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WIP Dup Test

This commit is contained in:
Nick Goupinets 2021-09-02 17:41:57 -04:00
parent 528c429a4e
commit 2a60e91713
3 changed files with 193 additions and 30 deletions
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1
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmMatchLinkSvc.java
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@ -101,6 +101,7 @@ public class MdmMatchLinkSvc {
handleMdmWithSingleCandidate(theResource, firstMatch, theMdmTransactionContext);
} else {
log(theMdmTransactionContext, "MDM received multiple match candidates, that were linked to different Golden Resources. Setting POSSIBLE_DUPLICATES and POSSIBLE_MATCHES.");
//Set them all as POSSIBLE_MATCH
List<IAnyResource> goldenResources = new ArrayList<>();
for (MatchedGoldenResourceCandidate matchedGoldenResourceCandidate : theCandidateList.getCandidates()) {

190
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmEventIT.java Normal file
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@ -0,0 +1,190 @@
package ca.uhn.fhir.jpa.mdm.interceptor;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer;
import ca.uhn.fhir.mdm.api.MdmLinkEvent;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
import org.hibernate.dialect.H2Dialect;
import org.hibernate.search.backend.lucene.cfg.LuceneBackendSettings;
import org.hibernate.search.backend.lucene.cfg.LuceneIndexSettings;
import org.hibernate.search.engine.cfg.BackendSettings;
import org.hibernate.search.mapper.orm.cfg.HibernateOrmMapperSettings;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.slf4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Primary;
import org.springframework.data.domain.Example;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.TestPropertySource;
import java.util.Properties;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.slf4j.LoggerFactory.getLogger;
@TestPropertySource(properties = {
"mdm.prevent_multiple_eids=false"
})
@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
@ContextConfiguration(classes = {MdmHelperConfig.class})
public class MdmEventIT extends BaseMdmR4Test {
private static final Logger ourLog = getLogger(MdmEventIT.class);
@RegisterExtension
@Autowired
public MdmHelperR4 myMdmHelper;
@Autowired
private IdHelperService myIdHelperService;
@Bean
@Primary
public Properties jpaProperties() {
Properties extraProperties = new Properties();
extraProperties.put("hibernate.format_sql", "true");
extraProperties.put("hibernate.show_sql", "true");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.dialect", H2Dialect.class.getName());
extraProperties.put(BackendSettings.backendKey(BackendSettings.TYPE), "lucene");
extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.ANALYSIS_CONFIGURER), HapiLuceneAnalysisConfigurer.class.getName());
extraProperties.put(BackendSettings.backendKey(LuceneIndexSettings.DIRECTORY_TYPE), "local-heap");
extraProperties.put(BackendSettings.backendKey(LuceneBackendSettings.LUCENE_VERSION), "LUCENE_CURRENT");
extraProperties.put(HibernateOrmMapperSettings.ENABLED, "true");
return extraProperties;
}
@Test
public void testDuplicateLinkChangeEvent() throws InterruptedException {
Patient patient1 = buildJanePatient();
addExternalEID(patient1, "eid-1");
addExternalEID(patient1, "eid-11");
patient1 = createPatientAndUpdateLinks(patient1);
Patient patient2 = buildPaulPatient();
addExternalEID(patient2, "eid-2");
addExternalEID(patient2, "eid-22");
patient2 = createPatientAndUpdateLinks(patient2);
Patient patient3 = buildPaulPatient();
addExternalEID(patient3, "eid-22");
patient3 = createPatientAndUpdateLinks(patient3);
patient2.getIdentifier().clear();
addExternalEID(patient2, "eid-11");
addExternalEID(patient2, "eid-22");
patient2 = (Patient) myPatientDao.update(patient2).getResource();
MdmTransactionContext ctx = myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient2, createContextForUpdate(patient2.getIdElement().getResourceType()));
MdmLinkEvent mdmLinkEvent = ctx.getMdmLinkEvent();
