added provenance to replace-references and added provenance tests for…

… merge as well

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

@@ -191,7 +191,7 @@ public IBaseParameters replaceReferences(
 			RequestPartitionId partitionId = myRequestPartitionHelperSvc.determineReadPartitionForRequest(
 					theServletRequest, ReadPartitionIdRequestDetails.forRead(targetId));
 			ReplaceReferencesRequest replaceReferencesRequest =
-					new ReplaceReferencesRequest(sourceId, targetId, resourceLimit, partitionId);
+					new ReplaceReferencesRequest(sourceId, targetId, resourceLimit, partitionId, true);
 			IBaseParameters retval =
 					getReplaceReferencesSvc().replaceReferences(replaceReferencesRequest, theServletRequest);
 			if (ParametersUtil.getNamedParameter(getContext(), retval, OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_TASK)

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

@@ -21,6 +21,7 @@
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.jobs.replacereferences.ReplaceReferencesJobParameters;
+import ca.uhn.fhir.batch2.jobs.replacereferences.ReplaceReferencesProvenanceSvc;
 import ca.uhn.fhir.batch2.util.Batch2TaskHelper;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
@@ -42,6 +43,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.Date;
+import java.util.List;
 import java.util.stream.Stream;
 
 import static ca.uhn.fhir.batch2.jobs.replacereferences.ReplaceReferencesAppCtx.JOB_REPLACE_REFERENCES;
@@ -58,6 +61,7 @@ public class ReplaceReferencesSvcImpl implements IReplaceReferencesSvc {
 	private final ReplaceReferencesPatchBundleSvc myReplaceReferencesPatchBundleSvc;
 	private final Batch2TaskHelper myBatch2TaskHelper;
 	private final JpaStorageSettings myStorageSettings;
+	private final ReplaceReferencesProvenanceSvc myReplaceReferencesProvenanceSvc;
 
 	public ReplaceReferencesSvcImpl(
 			DaoRegistry theDaoRegistry,
@@ -74,6 +78,7 @@ public ReplaceReferencesSvcImpl(
 		myReplaceReferencesPatchBundleSvc = theReplaceReferencesPatchBundleSvc;
 		myBatch2TaskHelper = theBatch2TaskHelper;
 		myStorageSettings = theStorageSettings;
+		myReplaceReferencesProvenanceSvc = new ReplaceReferencesProvenanceSvc(theDaoRegistry);
 	}
 
 	@Override
@@ -123,6 +128,7 @@ private IBaseParameters replaceReferencesPreferAsync(
 	private IBaseParameters replaceReferencesPreferSync(
 			ReplaceReferencesRequest theReplaceReferencesRequest, RequestDetails theRequestDetails) {
 
+		Date startTime = new Date();
 		// TODO KHS get partition from request
 		StopLimitAccumulator<IdDt> accumulator = myHapiTransactionService
 				.withRequest(theRequestDetails)
@@ -139,6 +145,15 @@ private IBaseParameters replaceReferencesPreferSync(
 		Bundle result = myReplaceReferencesPatchBundleSvc.patchReferencingResources(
 				theReplaceReferencesRequest, accumulator.getItemList(), theRequestDetails);
 
+		if (theReplaceReferencesRequest.createProvenance) {
+			myReplaceReferencesProvenanceSvc.createProvenance(
+					theReplaceReferencesRequest.targetId,
+					theReplaceReferencesRequest.sourceId,
+					List.of(result),
+					startTime,
+					theRequestDetails);
+		}
+
 		Parameters retval = new Parameters();
 		retval.addParameter()
 				.setName(OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_OUTCOME)

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

@@ -21,6 +21,7 @@
 
 import ca.uhn.fhir.batch2.api.IJobCoordinator;
 import ca.uhn.fhir.batch2.jobs.merge.MergeJobParameters;
+import ca.uhn.fhir.batch2.jobs.merge.MergeProvenanceSvc;
 import ca.uhn.fhir.batch2.jobs.merge.MergeResourceHelper;
 import ca.uhn.fhir.batch2.util.Batch2TaskHelper;
 import ca.uhn.fhir.context.FhirContext;
@@ -36,20 +37,24 @@
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
 import ca.uhn.fhir.util.OperationOutcomeUtil;
+import ca.uhn.fhir.util.ParametersUtil;
 import org.hl7.fhir.instance.model.api.IBase;
 import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
+import org.hl7.fhir.instance.model.api.IBaseParameters;
+import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Patient;
-import org.hl7.fhir.r4.model.Provenance;
 import org.hl7.fhir.r4.model.Task;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import java.util.Date;
+import java.util.List;
 
 import static ca.uhn.fhir.batch2.jobs.merge.MergeAppCtx.JOB_MERGE;
 import static ca.uhn.fhir.rest.api.Constants.STATUS_HTTP_200_OK;
 import static ca.uhn.fhir.rest.api.Constants.STATUS_HTTP_202_ACCEPTED;
 import static ca.uhn.fhir.rest.api.Constants.STATUS_HTTP_500_INTERNAL_ERROR;
+import static ca.uhn.fhir.rest.server.provider.ProviderConstants.OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_OUTCOME;
 
