docker-compose.yml

services:

  # ── Infrastructure ─────────────────────────────────────────────────────────

  redis:
    image: redis:7.4-alpine
    container_name: metaboflow-redis
    restart: unless-stopped
    ports:
      - "6379:6379"
    healthcheck:
      test: ["CMD", "redis-cli", "ping"]
      interval: 10s
      timeout: 3s
      retries: 3

  postgres:
    image: postgres:16-alpine
    container_name: metaboflow-postgres
    restart: unless-stopped
    environment:
      POSTGRES_DB: metaboflow
      POSTGRES_USER: metaboflow
      POSTGRES_PASSWORD: metaboflow_dev
    ports:
      - "5432:5432"
    volumes:
      - pgdata:/var/lib/postgresql/data
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U metaboflow"]
      interval: 10s
      timeout: 3s
      retries: 3

  # ── Backend ────────────────────────────────────────────────────────────────

  backend:
    build:
      context: ./packages/backend
      dockerfile: Dockerfile
    container_name: metaboflow-backend
    restart: unless-stopped
    ports:
      - "8000:8000"
    environment:
      METABOFLOW_DATABASE_URL: postgresql://metaboflow:metaboflow_dev@postgres:5432/metaboflow
      METABOFLOW_REDIS_URL: redis://redis:6379/0
      METABOFLOW_CELERY_BROKER_URL: redis://redis:6379/0
      METABOFLOW_CELERY_RESULT_BACKEND: redis://redis:6379/1
      METABOFLOW_XCMS_WORKER_URL: http://xcms-worker:8001
      METABOFLOW_STATS_WORKER_URL: http://stats-worker:8002
      METABOFLOW_CHART_SERVICE_URL: http://chart-service:8005
      METABOFLOW_ANNOT_WORKER_URL: http://annot-worker:8006
      METABOFLOW_SIRIUS_WORKER_URL: http://sirius-worker:8007
      METABOFLOW_CHART_R_WORKER_URL: http://chart-r-worker:8008
      METABOFLOW_REPORT_WORKER_URL: http://report-worker:8009
      METABOFLOW_CORS_ORIGINS: '["http://localhost:3000","http://localhost:3001","http://localhost:3005"]'
    volumes:
      - ./data:/data
    depends_on:
      redis:
        condition: service_healthy
      postgres:
        condition: service_healthy
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8000/health"]
      interval: 15s
      timeout: 5s
      retries: 3

  celery-worker:
    build:
      context: ./packages/backend
      dockerfile: Dockerfile
    container_name: metaboflow-celery
    command: uv run celery -A app.tasks.celery_app worker --loglevel=info -I app.tasks.analysis_tasks
    restart: unless-stopped
    environment:
      METABOFLOW_DATABASE_URL: postgresql://metaboflow:metaboflow_dev@postgres:5432/metaboflow
      METABOFLOW_REDIS_URL: redis://redis:6379/0
      METABOFLOW_CELERY_BROKER_URL: redis://redis:6379/0
      METABOFLOW_CELERY_RESULT_BACKEND: redis://redis:6379/1
      METABOFLOW_XCMS_WORKER_URL: http://xcms-worker:8001
      METABOFLOW_STATS_WORKER_URL: http://stats-worker:8002
      METABOFLOW_ANNOT_WORKER_URL: http://annot-worker:8006
      METABOFLOW_SIRIUS_WORKER_URL: http://sirius-worker:8007
      METABOFLOW_CHART_R_WORKER_URL: http://chart-r-worker:8008
      METABOFLOW_REPORT_WORKER_URL: http://report-worker:8009
    volumes:
      - ./data:/data
    depends_on:
      redis:
        condition: service_healthy

