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Survivorship 2

This commit is contained in:
Nick 2021-01-05 17:59:26 -05:00
parent f4cf4bf54a
commit a4a173d5c7
6 changed files with 22 additions and 26 deletions
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16
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java
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@ -65,21 +65,23 @@ public class MdmEidUpdateService {
@Autowired
private IMdmSurvivorshipService myMdmSurvivorshipService;
void handleMdmUpdate(IAnyResource theResource, MatchedGoldenResourceCandidate theMatchedGoldenResourceCandidate, MdmTransactionContext theMdmTransactionContext) {
MdmUpdateContext updateContext = new MdmUpdateContext(theMatchedGoldenResourceCandidate, theResource);
void handleMdmUpdate(IAnyResource theTargetResource, MatchedGoldenResourceCandidate theMatchedGoldenResourceCandidate, MdmTransactionContext theMdmTransactionContext) {
MdmUpdateContext updateContext = new MdmUpdateContext(theMatchedGoldenResourceCandidate, theTargetResource);
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(theTargetResource, updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
if (updateContext.isRemainsMatchedToSameGoldenResource()) {
// Copy over any new external EIDs which don't already exist.
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(theResource, updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
if (!updateContext.isIncomingResourceHasAnEid() || updateContext.isHasEidsInCommon()) {
//update to patient that uses internal EIDs only.
myMdmLinkSvc.updateLink(updateContext.getMatchedGoldenResource(), theResource, theMatchedGoldenResourceCandidate.getMatchResult(), MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
myMdmLinkSvc.updateLink(updateContext.getMatchedGoldenResource(), theTargetResource, theMatchedGoldenResourceCandidate.getMatchResult(), MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
} else if (!updateContext.isHasEidsInCommon()) {
handleNoEidsInCommon(theResource, theMatchedGoldenResourceCandidate, theMdmTransactionContext, updateContext);
handleNoEidsInCommon(theTargetResource, theMatchedGoldenResourceCandidate, theMdmTransactionContext, updateContext);
}
} 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(theResource, updateContext.getExistingGoldenResource(), updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
linkToNewGoldenResourceAndFlagAsDuplicate(theTargetResource, updateContext.getExistingGoldenResource(), updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
// TODO NG - Do we need to merge fields from the old golden resource to the new golden resource?
}
}
@ -111,7 +113,7 @@ public class MdmEidUpdateService {
private void createNewGoldenResourceAndFlagAsDuplicate(IAnyResource theResource, MdmTransactionContext theMdmTransactionContext, IAnyResource theOldGoldenResource) {
log(theMdmTransactionContext, "Duplicate detected based on the fact that both resources have different external EIDs.");
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theResource);
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theResource, theMdmTransactionContext);
myMdmLinkSvc.updateLink(newGoldenResource, theResource, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
myMdmLinkSvc.updateLink(newGoldenResource, theOldGoldenResource, MdmMatchOutcome.POSSIBLE_DUPLICATE, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);

3
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImpl.java
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@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.mdm.svc;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
@ -63,6 +64,8 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
IMdmSettings myMdmSettings;
@Autowired
MessageHelper myMessageHelper;
@Autowired
IMdmSurvivorshipService myMdmSurvivorshipService;
@Transactional
@Override

5
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java
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@ -122,7 +122,7 @@ public class MdmMatchLinkSvc {
private void handleMdmWithNoCandidates(IAnyResource theResource, MdmTransactionContext theMdmTransactionContext) {
log(theMdmTransactionContext, String.format("There were no matched candidates for MDM, creating a new %s.", theResource.getIdElement().getResourceType()));
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theResource);
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theResource, theMdmTransactionContext);
// TODO GGG :)
// 1. Get the right helper
// 2. Create source resource for the MDM source
@ -136,13 +136,12 @@ public class MdmMatchLinkSvc {
if (myGoldenResourceHelper.isPotentialDuplicate(golenResource, theSourceResource)) {
log(theMdmTransactionContext, "Duplicate detected based on the fact that both resources have different external EIDs.");
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theSourceResource);
IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theSourceResource, theMdmTransactionContext);
myMdmLinkSvc.updateLink(newGoldenResource, theSourceResource, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
myMdmLinkSvc.updateLink(newGoldenResource, golenResource, MdmMatchOutcome.POSSIBLE_DUPLICATE, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
} else {
if (theGoldenResourceCandidate.isMatch()) {
myGoldenResourceHelper.handleExternalEidAddition(golenResource, theSourceResource, theMdmTransactionContext);
//TODO MDM GGG/NG: eventually we need to add survivorship rules of attributes here. Currently no data is copied over except EIDs.
}
myMdmLinkSvc.updateLink(golenResource, theSourceResource, theGoldenResourceCandidate.getMatchResult(), MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
}

