(odm_vendor_namespace_value:OdmVendorNamespaceValue) MATCH (odm_vendor_element_root1:OdmVendorElementRoot {uid:"odm_vendor_element1"})-[:LATEST]->(odm_vendor_element_value1:OdmVendorElementValue) MATCH (odm_vendor_element_root3:OdmVendorElementRoot {uid:"odm_vendor_element3"})-[:LATEST]->(odm_vendor_element_value3:OdmVendorElementValue) -MERGE (odm_vendor_attribute_root1:ConceptRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute1"}) -MERGE (odm_vendor_attribute_value1:ConceptValue:OdmVendorAttributeValue {name: "nameOne", data_type: "string", value_regex: "^[a-zA-Z]+$"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_attribute_root1) +MERGE (odm_vendor_attribute_root1:Odm:OdmRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute1"}) +MERGE (odm_vendor_attribute_value1:Odm:OdmValue:OdmVendorAttributeValue {name: "nameOne", data_type: "string", value_regex: "^[a-zA-Z]+$"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_attribute_root1) MERGE (odm_vendor_attribute_root1)-[r1:LATEST_FINAL]->(odm_vendor_attribute_value1) MERGE (odm_vendor_attribute_root1)-[hv1:HAS_VERSION]->(odm_vendor_attribute_value1) MERGE (odm_vendor_attribute_root1)-[:LATEST]->(odm_vendor_attribute_value1) MERGE (odm_vendor_element_value1)-[:HAS_VENDOR_ATTRIBUTE {value: "value1"}]->(odm_vendor_attribute_value1) SET hv1 = final_properties -MERGE (odm_vendor_attribute_root2:ConceptRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute2"}) -MERGE (odm_vendor_attribute_value2:ConceptValue:OdmVendorAttributeValue {name: "nameTwo", data_type: "string"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_attribute_root2) +MERGE (odm_vendor_attribute_root2:Odm:OdmRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute2"}) +MERGE (odm_vendor_attribute_value2:Odm:OdmValue:OdmVendorAttributeValue {name: "nameTwo", data_type: "string"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_attribute_root2) MERGE (odm_vendor_attribute_root2)-[r2:LATEST_FINAL]->(odm_vendor_attribute_value2) MERGE (odm_vendor_attribute_root2)-[hv2:HAS_VERSION]->(odm_vendor_attribute_value2) MERGE (odm_vendor_attribute_root2)-[:LATEST]->(odm_vendor_attribute_value2) MERGE (odm_vendor_element_value1)-[:HAS_VENDOR_ATTRIBUTE {value: "value2"}]->(odm_vendor_attribute_value2) SET hv2 = final_properties -MERGE (odm_vendor_attribute_root3:ConceptRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute3"}) -MERGE (odm_vendor_attribute_value3:ConceptValue:OdmVendorAttributeValue {name: "nameThree", compatible_types: '["FormDef","ItemGroupDef","ItemDef","ItemGroupRef","ItemRef"]', data_type: "string", value_regex: "^[a-zA-Z]+$"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_attribute_root3) +MERGE (odm_vendor_attribute_root3:Odm:OdmRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute3"}) +MERGE (odm_vendor_attribute_value3:Odm:OdmValue:OdmVendorAttributeValue {name: "nameThree", compatible_types: '["FormDef","ItemGroupDef","ItemDef","ItemGroupRef","ItemRef"]', data_type: "string", value_regex: "^[a-zA-Z]+$"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_attribute_root3) MERGE (odm_vendor_attribute_root3)-[r4:LATEST_FINAL]->(odm_vendor_attribute_value3) MERGE (odm_vendor_attribute_root3)-[hv4:HAS_VERSION]->(odm_vendor_attribute_value3) MERGE (odm_vendor_attribute_root3)-[:LATEST]->(odm_vendor_attribute_value3) MERGE (odm_vendor_namespace_value)-[:HAS_VENDOR_ATTRIBUTE {value: "value3"}]->(odm_vendor_attribute_value3) SET hv4 = final_properties -MERGE (odm_vendor_attribute_root4:ConceptRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute4"}) -MERGE (odm_vendor_attribute_value4:ConceptValue:OdmVendorAttributeValue {name: "nameFour", compatible_types: '["FormDef","ItemGroupDef","ItemDef","ItemGroupRef","ItemRef"]', data_type: "string"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_attribute_root4) +MERGE (odm_vendor_attribute_root4:Odm:OdmRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute4"}) +MERGE (odm_vendor_attribute_value4:Odm:OdmValue:OdmVendorAttributeValue {name: "nameFour", compatible_types: '["FormDef","ItemGroupDef","ItemDef","ItemGroupRef","ItemRef"]', data_type: "string"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_attribute_root4) MERGE (odm_vendor_attribute_root4)-[r5:LATEST_FINAL]->(odm_vendor_attribute_value4) MERGE (odm_vendor_attribute_root4)-[hv5:HAS_VERSION]->(odm_vendor_attribute_value4) MERGE (odm_vendor_attribute_root4)-[:LATEST]->(odm_vendor_attribute_value4) MERGE (odm_vendor_namespace_value)-[:HAS_VENDOR_ATTRIBUTE {value: "value4"}]->(odm_vendor_attribute_value4) SET hv5 = final_properties -MERGE (odm_vendor_attribute_root5:ConceptRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute5"}) -MERGE (odm_vendor_attribute_value5:ConceptValue:OdmVendorAttributeValue {name: "nameFive", compatible_types: '["NonCompatibleVendor"]', data_type: "string"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_attribute_root5) +MERGE (odm_vendor_attribute_root5:Odm:OdmRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute5"}) +MERGE (odm_vendor_attribute_value5:Odm:OdmValue:OdmVendorAttributeValue {name: "nameFive", compatible_types: '["NonCompatibleVendor"]', data_type: "string"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_attribute_root5) MERGE (odm_vendor_attribute_root5)-[r6:LATEST_FINAL]->(odm_vendor_attribute_value5) MERGE (odm_vendor_attribute_root5)-[hv6:HAS_VERSION]->(odm_vendor_attribute_value5) MERGE (odm_vendor_attribute_root5)-[:LATEST]->(odm_vendor_attribute_value5) MERGE (odm_vendor_namespace_value)-[:HAS_VENDOR_ATTRIBUTE {value: "value5"}]->(odm_vendor_attribute_value5) SET hv6 = final_properties -MERGE (odm_vendor_attribute_root7:ConceptRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute7"}) -MERGE (odm_vendor_attribute_value7:ConceptValue:OdmVendorAttributeValue {name: "nameSeven", data_type: "string"}) -MERGE (library)-[:CONTAINS_CONCEPT]->(odm_vendor_attribute_root7) +MERGE (odm_vendor_attribute_root7:Odm:OdmRoot:OdmVendorAttributeRoot {uid: "odm_vendor_attribute7"}) +MERGE (odm_vendor_attribute_value7:Odm:OdmValue:OdmVendorAttributeValue {name: "nameSeven", data_type: "string"}) +MERGE (library)-[:CONTAINS_ODM]->(odm_vendor_attribute_root7) MERGE (odm_vendor_attribute_root7)-[r7:LATEST_FINAL]->(odm_vendor_attribute_value7) MERGE (odm_vendor_attribute_root7)-[hv7:HAS_VERSION]->(odm_vendor_attribute_value7) MERGE (odm_vendor_attribute_root7)-[:LATEST]->(odm_vendor_attribute_value7) @@ -1331,7 +1331,7 @@ ActivityInstanceValue:FindingValue:NumericFindingValue { name:"name1"}) MERGE (activity_instance_value1)-[:HAS_ACTIVITY]->(activity_grouping) -SET activity_instance_value1=new_activity_instance_value1 +SET activity_instance_value1=properties(new_activity_instance_value1) SET activity_instance_value1.molecular_weight = 0.0 SET activity_instance_value1.name="name1" SET hv3a = final_properties @@ -2793,8 +2793,8 @@ set hv.status = "DRAFT" set hv.start_date = datetime() set hv.author_id = "unknown-user" -set hv2 = hv -set ld = hv +set hv2 = properties(hv) +set ld = properties(hv) MERGE (ot:ObjectiveTemplateRoot:SyntaxTemplateRoot:SyntaxIndexingTemplateRoot {uid:"ObjectiveTemplate_000001", sequence_id: "O1"})-[relt:LATEST_FINAL]->(otv:ObjectiveTemplateValue:SyntaxTemplateValue:SyntaxIndexingTemplateValue {name :"objective_1", name_plain : "objective_1"}) MERGE (or:ObjectiveRoot:SyntaxInstanceRoot:SyntaxIndexingInstanceRoot)-[rel:LATEST_FINAL]->(ov:ObjectiveValue:SyntaxInstanceValue:SyntaxIndexingInstanceValue {name : "objective_1", name_plain : "objective_1"}) @@ -2890,7 +2890,7 @@ set hv.status = "DRAFT" set hv.start_date = datetime() set hv.author_id = "unknown-user" -set ld = hv +set ld = properties(hv) MERGE (ot:ObjectiveTemplateRoot:SyntaxTemplateRoot:SyntaxIndexingTemplateRoot {uid:"ObjectiveTemplate_000001", sequence_id: "O1"})-[relt:LATEST_FINAL]->(otv:ObjectiveTemplateValue:SyntaxTemplateValue:SyntaxIndexingTemplateValue {name : "objective_1", name_plain : "objective_1"}) MERGE (or:ObjectiveRoot:SyntaxInstanceRoot:SyntaxIndexingInstanceRoot)-[rel:LATEST_FINAL]->(ov:ObjectiveValue:SyntaxInstanceValue:SyntaxIndexingInstanceValue {name : "objective_1", name_plain : "objective_1"}) @@ -2975,7 +2975,7 @@ set hv.status = "DRAFT" set hv.start_date = datetime() set hv.author_id = "unknown-user" -set ld = hv +set ld = properties(hv) // Compound CREATE (cr:ConceptRoot:CompoundRoot:TemplateParameterTermRoot {uid : "TemplateParameter_000001"}) @@ -3371,7 +3371,7 @@ def get_codelist_with_term_cypher( set hv.status = "DRAFT" set hv.start_date = datetime() set hv.author_id = "unknown-user" -set ld = hv +set ld = properties(hv) MERGE (ot:ObjectiveTemplateRoot:SyntaxTemplateRoot:SyntaxIndexingTemplateRoot {uid:"ObjectiveTemplate_000001", sequence_id: "O1"})-[relt:LATEST_FINAL]->(otv:ObjectiveTemplateValue:SyntaxTemplateValue:SyntaxIndexingTemplateValue {name : "objective_1", name_plain : "objective_1"}) @@ -3479,7 +3479,7 @@ def get_codelist_with_term_cypher( set hv.status = "DRAFT" set hv.start_date = datetime() set hv.author_id = "unknown-user" -set ld = hv +set ld = properties(hv) MERGE (ot:ObjectiveTemplateRoot:SyntaxTemplateRoot:SyntaxIndexingTemplateRoot {uid:"ObjectiveTemplate_000001", sequence_id: "O1"})-[relt:LATEST_FINAL]->(otv:ObjectiveTemplateValue:SyntaxTemplateValue:SyntaxIndexingTemplateValue {name : "objective_1", name_plain : "objective_1"}) MERGE (or:ObjectiveRoot:SyntaxInstanceRoot:SyntaxIndexingInstanceRoot)-[rel:LATEST_FINAL]->(ov:ObjectiveValue:SyntaxInstanceValue:SyntaxIndexingInstanceValue {name : "objective_1", name_plain : "objective_1"}) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_visit.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_visit.py index aa6cb7ef..9a5a42f8 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_visit.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/factory_visit.py @@ -69,9 +69,9 @@ def generate_default_input_data_for_visit(): "description": "description", "start_rule": "start_rule", "end_rule": "end_rule", - "visit_contact_mode_uid": "VisitContactMode_0001", - "visit_type_uid": "VisitType_0003", - "time_reference_uid": "VisitSubType_0005", + "visit_contact_mode": {"term_uid": "VisitContactMode_0001"}, + "visit_type": {"term_uid": "VisitType_0003"}, + "time_reference": {"term_uid": "VisitSubType_0005"}, "is_global_anchor_visit": False, "visit_class": "SINGLE_VISIT", "visit_subclass": "SINGLE_VISIT", @@ -566,24 +566,24 @@ def create_some_visits( create_visit_with_update( study_uid=study_uid, study_epoch_uid=epoch1.uid, - visit_type_uid="VisitType_0001", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0001"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=0, time_unit_uid=day_uid, ) create_visit_with_update( study_uid=study_uid, study_epoch_uid=epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=12, time_unit_uid=day_uid, ) create_visit_with_update( study_uid=study_uid, study_epoch_uid=epoch1.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=10, time_unit_uid=day_uid, ) @@ -591,16 +591,16 @@ def create_some_visits( version3 = create_visit_with_update( study_uid=study_uid, study_epoch_uid=epoch1.uid, - visit_type_uid="VisitType_0004", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0004"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=20, time_unit_uid=day_uid, ) version4 = create_visit_with_update( study_uid=study_uid, study_epoch_uid=epoch2.uid, - visit_type_uid="VisitType_0002", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0002"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=30, time_unit_uid=day_uid, visit_sublabel_reference=None, @@ -610,8 +610,8 @@ def create_some_visits( create_visit_with_update( study_uid=study_uid, study_epoch_uid=epoch2.uid, - visit_type_uid="VisitType_0003", - time_reference_uid="VisitSubType_0002", + visit_type={"term_uid": "VisitType_0003"}, + time_reference={"term_uid": "VisitSubType_0002"}, time_value=31, time_unit_uid=day_uid, visit_sublabel_reference=version4.uid, @@ -624,8 +624,8 @@ def create_some_visits( study_uid=study_uid, uid=version3.uid, study_epoch_uid=epoch2.uid, - visit_type_uid="VisitType_0004", - time_reference_uid="VisitSubType_0001", + visit_type={"term_uid": "VisitType_0004"}, + time_reference={"term_uid": "VisitSubType_0001"}, time_value=35, time_unit_uid=day_uid, ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/utils.py b/clinical-mdr-api/clinical_mdr_api/tests/integration/utils/utils.py index af6f8785..40999fff 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 @@ -32,6 +32,9 @@ StudySourceVariableEnum, ValidationMode, ) +from clinical_mdr_api.domains.study_definition_aggregates.study_metadata import ( + StudyStatus, +) from clinical_mdr_api.main import app from clinical_mdr_api.models.biomedical_concepts.activity_instance_class import ( ActivityInstanceClass, @@ -92,41 +95,6 @@ MedicinalProduct, MedicinalProductCreateInput, ) -from clinical_mdr_api.models.concepts.odms.odm_common_models import ( - OdmAliasModel, - OdmFormalExpressionModel, - OdmTranslatedTextModel, -) -from clinical_mdr_api.models.concepts.odms.odm_condition import ( - OdmCondition, - OdmConditionPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_form import OdmForm, OdmFormPostInput -from clinical_mdr_api.models.concepts.odms.odm_item import ( - OdmItem, - OdmItemCodelist, - OdmItemPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_item_group import ( - OdmItemGroup, - OdmItemGroupPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_study_event import ( - OdmStudyEvent, - OdmStudyEventPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_vendor_attribute import ( - OdmVendorAttribute, - OdmVendorAttributePostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_vendor_element import ( - OdmVendorElement, - OdmVendorElementPostInput, -) -from clinical_mdr_api.models.concepts.odms.odm_vendor_namespace import ( - OdmVendorNamespace, - OdmVendorNamespacePostInput, -) from clinical_mdr_api.models.concepts.pharmaceutical_product import ( PharmaceuticalProduct, PharmaceuticalProductCreateInput, @@ -149,6 +117,11 @@ CTTermCodelistInput, CTTermCreateInput, CTTermNameAndAttributes, + CTTermUidInput, +) +from clinical_mdr_api.models.data_completeness_tag import ( + DataCompletenessTag, + DataCompletenessTagInput, ) from clinical_mdr_api.models.data_suppliers.data_supplier import ( DataSupplier, @@ -168,6 +141,31 @@ NotificationPostInput, NotificationType, ) +from clinical_mdr_api.models.odms.common_models import ( + OdmAliasModel, + OdmFormalExpressionModel, + OdmTranslatedTextModel, +) +from clinical_mdr_api.models.odms.condition import OdmCondition, OdmConditionPostInput +from clinical_mdr_api.models.odms.form import OdmForm, OdmFormPostInput +from clinical_mdr_api.models.odms.item import OdmItem, OdmItemCodelist, OdmItemPostInput +from clinical_mdr_api.models.odms.item_group import OdmItemGroup, OdmItemGroupPostInput +from clinical_mdr_api.models.odms.study_event import ( + OdmStudyEvent, + OdmStudyEventPostInput, +) +from clinical_mdr_api.models.odms.vendor_attribute import ( + OdmVendorAttribute, + OdmVendorAttributePostInput, +) +from clinical_mdr_api.models.odms.vendor_element import ( + OdmVendorElement, + OdmVendorElementPostInput, +) +from clinical_mdr_api.models.odms.vendor_namespace import ( + OdmVendorNamespace, + OdmVendorNamespacePostInput, +) from clinical_mdr_api.models.projects.project import Project, ProjectCreateInput from clinical_mdr_api.models.standard_data_models.data_model import DataModel from clinical_mdr_api.models.standard_data_models.data_model_ig import DataModelIG @@ -208,6 +206,7 @@ Study, StudyCreateInput, StudyDescriptionJsonModel, + StudyIdentificationMetadataJsonModel, StudyMetadataJsonModel, StudyPatchRequestJsonModel, StudyPreferredTimeUnit, @@ -377,22 +376,6 @@ from clinical_mdr_api.services.concepts.medicinal_products_service import ( MedicinalProductService, ) -from clinical_mdr_api.services.concepts.odms.odm_conditions import OdmConditionService -from clinical_mdr_api.services.concepts.odms.odm_forms import OdmFormService -from clinical_mdr_api.services.concepts.odms.odm_item_groups import OdmItemGroupService -from clinical_mdr_api.services.concepts.odms.odm_items import OdmItemService -from clinical_mdr_api.services.concepts.odms.odm_study_events import ( - OdmStudyEventService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_attributes import ( - OdmVendorAttributeService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_elements import ( - OdmVendorElementService, -) -from clinical_mdr_api.services.concepts.odms.odm_vendor_namespaces import ( - OdmVendorNamespaceService, -) from clinical_mdr_api.services.concepts.pharmaceutical_products_service import ( PharmaceuticalProductService, ) @@ -428,6 +411,7 @@ from clinical_mdr_api.services.controlled_terminologies.ct_term_name import ( CTTermNameService, ) +from clinical_mdr_api.services.data_completeness_tags import DataCompletenessTagService from clinical_mdr_api.services.data_suppliers.data_supplier import DataSupplierService from clinical_mdr_api.services.dictionaries.dictionary_codelist_generic_service import ( DictionaryCodelistGenericService as DictionaryCodelistService, @@ -438,6 +422,14 @@ from clinical_mdr_api.services.feature_flags import FeatureFlagService from clinical_mdr_api.services.libraries import libraries as library_service from clinical_mdr_api.services.notifications import NotificationService +from clinical_mdr_api.services.odms.conditions import OdmConditionService +from clinical_mdr_api.services.odms.forms import OdmFormService +from clinical_mdr_api.services.odms.item_groups import OdmItemGroupService +from clinical_mdr_api.services.odms.items import OdmItemService +from clinical_mdr_api.services.odms.study_events import OdmStudyEventService +from clinical_mdr_api.services.odms.vendor_attributes import OdmVendorAttributeService +from clinical_mdr_api.services.odms.vendor_elements import OdmVendorElementService +from clinical_mdr_api.services.odms.vendor_namespaces import OdmVendorNamespaceService from clinical_mdr_api.services.projects.project import ProjectService from clinical_mdr_api.services.standard_data_models.data_model import DataModelService from clinical_mdr_api.services.standard_data_models.data_model_ig import ( @@ -633,6 +625,20 @@ def __init__(self, **kwargs: str): DICTIONARY_CODELIST_LIBRARY = "UCUM" +def _resolve_ct_term( + nested: dict | CTTermUidInput | None, + flat_uid: str | None, +) -> CTTermUidInput | None: + """Resolve a CT term field from either a nested object or a flat UID string.""" + if nested is not None: + if isinstance(nested, dict): + return CTTermUidInput(**nested) + return nested + if flat_uid is not None: + return CTTermUidInput(term_uid=flat_uid) + return None + + class TestUtils: """Class containing methods that create all kinds of entities, e.g. library compounds""" @@ -837,6 +843,15 @@ def create_feature_flag( payload = FeatureFlagInput(name=name, enabled=enabled, description=description) return service.create_feature_flag(payload) + @classmethod + def create_data_completeness_tag( + cls, + name: str = "Data Completeness Tag Name", + ) -> DataCompletenessTag: + service: DataCompletenessTagService = DataCompletenessTagService() + payload = DataCompletenessTagInput(name=name) + return service.create_data_completeness_tag(payload) + @classmethod def create_notification( cls, @@ -1127,12 +1142,10 @@ def create_footnote( ) -> Footnote: if not footnote_template_uid: # find the footnote type codelist - codelist_uid = db.cypher_query( - """ + codelist_uid = db.cypher_query(""" MATCH (clr:CTCodelistRoot)-[:HAS_ATTRIBUTES_ROOT]->(:CTCodelistAttributesRoot)-[:LATEST]->(:CTCodelistAttributesValue {submission_value: 'FTNTTP'}) RETURN clr.uid - """ - )[0][0][0] + """)[0][0][0] footnote_template_uid = cls.create_footnote_template( name="test name", @@ -1961,9 +1974,7 @@ def batch_select_study_activity_instances( @classmethod def delete_study(cls, study_uid: str): - db.cypher_query( - f"MATCH (r:StudyRoot {{uid:'{study_uid}'}})-[]-(v:StudyValue) DETACH DELETE r, v" - ) + StudyService().soft_delete(uid=study_uid) @classmethod def create_study_activity_schedule( @@ -2037,12 +2048,20 @@ def create_study_visit( cls, study_uid: str, study_epoch_uid: str, - visit_type_uid: str, - show_visit: bool, - visit_contact_mode_uid: str, - visit_class: VisitClass, - is_global_anchor_visit: bool, + # Flat UID params (for explicit callers) + visit_type_uid: str | None = None, + visit_contact_mode_uid: str | None = None, time_reference_uid: str | None = None, + epoch_allocation_uid: str | None = None, + # Nested CT term params (for **datadict unpacking) + visit_type: dict | CTTermUidInput | None = None, + visit_contact_mode: dict | CTTermUidInput | None = None, + time_reference: dict | CTTermUidInput | None = None, + epoch_allocation: dict | CTTermUidInput | None = None, + # Common params + show_visit: bool = True, + visit_class: VisitClass = "SINGLE_VISIT", # type: ignore[assignment] + is_global_anchor_visit: bool = False, time_value: int | None = None, time_unit_uid: str | None = None, visit_sublabel_reference: str | None = None, @@ -2052,14 +2071,21 @@ def create_study_visit( description: str | None = None, start_rule: str | None = None, end_rule: str | None = None, - epoch_allocation_uid: str | None = None, visit_subclass: VisitSubclass | None = None, ) -> StudyVisit: + # Resolve CT term fields: prefer nested object, fall back to flat UID + _visit_type = _resolve_ct_term(visit_type, visit_type_uid) + _visit_contact_mode = _resolve_ct_term( + visit_contact_mode, visit_contact_mode_uid + ) + _time_reference = _resolve_ct_term(time_reference, time_reference_uid) + _epoch_allocation = _resolve_ct_term(epoch_allocation, epoch_allocation_uid) + service: StudyVisitService = StudyVisitService(study_uid=study_uid) study_visit_input: StudyVisitCreateInput = StudyVisitCreateInput( study_epoch_uid=study_epoch_uid, - visit_type_uid=visit_type_uid, - time_reference_uid=time_reference_uid, + visit_type=_visit_type, # type: ignore[arg-type] + time_reference=_time_reference, time_value=time_value, time_unit_uid=time_unit_uid, visit_sublabel_reference=visit_sublabel_reference, @@ -2070,8 +2096,8 @@ def create_study_visit( description=description, start_rule=start_rule, end_rule=end_rule, - visit_contact_mode_uid=visit_contact_mode_uid, - epoch_allocation_uid=epoch_allocation_uid, + visit_contact_mode=_visit_contact_mode, # type: ignore[arg-type] + epoch_allocation=_epoch_allocation, visit_class=visit_class, visit_subclass=visit_subclass, is_global_anchor_visit=is_global_anchor_visit, @@ -2341,7 +2367,7 @@ def create_odm_study_event( display_in_tree=display_in_tree, ) - result: OdmStudyEvent = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmStudyEvent = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2375,7 +2401,7 @@ def create_odm_form( aliases=aliases, ) - result: OdmForm = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmForm = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2421,7 +2447,7 @@ def create_odm_item_group( sdtm_domain_uids=sdtm_domain_uids, ) - result: OdmItemGroup = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmItemGroup = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2477,7 +2503,7 @@ def create_odm_item( terms=terms, ) - result: OdmItem = service.create(concept_input=payload) + result: OdmItem = service.create(odm_input=payload) if approve: service.approve(result.uid) return result @@ -2511,7 +2537,7 @@ def create_odm_condition( aliases=aliases, ) - result: OdmCondition = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmCondition = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2534,7 +2560,7 @@ def create_odm_vendor_namespace( url=url, ) - result: OdmVendorNamespace = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmVendorNamespace = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2560,7 +2586,7 @@ def create_odm_vendor_element( vendor_namespace_uid=vendor_namespace_uid, ) - result: OdmVendorElement = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmVendorElement = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2592,7 +2618,7 @@ def create_odm_vendor_attribute( vendor_element_uid=vendor_element_uid, ) - result: OdmVendorAttribute = service.create(concept_input=payload) # type: ignore[assignment] + result: OdmVendorAttribute = service.create(odm_input=payload) # type: ignore[assignment] if approve: service.approve(result.uid) return result @@ -2677,6 +2703,25 @@ def create_study( ) return service.create(payload) + @classmethod + def patch_study( + cls, + uid: str, + study_parent_part_uid: str | None = None, + dry: bool = False, + **kwargs, + ) -> Study: + study_service: StudyService = StudyService() + + payload = StudyPatchRequestJsonModel( + study_parent_part_uid=study_parent_part_uid, + current_metadata=StudyMetadataJsonModel( + identification_metadata=StudyIdentificationMetadataJsonModel(**kwargs) + ), + ) + + return study_service.patch(uid=uid, dry=dry, study_patch_request=payload) + @classmethod def create_study_standard_version( cls, @@ -3602,6 +3647,7 @@ def create_data_model_ig( def create_dataset_class( cls, data_model_uid: str, + data_model_name: str, data_model_catalogue_name: str, label: str = "label", description: str = "description", @@ -3641,7 +3687,9 @@ def create_dataset_class( "library_name": library_name, }, ) - return DatasetClassService().get_by_uid(uid=dataset_class_uid) + return DatasetClassService().get_by_uid( + uid=dataset_class_uid, data_model_name=data_model_name + ) @classmethod def create_dataset( @@ -4297,30 +4345,51 @@ def create_comment_thread_reply( def lock_study(cls, study_uid, reason_for_lock_term_uid: str) -> str: """locks a study version (giving it a study-title first), returns locked study version""" - study_service = StudyService() - - study_service.patch( - uid=study_uid, - dry=False, - study_patch_request=StudyPatchRequestJsonModel( - current_metadata=StudyMetadataJsonModel( - study_description=StudyDescriptionJsonModel( - study_title=cls.random_str(prefix="Title ") - ) - ) - ), - ) + cls.set_study_title(study_uid) + study_service = StudyService() study = study_service.lock( uid=study_uid, change_description=cls.random_str(prefix="v"), reason_for_lock_term_uid=reason_for_lock_term_uid, ) - latest_study_version = str( - study.current_metadata.version_metadata.version_number + latest_study_version = study.current_metadata.version_metadata.version_number + + return str(latest_study_version) + + @classmethod + def release_study(cls, study_uid: str, reason_for_release_term_uid: str) -> str: + """releases a study version, returns released study version""" + + cls.set_study_title(study_uid) + + study_service = StudyService() + + study_service.release( + uid=study_uid, + change_description=cls.random_str(prefix="release "), + reason_for_release_uid=reason_for_release_term_uid, + ) + + study_history = study_service.get_study_snapshot_history( + study_uid=study_uid + ).items + release_history = sorted( + ( + item + for item in study_history + if StudyStatus.RELEASED in item.study_status + ), + key=lambda item: item.modified_date, + reverse=True, ) - return latest_study_version + if not release_history: + raise RuntimeError( + f"No released study version was found in history of study {study_uid}" + ) + + return str(release_history[0].metadata_version) @classmethod def unlock_study(cls, study_uid, reason_for_unlock_term_uid: str): 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 dc93b537..75511871 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 @@ -73,6 +73,7 @@ def create_random_activity_instance_vo() -> ActivityInstanceVO: ActivityItemVO.from_repository_values( activity_item_class_uid=random_str(), activity_item_class_name=random_str(), + ct_codelist=None, ct_terms=[ CTTermItem( uid=random_str(), name=random_str(), codelist_uid=random_str() @@ -88,6 +89,7 @@ def create_random_activity_instance_vo() -> ActivityInstanceVO: ActivityItemVO.from_repository_values( activity_item_class_uid=random_str(), activity_item_class_name=random_str(), + ct_codelist=None, ct_terms=[ CTTermItem( uid=random_str(), name=random_str(), codelist_uid=random_str() @@ -314,6 +316,7 @@ def test__init__ar_validation_failure(self): ActivityItemVO.from_repository_values( activity_item_class_uid=random_str(), activity_item_class_name=random_str(), + ct_codelist=None, ct_terms={"name": random_str(), "uid": random_str()}, unit_definitions=[ CompactUnitDefinition( @@ -326,6 +329,7 @@ def test__init__ar_validation_failure(self): ActivityItemVO.from_repository_values( activity_item_class_uid=random_str(), activity_item_class_name=random_str(), + ct_codelist=None, ct_terms={"name": random_str(), "uid": random_str()}, unit_definitions=[ CompactUnitDefinition( diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/clinical_programme_aggregate/test_clinical_programme.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/clinical_programme_aggregate/test_clinical_programme.py index 72800a9a..45ab29e4 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/clinical_programme_aggregate/test_clinical_programme.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/clinical_programme_aggregate/test_clinical_programme.py @@ -7,7 +7,7 @@ def create_random_clinical_programme( - generate_uid_callback: Callable[[], str] + generate_uid_callback: Callable[[], str], ) -> ClinicalProgrammeAR: random_clinical_programme = ClinicalProgrammeAR.from_input_values( name=random_str(), generate_uid_callback=generate_uid_callback diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/generic.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/generic.py index ce2b3642..d66992ac 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/generic.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/generic.py @@ -79,18 +79,16 @@ def get_next_free_uid_and_increment_counter(cls) -> str: object_name = cls.__name__.removesuffix("Root") return str( - db.cypher_query( - """ + db.cypher_query(""" MERGE (m:Counter{{counterId:'{LABEL}Counter'}}) ON CREATE SET m:{LABEL}Counter, m.count=0 WITH m CALL apoc.atomic.add(m,'count',1,1) yield oldValue, newValue WITH newValue(newValue) as uid_number RETURN "{LABEL}_"+apoc.text.lpad(""+(uid_number), {number_of_digits}, "0") - """.format( - LABEL=object_name, number_of_digits=settings.number_of_uid_digits - ) - )[0][0][0] + """.format(LABEL=object_name, number_of_digits=settings.number_of_uid_digits))[ + 0 + ][0][0] ) @classmethod @@ -144,17 +142,13 @@ def save(self): else type(self).__name__ ) - new_uid = db.cypher_query( - """ + new_uid = db.cypher_query(""" MERGE (m:Counter{{counterId:'{LABEL}Counter'}}) ON CREATE SET m:{LABEL}Counter, m.count=1 ON MATCH SET m.count = m.count + 1 WITH m RETURN m.count as number - """.format( - LABEL=object_name - ) - )[0][0][0] + """.format(LABEL=object_name))[0][0][0] self.uid = ( str(object_name) + "_" diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/study_definition_aggregate/test_root.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/study_definition_aggregate/test_root.py index 36c9bc5b..ccd319c4 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/study_definition_aggregate/test_root.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/study_definition_aggregate/test_root.py @@ -92,6 +92,7 @@ def create_random_study( initial_id_metadata=initial_id_metadata, project_exists_callback=lambda _: True, study_number_exists_callback=lambda x, y: False, + study_acronym_exists_callback=lambda x, y: False, initial_high_level_study_design=( initial_high_level_study_design if not is_study_after_create @@ -436,6 +437,7 @@ def generate_uid_callback() -> str: study_title_exists_callback=lambda _, study_number: False, study_short_title_exists_callback=lambda _, study_number: False, study_number_exists_callback=lambda x, y: False, + study_acronym_exists_callback=lambda x, y: False, author_id=author, ) diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/test_template_vo.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/test_template_vo.py index 925bddc2..2e2550de 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/test_template_vo.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/test_template_vo.py @@ -35,7 +35,7 @@ def template_string_with_valid_syntax(draw): @given(template_and_parameter_list=valid_template_with_list_of_parameter_names()) def test__template_vo_from_input_values__success( - template_and_parameter_list: tuple[str, list[str]] + template_and_parameter_list: tuple[str, list[str]], ): # event(f"template_string={template_string}") template_string = template_and_parameter_list[0] diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/unit_definition/test_unit_definition.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/unit_definition/test_unit_definition.py index 30608fe7..fe3a9e7e 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/unit_definition/test_unit_definition.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain/unit_definition/test_unit_definition.py @@ -61,12 +61,12 @@ def item_metadata(draw): author_id = _item_metadata.author_id author_username = AUTHOR_USERNAME change_description = _item_metadata.change_description - (major_version, minor_version) = draw( + major_version, minor_version = draw( tuples(integers(min_value=0), integers(min_value=0)).filter( lambda t: t[0] > 0 or t[1] > 0 ) ) - (start_date, end_date) = draw( + start_date, end_date = draw( tuples( datetimes(max_value=datetime.now()), one_of(none(), datetimes(max_value=datetime.now())), diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py index 26416485..b34ad8cd 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/domain_repositories/test_study_definition_repository_base.py @@ -298,6 +298,12 @@ def remove_soa_splits( ) -> None: return + @staticmethod + def get_study_id( + study_uid: str, study_value_version: str | None = None + ) -> str | None: + return None + def _random_study_number() -> str: choice = [str(_) for _ in range(0, 10)] 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 ce7084c7..a1f8b17e 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 @@ -477,7 +477,7 @@ def compare_docx_table( if cell.footnotes: # THEN footnote symbols match - symbols = parax0.runs[1].text.split("\u00A0") + symbols = parax0.runs[1].text.split("\u00a0") assert ( symbols == cell.footnotes ), f"footnote symbols don't match in {row_idx} column {col_idx}" diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py index 1e6af645..db07355e 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/soa_test_data.py @@ -7,7 +7,9 @@ ActivityForStudyActivity, ActivityGroupingHierarchySimpleModel, ) -from clinical_mdr_api.models.libraries.library import Library +from clinical_mdr_api.models.controlled_terminologies.ct_term import ( + SimpleCTTermNameWithConflictFlag, +) from clinical_mdr_api.models.study_selections.study_selection import ( ReferencedItem, SimpleStudyActivityGroup, @@ -16,12 +18,11 @@ StudyActivitySchedule, StudySelectionActivity, ) -from clinical_mdr_api.models.study_selections.study_soa_footnote import StudySoAFootnote -from clinical_mdr_api.models.study_selections.study_visit import StudyVisit -from clinical_mdr_api.models.syntax_instances.footnote import ( - Footnote, - FootnoteTemplateWithType, +from clinical_mdr_api.models.study_selections.study_soa_footnote import ( + CompactFootnote, + StudySoAFootnote, ) +from clinical_mdr_api.models.study_selections.study_visit import StudyVisitLite from clinical_mdr_api.services.utils.table_f import ( Ref, SimpleFootnote, @@ -30,956 +31,403 @@ TableWithFootnotes, ) from common.config import settings +from common.utils import VisitClass, VisitSubclass AUTHOR_USERNAME = "unknown-user" STUDY_VISITS = [ - StudyVisit( - study_epoch_uid="StudyEpoch_000004", - visit_type_uid="CTTerm_000182", - time_reference_uid="CTTerm_000122", - time_value=-14, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000012", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000012", - study_uid="Study_000002", - study_epoch_name="Screening", - study_epoch={ - "term_uid": "C48262_SCREENING", - "sponsor_preferred_name": "Screening", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="C48262_SCREENING", - order=1, - visit_type_name="Screening", - visit_type={ - "term_uid": "CTTerm_000182", - "sponsor_preferred_name": "Screening", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=-1209600.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000004", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="C48262_SCREENING", + sponsor_preferred_name="Screening", + ), study_day_number=-14, study_duration_days=-15, - study_duration_days_label="-15 days", - study_day_label="Day -14", study_week_number=-2, study_duration_weeks=-3, - study_duration_weeks_label="-3 weeks", - week_in_study_label="Week -3", - study_week_label="Week -2", - visit_number=1, - visit_subnumber=0, + visit_number=1.0, unique_visit_number=100, - visit_subname="Visit 1", - visit_name="Visit 1", visit_short_name="V1", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 41, 55, 138405, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000182", + sponsor_preferred_name="Screening", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000005", - visit_type_uid="CTTerm_000184", - time_reference_uid="CTTerm_000122", - time_value=-3, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000013", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000013", - study_uid="Study_000002", - study_epoch_name="Run-in", - study_epoch={ - "term_uid": "C98779_RUN-IN", - "sponsor_preferred_name": "Run-in", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="C98779_RUN-IN", - order=2, - visit_type_name="Start of run-in", - visit_type={ - "term_uid": "CTTerm_000184", - "sponsor_preferred_name": "Start of run-in", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=-259200.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000005", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="C98779_RUN-IN", + sponsor_preferred_name="Run-in", + ), study_day_number=-3, study_duration_days=-4, - study_duration_days_label="-4 days", - study_day_label="Day -3", study_week_number=1, study_duration_weeks=0, - study_duration_weeks_label="0 weeks", - week_in_study_label="Week 0", - study_week_label="Week 1", - visit_number=2, - visit_subnumber=0, + visit_number=2.0, unique_visit_number=200, - visit_subname="Visit 2", - visit_name="Visit 2", visit_short_name="V2", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 41, 56, 604440, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000184", + sponsor_preferred_name="Start of run-in", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000005", - visit_type_uid="CTTerm_000177", - time_reference_uid="CTTerm_000122", - time_value=-2, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000014", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=False, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid="CTTerm_000194", - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000014", - study_uid="Study_000002", - study_epoch_name="Run-in", - study_epoch={ - "term_uid": "C98779_RUN-IN", - "sponsor_preferred_name": "Run-in", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="C98779_RUN-IN", - order=3, - visit_type_name="Pre-treatment", - visit_type={ - "term_uid": "CTTerm_000177", - "sponsor_preferred_name": "Pre-treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name="Current Visit", - duration_time=-172800.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000005", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="C98779_RUN-IN", + sponsor_preferred_name="Run-in", + ), study_day_number=-2, study_duration_days=-3, - study_duration_days_label="-3 days", - study_day_label="Day -2", study_week_number=1, study_duration_weeks=0, - study_duration_weeks_label="0 weeks", - week_in_study_label="Week 0", - study_week_label="Week 1", - visit_number=3, - visit_subnumber=0, + visit_number=3.0, unique_visit_number=300, - visit_subname="Visit 3", - visit_name="Visit 3", visit_short_name="V3", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 27, 12, 50, 50, 931022, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000177", + sponsor_preferred_name="Pre-treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000005", - visit_type_uid="CTTerm_000177", - time_reference_uid="CTTerm_000122", - time_value=-1, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000015", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000015", - study_uid="Study_000002", - study_epoch_name="Run-in", - study_epoch={ - "term_uid": "C98779_RUN-IN", - "sponsor_preferred_name": "Run-in", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="C98779_RUN-IN", - order=4, - visit_type_name="Pre-treatment", - visit_type={ - "term_uid": "CTTerm_000177", - "sponsor_preferred_name": "Pre-treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=-86400.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000005", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="C98779_RUN-IN", + sponsor_preferred_name="Run-in", + ), study_day_number=-1, study_duration_days=-2, - study_duration_days_label="-2 days", - study_day_label="Day -1", study_week_number=1, study_duration_weeks=0, - study_duration_weeks_label="0 weeks", - week_in_study_label="Week 0", - study_week_label="Week 1", - visit_number=4, - visit_subnumber=0, + visit_number=4.0, unique_visit_number=400, - visit_subname="Visit 4", - visit_name="Visit 4", visit_short_name="V4", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 41, 58, 200939, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000177", + sponsor_preferred_name="Pre-treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000006", - visit_type_uid="CTTerm_000187", - time_reference_uid="CTTerm_000122", - time_value=0, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000016", consecutive_visit_group="V5-V7", + consecutive_visit_group_uid="StudyVisitGroup_000007", show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description="CYCLE 1, TREATMENT DAY 1", - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=True, - is_soa_milestone=False, - uid="StudyVisit_000016", - study_uid="Study_000002", - study_epoch_name="Treatment 1", - study_epoch={ - "term_uid": "CTTerm_001163", - "sponsor_preferred_name": "Treatment 1", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_001163", - order=5, - visit_type_name="Treatment", - visit_type={ - "term_uid": "CTTerm_000187", - "sponsor_preferred_name": "Treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=0.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000006", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_001163", + sponsor_preferred_name="Treatment 1", + ), study_day_number=1, study_duration_days=0, - study_duration_days_label="0 days", - study_day_label="Day 1", study_week_number=1, study_duration_weeks=0, - study_duration_weeks_label="0 weeks", - week_in_study_label="Week 0", - study_week_label="Week 1", - visit_number=5, - visit_subnumber=0, + visit_number=5.0, unique_visit_number=500, - visit_subname="Visit 5", - visit_name="Visit 5", visit_short_name="V5", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 28, 7, 8, 37, 273657, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=True, + is_soa_milestone=True, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000187", + sponsor_preferred_name="Treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000006", - visit_type_uid="CTTerm_000187", - time_reference_uid="CTTerm_000122", - time_value=2, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000017", consecutive_visit_group="V5-V7", + consecutive_visit_group_uid="StudyVisitGroup_000007", show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description="CYCLE 1, TREATMENT DAY 3", - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000017", - study_uid="Study_000002", - study_epoch_name="Treatment 1", - study_epoch={ - "term_uid": "CTTerm_001163", - "sponsor_preferred_name": "Treatment 1", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_001163", - order=6, - visit_type_name="Treatment", - visit_type={ - "term_uid": "CTTerm_000187", - "sponsor_preferred_name": "Treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=172800.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000006", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_001163", + sponsor_preferred_name="Treatment 1", + ), study_day_number=3, study_duration_days=2, - study_duration_days_label="2 days", - study_day_label="Day 3", study_week_number=1, study_duration_weeks=0, - study_duration_weeks_label="0 weeks", - week_in_study_label="Week 0", - study_week_label="Week 1", - visit_number=6, - visit_subnumber=0, + visit_number=6.0, unique_visit_number=600, - visit_subname="Visit 6", - visit_name="Visit 6", visit_short_name="V6", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 28, 7, 8, 37, 539422, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000187", + sponsor_preferred_name="Treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000006", - visit_type_uid="CTTerm_000187", - time_reference_uid="CTTerm_000122", - time_value=4, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000018", consecutive_visit_group="V5-V7", + consecutive_visit_group_uid="StudyVisitGroup_000007", show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description="CYCLE 1, TREATMENT DAY 5", - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000018", - study_uid="Study_000002", - study_epoch_name="Treatment 1", - study_epoch={ - "term_uid": "CTTerm_001163", - "sponsor_preferred_name": "Treatment 1", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_001163", - order=7, - visit_type_name="Treatment", - visit_type={ - "term_uid": "CTTerm_000187", - "sponsor_preferred_name": "Treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=345600.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000006", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_001163", + sponsor_preferred_name="Treatment 1", + ), study_day_number=5, study_duration_days=4, - study_duration_days_label="4 days", - study_day_label="Day 5", study_week_number=1, study_duration_weeks=0, - study_duration_weeks_label="0 weeks", - week_in_study_label="Week 0", - study_week_label="Week 1", - visit_number=7, - visit_subnumber=0, + visit_number=7.0, unique_visit_number=700, - visit_subname="Visit 7", - visit_name="Visit 7", visit_short_name="V7", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 28, 7, 8, 37, 794881, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000187", + sponsor_preferred_name="Treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000007", - visit_type_uid="CTTerm_000187", - time_reference_uid="CTTerm_000122", - time_value=14, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000019", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description="CYCLE 2, TREATMENT DAY 1", - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000019", - study_uid="Study_000002", - study_epoch_name="Treatment 2", - study_epoch={ - "term_uid": "CTTerm_001162", - "sponsor_preferred_name": "Treatment 2", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_001162", - order=8, - visit_type_name="Treatment", - visit_type={ - "term_uid": "CTTerm_000187", - "sponsor_preferred_name": "Treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=1209600.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000007", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_001162", + sponsor_preferred_name="Treatment 2", + ), study_day_number=15, study_duration_days=14, - study_duration_days_label="14 days", - study_day_label="Day 15", study_week_number=3, study_duration_weeks=2, - study_duration_weeks_label="2 weeks", - week_in_study_label="Week 2", - study_week_label="Week 3", - visit_number=8, - visit_subnumber=0, + visit_number=8.0, unique_visit_number=800, - visit_subname="Visit 8", - visit_name="Visit 8", visit_short_name="V8", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 42, 1, 370897, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=True, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000187", + sponsor_preferred_name="Treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000007", - visit_type_uid="CTTerm_000187", - time_reference_uid="CTTerm_000122", - time_value=16, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000020", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description="CYCLE 2, TREATMENT DAY 2", - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000020", - study_uid="Study_000002", - study_epoch_name="Treatment 2", - study_epoch={ - "term_uid": "CTTerm_001162", - "sponsor_preferred_name": "Treatment 2", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_001162", - order=9, - visit_type_name="Treatment", - visit_type={ - "term_uid": "CTTerm_000187", - "sponsor_preferred_name": "Treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=1382400.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000007", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_001162", + sponsor_preferred_name="Treatment 2", + ), study_day_number=17, study_duration_days=16, - study_duration_days_label="16 days", - study_day_label="Day 17", study_week_number=3, study_duration_weeks=2, - study_duration_weeks_label="2 weeks", - week_in_study_label="Week 2", - study_week_label="Week 3", - visit_number=9, - visit_subnumber=0, + visit_number=9.0, unique_visit_number=900, - visit_subname="Visit 9", - visit_name="Visit 9", visit_short_name="V9", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 42, 2, 213618, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000187", + sponsor_preferred_name="Treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000007", - visit_type_uid="CTTerm_000187", - time_reference_uid="CTTerm_000122", - time_value=18, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000021", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description="CYCLE 2, TREATMENT DAY 5", - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000021", - study_uid="Study_000002", - study_epoch_name="Treatment 2", - study_epoch={ - "term_uid": "CTTerm_001162", - "sponsor_preferred_name": "Treatment 2", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_001162", - order=10, - visit_type_name="Treatment", - visit_type={ - "term_uid": "CTTerm_000187", - "sponsor_preferred_name": "Treatment", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=1555200.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000007", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_001162", + sponsor_preferred_name="Treatment 2", + ), study_day_number=19, study_duration_days=18, - study_duration_days_label="18 days", - study_day_label="Day 19", study_week_number=3, study_duration_weeks=2, - study_duration_weeks_label="2 weeks", - week_in_study_label="Week 2", - study_week_label="Week 3", - visit_number=10, - visit_subnumber=0, + visit_number=10.0, unique_visit_number=1000, - visit_subname="Visit 10", - visit_name="Visit 10", visit_short_name="V10", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 42, 3, 81758, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000187", + sponsor_preferred_name="Treatment", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000008", - visit_type_uid="CTTerm_000175", - time_reference_uid="CTTerm_000122", - time_value=21, - time_unit_uid="UnitDefinition_000364", - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000022", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=0, max_visit_window_value=0, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000081", - epoch_allocation_uid=None, - visit_class="SINGLE_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000022", - study_uid="Study_000002", - study_epoch_name="Follow-up", - study_epoch={ - "term_uid": "C99158_FOLLOW-UP", - "sponsor_preferred_name": "Follow-up", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="C99158_FOLLOW-UP", - order=11, - visit_type_name="Follow-up", - visit_type={ - "term_uid": "CTTerm_000175", - "sponsor_preferred_name": "Follow-up", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name="Global anchor visit", - time_unit_name="days", - visit_contact_mode_name="On Site Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000081", - "sponsor_preferred_name": "On Site Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name=None, - duration_time=1814400.0, - duration_time_unit="UnitDefinition_000364", + study_epoch_uid="StudyEpoch_000008", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="C99158_FOLLOW-UP", + sponsor_preferred_name="Follow-up", + ), study_day_number=22, study_duration_days=21, - study_duration_days_label="21 days", - study_day_label="Day 22", study_week_number=4, study_duration_weeks=3, - study_duration_weeks_label="3 weeks", - week_in_study_label="Week 3", - study_week_label="Week 4", - visit_number=11, - visit_subnumber=0, + visit_number=11.0, unique_visit_number=1100, - visit_subname="Visit 11", - visit_name="Visit 11", visit_short_name="V11", visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 25, 11, 42, 4, 15590, tzinfo=datetime.timezone.utc + visit_class=VisitClass.SINGLE_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=True, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000175", + sponsor_preferred_name="Follow-up", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000009", - visit_type_uid="CTTerm_000192", - time_reference_uid=None, - time_value=None, - time_unit_uid=None, - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000023", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=-9999, max_visit_window_value=9999, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000079", - epoch_allocation_uid="CTTerm_000196", - visit_class="UNSCHEDULED_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000023", - study_uid="Study_000002", - study_epoch_name="Basic", - study_epoch={ - "term_uid": "CTTerm_000009", - "sponsor_preferred_name": "Basic", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_000009", - order=settings.unscheduled_visit_number, - visit_type_name="Unscheduled", - visit_type={ - "term_uid": "CTTerm_000192", - "sponsor_preferred_name": "Unscheduled", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name=None, - time_unit_name=None, - visit_contact_mode_name="Virtual Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000079", - "sponsor_preferred_name": "Virtual Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name="Date Current Visit", - duration_time=None, - duration_time_unit=None, + study_epoch_uid="StudyEpoch_000009", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000009", + sponsor_preferred_name="Basic", + ), study_day_number=None, - study_duration_days_label=None, - study_day_label=None, + study_duration_days=None, study_week_number=None, - study_duration_weeks_label=None, - week_in_study_label=None, - study_week_label=None, + study_duration_weeks=None, visit_number=settings.unscheduled_visit_number, - visit_subnumber=0, unique_visit_number=settings.unscheduled_visit_number, - visit_subname=f"Visit {settings.unscheduled_visit_number}", - visit_name=f"Visit {settings.unscheduled_visit_number}", - visit_short_name=f"{settings.unscheduled_visit_number}", + visit_short_name=str(settings.unscheduled_visit_number), visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 28, 7, 9, 58, 725540, tzinfo=datetime.timezone.utc + visit_class=VisitClass.UNSCHEDULED_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000192", + sponsor_preferred_name="Unscheduled", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), - StudyVisit( - study_epoch_uid="StudyEpoch_000009", - visit_type_uid="CTTerm_000190", - time_reference_uid=None, - time_value=None, - time_unit_uid=None, - visit_sublabel_reference=None, + StudyVisitLite( + uid="StudyVisit_000024", consecutive_visit_group=None, + consecutive_visit_group_uid=None, show_visit=True, min_visit_window_value=-9999, max_visit_window_value=9999, visit_window_unit_uid="UnitDefinition_000364", - description=None, - start_rule=None, - end_rule=None, - visit_contact_mode_uid="CTTerm_000079", - epoch_allocation_uid="CTTerm_000196", - visit_class="NON_VISIT", - visit_subclass="SINGLE_VISIT", - is_global_anchor_visit=False, - is_soa_milestone=False, - uid="StudyVisit_000024", - study_uid="Study_000002", - study_epoch_name="Basic", - study_epoch={ - "term_uid": "CTTerm_000009", - "sponsor_preferred_name": "Basic", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_uid="CTTerm_000009", - order=settings.non_visit_number, - visit_type_name="Non-visit", - visit_type={ - "term_uid": "CTTerm_000190", - "sponsor_preferred_name": "Non-visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - time_reference_name=None, - time_unit_name=None, - visit_contact_mode_name="Virtual Visit", - visit_contact_mode={ - "term_uid": "CTTerm_000079", - "sponsor_preferred_name": "Virtual Visit", - "sponsor_preferred_name_sentence_case": "screening", - }, - epoch_allocation_name="Date Current Visit", - duration_time=None, - duration_time_unit=None, + study_epoch_uid="StudyEpoch_000009", + study_epoch=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000009", + sponsor_preferred_name="Basic", + ), study_day_number=None, - study_duration_days_label=None, - study_day_label=None, + study_duration_days=None, study_week_number=None, - study_duration_weeks_label=None, - week_in_study_label=None, - study_week_label=None, + study_duration_weeks=None, visit_number=settings.non_visit_number, - visit_subnumber=0, unique_visit_number=settings.non_visit_number, - visit_subname=f"Visit {settings.non_visit_number}", - visit_name=f"Visit {settings.non_visit_number}", - visit_short_name=f"{settings.non_visit_number}", + visit_short_name=str(settings.non_visit_number), visit_window_unit_name="days", - status="DRAFT", - start_date=datetime.datetime( - 2023, 9, 28, 7, 9, 40, 605585, tzinfo=datetime.timezone.utc + visit_class=VisitClass.NON_VISIT, + visit_subclass=VisitSubclass.SINGLE_VISIT, + is_global_anchor_visit=False, + is_soa_milestone=False, + visit_type=SimpleCTTermNameWithConflictFlag( + term_uid="CTTerm_000190", + sponsor_preferred_name="Non-visit", ), - end_date=None, - author_username=AUTHOR_USERNAME, - possible_actions=["edit", "delete", "lock"], - change_type=None, ), ] + STUDY_ACTIVITIES = [ StudySelectionActivity( study_uid="Study_000002", @@ -1600,734 +1048,340 @@ accepted_version=False, ), ] + STUDY_ACTIVITY_SCHEDULES = [ StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000237", study_activity_uid="StudyActivity_000033", - study_activity_name="Informed Consent Obtained", study_visit_uid="StudyVisit_000021", - study_visit_name="Visit 10", - start_date=datetime.datetime(2023, 9, 28, 12, 16, 13, 789294), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000224", study_activity_uid="StudyActivity_000033", - study_activity_name="Informed Consent Obtained", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 18, 41, 289272), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000223", study_activity_uid="StudyActivity_000033", - study_activity_name="Informed Consent Obtained", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 18, 41, 200554), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000222", study_activity_uid="StudyActivity_000033", - study_activity_name="Informed Consent Obtained", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 28, 7, 18, 41, 106152), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000180", study_activity_uid="StudyActivity_000033", - study_activity_name="Informed Consent Obtained", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 44, 925699), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000167", study_activity_uid="StudyActivity_000033", - study_activity_name="Informed Consent Obtained", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 40, 4090), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000239", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 28, 12, 16, 36, 941563), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000148", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000014", - study_visit_name="Visit 3", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 29, 963794), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000174", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 42, 799372), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000150", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000015", - study_visit_name="Visit 4", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 30, 666424), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000146", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 29, 284104), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000209", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 33, 792658), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000152", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 31, 375534), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000186", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000015", - study_visit_name="Visit 4", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 47, 957960), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000184", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 47, 259826), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000213", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 35, 538906), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000172", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 41, 800992), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000140", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 27, 180162), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000207", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 33, 659383), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000215", study_activity_uid="StudyActivity_000041", - study_activity_name="Date of Birth", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 35, 692353), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000235", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000021", - study_visit_name="Visit 10", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 53, 81287), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000232", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000019", - study_visit_name="Visit 8", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 12, 896228), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000231", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 11, 30893), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000230", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 10, 952933), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000229", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 10, 870893), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000228", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000014", - study_visit_name="Visit 3", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 2, 996469), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000227", study_activity_uid="StudyActivity_000040", - study_activity_name="Diastolic Blood Pressure", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 28, 12, 14, 1, 609735), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000212", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 35, 462210), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000210", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 33, 886820), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000177", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 43, 881792), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000145", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 28, 934309), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000216", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 35, 761803), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000187", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000015", - study_visit_name="Visit 4", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 48, 294076), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000185", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 47, 610633), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000171", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 41, 454736), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000137", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 25, 836096), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000206", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 33, 595642), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000147", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000014", - study_visit_name="Visit 3", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 29, 622008), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000163", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000022", - study_visit_name="Visit 11", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 37, 404001), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000151", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 31, 24714), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000179", study_activity_uid="StudyActivity_000039", - study_activity_name="Systolic Blood Pressure", study_visit_uid="StudyVisit_000014", - study_visit_name="Visit 3", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 44, 578341), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000181", study_activity_uid="StudyActivity_000038", - study_activity_name="Erythrocytes", study_visit_uid="StudyVisit_000015", - study_visit_name="Visit 4", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 45, 285530), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000139", study_activity_uid="StudyActivity_000038", - study_activity_name="Erythrocytes", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 26, 830628), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000173", study_activity_uid="StudyActivity_000038", - study_activity_name="Erythrocytes", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 42, 455121), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000165", study_activity_uid="StudyActivity_000038", - study_activity_name="Erythrocytes", study_visit_uid="StudyVisit_000022", - study_visit_name="Visit 11", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 38, 392756), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000166", study_activity_uid="StudyActivity_000038", - study_activity_name="Erythrocytes", study_visit_uid="StudyVisit_000015", - study_visit_name="Visit 4", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 39, 653893), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000141", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 27, 524314), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000136", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 25, 471663), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000143", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000019", - study_visit_name="Visit 8", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 28, 215687), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000142", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 27, 860010), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000208", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 33, 734000), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000170", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 41, 88442), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000144", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000022", - study_visit_name="Visit 11", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 28, 558020), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000211", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 35, 385759), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000176", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000016", - study_visit_name="Visit 5", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 43, 507686), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000205", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000017", - study_visit_name="Visit 6", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 33, 509835), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000214", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000018", - study_visit_name="Visit 7", - start_date=datetime.datetime(2023, 9, 28, 7, 8, 35, 607005), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000175", study_activity_uid="StudyActivity_000037", - study_activity_name="Weight", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 43, 151406), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000221", study_activity_uid="StudyActivity_000036", - study_activity_name="Height", study_visit_uid="StudyVisit_000020", - study_visit_name="Visit 9", - start_date=datetime.datetime(2023, 9, 28, 7, 18, 20, 595234), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000169", study_activity_uid="StudyActivity_000036", - study_activity_name="Height", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 40, 711597), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000220", study_activity_uid="StudyActivity_000036", - study_activity_name="Height", study_visit_uid="StudyVisit_000014", - study_visit_name="Visit 3", - start_date=datetime.datetime(2023, 9, 28, 7, 18, 16, 760068), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000219", study_activity_uid="StudyActivity_000035", - study_activity_name="Medical History/Concomitant Illness", study_visit_uid="StudyVisit_000022", - study_visit_name="Visit 11", - start_date=datetime.datetime(2023, 9, 28, 7, 17, 58, 133816), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000218", study_activity_uid="StudyActivity_000035", - study_activity_name="Medical History/Concomitant Illness", study_visit_uid="StudyVisit_000013", - study_visit_name="Visit 2", - start_date=datetime.datetime(2023, 9, 28, 7, 17, 53, 408971), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000217", study_activity_uid="StudyActivity_000035", - study_activity_name="Medical History/Concomitant Illness", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 28, 7, 17, 50, 576524), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000134", study_activity_uid="StudyActivity_000034", - study_activity_name="Eligibility Criteria Met", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 24, 778118), - author_username=AUTHOR_USERNAME, - end_date=None, ), StudyActivitySchedule( - study_uid="Study_000002", study_activity_schedule_uid="StudyActivitySchedule_000168", study_activity_uid="StudyActivity_000034", - study_activity_name="Eligibility Criteria Met", study_visit_uid="StudyVisit_000012", - study_visit_name="Visit 1", - start_date=datetime.datetime(2023, 9, 25, 11, 42, 40, 366106), - author_username=AUTHOR_USERNAME, - end_date=None, ), ] + COORDINATES = { "StudyEpoch_000004": (0, 1), "StudyVisit_000012": (1, 1), @@ -2429,6 +1483,7 @@ "StudyActivitySchedule_000207": (27, 5), "StudyActivitySchedule_000215": (27, 5), } + FOOTNOTES: list[StudySoAFootnote] = [ StudySoAFootnote( uid="StudySoAFootnote_000011", @@ -2447,30 +1502,13 @@ item_type=SoAItemType.STUDY_VISIT, ), ], - footnote=Footnote( + footnote=CompactFootnote( uid="Footnote_000011", name="

The beginning is the most important part of the work

", name_plain="The beginning is the most important part of the work", - start_date=datetime.datetime(2023, 9, 26, 21, 42, 25, 947953), - end_date=None, status="Final", version="1.0", - change_description="Approved version", - author_username=AUTHOR_USERNAME, - possible_actions=["inactivate"], - footnote_template=FootnoteTemplateWithType( - name="

The beginning is the most important part of the work

", - name_plain="The beginning is the most important part of the work", - uid="FootnoteTemplate_000012", - sequence_id="FSA12", - library_name="User Defined", - type=None, - ), - parameter_terms=[], - library=Library(name="User Defined", is_editable=True), - study_count=0, ), - footnote_template=None, ), StudySoAFootnote( uid="StudySoAFootnote_000012", @@ -2524,30 +1562,13 @@ item_type=SoAItemType.STUDY_ACTIVITY_SCHEDULE, ), ], - footnote=Footnote( + footnote=CompactFootnote( uid="Footnote_000012", name="

For a man to conquer himself is the first and nobles of all victories

", name_plain="For a man to conquer himself is the first and nobles of all victories", - start_date=datetime.datetime(2023, 9, 26, 21, 43, 13, 45570), - end_date=None, status="Final", version="1.0", - change_description="Approved version", - author_username=AUTHOR_USERNAME, - possible_actions=["inactivate"], - footnote_template=FootnoteTemplateWithType( - name="

For a man to conquer himself is the first and nobles of all victories

", - name_plain="For a man to conquer himself is the first and nobles of all victories", - uid="FootnoteTemplate_000013", - sequence_id="FSA13", - library_name="User Defined", - type=None, - ), - parameter_terms=[], - library=Library(name="User Defined", is_editable=True), - study_count=0, ), - footnote_template=None, ), StudySoAFootnote( uid="StudySoAFootnote_000013", @@ -2601,30 +1622,13 @@ item_type=SoAItemType.STUDY_ACTIVITY_SCHEDULE, ), ], - footnote=Footnote( + footnote=CompactFootnote( uid="Footnote_000013", name="

Friendship is a single soul dwelling in two bodies

", name_plain="Friendship is a single soul dwelling in two bodies", - start_date=datetime.datetime(2023, 9, 26, 21, 43, 48, 36499), - end_date=None, status="Final", version="1.0", - change_description="Approved version", - author_username=AUTHOR_USERNAME, - possible_actions=["inactivate"], - footnote_template=FootnoteTemplateWithType( - name="

Friendship is a single soul dwelling in two bodies

", - name_plain="Friendship is a single soul dwelling in two bodies", - uid="FootnoteTemplate_000014", - sequence_id="FSA14", - library_name="User Defined", - type=None, - ), - parameter_terms=[], - library=Library(name="User Defined", is_editable=True), - study_count=0, ), - footnote_template=None, ), StudySoAFootnote( uid="StudySoAFootnote_000014", @@ -2688,32 +1692,16 @@ item_type=SoAItemType.STUDY_ACTIVITY_SCHEDULE, ), ], - footnote=Footnote( + footnote=CompactFootnote( uid="Footnote_000008", name='

The best way to predict the future is to create it"

', name_plain='The best way to predict the future is to create it"', - start_date=datetime.datetime(2023, 9, 26, 10, 50, 43, 523495), - end_date=None, status="Final", version="1.0", - change_description="Approved version", - author_username=AUTHOR_USERNAME, - possible_actions=["inactivate"], - footnote_template=FootnoteTemplateWithType( - name='

The best way to predict the future is to create it"

