Create __init__.py #3
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| name: Schema Submission | ||
| on: | ||
| issues: | ||
| types: [opened] | ||
| jobs: | ||
| ingest: | ||
| # Only run if issue title starts with "schema-submission:" | ||
| if: startsWith(github.event.issue.title, 'schema-submission:') | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: write | ||
| issues: write | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
| - name: Set up Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
| - name: Install dependencies | ||
| run: pip install -r requirements.txt | ||
| - name: Extract schema name from issue title | ||
| id: meta | ||
| run: | | ||
| TITLE="${{ github.event.issue.title }}" | ||
| # title format: "schema-submission:my-schema-name" | ||
| SCHEMA_NAME="${TITLE#schema-submission:}" | ||
| SCHEMA_NAME=$(echo "$SCHEMA_NAME" | tr -s ' ' | xargs | tr ' ' '-' | tr '[:upper:]' '[:lower:]') | ||
| echo "schema_name=$SCHEMA_NAME" >> $GITHUB_OUTPUT | ||
| - name: Extract YAML from issue body | ||
| id: extract | ||
| env: | ||
| ISSUE_BODY: ${{ github.event.issue.body }} | ||
| run: | | ||
| python3 - << 'PYEOF' | ||
| import os, re, sys | ||
| body = os.environ["ISSUE_BODY"] | ||
| # Accept YAML fenced in ```yaml ... ``` or bare (no fence) | ||
| fenced = re.search(r'```ya?ml\s*\n(.*?)```', body, re.DOTALL) | ||
| if fenced: | ||
| yaml_content = fenced.group(1) | ||
| else: | ||
| yaml_content = body.strip() | ||
| # Basic sanity check — must look like LinkML | ||
| if "classes:" not in yaml_content: | ||
| print("ERROR: issue body does not contain a valid LinkML schema (missing 'classes:' key).") | ||
| sys.exit(1) | ||
| schema_name = os.environ.get("SCHEMA_NAME", "unknown") | ||
| out_path = f"schemas/{schema_name}.yml" | ||
| os.makedirs("schemas", exist_ok=True) | ||
| with open(out_path, "w") as f: | ||
| f.write(yaml_content) | ||
| print(f"Wrote {out_path}") | ||
| PYEOF | ||
| env: | ||
| SCHEMA_NAME: ${{ steps.meta.outputs.schema_name }} | ||
| - name: Validate YAML parses as LinkML | ||
| run: | | ||
| python3 - << 'PYEOF' | ||
| import yaml, sys | ||
| name = "${{ steps.meta.outputs.schema_name }}" | ||
| path = f"schemas/{name}.yml" | ||
| with open(path) as f: | ||
| data = yaml.safe_load(f) | ||
| required = ["classes", "slots"] | ||
| missing = [k for k in required if k not in data] | ||
| if missing: | ||
| print(f"ERROR: schema missing required keys: {missing}") | ||
| sys.exit(1) | ||
| print(f"Valid LinkML schema: {len(data.get('classes', {}))} classes, {len(data.get('slots', {}))} slots") | ||
| PYEOF | ||
| - name: Ingest schema into registry | ||
| run: | | ||
| python neuro_registry/ingest_linkml.py \ | ||
| --file schemas/${{ steps.meta.outputs.schema_name }}.yml \ | ||
| --db registry.lbug | ||
| - name: Run alignment | ||
| run: | | ||
| python neuro_registry/align.py \ | ||
| --source ${{ steps.meta.outputs.schema_name }} \ | ||
| --db registry.lbug | ||
| - name: Export registry snapshot to JSON | ||
| run: | | ||
| python neuro_registry/export_json.py \ | ||
| --db registry.lbug \ | ||
| --out data/registry.json | ||
| - name: Commit schema file + updated data snapshot | ||
| run: | | ||
| git config user.name "github-actions[bot]" | ||
| git config user.email "github-actions[bot]@users.noreply.github.com" | ||
| git add schemas/${{ steps.meta.outputs.schema_name }}.yml data/registry.json | ||
| git diff --cached --quiet || git commit -m \ | ||
| "feat(schema): ingest ${{ steps.meta.outputs.schema_name }} from issue #${{ github.event.issue.number }}" | ||
| git push | ||
| - name: Comment on issue — success | ||
| if: success() | ||
| uses: actions/github-script@v7 | ||
| with: | ||
| script: | | ||
| const name = "${{ steps.meta.outputs.schema_name }}"; | ||
| const pagesUrl = `https://${context.repo.owner}.github.io/${context.repo.repo}`; | ||
| await github.rest.issues.createComment({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| issue_number: context.issue.number, | ||
| body: [ | ||
| `✅ **Schema \`${name}\` ingested successfully.**`, | ||
| ``, | ||
| `- Classes and properties have been added to the registry.`, | ||
| `- Alignment against existing schemas has been computed.`, | ||
| `- Registry snapshot updated at \`data/registry.json\`.`, | ||
| ``, | ||
| `Browse the updated schema at: ${pagesUrl}`, | ||
| ].join("\n"), | ||
| }); | ||
| await github.rest.issues.update({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| issue_number: context.issue.number, | ||
| state: "closed", | ||
| }); | ||
| - name: Comment on issue — failure | ||
| if: failure() | ||
| uses: actions/github-script@v7 | ||
| with: | ||
| script: | | ||
| await github.rest.issues.createComment({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| issue_number: context.issue.number, | ||
| body: [ | ||
| `❌ **Schema ingestion failed.**`, | ||
| ``, | ||
| `Please check that your issue body contains a valid LinkML YAML schema`, | ||
| `with both \`classes:\` and \`slots:\` keys, optionally fenced in \`\`\`yaml ... \`\`\`.`, | ||
| ``, | ||
| `[View the workflow run for details](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }})`, | ||
| ].join("\n"), | ||
| }); | ||
