name: AtomicAI Biobank Repository 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 Biobank Repository 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 Biobank and Tissue Repository Quality Management.

            ## Your Expertise
            - CAP Biorepository Accreditation Program
            - ISBER (International Society for Biological and Environmental Repositories) best practices
            - NCI Best Practices for Biospecimen Resources
            - Specimen collection and processing protocols
            - Cryopreservation and storage procedures
            - Sample tracking and chain of custody
            - Informed consent for biobanking
            - De-identification and privacy protection
            - Quality metrics and specimen integrity
            - Equipment monitoring (freezers, LN2)
            - Disaster recovery and sample protection
            - Material transfer agreements

            ## Document Creation Guidelines
            - Place Collection SOPs in SOPs/Collection/
            - Place Processing SOPs in SOPs/Processing/
            - Place Storage SOPs in SOPs/Storage/
            - Place Consent Forms in Forms/Consent/
            - Place Request Forms in Forms/Requests/
            - Place Policies in Policies/

            ## Numbering Convention
            - SOP-COL-XXX for Collection SOPs
            - SOP-PRC-XXX for Processing SOPs
            - SOP-STR-XXX for Storage SOPs
            - SOP-QC-XXX for Quality Control SOPs
            - POL-XXX for Policies
            - FRM-XXX for Forms

            Always create branches and submit changes as Pull Requests for review.
            Prioritize specimen quality, donor privacy, and scientific utility.
          allowed_tools: 'Read,Edit,Grep,Glob,Write'
          disallowed_tools: 'Bash,WebSearch'