further mcp integration #398

.github/workflows/angular_test.yml

@@ -16,10 +16,10 @@ jobs:
         uses: actions/checkout@v5
 
       - name: Setup Node.js
-        uses: actions/setup-node@v5
+        uses: actions/setup-node@v6
         with:
           # https://github.com/actions/setup-node
-          node-version: 20
+          node-version: 24
           cache: npm
           cache-dependency-path: matchbox-frontend/package-lock.json
 

docs/changelog.md

@@ -1,3 +1,7 @@
+2025/10/21 Release 4.0.14
+
+- Further MCP Server integration [#398](https://github.com/ahdis/matchbox/issues/398)
+
 2025/10/04 Release 4.0.13
 
 - MCP Server integration (#398)

docs/validation-with-ai-tutorial.md

@@ -87,7 +87,7 @@ spring:
         enabled: true
 ```
 
-The MCP-Server can be reached at the endpoint `http://<<your-url>>/matchbox/mcp/sse`
+The MCP-Server can be reached at the endpoint `http://<<your-url>>/matchbox(v3)/mcp/message`
 
 ### Setting up matchbox for Claude Desktop
 
@@ -98,6 +98,20 @@ For Free users connecting to remote servers is currently not officially supporte
 Example Claude Desktop:
 ![Claude Desktop MCP example](assets/claude_desktop_mcp_example.png)
 
+```json
+  {
+      "mcpServers": {
+        "matchbox": {
+          "command": "npx",
+          "args": [
+            "mcp-remote@latest",
+            "http://localhost:8080/matchboxv3/mcp/message"
+          ]
+        }
+      }
+    }
+```
+
 ### Setting up matchbox for VS Code GitHub Copilot
 
 First, make sure the `chat.mcp.enabled` setting in VS Code is enabled.
@@ -112,7 +126,7 @@ Add matchbox as MCP-Server as such:
     "mcp": {
         "servers": {
             "matchbox": {
-                "url": "http://<<your-url>>/matchbox/mcp/sse"
+                "url": "http://<<your-url>>/matchboxv3/mcp/message"
             }
         }
     },

matchbox-engine/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>4.0.13</version>
+        <version>4.0.14</version>
     </parent>
 
     <artifactId>matchbox-engine</artifactId>

matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/MatchboxEngine.java

@@ -889,6 +889,8 @@ public List<ValidationMessage> validate(final @NonNull FhirFormat format,
 		final List<ValidationMessage> messages = new ArrayList<>();
 		final InstanceValidator validator = getValidator(format);
 		validator.validate(null, messages, stream, format, (sd != null) ? new ArrayList<>(List.of(sd)) :  new ArrayList<>());
+			log.info("finished validation " + sd.getUrl() + "|" + sd.getVersion() + " "
+						+ (sd.getDateElement() != null ? "(" + sd.getDateElement().asStringValue() + ")" : ""));
 		return this.filterValidationMessages(messages);
 	}
 

matchbox-frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matchbox",
-  "version": "3.9.13",
+  "version": "3.9.14",
   "license": "MIT",
   "scripts": {
     "ng": "ng",

matchbox-frontend/src/app/home/home.component.html

@@ -24,7 +24,7 @@
   </mat-card-content>
   <mat-card-footer>
     <p>
-      matchbox version: {{ version }} | <a href="https://www.ahdis.ch" rel="external nofollow noopener" target="_blank">
+      Matchbox version: {{ version }} | <a href="https://www.ahdis.ch" rel="external nofollow noopener" target="_blank">
       contact</a>
     </p>
   </mat-card-footer>

matchbox-server/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>matchbox</artifactId>
         <groupId>health.matchbox</groupId>
-        <version>4.0.13</version>
+        <version>4.0.14</version>
     </parent>
 
     <artifactId>matchbox-server</artifactId>

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

@@ -114,6 +114,15 @@ public MockHttpServletRequest buildRequest() {
 				if (profile != null && !profile.isBlank()) {
 					req.addParameter("profile", profile);
 				}
+				Map<?, ?> sp = null;
+				if (config.get("query") instanceof Map<?, ?> q) {
+					sp = q;
+				} else if (config.get("searchParams") instanceof Map<?, ?> s) {
+					sp = s;
+				}
+				if (sp != null) {
+					sp.forEach((k, v) -> req.addParameter(k.toString(), v.toString()));
+				}
 				req.addHeader("Content-Type", "text/plain; charset=UTF-8");
