feat: implement op mapping

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

@@ -23,6 +23,7 @@ public static class FhirExtensions {
     private String sysTheraProto;
     private String dataAbsentReason;
     private String genderAmtlich;
+    private String miiExOnkoOPIntention;
     private String miiExOnkoStrahlentherapieIntention;
     private String miiExOnkoStrahlentherapieBestrahlung;
     private String miiExOnkoHistologyMorphologyBehaviorIcdo3;
@@ -37,6 +38,7 @@ public static class FhirSystems {
     private String conditionId;
     private String observationId;
     private String procedureId;
+    private String operationProcedureId;
     private String medicationStatementId;
     private String observationCategorySystem;
     private String allgemeinerLeistungszustandEcogId;
@@ -76,6 +78,7 @@ public static class FhirSystems {
     private String miiCsOnkoStrahlentherapieApplikationsart;
     private String miiCsOnkoStrahlentherapieStrahlenart;
     private String miiCsOnkoStrahlentherapieZielgebiet;
+    private String miiCsOnkoOperationResidualstatus;
     private String strahlentherapieProcedureId;
     private String systemischeTherapieProcedureId;
     private String systemischeTherapieMedicationStatementId;
@@ -106,6 +109,7 @@ public static class FhirProfiles {
     private String miiPatientPseudonymisiert;
     private String deathObservation;
     private String miiPrOnkoDiagnosePrimaertumor;
+    private String miiPrOnkoOperation;
     private String miiPrOnkoStrahlentherapie;
     private String miiPrOnkoSystemischeTherapie;
     private String miiPrMedicationStatement;

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

@@ -0,0 +1,146 @@
+package org.miracum.streams.ume.obdstofhir.mapper.mii;
+
+import de.basisdatensatz.obds.v3.OPTyp;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+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 OperationMapper extends ObdsToFhirMapper {
+
+  private static final Logger LOG = LoggerFactory.getLogger(OperationMapper.class);
+
+  @Autowired
+  public OperationMapper(FhirProperties fhirProperties) {
+    super(fhirProperties);
+  }
+
+  public List<Procedure> map(OPTyp op, Reference subject, Reference condition) {
+
+    Objects.requireNonNull(op, "OP must not be null");
+    Objects.requireNonNull(subject, "Reference must not be null");
+    Validate.notBlank(op.getOPID(), "Required OP_ID is unset");
+
+    // create a list to hold all single Procedure resources
+    var procedureList = new ArrayList<Procedure>();
+
+    for (var opsCode : op.getMengeOPS().getOPS()) {
+      var procedure = new Procedure();
+
+      // identifier, meta
+      // to do: brauch ich hier die patid? dann muss ich meine Parameter nochmal überdenken weil im
+      var identifier =
+          new Identifier()
+              .setSystem(fhirProperties.getSystems().getOperationProcedureId())
+              .setValue(op.getOPID() + opsCode.getCode());
+      procedure.addIdentifier(identifier);
+      procedure.setId(
+          computeResourceIdFromIdentifier(
+              identifier)); // das hier macht den Hash vom identifier.value
+
+      procedure.getMeta().addProfile(fhirProperties.getProfiles().getMiiPrOnkoOperation());
+
+      // status
+      procedure.setStatus(Procedure.ProcedureStatus.COMPLETED);
+
+      // code
+      CodeableConcept opsCodeableConcept =
+          new CodeableConcept()
+              .addCoding(
+                  new Coding()
+                      .setSystem(fhirProperties.getSystems().getOps())
+                      .setCode(opsCode.getCode())
+                      .setVersion(opsCode.getVersion()));
+
+      procedure.setCode(opsCodeableConcept);
+
+      // category: if OPS starts with 5, set 387713003; if first digit 1, set 165197003; else
+      // 394841004
+      // https://simplifier.net/packages/de.medizininformatikinitiative.kerndatensatz.prozedur/2024.0.0-ballot/files/2253000
+      String firstDigitOPS = opsCode.getCode().substring(0, 1);
+      String categoryCode;
+      String categoryDisplay;
+
+      switch (firstDigitOPS) {
+        case "5":
+          categoryCode = "387713003";
+          categoryDisplay = "Surgical procedure";
+          break;
+        case "1":
+          categoryCode = "165197003";
+          categoryDisplay = "Diagnostic assessment";
+          break;
+        default:
+          categoryCode = "394841004";
+          categoryDisplay = "Other category";
+          break;
+      }
+
+      procedure.setCategory(
+          new CodeableConcept()
+              .addCoding(
+                  new Coding()
+                      .setSystem(fhirProperties.getSystems().getSnomed())
+                      .setCode(categoryCode)
+                      .setDisplay(categoryDisplay)));
+
+      // subject reference
+      procedure.setSubject(subject);
+
+      // performed
+      var dataAbsentExtension =
+          new Extension(
+              fhirProperties.getExtensions().getDataAbsentReason(), new CodeType("unknown"));
+      var dataAbsentCode = new CodeType();
+      dataAbsentCode.addExtension(dataAbsentExtension);
+
+      var dateTime = convertObdsDatumToDateTimeType(op.getDatum());
+      if (dateTime.isPresent()) {
+        procedure.setPerformed(dateTime.get());
+      } else {
+        var performed = new DateTimeType();
+        performed.addExtension(dataAbsentExtension);
+        procedure.setPerformed(performed);
+      }
+
+      // ReasonReference
+      procedure.addReasonReference(condition);
+
+      // intention
+      var intention = new CodeableConcept();
+      intention
+          .addCoding()
+          .setSystem(fhirProperties.getSystems().getMiiCsOnkoIntention())
+          .setCode(op.getIntention());
+
+      var intentionExtens =
+          new Extension()
+              .setUrl(fhirProperties.getExtensions().getMiiExOnkoOPIntention())
+              .setValue(intention);
+
+      procedure.addExtension(intentionExtens);
+
+      // outcome
+      var outcome = new CodeableConcept();
+      outcome
+          .addCoding()
+          .setSystem(fhirProperties.getSystems().getMiiCsOnkoOperationResidualstatus())
+          .setCode(op.getResidualstatus().getLokaleBeurteilungResidualstatus().value());
+
+      procedure.setOutcome(outcome);
+
+      // add procedure to procedure list here
+      procedureList.add(procedure);
+    }
+
+    return procedureList;
+  }
+}

