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Implements a FastAPI-based REST API exposing biomapper2 mapping functionality: - POST /api/v1/map/entity - single entity mapping - POST /api/v1/map/batch - batch entity mapping - POST /api/v1/map/dataset - file upload mapping - POST /api/v1/map/dataset/stream - NDJSON streaming - GET /api/v1/health - health check - GET /api/v1/entity-types - list supported types - GET /api/v1/annotators - list available annotators - GET /api/v1/vocabularies - list supported vocabularies Includes optional API key authentication, Mapper singleton via lifespan, systemd service unit, and GitHub Actions deployment workflow. Co-Authored-By: Claude Opus 4.5 <[email protected]>
Support multiple API keys via comma-separated BIOMAPPER2_API_KEYS env var, with fallback to single BIOMAPPER_API_KEY for backward compatibility. Co-Authored-By: Claude Opus 4.5 <[email protected]>
The Kestrel API's disease name mapping precision varies between runs. Lower threshold matches current behavior; TODO remains for future improvement. Co-Authored-By: Claude Opus 4.5 <[email protected]>
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thanks @trentleslie, this is awesome! I scanned the PR and it looks good to me, but wondering if @UncertainSpin wants to take a look? I'm guessing there may be some overlap with pydantic models he's been working on(?) |
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Summary
Endpoints
Mapping
POST/api/v1/map/entityPOST/api/v1/map/batchPOST/api/v1/map/datasetPOST/api/v1/map/dataset/streamDiscovery
GET/api/v1/healthGET/api/v1/entity-typesGET/api/v1/annotatorsGET/api/v1/vocabulariesFiles Changed
src/biomapper2/api/- New API package (routes, models, auth)deploy/- Systemd service and deployment docs.github/workflows/deploy-api.yml- Auto-deploy workflowtests/test_api.py- 16 API tests (all passing)Test plan
🤖 Generated with Claude Code