Launching The BGP

This guide provides instructions for launching the BioGenome Portal and configuring all the necessary environment variables. The app uses Docker Compose to manage multiple services, including the database, server, cronjobs, and Celery worker.

Launching the Application

To launch the application, ensure you have Docker and Docker Compose installed on your machine. Then, follow these steps:

1. Clone the Repository: If you haven’t already, clone the repository that contains the app code:

   git clone <your-repo-url>
   cd <repo-directory>

2. Set Up Environment Variables: Before launching the app, ensure that the environment variables in your .env file are correctly configured. The app requires various settings for database access, API configuration, and external integrations.

3. Build and Run the Containers: Use the following command to build and start the application:

   docker-compose up --build

   This will start the following services:

   • MongoDB for database management
   • Flask API for the back-end server
   • Cronjob container for scheduled tasks
   • Nginx for front-end serving
   • Celery worker for background tasks
   • Redis as a message broker for Celery

4. Access the App: Once the app is running, you can access it via the port defined for Nginx (default: http://localhost:91).

Environment Variables

The following environment variables are required to properly configure the application:

Database Variables

• DB_NAME: The name of the MongoDB database.
• DB_USER: Username for the MongoDB instance, it will also correspond to the first admin username.
• DB_PASS: Password for the MongoDB instance, it will also correspond to the first admin password.
• DB_HOST: The host for the MongoDB instance.
• DB_PORT: Port used to connect to the MongoDB instance (default: 27017).
• MONGO_INITDB_ROOT_USERNAME: MongoDB root username.
• MONGO_INITDB_ROOT_PASSWORD: MongoDB root password.
• MONGO_INITDB_DATABASE: Default database created on initialization.
• MONGODB_DATA_DIR: Directory to store MongoDB data.
• MONDODB_LOG_DIR: Directory for MongoDB logs (default: /dev/null).

Celery and Redis Variables

• CELERY_BROKER_URL: URL of the Redis broker used by Celery (default: redis://redis/0).
• CELERY_RESULT_BACKEND: Redis URL for storing task results (default: redis://redis/0).

API Variables

• APP_NAME: Name of the application (default: BioGenomePortal).
• API_PORT: Port used by the Flask API (default: 80).
• API_HOST: Hostname for the Flask API (default: biogenome_server).
• PROXY_HOST: Hostname for the Nginx proxy (default: biogenome_nginx).
• PROCESSES: Number of processes for the Flask app (default: 4).
• THREADS: Number of threads per process for the Flask app (default: 2).

Authentication Variables

• JWT_SECRET_KEY: Secret key used for JWT authentication in the Flask API.

Project Variables

• PROJECT_ACCESSION: INSDC Accession number for the project (ex: PRJNA489243).
• PROJECTS: List of projects acronyms (ex: DTOL, VGP, CBP), used to import biosamples containing the acronym in the project_name attribute
• ANNOTATIONS_PATH: Path to the directory containing annotation data, uploaded gffs files will be stored in the mounted volume.
• ROOT_NODE: Root Taxonomic ID (default: 2759 for Eukaryots).

External Service Variables

• CESIUM_TOKEN: Cesium API token for accessing external services.

GoaT Project Variables

• GOAT_PROJECT_NAME: Name of the GoaT project (default: CBP).
• GOAT_PRIMARY_CONTACT: Primary contact for the GoaT project (e.g., Montserrat Corominas).
• GOAT_PRIMARY_CONTACT_EMAIL: Contact email for the GoaT project.
• GOAT_PRIMARY_CONTACT_INSTITUTION: Institution of the primary contact (default: UB, 08028, Spain).
• GOAT_SCHEMA_VERSION: GoaT schema version (default: ebp_species_goat_2.6).

Nginx Variables

• BASE_PATH: Base path for the application (default: /ebp), use it to deploy in the app in subpaths

Docker Compose Services

The application is structured into multiple services that work together:

• biogenome_db: MongoDB database container.
• biogenome_server: Flask back-end server.
• biogenome_cron: Container handling scheduled cronjobs.
• biogenome_nginx: Nginx container for serving the front-end.
• celery: Celery worker for handling background tasks.
• redis: Redis container for Celery message brokering.

Example docker-compose.yml

version: '3'

services:

  biogenome_db:
    image: mongo:6.0
    container_name: "${DB_HOST}"
    env_file:
      - .env
    volumes:
     - ./mongo-init.sh:/docker-entrypoint-initdb.d/mongo-init.sh
     - /home/emilior/ebp-data:/data/db
    ports:
      - "27010:27017"

  biogenome_server:
    build: ./server
    container_name: "biogenome_server"
    restart: always
    volumes:
      - ./server:/server
      - ${ANNOTATIONS_PATH}:/server/annotations_data
    env_file:
      - .env
    depends_on:
      - redis

  biogenome_cron:
    build: ./cronjobs
    container_name: biogenome_cron
    env_file:
      - .env

  biogenome_nginx:
    build:
      context: ./biogenome-client
      dockerfile: Dockerfile
      args:
        - ROOT_NODE=$ROOT_NODE
        - CESIUM_TOKEN=$CESIUM_TOKEN
        - BASE_PATH=$BASE_PATH
    container_name: "biogenome_nginx"
    restart: always
    volumes:
      - node_modules:/biogenome-client/node_modules
    environment:
      - API_PORT=${API_PORT}
      - API_HOST=${API_HOST}
      - BASE_PATH=${BASE_PATH}
    ports:
      - "91:${API_PORT}"

  celery:
    build: ./server
    command: celery --app app.celery_app worker --loglevel=info --autoscale=1,1 --max-tasks-per-child=1
    restart: always
    volumes:
      - ${ANNOTATIONS_PATH}:/annotations_data
    env_file:
      - .env
    depends_on:
      - biogenome_server
      - biogenome_db
      - redis

  redis:
    image: "redis:alpine"

volumes:
  app:
  mongodb-data:
  node_modules: