Survivorship 4
This commit is contained in:
Nick
parent
ebefb141f3
commit
bec056cf9d
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@ -23,7 +23,9 @@ package ca.uhn.fhir.jpa.mdm.svc;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
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import ca.uhn.fhir.mdm.model.MdmTransactionContext;
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import ca.uhn.fhir.mdm.util.TerserUtil;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.springframework.beans.factory.annotation.Autowired;
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public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
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@ -31,8 +33,42 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
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@Autowired
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private FhirContext myFhirContext;
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/**
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* Survivorship rules may include the following data consolidation methods:
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*
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* <ul>
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* <li>
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* Length of field - apply the field value containing most or least number of characters - e.g. longest name
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* </li>
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* <li>
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* Date time - all the field value from the oldest or the newest recrod - e.g. use the most recent phone number
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* </li>
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* <li>
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* Frequency - use the most or least frequent number of occurrence - e.g. most common phone number
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* </li>
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* <li>
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* Integer - number functions (largest, sum, avg) - e.g. number of patient encounters
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* </li>
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* <li>
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* Quality of data - best quality data - e.g. data coming from a certain system is considered trusted and overrides all other values
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* </li>
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* <li>
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* A hybrid approach combining all methods listed above as best fits
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* </li>
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* </ul>
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*
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* @param theTargetResource Target resource to merge fields from
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* @param theGoldenResource Golden resource to merge fields into
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* @param theMdmTransactionContext Current transaction context
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* @param <T>
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*/
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@Override
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public <T extends IBase> void applySurvivorshipRulesToGoldenResource(T theTargetResource, T theGoldenResource, MdmTransactionContext theMdmTransactionContext) {
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// TerserUtil.cloneFields(myFhirContext, (IBaseResource) theTargetResource, (IBaseResource) theGoldenResource);
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// TerserUtil.mergeFields(myFhirContext, (IBaseResource) theTargetResource, (IBaseResource) theGoldenResource, TerserUtil.DEFAULT_EXCLUDED_FIELDS);
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if (MdmTransactionContext.OperationType.MERGE_GOLDEN_RESOURCES == theMdmTransactionContext.getRestOperation()) {
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TerserUtil.mergeFieldsExceptIdAndMeta(myFhirContext, (IBaseResource) theTargetResource, (IBaseResource) theGoldenResource);
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} else {
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TerserUtil.overwriteFields(myFhirContext, (IBaseResource) theTargetResource, (IBaseResource) theGoldenResource, TerserUtil.EXCLUDE_IDS_AND_META);
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}
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}
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}
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@ -161,8 +161,10 @@ public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
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public void emptyFromFullTo() {
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myFromGoldenPatient.getName().add(new HumanName().addGiven(BAD_GIVEN_NAME));
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populatePatient(myToGoldenPatient);
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print(myFromGoldenPatient);
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Patient mergedSourcePatient = mergeGoldenPatients();
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print(mergedSourcePatient);
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HumanName returnedName = mergedSourcePatient.getNameFirstRep();
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assertEquals(GIVEN_NAME, returnedName.getGivenAsSingleString());
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assertEquals(FAMILY_NAME, returnedName.getFamily());
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@ -393,20 +395,19 @@ public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
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@Test
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public void testMergeNamesAllSame() {
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// TODO NG - Revisit when rules are available
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// myFromSourcePatient.addName().addGiven("Jim");
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// myFromSourcePatient.getNameFirstRep().addGiven("George");
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// assertThat(myFromSourcePatient.getName(), hasSize(1));
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// assertThat(myFromSourcePatient.getName().get(0).getGiven(), hasSize(2));
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//
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// myToSourcePatient.addName().addGiven("Jim");
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// myToSourcePatient.getNameFirstRep().addGiven("George");
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// assertThat(myToSourcePatient.getName(), hasSize(1));
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// assertThat(myToSourcePatient.getName().get(0).getGiven(), hasSize(2));
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//
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// mergeSourcePatients();
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// assertThat(myToSourcePatient.getName(), hasSize(1));
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// assertThat(myToSourcePatient.getName().get(0).getGiven(), hasSize(2));
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myFromGoldenPatient.addName().addGiven("Jim");
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myFromGoldenPatient.getNameFirstRep().addGiven("George");
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assertThat(myFromGoldenPatient.getName(), hasSize(1));
