Feature/cds config (#857)

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

* Reverted change that IntelliJ complains about

* Pre-rework

* Cleaned up the code a fair bit

* Renamed

* Renamed

* Running spotless

* Reuse FhirContext in result serialization to make MCP server work with R5

* Added support for transactions

* PoC tool for CDS Hooks

* some cleanup

* Upgrade of model protocol

* Added comments

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

* Adjusted to new builder pattern

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

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

* A bit of restructuring

* More rework

* Removing (suspected unnecessary) formatting

* Add more example doc

* Added a smoke- / passthrough-test

* Applied spotless

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

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

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

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

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

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

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

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

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

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

* Formatting

* Added some documentation

* spotless cares about MD?

* Reverting back to default values

* minor refinements

* Fixed CDS hooks configuration

* Fixed some wirings

* Readded missing elements

* getting closer to get test running again ...

* applying review

* Readded exclude

* Bumped spring-ai deps

* added agents file

* Updated according to review

---------

Co-authored-by: Ádám Z. Kövér <[email protected]>
Co-authored-by: Copilot <[email protected]>

Author: 3 people

AGENTS.md

@@ -0,0 +1,38 @@
+# Repository Guidelines
+
+## Project Structure & Module Organization
+- `src/main/java`: Spring Boot entry point `ca.uhn.fhir.jpa.starter.Application`, resource providers, config.
+- `src/main/resources`: Application YAML, search parameter bundles, capability statements packaged with the WAR.
+- `src/main/webapp`: HAPI Testpage overlay shipped for the default UI.
+- `src/test/java` & `src/test/resources`: JUnit 5 suites (interceptors, MCP, MDM) plus matching fixtures grouped by FHIR version.
+- `charts/`, `docker-compose.yml`, `configs/`: Deployment templates for Helm, Docker, and Tomcat/server overrides.
+- `Dockerfile`, `build-docker-image.sh`: Reference container build scripts used by CI/CD.
+
+## Build, Test, and Development Commands
+- `mvn clean install`: Compile, run Surefire + Failsafe, and emit `target/ROOT.war`.
+- `mvn spring-boot:run -Pboot`: Start the server on port 8080 with hot reload-friendly Boot profile.
+- `mvn clean package spring-boot:repackage -Pboot && java -jar target/ROOT.war`: Build and exercise the bootable WAR.
+- `docker-compose up -d --build`: Launch JPAServer + PostgreSQL using the local Dockerfile.
+- `docker run -p 8080:8080 hapiproject/hapi:latest`: Compare against the upstream binary distribution.
+
+## Coding Style & Naming Conventions
+- Target Java 17, four-space indents, alphabetized imports, no wildcards.
+- Keep code under `ca.uhn.fhir.jpa.starter` and mirror packages in tests.
+- Prefer descriptive class suffixes (`*Provider`, `*Service`, `*Config`) and constructor injection with `final` collaborators.
+- YAML keys stay kebab-case; JSON fixtures use lower_snake_case filenames.
+
+## Testing Guidelines
+- `mvn test`: Runs JUnit Jupiter unit suites such as `CustomBeanTest` and `ParallelUpdatesVersionConflictTest`.
+- `mvn verify`: Adds integration coverage through Failsafe with the default H2 datasource; if you pivot to PostgreSQL, run `mvn install -DskipTests` until fixtures are updated.
+- Store integration suites as `*IT.java` so Failsafe detects them and colocate datasets in `src/test/resources`.
+- Leverage Testcontainers and HAPI FHIR test utilities already declared in `pom.xml`.
+
+## Commit & Pull Request Guidelines
+- Follow repository precedent: imperative summary, optional scope (`Feature/mcp`), and linked issue `(#123)` when applicable.
+- Keep commits narrowly scoped and include config or fixture updates with the code they support.
+- PRs should describe runtime impact (profiles, ports, env vars), reference issues, and include UI screenshots when behaviour changes.
+- Run `mvn verify` or the relevant Docker workflow before review; note any skipped checks and how to reproduce the result.
+
+## Security & Configuration Tips
+- Do not commit secrets; stash overrides under `configs/` and explain required env vars in the PR.
+- When enabling external services, update `src/main/resources/application.yaml` plus sample overrides and mention connection expectations for reviewers.

