Synapse MCP Server

A Model Context Protocol (MCP) server that exposes Synapse Entities (Datasets, Projects, Folders, Files, Tables) with their annotations.

Overview

This server provides a RESTful API for accessing Synapse entities and their annotations through the Model Context Protocol (MCP). It allows you to:

Authenticate with Synapse
Retrieve entities by ID
Get entity annotations
Get entity children
Query entities based on various criteria
Query Synapse tables

Installation

# Clone the repository
git clone https://github.com/SageBionetworks/synapse-mcp.git
cd synapse-mcp

# Create a virtual environment
python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate

# Install dependencies
pip install -e .

Installing from PyPI

# Install from PyPI
pip install synapse-mcp

Usage

Starting the Server

python server.py

This will start the MCP server on the default port (9000).

Using the CLI

# Start the server using the CLI
synapse-mcp --host 127.0.0.1 --port 9000 --debug

Command-line Options

usage: server.py [-h] [--host HOST] [--port PORT] [--debug]

Run the Synapse MCP server

options:
  -h, --help     show this help message and exit
  --host HOST    Host to bind to
  --port PORT    Port to listen on
  --debug        Enable debug logging

Running Tests

# Run all tests with coverage
./run_tests.sh

# Or run pytest directly
python -m pytest

Testing the Server

python examples/client_example.py

API Endpoints

Server Information

GET /info - Get server information

Tools

GET /tools - List available tools
POST /tools/authenticate - Authenticate with Synapse
POST /tools/get_entity - Get an entity by ID
POST /tools/get_entity_annotations - Get annotations for an entity
POST /tools/get_entity_children - Get child entities of a container entity
POST /tools/query_entities - Query entities based on various criteria
POST /tools/query_table - Query a Synapse table

Resources

GET /resources - List available resources
GET /resources/entity/{id} - Get entity by ID
GET /resources/entity/{id}/annotations - Get entity annotations
GET /resources/entity/{id}/children - Get entity children
GET /resources/query/entities/{entity_type} - Query entities by type
GET /resources/query/entities/parent/{parent_id} - Query entities by parent ID
GET /resources/query/entities/name/{name} - Query entities by name
GET /resources/query/table/{id}/{query} - Query a table with SQL-like syntax

Examples

Authentication

You need to authenticate with real Synapse credentials to use the server:

import requests

# Authenticate with Synapse
response = requests.post("http://127.0.0.1:9000/tools/authenticate", json={
    "email": "your-synapse-email@example.com",
    "password": "your-synapse-password"
})
result = response.json()
print(result)

# Alternatively, you can authenticate with an API key
response = requests.post("http://127.0.0.1:9000/tools/authenticate", json={
    "api_key": "your-synapse-api-key"
})

Getting an Entity

import requests

# Get an entity by ID
response = requests.get("http://127.0.0.1:9000/resources/entity/syn123456")  # Replace with a real Synapse ID
entity = response.json()
print(entity)

Getting Entity Annotations

import requests

# Get annotations for an entity
response = requests.get("http://127.0.0.1:9000/resources/entity/syn123456/annotations")  # Replace with a real Synapse ID
annotations = response.json()
print(annotations)

Querying Entities

import requests

# Query for files in a project
response = requests.get("http://127.0.0.1:9000/resources/query/entities/parent/syn123456", params={  # Replace with a real Synapse ID
    "entity_type": "file"
})
files = response.json()
print(files)

Querying a Table

import requests

# Query a table
table_id = "syn123456"  # Replace with a real Synapse table ID
query = "SELECT * FROM syn123456 LIMIT 10"  # Replace with a real Synapse table ID
response = requests.get(f"http://127.0.0.1:9000/resources/query/table/{table_id}/{query}")
table_data = response.json()
print(table_data)

Getting Datasets in Croissant Format

import requests
import json

# Get public datasets in Croissant format
response = requests.get("http://127.0.0.1:9000/resources/croissant/datasets")
croissant_data = response.json()

# Save to file
with open("croissant_metadata.json", "w") as f:
    json.dump(croissant_data, f, indent=2)

License

MIT

Integrations