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assertThat(myFromGoldenPatient.getName().get(0).getGiven(), hasSize(2));
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myToGoldenPatient.addName().addGiven("Jim");
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myToGoldenPatient.getNameFirstRep().addGiven("George");
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assertThat(myToGoldenPatient.getName(), hasSize(1));
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assertThat(myToGoldenPatient.getName().get(0).getGiven(), hasSize(2));
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mergeGoldenPatients();
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assertThat(myToGoldenPatient.getName(), hasSize(1));
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assertThat(myToGoldenPatient.getName().get(0).getGiven(), hasSize(2));
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}
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@Test
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@ -426,8 +427,6 @@ public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
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}
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private MdmLink createMdmLink(Patient theSourcePatient, Patient theTargetPatient) {
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//TODO GGG Ensure theis comment can be safely removed
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//theSourcePatient.addLink().setTarget(new Reference(theTargetPatient));
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return myMdmLinkDaoSvc.createOrUpdateLinkEntity(theSourcePatient, theTargetPatient, POSSIBLE_MATCH, MdmLinkSourceEnum.AUTO, createContextForCreate("Patient"));
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}
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@ -35,12 +35,7 @@ import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.NO_MATCH;
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import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.POSSIBLE_DUPLICATE;
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import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.POSSIBLE_MATCH;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.blankOrNullString;
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import static org.hamcrest.Matchers.equalTo;
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import static org.hamcrest.Matchers.hasSize;
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import static org.hamcrest.Matchers.in;
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import static org.hamcrest.Matchers.is;
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import static org.hamcrest.Matchers.not;
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import static org.hamcrest.Matchers.*;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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@ -184,13 +179,13 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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Optional<MdmLink> mdmLink = myMdmLinkDaoSvc.getMatchedLinkForSourcePid(patient.getIdElement().getIdPartAsLong());
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Patient read = getTargetResourceFromMdmLink(mdmLink.get(), "Patient");
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// TODO NG - rules haven't been determined yet revisit once implemented...
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// assertThat(read.getNameFirstRep().getFamily(), is(equalTo(patient.getNameFirstRep().getFamily())));
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// assertThat(read.getNameFirstRep().getGivenAsSingleString(), is(equalTo(patient.getNameFirstRep().getGivenAsSingleString())));
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// assertThat(read.getBirthDateElement().toHumanDisplay(), is(equalTo(patient.getBirthDateElement().toHumanDisplay())));
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// assertThat(read.getTelecomFirstRep().getValue(), is(equalTo(patient.getTelecomFirstRep().getValue())));
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// assertThat(read.getPhoto().getData(), is(equalTo(patient.getPhotoFirstRep().getData())));
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// assertThat(read.getGender(), is(equalTo(patient.getGender())));
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assertThat(read.getNameFirstRep().getFamily(), is(equalTo(patient.getNameFirstRep().getFamily())));
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assertThat(read.getNameFirstRep().getGivenAsSingleString(), is(equalTo(patient.getNameFirstRep().getGivenAsSingleString())));
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assertThat(read.getBirthDateElement().toHumanDisplay(), is(equalTo(patient.getBirthDateElement().toHumanDisplay())));
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assertThat(read.getTelecomFirstRep().getValue(), is(equalTo(patient.getTelecomFirstRep().getValue())));
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assertThat(read.getPhoto().size(), is(equalTo(patient.getPhoto().size())));
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assertThat(read.getPhotoFirstRep().getData(), is(equalTo(patient.getPhotoFirstRep().getData())));
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assertThat(read.getGender(), is(equalTo(patient.getGender())));
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}
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@Test
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@ -246,7 +241,6 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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@Test
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public void testHavingMultipleEIDsOnIncomingPatientMatchesCorrectly() {
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Patient patient1 = buildJanePatient();
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addExternalEID(patient1, "id_1");
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addExternalEID(patient1, "id_2");
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@ -274,7 +268,6 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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List<MdmLink> possibleDuplicates = myMdmLinkDaoSvc.getPossibleDuplicates();
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assertThat(possibleDuplicates, hasSize(1));
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List<Long> duplicatePids = Stream.of(patient1, patient2)
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.map(this::getGoldenResourceFromTargetResource)
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.map(myIdHelperService::getPidOrNull)
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@ -480,8 +473,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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Patient sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(janePaulPatient);
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HumanName nameFirstRep = sourcePatientFromTarget.getNameFirstRep();
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// TODO NG attribute propagation has been removed - revisit once source survivorship rules are defined
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// assertThat(nameFirstRep.getGivenAsSingleString(), is(equalToIgnoringCase("paul")));
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assertThat(nameFirstRep.getGivenAsSingleString(), is(equalToIgnoringCase("paul")));
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}
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@Test
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@ -492,8 +484,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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Patient sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(paul);
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// TODO NG - rules haven't been determined yet revisit once implemented...
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// assertThat(sourcePatientFromTarget.getGender(), is(equalTo(Enumerations.AdministrativeGender.MALE)));
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assertThat(sourcePatientFromTarget.getGender(), is(equalTo(Enumerations.AdministrativeGender.MALE)));
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Patient paul2 = buildPaulPatient();
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paul2.setGender(Enumerations.AdministrativeGender.FEMALE);
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@ -504,7 +495,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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//Newly matched patients aren't allowed to overwrite GoldenResource Attributes unless they are empty,
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// so gender should still be set to male.
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Patient paul2GoldenResource = (Patient) getGoldenResourceFromTargetResource(paul2);
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// assertThat(paul2GoldenResource.getGender(), is(equalTo(Enumerations.AdministrativeGender.MALE)));
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assertThat(paul2GoldenResource.getGender(), is(equalTo(Enumerations.AdministrativeGender.MALE)));
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}
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@Test
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@ -516,8 +507,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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paul = createPatientAndUpdateLinks(paul);
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Patient sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(paul);
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// TODO NG - rules haven't been determined yet revisit once implemented...
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// assertThat(sourcePatientFromTarget.getBirthDateElement().getValueAsString(), is(incorrectBirthdate));
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assertThat(sourcePatientFromTarget.getBirthDateElement().getValueAsString(), is(incorrectBirthdate));
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String correctBirthdate = "1990-06-28";
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paul.getBirthDateElement().setValueAsString(correctBirthdate);
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@ -525,8 +515,7 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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paul = updatePatientAndUpdateLinks(paul);
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sourcePatientFromTarget = (Patient) getGoldenResourceFromTargetResource(paul);
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// TODO NG - rules haven't been determined yet revisit once implemented...
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// assertThat(sourcePatientFromTarget.getBirthDateElement().getValueAsString(), is(equalTo(correctBirthdate)));
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assertThat(sourcePatientFromTarget.getBirthDateElement().getValueAsString(), is(equalTo(correctBirthdate)));
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assertLinkCount(1);
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}
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@ -613,6 +602,5 @@ public class MdmMatchLinkSvcTest extends BaseMdmR4Test {
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List<MdmLink> possibleDuplicates = myMdmLinkDaoSvc.getPossibleDuplicates();
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assertThat(possibleDuplicates, hasSize(1));
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assertThat(patient3, is(possibleDuplicateOf(patient1)));
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}
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}
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@ -144,6 +144,7 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
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@Operation(name = ProviderConstants.MDM_MERGE_GOLDEN_RESOURCES)
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public IBaseResource mergeGoldenResources(@OperationParam(name = ProviderConstants.MDM_MERGE_GR_FROM_GOLDEN_RESOURCE_ID, min = 1, max = 1, typeName = "string") IPrimitiveType<String> theFromGoldenResourceId,
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@OperationParam(name = ProviderConstants.MDM_MERGE_GR_TO_GOLDEN_RESOURCE_ID, min = 1, max = 1, typeName = "string") IPrimitiveType<String> theToGoldenResourceId,
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@OperationParam()
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RequestDetails theRequestDetails) {
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validateMergeParameters(theFromGoldenResourceId, theToGoldenResourceId);
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@ -29,11 +29,34 @@ import ca.uhn.fhir.util.FhirTerser;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import java.lang.reflect.Method;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.List;
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import java.util.function.Predicate;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import static ca.uhn.fhir.mdm.util.GoldenResourceHelper.FIELD_NAME_IDENTIFIER;
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final class TerserUtil {
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public final class TerserUtil {
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public static final Collection<String> IDS_AND_META_EXCLUDES =
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Collections.unmodifiableSet(Stream.of("id", "meta", "identifier").collect(Collectors.toSet()));
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public static final Predicate<String> EXCLUDE_IDS_AND_META = new Predicate<String>() {
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@Override
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public boolean test(String s) {
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return !IDS_AND_META_EXCLUDES.contains(s);
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}
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};
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public static final Predicate<String> INCLUDE_ALL = new Predicate<String>() {
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@Override
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public boolean test(String s) {
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return true;
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}
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};
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private TerserUtil() {
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}
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@ -41,9 +64,9 @@ final class TerserUtil {
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/**
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* Clones the specified canonical EID into the identifier field on the resource
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*
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* @param theFhirContext Context to pull resource definitions from
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* @param theFhirContext Context to pull resource definitions from
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* @param theResourceToCloneInto Resource to set the EID on
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* @param theEid EID to be set
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* @param theEid EID to be set
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*/
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public static void cloneEidIntoResource(FhirContext theFhirContext, IBaseResource theResourceToCloneInto, CanonicalEID theEid) {
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// get a ref to the actual ID Field
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@ -84,7 +107,7 @@ final class TerserUtil {
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List<IBase> theToFieldValues = childDefinition.getAccessor().getValues(theTo);
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for (IBase theFromFieldValue : theFromFieldValues) {
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if (contains(theFromFieldValue, theToFieldValues)) {
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if (containsPrimitiveValue(theFromFieldValue, theToFieldValues)) {
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continue;
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}
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@ -95,11 +118,87 @@ final class TerserUtil {
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}
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}
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private static boolean contains(IBase theItem, List<IBase> theItems) {
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private static boolean containsPrimitiveValue(IBase theItem, List<IBase> theItems) {
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PrimitiveTypeEqualsPredicate predicate = new PrimitiveTypeEqualsPredicate();
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return theItems.stream().anyMatch(i -> {
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return predicate.test(i, theItem);
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});
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}
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private static boolean contains(IBase theItem, List<IBase> theItems) {
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Method method = null;
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for (Method m : theItem.getClass().getDeclaredMethods()) {
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if (m.getName().equals("equalsDeep")) {
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method = m;
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break;
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}
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}
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final Method m = method;
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return theItems.stream().anyMatch(i -> {
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if (m != null) {
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try {
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return (Boolean) m.invoke(theItem, i);
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} catch (Exception e) {
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throw new RuntimeException("Unable to compare equality via equalsDeep", e);
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}
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}
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return theItem.equals(i);
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});
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}
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public static void mergeAllFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo) {
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mergeFields(theFhirContext, theFrom, theTo, INCLUDE_ALL);
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}
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public static void overwriteFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<String> inclusionStrategy) {
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FhirTerser terser = theFhirContext.newTerser();
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RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
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for (BaseRuntimeChildDefinition childDefinition : definition.getChildrenAndExtension()) {
