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feat: add initial SystemischeTherapieMapper
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src/main/java/org/miracum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieMapper.java
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| package org.miracum.streams.ume.obdstofhir.mapper.mii; | ||
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| 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.Coding; | ||
| 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; | ||
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| @Service | ||
| public class SystemischeTherapieMapper extends ObdsToFhirMapper { | ||
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| private static final Logger LOG = LoggerFactory.getLogger(SystemischeTherapieMapper.class); | ||
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| public SystemischeTherapieMapper(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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| 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(); | ||
| var performedStart = new DateTimeType(); | ||
| performedStart.setValue(syst.getBeginn().getValue().toGregorianCalendar().getTime()); | ||
| performed.setStartElement(performedStart); | ||
| if (syst.getEnde() != null) { | ||
| var performedEnd = new DateTimeType(); | ||
| performedEnd.setValue(syst.getEnde().toGregorianCalendar().getTime()); | ||
| performed.setEndElement(performedEnd); | ||
| } | ||
| procedure.setPerformed(performed); | ||
| } | ||
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| // TODO: Same as in Strahlentherapie? | ||
| var category = | ||
| new CodeableConcept( | ||
| new Coding( | ||
| fhirProperties.getSystems().getSnomed(), "277132007", "Therapeutic procedure")); | ||
| procedure.setCategory(category); | ||
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| return procedure; | ||
| } | ||
| } |
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63 changes: 63 additions & 0 deletions
63
...est/java/org/miracum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieMapperTest.java
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| @@ -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 SystemischeTherapieMapperTest { | ||
| private static SystemischeTherapieMapper sut; | ||
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| @BeforeAll | ||
| static void beforeEach(@Autowired FhirProperties fhirProps) { | ||
| sut = new SystemischeTherapieMapper(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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...perTest.map_withGivenObds_shouldCreateValidProcedure.Testpatient_1.xml.approved.fhir.json
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| { | ||
| "resourceType": "Procedure", | ||
| "id": "8e5a61d808bb30074e894fc702086b24763c410267b91c86f75de0b3b6507ccf", | ||
| "meta": { | ||
| "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-systemische-therapie" ] | ||
| }, | ||
| "identifier": [ { | ||
| "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-procedure-id", | ||
| "value": "101_IN-1" | ||
| } ], | ||
| "status": "completed", | ||
| "category": { | ||
| "coding": [ { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "277132007", | ||
| "display": "Therapeutic procedure" | ||
| } ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/any" | ||
| }, | ||
| "performedPeriod": { | ||
| "start": "2020-05-01T02:00:00+02:00", | ||
| "end": "2020-10-15T02:00:00+02:00" | ||
| } | ||
| } |
25 changes: 25 additions & 0 deletions
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...perTest.map_withGivenObds_shouldCreateValidProcedure.Testpatient_2.xml.approved.fhir.json
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,25 @@ | ||
| { | ||
| "resourceType": "Procedure", | ||
| "id": "fbc045f02f136bf06dcbf1c9002d85d86ae87ec317fdb0b10a23a4cc76ba2fc2", | ||
| "meta": { | ||
| "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-systemische-therapie" ] | ||
| }, | ||
| "identifier": [ { | ||
| "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-procedure-id", | ||
| "value": "11_1_Innere.1" | ||
| } ], | ||
| "status": "in-progress", | ||
| "category": { | ||
| "coding": [ { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "277132007", | ||
| "display": "Therapeutic procedure" | ||
| } ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/any" | ||
| }, | ||
| "performedPeriod": { | ||
| "start": "2021-11-08T01:00:00+01:00" | ||
| } | ||
| } |
25 changes: 25 additions & 0 deletions
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...perTest.map_withGivenObds_shouldCreateValidProcedure.Testpatient_3.xml.approved.fhir.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| { | ||
| "resourceType": "Procedure", | ||
| "id": "e722bcc3a86e05e00a0fe5566607b4293be976500750ed2de2f48280b7fba359", | ||
| "meta": { | ||
| "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-systemische-therapie" ] | ||
| }, | ||
| "identifier": [ { | ||
| "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-procedure-id", | ||
| "value": "12_1_Innere.1" | ||
| } ], | ||
| "status": "in-progress", | ||
| "category": { | ||
| "coding": [ { | ||
| "system": "http://snomed.info/sct", | ||
| "code": "277132007", | ||
| "display": "Therapeutic procedure" | ||
| } ] | ||
| }, | ||
| "subject": { | ||
| "reference": "Patient/any" | ||
| }, | ||
| "performedPeriod": { | ||
| "start": "2018-03-17T01:00:00+01:00" | ||
| } | ||
| } |