Spaces:
Sleeping
Sleeping
Upload 6 files
Browse files- Dockerfile +15 -12
- README.md +71 -22
- mcp_service.py +378 -0
- requirements.txt +24 -26
- start_mcp.py +35 -13
Dockerfile
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# MaTableGPT MCP Service Docker Image
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# ====================================
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# For HuggingFace Spaces Deployment
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FROM python:3.10-slim
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# Set environment variables
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ENV PYTHONDONTWRITEBYTECODE=1
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ENV PYTHONUNBUFFERED=1
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-
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# Install system dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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build-essential \
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git \
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&& rm -rf /var/lib/apt/lists/*
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# Copy requirements first for better caching
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pip install --no-cache-dir -r requirements.txt
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# Download NLTK data for table splitting
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RUN python -c "import nltk; nltk.download('punkt')"
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# Copy application code
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COPY . .
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# Set permissions for HuggingFace Spaces
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RUN chmod -R 777 /app/sessions /app/temp
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# Expose
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-
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EXPOSE 7860 7865
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# Health check
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HEALTHCHECK --interval=30s --timeout=30s --start-period=
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CMD
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# Run
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CMD ["python", "
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# MaTableGPT MCP Service Docker Image
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# ====================================
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# For HuggingFace Spaces Deployment (SSE Mode)
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FROM python:3.10-slim
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# Set environment variables
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ENV PYTHONDONTWRITEBYTECODE=1
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ENV PYTHONUNBUFFERED=1
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# MCP SSE Server Configuration
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# HuggingFace Spaces 使用端口 7860
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ENV MCP_HOST=0.0.0.0
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ENV MCP_PORT=7860
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# Install system dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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build-essential \
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git \
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curl \
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&& rm -rf /var/lib/apt/lists/*
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# Copy requirements first for better caching
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pip install --no-cache-dir -r requirements.txt
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# Download NLTK data for table splitting
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RUN python -c "import nltk; nltk.download('punkt')" || true
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# Copy application code
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COPY . .
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# Set permissions for HuggingFace Spaces
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RUN chmod -R 777 /app/sessions /app/temp
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# Expose MCP SSE port (HuggingFace Spaces uses 7860)
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EXPOSE 7860
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# Health check for MCP SSE endpoint
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HEALTHCHECK --interval=30s --timeout=30s --start-period=10s --retries=3 \
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CMD curl -f http://localhost:7860/sse || exit 1
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# Run MCP service in SSE mode
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CMD ["python", "start_mcp.py", "--mode", "sse", "--host", "0.0.0.0", "--port", "7860"]
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README.md
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- Store representations and extractions
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- Export session data for analysis
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## 📦 Installation
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### Prerequisites
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- Python 3.8+
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- OpenAI API key (for GPT extraction)
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### Local Installation
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## 🚀 Usage
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### Start MCP Server (
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```bash
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python start_mcp.py
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```
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### Start MCP Server (SSE mode for web integration)
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python start_mcp.py --mode sse --port
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```
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### Start
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```bash
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python
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```
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## 🔧 MCP Tools Reference
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| `extract_catalyst_data_zero_shot` | Extract using zero-shot GPT |
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| `extract_catalyst_data_few_shot` | Extract with example pairs |
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| `extract_catalyst_data_fine_tuned` | Extract using fine-tuned model |
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### Utilities
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| Tool | Description |
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|------|-------------|
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| `list_performance_types` | List supported catalyst performance types |
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| `validate_extraction_result` | Validate extraction against schema |
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| `get_extraction_code_template` | Get Python code for local extraction |
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| `get_environment_requirements` | Get setup requirements |
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docker build -t matablgpt-mcp .
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```
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### Run container
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```bash
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docker run -p 7860:7860
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-e
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matablgpt-mcp
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```
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## 🤗 HuggingFace Spaces Deployment
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1. Create a new Space with Docker SDK
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2. Upload all files from `mcp_output/`
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3. Add
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-
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## 📝 MCP Client Configuration
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-
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```json
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{
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"mcpServers": {
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"matablgpt": {
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"command": "python",
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"args": ["
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"env": {
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"
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}
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}
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}
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}
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```
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-
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```json
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{
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"mcpServers": {
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"matablgpt": {
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"url": "
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}
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}
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}
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## 🙏 Acknowledgments
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Based on [MaTableGPT](https://github.com/
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## 📜 License
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- Store representations and extractions
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- Export session data for analysis
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## 🚀 Quick Start (HuggingFace Space SSE Mode)
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This service runs as a **pure MCP SSE server** on HuggingFace Space, accessible via SSE endpoint.
