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Online system for the FIU Plugin-based Microbiome Analysis application

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PluMA Online

The frontend and backend application for the PluMA Online ecosystem.

code style: prettier Testing CI

Requirements

  1. nodejs >= 14.0.0
  2. pnpm >= 6.28.0
  3. docker
  4. WINDOWS Windows Subsystem for Linux <-- Strongly recommended
  5. WINDOWS Docker Desktop
  6. MacOS Vagrant
  7. MacOS VirtualBox or VMWare Player
  8. VSCode (preferred IDE)
  9. (Optional) MongoDB Compass <-- GUI for database

Installation

Prerequesite

If you have a previous working version of the repository prior to Feb. 07, 2022, you'll need to re-create the database files from scratch:

  1. Bring down your containers with:
docker-compose down
  1. Delete all unconnected volumes with:
docker volumes prune

Commands

  1. Clone the repository
  2. Install pnpm:
npm i -g pnpm
  1. Copy .env.example to a new file named .env and fill in ALL variables as appropriate

Each variable must be filled in and must be unique to each environment. Passswords must be valid passwords, secrets must be valid secrets, and DATABASE_URL must be a valid MongoDB connection URI.

The database hostname is database. Do not use an IP address in the MongoDB connection URI.

  1. Create a new file docker-compose.override.yml and copy the below into the file:
version: "3"

services:
  webapp:
    container_name: pluma-online
    build:
      context: ./
      dockerfile: Dockerfile-devel
    depends_on:
      - database
    networks:
      - web
    ports:
      - "4200:4200"
    volumes:
      - ./:/app
    restart: unless-stopped
    environment:
      APP_HOST: ${APP_HOST}
      APP_SETUP_PASSWORD: ${APP_SETUP_PASSWORD}
      APP_ADMIN_EMAIL: ${APP_ADMIN_EMAIL}
      APP_ADMIN_PASSWORD: ${APP_ADMIN_PASSWORD}
      APP_JWT_SECRET: ${APP_JWT_SECRET}
      MONGO_INITDB_ROOT_USERNAME: ${MONGO_INITDB_ROOT_USERNAME}
      MONGO_INITDB_ROOT_PASSWORD: ${MONGO_INITDB_ROOT_PASSWORD}
      MONGO_INITDB_DATABASE: ${MONGO_INITDB_DATABASE}
      DATABASE_URL: mongodb://${MONGO_INITDB_ROOT_USERNAME}:${MONGO_INITDB_ROOT_PASSWORD}@database/${MONGO_INITDB_DATABASE}?authSource=admin
      REDIS_HOST: ${REDIS_HOST}
      REDIS_PORT: ${REDIS_PORT}
  1. Run
pnpm run generate-key

This should create a keyfile at ./docker/mongodb/mongodb.key. sudo must be properly installed on your distro for this command to work correctly.

  1. Run:

NOTE: MacOS The following commands must be run inside the Vagrant virutal machine via vagrant ssh. See the Vagrant Documentation for more info.

docker-compose up -d database

and allow the database instance to load.

  1. Run:
docker-compose exec database /docker-entrypoint-initdb/01-mongo-init.sh

The output for this command should return successfully.

  1. Run:
docker-compose up -d

in the project folder to bring up the containers. Allow the webapp container to fully build the web application (it will take a few minutes). Follow the logs of each container by using the command docker-compose logs -f [container]

  1. Run:
docker-compose exec webapp pnpm run get-plugins && pnpm run prisma db seed

The output for this command should show a successful seeding of the database with at least 500 plugins and 20 pipelines.

  1. Hack on the code base.

Windows

Since docker is using a containerized Linux system, all shellscript files must end each line with a LF character. If issues are encountered with running shellscripts in the repository, this is likely due to the line endings being rewritten as CRLF. Use a text editor to batch change the end of line characters if this occurs.

docker-compose on Windows must be run through the installation of Docker Desktop. Do not use the docker-compose binary distributed through the package manager of your WSL2 distro.

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