', - name_plain='The best way to predict the future is to create it"', - uid="FootnoteTemplate_000009", - sequence_id="FSA9", - library_name="User Defined", - type=None, - ), - parameter_terms=[], - library=Library(name="User Defined", is_editable=True), - study_count=0, ), - footnote_template=None, ), ] + DETAILED_SOA_TABLE = TableWithFootnotes( rows=[ TableRow( @@ -3817,6 +2805,7 @@ title="Protocol Flowchart", id=None, ) + PROTOCOL_SOA_TABLE = TableWithFootnotes( rows=[ TableRow( @@ -4966,6 +3955,7 @@ title="Protocol Flowchart", id=None, ) + PROTOCOL_SOA_TABLE_WITH_REF_PROPAGATION = TableWithFootnotes( rows=[ TableRow( @@ -6297,6 +5287,7 @@ title="Protocol Flowchart", id=None, ) + ADD_PROTOCOL_SECTION_COLUMN_CASE1 = ( TableWithFootnotes( rows=[ @@ -6391,6 +5382,7 @@ num_header_cols=2, ), ) + ADD_PROTOCOL_SECTION_COLUMN_CASE2 = ( TableWithFootnotes( rows=[ @@ -6422,6 +5414,7 @@ num_header_cols=0, ), ) + ADD_PROTOCOL_SECTION_COLUMN_CASE3 = ( TableWithFootnotes( rows=[ diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_design_figure.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_design_figure.py index 300b1298..e5b2966a 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_design_figure.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/services/test_study_design_figure.py @@ -694,8 +694,6 @@ STUDY_VISITS = ( StudyVisit( study_epoch_uid="StudyEpoch_000001", - visit_type_uid="CTTerm_000171", - time_reference_uid="CTTerm_000117", time_value=-2, time_unit_uid="UnitDefinition_000171", visit_sublabel_reference=None, @@ -707,8 +705,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -721,15 +717,12 @@ "sponsor_preferred_name": "Screening", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C48262_SCREENING", order=1, - visit_type_name="Screening", visit_type={ "term_uid": "CTTerm_000171", "sponsor_preferred_name": "Screening", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="weeks", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -761,8 +754,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=0, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -774,8 +765,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=True, @@ -788,15 +777,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=2, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -828,8 +814,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=7, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -841,8 +825,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -855,15 +837,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=3, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -895,8 +874,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=14, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -908,8 +885,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -922,15 +897,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=4, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -962,8 +934,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=21, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -975,8 +945,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -989,15 +957,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=5, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1029,8 +994,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=28, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1042,8 +1005,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1056,15 +1017,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=6, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1096,8 +1054,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=35, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1109,8 +1065,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1123,15 +1077,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=7, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1163,8 +1114,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=42, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1176,8 +1125,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1190,15 +1137,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=8, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1230,8 +1174,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=49, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1243,8 +1185,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1257,15 +1197,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=9, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1297,8 +1234,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000002", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000117", time_value=56, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1310,8 +1245,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1324,15 +1257,12 @@ "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C101526_TREATMENT", order=10, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1364,8 +1294,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000042", - visit_type_uid="CTTerm_000176", - time_reference_uid="CTTerm_000113", time_value=1, time_unit_uid="UnitDefinition_000166", visit_sublabel_reference=None, @@ -1377,8 +1305,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1391,15 +1317,12 @@ "sponsor_preferred_name": "Extension", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="CTTerm_000007", order=11, - visit_type_name="Treatment", visit_type={ "term_uid": "CTTerm_000176", "sponsor_preferred_name": "Treatment", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Previous Visit", time_unit_name="week", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1431,8 +1354,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000003", - visit_type_uid="CTTerm_000161", - time_reference_uid="CTTerm_000117", time_value=182, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1444,8 +1365,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000080", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1458,15 +1377,12 @@ "sponsor_preferred_name": "Follow-up", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="C99158_FOLLOW-UP", order=12, - visit_type_name="Follow-up", visit_type={ "term_uid": "CTTerm_000161", "sponsor_preferred_name": "Follow-up", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Global Anchor Visit", time_unit_name="days", visit_contact_mode_name="On Site Visit", visit_contact_mode={ @@ -1498,8 +1414,6 @@ ), StudyVisit( study_epoch_uid="StudyEpoch_000034", - visit_type_uid="CTTerm_000164", - time_reference_uid="CTTerm_000113", time_value=183, time_unit_uid="UnitDefinition_000151", visit_sublabel_reference=None, @@ -1511,8 +1425,6 @@ description=None, start_rule=None, end_rule=None, - visit_contact_mode_uid="CTTerm_000079", - epoch_allocation_uid=None, visit_class="SINGLE_VISIT", visit_subclass="SINGLE_VISIT", is_global_anchor_visit=False, @@ -1525,15 +1437,12 @@ "sponsor_preferred_name": "Elimination", "sponsor_preferred_name_sentence_case": "screening", }, - epoch_uid="CTTerm_000008", order=13, - visit_type_name="Post treatment activity", visit_type={ "term_uid": "CTTerm_000164", "sponsor_preferred_name": "Post treatment activity", "sponsor_preferred_name_sentence_case": "screening", }, - time_reference_name="Previous Visit", time_unit_name="days", visit_contact_mode_name="Phone Contact", visit_contact_mode={ 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 46c3548f..bf2fa7bf 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 @@ -16,7 +16,10 @@ 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_visit import StudyVisit +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 @@ -66,7 +69,9 @@ def _validate_parameters(self, *_args, **_kwargs): pass def _get_soa_preferences(self, *_args, **_kwargs) -> StudySoaPreferencesInput: - return StudySoaPreferencesInput() + return StudySoaPreferencesInput( + show_epochs=True, show_milestones=False, baseline_as_time_zero=False + ) def get_preferred_time_unit(self, *_args, **_kwargs) -> str: return "week" @@ -174,7 +179,7 @@ def check_flowchart_table_first_rows( first_visit_of_each_group.setdefault( collapse_visit_groups and visit.consecutive_visit_group - or visit.visit_name, + or visit.visit_short_name, visit, ) @@ -189,7 +194,7 @@ def check_flowchart_table_first_rows( i += 1 if visit.is_soa_milestone: - if prev_visit_type_uid == visit.visit_type_uid: + if prev_visit_type_uid == visit.visit_type.term_uid: # Same visit_type, then merged with the previous cell assert row.cells[i].text == "" assert row.cells[i].span == 0 @@ -197,7 +202,7 @@ def check_flowchart_table_first_rows( else: # Different visit_type, new label - prev_visit_type_uid = visit.visit_type_uid + prev_visit_type_uid = visit.visit_type.term_uid assert row.cells[i].text == visit.visit_type.sponsor_preferred_name assert row.cells[i].style == "header1" assert row.cells[i].span > 0 @@ -334,7 +339,7 @@ def check_flowchart_table_visit_rows( for visit in study_visits: group_name = ( not operational and visit.consecutive_visit_group - ) or visit.visit_name + ) or visit.visit_short_name visit_groups.setdefault(group_name, []).append(visit) visit_idx_by_uid[visit.uid] = len(visit_groups) + (2 if operational else 0) @@ -347,7 +352,7 @@ def check_flowchart_table_visit_rows( assert ( table.rows[row_idx].cells[i].text == (not operational and visit.consecutive_visit_group) - or visit.visit_name + or visit.visit_short_name ) # THEN visits ref in second row @@ -570,7 +575,7 @@ def test_group_visits( for visit in visit_group: count_visits += 1 - assert isinstance(visit, StudyVisit) + assert isinstance(visit, (StudyVisit, StudyVisitLite)) assert study_epoch_uid == visit.study_epoch_uid if len(visit_group) == 1: diff --git a/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_api_version.py b/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_api_version.py index 397ff4fc..cc993390 100644 --- a/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_api_version.py +++ b/clinical-mdr-api/clinical_mdr_api/tests/unit/utils/test_api_version.py @@ -30,12 +30,12 @@ def test_increment_api_version_if_needed(): api_spec_new = { "openapi": "3.0.2", "info": {"title": "OpenStudyBuilder API", "version": "2.0.0"}, - "paths": {"/concepts/odms/study-events": {}}, + "paths": {"/odms/study-events": {}}, } api_spec_old = { "openapi": "3.0.2", "info": {"title": "OpenStudyBuilder API", "version": "2.0.0"}, - "paths": {"/concepts/odms/study-events-old": {}}, + "paths": {"/odms/study-events-old": {}}, } api_spec_final = utils.increment_api_version_if_needed(api_spec_new, api_spec_old) @@ -52,12 +52,12 @@ def test_increment_api_version_if_needed(): api_spec_new = { "openapi": "3.0.2", "info": {"title": "OpenStudyBuilder API", "version": "2.0.2"}, - "paths": {"/concepts/odms/study-events": {}}, + "paths": {"/odms/study-events": {}}, } api_spec_old = { "openapi": "3.0.2", "info": {"title": "OpenStudyBuilder API", "version": "2.0.0"}, - "paths": {"/concepts/odms/study-events-old": {}}, + "paths": {"/odms/study-events-old": {}}, } api_spec_final = utils.increment_api_version_if_needed(api_spec_new, api_spec_old) @@ -68,12 +68,12 @@ def test_increment_api_version_if_needed(): api_spec_new = { "openapi": "3.0.2", "info": {"title": "OpenStudyBuilder API", "version": "2.0.0"}, - "paths": {"/concepts/odms/study-events": {}}, + "paths": {"/odms/study-events": {}}, } api_spec_old = { "openapi": "3.0.2", "info": {"title": "OpenStudyBuilder API", "version": "2.0.0"}, - "paths": {"/concepts/odms/study-events": {}}, + "paths": {"/odms/study-events": {}}, } api_spec_final = utils.increment_api_version_if_needed(api_spec_new, api_spec_old) diff --git a/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py b/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py index 7a0a2672..0726c0ee 100644 --- a/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py +++ b/clinical-mdr-api/clinical_mdr_api/utils/db_integrity_checks.py @@ -113,8 +113,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): WITH root, collect(v) as versions WITH root, [v IN tail(versions) WHERE v.end_date IS NULL] as bad WITH root WHERE size(bad) > 0 - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "only_one_latest_for_study_root", @@ -123,8 +122,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): MATCH (root:StudyRoot {uid: $study_uid})-[v:LATEST|LATEST_DRAFT|LATEST_FINAL|LATEST_RETIRED]->() WITH root, collect(type(v)) as types WHERE size(apoc.coll.duplicates(types)) > 0 - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "test_no_duplicated_study_version_by_status_and_dates", @@ -134,8 +132,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): WITH root, collect(v.status) as statuses, v WITH root, statuses, collect(v.start_date) as starts, collect(v.end_date) as ends WHERE (size(apoc.coll.duplicates(starts)) > 0 OR size(apoc.coll.duplicates(ends)) > 0) - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "no_study_version_has_negative_duration", @@ -143,8 +140,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): """ MATCH (root:StudyRoot {uid: $study_uid})-[v:HAS_VERSION|LATEST_DRAFT|LATEST_FINAL|LATEST_LOCKED|LATEST_RETIRED|LATEST_RELEASED]->() WHERE v.end_date IS NOT NULL AND v.end_date < v.start_date - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "no_study_version_lacks_start_date", @@ -152,8 +148,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): """ MATCH (root:StudyRoot {uid: $study_uid})-[v:HAS_VERSION|LATEST_DRAFT|LATEST_FINAL|LATEST_LOCKED|LATEST_RETIRED|LATEST_RELEASED]->() WHERE v.start_date IS NULL - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "no_study_version_lacks_end_date", @@ -161,8 +156,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): """ MATCH (root:StudyRoot {uid: $study_uid})-[v:HAS_VERSION]->(sv) WHERE v.end_date IS NULL AND NOT (root)-[:LATEST]->(sv) - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "study_versions_in_chronologic_order", @@ -199,8 +193,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): WITH root, latest, collect(value) as values WITH root, latest, last(values) as latest_by_date WITH root WHERE latest <> latest_by_date - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "no_latest_without_has_version", @@ -209,8 +202,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): MATCH (root:StudyRoot {uid: $study_uid})-[lat:LATEST_DRAFT|LATEST_FINAL|LATEST_LOCKED|LATEST_RETIRED|LATEST_RELEASED]->(value) WHERE lat.version IS NOT NULL AND lat.status IS NOT NULL AND NOT (root)-[:HAS_VERSION {version: lat.version, status: lat.status}]->(value) - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "no_released_without_locked", @@ -218,8 +210,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): """ MATCH (root:StudyRoot {uid: $study_uid})-[hvl:HAS_VERSION {status: "LOCKED"}]->(value) WHERE NOT (root)-[:HAS_VERSION {change_description: hvl.change_description, status: "RELEASED"}]->(value) - """ - + build_root_summary_return_statement("root"), + """ + build_root_summary_return_statement("root"), ), ( "unique_study_selection_on_each_study_value", @@ -232,8 +223,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): WHERE ss_uid_count>=2 MATCH (sv)--(n) WHERE n.uid = ss_uid - """ - + build_root_summary_return_statement("n"), + """ + build_root_summary_return_statement("n"), ), # test_study_selection_audit_trail.py ( @@ -242,8 +232,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): """ MATCH (sr:StudyRoot {uid: $study_uid})-[:AUDIT_TRAIL]->(all_sa:StudyAction)-->(ss:StudySelection) WHERE NOT (:StudyAction)-[:AFTER]->(ss) AND NOT (:UpdateSoASnapshot)-[:AFTER]->(ss) - """ - + build_root_summary_return_statement("ss"), + """ + build_root_summary_return_statement("ss"), ), ( "study_action_after_relation", @@ -254,8 +243,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): NOT (sa)-[:AFTER]->() AND NOT sa:UpdateSoASnapshot //TODO: will change to StudyActionLog AND NOT (sa)-[:BEFORE]->(:StudyValue) - """ - + build_root_summary_return_statement("sa"), + """ + build_root_summary_return_statement("sa"), ), ( "study_selection_labels", @@ -265,8 +253,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): WHERE NOT ss:StudySelection AND NOT ss.uid is NULL WITH ss - """ - + build_root_summary_return_statement("ss"), + """ + build_root_summary_return_statement("ss"), ), ( "time_coherence_on_each_study_selection_required_relationship", @@ -311,8 +298,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): AND ss3.uid<>ss1.uid WITH ss1, ss1_ss2, ss2, ss2_saction, ss2_old_version WHERE ss3 IS NULL - """ - + build_root_summary_return_statement("ss1"), + """ + build_root_summary_return_statement("ss1"), ), ( "study_actions_are_in_chronological_order", @@ -327,8 +313,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): RETURN ALL(i IN RANGE(1, SIZE(dates)-1) WHERE dates[i-1] <= dates[i]) AS inOrder } WITH sr, ss WHERE NOT inOrder - """ - + build_root_summary_return_statement("ss"), + """ + build_root_summary_return_statement("ss"), ), # test_study_selection.py ( @@ -339,8 +324,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): OPTIONAL MATCH (av)<-[ahv:HAS_VERSION]-(ar:ActivityRoot) WHERE ahv.start_date < sa.date AND (ahv.end_date IS NULL OR ahv.end_date > sa.date) AND ahv.status = "Final" WITH sa, sact, av WHERE ar IS NULL - """ - + build_root_summary_return_statement("sact"), + """ + build_root_summary_return_statement("sact"), ), # testing study versions and study definition documents ( @@ -352,8 +336,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): OPTIONAL MATCH (study_value)-[:HAS_STUDY_VERSION]->(study_version:StudyVersion) WITH study_version, collect(DISTINCT study_definition_document) as study_definition_documents WHERE size(study_definition_documents) > 1 - """ - + build_root_summary_return_statement("study_version"), + """ + build_root_summary_return_statement("study_version"), ), ( "study_version_exists_if_has_protocol_soa_cell_and_study_definition_document_exists", @@ -363,8 +346,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): MATCH (study_value)-[:HAS_STUDY_DEFINITION_DOCUMENT]->(study_definition_document:StudyDefinitionDocument) OPTIONAL MATCH (study_value)-[:HAS_STUDY_VERSION]->(study_version:StudyVersion) WHERE soa_cell IS NOT NULL AND study_definition_document IS NOT NULL AND study_version IS NULL - """ - + build_root_summary_return_statement("study_definition_document"), + """ + build_root_summary_return_statement("study_definition_document"), ), ( "study_version_exists_if_study_definition_document_exists", @@ -372,8 +354,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): """ MATCH (study_root:StudyRoot {uid: $study_uid})-[:HAS_VERSION]->(study_value:StudyValue)-[:HAS_STUDY_DEFINITION_DOCUMENT]->(study_definition_document:StudyDefinitionDocument) WHERE study_definition_document IS NOT NULL AND NOT (study_value)-[:HAS_STUDY_VERSION]->(:StudyVersion) - """ - + build_root_summary_return_statement("study_definition_document"), + """ + build_root_summary_return_statement("study_definition_document"), ), ( "FINAL_or_RELEASED_study_version_exisits_if_study_version_node_exists", @@ -383,8 +364,7 @@ def build_root_summary_return_statement(root_alias, extra_return=None): WHERE has_version.status IN ["FINAL", "RELEASED"] WITH study_version, collect(has_version) as final_or_released_versions WHERE size(final_or_released_versions) = 0 - """ - + build_root_summary_return_statement("study_version"), + """ + build_root_summary_return_statement("study_version"), ), ] diff --git a/clinical-mdr-api/common/auth/user.py b/clinical-mdr-api/common/auth/user.py index 2b1b3811..c067f12a 100644 --- a/clinical-mdr-api/common/auth/user.py +++ b/clinical-mdr-api/common/auth/user.py @@ -2,7 +2,7 @@ from cachetools import TTLCache, cached from neo4j.exceptions import Forbidden -from neomodel.sync_.core import db +from neomodel import db from starlette_context import context from common.auth.models import Auth, User diff --git a/clinical-mdr-api/common/config.py b/clinical-mdr-api/common/config.py index 034d9ce9..d0bb8a12 100644 --- a/clinical-mdr-api/common/config.py +++ b/clinical-mdr-api/common/config.py @@ -67,6 +67,9 @@ def cast_to_bool(cls, value: str | bool) -> bool: neo4j_dsn: str neo4j_connection_lifetime: float = 29 * 60 neo4j_liveness_check_timeout: float = 5 * 60 + soft_cardinality_check: bool = ( + True # This will prevent cardinality violations from being raised as errors. + ) # Cache Configuration cache_max_size: int = 1000 diff --git a/clinical-mdr-api/common/database.py b/clinical-mdr-api/common/database.py index a626dbdd..d65d227d 100644 --- a/clinical-mdr-api/common/database.py +++ b/clinical-mdr-api/common/database.py @@ -12,7 +12,9 @@ urllib.parse.uses_netloc.append(scheme) -def configure_database(neo4j_dsn: str, /, **driver_options) -> Driver: +def configure_database( + neo4j_dsn: str, /, soft_cardinality_check: bool = True, **driver_options +) -> Driver: parsed = urllib.parse.urlparse(neo4j_dsn) if parsed.scheme not in ( @@ -39,6 +41,7 @@ def configure_database(neo4j_dsn: str, /, **driver_options) -> Driver: neomodel_config.DRIVER = driver neomodel_config.DATABASE_NAME = database_name neomodel_config.DATABASE_URL = None + neomodel_config.SOFT_CARDINALITY_CHECK = soft_cardinality_check return driver diff --git a/clinical-mdr-api/common/neomodel.py b/clinical-mdr-api/common/neomodel.py new file mode 100644 index 00000000..34781c90 --- /dev/null +++ b/clinical-mdr-api/common/neomodel.py @@ -0,0 +1,42 @@ +"""Proxy types to make mypy happy...""" + +import datetime +from typing import TYPE_CHECKING + +import neomodel + +if TYPE_CHECKING: + from typing import Any, Generic, TypeVar, overload + + T = TypeVar("T") + + class _Property(Generic[T]): + @overload + def __get__(self, obj: None, objtype: type) -> "_Property[T]": ... + @overload + def __get__(self, obj: Any, objtype: type) -> T: ... + def __get__(self, obj: Any, objtype: type) -> Any: ... + def __set__(self, obj: Any, value: T) -> None: ... + def __init__( + self, *args: Any, **kwargs: Any # pylint: disable=unused-argument + ) -> None: ... + + class StringProperty(_Property[str]): ... + + class IntegerProperty(_Property[int]): ... + + class BooleanProperty(_Property[bool]): ... + + class FloatProperty(_Property[float]): ... + + class DateProperty(_Property[datetime.date]): ... + + class ArrayProperty(_Property[list[Any]]): ... + +else: + StringProperty = neomodel.StringProperty + IntegerProperty = neomodel.IntegerProperty + BooleanProperty = neomodel.BooleanProperty + FloatProperty = neomodel.FloatProperty + DateProperty = neomodel.DateProperty + ArrayProperty = neomodel.ArrayProperty diff --git a/clinical-mdr-api/common/queries.py b/clinical-mdr-api/common/queries.py index 57f65e24..26397e71 100644 --- a/clinical-mdr-api/common/queries.py +++ b/clinical-mdr-api/common/queries.py @@ -1,22 +1,21 @@ """Common query patterns""" +# pylint: disable=invalid-name + from textwrap import dedent # Gives ct_terms_datetime for effective study_standard_version of a StudyValue -study_standard_version_ct_terms_datetime = dedent( - """ +study_standard_version_ct_terms_datetime = dedent(""" CALL { WITH study_value OPTIONAL MATCH (study_value)-[:HAS_STUDY_STANDARD_VERSION]->(study_standard_version:StudyStandardVersion)-[:HAS_CT_PACKAGE]->(ct_package:CTPackage) WHERE ct_package.uid CONTAINS "SDTM CT" RETURN datetime(toString(date(ct_package.effective_date)) + 'T23:59:59.999999000Z') AS ct_terms_datetime } -""" -) +""") # Gives CTTermNameValue as {value} for a CTTermRoot {root} at given ct_terms_datetime (f-string) -ct_term_name_at_datetime = dedent( - """ +ct_term_name_at_datetime = dedent(""" CALL {{ WITH {root}, ct_terms_datetime OPTIONAL MATCH ({root})-[:HAS_NAME_ROOT]->(:CTTermNameRoot)-[version:HAS_VERSION]->(value:CTTermNameValue) @@ -34,5 +33,4 @@ date_conflict: NOT dates_match }} AS {value} }} -""" -).rstrip() +""").rstrip() diff --git a/clinical-mdr-api/common/telemetry/request_metrics.py b/clinical-mdr-api/common/telemetry/request_metrics.py index 3f694d95..926cdc45 100644 --- a/clinical-mdr-api/common/telemetry/request_metrics.py +++ b/clinical-mdr-api/common/telemetry/request_metrics.py @@ -5,8 +5,8 @@ from functools import wraps from typing import Mapping -import neomodel import opencensus.trace +from neomodel.sync_.database import Database as NeomodelDatabase from pydantic import BaseModel, Field from starlette.datastructures import MutableHeaders from starlette.responses import Response @@ -130,7 +130,7 @@ def cypher_tracing(query: str, params: Mapping): def patch_neomodel_database(): - """Monkey-patch neomodel.core.db singleton to trace Cypher queries""" + """Monkey-patch neomodel db singleton to trace Cypher queries""" def wrap(func): @wraps(func) @@ -158,8 +158,6 @@ def _run_cypher_query( return _run_cypher_query - log.info("Patching neomodel.util.Database") + log.info("Patching neomodel.sync_.database.Database") - neomodel.sync_.core.Database._run_cypher_query = wrap( - neomodel.sync_.core.Database._run_cypher_query - ) + NeomodelDatabase._run_cypher_query = wrap(NeomodelDatabase._run_cypher_query) # type: ignore[method-assign] diff --git a/clinical-mdr-api/consumer_api/apiVersion b/clinical-mdr-api/consumer_api/apiVersion index 841597f0..27f3bc3e 100644 --- a/clinical-mdr-api/consumer_api/apiVersion +++ b/clinical-mdr-api/consumer_api/apiVersion @@ -1 +1 @@ -0.1.119 +0.1.120 diff --git a/clinical-mdr-api/consumer_api/openapi.json b/clinical-mdr-api/consumer_api/openapi.json index c9d9d7f8..7cd05cd7 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": "0.1.119" + "version": "0.1.120" }, "paths": { "/": { @@ -3255,6 +3255,14 @@ "type": "array", "title": "Versions", "description": "Study versions" + }, + "data_completeness_tags": { + "items": { + "type": "string" + }, + "type": "array", + "title": "Data Completeness Tags", + "description": "List of data completeness tag names assigned to the study." } }, "type": "object", @@ -3281,6 +3289,7 @@ "study_activity_subgroup": { "anyOf": [ { + "additionalProperties": true, "type": "object" }, { @@ -3294,6 +3303,7 @@ "study_activity_group": { "anyOf": [ { + "additionalProperties": true, "type": "object" }, { @@ -3305,6 +3315,7 @@ "nullable": true }, "soa_group": { + "additionalProperties": true, "type": "object", "title": "Soa Group", "description": "SoA Group" 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 f9b1b558..26332488 100644 --- a/clinical-mdr-api/consumer_api/requirements/fs/fs-studies.md +++ b/clinical-mdr-api/consumer_api/requirements/fs/fs-studies.md @@ -204,7 +204,7 @@ The endpoint must return audit trail entries in CSV format with the following co - `action`: Action performed (Create, Edit, Delete) - `entity_uid`: UID of the entity affected by the action - `entity_type`: Type (node labels) of the entity affected by the action. Multiple labels are separated by '|' character. -- `changed_properties`: List of properties that were changed during the Edit action +- `changed_properties`: List of properties that were changed during the Edit action separated by '|' character. - `author`: Hashed (MD5) value of the ID of a user that performed the action The response must have a media type of `text/csv`. diff --git a/clinical-mdr-api/consumer_api/shared/common.py b/clinical-mdr-api/consumer_api/shared/common.py index 9e26d88b..ce5bebe5 100644 --- a/clinical-mdr-api/consumer_api/shared/common.py +++ b/clinical-mdr-api/consumer_api/shared/common.py @@ -5,7 +5,7 @@ from typing import Any from fastapi import Query -from neomodel.sync_.core import db +from neomodel import db from common.config import settings from common.exceptions import ValidationException diff --git a/clinical-mdr-api/consumer_api/system/service.py b/clinical-mdr-api/consumer_api/system/service.py index 3e1e9e93..ec32ede5 100644 --- a/clinical-mdr-api/consumer_api/system/service.py +++ b/clinical-mdr-api/consumer_api/system/service.py @@ -2,7 +2,7 @@ import urllib.parse from typing import Annotated -from neomodel.sync_.core import db +from neomodel import db from pydantic import BaseModel, Field diff --git a/clinical-mdr-api/consumer_api/tests/utils.py b/clinical-mdr-api/consumer_api/tests/utils.py index 83625b17..40a287b2 100644 --- a/clinical-mdr-api/consumer_api/tests/utils.py +++ b/clinical-mdr-api/consumer_api/tests/utils.py @@ -13,7 +13,7 @@ import neo4j.exceptions import openpyxl from fastapi.testclient import TestClient -from neomodel.sync_.core import db +from neomodel import db from common.config import settings from common.database import configure_database @@ -87,6 +87,25 @@ def assert_response_status_code(response: httpx.Response, status: int | Iterable ) +def assert_csv_format(csv_content: str, delimiter: str = ",") -> None: + """Assert that the CSV content is well-formed: + - Delimiter is the expected delimiter + - Each row has the same number of fields as the header + - No unexpected unescaped delimiters (field count mismatch would reveal this) + """ + lines = csv_content.splitlines() + assert len(lines) >= 2, "CSV must have at least a header and one data row" + reader = csv.reader(lines, delimiter=delimiter) + header = next(reader) + expected_fields = len(header) + assert expected_fields > 0, "CSV header must have at least one field" + for line_num, row in enumerate(reader, start=2): + assert len(row) == expected_fields, ( + f"Row {line_num} has {len(row)} fields, expected {expected_fields}. " + f"Row content: {row}" + ) + + class TestUtils: """Test utility functions for API tests.""" 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 65304120..924a2fca 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 @@ -9,7 +9,7 @@ import pytest from fastapi.testclient import TestClient -from neomodel.sync_.core import Database +from neomodel.sync_.database import Database from clinical_mdr_api.services.studies.study import StudyService from clinical_mdr_api.services.studies.study_flowchart import StudyFlowchartService @@ -25,7 +25,11 @@ ) from clinical_mdr_api.tests.integration.utils.utils import TestUtils from consumer_api.consumer_api import app -from consumer_api.tests.utils import assert_response_status_code, set_db +from consumer_api.tests.utils import ( + assert_csv_format, + assert_response_status_code, + set_db, +) from consumer_api.v1 import models BASE_URL = "/v1" @@ -273,6 +277,7 @@ def test_get_study_audit_trail(api_client): assert_response_status_code(response, 200) csv_content = response.content.decode("utf-8") + assert_csv_format(csv_content) csv_reader = csv.DictReader(csv_content.splitlines()) rows = list(csv_reader) assert len(rows) > 0 @@ -283,6 +288,7 @@ def test_get_study_audit_trail(api_client): assert_response_status_code(response, 200) csv_content = response.content.decode("utf-8") + assert_csv_format(csv_content) csv_reader = csv.DictReader(csv_content.splitlines()) rows = list(csv_reader) assert len(rows) > 0 @@ -330,6 +336,7 @@ def test_count_create_and_edit_actions_per_entity_type(api_client): assert_response_status_code(response, 200) csv_content = response.content.decode("utf-8") + assert_csv_format(csv_content) csv_reader = csv.DictReader(csv_content.splitlines()) rows = list(csv_reader) assert len(rows) > 0 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 73299e4b..4ce0319a 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 @@ -6,6 +6,7 @@ import pytest from fastapi.testclient import TestClient +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_flowchart import StudyFlowchartService from clinical_mdr_api.tests.integration.utils.api import inject_base_data @@ -33,6 +34,7 @@ "number", "acronym", "versions", + "data_completeness_tags", ] STUDY_FIELDS_NOT_NULL = [ @@ -475,6 +477,40 @@ def test_get_studies(api_client): ), f"Study {study.uid} not found in response" +def test_get_studies_returns_data_completeness_tags(api_client): + """Verify that data_completeness_tags are properly returned for studies.""" + # Create tags and assign them to a study + tag1 = TestUtils.create_data_completeness_tag(name="Consumer API Tag A") + tag2 = TestUtils.create_data_completeness_tag(name="Consumer API Tag B") + + service = DataCompletenessTagService() + service.assign_tag_to_study(study_uid=studies[0].uid, tag_uid=tag1.uid) + service.assign_tag_to_study(study_uid=studies[0].uid, tag_uid=tag2.uid) + + 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_completeness_tags" in study_item + assert isinstance(study_item["data_completeness_tags"], list) + assert tag1.name in study_item["data_completeness_tags"] + assert tag2.name in study_item["data_completeness_tags"] + + # Verify a study without tags returns an empty list + study_without_tags = next( + (s for s in res["items"] if s["uid"] == studies[1].uid), None + ) + assert study_without_tags is not None + assert study_without_tags["data_completeness_tags"] == [] + + # Cleanup + service.remove_tag_from_study(study_uid=studies[0].uid, tag_uid=tag1.uid) + service.remove_tag_from_study(study_uid=studies[0].uid, tag_uid=tag2.uid) + + 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 48dce8a9..0647e160 100644 --- a/clinical-mdr-api/consumer_api/tests/v2/test_api.py +++ b/clinical-mdr-api/consumer_api/tests/v2/test_api.py @@ -21,6 +21,7 @@ "acronym", "id_prefix", "number", + "data_completeness_tags", ] STUDY_FIELDS_NOT_NULL = [ diff --git a/clinical-mdr-api/consumer_api/v1/db.py b/clinical-mdr-api/consumer_api/v1/db.py index 8df4552b..c7a6b3f3 100644 --- a/clinical-mdr-api/consumer_api/v1/db.py +++ b/clinical-mdr-api/consumer_api/v1/db.py @@ -105,6 +105,7 @@ def get_studies( }}) AS authors ORDER BY hv.start_date DESC WITH + study_root, study_root.uid as uid, study_value.study_acronym as acronym, study_value.study_id_prefix as id_prefix, @@ -136,7 +137,8 @@ def get_studies( id_prefix, number, id, - versions + versions, + [(study_root)-[:HAS_COMPLETENESS_TAG]->(t:DataCompletenessTag) | t.name] as data_completeness_tags """ full_query = " ".join( diff --git a/clinical-mdr-api/consumer_api/v1/main.py b/clinical-mdr-api/consumer_api/v1/main.py index de26c734..09eb1cb9 100644 --- a/clinical-mdr-api/consumer_api/v1/main.py +++ b/clinical-mdr-api/consumer_api/v1/main.py @@ -661,6 +661,14 @@ def get_studies_audit_trail( ] csv_output = ",".join(keys) + "\n" for entry in audit_trail: + # None values are returned as empty string + # lists are returned as val1|val2 + for key in keys: + if entry[key] is None: + entry[key] = "" + elif isinstance(entry[key], list): + entry[key] = "|".join(entry[key]) + csv_output += ",".join(str(entry[key]) for key in keys) csv_output += "\n" diff --git a/clinical-mdr-api/consumer_api/v1/models.py b/clinical-mdr-api/consumer_api/v1/models.py index 1c015f2d..18a47ef0 100644 --- a/clinical-mdr-api/consumer_api/v1/models.py +++ b/clinical-mdr-api/consumer_api/v1/models.py @@ -124,6 +124,10 @@ def from_input(cls, val: dict[str, Any]): Field(description="Study acronym", json_schema_extra={"nullable": True}), ] = None versions: Annotated[list[StudyVersion], Field(description="Study versions")] + data_completeness_tags: list[str] = Field( + description="List of data completeness tag names assigned to the study.", + default_factory=list, + ) @classmethod def from_input(cls, val: dict[str, Any]): @@ -138,6 +142,7 @@ def from_input(cls, val: dict[str, Any]): Study.StudyVersion.from_input(version) for version in val.get("versions", []) ], + data_completeness_tags=val.get("data_completeness_tags", []), ) diff --git a/clinical-mdr-api/consumer_api/v2/models.py b/clinical-mdr-api/consumer_api/v2/models.py index e12a4a60..9662dc51 100644 --- a/clinical-mdr-api/consumer_api/v2/models.py +++ b/clinical-mdr-api/consumer_api/v2/models.py @@ -29,6 +29,10 @@ class Study(BaseModel): str | None, Field(description="Study number", json_schema_extra={"nullable": True}), ] = None + data_completeness_tags: list[str] = Field( + description="List of data completeness tag names assigned to the study.", + default_factory=list, + ) @classmethod def from_input(cls, val: dict[str, Any]): @@ -38,4 +42,5 @@ def from_input(cls, val: dict[str, Any]): acronym=val["acronym"], id_prefix=val["id_prefix"], number=val["number"], + data_completeness_tags=val.get("data_completeness_tags", []), ) diff --git a/clinical-mdr-api/doc/licenses/fhir_core-1.1.4.txt b/clinical-mdr-api/doc/licenses/fhir.resources-8.2.0.txt similarity index 100% rename from clinical-mdr-api/doc/licenses/fhir_core-1.1.4.txt rename to clinical-mdr-api/doc/licenses/fhir.resources-8.2.0.txt diff --git a/clinical-mdr-api/doc/licenses/fhir_core-1.1.5.txt b/clinical-mdr-api/doc/licenses/fhir_core-1.1.5.txt new file mode 100644 index 00000000..f7d404a1 --- /dev/null +++ b/clinical-mdr-api/doc/licenses/fhir_core-1.1.5.txt @@ -0,0 +1,29 @@ +BSD License + +Copyright (c) 2019, Md Nazrul Islam +All rights reserved. + +Redistribution and use in source