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**SSE Endpoint**: `https://your-space-name.hf.space/sse`
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### Connect from Cursor/Claude Desktop
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```json
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{
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"mcpServers": {
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"matablgpt": {
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"url": "https://your-space-name.hf.space/sse"
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}
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}
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}
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```
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## 📦 Installation
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### Prerequisites
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- Python 3.8+
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- OpenAI-compatible API key (for GPT extraction)
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### Local Installation
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## 🚀 Usage
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### Start MCP Server (SSE mode - Default for HuggingFace Space)
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```bash
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# Default: SSE mode on port 7860
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python start_mcp.py
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# Custom port
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python start_mcp.py --mode sse --port 8080
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```
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### Start MCP Server (stdio mode - For local Cursor integration)
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```bash
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python start_mcp.py --mode stdio
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```
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## 🔧 MCP Tools Reference
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| `extract_catalyst_data_zero_shot` | Extract using zero-shot GPT |
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| `extract_catalyst_data_few_shot` | Extract with example pairs |
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| `extract_catalyst_data_fine_tuned` | Extract using fine-tuned model |
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| `batch_extract_tables` | Extract from multiple tables in batch |
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### Follow-up & Refinement
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| Tool | Description |
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|------|-------------|
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| `apply_follow_up_questions` | Refine extraction with iterative Q&A (from original MaTableGPT) |
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### Evaluation
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| Tool | Description |
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|------|-------------|
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| `evaluate_extraction` | Compute Structure F1 Score and Value Accuracy |
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| `validate_extraction_result` | Validate extraction against schema |
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### Utilities
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| Tool | Description |
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|------|-------------|
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| `list_performance_types` | List supported catalyst performance types |
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| `get_extraction_code_template` | Get Python code for local extraction |
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| `get_environment_requirements` | Get setup requirements |
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docker build -t matablgpt-mcp .
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```
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### Run container (SSE mode)
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```bash
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docker run -p 7860:7860 \
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-e LLM_API_KEY=your_key \
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-e LLM_API_BASE=https://api.your-service.com/v1 \
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matablgpt-mcp
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```
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## 🤗 HuggingFace Spaces Deployment
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1. Create a new Space with **Docker SDK**
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2. Upload all files from `mcp_output/`
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3. Add secrets in Space settings:
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- `LLM_API_KEY`: Your API key
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- `LLM_API_BASE`: Your API base URL (e.g., `https://api.your-service.com/v1`)
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- `LLM_MODEL`: (Optional) Model name
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4. Space will auto-build and deploy the MCP SSE service
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5. Connect via: `https://your-space-name.hf.space/sse`
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## 📝 MCP Client Configuration
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### For Cursor (SSE mode - HuggingFace Space)
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Add to `~/.cursor/mcp.json`:
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```json
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{
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"mcpServers": {
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"matablgpt": {
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"url": "https://your-space-name.hf.space/sse"
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}
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}
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}
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```
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### For Cursor (stdio mode - Local)
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```json
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{
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"mcpServers": {
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"matablgpt": {
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"command": "python",
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"args": ["F:/Material_Agent/MaTableGPT/mcp_output/start_mcp.py", "--mode", "stdio"],
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"env": {
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"LLM_API_KEY": "your_key",
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"LLM_API_BASE": "https://api.your-service.com/v1"
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}
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}
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}
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}
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```
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### For Claude Desktop
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```json
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{
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"mcpServers": {
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"matablgpt": {
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"url": "https://your-space-name.hf.space/sse"
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}
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}
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}
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## 🙏 Acknowledgments
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Based on [MaTableGPT](https://github.com/KIST-CSRC/MaTableGPT) - GPT-based Table Data Extractor from Materials Science Literature.
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## 📜 License
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mcp_service.py
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|
| 1326 |
@mcp.tool()
|
| 1327 |
def get_environment_requirements() -> Dict:
|
| 1328 |
"""
|
|
|
|
| 1323 |
}
|
| 1324 |
|
| 1325 |
|
| 1326 |
+
@mcp.tool()
|
| 1327 |
+
def apply_follow_up_questions(
|
| 1328 |
+
extraction_result: Dict,
|
| 1329 |
+
table_representation: str,
|
| 1330 |
+
session_id: str = "",
|
| 1331 |
+
table_name: str = ""
|
| 1332 |
+
) -> Dict:
|
| 1333 |
+
"""
|
| 1334 |
+
Apply follow-up questions to refine and validate extraction results.
|
| 1335 |
+
|
| 1336 |
+
This implements the iterative questioning process from the original MaTableGPT
|
| 1337 |
+
to improve extraction accuracy by:
|
| 1338 |
+
1. Verifying catalyst names against the table
|
| 1339 |
+
2. Checking performance types
|
| 1340 |
+
3. Validating property values
|
| 1341 |
+
4. Checking for reaction_type, electrolyte, substrate in title/caption
|
| 1342 |
+
|
| 1343 |
+
Args:
|
| 1344 |
+
extraction_result: Initial extraction result to refine
|
| 1345 |
+
table_representation: Original table representation for verification
|
| 1346 |
+
session_id: Optional session ID to save refined results
|
| 1347 |
+
table_name: Optional table name
|
| 1348 |
+
|
| 1349 |
+
Returns:
|
| 1350 |
+
Dictionary containing refined extraction result
|
| 1351 |
+
"""
|
| 1352 |
+
try:
|
| 1353 |
+
extractor = get_extractor()
|
| 1354 |
+
|
| 1355 |
+
# Initialize message context
|
| 1356 |
+
system_prompt = """You need to modify the JSON representing the table.
