docs: add Ralph project structure
- PROMPT.md: Ralph development instructions with BtToxin Pipeline specifics - specs/requirements.md: Technical specifications (API, file formats, concurrency) - @AGENT.md: Build, test, and deployment commands Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
zly
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@AGENT.md
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@AGENT.md
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# Agent Build Instructions
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## Project Setup
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### Frontend (Vue 3 + Vite)
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```bash
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cd frontend
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pnpm install
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```
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### Backend (FastAPI)
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```bash
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# Using pixi (recommended)
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cd web/zly
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pixi run -e webbackend api-dev
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# Or using python directly
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cd web/backend
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pip install -r requirements.txt
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uvicorn main:app --reload --host 0.0.0.0 --port 8000
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```
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### Pixi Environment Setup
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```bash
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cd web/zly
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pixi install
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pixi run -e digger --help
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pixi run -e pipeline --help
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```
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## Running Tests
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### Frontend Tests
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```bash
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cd frontend
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pnpm test:unit
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pnpm test:unit --run # Run once without watch
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```
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### Backend Tests
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```bash
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cd web/backend
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pytest -v
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pytest --cov=src tests/ # With coverage
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```
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## Build Commands
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### Frontend Production Build
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```bash
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cd frontend
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pnpm build
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# Output: dist/
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```
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### Backend Production
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```bash
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# Build with pixi
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cd web/zly
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pixi run -e webbackend api-prod
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```
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## Development Server
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### Frontend Dev Server
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```bash
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cd frontend
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pnpm dev --host # Access at http://localhost:5173
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```
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### Backend Dev Server
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```bash
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cd web/zly
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pixi run -e webbackend api-dev
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# Access at http://localhost:8000
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```
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## Docker Deployment
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```bash
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cd web/zly/docker
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docker-compose up -d --build
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```
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## Key Learnings
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- Update this section when you learn new build optimizations
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- Document any gotchas or special setup requirements
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- Keep track of the fastest test/build cycle
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## Feature Development Quality Standards
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**CRITICAL**: All new features MUST meet the following mandatory requirements before being considered complete.
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### Testing Requirements
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- **Minimum Coverage**: 85% code coverage ratio required for all new code
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- **Test Pass Rate**: 100% - all tests must pass, no exceptions
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- **Test Types Required**:
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- Unit tests for all business logic and services
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- Integration tests for API endpoints or main functionality
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- End-to-end tests for critical user workflows
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- **Coverage Validation**: Run coverage reports before marking features complete:
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```bash
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# Examples by language/framework
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npm run test:coverage
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pytest --cov=src tests/ --cov-report=term-missing
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cargo tarpaulin --out Html
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```
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- **Test Quality**: Tests must validate behavior, not just achieve coverage metrics
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- **Test Documentation**: Complex test scenarios must include comments explaining the test strategy
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### Git Workflow Requirements
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Before moving to the next feature, ALL changes must be:
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1. **Committed with Clear Messages**:
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```bash
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git add .
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git commit -m "feat(module): descriptive message following conventional commits"
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```
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- Use conventional commit format: `feat:`, `fix:`, `docs:`, `test:`, `refactor:`, etc.
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- Include scope when applicable: `feat(api):`, `fix(ui):`, `test(auth):`
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- Write descriptive messages that explain WHAT changed and WHY
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2. **Pushed to Remote Repository**:
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```bash
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git push origin <branch-name>
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```
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- Never leave completed features uncommitted
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- Push regularly to maintain backup and enable collaboration
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- Ensure CI/CD pipelines pass before considering feature complete
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3. **Branch Hygiene**:
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- Work on feature branches, never directly on `main`
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- Branch naming convention: `feature/<feature-name>`, `fix/<issue-name>`, `docs/<doc-update>`
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- Create pull requests for all significant changes
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4. **Ralph Integration**:
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- Update @fix_plan.md with new tasks before starting work
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- Mark items complete in @fix_plan.md upon completion
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- Update PROMPT.md if development patterns change
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- Test features work within Ralph's autonomous loop
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### Documentation Requirements
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**ALL implementation documentation MUST remain synchronized with the codebase**:
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1. **Code Documentation**:
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- Language-appropriate documentation (JSDoc, docstrings, etc.)
