Client walkthrough (curl) of submit/monitor over WES v1.0.0: state mapping,
gxworkflow:// scheme, engine params, tasks, pagination, errors, limitations.
Cross-link admin <-> dev docs; point at gxy-wes / gxy-wes-bioblend examples.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Implement full Workflow Execution Service (WES) API support for running Galaxy
workflows via the GA4GH standard. Includes complete core functionality with run
submission, status tracking, cancellation, input/output handling, and task logs.
Core WES Features:
- 6 WES API endpoints (service-info, runs CRUD, cancel, status)
- Support for both workflow_url and workflow_attachment input methods
- Support for gxworkflow:// URI scheme for direct database workflow references
- Automatic history creation with optional custom naming
- Full workflow support: gx_workflow_ga and gx_workflow_format2
- DRS URI generation for all workflow outputs
- State mapping between Galaxy invocation states and WES states
- Cursor-based pagination for run listings
Task Log Features:
- /api/jobs/{job_id}/stdout - Job stdout as plain text
- /api/jobs/{job_id}/stderr - Job stderr as plain text
- /ga4gh/wes/v1/runs/{run_id}/tasks - Paginated task list
- /ga4gh/wes/v1/runs/{run_id}/tasks/{task_id} - Task details
- Build TaskLogs from workflow invocation steps
- Populate RunLog with task_logs list and task_logs_url
Implementation Highlights:
- Auto-generated Pydantic models from GA4GH WES OpenAPI spec
- FastAPI CBV router following Galaxy API patterns
- Service layer with full workflow submission/execution pipeline
- Shared GA4GH utilities for DRS code reuse
- Reduced test duplication with helper functions
Files Added:
- lib/galaxy/schema/wes/__init__.py - Generated Pydantic models
- lib/galaxy/webapps/galaxy/api/wes.py - WES API router
- lib/galaxy/webapps/galaxy/services/wes.py - WesService
- lib/galaxy/webapps/galaxy/services/ga4gh.py - Shared GA4GH utilities
- WES_PLAN.md - Implementation plan
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Add an ascp handler to the frontend, so users can paste ascp:// urls
- Add ssh key passphrase config option, without this downloads hang
waiting for password
- Bypass is_dir / is_file checks, they'll always fail. We assume files
for now.
- Implement top-level get_file. `_get_file` would require implementing
`get_info` which doesn't really make sense for this file source.
