feat: add initial SystemischeTherapieMedicationStatementMapper

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

@@ -81,6 +81,8 @@ public static class FhirSystems {
     private String miiCsTherapieGrundEnde;
     private String conditionVerStatus;
     private String icdo3MorphologieOid;
+    private String atcBfarm;
+    private String atcWho;
   }
 
   @Data
@@ -100,6 +102,7 @@ public static class FhirProfiles {
     private String miiPrOnkoDiagnosePrimaertumor;
     private String miiPrOnkoStrahlentherapie;
     private String miiPrOnkoSystemischeTherapie;
+    private String miiPrMedicationStatement;
   }
 
   @Data

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

@@ -0,0 +1,106 @@
+package org.miracum.streams.ume.obdstofhir.mapper.mii;
+
+import de.basisdatensatz.obds.v3.SYSTTyp;
+import de.basisdatensatz.obds.v3.SYSTTyp.Meldeanlass;
+import java.util.Objects;
+import org.apache.commons.lang3.Validate;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
+import org.hl7.fhir.r4.model.Enumerations.ResourceType;
+import org.hl7.fhir.r4.model.Identifier;
+import org.hl7.fhir.r4.model.MedicationStatement;
+import org.hl7.fhir.r4.model.Period;
+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;
+import org.springframework.util.StringUtils;
+
+@Service
+public class SystemischeTherapieMedicationStatementMapper extends ObdsToFhirMapper {
+
+  private static final Logger LOG =
+      LoggerFactory.getLogger(SystemischeTherapieProcedureMapper.class);
+
+  public SystemischeTherapieMedicationStatementMapper(FhirProperties fhirProperties) {
+    super(fhirProperties);
+  }
+
+  public Bundle map(SYSTTyp syst, Reference patient, Reference procedure) {
+    Objects.requireNonNull(syst, "Systemtherapie must not be null");
+    Objects.requireNonNull(patient, "Reference to Patient must not be null");
+    Objects.requireNonNull(procedure, "Reference to Procedure must not be null");
+
+    Validate.notBlank(syst.getSYSTID(), "Required SYST_ID is unset");
+    Validate.isTrue(
+        Objects.equals(
+            patient.getReferenceElement().getResourceType(), ResourceType.PATIENT.toCode()),
+        "The subject reference should point to a Patient resource");
+    Validate.isTrue(
+        Objects.equals(
+            procedure.getReferenceElement().getResourceType(), ResourceType.PROCEDURE.toCode()),
+        "The subject reference should point to a Procedure resource");
+
+    var bundle = new Bundle();
+    bundle.setType(Bundle.BundleType.TRANSACTION);
+
+    for (var substanz : syst.getMengeSubstanz().getSubstanz()) {
+      var systMedicationStatement = new MedicationStatement();
+      systMedicationStatement
+          .getMeta()
+          .addProfile(fhirProperties.getProfiles().getMiiPrMedicationStatement());
+
+      if ((null != substanz.getATC() && StringUtils.hasText(substanz.getATC().getCode()))
+          || StringUtils.hasText(substanz.getBezeichnung())) {
+        var substanzId = "";
+        if (null != substanz.getATC() && StringUtils.hasText(substanz.getATC().getCode())) {
+          substanzId = substanz.getATC().getCode();
+          var atcCoding =
+              new Coding(
+                  fhirProperties.getSystems().getAtcBfarm(), substanz.getATC().getCode(), "");
+          systMedicationStatement.setMedication(new CodeableConcept(atcCoding));
+        } else {
+          substanzId = substanz.getBezeichnung().replaceAll("[^A-Za-z0-9]", "");
+          systMedicationStatement.setMedication(
+              new CodeableConcept().setText(substanz.getBezeichnung()));
+        }
+
+        // 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(String.format("%s_%s", syst.getSYSTID(), substanzId));
+        systMedicationStatement.addIdentifier(identifier);
+        systMedicationStatement.setId(computeResourceIdFromIdentifier(identifier));
+
+        // Status / Effective
+        var meldeanlass = syst.getMeldeanlass();
+        var period = new Period();
+        if (meldeanlass == Meldeanlass.BEHANDLUNGSENDE) {
+          systMedicationStatement.setStatus(
+              MedicationStatement.MedicationStatementStatus.COMPLETED);
+          convertObdsDatumToDateTimeType(syst.getBeginn())
+              .ifPresent(start -> period.setStart(start.getValue(), start.getPrecision()));
+          convertObdsDatumToDateTimeType(syst.getEnde())
+              .ifPresent(end -> period.setEnd(end.getValue(), end.getPrecision()));
+        } else {
+          systMedicationStatement.setStatus(MedicationStatement.MedicationStatementStatus.ACTIVE);
+          convertObdsDatumToDateTimeType(syst.getBeginn())
+              .ifPresent(start -> period.setStart(start.getValue(), start.getPrecision()));
+        }
+        systMedicationStatement.setEffective(period);
+
+        // Subject
+        systMedicationStatement.setSubject(patient);
+
+        bundle = addResourceAsEntryInBundle(bundle, systMedicationStatement);
+      }
+    }
+
+    return bundle;
+  }
+}

src/main/resources/application.yml

@@ -69,6 +69,8 @@ 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"
+    atcBfarm: "http://fhir.de/CodeSystem/bfarm/atc"
+    atcWho: "http://www.whocc.no/atc"
   profiles:
     histologie: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Observation-Histologie"
     grading: "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Observation-Grading"
@@ -86,6 +88,7 @@ fhir:
     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"
+    mii-pr-medication-statement: "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement"
   display:
     histologyLoinc: "Histology and Behavior ICD-O-3 Cancer"
     gradingLoinc: "Grade pathology value Cancer"