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- Update inline comments when implementation changes
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- Remove outdated comments immediately
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2. **Implementation Documentation**:
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- Update relevant sections in this AGENT.md file
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- Keep build and test commands current
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- Update configuration examples when defaults change
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- Document breaking changes prominently
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3. **README Updates**:
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- Keep feature lists current
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- Update setup instructions when dependencies change
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- Maintain accurate command examples
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- Update version compatibility information
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4. **AGENT.md Maintenance**:
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- Add new build patterns to relevant sections
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- Update "Key Learnings" with new insights
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- Keep command examples accurate and tested
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- Document new testing patterns or quality gates
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### Feature Completion Checklist
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Before marking ANY feature as complete, verify:
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- [ ] All tests pass with appropriate framework command
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- [ ] Code coverage meets 85% minimum threshold
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- [ ] Coverage report reviewed for meaningful test quality
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- [ ] Code formatted according to project standards
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- [ ] Type checking passes (if applicable)
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- [ ] All changes committed with conventional commit messages
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- [ ] All commits pushed to remote repository
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- [ ] @fix_plan.md task marked as complete
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- [ ] Implementation documentation updated
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- [ ] Inline code comments updated or added
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- [ ] AGENT.md updated (if new patterns introduced)
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- [ ] Breaking changes documented
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- [ ] Features tested within Ralph loop (if applicable)
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- [ ] CI/CD pipeline passes
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### Rationale
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These standards ensure:
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- **Quality**: High test coverage and pass rates prevent regressions
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- **Traceability**: Git commits and @fix_plan.md provide clear history of changes
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- **Maintainability**: Current documentation reduces onboarding time and prevents knowledge loss
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- **Collaboration**: Pushed changes enable team visibility and code review
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- **Reliability**: Consistent quality gates maintain production stability
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- **Automation**: Ralph integration ensures continuous development practices
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**Enforcement**: AI agents should automatically apply these standards to all feature development tasks without requiring explicit instruction for each task.
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PROMPT.md
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PROMPT.md
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# Ralph Development Instructions
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## Context
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You are Ralph, an autonomous AI development agent working on a **BtToxin Pipeline** project - an automated analysis platform for identifying and evaluating insecticidal toxin genes from Bacillus thuringiensis genomes.
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## Current Objectives
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1. **Core Analysis Pipeline**: Implement genome/protein file upload and toxin gene identification using BtToxin_Digger
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2. **Toxicity Assessment**: Integrate BtToxin_Shoter module for toxin-insect target activity prediction based on BPPRC database
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3. **Task Management System**: Build async task queue with 16 concurrent limit, Redis-backed status tracking, and 30-day result retention
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4. **Web Interface**: Create Vue 3 frontend with Element Plus for file upload, task monitoring, and result visualization
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5. **Internationalization**: Implement bilingual support (Chinese/English) with vue-i18n
