test.yml

name: Github Actions Test

on: [push]
jobs:
  build:
    env:
      POSTGRES_USER: admin
      POSTGRES_PASSWORD: OG0pjmnQDWUTvLotYrxPrg
      POSTGRES_HOST: localhost
      POSTGRES_HOST_AUTH_METHOD: password
      POSTGRES_DB: metadata
      POSTGRES_PORT: 5432
      HTSGET_TEST_KEY: thisisatest
      DB_PATH: localhost
      SERVER_LOCAL_DATA: ${{github.workspace}}/data
      PGPASSWORD: OG0pjmnQDWUTvLotYrxPrg
      INDEXING_PATH: ${{github.workspace}}/tmp
      INDEXING_SWITCH_FILE: ${{github.workspace}}/indexer_on
      TESTENV_URL: http://localhost:3000
      AGGREGATE_COUNT_THRESHOLD: 5
      POSTGRES_USERNAME: admin
    runs-on: ubuntu-latest
    # Add in environment variables for the entire "build" job
    services:
      postgres_main:
        image: postgres:latest
        env:
          POSTGRES_USER: ${{ env.POSTGRES_USER }}
          POSTGRES_PASSWORD: ${{ env.POSTGRES_PASSWORD }}
          POSTGRES_DB: ${{ env.POSTGRES_DB }}
        ports:
          - 5432:5432
        options: >-
          --health-cmd pg_isready
          --health-interval 10s
          --health-timeout 5s
          --health-retries 5
    strategy:
      matrix:
        python-version: ['3.12']
    steps:
    - name: Checkout code
      uses: actions/checkout@v4
      with:
        submodules: true
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install requirements
      run: |
        pip install -r requirements.txt
        bash create_db.sh
        mkdir -p ${{ env.INDEXING_PATH }}
        touch ${{ env.INDEXING_SWITCH_FILE }}
        sed -i s@\<AGGREGATE_COUNT_THRESHOLD\>@${{env.AGGREGATE_COUNT_THRESHOLD}}@ config.ini
        sed -i s@\<POSTGRES_USERNAME\>@${{env.POSTGRES_USERNAME}}@ config.ini
    - name: Test
      run: |
        python htsget_server/server.py &
        python htsget_server/indexing.py &
        sleep 5
        pytest tests/test_htsget_server.py