change ms-based attribute to match depends on in assay. #37
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Lint, validate and convert CSV to JSON-LD | |
| on: | |
| pull_request: | |
| branches: 'main' | |
| paths: 'HTAN.model.csv' | |
| workflow_dispatch: | |
| jobs: | |
| lint: | |
| name: Lint CSV | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: csvlinter | |
| uses: kcheriyath/[email protected] | |
| with: | |
| find_pattern: "*.csv" | |
| validate: | |
| name: Validate CSV | |
| 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_check: | |
| name: Check Component DependsOn entries | |
| 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 | |
| convert: | |
| name: Convert CSV to JSON-LD | |
| needs: | |
| - lint | |
| - validate | |
| - component_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 }} |