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6. **Docker Deployment**: Configure Docker Compose with Traefik reverse proxy for production deployment
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## Key Principles
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- ONE task per loop - focus on the most important thing
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- Search the codebase before assuming something isn't implemented
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- Use subagents for expensive operations (file searching, analysis)
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- Write comprehensive tests with clear documentation
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- Update @fix_plan.md with your learnings
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- Commit working changes with descriptive messages
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## Testing Guidelines (CRITICAL)
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- LIMIT testing to ~20% of your total effort per loop
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- PRIORITIZE: Implementation > Documentation > Tests
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- Only write tests for NEW functionality you implement
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- Do NOT refactor existing tests unless broken
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- Focus on CORE functionality first, comprehensive testing later
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## Project Requirements
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### File Upload Requirements
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- Accept genome files (.fna, .fa, .fasta) and protein files (.faa)
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- Single file per task - genome and protein cannot be mixed
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- Maximum file size: 100MB
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- Drag-and-drop upload support with format validation
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### Analysis Pipeline Stages
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1. **Digger**: Identify Bt toxin genes using BtToxin_Digger + BLAST + Perl
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2. **Shoter**: Evaluate toxin activity against insect targets using BPPRC database
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3. **Plots**: Generate heatmaps for toxin-target relationships
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4. **Bundle**: Package results into .tar.gz download
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### Task States
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- `pending`: Waiting to enter queue
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- `queued`: Waiting for available slot (shows queue position)
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- `running`: Currently executing (shows progress % and stage)
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- `completed`: Finished successfully
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- `failed`: Error occurred (shows error message)
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### API Endpoints
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| Method | Endpoint | Description |
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|--------|----------|-------------|
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| POST | `/api/tasks` | Create new analysis task |
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| GET | `/api/tasks/{task_id}` | Get task status and progress |
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| GET | `/api/tasks/{task_id}/download` | Download result bundle |
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| DELETE | `/api/tasks/{task_id}` | Delete task and results |
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## Technical Constraints
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### Frontend Stack
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- Vue 3 (Composition API + script setup)
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- Vite build tool
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- Element Plus UI components
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- Pinia state management
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- Vue Router 4
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- vue-i18n for i18n
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- fetch API for HTTP requests
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### Backend Stack
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- FastAPI + Uvicorn
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- asyncio + Semaphore for 16 concurrent task limit
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- Redis for task status and queue management
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- pixi for environment management (conda alternative)
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- digger env: BtToxin_Digger + BLAST + Perl
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- pipeline env: Python 3.9+ (pandas, matplotlib, seaborn)
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### Database Files
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- BPPRC Specificity Database: `toxicity-data.csv`
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- BtToxin database: `external_dbs/bt_toxin`
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### Scoring Parameters (configurable)
