Feature/mcp #846

jkiddo · 2025-08-10T05:12:42Z

No description provided.

…h R5

Reuse FhirContext in result serialization

…tarter into feature/mcp

PoC tool for CDS Hooks

jkiddo · 2025-08-23T20:51:13Z

Currently awaiting next release of https://github.com/spring-projects/spring-ai

# Conflicts: # src/main/resources/application.yaml

robogary · 2025-08-24T15:55:55Z

Formatting check succeeded!

Copilot

Pull Request Overview

This PR implements MCP (Model Context Protocol) integration to provide a bridge between AI models and the FHIR server. The feature adds an MCP server that exposes FHIR operations and CDS Hooks as tools that can be called by AI systems.

Key changes:

Added MCP server configuration and bridge implementation
Created tool specifications for FHIR CRUD operations and CDS Hooks calls
Enabled CR (Clinical Reasoning) and CDS Hooks modules to support MCP functionality

Reviewed Changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
pom.xml	Added Spring AI MCP and Model Context Protocol SDK dependencies
src/main/resources/application.yaml	Added MCP server configuration and enabled CR/CDS Hooks modules
src/main/java/ca/uhn/fhir/jpa/starter/AppProperties.java	Fixed annotation ordering for proper configuration
src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java	Main bridge class connecting MCP tools to FHIR operations
src/main/java/ca/uhn/fhir/jpa/starter/mcp/*.java	MCP-specific classes for tool definitions, request building, and result handling
src/test/resources/mcp/.xml, .json	Test resources for MCP functionality
src/test/java/ca/uhn/fhir/jpa/starter/McpTests.java	Test class for MCP client integration

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Copilot · 2025-08-24T15:58:35Z

src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java

+		// Print the keys of contextMap
+		for (String key : contextMap.keySet()) {
+			System.out.println("Context map key: " + key);


Debug code with System.out.println statements (lines 170-173) should be removed from production code. Use proper logging instead.

Suggested change

// Print the keys of contextMap

for (String key : contextMap.keySet()) {

System.out.println("Context map key: " + key);

logger.debug("Context map key: {}", key);

Copilot · 2025-08-24T15:58:36Z

src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java

+		Object patchBody = config.get("patch");
+		if (patchBody == null) {
+			throw new IllegalArgumentException("Missing 'patch' for patch interaction");


The RequestBuilder looks for a 'patch' parameter but the ToolFactory schemas define the parameter as 'resource' for patch operations. This will cause patch operations to fail.

Suggested change

Object patchBody = config.get("patch");

if (patchBody == null) {

throw new IllegalArgumentException("Missing 'patch' for patch interaction");

Object patchBody = config.get("resource");

if (patchBody == null) {

throw new IllegalArgumentException("Missing 'resource' for patch interaction");

Copilot

Pull Request Overview

This PR implements Model Context Protocol (MCP) integration to enable AI agents to interact with FHIR resources and CDS Hooks through standardized tooling. The implementation provides a bridge between MCP clients and the HAPI FHIR server, exposing FHIR operations as MCP tools.

Adds MCP server configuration and dependency management for Spring AI MCP integration
Implements FHIR resource manipulation tools (CRUD operations, search, transactions) accessible via MCP
Enables CDS Hooks invocation through MCP tooling with proper request/response handling

Reviewed Changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
pom.xml	Adds Spring AI MCP and MCP SDK dependencies for protocol support
src/main/resources/application.yaml	Configures MCP server settings and enables CR/CDS Hooks modules
src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java	Core bridge component that translates MCP tool calls to FHIR operations
src/main/java/ca/uhn/fhir/jpa/starter/mcp/	MCP-specific classes for tool definitions, request building, and result handling
src/test/	Test resources and integration tests for MCP functionality

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Copilot · 2025-08-24T18:35:01Z

src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java

+		// Print the keys of contextMap
+		for (String key : contextMap.keySet()) {
+			System.out.println("Context map key: " + key);


Debug print statements should be removed from production code. Use proper logging instead of System.out.println for debugging purposes.