 /**
  * Service for the FHIR $merge operation. Currently only supports Patient/$merge. The plan is to expand to other resource types.
@@ -68,6 +73,7 @@ public class ResourceMergeService {
 	private final MergeResourceHelper myMergeResourceHelper;
 	private final Batch2TaskHelper myBatch2TaskHelper;
 	private final MergeValidationService myMergeValidationService;
+	private final MergeProvenanceSvc myMergeProvenanceSvc;
 
 	public ResourceMergeService(
 			JpaStorageSettings theStorageSettings,
@@ -87,8 +93,8 @@ public ResourceMergeService(
 		myBatch2TaskHelper = theBatch2TaskHelper;
 		myFhirContext = myPatientDao.getContext();
 		myHapiTransactionService = theHapiTransactionService;
-		IFhirResourceDao<Provenance> provenanceDao = theDaoRegistry.getResourceDao(Provenance.class);
-		myMergeResourceHelper = new MergeResourceHelper(myPatientDao, provenanceDao);
+		myMergeProvenanceSvc = new MergeProvenanceSvc(theDaoRegistry);
+		myMergeResourceHelper = new MergeResourceHelper(theDaoRegistry, myMergeProvenanceSvc);
 		myMergeValidationService = new MergeValidationService(myFhirContext, theDaoRegistry);
 	}
 
@@ -224,18 +230,28 @@ private void doMergeSync(
 				theSourceResource.getIdElement(),
 				theTargetResource.getIdElement(),
 				theMergeOperationParameters.getResourceLimit(),
-				partitionId);
+				partitionId,
+				// don't create provenance as part of replace-references,
+				// we create it after updating source and target for merge
+				false);
 
-		myReplaceReferencesSvc.replaceReferences(replaceReferencesRequest, theRequestDetails);
+		IBaseParameters outParams =
+				myReplaceReferencesSvc.replaceReferences(replaceReferencesRequest, theRequestDetails);
 
-		Patient updatedTarget = myMergeResourceHelper.updateMergedResourcesAfterReferencesReplaced(
+		Bundle patchResultBundle = (Bundle) ParametersUtil.getNamedParameterResource(
+						myFhirContext, outParams, OPERATION_REPLACE_REFERENCES_OUTPUT_PARAM_OUTCOME)
+				.orElseThrow();
+
+		Patient updatedTarget = myMergeResourceHelper.updateMergedResourcesAndCreateProvenance(
 				myHapiTransactionService,
 				theSourceResource,
 				theTargetResource,
+				List.of(patchResultBundle),
 				(Patient) theMergeOperationParameters.getResultResource(),
 				theMergeOperationParameters.getDeleteSource(),
 				theRequestDetails,
 				startTime);
+
 		theMergeOutcome.setUpdatedTargetResource(updatedTarget);
 
 		String detailsText = "Merge operation completed successfully.";

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/merge/ResourceMergeServiceTest.java

@@ -23,6 +23,7 @@
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.util.CanonicalIdentifier;
 import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Identifier;
@@ -1464,9 +1465,14 @@ private void verifyProvenanceCreated(boolean theDeleteSource) {
 
 
 	private void setupReplaceReferencesForSuccessForSync() {
-		// set the count to less that the page size for sync processing
+		Parameters parameters = new Parameters();
+		Parameters.ParametersParameterComponent outcomeParameter = new Parameters.ParametersParameterComponent();
+		outcomeParameter.setName("outcome");
+		outcomeParameter.setResource(new Bundle());
+		parameters.addParameter(outcomeParameter);
+
 		when(myReplaceReferencesSvcMock.replaceReferences(isA(ReplaceReferencesRequest.class),
-			eq(myRequestDetailsMock))).thenReturn(new Parameters());
+			eq(myRequestDetailsMock))).thenReturn(parameters);
 	}
 
 	private void setupBatch2JobTaskHelperMock(Task theTaskToReturn) {

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/PatientMergeR4Test.java

@@ -12,6 +12,7 @@
 import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
 import jakarta.annotation.Nonnull;
 import jakarta.servlet.http.HttpServletResponse;
+import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Encounter;
@@ -32,7 +33,9 @@
 import org.junit.jupiter.params.provider.CsvSource;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.jpa.provider.ReplaceReferencesSvcImpl.RESOURCE_TYPES_SYSTEM;
@@ -143,6 +146,7 @@ public void testMerge(boolean withDelete, boolean withInputResultPatient, boolea
 		List<Identifier> expectedIdentifiersOnTargetAfterMerge =
 			myTestHelper.getExpectedIdentifiersForTargetAfterMerge(withInputResultPatient);
 
+
 		// Assert Task inAsync mode, unless it is preview in which case we don't return a task
 		if (isAsync && !withPreview) {
 			assertThat(getLastHttpStatusCode()).isEqualTo(HttpServletResponse.SC_ACCEPTED);
@@ -246,6 +250,55 @@ void testMerge_smallResourceLimit() {
 			.satisfies(ex -> assertThat(extractFailureMessage((BaseServerResponseException) ex)).isEqualTo("HAPI-2597: Number of resources with references to "+ myTestHelper.getSourcePatientId() + " exceeds the resource-limit 5. Submit the request asynchronsly by adding the HTTP Header 'Prefer: respond-async'."));
 	}
 
