fix: handle Primaertumor_ICD_Version being unset or not matching regex (

#39) * fix: handle Primaertumor_ICD_Version being unset or not matching regex * fix: handle Meldung.Diagnose.Primaertumor_* unset and default to TumorZuordnung * fix: use distinct ID when condition is generated from a tumorzuordnung avoids overriding existing resources but may cause duplicate diagnosis being present * test: added snapshot tests for previously failing data
bzkf · May 7, 2024 · 87a6b63 · 87a6b63
1 parent bbaceb5
commit 87a6b63
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Showing 7 changed files with 374 additions and 14 deletions.
diff --git a/src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsConditionMapper.java b/src/main/java/org/miracum/streams/ume/obdstofhir/mapper/ObdsConditionMapper.java
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.regex.Pattern;
 import org.hl7.fhir.r4.model.*;
 import org.miracum.streams.ume.obdstofhir.FhirProperties;
 import org.miracum.streams.ume.obdstofhir.lookup.*;
@@ -12,12 +13,16 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.util.StringUtils;
 
 @Configuration
 public class ObdsConditionMapper extends ObdsToFhirMapper {
 
   private static final Logger LOG = LoggerFactory.getLogger(ObdsConditionMapper.class);
 
+  private static final Pattern icdVersionPattern =
+      Pattern.compile("^(10 (?<versionYear>20\\d{2}) ((GM)|(WHO))|Sonstige)$");
+
   @Value("${app.version}")
   private String appVersion;
 
@@ -64,8 +69,12 @@ public Bundle mapOnkoResourcesToCondition(
 
     ADT_GEKID.PrimaryConditionAbs primDia = meldung.getDiagnose();
 
-    // diagnose Tag ist only specified in meldeanlass 'diagnose', otherwise use tag 'Tumorzuordung'
-    if (primDia == null) {
+    // Diagnose Element is only fully specified in meldeanlass 'diagnose', otherwise use element
+    // 'Tumorzuordung'
+    // It's possible that 'Meldung.Diagnose' is set but 'Meldung.Diagnose.Primaertumor_*' is not,
+    // in that case also use the TumorZuordnung to construct the Condition.
+    var useTumorZuordnung = primDia == null || primDia.getPrimaertumor_ICD_Code() == null;
+    if (useTumorZuordnung) {
       primDia = meldung.getTumorzuordnung();
 
       if (primDia == null) {
@@ -80,6 +89,9 @@ public Bundle mapOnkoResourcesToCondition(
     }
 
     var conIdentifier = pid + "condition" + primDia.getTumor_ID();
+    if (useTumorZuordnung) {
+      conIdentifier += "-from-tumorzuordnung";
+    }
 
     onkoCondition.setId(this.getHash(ResourceType.Condition, conIdentifier));
 
@@ -94,18 +106,26 @@ public Bundle mapOnkoResourcesToCondition(
         .getMeta()
         .setProfile(List.of(new CanonicalType(fhirProperties.getProfiles().getCondition())));
 
-    var coding = new Coding();
-    var icd10Version = primDia.getPrimaertumor_ICD_Version();
-    // Aufbau: "10 2021 GM"
-    String[] icdVersionArray = icd10Version.split(" ");
-
-    if (icdVersionArray.length == 3 && icdVersionArray[1].matches("^20\\d{2}$")) {
-      coding.setVersion(icdVersionArray[1]);
-    } // FIXME: else throw exception?
+    var coding =
+        new Coding()
+            .setCode(primDia.getPrimaertumor_ICD_Code())
+            .setSystem(fhirProperties.getSystems().getIcd10gm());
 
-    coding
-        .setCode(primDia.getPrimaertumor_ICD_Code())
-        .setSystem(fhirProperties.getSystems().getIcd10gm());
+    // Aufbau: "10 2021 GM"
+    var icd10Version = primDia.getPrimaertumor_ICD_Version();
+    if (StringUtils.hasLength(icd10Version)) {
+      var matcher = icdVersionPattern.matcher(icd10Version);
+      if (matcher.matches()) {
+        coding.setVersion(matcher.group("versionYear"));
+      } else {
+        LOG.warn(
+            "Primaertumor_ICD_Version doesn't match expected format. Expected: '{}', actual: '{}'",
+            icdVersionPattern.pattern(),
+            icd10Version);
+      }
+    } else {
+      LOG.warn("Primaertumor_ICD_Version is unset or contains only whitespaces");
+    }
 
