pr-wf.yaml

name: PR pipeline to verify tests and code rules
on: [pull_request]
jobs:
  Python-tests:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 4
      matrix:
        python-version: [3.8]
    services:
      redis:
        image: redis
        options: >-
          --health-cmd "redis-cli ping"
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 6379:6379
      postgres:
        image: postgres:13
        env:
          POSTGRES_PASSWORD: multiomics
          POSTGRES_USER: multiomics
          POSTGRES_DB: multiomics
          POSTGRES_HOST_AUTH_METHOD: trust
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5  
        ports:
          - 5432:5432         
      mongo:
        image: "mongo:4.2"
        env:
          MONGO_INITDB_ROOT_USERNAME: multiomics
          MONGO_INITDB_ROOT_PASSWORD: multiomics
          MONGO_INITDB_DATABASE: multiomics
        options: >-
          --health-cmd "/bin/bash -c 'mongo --norc --quiet --host=localhost:27017 --eval \"db.getMongo()\"'"
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
        ports:
          - 27017:27017
    env:
      REDIS_HOST: localhost
      REDIS_PORT: 6379
      MONGO_HOST: localhost
      MONGO_DB: multiomics
      MONGO_USERNAME: multiomics
      MONGO_PASSWORD: multiomics
      POSTGRES_USERNAME: multiomics
      POSTGRES_PASSWORD: multiomics
      POSTGRES_HOST: localhost
      POSTGRES_DB: multiomics

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Create virtual environment
      run: |
        pip install virtualenv
        virtualenv venv
    - name: Install Dependencies
      run: |
        . venv/bin/activate
        pip install -r config/requirements.txt
    - name: Run Tests
      run: |
        . venv/bin/activate
        python src/manage.py test src --settings=multiomics_intermediate.settings_ci
  Node-checks:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 4
      matrix:
        node-version: [16.x]

    steps:
    - uses: actions/checkout@v2
    - name: Use Node.js ${{ matrix.node-version }}
      uses: actions/setup-node@v1
      with:
        node-version: ${{ matrix.node-version }}
    - name: NPM install
      run: npm --prefix src/frontend/static/frontend i
    - name: NPM linter checks
      run: npm --prefix src/frontend/static/frontend run check-all