Find UniProt names of ChEBI compounds #18
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| name: Add SPARQL query example | |
| on: | |
| issues: | |
| types: [opened] | |
| permissions: | |
| issues: write | |
| contents: write | |
| pull-requests: write | |
| # NOTE: You will need to enable gh actions workflows to create PRs in your org and repo settings | |
| # At the bottom of the "Actions" tab check "Allow GitHub Actions to create and approve pull requests" | |
| jobs: | |
| add_example: | |
| runs-on: ubuntu-latest | |
| if: contains(github.event.issue.labels.*.name, 'add-example') | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v5 | |
| - name: Set up Java | |
| uses: actions/setup-java@v5 | |
| with: | |
| distribution: 'graalvm' | |
| java-version: '25' | |
| - name: Set up Python | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: '3.x' | |
| - name: Download sparql-examples-utils.jar | |
| run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.24/sparql-examples-utils-2.0.24-uber.jar" -O sparql-examples-utils.jar | |
| - name: Parse issue and create turtle file | |
| id: create_ttl | |
| run: java -Xss8m -jar sparql-examples-utils.jar import-github-issue -i ./examples -t tmp 2> error.log >> $GITHUB_OUTPUT | |
| env: | |
| GITHUB_ISSUE_BODY: ${{ github.event.issue.body }} | |
| - name: Validate generated SPARQL query example | |
| id: validate | |
| if: success() | |
| run: java -jar sparql-examples-utils.jar test -i ./examples -p tmp --also-run-slow-tests > error.log 2>&1 | |
| - name: Clean up temporary files | |
| if: success() | |
| run: | | |
| rm -f error.log | |
| rm -rf examples/tmp | |
| - name: Create Pull Request with validated query | |
| if: success() | |
| uses: peter-evans/create-pull-request@v7 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| commit-message: "Add SPARQL query example `${{ steps.create_ttl.outputs.output_file }}` (from issue #${{ github.event.issue.number }})" | |
| title: "Add example: ${{ steps.create_ttl.outputs.output_file }}" | |
| body: | | |
| ## Adding SPARQL Query | |
| This PR adds the SPARQL query example `${{ steps.create_ttl.outputs.output_file }}` submitted in issue #${{ github.event.issue.number }} with the following description: | |
| > ${{ steps.create_ttl.outputs.query_description }} | |
| This PR was automatically created after successful validation and execution of the SPARQL query. | |
| Closes #${{ github.event.issue.number }} | |
| branch: add-example-${{ github.event.issue.number }} | |
| delete-branch: true | |
| labels: | | |
| add-example | |
| automated-pr | |
| - name: Comment successful validation in issue | |
| if: success() | |
| uses: actions/github-script@v8 | |
| with: | |
| script: | | |
| const targetPath = '${{ steps.create_ttl.outputs.output_file }}'; | |
| const comment = `## ✅ Query validation successful | |
| Your SPARQL query \`${targetPath}\` has been validated and a pull request has been created for review. | |
| The query will be added to the SPARQL examples collection once the pull request is reviewed and merged. | |
| Thank you for your contribution!`; | |
| await github.rest.issues.createComment({ | |
| issue_number: context.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| body: comment | |
| }); | |
| - name: Comment on validation failure and close issue | |
| if: failure() | |
| uses: actions/github-script@v8 | |
| with: | |
| script: | | |
| const fs = require('fs'); | |
| let errorMessage = 'No error details available'; | |
| try { | |
| const log = fs.readFileSync('error.log', 'utf8').trim(); | |
| if (log) errorMessage = log; | |
| } catch (e) {} | |
| const comment = `## ❌ Query validation failed | |
| Your SPARQL query did not pass validation. Please check the following: | |
| 1. **Syntax**: Ensure your SPARQL query syntax is correct | |
| 2. **Prefixes**: Make sure all prefixes used in the query are properly defined | |
| 3. **Endpoint compatibility**: Verify that your query is compatible with the selected endpoint | |
| **⚠️ Error details:** | |
| \`\`\` | |
| ${errorMessage} | |
| \`\`\` | |
| Please fix the query, and make sure of the following: | |
| 1. **Syntax**: Ensure your SPARQL query syntax is correct | |
| 2. **Prefixes**: Make sure all prefixes used in the query are properly defined | |
| 3. **Results**: Verify that your query returns results with the selected endpoint(s) | |
| Then **create a new issue** with the corrected version. The validation will run again automatically.`; | |
| await github.rest.issues.createComment({ | |
| issue_number: context.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| body: comment | |
| }); | |
| await github.rest.issues.update({ | |
| issue_number: context.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| state: 'closed' | |
| }); |