feat: initial implementation and project setup for Python-based FHIR MCP server

Establish project structure and environment configuration

Implement core FHIR MCP server logic and OAuth modules

Add utility functions and supporting files
This commit is contained in:
vimukthiRajapaksha
2025-06-20 12:03:12 +05:30
parent ed0d9c8ec2
commit 27ff7e626a
15 changed files with 2755 additions and 2 deletions

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.env.example Normal file
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HEALTHCARE_MCP_HOST="localhost"
HEALTHCARE_MCP_PORT="8000"
# (Optional) If set, this value will be used as the server's base URL instead of generating it from host and port
HEALTHCARE_MCP_SERVER_URL=""
HEALTHCARE_MCP_FHIR__CLIENT_ID=""
HEALTHCARE_MCP_FHIR__CLIENT_SECRET=""
HEALTHCARE_MCP_FHIR__BASE_URL=""
HEALTHCARE_MCP_FHIR__SCOPE=""
# Timeout for FHIR server requests, in seconds
HEALTHCARE_MCP_FHIR__TIMEOUT=60
# (Optional) If set, the authorization flow will be skipped and this access token will be used directly
HEALTHCARE_MCP_FHIR__ACCESS_TOKEN=""
HEALTHCARE_MCP_OAUTH__CLIENT_ID=""
HEALTHCARE_MCP_OAUTH__CLIENT_SECRET=""
HEALTHCARE_MCP_OAUTH__METADATA_URL=""
HEALTHCARE_MCP_OAUTH__SCOPE=""

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.gitignore vendored
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# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
replay_pid*
# Python-generated files
__pycache__/
*.py[oc]
build/
dist/
wheels/
*.egg-info
# Virtual environments
.venv
# IDE specific
.vscode/
.idea/
# Environment variables
.env
*.env

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.python-version Normal file
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3.12

202
README.md
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# fhir-mcp-server
This server lets you interact with Fast Healthcare Interoperability Resources (FHIR) resources on a specified FHIR server.
# Model Context Protocol (MCP) Server for Fast Healthcare Interoperability Resources (FHIR)
[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/wso2/fhir-mcp-server/blob/main/LICENSE)
[![Get Support on Stack Overflow](https://img.shields.io/badge/stackoverflow-wso2-orange)](https://stackoverflow.com/questions/tagged/wso2)
[![Join the community on Discord](https://img.shields.io/badge/Join%20us%20on-Discord-%23e01563.svg)](https://discord.com/invite/wso2)
[![X](https://img.shields.io/twitter/follow/wso2.svg?style=social&label=Follow)](https://twitter.com/intent/follow?screen_name=wso2)
## Overview
The MCP Server for FHIR is a Python-based service that provides seamless, standardized access to FHIR data from any compatible FHIR server. Designed for developers, integrators, and healthcare innovators, this server acts as a bridge between modern AI/LLM tools and healthcare data, making it easy to search, retrieve, and analyze clinical information.
**Key features:**
- **Flexible Integration:** Use the server from the command line, in Docker, or directly within tools like VS Code, Claude Desktop, and MCP Inspector.
- **Natural Language FHIR Search:** Query for patients, allergies, immunizations, care plans, and more using simple prompts or programmatic requests.
- **Configurable & Secure:** Easily connect to any FHIR server, with support for environment-based configuration and secure access tokens.
- **Developer Friendly:** Quick setup with modern Python tooling (`uv`), clear documentation, and ready-to-use integration examples for rapid prototyping and deployment.
Whether you are building healthcare applications, integrating with AI assistants, or exploring clinical datasets, the MCP server provides a robust foundation for accessing and working with FHIR data in a standardized, extensible way.
## Prerequisites
- Python 3.8+
- [uv](https://github.com/astral-sh/uv) (for dependency management)
- An accessible FHIR server (defaults to the public HAPI FHIR test server)
## Setup
1. **Clone the repository:**
```bash
git clone <repository_url>
cd <repository_directory>
```
2. **Create a virtual environment and install dependencies:**
```bash
uv venv
source .venv/bin/activate
uv pip sync requirements.txt
```
Or with pip:
```bash
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt
```
3. **Configure Environment Variables:**
Copy the example file and customize if needed:
```bash
cp .env.example .env
```
## Usage
Run the server:
```bash
uv run fhir-mcp-server
```
You can also run the server directly from the PyPI package (without cloning the repository) using:
```bash
uvx fhir-mcp-server
```
## VS Code Integration
Add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing Ctrl + Shift + P and typing Preferences: Open User Settings (JSON).
<table>
<tr><th>Streamable HTTP</th><th>stdio</th></tr>
<tr valign=top>
<td>
```json
"mcp": {
"servers": {
"fhir": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"http://localhost:8000/mcp"
]
}
}
}
```
</td>
<td>
```json
"mcp": {
"servers": {
"fhir": {
"command": "uv",
"args": [
"--directory",
"/path/to/fhir-mcp-server",
"run",
"fhir-mcp-server",
"--transport",
"stdio"
],
"env": {
"HEALTHCARE_MCP_FHIR__ACCESS_TOKEN": "Your FHIR Access Token"
}
}
}
}
```
</td>
</tr>
</table>
## Claude Desktop Integration
Add the following JSON block to your Claude Desktop settings to connect to your local MCP server.
- Launch the Claude Desktop app, click on the Claude menu in the top bar, and select "Settings…".
- In the Settings pane, click “Developer” in the left sidebar. Then click "Edit Config". This will open your configuration file in your file system. If it doesnt exist yet, Claude will create one automatically at:
- macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
- Windows: %APPDATA%\Claude\claude_desktop_config.json
- Open the claude_desktop_config.json file in any text editor. Replace its contents with the following JSON block to register the MCP server:
<table>
<tr><th>Streamable HTTP</th><th>stdio</th></tr>
<tr valign=top>
<td>
```json
{
"mcpServers": {
"fhir": {
"command": "npx",
"args": [
"-y",
"mcp-remote",
"http://localhost:8000/mcp"
]
}
}
}
```
</td>
<td>
```json
{
"mcpServers": {
"fhir": {
"command": "uv",
"args": [
"--directory",
"/path/to/fhir-mcp-server",
"run",
"fhir-mcp-server",
"--transport",
"stdio"
],
"env": {
"HEALTHCARE_MCP_FHIR__ACCESS_TOKEN": "Your FHIR Access Token"
}
}
}
}
```
</td>
</tr>
</table>
## MCP Inspector Integration
Follow these steps to get the MCP Inspector up and running:
- Open a terminal and run the following command:
`npx -y @modelcontextprotocol/inspector`
- In the MCP Inspector interface:
<table>
<tr><th>Streamable HTTP</th><th>stdio</th></tr>
<tr valign=top>
<td>
- Transport Type: `Streamable HTTP`
- URL: `http://localhost:8000/mcp`
</td>
<td>
- Transport Type: `STDIO`
- Command: `uv`
- Arguments: `--directory /path/to/fhir-mcp-server run fhir-mcp-server --transport stdio`
</td>
</tr>
</table>
Make sure your MCP server is already running and listening on the above endpoint.
Once connected, MCP Inspector will allow you to visualize tool invocations, inspect request/response payloads, and debug your tool implementations easily.
## Example Prompts
- Get allergy history for patient 53373
- Fetch the immunization records for patient ID 53373
- List all active care plans for patient 22
- Provide a consolidated report for patient 53373 that includes their complete allergy history as well as all available immunization records, organized by date and highlighting any critical alerts
- Retrieve all active care plans for patient ID 22 and present them in a markdown table showing each plans ID, title, status, intent, and start date

