Fix NPE in MDM post-mdm-clear on UPDATE operations. (#3851)

* Fix bug, imlpementation, changelog

* wip

* wip

* wip

* Add test

* wip

* wip

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/7_0_0/3786-mdm-npe.yaml

@@ -0,0 +1,4 @@
+---
+type: fix
+issue: 3786
+title: "Previously, when executing an update on a resource that had to undergo MDM, a nullpointer could occur. This has been fixed."

hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java

@@ -19,7 +19,6 @@
  */
 package ca.uhn.fhir.jpa.mdm.svc;
 
-import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.mdm.dao.MdmLinkDaoSvc;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.MatchedGoldenResourceCandidate;
 import ca.uhn.fhir.jpa.mdm.svc.candidate.MdmGoldenResourceFindingSvc;
@@ -35,7 +34,6 @@ import ca.uhn.fhir.mdm.model.MdmTransactionContext;
 import ca.uhn.fhir.mdm.util.EIDHelper;
 import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.hl7.fhir.instance.model.api.IAnyResource;
 import org.slf4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -82,6 +80,7 @@ public class MdmEidUpdateService {
 		myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(
 				theTargetResource, updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
 
+		IAnyResource theOldGoldenResource = updateContext.getExistingGoldenResource();
 		if (updateContext.isRemainsMatchedToSameGoldenResource()) {
 			// Copy over any new external EIDs which don't already exist.
 			if (!updateContext.isIncomingResourceHasAnEid() || updateContext.isHasEidsInCommon()) {
@@ -96,17 +95,24 @@ public class MdmEidUpdateService {
 				handleNoEidsInCommon(
 						theTargetResource, theMatchedGoldenResourceCandidate, theMdmTransactionContext, updateContext);
 			}
+		} else if (theOldGoldenResource == null) {
+			// If we are in an update, and there is no existing golden resource, it is likely due to a clear operation,
+			// and we need to start from scratch.
+			myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(
+					theTargetResource, updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
+			myMdmResourceDaoSvc.upsertGoldenResource(
+					updateContext.getMatchedGoldenResource(), theMdmTransactionContext.getResourceType());
+			myMdmLinkSvc.updateLink(
+					updateContext.getMatchedGoldenResource(),
+					theTargetResource,
+					theMatchedGoldenResourceCandidate.getMatchResult(),
+					MdmLinkSourceEnum.AUTO,
+					theMdmTransactionContext);
 		} else {
 			// This is a new linking scenario. we have to break the existing link and link to the new Golden Resource.
 			// For now, we create duplicate.
 			// updated patient has an EID that matches to a new candidate. Link them, and set the Golden Resources
 			// possible duplicates
-			IAnyResource theOldGoldenResource = updateContext.getExistingGoldenResource();
-			if (theOldGoldenResource == null) {
-				throw new InternalErrorException(
-						Msg.code(2362)
-								+ "Old golden resource was null while updating MDM links with new golden resource. It is likely that a $mdm-clear was performed without a $mdm-submit. Link will not be updated.");
-			} else {
 			linkToNewGoldenResourceAndFlagAsDuplicate(
 					theTargetResource,
 					theMatchedGoldenResourceCandidate.getMatchResult(),
@@ -120,7 +126,6 @@ public class MdmEidUpdateService {
 					updateContext.getMatchedGoldenResource(), theMdmTransactionContext.getResourceType());
 		}
 	}
-	}
 
 	private void handleNoEidsInCommon(
 			IAnyResource theResource,
@@ -283,5 +288,9 @@ public class MdmEidUpdateService {
 		public boolean isRemainsMatchedToSameGoldenResource() {
 			return myRemainsMatchedToSameGoldenResource;
 		}
+
+		public boolean hasExistingGoldenResource() {
+			return myExistingGoldenResource != null;
+		}
 	}
 }

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/BaseMdmR4Test.java

@@ -626,6 +626,14 @@ abstract public class BaseMdmR4Test extends BaseJpaR4Test {
 		return retval;
 	}
 
+	@Nonnull
+	protected MdmTransactionContext buildUpdateResourceMdmTransactionContext() {
+		MdmTransactionContext retval = new MdmTransactionContext();
+		retval.setResourceType("Patient");
+		retval.setRestOperation(MdmTransactionContext.OperationType.UPDATE_RESOURCE);
+		return retval;
+	}
+
 	protected MdmLink createGoldenPatientAndLinkToSourcePatient(Long thePatientPid, MdmMatchResultEnum theMdmMatchResultEnum) {
 		Patient patient = createPatient();
 

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java

@@ -1,5 +1,8 @@
 package ca.uhn.fhir.jpa.mdm.interceptor;
 
+import ca.uhn.fhir.batch2.api.StepExecutionDetails;
+import ca.uhn.fhir.batch2.jobs.chunk.ResourceIdListWorkChunkJson;
+import ca.uhn.fhir.batch2.model.JobInstance;
 import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
 import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
@@ -7,7 +10,11 @@ import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
 import ca.uhn.fhir.mdm.model.mdmevents.MdmLinkEvent;
 import ca.uhn.fhir.mdm.model.mdmevents.MdmLinkJson;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
+import ca.uhn.fhir.mdm.batch2.clear.MdmClearJobParameters;
+import ca.uhn.fhir.mdm.batch2.clear.MdmClearStep;
 import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.api.server.RequestDetails;
+import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Patient;
@@ -20,7 +27,11 @@ import org.springframework.data.domain.Example;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.TestPropertySource;
 
+import javax.annotation.Nonnull;
 import java.util.List;
+import java.util.Set;
+import java.util.UUID;
+import java.util.stream.Collectors;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java

@@ -1,6 +1,8 @@
 package ca.uhn.fhir.jpa.mdm.svc;
 
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
+import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
 import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
 import ca.uhn.fhir.jpa.mdm.config.BaseTestMdmConfig;
@@ -80,7 +82,6 @@ public class MdmMatchLinkSvcTest {
 
 	private static final Logger ourLog = getLogger(MdmMatchLinkSvcTest.class);
 
-
 	@Nested
 	public class NoBlockLinkTest extends BaseMdmR4Test {
 		@Autowired
@@ -231,6 +232,23 @@ public class MdmMatchLinkSvcTest {
 			assertLinksMatchVector(null, null, null);
 		}
 
+	@Test
+	public void updateMdmLinksForMdmSource_singleCandidateDuringUpdate_DoesNotNullPointer() {
+
+		//Given: A patient exists with a matched golden resource.
+		Patient jane = createPatientAndUpdateLinks(buildJanePatient());
+		Patient goldenJane = getGoldenResourceFromTargetResource(jane);
+
+		//When: A patient who has no existing MDM links comes in as an update
+		Patient secondaryJane = createPatient(buildJanePatient(), false, false);
+		secondaryJane.setActive(true);
+		IAnyResource resource = (IAnyResource) myPatientDao.update(secondaryJane).getResource();
+
+		//Then: The secondary jane should link to the first jane.
+		myMdmMatchLinkSvc.updateMdmLinksForMdmSource(resource, buildUpdateResourceMdmTransactionContext());
+		assertThat(secondaryJane, is(sameGoldenResourceAs(jane)));
+	}
+
 	@Test
 	public void testWhenPOSSIBLE_MATCHOccursOnGoldenResourceThatHasBeenManuallyNOMATCHedThatItIsBlocked() {
 		Patient originalJane = createPatientAndUpdateLinks(buildJanePatient());