Update to 6.9.8

pom.xml

@@ -14,7 +14,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>hapi-fhir</artifactId>
-            <version>6.9.7-SNAPSHOT</version>
+            <version>6.9.8-SNAPSHOT</version>
     </parent>
 
     <artifactId>hapi-fhir-jpaserver-starter</artifactId>
@@ -132,6 +132,12 @@
             <artifactId>hapi-fhir-jpaserver-mdm</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <!-- This dependency includes the CDS Hooks Server -->
+        <dependency>
+          <groupId>ca.uhn.hapi.fhir</groupId>
+          <artifactId>hapi-fhir-server-cds-hooks</artifactId>
+          <version>${project.version}</version>
+        </dependency>
         <!-- This dependency includes the OpenAPI Server -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>

src/main/java/ca/uhn/fhir/jpa/starter/Application.java

@@ -1,8 +1,12 @@
 package ca.uhn.fhir.jpa.starter;
 
 import ca.uhn.fhir.batch2.jobs.config.Batch2JobsConfig;
+import ca.uhn.fhir.cr.common.IRepositoryFactory;
+import ca.uhn.fhir.cr.repo.HapiFhirRepository;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.batch2.JpaBatch2Config;
 import ca.uhn.fhir.jpa.starter.annotations.OnEitherVersion;
+import ca.uhn.fhir.jpa.starter.cdshooks.StarterCdsHooksConfig;
 import ca.uhn.fhir.jpa.starter.common.FhirTesterConfig;
 import ca.uhn.fhir.jpa.starter.cr.StarterCrDstu3Config;
 import ca.uhn.fhir.jpa.starter.cr.StarterCrR4Config;
@@ -33,6 +37,7 @@ import org.springframework.web.servlet.DispatcherServlet;
 @Import({
 		StarterCrR4Config.class,
 		StarterCrDstu3Config.class,
+		StarterCdsHooksConfig.class,
 		SubscriptionSubmitterConfig.class,
 		SubscriptionProcessorConfig.class,
 		SubscriptionChannelConfig.class,
@@ -90,4 +95,9 @@ public class Application extends SpringBootServletInitializer {
 		return registrationBean;
 
 	}
+
+	@Bean
+	IRepositoryFactory repositoryFactory(DaoRegistry theDaoRegistry, RestfulServer theRestfulServer) {
+		return rd -> new HapiFhirRepository(theDaoRegistry, rd, theRestfulServer);
+	}
 }

