Make JSON-LD and Build Dependencies Table #258
Workflow file for this run
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| name: Make JSON-LD and Build Dependencies Table | |
| on: | |
| pull_request: | |
| branches: 'main' | |
| paths: 'HTAN.model.csv' | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| concurrency: | |
| 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: | | |
| 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 }} | |
| build-dependencies: | |
| name: Build Dependencies Table | |
| needs: convert | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Fetch latest changes | |
| run: git pull origin main | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install requests pandas | |
| - name: Fetch attribute table | |
| run: | | |
| python - <<EOF | |
| import requests | |
| import pandas as pd | |
| from io import StringIO | |
| def fetch_and_save_attribute_table(): | |
| url = "https://schematic.api.sagebionetworks.org/v1/visualize/attributes" | |
| jsonld_url = "https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld" | |
| params = {'schema_url': jsonld_url} | |
| print("Fetching attribute table...") | |
| response = requests.get(url, params=params) | |
| print(f"Status Code: {response.status_code}") | |
| if response.status_code == 200: | |
| content_type = response.headers.get('Content-Type', '') | |
| if 'text/html' in content_type: | |
| print("Response in text/html format, converting to CSV...") | |
| try: | |
| df = pd.read_csv(StringIO(response.text)) | |
| print("Fetched attribute table.") | |
| df.to_csv('HTAN.dependencies.csv', index=False) | |
| print("Saved to HTAN.dependencies.csv.") | |
| except Exception as e: | |
| print(f"Error processing CSV: {e}") | |
| else: | |
| print("Unexpected content type. Expected text/html but got:", content_type) | |
| else: | |
| print(f"Failed to fetch data. Status Code: {response.status_code}") | |
| fetch_and_save_attribute_table() | |
| EOF | |
| - name: Commit changes | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git add HTAN.dependencies.csv | |
| git commit -m "Update HTAN.dependencies.csv with the latest attribute table" || echo "No changes to commit" | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| commit-message: "Update HTAN.dependencies.csv" | |
| branch: update-attribute-table | |
| title: "Update HTAN.dependencies.csv" | |
| body: "This PR updates HTAN.dependencies.csv with the latest attribute table." |