ai integrations #11

cmungall · 2025-12-13T00:10:44Z

adding AI integrations
adding AI integrations

Copilot

Pull request overview

This PR adds comprehensive AI integrations to enable multiple AI coding assistants (Claude Code, Dragon AI Agent, and GitHub Copilot) to work with the repository through GitHub Actions workflows and configuration files.

Key changes:

Added justfile recipes for setting up AI-related symlinks, GitHub topics, and repository secrets
Created GitHub Actions workflows for Claude Code, Dragon AI Agent, and automated code review/issue triage
Added configuration files for Claude (.claude/settings.json, .claude/.mcp.json) and Copilot instructions

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
ai.just	Provides justfile recipes for AI setup tasks including symlink creation, GitHub configuration, and secret management
.github/workflows/dragon-ai.yml	Workflow to respond to @dragon-ai-agent mentions in issues/PRs with automated AI assistance
.github/workflows/claude.yml	Workflow to handle @claude mentions across issues, PRs, and comments
.github/workflows/claude-ontology-review.yml	Automated PR review workflow specifically for ontology file changes
.github/workflows/claude-issue-triage.yml	Workflow for automatic issue triage using Claude Code
.github/workflows/claude-issue-summarize.yml	Workflow for automatic issue summarization using Claude Code
.github/workflows/claude-code-review.yml	General-purpose automated PR code review workflow
.github/copilot-instructions.md	Instructions for AI assistants about repository structure and conventions
.github/actions/claude-issue-triage-action/action.yml	Updated to support Claude OAuth token authentication as optional
.github/actions/claude-issue-summarize-action/action.yml	Updated to support Claude OAuth token authentication as optional
.github/actions/claude-code-action/action.yml	Major changes to authentication handling, switching from CBORG to direct Anthropic/OAuth, and removed timeout enforcement
.claude/settings.json	Claude Code permissions configuration allowing various file operations
.claude/.mcp.json	Model Context Protocol server configuration for OLS and PubMed integrations

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2025-12-13T00:15:51Z

.github/actions/claude-code-action/action.yml

+          echo CLAUDE AUTH TOKEN IS NOT SET
+        else
+          echo CLAUDE AUTH TOKEN IS SET
+          export ANTHROPIC_API_KEY=


The logic in this conditional check is inverted. The condition checks if the token is NOT empty (! -z means "not zero length"), but then echoes "IS NOT SET". When the token exists, it should say "IS SET", and when it doesn't exist, it should say "IS NOT SET". Additionally, line 137 sets ANTHROPIC_API_KEY to empty without a value assignment operator, which will cause a syntax error.

Suggested change

echo CLAUDE AUTH TOKEN IS NOT SET

else

echo CLAUDE AUTH TOKEN IS SET

export ANTHROPIC_API_KEY=

echo CLAUDE AUTH TOKEN IS SET

else

echo CLAUDE AUTH TOKEN IS NOT SET

export ANTHROPIC_API_KEY=""

Copilot · 2025-12-13T00:15:52Z

.github/workflows/dragon-ai.yml

+        id: claude-response
+        env:
+          CLAUDE_CODE_OAUTH_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}


The workflow step uses GITHUB_TOKEN but line 151 sets GH_TOKEN to use PAT_FOR_PR. This inconsistency means the Claude Code execution will use the limited default GITHUB_TOKEN instead of the PAT, which may not have sufficient permissions to create PRs or perform other privileged operations that the PAT was intended to enable.

Suggested change

GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

GH_TOKEN: ${{ secrets.PAT_FOR_PR }}

Copilot · 2025-12-13T00:15:52Z

.github/workflows/claude-issue-triage.yml

@@ -0,0 +1,27 @@
+name: Claude Issue Triage
+description: "Automatically triage GitHub issues using Claude Code"


The 'description' field is not valid in GitHub Actions workflow syntax at the top level. This field should be removed as it's only valid within action.yml files, not workflow files.

Suggested change

description: "Automatically triage GitHub issues using Claude Code"

Copilot · 2025-12-13T00:15:53Z

.github/copilot-instructions.md

+# CLAUDE.md for 
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.


The file is named "copilot-instructions.md" but the header says "CLAUDE.md for". This appears to be copied from a Claude-specific file without updating the header. The header should either reference GitHub Copilot or be more generic to match the filename.

Suggested change

# CLAUDE.md for

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

# Copilot Instructions

This file provides guidance to GitHub Copilot when working with code in this repository.

Copilot · 2025-12-13T00:15:53Z

.github/copilot-instructions.md

@@ -0,0 +1,22 @@
+# CLAUDE.md for 
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.


The file provides guidance for "Claude Code" but is placed in a file specifically named for GitHub Copilot instructions. This creates confusion about which AI tool the instructions are intended for. Either the content should be made generic to cover both tools, or separate instruction files should be created for each tool.