src/main/java/ca/uhn/fhir/jpa/starter/cr/CrR4Config.java

@@ -0,0 +1,182 @@
+package ca.uhn.fhir.jpa.starter.cr;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.cr.common.IRepositoryFactory;
+import ca.uhn.fhir.cr.config.ProviderLoader;
+import ca.uhn.fhir.cr.config.ProviderSelector;
+import ca.uhn.fhir.cr.r4.IActivityDefinitionProcessorFactory;
+import ca.uhn.fhir.cr.r4.ICareGapsServiceFactory;
+import ca.uhn.fhir.cr.r4.ICqlExecutionServiceFactory;
+import ca.uhn.fhir.cr.r4.IMeasureServiceFactory;
+import ca.uhn.fhir.cr.r4.IPlanDefinitionProcessorFactory;
+import ca.uhn.fhir.cr.r4.IQuestionnaireProcessorFactory;
+import ca.uhn.fhir.cr.r4.IQuestionnaireResponseProcessorFactory;
+import ca.uhn.fhir.cr.r4.ISubmitDataProcessorFactory;
+import ca.uhn.fhir.cr.r4.activitydefinition.ActivityDefinitionApplyProvider;
+import ca.uhn.fhir.cr.r4.cqlexecution.CqlExecutionOperationProvider;
+import ca.uhn.fhir.cr.r4.measure.CareGapsOperationProvider;
+import ca.uhn.fhir.cr.r4.measure.MeasureOperationsProvider;
+import ca.uhn.fhir.cr.r4.measure.MeasureService;
+import ca.uhn.fhir.cr.r4.measure.SubmitDataProvider;
+import ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionApplyProvider;
+import ca.uhn.fhir.cr.r4.plandefinition.PlanDefinitionPackageProvider;
+import ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePackageProvider;
+import ca.uhn.fhir.cr.r4.questionnaire.QuestionnairePopulateProvider;
+import ca.uhn.fhir.cr.r4.questionnaireresponse.QuestionnaireResponseExtractProvider;
+import ca.uhn.fhir.rest.server.RestfulServer;
+import org.opencds.cqf.fhir.cql.EvaluationSettings;
+import org.opencds.cqf.fhir.cr.activitydefinition.r4.ActivityDefinitionProcessor;
+import org.opencds.cqf.fhir.cr.cql.r4.R4CqlExecutionService;
+import org.opencds.cqf.fhir.cr.measure.CareGapsProperties;
+import org.opencds.cqf.fhir.cr.measure.MeasureEvaluationOptions;
+import org.opencds.cqf.fhir.cr.measure.r4.R4CareGapsService;
+import org.opencds.cqf.fhir.cr.measure.r4.R4SubmitDataService;
+import org.opencds.cqf.fhir.cr.plandefinition.r4.PlanDefinitionProcessor;
+import org.opencds.cqf.fhir.cr.questionnaire.r4.QuestionnaireProcessor;
+import org.opencds.cqf.fhir.cr.questionnaireresponse.r4.QuestionnaireResponseProcessor;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+import java.util.Arrays;
+import java.util.Map;
+import java.util.concurrent.Executor;
+
+@Configuration
+public class CrR4Config {
+
+	@Bean
+	IMeasureServiceFactory r4MeasureServiceFactory(
+			IRepositoryFactory theRepositoryFactory, MeasureEvaluationOptions theEvaluationOptions) {
+		return rd -> new MeasureService(theRepositoryFactory.create(rd), theEvaluationOptions);
+	}
+
+	@Bean
+	ISubmitDataProcessorFactory r4SubmitDataProcessorFactory(IRepositoryFactory theRepositoryFactory) {
+		return rd -> new R4SubmitDataService(theRepositoryFactory.create(rd));
+	}
+
+	@Bean
+	ICqlExecutionServiceFactory r4CqlExecutionServiceFactory(
+			IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
+		return rd -> new R4CqlExecutionService(theRepositoryFactory.create(rd), theEvaluationSettings);
+	}
+
+	@Bean
+	CqlExecutionOperationProvider r4CqlExecutionOperationProvider() {
+		return new CqlExecutionOperationProvider();
+	}
+
+	@Bean
+	ICareGapsServiceFactory careGapsServiceFactory(
+			IRepositoryFactory theRepositoryFactory,
+			CareGapsProperties theCareGapsProperties,
+			MeasureEvaluationOptions theMeasureEvaluationOptions,
+			@Qualifier("cqlExecutor") Executor theExecutor) {
+		return rd -> new R4CareGapsService(
+				theCareGapsProperties,
+				theRepositoryFactory.create(rd),
+				theMeasureEvaluationOptions,
+				theExecutor,
+				rd.getFhirServerBase());
+	}
+
+	@Bean
+	CareGapsOperationProvider r4CareGapsOperationProvider() {
+		return new CareGapsOperationProvider();
+	}
+
+	@Bean
+	SubmitDataProvider r4SubmitDataProvider() {
+		return new SubmitDataProvider();
+	}
+
+	@Bean
+	MeasureOperationsProvider r4MeasureOperationsProvider() {
+		return new MeasureOperationsProvider();
+	}
+
+	@Bean
+	IActivityDefinitionProcessorFactory r4ActivityDefinitionProcessorFactory(
+			IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
+		return rd -> new ActivityDefinitionProcessor(
+				theRepositoryFactory.create(rd), theEvaluationSettings);
+	}
+
+	@Bean
+	IPlanDefinitionProcessorFactory r4PlanDefinitionProcessorFactory(
+			IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
+		return rd -> new PlanDefinitionProcessor(
+				theRepositoryFactory.create(rd), theEvaluationSettings);
+	}
+
+	@Bean
+	IQuestionnaireProcessorFactory r4QuestionnaireProcessorFactory(
+			IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
+		return rd -> new QuestionnaireProcessor(
+				theRepositoryFactory.create(rd), theEvaluationSettings);
+	}
+
+	@Bean
+	IQuestionnaireResponseProcessorFactory r4QuestionnaireResponseProcessorFactory(
+			IRepositoryFactory theRepositoryFactory, EvaluationSettings theEvaluationSettings) {
+		return rd -> new QuestionnaireResponseProcessor(
+				theRepositoryFactory.create(rd), theEvaluationSettings);
+	}
+
+	@Bean
+	ActivityDefinitionApplyProvider r4ActivityDefinitionApplyProvider() {
+		return new ActivityDefinitionApplyProvider();
+	}
+
+	@Bean
+	PlanDefinitionApplyProvider r4PlanDefinitionApplyProvider() {
+		return new PlanDefinitionApplyProvider();
+	}
+
+	@Bean
+	QuestionnaireResponseExtractProvider
+			r4QuestionnaireResponseExtractProvider() {
+		return new QuestionnaireResponseExtractProvider();
+	}
+
+	@Bean
+	PlanDefinitionPackageProvider r4PlanDefinitionPackageProvider() {
+		return new PlanDefinitionPackageProvider();
+	}
+
+	@Bean
+	QuestionnairePackageProvider r4QuestionnairePackageProvider() {
+		return new QuestionnairePackageProvider();
+	}
+
+	@Bean
+	QuestionnairePopulateProvider r4QuestionnairePopulateProvider() {
+		return new QuestionnairePopulateProvider();
+	}
+
+	@Bean
+	public ProviderLoader r4PdLoader(
+			ApplicationContext theApplicationContext, FhirContext theFhirContext, RestfulServer theRestfulServer) {
+
+		var selector = new ProviderSelector(
+				theFhirContext,
+				Map.of(
+						FhirVersionEnum.R4,
+						Arrays.asList(
+								MeasureOperationsProvider.class,
+								SubmitDataProvider.class,
+								CareGapsOperationProvider.class,
+								CqlExecutionOperationProvider.class,
+								ActivityDefinitionApplyProvider.class,
+								PlanDefinitionApplyProvider.class,
+								QuestionnaireResponseExtractProvider.class,
+								QuestionnairePackageProvider.class,
+								PlanDefinitionPackageProvider.class,
+								QuestionnairePopulateProvider.class)));
+
+		return new ProviderLoader(theRestfulServer, theApplicationContext, selector);
+	}
+}