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pyproject.toml Normal file
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[project]
authors = [
{name = "WSO2", email = "dev@wso2.org"},
]
classifiers = [
"Development Status :: 4 - Beta",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.12",
"Intended Audience :: Developers",
"Operating System :: OS Independent",
]
dependencies = [
"mcp[cli]>=1.9.1",
"aiohttp>=3.12.13",
"fhirpy>=2.0.15",
]
description = "A Model Context Protocol (MCP) server that provides seamless, standardized access to Fast Healthcare Interoperability Resources (FHIR) data from any compatible FHIR server. Designed for easy integration with AI tools, developer workflows, and healthcare applications, it enables natural language and programmatic search, retrieval, and analysis of clinical data."
keywords = [
"fhir",
"healthcare",
"mcp",
"model-context-protocol",
"llm",
]
license = "Apache-2.0"
license-files = ["LICEN[CS]E*"]
name = "fhir-mcp-server"
readme = {file = "README.md", content-type = "text/markdown"}
requires-python = ">=3.12"
version = "1.0.0"
[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[tool.hatch.build.targets.wheel]
packages = ["src/fhir_mcp_server"]
[project.scripts]
fhir-mcp-server = "fhir_mcp_server.server:main"
[[tool.uv.index]]
name = "pypi"
publish-url = "https://upload.pypi.org/legacy/"
url = "https://pypi.org/simple/"
[project.urls]
"Bug Tracker" = "https://github.com/wso2/fhir-mcp-server/issues"
"Documentation" = "https://github.com/wso2/fhir-mcp-server/blob/development/README.md"
"Homepage" = "https://github.com/wso2/fhir-mcp-server"

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requirements.txt Normal file
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aiohappyeyeballs==2.6.1
aiohttp==3.12.2
aiosignal==1.3.2
annotated-types==0.7.0
anyio==4.9.0
attrs==25.3.0
certifi==2025.4.26
charset-normalizer==3.4.2
click==8.2.1
fhirpy==2.0.15
frozenlist==1.6.0
h11==0.16.0
httpcore==1.0.9
httpx==0.28.1
httpx-sse==0.4.0
idna==3.10
markdown-it-py==3.0.0
mcp==1.9.1
mdurl==0.1.2
multidict==6.4.4
propcache==0.3.1
pydantic==2.11.5
pydantic-core==2.33.2
pydantic-settings==2.9.1
pygments==2.19.1
python-dotenv==1.1.0
python-multipart==0.0.20
pytz==2025.2
requests==2.32.3
rich==14.0.0
shellingham==1.5.4
sniffio==1.3.1
sse-starlette==2.3.5
starlette==0.46.2
typer==0.16.0
typing-extensions==4.13.2
typing-inspection==0.4.1
urllib3==2.4.0
uvicorn==0.34.2
yarl==1.20.0

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# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.

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# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
from .client_provider import FHIRClientProvider
from .common import handle_successful_authentication, handle_failed_authentication
from .server_provider import OAuthServerProvider
from .types import FHIROAuthConfigs, ServerConfigs, OAuthToken
__all__ = [
"FHIRClientProvider",
"FHIROAuthConfigs",
"handle_successful_authentication",
"handle_failed_authentication",
"OAuthServerProvider",
"OAuthToken",
"ServerConfigs",
]

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# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
import asyncio
import anyio
import httpx
import logging
import secrets
import webbrowser
from collections.abc import Awaitable, Callable
from typing import Dict
from urllib.parse import urlencode
from http.client import HTTPException
from pydantic import AnyHttpUrl
from fhir_mcp_server.oauth.types import FHIROAuthConfigs, OAuthMetadata, OAuthToken
from fhir_mcp_server.oauth.common import (
discover_oauth_metadata,
is_token_expired,
get_endpoint,
generate_code_verifier,
generate_code_challenge,
perform_token_flow,
)
logger = logging.getLogger(__name__)
async def webbrowser_redirect_handler(authorization_url: str):
print(f"Opening user's browser with URL: {authorization_url}")
webbrowser.open_new_tab(authorization_url)
class FHIRClientProvider(httpx.Auth):
"""
Authentication for httpx using anyio.
Handles OAuth flow and token storage.
"""
def __init__(
self,
callback_url: AnyHttpUrl,
configs: FHIROAuthConfigs,
redirect_handler: Callable[
[str], Awaitable[None]
] = webbrowser_redirect_handler,
):
"""
Initialize OAuth2 authentication.
Args:
callback_url: Callback URL of the FHIR client
configs: FHIR server configurations
redirect_handler: Function to handle authorization URL like opening browser
"""
self.callback_url = callback_url
self.redirect_handler = redirect_handler
self.configs = configs
self.state_mapping: dict[str, dict[str, str]] = {}
self.token_mapping: Dict[str, OAuthToken | None] = {}
# Thread safety lock
self._token_lock = anyio.Lock()
self._metadata: OAuthMetadata | None = None
def _generate_code_verifier(self) -> str:
"""Generate a cryptographically random code verifier for PKCE."""
return generate_code_verifier(128)
def _generate_code_challenge(self, code_verifier: str) -> str:
"""Generate a code challenge from a code verifier using SHA256."""
return generate_code_challenge(code_verifier)
async def _discover_oauth_metadata(
self, discovery_url: str
) -> OAuthMetadata | None:
"""
Discover OAuth metadata from server's well-known endpoint.
"""
return await discover_oauth_metadata(metadata_url=discovery_url)
def _is_valid_token(self, token_id: str) -> bool:
"""Check if current token is valid."""
current_token: OAuthToken | None = self.token_mapping.get(token_id)
return not is_token_expired(current_token)
async def _validate_token_scopes(self, token_response: OAuthToken) -> None:
"""
Validate returned scopes against requested scopes.
Per OAuth 2.1 Section 3.3: server may grant subset, not superset.
"""
if not token_response.scope:
# No scope returned = validation passes
return
# Check explicitly requested scopes only
requested_scopes: set[str] = set()
if self.configs.scope:
# Validate against explicit scope request
requested_scopes = set(self.configs.scopes)
# Check for unauthorized scopes
returned_scopes = set(token_response.scope.split(" "))
unauthorized_scopes = returned_scopes - requested_scopes
if unauthorized_scopes:
logger.debug(
f"Server granted unauthorized scopes: {unauthorized_scopes}. "
f"Requested: {requested_scopes}, Returned: {returned_scopes}"
)
raise ValueError("scope validation failed!")
else:
# No explicit scopes requested - accept server defaults
logger.debug(
f"No explicit scopes requested, accepting server-granted "
f"scopes: {token_response.scope}"
)
async def ensure_token(self, token_id: str) -> None:
"""Ensure valid access token, refreshing or re-authenticating as needed."""
async with self._token_lock:
# Return early if token is valid
if self._is_valid_token(token_id):
return
# Try refreshing existing token
if await self._refresh_access_token(token_id):
return
# Fall back to full OAuth flow
await self._perform_oauth_flow(token_id)
async def _perform_oauth_flow(self, token_id: str) -> None:
"""Execute OAuth2 authorization code flow with PKCE."""
logger.debug("Starting authentication flow.")
# Discover OAuth metadata
if not self._metadata:
self._metadata = await self._discover_oauth_metadata(
self.configs.discovery_url
)
# Generate PKCE challenge
code_verifier: str = self._generate_code_verifier()
code_challenge: str = self._generate_code_challenge(code_verifier)
authorization_endpoint: str = self._get_authorization_endpoint()
# Build authorization URL
state: str = secrets.token_urlsafe(32)
auth_params: Dict[str, str] = {
"response_type": "code",
"client_id": self.configs.client_id,
"redirect_uri": str(self.callback_url),
"state": state,
"code_challenge": code_challenge,
"code_challenge_method": "S256",
}
# Include explicit scopes only
if self.configs.scope:
auth_params["scope"] = self.configs.scope
auth_url: str = f"{authorization_endpoint}?{urlencode(auth_params)}"
self.state_mapping[state] = {
**auth_params,
"token_id": token_id,
"code_verifier": code_verifier,
}
# Redirect user for authorization
await self.redirect_handler(auth_url)
async def handle_fhir_oauth_callback(self, code: str, state: str) -> None:
state_mapping: Dict[str, str] | None = self.state_mapping.get(state)
if not state_mapping:
raise HTTPException(400, "Invalid state parameter")
code_verifier: str = state_mapping["code_verifier"]
token_id: str = state_mapping["token_id"]
# Exchange authorization code for tokens
await self._exchange_code_for_token(token_id, code, code_verifier)
async def _exchange_code_for_token(
self,
token_id: str,
auth_code: str,
code_verifier: str,
) -> None:
"""Exchange authorization code for access token."""
access_token_payload: dict = {
"grant_type": "authorization_code",
"code": auth_code,
"redirect_uri": str(self.callback_url),
"client_id": self.configs.client_id,
"client_secret": self.configs.client_secret,
"code_verifier": code_verifier,
}
try:
token: OAuthToken = await perform_token_flow(
url=self._get_token_endpoint(),
data=access_token_payload,
timeout=self.configs.timeout,
)
await self._validate_token_scopes(token)
self.token_mapping[token_id] = token
except Exception as ex:
logger.exception("Access token request failed. Caused by, ", exc_info=ex)
raise ValueError("Access token request failed")
def _get_authorization_endpoint(self) -> str:
"""Get authorization endpoint."""
return get_endpoint(self._metadata, "authorization_endpoint")
def _get_token_endpoint(self) -> str:
"""Get token endpoint."""
return get_endpoint(self._metadata, "token_endpoint")
async def _refresh_access_token(self, token_id: str) -> None:
"""Refresh access token using refresh token."""
current_token: OAuthToken | None = self.token_mapping.get(token_id)
if not current_token:
logger.debug("Unable to perform token refresh. No access token found!")
return None
refresh_token_payload: dict = {
"grant_type": "refresh_token",
"refresh_token": current_token.refresh_token,
"client_id": self.configs.client_id,
"client_secret": self.configs.client_secret,
}
try:
new_token: OAuthToken = await perform_token_flow(
url=self._get_token_endpoint(),
data=refresh_token_payload,
timeout=self.configs.timeout,
)
await self._validate_token_scopes(new_token)
self.token_mapping[token_id] = new_token
except Exception as ex:
logger.exception("Token refresh failed. Caused by, ", exc_info=ex)
raise ValueError("Token refresh failed")
async def get_access_token(self, token_id: str) -> OAuthToken | None:
"""Get access token for the given token ID."""
await self.ensure_token(token_id)
access_token: OAuthToken | None = self.token_mapping.get(token_id)
if not access_token:
# Wait for user_access_token to become available, with a timeout
for _ in range(self.configs.timeout):
access_token: OAuthToken | None = self.token_mapping.get(token_id)
if access_token:
break
await asyncio.sleep(1)
if not access_token:
logger.error("Failed to obtain user access token.")
raise ValueError("Failed to obtain user access token.")
return access_token

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# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
import logging
import time
import secrets
import string
import hashlib
import base64
from typing import Dict
from httpx import Response
from fhir_mcp_server.oauth.types import OAuthMetadata, OAuthToken
from mcp.shared._httpx_utils import create_mcp_http_client
from starlette.responses import HTMLResponse
logger = logging.getLogger(__name__)
async def discover_oauth_metadata(
metadata_url: str, headers: Dict[str, str] = {"Accept": "application/fhir+json"}
) -> OAuthMetadata | None:
"""
Discover OAuth metadata from server's well-known endpoint.
"""
async with create_mcp_http_client() as client:
try:
response = await client.get(url=metadata_url, headers=headers)
if response.status_code == 404:
return None
response.raise_for_status()
metadata_json = response.json()
logger.debug(f"OAuth metadata discovered: {metadata_json}")
return OAuthMetadata.model_validate(metadata_json)
except Exception as ex:
logger.exception("Failed to discover OAuth metadata. Caused by, ", ex)
return None
def is_token_expired(token) -> bool:
"""Return True if the token is missing or expired."""
if not token or not getattr(token, "expires_at", None):
return True
return time.time() > token.expires_at
def get_endpoint(metadata, endpoint: str) -> str:
"""Get an endpoint URL from OAuthMetadata, raise if missing."""
value = getattr(metadata, endpoint, None)
if not value:
raise Exception(f"{endpoint} not found in metadata")
return str(value)
def handle_successful_authentication() -> HTMLResponse:
return HTMLResponse(
f"""
<!DOCTYPE html>
<html>
<head>
<title>FHIR MCP Server | Authentication Complete</title>
</head>
<body style="font-family:Arial,sans-serif;display:flex;justify-content:center;align-items:center;height:100vh;margin:0;background:#F5F5F5;">
<div style="text-align:center;padding:20px;background:#E5F5E0;border-radius:8px;box-shadow:0 2px 4px rgba(0,0,0,0.1);width:400px;">
<h2 style="color:#000000;margin:0 0 16px;">Authentication Successful!</h2>
<p style="color:#000000;margin:0 0 20px;">You can close this window and return to the application.</p>
</div>
<script>setTimeout(() => window.close(), 2000);</script>
</body>
</html>
"""
)
def handle_failed_authentication(error_desc: str = "") -> HTMLResponse:
return HTMLResponse(
f"""
<!DOCTYPE html>
<html>
<head>
<title>FHIR MCP Server | Authentication Complete</title>
</head>
<body style="font-family:Arial,sans-serif;display:flex;justify-content:center;align-items:center;height:100vh;margin:0;background:#F5F5F5;">
<div style="text-align:center;padding:20px;background:#F7C6C7;border-radius:8px;box-shadow:0 2px 4px rgba(0,0,0,0.1);width:400px;">
<h2 style="color:#000000;margin:0 0 16px;">Authentication Failed!</h2>
<p style="color:#000000;margin:0 0 20px;">{error_desc}. Please try again!</p>
</div>
</body>
</html>
"""
)
def generate_code_verifier(length: int = 128) -> str:
"""Generate a cryptographically random code verifier for PKCE (RFC 7636)."""
if not (43 <= length <= 128):
raise ValueError("Code verifier length must be between 43 and 128.")
return "".join(
secrets.choice(string.ascii_letters + string.digits + "-._~")
for _ in range(length)
)
def generate_code_challenge(code_verifier: str) -> str:
"""Generate a code challenge from a code verifier using SHA256 (RFC 7636)."""
digest = hashlib.sha256(code_verifier.encode("ascii")).digest()
challenge = base64.urlsafe_b64encode(digest).decode("ascii")
return challenge.rstrip("=")
async def perform_token_flow(
url: str,
data: Dict[str, str],
headers: Dict[str, str] = {"Content-Type": "application/x-www-form-urlencoded"},
timeout: float = 30.0,
) -> OAuthToken:
try:
async with create_mcp_http_client() as client:
response: Response = await client.post(
url=url,
data=data,
headers=headers,
timeout=timeout,
)
if response.status_code != 200:
logger.error(
f"Token call failed with status: {response.status_code}: {response.text}"
)
raise ValueError(f"Token endpoint call failed")
# Parse token response
token_response: OAuthToken = OAuthToken.model_validate(response.json())
# Calculate token expiry
if not token_response.expires_at:
if token_response.expires_in:
token_response.expires_at = time.time() + token_response.expires_in
else:
token_response.expires_at = time.time() + 3600
return token_response
except Exception as ex:
logger.exception(
"Unable to invoke the token endpoint. Caused by, ", exc_info=ex
)
raise ValueError("Token endpoint call failed")