|
| 1357 |
+
JSON template: {'catalyst_name': {'performance_name': {property_template}}}
|
| 1358 |
+
property_template: {'electrolyte': '', 'reaction_type': '', 'value': '', 'current_density': '', 'overpotential': '', 'potential': '', 'substrate': '', 'versus': '', 'condition': ''}
|
| 1359 |
+
performance_list = """ + str(GPTExtractor.PERFORMANCE_LIST) + """
|
| 1360 |
+
Replace 'catalyst_name' and 'performance_name' with actual names from the table."""
|
| 1361 |
+
|
| 1362 |
+
messages = [{"role": "system", "content": system_prompt}]
|
| 1363 |
+
|
| 1364 |
+
# Step 1: Verify catalysts in table
|
| 1365 |
+
verify_q = f"""<input representation>
|
| 1366 |
+
{table_representation}
|
| 1367 |
+
|
| 1368 |
+
Question 1: List all catalyst names in the table representation as a Python list. Only output the Python list."""
|
| 1369 |
+
|
| 1370 |
+
messages.append({"role": "user", "content": verify_q})
|
| 1371 |
+
response = extractor.client.chat.completions.create(
|
| 1372 |
+
model=extractor.get_model(),
|
| 1373 |
+
messages=messages,
|
| 1374 |
+
temperature=0
|
| 1375 |
+
)
|
| 1376 |
+
catalysts_in_table = response.choices[0].message.content.strip()
|
| 1377 |
+
messages.append({"role": "assistant", "content": catalysts_in_table})
|
| 1378 |
+
|
| 1379 |
+
# Step 2: Get catalysts from extraction
|
| 1380 |
+
extraction_catalysts_q = f"""<input json>
|
| 1381 |
+
{json.dumps(extraction_result)}
|
| 1382 |
+
|
| 1383 |
+
Question 2: List all catalyst names from the input json as a Python list. Only output the Python list."""
|
| 1384 |
+
|
| 1385 |
+
messages.append({"role": "user", "content": extraction_catalysts_q})
|
| 1386 |
+
response = extractor.client.chat.completions.create(
|
| 1387 |
+
model=extractor.get_model(),
|
| 1388 |
+
messages=messages,
|
| 1389 |
+
temperature=0
|
| 1390 |
+
)
|
| 1391 |
+
catalysts_in_json = response.choices[0].message.content.strip()
|
| 1392 |
+
messages.append({"role": "assistant", "content": catalysts_in_json})
|
| 1393 |
+
|
| 1394 |
+
# Step 3: Reconcile catalysts
|
| 1395 |
+
reconcile_q = """Question 3: Based on answers to Question 1 and 2, modify or remove any catalysts
|
| 1396 |
+
from Question 2 that don't match Question 1. Output the corrected Python list."""
|
| 1397 |
+
|
| 1398 |
+
messages.append({"role": "user", "content": reconcile_q})
|
| 1399 |
+
response = extractor.client.chat.completions.create(
|
| 1400 |
+
model=extractor.get_model(),
|
| 1401 |
+
messages=messages,
|
| 1402 |
+
temperature=0
|
| 1403 |
+
)
|
| 1404 |
+
reconciled_catalysts = response.choices[0].message.content.strip()
|
| 1405 |
+
messages.append({"role": "assistant", "content": reconciled_catalysts})
|
| 1406 |
+
|
| 1407 |
+
# Step 4: Check for title/caption info
|
| 1408 |
+
title_caption_q = f"""<input representation>
|
| 1409 |
+
{table_representation}
|
| 1410 |
+
|
| 1411 |
+
Question 4: Check the title and caption of the table.
|
| 1412 |
+
- Is there reaction type info (OER, HER, oxygen evolution, hydrogen evolution)?
|
| 1413 |
+
- Is there electrolyte info?
|
| 1414 |
+
- Is there substrate info?
|
| 1415 |
+
Answer in format: {{"reaction_type": "yes/no", "electrolyte": "yes/no", "substrate": "yes/no"}}"""
|
| 1416 |
+
|
| 1417 |
+
messages.append({"role": "user", "content": title_caption_q})
|
| 1418 |
+
response = extractor.client.chat.completions.create(
|
| 1419 |
+
model=extractor.get_model(),
|
| 1420 |
+
messages=messages,
|
| 1421 |
+
temperature=0
|
| 1422 |
+
)
|
| 1423 |
+
metadata_check = response.choices[0].message.content.strip()
|
| 1424 |
+
messages.append({"role": "assistant", "content": metadata_check})
|
| 1425 |
+
|
| 1426 |
+
# Step 5: Apply refinements
|
| 1427 |
+
refine_q = f"""<input json>
|
| 1428 |
+
{json.dumps(extraction_result)}
|
| 1429 |
+
|
| 1430 |
+
Based on the above analysis:
