generic merge draft

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/JpaR4Config.java

@@ -20,6 +20,10 @@
 package ca.uhn.fhir.jpa.config.r4;
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
+import ca.uhn.fhir.batch2.jobs.merge.ExtensionBasedLinkService;
+import ca.uhn.fhir.batch2.jobs.merge.MergeResourceHelper;
+import ca.uhn.fhir.batch2.jobs.merge.PatientNativeLinkService;
+import ca.uhn.fhir.batch2.jobs.merge.ResourceLinkServiceFactory;
 import ca.uhn.fhir.batch2.util.Batch2TaskHelper;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.support.IValidationSupport;
@@ -28,6 +32,7 @@
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
+import ca.uhn.fhir.jpa.api.svc.IMergeOperationProviderSvc;
 import ca.uhn.fhir.jpa.config.GeneratedDaoAndResourceProviderConfigR4;
 import ca.uhn.fhir.jpa.config.JpaConfig;
 import ca.uhn.fhir.jpa.dao.ITransactionProcessorVersionAdapter;
@@ -38,6 +43,7 @@
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.jpa.provider.IReplaceReferencesSvc;
 import ca.uhn.fhir.jpa.provider.JpaSystemProvider;
+import ca.uhn.fhir.jpa.provider.merge.MergeOperationProviderSvc;
 import ca.uhn.fhir.jpa.provider.merge.MergeValidationService;
 import ca.uhn.fhir.jpa.provider.merge.PatientMergeProvider;
 import ca.uhn.fhir.jpa.provider.merge.ResourceMergeService;
@@ -112,15 +118,42 @@ public ITermLoaderSvc termLoaderService(
 	}
 
 	@Bean
-	public MergeValidationService mergeValidationService(FhirContext theFhirContext, DaoRegistry theDaoRegistry) {
-		return new MergeValidationService(theFhirContext, theDaoRegistry);
+	public MergeValidationService mergeValidationService(
+			FhirContext theFhirContext,
+			DaoRegistry theDaoRegistry,
+			ResourceLinkServiceFactory theResourceLinkServiceFactory) {
+		return new MergeValidationService(theFhirContext, theDaoRegistry, theResourceLinkServiceFactory);
 	}
 
 	@Bean
 	public MergeProvenanceSvc mergeProvenanceSvc(DaoRegistry theDaoRegistry) {
 		return new MergeProvenanceSvc(theDaoRegistry);
 	}
 
+	@Bean
+	public PatientNativeLinkService patientNativeLinkService() {
+		return new PatientNativeLinkService();
+	}
+
+	@Bean
+	public ExtensionBasedLinkService extensionBasedLinkService() {
+		return new ExtensionBasedLinkService();
+	}
+
+	@Bean
+	public ResourceLinkServiceFactory resourceLinkServiceFactory(
+			PatientNativeLinkService thePatientService, ExtensionBasedLinkService theExtensionService) {
+		return new ResourceLinkServiceFactory(thePatientService, theExtensionService);
+	}
+
+	@Bean
+	public MergeResourceHelper mergeResourceHelper(
+			DaoRegistry theDaoRegistry,
+			MergeProvenanceSvc theMergeProvenanceSvc,
+			ResourceLinkServiceFactory theResourceLinkServiceFactory) {
+		return new MergeResourceHelper(theDaoRegistry, theMergeProvenanceSvc, theResourceLinkServiceFactory);
+	}
+
 	@Bean
 	public ResourceMergeService resourceMergeService(
 			DaoRegistry theDaoRegistry,
@@ -131,7 +164,8 @@ public ResourceMergeService resourceMergeService(
 			Batch2TaskHelper theBatch2TaskHelper,
 			JpaStorageSettings theStorageSettings,
 			MergeValidationService theMergeValidationService,
-			MergeProvenanceSvc theMergeProvenanceSvc) {
+			MergeProvenanceSvc theMergeProvenanceSvc,
+			MergeResourceHelper theMergeResourceHelper) {
 
 		return new ResourceMergeService(
 				theStorageSettings,
@@ -142,7 +176,8 @@ public ResourceMergeService resourceMergeService(
 				theJobCoordinator,
 				theBatch2TaskHelper,
 				theMergeValidationService,
-				theMergeProvenanceSvc);
+				theMergeProvenanceSvc,
+				theMergeResourceHelper);
 	}
 
