albertorb/mcp-server-fhir

Epic FHIR MCP Server

A production-ready Model Context Protocol (MCP) server that connects LLMs to Epic's FHIR API. Supports both stdio (for Claude Desktop) and HTTP/SSE transports with OAuth2 backend systems authentication.

Features

• OAuth2 Backend Systems Flow - Secure server-to-server authentication with JWT
• Epic FHIR R4 API - Access patient data, medications, observations, and more
• Dual Transport - Stdio for Claude Desktop, Streamable HTTP for web clients

Architecture

Stdio Transport (Claude Desktop):

┌─────────────┐    stdin/stdout    ┌─────────────┐    OAuth2/FHIR    ┌─────────────┐
│   Claude    │ ◄───────────────► │ MCP Server  │ ◄──────────────► │  Epic FHIR  │
│   Desktop   │                    │  (Python)   │                   │     API     │
└─────────────┘                    └─────────────┘                   └─────────────┘

Streamable HTTP Transport (Web Clients):

┌─────────────┐  Streamable HTTP  ┌─────────────┐    OAuth2/FHIR    ┌─────────────┐
│   Web/API   │ ◄────────────────► │ MCP Server  │ ◄──────────────► │  Epic FHIR  │
│   Client    │                    │  (Python)   │                   │     API     │
└─────────────┘                    └─────────────┘                   └─────────────┘

Quick Start

Prerequisites

• Python 3.12+
• Epic FHIR Sandbox account (Sign up)
• OpenSSL (for key generation)
• uv (recommended) or pip

1. Clone and Install

git clone <your-repo-url>
cd fhir-epic-mcpserver

# Install dependencies
uv sync
# or: pip install -e .

2. Generate Keys and JWKS

# Run setup script to generate RSA keys and JWKS
uv run python create_keys.py

This will create:

• private_key.pem - Your private key (keep secret!)
• public_key.pem - Public key
• certificate.pem - X.509 certificate
• jwks.json - JSON Web Key Set for Epic
• .env - Environment configuration

3. Host JWKS Publicly

Epic requires your JWKS to be accessible via public HTTPS URL.

Option A: GitHub Gist (Quick)

1. Go to https://gist.github.com
2. Create new gist with filename jwks.json
3. Paste contents from your jwks.json file
4. Create public gist
5. Click "Raw" and copy the URL

Option B: Production Hosting

• Your domain: https://yourdomain.com/.well-known/jwks.json
• AWS S3, Azure Blob, or Google Cloud Storage (public)

4. Configure Epic App

1. Go to https://fhir.epic.com/Developer/Apps
2. Create Backend Systems app
3. Select FHIR R4 APIs you need:
   • Patient.Read
   • Observation.Read
   • Condition.Read
   • MedicationRequest.Read
   • AllergyIntolerance.Read
   • Immunization.Read
4. In Non-Production section:
   • Add your JWKS URL
   • Click Test to validate
   • Click Save & Ready for Sandbox
5. Wait 30 minutes for Epic to sync

5. Configure Environment

Update .env with your Epic credentials:

EPIC_CLIENT_ID=your-client-id-from-epic
EPIC_PRIVATE_KEY_PATH=./private_key.pem
EPIC_TOKEN_URL=https://fhir.epic.com/interconnect-fhir-oauth/oauth2/token
EPIC_FHIR_BASE_URL=https://fhir.epic.com/interconnect-fhir-oauth/api/FHIR/R4

# Server config
HOST=0.0.0.0
PORT=8000
LOG_LEVEL=INFO

6. Run Server

# For Claude Desktop (stdio mode - default)
uv run python src/server.py

# For HTTP/SSE mode (web/API usage)
uv run python src/server.py --transport sse --port 8000

# Production with uvicorn (SSE mode)
uv run uvicorn src.server:app --host 0.0.0.0 --port 8000

Stdio mode runs on stdin/stdout for Claude Desktop
SSE mode runs HTTP server on http://localhost:8000

Available Tools

The MCP server exposes these tools to LLMs:

Testing with Epic Sandbox

Epic provides test patients with realistic data:

See full list: https://fhir.epic.com/Documentation?docId=testpatients

MCP Client Configuration

Claude Desktop

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

{
  "mcpServers": {
    "epic-fhir": {
      "command": "uv",
      "args": [
        "run",
        "python",
        "/path/to/fhir-epic-mcpserver/src/server.py"
      ],
      "env": {
        "EPIC_CLIENT_ID": "your-client-id-here",
        "EPIC_PRIVATE_KEY_PATH": "/path/to/fhir-epic-mcpserver/private_key.pem",
        "EPIC_TOKEN_URL": "https://fhir.epic.com/interconnect-fhir-oauth/oauth2/token",
        "EPIC_FHIR_BASE_URL": "https://fhir.epic.com/interconnect-fhir-oauth/api/FHIR/R4"
      }
    }
  }
}

Important:

• Use absolute paths for the script and private key
• Replace your-client-id-here with your actual Epic Client ID
• Replace /path/to/fhir-epic-mcpserver with your actual project path
• Restart Claude Desktop after updating the config

Quick setup:

1. Copy claude_desktop_config.example.json content
2. Update the paths to your actual project location
3. Add your Epic Client ID
4. Paste into Claude Desktop config at:
   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
   • Windows: %APPDATA%\Claude\claude_desktop_config.json

Other MCP Clients (HTTP/SSE)

For web-based or HTTP clients, run in SSE mode:

uv run python src/server.py --transport sse --port 8000

Connect to SSE endpoint: http://localhost:8000/sse

Development

Project Structure

epic-fhir-mcp-server/
├── src/
│   ├── __init__.py
│   ├── server.py          # HTTP/SSE MCP server
│   ├── epic_client.py     # Epic OAuth2 + FHIR client
│   ├── tools.py           # MCP tool definitions
│   └── config.py          # Configuration management
├── create_keys.py         # Key generation script
├── pyproject.toml         # Dependencies
├── .env.example           # Environment template
└── README.md

Running Tests

# Install dev dependencies
uv sync --dev

# Run tests
uv run pytest

# With coverage
uv run pytest --cov=src

Code Quality

# Format code
uv run ruff format src/

# Lint
uv run ruff check src/

Troubleshooting

invalid_client Error

Causes:

• App not "Ready for Sandbox"
• Epic configuration not synced (wait 30 min)
• Wrong client ID
• JWKS URL not accessible

Solutions:

1. Verify app status in Epic portal
2. Wait 30 minutes after configuration changes
3. Test JWKS URL: curl https://your-jwks-url
4. Check kid matches between JWT and JWKS

401 Unauthorized on FHIR Requests

Causes:

• Token expired (1-hour lifetime)
• Missing Authorization header
• Insufficient scopes

Solutions:

• Token is cached automatically
• Check logs for authentication errors
• Verify required scopes in Epic app config

Connection Issues

# Check server is running
curl http://localhost:8000/sse

# View logs
LOG_LEVEL=DEBUG uv run python src/server.py

OpenAI Agent Integration

This MCP server can be used with the OpenAI Agents SDK to create AI agents that can interact with Epic FHIR data.

Quick Start with Agent

1. Install the OpenAI Agents SDK:

   pip install openai-agents
   # or
   uv add openai-agents
   

2. Set your OpenAI API key:

   export OPENAI_API_KEY="your-api-key-here"
   

3. Run the simple test agent:

   python test_agent_simple.py
   

Example Agent Code

import asyncio
from agents import Agent, Runner
from agents.mcp import MCPServerStdio

async def main():
    async with MCPServerStdio(
        name="Epic FHIR",
        params={"command": "uv", "args": ["run", "python", "-m", "src.server"]},
    ) as mcp_server:
        agent = Agent(
            name="FHIR Assistant",
            instructions="You are a helpful medical assistant.",
            mcp_servers=[mcp_server],
        )
        
        result = await Runner.run(
            starting_agent=agent,
            input="Search for patient Derrick Borer"
        )
        print(result.final_output)

asyncio.run(main())