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- `min_identity`: Minimum similarity (0-1, default: 0.8)
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- `min_coverage`: Minimum coverage (0-1, default: 0.6)
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- `allow_unknown_families`: Allow unknown families (default: false)
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- `require_index_hit`: Require index hit (default: true)
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### Reserved / Future Features
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- CRISPR-Cas analysis module (prepare `crispr_cas/` directory)
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- Direct protein sequence analysis (sequence_type=prot)
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## Success Criteria
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1. [ ] Users can upload genome (.fna/.fa/.fasta) or protein (.faa) files for analysis
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2. [ ] System supports 16 concurrent tasks with automatic queue management
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3. [ ] Chinese/English language switching works correctly
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4. [ ] Toxin-target activity assessment displays in heatmap format
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5. [ ] Results available for download as .tar.gz within 30 days
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6. [ ] Docker deployment successful with Traefik reverse proxy at bttiaw.hzau.edu.cn
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## Current Task
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Follow @fix_plan.md and choose the most important item to implement next.
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specs/requirements.md
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specs/requirements.md
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# Technical Specifications
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## BtToxin Pipeline - Technical Requirements
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### 1. System Architecture
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#### 1.1 Overview
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BtToxin Pipeline is a web-based genomic analysis platform consisting of:
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- **Frontend**: Vue 3 SPA with Element Plus components
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- **Backend**: FastAPI REST API with async task processing
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- **Task Queue**: Redis-backed queue with semaphore-based concurrency control
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- **Analysis Engine**: BtToxin_Digger and BtToxin_Shoter modules
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#### 1.2 Component Architecture
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```
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┌─────────────────┐ ┌─────────────────┐ ┌─────────────────┐
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│ Vue 3 SPA │────▶│ FastAPI API │────▶│ Task Queue │
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│ (Frontend) │ │ (Backend) │ │ (Redis) │
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└─────────────────┘ └─────────────────┘ └─────────────────┘
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│ │
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│ ▼
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┌───────┴────────┐ ┌─────────────────┐
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│ Pixi/Conda │ │ Task Workers │
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│ Environments │ │ (16 concurrent)│
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└────────────────┘ └─────────────────┘
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│
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▼
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┌─────────────────┐
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│ BtToxin Tools │
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│ (Digger/Shoter)│
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└─────────────────┘
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```
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### 2. Frontend Specifications
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#### 2.1 Technology Stack
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| Component | Version/Requirement |
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|-----------|---------------------|
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| Vue 3 | Composition API + script setup |
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| Vite | Latest stable |
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| Element Plus | Latest compatible |
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| Pinia | Latest stable |
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| Vue Router | v4 |
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| vue-i18n | v9+ |
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| HTTP Client | fetch API (no axios) |
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#### 2.2 Page Structure
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| Page | Route | Description |
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|------|-------|-------------|
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| Home | `/` | System introduction, quick start |
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| About | `/about` | Features, usage, limitations |
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| Submit | `/submit` | File upload, parameters, submit |
