test_modules.yml

name: test_modules

on:
  push:
    branches: "**"
  pull_request:
    types: [opened, reopened, synchronize, closed]
    branches: "**"

jobs:
  test_map:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 2
      matrix:
        map_args: ["-d 'ENA' -f relecov_tools/schema/ena_schema.json", "-d 'GISAID' -f relecov_tools/schema/gisaid_schema.json"]
    steps:
    - name: Set up Python 3.9.16
      uses: actions/setup-python@v3
      with:
        python-version: '3.9.16'
    - name: Checkout code
      uses: actions/checkout@v3
      with:
        ref: ${{ github.event.pull_request.head.sha }}
        fetch-depth: 0
    - name: Install package and dependencies
      run: |
        pip install -r requirements.txt
        pip install .
    - name: Run each module tests
      run: |
        relecov-tools map -j tests/data/map_validate/processed_metadata_lab_test.json -p relecov_tools/schema/relecov_schema.json ${{ matrix.map_args }} -o .
      env:
        OUTPUT_LOCATION: ${{ github.workspace }}/tests/
    - name: Upload output file
      uses: actions/upload-artifact@v4
      with:
        name: test-output
        path: output.txt

  test_all_modules:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 3
      matrix:
        modules: ["read-lab-metadata", "read-bioinfo-metadata", "validate"]
    steps:

    - name: Set up Python 3.9.16
      uses: actions/setup-python@v3
      with:
        python-version: '3.9.16'

    - name: Checkout code
      uses: actions/checkout@v3
      with:
        ref: ${{ github.event.pull_request.head.sha }}
        fetch-depth: 0

    - name: Install package and dependencies
      run: |
        pip install -r requirements.txt
        pip install .

    - name: Run each module tests
      run: |
        if [ "${{ matrix.modules }}" == "read-lab-metadata" ]; then
          relecov-tools read-lab-metadata -m tests/data/read_lab_metadata/metadata_lab_test.xlsx -s tests/data/read_lab_metadata/samples_data_test.json -o $OUTPUT_LOCATION
        elif [ "${{ matrix.modules }}" == "validate" ]; then
          relecov-tools validate -j tests/data/map_validate/processed_metadata_lab_test.json -s relecov_tools/schema/relecov_schema.json -m tests/data/map_validate/metadata_lab_test.xlsx -o $OUTPUT_LOCATION
        fi
      env:
        OUTPUT_LOCATION: ${{ github.workspace }}/tests/
    - name: Upload output file
      uses: actions/upload-artifact@v4
      with:
        name: test-output
        path: output.txt