|
| 1431 |
+
1. Keep only catalysts that exist in the table
|
| 1432 |
+
2. Remove any 'NA', 'unknown', or empty values
|
| 1433 |
+
3. If title/caption lacks reaction_type/electrolyte/substrate info, remove those keys
|
| 1434 |
+
4. Output the refined JSON only. No explanation."""
|
| 1435 |
+
|
| 1436 |
+
messages.append({"role": "user", "content": refine_q})
|
| 1437 |
+
response = extractor.client.chat.completions.create(
|
| 1438 |
+
model=extractor.get_model(),
|
| 1439 |
+
messages=messages,
|
| 1440 |
+
temperature=0
|
| 1441 |
+
)
|
| 1442 |
+
refined_result = response.choices[0].message.content.strip()
|
| 1443 |
+
|
| 1444 |
+
# Parse result
|
| 1445 |
+
if "```" in refined_result:
|
| 1446 |
+
refined_result = refined_result.replace("```json", "").replace("```", "")
|
| 1447 |
+
|
| 1448 |
+
try:
|
| 1449 |
+
refined_json = json.loads(refined_result)
|
| 1450 |
+
except json.JSONDecodeError:
|
| 1451 |
+
refined_json = extraction_result # Fall back to original
|
| 1452 |
+
|
| 1453 |
+
# Save if session provided
|
| 1454 |
+
if session_id:
|
| 1455 |
+
extraction_record = ExtractionResult(
|
| 1456 |
+
session_id=session_id,
|
| 1457 |
+
table_name=table_name or "unnamed",
|
| 1458 |
+
model_type="follow-up-refined",
|
| 1459 |
+
result=refined_json,
|
| 1460 |
+
timestamp=datetime.now().isoformat(),
|
| 1461 |
+
follow_up_applied=True
|
| 1462 |
+
)
|
| 1463 |
+
session_manager.save_extraction(session_id, extraction_record)
|
| 1464 |
+
|
| 1465 |
+
return {
|
| 1466 |
+
"success": True,
|
| 1467 |
+
"original": extraction_result,
|
| 1468 |
+
"refined": refined_json,
|
| 1469 |
+
"follow_up_applied": True,
|
| 1470 |
+
"verification_steps": {
|
| 1471 |
+
"catalysts_in_table": catalysts_in_table,
|
| 1472 |
+
"catalysts_in_json": catalysts_in_json,
|
| 1473 |
+
"reconciled": reconciled_catalysts,
|
| 1474 |
+
"metadata_check": metadata_check
|
| 1475 |
+
}
|
| 1476 |
+
}
|
| 1477 |
+
|
| 1478 |
+
except Exception as e:
|
| 1479 |
+
return {
|
| 1480 |
+
"success": False,
|
| 1481 |
+
"error": str(e),
|
| 1482 |
+
"original": extraction_result,
|
| 1483 |
+
"follow_up_applied": False
|
| 1484 |
+
}
|
| 1485 |
+
|
| 1486 |
+
|
| 1487 |
+
@mcp.tool()
|
| 1488 |
+
def evaluate_extraction(
|
| 1489 |
+
prediction: Dict,
|
| 1490 |
+
ground_truth: Dict,
|
| 1491 |
+
evaluation_type: str = "both"
|
| 1492 |
+
) -> Dict:
|
| 1493 |
+
"""
|
| 1494 |
+
Evaluate extraction results against ground truth.
|
| 1495 |
+
|
| 1496 |
+
Computes metrics from the original MaTableGPT evaluation:
|
| 1497 |
+
- Structure F1 Score: Measures correctness of JSON structure
|
| 1498 |
+
- Value Accuracy: Measures correctness of extracted values
|
| 1499 |
+
|
| 1500 |
+
Args:
|
| 1501 |
+
prediction: The extracted/predicted result
|
| 1502 |
+
ground_truth: The expected correct result
|
| 1503 |
+
evaluation_type: "structure", "value", or "both"
|
| 1504 |
+
|
| 1505 |
+
Returns:
|
| 1506 |
+
Dictionary containing evaluation metrics
|
| 1507 |
+
"""
|
| 1508 |
+
import re
|
| 1509 |
+
import unicodedata
|
| 1510 |
+
|
| 1511 |
+
def normalize_text(text: str) -> str:
|
| 1512 |
+
"""Normalize text for comparison."""
|
| 1513 |
+
if not isinstance(text, str):
|
| 1514 |
+
return str(text)
|
| 1515 |
+
# Remove unicode variations
|
| 1516 |
+
text = unicodedata.normalize('NFKD', text)
|
| 1517 |
+
# Common substitutions
|
| 1518 |
+
text = re.sub(r'–|−', '-', text)
|
| 1519 |
+
text = re.sub(r'<sup>|</sup>', '', text)
|
| 1520 |
+
text = re.sub(r'm2 g−1', 'm2/g', text)
|
| 1521 |
+
text = re.sub(r'mA cm−2', 'mA/cm2', text)
|
| 1522 |
+
text = re.sub(r'\s+', '', text)
|
| 1523 |
+
return text.lower()
|
| 1524 |
+
|
| 1525 |
+
def get_all_keys(d: Dict, parent_key: str = '', sep: str = '//') -> List[str]:
|
| 1526 |
+
"""Recursively get all keys from nested dict."""
|
| 1527 |
+
keys = []
|
| 1528 |
+
if isinstance(d, dict):
|
| 1529 |
+
for k, v in d.items():
|
| 1530 |
+
new_key = f"{parent_key}{sep}{k}" if parent_key else k
|
| 1531 |
+
keys.append(new_key)
|
| 1532 |
+
keys.extend(get_all_keys(v, new_key, sep))
|
| 1533 |
+
elif isinstance(d, list):
|
| 1534 |
+
for i, item in enumerate(d):
|
| 1535 |
+
keys.extend(get_all_keys(item, f"{parent_key}[{i}]", sep))
|
| 1536 |
+
return keys
|
| 1537 |
+
|
| 1538 |
+
def get_key_value_pairs(d: Dict, parent_key: str = '') -> List[tuple]:
|
| 1539 |
+
"""Get all key-value pairs from nested dict."""