Suggested change

// Print the keys of contextMap

for (String key : contextMap.keySet()) {

System.out.println("Context map key: " + key);

logger.debug("Context map key: {}", key);

Copilot · 2025-08-24T18:35:01Z

src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java

+			// TODO Return MCP Error
+			logger.error(e.getMessage(), e);
+			e.printStackTrace();


Remove the printStackTrace() call as the exception is already being logged via the logger. The printStackTrace() is redundant and can clutter output.

Suggested change

// TODO Return MCP Error

logger.error(e.getMessage(), e);

e.printStackTrace();

robogary · 2025-08-24T19:23:15Z

Formatting check succeeded!

Co-authored-by: Copilot <[email protected]>

robogary · 2025-08-24T19:24:59Z

Formatting check succeeded!

jkiddo · 2025-08-25T12:12:40Z

Some live testing here: https://www.youtube.com/watch?v=yb2q-k41GKQ&ab_channel=ChristopherGyldenk%C3%A6rne

robogary · 2025-08-26T18:37:41Z

Formatting check succeeded!

robogary · 2025-08-26T18:38:22Z

Formatting check succeeded!

robogary · 2025-08-26T21:29:07Z

Formatting check succeeded!

Copilot

Pull Request Overview

This PR implements Model Context Protocol (MCP) server functionality to the HAPI FHIR starter project, enabling LLM clients to interact with FHIR resources through standardized MCP tools.

Adds MCP server configuration and bridge components for FHIR operations and CDS Hooks
Implements comprehensive FHIR resource tools (CRUD operations, search, transactions)
Enables CDS Hooks integration through MCP protocol

Reviewed Changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
pom.xml	Adds Spring AI MCP and MCP SDK dependencies
application.yaml	Configures MCP server settings and enables CR/CDS Hooks modules
McpServerConfig.java	Spring configuration for MCP server with servlet registration
McpFhirBridge.java	Bridge component connecting MCP tools to FHIR operations
McpCdsBridge.java	Bridge component for CDS Hooks integration via MCP
ToolFactory.java	Factory creating MCP tool definitions for FHIR and CDS operations
RequestBuilder.java	Builds HTTP requests for different FHIR interactions
Interaction.java	Enum mapping MCP interactions to HTTP request types
CallToolResultFactory.java	Factory for creating MCP tool call responses
McpBridge.java	Interface for MCP bridge implementations
AppProperties.java	Moves annotation to fix configuration loading order
.dockerignore	Removes obsolete duplicate-finder-result.xml entry
Test resources	JSON/XML test files for MCP CDS Hooks integration testing
McpTests.java	Disabled integration test for MCP client functionality

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Copilot · 2025-08-26T22:29:32Z

src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java

+			case SEARCH -> {
+				method = "GET";
+				req = new MockHttpServletRequest(method, basePath);
+				if (config.get("searchParams") instanceof Map<?, ?> sp) {


The code checks for 'searchParams' but the SEARCH_FHIR_RESOURCES_SCHEMA defines the parameter as 'query'. This mismatch will cause search parameters to never be applied.

Suggested change

if (config.get("searchParams") instanceof Map<?, ?> sp) {

if (config.get("query") instanceof Map<?, ?> sp) {

Copilot · 2025-08-26T22:29:33Z

src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java

+		Object patchBody = config.get("patch");
+		if (patchBody == null) {
+			throw new IllegalArgumentException("Missing 'patch' for patch interaction");


The code looks for 'patch' key but the PATCH_FHIR_RESOURCE_SCHEMA and CONDITIONAL_PATCH_FHIR_RESOURCE_SCHEMA define the parameter as 'resource'. This will cause patch operations to fail.

Suggested change

Object patchBody = config.get("patch");

if (patchBody == null) {

throw new IllegalArgumentException("Missing 'patch' for patch interaction");

Object patchBody = config.get("resource");

if (patchBody == null) {

throw new IllegalArgumentException("Missing 'resource' for patch interaction");

Copilot · 2025-08-26T22:29:33Z

src/main/java/ca/uhn/fhir/jpa/starter/mcp/ToolFactory.java

+				"description": "Additional data to prefetch for the CDS service call."
+			}
+		},
+		"required": ["service", "hook", "hookInstance", "context"]


The required field lists 'context' but the property is actually named 'hookContext' in the schema above. This will cause validation failures for CDS Hook calls.

Suggested change

"required": ["service", "hook", "hookInstance", "context"]

"required": ["service", "hook", "hookInstance", "hookContext"]

Copilot · 2025-08-26T22:29:33Z

src/main/java/ca/uhn/fhir/rest/server/McpCdsBridge.java

+		var hookContext = (Map<String, String>) contextMap.get("hookContext");
+		if (hookContext.containsKey("userId")) {
+			context.put("userId", hookContext.get("userId").toString());
+		}
+		if (hookContext.containsKey("patientId")) {
+			context.put("patientId", hookContext.get("patientId").toString());
+		}
+		if (hookContext.containsKey("encounterId")) {
+			context.put("encounterId", hookContext.get("encounterId").toString());
+		}


Unsafe cast to Map<String, String> without type checking. If hookContext contains non-String values, this will throw a ClassCastException at runtime.

Suggested change

var hookContext = (Map<String, String>) contextMap.get("hookContext");

if (hookContext.containsKey("userId")) {

context.put("userId", hookContext.get("userId").toString());

}

if (hookContext.containsKey("patientId")) {

context.put("patientId", hookContext.get("patientId").toString());

}

if (hookContext.containsKey("encounterId")) {

context.put("encounterId", hookContext.get("encounterId").toString());

}

var hookContextObj = contextMap.get("hookContext");

if (hookContextObj instanceof Map<?, ?> hookContext) {

if (hookContext.containsKey("userId")) {

var userId = hookContext.get("userId");

if (userId != null) {

context.put("userId", userId.toString());

}

}

if (hookContext.containsKey("patientId")) {

var patientId = hookContext.get("patientId");

if (patientId != null) {

context.put("patientId", patientId.toString());

}

}

if (hookContext.containsKey("encounterId")) {

var encounterId = hookContext.get("encounterId");

if (encounterId != null) {

context.put("encounterId", encounterId.toString());

}

}

}

Copilot · 2025-08-26T22:29:34Z

src/main/java/ca/uhn/fhir/rest/server/McpCdsBridge.java

+			// TODO Return MCP Error
+			logger.error(e.getMessage(), e);
+			e.printStackTrace();


The printStackTrace() call is redundant since the exception is already being logged. Remove this line to avoid duplicate stack traces in logs.

Suggested change

// TODO Return MCP Error

logger.error(e.getMessage(), e);

e.printStackTrace();

Copilot · 2025-08-26T22:29:34Z

src/main/java/ca/uhn/fhir/jpa/starter/mcp/RequestBuilder.java

+				if (config.get("searchParams") instanceof Map<?, ?> sp) {
+					sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));


The code should handle the case where the 'query' parameter (as defined in the schema) needs to be parsed into individual search parameters. Currently it expects a Map but the schema defines it as a comma-separated string.

Suggested change

if (config.get("searchParams") instanceof Map<?, ?> sp) {

sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));

Object searchParamsObj = config.get("searchParams");

if (searchParamsObj instanceof Map<?, ?> sp) {

sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));

} else if (searchParamsObj instanceof String spStr && !spStr.isBlank()) {

// Parse comma-separated string, e.g. "name=John,age=30"

String[] pairs = spStr.split(",");

for (String pair : pairs) {

String[] kv = pair.split("=", 2);

if (kv.length == 2) {

req.addParameter(kv[0].trim(), kv[1].trim());

}

}

robogary · 2025-08-27T09:09:40Z

Formatting check succeeded!

robogary · 2025-08-27T09:16:07Z

Formatting check succeeded!

robogary · 2025-08-27T09:38:51Z

Formatting check succeeded!

robogary · 2025-08-29T10:14:26Z

Formatting check succeeded!

