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Code Issues Packages Projects Releases Wiki Activity

Ks 20211203 mdm possible match (#3216) 

* begin with failing test

* fix issue

* change log

* code review
This commit is contained in:
Ken Stevens 2021-12-03 14:44:25 -05:00 committed by GitHub
parent 84a9609236
commit 0656037c8d
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6 changed files with 62 additions and 9 deletions
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3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3216-mdm-possible-match-to-match.yaml Normal file
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@ -0,0 +1,3 @@
---
type: fix
title: "MDM was throwing a NullPointerException when upgrading a match from POSSIBLE_MATCH to MATCH. This has been corrected."

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
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@ -627,7 +627,7 @@ public class IdHelperService {
}
@Nonnull
public Long getPidOrThrowException(IAnyResource theResource) {
public Long getPidOrThrowException(@Nonnull IAnyResource theResource) {
Long retVal = (Long) theResource.getUserData(RESOURCE_PID);
if (retVal == null) {
throw new IllegalStateException(

21
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/dao/MdmLinkDaoSvc.java
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@ -30,7 +30,9 @@ import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
import ca.uhn.fhir.mdm.log.Logs;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Example;
@ -146,6 +148,15 @@ public class MdmLinkDaoSvc {
* @return the {@link MdmLink} that contains the Match information for the source.
*/
public Optional<MdmLink> getMatchedLinkForSource(IBaseResource theSourceResource) {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.MATCH);
}
public Optional<MdmLink> getPossibleMatchedLinkForSource(IBaseResource theSourceResource) {
return getMdmLinkWithMatchResult(theSourceResource, MdmMatchResultEnum.POSSIBLE_MATCH);
}
@NotNull
private Optional<MdmLink> getMdmLinkWithMatchResult(IBaseResource theSourceResource, MdmMatchResultEnum theMatchResult) {
Long pid = myIdHelperService.getPidOrNull(theSourceResource);
if (pid == null) {
return Optional.empty();
@ -153,7 +164,7 @@ public class MdmLinkDaoSvc {
MdmLink exampleLink = myMdmLinkFactory.newMdmLink();
exampleLink.setSourcePid(pid);
exampleLink.setMatchResult(MdmMatchResultEnum.MATCH);
exampleLink.setMatchResult(theMatchResult);
Example<MdmLink> example = Example.of(exampleLink);
return myMdmLinkDao.findOne(example);
}
@ -298,4 +309,12 @@ public class MdmLinkDaoSvc {
return myMdmLinkFactory.newMdmLink();
}
public Optional<MdmLink> getMatchedOrPossibleMatchedLinkForSource(IAnyResource theResource) {
// TODO KHS instead of two queries, just do one query with an OR
Optional<MdmLink> retval = getMatchedLinkForSource(theResource);
if (!retval.isPresent()) {
retval = getPossibleMatchedLinkForSource(theResource);
}
return retval;
}
}

