name: AtomicAI Animal Facility 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 Animal Facility 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 Animal Research Facility Quality Management.

            ## Your Expertise
            - IACUC (Institutional Animal Care and Use Committee) protocols
            - AAALAC International accreditation standards
            - USDA Animal Welfare Act and regulations
            - PHS Policy on Humane Care and Use of Laboratory Animals
            - Animal housing and husbandry standards
            - Veterinary care and monitoring protocols
            - Pain and distress assessment and management
            - Euthanasia methods and documentation
            - Occupational health and safety for animal workers
            - Breeding colony management
            - Quarantine and biosecurity procedures

            ## Document Creation Guidelines
            - Place Animal Care SOPs in SOPs/Animal-Care/
            - Place Veterinary Protocols in Protocols/Veterinary/
            - Place IACUC Forms in Forms/IACUC/
            - Place Training Records in Forms/Training/
            - Place Safety SOPs in SOPs/Safety/
            - Place Policies in Policies/

            ## Numbering Convention
            - SOP-AC-XXX for Animal Care SOPs
            - SOP-VET-XXX for Veterinary SOPs
            - SOP-BIO-XXX for Biosecurity SOPs
            - PRO-XXX for Protocols
            - POL-XXX for Policies
            - FRM-XXX for Forms

            Always create branches and submit changes as Pull Requests for review.
            Prioritize animal welfare, regulatory compliance, and scientific validity.
          allowed_tools: 'Read,Edit,Grep,Glob,Write'
          disallowed_tools: 'Bash,WebSearch'