and binary forms, with or without modification, +are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, this + list of conditions and the following disclaimer in the documentation and/or + other materials provided with the distribution. + +* Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from this + software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. +IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, +INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, +BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY +OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE +OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED +OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/clinical-mdr-api/extensions/README.md b/clinical-mdr-api/extensions/README.md index 9d0ef315..8cc417e8 100644 --- a/clinical-mdr-api/extensions/README.md +++ b/clinical-mdr-api/extensions/README.md @@ -65,7 +65,7 @@ extensions/ ## How to run extensions locally ### Prerequisites -- Python 3.13+ installed +- Python 3.14 installed - Pipenv installed - Neo4j database running (configure `NEO4J_DSN` environment variable) - Dependencies installed: `pipenv install` diff --git a/clinical-mdr-api/extensions/common.py b/clinical-mdr-api/extensions/common.py index 00d4be32..d4bbddf9 100644 --- a/clinical-mdr-api/extensions/common.py +++ b/clinical-mdr-api/extensions/common.py @@ -6,7 +6,7 @@ from typing import Annotated, Any, Generic, Self, TypeVar from fastapi import Query, Request -from neomodel.sync_.core import db +from neomodel import db from pydantic import BaseModel, Field from requests.utils import requote_uri diff --git a/clinical-mdr-api/extensions/hello/db.py b/clinical-mdr-api/extensions/hello/db.py index cf967bfd..8eeaa664 100644 --- a/clinical-mdr-api/extensions/hello/db.py +++ b/clinical-mdr-api/extensions/hello/db.py @@ -5,10 +5,8 @@ def get_node_count() -> int: - result = query( - """ + result = query(""" MATCH (n) RETURN count(n) AS node_count - """ - ) + """) return result[0]["node_count"] if result else 0 diff --git a/clinical-mdr-api/openapi.json b/clinical-mdr-api/openapi.json index f8eb9cbf..c054dbe4 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": "3.0.610" + "version": "3.0.628" }, "paths": { "/": { @@ -178,6 +178,174 @@ } } }, + "/user-preferences": { + "get": { + "tags": [ + "User Preferences" + ], + "summary": "Returns user preferences", + "operationId": "get_user_preferences_user_preferences_get", + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/UserPreferencesResponse" + } + } + } + }, + "401": { + "description": "Unauthorized", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + }, + "patch": { + "tags": [ + "User Preferences" + ], + "summary": "Update user preferences", + "description": "Update one or more user preference settings", + "operationId": "patch_user_preferences_user_preferences_patch", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/UserPreferencesPatchInput" + } + } + }, + "required": true + }, + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/UserPreferencesResponse" + } + } + } + }, + "401": { + "description": "Unauthorized", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + } + }, + "/user-preferences/{preference_key}": { + "delete": { + "tags": [ + "User Preferences" + ], + "summary": "Delete user preference", + "description": "Reset a user preference to global default by deleting the user override", + "operationId": "delete_user_preference_user_preferences__preference_key__delete", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "preference_key", + "in": "path", + "required": true, + "schema": { + "type": "string", + "title": "Preference Key" + } + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/UserPreferencesResponse" + } + } + } + }, + "401": { + "description": "Unauthorized", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, "/feature-flags": { "get": { "tags": [ @@ -519,13 +687,13 @@ } } }, - "/notifications": { + "/data-completeness-tags": { "get": { "tags": [ - "Notifications" + "Data Completeness Tags" ], - "summary": "Returns all notifications.", - "operationId": "get_all_notifications_notifications_get", + "summary": "Returns all data completeness tags.", + "operationId": "get_all_data_completeness_tags_data_completeness_tags_get", "responses": { "200": { "description": "Successful Response", @@ -533,10 +701,10 @@ "application/json": { "schema": { "items": { - "$ref": "#/components/schemas/Notification" + "$ref": "#/components/schemas/DataCompletenessTag" }, "type": "array", - "title": "Response Get All Notifications Notifications Get" + "title": "Response Get All Data Completeness Tags Data Completeness Tags Get" } } } @@ -583,15 +751,15 @@ }, "post": { "tags": [ - "Notifications" + "Data Completeness Tags" ], - "summary": "Creates a notification.", - "operationId": "create_notification_notifications_post", + "summary": "Creates a data completeness tag.", + "operationId": "create_data_completeness_tag_data_completeness_tags_post", "requestBody": { "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/NotificationPostInput" + "$ref": "#/components/schemas/DataCompletenessTagInput" } } }, @@ -603,7 +771,7 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Notification" + "$ref": "#/components/schemas/DataCompletenessTag" } } } @@ -628,6 +796,16 @@ } } }, + "409": { + "description": "The request could not be completed due to a conflict with the current state of the target resource. This typically occurs when attempting to create or modify a resource that already exists or violates a uniqueness constraint.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, "400": { "description": "Bad Request", "content": { @@ -649,58 +827,13 @@ ] } }, - "/notifications/actives": { - "get": { - "tags": [ - "Notifications" - ], - "summary": "Returns all notifications that are currently published and active.", - "operationId": "get_all_active_notifications_notifications_actives_get", - "responses": { - "200": { - "description": "Successful Response", - "content": { - "application/json": { - "schema": { - "items": { - "$ref": "#/components/schemas/Notification" - }, - "type": "array", - "title": "Response Get All Active Notifications Notifications Actives Get" - } - } - } - }, - "404": { - "description": "Entity not found", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - }, - "400": { - "description": "Bad Request", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ErrorResponse" - } - } - } - } - } - } - }, - "/notifications/{serial_number}": { - "get": { + "/data-completeness-tags/{uid}": { + "put": { "tags": [ - "Notifications" + "Data Completeness Tags" ], - "summary": "Returns the notification identified by the provided Serial Number.", - "operationId": "get_notification_notifications__serial_number__get", + "summary": "Updates the data completeness tag identified by the provided UID.", + "operationId": "update_data_completeness_tag_data_completeness_tags__uid__put", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -711,22 +844,32 @@ ], "parameters": [ { - "name": "serial_number", + "name": "uid", "in": "path", "required": true, "schema": { - "type": "integer", - "title": "Serial Number of the notification" + "type": "string", + "title": "UID of the data completeness tag" } } ], + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/DataCompletenessTagInput" + } + } + } + }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Notification" + "$ref": "#/components/schemas/DataCompletenessTag" } } } @@ -751,6 +894,16 @@ } } }, + "409": { + "description": "The request could not be completed due to a conflict with the current state of the target resource. This typically occurs when attempting to create or modify a resource that already exists or violates a uniqueness constraint.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, "400": { "description": "Bad Request", "content": { @@ -763,12 +916,12 @@ } } }, - "patch": { + "delete": { "tags": [ - "Notifications" + "Data Completeness Tags" ], - "summary": "Updates the notification identified by the provided Serial Number.", - "operationId": "update_notification_notifications__serial_number__patch", + "summary": "Deletes the data completeness tag identified by the provided UID.", + "operationId": "delete_data_completeness_tag_data_completeness_tags__uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -779,35 +932,341 @@ ], "parameters": [ { - "name": "serial_number", + "name": "uid", "in": "path", "required": true, "schema": { - "type": "integer", - "title": "Serial Number of the notification" + "type": "string", + "title": "UID of the data completeness tag" } } ], - "requestBody": { - "required": true, - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/NotificationPatchInput" - } - } - } - }, "responses": { - "200": { - "description": "Successful Response", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Notification" - } - } - } + "204": { + "description": "Successful Response" + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$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" + } + } + } + } + } + } + }, + "/notifications": { + "get": { + "tags": [ + "Notifications" + ], + "summary": "Returns all notifications.", + "operationId": "get_all_notifications_notifications_get", + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Notification" + }, + "type": "array", + "title": "Response Get All Notifications Notifications Get" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + }, + "post": { + "tags": [ + "Notifications" + ], + "summary": "Creates a notification.", + "operationId": "create_notification_notifications_post", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/NotificationPostInput" + } + } + }, + "required": true + }, + "responses": { + "201": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Notification" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + } + }, + "/notifications/actives": { + "get": { + "tags": [ + "Notifications" + ], + "summary": "Returns all notifications that are currently published and active.", + "operationId": "get_all_active_notifications_notifications_actives_get", + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "items": { + "$ref": "#/components/schemas/Notification" + }, + "type": "array", + "title": "Response Get All Active Notifications Notifications Actives Get" + } + } + } + }, + "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" + } + } + } + } + } + } + }, + "/notifications/{serial_number}": { + "get": { + "tags": [ + "Notifications" + ], + "summary": "Returns the notification identified by the provided Serial Number.", + "operationId": "get_notification_notifications__serial_number__get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "serial_number", + "in": "path", + "required": true, + "schema": { + "type": "integer", + "title": "Serial Number of the notification" + } + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Notification" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$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" + } + } + } + } + } + }, + "patch": { + "tags": [ + "Notifications" + ], + "summary": "Updates the notification identified by the provided Serial Number.", + "operationId": "update_notification_notifications__serial_number__patch", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "serial_number", + "in": "path", + "required": true, + "schema": { + "type": "integer", + "title": "Serial Number of the notification" + } + } + ], + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/NotificationPatchInput" + } + } + } + }, + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Notification" + } + } + } }, "403": { "description": "Forbidden", @@ -947,14 +1406,14 @@ ] } }, - "/concepts/odms/study-events": { + "/odms/study-events": { "get": { "tags": [ "ODM Study Events" ], "summary": "Return every variable related to the selected status and version of the ODM Study Events", "description": "Response 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_all_odm_study_events_concepts_odms_study_events_get", + "operationId": "get_all_odm_study_events_odms_study_events_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1151,7 +1610,7 @@ "ODM Study Events" ], "summary": "Creates a new Study Event in 'Draft' status with version 0.1", - "operationId": "create_odm_study_event_concepts_odms_study_events_post", + "operationId": "create_odm_study_event_odms_study_events_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1214,14 +1673,14 @@ } } }, - "/concepts/odms/study-events/headers": { + "/odms/study-events/headers": { "get": { "tags": [ "ODM Study Events" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_study_events_headers_get", + "operationId": "get_distinct_values_for_header_odms_study_events_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1345,7 +1804,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Study Events Headers Get" + "title": "Response Get Distinct Values For Header Odms Study Events Headers Get" } } } @@ -1383,13 +1842,13 @@ } } }, - "/concepts/odms/study-events/{odm_study_event_uid}": { + "/odms/study-events/{odm_study_event_uid}": { "get": { "tags": [ "ODM Study Events" ], "summary": "Get details on a specific ODM Study Event (in a specific version)", - "operationId": "get_odm_study_event_concepts_odms_study_events__odm_study_event_uid__get", + "operationId": "get_odm_study_event_odms_study_events__odm_study_event_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1477,7 +1936,7 @@ "ODM Study Events" ], "summary": "Update ODM Study Event", - "operationId": "edit_odm_study_event_concepts_odms_study_events__odm_study_event_uid__patch", + "operationId": "edit_odm_study_event_odms_study_events__odm_study_event_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1557,7 +2016,7 @@ "ODM Study Events" ], "summary": "Delete draft version of ODM Study Event", - "operationId": "delete_odm_study_event_concepts_odms_study_events__odm_study_event_uid__delete", + "operationId": "delete_odm_study_event_odms_study_events__odm_study_event_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1616,13 +2075,13 @@ } } }, - "/concepts/odms/study-events/{odm_study_event_uid}/relationships": { + "/odms/study-events/{odm_study_event_uid}/relationships": { "get": { "tags": [ "ODM Study Events" ], "summary": "Get UIDs of a specific ODM Study Event's relationships", - "operationId": "get_active_relationships_concepts_odms_study_events__odm_study_event_uid__relationships_get", + "operationId": "get_active_relationships_odms_study_events__odm_study_event_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1657,7 +2116,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Study Events Odm Study Event Uid Relationships Get" + "title": "Response Get Active Relationships Odms Study Events Odm Study Event Uid Relationships Get" } } } @@ -1695,14 +2154,14 @@ } } }, - "/concepts/odms/study-events/{odm_study_event_uid}/versions": { + "/odms/study-events/{odm_study_event_uid}/versions": { "get": { "tags": [ "ODM Study Events" ], "summary": "List version history for ODM Study Event", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Study Events.\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_odm_study_event_versions_concepts_odms_study_events__odm_study_event_uid__versions_get", + "operationId": "get_odm_study_event_versions_odms_study_events__odm_study_event_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1734,7 +2193,7 @@ "items": { "$ref": "#/components/schemas/OdmStudyEvent" }, - "title": "Response Get Odm Study Event Versions Concepts Odms Study Events Odm Study Event Uid Versions Get" + "title": "Response Get Odm Study Event Versions Odms Study Events Odm Study Event Uid Versions Get" } } } @@ -1777,7 +2236,7 @@ ], "summary": " Create a new version of ODM Study Event", "description": "State before:\n - uid must exist and the ODM Study Event must be in status Final.\n\nBusiness logic:\n- The ODM Study Event is changed to a draft state.\n\nState after:\n - ODM Study Event 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_odm_study_event_version_concepts_odms_study_events__odm_study_event_uid__versions_post", + "operationId": "create_odm_study_event_version_odms_study_events__odm_study_event_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1855,13 +2314,13 @@ } } }, - "/concepts/odms/study-events/{odm_study_event_uid}/approvals": { + "/odms/study-events/{odm_study_event_uid}/approvals": { "post": { "tags": [ "ODM Study Events" ], "summary": "Approve draft version of ODM Study Event", - "operationId": "approve_odm_study_event_concepts_odms_study_events__odm_study_event_uid__approvals_post", + "operationId": "approve_odm_study_event_odms_study_events__odm_study_event_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -1927,13 +2386,13 @@ } } }, - "/concepts/odms/study-events/{odm_study_event_uid}/activations": { + "/odms/study-events/{odm_study_event_uid}/activations": { "delete": { "tags": [ "ODM Study Events" ], "summary": " Inactivate final version of ODM Study Event", - "operationId": "inactivate_odm_study_event_concepts_odms_study_events__odm_study_event_uid__activations_delete", + "operationId": "inactivate_odm_study_event_odms_study_events__odm_study_event_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2003,7 +2462,7 @@ "ODM Study Events" ], "summary": "Reactivate retired version of a ODM Study Event", - "operationId": "reactivate_odm_study_event_concepts_odms_study_events__odm_study_event_uid__activations_post", + "operationId": "reactivate_odm_study_event_odms_study_events__odm_study_event_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2069,13 +2528,13 @@ } } }, - "/concepts/odms/study-events/{odm_study_event_uid}/forms": { + "/odms/study-events/{odm_study_event_uid}/forms": { "post": { "tags": [ "ODM Study Events" ], "summary": "Adds forms to the ODM Study Event.", - "operationId": "add_forms_to_odm_study_event_concepts_odms_study_events__odm_study_event_uid__forms_post", + "operationId": "add_forms_to_odm_study_event_odms_study_events__odm_study_event_uid__forms_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2167,14 +2626,14 @@ } } }, - "/concepts/odms/forms": { + "/odms/forms": { "get": { "tags": [ "ODM Forms" ], "summary": "Return every variable related to the selected status and version of the ODM Forms", "description": "Response 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_all_odm_forms_concepts_odms_forms_get", + "operationId": "get_all_odm_forms_odms_forms_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2371,7 +2830,7 @@ "ODM Forms" ], "summary": "Creates a new Form in 'Draft' status with version 0.1", - "operationId": "create_odm_form_concepts_odms_forms_post", + "operationId": "create_odm_form_odms_forms_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2434,14 +2893,14 @@ } } }, - "/concepts/odms/forms/headers": { + "/odms/forms/headers": { "get": { "tags": [ "ODM Forms" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_forms_headers_get", + "operationId": "get_distinct_values_for_header_odms_forms_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2565,7 +3024,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Forms Headers Get" + "title": "Response Get Distinct Values For Header Odms Forms Headers Get" } } } @@ -2603,14 +3062,14 @@ } } }, - "/concepts/odms/forms/study-events": { + "/odms/forms/study-events": { "get": { "tags": [ "ODM Forms" ], "summary": "Get all ODM Forms that belongs to an ODM Study Event", "description": "Response 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_odm_form_that_belongs_to_study_event_concepts_odms_forms_study_events_get", + "operationId": "get_odm_form_that_belongs_to_study_event_odms_forms_study_events_get", "responses": { "200": { "description": "Successful Response", @@ -2621,7 +3080,7 @@ "$ref": "#/components/schemas/OdmElementWithParentUid" }, "type": "array", - "title": "Response Get Odm Form That Belongs To Study Event Concepts Odms Forms Study Events Get" + "title": "Response Get Odm Form That Belongs To Study Event Odms Forms Study Events Get" } } } @@ -2667,13 +3126,13 @@ ] } }, - "/concepts/odms/forms/{odm_form_uid}": { + "/odms/forms/{odm_form_uid}": { "get": { "tags": [ "ODM Forms" ], "summary": "Get details on a specific ODM Form (in a specific version)", - "operationId": "get_odm_form_concepts_odms_forms__odm_form_uid__get", + "operationId": "get_odm_form_odms_forms__odm_form_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2761,7 +3220,7 @@ "ODM Forms" ], "summary": "Update ODM Form", - "operationId": "edit_odm_form_concepts_odms_forms__odm_form_uid__patch", + "operationId": "edit_odm_form_odms_forms__odm_form_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2841,7 +3300,7 @@ "ODM Forms" ], "summary": "Delete draft version of ODM Form", - "operationId": "delete_odm_form_concepts_odms_forms__odm_form_uid__delete", + "operationId": "delete_odm_form_odms_forms__odm_form_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2900,13 +3359,13 @@ } } }, - "/concepts/odms/forms/{odm_form_uid}/relationships": { + "/odms/forms/{odm_form_uid}/relationships": { "get": { "tags": [ "ODM Forms" ], "summary": "Get UIDs of a specific ODM Form's relationships", - "operationId": "get_active_relationships_concepts_odms_forms__odm_form_uid__relationships_get", + "operationId": "get_active_relationships_odms_forms__odm_form_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -2941,7 +3400,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Forms Odm Form Uid Relationships Get" + "title": "Response Get Active Relationships Odms Forms Odm Form Uid Relationships Get" } } } @@ -2979,14 +3438,14 @@ } } }, - "/concepts/odms/forms/{odm_form_uid}/versions": { + "/odms/forms/{odm_form_uid}/versions": { "get": { "tags": [ "ODM Forms" ], "summary": "List version history for ODM Form", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Forms.\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_odm_form_versions_concepts_odms_forms__odm_form_uid__versions_get", + "operationId": "get_odm_form_versions_odms_forms__odm_form_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3018,7 +3477,7 @@ "items": { "$ref": "#/components/schemas/OdmForm" }, - "title": "Response Get Odm Form Versions Concepts Odms Forms Odm Form Uid Versions Get" + "title": "Response Get Odm Form Versions Odms Forms Odm Form Uid Versions Get" } } } @@ -3061,7 +3520,7 @@ ], "summary": " Create a new version of ODM Form", "description": "State before:\n - uid must exist and the ODM Form must be in status Final.\n\nBusiness logic:\n- The ODM Form is changed to a draft state.\n\nState after:\n - ODM Form 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_odm_form_version_concepts_odms_forms__odm_form_uid__versions_post", + "operationId": "create_odm_form_version_odms_forms__odm_form_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3139,13 +3598,13 @@ } } }, - "/concepts/odms/forms/{odm_form_uid}/approvals": { + "/odms/forms/{odm_form_uid}/approvals": { "post": { "tags": [ "ODM Forms" ], "summary": "Approve draft version of ODM Form", - "operationId": "approve_odm_form_concepts_odms_forms__odm_form_uid__approvals_post", + "operationId": "approve_odm_form_odms_forms__odm_form_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3211,13 +3670,13 @@ } } }, - "/concepts/odms/forms/{odm_form_uid}/activations": { + "/odms/forms/{odm_form_uid}/activations": { "delete": { "tags": [ "ODM Forms" ], "summary": " Inactivate final version of ODM Form", - "operationId": "inactivate_odm_form_concepts_odms_forms__odm_form_uid__activations_delete", + "operationId": "inactivate_odm_form_odms_forms__odm_form_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3287,7 +3746,7 @@ "ODM Forms" ], "summary": "Reactivate retired version of a ODM Form", - "operationId": "reactivate_odm_form_concepts_odms_forms__odm_form_uid__activations_post", + "operationId": "reactivate_odm_form_odms_forms__odm_form_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3353,13 +3812,13 @@ } } }, - "/concepts/odms/forms/{odm_form_uid}/item-groups": { + "/odms/forms/{odm_form_uid}/item-groups": { "post": { "tags": [ "ODM Forms" ], "summary": "Adds item groups to the ODM Form.", - "operationId": "add_item_groups_to_odm_form_concepts_odms_forms__odm_form_uid__item_groups_post", + "operationId": "add_item_groups_to_odm_form_odms_forms__odm_form_uid__item_groups_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3451,14 +3910,14 @@ } } }, - "/concepts/odms/item-groups": { + "/odms/item-groups": { "get": { "tags": [ "ODM Item Groups" ], "summary": "Return every variable related to the selected status and version of the ODM Item Groups", "description": "Response 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_all_odm_item_groups_concepts_odms_item_groups_get", + "operationId": "get_all_odm_item_groups_odms_item_groups_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3655,7 +4114,7 @@ "ODM Item Groups" ], "summary": "Creates a new Item Group in 'Draft' status with version 0.1", - "operationId": "create_odm_item_group_concepts_odms_item_groups_post", + "operationId": "create_odm_item_group_odms_item_groups_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3718,14 +4177,14 @@ } } }, - "/concepts/odms/item-groups/headers": { + "/odms/item-groups/headers": { "get": { "tags": [ "ODM Item Groups" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_item_groups_headers_get", + "operationId": "get_distinct_values_for_header_odms_item_groups_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -3849,7 +4308,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Item Groups Headers Get" + "title": "Response Get Distinct Values For Header Odms Item Groups Headers Get" } } } @@ -3887,14 +4346,14 @@ } } }, - "/concepts/odms/item-groups/forms": { + "/odms/item-groups/forms": { "get": { "tags": [ "ODM Item Groups" ], "summary": "Get all ODM Item Groups that belongs to an ODM Form", "description": "Response 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_odm_item_group_that_belongs_to_form_concepts_odms_item_groups_forms_get", + "operationId": "get_odm_item_group_that_belongs_to_form_odms_item_groups_forms_get", "responses": { "200": { "description": "Successful Response", @@ -3905,7 +4364,7 @@ "$ref": "#/components/schemas/OdmElementWithParentUid" }, "type": "array", - "title": "Response Get Odm Item Group That Belongs To Form Concepts Odms Item Groups Forms Get" + "title": "Response Get Odm Item Group That Belongs To Form Odms Item Groups Forms Get" } } } @@ -3951,13 +4410,13 @@ ] } }, - "/concepts/odms/item-groups/{odm_item_group_uid}": { + "/odms/item-groups/{odm_item_group_uid}": { "get": { "tags": [ "ODM Item Groups" ], "summary": "Get details on a specific ODM Item Group (in a specific version)", - "operationId": "get_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__get", + "operationId": "get_odm_item_group_odms_item_groups__odm_item_group_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4045,7 +4504,7 @@ "ODM Item Groups" ], "summary": "Update ODM Item Group", - "operationId": "edit_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__patch", + "operationId": "edit_odm_item_group_odms_item_groups__odm_item_group_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4125,7 +4584,7 @@ "ODM Item Groups" ], "summary": "Delete draft version of ODM Item Group", - "operationId": "delete_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__delete", + "operationId": "delete_odm_item_group_odms_item_groups__odm_item_group_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4184,13 +4643,13 @@ } } }, - "/concepts/odms/item-groups/{odm_item_group_uid}/relationships": { + "/odms/item-groups/{odm_item_group_uid}/relationships": { "get": { "tags": [ "ODM Item Groups" ], "summary": "Get UIDs of a specific ODM Item Group's relationships", - "operationId": "get_active_relationships_concepts_odms_item_groups__odm_item_group_uid__relationships_get", + "operationId": "get_active_relationships_odms_item_groups__odm_item_group_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4225,7 +4684,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Item Groups Odm Item Group Uid Relationships Get" + "title": "Response Get Active Relationships Odms Item Groups Odm Item Group Uid Relationships Get" } } } @@ -4263,14 +4722,14 @@ } } }, - "/concepts/odms/item-groups/{odm_item_group_uid}/versions": { + "/odms/item-groups/{odm_item_group_uid}/versions": { "get": { "tags": [ "ODM Item Groups" ], "summary": "List version history for ODM Item Group", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Item Groups.\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_odm_item_group_versions_concepts_odms_item_groups__odm_item_group_uid__versions_get", + "operationId": "get_odm_item_group_versions_odms_item_groups__odm_item_group_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4302,7 +4761,7 @@ "items": { "$ref": "#/components/schemas/OdmItemGroup" }, - "title": "Response Get Odm Item Group Versions Concepts Odms Item Groups Odm Item Group Uid Versions Get" + "title": "Response Get Odm Item Group Versions Odms Item Groups Odm Item Group Uid Versions Get" } } } @@ -4345,7 +4804,7 @@ ], "summary": " Create a new version of ODM Item Group", "description": "State before:\n - uid must exist and the ODM Item Group must be in status Final.\n\nBusiness logic:\n- The ODM Item Group is changed to a draft state.\n\nState after:\n - ODM Item Group 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_odm_item_group_version_concepts_odms_item_groups__odm_item_group_uid__versions_post", + "operationId": "create_odm_item_group_version_odms_item_groups__odm_item_group_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4423,13 +4882,13 @@ } } }, - "/concepts/odms/item-groups/{odm_item_group_uid}/approvals": { + "/odms/item-groups/{odm_item_group_uid}/approvals": { "post": { "tags": [ "ODM Item Groups" ], "summary": "Approve draft version of ODM Item Group", - "operationId": "approve_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__approvals_post", + "operationId": "approve_odm_item_group_odms_item_groups__odm_item_group_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4495,13 +4954,13 @@ } } }, - "/concepts/odms/item-groups/{odm_item_group_uid}/activations": { + "/odms/item-groups/{odm_item_group_uid}/activations": { "delete": { "tags": [ "ODM Item Groups" ], "summary": " Inactivate final version of ODM Item Group", - "operationId": "inactivate_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__activations_delete", + "operationId": "inactivate_odm_item_group_odms_item_groups__odm_item_group_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4571,7 +5030,7 @@ "ODM Item Groups" ], "summary": "Reactivate retired version of a ODM Item Group", - "operationId": "reactivate_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__activations_post", + "operationId": "reactivate_odm_item_group_odms_item_groups__odm_item_group_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4637,13 +5096,13 @@ } } }, - "/concepts/odms/item-groups/{odm_item_group_uid}/items": { + "/odms/item-groups/{odm_item_group_uid}/items": { "post": { "tags": [ "ODM Item Groups" ], "summary": "Adds items to the ODM Item Group.", - "operationId": "add_item_to_odm_item_group_concepts_odms_item_groups__odm_item_group_uid__items_post", + "operationId": "add_item_to_odm_item_group_odms_item_groups__odm_item_group_uid__items_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4735,14 +5194,14 @@ } } }, - "/concepts/odms/items": { + "/odms/items": { "get": { "tags": [ "ODM Items" ], "summary": "Return every variable related to the selected status and version of the ODM Items", "description": "Response 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_all_odm_items_concepts_odms_items_get", + "operationId": "get_all_odm_items_odms_items_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -4939,7 +5398,7 @@ "ODM Items" ], "summary": "Creates a new Item in 'Draft' status with version 0.1", - "operationId": "create_odm_item_concepts_odms_items_post", + "operationId": "create_odm_item_odms_items_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5002,14 +5461,14 @@ } } }, - "/concepts/odms/items/headers": { + "/odms/items/headers": { "get": { "tags": [ "ODM Items" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_items_headers_get", + "operationId": "get_distinct_values_for_header_odms_items_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5133,7 +5592,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Items Headers Get" + "title": "Response Get Distinct Values For Header Odms Items Headers Get" } } } @@ -5171,13 +5630,13 @@ } } }, - "/concepts/odms/items/item-groups": { + "/odms/items/item-groups": { "get": { "tags": [ "ODM Items" ], "summary": "Get all ODM Items that belongs to an ODM Item Group", - "operationId": "get_odm_items_that_belongs_to_item_group_concepts_odms_items_item_groups_get", + "operationId": "get_odm_items_that_belongs_to_item_group_odms_items_item_groups_get", "responses": { "200": { "description": "Successful Response", @@ -5188,7 +5647,7 @@ "$ref": "#/components/schemas/OdmElementWithParentUid" }, "type": "array", - "title": "Response Get Odm Items That Belongs To Item Group Concepts Odms Items Item Groups Get" + "title": "Response Get Odm Items That Belongs To Item Group Odms Items Item Groups Get" } } } @@ -5234,13 +5693,13 @@ ] } }, - "/concepts/odms/items/{odm_item_uid}": { + "/odms/items/{odm_item_uid}": { "get": { "tags": [ "ODM Items" ], "summary": "Get details on a specific ODM Item (in a specific version)", - "operationId": "get_odm_item_concepts_odms_items__odm_item_uid__get", + "operationId": "get_odm_item_odms_items__odm_item_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5328,7 +5787,7 @@ "ODM Items" ], "summary": "Update ODM Item", - "operationId": "edit_odm_item_concepts_odms_items__odm_item_uid__patch", + "operationId": "edit_odm_item_odms_items__odm_item_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5408,7 +5867,7 @@ "ODM Items" ], "summary": "Delete draft version of ODM Item", - "operationId": "delete_odm_item_concepts_odms_items__odm_item_uid__delete", + "operationId": "delete_odm_item_odms_items__odm_item_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5467,13 +5926,13 @@ } } }, - "/concepts/odms/items/{odm_item_uid}/relationships": { + "/odms/items/{odm_item_uid}/relationships": { "get": { "tags": [ "ODM Items" ], "summary": "Get UIDs of a specific ODM Item's relationships", - "operationId": "get_active_relationships_concepts_odms_items__odm_item_uid__relationships_get", + "operationId": "get_active_relationships_odms_items__odm_item_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5508,7 +5967,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Items Odm Item Uid Relationships Get" + "title": "Response Get Active Relationships Odms Items Odm Item Uid Relationships Get" } } } @@ -5546,14 +6005,14 @@ } } }, - "/concepts/odms/items/{odm_item_uid}/versions": { + "/odms/items/{odm_item_uid}/versions": { "get": { "tags": [ "ODM Items" ], "summary": "List version history for ODM Item", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Items.\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_odm_item_versions_concepts_odms_items__odm_item_uid__versions_get", + "operationId": "get_odm_item_versions_odms_items__odm_item_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5585,7 +6044,7 @@ "items": { "$ref": "#/components/schemas/OdmItem" }, - "title": "Response Get Odm Item Versions Concepts Odms Items Odm Item Uid Versions Get" + "title": "Response Get Odm Item Versions Odms Items Odm Item Uid Versions Get" } } } @@ -5628,7 +6087,7 @@ ], "summary": " Create a new version of ODM Item", "description": "State before:\n - uid must exist and the ODM Item must be in status Final.\n\nBusiness logic:\n- The ODM Item is changed to a draft state.