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# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
import logging
import secrets
import time
from typing import Dict
from pydantic import AnyHttpUrl
from starlette.exceptions import HTTPException
from urllib.parse import urlencode
from mcp.server.auth.provider import (
AccessToken,
OAuthAuthorizationServerProvider,
RefreshToken,
AuthorizationParams,
construct_redirect_uri,
)
from mcp.shared.auth import OAuthClientInformationFull, OAuthToken
from fhir_mcp_server.oauth.types import (
AuthorizationCode,
OAuthMetadata,
OAuthToken as OAuth2Token,
)
from fhir_mcp_server.oauth.types import OAuthMetadata, ServerConfigs
from fhir_mcp_server.oauth.common import (
discover_oauth_metadata,
get_endpoint,
generate_code_challenge,
generate_code_verifier,
perform_token_flow,
)
logger = logging.getLogger(__name__)
class OAuthServerProvider(OAuthAuthorizationServerProvider):
def __init__(self, configs: ServerConfigs):
self.configs = configs
self.clients: Dict[str, OAuthClientInformationFull] = {}
self.auth_code_mapping: Dict[str, AuthorizationCode] = {}
self.token_mapping: Dict[str, AccessToken | RefreshToken] = {}
self.state_mapping: Dict[str, Dict[str, str]] = {}
self._metadata: OAuthMetadata | None = None
async def initialize(self) -> None:
"""Initialize the OAuth server."""
self._metadata = await self._discover_oauth_metadata()
async def get_client(self, client_id: str) -> OAuthClientInformationFull | None:
"""Get OAuth client information."""
return self.clients.get(client_id)
async def register_client(self, client_info: OAuthClientInformationFull):
"""Register a new OAuth client."""
self.clients[client_info.client_id] = client_info
async def authorize(
self, client: OAuthClientInformationFull, params: AuthorizationParams
) -> str:
"""Generate an authorization URL for OAuth flow."""
if not self._metadata:
self._metadata = await self._discover_oauth_metadata()
authorization_endpoint: str = await self._get_authorization_endpoint()
# Generate PKCE challenge
code_verifier: str = self._generate_code_verifier()
code_challenge: str = self._generate_code_challenge(code_verifier)
state: str = params.state or secrets.token_hex(16)
# Store the state mapping
self.state_mapping[state] = {
"redirect_uri": str(params.redirect_uri),
"code_verifier": code_verifier,
"code_challenge": params.code_challenge,
"redirect_uri_provided_explicitly": str(
params.redirect_uri_provided_explicitly
),
"client_id": client.client_id,
**({"scope": " ".join(params.scopes)} if params.scopes else {}),
}
auth_params: Dict[str, str] = {
"response_type": "code",
"scope": self.configs.oauth.scope,
"client_id": self.configs.oauth.client_id,
"redirect_uri": str(
self.configs.oauth.callback_url(self.configs.effective_server_url)
),
"state": state,
"code_challenge": code_challenge,
"code_challenge_method": "S256",
}
auth_url: str = f"{authorization_endpoint}?{urlencode(auth_params)}"
logger.debug(f"Redirecting the request to authorization URL: {auth_url}")
return auth_url
async def handle_mcp_oauth_callback(self, code: str, state: str) -> str:
"""Handle OAuth redirect."""
state_data: Dict[str, str] | None = self.state_mapping.get(state)
if not state_data:
raise HTTPException(400, "Invalid state parameter")
redirect_uri: str = state_data["redirect_uri"]
code_challenge: str = state_data["code_challenge"]
redirect_uri_provided_explicitly: bool = (
state_data["redirect_uri_provided_explicitly"] == "True"
)
client_id: str = state_data["client_id"]
code_verifier: str = state_data["code_verifier"]
scope: str | None = state_data.get("scope")
# Create MCP authorization code
mcp_auth_code: str = f"fhir_mcp_{secrets.token_hex(16)}"
self.auth_code_mapping[mcp_auth_code] = AuthorizationCode(
code=code,
client_id=client_id,
redirect_uri=AnyHttpUrl(redirect_uri),
redirect_uri_provided_explicitly=redirect_uri_provided_explicitly,
expires_at=int(time.time() + 600), # 10 min
scopes=scope.strip().split(" ") if scope else [],
code_verifier=code_verifier,
code_challenge=code_challenge,
)
del self.state_mapping[state]
return construct_redirect_uri(redirect_uri, code=mcp_auth_code, state=state)
async def load_authorization_code(
self, client: OAuthClientInformationFull, authorization_code: str
) -> AuthorizationCode | None:
"""Load an validate authorization code."""
auth_code: AuthorizationCode | None = self.auth_code_mapping.get(
authorization_code
)
if not auth_code:
return None
if auth_code.client_id != client.client_id:
return None
if auth_code.expires_at < time.time():
return None
del self.auth_code_mapping[authorization_code]
return auth_code
async def exchange_authorization_code(
self, client: OAuthClientInformationFull, authorization_code: AuthorizationCode
) -> OAuthToken:
"""Exchange authorization code for tokens."""
if client.client_id != authorization_code.client_id:
raise ValueError("Client authentication failed")
access_token_payload: Dict = {
"grant_type": "authorization_code",
"code": authorization_code.code,
"code_verifier": authorization_code.code_verifier,
"client_id": self.configs.oauth.client_id,
"client_secret": self.configs.oauth.client_secret,
"redirect_uri": self.configs.oauth.callback_url(self.configs.effective_server_url),
}
token: OAuth2Token = await perform_token_flow(
url=await self._get_token_endpoint(),
data=access_token_payload,
headers={"Accept": "application/json"},
)
# Generate MCP tokens
mcp_access_token: str = f"fhir_mcp_{secrets.token_hex(32)}"
mcp_refresh_token: str = f"fhir_mcp_{secrets.token_hex(32)}"
self.token_mapping[mcp_access_token] = AccessToken(
token=token.access_token,
client_id=self.configs.oauth.client_id,
scopes=token.scopes,
expires_at=int(token.expires_at or 3600),
)
if token.refresh_token:
self.token_mapping[mcp_refresh_token] = RefreshToken(
token=token.refresh_token,
client_id=self.configs.oauth.client_id,
scopes=token.scopes,
expires_at=int(token.expires_at or 3600),
)
return OAuthToken(
access_token=mcp_access_token,
refresh_token=mcp_refresh_token,
token_type="bearer",
expires_in=token.expires_in,
scope=" ".join(authorization_code.scopes),
)
async def load_access_token(self, token: str) -> AccessToken | None:
"""Load and validate an access token."""
access_token: AccessToken | RefreshToken | None = self.token_mapping.get(token)
if not access_token:
return None
if access_token.expires_at and access_token.expires_at < time.time():
return None
if isinstance(access_token, AccessToken):
return access_token
return None
async def load_refresh_token(
self, client: OAuthClientInformationFull, refresh_token: str
) -> RefreshToken | None:
"""Load and validate refresh token."""
token = self.token_mapping.get(refresh_token)
if not token:
return None
if token.client_id != client.client_id:
return None
if token.expires_at and token.expires_at < time.time():
return None
if isinstance(token, RefreshToken):
return token
return None
async def exchange_refresh_token(
self,
client: OAuthClientInformationFull,
refresh_token: RefreshToken,
scopes: list[str],
) -> OAuthToken:
"""Exchange refresh token"""
if refresh_token.client_id != client.client_id:
raise ValueError("Client authentication failed")
refresh_token_payload: Dict = {
"grant_type": "refresh_token",
"refresh_token": refresh_token,
"client_id": self.configs.oauth.client_id,
"client_secret": self.configs.oauth.client_secret,
"scopes": " ".join(scopes),
}
new_token: OAuth2Token = await perform_token_flow(
url=await self._get_token_endpoint(),
data=refresh_token_payload,
headers={"Accept": "application/json"},
)
# Generate new MCP tokens
mcp_access_token: str = f"fhir_mcp_{secrets.token_hex(32)}"
mcp_refresh_token: str = f"fhir_mcp_{secrets.token_hex(32)}"
self.token_mapping[mcp_access_token] = AccessToken(
token=new_token.access_token,
scopes=new_token.scopes,
expires_at=int(new_token.expires_at or 3600),
client_id=client.client_id,
)
if new_token.refresh_token:
self.token_mapping[mcp_refresh_token] = RefreshToken(
token=new_token.refresh_token,
scopes=new_token.scopes,
expires_at=int(new_token.expires_at or 3600),
client_id=client.client_id,
)
return OAuthToken(
access_token=mcp_access_token,
refresh_token=mcp_refresh_token,
token_type="bearer",
expires_in=int(new_token.expires_in or 3600),
scope=new_token.scope,
)
async def revoke_token(
self, token: str, token_type_hint: str | None = None
) -> None:
"""Revoke a token."""
if token in self.token_mapping:
del self.token_mapping[token]
async def _discover_oauth_metadata(self) -> OAuthMetadata | None:
return await discover_oauth_metadata(
metadata_url=self.configs.oauth.metadata_url,
headers={"Accept": "application/json"},
)
async def _get_authorization_endpoint(self) -> str:
return get_endpoint(self._metadata, "authorization_endpoint")
async def _get_token_endpoint(self) -> str:
return get_endpoint(self._metadata, "token_endpoint")
def _generate_code_verifier(self) -> str:
"""Generate a cryptographically random code verifier for PKCE."""
return generate_code_verifier(128)
def _generate_code_challenge(self, code_verifier: str) -> str:
"""Generate a code challenge from a code verifier using SHA256."""
return generate_code_challenge(code_verifier)