11
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkSvcTest.java
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@ -51,23 +51,16 @@ public class MdmLinkSvcTest extends BaseMdmR4Test {
assertLinkCount(0);
Patient goldenPatient = createGoldenPatient();
IdType sourcePatientId = goldenPatient.getIdElement().toUnqualifiedVersionless();
// TODO NG should be ok to remove - assertEquals(0, goldenPatient.getLink().size());
Patient patient = createPatient();
{
myMdmLinkSvc.updateLink(goldenPatient, patient, POSSIBLE_MATCH, MdmLinkSourceEnum.AUTO, createContextForCreate("Patient"));
assertLinkCount(1);
// TODO NG should be ok to remove
// Patient newSourcePatient = myPatientDao.read(sourcePatientId);
// assertEquals(1, newSourcePatient.getLink().size());
}
{
myMdmLinkSvc.updateLink(goldenPatient, patient, MdmMatchOutcome.NO_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
assertLinkCount(1);
// TODO NG should be ok to remove
// Patient newSourcePatient = myPatientDao.read(sourcePatientId);
// assertEquals(0, newSourcePatient.getLink().size());
}
}
@ -129,7 +122,6 @@ public class MdmLinkSvcTest extends BaseMdmR4Test {
@Test
public void testManualMdmLinksCannotBeModifiedBySystem() {
// Patient goldenPatient = createGoldenPatient(buildJaneSourcePatient());
Patient goldenPatient = createGoldenPatient(buildJanePatient());
Patient patient = createPatient(buildJanePatient());
@ -144,7 +136,6 @@ public class MdmLinkSvcTest extends BaseMdmR4Test {
@Test
public void testAutomaticallyAddedNO_MATCHMdmLinksAreNotAllowed() {
// Patient goldenPatient = createGoldenPatient(buildJaneSourcePatient());
Patient goldenPatient = createGoldenPatient(buildJanePatient());
Patient patient = createPatient(buildJanePatient());
@ -159,7 +150,6 @@ public class MdmLinkSvcTest extends BaseMdmR4Test {
@Test
public void testSyncDoesNotSyncNoMatchLinks() {
// Patient sourcePatient = createGoldenPatient(buildJaneSourcePatient());
Patient goldenPatient = createGoldenPatient(buildJanePatient());
Patient patient1 = createPatient(buildJanePatient());
Patient patient2 = createPatient(buildJanePatient());
@ -171,7 +161,6 @@ public class MdmLinkSvcTest extends BaseMdmR4Test {
List<MdmLink> targets = myMdmLinkDaoSvc.findMdmLinksByGoldenResource(goldenPatient);
assertFalse(targets.isEmpty());
assertEquals(2, targets.size());
// TODO NG - OK? original assertTrue(goldenPatient.hasLink());
//TODO GGG update this test once we decide what has to happen here. There is no more "syncing links"
//assertEquals(patient1.getIdElement().toVersionless().getValue(), sourcePatient.getLinkFirstRep().getTarget().getReference());

5
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvcTest.java
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@ -8,6 +8,7 @@ import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
import ca.uhn.fhir.mdm.api.MdmMatchOutcome;
import ca.uhn.fhir.mdm.model.CanonicalEID;
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.mdm.util.MdmResourceUtil;
@ -352,7 +353,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
//In a normal situation, janePatient2 would just match to jane patient, but here we need to hack it so they are their
//own individual GoldenResource for the purpose of this test.
IAnyResource goldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(janePatient2);
IAnyResource goldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(janePatient2, new MdmTransactionContext());
myMdmLinkSvc.updateLink(goldenResource, janePatient2, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.AUTO, createContextForCreate("Patient"));
assertThat(janePatient, is(not(sameGoldenResourceAs(janePatient2))));
@ -443,7 +444,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
public void testCreateGoldenResourceFromMdmTarget() {
// Create Use Case #2 - adding patient with no EID
Patient janePatient = buildJanePatient();
Patient janeGoldenResourcePatient = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(janePatient);
Patient janeGoldenResourcePatient = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(janePatient, new MdmTransactionContext());
// golden record now contains HAPI-generated EID and HAPI tag
assertTrue(MdmResourceUtil.isMdmManaged(janeGoldenResourcePatient));

6
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/GoldenResourceHelper.java
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@ -73,17 +73,19 @@ public class GoldenResourceHelper {
/**
* Creates a copy of the specified resource. This method will carry over resource EID if it exists. If it does not exist,
* a randomly generated UUID EID will be created.
*
* @param <T> Supported MDM resource type (e.g. Patient, Practitioner)
* @param theIncomingResource The resource that will be used as the starting point for the MDM linking.
* @param theMdmTransactionContext
*/
public <T extends IAnyResource> T createGoldenResourceFromMdmSourceResource(T theIncomingResource) {
public <T extends IAnyResource> T createGoldenResourceFromMdmSourceResource(T theIncomingResource, MdmTransactionContext theMdmTransactionContext) {
validateContextSupported();
// get a ref to the actual ID Field
RuntimeResourceDefinition resourceDefinition = myFhirContext.getResourceDefinition(theIncomingResource);
IBaseResource newGoldenResource = resourceDefinition.newInstance();
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(theIncomingResource, newGoldenResource, theMdmTransactionContext);
// hapi has 2 metamodels: for children and types
BaseRuntimeChildDefinition goldenResourceIdentifier = resourceDefinition.getChildByName(FIELD_NAME_IDENTIFIER);