+	@ParameterizedTest(name = "{index}: deleteSource={0}, async={1}")
+	@CsvSource({
+		"true, false",
+		"false, false",
+		"true, true",
+		"false, true",
+	})
+	void testMerge_resourcesWithNoReferences(boolean theDeleteSource, boolean theAsync) {
+
+		Patient sourcePatient = new Patient();
+		sourcePatient = (Patient )myPatientDao.create(sourcePatient, mySrd).getResource();
+
+
+		Patient targetPatient = new Patient();
+		targetPatient = (Patient) myPatientDao.create(targetPatient, mySrd).getResource();
+
+		ReplaceReferencesTestHelper.PatientMergeInputParameters inParams = new ReplaceReferencesTestHelper.PatientMergeInputParameters();
+		inParams.sourcePatient = new Reference(sourcePatient.getIdElement().toVersionless());
+		inParams.targetPatient = new Reference(targetPatient.getIdElement().toVersionless());
+		if (theDeleteSource) {
+			inParams.deleteSource = true;
+		}
+
+		Parameters outParams = callMergeOperation(inParams.asParametersResource(), theAsync);
+
+		if (theAsync) {
+			assertThat(getLastHttpStatusCode()).isEqualTo(HttpServletResponse.SC_ACCEPTED);
+			Task task = (Task) outParams.getParameter(OPERATION_MERGE_OUTPUT_PARAM_TASK).getResource();
+			assertNull(task.getIdElement().getVersionIdPart());
+			ourLog.info("Got task {}", task.getId());
+			String jobId = myTestHelper.getJobIdFromTask(task);
+			myBatch2JobHelper.awaitJobCompletion(jobId);
+		}
+
+		IIdType theExpectedTargetIdWithVersion = targetPatient.getIdElement().withVersion("2");
+		if (theDeleteSource) {
+			// when the source resource is being deleted and since there is no identifiers to copy over to the target
+			// in this test, the target is not actually updated, so its version will remain the same
+			theExpectedTargetIdWithVersion = targetPatient.getIdElement().withVersion("1");
+		}
+
+		myTestHelper.assertMergeProvenance(theDeleteSource,
+			sourcePatient.getIdElement().withVersion("2"),
+			theExpectedTargetIdWithVersion,
+			0,
+			Collections.EMPTY_SET);
+	}
+
+
 	@Test
 	void testMerge_SourceResourceCannotBeDeletedBecauseAnotherResourceReferencingSourceWasAddedWhileJobIsRunning_JobFails() {
 		ReplaceReferencesTestHelper.PatientMergeInputParameters inParams = new ReplaceReferencesTestHelper.PatientMergeInputParameters();
@@ -284,7 +337,7 @@ void testMerge_SourceResourceCannotBeDeletedBecauseAnotherResourceReferencingSou
 		assertThat(taskAfterJobFailure.getStatus()).isEqualTo(Task.TaskStatus.FAILED);
 	}
 
-	@ParameterizedTest
+	@ParameterizedTest(name = "{index}: deleteSource={0}, resultPatient={1}, preview={2}")
 	@CsvSource({
 		// withDelete, withInputResultPatient, withPreview
 		"true, true, true",
@@ -305,7 +358,7 @@ public void testMultipleTargetMatchesFails(boolean withDelete, boolean withInput
 	}
 
 
-	@ParameterizedTest
+	@ParameterizedTest(name = "{index}: deleteSource={0}, resultPatient={1}, preview={2}")
 	@CsvSource({
 		// withDelete, withInputResultPatient, withPreview
 		"true, true, true",

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ReplaceReferencesR4Test.java

@@ -45,6 +45,10 @@ public void after() throws Exception {
 	@BeforeEach
 	public void before() throws Exception {
 		super.before();
+		// keep the version on Provenance.target fields to verify that Provenance resources were saved
+		// with versioned target references
+		myFhirContext.getParserOptions()
+			.setDontStripVersionsFromReferencesAtPaths("Provenance.target");
 
 		myTestHelper = new ReplaceReferencesTestHelper(myFhirContext, myDaoRegistry);
 		myTestHelper.beforeEach();
@@ -81,6 +85,7 @@ void testReplaceReferences(boolean isAsync) {
 		// Check that the linked resources were updated
 
 		myTestHelper.assertAllReferencesUpdated();
+		myTestHelper.assertReplaceReferencesProvenance();
 	}
 
 	private JobInstance awaitJobCompletion(Task task) {
@@ -157,6 +162,7 @@ void testReplaceReferencesSmallTransactionEntriesSize() {
 		// Check that the linked resources were updated
 
 		myTestHelper.assertAllReferencesUpdated();
+		myTestHelper.assertReplaceReferencesProvenance();
 	}
 
 	// TODO ED we should add some tests for the invalid request error cases (and assert 4xx status code)