Added 'added_by_HRA' annotations to 163 terms #136
Workflow file for this run
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| # AI review of pull requests. | |
| # | |
| # Authenticates as the `ai4c-reviewer` GitHub App, NOT `ai4c-agent`. The two are | |
| # deliberately separate identities: ai4c-agent authors PRs, so having it also | |
| # approve them would make the approval meaningless. Reviews now come from | |
| # ai4c-reviewer[bot] (app id 4388239, bot user 308941448). | |
| # | |
| # Required secrets: | |
| # - AI4C_REVIEWER_APP_ID | |
| # - AI4C_REVIEWER_PRIVATE_KEY | |
| # - CLAUDE_CODE_OAUTH_TOKEN | |
| name: Claude Code Review | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened, ready_for_review] | |
| workflow_dispatch: | |
| inputs: | |
| pr_number: | |
| description: "PR number to review" | |
| required: true | |
| type: number | |
| concurrency: | |
| group: claude-review-${{ github.event.pull_request.number || github.event.inputs.pr_number }} | |
| cancel-in-progress: true | |
| jobs: | |
| claude-review: | |
| if: github.event_name == 'workflow_dispatch' || github.event.pull_request.draft == false | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| pull-requests: write | |
| issues: read | |
| id-token: write | |
| env: | |
| PR_NUMBER: ${{ github.event.pull_request.number || github.event.inputs.pr_number }} | |
| TOOLS_DIR: ${{ github.workspace }}/tools | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 1 | |
| # create-github-app-token fails obscurely on an empty app-id, which reads | |
| # as a token problem rather than a missing secret. Fail with the actual | |
| # cause and the fix instead. | |
| - name: Check reviewer app secrets are configured | |
| env: | |
| APP_ID: ${{ secrets.AI4C_REVIEWER_APP_ID }} | |
| PRIVATE_KEY: ${{ secrets.AI4C_REVIEWER_PRIVATE_KEY }} | |
| run: | | |
| set -euo pipefail | |
| missing="" | |
| [[ -n "${APP_ID:-}" ]] || missing="$missing AI4C_REVIEWER_APP_ID" | |
| [[ -n "${PRIVATE_KEY:-}" ]] || missing="$missing AI4C_REVIEWER_PRIVATE_KEY" | |
| if [[ -n "$missing" ]]; then | |
| echo "::error title=ai4c-reviewer not configured::Missing secret(s):$missing. This workflow authenticates as the ai4c-reviewer GitHub App, which is separate from ai4c-agent. Install the app on this repository and add the secrets; app id is 4388239." | |
| exit 1 | |
| fi | |
| - name: Generate ai4c-reviewer token | |
| id: reviewer-token | |
| uses: actions/create-github-app-token@v3 | |
| with: | |
| app-id: ${{ secrets.AI4C_REVIEWER_APP_ID }} | |
| private-key: ${{ secrets.AI4C_REVIEWER_PRIVATE_KEY }} | |
| - name: Checkout PR branch (for workflow_dispatch) | |
| if: github.event_name == 'workflow_dispatch' | |
| env: | |
| GH_TOKEN: ${{ steps.reviewer-token.outputs.token }} | |
| run: gh pr checkout "${{ env.PR_NUMBER }}" | |
| - name: Create tools directory | |
| run: mkdir -p "${{ env.TOOLS_DIR }}" | |
| - name: Add tools to PATH | |
| run: echo "${{ env.TOOLS_DIR }}" >> "$GITHUB_PATH" | |
| - name: Add obo-scripts to PATH | |
| run: | | |
| git clone --depth 1 https://github.com/cmungall/obo-scripts.git "${{ env.TOOLS_DIR }}/obo-scripts" | |
| echo "${{ env.TOOLS_DIR }}/obo-scripts" >> "$GITHUB_PATH" | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| - name: Install Python tools | |
| run: | | |
| uv venv | |
| . .venv/bin/activate | |
| uv pip install aurelian "wrapt>=1.17.2" | |
| echo "${{ github.workspace }}/.venv/bin" >> "$GITHUB_PATH" | |
| - name: Run Claude Code Review | |
| uses: anthropics/claude-code-action@v1 | |
| with: | |
| claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} | |
| github_token: ${{ steps.reviewer-token.outputs.token }} | |
| track_progress: ${{ github.event_name == 'pull_request' }} | |
| # This lists the PR *author* to accept, not the reviewer identity: | |
| # ai4c-agent opens PRs and reviewing them is the main point, so it must | |
| # stay here even though the job now authenticates as ai4c-reviewer. | |
| allowed_bots: "claude,github-actions,ai4c-agent" | |
| claude_args: | | |
| --allowedTools "mcp__github_inline_comment__create_inline_comment,Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr review:*),Bash(gh api:*),Bash(obo-grep.pl:*),Bash(aurelian:*),Bash(cat:*),Bash(sed:*),Bash(head:*),Bash(tail:*),Bash(wc:*),Bash(find:*),Bash(ls:*),Bash(rg:*)" | |
| prompt: | | |
| REPO: ${{ github.repository }} | |
| PR NUMBER: ${{ env.PR_NUMBER }} | |
| Review this pull request for the Uberon ontology repository. | |
| Follow the repository instructions in `CLAUDE.md`. | |
| When you need to inspect ontology content in `src/ontology/uberon-edit.obo`, use only: | |
| - `obo-grep.pl -r 'id: UBERON:NNNNNNN' src/ontology/uberon-edit.obo` | |
| - `obo-grep.pl -r 'UBERON:NNNNNNN' src/ontology/uberon-edit.obo` | |
| Focus on: | |
| - Hierarchy and proposed parents being anatomically and logically consistent | |
| - Definitions, xrefs, and PMIDs being real and adequately supportive | |
| - Obsolete-term handling and replacement or consider tags being safe | |
| - OBO and ODK conventions being preserved | |
| - Workflow, auth, and repo-configuration regressions when the PR touches `.github` or `.claude` | |
| Be constructive and specific. For each issue found, indicate severity: | |
| - 🔴 CRITICAL: Must fix before merge | |
| - 🟡 IMPORTANT: Should fix before merge | |
| - 🔵 SUGGESTION: Optional improvement | |
| Prefer inline comments for concrete file-level issues. Use the overall review summary to explain the main risks and the merge recommendation. | |
| After reviewing, set the GitHub PR review status: | |
| If there are any 🔴 CRITICAL or 🟡 IMPORTANT issues, submit a REQUEST_CHANGES review: | |
| ``` | |
| gh pr review ${{ env.PR_NUMBER }} --request-changes --body "<your review summary>" | |
| ``` | |
| If there are only 🔵 SUGGESTIONs or no issues, submit an APPROVE review: | |
| ``` | |
| gh pr review ${{ env.PR_NUMBER }} --approve --body "<your review summary>" | |
| ``` | |
| Always include a checklist at the top of your review: | |
| - [ ] Hierarchy and parents are consistent | |
| - [ ] Definitions and supporting references look adequate | |
| - [ ] Obsolete or replacement handling is safe | |
| - [ ] OBO and ODK conventions appear preserved | |
| - [ ] No obvious CI, auth, or workflow regression |