 	@Bean
@@ -160,19 +195,25 @@ public ResourceUndoMergeService resourceUndoMergeService(
 				theRequestPartitionHelperSvc);
 	}
 
+	@Bean
+	public IMergeOperationProviderSvc mergeOperationProviderSvc(
+			FhirContext theFhirContext,
+			ResourceMergeService theResourceMergeService,
+			IInterceptorBroadcaster theInterceptorBroadcaster,
+			JpaStorageSettings theStorageSettings) {
+
+		return new MergeOperationProviderSvc(
+				theFhirContext, theResourceMergeService, theInterceptorBroadcaster, theStorageSettings);
+	}
+
 	@Bean
 	public PatientMergeProvider patientMergeProvider(
 			FhirContext theFhirContext,
 			DaoRegistry theDaoRegistry,
-			ResourceMergeService theResourceMergeService,
-			ResourceUndoMergeService theResourceUndoMergeService,
-			IInterceptorBroadcaster theInterceptorBroadcaster) {
+			IMergeOperationProviderSvc theMergeOperationProviderSvc,
+			ResourceUndoMergeService theResourceUndoMergeService) {
 
 		return new PatientMergeProvider(
-				theFhirContext,
-				theDaoRegistry,
-				theResourceMergeService,
-				theResourceUndoMergeService,
-				theInterceptorBroadcaster);
+				theFhirContext, theDaoRegistry, theMergeOperationProviderSvc, theResourceUndoMergeService);
 	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/merge/MergeOperationInputParameters.java

@@ -26,8 +26,10 @@
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
 import ca.uhn.fhir.model.api.IProvenanceAgent;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseReference;
 import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.hl7.fhir.r4.model.Patient;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
 
 import java.util.List;
 
@@ -98,9 +100,10 @@ public void setOriginalInputParameters(IBaseResource theOriginalInputParameters)
 	public MergeJobParameters asMergeJobParameters(
 			FhirContext theFhirContext,
 			JpaStorageSettings theStorageSettings,
-			Patient theSourceResource,
-			Patient theTargetResource,
-			RequestPartitionId thePartitionId) {
+			IBaseResource theSourceResource,
+			IBaseResource theTargetResource,
+			RequestPartitionId thePartitionId,
+			String theOperationName) {
 		MergeJobParameters retval = new MergeJobParameters();
 		retval.setOriginalInputParameters(
 				theFhirContext.newJsonParser().encodeResourceToString(myOriginalInputParameters));
@@ -110,6 +113,57 @@ public MergeJobParameters asMergeJobParameters(
 		retval.setPartitionId(thePartitionId);
 		retval.setProvenanceAgents(ProvenanceAgentJson.from(myProvenanceAgents, theFhirContext));
 		retval.setCreateProvenance(myCreateProvenance);
+		retval.setOperationName(theOperationName);
 		return retval;
 	}
+
+	/**
+	 * Static factory method to create MergeOperationInputParameters from operation parameters.
+	 * Version-agnostic - uses IBase for identifiers to support all FHIR versions.
+	 *
+	 * @param theSourceIdentifiers List of source resource identifiers (IBase to support all FHIR versions)
+	 * @param theTargetIdentifiers List of target resource identifiers (IBase to support all FHIR versions)
+	 * @param theSourceResource Reference to the source resource
+	 * @param theTargetResource Reference to the target resource
+	 * @param thePreview Preview mode flag
+	 * @param theDeleteSource Delete source flag
+	 * @param theResultResource Result resource template
+	 * @param theResourceLimit Resource processing limit
+	 * @param theProvenanceAgents Provenance agents for tracking
+	 * @param theOriginalInputParameters Original input parameters for audit trail
+	 * @return Populated MergeOperationInputParameters object
+	 */
+	public static MergeOperationInputParameters from(
+			List<IBase> theSourceIdentifiers,
+			List<IBase> theTargetIdentifiers,
+			IBaseReference theSourceResource,
+			IBaseReference theTargetResource,
+			IPrimitiveType<Boolean> thePreview,
+			IPrimitiveType<Boolean> theDeleteSource,
+			IBaseResource theResultResource,
+			int theResourceLimit,
+			List<IProvenanceAgent> theProvenanceAgents,
+			IBaseResource theOriginalInputParameters) {
+
+		MergeOperationInputParameters parameters = new MergeOperationInputParameters(theResourceLimit);
+
+		// Set common parameters (identifiers and resource references)
+		MergeOperationsCommonInputParameters.setParameters(
+				parameters, theSourceIdentifiers, theTargetIdentifiers, theSourceResource, theTargetResource);
+
+		// Set merge-specific parameters
+		parameters.setPreview(thePreview != null && thePreview.getValue());
+		parameters.setDeleteSource(theDeleteSource != null && theDeleteSource.getValue());
+
+		if (theResultResource != null) {
+			// Pass in a copy of the result resource as we don't want it to be modified.
+			// It will be returned back to the client as part of the response.
+			parameters.setResultResource(theResultResource);
+		}
+
+		parameters.setProvenanceAgents(theProvenanceAgents);
+		parameters.setOriginalInputParameters(theOriginalInputParameters);
+
+		return parameters;
+	}
 }