jkiddo and others added 16 commits August 4, 2025 11:26

Added MCP support using SSE on http://localhost:8080/sse

ceb788d

Reverted change that IntelliJ complains about

1cffe6f

Pre-rework

2a37f2e

Cleaned up the code a fair bit

5dcbfdb

Renamed

56f9b8f

Renamed

70c07c2

Running spotless

4fbab92

Reuse FhirContext in result serialization to make MCP server work wit…

a930457

…h R5

Merge pull request #4 from adamzkover/feature/mcp

1059bbf

Reuse FhirContext in result serialization

Added support for transactions

1bb3e53

Merge branch 'feature/mcp' of github.com:jkiddo/hapi-fhir-jpaserver-s…

37a5a72

…tarter into feature/mcp

PoC tool for CDS Hooks

785b0a4

Merge pull request #5 from adamzkover/feature/mcp

c672b79

PoC tool for CDS Hooks

some cleanup

0f96854

Upgrade of model protocol

758e395

Added comments

8eff66e

jkiddo added 2 commits August 24, 2025 17:08

Removed field injection ... CDS to be changed to AutoConfig eventually

bd2abc3

Merge branch 'master' into feature/mcp

56ba7e3

# Conflicts: # src/main/resources/application.yaml

jkiddo requested a review from Copilot August 24, 2025 15:57

Copilot AI reviewed Aug 24, 2025

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jkiddo requested a review from Copilot August 24, 2025 18:34

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Adjusted to new builder pattern

269c50c

jkiddo requested a review from Copilot August 24, 2025 19:23

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Update src/main/java/ca/uhn/fhir/rest/server/MCPBridge.java

b63b1ae

Co-authored-by: Copilot <[email protected]>

A bit of restructuring

6f66ecf

Merge branch 'hapifhir:master' into feature/mcp

1d851e9

More rework

3b7eb46

jkiddo requested a review from Copilot August 26, 2025 21:32

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jkiddo requested a review from Copilot August 26, 2025 22:28

Copilot AI reviewed Aug 26, 2025

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Merge branch 'hapifhir:master' into feature/mcp

7246f29

Removing (suspected unnecessary) formatting

154d01c

Add more example doc

dfc1b99

Merge branch 'hapifhir:master' into feature/mcp

8d7b35d

	// TODO Return MCP Error
	logger.error(e.getMessage(), e);
	e.printStackTrace();

	if (config.get("searchParams") instanceof Map<?, ?> sp) {
	if (config.get("query") instanceof Map<?, ?> sp) {

	"required": ["service", "hook", "hookInstance", "context"]
	"required": ["service", "hook", "hookInstance", "hookContext"]

-		var hookContext = (Map<String, String>) contextMap.get("hookContext");
-		if (hookContext.containsKey("userId")) {
-			context.put("userId", hookContext.get("userId").toString());
-		}
-		if (hookContext.containsKey("patientId")) {
-			context.put("patientId", hookContext.get("patientId").toString());
-		}
-		if (hookContext.containsKey("encounterId")) {
-			context.put("encounterId", hookContext.get("encounterId").toString());
-		}
+		var hookContextObj = contextMap.get("hookContext");
+		if (hookContextObj instanceof Map<?, ?> hookContext) {
+			if (hookContext.containsKey("userId")) {
+				var userId = hookContext.get("userId");
+				if (userId != null) {
+					context.put("userId", userId.toString());
+				}
+			}
+			if (hookContext.containsKey("patientId")) {
+				var patientId = hookContext.get("patientId");
+				if (patientId != null) {
+					context.put("patientId", patientId.toString());
+				}
+			}
+			if (hookContext.containsKey("encounterId")) {
+				var encounterId = hookContext.get("encounterId");
+				if (encounterId != null) {
+					context.put("encounterId", encounterId.toString());
+				}
+			}
+		}

		if (config.get("searchParams") instanceof Map<?, ?> sp) {
		sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));

-				if (config.get("searchParams") instanceof Map<?, ?> sp) {
-					sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));
+				Object searchParamsObj = config.get("searchParams");
+				if (searchParamsObj instanceof Map<?, ?> sp) {
+					sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));
+				} else if (searchParamsObj instanceof String spStr && !spStr.isBlank()) {
+					// Parse comma-separated string, e.g. "name=John,age=30"
+					String[] pairs = spStr.split(",");
+					for (String pair : pairs) {
+						String[] kv = pair.split("=", 2);
+						if (kv.length == 2) {
+							req.addParameter(kv[0].trim(), kv[1].trim());
+						}
+					}

Feature/mcp #846

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Feature/mcp #846

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