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feat: add initial SystemischeTherapieProcedureMapper (#165)
* feat: add initial SystemischeTherapieMapper * feat: set code.systemische_therapie_art if available * fix: handle oBDS DatumTagOderMonatGenauTyp * fix: use absent category * test: add tests for conversion to DateTimeType * refactor: rename mapper class to reflect destination type * refactor: rename init method * feat: add outcome if available in oBDS
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117 changes: 117 additions & 0 deletions
117
...ava/org/miracum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieProcedureMapper.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| package org.miracum.streams.ume.obdstofhir.mapper.mii; | ||
|
|
||
| import de.basisdatensatz.obds.v3.SYSTTyp; | ||
| import java.util.Objects; | ||
| import org.apache.commons.lang3.Validate; | ||
| import org.hl7.fhir.r4.model.CodeType; | ||
| import org.hl7.fhir.r4.model.CodeableConcept; | ||
| import org.hl7.fhir.r4.model.DateTimeType; | ||
| import org.hl7.fhir.r4.model.Enumerations.ResourceType; | ||
| import org.hl7.fhir.r4.model.Extension; | ||
| import org.hl7.fhir.r4.model.Identifier; | ||
| import org.hl7.fhir.r4.model.Period; | ||
| import org.hl7.fhir.r4.model.Procedure; | ||
| import org.hl7.fhir.r4.model.Reference; | ||
| import org.miracum.streams.ume.obdstofhir.FhirProperties; | ||
| import org.miracum.streams.ume.obdstofhir.mapper.ObdsToFhirMapper; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
| import org.springframework.stereotype.Service; | ||
|
|
||
| @Service | ||
| public class SystemischeTherapieProcedureMapper extends ObdsToFhirMapper { | ||
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| private static final Logger LOG = | ||
| LoggerFactory.getLogger(SystemischeTherapieProcedureMapper.class); | ||
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| public SystemischeTherapieProcedureMapper(FhirProperties fhirProperties) { | ||
| super(fhirProperties); | ||
| } | ||
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| public Procedure map(SYSTTyp syst, Reference subject) { | ||
| Objects.requireNonNull(syst, "Systemtherapie must not be null"); | ||
| Objects.requireNonNull(subject, "Reference must not be null"); | ||
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|
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| Validate.notBlank(syst.getSYSTID(), "Required SYST_ID is unset"); | ||
| Validate.isTrue( | ||
| Objects.equals( | ||
| subject.getReferenceElement().getResourceType(), ResourceType.PATIENT.toCode()), | ||
| "The subject reference should point to a Patient resource"); | ||
|
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| var procedure = new Procedure(); | ||
| procedure.getMeta().addProfile(fhirProperties.getProfiles().getMiiPrOnkoSystemischeTherapie()); | ||
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| // TODO: can we be sure that this SYST-ID is globally unqiue across all SYSTs? - | ||
| // if not we may instead need to construct the ID from the patient-id + others. | ||
| var identifier = | ||
| new Identifier() | ||
| .setSystem(fhirProperties.getSystems().getSystemischeTherapieProcedureId()) | ||
| .setValue(syst.getSYSTID()); | ||
| procedure.addIdentifier(identifier); | ||
| procedure.setId(computeResourceIdFromIdentifier(identifier)); | ||
|
|
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| // Status | ||
| if (syst.getMeldeanlass() == SYSTTyp.Meldeanlass.BEHANDLUNGSENDE) { | ||
| procedure.setStatus(Procedure.ProcedureStatus.COMPLETED); | ||
| } else { | ||
| procedure.setStatus(Procedure.ProcedureStatus.INPROGRESS); | ||
| } | ||
|
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| procedure.setSubject(subject); | ||
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| var dataAbsentExtension = | ||
| new Extension( | ||
| fhirProperties.getExtensions().getDataAbsentReason(), new CodeType("unknown")); | ||
| var dataAbsentCode = new CodeType(); | ||
| dataAbsentCode.addExtension(dataAbsentExtension); | ||
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| if (syst.getBeginn() == null && syst.getEnde() == null) { | ||
| var performedStart = new DateTimeType(); | ||
| performedStart.addExtension(dataAbsentExtension); | ||
| var performed = new Period().setStartElement(performedStart); | ||
| procedure.setPerformed(performed); | ||
| } else { | ||
| var performed = new Period(); | ||
| convertObdsDatumToDateTimeType(syst.getBeginn()).ifPresent(performed::setStartElement); | ||
| convertObdsDatumToDateTimeType(syst.getEnde()).ifPresent(performed::setEndElement); | ||
| procedure.setPerformed(performed); | ||
| } | ||
|
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| var code = new CodeableConcept(); | ||
| // Always add absent OPS | ||
| code.addCoding().setSystem(fhirProperties.getSystems().getOps()).setCodeElement(dataAbsentCode); | ||
