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refactor: add method to create FHIR references #102

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refactor: add method to create FHIR references #102

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2 changes: 1 addition & 1 deletion src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsConditionMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@ public Bundle mapOnkoResourcesToCondition(

onkoCondition.setSubject(
new Reference()
.setReference(ResourceType.Patient + "/" + this.getHash(ResourceType.Patient, pid))
.setReference(this.getReference(ResourceType.Patient, pid))
.setIdentifier(
new Identifier()
.setSystem(fhirProperties.getSystems().getPatientId())
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5 changes: 1 addition & 4 deletions src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsMedicationStatementMapper.java
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Expand Up @@ -149,10 +149,7 @@ public MedicationStatement createSystemtherapyMedicationStatement(
stMedicationStatement.setPartOf(
List.of(
new Reference()
.setReference(
ResourceType.MedicationStatement
+ "/"
+ this.getHash(ResourceType.MedicationStatement, partOfId))));
.setReference(this.getReference(ResourceType.MedicationStatement, partOfId))));
}

} else {
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7 changes: 2 additions & 5 deletions src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsObservationMapper.java
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Expand Up @@ -318,7 +318,7 @@ public Bundle mapOnkoResourcesToObservationsBundle(

var patientReference =
new Reference()
.setReference(ResourceType.Patient + "/" + this.getHash(ResourceType.Patient, patId))
.setReference(this.getReference(ResourceType.Patient, patId))
.setIdentifier(
new Identifier()
.setSystem(fhirProperties.getSystems().getPatientId())
Expand Down Expand Up @@ -556,10 +556,7 @@ public Bundle createHistologieAndGradingObservation(
if (grading != null) {
histObs.addHasMember(
new Reference()
.setReference(
ResourceType.Observation
+ "/"
+ this.getHash(ResourceType.Observation, gradingObsIdentifier)));
.setReference(this.getReference(ResourceType.Observation, gradingObsIdentifier)));
}

bundle = addResourceAsEntryInBundle(bundle, histObs);
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6 changes: 1 addition & 5 deletions src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsProcedureMapper.java
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Expand Up @@ -167,11 +167,7 @@ public Procedure createOpProcedure(
if (distinctOpsSet.size() > 1) {
opProcedure.setPartOf(
List.of(
new Reference()
.setReference(
ResourceType.Procedure
+ "/"
+ this.getHash(ResourceType.Procedure, partOfId))));
new Reference().setReference(this.getReference(ResourceType.Procedure, partOfId))));
}

// Code
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4 changes: 4 additions & 0 deletions src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsToFhirMapper.java
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Expand Up @@ -67,6 +67,10 @@ protected String getHash(ResourceType type, String id) {
return Hashing.sha256().hashString(idToHash + "|" + id, StandardCharsets.UTF_8).toString();
}

protected String getReference(ResourceType type, String id) {
return type + "/" + this.getHash(type, id);
}

protected String computeResourceIdFromIdentifier(Identifier identifier) {
return Hashing.sha256()
.hashString(identifier.getSystem() + "|" + identifier.getValue(), StandardCharsets.UTF_8)
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26 changes: 25 additions & 1 deletion src/test/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsToFhirIntegrationTest.java
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@@ -1,9 +1,12 @@
package org.miracum.streams.ume.obdstofhir.mapper;

import static org.assertj.core.api.Assertions.assertThat;
import static org.mockito.Mockito.doAnswer;

import org.hl7.fhir.r4.model.ResourceType;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.CsvSource;
Expand All @@ -17,9 +20,10 @@

@ExtendWith(SpringExtension.class)
@Import({ObdsTestMapper.class})
@MockBean(FhirProperties.class)
public class ObdsToFhirIntegrationTest {

@MockBean FhirProperties fhirProperties;

ObdsTestMapper mapper;

@BeforeEach
Expand Down Expand Up @@ -96,6 +100,26 @@ void applyPatientIdPattern(String input, String output) {
assertThat(actual).isEqualTo(output);
}
}

@Nested
class References {

@Test
void shouldCreateReferenceString() {
doAnswer(
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das müsste man sich einsparen können indem man analog zu zB https://github.com/bzkf/obds-to-fhir/blob/master/src/test/java/org/miracum/streams/ume/obdstofhir/mapper/GleasonScoreToObservationMapperTests.java#L30-L33 einen

@SpringBootTest daraus macht

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@pcvolkmer pcvolkmer Oct 3, 2024 •
edited
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Bei Verwendung von @SpringBootTest wird die komplette Anwendung konfiguriert und es ist z.B. auch eine Kafka-Instanz erforderlich (@ExtendWith(SpringExtension.class)). Mit dem Ansatz, müsste der benötigte Test-Slices explizit konfiguriert werden.

Mit dem hier gewählten Ansatz wird lediglich die Integration der Konfiguration(sparameter) - hier mit Mockitos doAnswer(..) gemockt um einen Wert für fhirSystems.setPatientId zu liefern - und der Methoden getHash(..) der abstrakten Klasse ObdsToFhir in einer konkreten (Test-)Implementierung (hier: ObdsTestMapper) von ObdsToFhir zur Erzeugung eines Resource-Strings getestet, ohne größere Teile der Anwendung konfigurieren zu müssen.

invocationOnMock -> {
final var fhirSystems = new FhirProperties.FhirSystems();
fhirSystems.setPatientId("https://fhir.diz.uk-erlangen.de/identifiers/patient-id");
return fhirSystems;
})
.when(fhirProperties)
.getSystems();

final var actual = mapper.getReference(ResourceType.Patient, "1");
assertThat(actual)
.isEqualTo("Patient/82a86769573e519a1fa2d79911fb19fbdceabe2416a5c9230b503618a23a31c1");
}
}
}

@Component
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