127 lines
4.2 KiB
Markdown
Executable File
127 lines
4.2 KiB
Markdown
Executable File
# Gene Family MAS Project Progress
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## Backup Location
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- `/home/xia-lab/gene-family-mas-backup-20260221-053220`
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## Papers Location
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- `/home/xia-lab/wutx/00test/bbav2/paper/gfpaper/buchong/` (33+ PDFs)
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## Completed Modules (2026-02-21)
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### 1. LLM Multi-Provider System (`src/llm/`)
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- `base.py`: BaseLLMProvider, LLMResponse, LLMMessage
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- `manager.py`: LLMManager with auto-fallback (GLM-4 → Kimi → MiniMax → DeepSeek)
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- `providers/glm.py`: GLM-4 via zhipuai
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- `providers/kimi.py`: Kimi via OpenAI-compatible API
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- `providers/minimax.py`: MiniMax via OpenAI-compatible API
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- `providers/deepseek.py`: DeepSeek via OpenAI-compatible API
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### 2. Memory System (`src/memory/`)
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- `base.py`: BaseMemory, MemoryEntry, SearchResult
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- `session.py`: SessionMemory (in-memory with TTL)
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- `case.py`: CaseMemory (SQLite persistence)
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- `knowledge.py`: KnowledgeMemory (vector embeddings)
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- `manager.py`: MemoryManager orchestrating all layers
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### 3. Core Orchestrator (`src/core/`)
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- `state.py`: GraphState (TypedDict for LangGraph)
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- `orchestrator.py`: LangGraph flow with intent routing (FAQ/Analysis modes)
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### 4. RAG Knowledge System (`src/rag/`) ✅
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- `base.py`: Document, Chunk, SearchResult dataclasses
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- `pdf_extractor.py`: PDF text extraction using PyMuPDF
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- `chunker.py`: 50-30 chunking strategy
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- `embeddings.py`: GLMEmbedding with fake embedding fallback
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- `vector_store.py`: In-memory vector store with cosine similarity
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- `retriever.py`: RAGRetriever orchestrating extraction → chunking → embedding → search
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### 5. Tool Execution System (`src/tools/`) ✅
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- `registry.py`: ToolRegistry with HMMER, BLAST, MAFFT, IQ-TREE, MCScanX, MEME
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- `adapter.py`: ToolAdapter for command execution
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- `executor.py`: ToolExecutor with Docker support
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- `workflow.py`: GeneFamilyWorkflow for chaining tools
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### 6. FastAPI Backend (`api/`)
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- `main.py`: FastAPI app with CORS, dotenv loading
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- `routes.py`: Full REST API endpoints
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- `/session`, `/query`, `/case`, `/feedback`
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- `/providers` - List available LLM providers
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- `/tools` - List available analysis tools
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- `/tools/{tool_id}/execute` - Execute a specific tool
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- `/workflow/gene-family` - Run gene family workflow
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- `/upload` - Single file upload
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- `/upload/batch` - Batch file upload
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- `/ws/{session_id}` - WebSocket for real-time progress
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- `schemas.py`: Pydantic request/response models
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- `websocket.py`: WebSocket connection manager
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### 7. Frontend (`frontend/`)
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- Next.js 14 + TypeScript + Tailwind CSS
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- Chat interface with message history
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- File upload support
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- WebSocket for real-time progress
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## API Endpoints Summary
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| Endpoint | Method | Description |
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|----------|--------|-------------|
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| `/health` | GET | Health check |
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| `/api/v1/providers` | GET | List LLM providers |
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| `/api/v1/session` | POST | Create session |
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| `/api/v1/query` | POST | Submit query (FAQ/Analysis) |
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| `/api/v1/case` | POST/GET | Create/get case |
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| `/api/v1/feedback` | POST | Submit feedback |
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| `/api/v1/tools` | GET | List available tools |
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| `/api/v1/tools/{tool_id}/execute` | POST | Execute tool |
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| `/api/v1/workflow/gene-family` | POST | Run analysis workflow |
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| `/api/v1/upload` | POST | Upload single file |
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| `/api/v1/upload/batch` | POST | Upload multiple files |
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| `/api/v1/ws/{session_id}` | WS | WebSocket connection |
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## Configuration
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### Environment Variables (.env)
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```
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ZHIPUAI_API_KEY=configured
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MOONSHOT_API_KEY=configured
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MINIMAX_API_KEY=configured
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DEEPSEEK_API_KEY=configured
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```
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### LLM Config (config/llm.yaml)
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- Default: GLM-4-flash
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- Models: glm-4-flash, glm-4, glm-4-plus
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- Fallback: Kimi → MiniMax → DeepSeek
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## Running Commands
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### Backend
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```bash
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cd /home/xia-lab/gene-family-mas
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poetry shell
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uvicorn api.main:app --host 0.0.0.0 --port 8000
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```
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### Frontend
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```bash
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cd /home/xia-lab/gene-family-mas/frontend
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npm run dev
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```
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### Test Queries
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```bash
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# FAQ query
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curl -X POST http://localhost:8000/api/v1/query \
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-H "Content-Type: application/json" \
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-d '{"session_id": "test", "query": "什么是基因家族？"}'
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# Analysis query
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curl -X POST http://localhost:8000/api/v1/query \
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-H "Content-Type: application/json" \
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-d '{"session_id": "test", "query": "帮我鉴定苦荞的SPL基因家族"}'
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# File upload
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curl -X POST http://localhost:8000/api/v1/upload \
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-F "file=@sequences.fasta"
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```
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