|
| 1540 |
+
pairs = []
|
| 1541 |
+
if isinstance(d, dict):
|
| 1542 |
+
for k, v in d.items():
|
| 1543 |
+
new_key = f"{parent_key}//{k}" if parent_key else k
|
| 1544 |
+
if isinstance(v, (dict, list)):
|
| 1545 |
+
pairs.extend(get_key_value_pairs(v, new_key))
|
| 1546 |
+
else:
|
| 1547 |
+
pairs.append((new_key, normalize_text(str(v))))
|
| 1548 |
+
elif isinstance(d, list):
|
| 1549 |
+
for i, item in enumerate(d):
|
| 1550 |
+
pairs.extend(get_key_value_pairs(item, f"{parent_key}[{i}]"))
|
| 1551 |
+
return pairs
|
| 1552 |
+
|
| 1553 |
+
results = {"success": True}
|
| 1554 |
+
|
| 1555 |
+
try:
|
| 1556 |
+
# Normalize both inputs
|
| 1557 |
+
pred_keys = get_all_keys(prediction)
|
| 1558 |
+
gt_keys = get_all_keys(ground_truth)
|
| 1559 |
+
|
| 1560 |
+
# Structure F1 Score
|
| 1561 |
+
if evaluation_type in ["structure", "both"]:
|
| 1562 |
+
# Remove 'condition' keys as per original
|
| 1563 |
+
pred_keys = [k for k in pred_keys if 'condition' not in k]
|
| 1564 |
+
gt_keys = [k for k in gt_keys if 'condition' not in k]
|
| 1565 |
+
|
| 1566 |
+
# Calculate TP, FP, FN for structure
|
| 1567 |
+
tp = len(set(pred_keys) & set(gt_keys))
|
| 1568 |
+
fp = len(set(pred_keys) - set(gt_keys))
|
| 1569 |
+
fn = len(set(gt_keys) - set(pred_keys))
|
| 1570 |
+
|
| 1571 |
+
if tp + fp + fn > 0:
|
| 1572 |
+
f1_score = tp / (tp + 0.5 * (fp + fn))
|
| 1573 |
+
else:
|
| 1574 |
+
f1_score = 1.0 if len(gt_keys) == 0 else 0.0
|
| 1575 |
+
|
| 1576 |
+
results["structure_f1"] = round(f1_score, 4)
|
| 1577 |
+
results["structure_details"] = {
|
| 1578 |
+
"true_positives": tp,
|
| 1579 |
+
"false_positives": fp,
|
| 1580 |
+
"false_negatives": fn,
|
| 1581 |
+
"matched_keys": list(set(pred_keys) & set(gt_keys))[:10], # Sample
|
| 1582 |
+
"missing_keys": list(set(gt_keys) - set(pred_keys))[:10],
|
| 1583 |
+
"extra_keys": list(set(pred_keys) - set(gt_keys))[:10]
|
| 1584 |
+
}
|
| 1585 |
+
|
| 1586 |
+
# Value Accuracy
|
| 1587 |
+
if evaluation_type in ["value", "both"]:
|
| 1588 |
+
pred_pairs = get_key_value_pairs(prediction)
|
| 1589 |
+
gt_pairs = get_key_value_pairs(ground_truth)
|
| 1590 |
+
|
| 1591 |
+
# Compare values
|
| 1592 |
+
correct = 0
|
| 1593 |
+
total = len(gt_pairs)
|
| 1594 |
+
|
| 1595 |
+
pred_dict = {k: v for k, v in pred_pairs}
|
| 1596 |
+
|
| 1597 |
+
for key, value in gt_pairs:
|
| 1598 |
+
if key in pred_dict:
|
| 1599 |
+
# Normalize and compare
|
| 1600 |
+
if normalize_text(pred_dict[key]) == normalize_text(value):
|
| 1601 |
+
correct += 1
|
| 1602 |
+
|
| 1603 |
+
value_accuracy = correct / total if total > 0 else 1.0
|
| 1604 |
+
|
| 1605 |
+
results["value_accuracy"] = round(value_accuracy, 4)
|
| 1606 |
+
results["value_details"] = {
|
| 1607 |
+
"correct_values": correct,
|
| 1608 |
+
"total_values": total,
|
| 1609 |
+
"accuracy_percentage": round(value_accuracy * 100, 2)
|
| 1610 |
+
}
|
| 1611 |
+
|
| 1612 |
+
# Overall score
|
| 1613 |
+
if evaluation_type == "both":
|
| 1614 |
+
results["overall_score"] = round(
|
| 1615 |
+
(results["structure_f1"] + results["value_accuracy"]) / 2, 4
|
| 1616 |
+
)
|
| 1617 |
+
|
| 1618 |
+
except Exception as e:
|
| 1619 |
+
results["success"] = False
|
| 1620 |
+
results["error"] = str(e)
|
| 1621 |
+
|
| 1622 |
+
return results
|
| 1623 |
+
|
| 1624 |
+
|
| 1625 |
+
@mcp.tool()
|
| 1626 |
+
def batch_extract_tables(
|
| 1627 |
+
tables: List[Dict],
|
| 1628 |
+
model_type: str = "zero-shot",
|
| 1629 |
+
apply_follow_up: bool = False,
|
| 1630 |
+
session_id: str = ""
|
| 1631 |
+
) -> Dict:
|
| 1632 |
+
"""
|
| 1633 |
+
Extract data from multiple tables in batch.
