Implement CDS on FHIR in CDS Hooks

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/5238-add-cds-on-fhir.yaml

@@ -0,0 +1,6 @@
+---
+type: add
+issue: 5238
+title: "Added an implementation of Clinical Reasoning CDS on FHIR to the CDS Hooks module that allows PlanDefinition
+worfklows to be processed as CDS Services using the $apply operation.
+"

hapi-fhir-server-cds-hooks/pom.xml

@@ -33,6 +33,11 @@
 			<artifactId>hapi-fhir-storage</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-storage-cr</artifactId>
+			<version>${project.version}</version>
+		</dependency>
 
 		<dependency>
 			<groupId>org.springframework</groupId>

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/ICdsConfigService.java

@@ -20,8 +20,14 @@
 package ca.uhn.hapi.fhir.cdshooks.api;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.cr.common.IRepositoryFactory;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
+import ca.uhn.fhir.rest.api.server.SystemRestfulResponse;
+import ca.uhn.fhir.rest.server.RestfulServer;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.opencds.cqf.fhir.utility.Ids;
 
 import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
@@ -37,4 +43,22 @@ public interface ICdsConfigService {
 	default DaoRegistry getDaoRegistry() {
 		return null;
 	}
+
+	@Nullable
+	default IRepositoryFactory getRepositoryFactory() {
+		return null;
+	}
+
+	@Nullable
+	default RestfulServer getRestfulServer() {
+		return null;
+	}
+
+	default RequestDetails createRequestDetails(FhirContext theFhirContext, String theId, String theResourceType) {
+		SystemRequestDetails rd = new SystemRequestDetails();
+		rd.setServer(getRestfulServer());
+		rd.setResponse(new SystemRestfulResponse(rd));
+		rd.setId(Ids.newId(theFhirContext.getVersion().getVersion(), theResourceType, theId));
+		return rd;
+	}
 }

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/api/ICdsServiceRegistry.java

@@ -72,6 +72,14 @@ void registerService(
 			boolean theAllowAutoFhirClientPrefetch,
 			String theModuleId);
 
+	/**
+	 * Register a new Clinical Reasoning CDS Service with the endpoint.
+	 *
+	 * @param theServiceId the id of the service PlanDefinition
+	 * @return the service was registered
+	 */
+	boolean registerCrService(String theServiceId);
+
 	/**
 	 * Remove registered CDS service with the service ID, only removes dynamically registered service
 	 *

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/config/CdsHooksConfig.java

@@ -20,20 +20,35 @@
 package ca.uhn.hapi.fhir.cdshooks.config;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.cr.common.IRepositoryFactory;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.jpa.cache.IResourceChangeListenerRegistry;
 import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
+import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsHooksDaoAuthorizationSvc;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceRegistry;
 import ca.uhn.hapi.fhir.cdshooks.module.CdsHooksObjectMapperFactory;
 import ca.uhn.hapi.fhir.cdshooks.svc.CdsConfigServiceImpl;
 import ca.uhn.hapi.fhir.cdshooks.svc.CdsHooksContextBooter;
 import ca.uhn.hapi.fhir.cdshooks.svc.CdsServiceRegistryImpl;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceDstu3;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR4;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrServiceR5;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsServiceInterceptor;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceFactory;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceDstu3;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR4;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.CrDiscoveryServiceR5;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICrDiscoveryServiceFactory;
 import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchDaoSvc;
 import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchFhirClientSvc;
 import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsPrefetchSvc;
 import ca.uhn.hapi.fhir.cdshooks.svc.prefetch.CdsResolutionStrategySvc;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.opencds.cqf.fhir.api.Repository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.context.annotation.Bean;
@@ -44,12 +59,23 @@ public class CdsHooksConfig {
 
 	public static final String CDS_HOOKS_OBJECT_MAPPER_FACTORY = "cdsHooksObjectMapperFactory";
 
+	public static final String PLAN_DEFINITION_RESOURCE_NAME = "PlanDefinition";
+
 	@Autowired(required = false)
 	private DaoRegistry myDaoRegistry;
 
 	@Autowired(required = false)
 	private MatchUrlService myMatchUrlService;
 
