gapforge/docker-compose.bulk.yml at main · LordKay-sudo/gapforge · GitHub

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# Bulk Open Targets ingest overlay (roadmap scale path).
#
# Prerequisite: generate bulk JSON on the host (gitignored):
#   py -3 scripts/download_opentargets_bulk.py --release 24.06 --max-genes 500 --with-evidence
#   py -3 scripts/etl_opentargets.py --input data/raw/opentargets_bulk.json --strict
#
# Then:
#   docker compose -f docker-compose.yml -f docker-compose.bulk.yml up --build
#
# Default compose still uses the frozen slice via Dockerfile.seed.

services:
  seed:
    environment:
      OT_RAW_JSON: /app/data/raw/opentargets_bulk.json
    volumes:
      - ./data/raw/opentargets_bulk.json:/app/data/raw/opentargets_bulk.json:ro
      - ./data/processed:/app/data/processed
    command:
      - /bin/sh
      - -c
      - |
        if [ ! -f "$$OT_RAW_JSON" ]; then
          echo "Missing $$OT_RAW_JSON — run download_opentargets_bulk.py on the host first." >&2
          exit 1
        fi
        python /app/scripts/etl_opentargets.py --input "$$OT_RAW_JSON" --strict
        python /app/scripts/seed_neo4j.py --strict