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Fixed implementation based on the feedback.

This commit is contained in:
Nick Goupinets 2020-10-28 15:09:15 -04:00
parent 170cf245cc
commit 954fbf054f
6 changed files with 91 additions and 20 deletions
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43
hapi-fhir-jpaserver-empi/src/test/java/ca/uhn/fhir/jpa/empi/provider/EmpiProviderMatchR4Test.java
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@ -1,23 +1,28 @@
package ca.uhn.fhir.jpa.empi.provider;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.empi.api.EmpiConstants;
import com.google.common.collect.Ordering;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.codesystems.MatchGrade;
import org.junit.Assert;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import java.util.List;
import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.*;
public class EmpiProviderMatchR4Test extends BaseProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(EmpiProviderMatchR4Test.class);
public static final String NAME_GIVEN_JANET = NAME_GIVEN_JANE + "t";
@Override
@BeforeEach
public void before() {
@ -41,12 +46,38 @@ public class EmpiProviderMatchR4Test extends BaseProviderR4Test {
Bundle.BundleEntrySearchComponent searchComponent = entry0.getSearch();
assertEquals(Bundle.SearchEntryMode.MATCH, searchComponent.getMode());
assertEquals(2.0/3.0, searchComponent.getScore().doubleValue(), 0.01);
Extension matchGradeExtension = searchComponent.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/match-grade");
assertEquals(2.0 / 3.0, searchComponent.getScore().doubleValue(), 0.01);
Extension matchGradeExtension = searchComponent.getExtensionByUrl(EmpiConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE);
assertNotNull(matchGradeExtension);
assertEquals(MatchGrade.CERTAIN.toCode(), matchGradeExtension.getValue().toString());
}
@Test
public void testMatchOrder() throws Exception {
Patient jane0 = buildJanePatient();
Patient createdJane1 = createPatient(jane0);
Patient jane1 = buildPatientWithNameAndId(NAME_GIVEN_JANET, JANE_ID);
jane1.setActive(true);
Patient createdJane2 = createPatient(jane1);
Patient newJane = buildJanePatient();
Bundle result = myEmpiProviderR4.match(newJane);
assertEquals(2, result.getEntry().size());
Bundle.BundleEntryComponent entry0 = result.getEntry().get(0);
assertTrue(jane0.getId().equals(((Patient) entry0.getResource()).getId()), "First match should be Jane");
Bundle.BundleEntryComponent entry1 = result.getEntry().get(1);
assertTrue(jane1.getId().equals(((Patient) entry1.getResource()).getId()), "Second match should be Janet");
List<Double> scores = result.getEntry()
.stream()
.map(bec -> bec.getSearch().getScore().doubleValue())
.collect(Collectors.toList());
assertTrue(Ordering.<Double>natural().reverse().isOrdered(scores), "Match scores must be descending");
}
@Test
public void testMismatch() throws Exception {
Patient jane = buildJanePatient();

1
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/api/EmpiConstants.java
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@ -32,5 +32,6 @@ public class EmpiConstants {
public static final String HAPI_ENTERPRISE_IDENTIFIER_SYSTEM = "http://hapifhir.io/fhir/NamingSystem/empi-person-enterprise-id";
public static final String ALL_RESOURCE_SEARCH_PARAM_TYPE = "*";
public static final String FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE = "http://hl7.org/fhir/StructureDefinition/match-grade";
}

7
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/api/EmpiMatchOutcome.java
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@ -117,7 +117,12 @@ public final class EmpiMatchOutcome {
} else if (score > vector) {
return 1.0;
}
return score / vector;
double retVal = score / vector;
if (retVal < 0) {
retVal = 0.0;
}
return retVal;
}
@Override