+	@Autowired(required = false)
+	private IResourceChangeListenerRegistry myResourceChangeListenerRegistry;
+
+	@Autowired(required = false)
+	private IRepositoryFactory myRepositoryFactory;
+
+	@Autowired(required = false)
+	private RestfulServer myRestfulServer;
+
 	@Bean(name = CDS_HOOKS_OBJECT_MAPPER_FACTORY)
 	public ObjectMapper objectMapper(FhirContext theFhirContext) {
 		return new CdsHooksObjectMapperFactory(theFhirContext).newMapper();
@@ -59,14 +85,78 @@ public ObjectMapper objectMapper(FhirContext theFhirContext) {
 	public ICdsServiceRegistry cdsServiceRegistry(
 			CdsHooksContextBooter theCdsHooksContextBooter,
 			CdsPrefetchSvc theCdsPrefetchSvc,
-			@Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY) ObjectMapper theObjectMapper) {
-		return new CdsServiceRegistryImpl(theCdsHooksContextBooter, theCdsPrefetchSvc, theObjectMapper);
+			@Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY) ObjectMapper theObjectMapper,
+			ICdsCrServiceFactory theCdsCrServiceFactory,
+			ICrDiscoveryServiceFactory theCrDiscoveryServiceFactory) {
+		return new CdsServiceRegistryImpl(
+				theCdsHooksContextBooter,
+				theCdsPrefetchSvc,
+				theObjectMapper,
+				theCdsCrServiceFactory,
+				theCrDiscoveryServiceFactory);
+	}
+
+	@Bean
+	public ICdsCrServiceFactory cdsCrServiceFactory(FhirContext theFhirContext, ICdsConfigService theCdsConfigService) {
+		return id -> {
+			if (myRepositoryFactory == null) {
+				return null;
+			}
+			RequestDetails rd =
+					theCdsConfigService.createRequestDetails(theFhirContext, id, PLAN_DEFINITION_RESOURCE_NAME);
+			Repository repository = myRepositoryFactory.create(rd);
+			switch (theFhirContext.getVersion().getVersion()) {
+				case DSTU3:
+					return new CdsCrServiceDstu3(rd, repository);
+				case R4:
+					return new CdsCrServiceR4(rd, repository);
+				case R5:
+					return new CdsCrServiceR5(rd, repository);
+				default:
+					return null;
+			}
+		};
+	}
+
+	@Bean
+	public ICrDiscoveryServiceFactory crDiscoveryServiceFactory(
+			FhirContext theFhirContext, ICdsConfigService theCdsConfigService) {
+		return id -> {
+			if (myRepositoryFactory == null) {
+				return null;
+			}
+			RequestDetails rd =
+					theCdsConfigService.createRequestDetails(theFhirContext, id, PLAN_DEFINITION_RESOURCE_NAME);
+			Repository repository = myRepositoryFactory.create(rd);
+			switch (theFhirContext.getVersion().getVersion()) {
+				case DSTU3:
+					return new CrDiscoveryServiceDstu3(rd.getId(), repository);
+				case R4:
+					return new CrDiscoveryServiceR4(rd.getId(), repository);
+				case R5:
+					return new CrDiscoveryServiceR5(rd.getId(), repository);
+				default:
+					return null;
+			}
+		};
+	}
+
+	@Bean
+	public CdsServiceInterceptor cdsServiceInterceptor() {
+		if (myResourceChangeListenerRegistry == null) {
+			return null;
+		}
+		CdsServiceInterceptor listener = new CdsServiceInterceptor();
+		myResourceChangeListenerRegistry.registerResourceResourceChangeListener(
+				PLAN_DEFINITION_RESOURCE_NAME, SearchParameterMap.newSynchronous(), listener, 1000);
+		return listener;
 	}
 
 	@Bean
 	public ICdsConfigService cdsConfigService(
 			FhirContext theFhirContext, @Qualifier(CDS_HOOKS_OBJECT_MAPPER_FACTORY) ObjectMapper theObjectMapper) {
-		return new CdsConfigServiceImpl(theFhirContext, theObjectMapper, myDaoRegistry);
+		return new CdsConfigServiceImpl(
+				theFhirContext, theObjectMapper, myDaoRegistry, myRepositoryFactory, myRestfulServer);
 	}
 
 	@Bean

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/svc/BaseCdsCrMethod.java

@@ -0,0 +1,47 @@
+/*-
+ * #%L
+ * HAPI FHIR - CDS Hooks
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a 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.
+ * #L%
+ */
+package ca.uhn.hapi.fhir.cdshooks.svc;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.i18n.Msg;
+import ca.uhn.fhir.model.api.IModelJson;
+import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsMethod;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceFactory;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+abstract class BaseCdsCrMethod implements ICdsMethod {
+	private ICdsCrServiceFactory myCdsCrServiceFactory;
+
+	public BaseCdsCrMethod(ICdsCrServiceFactory theCdsCrServiceFactory) {
+		myCdsCrServiceFactory = theCdsCrServiceFactory;
+	}
+
+	public Object invoke(ObjectMapper theObjectMapper, IModelJson theJson, String theServiceId) {
+		try {
+			return myCdsCrServiceFactory.create(theServiceId).invoke(theJson);
+		} catch (Exception e) {
+			if (e.getCause() != null && e.getCause() instanceof BaseServerResponseException) {
+				throw (BaseServerResponseException) e.getCause();
+			}
+			throw new ConfigurationException(Msg.code(2434) + "Failed to invoke $apply on " + theServiceId, e);
+		}
+	}
+}

