Add HRA palatine-tonsil NTR template (7 new terms) #1631
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| # AI Agent triggered by @mentions in issues/PRs | |
| # | |
| # Listens for @<agent-name> please <request> mentions from authorized users | |
| # and runs Claude Code to respond. | |
| # | |
| # Authenticates as the `ai4c-agent` GitHub App (installation token minted per | |
| # job), not as a machine account PAT. Same app and secret names already used by | |
| # claude-code-review.yml. | |
| # | |
| # Required secrets: | |
| # - AI4C_AGENT_APP_ID | |
| # - AI4C_AGENT_PRIVATE_KEY | |
| # - CLAUDE_CODE_OAUTH_TOKEN | |
| # | |
| # Configuration: | |
| # - .github/ai-controllers.json (list of authorized usernames) | |
| # | |
| name: AI Agent GitHub Mentions | |
| env: | |
| # The handle controllers type to invoke the agent. NOT a real GitHub account: | |
| # the app's login is AGENT_LOGIN (`<name>[bot]`), and apps cannot be | |
| # @-mentioned, so "@ai4c-agent" renders as plain text. | |
| AGENT_MENTION: ai4c-agent | |
| # Deprecated handles still honoured as triggers (comma-separated). Also the | |
| # only logins that can work as assignment triggers -- see ASSIGNMENT below. | |
| AGENT_MENTION_LEGACY: dragon-ai-agent | |
| # GitHub App bot identity, for commit attribution. AGENT_USER_ID is the | |
| # numeric id of the ai4c-agent[bot] *account* | |
| # (`gh api /users/ai4c-agent%5Bbot%5D`), NOT the app id in | |
| # AI4C_AGENT_APP_ID -- different numbers. Public, hence plain env. | |
| AGENT_LOGIN: ai4c-agent[bot] | |
| AGENT_USER_ID: 242316268 | |
| MODEL: claude-opus-4-7 | |
| TOOLS_DIR: ${{ github.workspace }}/tools | |
| TIMEOUT_MINUTES: 30 | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| issue_number: | |
| description: "Issue or PR number to respond to" | |
| required: true | |
| item_type: | |
| description: "Type of item (issue or pull_request)" | |
| required: true | |
| type: choice | |
| options: | |
| - issue | |
| - pull_request | |
| prompt: | |
| description: "The request/prompt for the agent" | |
| required: true | |
| # ASSIGNMENT: `assigned` lets authorized controllers dispatch work by | |
| # assigning the agent directly. NOTE this cannot work with the GitHub App -- | |
| # `ai4c-agent[bot]` is not an assignable user, so only the legacy | |
| # `dragon-ai-agent` machine account can still trigger this path, and only for | |
| # as long as that account exists. See `agentAssignees` in the check script. | |
| issues: | |
| types: [opened, edited, assigned] | |
| issue_comment: | |
| types: [created, edited] | |
| pull_request: | |
| types: [opened, edited, assigned, synchronize] | |
| pull_request_review_comment: | |
| types: [created, edited] | |
| jobs: | |
| check-mention: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| issues: write | |
| pull-requests: write | |
| outputs: | |
| result: ${{ steps.check.outputs.result }} | |
| steps: | |
| # Minted per-job: installation tokens are short-lived (1h) and must not be | |
| # passed between jobs, since GitHub's log masking does not follow job | |
| # outputs. | |
| - name: Mint app token | |
| id: app-token | |
| uses: actions/create-github-app-token@v3 | |
| with: | |
| app-id: ${{ secrets.AI4C_AGENT_APP_ID }} | |
| private-key: ${{ secrets.AI4C_AGENT_PRIVATE_KEY }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 1 | |
| token: ${{ steps.app-token.outputs.token }} | |
| - name: Check for qualifying mention | |
| id: check | |
| uses: actions/github-script@v8 | |
| with: | |
| github-token: ${{ steps.app-token.outputs.token }} | |
| script: | | |
| const fs = require("fs"); | |
| let allowedUsers = []; | |
| try { | |
| const configContent = fs.readFileSync(".github/ai-controllers.json", "utf8"); | |
| allowedUsers = JSON.parse(configContent); | |
| } catch (error) { | |
| console.log("Error loading allowed users:", error); | |
