Skill: Rebuild the ChromaDB Gold Index

Use when: BDPM/ANSM source data has changed, Silver models were updated, or ChromaDB collections are missing/stale.

Steps

1. Ensure Docker stack is running:

   docker compose up -d
   docker ps    # verify chromadb and postgres containers are healthy
   

2. Ensure Silver is up to date (run if source data changed):

   uv run dotenv -f dbt/.env run -- uv run dbt run --project-dir dbt --profiles-dir dbt
   uv run dotenv -f dbt/.env run -- uv run dbt test --project-dir dbt --profiles-dir dbt
   

3. Materialize the Gold asset:

   uv run dotenv -f .env run -- uv run dagster asset materialize --select gold_embeddings
   

4. Verify collections via chromadb-inspector agent or directly:

   uv run dotenv -f .env run -- python -c "
   import chromadb, os
   c = chromadb.HttpClient(host=os.environ['CHROMA_HOST'], port=int(os.environ['CHROMA_PORT']))
   for name in ['idx_bdpm_medicament_v1', 'idx_ansm_interaction_v1']:
       print(name, c.get_collection(name).count())
   "
   

5. Smoke-test the agent tools:

   uv run dotenv -f .env run -- python -c "
   from medox.agent.tools.tool_search_drug import search_drug
   from medox.agent.tools.tool_check_interactions import check_interactions
   print(search_drug.invoke({'query': 'doliprane'}))
   print(check_interactions.invoke({'substance_a': 'warfarine', 'substance_b': 'ibuprofene'}))
   "
   

Collection naming

idx_bdpm_medicament_v1

silver_bdpm__medicament

idx_ansm_interaction_v1

silver_ansm__interaction

Rules

• Always run dbt tests before reindexing — bad Silver data produces bad embeddings
• Full reindex deletes and recreates the collection — expect a few minutes
• If

  gold_embeddings

  fails: check

  CHROMA_HOST

  /

  CHROMA_PORT

  in

  .env

  and Docker status