Reorganization of SDCs #132
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| name: PR Quality Checks | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| jobs: | |
| pr-checks: | |
| name: PR Quality Checks | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.6 | |
| outputs: | |
| annotations_added: ${{ steps.fix.outputs.annotations_added }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.head_ref }} | |
| # --- ODK tests on the committed workspace --- | |
| - name: ODK tests (IRI ranges, consistency, SPARQL checks, OBO report) | |
| run: | | |
| cd src/ontology/ | |
| make IMP=false PAT=false COMP=false MIR=false validate_idranges reason_test sparql_test robot_reports | |
| # --- Merge + DL profile check (reuse ODK's merged file) --- | |
| - name: Merge and validate OWL DL profile | |
| run: | | |
| cd src/ontology | |
| robot --catalog catalog-v001.xml \ | |
| validate-profile --profile DL \ | |
| --input tmp/merged-pmdco-edit.ofn \ | |
| --output ../../validation.txt \ | |
| || { cat ../../validation.txt; exit 1; } | |
| # --- Determine curation status via SPARQL, then auto-annotate --- | |
| - name: Query other violations for curation status | |
| run: | | |
| cd src/ontology | |
| robot --catalog catalog-v001.xml query \ | |
| --input tmp/merged-pmdco-edit.ofn \ | |
| --query ../../.github/workflow_resources/q_pmdco_other_violations.sparql \ | |
| ../../other_violations.csv | |
| - id: fix | |
| name: Add missing IAO_0000114 / IAO_0000117 to component files | |
| run: | | |
| python3 scripts/fix_missing_annotations.py \ | |
| src/ontology/components \ | |
| --violations-report other_violations.csv | tee annotation_log.txt | |
| if grep -q "No missing annotations" annotation_log.txt; then | |
| echo "annotations_added=false" >> $GITHUB_OUTPUT | |
| else | |
| echo "annotations_added=true" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Upload patched component files | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: patched-components | |
| path: src/ontology/components/ | |
| retention-days: 1 | |
| # --- Final check and report on patched ontology --- | |
| - name: Merge patched ontology | |
| run: | | |
| cd src/ontology | |
| robot merge --catalog catalog-v001.xml \ | |
| --input pmdco-edit.owl \ | |
| --output ../../pmdco-merged.ttl | |
| - name: Check for blocking violations (robot verify) | |
| run: | | |
| cd src/ontology | |
| robot --catalog catalog-v001.xml verify \ | |
| --input ../../pmdco-merged.ttl \ | |
| --queries ../../.github/workflow_resources/q_pmdco_blocking.sparql | |
| - name: Generate and render violations report | |
| if: always() | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| cd src/ontology | |
| robot --catalog catalog-v001.xml query \ | |
| --input ../../pmdco-merged.ttl \ | |
| --query ../../.github/workflow_resources/q_pmdco_blocking.sparql \ | |
| ../../violations.csv | |
| robot --catalog catalog-v001.xml query \ | |
| --input ../../pmdco-merged.ttl \ | |
| --query ../../.github/workflow_resources/q_pmdco_warnings.sparql \ | |
| ../../warnings.csv | |
| cd ../.. | |
| python3 - <<'EOF' | |
| import csv, os, re, subprocess | |
| def annotation_table(log_path): | |
| try: | |
| lines = open(log_path).readlines() | |
| except FileNotFoundError: | |
| return "_Annotation log not available._" | |
| rows = [] | |
| for line in lines: | |
| m = re.search(r'(\S+\.owl):\s+\+(\d+) annotation\(s\) on (\d+) term\(s\)', line) | |
| if m: | |
| rows.append((m.group(1), m.group(3), m.group(2))) | |
| if not rows: | |
| return "_No annotations were auto-added._" | |
| total_terms = sum(int(r[1]) for r in rows) | |
| total_ann = sum(int(r[2]) for r in rows) | |
| tbl = "| file | terms | annotations added |\n" | |
| tbl += "| --- | --- | --- |\n" | |
| for fname, terms, ann in rows: | |
| tbl += f"| {fname} | {terms} | {ann} |\n" | |
| tbl += f"| **Total** | **{total_terms}** | **{total_ann}** |\n" | |
| return tbl | |
| def issues_table(violations_path, warnings_path): | |
| rows = [] | |
| for path, severity in [(violations_path, "Blocking"), (warnings_path, "Warning")]: | |
| try: | |
| for row in csv.DictReader(open(path)): | |
| rows.append((row.get("term",""), row.get("issue",""), severity)) | |
| except FileNotFoundError: | |
| pass | |
| if not rows: | |
| return "_No issues found — all terms conform._" | |
| tbl = "| term | issue | severity |\n" | |
| tbl += "| --- | --- | --- |\n" | |
| for term, issue, sev in rows: | |
| tbl += f"| {term} | {issue} | {sev} |\n" | |
| return tbl | |
| ann_md = annotation_table("annotation_log.txt") | |
| issues_md = issues_table("violations.csv", "warnings.csv") | |
| md = ( | |
| "## PMDco Quality Check\n\n" | |
| "### Auto-added annotations\n" + ann_md + "\n\n" | |
| "### Hygiene issues\n" + issues_md + "\n" | |
| ) | |
| with open(os.environ["GITHUB_STEP_SUMMARY"], "a") as f: | |
| f.write(md) | |
| marker = "<!-- pmdco-quality-report -->" | |
| body = marker + "\n" + md | |
| pr = os.environ.get("GITHUB_REF", "").replace("refs/pull/", "").replace("/merge", "") | |
| if pr.isdigit(): | |
| repo = os.environ["GITHUB_REPOSITORY"] | |
| result = subprocess.run( | |
| ["gh", "api", f"repos/{repo}/issues/{pr}/comments", "--jq", | |
| f'[.[] | select(.body | startswith("{marker}")) | .id][0]'], | |
| capture_output=True, text=True | |
| ) | |
| comment_id = result.stdout.strip() | |
| if comment_id and comment_id != "null": | |
| subprocess.run(["gh", "api", f"repos/{repo}/issues/comments/{comment_id}", | |
| "-X", "PATCH", "-f", f"body={body}"], check=True) | |
| else: | |
| subprocess.run(["gh", "pr", "comment", pr, "--repo", repo, | |
| "--body", body], check=True) | |
| EOF | |
| - name: Archive violations report | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: violations-report | |
| path: | | |
| violations.csv | |
| warnings.csv | |
| annotation_log.txt | |
| commit-annotations: | |
| name: Commit annotation fixes | |
| needs: pr-checks | |
| if: | | |
| needs.pr-checks.outputs.annotations_added == 'true' && | |
| needs.pr-checks.result == 'success' && | |
| github.event.pull_request.head.repo.full_name == github.repository | |
| permissions: | |
| contents: write | |
| statuses: write | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.head_ref }} | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Apply patched component files | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: patched-components | |
| path: src/ontology/components/ | |
| - name: Commit and push | |
| run: | | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| git config user.name "github-actions[bot]" | |
| git add src/ontology/components/ | |
| git diff --cached --quiet && echo "Nothing to commit." || \ | |
| git commit -m "chore: auto-fill missing IAO_0000114/IAO_0000117 annotations" | |
| git push | |
| - name: Forward check status to new commit | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| NEW_SHA=$(git rev-parse HEAD) | |
| gh api repos/${{ github.repository }}/statuses/$NEW_SHA \ | |
| -f state=success \ | |
| -f context="PR Quality Checks / pr-checks" \ | |
| -f description="All checks passed (annotations auto-filled)" \ | |
| -f target_url="https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}" |