src/main/java/ca/uhn/fhir/jpa/starter/cr/StarterCrR4Config.java

@@ -1,18 +1,13 @@
 package ca.uhn.fhir.jpa.starter.cr;
 
 
-import ca.uhn.fhir.cr.config.r4.ApplyOperationConfig;
+import ca.uhn.fhir.cr.repo.HapiFhirRepository;
-import ca.uhn.fhir.cr.config.r4.CrR4Config;
-import ca.uhn.fhir.cr.config.r4.ExtractOperationConfig;
-import ca.uhn.fhir.cr.config.r4.PackageOperationConfig;
-import ca.uhn.fhir.cr.config.r4.PopulateOperationConfig;
 import ca.uhn.fhir.jpa.starter.annotations.OnR4Condition;
 import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.provider.ResourceProviderFactory;
-import org.springframework.context.annotation.Conditional;
-import org.springframework.context.annotation.Import;
-
 import ca.uhn.fhir.cr.common.CqlThreadFactory;
+import ca.uhn.fhir.cr.common.IRepositoryFactory;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.starter.AppProperties;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
@@ -38,11 +33,7 @@ import java.util.concurrent.Executors;
 
 @Configuration
 @Conditional({ OnR4Condition.class, CrConfigCondition.class })
-@Import({ CrR4Config.class,
+@Import(CrR4Config.class)
-	ApplyOperationConfig.class,
-	ExtractOperationConfig.class,
-	PackageOperationConfig.class,
-	PopulateOperationConfig.class})
 public class StarterCrR4Config {
 	private static final Logger ourLogger = LoggerFactory.getLogger(StarterCrR4Config.class);
 
@@ -57,6 +48,7 @@ public class StarterCrR4Config {
 
 		return executor;
 	}
+
 	@Bean
 	CareGapsProperties careGapsProperties(AppProperties theAppProperties)  {
 		var careGapsProperties = new CareGapsProperties();
@@ -75,6 +67,7 @@ public class StarterCrR4Config {
 		}
 		return measureEvalOptions;
 	}
+
 	@Bean
 	public EvaluationSettings evaluationSettings(
 		AppProperties theAppProperties,