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# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
from pydantic import AnyHttpUrl, BaseModel
from pydantic_settings import BaseSettings, SettingsConfigDict
class BaseOAuthConfigs(BaseSettings):
client_id: str
client_secret: str
scope: str
@property
def scopes(self) -> list[str]:
# If the raw value is a string, split on empty spaces
if isinstance(self.scope, str):
return [scope.strip() for scope in self.scope.split(" ") if scope.strip()]
return [self.scope]
class MCPOAuthConfigs(BaseOAuthConfigs):
metadata_url: str
def callback_url(
self, server_url: str, suffix: str = "/oauth/callback"
) -> AnyHttpUrl:
return AnyHttpUrl(f"{server_url.rstrip('/')}{suffix}")
class FHIROAuthConfigs(BaseOAuthConfigs):
base_url: str
timeout: int = 30 # in secs
access_token: str | None = None
def callback_url(
self, server_url: str, suffix: str = "/fhir/callback"
) -> AnyHttpUrl:
return AnyHttpUrl(f"{server_url.rstrip('/')}{suffix}")
@property
def discovery_url(self) -> str:
return f"{self.base_url.rstrip('/')}/.well-known/smart-configuration"
@property
def metadata_url(self) -> str:
return f"{self.base_url.rstrip('/')}/metadata?_format=json"
class ServerConfigs(BaseSettings):
"""Contains environment configurations of the MCP server."""
model_config = SettingsConfigDict(
env_prefix="HEALTHCARE_MCP_",
env_file=".env",
env_file_encoding="utf-8",
env_nested_delimiter="__",
extra="ignore",
)
# Server settings
host: str = "localhost"
port: int = 8000
server_url: str | None = None
# OAuth2 settings
oauth: MCPOAuthConfigs
# FHIR settings
fhir: FHIROAuthConfigs
@property
def effective_server_url(self) -> str:
return self.server_url or f"http://{self.host}:{self.port}"
def __init__(self, **data):
"""Initialize settings with values from environment variables"""
super().__init__(**data)
class OAuthMetadata(BaseModel):
"""
OAuth 2.0 Authorization Server Metadata.
"""
issuer: AnyHttpUrl
authorization_endpoint: AnyHttpUrl
token_endpoint: AnyHttpUrl
registration_endpoint: AnyHttpUrl | None = None
scopes_supported: list[str] | None = None
response_types_supported: list[str]
response_modes_supported: list[str] | None = None
grant_types_supported: list[str] | None = None
token_endpoint_auth_methods_supported: list[str] | None = None
token_endpoint_auth_signing_alg_values_supported: list[str] | None = None
service_documentation: AnyHttpUrl | None = None
ui_locales_supported: list[str] | None = None
op_policy_uri: AnyHttpUrl | None = None
op_tos_uri: AnyHttpUrl | None = None
revocation_endpoint: AnyHttpUrl | None = None
revocation_endpoint_auth_methods_supported: list[str] | None = None
revocation_endpoint_auth_signing_alg_values_supported: None = None
introspection_endpoint: AnyHttpUrl | None = None
introspection_endpoint_auth_methods_supported: list[str] | None = None
introspection_endpoint_auth_signing_alg_values_supported: None = None
code_challenge_methods_supported: list[str] | None = None
class OAuthToken(BaseModel):
"""
OAuth 2.0 token with metadata.
"""
access_token: str
token_type: str
expires_in: int | None = None
scope: str | None = None
refresh_token: str | None = None
expires_at: float | None = None
@property
def scopes(self) -> list[str]:
return self.scope.split(" ") if self.scope else []
class AuthorizationCode(BaseModel):
code: str
scopes: list[str]
expires_at: float
client_id: str
code_verifier: str
code_challenge: str
redirect_uri: AnyHttpUrl
redirect_uri_provided_explicitly: bool

