test_modules.yml

name: Python Package using Conda

on: 
  push:
    branches: "**"
  pull_request_target:
    types:
      - opened
    branches: "**"

env:
  GITHUB_TOKEN: ${{ secrets.TOKEN_ACTIONS }}

jobs:
  security_check:
    runs-on: ubuntu-latest
    steps:
      - name: Get User Permission
        id: checkAccess
        uses: actions-cool/check-user-permission@v2
        with:
          require: write
          username: ${{ github.triggering_actor }}
      - name: Check User Permission
        if: steps.checkAccess.outputs.require-result == 'false'
        run: |
          echo "${{ github.triggering_actor }} does not have permissions on this repo."
          echo "Current permission level is ${{ steps.checkAccess.outputs.user-permission }}"
          echo "Job originally triggered by ${{ github.actor }}"
          exit 1

  test_sftp_handle:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 1
      matrix:
        download_options: ["download_only", "download_clean", "delete_only"]
        target_folders: ["", "-t COD-test-1"]

    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:
        path: .

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

    - name: Run sftp_handle tests
      run: |
        python3 tests/test_sftp_handle.py --download_option ${{ matrix.download_options }} ${{ matrix.target_folders }}
      env:
        TEST_USER: ${{ secrets.TEST_USER }}
        TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }}
        TEST_PORT: ${{ secrets.TEST_PORT }}
        OUTPUT_LOCATION: ${{ github.workspace }}/tests/

  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:
        path: .
    - 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@v2
      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:
        path: .
    - 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@v2
      with:
        name: test-output
        path: output.txt