Copilot · 2025-12-13T00:15:54Z

.github/actions/claude-code-action/action.yml

        else
          # Run Claude Code and tee output to console and file
-          timeout $timeout_seconds claude \
+          claude \


The timeout command has been removed from this line. This means Claude Code will run without a timeout, potentially causing the workflow to hang indefinitely if Claude doesn't complete. The timeout_seconds variable is still calculated but no longer used, making the timeout_minutes input parameter ineffective.

Copilot · 2025-12-13T00:15:54Z

ai.just

+setup-gh: gh-add-topics gh-add-secrets
+
+gh-add-topics:
+  gh repo edit --add-topic "monarchinitiative,ai4curation"


The command uses hardcoded topic values "monarchinitiative,ai4curation" without considering that this file may be copied to other repositories via the copier template. These topics are specific to the Monarch Initiative and may not be appropriate for all repositories using this template. Consider making these configurable or documenting that users should modify this line.

Suggested change

gh repo edit --add-topic "monarchinitiative,ai4curation"

# TODO: Set repository topics. Edit the 'topics' variable in your copier template context.

gh repo edit --add-topic "{{ topics }}"

Copilot · 2025-12-13T00:15:55Z

.github/workflows/dragon-ai.yml

+            
+            // Check if user is allowed and mention exists
+            const isAllowed = allowedUsers.includes(userLogin);
+            const mentionRegex = /@dragon-ai-agent\s+please\s+(.*)/i;


The regex pattern uses a case-insensitive flag but requires the exact phrase "please" between the mention and the command. This creates a rigid user experience where users must remember to include "please" in their commands. Consider whether this politeness requirement is necessary, or if it should be made optional in the regex pattern.

Suggested change

const mentionRegex = /@dragon-ai-agent\s+please\s+(.*)/i;

const mentionRegex = /@dragon-ai-agent\s+(?:please\s+)?(.*)/i;

Copilot · 2025-12-13T00:15:55Z

.github/workflows/dragon-ai.yml

+          # Run Claude with proper permissions
+          claude -p "$(cat /tmp/claude-input/claude_prompt.txt)" \
+            --permission-mode bypassPermissions \


The Claude CLI is invoked with --permission-mode bypassPermissions, which disables all permission checks. This is a significant security risk as it allows the AI to execute any command without restrictions. This should be documented with clear warnings, and consideration should be given to using a more restrictive permission mode or at least limiting allowed tools.

Suggested change

# Run Claude with proper permissions

claude -p "$(cat /tmp/claude-input/claude_prompt.txt)" \

--permission-mode bypassPermissions \

# Run Claude with default (safer) permissions.

# The --permission-mode bypassPermissions flag has been removed to avoid disabling all permission checks.

claude -p "$(cat /tmp/claude-input/claude_prompt.txt)" \

Copilot · 2025-12-13T00:15:55Z

ai.just

+      gh secret set "$secret_name" --body "${!gh_var}"
+    elif [ -n "${!plain_var:-}" ]; then
+      echo "Setting $secret_name from $plain_var"
+      gh secret set "$secret_name" --body "${!plain_var}"


Using gh secret set with --body "${!gh_var}" and --body "${!plain_var}" passes secret values on the process command line, which can be read by other users on the same host via tools like ps or /proc/*/cmdline. This risks leaking highly sensitive tokens such as PAT_FOR_PR or API keys to local attackers or in multi-tenant CI environments. To avoid this, feed secret values to gh secret set via stdin or a file (or an environment variable only read internally) instead of including them as command-line arguments.

Suggested change

gh secret set "$secret_name" --body "${!gh_var}"

elif [ -n "${!plain_var:-}" ]; then

echo "Setting $secret_name from $plain_var"

gh secret set "$secret_name" --body "${!plain_var}"

echo "${!gh_var}" | gh secret set "$secret_name" --body -

elif [ -n "${!plain_var:-}" ]; then

echo "Setting $secret_name from $plain_var"

echo "${!plain_var}" | gh secret set "$secret_name" --body -

cmungall added 2 commits December 12, 2025 16:10

adding AI integrations

0fbbeae

adding AI integrations

64a905f

Copilot AI review requested due to automatic review settings December 13, 2025 00:10

Copilot started reviewing on behalf of cmungall December 13, 2025 00:11 View session

Copilot AI reviewed Dec 13, 2025

View reviewed changes

cmungall merged commit 78fbb5d into main Dec 13, 2025
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	GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	GH_TOKEN: ${{ secrets.PAT_FOR_PR }}

		@@ -0,0 +1,27 @@
		name: Claude Issue Triage
		description: "Automatically triage GitHub issues using Claude Code"

		# CLAUDE.md for

		This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

		@@ -0,0 +1,22 @@
		# CLAUDE.md for

		This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

	gh repo edit --add-topic "monarchinitiative,ai4curation"
	# TODO: Set repository topics. Edit the 'topics' variable in your copier template context.
	gh repo edit --add-topic "{{ topics }}"

	const mentionRegex = /@dragon-ai-agent\s+please\s+(.*)/i;
	const mentionRegex = /@dragon-ai-agent\s+(?:please\s+)?(.*)/i;

ai integrations #11

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