18
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/provider/EmpiProviderDstu3.java
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@ -21,6 +21,7 @@ package ca.uhn.fhir.empi.provider;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.empi.api.EmpiConstants;
import ca.uhn.fhir.empi.api.EmpiLinkJson;
import ca.uhn.fhir.empi.api.IEmpiControllerSvc;
import ca.uhn.fhir.empi.api.IEmpiExpungeSvc;
@ -52,6 +53,7 @@ import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IIdType;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import java.util.UUID;
import java.util.stream.Stream;
@ -77,11 +79,13 @@ public class EmpiProviderDstu3 extends BaseEmpiProvider {
}
@Operation(name = ProviderConstants.EMPI_MATCH, type = Patient.class)
public Bundle match(@OperationParam(name=ProviderConstants.EMPI_MATCH_RESOURCE, min = 1, max = 1) Patient thePatient) {
public Bundle match(@OperationParam(name = ProviderConstants.EMPI_MATCH_RESOURCE, min = 1, max = 1) Patient thePatient) {
if (thePatient == null) {
throw new InvalidRequestException("resource may not be null");
}
List<MatchedTarget> matches = myEmpiMatchFinderSvc.getMatchedTargets("Patient", thePatient);
matches.sort(Comparator.comparing((MatchedTarget m) -> m.getMatchResult().getNormalizedScore()).reversed());
Bundle retVal = new Bundle();
retVal.setType(Bundle.BundleType.SEARCHSET);
@ -104,19 +108,19 @@ public class EmpiProviderDstu3 extends BaseEmpiProvider {
return retVal;
}
private Bundle.BundleEntrySearchComponent toBundleEntrySearchComponent(MatchedTarget next) {
private Bundle.BundleEntrySearchComponent toBundleEntrySearchComponent(MatchedTarget theMatchedTarget) {
Bundle.BundleEntrySearchComponent searchComponent = new Bundle.BundleEntrySearchComponent();
searchComponent.setMode(Bundle.SearchEntryMode.MATCH);
searchComponent.setScore(next.getMatchResult().getNormalizedScore());
searchComponent.setScore(theMatchedTarget.getMatchResult().getNormalizedScore());
MatchGrade matchGrade = MatchGrade.PROBABLE;
if (next.isMatch()) {
if (theMatchedTarget.isMatch()) {
matchGrade = MatchGrade.CERTAIN;
} else if (next.isPossibleMatch()) {
} else if (theMatchedTarget.isPossibleMatch()) {
matchGrade = MatchGrade.POSSIBLE;
}
searchComponent.addExtension("http://hl7.org/fhir/StructureDefinition/match-grade",
new CodeType(matchGrade.toCode()));
searchComponent.addExtension(EmpiConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE, new CodeType(matchGrade.toCode()));
return searchComponent;
}

15
hapi-fhir-server-empi/src/main/java/ca/uhn/fhir/empi/provider/EmpiProviderR4.java
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@ -21,6 +21,7 @@ package ca.uhn.fhir.empi.provider;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.empi.api.EmpiConstants;
import ca.uhn.fhir.empi.api.EmpiLinkJson;
import ca.uhn.fhir.empi.api.IEmpiControllerSvc;
import ca.uhn.fhir.empi.api.IEmpiExpungeSvc;
@ -54,6 +55,7 @@ import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.codesystems.MatchGrade;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import java.util.UUID;
import java.util.stream.Stream;
@ -85,6 +87,7 @@ public class EmpiProviderR4 extends BaseEmpiProvider {
}
List<MatchedTarget> matches = myEmpiMatchFinderSvc.getMatchedTargets("Patient", thePatient);
matches.sort(Comparator.comparing((MatchedTarget m) -> m.getMatchResult().getNormalizedScore()).reversed());
Bundle retVal = new Bundle();
retVal.setType(Bundle.BundleType.SEARCHSET);
@ -107,19 +110,19 @@ public class EmpiProviderR4 extends BaseEmpiProvider {
return retVal;
}
private Bundle.BundleEntrySearchComponent toBundleEntrySearchComponent(MatchedTarget next) {
private Bundle.BundleEntrySearchComponent toBundleEntrySearchComponent(MatchedTarget theMatchedTarget) {
Bundle.BundleEntrySearchComponent searchComponent = new Bundle.BundleEntrySearchComponent();
searchComponent.setMode(Bundle.SearchEntryMode.MATCH);
searchComponent.setScore(next.getMatchResult().getNormalizedScore());
searchComponent.setScore(theMatchedTarget.getMatchResult().getNormalizedScore());
MatchGrade matchGrade = MatchGrade.PROBABLE;
if (next.isMatch()) {
if (theMatchedTarget.isMatch()) {
matchGrade = MatchGrade.CERTAIN;
} else if (next.isPossibleMatch()) {
} else if (theMatchedTarget.isPossibleMatch()) {
matchGrade = MatchGrade.POSSIBLE;
}
searchComponent.addExtension("http://hl7.org/fhir/StructureDefinition/match-grade",
new CodeType(matchGrade.toCode()));
searchComponent.addExtension(EmpiConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE, new CodeType(matchGrade.toCode()));
return searchComponent;
}

27
hapi-fhir-server-empi/src/test/java/ca/uhn/fhir/empi/api/EmpiMatchOutcomeTest.java Normal file
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@ -0,0 +1,27 @@
package ca.uhn.fhir.empi.api;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*;
class EmpiMatchOutcomeTest {
@Test
void testNormalizedScore() {
EmpiMatchOutcome outcome = new EmpiMatchOutcome(0l, 0.0);
assertEquals(0.0, outcome.getNormalizedScore());
outcome = new EmpiMatchOutcome(10l, 10.0);
assertEquals(1.0, outcome.getNormalizedScore());
outcome = new EmpiMatchOutcome(10l, -10.0);
assertEquals(0.0, outcome.getNormalizedScore());
outcome = new EmpiMatchOutcome(3l, 2.0);
assertEquals(2.0 / 3.0, outcome.getNormalizedScore(), 0.0001);
outcome = new EmpiMatchOutcome(5l, 19.0);
assertEquals(1.0, outcome.getNormalizedScore());
}
}