Nmdc

A fastmcp-based tool for writing prompts against data in the NMDC database.

Installation

You can install the package from source using uv:

uv sync

Usage

You can use the CLI:

nmdc-mcp

Or import in your Python code: # TODO incorrect instructions

from nmdc_mcp.main import create_mcp

mcp = create_mcp()
mcp.run()

Or utilize the nmdc_mcp.client. This client uses OpenAI API and assumes you have API_KEY set in a .env file in the root directory of this repo. The BASE_URL and MODEL are also customizable in .env. For PNNL staff that want to run via this client - the BASE_URL and MODEL are specific. Contact Olivia Hess if you need help setting these values up.

uv run 'path/to/nmdc_mcp/client.py' 'path/to/nmdc_mcp/main.py'

Or using python

python 'path/to/nmdc_mcp/client.py' 'path/to/nmdc_mcp/main.py'

Development

Local Setup

# Clone the repository
git clone https://github.com/microbiomedata/nmdc-mcp.git
cd nmdc-mcp

# Install development dependencies
make dev

Development Workflow

The project uses a comprehensive Makefile for development tasks:

# Run all development checks (tests, formatting, linting, type checking)
make all

# Individual commands
make dev           # Install development dependencies
make test-coverage # Run tests with coverage
make format        # Format code with black
make lint          # Lint with ruff
make mypy          # Type checking
make deptry        # Check for unused dependencies
make build         # Build package

Testing

# Run all tests with coverage
make test-coverage

# Run specific test types
make test-unit         # Unit tests only
make test-integration  # Integration tests
make test-real-api     # Tests against real NMDC API
make test-mcp          # Test MCP protocol

MCP Integration

Claude Desktop Setup

Add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{
  "mcpServers": {
    "nmdc-mcp": {
      "command": "uvx",
      "args": ["nmdc-mcp"]
    }
  }
}

Claude Code MCP Setup

claude mcp add -s project nmdc-mcp uvx nmdc-mcp

Goose Setup

goose session --with-extension "uvx nmdc-mcp"

License

MIT