 			}
 			default -> throw new IllegalArgumentException("Unsupported interaction: " + interaction);

matchbox-server/src/main/java/ca/uhn/fhir/rest/server/McpMatchboxBridge.java

@@ -2,7 +2,8 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ch.ahdis.matchbox.mcp.ToolFactory;
-import ca.uhn.fhir.jpa.starter.AppProperties;
+import ch.ahdis.matchbox.util.CrossVersionResourceUtils;
+import ch.ahdis.matchbox.util.http.MatchboxFhirFormat;
 import ca.uhn.fhir.jpa.starter.mcp.CallToolResultFactory;
 import ca.uhn.fhir.jpa.starter.mcp.Interaction;
 import ca.uhn.fhir.jpa.starter.mcp.RequestBuilder;
@@ -11,12 +12,16 @@
 import io.modelcontextprotocol.server.McpServerFeatures;
 import io.modelcontextprotocol.spec.McpSchema;
 
+import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
+import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.Enumerations.OperationParameterUse;
 import org.hl7.fhir.r5.model.OperationDefinition;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.mock.web.MockHttpServletResponse;
 import org.springframework.stereotype.Component;
 
+import java.io.StringWriter;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -46,6 +51,10 @@ public List<McpServerFeatures.SyncToolSpecification> generateTools() {
 					new McpServerFeatures.SyncToolSpecification.Builder()
 							.tool(ToolFactory.listFhirProfilesToValidateFor())
 							.callHandler((exchange, request) -> getFhirProfilesToValidateFor(request, Interaction.READ))
+					 		.build(),
+					new McpServerFeatures.SyncToolSpecification.Builder()
+							.tool(ToolFactory.listValidationParameters())
+							.callHandler((exchange, request) -> getExtraValidationParameters(request, Interaction.READ))
 					 		.build()
 							);
 		} catch (JsonProcessingException e) {
@@ -97,6 +106,52 @@ private McpSchema.CallToolResult getFhirProfilesToValidateFor(McpSchema.CallTool
 		}
 	}
 
+	private McpSchema.CallToolResult getExtraValidationParameters(McpSchema.CallToolRequest contextMap, Interaction interaction) {
+		var response = new MockHttpServletResponse();
+		contextMap.arguments().put("resourceType", "OperationDefinition");
+		contextMap.arguments().put("id", "-s-validate");
+		var request = new RequestBuilder(restfulServer, contextMap.arguments(), interaction).buildRequest();
+		try {
+			restfulServer.handleRequest(interaction.asRequestType(), request, response);
+			var status = response.getStatus();
+			var body = response.getContentAsString();
+
+			if (status >= 200 && status < 300) {
+				if (body.isBlank()) {
+					return CallToolResultFactory.failure("Empty successful response for " + interaction);
+				}
+
+				FhirContext fhirR5Context = FhirContext.forR5Cached();
+				OperationDefinition operationDefinition = fhirR5Context.newJsonParser().parseResource(OperationDefinition.class, body);
+				List<OperationDefinitionParameterComponent> parameters = operationDefinition.getParameter().stream()
+					.filter(p -> OperationParameterUse.IN.equals(p.getUse()))
+					.filter(p -> !"resource".equals(p.getName()))
+					.filter(p -> !"profile".equals(p.getName()))
+					.map(p -> {
+						p.setUse(null);
+						return p;
+					}).toList();
+
+
+				StringWriter result = new StringWriter();
+				result.append("[ ");
+				for (int i = 0; i < parameters.size(); i++) {
+					CrossVersionResourceUtils.serializeR5(parameters.get(i), MatchboxFhirFormat.JSON, result);
+					result.append(",");
+				}
+				result.append("]");
+
+				String json = result.toString();
+		        return CallToolResultFactory.successFhirBody(json);
+			} else {
+				return CallToolResultFactory.failure(String.format("FHIR server error %d: %s", status, body));
+			}
+		} catch (Exception e) {
+			logger.error(e.getMessage(), e);
+			return CallToolResultFactory.failure("Unexpected error: " + e.getMessage());
+		}
+	}
+
 	private McpSchema.CallToolResult getFhirImplementationGuides(McpSchema.CallToolRequest contextMap, Interaction interaction) {
 		var response = new MockHttpServletResponse();
 		contextMap.arguments().put("resourceType", "ImplementationGuide");