\n\nState after:\n - ODM Item 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_odm_item_version_concepts_odms_items__odm_item_uid__versions_post", + "operationId": "create_odm_item_version_odms_items__odm_item_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5694,13 +6153,13 @@ } } }, - "/concepts/odms/items/{odm_item_uid}/approvals": { + "/odms/items/{odm_item_uid}/approvals": { "post": { "tags": [ "ODM Items" ], "summary": "Approve draft version of ODM Item", - "operationId": "approve_odm_item_concepts_odms_items__odm_item_uid__approvals_post", + "operationId": "approve_odm_item_odms_items__odm_item_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5766,13 +6225,13 @@ } } }, - "/concepts/odms/items/{odm_item_uid}/activations": { + "/odms/items/{odm_item_uid}/activations": { "delete": { "tags": [ "ODM Items" ], "summary": " Inactivate final version of ODM Item", - "operationId": "inactivate_odm_item_concepts_odms_items__odm_item_uid__activations_delete", + "operationId": "inactivate_odm_item_odms_items__odm_item_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5842,7 +6301,7 @@ "ODM Items" ], "summary": "Reactivate retired version of a ODM Item", - "operationId": "reactivate_odm_item_concepts_odms_items__odm_item_uid__activations_post", + "operationId": "reactivate_odm_item_odms_items__odm_item_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -5908,13 +6367,13 @@ } } }, - "/concepts/odms/conditions": { + "/odms/conditions": { "get": { "tags": [ "ODM Conditions" ], "summary": "Return every variable related to the selected status and version of the ODM Conditions", - "operationId": "get_all_odm_conditions_concepts_odms_conditions_get", + "operationId": "get_all_odm_conditions_odms_conditions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6111,7 +6570,7 @@ "ODM Conditions" ], "summary": "Creates a new Condition in 'Draft' status with version 0.1", - "operationId": "create_odm_condition_concepts_odms_conditions_post", + "operationId": "create_odm_condition_odms_conditions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6174,14 +6633,14 @@ } } }, - "/concepts/odms/conditions/headers": { + "/odms/conditions/headers": { "get": { "tags": [ "ODM Conditions" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_conditions_headers_get", + "operationId": "get_distinct_values_for_header_odms_conditions_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6305,7 +6764,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Conditions Headers Get" + "title": "Response Get Distinct Values For Header Odms Conditions Headers Get" } } } @@ -6343,13 +6802,13 @@ } } }, - "/concepts/odms/conditions/{odm_condition_uid}": { + "/odms/conditions/{odm_condition_uid}": { "get": { "tags": [ "ODM Conditions" ], "summary": "Get details on a specific ODM Condition (in a specific version)", - "operationId": "get_odm_condition_concepts_odms_conditions__odm_condition_uid__get", + "operationId": "get_odm_condition_odms_conditions__odm_condition_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6437,7 +6896,7 @@ "ODM Conditions" ], "summary": "Update ODM Condition", - "operationId": "edit_odm_condition_concepts_odms_conditions__odm_condition_uid__patch", + "operationId": "edit_odm_condition_odms_conditions__odm_condition_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6527,7 +6986,7 @@ "ODM Conditions" ], "summary": "Delete draft version of ODM Condition", - "operationId": "delete_odm_condition_concepts_odms_conditions__odm_condition_uid__delete", + "operationId": "delete_odm_condition_odms_conditions__odm_condition_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6586,13 +7045,13 @@ } } }, - "/concepts/odms/conditions/{odm_condition_uid}/relationships": { + "/odms/conditions/{odm_condition_uid}/relationships": { "get": { "tags": [ "ODM Conditions" ], "summary": "Get UIDs of a specific ODM Condition's relationships", - "operationId": "get_active_relationships_concepts_odms_conditions__odm_condition_uid__relationships_get", + "operationId": "get_active_relationships_odms_conditions__odm_condition_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6627,7 +7086,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Conditions Odm Condition Uid Relationships Get" + "title": "Response Get Active Relationships Odms Conditions Odm Condition Uid Relationships Get" } } } @@ -6665,14 +7124,14 @@ } } }, - "/concepts/odms/conditions/{odm_condition_uid}/versions": { + "/odms/conditions/{odm_condition_uid}/versions": { "get": { "tags": [ "ODM Conditions" ], "summary": "List version history for ODM Condition", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Conditions.\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_odm_condition_versions_concepts_odms_conditions__odm_condition_uid__versions_get", + "operationId": "get_odm_condition_versions_odms_conditions__odm_condition_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6704,7 +7163,7 @@ "items": { "$ref": "#/components/schemas/OdmCondition" }, - "title": "Response Get Odm Condition Versions Concepts Odms Conditions Odm Condition Uid Versions Get" + "title": "Response Get Odm Condition Versions Odms Conditions Odm Condition Uid Versions Get" } } } @@ -6747,7 +7206,7 @@ ], "summary": " Create a new version of ODM Condition", "description": "State before:\n - uid must exist and the ODM Condition must be in status Final.\n\nBusiness logic:\n- The ODM Condition is changed to a draft state.\n\nState after:\n - ODM Condition 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_odm_condition_version_concepts_odms_conditions__odm_condition_uid__versions_post", + "operationId": "create_odm_condition_version_odms_conditions__odm_condition_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6813,13 +7272,13 @@ } } }, - "/concepts/odms/conditions/{odm_condition_uid}/approvals": { + "/odms/conditions/{odm_condition_uid}/approvals": { "post": { "tags": [ "ODM Conditions" ], "summary": "Approve draft version of ODM Condition", - "operationId": "approve_odm_condition_concepts_odms_conditions__odm_condition_uid__approvals_post", + "operationId": "approve_odm_condition_odms_conditions__odm_condition_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6885,13 +7344,13 @@ } } }, - "/concepts/odms/conditions/{odm_condition_uid}/activations": { + "/odms/conditions/{odm_condition_uid}/activations": { "delete": { "tags": [ "ODM Conditions" ], "summary": " Inactivate final version of ODM Condition", - "operationId": "inactivate_odm_condition_concepts_odms_conditions__odm_condition_uid__activations_delete", + "operationId": "inactivate_odm_condition_odms_conditions__odm_condition_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -6961,7 +7420,7 @@ "ODM Conditions" ], "summary": "Reactivate retired version of a ODM Condition", - "operationId": "reactivate_odm_condition_concepts_odms_conditions__odm_condition_uid__activations_post", + "operationId": "reactivate_odm_condition_odms_conditions__odm_condition_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7027,13 +7486,13 @@ } } }, - "/concepts/odms/methods": { + "/odms/methods": { "get": { "tags": [ "ODM Methods" ], "summary": "Return every variable related to the selected status and version of the ODM Methods", - "operationId": "get_all_odm_methods_concepts_odms_methods_get", + "operationId": "get_all_odm_methods_odms_methods_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7230,7 +7689,7 @@ "ODM Methods" ], "summary": "Creates a new Method in 'Draft' status with version 0.1", - "operationId": "create_odm_method_concepts_odms_methods_post", + "operationId": "create_odm_method_odms_methods_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7293,14 +7752,14 @@ } } }, - "/concepts/odms/methods/headers": { + "/odms/methods/headers": { "get": { "tags": [ "ODM Methods" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_methods_headers_get", + "operationId": "get_distinct_values_for_header_odms_methods_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7424,7 +7883,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Methods Headers Get" + "title": "Response Get Distinct Values For Header Odms Methods Headers Get" } } } @@ -7462,13 +7921,13 @@ } } }, - "/concepts/odms/methods/{odm_method_uid}": { + "/odms/methods/{odm_method_uid}": { "get": { "tags": [ "ODM Methods" ], "summary": "Get details on a specific ODM Method (in a specific version)", - "operationId": "get_odm_method_concepts_odms_methods__odm_method_uid__get", + "operationId": "get_odm_method_odms_methods__odm_method_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7556,7 +8015,7 @@ "ODM Methods" ], "summary": "Update ODM Method", - "operationId": "edit_odm_method_concepts_odms_methods__odm_method_uid__patch", + "operationId": "edit_odm_method_odms_methods__odm_method_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7646,7 +8105,7 @@ "ODM Methods" ], "summary": "Delete draft version of ODM Method", - "operationId": "delete_odm_method_concepts_odms_methods__odm_method_uid__delete", + "operationId": "delete_odm_method_odms_methods__odm_method_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7705,13 +8164,13 @@ } } }, - "/concepts/odms/methods/{odm_method_uid}/relationships": { + "/odms/methods/{odm_method_uid}/relationships": { "get": { "tags": [ "ODM Methods" ], "summary": "Get UIDs of a specific ODM Method's relationships", - "operationId": "get_active_relationships_concepts_odms_methods__odm_method_uid__relationships_get", + "operationId": "get_active_relationships_odms_methods__odm_method_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7746,7 +8205,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Methods Odm Method Uid Relationships Get" + "title": "Response Get Active Relationships Odms Methods Odm Method Uid Relationships Get" } } } @@ -7784,14 +8243,14 @@ } } }, - "/concepts/odms/methods/{odm_method_uid}/versions": { + "/odms/methods/{odm_method_uid}/versions": { "get": { "tags": [ "ODM Methods" ], "summary": "List version history for ODM Method", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Methods.\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_odm_method_versions_concepts_odms_methods__odm_method_uid__versions_get", + "operationId": "get_odm_method_versions_odms_methods__odm_method_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7823,7 +8282,7 @@ "items": { "$ref": "#/components/schemas/OdmMethod" }, - "title": "Response Get Odm Method Versions Concepts Odms Methods Odm Method Uid Versions Get" + "title": "Response Get Odm Method Versions Odms Methods Odm Method Uid Versions Get" } } } @@ -7866,7 +8325,7 @@ ], "summary": " Create a new version of ODM Method", "description": "State before:\n - uid must exist and the ODM Method must be in status Final.\n\nBusiness logic:\n- The ODM Method is changed to a draft state.\n\nState after:\n - ODM Method 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_odm_method_version_concepts_odms_methods__odm_method_uid__versions_post", + "operationId": "create_odm_method_version_odms_methods__odm_method_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -7932,13 +8391,13 @@ } } }, - "/concepts/odms/methods/{odm_method_uid}/approvals": { + "/odms/methods/{odm_method_uid}/approvals": { "post": { "tags": [ "ODM Methods" ], "summary": "Approve draft version of ODM Method", - "operationId": "approve_odm_method_concepts_odms_methods__odm_method_uid__approvals_post", + "operationId": "approve_odm_method_odms_methods__odm_method_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8004,13 +8463,13 @@ } } }, - "/concepts/odms/methods/{odm_method_uid}/activations": { + "/odms/methods/{odm_method_uid}/activations": { "delete": { "tags": [ "ODM Methods" ], "summary": " Inactivate final version of ODM Method", - "operationId": "inactivate_odm_method_concepts_odms_methods__odm_method_uid__activations_delete", + "operationId": "inactivate_odm_method_odms_methods__odm_method_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8080,7 +8539,7 @@ "ODM Methods" ], "summary": "Reactivate retired version of a ODM Method", - "operationId": "reactivate_odm_method_concepts_odms_methods__odm_method_uid__activations_post", + "operationId": "reactivate_odm_method_odms_methods__odm_method_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8146,13 +8605,13 @@ } } }, - "/concepts/odms/vendor-namespaces": { + "/odms/vendor-namespaces": { "get": { "tags": [ "ODM Vendor Namespaces" ], "summary": "Return every variable related to the selected status and version of the ODM Vendor Namespaces", - "operationId": "get_all_odm_vendor_namespaces_concepts_odms_vendor_namespaces_get", + "operationId": "get_all_odm_vendor_namespaces_odms_vendor_namespaces_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8349,7 +8808,7 @@ "ODM Vendor Namespaces" ], "summary": "Creates a new Vendor Namespace in 'Draft' status with version 0.1", - "operationId": "create_odm_vendor_namespace_concepts_odms_vendor_namespaces_post", + "operationId": "create_odm_vendor_namespace_odms_vendor_namespaces_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8412,14 +8871,14 @@ } } }, - "/concepts/odms/vendor-namespaces/headers": { + "/odms/vendor-namespaces/headers": { "get": { "tags": [ "ODM Vendor Namespaces" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_vendor_namespaces_headers_get", + "operationId": "get_distinct_values_for_header_odms_vendor_namespaces_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8543,7 +9002,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Vendor Namespaces Headers Get" + "title": "Response Get Distinct Values For Header Odms Vendor Namespaces Headers Get" } } } @@ -8581,13 +9040,13 @@ } } }, - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}": { + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}": { "get": { "tags": [ "ODM Vendor Namespaces" ], "summary": "Get details on a specific ODM Vendor Namespace (in a specific version)", - "operationId": "get_odm_vendor_namespace_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__get", + "operationId": "get_odm_vendor_namespace_odms_vendor_namespaces__odm_vendor_namespace_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8675,7 +9134,7 @@ "ODM Vendor Namespaces" ], "summary": "Update ODM Vendor Namespace", - "operationId": "edit_odm_vendor_namespace_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__patch", + "operationId": "edit_odm_vendor_namespace_odms_vendor_namespaces__odm_vendor_namespace_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8755,7 +9214,7 @@ "ODM Vendor Namespaces" ], "summary": "Delete draft version of ODM Vendor Namespace", - "operationId": "delete_odm_vendor_namespace_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__delete", + "operationId": "delete_odm_vendor_namespace_odms_vendor_namespaces__odm_vendor_namespace_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8814,13 +9273,13 @@ } } }, - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/relationships": { + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/relationships": { "get": { "tags": [ "ODM Vendor Namespaces" ], "summary": "Get UIDs of a specific ODM Vendor Namespace's relationships", - "operationId": "get_active_relationships_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__relationships_get", + "operationId": "get_active_relationships_odms_vendor_namespaces__odm_vendor_namespace_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8855,7 +9314,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Vendor Namespaces Odm Vendor Namespace Uid Relationships Get" + "title": "Response Get Active Relationships Odms Vendor Namespaces Odm Vendor Namespace Uid Relationships Get" } } } @@ -8893,14 +9352,14 @@ } } }, - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/versions": { + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/versions": { "get": { "tags": [ "ODM Vendor Namespaces" ], "summary": "List version history for ODM Vendor Namespace", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Vendor Namespaces.\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_odm_vendor_namespace_versions_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__versions_get", + "operationId": "get_odm_vendor_namespace_versions_odms_vendor_namespaces__odm_vendor_namespace_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -8932,7 +9391,7 @@ "items": { "$ref": "#/components/schemas/OdmVendorNamespace" }, - "title": "Response Get Odm Vendor Namespace Versions Concepts Odms Vendor Namespaces Odm Vendor Namespace Uid Versions Get" + "title": "Response Get Odm Vendor Namespace Versions Odms Vendor Namespaces Odm Vendor Namespace Uid Versions Get" } } } @@ -8975,7 +9434,7 @@ ], "summary": " Create a new version of ODM Vendor Namespace", "description": "State before:\n - uid must exist and the ODM Vendor Namespace must be in status Final.\n\nBusiness logic:\n- The ODM Vendor Namespace is changed to a draft state.\n\nState after:\n - ODM Vendor Namespace 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_odm_vendor_namespace_version_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__versions_post", + "operationId": "create_odm_vendor_namespace_version_odms_vendor_namespaces__odm_vendor_namespace_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9041,13 +9500,13 @@ } } }, - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/approvals": { + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/approvals": { "post": { "tags": [ "ODM Vendor Namespaces" ], "summary": "Approve draft version of ODM Vendor Namespace", - "operationId": "approve_odm_vendor_namespace_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__approvals_post", + "operationId": "approve_odm_vendor_namespace_odms_vendor_namespaces__odm_vendor_namespace_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9113,13 +9572,13 @@ } } }, - "/concepts/odms/vendor-namespaces/{odm_vendor_namespace_uid}/activations": { + "/odms/vendor-namespaces/{odm_vendor_namespace_uid}/activations": { "delete": { "tags": [ "ODM Vendor Namespaces" ], "summary": " Inactivate final version of ODM Vendor Namespace", - "operationId": "inactivate_odm_vendor_namespace_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__activations_delete", + "operationId": "inactivate_odm_vendor_namespace_odms_vendor_namespaces__odm_vendor_namespace_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9189,7 +9648,7 @@ "ODM Vendor Namespaces" ], "summary": "Reactivate retired version of a ODM Vendor Namespace", - "operationId": "reactivate_odm_vendor_namespace_concepts_odms_vendor_namespaces__odm_vendor_namespace_uid__activations_post", + "operationId": "reactivate_odm_vendor_namespace_odms_vendor_namespaces__odm_vendor_namespace_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9255,13 +9714,13 @@ } } }, - "/concepts/odms/vendor-attributes": { + "/odms/vendor-attributes": { "get": { "tags": [ "ODM Vendor Attributes" ], "summary": "Return every variable related to the selected status and version of the ODM Vendor Attributes", - "operationId": "get_all_odm_vendor_attributes_concepts_odms_vendor_attributes_get", + "operationId": "get_all_odm_vendor_attributes_odms_vendor_attributes_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9458,7 +9917,7 @@ "ODM Vendor Attributes" ], "summary": "Creates a new Vendor Attribute in 'Draft' status with version 0.1", - "operationId": "create_odm_vendor_attribute_concepts_odms_vendor_attributes_post", + "operationId": "create_odm_vendor_attribute_odms_vendor_attributes_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9511,14 +9970,14 @@ } } }, - "/concepts/odms/vendor-attributes/headers": { + "/odms/vendor-attributes/headers": { "get": { "tags": [ "ODM Vendor Attributes" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_vendor_attributes_headers_get", + "operationId": "get_distinct_values_for_header_odms_vendor_attributes_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9642,7 +10101,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Vendor Attributes Headers Get" + "title": "Response Get Distinct Values For Header Odms Vendor Attributes Headers Get" } } } @@ -9680,13 +10139,13 @@ } } }, - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}": { + "/odms/vendor-attributes/{odm_vendor_attribute_uid}": { "get": { "tags": [ "ODM Vendor Attributes" ], "summary": "Get details on a specific ODM Vendor Attribute (in a specific version)", - "operationId": "get_odm_vendor_attribute_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__get", + "operationId": "get_odm_vendor_attribute_odms_vendor_attributes__odm_vendor_attribute_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9774,7 +10233,7 @@ "ODM Vendor Attributes" ], "summary": "Update ODM Vendor Attribute", - "operationId": "edit_odm_vendor_attribute_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__patch", + "operationId": "edit_odm_vendor_attribute_odms_vendor_attributes__odm_vendor_attribute_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9854,7 +10313,7 @@ "ODM Vendor Attributes" ], "summary": "Delete draft version of ODM Vendor Attribute", - "operationId": "delete_odm_vendor_attribute_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__delete", + "operationId": "delete_odm_vendor_attribute_odms_vendor_attributes__odm_vendor_attribute_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9913,13 +10372,13 @@ } } }, - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/relationships": { + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/relationships": { "get": { "tags": [ "ODM Vendor Attributes" ], "summary": "Get UIDs of a specific ODM Vendor Attribute's relationships", - "operationId": "get_active_relationships_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__relationships_get", + "operationId": "get_active_relationships_odms_vendor_attributes__odm_vendor_attribute_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -9954,7 +10413,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Vendor Attributes Odm Vendor Attribute Uid Relationships Get" + "title": "Response Get Active Relationships Odms Vendor Attributes Odm Vendor Attribute Uid Relationships Get" } } } @@ -9992,14 +10451,14 @@ } } }, - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/versions": { + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/versions": { "get": { "tags": [ "ODM Vendor Attributes" ], "summary": "List version history for ODM Vendor Attribute", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Vendor Attributes.\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_odm_vendor_attribute_versions_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__versions_get", + "operationId": "get_odm_vendor_attribute_versions_odms_vendor_attributes__odm_vendor_attribute_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10031,7 +10490,7 @@ "items": { "$ref": "#/components/schemas/OdmVendorAttribute" }, - "title": "Response Get Odm Vendor Attribute Versions Concepts Odms Vendor Attributes Odm Vendor Attribute Uid Versions Get" + "title": "Response Get Odm Vendor Attribute Versions Odms Vendor Attributes Odm Vendor Attribute Uid Versions Get" } } } @@ -10074,7 +10533,7 @@ ], "summary": " Create a new version of ODM Vendor Attribute", "description": "State before:\n - uid must exist and the ODM Vendor Attribute must be in status Final.\n\nBusiness logic:\n- The ODM Vendor Attribute is changed to a draft state.\n\nState after:\n - ODM Vendor Attribute 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_odm_vendor_attribute_version_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__versions_post", + "operationId": "create_odm_vendor_attribute_version_odms_vendor_attributes__odm_vendor_attribute_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10140,13 +10599,13 @@ } } }, - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/approvals": { + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/approvals": { "post": { "tags": [ "ODM Vendor Attributes" ], "summary": "Approve draft version of ODM Vendor Attribute", - "operationId": "approve_odm_vendor_attribute_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__approvals_post", + "operationId": "approve_odm_vendor_attribute_odms_vendor_attributes__odm_vendor_attribute_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10212,13 +10671,13 @@ } } }, - "/concepts/odms/vendor-attributes/{odm_vendor_attribute_uid}/activations": { + "/odms/vendor-attributes/{odm_vendor_attribute_uid}/activations": { "delete": { "tags": [ "ODM Vendor Attributes" ], "summary": " Inactivate final version of ODM Vendor Attribute", - "operationId": "inactivate_odm_vendor_attribute_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__activations_delete", + "operationId": "inactivate_odm_vendor_attribute_odms_vendor_attributes__odm_vendor_attribute_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10288,7 +10747,7 @@ "ODM Vendor Attributes" ], "summary": "Reactivate retired version of a ODM Vendor Attribute", - "operationId": "reactivate_odm_vendor_attribute_concepts_odms_vendor_attributes__odm_vendor_attribute_uid__activations_post", + "operationId": "reactivate_odm_vendor_attribute_odms_vendor_attributes__odm_vendor_attribute_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10354,13 +10813,13 @@ } } }, - "/concepts/odms/vendor-elements": { + "/odms/vendor-elements": { "get": { "tags": [ "ODM Vendor Elements" ], "summary": "Return every variable related to the selected status and version of the ODM Vendor Elements", - "operationId": "get_all_odm_vendor_elements_concepts_odms_vendor_elements_get", + "operationId": "get_all_odm_vendor_elements_odms_vendor_elements_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10557,7 +11016,7 @@ "ODM Vendor Elements" ], "summary": "Creates a new Vendor Element in 'Draft' status with version 0.1", - "operationId": "create_odm_vendor_element_concepts_odms_vendor_elements_post", + "operationId": "create_odm_vendor_element_odms_vendor_elements_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10610,14 +11069,14 @@ } } }, - "/concepts/odms/vendor-elements/headers": { + "/odms/vendor-elements/headers": { "get": { "tags": [ "ODM Vendor Elements" ], "summary": "Returns possible values from the database for a given header", "description": "Allowed parameters include : field name for which to get possible\n values, search string to provide filtering for the field name, additional filters to apply on other fields", - "operationId": "get_distinct_values_for_header_concepts_odms_vendor_elements_headers_get", + "operationId": "get_distinct_values_for_header_odms_vendor_elements_headers_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10741,7 +11200,7 @@ "schema": { "type": "array", "items": {}, - "title": "Response Get Distinct Values For Header Concepts Odms Vendor Elements Headers Get" + "title": "Response Get Distinct Values For Header Odms Vendor Elements Headers Get" } } } @@ -10779,13 +11238,13 @@ } } }, - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}": { + "/odms/vendor-elements/{odm_vendor_element_uid}": { "get": { "tags": [ "ODM Vendor Elements" ], "summary": "Get details on a specific ODM Vendor Element (in a specific version)", - "operationId": "get_odm_vendor_element_concepts_odms_vendor_elements__odm_vendor_element_uid__get", + "operationId": "get_odm_vendor_element_odms_vendor_elements__odm_vendor_element_uid__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10873,7 +11332,7 @@ "ODM Vendor Elements" ], "summary": "Update ODM Vendor Element", - "operationId": "edit_odm_vendor_element_concepts_odms_vendor_elements__odm_vendor_element_uid__patch", + "operationId": "edit_odm_vendor_element_odms_vendor_elements__odm_vendor_element_uid__patch", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -10953,7 +11412,7 @@ "ODM Vendor Elements" ], "summary": "Delete draft version of ODM Vendor Element", - "operationId": "delete_odm_vendor_element_concepts_odms_vendor_elements__odm_vendor_element_uid__delete", + "operationId": "delete_odm_vendor_element_odms_vendor_elements__odm_vendor_element_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11012,13 +11471,13 @@ } } }, - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/relationships": { + "/odms/vendor-elements/{odm_vendor_element_uid}/relationships": { "get": { "tags": [ "ODM Vendor Elements" ], "summary": "Get UIDs of a specific ODM Vendor Element's relationships", - "operationId": "get_active_relationships_concepts_odms_vendor_elements__odm_vendor_element_uid__relationships_get", + "operationId": "get_active_relationships_odms_vendor_elements__odm_vendor_element_uid__relationships_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11053,7 +11512,7 @@ "type": "string" } }, - "title": "Response Get Active Relationships Concepts Odms Vendor Elements Odm Vendor Element Uid Relationships Get" + "title": "Response Get Active Relationships Odms Vendor Elements Odm Vendor Element Uid Relationships Get" } } } @@ -11091,14 +11550,14 @@ } } }, - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/versions": { + "/odms/vendor-elements/{odm_vendor_element_uid}/versions": { "get": { "tags": [ "ODM Vendor Elements" ], "summary": "List version history for ODM Vendor Element", "description": "State before:\n - uid must exist.\n\nBusiness logic:\n - List version history for ODM Vendor Elements.\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_odm_vendor_element_versions_concepts_odms_vendor_elements__odm_vendor_element_uid__versions_get", + "operationId": "get_odm_vendor_element_versions_odms_vendor_elements__odm_vendor_element_uid__versions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11130,7 +11589,7 @@ "items": { "$ref": "#/components/schemas/OdmVendorElement" }, - "title": "Response Get Odm Vendor Element Versions Concepts Odms Vendor Elements Odm Vendor Element Uid Versions Get" + "title": "Response Get Odm Vendor Element Versions Odms Vendor Elements Odm Vendor Element Uid Versions Get" } } } @@ -11173,7 +11632,7 @@ ], "summary": " Create a new version of ODM Vendor Element", "description": "State before:\n - uid must exist and the ODM Vendor Element must be in status Final.\n\nBusiness logic:\n- The ODM Vendor Element is changed to a draft state.\n\nState after:\n - ODM Vendor Element 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_odm_vendor_element_version_concepts_odms_vendor_elements__odm_vendor_element_uid__versions_post", + "operationId": "create_odm_vendor_element_version_odms_vendor_elements__odm_vendor_element_uid__versions_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11239,13 +11698,13 @@ } } }, - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/approvals": { + "/odms/vendor-elements/{odm_vendor_element_uid}/approvals": { "post": { "tags": [ "ODM Vendor Elements" ], "summary": "Approve draft version of ODM Vendor Element", - "operationId": "approve_odm_vendor_element_concepts_odms_vendor_elements__odm_vendor_element_uid__approvals_post", + "operationId": "approve_odm_vendor_element_odms_vendor_elements__odm_vendor_element_uid__approvals_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11311,13 +11770,13 @@ } } }, - "/concepts/odms/vendor-elements/{odm_vendor_element_uid}/activations": { + "/odms/vendor-elements/{odm_vendor_element_uid}/activations": { "delete": { "tags": [ "ODM Vendor Elements" ], "summary": " Inactivate final version of ODM Vendor Element", - "operationId": "inactivate_odm_vendor_element_concepts_odms_vendor_elements__odm_vendor_element_uid__activations_delete", + "operationId": "inactivate_odm_vendor_element_odms_vendor_elements__odm_vendor_element_uid__activations_delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11387,7 +11846,7 @@ "ODM Vendor Elements" ], "summary": "Reactivate retired version of a ODM Vendor Element", - "operationId": "reactivate_odm_vendor_element_concepts_odms_vendor_elements__odm_vendor_element_uid__activations_post", + "operationId": "reactivate_odm_vendor_element_odms_vendor_elements__odm_vendor_element_uid__activations_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11453,13 +11912,13 @@ } } }, - "/concepts/odms/metadata/aliases": { + "/odms/metadata/aliases": { "get": { "tags": [ "ODM Metadata" ], "summary": "Listing of ODM Aliases", - "operationId": "get_aliases_concepts_odms_metadata_aliases_get", + "operationId": "get_aliases_odms_metadata_aliases_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11578,13 +12037,13 @@ } } }, - "/concepts/odms/metadata/translated-texts": { + "/odms/metadata/translated-texts": { "get": { "tags": [ "ODM Metadata" ], "summary": "Listing of ODM Translated Texts", - "operationId": "get_translated_texts_concepts_odms_metadata_translated_texts_get", + "operationId": "get_translated_texts_odms_metadata_translated_texts_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11703,13 +12162,13 @@ } } }, - "/concepts/odms/metadata/formal-expressions": { + "/odms/metadata/formal-expressions": { "get": { "tags": [ "ODM Metadata" ], "summary": "Listing of ODM Formal Expressions", - "operationId": "get_formal_expressions_concepts_odms_metadata_formal_expressions_get", + "operationId": "get_formal_expressions_odms_metadata_formal_expressions_get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11828,13 +12287,13 @@ } } }, - "/concepts/odms/metadata/report": { + "/odms/metadata/report": { "post": { "tags": [ "ODM Metadata" ], "summary": "Export ODM Report", - "operationId": "get_odm_report_concepts_odms_metadata_report_post", + "operationId": "get_odm_report_odms_metadata_report_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -11907,13 +12366,13 @@ } } }, - "/concepts/odms/metadata/xmls/export": { + "/odms/metadata/xmls/export": { "post": { "tags": [ "ODM Metadata" ], "summary": "Export ODM XML", - "operationId": "get_odm_document_concepts_odms_metadata_xmls_export_post", + "operationId": "get_odm_document_odms_metadata_xmls_export_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -12002,7 +12461,7 @@ "content": { "multipart/form-data": { "schema": { - "$ref": "#/components/schemas/Body_get_odm_document_concepts_odms_metadata_xmls_export_post" + "$ref": "#/components/schemas/Body_get_odm_document_odms_metadata_xmls_export_post" } } } @@ -12048,13 +12507,13 @@ } } }, - "/concepts/odms/metadata/csvs/export": { + "/odms/metadata/csvs/export": { "post": { "tags": [ "ODM Metadata" ], "summary": "Export ODM CSV", - "operationId": "get_odm_csv_concepts_odms_metadata_csvs_export_post", + "operationId": "get_odm_csv_odms_metadata_csvs_export_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -12122,13 +12581,13 @@ } } }, - "/concepts/odms/metadata/xmls/import": { + "/odms/metadata/xmls/import": { "post": { "tags": [ "ODM Metadata" ], "summary": "Import ODM XML", - "operationId": "store_odm_xml_concepts_odms_metadata_xmls_import_post", + "operationId": "store_odm_xml_odms_metadata_xmls_import_post", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -12173,7 +12632,7 @@ "content": { "multipart/form-data": { "schema": { - "$ref": "#/components/schemas/Body_store_odm_xml_concepts_odms_metadata_xmls_import_post" + "$ref": "#/components/schemas/Body_store_odm_xml_odms_metadata_xmls_import_post" } } } @@ -12220,13 +12679,13 @@ } } }, - "/concepts/odms/metadata/xmls/stylesheets": { + "/odms/metadata/xmls/stylesheets": { "get": { "tags": [ "ODM Metadata" ], "summary": "Listing of all available ODM XML Stylesheet names", - "operationId": "get_available_stylesheet_names_concepts_odms_metadata_xmls_stylesheets_get", + "operationId": "get_available_stylesheet_names_odms_metadata_xmls_stylesheets_get", "responses": { "200": { "description": "Successful Response", @@ -12237,7 +12696,7 @@ "type": "string" }, "type": "array", - "title": "Response Get Available Stylesheet Names Concepts Odms Metadata Xmls Stylesheets Get" + "title": "Response Get Available Stylesheet Names Odms Metadata Xmls Stylesheets Get" } } } @@ -12283,13 +12742,13 @@ ] } }, - "/concepts/odms/metadata/xmls/stylesheets/{stylesheet}": { + "/odms/metadata/xmls/stylesheets/{stylesheet}": { "get": { "tags": [ "ODM Metadata" ], "summary": "Get a specific ODM XML Stylesheet", - "operationId": "get_specific_stylesheet_concepts_odms_metadata_xmls_stylesheets__stylesheet__get", + "operationId": "get_specific_stylesheet_odms_metadata_xmls_stylesheets__stylesheet__get", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -13840,6 +14299,24 @@ "title": "Activity Instruction Template Uid" }, "description": "The unique id of the activity instruction template." + }, + { + "name": "study_uid", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + "title": "Study Uid" + }, + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)" } ], "responses": { @@ -18079,6 +18556,24 @@ "title": "Footnote Template Uid" }, "description": "The unique id of the footnote template." + }, + { + "name": "study_uid", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + "title": "Study Uid" + }, + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)" } ], "responses": { @@ -22249,6 +22744,24 @@ "title": "Criteria Template Uid" }, "description": "The unique id of the criteria template." + }, + { + "name": "study_uid", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + "title": "Study Uid" + }, + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)" } ], "responses": { @@ -30665,6 +31178,24 @@ "title": "Endpoint Template Uid" }, "description": "The unique id of the endpoint template." + }, + { + "name": "study_uid", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)", + "title": "Study Uid" + }, + "description": "Optionally, the uid of the study to subset the parameters to (e.g. for StudyEndpoints parameters)" } ], "responses": { @@ -68849,7 +69380,8 @@ "schema": { "type": "array", "items": { - "type": "object" + "type": "object", + "additionalProperties": true }, "title": "Response Get Caches Admin Caches Get" } @@ -68910,7 +69442,8 @@ "schema": { "type": "array", "items": { - "type": "object" + "type": "object", + "additionalProperties": true }, "title": "Response Clear Caches Admin Caches Delete" } @@ -69327,6 +69860,133 @@ } } }, + "/admin/global-preferences": { + "get": { + "tags": [ + "Admin" + ], + "summary": "Returns global preferences", + "operationId": "get_global_preferences_admin_global_preferences_get", + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/PreferencesResponse" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + }, + "patch": { + "tags": [ + "Admin" + ], + "summary": "Update global preferences", + "description": "Update one or more global preference settings", + "operationId": "patch_global_preferences_admin_global_preferences_patch", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/GlobalPreferencesPatchInput" + } + } + }, + "required": true + }, + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/PreferencesResponse" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + }, + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ] + } + }, "/brands": { "get": { "tags": [ @@ -70895,6 +71555,114 @@ }, "description": "Indicates whether to return minimal response with only `uid`, `id` and `acronym`." }, + { + "name": "has_study_objective", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "description": "Filter studies by Study Objectives presence: `true` (has objectives), `false` (no objectives), or omit (all studies).", + "title": "Has Study Objective" + }, + "description": "Filter studies by Study Objectives presence: `true` (has objectives), `false` (no objectives), or omit (all studies)." + }, + { + "name": "has_study_footnote", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "description": "Filter studies by Study Objectives presence: `true` (has objectives), `false` (no objectives), or omit (all studies).", + "title": "Has Study Footnote" + }, + "description": "Filter studies by Study Objectives presence: `true` (has objectives), `false` (no objectives), or omit (all studies)." + }, + { + "name": "has_study_endpoint", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "description": "Filter studies by Study Endpoints presence: `true` (has endpoints), `false` (no endpoints), or omit (all studies).", + "title": "Has Study Endpoint" + }, + "description": "Filter studies by Study Endpoints presence: `true` (has endpoints), `false` (no endpoints), or omit (all studies)." + }, + { + "name": "has_study_criteria", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "description": "Filter studies by Study Criteria presence: `true` (has criteria), `false` (no criteria), or omit (all studies).", + "title": "Has Study Criteria" + }, + "description": "Filter studies by Study Criteria presence: `true` (has criteria), `false` (no criteria), or omit (all studies)." + }, + { + "name": "has_study_activity", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "description": "Filter studies by Study Activities presence: `true` (has activities), `false` (no activities), or omit (all studies).", + "title": "Has Study Activity" + }, + "description": "Filter studies by Study Activities presence: `true` (has activities), `false` (no activities), or omit (all studies)." + }, + { + "name": "has_study_activity_instruction", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "description": "Filter studies by Study Activity Instructions presence: `true` (has activity instructions), `false` (no activity instructions), or omit (all studies).", + "title": "Has Study Activity Instruction" + }, + "description": "Filter studies by Study Activity Instructions presence: `true` (has activity instructions), `false` (no activity instructions), or omit (all studies)." + }, { "name": "deleted", "in": "query", @@ -71695,7 +72463,7 @@ ], "summary": "Deletes a Study", "description": "State before:\n - uid must exist\n - The Study must be in status Draft and it couldn't be locked before.