Patch CITE-seq L1 cDNA #245
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: Make 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 | |
| env: | |
| SCHEMATIC_VERSION: '24.2.1' | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| lint: | |
| name: Lint CSV | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: csvlinter | |
| uses: kcheriyath/[email protected] | |
| with: | |
| find_pattern: "*.csv" | |
| validate: | |
| name: Validate CSV | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install IPython | |
| run: | | |
| pip install ipython==8.18.1 | |
| - name: Install Schematic | |
| run: | | |
| pip install schematicpy==$SCHEMATIC_VERSION | |
| - name: Convert CSV schema | |
| run: | | |
| schematic schema convert .github/CSV.model.csv | |
| - name: Validate data model CSV | |
| 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." | |
| convert: | |
| name: Convert CSV to JSON-LD | |
| needs: | |
| - lint | |
| - validate | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install IPython | |
| run: | | |
| pip install ipython==8.18.1 | |
| - name: Install Schematic | |
| run: | | |
| pip install schematicpy==$SCHEMATIC_VERSION | |
| - name: Convert .csv to .jsonld | |
| run: | | |
| schematic schema convert HTAN.model.csv | |
| - name: Set up Git user | |
| run: | | |
| git config --local user.name "github-actions[bot]" | |
| git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| - name: Fetch PR details | |
| if: github.event_name == 'pull_request' | |
| uses: r-lib/actions/pr-fetch@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Commit the changes | |
| run: | | |
| # Specifying the full email allows the avatar to show up: https://github.com/orgs/community/discussions/26560 | |
| git add HTAN.model.jsonld | |
| git commit -m "GitHub Action: convert *.model.csv to *.model.jsonld" || echo "No changes to commit" | |
| - name: Push changes back to PR | |
| if: github.event_name == 'pull_request' | |
| uses: r-lib/actions/pr-push@v2 | |
| with: | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} |