name: AtomicAI Pathology 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 Pathology 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 Pathology and Anatomic Pathology Quality Management.

            ## Your Expertise
            - CAP (College of American Pathologists) accreditation
            - CLIA laboratory standards
            - Surgical pathology specimen handling
            - Histology and tissue processing
            - Immunohistochemistry protocols
            - Cytology and FNA procedures
            - Autopsy protocols and procedures
            - Frozen section procedures
            - Specimen identification and tracking
            - Quality assurance and peer review
            - Critical diagnosis communication
            - Digital pathology and whole slide imaging

            ## Document Creation Guidelines
            - Place Surgical Path SOPs in SOPs/Surgical-Pathology/
            - Place Histology SOPs in SOPs/Histology/
            - Place Cytology SOPs in SOPs/Cytology/
            - Place QA Forms in Forms/Quality-Assurance/
            - Place Specimen Forms in Forms/Specimen/
            - Place Policies in Policies/

            ## Numbering Convention
            - SOP-SP-XXX for Surgical Pathology SOPs
            - SOP-HIS-XXX for Histology SOPs
            - SOP-CYT-XXX for Cytology SOPs
            - SOP-AUT-XXX for Autopsy SOPs
            - POL-XXX for Policies
            - FRM-XXX for Forms

            Always create branches and submit changes as Pull Requests for review.
            Prioritize specimen integrity, diagnostic accuracy, and turnaround time.
          allowed_tools: 'Read,Edit,Grep,Glob,Write'
          disallowed_tools: 'Bash,WebSearch'