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@@ -0,0 +1,567 @@
# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
import click
import logging
import sys
from fhir_mcp_server.utils import (
create_async_fhir_client,
get_bundle_entries,
get_default_headers,
get_operation_outcome_error,
get_operation_outcome_exception,
get_operation_outcome_required_error,
get_capability_statement,
trim_resource,
)
from fhir_mcp_server.oauth import (
handle_failed_authentication,
handle_successful_authentication,
OAuthServerProvider,
FHIRClientProvider,
OAuthToken,
ServerConfigs,
)
from fhirpy import AsyncFHIRClient
from fhirpy.lib import AsyncFHIRResource
from fhirpy.base.exceptions import OperationOutcome
from fhirpy.base.searchset import Raw
from typing import Dict, Any, Optional
from pydantic import AnyHttpUrl
from starlette.requests import Request
from starlette.responses import RedirectResponse, Response, HTMLResponse
from mcp.server.auth.middleware.auth_context import get_access_token
from mcp.server.auth.provider import AccessToken
from mcp.server.auth.settings import AuthSettings, ClientRegistrationOptions
from mcp.server.fastmcp.server import FastMCP
logger: logging.Logger = logging.getLogger(__name__)
configs: ServerConfigs = ServerConfigs()
server_provider: OAuthServerProvider = OAuthServerProvider(configs=configs)
auth_settings: AuthSettings = AuthSettings(
issuer_url=AnyHttpUrl(configs.effective_server_url),
client_registration_options=ClientRegistrationOptions(
enabled=True,
valid_scopes=configs.oauth.scopes,
default_scopes=configs.oauth.scopes,
),
)
mcp: FastMCP = FastMCP(
name="FHIR MCP Server",
instructions="This server implements the HL7 FHIR MCP for secure, standards-based access to FHIR resources",
auth_server_provider=server_provider,
host=configs.host,
port=configs.port,
auth=auth_settings,
json_response=True,
stateless_http=True,
)
client_provider: FHIRClientProvider = FHIRClientProvider(
callback_url=AnyHttpUrl(configs.fhir.callback_url(configs.effective_server_url)),
configs=configs.fhir,
)
@mcp.custom_route("/fhir/callback", methods=["GET"])
async def handle_fhir_server_callback(request: Request) -> HTMLResponse:
"""Handle FHIR OAuth redirect."""
code: str | None = request.query_params.get("code")
state: str | None = request.query_params.get("state")
if not code or not state:
return handle_failed_authentication("Missing code or state parameter")
try:
await client_provider.handle_fhir_oauth_callback(code, state)
return handle_successful_authentication()
except Exception as ex:
logger.error(
"Error occurred while handling FHIR oauth callback. Caused by, ",
exc_info=ex,
)
return handle_failed_authentication("Something went wrong.")
@mcp.custom_route("/oauth/callback", methods=["GET"])
async def handle_auth_server_callback(request: Request) -> Response:
"""Handle MCP OAuth redirect."""
code: str | None = request.query_params.get("code")
state: str | None = request.query_params.get("state")
if not code or not state:
return handle_failed_authentication("Missing code or state parameter")
try:
redirect_uri: str = await server_provider.handle_mcp_oauth_callback(code, state)
return RedirectResponse(status_code=302, url=redirect_uri)
except Exception as ex:
logger.error(
"Error occurred while handling MCP oauth callback. Caused by, ", exc_info=ex
)
return handle_failed_authentication("Something went wrong.")
async def get_user_access_token() -> OAuthToken | None:
"""Get the access token for the authenticated user."""
if configs.fhir.access_token:
logger.debug("Using configured FHIR access token for user.")
return OAuthToken(access_token=configs.fhir.access_token, token_type="Bearer")
client_access_token: AccessToken | None = get_access_token()
if not client_access_token:
raise ValueError("Failed to obtain client access token.")
return await client_provider.get_access_token(client_access_token.token)
async def get_async_fhir_client() -> AsyncFHIRClient:
"""Get an async FHIR client with user access token."""
user_token: OAuthToken | None = await get_user_access_token()
if not user_token:
raise ValueError("User is not authenticated")
logger.debug(
f"Creating async FHIR client with access token: {user_token.access_token}"
)
return await create_async_fhir_client(
config=configs.fhir,
access_token=user_token.access_token,
extra_headers=get_default_headers(),
)
@mcp.tool()
async def get_capabilities(type: str) -> Dict[str, Any]:
"""
Retrieves metadata about a specified FHIR resource type, including its supported search parameters and custom operations.
This tool should be used at the start of any workflow where you need to discover what queries or operations are permitted
against that resource (e.g., before calling search, read, or create). Do not use this tool to fetch actual resources.
It only returns definitions and descriptions of capabilities, not resource instances. Because FHIR defines different search
parameters and operations per resource type, this tool ensures your subsequent calls use valid inputs.
Args:
type (str): The FHIR resource type name (e.g., "Patient", "Observation", "Encounter").
Must exactly match one of the core or profile-defined resource types supported by the server.
Returns:
Dict[str, Any]:
A dictionary containing:
- "type" (str): The requested resource type (if available) or empty.
- "searchParam" (Dict[str, str]): A map of FHIR search-parameter names. Each key is the parameter name
(e.g., "family", "_id", "_lastUpdated"), and each value is the FHIR-provided description of that parameter's meaning and usage constraints.
- "operation" (Dict[str, str]): A map of custom FHIR operation names to their descriptions.
Each key is the operation name (e.g., "$validate"), and each value explains the operation's purpose.
"""
try:
logger.debug(f"Invoked with resource_type='{type}'")
data: Dict[str, Any] = await get_capability_statement(configs.fhir.metadata_url)
for resource in data["rest"][0]["resource"]:
if resource.get("type") == type:
logger.info(f"Resource type '{type}' found in the CapabilityStatement.")
return {
"type": resource.get("type"),
"searchParam": trim_resource(resource.get("searchParam", [])),
"operation": trim_resource(resource.get("operation", [])),
}
logger.info(f"Resource type '{type}' not found in the CapabilityStatement.")
return await get_operation_outcome_error(
code="not-supported",
diagnostics=f"The interaction, operation, resource or profile {type} is not supported.",
)
except Exception as ex:
logger.exception(
f"Error while executing the FHIR metadata interaction for resource_type '{type}'. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_exception()
@mcp.tool()
async def search(
type: str, searchParam: Dict[str, str]
) -> list[AsyncFHIRResource] | Dict[str, Any]:
"""
Executes a standard FHIR search interaction on a given resource type, returning a bundle or list of matching resources.
Use this when you need to query for multiple resources based on one or more search-parameters.
Do not use this tool for create, update, or delete operations, and be aware that large result sets may be paginated by the FHIR server.
Args:
type (str): The FHIR resource type name (e.g., "MedicationRequest", "Condition", "Procedure").
Must exactly match one of the core or profile-defined resource types supported by the server.
searchParam (Dict[str, str]): A mapping of FHIR search parameter names to their desired values (e.g., {"family":"Smith","birthdate":"1970-01-01"}).
These parameters refine queries for operation-specific query qualifiers.
Only parameters exposed by `get_capabilities` for that resource type are valid.
Returns:
Dict[str, Any]: A dictionary containing the full FHIR resource instance matching the search criteria.
"""
try:
logger.debug(f"Invoked with type='{type}' and searchParam={searchParam}")
if not type:
logger.error(
"Unable to perform search operation: 'type' is a mandatory field."
)
return await get_operation_outcome_required_error("type")
client: AsyncFHIRClient = await get_async_fhir_client()
return await client.resources(type).search(Raw(**searchParam)).fetch()
except ValueError as ex:
logger.exception(
f"User does not have permission to perform FHIR '{type}' resource search operation. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_error(
code="forbidden",
diagnostics=f"The user does not have the rights to perform search operation.",
)
except OperationOutcome as ex:
logger.exception(
f"FHIR server returned an OperationOutcome error while searching the resource: '{type}', Caused by,",
exc_info=ex,
)
return ex.resource["issue"] or await get_operation_outcome_exception()
except Exception as ex:
logger.exception(
f"An unexpected error occurred during the FHIR search operation for resource: '{type}'. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_exception()
@mcp.tool()
async def read(
type: str,
id: str,
searchParam: Optional[Dict[str, str]] = None,
operation: Optional[str] = "",
) -> Dict[str, Any]:
"""
Performs a FHIR "read" interaction to retrieve a single resource instance by its type and resource ID,
optionally refining the response with search parameters or custom operations.
Use it when you know the exact resource ID and require that one resource; do not use it for bulk queries.
If additional query-level parameters or operations are needed (e.g., _elements or $validate), include them in searchParam or operation.
Args:
type (str): The FHIR resource type name (e.g., "DiagnosticReport", "AllergyIntolerance", "Immunization").
Must exactly match one of the core or profile-defined resource types supported by the server.
id (str): The logical ID of a specific FHIR resource instance.
searchParam (Dict[str, str]): A mapping of FHIR search parameter names to their desired values (e.g., {"device-name":"glucometer"}).
These parameters refine queries for operation-specific query qualifiers.
Only parameters exposed by `get_capabilities` for that resource type are valid.
operation (Optional[str]): The name of a custom FHIR operation or extended query defined for the resource (e.g., "$everything").
Must match one of the operation names returned by `get_capabilities`.
Returns:
Dict[str, Any]: A dictionary containing the single FHIR resource instance of the requested type and id.
"""
try:
logger.debug(
f"Invoked with type='{type}', id={id}, searchParam={searchParam}, and operation={operation}"
)
if not type:
logger.error(
"Unable to perform read operation: 'type' is a mandatory field."
)
return await get_operation_outcome_required_error("type")
client: AsyncFHIRClient = await get_async_fhir_client()
bundle: dict = await client.resource(resource_type=type, id=id).execute(
operation=operation or "", method="GET", params=searchParam
)
return await get_bundle_entries(bundle=bundle)
except ValueError as ex:
logger.exception(
f"User does not have permission to perform FHIR '{type}' resource read operation. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_error(
code="forbidden",
diagnostics=f"The user does not have the rights to perform read operation.",
)
except OperationOutcome as ex:
logger.exception(
f"FHIR server returned an OperationOutcome error while reading the resource: '{type}', Caused by,",
exc_info=ex,
)
return ex.resource["issue"] or await get_operation_outcome_exception()
except Exception as ex:
logger.exception(
f"An unexpected error occurred during the FHIR read operation for resource: '{type}'. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_exception()
@mcp.tool()
async def create(
type: str,
payload: Dict[str, Any],
searchParam: Optional[Dict[str, str]] = None,
operation: Optional[str] = "",
) -> Dict[str, Any]:
"""
Executes a FHIR "create" interaction to persist a new resource of the specified type. It is required to supply the full resource payload in JSON form.
Use this tool when you need to add new data (e.g., a new Patient or Observation). Do not call it to update existing resources; for updates, use patch.
Note that servers may reject resources that violate profiles or mandatory bindings.
Args:
type (str): The FHIR resource type name (e.g., "Device", "CarePlan", "Goal").
Must exactly match one of the core or profile-defined resource types supported by the server.
payload (Dict[str, str]): A JSON object representing the full FHIR resource body to be created.
It must include all required elements of the resource's profile.
searchParam (Dict[str, str]): A mapping of FHIR search parameter names to their desired values (e.g., {"address-city":"Boston"}).
These parameters refine queries for operation-specific query qualifiers.
Only parameters exposed by `get_capabilities` for that resource type are valid.
operation (Optional[str]): The name of a custom FHIR operation or extended query defined for the resource (e.g., "$evaluate").
Must match one of the operation names returned by `get_capabilities`.
Returns:
Dict[str, Any]: A dictionary containing the newly created FHIR resource, including server-assigned fields (id, meta.versionId, meta.lastUpdated,
and any server-added extensions). Reflects exactly what was persisted.
"""
try:
logger.debug(
f"Invoked with type='{type}', payload={payload}, searchParam={searchParam}, and operation={operation}"
)
if not type:
logger.error(
"Unable to perform create operation: 'type' is a mandatory field."
)
return await get_operation_outcome_required_error("type")
client: AsyncFHIRClient = await get_async_fhir_client()
bundle: dict = await client.resource(resource_type=type).execute(
operation=operation or "", data=payload, params=searchParam
)
return await get_bundle_entries(bundle=bundle)
except ValueError as ex:
logger.exception(
f"User does not have permission to perform FHIR '{type}' resource create operation. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_error(
code="forbidden",
diagnostics=f"The user does not have the rights to perform create operation.",
)
except OperationOutcome as ex:
logger.exception(
f"FHIR server returned an OperationOutcome error while creating the resource: '{type}', Caused by,",
exc_info=ex,
)
return ex.resource["issue"] or await get_operation_outcome_exception()
except Exception as ex:
logger.exception(
f"An unexpected error occurred during the FHIR create operation for resource: '{type}'. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_exception()
@mcp.tool()
async def update(
type: str,
id: str,
payload: Dict[str, Any],
searchParam: Optional[Dict[str, str]] = None,
operation: Optional[str] = "",
) -> Dict[str, Any]:
"""
Performs a FHIR "update" interaction by replacing an existing resource instance's content with the provided payload.
Use it when you need to overwrite a resource's data in its entirety, such as correcting or completing a record, and you already know the resource's logical id.
Optionally, you can include searchParam for conditional updates (e.g., only update if the resource matches certain criteria) or specify a
custom operation (e.g., "$validate" to run validation before updating). The tool returns the updated resource or an OperationOutcome detailing any errors.
Args:
type (str): The FHIR resource type name (e.g., "Location", "Organization", "Coverage").
id (str): The logical ID of a specific FHIR resource instance.
Must exactly match one of the core or profile-defined resource types supported by the server.
payload (Dict[str, Any]): The complete JSON representation of the FHIR resource, containing all required elements and any optional data.
Servers replace the existing resource with this exact content, so the payload must include all mandatory fields defined by the resource's profile
and any previous data you wish to preserve.
searchParam (Dict[str, str]): A mapping of FHIR search parameter names to their desired values (e.g., {"patient":"Patient/54321","relationship":"father"}).
These parameters refine queries for operation-specific query qualifiers.
Only parameters exposed by `get_capabilities` for that resource type are valid.
operation (Optional[str]): The name of a custom FHIR operation or extended query defined for the resource (e.g., "$lastn").
Must match one of the operation names returned by `get_capabilities`.
Returns:
Dict[str, Any]: A dictionary containing the updated FHIR resource after applying the JSON Patch operations..
"""
try:
logger.debug(
f"Invoked with type='{type}', id={id}, payload={payload}, searchParam={searchParam}, and operation={operation}"
)
if not type:
logger.error(
"Unable to perform update operation: 'type' is a mandatory field."
)
return await get_operation_outcome_required_error("type")
client: AsyncFHIRClient = await get_async_fhir_client()
bundle: dict = await client.resource(resource_type=type, id=id).execute(
operation=operation or "",
method="PUT",
data={id: id, **payload},
params=searchParam,
)
return await get_bundle_entries(bundle=bundle)
except ValueError as ex:
logger.exception(
f"User does not have permission to perform FHIR '{type}' resource update operation. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_error(
code="forbidden",
diagnostics=f"The user does not have the rights to perform update operation.",
)
except OperationOutcome as ex:
logger.exception(
f"FHIR server returned an OperationOutcome error while updating the resource: '{type}', Caused by,",
exc_info=ex,
)
return ex.resource["issue"] or await get_operation_outcome_exception()
except Exception as ex:
logger.exception(
f"An unexpected error occurred during the FHIR update operation for resource: '{type}'. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_exception()
@mcp.tool()
async def delete(
type: str,
id: Optional[str] = "",
searchParam: Optional[Dict[str, str]] = None,
operation: Optional[str] = "",
) -> Dict[str, Any]:
"""
Execute a FHIR "delete" interaction on a specific resource instance.
Use this tool when you need to remove a single resource identified by its logical ID or optionally filtered by search parameters.
The optional `id` parameter must match an existing resource instance when present. If you include `searchParam`,
the server will perform a conditional delete, deleting the resource only if it matches the given criteria. If you supply `operation`,
it will execute the named FHIR operation (e.g., `$expunge`) on the resource. Do not use this tool for bulk deletes across multiple
This tool returns a FHIR `OperationOutcome` describing success or failure of the deletion.
Args:
type (str): The FHIR resource type name (e.g., "ServiceRequest", "Appointment", "HealthcareService").
id (str): The logical ID of a specific FHIR resource instance.
Must exactly match one of the core or profile-defined resource types supported by the server.
payload (Dict[str, str]): A JSON object following the RFC 6902 patch syntax (an array of operations) of the FHIR resource to be patched
(e.g., [{"op": "replace", "path": "/name/family", "value": "Doe"}]).
searchParam (Dict[str, str]): A mapping of FHIR search parameter names to their desired values (e.g., {"category":"laboratory","issued:"2025-05-01"}).
These parameters refine queries for operation-specific query qualifiers.
Only parameters exposed by `get_capabilities` for that resource type are valid.
operation (Optional[str]): The name of a custom FHIR operation or extended query defined for the resource (e.g., "$expand").
Must match one of the operation names returned by `get_capabilities`.
Returns:
Dict[str, Any]: A dictionary containing the confirmation of deletion or details on why deletion failed.
"""
try:
logger.debug(
f"Invoked with type='{type}', id={id}, searchParam={searchParam}, and operation={operation}"
)
if not type:
logger.error(
"Unable to perform delete operation: 'type' is a mandatory field."
)
return await get_operation_outcome_required_error("type")
client: AsyncFHIRClient = await get_async_fhir_client()
bundle: dict = await client.resource(resource_type=type, id=id).execute(
operation=operation or "", method="DELETE", params=searchParam
)
return await get_bundle_entries(bundle=bundle)
except ValueError as ex:
logger.exception(
f"User does not have permission to perform FHIR '{type}' resource delete operation. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_error(
code="forbidden",
diagnostics=f"The user does not have the rights to perform delete operation.",
)
except OperationOutcome as ex:
logger.exception(
f"FHIR server returned an OperationOutcome error while deleting the resource: '{type}', Caused by,",
exc_info=ex,
)
return ex.resource["issue"] or await get_operation_outcome_exception()
except Exception as ex:
logger.exception(
f"An unexpected error occurred during the FHIR delete operation for resource: '{type}'. Caused by, ",
exc_info=ex,
)
return await get_operation_outcome_exception()
@click.command()
@click.option(
"--transport",
type=click.Choice(["stdio", "sse", "streamable-http"]),
default="streamable-http",
show_default=True,
help="Transport protocol to use",
)
@click.option(
"--log-level",
type=click.Choice(["DEBUG", "INFO", "WARN", "ERROR"], case_sensitive=False),
default="INFO",
show_default=True,
help="Log level to use",
)
def main(transport, log_level) -> None:
"""Start the FHIR MCP server."""
logger.setLevel(log_level.upper())
try:
logger.info(f"Starting FHIR MCP server with {transport} transport")
mcp.run(transport=transport)
except Exception as ex:
logger.error(
f"Unable to run the FHIR MCP server. Caused by, %s", ex, exc_info=True
)
sys.exit(1)
sys.exit(0)
if __name__ == "__main__":
logging.basicConfig(
level=logging.INFO,
format="[%(asctime)s] %(levelname)s {%(name)s.%(funcName)s:%(lineno)d} - %(message)s",
)
main()