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/merge/MergeOperationProviderSvc.java

@@ -0,0 +1,164 @@
+// Created by claude-sonnet-4-5
+/*-
+ * #%L
+ * HAPI FHIR JPA Server
+ * %%
+ * Copyright (C) 2014 - 2025 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.fhir.jpa.provider.merge;
+
+import ca.uhn.fhir.batch2.jobs.merge.MergeResourceHelper;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster;
+import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
+import ca.uhn.fhir.jpa.api.svc.IMergeOperationProviderSvc;
+import ca.uhn.fhir.jpa.interceptor.ProvenanceAgentsPointcutUtil;
+import ca.uhn.fhir.model.api.IProvenanceAgent;
+import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
+import ca.uhn.fhir.util.FhirTerser;
+import ca.uhn.fhir.util.ParametersUtil;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
+import org.hl7.fhir.instance.model.api.IBase;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.instance.model.api.IBaseReference;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.instance.model.api.IPrimitiveType;
+
+import java.util.List;
+
+import static ca.uhn.fhir.jpa.provider.BaseJpaProvider.endRequest;
+import static ca.uhn.fhir.jpa.provider.BaseJpaProvider.startRequest;
+import static ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_MERGE_OUTPUT_PARAM_RESULT;
+
+/**
+ * Service that handles the common logic for merge operations across different resource types.
+ * This service extracts the shared merge operation logic that was previously duplicated
+ * in resource-specific providers.
+ */
+public class MergeOperationProviderSvc implements IMergeOperationProviderSvc {
+
+	private final FhirContext myFhirContext;
+	private final ResourceMergeService myResourceMergeService;
+	private final IInterceptorBroadcaster myInterceptorBroadcaster;
+	private final JpaStorageSettings myStorageSettings;
+
+	public MergeOperationProviderSvc(
+			FhirContext theFhirContext,
+			ResourceMergeService theResourceMergeService,
+			IInterceptorBroadcaster theInterceptorBroadcaster,
+			JpaStorageSettings theStorageSettings) {
+		myFhirContext = theFhirContext;
+		myResourceMergeService = theResourceMergeService;
+		myInterceptorBroadcaster = theInterceptorBroadcaster;
+		myStorageSettings = theStorageSettings;
+	}
+
+	/**
+	 * Executes a merge operation for any resource type.
+	 *
+	 * @param theSourceIdentifiers Source resource identifiers
+	 * @param theTargetIdentifiers Target resource identifiers
+	 * @param theSourceReference   Source resource reference
+	 * @param theTargetReference   Target resource reference
+	 * @param thePreview           Preview mode flag
+	 * @param theDeleteSource      Delete source flag
+	 * @param theResultResource    Optional result resource provided by client
+	 * @param theResourceLimit     Optional batch size limit
+	 * @param theRequestDetails    Servlet request details containing HTTP request/response and context
+	 * @return Parameters resource containing merge operation results
+	 */
+	@Override
+	public IBaseParameters merge(
+			List<IBase> theSourceIdentifiers,
+			List<IBase> theTargetIdentifiers,
+			IBaseReference theSourceReference,
+			IBaseReference theTargetReference,
+			IPrimitiveType<Boolean> thePreview,
+			IPrimitiveType<Boolean> theDeleteSource,
+			IBaseResource theResultResource,
+			IPrimitiveType<Integer> theResourceLimit,
+			ServletRequestDetails theRequestDetails) {
+
+		HttpServletRequest servletRequest = theRequestDetails.getServletRequest();
+		HttpServletResponse servletResponse = theRequestDetails.getServletResponse();
+
+		startRequest(servletRequest);
+		try {
+			int resourceLimit = MergeResourceHelper.setResourceLimitFromParameter(myStorageSettings, theResourceLimit);
+
+			List<IProvenanceAgent> provenanceAgents =
+					ProvenanceAgentsPointcutUtil.ifHasCallHooks(theRequestDetails, myInterceptorBroadcaster);
+
+			FhirTerser terser = myFhirContext.newTerser();
+			IBaseResource resultResourceCopy = theResultResource != null ? terser.clone(theResultResource) : null;
+			IBaseResource originalParametersCopy = terser.clone(theRequestDetails.getResource());
+
+			MergeOperationInputParameters mergeOperationParameters = MergeOperationInputParameters.from(
+					theSourceIdentifiers,
+					theTargetIdentifiers,
+					theSourceReference,
+					theTargetReference,
+					thePreview,
+					theDeleteSource,
+					resultResourceCopy,
+					resourceLimit,
+					provenanceAgents,
+					originalParametersCopy);
+
+			MergeOperationOutcome mergeOutcome =
+					myResourceMergeService.merge(mergeOperationParameters, theRequestDetails);
+			servletResponse.setStatus(mergeOutcome.getHttpStatusCode());
+			return buildMergeOperationOutputParameters(mergeOutcome, theRequestDetails.getResource());
+		} finally {
+			endRequest(servletRequest);
+		}
+	}
+
+	private IBaseParameters buildMergeOperationOutputParameters(
+			MergeOperationOutcome theMergeOutcome, IBaseResource theInputParameters) {
+
+		IBaseParameters retVal = ParametersUtil.newInstance(myFhirContext);
+		ParametersUtil.addParameterToParameters(
+				myFhirContext,
+				retVal,
+				ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_MERGE_OUTPUT_PARAM_INPUT,
+				theInputParameters);
+
+		ParametersUtil.addParameterToParameters(
+				myFhirContext,
+				retVal,
+				ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_MERGE_OUTPUT_PARAM_OUTCOME,
+				theMergeOutcome.getOperationOutcome());
+
+		if (theMergeOutcome.getUpdatedTargetResource() != null) {
+			ParametersUtil.addParameterToParameters(
+					myFhirContext,
+					retVal,
+					OPERATION_MERGE_OUTPUT_PARAM_RESULT,
+					theMergeOutcome.getUpdatedTargetResource());
+		}
+
+		if (theMergeOutcome.getTask() != null) {
+			ParametersUtil.addParameterToParameters(
+					myFhirContext,
+					retVal,
+					ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_MERGE_OUTPUT_PARAM_TASK,
+					theMergeOutcome.getTask());
+		}
+		return retVal;
+	}
+}