|
| 1634 |
+
|
| 1635 |
+
Args:
|
| 1636 |
+
tables: List of {"html": html_table, "title": title, "caption": caption, "name": table_name}
|
| 1637 |
+
model_type: "zero-shot", "few-shot", or "fine-tuning"
|
| 1638 |
+
apply_follow_up: Whether to apply follow-up questions for refinement
|
| 1639 |
+
session_id: Optional session ID
|
| 1640 |
+
|
| 1641 |
+
Returns:
|
| 1642 |
+
Dictionary containing all extraction results
|
| 1643 |
+
"""
|
| 1644 |
+
if not session_id:
|
| 1645 |
+
session_id = session_manager.create_session()
|
| 1646 |
+
|
| 1647 |
+
results = {
|
| 1648 |
+
"success": True,
|
| 1649 |
+
"session_id": session_id,
|
| 1650 |
+
"total_tables": len(tables),
|
| 1651 |
+
"extractions": []
|
| 1652 |
+
}
|
| 1653 |
+
|
| 1654 |
+
for i, table_info in enumerate(tables):
|
| 1655 |
+
html = table_info.get("html", "")
|
| 1656 |
+
title = table_info.get("title", "")
|
| 1657 |
+
caption = table_info.get("caption", "")
|
| 1658 |
+
table_name = table_info.get("name", f"table_{i+1}")
|
| 1659 |
+
|
| 1660 |
+
try:
|
| 1661 |
+
# Convert to representation
|
| 1662 |
+
representation = table_representer.html_to_tsv(html, title, caption)
|
| 1663 |
+
|
| 1664 |
+
# Extract based on model type
|
| 1665 |
+
extractor = get_extractor()
|
| 1666 |
+
if model_type == "zero-shot":
|
| 1667 |
+
extraction = extractor.extract_zero_shot(representation)
|
| 1668 |
+
elif model_type == "few-shot":
|
| 1669 |
+
extraction = extractor.extract_few_shot(representation)
|
| 1670 |
+
else:
|
| 1671 |
+
extraction = {"error": "Fine-tuning requires model_name parameter"}
|
| 1672 |
+
|
| 1673 |
+
# Apply follow-up if requested
|
| 1674 |
+
if apply_follow_up and "error" not in extraction:
|
| 1675 |
+
from copy import deepcopy
|
| 1676 |
+
follow_up_result = apply_follow_up_questions(
|
| 1677 |
+
deepcopy(extraction),
|
| 1678 |
+
representation,
|
| 1679 |
+
session_id,
|
| 1680 |
+
table_name
|
| 1681 |
+
)
|
| 1682 |
+
if follow_up_result.get("success"):
|
| 1683 |
+
extraction = follow_up_result.get("refined", extraction)
|
| 1684 |
+
|
| 1685 |
+
results["extractions"].append({
|
| 1686 |
+
"table_name": table_name,
|
| 1687 |
+
"success": True,
|
| 1688 |
+
"extraction": extraction
|
| 1689 |
+
})
|
| 1690 |
+
|
| 1691 |
+
except Exception as e:
|
| 1692 |
+
results["extractions"].append({
|
| 1693 |
+
"table_name": table_name,
|
| 1694 |
+
"success": False,
|
| 1695 |
+
"error": str(e)
|
| 1696 |
+
})
|
| 1697 |
+
|
| 1698 |
+
results["successful_extractions"] = sum(1 for e in results["extractions"] if e["success"])
|
| 1699 |
+
results["failed_extractions"] = results["total_tables"] - results["successful_extractions"]
|
| 1700 |
+
|
| 1701 |
+
return results
|
| 1702 |
+
|
| 1703 |
+
|
| 1704 |
@mcp.tool()
|
| 1705 |
def get_environment_requirements() -> Dict:
|
| 1706 |
"""
|
requirements.txt
CHANGED
|
@@ -1,26 +1,24 @@
|
|
| 1 |
-
# MaTableGPT MCP Service Requirements
|
| 2 |
-
# ====================================
|
| 3 |
-
|
| 4 |
-
# Core MCP Framework
|
| 5 |
-
mcp>=
|
| 6 |
-
|
| 7 |
-
# OpenAI-compatible API client
|
| 8 |
-
openai>=1.0.0
|
| 9 |
-
|
| 10 |
-
# HTML Parsing
|
| 11 |
-
beautifulsoup4>=4.12.0