assertFalse(mdmLinkEvent.getDuplicateGoldenResourceIds().isEmpty());
}
// @Test
public void testCreateLinkChangeEvent() throws InterruptedException {
Practitioner pr = buildPractitionerWithNameAndId("Young", "AC-DC");
myMdmHelper.createWithLatch(pr);
ResourceOperationMessage resourceOperationMessage = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(ResourceOperationMessage.class);
assertNotNull(resourceOperationMessage);
assertEquals(pr.getId(), resourceOperationMessage.getId());
MdmLink link = getLinkByTargetId(pr);
MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
assertNotNull(linkChangeEvent);
assertEquals(link.getGoldenResourcePid(), new IdDt(linkChangeEvent.getGoldenResourceId()).getIdPartAsLong());
assertEquals(link.getSourcePid(), new IdDt(linkChangeEvent.getTargetResourceId()).getIdPartAsLong());
}
/*
@Test
public void testDuplicateLinkChangeEvent() throws InterruptedException {
logAllLinks();
for (IBaseResource r : myPatientDao.search(new SearchParameterMap()).getAllResources()) {
ourLog.info("Found {}", r);
}
Patient myPatient = createPatientAndUpdateLinks(buildPaulPatient());
StringType myPatientId = new StringType(myPatient.getIdElement().getValue());
Patient mySourcePatient = getGoldenResourceFromTargetResource(myPatient);
StringType mySourcePatientId = new StringType(mySourcePatient.getIdElement().getValue());
StringType myVersionlessGodlenResourceId = new StringType(mySourcePatient.getIdElement().toVersionless().getValue());
MdmLink myLink = myMdmLinkDaoSvc.findMdmLinkBySource(myPatient).get();
// Tests require our initial link to be a POSSIBLE_MATCH
myLink.setMatchResult(MdmMatchResultEnum.POSSIBLE_MATCH);
saveLink(myLink);
assertEquals(MdmLinkSourceEnum.AUTO, myLink.getLinkSource());
// myDaoConfig.setExpungeEnabled(true);
// Add a second patient
createPatientAndUpdateLinks(buildJanePatient());
// Add a possible duplicate
StringType myLinkSource = new StringType(MdmLinkSourceEnum.AUTO.name());
Patient sourcePatient1 = createGoldenPatient();
StringType myGoldenResource1Id = new StringType(sourcePatient1.getIdElement().toVersionless().getValue());
Long sourcePatient1Pid = myIdHelperService.getPidOrNull(sourcePatient1);
Patient sourcePatient2 = createGoldenPatient();
StringType myGoldenResource2Id = new StringType(sourcePatient2.getIdElement().toVersionless().getValue());
Long sourcePatient2Pid = myIdHelperService.getPidOrNull(sourcePatient2);
MdmLink possibleDuplicateMdmLink = myMdmLinkDaoSvc.newMdmLink().setGoldenResourcePid(sourcePatient1Pid).setSourcePid(sourcePatient2Pid).setMatchResult(MdmMatchResultEnum.POSSIBLE_DUPLICATE).setLinkSource(MdmLinkSourceEnum.AUTO);
saveLink(possibleDuplicateMdmLink);
logAllLinks();
ResourceOperationMessage resourceOperationMessage = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(ResourceOperationMessage.class);
assertNotNull(resourceOperationMessage);
assertEquals(sourcePatient2.getId(), resourceOperationMessage.getId());
}
*/
private MdmLink getLinkByTargetId(IBaseResource theResource) {
MdmLink example = new MdmLink();
example.setSourcePid(theResource.getIdElement().getIdPartAsLong());
return myMdmLinkDao.findAll(Example.of(example)).get(0);
}
@Test
public void testUpdateLinkChangeEvent() throws InterruptedException {
Patient patient1 = addExternalEID(buildJanePatient(), "eid-1");
myMdmHelper.createWithLatch(patient1);
MdmTransactionContext ctx = createContextForCreate("Patient");
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient1, ctx);
ourLog.info(ctx.getMdmLinkEvent().toString());
assertEquals(patient1.getIdElement().getValue(), ctx.getMdmLinkEvent().getTargetResourceId());
assertEquals(getLinkByTargetId(patient1).getGoldenResourcePid(), new IdDt(ctx.getMdmLinkEvent().getGoldenResourceId()).getIdPartAsLong());
Patient patient2 = addExternalEID(buildJanePatient(), "eid-2");
myMdmHelper.createWithLatch(patient2);
ctx = createContextForCreate("Patient");
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient2, ctx);
ourLog.info(ctx.getMdmLinkEvent().toString());
assertEquals(patient2.getIdElement().getValue(), ctx.getMdmLinkEvent().getTargetResourceId());
assertEquals(getLinkByTargetId(patient2).getGoldenResourcePid(), new IdDt(ctx.getMdmLinkEvent().getGoldenResourceId()).getIdPartAsLong());
}
}

32
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/interceptor/MdmStorageInterceptorIT.java
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@ -6,12 +6,7 @@ import ca.uhn.fhir.jpa.entity.MdmLink;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperConfig;
import ca.uhn.fhir.jpa.mdm.helper.MdmHelperR4;
import ca.uhn.fhir.jpa.mdm.svc.MdmLinkSvcImpl;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.mdm.api.IMdmLinkSvc;
import ca.uhn.fhir.mdm.api.MdmLinkEvent;
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.rules.config.MdmSettings;
@ -21,7 +16,6 @@ import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.server.TransactionLogMessages;
import ca.uhn.fhir.rest.server.exceptions.ForbiddenOperationException;
import ca.uhn.fhir.rest.server.messaging.ResourceOperationMessage;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -29,7 +23,6 @@ import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Practitioner;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
@ -55,9 +48,7 @@ import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.nullValue;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.slf4j.LoggerFactory.getLogger;
@ -72,8 +63,6 @@ public class MdmStorageInterceptorIT extends BaseMdmR4Test {
public MdmHelperR4 myMdmHelper;
@Autowired
private IdHelperService myIdHelperService;
@Autowired
private IMdmLinkSvc myMdmLinkSvc;
@Test
public void testCreatePractitioner() throws InterruptedException {
@ -81,23 +70,6 @@ public class MdmStorageInterceptorIT extends BaseMdmR4Test {
assertLinkCount(1);
}
@Test
public void testCreateLinkChangeEvent() throws InterruptedException {
Practitioner pr = buildPractitionerWithNameAndId("Young", "AC-DC");
myMdmHelper.createWithLatch(pr);
ResourceOperationMessage resourceOperationMessage = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(ResourceOperationMessage.class);
assertNotNull(resourceOperationMessage);
assertEquals(pr.getId(), resourceOperationMessage.getId());
MdmLink link = getLinkByTargetId(pr);
MdmLinkEvent linkChangeEvent = myMdmHelper.getAfterMdmLatch().getLatchInvocationParameterOfType(MdmLinkEvent.class);
assertNotNull(linkChangeEvent);
assertEquals(link.getGoldenResourcePid(), new IdDt(linkChangeEvent.getGoldenResourceId()).getIdPartAsLong());
assertEquals(link.getSourcePid(), new IdDt(linkChangeEvent.getTargetResourceId()).getIdPartAsLong());
}
private MdmLink getLinkByTargetId(IBaseResource theResource) {
MdmLink example = new MdmLink();
example.setSourcePid(theResource.getIdElement().getIdPartAsLong());
@ -113,7 +85,7 @@ public class MdmStorageInterceptorIT extends BaseMdmR4Test {
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient1, ctx);
ourLog.info(ctx.getMdmLinkEvent().toString());
assertEquals(patient1.getIdElement().getValue(), ctx.getMdmLinkEvent().getTargetResourceId());
assertEquals(getLinkByTargetId(patient1).getGoldenResourcePid(), new IdDt(ctx.getMdmLinkEvent().getGoldenResourceId()).getIdPartAsLong());
assertEquals(getLinkByTargetId(patient1).getGoldenResourcePid(), new IdDt(ctx.getMdmLinkEvent().getGoldenResourceId()).getIdPartAsLong());
Patient patient2 = addExternalEID(buildJanePatient(), "eid-2");
myMdmHelper.createWithLatch(patient2);
@ -121,7 +93,7 @@ public class MdmStorageInterceptorIT extends BaseMdmR4Test {
myMdmMatchLinkSvc.updateMdmLinksForMdmSource(patient2, ctx);
ourLog.info(ctx.getMdmLinkEvent().toString());
assertEquals(patient2.getIdElement().getValue(), ctx.getMdmLinkEvent().getTargetResourceId());
assertEquals(getLinkByTargetId(patient2).getGoldenResourcePid(), new IdDt(ctx.getMdmLinkEvent().getGoldenResourceId()).getIdPartAsLong());
assertEquals(getLinkByTargetId(patient2).getGoldenResourcePid(), new IdDt(ctx.getMdmLinkEvent().getGoldenResourceId()).getIdPartAsLong());
}
@Test