@@ -135,12 +190,25 @@ private McpSchema.CallToolResult getFhirImplementationGuides(McpSchema.CallToolR
 	private McpSchema.CallToolResult getValidationResult(McpSchema.CallToolRequest contextMap, Interaction interaction) {
 
 		var response = new MockHttpServletResponse();
-		var request = new RequestBuilder(restfulServer, contextMap.arguments(), interaction).buildRequest();
+		if (contextMap.arguments().containsKey("validationparams")) {
+			Map<String, Object> map = new java.util.HashMap<>();
+			String validationParams = (String) contextMap.arguments().get("validationparams");
+			// Parse the validationParams string into a Map
+			String[] params = validationParams.split(",");
+			for (String param : params) {
+				String[] keyValue = param.split("=");
+				if (keyValue.length == 2) {
+					map.put(keyValue[0].trim(), keyValue[1].trim());
+				}
+			}
+			contextMap.arguments().put("query", map);
+		} else {
+			Map<String, Object> map = new java.util.HashMap<>();
+			map.put("analyzeOutcomeWithAI", "false");
+			contextMap.arguments().put("query", map);
+		}
 
-		Map<String, Object> map = new java.util.HashMap<>();
-		// we do not want to use AI for validation, this can do mcp client itself
-		map.put("analyzeOutcomeWithAI", "false");
-		contextMap.arguments().put("query", map);
+		var request = new RequestBuilder(restfulServer, contextMap.arguments(), interaction).buildRequest();
 
 		try {
 			restfulServer.handleRequest(interaction.asRequestType(), request, response);

matchbox-server/src/main/java/ch/ahdis/matchbox/mcp/ToolFactory.java

@@ -21,6 +21,10 @@ public class ToolFactory {
 			"profile": {
 			"type": "string",
 			"description": "The FHIR profile to validate against"
+			},
+			"validationparams": {
+			"type": "string",
+			"description": "Additional validation parameters separated by \\",\\". For example: \\"txServer=http://tx.fhir.org,txUseEcosystem=false\\"."
 			}
 		},
 		"required": ["resource", "profile"]
@@ -35,9 +39,9 @@ public class ToolFactory {
 			"includeVersions": {
 				"type": "boolean",
 				"description": "include older versions of the installed FHIR Implementation Guides, defaults to false"
+				}
 			}
 		}
-		}
 		""";
 
 	private static final String LIST_PROFILES_SCHEMA =
@@ -57,6 +61,15 @@ public class ToolFactory {
 	}
 		""";
 
+	private static final String LIST_VALIDATIONPARAMETERS_SCHEMA =
+		"""
+		{
+		"type": "object",
+		"properties": {
+			}
+		}
+		""";
+
 	private static final String LIST_FHIR_IGS_OUTPUT_SCHEMA =
 		"""
 	{
@@ -123,6 +136,16 @@ public static Tool listFhirProfilesToValidateFor() throws JsonProcessingExceptio
 				.build();
 	}
 
+	public static Tool listValidationParameters() throws JsonProcessingException {
+		return new Tool.Builder()
+				.name("list-validation-parameters")
+				.description("List additional available parameters for validation")
+				.inputSchema(mapper.readValue(LIST_VALIDATIONPARAMETERS_SCHEMA, McpSchema.JsonSchema.class))
+//				.outputSchema(LIST_FHIR_IGS_OUTPUT_SCHEMA)
+				.build();
+	}
+
+
 	public static final ObjectMapper mapper = new ObjectMapper()
 			.enable(JsonParser.Feature.ALLOW_COMMENTS)
 			.enable(JsonParser.Feature.ALLOW_SINGLE_QUOTES)

matchbox-server/src/main/java/ch/ahdis/matchbox/util/CrossVersionResourceUtils.java

@@ -8,6 +8,7 @@
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.instance.model.api.IBase;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
@@ -67,6 +68,14 @@ public static void serializeR5(final Resource resource,
 		parser.encodeResourceToWriter(resource, writer);
 	}
 
+	public static void serializeR5(final IBase theElement,
+											 final MatchboxFhirFormat format,
+											 final Writer writer) throws IOException {
+		final var parser = getHapiParser(format, FhirVersionEnum.R5);
+		parser.setPrettyPrint(true);
+		writer.append(parser.encodeToString(theElement));
+	}
+
 	public static org.hl7.fhir.r4.model.Resource convertResource(final org.hl7.fhir.r4b.model.Resource resource) {
 		// Is there a better way of doing this?
 		return VersionConvertorFactory_40_50.convertResource(VersionConvertorFactory_43_50.convertResource(resource));