| if (null != syst.getTherapieart()) { | ||
| code.addCoding() | ||
| .setSystem(fhirProperties.getSystems().getMiiCsOnkoSystemischeTherapieArt()) | ||
| .setCode(syst.getTherapieart().value()); | ||
| } | ||
|
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| procedure.setCode(code); | ||
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| var category = new CodeableConcept(); | ||
| category | ||
| .addCoding() | ||
| .setSystem(fhirProperties.getSystems().getSnomed()) | ||
| .setCodeElement(dataAbsentCode); | ||
| procedure.setCategory(category); | ||
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| var intention = new CodeableConcept(); | ||
| intention | ||
| .addCoding() | ||
| .setSystem(fhirProperties.getSystems().getMiiCsOnkoIntention()) | ||
| .setCode(syst.getIntention()); // Direct mapping from oBDS value | ||
| procedure.addExtension( | ||
| fhirProperties.getExtensions().getMiiExOnkoSystemischeTherapieIntention(), intention); | ||
|
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| if (null != syst.getEndeGrund()) { | ||
| var outcome = new CodeableConcept(); | ||
| outcome | ||
| .addCoding() | ||
| .setSystem(fhirProperties.getSystems().getMiiCsTherapieGrundEnde()) | ||
| .setCode(syst.getEndeGrund().value()); | ||
| procedure.setOutcome(outcome); | ||
| } | ||
|
|
||
| return procedure; | ||
| } | ||
| } |
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63 changes: 63 additions & 0 deletions
63
...org/miracum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieProcedureMapperTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| package org.miracum.streams.ume.obdstofhir.mapper.mii; | ||
|
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| import static org.assertj.core.api.Assertions.assertThat; | ||
|
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| import ca.uhn.fhir.context.FhirContext; | ||
| import com.fasterxml.jackson.databind.DeserializationFeature; | ||
| import com.fasterxml.jackson.dataformat.xml.XmlMapper; | ||
| import com.fasterxml.jackson.datatype.jdk8.Jdk8Module; | ||
| import com.fasterxml.jackson.module.jakarta.xmlbind.JakartaXmlBindAnnotationModule; | ||
| import de.basisdatensatz.obds.v3.OBDS; | ||
| import java.io.IOException; | ||
| import org.approvaltests.Approvals; | ||
| import org.hl7.fhir.r4.model.Reference; | ||
| import org.junit.jupiter.api.BeforeAll; | ||
| import org.junit.jupiter.params.ParameterizedTest; | ||
| import org.junit.jupiter.params.provider.CsvSource; | ||
| import org.miracum.streams.ume.obdstofhir.FhirProperties; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.context.properties.EnableConfigurationProperties; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
|
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| @SpringBootTest(classes = {FhirProperties.class}) | ||
| @EnableConfigurationProperties | ||
| class SystemischeTherapieProcedureMapperTest { | ||
| private static SystemischeTherapieProcedureMapper sut; | ||
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| @BeforeAll | ||
| static void beforeAll(@Autowired FhirProperties fhirProps) { | ||
| sut = new SystemischeTherapieProcedureMapper(fhirProps); | ||
| } | ||
|
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| @ParameterizedTest | ||
| @CsvSource({"Testpatient_1.xml", "Testpatient_2.xml", "Testpatient_3.xml"}) | ||
| void map_withGivenObds_shouldCreateValidProcedure(String sourceFile) throws IOException { | ||
| final var resource = this.getClass().getClassLoader().getResource("obds3/" + sourceFile); | ||
| assertThat(resource).isNotNull(); | ||
|
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| final var xmlMapper = | ||
| XmlMapper.builder() | ||
| .defaultUseWrapper(false) | ||
| .addModule(new JakartaXmlBindAnnotationModule()) | ||
| .addModule(new Jdk8Module()) | ||
| .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false) | ||
| .build(); | ||
|
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| final var obds = xmlMapper.readValue(resource.openStream(), OBDS.class); | ||
|
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| var obdsPatient = obds.getMengePatient().getPatient().getFirst(); | ||
|
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| var subject = new Reference("Patient/any"); | ||
| var systMeldung = | ||
| obdsPatient.getMengeMeldung().getMeldung().stream() | ||
| .filter(m -> m.getSYST() != null) | ||
| .findFirst() | ||
| .get(); | ||
| var procedure = sut.map(systMeldung.getSYST(), subject); | ||
|
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| var fhirParser = FhirContext.forR4().newJsonParser().setPrettyPrint(true); | ||
| var fhirJson = fhirParser.encodeResourceToString(procedure); | ||
| Approvals.verify( | ||
| fhirJson, Approvals.NAMES.withParameters(sourceFile).forFile().withExtension(".fhir.json")); | ||
| } | ||
| } |
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