name: AtomicAI Clinical Research Assistant

on:
  issue_comment:
    types: [created]
  issues:
    types: [opened, assigned]
  pull_request:
    types: [opened, synchronize, assigned]
  pull_request_review_comment:
    types: [created]

jobs:
  claude-assistant:
    runs-on: ubuntu-latest
    if: |
      github.actor != 'atomicqms-service' &&
      (
      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@atomicai') && github.event.comment.user.login != 'atomicqms-service') ||
      (github.event_name == 'issues' && github.event.action == 'opened' && contains(github.event.issue.body, '@atomicai')) ||
      (github.event_name == 'pull_request' && github.event.action == 'opened' && contains(github.event.pull_request.body, '@atomicai')) ||
      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@atomicai') && github.event.comment.user.login != 'atomicqms-service') ||
      (github.event.action == 'assigned' && github.event.assignee.login == 'atomicai')

      )
    permissions:
      contents: write
      issues: write
      pull-requests: write

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Run AtomicAI Clinical Research Assistant
        uses: https://beta.atomicqms.com/atomicqms-service/actions/claude-code-gitea-action-slim@main
        with:
          trigger_phrase: '@atomicai'
          assignee_trigger: 'atomicai'
          claude_git_name: 'AtomicAI'
          claude_git_email: 'atomicai@atomicqms.local'
          custom_instructions: |
            You are AtomicAI, an AI assistant specialized in Clinical Research Quality Management.
            
            ## Your Expertise
            - ICH-GCP E6(R2) Good Clinical Practice guidelines
            - 21 CFR Part 11 Electronic Records compliance
            - FDA regulations (21 CFR 50, 56, 312, 812)
            - Clinical trial operations and site management
            - Informed consent form development
            - Adverse event reporting procedures
            - Clinical data management and CDISC standards
            
            ## Document Creation Guidelines
            - Place Clinical SOPs in SOPs/Clinical/
            - Place Regulatory SOPs in SOPs/Regulatory/
            - Place Data Management SOPs in SOPs/Data-Management/
            - Place Safety SOPs in SOPs/Safety/
            - Place Informed Consent templates in Forms/Informed-Consent/
            - Place Case Report Forms in Forms/Case-Report/
            - Place Monitoring forms in Forms/Monitoring/
            
            ## Numbering Convention
            - SOP-CL-XXX for Clinical SOPs
            - SOP-REG-XXX for Regulatory SOPs
            - SOP-DM-XXX for Data Management SOPs
            - SOP-SAF-XXX for Safety SOPs
            - ICF-XXX for Informed Consent Forms
            
            Always create branches and submit changes as Pull Requests for review.
            Include regulatory references where applicable.
          allowed_tools: 'Read,Edit,Grep,Glob,Write'
          disallowed_tools: 'Bash,WebSearch'