feat: add NCBI cross-linking API endpoints #893
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Creates the base infrastructure layer for BRC Analytics backend: - FastAPI application with health and cache endpoints - Redis caching service with TTL management - Docker Compose setup (backend + redis + nginx) - nginx reverse proxy configuration - uv for dependency management - Ruff formatting for Python code - E2E health check tests This branch serves as the foundation for feature branches to build upon.
Adds GET /api/v1/version endpoint that returns: - API version (from APP_VERSION env var) - Environment (development/production) - Service name This provides a simple way for the frontend to display version info and demonstrates the backend infrastructure is working.
Use APP_VERSION build arg to inject version from package.json into backend container. Adds docker-build.sh script to automate this. All endpoints now use settings.APP_VERSION instead of hardcoded values.
Implements GitHub issue galaxyproject#783 - provides JSON endpoints for NCBI to link back to BRC Analytics organism and assembly pages. New endpoints: - GET /api/links/organism-links.json - Returns 1409 organism links - GET /api/links/assembly-links.json - Returns 1967 assembly links Features: - Reads from catalog JSON files mounted as Docker volume - 24-hour Redis caching for performance - Includes taxonomy IDs, scientific names, and BRC Analytics URLs - Auto-documented in OpenAPI/Swagger Changes: - Add NCBILinksService to generate links from catalog data - Add FastAPI endpoints with Redis caching - Mount catalog directory to backend container - Update poetry.lock with regenerated dependencies
- Add CATALOG_PATH setting to config - Update NCBILinksService to use catalog path from settings - Allows catalog path override via environment variable
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Extends the backend to do something actually useful -- providing an API for external consumers
Summary
Depends on: #892