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if (!inclusionStrategy.test(childDefinition.getElementName())) {
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continue;
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}
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childDefinition.getAccessor().getFirstValueOrNull(theFrom).ifPresent( v -> {
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childDefinition.getMutator().setValue(theTo, v);
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}
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);
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}
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}
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public static void mergeFieldsExceptIdAndMeta(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo) {
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mergeFields(theFhirContext, theFrom, theTo, EXCLUDE_IDS_AND_META);
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}
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public static void mergeFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<String> inclusionStrategy) {
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FhirTerser terser = theFhirContext.newTerser();
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RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
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for (BaseRuntimeChildDefinition childDefinition : definition.getChildrenAndExtension()) {
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if (!inclusionStrategy.test(childDefinition.getElementName())) {
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continue;
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}
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List<IBase> theFromFieldValues = childDefinition.getAccessor().getValues(theFrom);
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List<IBase> theToFieldValues = childDefinition.getAccessor().getValues(theTo);
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for (IBase theFromFieldValue : theFromFieldValues) {
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if (contains(theFromFieldValue, theToFieldValues)) {
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continue;
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}
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IBase newFieldValue = childDefinition.getChildByName(childDefinition.getElementName()).newInstance();
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terser.cloneInto(theFromFieldValue, newFieldValue, true);
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try {
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theToFieldValues.add(newFieldValue);
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} catch (UnsupportedOperationException e) {
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childDefinition.getMutator().setValue(theTo, newFieldValue);
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break;
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}
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}
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}
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}
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}
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@ -8,7 +8,9 @@ import org.junit.jupiter.api.Test;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.hasSize;
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import static org.junit.jupiter.api.Assertions.*;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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||||
import static org.junit.jupiter.api.Assertions.assertNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
class TerserUtilTest extends BaseR4Test {
|
||||
|
||||
|
|
@ -28,12 +30,12 @@ class TerserUtilTest extends BaseR4Test {
|
|||
assertEquals(p1.getIdentifier().get(0).getValue(), p2.getIdentifier().get(0).getValue());
|
||||
}
|
||||
|
||||
// @Test
|
||||
@Test
|
||||
void testCloneFields() {
|
||||
Patient p1 = buildJohny();
|
||||
Patient p2 = new Patient();
|
||||
|
||||
// TerserUtil.cloneFields(ourFhirContext, p1, p2);
|
||||
TerserUtil.mergeFieldsExceptIdAndMeta(ourFhirContext, p1, p2);
|
||||
|
||||
assertTrue(p2.getIdentifier().isEmpty());
|
||||
|
||||
|
|
@ -42,8 +44,8 @@ class TerserUtilTest extends BaseR4Test {
|
|||
assertEquals(p1.getName().get(0).getNameAsSingleString(), p2.getName().get(0).getNameAsSingleString());
|
||||
}
|
||||
|
||||
// @Test
|
||||
void testAnotherCloneFields() {
|
||||
@Test
|
||||
void testCloneWithNonPrimitves() {
|
||||
Patient p1 = new Patient();
|
||||
Patient p2 = new Patient();
|
||||
|
||||
|
|
@ -57,9 +59,32 @@ class TerserUtilTest extends BaseR4Test {
|
|||
assertThat(p2.getName(), hasSize(1));
|
||||
assertThat(p2.getName().get(0).getGiven(), hasSize(2));
|
||||
|
||||
// TerserUtil.cloneFields(ourFhirContext, p1, p2);
|
||||
TerserUtil.mergeAllFields(ourFhirContext, p1, p2);
|
||||
assertThat(p2.getName(), hasSize(2));
|
||||
assertThat(p2.getName().get(0).getGiven(), hasSize(2));
|
||||
assertThat(p2.getName().get(1).getGiven(), hasSize(2));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testCloneWithDuplicateNonPrimitives() {
|
||||
Patient p1 = new Patient();
|
||||
Patient p2 = new Patient();
|
||||
|
||||
p1.addName().addGiven("Jim");
|
||||
p1.getNameFirstRep().addGiven("George");
|
||||
|
||||
assertThat(p1.getName(), hasSize(1));
|
||||
assertThat(p1.getName().get(0).getGiven(), hasSize(2));
|
||||
|
||||
p2.addName().addGiven("Jim");
|
||||
p2.getNameFirstRep().addGiven("George");
|
||||
|
||||
assertThat(p2.getName(), hasSize(1));
|
||||
assertThat(p2.getName().get(0).getGiven(), hasSize(2));
|
||||
|
||||
TerserUtil.mergeAllFields(ourFhirContext, p1, p2);
|
||||
|
||||
assertThat(p2.getName(), hasSize(1));
|
||||
assertThat(p2.getName().get(0).getGiven(), hasSize(2));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue