README.md•3.83 kB
# CEDAR MCP Server
A Model Context Protocol (MCP) server for interacting with the CEDAR (Center for Expanded Data Annotation and Retrieval) metadata repository.
## 🚀 快速启动（推荐）
### 使用 UVX 一键启动
```bash
uvx bach-cedar-mcp
```
### 在 Cursor/Cherry Studio 中配置
```json
{
"mcpServers": {
"cedar-mcp": {
"command": "uvx",
"args": ["bach-cedar-mcp"],
"env": {
"CEDAR_API_KEY": "<YOUR_CEDAR_API_KEY>",
"BIOPORTAL_API_KEY": "<YOUR_BIOPORTAL_API_KEY>"
}
}
}
}
```
**PyPI 包地址**: https://pypi.org/project/bach-cedar-mcp/
---
## Prerequisites
Before using this MCP server, you'll need API keys from:
### CEDAR API Key
- Go to [cedar.metadatacenter.org](https://cedar.metadatacenter.org)
- Create an account or log in
- Navigate to: Profile → API Key
- Copy your API key
### BioPortal API Key
- Go to [bioportal.bioontology.org](https://bioportal.bioontology.org)
- Create an account or log in
- Navigate to: Account Settings → API Key
- Copy your API key
## Running the CEDAR MCP Server
### Option 1: Using UVX from PyPI (Recommended)
Run directly without installation using `uvx`:
```bash
uvx bach-cedar-mcp \
--cedar-api-key "your-cedar-key" \
--bioportal-api-key "your-bioportal-key"
```
### Option 2: Install from PyPI
Install using pip and run:
```bash
# Install from PyPI
pip install bach-cedar-mcp
# Run the server
bach-cedar-mcp \
--cedar-api-key "your-cedar-key" \
--bioportal-api-key "your-bioportal-key"
```
### Option 3: Using Environment Variables
Set environment variables instead of command-line arguments:
```bash
# Set environment variables
export CEDAR_API_KEY="your-cedar-key"
export BIOPORTAL_API_KEY="your-bioportal-key"
# Run with uvx
uvx bach-cedar-mcp
# Or if installed with pip
bach-cedar-mcp
```
### Option 4: Local Development
Clone and run from source:
```bash
# Clone the repository
git clone https://github.com/BACH-AI-Tools/cedar-mcp.git
cd cedar-mcp
# Install dependencies and run
uv run python -m cedar_mcp.server \
--cedar-api-key "your-cedar-key" \
--bioportal-api-key "your-bioportal-key"
```
## Using with Claude Code
Add the CEDAR MCP server to Claude Code:
```bash
# Add using uvx (from PyPI)
claude mcp add cedar-mcp --uvx bach-cedar-mcp \
--cedar-api-key "your-cedar-key" \
--bioportal-api-key "your-bioportal-key"
```
## Using with Claude Desktop
To use with Claude Desktop app:
1. **Install the MCP server** using one of the methods above
2. **Add to Claude Desktop configuration** in your `claude_desktop_config.json`:
```json
{
"mcpServers": {
"cedar-mcp": {
"command": "uvx",
"args": ["bach-cedar-mcp"],
"env": {
"CEDAR_API_KEY": "your-cedar-key",
"BIOPORTAL_API_KEY": "your-bioportal-key"
}
}
}
}
```
Or if you have it installed with pip:
```json
{
"mcpServers": {
"cedar-mcp": {
"command": "bach-cedar-mcp",
"env": {
"CEDAR_API_KEY": "your-cedar-key",
"BIOPORTAL_API_KEY": "your-bioportal-key"
}
}
}
}
```
## Available Tools
Here is the list of CEDAR tools with a short description
* `get_template`: Fetches a template from the CEDAR repository.
* `get_instances_based_on_template`: Gets template instances that belong to a specific template with pagination support.
## Development
### Install Development Dependencies
```bash
pip install -r requirements-dev.txt
```
### Running Tests
This project includes comprehensive integration tests that validate real API interactions with both CEDAR and BioPortal APIs.
For detailed testing information, see [test/README.md](test/README.md).
## Contributing
Contributions are welcome! Please ensure all tests pass before submitting a Pull Request:
```bash
python run_tests.py --integration
```