  # ── Engine Workers ─────────────────────────────────────────────────────────

  xcms-worker:
    build:
      context: ./packages/engines/xcms-worker
      dockerfile: Dockerfile
    image: metaboflow/xcms-worker:0.1.0
    container_name: metaboflow-xcms-worker
    restart: unless-stopped
    volumes:
      - ./data:/data
      - ${HOME}/spectral_libraries:/spectral_libraries:ro
    healthcheck:
      test: ["CMD", "Rscript", "-e", "cat('ok')"]
      interval: 30s
      timeout: 10s
      retries: 3
      start_period: 15s

  stats-worker:
    build:
      context: ./packages/engines/stats-worker
      dockerfile: Dockerfile
    image: metaboflow/stats-worker:0.1.0
    container_name: metaboflow-stats-worker
    restart: unless-stopped
    volumes:
      - ./data:/data
    healthcheck:
      test: ["CMD", "Rscript", "-e", "cat('ok')"]
      interval: 30s
      timeout: 10s
      retries: 3
      start_period: 15s

  annot-worker:
    build:
      context: ./packages/engines/annot-worker
      dockerfile: Dockerfile
    image: metaboflow/annot-worker:0.1.0
    container_name: metaboflow-annot-worker
    restart: unless-stopped
    ports:
      - "8006:8006"
    volumes:
      - ${HOME}/spectral_libraries:/spectral_libraries:ro
      - ./data:/data
    environment:
      ANNOTWORKER_LIBRARY_DIR: /spectral_libraries
      ANNOTWORKER_REGISTRY_DB: /spectral_libraries/registry.db
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8006/health"]
      interval: 15s
      timeout: 5s
      retries: 3

  sirius-worker:
    build:
      context: ./packages/engines/sirius-worker
      dockerfile: Dockerfile
    image: metaboflow/sirius-worker:0.1.0
    container_name: metaboflow-sirius-worker
    restart: unless-stopped
    ports:
      - "8007:8007"
    volumes:
      - ./data:/data
    environment:
      SIRIUS_USER: ${SIRIUS_USER:-}
      SIRIUS_PASSWORD: ${SIRIUS_PASSWORD:-}
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8007/health"]
      interval: 30s
      timeout: 10s
      retries: 3
      start_period: 30s

  # ── Chart Service ────────────────────────────────────────────────────────

  chart-service:
    build:
      context: ./packages/chart-service
      dockerfile: Dockerfile
    image: metaboflow/chart-service:0.1.0
    container_name: metaboflow-chart-service
    restart: unless-stopped
    environment:
      CHART_OUTPUT_DIR: /data/charts
      CHART_DPI: "300"
    volumes:
      - ./data:/data
    healthcheck:
      test: ["CMD", "curl", "-f", "http://localhost:8005/health"]
      interval: 15s
      timeout: 5s
      retries: 3

  # ── Chart R Worker ───────────────────────────────────────────────────────

  chart-r-worker:
    build:
      context: ./packages/engines/chart-r-worker
    image: metaboflow/chart-r-worker:0.1.0
    container_name: metaboflow-chart-r-worker
    restart: unless-stopped
    volumes:
      - ./data:/data
    expose:
      - "8008"
    healthcheck:
      test: ["CMD", "Rscript", "-e", "con <- url('http://localhost:8008/health'); r <- readLines(con, warn=FALSE); close(con); if(length(r)==0) quit(status=1)"]
      interval: 30s
      timeout: 10s
      retries: 3

  # ── Report Worker ───────────────────────────────────────────────────────

  report-worker:
    build:
      context: ./packages/engines/report-worker
    image: metaboflow/report-worker:0.1.0
    container_name: metaboflow-report-worker
    restart: unless-stopped
    volumes:
      - ./data:/data
    expose:
      - "8009"
    healthcheck:
      test: ["CMD", "Rscript", "-e", "con <- url('http://localhost:8009/health'); r <- readLines(con, warn=FALSE); close(con); if(length(r)==0) quit(status=1)"]
      interval: 30s
      timeout: 10s
      retries: 3

  # ── Frontend ─────────────────────────────────────────────────────────────

  frontend:
    build:
      context: ./packages/frontend
      dockerfile: Dockerfile
    container_name: metaboflow-frontend
    restart: unless-stopped
    ports:
      - "${FRONTEND_PORT:-3001}:3000"
    environment:
      NEXT_PUBLIC_API_URL: http://backend:8000
    depends_on:
      backend:
        condition: service_healthy

volumes:
  pgdata: