feat: implement death mapping

src/main/java/org/miracum/streams/ume/obdstofhir/FhirProperties.java

@@ -80,6 +80,7 @@ public static class FhirSystems {
     private String miiCsOnkoSystemischeTherapieArt;
     private String miiCsOnkoSeitenlokalisation;
     private String miiCsTherapieGrundEnde;
+    private String miiCsOnkoTodInterpretation;
     private String conditionVerStatus;
     private String icdo3MorphologieOid;
     private String atcBfarm;
@@ -104,6 +105,7 @@ public static class FhirProfiles {
     private String miiPrOnkoStrahlentherapie;
     private String miiPrOnkoSystemischeTherapie;
     private String miiPrMedicationStatement;
+    private String miiPrOnkoTod;
   }
 
   @Data

src/main/java/org/miracum/streams/ume/obdstofhir/mapper/mii/TodMapper.java

@@ -0,0 +1,100 @@
+package org.miracum.streams.ume.obdstofhir.mapper.mii;
+
+import de.basisdatensatz.obds.v3.AllgemeinICDTyp;
+import de.basisdatensatz.obds.v3.OBDS;
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.regex.Pattern;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.r4.model.*;
+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.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class TodMapper extends ObdsToFhirMapper {
+
+  private static final Logger LOG = LoggerFactory.getLogger(TodMapper.class);
+  private static final Pattern icdVersionPattern =
+      Pattern.compile("^(10 (?<versionYear>20\\d{2}) ((GM)|(WHO))|Sonstige)$");
+
+  @Autowired
+  public TodMapper(FhirProperties fhirProperties) {
+    super(fhirProperties);
+  }
+
+  public Observation map(
+      OBDS.MengePatient.Patient.MengeMeldung.Meldung meldung, Reference patient) {
+    // Validation
+    Objects.requireNonNull(meldung.getTod());
+    Objects.requireNonNull(patient);
+    // Objects.requireNonNull(condition);
+
+    Validate.notBlank(meldung.getTod().getAbschlussID(), "Required ABSCHLUSS_ID is unset");
+    Validate.isTrue(
+        Objects.equals(
+            patient.getReferenceElement().getResourceType(),
+            Enumerations.ResourceType.PATIENT.toCode()),
+        "The subject reference should point to a Patient resource");
+    /*
+    Validate.isTrue(
+      Objects.equals(
+        condition.getReferenceElement().getResourceType(), Enumerations.ResourceType.CONDITION.toCode()),
+      "The condition reference should point to a Condition resource");
+    */
+
+    var observation = new Observation();
+    observation.getMeta().addProfile(fhirProperties.getProfiles().getMiiPrOnkoTod());
+    observation.setStatus(Observation.ObservationStatus.FINAL);
+
+    // Code | 184305005 | Cause of death (observable entity)
+    var snomedCode = new CodeableConcept();
+    snomedCode.addCoding().setSystem(fhirProperties.getSystems().getSnomed()).setCode("184305005");
+    observation.setCode(snomedCode);
+
+    // Subject
+    observation.setSubject(patient);
+
+    // Effective | Sterbedatum
+    var todesZeitpunkt = convertObdsDatumToDateTimeType(meldung.getTod().getSterbedatum());
+    if (todesZeitpunkt.isPresent()) {
+      observation.setEffective(todesZeitpunkt.get());
+    }
+
+    /*
+    // Focus | Bezugsdiagnose
+    var focusList = new ArrayList<Reference>();
+    focusList.add(condition);
+    observation.setFocus(focusList);
+    */
+
+    // Value | Todesursache(n) ICD10GM
+    if (meldung.getTod().getMengeTodesursachen() != null) {
+      var todesursacheConcept = new CodeableConcept();
+      for (AllgemeinICDTyp todesursache :
+          meldung.getTod().getMengeTodesursachen().getTodesursacheICD()) {
+        todesursacheConcept
+            .addCoding()
+            .setSystem(fhirProperties.getSystems().getIcd10gm())
+            .setCode(todesursache.getCode())
+            .setVersion(todesursache.getVersion());
+      }
+      observation.setValue(todesursacheConcept);
+    }
+
+    // Interpretation | Tod Tumorbedingt
+    if (meldung.getTod().getTodTumorbedingt() != null) {
+      var interpretation = new CodeableConcept();
+      interpretation
+          .addCoding()
+          .setSystem(fhirProperties.getSystems().getMiiCsOnkoTodInterpretation())
+          .setCode(meldung.getTod().getTodTumorbedingt().value());
+      observation.setInterpretation(Arrays.asList(interpretation));
+    }
+
+    return observation;
+  }
+}

src/main/resources/application.yml

@@ -70,6 +70,7 @@ fhir:
     mii-cs-onko-seitenlokalisation: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-seitenlokalisation"
     mii-cs-onko-systemische-therapie-art: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-therapie-typ"
     mii-cs-therapie-grund-ende: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-therapie-grund-ende"
+    mii-cs-onko-tod-interpretation: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-tod"
     atcBfarm: "http://fhir.de/CodeSystem/bfarm/atc"
     atcWho: "http://www.whocc.no/atc"
   profiles:
@@ -90,6 +91,7 @@ fhir:
     mii-pr-onko-strahlentherapie: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-strahlentherapie"
     mii-pr-onko-systemische-therapie: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-systemische-therapie"
     mii-pr-medication-statement: "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement"
+    mii-pr-onko-tod: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-tod"
   display:
     histologyLoinc: "Histology and Behavior ICD-O-3 Cancer"
     gradingLoinc: "Grade pathology value Cancer"

src/test/java/org/miracum/streams/ume/obdstofhir/mapper/mii/TodMapperTest.java

@@ -0,0 +1,63 @@
+package org.miracum.streams.ume.obdstofhir.mapper.mii;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+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;
+
+@SpringBootTest(classes = {FhirProperties.class})
+@EnableConfigurationProperties
+class TodMapperTest {
+  private static TodMapper tm;
+
+  @BeforeAll
+  static void beforeEach(@Autowired FhirProperties fhirProps) {
+    tm = new TodMapper(fhirProps);
+  }
+
+  @ParameterizedTest
+  @CsvSource({"Testpatient_1.xml"})
+  void map_withGivenObds_shouldCreateValidProcedure(String sourceFile) throws IOException {
+    final var resource = this.getClass().getClassLoader().getResource("obds3/" + sourceFile);
+    assertThat(resource).isNotNull();
+
+    final var xmlMapper =
+        XmlMapper.builder()
+            .defaultUseWrapper(false)
+            .addModule(new JakartaXmlBindAnnotationModule())
+            .addModule(new Jdk8Module())
+            .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
+            .build();
+
+    final var obds = xmlMapper.readValue(resource.openStream(), OBDS.class);
+
+    var obdsPatient = obds.getMengePatient().getPatient().getFirst();
+
+    var subject = new Reference("Patient/any");
+    var tMeldung =
+        obdsPatient.getMengeMeldung().getMeldung().stream()
+            .filter(m -> m.getTod() != null)
+            .findFirst()
+            .get();
+    var procedure = tm.map(tMeldung, subject);
+
+    var fhirParser = FhirContext.forR4().newJsonParser().setPrettyPrint(true);
+    var fhirJson = fhirParser.encodeResourceToString(procedure);
+    Approvals.verify(
+        fhirJson, Approvals.NAMES.withParameters(sourceFile).forFile().withExtension(".fhir.json"));
+  }
+}

src/test/java/snapshots/org/miracum/streams/ume/obdstofhir/mapper/mii/TodMapperTest.map_withGivenObds_shouldCreateValidProcedure.Testpatient_1.xml.approved.fhir.json

@@ -0,0 +1,34 @@
+{
+  "resourceType": "Observation",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-tod" ]
+  },
+  "status": "final",
+  "code": {
+    "coding": [ {
+      "system": "http://snomed.info/sct",
+      "code": "184305005"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "effectiveDateTime": "2022-08-01",
+  "valueCodeableConcept": {
+    "coding": [ {
+      "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+      "version": "10 2020 GM",
+      "code": "C50.9"
+    }, {
+      "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+      "version": "10 2020 GM",
+      "code": "T57.3"
+    } ]
+  },
+  "interpretation": [ {
+    "coding": [ {
+      "system": "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-tod",
+      "code": "J"
+    } ]
+  } ]
+}