pom.xml

@@ -391,20 +391,14 @@
         <dependency>
             <groupId>org.springframework.ai</groupId>
             <artifactId>spring-ai-mcp</artifactId>
-            <version>1.1.0-M1</version>
+            <version>1.1.0-M2</version>
         </dependency>
 
         <!--implementation("org.springframework.ai:spring-ai-starter-mcp-server-webmvc:1.1.0-M1")-->
         <dependency>
             <groupId>org.springframework.ai</groupId>
             <artifactId>spring-ai-starter-mcp-server</artifactId>
-            <version>1.1.0-M1</version>
-        </dependency>
-
-        <dependency>
-            <groupId>io.modelcontextprotocol.sdk</groupId>
-            <artifactId>mcp</artifactId>
-            <version>0.12.1</version>
+            <version>1.1.0-M2</version>
         </dependency>
 
         <dependency>

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksProperties.java

@@ -1,7 +1,9 @@
 package ca.uhn.fhir.jpa.starter.cdshooks;
 
 import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
 
+@Configuration
 @ConfigurationProperties(prefix = "hapi.fhir.cdshooks")
 public class CdsHooksProperties {
 

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/CdsHooksServlet.java

@@ -2,7 +2,6 @@
 
 import ca.uhn.fhir.jpa.starter.AppProperties;
 import ca.uhn.fhir.rest.api.server.cdshooks.CdsServiceRequestJson;
-import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
 import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
@@ -43,9 +42,6 @@ public class CdsHooksServlet extends HttpServlet {
 	@Autowired
 	ICdsServiceRegistry cdsServiceRegistry;
 
-	@Autowired
-	RestfulServer restfulServer;
-
 	@Autowired
 	@Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY)
 	ObjectMapper objectMapper;

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/ProviderConfiguration.java

@@ -1,6 +1,6 @@
 package ca.uhn.fhir.jpa.starter.cdshooks;
 
-import ca.uhn.fhir.jpa.starter.cr.CrProperties;
+import ca.uhn.fhir.jpa.starter.cr.CqlRuntimeProperties;
 
 public class ProviderConfiguration {
 	private final String clientIdHeaderName;
@@ -11,8 +11,8 @@ public ProviderConfiguration(boolean cqlLoggingEnabled, String clientIdHeaderNam
 		this.clientIdHeaderName = clientIdHeaderName;
 	}
 
-	public ProviderConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
-		this(crProperties.getCql().getRuntime().isDebugLoggingEnabled(), cdsProperties.getClientIdHeaderName());
+	public ProviderConfiguration(CdsHooksProperties cdsProperties, CqlRuntimeProperties cqlRuntimeProperties) {
+		this(cqlRuntimeProperties.isDebugLoggingEnabled(), cdsProperties.getClientIdHeaderName());
 	}
 
 	public String getClientIdHeaderName() {

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/StarterCdsHooksConfig.java

@@ -1,20 +1,13 @@
 package ca.uhn.fhir.jpa.starter.cdshooks;
 
