Update CI tests and add pre-commit #108
Workflow file for this run
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| name: Lint, validate and convert CSV to JSON-LD | |
| on: | |
| pull_request: | |
| branches: 'main' | |
| paths: 'HTAN.model.csv' | |
| workflow_dispatch: | |
| concurrency: | |
| # cancel the current running workflow from the same branch, PR when a new workflow is triggered | |
| # when the trigger is not a PR but a push, it will use the commit sha to generate the concurrency group | |
| # {{ github.workflow }}: the workflow name is used to generate the concurrency group. This allows you to have more than one workflows | |
| # {{ github.ref_type }}: the type of Git ref object created in the repository. Can be either branch or tag | |
| # {{ github.sha }}: full commit sha | |
| # credit: https://github.com/Sage-Bionetworks-Workflows/sagetasks/blob/main/.github/workflows/ci.yml | |
| group: >- | |
| ${{ github.workflow }}-${{ github.ref_type }}- | |
| ${{ github.sha }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| name: Lint CSV | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: csvlinter | |
| uses: kcheriyath/[email protected] | |
| with: | |
| find_pattern: "*.csv" | |
| validate: | |
| name: Validate CSV | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Schematic | |
| shell: bash | |
| run: | | |
| pip3 install poetry | |
| git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git | |
| cd schematic | |
| poetry build | |
| pip3 install dist/schematicpy-*-py3-none-any.whl | |
| pip install --force-reinstall typing-extensions==4.5.0 | |
| - name: Convert CSV schema | |
| shell: bash | |
| run: | | |
| schematic schema convert .github/CSV.model.csv | |
| - name: Validate data model CSV | |
| shell: bash | |
| run: | | |
| schematic model -c .github/CSV_schematic_config.yml validate -mp HTAN.model.csv -dt "DataModel" | | |
| grep "Your manifest has been validated successfully. There are no errors in your manifest, and it can be submitted without any modifications." | |
| component_requirements_check: | |
| name: Check component requirements | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_components.py | |
| attributes_exist_check: | |
| name: Check attributes exist | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_attributes_exist.py | |
| attributes_used_check: | |
| name: Check attributes are used | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_attributes_are_used.py | |
| attributes_unique_check: | |
| name: Check attributes are unique | |
| if: always() | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pandas | |
| - name: Run script | |
| shell: bash | |
| run: | | |
| python .github/workflows/check_attributes_are_unique.py | |
| convert: | |
| name: Convert CSV to JSON-LD | |
| needs: | |
| - lint | |
| - validate | |
| - component_requirements_check | |
| - attributes_exist_check | |
| - attributes_used_check | |
| - attributes_unique_check | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.9' | |
| - name: Install Schematic | |
| shell: bash | |
| run: | | |
| pip3 install poetry | |
| git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git | |
| cd schematic | |
| poetry build | |
| pip3 install dist/schematicpy-*-py3-none-any.whl | |
| - name: Convert .csv to .jsonld | |
| shell: bash | |
| run: | | |
| schematic schema convert HTAN.model.csv | |
| - uses: r-lib/actions/pr-fetch@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit the changes | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| git add HTAN.model.jsonld | |
| git commit -m "GitHub Action: convert *.model.csv to *.model.jsonld" || echo "No changes to commit" | |
| - uses: r-lib/actions/pr-push@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} |