|
| 12 |
-
lxml>=4.9.0
|
| 13 |
-
|
| 14 |
-
# Data Processing
|
| 15 |
-
pandas>=2.0.0
|
| 16 |
-
|
| 17 |
-
#
|
| 18 |
-
|
| 19 |
-
|
| 20 |
-
|
| 21 |
-
|
| 22 |
-
|
| 23 |
-
|
| 24 |
-
|
| 25 |
-
# Optional: For table splitting analysis
|
| 26 |
-
nltk>=3.8.0
|
|
|
|
| 1 |
+
# MaTableGPT MCP Service Requirements
|
| 2 |
+
# ====================================
|
| 3 |
+
|
| 4 |
+
# Core MCP Framework (with SSE support)
|
| 5 |
+
mcp[cli]>=1.0.0
|
| 6 |
+
|
| 7 |
+
# OpenAI-compatible API client
|
| 8 |
+
openai>=1.0.0
|
| 9 |
+
|
| 10 |
+
# HTML Parsing
|
| 11 |
+
beautifulsoup4>=4.12.0
|
| 12 |
+
lxml>=4.9.0
|
| 13 |
+
|
| 14 |
+
# Data Processing
|
| 15 |
+
pandas>=2.0.0
|
| 16 |
+
|
| 17 |
+
# SSE/HTTP Support
|
| 18 |
+
starlette>=0.27.0
|
| 19 |
+
uvicorn>=0.23.0
|
| 20 |
+
sse-starlette>=1.6.0
|
| 21 |
+
httpx>=0.25.0
|
| 22 |
+
|
| 23 |
+
# Optional: For table splitting analysis
|
| 24 |
+
nltk>=3.8.0
|
|
|
|
|
|
start_mcp.py
CHANGED
|
@@ -11,8 +11,15 @@ Usage:
|
|
| 11 |
|
| 12 |
Arguments:
|
| 13 |
--host Host address (default: 0.0.0.0)
|
| 14 |
-
--port Port number (default:
|
| 15 |
-
--mode Run mode: 'stdio' or 'sse' (default:
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 16 |
"""
|
| 17 |
|
| 18 |
import os
|
|
@@ -35,13 +42,19 @@ def check_environment():
|
|
| 35 |
"""Check if required environment variables are set."""
|
| 36 |
warnings = []
|
| 37 |
|
| 38 |
-
|
|
|
|
|
|
|
| 39 |
warnings.append(
|
| 40 |
-
"OPENAI_API_KEY not set. GPT extraction features will not work. "
|
| 41 |
-
"Set it
|
| 42 |
-
"set OPENAI_API_KEY=your_key (Windows)"
|
| 43 |
)
|
| 44 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 45 |
return warnings
|
| 46 |
|
| 47 |
|
|
@@ -50,7 +63,7 @@ def check_dependencies():
|
|
| 50 |
missing = []
|
| 51 |
|
| 52 |
required = [
|
| 53 |
-
('mcp', 'mcp'),
|
| 54 |
('openai', 'openai'),
|
| 55 |
('bs4', 'beautifulsoup4'),
|
| 56 |
('pandas', 'pandas'),
|
|
@@ -68,25 +81,29 @@ def check_dependencies():
|
|
| 68 |
|
| 69 |
def main():
|
| 70 |
"""Main entry point."""
|
|
|
|
|
|
|
|
|
|
|
|
|
| 71 |
parser = argparse.ArgumentParser(
|
| 72 |
description="MaTableGPT MCP Server - Table Data Extraction from Materials Science Literature"
|
| 73 |
)
|
| 74 |
parser.add_argument(
|
| 75 |
'--host',
|
| 76 |
-
default=
|
| 77 |
-
help='Host address (default:
|
| 78 |
)
|
| 79 |
parser.add_argument(
|
| 80 |
'--port',
|
| 81 |
type=int,
|
| 82 |
-
default=
|
| 83 |
-
help='Port number (default:
|
| 84 |
)
|
| 85 |
parser.add_argument(
|
| 86 |
'--mode',
|
| 87 |
choices=['stdio', 'sse'],
|
| 88 |
-
default='
|
| 89 |
-
help='Run mode: stdio for standard I/O, sse for Server-Sent Events (default:
|
| 90 |
)
|
| 91 |
parser.add_argument(
|
| 92 |
'--debug',
|
|
@@ -119,6 +136,7 @@ def main():
|
|
| 119 |
if args.mode == 'sse':
|
| 120 |
logger.info(f"Host: {args.host}")
|
| 121 |
logger.info(f"Port: {args.port}")
|
|
|
|
| 122 |
logger.info("=" * 60)
|
| 123 |
|
| 124 |
# Import and run MCP service
|
|
@@ -130,13 +148,17 @@ def main():
|
|
| 130 |
mcp.run()
|
| 131 |
else:
|
| 132 |
logger.info(f"Starting MCP server in SSE mode on {args.host}:{args.port}...")
