bioflow / docs /OBSERVABILITY.md
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Fix explorer/ingestion UI and 3D endpoints
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Observability (Phase 6)

Structured Logs

FastAPI emits JSON logs for key actions:

  • search / search_error
  • ingest_single / ingest_single_error
  • workflow / workflow_error

Each log includes:

  • event
  • request_id
  • timestamp
  • relevant fields (query, top_k, duration_ms, etc.)

Health Metrics Endpoint

GET /api/health/metrics

Returns:

{
  "status": "ok",
  "timestamp": "...",
  "qdrant": {
    "available": true,
    "collections": ["molecules", "proteins"],
    "stats": { "molecules": { "points_count": 1234 } }
  },
  "models": {
    "available": true,
    "device": "cuda",
    "obm_loaded": true
  }
}

CI-Style Test Runner

python scripts/run_tests.py

Runs:

  • test_search_api.py
  • test_agent_api.py
  • test_search_filters.py
  • test_phase4_ui.py
  • test_ingestion_api.py