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsConfigServiceImpl.java

@@ -20,7 +20,9 @@
 package ca.uhn.hapi.fhir.cdshooks.svc;
 
 import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.cr.common.IRepositoryFactory;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
+import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.hapi.fhir.cdshooks.api.ICdsConfigService;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -31,14 +33,20 @@ public class CdsConfigServiceImpl implements ICdsConfigService {
 	private final FhirContext myFhirContext;
 	private final ObjectMapper myObjectMapper;
 	private final DaoRegistry myDaoRegistry;
+	private final IRepositoryFactory myRepositoryFactory;
+	private final RestfulServer myRestfulServer;
 
 	public CdsConfigServiceImpl(
 			@Nonnull FhirContext theFhirContext,
 			@Nonnull ObjectMapper theObjectMapper,
-			@Nullable DaoRegistry theDaoRegistry) {
+			@Nullable DaoRegistry theDaoRegistry,
+			@Nullable IRepositoryFactory theRepositoryFactory,
+			@Nullable RestfulServer theRestfulServer) {
 		myFhirContext = theFhirContext;
 		myObjectMapper = theObjectMapper;
 		myDaoRegistry = theDaoRegistry;
+		myRepositoryFactory = theRepositoryFactory;
+		myRestfulServer = theRestfulServer;
 	}
 
 	@Nonnull
@@ -58,4 +66,16 @@ public ObjectMapper getObjectMapper() {
 	public DaoRegistry getDaoRegistry() {
 		return myDaoRegistry;
 	}
+
+	@Nullable
+	@Override
+	public IRepositoryFactory getRepositoryFactory() {
+		return myRepositoryFactory;
+	}
+
+	@Nullable
+	@Override
+	public RestfulServer getRestfulServer() {
+		return myRestfulServer;
+	}
 }

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsCrServiceMethod.java

@@ -0,0 +1,45 @@
+/*-
+ * #%L
+ * HAPI FHIR - CDS Hooks
+ * %%
+ * Copyright (C) 2014 - 2023 Smile CDR, Inc.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a 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.
+ * #L%
+ */
+package ca.uhn.hapi.fhir.cdshooks.svc;
+
+import ca.uhn.hapi.fhir.cdshooks.api.ICdsServiceMethod;
+import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceJson;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceFactory;
+
+public class CdsCrServiceMethod extends BaseCdsCrMethod implements ICdsServiceMethod {
+	private final CdsServiceJson myCdsServiceJson;
+
+	public CdsCrServiceMethod(CdsServiceJson theCdsServiceJson, ICdsCrServiceFactory theCdsCrServiceFactory) {
+		super(theCdsCrServiceFactory);
+		myCdsServiceJson = theCdsServiceJson;
+	}
+
+	@Override
+	public CdsServiceJson getCdsServiceJson() {
+		return myCdsServiceJson;
+	}
+
+	@Override
+	public boolean isAllowAutoFhirClientPrefetch() {
+		// The $apply operation will make FHIR requests for any data it needs
+		// directly against the fhirServer of the ServiceRequest.
+		return false;
+	}
+}

hapi-fhir-server-cds-hooks/src/main/java/ca/uhn/hapi/fhir/cdshooks/svc/CdsServiceCache.java

@@ -25,6 +25,8 @@
 import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceRequestJson;
 import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServiceResponseJson;
 import ca.uhn.hapi.fhir.cdshooks.api.json.CdsServicesJson;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.ICdsCrServiceFactory;
+import ca.uhn.hapi.fhir.cdshooks.svc.cr.discovery.ICrDiscoveryServiceFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -33,6 +35,8 @@
 import java.util.Map;
 import java.util.function.Function;
 
+import static ca.uhn.hapi.fhir.cdshooks.svc.cr.CdsCrConstants.CDS_CR_MODULE_ID;
+
 public class CdsServiceCache {
 	static final Logger ourLog = LoggerFactory.getLogger(CdsServiceCache.class);
 	final Map<String, ICdsMethod> myServiceMap = new LinkedHashMap<>();
@@ -66,6 +70,23 @@ public void registerDynamicService(
 		}
 	}
 
+	public void registerCrService(
+			String theServiceId,
+			ICrDiscoveryServiceFactory theDiscoveryServiceFactory,
+			ICdsCrServiceFactory theCrServiceFactory) {
+		if (!isCdsServiceAlreadyRegistered(theServiceId, CDS_CR_MODULE_ID)) {
+			CdsServiceJson cdsServiceJson =
+					theDiscoveryServiceFactory.create(theServiceId).resolveService();
+			if (cdsServiceJson != null) {
+				final CdsCrServiceMethod cdsCrServiceMethod =
+						new CdsCrServiceMethod(cdsServiceJson, theCrServiceFactory);
+				myServiceMap.put(theServiceId, cdsCrServiceMethod);
+				myCdsServiceJson.addService(cdsServiceJson);
+				ourLog.info("Created service for {}", theServiceId);
+			}
+		}
+	}
+
 	public void registerFeedback(String theServiceId, Object theServiceBean, Method theMethod) {
 		final CdsFeedbackMethod cdsFeedbackMethod = new CdsFeedbackMethod(theServiceBean, theMethod);
 		myFeedbackMap.put(theServiceId, cdsFeedbackMethod);