|
|
|
|
| 133 |
mcp.run(transport='sse', host=args.host, port=args.port)
|
| 134 |
|
| 135 |
except ImportError as e:
|
| 136 |
logger.error(f"Failed to import MCP service: {e}")
|
|
|
|
| 137 |
sys.exit(1)
|
| 138 |
except Exception as e:
|
| 139 |
logger.error(f"Error starting MCP server: {e}")
|
|
|
|
|
|
|
| 140 |
sys.exit(1)
|
| 141 |
|
| 142 |
|
|
|
|
| 11 |
|
| 12 |
Arguments:
|
| 13 |
--host Host address (default: 0.0.0.0)
|
| 14 |
+
--port Port number (default: 7860)
|
| 15 |
+
--mode Run mode: 'stdio' or 'sse' (default: sse for HuggingFace Space)
|
| 16 |
+
|
| 17 |
+
Environment Variables:
|
| 18 |
+
LLM_API_KEY / OPENAI_API_KEY - API key for LLM service
|
| 19 |
+
LLM_API_BASE / OPENAI_API_BASE - Custom API base URL (for third-party services)
|
| 20 |
+
LLM_MODEL / OPENAI_MODEL - Model name (default: gpt-4-turbo-preview)
|
| 21 |
+
MCP_HOST - Server host (default: 0.0.0.0)
|
| 22 |
+
MCP_PORT - Server port (default: 7860)
|
| 23 |
"""
|
| 24 |
|
| 25 |
import os
|
|
|
|
| 42 |
"""Check if required environment variables are set."""
|
| 43 |
warnings = []
|
| 44 |
|
| 45 |
+
# Check for API key (support both naming conventions)
|
| 46 |
+
api_key = os.environ.get('LLM_API_KEY') or os.environ.get('OPENAI_API_KEY')
|
| 47 |
+
if not api_key:
|
| 48 |
warnings.append(
|
| 49 |
+
"LLM_API_KEY/OPENAI_API_KEY not set. GPT extraction features will not work. "
|
| 50 |
+
"Set it in HuggingFace Space secrets or environment variables."
|
|
|
|
| 51 |
)
|
| 52 |
|
| 53 |
+
# Check for API base (for third-party services)
|
| 54 |
+
api_base = os.environ.get('LLM_API_BASE') or os.environ.get('OPENAI_API_BASE')
|
| 55 |
+
if api_base:
|
| 56 |
+
logger.info(f"Using custom API base: {api_base}")
|
| 57 |
+
|
| 58 |
return warnings
|
| 59 |
|
| 60 |
|
|
|
|
| 63 |
missing = []
|
| 64 |
|
| 65 |
required = [
|
| 66 |
+
('mcp', 'mcp[cli]'),
|
| 67 |
('openai', 'openai'),
|
| 68 |
('bs4', 'beautifulsoup4'),
|
| 69 |
('pandas', 'pandas'),
|
|
|
|
| 81 |
|
| 82 |
def main():
|
| 83 |
"""Main entry point."""
|
| 84 |
+
# Get default values from environment variables
|
| 85 |
+
default_host = os.environ.get('MCP_HOST', '0.0.0.0')
|
| 86 |
+
default_port = int(os.environ.get('MCP_PORT', '7860'))
|
| 87 |
+
|
| 88 |
parser = argparse.ArgumentParser(
|
| 89 |
description="MaTableGPT MCP Server - Table Data Extraction from Materials Science Literature"
|
| 90 |
)
|
| 91 |
parser.add_argument(
|
| 92 |
'--host',
|
| 93 |
+
default=default_host,
|
| 94 |
+
help=f'Host address (default: {default_host})'
|
| 95 |
)
|
| 96 |
parser.add_argument(
|
| 97 |
'--port',
|
| 98 |
type=int,
|
| 99 |
+
default=default_port,
|
| 100 |
+
help=f'Port number (default: {default_port})'
|
| 101 |
)
|
| 102 |
parser.add_argument(
|
| 103 |
'--mode',
|
| 104 |
choices=['stdio', 'sse'],
|
| 105 |
+
default='sse',
|
| 106 |
+
help='Run mode: stdio for standard I/O, sse for Server-Sent Events (default: sse)'
|
| 107 |
)
|
| 108 |
parser.add_argument(
|
| 109 |
'--debug',
|
|
|
|
| 136 |
if args.mode == 'sse':
|
| 137 |
logger.info(f"Host: {args.host}")
|
| 138 |
logger.info(f"Port: {args.port}")
|
| 139 |
+
logger.info(f"SSE Endpoint: http://{args.host}:{args.port}/sse")
|
| 140 |
logger.info("=" * 60)
|
| 141 |
|
| 142 |
# Import and run MCP service
|
|
|
|
| 148 |
mcp.run()
|
| 149 |
else:
|
| 150 |
logger.info(f"Starting MCP server in SSE mode on {args.host}:{args.port}...")
|
| 151 |
+
logger.info("MCP SSE service is ready to accept connections!")
|
| 152 |
mcp.run(transport='sse', host=args.host, port=args.port)
|
| 153 |
|
| 154 |
except ImportError as e:
|
| 155 |
logger.error(f"Failed to import MCP service: {e}")
|
| 156 |
+
logger.error("Make sure mcp_service.py is in the same directory")
|
| 157 |
sys.exit(1)
|
| 158 |
except Exception as e:
|
| 159 |
logger.error(f"Error starting MCP server: {e}")
|
| 160 |
+
import traceback
|
| 161 |
+
traceback.print_exc()
|
| 162 |
sys.exit(1)
|
| 163 |
|
| 164 |
|