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| Status | `/status` | Task progress, results |
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| Tools | `/tools` | BtToxin_Shoter methodology |
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#### 2.3 File Upload Component Requirements
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- Drag and drop zone
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- File type auto-detection
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- Size limit: 100MB
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- Pre-upload format validation
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- Progress indicator during upload
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#### 2.4 Internationalization (i18n)
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- Languages: Chinese (zh), English (en)
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- Language switcher in header/nav
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- Persist selection via localStorage
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- Refresh page on language change
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### 3. Backend Specifications
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#### 3.1 Technology Stack
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| Component | Version/Requirement |
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||||||
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|-----------|---------------------|
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||||||
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| FastAPI | Latest stable |
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| Uvicorn | Latest stable |
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| Python | 3.9+ |
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| Redis | Latest stable |
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| pixi | Latest (conda alternative) |
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#### 3.2 API Specifications
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||||||
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##### 3.2.1 Create Task
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||||||
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```
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POST /api/tasks
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Content-Type: multipart/form-data
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||||||
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||||||
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Request Parameters:
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||||||
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| Name | Type | Required | Default | Description |
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||||||
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|-------------------------|---------|----------|---------|-------------|
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||||||
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| file | File | Yes | - | Uploaded file |
|
||||||
|
| file_type | string | Yes | - | genome/protein |
|
||||||
|
| min_identity | float | No | 0.8 | Min similarity (0-1) |
|
||||||
|
| min_coverage | float | No | 0.6 | Min coverage (0-1) |
|
||||||
|
| allow_unknown_families | boolean | No | false | Allow unknown families |
|
||||||
|
| require_index_hit | boolean | No | true | Require index hit |
|
||||||
|
| lang | string | No | zh | Report language (zh/en) |
|
||||||
|
|
||||||
|
Response:
|
||||||
|
{
|
||||||
|
"task_id": "uuid-string",
|
||||||
|
"status": "pending",
|
||||||
|
"created_at": "ISO-timestamp",
|
||||||
|
"expires_at": "ISO-timestamp"
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
##### 3.2.2 Get Task Status
|
||||||
|
```
|
||||||
|
GET /api/tasks/{task_id}
|
||||||
|
|
||||||
|
Response:
|
||||||
|
{
|
||||||
|
"task_id": "uuid-string",
|
||||||
|
"status": "queued|running|completed|failed",
|
||||||
|
"progress": 0-100,
|
||||||
|
"current_stage": "digger|shoter|plots|bundle",
|
||||||
|
"submission_time": "ISO-timestamp",
|
||||||
|
"start_time": "ISO-timestamp|null",
|
||||||
|
"completion_time": "ISO-timestamp|null",
|
||||||
|
"filename": "original-filename",
|
||||||
|
"error": "error-message|null",
|
||||||
|
"estimated_remaining_seconds": number|null,
|
||||||
|
"queue_position": number|null
|
||||||
|
}
|
||||||
|
```
|
||||||
|
|
||||||
|
##### 3.2.3 Download Results
|
||||||
|
```
|
||||||
|
GET /api/tasks/{task_id}/download
|
||||||
|
|
||||||
|
Response: .tar.gz file (Content-Disposition: attachment)
|
||||||
|
```
|
||||||
|
|
||||||
|
##### 3.2.4 Delete Task
|
||||||
|
```
|
||||||
|
DELETE /api/tasks/{task_id}
|
||||||
|
|
||||||
|
Response: 204 No Content
|
||||||
|
```
|
||||||
|
|
||||||
|
#### 3.3 Task Queue Specifications
|
||||||
|
|
||||||
|
##### Concurrency Control
|
||||||
|
- Maximum concurrent tasks: 16
|
||||||
|
- Implementation: asyncio.Semaphore(16)
|
||||||
|
- Queue overflow: Tasks wait in Redis queue
|
||||||
|
- Queue position: Track and display position for queued tasks
|
||||||
|
|
||||||
|
##### Task Lifecycle
|
||||||
|
```
|
||||||
|
pending → queued → running → completed
|
||||||
|
→ failed
|
||||||
|
```
|
||||||
|
|
||||||
|
##### Task Status Values
|
||||||
|
| Status | Description |
|
||||||
|
|--------|-------------|
|
||||||
|
| pending | Created, waiting to enter queue |
|
||||||
|
| queued | Waiting for available slot (has queue_position) |
|
||||||
|
| running | Currently processing (has progress, current_stage) |
|
||||||
|
| completed | Successfully finished (has download URL) |