\n\nBusiness logic:\n - The draft Study is deleted.\n\nState after:\n - Study is successfully deleted.\n\nPossible errors:\n - Invalid uid or status not Draft or Study was previously locked.", - "operationId": "delete_activity_studies__study_uid__delete", + "operationId": "delete_study_studies__study_uid__delete", "security": [ { "OAuth2AuthorizationCodeBearer": [] @@ -72393,14 +73161,14 @@ "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." }, { - "name": "only_latest_major_protcol_version", + "name": "only_latest_major_protocol_version", "in": "query", "required": false, "schema": { "type": "boolean", "description": "Indicates whether Study snapshots without protocol header version should be returned", "default": false, - "title": "Only Latest Major Protcol Version" + "title": "Only Latest Major Protocol Version" }, "description": "Indicates whether Study snapshots without protocol header version should be returned" } @@ -73859,7 +74627,11 @@ "title": "Study Value Version" }, "description": "Study Version Number", - "example": "2.1" + "examples": { + "2.1": { + "value": "2.1" + } + } } ], "responses": { @@ -75244,7 +76016,8 @@ "schema": { "type": "array", "items": { - "type": "object" + "type": "object", + "additionalProperties": true }, "title": "Response Export Detailed Soa Content Studies Study Uid Detailed Soa Exports Get" } @@ -75339,7 +76112,8 @@ "schema": { "type": "array", "items": { - "type": "object" + "type": "object", + "additionalProperties": true }, "title": "Response Export Operational Soa Content Studies Study Uid Operational Soa Exports Get" } @@ -75434,7 +76208,8 @@ "schema": { "type": "array", "items": { - "type": "object" + "type": "object", + "additionalProperties": true }, "title": "Response Export Protocol Soa Content Studies Study Uid Protocol Soa Exports Get" } @@ -75906,7 +76681,8 @@ "schema": { "type": "array", "items": { - "type": "object" + "type": "object", + "additionalProperties": true }, "title": "Response Get A Paginated List Of Study Crfs Of A Study Studies Study Uid Odm Forms Get" } @@ -93539,6 +94315,236 @@ } } }, + "/studies/{study_uid}/data-completeness-tags": { + "get": { + "tags": [ + "Study Selections" + ], + "summary": "Returns all data completeness tags assigned to the given study.", + "operationId": "get_study_data_completeness_tags_studies__study_uid__data_completeness_tags_get", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + } + ], + "responses": { + "200": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/DataCompletenessTag" + }, + "title": "Response Get Study Data Completeness Tags Studies Study Uid Data Completeness Tags Get" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "404": { + "description": "Entity not found", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + }, + "400": { + "description": "Bad Request", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + }, + "post": { + "tags": [ + "Study Selections" + ], + "summary": "Assigns a data completeness tag to the given study.", + "operationId": "assign_data_completeness_tag_to_study_studies__study_uid__data_completeness_tags_post", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + } + ], + "requestBody": { + "required": true, + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Body_assign_data_completeness_tag_to_study_studies__study_uid__data_completeness_tags_post" + } + } + } + }, + "responses": { + "201": { + "description": "Successful Response", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/DataCompletenessTag" + } + } + } + }, + "403": { + "description": "Forbidden", + "content": { + "application/json": { + "schema": { + "$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" + } + } + } + } + } + } + }, + "/studies/{study_uid}/data-completeness-tags/{uid}": { + "delete": { + "tags": [ + "Study Selections" + ], + "summary": "Removes a data completeness tag from the given study.", + "operationId": "remove_data_completeness_tag_from_study_studies__study_uid__data_completeness_tags__uid__delete", + "security": [ + { + "OAuth2AuthorizationCodeBearer": [] + }, + { + "BearerJwtAuth": [] + } + ], + "parameters": [ + { + "name": "study_uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "description": "The unique id of the study.", + "title": "Study Uid" + }, + "description": "The unique id of the study." + }, + { + "name": "uid", + "in": "path", + "required": true, + "schema": { + "type": "string", + "title": "UID of the data completeness tag" + } + } + ], + "responses": { + "204": { + "description": "Successful Response" + }, + "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": { + "$ref": "#/components/schemas/ErrorResponse" + } + } + } + } + } + } + }, "/studies/{study_uid}/ctr/odm.xml": { "get": { "tags": [ @@ -101587,6 +102593,18 @@ "title": "Derive Props Based On Timeline" }, "description": "Indicates whether the (visit_name, visit_short_name, unique_visit_number) properties are derived based on the study visit timeline and not from database values." + }, + { + "name": "lite", + "in": "query", + "required": false, + "schema": { + "type": "boolean", + "description": "Whether to use the lightweight implementation of this endpoint, which doesn't support `filters` and `operator` parameters.", + "default": false, + "title": "Lite" + }, + "description": "Whether to use the lightweight implementation of this endpoint, which doesn't support `filters` and `operator` parameters." } ], "responses": { @@ -101595,7 +102613,7 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/CustomPage_StudyVisit_" + "$ref": "#/components/schemas/CustomPage_Union_StudyVisitLite__StudyVisit__" } } } @@ -110108,6 +111126,28 @@ } ], "parameters": [ + { + "name": "sponsor_model_name", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + "title": "Sponsor Model Name" + }, + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'" + }, + { + "name": "sponsor_model_version", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The version of the sponsor model, for instance '15'", + "title": "Sponsor Model Version" + }, + "description": "The version of the sponsor model, for instance '15'" + }, { "name": "sort_by", "in": "query", @@ -110324,12 +111364,24 @@ ], "parameters": [ { - "name": "field_name", + "name": "sponsor_model_name", "in": "query", "required": true, + "schema": { + "type": "string", + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + "title": "Sponsor Model Name" + }, + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'" + }, + { + "name": "field_name", + "in": "query", + "required": false, "schema": { "type": "string", "description": "The field name for which to lookup possible values in the database.\n\nFunctionality: searches for possible values (aka 'headers') of this field in the database.Errors: invalid field name specified", + "default": "", "title": "Field Name" }, "description": "The field name for which to lookup possible values in the database.\n\nFunctionality: searches for possible values (aka 'headers') of this field in the database.Errors: invalid field name specified" @@ -110476,6 +111528,28 @@ } ], "parameters": [ + { + "name": "sponsor_model_name", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + "title": "Sponsor Model Name" + }, + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'" + }, + { + "name": "sponsor_model_version", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The version number of the sponsor model, for instance '15'", + "title": "Sponsor Model Version" + }, + "description": "The version number of the sponsor model, for instance '15'" + }, { "name": "sort_by", "in": "query", @@ -110692,12 +111766,42 @@ ], "parameters": [ { - "name": "field_name", + "name": "sponsor_model_name", "in": "query", "required": true, + "schema": { + "type": "string", + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'", + "title": "Sponsor Model Name" + }, + "description": "The name of the sponsor model, for instance 'sdtmig_sponsormodel_3.2-NN15'" + }, + { + "name": "sponsor_model_version_number", + "in": "query", + "required": false, + "schema": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "description": "The version number of the sponsor model", + "title": "Sponsor Model Version Number" + }, + "description": "The version number of the sponsor model" + }, + { + "name": "field_name", + "in": "query", + "required": false, "schema": { "type": "string", "description": "The field name for which to lookup possible values in the database.\n\nFunctionality: searches for possible values (aka 'headers') of this field in the database.Errors: invalid field name specified", + "default": "", "title": "Field Name" }, "description": "The field name for which to lookup possible values in the database.\n\nFunctionality: searches for possible values (aka 'headers') of this field in the database.Errors: invalid field name specified" @@ -110844,6 +111948,17 @@ } ], "parameters": [ + { + "name": "data_model_name", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The full name of the model, for instance 'SDTM v2.0'", + "title": "Data Model Name" + }, + "description": "The full name of the model, for instance 'SDTM v2.0'" + }, { "name": "sort_by", "in": "query", @@ -111010,6 +112125,17 @@ } ], "parameters": [ + { + "name": "data_model_name", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The full name of the model, for instance 'SDTM v2.0'", + "title": "Data Model Name" + }, + "description": "The full name of the model, for instance 'SDTM v2.0'" + }, { "name": "field_name", "in": "query", @@ -111173,6 +112299,17 @@ "title": "Dataset Class Uid" }, "description": "The unique id of the DatasetClass" + }, + { + "name": "data_model_name", + "in": "query", + "required": true, + "schema": { + "type": "string", + "description": "The full name of the model, for instance 'SDTM v2.0'", + "title": "Data Model Name" + }, + "description": "The full name of the model, for instance 'SDTM v2.0'" } ], "responses": { @@ -117308,6 +118445,7 @@ "anyOf": [ { "items": { + "additionalProperties": true, "type": "object" }, "type": "array" @@ -119897,6 +121035,16 @@ "activity_item_class": { "$ref": "#/components/schemas/CompactActivityItemClassForActivityItem" }, + "ct_codelist": { + "anyOf": [ + { + "$ref": "#/components/schemas/CompactCodelist" + }, + { + "type": "null" + } + ] + }, "ct_terms": { "items": { "$ref": "#/components/schemas/CompactCTTerm" @@ -120601,6 +121749,17 @@ "minLength": 1, "title": "Activity Item Class Uid" }, + "ct_codelist_uid": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Ct Codelist Uid" + }, "ct_terms": { "items": { "$ref": "#/components/schemas/CTTermsInput" @@ -121282,6 +122441,19 @@ ], "title": "BatchErrorResponse" }, + "Body_assign_data_completeness_tag_to_study_studies__study_uid__data_completeness_tags_post": { + "properties": { + "uid": { + "type": "string", + "title": "UID of the data completeness tag" + } + }, + "type": "object", + "required": [ + "uid" + ], + "title": "Body_assign_data_completeness_tag_to_study_studies__study_uid__data_completeness_tags_post" + }, "Body_create_ct_packages_sponsor_post": { "properties": { "extends_package": { @@ -121315,7 +122487,7 @@ ], "title": "Body_create_ct_packages_sponsor_post" }, - "Body_get_odm_document_concepts_odms_metadata_xmls_export_post": { + "Body_get_odm_document_odms_metadata_xmls_export_post": { "properties": { "mapper_file": { "anyOf": [ @@ -121332,9 +122504,9 @@ } }, "type": "object", - "title": "Body_get_odm_document_concepts_odms_metadata_xmls_export_post" + "title": "Body_get_odm_document_odms_metadata_xmls_export_post" }, - "Body_store_odm_xml_concepts_odms_metadata_xmls_import_post": { + "Body_store_odm_xml_odms_metadata_xmls_import_post": { "properties": { "xml_file": { "type": "string", @@ -121360,7 +122532,7 @@ "required": [ "xml_file" ], - "title": "Body_store_odm_xml_concepts_odms_metadata_xmls_import_post" + "title": "Body_store_odm_xml_odms_metadata_xmls_import_post" }, "Brand": { "properties": { @@ -122728,6 +123900,30 @@ ], "title": "CTCodelistCreateInput" }, + "CTCodelistItem": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name" + } + }, + "type": "object", + "required": [ + "uid" + ], + "title": "CTCodelistItem" + }, "CTCodelistName": { "properties": { "catalogue_names": { @@ -125342,6 +126538,20 @@ ], "title": "CTTermRelatives" }, + "CTTermUidInput": { + "properties": { + "term_uid": { + "type": "string", + "title": "Term Uid" + } + }, + "type": "object", + "required": [ + "term_uid" + ], + "title": "CTTermUidInput", + "description": "Minimal input model accepting only a CT term UID.\n\nUsed in POST/PATCH input models to align the input shape with the\nnested-object shape returned by the corresponding GET response model." + }, "CTTermsInput": { "properties": { "term_uid": { @@ -125402,6 +126612,7 @@ "title": "Uid" }, "value_node": { + "additionalProperties": true, "type": "object", "title": "Value Node" }, @@ -126192,6 +127403,36 @@ "type": "object", "title": "CompactCTTerm" }, + "CompactCodelist": { + "properties": { + "uid": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Uid", + "nullable": true + }, + "name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Name", + "nullable": true + } + }, + "type": "object", + "title": "CompactCodelist" + }, "CompactFootnote": { "properties": { "uid": { @@ -133404,11 +134645,11 @@ ], "title": "CustomPage[StudyVisitListing]" }, - "CustomPage_StudyVisit_": { + "CustomPage_TextValue_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/StudyVisit" + "$ref": "#/components/schemas/TextValue" }, "type": "array", "title": "Items" @@ -133436,13 +134677,13 @@ "page", "size" ], - "title": "CustomPage[StudyVisit]" + "title": "CustomPage[TextValue]" }, - "CustomPage_TextValue_": { + "CustomPage_TimePoint_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/TextValue" + "$ref": "#/components/schemas/TimePoint" }, "type": "array", "title": "Items" @@ -133470,13 +134711,13 @@ "page", "size" ], - "title": "CustomPage[TextValue]" + "title": "CustomPage[TimePoint]" }, - "CustomPage_TimePoint_": { + "CustomPage_TimeframeTemplate_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/TimePoint" + "$ref": "#/components/schemas/TimeframeTemplate" }, "type": "array", "title": "Items" @@ -133504,13 +134745,13 @@ "page", "size" ], - "title": "CustomPage[TimePoint]" + "title": "CustomPage[TimeframeTemplate]" }, - "CustomPage_TimeframeTemplate_": { + "CustomPage_Timeframe_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/TimeframeTemplate" + "$ref": "#/components/schemas/Timeframe" }, "type": "array", "title": "Items" @@ -133538,13 +134779,13 @@ "page", "size" ], - "title": "CustomPage[TimeframeTemplate]" + "title": "CustomPage[Timeframe]" }, - "CustomPage_Timeframe_": { + "CustomPage_TopicCdDef_": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/Timeframe" + "$ref": "#/components/schemas/TopicCdDef" }, "type": "array", "title": "Items" @@ -133572,13 +134813,20 @@ "page", "size" ], - "title": "CustomPage[Timeframe]" + "title": "CustomPage[TopicCdDef]" }, - "CustomPage_TopicCdDef_": { + "CustomPage_Union_CTTermName__CTTermNameSimple__": { "properties": { "items": { "items": { - "$ref": "#/components/schemas/TopicCdDef" + "anyOf": [ + { + "$ref": "#/components/schemas/CTTermName" + }, + { + "$ref": "#/components/schemas/CTTermNameSimple" + } + ] }, "type": "array", "title": "Items" @@ -133606,18 +134854,21 @@ "page", "size" ], - "title": "CustomPage[TopicCdDef]" + "title": "CustomPage[Union[CTTermName, CTTermNameSimple]]" }, - "CustomPage_Union_CTTermName__CTTermNameSimple__": { + "CustomPage_Union_StudyVisitAdamListing__StudyEndpntAdamListing__FlowchartMetadataAdamListing__": { "properties": { "items": { "items": { "anyOf": [ { - "$ref": "#/components/schemas/CTTermName" + "$ref": "#/components/schemas/StudyVisitAdamListing" }, { - "$ref": "#/components/schemas/CTTermNameSimple" + "$ref": "#/components/schemas/StudyEndpntAdamListing" + }, + { + "$ref": "#/components/schemas/FlowchartMetadataAdamListing" } ] }, @@ -133647,21 +134898,18 @@ "page", "size" ], - "title": "CustomPage[Union[CTTermName, CTTermNameSimple]]" + "title": "CustomPage[Union[StudyVisitAdamListing, StudyEndpntAdamListing, FlowchartMetadataAdamListing]]" }, - "CustomPage_Union_StudyVisitAdamListing__StudyEndpntAdamListing__FlowchartMetadataAdamListing__": { + "CustomPage_Union_StudyVisitLite__StudyVisit__": { "properties": { "items": { "items": { "anyOf": [ { - "$ref": "#/components/schemas/StudyVisitAdamListing" + "$ref": "#/components/schemas/StudyVisitLite" }, { - "$ref": "#/components/schemas/StudyEndpntAdamListing" - }, - { - "$ref": "#/components/schemas/FlowchartMetadataAdamListing" + "$ref": "#/components/schemas/StudyVisit" } ] }, @@ -133691,7 +134939,7 @@ "page", "size" ], - "title": "CustomPage[Union[StudyVisitAdamListing, StudyEndpntAdamListing, FlowchartMetadataAdamListing]]" + "title": "CustomPage[Union[StudyVisitLite, StudyVisit]]" }, "CustomPage_UnitDefinitionModel_": { "properties": { @@ -133795,7 +135043,7 @@ ], "title": "CustomPage[VisitName]" }, - "DataModel": { + "DataCompletenessTag": { "properties": { "uid": { "type": "string", @@ -133803,56 +135051,31 @@ }, "name": { "type": "string", - "title": "Name", - "description": "The name or the data model. E.g. 'SDTM', 'ADAM', ..." - }, - "description": { - "type": "string", - "title": "Description" - }, - "implementation_guides": { - "items": { - "$ref": "#/components/schemas/SimpleImplementationGuide" - }, - "type": "array", - "title": "Implementation Guides" - }, - "version_number": { - "type": "string", - "title": "Version Number", - "description": "The version or the data model ig. E.g. '1.4'" - }, - "start_date": { - "type": "string", - "format": "date-time", - "title": "Start Date", - "description": "Version start date in ISO 8601 format with timezone, e.g. '2020-10-31T16:00:00+02:00' for October 31, 2020 at 4pm in UTC+2 timezone." - }, - "status": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Status", - "nullable": true + "title": "Name" } }, "type": "object", "required": [ "uid", - "name", - "description", - "implementation_guides", - "version_number", - "start_date" + "name" ], - "title": "DataModel" + "title": "DataCompletenessTag" }, - "DataModelIG": { + "DataCompletenessTagInput": { + "properties": { + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + } + }, + "type": "object", + "required": [ + "name" + ], + "title": "DataCompletenessTagInput" + }, + "DataModel": { "properties": { "uid": { "type": "string", @@ -133861,27 +135084,84 @@ "name": { "type": "string", "title": "Name", - "description": "The name or the data model ig. E.g. 'SDTM', 'ADAM', ..." + "description": "The name or the data model. E.g. 'SDTM', 'ADAM', ..." }, "description": { "type": "string", "title": "Description" }, - "implemented_data_model": { - "anyOf": [ - { - "$ref": "#/components/schemas/SimpleDataModel" - }, - { - "type": "null" - } - ], - "nullable": true + "implementation_guides": { + "items": { + "$ref": "#/components/schemas/SimpleImplementationGuide" + }, + "type": "array", + "title": "Implementation Guides" }, "version_number": { "type": "string", "title": "Version Number", - "description": "The version or the data model ig. E.g. '1.1.1'" + "description": "The version or the data model ig. E.g. '1.4'" + }, + "start_date": { + "type": "string", + "format": "date-time", + "title": "Start Date", + "description": "Version start date in ISO 8601 format with timezone, e.g. '2020-10-31T16:00:00+02:00' for October 31, 2020 at 4pm in UTC+2 timezone." + }, + "status": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Status", + "nullable": true + } + }, + "type": "object", + "required": [ + "uid", + "name", + "description", + "implementation_guides", + "version_number", + "start_date" + ], + "title": "DataModel" + }, + "DataModelIG": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name", + "description": "The name or the data model ig. E.g. 'SDTM', 'ADAM', ..." + }, + "description": { + "type": "string", + "title": "Description" + }, + "implemented_data_model": { + "anyOf": [ + { + "$ref": "#/components/schemas/SimpleDataModel" + }, + { + "type": "null" + } + ], + "nullable": true + }, + "version_number": { + "type": "string", + "title": "Version Number", + "description": "The version or the data model ig. E.g. '1.1.1'" }, "start_date": { "type": "string", @@ -134529,7 +135809,7 @@ "type": "string", "title": "Catalogue Name" }, - "parent_class": { + "parent_class_name": { "anyOf": [ { "type": "string" @@ -134538,22 +135818,18 @@ "type": "null" } ], - "title": "Parent Class", + "title": "Parent Class Name", "nullable": true }, - "data_models": { - "items": { - "$ref": "#/components/schemas/SimpleDataModelForDatasetClass" - }, - "type": "array", - "title": "Data Models" + "data_model": { + "$ref": "#/components/schemas/SimpleDataModelForDatasetClass" } }, "type": "object", "required": [ "uid", "catalogue_name", - "data_models" + "data_model" ], "title": "DatasetClass" }, @@ -134764,14 +136040,6 @@ "dataset": { "$ref": "#/components/schemas/SimpleDatasetForDatasetVariable" }, - "data_model_ig_names": { - "items": { - "type": "string" - }, - "type": "array", - "title": "Data Model Ig Names", - "description": "Versions of associated data model implementation guides" - }, "implements_variable": { "anyOf": [ { @@ -134813,8 +136081,7 @@ "type": "object", "required": [ "uid", - "dataset", - "data_model_ig_names" + "dataset" ], "title": "DatasetVariable" }, @@ -134872,6 +136139,7 @@ "required": [ "object_type", "description", + "action", "start_date" ], "title": "DetailedSoAHistory" @@ -140613,6 +141881,59 @@ ], "title": "GenericFilteringReturn[StudySelectionObjective]" }, + "GlobalPreferencesPatchInput": { + "properties": { + "language": { + "anyOf": [ + { + "type": "string", + "const": "en" + }, + { + "type": "null" + } + ], + "title": "Language" + }, + "rows_per_page": { + "anyOf": [ + { + "type": "integer", + "maximum": 100.0, + "minimum": 5.0 + }, + { + "type": "null" + } + ], + "title": "Rows Per Page" + }, + "sidebar_visible": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Sidebar Visible" + }, + "sidebar_auto_minimize": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Sidebar Auto Minimize" + } + }, + "type": "object", + "title": "GlobalPreferencesPatchInput" + }, "GraphUser": { "properties": { "id": { @@ -144730,6 +146051,18 @@ }, "OdmCondition": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -144774,18 +146107,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "oid": { "anyOf": [ { @@ -144828,13 +146149,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "oid", "formal_expressions", "translated_texts", @@ -144984,6 +146305,18 @@ }, "OdmForm": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -145028,18 +146361,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "oid": { "anyOf": [ { @@ -145128,13 +146449,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "translated_texts", "aliases", "item_groups", @@ -145480,6 +146801,18 @@ }, "OdmItem": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -145524,18 +146857,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "oid": { "anyOf": [ { @@ -145730,13 +147051,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "oid", "translated_texts", "aliases", @@ -145771,6 +147092,18 @@ }, "OdmItemGroup": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -145815,18 +147148,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "oid": { "anyOf": [ { @@ -145969,13 +147290,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "oid", "translated_texts", "aliases", @@ -147244,6 +148565,18 @@ }, "OdmMethod": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -147288,18 +148621,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "oid": { "anyOf": [ { @@ -147353,13 +148674,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "oid", "method_type", "formal_expressions", @@ -147612,6 +148933,18 @@ }, "OdmStudyEvent": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -147656,18 +148989,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "oid": { "anyOf": [ { @@ -147740,13 +149061,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "forms", "possible_actions" ], @@ -147981,6 +149302,18 @@ }, "OdmVendorAttribute": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -148025,18 +149358,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "compatible_types": { "items": { "type": "string" @@ -148100,13 +149421,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "compatible_types", "possible_actions" ], @@ -148392,6 +149713,18 @@ }, "OdmVendorElement": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -148436,18 +149769,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "compatible_types": { "items": { "type": "string" @@ -148475,13 +149796,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "compatible_types", "vendor_namespace", "vendor_attributes", @@ -148761,6 +150082,18 @@ }, "OdmVendorNamespace": { "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name" + }, + "library_name": { + "type": "string", + "title": "Library Name" + }, "start_date": { "type": "string", "format": "date-time", @@ -148805,18 +150138,6 @@ "type": "string", "title": "Change Description" }, - "uid": { - "type": "string", - "title": "Uid" - }, - "name": { - "type": "string", - "title": "Name" - }, - "library_name": { - "type": "string", - "title": "Library Name" - }, "prefix": { "anyOf": [ { @@ -148863,13 +150184,13 @@ }, "type": "object", "required": [ + "uid", + "name", + "library_name", "start_date", "status", "version", "change_description", - "uid", - "name", - "library_name", "prefix", "url", "vendor_elements", @@ -149138,6 +150459,11 @@ "type": "string", "title": "Uid" }, + "derived_name": { + "type": "string", + "title": "Derived Name", + "default": "" + }, "external_id": { "anyOf": [ { @@ -149315,6 +150641,117 @@ ], "title": "PharmaceuticalProductEditInput" }, + "PreferenceMetadata": { + "properties": { + "type": { + "type": "string", + "title": "Type" + }, + "label": { + "type": "string", + "title": "Label" + }, + "description": { + "type": "string", + "title": "Description" + }, + "min": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Min", + "nullable": true + }, + "max": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Max", + "nullable": true + }, + "default": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "boolean" + }, + { + "type": "string" + } + ], + "title": "Default" + }, + "allowed_values": { + "anyOf": [ + { + "items": { + "type": "string" + }, + "type": "array" + }, + { + "type": "null" + } + ], + "title": "Allowed Values", + "nullable": true + } + }, + "type": "object", + "required": [ + "type", + "label", + "description", + "default" + ], + "title": "PreferenceMetadata" + }, + "PreferencesResponse": { + "properties": { + "preferences": { + "additionalProperties": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "boolean" + }, + { + "type": "string" + } + ] + }, + "type": "object", + "title": "Preferences" + }, + "metadata": { + "additionalProperties": { + "$ref": "#/components/schemas/PreferenceMetadata" + }, + "type": "object", + "title": "Metadata" + } + }, + "type": "object", + "required": [ + "preferences", + "metadata" + ], + "title": "PreferencesResponse" + }, "Project": { "properties": { "uid": { @@ -149457,6 +150894,24 @@ ], "title": "Ref" }, + "ReferencedCodelist": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "submission_value": { + "type": "string", + "title": "Submission Value" + } + }, + "type": "object", + "required": [ + "uid", + "submission_value" + ], + "title": "ReferencedCodelist" + }, "ReferencedItem": { "properties": { "item_uid": { @@ -149498,6 +150953,24 @@ ], "title": "ReferencedItem" }, + "ReferencedTerm": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "submission_value": { + "type": "string", + "title": "Submission Value" + } + }, + "type": "object", + "required": [ + "uid", + "submission_value" + ], + "title": "ReferencedTerm" + }, "RegistryIdentifiersJsonModel": { "properties": { "ct_gov_id": { @@ -151299,7 +152772,7 @@ "ordinal": { "anyOf": [ { - "type": "string" + "type": "integer" }, { "type": "null" @@ -151738,6 +153211,78 @@ ], "title": "SimpleRoleTerm" }, + "SimpleSponsorModelDataModelIG": { + "properties": { + "ordinal": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Ordinal", + "nullable": true + }, + "name": { + "type": "string", + "title": "Name" + } + }, + "type": "object", + "required": [ + "name" + ], + "title": "SimpleSponsorModelDataModelIG" + }, + "SimpleSponsorModelDataset": { + "properties": { + "uid": { + "type": "string", + "title": "Uid" + }, + "ordinal": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Ordinal", + "nullable": true + }, + "key_order": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Key Order", + "nullable": true + }, + "version_number": { + "type": "integer", + "title": "Version Number" + }, + "sponsor_model_name": { + "type": "string", + "title": "Sponsor Model Name" + } + }, + "type": "object", + "required": [ + "uid", + "version_number", + "sponsor_model_name" + ], + "title": "SimpleSponsorModelDataset" + }, "SimpleStudyActivityGroup": { "properties": { "study_activity_group_uid": { @@ -152066,6 +153611,16 @@ }, "SimplifiedActivityItem": { "properties": { + "ct_codelist": { + "anyOf": [ + { + "$ref": "#/components/schemas/CTCodelistItem" + }, + { + "type": "null" + } + ] + }, "ct_terms": { "items": { "$ref": "#/components/schemas/CTTermItem" @@ -152132,6 +153687,22 @@ }, "SponsorModel": { "properties": { + "uid": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Uid" + }, + "name": { + "type": "string", + "title": "Name", + "description": "The name or the sponsor model. E.g. sdtm_sponsormodel_3.2-NN15" + }, "start_date": { "anyOf": [ { @@ -152173,57 +153744,9 @@ "nullable": true }, "version": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Version", - "nullable": true - }, - "change_description": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Change Description", - "nullable": true - }, - "author_username": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Author Username", - "nullable": true - }, - "uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Uid", - "nullable": true - }, - "name": { "type": "string", - "title": "Name", - "description": "The name or the sponsor model. E.g. sdtm_sponsormodel_3.2-NN15" + "title": "Version", + "description": "Version of the sponsor model." }, "extended_implementation_guide": { "anyOf": [ @@ -152236,23 +153759,13 @@ ], "title": "Extended Implementation Guide", "nullable": true - }, - "library_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Library Name", - "nullable": true } }, "type": "object", "required": [ - "name" + "uid", + "name", + "version" ], "title": "SponsorModel" }, @@ -152313,16 +153826,15 @@ "title": "Uid", "nullable": true }, - "library_name": { + "sponsor_model": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/SimpleSponsorModelDataModelIG" }, { "type": "null" } ], - "title": "Library Name", "nullable": true }, "is_basic_std": { @@ -152337,18 +153849,6 @@ "title": "Is Basic Std", "nullable": true }, - "implemented_dataset_class": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Implemented Dataset Class", - "nullable": true - }, "xml_path": { "anyOf": [ { @@ -152862,16 +154362,15 @@ "title": "Uid", "nullable": true }, - "library_name": { + "dataset": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/SimpleSponsorModelDataset" }, { "type": "null" } ], - "title": "Library Name", "nullable": true }, "is_basic_std": { @@ -152886,31 +154385,6 @@ "title": "Is Basic Std", "nullable": true }, - "implemented_parent_dataset_class": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Implemented Parent Dataset Class", - "nullable": true - }, - "implemented_variable_class": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Implemented Variable Class", - "nullable": true, - "souce": "has_sponsor_model_instance.implements_variable_class.is_instance_of.uid" - }, "label": { "anyOf": [ { @@ -152923,18 +154397,6 @@ "title": "Label", "nullable": true }, - "order": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Order", - "nullable": true - }, "variable_type": { "anyOf": [ { @@ -153261,6 +154723,20 @@ ], "title": "Enrich Rule", "nullable": true + }, + "referenced_codelists": { + "items": { + "$ref": "#/components/schemas/ReferencedCodelist" + }, + "type": "array", + "title": "Referenced Codelists" + }, + "referenced_terms": { + "items": { + "$ref": "#/components/schemas/ReferencedTerm" + }, + "type": "array", + "title": "Referenced Terms" } }, "additionalProperties": true, @@ -167871,6 +169347,14 @@ } ], "nullable": true + }, + "data_completeness_tags": { + "items": { + "type": "string" + }, + "type": "array", + "title": "Data Completeness Tags", + "description": "List of data completeness tag names assigned to the study." } }, "type": "object", @@ -169536,6 +171020,19 @@ "description": "Metadata version associated with a given Study version", "nullable": true }, + "original_metadata_version": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Original Metadata Version", + "description": "Metadata version of the first occurrence for the same protocol header version", + "nullable": true + }, "protocol_header_major_version": { "anyOf": [ { @@ -169645,7 +171142,8 @@ "type": "number" }, { - "type": "string" + "type": "string", + "pattern": "^(?!^[-+.]*$)[+-]?0*\\d*\\.?\\d*$" }, { "type": "null" @@ -169702,26 +171200,6 @@ "title": "Uid", "description": "Uid of the Visit" }, - "study_epoch_uid": { - "type": "string", - "title": "Study Epoch Uid" - }, - "visit_type_uid": { - "type": "string", - "title": "Visit Type Uid" - }, - "visit_sublabel_reference": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Visit Sublabel Reference", - "nullable": true - }, "consecutive_visit_group": { "anyOf": [ { @@ -169788,6 +171266,136 @@ "title": "Visit Window Unit Uid", "nullable": true }, + "study_epoch_uid": { + "type": "string", + "title": "Study Epoch Uid" + }, + "study_epoch": { + "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" + }, + "study_day_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Day Number", + "nullable": true + }, + "study_duration_days": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Duration Days", + "nullable": true + }, + "study_week_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Week Number", + "nullable": true + }, + "study_duration_weeks": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Duration Weeks", + "nullable": true + }, + "visit_number": { + "type": "number", + "title": "Visit Number" + }, + "unique_visit_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Unique Visit Number" + }, + "visit_short_name": { + "type": "string", + "title": "Visit Short Name" + }, + "visit_window_unit_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Visit Window Unit Name", + "nullable": true + }, + "visit_class": { + "$ref": "#/components/schemas/VisitClass" + }, + "visit_subclass": { + "anyOf": [ + { + "$ref": "#/components/schemas/VisitSubclass" + }, + { + "type": "null" + } + ], + "nullable": true + }, + "is_global_anchor_visit": { + "type": "boolean", + "title": "Is Global Anchor Visit" + }, + "is_soa_milestone": { + "type": "boolean", + "title": "Is Soa Milestone" + }, + "visit_type": { + "anyOf": [ + { + "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" + }, + { + "type": "null" + } + ] + }, + "visit_sublabel_reference": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Visit Sublabel Reference", + "nullable": true + }, "description": { "anyOf": [ { @@ -169854,52 +171462,6 @@ "description": "Study version number, if specified, otherwise None.", "nullable": true }, - "study_epoch": { - "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" - }, - "epoch_uid": { - "type": "string", - "title": "Epoch Uid", - "description": "The uid of the study epoch" - }, - "visit_type": { - "anyOf": [ - { - "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" - }, - { - "type": "null" - } - ] - }, - "visit_type_name": { - "type": "string", - "title": "Visit Type Name" - }, - "time_reference_uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Time Reference Uid", - "nullable": true - }, - "time_reference_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Time Reference Name", - "nullable": true - }, "time_reference": { "anyOf": [ { @@ -169958,10 +171520,6 @@ ], "nullable": true }, - "visit_contact_mode_uid": { - "type": "string", - "title": "Visit Contact Mode Uid" - }, "visit_contact_mode": { "anyOf": [ { @@ -169972,18 +171530,6 @@ } ] }, - "epoch_allocation_uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Epoch Allocation Uid", - "nullable": true - }, "epoch_allocation": { "anyOf": [ { @@ -170042,30 +171588,6 @@ "title": "Duration Time Unit", "nullable": true }, - "study_day_number": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Day Number", - "nullable": true - }, - "study_duration_days": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Duration Days", - "nullable": true - }, "study_duration_days_label": { "anyOf": [ { @@ -170090,30 +171612,6 @@ "title": "Study Day Label", "nullable": true }, - "study_week_number": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Week Number", - "nullable": true - }, - "study_duration_weeks": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Duration Weeks", - "nullable": true - }, "study_duration_weeks_label": { "anyOf": [ { @@ -170150,10 +171648,6 @@ "title": "Week In Study Label", "nullable": true }, - "visit_number": { - "type": "number", - "title": "Visit Number" - }, "visit_subnumber": { "type": "integer", "title": "Visit Subnumber" @@ -170162,17 +171656,6 @@ "type": "integer", "title": "Order" }, - "unique_visit_number": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Unique Visit Number" - }, "visit_subname": { "type": "string", "title": "Visit Subname" @@ -170181,44 +171664,6 @@ "type": "string", "title": "Visit Name" }, - "visit_short_name": { - "type": "string", - "title": "Visit Short Name" - }, - "visit_window_unit_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Visit Window Unit Name", - "nullable": true - }, - "visit_class": { - "$ref": "#/components/schemas/VisitClass" - }, - "visit_subclass": { - "anyOf": [ - { - "$ref": "#/components/schemas/VisitSubclass" - }, - { - "type": "null" - } - ], - "nullable": true - }, - "is_global_anchor_visit": { - "type": "boolean", - "title": "Is Global Anchor Visit" - }, - "is_soa_milestone": { - "type": "boolean", - "title": "Is Soa Milestone" - }, "status": { "type": "string", "title": "Status", @@ -170281,26 +171726,22 @@ "type": "object", "required": [ "uid", - "study_epoch_uid", - "visit_type_uid", "show_visit", - "study_uid", + "study_epoch_uid", "study_epoch", - "epoch_uid", - "visit_type", - "visit_type_name", - "visit_contact_mode_uid", - "visit_contact_mode", "visit_number", - "visit_subnumber", - "order", "unique_visit_number", - "visit_subname", - "visit_name", "visit_short_name", "visit_class", "is_global_anchor_visit", "is_soa_milestone", + "visit_type", + "study_uid", + "visit_contact_mode", + "visit_subnumber", + "order", + "visit_subname", + "visit_name", "status", "start_date", "possible_actions" @@ -170417,20 +171858,18 @@ "type": "string", "title": "Study Epoch Uid" }, - "visit_type_uid": { - "type": "string", - "title": "Visit Type Uid" + "visit_type": { + "$ref": "#/components/schemas/CTTermUidInput" }, - "time_reference_uid": { + "time_reference": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/CTTermUidInput" }, { "type": "null" } - ], - "title": "Time Reference Uid" + ] }, "time_value": { "anyOf": [ @@ -170546,20 +171985,18 @@ ], "title": "End Rule" }, - "visit_contact_mode_uid": { - "type": "string", - "title": "Visit Contact Mode Uid" + "visit_contact_mode": { + "$ref": "#/components/schemas/CTTermUidInput" }, - "epoch_allocation_uid": { + "epoch_allocation": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/CTTermUidInput" }, { "type": "null" } - ], - "title": "Epoch Allocation Uid" + ] }, "visit_class": { "$ref": "#/components/schemas/VisitClass" @@ -170645,9 +172082,9 @@ "type": "object", "required": [ "study_epoch_uid", - "visit_type_uid", + "visit_type", "show_visit", - "visit_contact_mode_uid", + "visit_contact_mode", "visit_class", "is_global_anchor_visit" ], @@ -170664,20 +172101,18 @@ "type": "string", "title": "Study Epoch Uid" }, - "visit_type_uid": { - "type": "string", - "title": "Visit Type Uid" + "visit_type": { + "$ref": "#/components/schemas/CTTermUidInput" }, - "time_reference_uid": { + "time_reference": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/CTTermUidInput" }, { "type": "null" } - ], - "title": "Time Reference Uid" + ] }, "time_value": { "anyOf": [ @@ -170793,20 +172228,18 @@ ], "title": "End Rule" }, - "visit_contact_mode_uid": { - "type": "string", - "title": "Visit Contact Mode Uid" + "visit_contact_mode": { + "$ref": "#/components/schemas/CTTermUidInput" }, - "epoch_allocation_uid": { + "epoch_allocation": { "anyOf": [ { - "type": "string" + "$ref": "#/components/schemas/CTTermUidInput" }, { "type": "null" } - ], - "title": "Epoch Allocation Uid" + ] }, "visit_class": { "anyOf": [ @@ -170900,9 +172333,9 @@ "required": [ "uid", "study_epoch_uid", - "visit_type_uid", + "visit_type", "show_visit", - "visit_contact_mode_uid", + "visit_contact_mode", "is_global_anchor_visit" ], "title": "StudyVisitEditInput" @@ -171148,22 +172581,154 @@ ], "title": "StudyVisitListingModel" }, - "StudyVisitVersion": { + "StudyVisitLite": { "properties": { "uid": { "type": "string", "title": "Uid", "description": "Uid of the Visit" }, + "consecutive_visit_group": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Consecutive Visit Group", + "nullable": true + }, + "consecutive_visit_group_uid": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Consecutive Visit Group Uid", + "nullable": true + }, + "show_visit": { + "type": "boolean", + "title": "Show Visit" + }, + "min_visit_window_value": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Min Visit Window Value", + "default": -9999, + "nullable": true + }, + "max_visit_window_value": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Max Visit Window Value", + "default": 9999, + "nullable": true + }, + "visit_window_unit_uid": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Visit Window Unit Uid", + "nullable": true + }, "study_epoch_uid": { "type": "string", "title": "Study Epoch Uid" }, - "visit_type_uid": { + "study_epoch": { + "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" + }, + "study_day_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Day Number", + "nullable": true + }, + "study_duration_days": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Duration Days", + "nullable": true + }, + "study_week_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Week Number", + "nullable": true + }, + "study_duration_weeks": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Duration Weeks", + "nullable": true + }, + "visit_number": { + "type": "number", + "title": "Visit Number" + }, + "unique_visit_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Unique Visit Number" + }, + "visit_short_name": { "type": "string", - "title": "Visit Type Uid" + "title": "Visit Short Name" }, - "visit_sublabel_reference": { + "visit_window_unit_name": { "anyOf": [ { "type": "string" @@ -171172,9 +172737,65 @@ "type": "null" } ], - "title": "Visit Sublabel Reference", + "title": "Visit Window Unit Name", "nullable": true }, + "visit_class": { + "$ref": "#/components/schemas/VisitClass" + }, + "visit_subclass": { + "anyOf": [ + { + "$ref": "#/components/schemas/VisitSubclass" + }, + { + "type": "null" + } + ], + "nullable": true + }, + "is_global_anchor_visit": { + "type": "boolean", + "title": "Is Global Anchor Visit" + }, + "is_soa_milestone": { + "type": "boolean", + "title": "Is Soa Milestone" + }, + "visit_type": { + "anyOf": [ + { + "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" + }, + { + "type": "null" + } + ] + } + }, + "type": "object", + "required": [ + "uid", + "show_visit", + "study_epoch_uid", + "study_epoch", + "visit_number", + "unique_visit_number", + "visit_short_name", + "visit_class", + "is_global_anchor_visit", + "is_soa_milestone", + "visit_type" + ], + "title": "StudyVisitLite" + }, + "StudyVisitVersion": { + "properties": { + "uid": { + "type": "string", + "title": "Uid", + "description": "Uid of the Visit" + }, "consecutive_visit_group": { "anyOf": [ { @@ -171241,6 +172862,136 @@ "title": "Visit Window Unit Uid", "nullable": true }, + "study_epoch_uid": { + "type": "string", + "title": "Study Epoch Uid" + }, + "study_epoch": { + "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" + }, + "study_day_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Day Number", + "nullable": true + }, + "study_duration_days": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Duration Days", + "nullable": true + }, + "study_week_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Week Number", + "nullable": true + }, + "study_duration_weeks": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Study Duration Weeks", + "nullable": true + }, + "visit_number": { + "type": "number", + "title": "Visit Number" + }, + "unique_visit_number": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "null" + } + ], + "title": "Unique Visit Number" + }, + "visit_short_name": { + "type": "string", + "title": "Visit Short Name" + }, + "visit_window_unit_name": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Visit Window Unit Name", + "nullable": true + }, + "visit_class": { + "$ref": "#/components/schemas/VisitClass" + }, + "visit_subclass": { + "anyOf": [ + { + "$ref": "#/components/schemas/VisitSubclass" + }, + { + "type": "null" + } + ], + "nullable": true + }, + "is_global_anchor_visit": { + "type": "boolean", + "title": "Is Global Anchor Visit" + }, + "is_soa_milestone": { + "type": "boolean", + "title": "Is Soa Milestone" + }, + "visit_type": { + "anyOf": [ + { + "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" + }, + { + "type": "null" + } + ] + }, + "visit_sublabel_reference": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Visit Sublabel Reference", + "nullable": true + }, "description": { "anyOf": [ { @@ -171307,52 +173058,6 @@ "description": "Study version number, if specified, otherwise None.", "nullable": true }, - "study_epoch": { - "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" - }, - "epoch_uid": { - "type": "string", - "title": "Epoch Uid", - "description": "The uid of the study epoch" - }, - "visit_type": { - "anyOf": [ - { - "$ref": "#/components/schemas/SimpleCTTermNameWithConflictFlag" - }, - { - "type": "null" - } - ] - }, - "visit_type_name": { - "type": "string", - "title": "Visit Type Name" - }, - "time_reference_uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Time Reference Uid", - "nullable": true - }, - "time_reference_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Time Reference Name", - "nullable": true - }, "time_reference": { "anyOf": [ { @@ -171411,10 +173116,6 @@ ], "nullable": true }, - "visit_contact_mode_uid": { - "type": "string", - "title": "Visit Contact Mode Uid" - }, "visit_contact_mode": { "anyOf": [ { @@ -171425,18 +173126,6 @@ } ] }, - "epoch_allocation_uid": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Epoch Allocation Uid", - "nullable": true - }, "epoch_allocation": { "anyOf": [ { @@ -171495,30 +173184,6 @@ "title": "Duration Time Unit", "nullable": true }, - "study_day_number": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Day Number", - "nullable": true - }, - "study_duration_days": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Duration Days", - "nullable": true - }, "study_duration_days_label": { "anyOf": [ { @@ -171543,30 +173208,6 @@ "title": "Study Day Label", "nullable": true }, - "study_week_number": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Week Number", - "nullable": true - }, - "study_duration_weeks": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Study Duration Weeks", - "nullable": true - }, "study_duration_weeks_label": { "anyOf": [ { @@ -171603,10 +173244,6 @@ "title": "Week In Study Label", "nullable": true }, - "visit_number": { - "type": "number", - "title": "Visit Number" - }, "visit_subnumber": { "type": "integer", "title": "Visit Subnumber" @@ -171622,17 +173259,6 @@ ], "title": "Order" }, - "unique_visit_number": { - "anyOf": [ - { - "type": "integer" - }, - { - "type": "null" - } - ], - "title": "Unique Visit Number" - }, "visit_subname": { "type": "string", "title": "Visit Subname" @@ -171641,44 +173267,6 @@ "type": "string", "title": "Visit Name" }, - "visit_short_name": { - "type": "string", - "title": "Visit Short Name" - }, - "visit_window_unit_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Visit Window Unit Name", - "nullable": true - }, - "visit_class": { - "$ref": "#/components/schemas/VisitClass" - }, - "visit_subclass": { - "anyOf": [ - { - "$ref": "#/components/schemas/VisitSubclass" - }, - { - "type": "null" - } - ], - "nullable": true - }, - "is_global_anchor_visit": { - "type": "boolean", - "title": "Is Global Anchor Visit" - }, - "is_soa_milestone": { - "type": "boolean", - "title": "Is Soa Milestone" - }, "status": { "type": "string", "title": "Status", @@ -171748,25 +173336,21 @@ "type": "object", "required": [ "uid", - "study_epoch_uid", - "visit_type_uid", "show_visit", - "study_uid", + "study_epoch_uid", "study_epoch", - "epoch_uid", - "visit_type", - "visit_type_name", - "visit_contact_mode_uid", - "visit_contact_mode", "visit_number", - "visit_subnumber", "unique_visit_number", - "visit_subname", - "visit_name", "visit_short_name", "visit_class", "is_global_anchor_visit", "is_soa_milestone", + "visit_type", + "study_uid", + "visit_contact_mode", + "visit_subnumber", + "visit_subname", + "visit_name", "status", "start_date", "possible_actions", @@ -172164,6 +173748,7 @@ "title": "Uid" }, "value_node": { + "additionalProperties": true, "type": "object", "title": "Value Node" }, @@ -174589,6 +176174,99 @@ "type": "object", "title": "UserInfoPatchInput" }, + "UserPreferencesPatchInput": { + "properties": { + "language": { + "anyOf": [ + { + "type": "string", + "const": "en" + }, + { + "type": "null" + } + ], + "title": "Language" + }, + "rows_per_page": { + "anyOf": [ + { + "type": "integer", + "maximum": 100.0, + "minimum": 5.0 + }, + { + "type": "null" + } + ], + "title": "Rows Per Page" + }, + "sidebar_visible": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Sidebar Visible" + }, + "sidebar_auto_minimize": { + "anyOf": [ + { + "type": "boolean" + }, + { + "type": "null" + } + ], + "title": "Sidebar Auto Minimize" + } + }, + "type": "object", + "title": "UserPreferencesPatchInput" + }, + "UserPreferencesResponse": { + "properties": { + "preferences": { + "additionalProperties": { + "anyOf": [ + { + "type": "integer" + }, + { + "type": "boolean" + }, + { + "type": "string" + } + ] + }, + "type": "object", + "title": "Preferences" + }, + "overrides": { + "additionalProperties": true, + "type": "object", + "title": "Overrides" + }, + "metadata": { + "additionalProperties": { + "$ref": "#/components/schemas/PreferenceMetadata" + }, + "type": "object", + "title": "Metadata" + } + }, + "type": "object", + "required": [ + "preferences", + "overrides", + "metadata" + ], + "title": "UserPreferencesResponse" + }, "ValidCodelistMappingInput": { "properties": { "valid_codelist_uids": { @@ -174861,38 +176539,23 @@ "dataset_class": { "$ref": "#/components/schemas/SimpleDatasetClassForVariableClass" }, - "dataset_variable_name": { - "anyOf": [ - { - "type": "string" - }, - { - "type": "null" - } - ], - "title": "Dataset Variable Name", - "nullable": true - }, "catalogue_name": { "type": "string", "title": "Catalogue Name" }, - "data_model_names": { - "items": { - "type": "string" - }, - "type": "array", - "title": "Data Model Names" - }, - "has_mapping_target": { + "has_mapping_targets": { "anyOf": [ { - "$ref": "#/components/schemas/SimpleMappingTarget" + "items": { + "$ref": "#/components/schemas/SimpleMappingTarget" + }, + "type": "array" }, { "type": "null" } ], + "title": "Has Mapping Targets", "nullable": true }, "referenced_codelists": { @@ -174910,15 +176573,19 @@ "title": "Referenced Codelists", "nullable": true }, - "qualifies_variable": { + "qualifies_variables": { "anyOf": [ { - "$ref": "#/components/schemas/SimpleVariableClass" + "items": { + "$ref": "#/components/schemas/SimpleVariableClass" + }, + "type": "array" }, { "type": "null" } ], + "title": "Qualifies Variables", "nullable": true } }, @@ -174928,8 +176595,7 @@ "label", "title", "dataset_class", - "catalogue_name", - "data_model_names" + "catalogue_name" ], "title": "VariableClass" }, diff --git a/clinical-mdr-api/pyproject.toml b/clinical-mdr-api/pyproject.toml index 18fe2406..04de5d23 100644 --- a/clinical-mdr-api/pyproject.toml +++ b/clinical-mdr-api/pyproject.toml @@ -1,7 +1,7 @@ [project] name = 'clinical-mdr-api' readme = 'README.md' -requires-python = '>=3.13' +requires-python = '>=3.14' license = 'TBD' authors = [ {name = 'OpenStudyBuilder', email = 'OpenStudyBuilder@gmail.com'} @@ -20,6 +20,7 @@ addopts = "--cov-config=.coveragerc" [tool.isort] profile = 'black' src_paths = ['clinical_mdr_api', 'consumer_api', 'common', 'sblint', 'extensions'] +known_third_party = ['neomodel'] [tool.pylint.'MASTER'] extension-pkg-allow-list = 'pydantic, lxml' diff --git a/clinical-mdr-api/sbom.md b/clinical-mdr-api/sbom.md index f3a694c1..f1abf6e2 100644 --- a/clinical-mdr-api/sbom.md +++ b/clinical-mdr-api/sbom.md @@ -1,97 +1,96 @@ ## Installed packages -| Package | Version | License | -|--------------------------|-------------|--------------------------------------------------------------| -| annotated-doc | 0.0.4 | [MIT](#annotated-doc) | -| annotated-types | 0.6.0 | [see below](#annotated-types) | -| anyio | 4.12.1 | [MIT](#anyio) | -| asyncache | 0.3.1 | [MIT](#asyncache) | -| attrs | 25.4.0 | [MIT](#attrs) | -| Authlib | 1.6.8 | [BSD-3-Clause](#authlib) | -| azure-core | 1.38.2 | [MIT License](#azure-core) | -| azure-identity | 1.25.2 | [MIT](#azure-identity) | -| beautifulsoup4 | 4.12.3 | [MIT License](#beautifulsoup4) | -| brotli | 1.2.0 | [MIT](#brotli) | -| cachetools | 5.5.2 | [MIT](#cachetools) | -| certifi | 2026.1.4 | [MPL-2.0](#certifi) | -| cffi | 2.0.0 | [MIT](#cffi) | -| charset-normalizer | 3.4.4 | [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) | -| cssselect2 | 0.9.0 | [see below](#cssselect2) | -| deepdiff | 8.6.1 | [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.resources | 8.2.0 | BSD license (missing) | -| fonttools | 4.61.1 | [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) | -| h11 | 0.16.0 | [MIT](#h11) | -| httpcore | 1.0.9 | [BSD-3-Clause](#httpcore) | -| httpx | 0.27.2 | [BSD-3-Clause](#httpx) | -| hypothesis | 6.115.6 | [MPL-2.0](#hypothesis) | -| idna | 3.11 | [BSD-3-Clause](#idna) | -| Jinja2 | 3.1.6 | [see below](#jinja2) | -| lxml | 5.3.2 | [BSD-3-Clause](#lxml) | -| MarkupSafe | 3.0.3 | [BSD-3-Clause](#markupsafe) | -| msal | 1.35.0 | [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) | -| nh3 | 0.2.22 | [MIT](#nh3) | -| numpy | 2.4.2 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | -| opencensus | 0.11.4 | [Apache-2.0](#opencensus) | -| opencensus-context | 0.1.3 | [Apache-2.0](#opencensus-context) | -| opencensus-ext-azure | 1.1.15 | [Apache-2.0](#opencensus-ext-azure) | -| openpyxl | 3.1.5 | [MIT](#openpyxl) | -| orderly-set | 5.5.0 | [see below](#orderly-set) | -| pandas | 3.0.1 | [see below](#pandas) | -| pillow | 12.1.1 | [MIT-CMU](#pillow) | -| proto-plus | 1.27.1 | [Apache 2.0](#proto-plus) | -| protobuf | 6.33.5 | [3-Clause BSD License](#protobuf) | -| psutil | 7.2.2 | [BSD-3-Clause](#psutil) | -| pyasn1 | 0.6.2 | [BSD-2-Clause](#pyasn1) | -| pyasn1_modules | 0.4.2 | [BSD](#pyasn1_modules) | -| pycparser | 3.0 | [BSD-3-Clause](#pycparser) | -| pydantic | 2.10.6 | [MIT](#pydantic) | -| pydantic_core | 2.27.2 | [MIT](#pydantic_core) | -| pydantic-settings | 2.7.1 | [MIT](#pydantic-settings) | -| pydyf | 0.12.1 | [see below](#pydyf) | -| PyJWT | 2.11.0 | [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) | -| python-dotenv | 1.2.1 | [BSD-3-Clause](#python-dotenv) | -| python-multipart | 0.0.22 | [Apache-2.0](#python-multipart) | -| pytz | 2025.2 | [MIT](#pytz) | -| PyYAML | 6.0.3 | [MIT](#pyyaml) | -| requests | 2.32.5 | [Apache-2.0](#requests) | -| rsa | 4.9.1 | [Apache-2.0](#rsa) | -| six | 1.17.0 | [MIT](#six) | -| sniffio | 1.3.1 | [MIT OR Apache-2.0](#sniffio) | -| sortedcontainers | 2.4.0 | [Apache 2.0](#sortedcontainers) | -| soupsieve | 2.8.3 | [MIT](#soupsieve) | -| starlette | 0.52.1 | [BSD-3-Clause](#starlette) | -| starlette-context | 0.4.0 | [MIT](#starlette-context) | -| stringcase | 1.2.0 | [MIT](#stringcase) | -| tinycss2 | 1.5.1 | [see below](#tinycss2) | -| tinyhtml5 | 2.0.0 | [see below](#tinyhtml5) | -| typing_extensions | 4.15.0 | [PSF-2.0](#typing_extensions) | -| typing-inspection | 0.4.2 | [MIT](#typing-inspection) | -| urllib3 | 2.6.3 | [MIT](#urllib3) | -| usdm | 0.65.0 | [see below](#usdm) | -| uvicorn | 0.32.1 | [BSD-3-Clause](#uvicorn) | -| weasyprint | 68.1 | [see below](#weasyprint) | -| webencodings | 0.5.1 | [BSD](#webencodings) | -| xsdata | 24.11 | [MIT](#xsdata) | -| yattag | 1.16.1 | [see below](#yattag) | -| zopfli | 0.4.1 | [Apache-2.0](#zopfli) | +| Package | Version | License | +|--------------------------|--------------|--------------------------------------------------------------| +| annotated-doc | 0.0.4 | [MIT](#annotated-doc) | +| annotated-types | 0.6.0 | [see below](#annotated-types) | +| anyio | 4.12.1 | [MIT](#anyio) | +| asyncache | 0.3.1 | [MIT](#asyncache) | +| attrs | 25.4.0 | [MIT](#attrs) | +| Authlib | 1.6.9 | [BSD-3-Clause](#authlib) | +| azure-core | 1.38.3 | [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 | 3.4.6 | [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) | +| cssselect2 | 0.9.0 | [see below](#cssselect2) | +| deepdiff | 8.6.1 | [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.resources | 8.2.0 | [BSD license](#fhirresources) | +| fonttools | 4.62.1 | [MIT](#fonttools) | +| google-api-core | 2.30.0 | [Apache 2.0](#google-api-core) | +| google-auth | 2.49.1 | [Apache 2.0](#google-auth) | +| googleapis-common-protos | 1.73.0 | [Apache 2.0](#googleapis-common-protos) | +| h11 | 0.16.0 | [MIT](#h11) | +| httpcore | 1.0.9 | [BSD-3-Clause](#httpcore) | +| httpx | 0.27.2 | [BSD-3-Clause](#httpx) | +| hypothesis | 6.115.6 | [MPL-2.0](#hypothesis) | +| idna | 3.11 | [BSD-3-Clause](#idna) | +| Jinja2 | 3.1.6 | [see below](#jinja2) | +| lxml | 5.3.2 | [BSD-3-Clause](#lxml) | +| MarkupSafe | 3.0.3 | [BSD-3-Clause](#markupsafe) | +| msal | 1.35.1 | [MIT](#msal) | +| msal-extensions | 1.3.1 | [MIT License](#msal-extensions) | +| neo4j | 6.1.0 | [Apache-2.0 AND Python-2.0](#neo4j) | +| neomodel | 6.1.0 | [MIT](#neomodel) | +| nh3 | 0.2.22 | [MIT](#nh3) | +| numpy | 2.4.3 | [BSD-3-Clause AND 0BSD AND MIT AND Zlib AND CC0-1.0](#numpy) | +| opencensus | 0.11.4 | [Apache-2.0](#opencensus) | +| opencensus-context | 0.1.3 | [Apache-2.0](#opencensus-context) | +| opencensus-ext-azure | 1.1.15 | [Apache-2.0](#opencensus-ext-azure) | +| openpyxl | 3.1.5 | [MIT](#openpyxl) | +| orderly-set | 5.5.0 | [see below](#orderly-set) | +| pandas | 3.0.1 | [see below](#pandas) | +| pillow | 12.1.1 | [MIT-CMU](#pillow) | +| proto-plus | 1.27.1 | [Apache 2.0](#proto-plus) | +| protobuf | 6.33.5 | [3-Clause BSD License](#protobuf) | +| psutil | 7.2.2 | [BSD-3-Clause](#psutil) | +| pyasn1 | 0.6.2 | [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 | 2.12.1 | [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) | +| python-dotenv | 1.2.2 | [BSD-3-Clause](#python-dotenv) | +| 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) | +| six | 1.17.0 | [MIT](#six) | +| sniffio | 1.3.1 | [MIT OR Apache-2.0](#sniffio) | +| sortedcontainers | 2.4.0 | [Apache 2.0](#sortedcontainers) | +| soupsieve | 2.8.3 | [MIT](#soupsieve) | +| starlette | 0.52.1 | [BSD-3-Clause](#starlette) | +| starlette-context | 0.4.0 | [MIT](#starlette-context) | +| stringcase | 1.2.0 | [MIT](#stringcase) | +| tinycss2 | 1.5.1 | [see below](#tinycss2) | +| tinyhtml5 | 2.1.0 | [see below](#tinyhtml5) | +| typing_extensions | 4.15.0 | [PSF-2.0](#typing_extensions) | +| typing-inspection | 0.4.2 | [MIT](#typing-inspection) | +| urllib3 | 2.6.3 | [MIT](#urllib3) | +| usdm | 0.65.0 | [see below](#usdm) | +| uvicorn | 0.32.1 | [BSD-3-Clause](#uvicorn) | +| weasyprint | 68.1 | [see below](#weasyprint) | +| webencodings | 0.5.1 | [BSD](#webencodings) | +| xsdata | 26.2 | [MIT](#xsdata) | +| yattag | 1.16.1 | [see below](#yattag) | +| zopfli | 0.4.1 | [Apache-2.0](#zopfli) | ## Third-party package licenses @@ -1304,6 +1303,39 @@ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +--- +### fhir.resources + + BSD License + + Copyright (c) 2019, Md Nazrul Islam + All rights reserved. + + Redistribution and use in source and binary forms, with or without modification, + are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, this + list of conditions and the following disclaimer in the documentation and/or + other materials provided with the distribution. + + * Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from this + software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED + WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. + IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, + INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY + OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE + OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED + OF THE POSSIBILITY OF SUCH DAMAGE. + --- ### fonttools @@ -9298,23 +9330,6 @@ 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. - --- ### six @@ -10882,7 +10897,7 @@ that what they have is not the original version, so that the original author's reputation will not be affected by problems that might be introduced by others. - + Finally, software patents pose a constant threat to the existence of any free program. We wish to make sure that a company cannot effectively restrict the users of a free program by obtaining a @@ -10938,7 +10953,7 @@ "work based on the library" and a "work that uses the library". The former contains code derived from the library, whereas the latter must be combined with the library in order to run. - + GNU LESSER GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION @@ -10985,7 +11000,7 @@ You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. - + 2. You may modify your copy or copies of the Library or any portion of it, thus forming a work based on the Library, and copy and distribute such modifications or work under the terms of Section 1 @@ -11043,7 +11058,7 @@ ordinary GNU General Public License has appeared, then you can specify that version instead if you wish.) Do not make any other change in these notices. - + Once this change is made in a given copy, it is irreversible for that copy, so the ordinary GNU General Public License applies to all subsequent copies and derivative works made from that copy. @@ -11094,7 +11109,7 @@ distribute the object code for the work under the terms of Section 6. Any executables containing that work also fall under Section 6, whether or not they are linked directly with the Library itself. - + 6. As an exception to the Sections above, you may also combine or link a "work that uses the Library" with the Library to produce a work containing portions of the Library, and distribute that work @@ -11156,7 +11171,7 @@ accompany the operating system. Such a contradiction means you cannot use both them and the Library together in an executable that you distribute. - + 7. You may place library facilities that are a work based on the Library side-by-side in a single library together with other library facilities not covered by this License, and distribute such a combined @@ -11197,7 +11212,7 @@ restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties with this License. - + 11. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or @@ -11249,7 +11264,7 @@ the Free Software Foundation. If the Library does not specify a license version number, you may choose any version ever published by the Free Software Foundation. - + 14. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these, write to the author to ask for permission. For software which is @@ -11283,7 +11298,7 @@ DAMAGES. END OF TERMS AND CONDITIONS - + How to Apply These Terms to Your New Libraries If you develop a new library, and you want it to be of the greatest @@ -11431,7 +11446,7 @@ that what they have is not the original version, so that the original author's reputation will not be affected by problems that might be introduced by others. - + Finally, software patents pose a constant threat to the existence of any free program. We wish to make sure that a company cannot effectively restrict the users of a free program by obtaining a @@ -11487,7 +11502,7 @@ "work based on the library" and a "work that uses the library". The former contains code derived from the library, whereas the latter must be combined with the library in order to run. - + GNU LESSER GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION @@ -11534,7 +11549,7 @@ You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. - + 2. You may modify your copy or copies of the Library or any portion of it, thus forming a work based on the Library, and copy and distribute such modifications or work under the terms of Section 1 @@ -11592,7 +11607,7 @@ ordinary GNU General Public License has appeared, then you can specify that version instead if you wish.) Do not make any other change in these notices. - + Once this change is made in a given copy, it is irreversible for that copy, so the ordinary GNU General Public License applies to all subsequent copies and derivative works made from that copy. @@ -11643,7 +11658,7 @@ distribute the object code for the work under the terms of Section 6. Any executables containing that work also fall under Section 6, whether or not they are linked directly with the Library itself. - + 6. As an exception to the Sections above, you may also combine or link a "work that uses the Library" with the Library to produce a work containing portions of the Library, and distribute that work @@ -11705,7 +11720,7 @@ accompany the operating system. Such a contradiction means you cannot use both them and the Library together in an executable that you distribute. - + 7. You may place library facilities that are a work based on the Library side-by-side in a single library together with other library facilities not covered by this License, and distribute such a combined @@ -11746,7 +11761,7 @@ restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties with this License. - + 11. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or @@ -11798,7 +11813,7 @@ the Free Software Foundation. If the Library does not specify a license version number, you may choose any version ever published by the Free Software Foundation. - + 14. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these, write to the author to ask for permission. For software which is @@ -11832,7 +11847,7 @@ DAMAGES. END OF TERMS AND CONDITIONS - + How to Apply These Terms to Your New Libraries If you develop a new library, and you want it to be of the greatest diff --git a/clinical-mdr-api/templates/odm/crf.html b/clinical-mdr-api/templates/odm/crf.html index 973ed4f1..5959c1e3 100644 --- a/clinical-mdr-api/templates/odm/crf.html +++ b/clinical-mdr-api/templates/odm/crf.html @@ -328,10 +328,18 @@ background-color: #D1D5DB; } + .bg-red-50 { + background-color: #FEF2F2; + } + .bg-red-100 { background-color: #FEE2E2; } + .bg-red-900 { + background-color: #7F1D1D; + } + .bg-cyan-300 { background-color: #67E8F9; } @@ -519,7 +527,7 @@
- COMPLETION INSTRUCTION + COMPLETION INSTRUCTIONS
{% for completion_instruction in completion_instructions %} @@ -545,7 +553,7 @@
- DESIGN NOTE + DESIGN NOTES
{% for design_note in design_notes %} @@ -565,24 +573,17 @@ {% macro render_units(units, item_uid, item_group_uid, form_uid) %} {% if units and units|length > 0 %} - - - - - -
Units: - {% for unit in units %} -
- - -
- - {% endfor %} -
+ {% for unit in units %} +
+ + + +
+ {% endfor %} {% endif %} {% endmacro %} @@ -616,7 +617,7 @@

Case Report Form (CRF)

- {% macro render_item(item_in, item_group_uid, form_uid, group_domains) %} + {% macro render_item(item_in, item_group_uid, form_uid, group_domains, form_integrations) %} {% set item = data.odm_items | selectattr('uid', '==', item_in.uid) | first | default('') %} {% if item_in.vendor %} {% set indent_attr = item_in.vendor.attributes | selectattr('name', '==', 'indentLevel') | first | default('') @@ -662,28 +663,39 @@

{% set seen = [] %} {% for item_activity_instance in item.activity_instances %} {% if item_activity_instance.activity_instance_uid not in seen %} {% set _ = seen.append(item_activity_instance.activity_instance_uid) %} -