relecov-tools/.github/workflows/test_modules.yml at 417a36bfe7de778dab866c29a6472375cc718062 · BU-ISCIII/relecov-tools · GitHub

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name: test_modules

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

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_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 3.12
      uses: actions/setup-python@v3
      with:
        python-version: '3.12'

    - 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: Load profile config (relecov)
      run: |
        relecov-tools add-extra-config \
          --config_file relecov_tools/conf/initial_config-relecov.yaml --force

    - name: Run each module tests
      run: |
        relecov-tools --debug 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: 4
      matrix:
        modules:
        - "read-lab-metadata"
        - "read-lab-metadata-mepram"
        - "read-bioinfo-metadata"
        - "validate"
        - "build-schema"
    env:
      OUTPUT_LOCATION: ${{ github.workspace }}/tests/

    steps:
    - name: Set up Python 3.12
      uses: actions/setup-python@v3
      with:
        python-version: '3.12'
    - 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: Load profile config (relecov)
      run: |
        relecov-tools add-extra-config \
          --config_file relecov_tools/conf/initial_config-relecov.yaml --force

    - name: Run read-lab-metadata module
      if: matrix.modules == 'read-lab-metadata'
      run: |
        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

    - name: Run read-lab-metadata module (MePRAM)
      if: matrix.modules == 'read-lab-metadata-mepram'
      run: |
        relecov-tools read-lab-metadata \
          -m tests/data/read_lab_metadata/mepram_metadata_lab_test.xlsx \
          -s tests/data/read_lab_metadata/mepram_samples_data_test.json \
          -p mepram \
          -o $OUTPUT_LOCATION

    - name: Run read-bioinfo-metadata module
      if: matrix.modules == 'read-bioinfo-metadata'
      run: |
        relecov-tools read-bioinfo-metadata \
          --json_file tests/data/read_bioinfo_metadata/validated_samples.json \
          --json_schema_file relecov_tools/schema/relecov_schema.json \
          --input_folder tests/data/read_bioinfo_metadata/analysis_folder/ \
          --software_name viralrecon \
          --soft_validation \
          -o $OUTPUT_LOCATION

    - name: Run validate module without --upload-files param (no sftp)
      if: matrix.modules == 'validate'
      run: |
        relecov-tools validate \
          -j tests/data/map_validate/processed_metadata_lab_test.json \
          -m tests/data/map_validate/metadata_lab_test.xlsx \
          -o tests/data/map_validate/ \
          -s relecov_tools/schema/relecov_schema.json \
          -l tests/data/map_validate/previous_processes_log_summary.json
      env:
        TEST_USER: ${{ secrets.TEST_USER }}
        TEST_PASSWORD: ${{ secrets.TEST_PASSWORD }}
        TEST_PORT: ${{ secrets.TEST_PORT }}
        GITHUB_WORKSPACE: ${{ github.workspace }}

    - name: Run build-schema module
      if: matrix.modules == 'build-schema'
      run: |
        relecov-tools build-schema \
          -i tests/data/build_schema/metadata_mapping_file.xlsx \
          --version $SCHEMA_DEFAULT_VERSION \
          --project $PROJECT_NAME \
          --non-interactive \
          -o $OUTPUT_LOCATION
      env:
        SCHEMA_DEFAULT_VERSION: "3.0.0"
        PROJECT_NAME: "relecov"

    - name: Upload output file
      uses: actions/upload-artifact@v4
      with:
        name: test-output
        path: ${{ github.workspace }}/output.txt