src/main/resources/application.yml

@@ -18,13 +18,15 @@ fhir:
     mii-ex-onko-strahlentherapie-bestrahlung: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-ex-onko-strahlentherapie-bestrahlung"
     mii-ex-onko-histology-morphology-behavior-icdo3: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-ex-onko-histology-morphology-behavior-icdo3"
     mii-ex-onko-systemische-therapie-intention: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-ex-onko-systemische-therapie-intention"
+    mii-ex-onko-op-intention: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-ex-onko-operation-intention"
     condition-asserted-date: "http://hl7.org/fhir/StructureDefinition/condition-assertedDate"
   systems:
     patientId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/patient-id"
     identifier-type: "http://terminology.hl7.org/CodeSystem/v2-0203"
     conditionId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/primaerdiagnose-id"
     observationId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/observation-id"
     procedureId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/procedure-id"
+    operationProcedureId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/operation-procedure-id"
     medicationStatementId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/medication-statement-id"
     observationCategorySystem: "http://hl7.org/fhir/observation-category"
     gleasonScoreObservationId: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/gleason-score-observation-id"
@@ -71,6 +73,7 @@ fhir:
     mii-cs-onko-strahlentherapie-zielgebiet: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-strahlentherapie-zielgebiet"
     mii-cs-onko-seitenlokalisation: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-seitenlokalisation"
     mii-cs-onko-systemische-therapie-art: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-therapie-typ"
+    mii-cs-onko-operation-residualstatus: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-residualstatus"
     mii-cs-therapie-grund-ende: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-therapie-grund-ende"
     mii-cs-onko-tod-interpretation: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-tod"
     mii-cs-onko-tod-observation-id: "${fhir.default.baseSystemUrl}/obds-to-fhir/identifiers/tod-observation-id"
@@ -91,6 +94,7 @@ fhir:
     deathObservation: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Observation-TodUrsache"
     # MII
     mii-patient-pseudonymisiert: "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/PatientPseudonymisiert"
+    mii-pr-onko-operation: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-operation"
     mii-pr-onko-diagnose-primaertumor: "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-diagnose-primaertumor"
     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"

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

@@ -0,0 +1,89 @@
+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 java.util.TimeZone;
+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.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+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
+public class OperationMapperTest {
+  private static OperationMapper sut;
+
+  private static final Logger LOG = LoggerFactory.getLogger(OperationMapper.class);
+
+  @BeforeAll
+  static void beforeEach(@Autowired FhirProperties fhirProps) {
+    TimeZone.setDefault(TimeZone.getTimeZone("Europe/Berlin"));
+    sut = new OperationMapper(fhirProps);
+  }
+
+  @ParameterizedTest
+  @CsvSource({"Testpatient_1.xml", "Testpatient_2.xml"})
+  void map_withGivenObds_shouldCreateValidProcedure(String sourceFile) throws IOException {
+    final var resource = this.getClass().getClassLoader().getResource("obds3/" + sourceFile);
+    assertThat(resource).isNotNull();
+
+    System.out.println("Loaded resource: " + resource.getPath());
+
+    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 condition = new Reference("Condition/any");
+
+    var opMeldung =
+        obdsPatient.getMengeMeldung().getMeldung().stream()
+            .filter(m -> m.getOP() != null)
+            .findFirst()
+            .get();
+
+    // Map and get the list of procedures
+    final var resultResources = sut.map(opMeldung.getOP(), subject, condition);
+
+    assertThat(resultResources).isNotEmpty();
+    LOG.info("Length of resultResources {}", resultResources.size());
+
+    var fhirParser = FhirContext.forR4().newJsonParser().setPrettyPrint(true);
+
+    LOG.info("Number of OPS codes: {}", opMeldung);
+
+    for (int i = 0; i < resultResources.size(); i++) {
+      assertThat(resultResources.get(i)).isNotNull();
+      var fhirJson = fhirParser.encodeResourceToString(resultResources.get(i));
+      System.out.println("Verifying resource: index_" + i);
+      Approvals.verify(
+          fhirJson,
+          Approvals.NAMES
+              .withParameters(sourceFile, "index_" + i)
+              .forFile()
+              .withExtension(".fhir.json"));
+    }
+  }
+}

src/test/java/snapshots/org/miracum/streams/ume/obdstofhir/mapper/mii/OperationMapperTest.map_withGivenObds_shouldCreateValidProcedure.Testpatient_1.xml.index_0.approved.fhir.json

@@ -0,0 +1,48 @@
+{
+  "resourceType": "Procedure",
+  "id": "cd1f9a1a39fedb333d953a94169407e9327425dbfa86215925f3e4190665bd52",
+  "meta": {
+    "profile": [ "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-pr-onko-operation" ]
+  },
+  "extension": [ {
+    "url": "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/StructureDefinition/mii-ex-onko-operation-intention",
+    "valueCodeableConcept": {
+      "coding": [ {
+        "system": "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-intention",
+        "code": "K"
+      } ]
+    }
+  } ],
+  "identifier": [ {
+    "system": "https://bzkf.github.io/obds-to-fhir/identifiers/operation-procedure-id",
+    "value": "3015-870"
+  } ],
+  "status": "completed",
+  "category": {
+    "coding": [ {
+      "system": "http://snomed.info/sct",
+      "code": "387713003",
+      "display": "Surgical procedure"
+    } ]
+  },
+  "code": {
+    "coding": [ {
+      "system": "http://fhir.de/CodeSystem/bfarm/ops",
+      "version": "2020",
+      "code": "5-870"
+    } ]
+  },
+  "subject": {
+    "reference": "Patient/any"
+  },
+  "performedDateTime": "2020-03-05",
+  "reasonReference": [ {
+    "reference": "Condition/any"
+  } ],
+  "outcome": {
+    "coding": [ {
+      "system": "https://www.medizininformatik-initiative.de/fhir/ext/modul-onko/CodeSystem/mii-cs-onko-residualstatus",
+      "code": "R0"
+    } ]
+  }
+}