git clone https://github.com/pankajrajdeo/lungmap-mcp-server.git
cd lungmap-mcp-server
pip install -e .

python scripts/test_server.py

{
  "mcpServers": {
    "lungmap": {
      "command": "python3",
      "args": ["/absolute/path/to/lungmap_mcp_server.py"]
    }
  }
}

import asyncio
from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client

async def main():
    server_params = StdioServerParameters(
        command="python3",
        args=["/absolute/path/to/lungmap_mcp_server.py"],
    )

    async with stdio_client(server_params) as (read, write):
        async with ClientSession(read, write) as session:
            # Initialize the session
            await session.initialize()

            # Call a tool: search_datasets
            result = await session.call_tool(
                "search_datasets",
                arguments={
                    "text_query": "lung development",
                    "species": "human",
                    "dataset_types": ["rna_seq"],
                    "limit": 5,
                },
            )
            print(result.content)

            # Call a tool: get_dataset_details
            details = await session.call_tool(
                "get_dataset_details",
                arguments={
                    "dataset_id": "LMEX0000000661",
                    "include_files": True,
                    "include_images": True,
                    "include_resources": True,
                },
            )
            print(details.content)

asyncio.run(main())

import asyncio
from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client
from langchain_mcp_adapters.tools import load_mcp_tools
from langgraph.prebuilt import create_react_agent

async def main():
    server_params = StdioServerParameters(
        command="python3",
        args=["/absolute/path/to/lungmap_mcp_server.py"],
    )

    async with stdio_client(server_params) as (read, write):
        async with ClientSession(read, write) as session:
            await session.initialize()

            # Load all MCP tools as LangChain tools
            tools = await load_mcp_tools(session)

            # Create a ReAct agent and invoke it
            agent = create_react_agent("openai:gpt-4o-mini", tools)
            response = await agent.ainvoke({
                "messages": [{"role": "user", "content": "Search everything about ACE2"}]
            })
            print(response)

asyncio.run(main())

lungmap-mcp-server/
├── 📄 README.md                    # This file
├── 📄 LICENSE                      # MIT License
├── 📄 pyproject.toml               # Python package config
├── 📄 lungmap_mcp_server.py        # Main MCP server
├── 📁 docs/                        # Documentation
│   ├── 📄 quickstart.md            # 5-minute setup guide
│   ├── 📄 installation_guide.md    # Detailed installation
│   ├── 📄 deployment_checklist.md  # Production checklist
│   └── 📄 mcp_config_examples.json # Configuration examples
├── 📁 scripts/                     # Utility scripts
│   ├── 🔧 setup_script.sh          # Automated setup
│   └── 🧪 test_server.py           # Server testing
├── 📁 tests/                       # Test suite
│   └── 🧪 test_tools.py            # Tool tests
└── 📁 tools/                       # Tool implementations
    ├── 📄 api_client.py            # API client utilities
    ├── 📄 constants.py             # Constants & mappings
    ├── 📄 types.py                 # Type definitions
    └── 📄 [8 lungmap tools].py     # Individual tools

git clone https://github.com/pankajrajdeo/lungmap-mcp-server.git
cd lungmap-mcp-server
pip install -e .

git clone https://github.com/pankajrajdeo/lungmap-mcp-server.git
cd lungmap-mcp-server
python -m venv venv
source venv/bin/activate  # Windows: venv\Scripts\activate
pip install -e .

git clone https://github.com/pankajrajdeo/lungmap-mcp-server.git
cd lungmap-mcp-server
uv venv
source .venv/bin/activate
uv pip install -e .

# Test server functionality
python scripts/test_server.py

# Test individual tools
python tests/test_tools.py

# Run with pytest (if installed)
pytest tests/

from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client
from langchain_mcp_adapters.tools import load_mcp_tools

server_params = StdioServerParameters(
    command="python3",
    args=["/path/to/lungmap_mcp_server.py"],
)

async with stdio_client(server_params) as (read, write):
    async with ClientSession(read, write) as session:
        await session.initialize()
        tools = await load_mcp_tools(session)
        # Use tools with your LangChain agent

# Transport
MCP_TRANSPORT=sse   # or stdio
HOST=0.0.0.0
PORT=8000
MCP_SSE_PATH=/sse

# Auth (optional but recommended for SSE)
LUNGMAP_MCP_TOKEN=your-secret-token

# Rate limiting
MAX_REQUESTS_PER_MINUTE=60

MCP_TRANSPORT=sse PORT=8000 LUNGMAP_MCP_TOKEN=dev-token \
python lungmap_mcp_server.py

from mcp import ClientSession, StdioServerParameters
from mcp.client.stdio import stdio_client

# For SSE, use appropriate client/URL; below shows stdio example

curl https://api.openai.com/v1/responses \
  -H "Authorization: Bearer $OPENAI_API_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "model": "o4-mini",
    "input": "Find human RNA-seq datasets about lung development",
    "tools": [{
      "type": "mcp",
      "server_label": "lungmap",
      "server_url": "http://localhost:8000/sse",
      "allowed_tools": ["search", "search_datasets", "get_dataset_details", "get_sample_details", "get_analysis_results", "get_molecular_entities", "get_infrastructure_resources", "list_controlled_vocabulary", "search_media", "fetch"],
      "require_approval": "never",
      "metadata": {
        "headers": {"Authorization": "Bearer dev-token"}
      }
    }]
  }'

{
  "mcpServers": {
    "lungmap-remote": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/client", "http://localhost:8000/sse"],
      "env": {
        "AUTHORIZATION": "Bearer dev-token"
      }
    }
  }
}

python lungmap_mcp_server.py   # stdio mode

python scripts/test_server.py

MCP_TRANSPORT=sse PORT=8000 LUNGMAP_MCP_TOKEN=dev-token \
python lungmap_mcp_server.py &

TEST_SSE_BASE=http://localhost:8000 pytest -q tests/test_remote.py

# Ensure you're in the project directory
cd lungmap-mcp-server
pip install -e .

# Check Python version
python3 --version  # Must be 3.10+

# Test server manually
python lungmap_mcp_server.py