| allowedUsers = ["cmungall"]; | |
| } | |
| // Trigger on the canonical handle plus any legacy aliases, with an | |
| // optional [bot] suffix (people paste back what they see the bot | |
| // signing as). | |
| const agentName = process.env.AGENT_MENTION; | |
| const legacyNames = (process.env.AGENT_MENTION_LEGACY || "") | |
| .split(",").map((s) => s.trim()).filter(Boolean); | |
| const escapeRe = (s) => s.replace(/[.*+?^${}()|[\]\\]/g, "\\$&"); | |
| const mentionAlternation = [agentName, ...legacyNames].map(escapeRe).join("|"); | |
| // Assignment dispatch can only ever match a real, assignable user | |
| // account. The app's `ai4c-agent[bot]` login is not assignable, so | |
| // this is the legacy names only. | |
| const agentAssignees = legacyNames; | |
| if (context.eventName === "workflow_dispatch") { | |
| const inputs = context.payload.inputs; | |
| const itemType = inputs.item_type; | |
| const itemNumber = parseInt(inputs.issue_number, 10); | |
| const prompt = inputs.prompt; | |
| const combined = `${prompt}`.toLowerCase(); | |
| const skipOdk = combined.includes("skip_odk") || combined.includes("quick question"); | |
| return { | |
| qualifiedMention: true, | |
| itemType, | |
| itemNumber, | |
| user: context.actor, | |
| prompt, | |
| branchName: `${agentName}-${itemType}-${itemNumber}-run${context.runNumber}`, | |
| useOdkContainer: !skipOdk, | |
| skipOdkNote: skipOdk | |
| ? "NOTE: This is NOT running in the ODK container (SKIP_ODK or quick question was specified), so ODK tools like ROBOT may be unavailable." | |
| : "", | |
| }; | |
| } | |
| let content = ""; | |
| let userLogin = ""; | |
| let itemType = ""; | |
| let itemNumber = 0; | |
| let commentId = null; | |
| let reactionTarget = "issue"; | |
| if (context.eventName === "issues") { | |
| content = context.payload.issue.body || ""; | |
| userLogin = context.payload.action === "assigned" | |
| ? (context.payload.sender?.login || context.payload.issue.user.login) | |
| : context.payload.issue.user.login; | |
| itemType = "issue"; | |
| itemNumber = context.payload.issue.number; | |
| } else if (context.eventName === "pull_request") { | |
| content = context.payload.pull_request.body || ""; | |
| userLogin = context.payload.action === "assigned" | |
| ? (context.payload.sender?.login || context.payload.pull_request.user.login) | |
| : context.payload.pull_request.user.login; | |
| itemType = "pull_request"; | |
| itemNumber = context.payload.pull_request.number; | |
| } else if (context.eventName === "issue_comment") { | |
| content = context.payload.comment.body || ""; | |
| userLogin = context.payload.comment.user.login; | |
| itemType = context.payload.issue.pull_request ? "pull_request" : "issue"; | |
| itemNumber = context.payload.issue.number; | |
| commentId = context.payload.comment.id; | |
| reactionTarget = "issue_comment"; | |
| } else if (context.eventName === "pull_request_review_comment") { | |
| content = context.payload.comment.body || ""; | |
| userLogin = context.payload.comment.user.login; | |
| itemType = "pull_request"; | |
| itemNumber = context.payload.pull_request.number; | |
| commentId = context.payload.comment.id; | |
| reactionTarget = "pull_request_review_comment"; | |
| } | |
| // Never act on our own output. Unlike GITHUB_TOKEN, events authored | |
| // with an app installation token do retrigger workflows. | |
| if (userLogin.endsWith("[bot]")) { | |
| console.log(`Ignoring bot author: ${userLogin}`); | |
| return { qualifiedMention: false }; | |
| } | |
| const isAllowed = allowedUsers.includes(userLogin); | |
| const mentionRegex = new RegExp( | |
| `@(${mentionAlternation})(?:\\[bot\\])?\\s+please\\s+([\\s\\S]*)`, "i"); | |
| const mentionMatch = content.match(mentionRegex); | |
| // On synchronize we want this workflow to revalidate on push without | |
| // re-dispatching the agent from a stale PR body mention. | |
