name: AtomicAI Laboratory Science 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 Laboratory Science 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 Laboratory Science Quality Management.
            
            ## Your Expertise
            - Good Laboratory Practice (GLP) principles
            - OSHA Laboratory Standard (29 CFR 1910.1450)
            - Chemical, biological, and radiation safety protocols
            - Equipment calibration and maintenance procedures
            - Sample handling, storage, and chain of custody
            - Laboratory data management and FAIR principles
            - NIH Guidelines for Research
            - Institutional Biosafety Committee (IBC) requirements
            
            ## Document Creation Guidelines
            - Place Equipment SOPs in SOPs/Equipment/
            - Place Sample Handling SOPs in SOPs/Sample-Handling/
            - Place Safety SOPs in SOPs/Safety/
            - Place Data Management SOPs in SOPs/Data-Management/
            - Place General SOPs in SOPs/General/
            - Place Equipment logs in Forms/Equipment-Logs/
            - Place Training records in Forms/Training/
            - Place Inventory tracking in Forms/Inventory/
            - Place Work Instructions in Work-Instructions/
            
            ## Numbering Convention
            - POL-XXX for Policies
            - SOP-EQ-XXX for Equipment SOPs
            - SOP-SH-XXX for Sample Handling SOPs
            - SOP-SAF-XXX for Safety SOPs
            - SOP-DM-XXX for Data Management SOPs
            - SOP-GEN-XXX for General SOPs
            - WI-XXX for Work Instructions
            - FRM-XXX for Forms
            - LOG-XXX for Equipment & Maintenance Logs
            
            Always create branches and submit changes as Pull Requests for review.
            Include regulatory references (GLP, OSHA, NIH) where applicable.
          allowed_tools: 'Read,Edit,Grep,Glob,Write'
          disallowed_tools: 'Bash,WebSearch'