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

@@ -0,0 +1,66 @@
+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 SystemischeTherapieMedicationStatementMapperTest {
+  private static SystemischeTherapieMedicationStatementMapper sut;
+
+  @BeforeAll
+  static void beforeAll(@Autowired FhirProperties fhirProps) {
+    sut = new SystemischeTherapieMedicationStatementMapper(fhirProps);
+  }
+
+  @ParameterizedTest
+  @CsvSource({"Testpatient_1.xml", "Testpatient_2.xml", "Testpatient_3.xml"})
+  void map_withGivenObds_shouldCreateValidMedicationStatement(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 patient = new Reference("Patient/any");
+    var procedure = new Reference("Procedure/any");
+    var systMeldung =
+        obdsPatient.getMengeMeldung().getMeldung().stream()
+            .filter(m -> m.getSYST() != null)
+            .findFirst()
+            .get();
+    var bundle = sut.map(systMeldung.getSYST(), patient, procedure);
+
+    var fhirParser = FhirContext.forR4().newJsonParser().setPrettyPrint(true);
+    var fhirJson = fhirParser.encodeResourceToString(bundle);
+
+    Approvals.verify(
+        fhirJson, Approvals.NAMES.withParameters(sourceFile).forFile().withExtension(".fhir.json"));
+  }
+}

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

@@ -0,0 +1,36 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [ {
+    "fullUrl": "MedicationStatement/99635bf8744dadda1f8b293046f2bfb3d021938263616e6228523113af2695c1",
+    "resource": {
+      "resourceType": "MedicationStatement",
+      "id": "99635bf8744dadda1f8b293046f2bfb3d021938263616e6228523113af2695c1",
+      "meta": {
+        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement" ]
+      },
+      "identifier": [ {
+        "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-procedure-id",
+        "value": "101_IN-1_L01FF05"
+      } ],
+      "status": "completed",
+      "medicationCodeableConcept": {
+        "coding": [ {
+          "system": "http://fhir.de/CodeSystem/bfarm/atc",
+          "code": "L01FF05"
+        } ]
+      },
+      "subject": {
+        "reference": "Patient/any"
+      },
+      "effectivePeriod": {
+        "start": "2020-05",
+        "end": "2020-10-15"
+      }
+    },
+    "request": {
+      "method": "PUT",
+      "url": "MedicationStatement/99635bf8744dadda1f8b293046f2bfb3d021938263616e6228523113af2695c1"
+    }
+  } ]
+}

src/test/java/snapshots/org/miracum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieMedicationStatementMapperTest.map_withGivenObds_shouldCreateValidMedicationStatement.Testpatient_2.xml.approved.fhir.json

@@ -0,0 +1,32 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [ {
+    "fullUrl": "MedicationStatement/d5925147316a1e8c6e69c3f663fad0301c1666ca5bf1b14f4c75cdda22ffce3b",
+    "resource": {
+      "resourceType": "MedicationStatement",
+      "id": "d5925147316a1e8c6e69c3f663fad0301c1666ca5bf1b14f4c75cdda22ffce3b",
+      "meta": {
+        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement" ]
+      },
+      "identifier": [ {
+        "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-procedure-id",
+        "value": "11_1_Innere.1_Bicalutamid"
+      } ],
+      "status": "active",
+      "medicationCodeableConcept": {
+        "text": "Bicalutamid"
+      },
+      "subject": {
+        "reference": "Patient/any"
+      },
+      "effectivePeriod": {
+        "start": "2021-11-08"
+      }
+    },
+    "request": {
+      "method": "PUT",
+      "url": "MedicationStatement/d5925147316a1e8c6e69c3f663fad0301c1666ca5bf1b14f4c75cdda22ffce3b"
+    }
+  } ]
+}

src/test/java/snapshots/org/miracum/streams/ume/obdstofhir/mapper/mii/SystemischeTherapieMedicationStatementMapperTest.map_withGivenObds_shouldCreateValidMedicationStatement.Testpatient_3.xml.approved.fhir.json

@@ -0,0 +1,32 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [ {
+    "fullUrl": "MedicationStatement/9d5246fd9512f352552a8ea37cbb65991f06e7497c6bf0575f81a49e1b9bfa35",
+    "resource": {
+      "resourceType": "MedicationStatement",
+      "id": "9d5246fd9512f352552a8ea37cbb65991f06e7497c6bf0575f81a49e1b9bfa35",
+      "meta": {
+        "profile": [ "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement" ]
+      },
+      "identifier": [ {
+        "system": "https://bzkf.github.io/obds-to-fhir/identifiers/systemische-therapie-procedure-id",
+        "value": "12_1_Innere.1_Paclitaxel"
+      } ],
+      "status": "active",
+      "medicationCodeableConcept": {
+        "text": "Paclitaxel"
+      },
+      "subject": {
+        "reference": "Patient/any"
+      },
+      "effectivePeriod": {
+        "start": "2018-03-17"
+      }
+    },
+    "request": {
+      "method": "PUT",
+      "url": "MedicationStatement/9d5246fd9512f352552a8ea37cbb65991f06e7497c6bf0575f81a49e1b9bfa35"
+    }
+  } ]
+}