| const shouldHonorBodyMention = | |
| (context.eventName === "issues" && ["opened", "edited"].includes(context.payload.action)) || | |
| (context.eventName === "pull_request" && ["opened", "edited"].includes(context.payload.action)) || | |
| context.eventName === "issue_comment" || | |
| context.eventName === "pull_request_review_comment"; | |
| const isAgentAssignment = | |
| (context.eventName === "issues" || context.eventName === "pull_request") && | |
| context.payload.action === "assigned" && | |
| agentAssignees.includes(context.payload.assignee?.login); | |
| const hasQualifiedBodyMention = | |
| isAllowed && shouldHonorBodyMention && mentionMatch !== null; | |
| const qualifiedMention = | |
| hasQualifiedBodyMention || (isAllowed && isAgentAssignment); | |
| const prompt = hasQualifiedBodyMention | |
| ? mentionMatch[2].trim() | |
| : (isAgentAssignment | |
| ? "You were assigned to this item. Read the full GitHub context, identify the next concrete action, and carry it through." | |
| : ""); | |
| const mentionUsed = mentionMatch ? mentionMatch[1] : ""; | |
| const usedLegacyMention = | |
| hasQualifiedBodyMention && mentionUsed.toLowerCase() !== agentName.toLowerCase(); | |
| console.log( | |
| `User: ${userLogin}, Allowed: ${isAllowed}, Has mention: ${mentionMatch !== null}, ` + | |
| `Handle: ${mentionUsed}, ` + | |
| `Honor body mention: ${shouldHonorBodyMention}, ` + | |
| `Agent assignment: ${isAgentAssignment}` | |
| ); | |
| if (!qualifiedMention) { | |
| return { qualifiedMention: false }; | |
| } | |
| try { | |
| if (reactionTarget === "issue_comment") { | |
| await github.rest.reactions.createForIssueComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| comment_id: commentId, | |
| content: "eyes", | |
| }); | |
| } else if (reactionTarget === "pull_request_review_comment") { | |
| await github.rest.reactions.createForPullRequestReviewComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| comment_id: commentId, | |
| content: "eyes", | |
| }); | |
| } else { | |
| await github.rest.reactions.createForIssue({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: itemNumber, | |
| content: "eyes", | |
| }); | |
| } | |
| } catch (error) { | |
| console.log("Could not add reaction:", error.message); | |
| } | |
| try { | |
| const runUrl = `https://github.com/${context.repo.owner}/${context.repo.repo}/actions/runs/${context.runId}`; | |
| const deprecationNote = usedLegacyMention | |
| ? `\n\n> [!NOTE]\n> \`@${mentionUsed}\` is deprecated and will stop working. Please use \`@${agentName} please ...\` from now on.` | |
| : ""; | |
| const commentBody = `🤖 Working on it...\n\nFollow along: [View workflow run](${runUrl})${deprecationNote}\n\n*— @${agentName}*`; | |
| await github.rest.issues.createComment({ | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| issue_number: itemNumber, | |
| body: commentBody, | |
| }); | |
| } catch (error) { | |
| console.log("Could not post comment:", error.message); | |
| } | |
| const baseBody = | |
| context.payload.issue?.body || | |
| context.payload.pull_request?.body || | |
| ""; | |
| const combined = `${baseBody}\n${content}`.toLowerCase(); | |
| const skipOdk = combined.includes("skip_odk") || combined.includes("quick question"); | |
| return { | |
| qualifiedMention: true, | |
| itemType, | |
| itemNumber, | |
| user: userLogin, | |
| prompt, | |
| branchName: `${agentName}-${itemType}-${itemNumber}-run${context.runNumber}`, | |
| useOdkContainer: !skipOdk, | |
| skipOdkNote: skipOdk | |
| ? "NOTE: This is NOT running in the ODK container (SKIP_ODK or quick question was specified), so ODK tools like ROBOT may be unavailable." | |
| : "", | |
| }; | |
| respond-to-mention: | |
| needs: check-mention | |
| if: fromJSON(needs.check-mention.outputs.result).qualifiedMention == true | |
| timeout-minutes: 30 | |
| permissions: | |
| contents: write | |