12
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java
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@ -80,7 +80,7 @@ public class MdmEidUpdateService {
} 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
linkToNewGoldenResourceAndFlagAsDuplicate(theTargetResource, updateContext.getExistingGoldenResource(), updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
linkToNewGoldenResourceAndFlagAsDuplicate(theTargetResource, theMatchedGoldenResourceCandidate.getMatchResult(), updateContext.getExistingGoldenResource(), updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(theTargetResource, updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
myMdmResourceDaoSvc.upsertGoldenResource(updateContext.getMatchedGoldenResource(), theMdmTransactionContext.getResourceType());
@ -121,10 +121,10 @@ public class MdmEidUpdateService {
myMdmLinkSvc.updateLink(newGoldenResource, theOldGoldenResource, MdmMatchOutcome.POSSIBLE_DUPLICATE, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
}
private void linkToNewGoldenResourceAndFlagAsDuplicate(IAnyResource theResource, IAnyResource theOldGoldenResource, IAnyResource theNewGoldenResource, MdmTransactionContext theMdmTransactionContext) {
private void linkToNewGoldenResourceAndFlagAsDuplicate(IAnyResource theResource, MdmMatchOutcome theMatchResult, IAnyResource theOldGoldenResource, IAnyResource theNewGoldenResource, MdmTransactionContext theMdmTransactionContext) {
log(theMdmTransactionContext, "Changing a match link!");
myMdmLinkSvc.deleteLink(theOldGoldenResource, theResource, theMdmTransactionContext);
myMdmLinkSvc.updateLink(theNewGoldenResource, theResource, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
myMdmLinkSvc.updateLink(theNewGoldenResource, theResource, theMatchResult, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
log(theMdmTransactionContext, "Duplicate detected based on the fact that both resources have different external EIDs.");
myMdmLinkSvc.updateLink(theNewGoldenResource, theOldGoldenResource, MdmMatchOutcome.POSSIBLE_DUPLICATE, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
}
@ -161,11 +161,11 @@ public class MdmEidUpdateService {
myHasEidsInCommon = myEIDHelper.hasEidOverlap(myMatchedGoldenResource, theResource);
myIncomingResourceHasAnEid = !myEIDHelper.getExternalEid(theResource).isEmpty();
Optional<MdmLink> theExistingMatchLink = myMdmLinkDaoSvc.getMatchedLinkForSource(theResource);
Optional<MdmLink> theExistingMatchOrPossibleMatchLink = myMdmLinkDaoSvc.getMatchedOrPossibleMatchedLinkForSource(theResource);
myExistingGoldenResource = null;
if (theExistingMatchLink.isPresent()) {
MdmLink mdmLink = theExistingMatchLink.get();
if (theExistingMatchOrPossibleMatchLink.isPresent()) {
MdmLink mdmLink = theExistingMatchOrPossibleMatchLink.get();
Long existingGoldenResourcePid = mdmLink.getGoldenResourcePid();
myExistingGoldenResource = myMdmResourceDaoSvc.readGoldenResourceByPid(new ResourcePersistentId(existingGoldenResourcePid), resourceType);
myRemainsMatchedToSameGoldenResource = candidateIsSameAsMdmLinkGoldenResource(mdmLink, theMatchedGoldenResourceCandidate);

6
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcImpl.java
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@ -36,6 +36,7 @@ import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import javax.transaction.Transactional;
import java.util.Optional;
@ -85,6 +86,9 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
@Override
public void deleteLink(IAnyResource theGoldenResource, IAnyResource theSourceResource, MdmTransactionContext theMdmTransactionContext) {
if (theGoldenResource == null) {
return;
}
Optional<MdmLink> optionalMdmLink = getMdmLinkForGoldenResourceSourceResourcePair(theGoldenResource, theSourceResource);
if (optionalMdmLink.isPresent()) {
MdmLink mdmLink = optionalMdmLink.get();
@ -122,7 +126,7 @@ public class MdmLinkSvcImpl implements IMdmLinkSvc {
return theIncomingSource == MdmLinkSourceEnum.AUTO && theExistingSource.isManual();
}
private Optional<MdmLink> getMdmLinkForGoldenResourceSourceResourcePair(IAnyResource theGoldenResource, IAnyResource theCandidate) {
private Optional<MdmLink> getMdmLinkForGoldenResourceSourceResourcePair(@Nonnull IAnyResource theGoldenResource, @Nonnull IAnyResource theCandidate) {
if (theGoldenResource.getIdElement().getIdPart() == null || theCandidate.getIdElement().getIdPart() == null) {
return Optional.empty();
} else {

27
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java
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@ -435,6 +435,33 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
assertThat(patient3, is(sameGoldenResourceAs(patient)));
}
@Test
public void testPossibleMatchUpdatedToMatch() {
// setup
Patient patient = buildJanePatient();
patient.getNameFirstRep().setFamily("familyone");
patient = createPatientAndUpdateLinks(patient);
assertThat(patient, is(sameGoldenResourceAs(patient)));
Patient patient2 = buildJanePatient();
patient2.getNameFirstRep().setFamily("pleasedonotmatchatall");
patient2 = createPatientAndUpdateLinks(patient2);
assertThat(patient2, is(not(sameGoldenResourceAs(patient))));
assertThat(patient2, is(not(linkedTo(patient))));
assertThat(patient2, is(possibleMatchWith(patient)));
patient2.getNameFirstRep().setFamily(patient.getNameFirstRep().getFamily());
// execute
updatePatientAndUpdateLinks(patient2);
// validate
assertThat(patient2, is(linkedTo(patient)));
assertThat(patient2, is(sameGoldenResourceAs(patient)));
}
@Test
public void testCreateGoldenResourceFromMdmTarget() {
// Create Use Case #2 - adding patient with no EID