-import ca.uhn.fhir.context.FhirVersionEnum;
-import ca.uhn.fhir.jpa.starter.cr.CrCommonConfig;
-import ca.uhn.fhir.jpa.starter.cr.CrConfigCondition;
-import ca.uhn.fhir.jpa.starter.cr.CrProperties;
+import ca.uhn.fhir.jpa.starter.cr.*;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
+import ca.uhn.hapi.fhir.cdshooks.config.CdsHooksConfig;
 import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrServiceRegistry;
 import org.opencds.cqf.fhir.cr.hapi.cdshooks.CdsCrSettings;
-import org.opencds.cqf.fhir.cr.hapi.cdshooks.ICdsCrServiceRegistry;
-import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.CdsCrDiscoveryServiceRegistry;
-import org.opencds.cqf.fhir.cr.hapi.cdshooks.discovery.ICdsCrDiscoveryServiceRegistry;
 import org.opencds.cqf.fhir.cr.hapi.config.CrCdsHooksConfig;
 import org.opencds.cqf.fhir.cr.hapi.config.RepositoryConfig;
-import org.opencds.cqf.fhir.cr.hapi.config.test.TestCdsHooksConfig;
 import org.springframework.beans.factory.config.AutowireCapableBeanFactory;
 import org.springframework.boot.web.servlet.ServletRegistrationBean;
 import org.springframework.context.annotation.Bean;
@@ -24,30 +17,9 @@
 
 @Configuration
 @Conditional({CdsHooksConfigCondition.class, CrConfigCondition.class})
-@Import({RepositoryConfig.class, TestCdsHooksConfig.class, CrCdsHooksConfig.class, CrCommonConfig.class})
+@Import({RepositoryConfig.class, CrCdsHooksConfig.class, CrCommonConfig.class, CdsHooksConfig.class})
 public class StarterCdsHooksConfig {
 
-	@Bean
-	public ICdsCrDiscoveryServiceRegistry cdsCrDiscoveryServiceRegistry() {
-		CdsCrDiscoveryServiceRegistry registry = new CdsCrDiscoveryServiceRegistry();
-		registry.unregister(FhirVersionEnum.R4);
-		registry.register(FhirVersionEnum.R4, UpdatedCrDiscoveryService.class);
-		return registry;
-	}
-
-	@Bean
-	public ICdsCrServiceRegistry cdsCrServiceRegistry() {
-		CdsCrServiceRegistry registry = new CdsCrServiceRegistry();
-		registry.unregister(FhirVersionEnum.R4);
-		registry.register(FhirVersionEnum.R4, UpdatedCdsCrService.class);
-		return registry;
-	}
-
-	@Bean
-	public CdsHooksProperties cdsHooksProperties() {
-		return new CdsHooksProperties();
-	}
-
 	@Bean
 	public CdsCrSettings cdsCrSettings(CdsHooksProperties cdsHooksProperties) {
 		CdsCrSettings settings = CdsCrSettings.getDefault();
@@ -67,8 +39,9 @@ public void authorizePreShow(IBaseResource theResource) {}
 	}
 
 	@Bean
-	public ProviderConfiguration providerConfiguration(CdsHooksProperties cdsProperties, CrProperties crProperties) {
-		return new ProviderConfiguration(cdsProperties, crProperties);
+	public ProviderConfiguration providerConfiguration(
+			CdsHooksProperties cdsProperties, CqlProperties cqlProperties, CqlRuntimeProperties cqlRuntimeProperties) {
+		return new ProviderConfiguration(cdsProperties, cqlRuntimeProperties);
 	}
 
 	@Bean

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCdsCrService.java

@@ -1,5 +1,10 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+@ConfigurationProperties(prefix = "hapi.fhir.cr.caregaps")
 public class CareGapsProperties {
 	private String reporter = "default";
 	private String section_author = "default";

src/main/java/ca/uhn/fhir/jpa/starter/cdshooks/UpdatedCrDiscoveryService.java

@@ -3,7 +3,11 @@
 import org.cqframework.cql.cql2elm.CqlCompilerException;
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.LibraryBuilder;
+import org.springframework.boot.context.properties.ConfigurationProperties;
+import org.springframework.context.annotation.Configuration;
 
+@Configuration
+@ConfigurationProperties(prefix = "hapi.fhir.cr.cql.compiler")
 public class CqlCompilerProperties {
 	private Boolean validate_units = true;
 	private Boolean verify_only = false;