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Code review updates

This commit is contained in:
Nick 2021-01-15 14:07:14 -05:00
parent 6cc40b134e
commit f10785ed43
6 changed files with 77 additions and 13 deletions
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4
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmEidUpdateService.java
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@ -81,7 +81,9 @@ public class MdmEidUpdateService {
//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);
// TODO NG - Do we need to merge fields from the old golden resource to the new golden resource?
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(theTargetResource, updateContext.getMatchedGoldenResource(), theMdmTransactionContext);
myMdmResourceDaoSvc.upsertGoldenResource(updateContext.getMatchedGoldenResource(), theMdmTransactionContext.getResourceType());
}
}

1
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkUpdaterSvcImpl.java
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@ -94,7 +94,6 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
mdmLink.setLinkSource(MdmLinkSourceEnum.MANUAL);
myMdmLinkDaoSvc.save(mdmLink);
// IAnyResource resource = (theManuallyMergedGoldenResource == null) ? theSourceResource : theManuallyMergedGoldenResource;
if (theMatchResult == MdmMatchResultEnum.MATCH) {
// only apply survivorship rules in case of a match
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(theSourceResource, theGoldenResource, theMdmContext);

9
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/svc/MdmSurvivorshipSvcImpl.java
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@ -34,12 +34,9 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
private FhirContext myFhirContext;
/**
* TODO NG Update docs to tell taht we also do that in non GR merge - like linking
*
* Merges two golden resources by overwriting all field values on theGoldenResource param for all REST operation methods
* except MERGE_GOLDEN_RESOURCES. In case of MERGE_GOLDEN_RESOURCES, it will attempt to copy field values from
* theTargetResource that do not exist in theGoldenResource. PID, indentifiers and meta values are not affected by
* this operation.
* Merges two golden resources by overwriting all field values on theGoldenResource param for CREATE_RESOURCE,
* UPDATE_RESOURCE, SUBMIT_RESOURCE_TO_MDM, UPDATE_LINK (when setting to MATCH) and MANUAL_MERGE_GOLDEN_RESOURCES.
* PID, identifiers and meta values are not affected by this operation.
*
* @param theTargetResource Target resource to retrieve fields from
* @param theGoldenResource Golden resource to merge fields into

14
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmGoldenResourceMergerSvcTest.java
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@ -18,6 +18,7 @@ import org.hl7.fhir.r4.model.DateType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
@ -34,8 +35,7 @@ import java.util.stream.Collectors;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasSize;
import static org.hamcrest.Matchers.is;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
import static org.junit.jupiter.api.Assertions.*;
public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
@ -409,6 +409,9 @@ public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
assertThat(mergedSourcePatient.getName(), hasSize(2));
assertThat(mergedSourcePatient.getName().get(0).getGiven(), hasSize(2));
assertThat(mergedSourcePatient.getName().get(1).getGiven(), hasSize(2));
assertThat(mergedSourcePatient.getName().get(0).getNameAsSingleString(), is("Jeff George"));
assertThat(mergedSourcePatient.getName().get(1).getNameAsSingleString(), is("Jim George"));
}
@Test
@ -426,6 +429,8 @@ public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
mergeGoldenPatients();
assertThat(myToGoldenPatient.getName(), hasSize(1));
assertThat(myToGoldenPatient.getName().get(0).getGiven(), hasSize(2));
assertThat(myToGoldenPatient.getName().get(0).getNameAsSingleString(), is("Jim George"));
}
@Test
@ -442,6 +447,11 @@ public class MdmGoldenResourceMergerSvcTest extends BaseMdmR4Test {
mergeGoldenPatients();
assertThat(myToGoldenPatient.getIdentifier(), hasSize(4));
assertTrue(myToGoldenPatient.getIdentifier().get(0).equalsDeep(new Identifier().setValue("aaa").setSystem("SYSTEM1")));
assertTrue(myToGoldenPatient.getIdentifier().get(1).equalsDeep(new Identifier().setValue("ccc").setSystem("SYSTEM1")));
assertTrue(myToGoldenPatient.getIdentifier().get(2).equalsDeep(new Identifier().setValue("bbb").setSystem("SYSTEM1")));
assertTrue(myToGoldenPatient.getIdentifier().get(3).equalsDeep(new Identifier().setValue("ccc").setSystem("SYSTEM2")));
}
private MdmLink createMdmLink(Patient theSourcePatient, Patient theTargetPatient) {

56
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmSurvivorshipSvcImplTest.java
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@ -1,7 +1,59 @@
package ca.uhn.fhir.jpa.mdm.svc;
import static org.junit.jupiter.api.Assertions.*;
import ca.uhn.fhir.jpa.mdm.BaseMdmR4Test;
import ca.uhn.fhir.mdm.api.IMdmSurvivorshipService;
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
import org.hl7.fhir.r4.model.Patient;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
class MdmSurvivorshipSvcImplTest {
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
class MdmSurvivorshipSvcImplTest extends BaseMdmR4Test {
@Autowired
private IMdmSurvivorshipService myMdmSurvivorshipService;
@Test
public void testRulesOnCreate() {
Patient p1 = buildFrankPatient();
Patient p2 = new Patient();
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(p1, p2, new MdmTransactionContext(MdmTransactionContext.OperationType.CREATE_RESOURCE));
assertFalse(p2.hasIdElement());
assertTrue(p2.getIdentifier().isEmpty());
assertTrue(p2.getMeta().isEmpty());
assertTrue(p1.getNameFirstRep().equalsDeep(p2.getNameFirstRep()));
assertNull(p2.getBirthDate());
assertEquals(p1.getTelecom().size(), p2.getTelecom().size());
assertTrue(p2.getTelecomFirstRep().equalsDeep(p1.getTelecomFirstRep()));
}
@Test
public void testRulesOnMerge() {
Patient p1 = buildFrankPatient();
String p1Name = p1.getNameFirstRep().getNameAsSingleString();
Patient p2 = buildPaulPatient();
String p2Name = p2.getNameFirstRep().getNameAsSingleString();
myMdmSurvivorshipService.applySurvivorshipRulesToGoldenResource(p1, p2, new MdmTransactionContext(MdmTransactionContext.OperationType.MERGE_GOLDEN_RESOURCES));
assertFalse(p2.hasIdElement());
assertFalse(p2.getIdentifier().isEmpty());
assertTrue(p2.getMeta().isEmpty());
assertEquals(2, p2.getName().size());
assertEquals(p2Name, p2.getName().get(0).getNameAsSingleString());
assertEquals(p1Name, p2.getName().get(1).getNameAsSingleString());
assertNull(p2.getBirthDate());
assertEquals(p1.getTelecom().size(), p1.getTelecom().size());
assertTrue(p2.getTelecomFirstRep().equalsDeep(p1.getTelecomFirstRep()));
}
}

6
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/util/TerserUtil.java
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@ -131,7 +131,11 @@ public final class TerserUtil {
IBase newFieldValue = childDefinition.getChildByName(field).newInstance();
terser.cloneInto(theFromFieldValue, newFieldValue, true);
theToFieldValues.add(newFieldValue);
try {
theToFieldValues.add(newFieldValue);
} catch (Exception e) {
childDefinition.getMutator().setValue(theTo, newFieldValue);
}
}
}