graph TD
    A[Research Topic Input] --> B[Query Generation]
    B --> C[Web Research]
    C --> D[Content Analysis]
    D --> E[Reflection & Gap Analysis]
    E --> F{Research Complete?}
    F -->|No| G[Generate Follow-up Queries]
    G --> C
    F -->|Yes| H[Final Report Generation]
    H --> I[Structured Output with Citations]
    
    subgraph "AI Models Used"
        J[Gemini 2.0 Flash<br/>Query Generation]
        K[Gemini 2.0 Flash<br/>Web Research]
        L[Gemini 2.5 Flash<br/>Reflection]
        M[Gemini 2.5 Pro<br/>Final Report]
    end
    
    B -.-> J
    C -.-> K
    E -.-> L
    H -.-> M

graph TB
    subgraph "Client Applications"
        A1[Claude Desktop]
        A2[Cursor IDE]
        A3[Custom MCP Client]
    end
    
    subgraph "MCP Server (FastMCP)"
        B1[HTTP Transport Layer]
        B2[Research Tool Handler]
        B3[Progress Streaming]
        B4[Health & Stats Endpoints]
    end
    
    subgraph "LangGraph Research Agent"
        C1[Query Generation Node]
        C2[Web Research Node]
        C3[Reflection Node]
        C4[Final Answer Node]
    end
    
    subgraph "External Services"
        D1[Google Search API]
        D2[Gemini AI Models]
    end
    
    A1 --> B1
    A2 --> B1
    A3 --> B1
    B1 --> B2
    B2 --> B3
    B2 --> C1
    C1 --> C2
    C2 --> C3
    C3 --> C4
    C2 --> D1
    C1 --> D2
    C3 --> D2
    C4 --> D2

graph TB
    subgraph "Development"
        A1[Local Development]
        A2[Docker Compose]
    end
    
    subgraph "Production Deployment"
        B1[Render Platform]
        B2[Docker Container]
        B3[Custom Cloud Deploy]
    end
    
    subgraph "MCP Server Container"
        C1[FastMCP HTTP Server]
        C2[LangGraph Agent]
        C3[Health Monitoring]
        C4[Environment Config]
    end
    
    A1 --> C1
    A2 --> C1
    B1 --> C1
    B2 --> C1
    B3 --> C1

# Clone repository
git clone https://github.com/your-username/deep-research-mcp.git
cd deep-research-mcp

# Install dependencies
pip install -r requirements.txt

# Set environment variables
export GEMINI_API_KEY=your_gemini_api_key_here

# Run MCP server
python -m src.mcp_server.server

# Build Docker image
docker build -t deep-research-mcp .

# Run container
docker run -p 8000:8000 \
  -e GEMINI_API_KEY=your_gemini_api_key \
  deep-research-mcp

{
  "topic": "Your research question",
  "max_research_loops": 2,
  "initial_search_query_count": 3,
  "reasoning_model": "gemini-2.5-pro"
}

{
  "mcpServers": {
    "deep-research": {
      "url": "https://your-service-name.onrender.com/mcp/"
    }
  }
}

{
  "mcpServers": {
    "deep-research": {
      "url": "https://your-service-name.onrender.com/mcp/"
    }
  }
}

from fastmcp import Client
import asyncio

async def research_example():
    client = Client("http://localhost:8000/mcp/")
    async with client:
        result = await client.call_tool("research", {
            "topic": "Latest developments in quantum computing",
            "max_research_loops": 3,
            "initial_search_query_count": 4
        })
        
        print("Research Report:")
        print(result["report"])
        print(f"\nSources: {len(result['sources'])}")
        print(f"Execution time: {result['metadata']['execution_time']:.2f}s")

asyncio.run(research_example())

deep-research-mcp/
├── src/
│   ├── agent/                    # LangGraph research agent
│   │   ├── app.py               # FastAPI app
│   │   ├── graph.py             # LangGraph workflow definition
│   │   ├── state.py             # State management
│   │   ├── prompts.py           # AI prompts
│   │   ├── tools_and_schemas.py # Tools and data schemas
│   │   ├── configuration.py     # Agent configuration
│   │   └── utils.py             # Utility functions
│   └── mcp_server/              # MCP server implementation
│       ├── server.py            # FastMCP server
│       ├── agent_adapter.py     # Agent wrapper
│       ├── config.py            # Configuration management
│       └── utils.py             # Server utilities
├── ClinicalTrials-MCP-Server/   # Additional MCP server example
├── examples/                    # Usage examples
├── requirements.txt             # Python dependencies
├── pyproject.toml              # Project configuration
├── render.yaml                 # Render deployment config
└── README.md                   # This file

# Install development dependencies
pip install -r requirements.txt

# Run tests
python -m pytest tests/

# Start server in development mode
python -m src.mcp_server.server

# Test health endpoint
curl http://localhost:8000/health

# Test MCP endpoint
curl -X POST http://localhost:8000/mcp/ \
  -H "Content-Type: application/json" \
  -d '{"method": "tools/list", "params": {}}'

curl https://your-service-name.onrender.com/health

{
  "status": "healthy",
  "service": "Deep Research MCP Server",
  "version": "1.0.0",
  "agent_status": "healthy"
}

curl https://your-service-name.onrender.com/stats