|
||||||
|
| failed | Error occurred (has error message) |
|
||||||
|
|
||||||
|
##### Pipeline Stages
|
||||||
|
| Stage | Description |
|
||||||
|
|-------|-------------|
|
||||||
|
| digger | BtToxin_Digger gene identification |
|
||||||
|
| shoter | BtToxin_Shoter toxicity assessment |
|
||||||
|
| plots | Heatmap generation |
|
||||||
|
| bundle | Result packaging (.tar.gz) |
|
||||||
|
|
||||||
|
#### 3.4 Redis Data Structures
|
||||||
|
|
||||||
|
| Key Pattern | Type | Description |
|
||||||
|
|-------------|------|-------------|
|
||||||
|
| `task:{task_id}:status` | Hash | Task status and metadata |
|
||||||
|
| `task:{task_id}:result` | String | Result bundle path |
|
||||||
|
| `queue:waiting` | List | Waiting task IDs |
|
||||||
|
| `queue:running` | Set | Currently running task IDs |
|
||||||
|
| `queue:position:{task_id}` | String | Individual queue position |
|
||||||
|
|
||||||
|
### 4. File Format Support
|
||||||
|
|
||||||
|
| Extension | File Type | MIME Type | sequence_type |
|
||||||
|
|-----------|-----------|-----------|---------------|
|
||||||
|
| .fna | Genome (nucleotide) | application/fasta | nucl |
|
||||||
|
| .fa | Genome (nucleotide) | application/fasta | nucl |
|
||||||
|
| .fasta | Auto-detect | application/fasta | auto |
|
||||||
|
| .faa | Protein | application/fasta | prot |
|
||||||
|
|
||||||
|
### 5. Database Specifications
|
||||||
|
|
||||||
|
#### 5.1 BPPRC Specificity Database
|
||||||
|
- File: `toxicity-data.csv`
|
||||||
|
- Contains: Historical toxin-insect activity records
|
||||||
|
- Used by: BtToxin_Shoter for activity prediction
|
||||||
|
|
||||||
|
#### 5.2 BtToxin Database
|
||||||
|
- Directory: `external_dbs/bt_toxin`
|
||||||
|
- Contains: Known Bt toxin sequences
|
||||||
|
- Used by: BtToxin_Digger for gene identification
|
||||||
|
|
||||||
|
### 6. Analysis Pipeline Specifications
|
||||||
|
|
||||||
|
#### 6.1 BtToxin_Digger
|
||||||
|
- Environment: digger (pixi)
|
||||||
|
- Dependencies: BtToxin_Digger, BLAST, Perl
|
||||||
|
- Input: Genome (.fna/.fa/.fasta) or protein (.faa) file
|
||||||
|
- Output: Identified toxin genes with coordinates
|
||||||
|
|
||||||
|
#### 6.2 BtToxin_Shoter
|
||||||
|
- Environment: pipeline (pixi)
|
||||||
|
- Dependencies: Python 3.9+, pandas, matplotlib, seaborn
|
||||||
|
- Input: Digger output, scoring parameters
|
||||||
|
- Output: Toxin-target activity predictions
|
||||||
|
|
||||||
|
#### 6.3 Scoring Parameters
|
||||||
|
| Parameter | Type | Range | Default | Description |
|
||||||
|
|-----------|------|-------|---------|-------------|
|
||||||
|
| min_identity | float | 0-1 | 0.8 | Minimum sequence identity |
|
||||||
|
| min_coverage | float | 0-1 | 0.6 | Minimum coverage |
|
||||||
|
| allow_unknown_families | boolean | - | false | Allow unknown toxin families |
|
||||||
|
| require_index_hit | boolean | - | true | Require database index hit |
|
||||||
|
|
||||||
|
### 7. Reserved Features
|
||||||
|
|
||||||
|
#### 7.1 CRISPR-Cas Analysis Module
|
||||||
|
- Directory: `crispr_cas/`
|
||||||
|
- Environment: Additional pixi environment
|
||||||
|
- Integration: Weighted scoring with Shotter
|
||||||
|
- Modes: Additive or subtractive weight adjustment
|
||||||
|
|
||||||
|
#### 7.2 Direct Protein Analysis
|
||||||
|
- Digger mode: sequence_type=prot
|
||||||
|
- Shoter: Process protein sequence hits normally
|
||||||
|
|
||||||
|
### 8. Performance Requirements
|
||||||
|
|
||||||
|
| Metric | Requirement |
|
||||||
|
|--------|-------------|
|
||||||
|
| Task timeout | 6 hours |
|
||||||
|
| API response time | < 1 second (excluding task execution) |
|
||||||
|
| Max concurrent tasks | 16 |
|
||||||
|
| Max file size | 100MB |
|
||||||
|
| Result retention | 30 days |
|
||||||
|
|
||||||
|
### 9. Security Requirements
|
||||||
|
|
||||||
|
- **Task isolation**: Each task has independent working directory
|
||||||
|
- **Input validation**: File format and size validation
|
||||||
|
- **Result protection**: 30-day automatic cleanup
|
||||||
|
- **File permissions**: Restricted access to task directories
|
||||||
|
|
||||||
|
### 10. Deployment Specifications
|
||||||
|
|
||||||
|
#### 10.1 Docker Configuration
|
||||||
|
- Docker Compose for orchestration
|
||||||
|
- Services: frontend, backend, redis, traefik
|
||||||
|
- Volume mounts for data persistence
|
||||||
|
|
||||||
|
#### 10.2 Traefik Configuration
|
||||||
|
- Domain: bttiaw.hzau.edu.cn
|
||||||
|
- HTTP/HTTPS support
|
||||||
|
- Automatic certificate management (Let's Encrypt)
|
||||||
|
- Router rules for each service
|
||||||
|
|
||||||
|
### 11. Environment Variables
|
||||||
|
|
||||||
|
| Variable | Description | Required |
|
||||||
|
|----------|-------------|----------|
|
||||||
|
| REDIS_HOST | Redis server hostname | Yes |
|
||||||
|
| REDIS_PORT | Redis server port | Yes |
|
||||||
|
| PIXI_ENV_PATH | Path to pixi environments | Yes |
|
||||||
|
| API_BASE_URL | Backend API base URL | Yes |
|
||||||
|
| MAX_CONCURRENT_TASKS | Maximum concurrent tasks | No (default: 16) |
|
||||||
|
| TASK_TIMEOUT_HOURS | Task timeout in hours | No (default: 6) |
|
||||||
|
| RESULT_RETENTION_DAYS | Result retention days | No (default: 30) |
|
||||||
|
|
||||||
|
### 12. Success Criteria Validation
|
||||||
|
|
||||||
|
| Criterion | Validation Method |
|
||||||
|
|-----------|-------------------|
|
||||||
|
| Genome/protein upload | Test with .fna and .faa files |
|
||||||
|
| 16 concurrent tasks | Load test with 20 simultaneous requests |
|
||||||
|
| Language switching | Verify zh/en toggle works on all pages |
|
||||||
|
| Heatmap visualization | Compare output with expected results |
|
||||||
|
| Docker deployment | Access via bttiaw.hzau.edu.cn |
|
||||||
Reference in New Issue
Block a user