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@@ -0,0 +1,115 @@
# Copyright (c) 2025, WSO2 LLC. (https://www.wso2.com/) All Rights Reserved.
# WSO2 LLC. licenses this file to you under the Apache License,
# Version 2.0 (the "License"); you may not use this file except
# in compliance with the License.
# You may obtain postgres_pgvector copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
import aiohttp
import logging
from fhir_mcp_server.oauth import FHIROAuthConfigs
from typing import Any, Dict, List, Optional
from fhirpy import AsyncFHIRClient
from mcp.shared._httpx_utils import create_mcp_http_client
logger: logging.Logger = logging.getLogger(__name__)
async def create_async_fhir_client(
config: FHIROAuthConfigs,
access_token: str,
extra_headers: dict | None = None,
) -> AsyncFHIRClient:
"""Create a FHIR AsyncClient with defaults."""
client: AsyncFHIRClient = AsyncFHIRClient(
url=config.base_url,
authorization=f"Bearer {access_token}",
aiohttp_config={
"timeout": aiohttp.ClientTimeout(total=config.timeout),
},
extra_headers=extra_headers,
)
return client
async def get_bundle_entries(bundle: Dict[str, Any]) -> Dict[str, Any]:
if "entry" in bundle and isinstance(bundle["entry"], list):
logger.debug(f"found {len(bundle['entry'])} entries for type '{type}'")
return {
"entry": [
entry.get("resource")
for entry in bundle["entry"]
if "resource" in entry
]
}
return bundle
def trim_resource(operations: List[Dict[str, Any]]) -> List[Dict[str, Optional[str]]]:
logger.debug(f"trim_resource called with {len(operations)} operations.")
trimmed = [
{"name": operation.get("name"), "documentation": operation.get("documentation")}
for operation in operations
if "name" in operation or "documentation" in operation
]
logger.debug(f"trim_resource returning {len(trimmed)} trimmed operations.")
return trimmed
async def get_operation_outcome_exception() -> dict:
return await get_operation_outcome_error(
code="exception", diagnostics="An unexpected internal error has occurred."
)
async def get_operation_outcome_required_error(element: str = "") -> dict:
return await get_operation_outcome_error(
code="required", diagnostics=f"A required element {element} is missing."
)
async def get_operation_outcome_error(code: str, diagnostics: str) -> dict:
return {
"resourceType": "OperationOutcome",
"issue": [
{
"severity": "error",
"code": code,
"diagnostics": diagnostics,
}
],
}
async def get_capability_statement(metadata_url: str) -> Dict[str, Any]:
"""
Discover CapabilityStatement from server's metadata endpoint.
"""
try:
async with create_mcp_http_client() as client:
response = await client.get(url=metadata_url, headers=get_default_headers())
response.raise_for_status()
metadata_json = response.json()
logger.debug(f"OAuth metadata discovered: {metadata_json}")
return metadata_json
except Exception as ex:
logger.exception(
"Unable to invoke the FHIR metadata endpoint. Caused by, ", exc_info=ex
)
raise ValueError("Unable to fetch FHIR metadata")
def get_default_headers() -> Dict[str, str]:
return {"Accept": "application/fhir+json"}

787
uv.lock generated Normal file
View File

@@ -0,0 +1,787 @@
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