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March 23, 2026 15:04
…egistration/Run FKs - Add VersionAlias enum (production, development) - Add WorkflowVersion table (version, definition_uri per workflow) - Add WorkflowVersionAlias table (named pointer to a version) - Re-point WorkflowRegistration FK from workflow.id to workflowversion.id - Re-point WorkflowRun FK from workflow.id to workflowversion.id - Remove version and definition_uri from Workflow table - Remove version from WorkflowSummary in pipeline models - Add new request/response schemas for versions and aliases - Update alembic/env.py imports - Autogenerated Alembic migration with data migration and full downgrade
…/run endpoints - Add create_workflow_version, get_workflow_versions, get_workflow_version_by_id - Add set_workflow_version_alias, get_workflow_version_aliases, delete_workflow_version_alias - Update create_workflow to no longer accept version/definition_uri - Update registration CRUD to use workflow_version_id with version validation - Update run CRUD to use workflow_version_id with version validation - Update workflow_to_public and workflow_run_to_public serialization - Add 3 version endpoints (POST/GET list/GET by id) - Add 3 alias endpoints (PUT/GET/DELETE) - Update registration endpoints to nest under versions - Update pipeline_to_public to build WorkflowSummary without version
- Rewrite test_workflows.py for new Workflow shape (no version/definition_uri) - Add test_workflow_versions.py (8 tests for version CRUD) - Add test_workflow_aliases.py (10 tests for alias CRUD) - Rewrite test_workflow_registrations.py (create version first, nested URLs) - Rewrite test_workflow_runs.py (create version first, body uses workflow_version_id) - Update test_pipeline_entity.py helper (remove definition_uri from Workflow) - Update test_qcmetrics.py helpers (WorkflowVersion creation for run tests)
…paration - Rewrite WORKFLOWS.md with new entities, ER diagram, and endpoint docs - Update PIPELINES.md design decisions for version-agnostic pipeline design - Update ER_DIAGRAM.md entities, relationships, constraints, and provenance section
…S.md - Combine ER diagrams, design decisions, database models, and API endpoints - Single unified reference for workflows, versions, aliases, registrations, runs, and pipelines - Fix stale version field in pipeline WorkflowSummary response examples - Remove superseded standalone files
- Rename WorkflowRegistration class/table/schemas to WorkflowDeployment - Rename all service functions: create/get/delete_workflow_deployment() - Rename all route URLs: /registrations -> /deployments, registration_id -> deployment_id - Update alembic/env.py import - Add Alembic migration: rename table + FK constraints (data-preserving) - Replace test_workflow_registrations.py with test_workflow_deployments.py - Update docs/ER_DIAGRAM.md and docs/WORKFLOWS_AND_PIPELINES.md - 416 tests pass
- Remove VersionAlias(str, enum.Enum) class and 'import enum' from models - Change alias field to str on WorkflowVersionAlias, WorkflowAliasSummary, WorkflowVersionAliasPublic - Update all service/route type hints from VersionAlias to str - Replace alias.value with alias in error messages - Change migration alias column from sa.Enum to AutoString - Replace test_set_alias_invalid_value (422) with test_set_alias_custom_value (accepts any string) - Update docs: enum→string in mermaid diagrams, field tables, and design rationale - 416 tests pass
Bare UUID() constructor calls in workflow services raised unhandled
ValueError when given non-UUID strings (e.g. 'not-a-uuid'), causing
FastAPI to return a 500 Internal Server Error.
Added _parse_uuid() helper that wraps UUID() in try/except and raises
HTTPException(400) with a descriptive message. Replaced all 7 bare
UUID() calls across get_workflow_by_id, get_workflow_version_by_id,
create_workflow_deployment, get_workflow_deployments,
delete_workflow_deployment, and get_workflow_run_by_id.
Added tests for invalid UUID (400) and nonexistent UUID (404) on
GET /workflows/{workflow_id}.
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This PR accomplishes the discussed changes to our workflow models:
Adds workflow versions, rather than storing version on the workflow itself; this means the workflow (eg WES Alignment) stays constant, but versions are updated.
Adds workflow version aliases - allows us to point to specific versions with aliases like "develop", "production" etc. like an AWS lambda function. Note - this was originally an enum, but following feedback was converted into a free string field in eeb5384.
Following feedback that it was annoying to have to make 2 calls and filter client side to get the external id of a specific workflow, we accept optional querystring parameters for GET /{workflow}/deployments endpoint like
GET /123-456/deployments?alias=production&engine=Arvadosto reduce to a single call with server-side filtering.Following feedback that the term registration wasn't very descriptive - workflow Registration is renamed Deployment throughout to reflect that it represents a specific deployment of the workflow to a platform.
Additional: