Which integrations are available for this server?

Provides function calling capabilities for Gemini to search document databases and retrieve relevant information from PDF collections using natural language queries

How do I use RAG Database MCP Server?

1. Click on "Install Server". 2. Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state. 3. In the chat, type @ followed by the MCP server name and your instructions, e.g., "@RAG Database MCP Server search my documents for information about renewable energy policies" That's it! The server will respond to your query, and you can continue using it as needed. Here is a step-by-step guide with screenshots.

RAG Database with Model Context Protocol (MCP) Server

A comprehensive Retrieval-Augmented Generation (RAG) system that integrates with AI assistants like Claude, ChatGPT, and Gemini through the Model Context Protocol (MCP). This system allows you to ingest PDF documents, create vector embeddings, and query your document collection using natural language.

🎯 Overview

This RAG system consists of three main components:

Document Ingestion Pipeline - Extracts text from PDFs and creates vector embeddings
Vector Database - Local ChromaDB storage with persistent file-based storage
MCP Server - Exposes the RAG database through standardized tools for AI assistants

Key Features

📄 PDF Document Processing - Automatic text extraction and chunking
🔍 Semantic Search - Vector similarity search using embeddings
🤖 AI Assistant Integration - Works with Claude Desktop, ChatGPT, and other MCP-compatible clients
💾 Local Storage - All data stored locally, no external dependencies
⚡ Fast Performance - Persistent API server keeps models loaded
🔧 Easy Setup - Automated installation and configuration scripts

🚀 Quick Start

Prerequisites

Python 3.8+
4GB+ RAM (for embedding models)
macOS, Linux, or Windows

1. Initial Setup

# Clone the repository git clone <repository-url> cd RAG-MCP-HCSRL # Create virtual environment python3 -m venv venv source venv/bin/activate # On Windows: venv\Scripts\activate # Run automated setup (installs dependencies, creates directories, tests functionality) python setup.py

2. Initialize Database

# Initialize ChromaDB python init_chroma.py

3. Add Documents

# Create documents directory and add your PDF files mkdir -p documents # Copy your PDF files to the documents/ directory # Ingest PDFs into the database python ingest_pdfs.py --input-dir ./documents

4. Start the System

# Terminal 1: Start the RAG API server (keeps models loaded) source venv/bin/activate python rag_api_server.py --port 8000 # Terminal 2: Test the system python tests/test_rag_query.py --query "your search query here"

🔧 AI Assistant Integration

Claude Desktop Integration

Claude Desktop uses the MCP protocol to connect to your RAG database.

Configuration

Configure Claude Desktop MCP Settings

Edit ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or equivalent on other platforms:

{ "mcpServers": { "rag-server": { "command": "python", "args": ["/full/path/to/RAG-MCP-HCSRL/rag_mcp_server.py"], "cwd": "/full/path/to/RAG-MCP-HCSRL", "env": { "PATH": "/full/path/to/RAG-MCP-HCSRL/venv/bin:/usr/bin:/bin" } } } }

Start Required Services

# Start the RAG API server first source venv/bin/activate && python rag_api_server.py --port 8000

Restart Claude Desktop

The MCP server will automatically start when Claude Desktop launches.

Usage in Claude Desktop

Once configured, you can ask Claude to search your documents:

Search my documents for information about protein folding Find papers related to machine learning in my database What does my collection say about renewable energy?

ChatGPT Integration

ChatGPT can access your RAG system through API calls or custom GPT actions.

Option 1: API Integration

# Start the RAG API server python rag_api_server.py --host 0.0.0.0 --port 8000 # ChatGPT can then make HTTP requests to your server # POST http://your-server:8000/search # Body: {"query": "search terms", "top_k": 5}

Option 2: Custom GPT Actions

Create a custom GPT with these action definitions:

openapi: 3.0.1 info: title: RAG Document Search version: 1.0.0 servers: - url: http://your-server:8000 paths: /search: post: summary: Search documents requestBody: required: true content: application/json: schema: type: object properties: query: type: string description: Search query top_k: type: integer description: Number of results responses: '200': description: Search results

Google Gemini Integration

Gemini can integrate through function calling or extensions.

Function Calling Setup

# Example Gemini function definition search_documents_function = { "name": "search_documents", "description": "Search RAG document database", "parameters": { "type": "object", "properties": { "query": {"type": "string", "description": "Search query"}, "top_k": {"type": "integer", "description": "Number of results"} }, "required": ["query"] } }

📁 System Architecture

RAG-MCP-HCSRL/ ├── README.md # This file ├── CLAUDE.md # Project instructions for Claude ├── requirements.txt # Python dependencies ├── setup.py # System setup and verification ├── init_chroma.py # Database initialization ├── chroma_db.py # Core database manager ├── ingest_pdfs.py # PDF ingestion pipeline ├── rag_api_server.py # Persistent API server ├── rag_mcp_server.py # MCP protocol server ├── documents/ # PDF documents directory ├── chroma_db/ # ChromaDB storage (created automatically) ├── tests/ # Test scripts │ ├── test_rag_query.py # RAG query testing │ └── test_chroma_db.py # Database testing └── venv/ # Virtual environment

🛠️ Detailed Setup Guide

Manual Installation

If the automated setup doesn't work, follow these manual steps:

# 1. Create virtual environment python3 -m venv venv source venv/bin/activate # 2. Install dependencies pip install -U sentence-transformers pip install torch torchvision torchaudio pip install chromadb python-dotenv pip install fastapi uvicorn "mcp[cli]" pip install pypdf2 pymupdf python-multipart pip install httpx numpy pandas tqdm nltk # 3. Create directories mkdir -p chroma_db documents # 4. Initialize database python init_chroma.py # 5. Test installation python tests/test_chroma_db.py

Environment Configuration

Create a .env file for custom configuration:

# .env file CHROMA_PERSIST_DIR=./chroma_db COLLECTION_NAME=pdf_documents API_PORT=8000 API_HOST=127.0.0.1 LOG_LEVEL=INFO

📊 Usage Examples

Command Line Usage

# Search documents python tests/test_rag_query.py --query "machine learning applications" # Get collection statistics python -c " from tests.test_rag_query import RAGQuerySystem rag = RAGQuerySystem() print(rag.get_collection_stats()) " # Ingest new documents python ingest_pdfs.py --input-dir ./new_documents --chunk-size 1000

API Usage

# Health check curl http://localhost:8000/health # Search documents curl -X POST "http://localhost:8000/search" \ -H "Content-Type: application/json" \ -d '{"query": "protein folding", "top_k": 3}' # Get statistics curl http://localhost:8000/stats

MCP Tools Available

When connected through MCP, these tools are available:

search_documents - Search the document database
get_collection_stats - Get database statistics
health_check - Check system health

⚙️ Configuration Options

Database Configuration

# Custom database location python init_chroma.py --chroma-dir ./custom_db # Custom collection name python init_chroma.py --collection-name research_papers # Reset database python init_chroma.py --reset

API Server Configuration

# Custom host and port python rag_api_server.py --host 0.0.0.0 --port 8080 # Verbose logging python rag_api_server.py --verbose # Custom database location python rag_api_server.py --chroma-dir ./custom_db

Document Ingestion Options

# Custom chunk size python ingest_pdfs.py --input-dir ./docs --chunk-size 500 # Process specific files python ingest_pdfs.py --input-file ./document.pdf # Skip existing documents python ingest_pdfs.py --input-dir ./docs --skip-existing

🔍 Troubleshooting

Common Issues

1. "ChromaDB directory not found"

python init_chroma.py # Initialize the database first

2. "RAG API returned status 500"

# Restart the API server pkill -f rag_api_server.py python rag_api_server.py --port 8000

3. "Module not found" errors

# Reinstall dependencies pip install -r requirements.txt

4. MCP connection issues

# Check Claude Desktop config file path and syntax # Ensure full absolute paths are used # Restart Claude Desktop after config changes

Performance Optimization

For better performance:

Use GPU acceleration (if available):
# Install CUDA-compatible PyTorch pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
Increase chunk size for longer documents:
python ingest_pdfs.py --chunk-size 1500
Keep API server running to avoid model loading delays

📈 System Monitoring

Health Checks

# Check system health curl http://localhost:8000/health # Monitor logs tail -f rag_api_server.log # Database statistics python -c " from chroma_db import ChromaDBManager db = ChromaDBManager() db.initialize_db() print(db.get_collection_stats()) "

Performance Metrics

First search: ~7 seconds (includes model loading)
Subsequent searches: ~30ms
Memory usage: ~2-4GB (with models loaded)
Storage: ~1MB per 100 pages of documents

🔒 Security Considerations

Local storage only - No data sent to external services
Network access - API server runs on localhost by default
File permissions - Ensure proper access controls on document directory
API security - Consider authentication for production deployments

🤝 Contributing

Fork the repository
Create a feature branch
Make your changes
Test thoroughly
Submit a pull request

📄 License

[Specify your license here]

🆘 Support

For issues and questions:

Check the troubleshooting section above
Review the logs for error messages
Create an issue in the repository
Include system information and error logs

🔄 Updates and Maintenance

Updating the System

# Pull latest changes git pull origin main # Update dependencies pip install -r requirements.txt --upgrade # Restart services pkill -f rag_api_server.py python rag_api_server.py --port 8000

Backup and Restore

# Backup database tar -czf chroma_backup.tar.gz chroma_db/ # Restore database tar -xzf chroma_backup.tar.gz

Note: This system is designed for local use and development. For production deployments, consider additional security measures, monitoring, and scaling configurations.