docker-compose.yml

# Node major version for the dev containers: set NODE_VERSION (shell or root .env) to try another, and keep the default in line with .nvmrc
services:
  backend:
    image: node:${NODE_VERSION:-24}-alpine
    working_dir: /backend-express
    volumes:
      - ./backend-express:/backend-express
      - /backend-express/node_modules
      - ./commons:/commons
      - ./data:/data
    ports:
      - "3001:3001"
    environment:
      - DB_HOST=postgres
      - DB_PORT=5432
      - DB_NAME=data_visualizer
      - DB_USERNAME=postgres
      - DB_PASSWORD=postgres
      - SHINY_URL=http://shiny:3838
      - SHINY_SECRET=${SHINY_SECRET:?set SHINY_SECRET in .env (see .env.example)}
      # Uploads are processed by the preprocess service below, which picks jobs up from this shared folder (inside ./data)
      - PREPROCESS_SPOOL_DIR=/data/jobs
    command: sh -c "rm -rf dist/ &&
                    npm install &&
                    npm run build &&
                    npm run db:migrate &&
                    npm run db:seed &&
                    npm run dev"
    depends_on:
      postgres:
        condition: service_healthy
    extra_hosts:
      - "host.docker.internal:host-gateway"
    restart: on-failure

  postgres:
    image: postgres:16-alpine
    environment:
      POSTGRES_USER: postgres
      POSTGRES_PASSWORD: postgres
      POSTGRES_DB: data_visualizer
    ports:
      - "5432:5432"
    volumes:
      - postgres-data:/var/lib/postgresql/data
    healthcheck:
      test: ["CMD-SHELL", "pg_isready -U postgres"]
      interval: 5s
      timeout: 5s
      retries: 5
    restart: on-failure

  # Only reachable from other services (no ports:); Express proxies to http://shiny:3838
  shiny:
    build: ./shiny
    volumes:
      - ./shiny/app:/srv/shiny-server/app
      - ./data/parquet:/data/parquet:ro
      - ./data/uploads/tissue:/data/tissue:ro
    environment:
      - PARQUET_DIR=/data/parquet
      - TISSUE_DIR=/data/tissue
      - SHINY_SECRET=${SHINY_SECRET:?set SHINY_SECRET in .env (see .env.example)}
      - SHINY_DEV=1

  # Turns uploaded .rds files into the Parquet the Shiny app reads: waits for jobs the backend drops in data/jobs and runs
  # preprocess.R on each (see shiny/preprocess/worker.sh). Needs RAM for the largest Seurat object (often 2-5x its file size)
  preprocess:
    build: ./shiny/preprocess
    image: preprocess
    entrypoint: ["/worker.sh"]
    volumes:
      - ./data:/data
      - ./shiny/preprocess/preprocess.R:/preprocess.R:ro
    restart: unless-stopped

  frontend:
    image: node:${NODE_VERSION:-24}-alpine
    working_dir: /app
    volumes:
      - ./frontend:/app
      - /app/node_modules
      - ./commons:/commons
    ports:
      - "3000:3000"
    command: sh -c "npm install && npm run dev --host"

volumes:
  postgres-data: