Release/6.0.0

[ddelpiano]

No description provided.

[Copilot]

Pull Request Overview

This PR implements version 6.0.0, a major release that introduces a redesigned dynamic relationship system for connectivity statements. The update splits the monolithic ConnectivityStatementTriple model into three specialized models (ConnectivityStatementTriple, ConnectivityStatementText, and ConnectivityStatementAnatomicalEntity) and adds support for custom ingestion code execution during the neurondm processing workflow.

Key Changes:

• Refactored dynamic relationships into type-specific models with dedicated serializers and API endpoints
• Implemented a three-step ingestion workflow with custom code execution support
• Added expert consultant functionality to track ORCID references separately from provenances
• Enhanced URI validation for provenances and expert consultants

Reviewed Changes

Copilot reviewed 68 out of 69 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
deployment/codefresh-dev.yaml	Updated CI/CD pipeline with new build stages, image cache support, and composer-neurondm task container
applications/composer/tasks/notify/notify.py	Extended notification system to support both export and ingestion workflows
applications/composer/tasks/neurondm/process_neurondm_standalone.py	New standalone script for neurondm processing without Django dependencies
applications/composer/tasks/neurondm/Dockerfile	New Dockerfile for lightweight neurondm task container
applications/composer/scripts/setup_cleanup_cron.sh	New script for setting up automated cleanup of old ingestion files
applications/composer/openapi/openapi.yaml	Updated API schema with new endpoints for text/anatomical relationships and expert consultants
applications/composer/nginx.conf	Fixed duplicate X-Forwarded-Proto header configuration
applications/composer/frontend/src/types/relationshipTypes.ts	New TypeScript types for relationship enums
applications/composer/frontend/src/services/StatementService.ts	Added service methods for text and anatomical entity relationships
applications/composer/frontend/src/services/JsonSchema.ts	Added expert consultants schema retrieval
applications/composer/frontend/src/services/ExpertConsultantService.tsx	New service for expert consultant CRUD operations
applications/composer/frontend/src/helpers/uriValidation.ts	Extracted URI validation logic into reusable utility functions
applications/composer/frontend/src/components/Widgets/CustomTextField.tsx	Added Enter key prevention for single-line text fields
applications/composer/frontend/src/components/Widgets/CustomEntitiesDropdown.tsx	Enhanced with configurable label positioning and styling
applications/composer/frontend/src/components/Forms/StatementForm.tsx	Major refactor to support new relationship types with dedicated widget configs
applications/composer/frontend/src/components/Forms/ProvenanceForm.tsx	Refactored to use shared URI validation utilities
applications/composer/frontend/src/components/Forms/ExpertConsultantForm.tsx	New form component for managing expert consultants
applications/composer/frontend/src/components/DistillationTab/DistillationTab.tsx	Added expert consultants form to distillation tab
applications/composer/frontend/package.json	Version bump to 6.0.0
applications/composer/backend/version.py	Version bump to 6.0.0
applications/composer/backend/tests/test_relationships.py	New test suite for relationship model validation
applications/composer/backend/tests/test_ingest_statements.py	Updated tests for new ingestion workflow and custom relationships
applications/composer/backend/test_serialization_standalone.py	New standalone test for NeuroDM serialization/deserialization
applications/composer/backend/requirements.txt	Updated django-filter version and removed django-silk
applications/composer/backend/composer/views.py	Added ingestion workflow trigger endpoint
applications/composer/backend/composer/urls.py	Added ingest-statements URL route
applications/composer/backend/composer/templates/admin/*	New admin templates for ingestion workflow and log downloads
applications/composer/backend/composer/services/workflows/*	New ingestion workflow modules with three-step processing
applications/composer/backend/composer/services/export/*	Updated export logic to handle new relationship models
applications/composer/backend/composer/services/errors_service.py	Updated import to use pure_enums
applications/composer/backend/composer/services/dynamic_schema_service.py	Updated to handle new relationship type names
applications/composer/backend/composer/services/cs_ingestion/*	Major refactor supporting custom code execution and split models
applications/composer/backend/composer/pure_enums.py	New Django-independent enum definitions
applications/composer/backend/composer/models.py	Split relationship models and added expert consultant model
applications/composer/backend/composer/migrations/*	New migrations for relationship refactoring and expert consultants
applications/composer/backend/composer/management/commands/*	New management commands for ingestion steps and cleanup
applications/composer/backend/composer/enums.py	Refactored to use pure_enums as source of truth
applications/composer/backend/composer/constants.py	New constants module for ingestion file paths
applications/composer/backend/composer/api/*	Updated API views and serializers for new relationship models
applications/composer/backend/composer/admin.py	Enhanced admin with relationship inline forms and custom code editor
applications/composer/backend/backend/urls.py	Removed django-silk URL configuration
applications/composer/backend/backend/settings.py	Removed django-silk and updated timezone

Comments suppressed due to low confidence (1)

applications/composer/backend/composer/services/workflows/export.py:12

• The scheme parameter is defined but never used in the function. This parameter should either be removed or utilized in constructing the file_url variable.

def run_export_workflow(user: User, scheme: str = "https") -> None:

---

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[Copilot]

[nitpick] The docstring states 'Django-independent' but this is a general Python enum. Consider clarifying that this enum can be used both with and without Django, or that it serves as the base for Django's TextChoices wrapper.

[Copilot]

[nitpick] The max_length of 20 may be insufficient if future relationship type values exceed this length. Consider increasing to 50 or making it a configurable constant to avoid future migrations.

Suggested change

	type = models.CharField(max_length=20, choices=RelationshipType.choices)
	type = models.CharField(max_length=50, choices=RelationshipType.choices)

[Copilot]

The anatomical_entities.all() query is executed during serialization without prefetch_related. While the ViewSet includes prefetch_related('anatomical_entities'), ensure this is consistently applied across all code paths that serialize this model to avoid N+1 queries.

Suggested change

	representation['anatomical_entities'] = AnatomicalEntitySerializer(
	instance.anatomical_entities.all(),
	# Use prefetched data if available to avoid N+1 queries
	anatomical_entities = getattr(instance, '_prefetched_objects_cache', {}).get('anatomical_entities')
	if anatomical_entities is None:
	anatomical_entities = instance.anatomical_entities.all()
	representation['anatomical_entities'] = AnatomicalEntitySerializer(
	anatomical_entities,