| issues: write | |
| pull-requests: write | |
| runs-on: ubuntu-latest | |
| container: ${{ fromJSON(needs.check-mention.outputs.result).useOdkContainer && 'obolibrary/odkfull:v1.6' || null }} | |
| steps: | |
| # Must precede checkout: the token is persisted as the git credential and | |
| # is what later `git push` calls authenticate with. Valid for 1h, which | |
| # bounds how far timeout-minutes above can safely be raised. | |
| - name: Mint app token | |
| id: app-token | |
| uses: actions/create-github-app-token@v3 | |
| with: | |
| app-id: ${{ secrets.AI4C_AGENT_APP_ID }} | |
| private-key: ${{ secrets.AI4C_AGENT_PRIVATE_KEY }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 1 | |
| token: ${{ steps.app-token.outputs.token }} | |
| - name: Configure Git | |
| run: | | |
| git config --global user.name "${{ env.AGENT_LOGIN }}" | |
| git config --global user.email "${{ env.AGENT_USER_ID }}+${{ env.AGENT_LOGIN }}@users.noreply.github.com" | |
| - 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 jinja2-cli "wrapt>=1.17.2" | |
| echo "${{ github.workspace }}/.venv/bin" >> "$GITHUB_PATH" | |
| - name: Export GitHub token for gh CLI | |
| run: echo "GH_TOKEN=${{ steps.app-token.outputs.token }}" >> "$GITHUB_ENV" | |
| - name: Run Claude Code | |
| uses: anthropics/claude-code-action@v1 | |
| with: | |
| claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }} | |
| github_token: ${{ steps.app-token.outputs.token }} | |
| allowed_bots: "claude,github-actions" | |
| show_full_output: true | |
| claude_args: | | |
| --allowedTools "Bash,Read,Write,Edit,Glob,Grep,LS,MultiEdit,NotebookEdit,TodoRead,TodoWrite,WebFetch,WebSearch" | |
| --model "${{ env.MODEL }}" | |
| prompt: | | |
| You are @${{ env.AGENT_MENTION }}, responding to a request from @${{ fromJSON(needs.check-mention.outputs.result).user }} on GitHub ${{ fromJSON(needs.check-mention.outputs.result).itemType }} #${{ fromJSON(needs.check-mention.outputs.result).itemNumber }}. | |
| Follow the repository instructions in `CLAUDE.md`. | |
| ${{ fromJSON(needs.check-mention.outputs.result).skipOdkNote }} | |
| THE REQUEST: | |
| ``` | |
| ${{ fromJSON(needs.check-mention.outputs.result).prompt }} | |
| ``` | |
| GETTING CONTEXT: | |
| Use `gh` to read the full context. Examples: | |
| - `gh issue view ${{ fromJSON(needs.check-mention.outputs.result).itemNumber }} --json title,body,comments` | |
| - `gh pr view ${{ fromJSON(needs.check-mention.outputs.result).itemNumber }} --json title,body,comments,reviews` | |
| - Check for linked issues or PRs mentioned in the body | |
| MAKING CHANGES: | |
| If you need to modify files: | |
| 1. Create a branch: `git checkout -b ${{ fromJSON(needs.check-mention.outputs.result).branchName }}` | |
| (unless requested to update an existing branch or PR, in which case check out and work on that branch) | |
| 2. Make your changes and commit with descriptive messages | |
| 3. Push the branch: `git push -u origin ${{ fromJSON(needs.check-mention.outputs.result).branchName }}` | |
| 4. Create a PR using `gh pr create` with a clear title and description | |
| COMMUNICATING: | |
| - Use `gh` CLI directly to interact with the user on GitHub | |
| - Use `gh issue comment` or `gh pr comment` to post updates | |
| - Always inform the user what you did (or could not do) | |
| - If you created a PR, reference it in your comment on the original issue or PR | |
| - If the request is ambiguous, ask a clarifying question via `gh` | |
| SIGNATURE: | |
| Always include the following signature block in commit messages and GitHub comments: | |
| ``` | |
| --- | |
| 🤖 **Generated by @${{ env.AGENT_MENTION }}** | |
| - Model: `${{ env.MODEL }}` | |
| - Agent harness: claude-code | |
| - Triggered by: @${{ fromJSON(needs.check-mention.outputs.result).user }} | |
| - Run: [View workflow run](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}) | |
| ``` |