     var conditionCode = new CodeableConcept().addCoding(coding);
     onkoCondition.setCode(conditionCode);

diff --git a/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsObservationProcessorTest.java b/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsObservationProcessorTest.java
@@ -6,11 +6,13 @@
 import java.io.IOException;
 import java.util.*;
 import java.util.stream.Stream;
+import org.apache.commons.lang3.tuple.Pair;
 import org.approvaltests.Approvals;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Observation;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.CsvSource;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.miracum.streams.ume.obdstofhir.FhirProperties;
 import org.miracum.streams.ume.obdstofhir.mapper.*;
@@ -194,4 +196,35 @@ void mapObservation_withGivenAdtXml(
               .withExtension(".fhir.json"));
     }
   }
+
+  @ParameterizedTest
+  @CsvSource({"diagnosis_set.xml", "diagnosis_unset.xml"})
+  void mapObservation_withGivenObdsXml_shouldMatchSnapshot(String resourceXmlName)
+      throws IOException {
+
+    var meldungExportList =
+        buildMeldungExportList(List.of(new Tupel<String, Integer>(resourceXmlName, 1)));
+
+    var onkoProcessor =
+        new ObdsProcessor(
+            fhirProps,
+            onkoMedicationStatementMapper,
+            onkoObservationMapper,
+            onkoProcedureMapper,
+            onkoPatientMapper,
+            onkoConditionMapper);
+
+    var observResultBundle =
+        onkoProcessor.getOnkoToObservationBundleMapper().apply(meldungExportList);
+
+    var resultBundle =
+        onkoProcessor
+            .getOnkoToConditionBundleMapper()
+            .apply(Pair.of(meldungExportList, observResultBundle));
+
+    var fhirJson = fhirParser.encodeResourceToString(resultBundle);
+    Approvals.verify(
+        fhirJson,
+        Approvals.NAMES.withParameters(resourceXmlName).forFile().withExtension(".fhir.json"));
+  }
 }
diff --git a/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsProcessorTest.java b/src/test/java/org/miracum/streams/ume/obdstofhir/processor/ObdsProcessorTest.java
@@ -64,7 +64,7 @@ protected MeldungExportList buildMeldungExportList(List<Tupel<String, Integer>>
       Map<String, Object> payloadOnkoRessource = new HashMap<>();
       payloadOnkoRessource.put("ID", payloadId);
       payloadOnkoRessource.put("REFERENZ_NUMMER", patId);
-      payloadOnkoRessource.put("LKR_MELDUNG", Integer.parseInt(meldungsId.replace(melderId, "")));
+      payloadOnkoRessource.put("LKR_MELDUNG", meldungsId.replace(melderId, ""));
       payloadOnkoRessource.put("VERSIONSNUMMER", xmlTupel.getSecond());
       payloadOnkoRessource.put("XML_DATEN", xmlContent);
 

diff --git a/....mapObservation_withGivenObdsXml_shouldMatchSnapshot.diagnosis_set.xml.approved.fhir.json b/....mapObservation_withGivenObdsXml_shouldMatchSnapshot.diagnosis_set.xml.approved.fhir.json
@@ -0,0 +1,39 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [ {
+    "fullUrl": "Condition/04c8f27ca021b8fd87ffd3abbde1f4b907bb3d6921fd61c5d4b9a0a756b8d110",
+    "resource": {
+      "resourceType": "Condition",
+      "id": "04c8f27ca021b8fd87ffd3abbde1f4b907bb3d6921fd61c5d4b9a0a756b8d110",
+      "meta": {
+        "source": "KR7X825X.ONKOSTAR:obds-to-fhir:0.0.0-test",
+        "profile": [ "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Condition-Primaerdiagnose" ]
+      },
+      "code": {
+        "coding": [ {
+          "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+          "version": "2010",
+          "code": "C43.5"
+        } ]
+      },
+      "subject": {
+        "reference": "Patient/19cc75fbfb51266ac0149828ae2f8522106e3ba176ceac2b40acb3cb1c9365f9",
+        "identifier": {
+          "type": {
+            "coding": [ {
+              "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+              "code": "MR"
+            } ]
+          },
+          "system": "https://fhir.diz.uk-erlangen.de/identifiers/patient-id",
+          "value": "0001234567"
+        }
+      }
+    },
+    "request": {
+      "method": "PUT",
+      "url": "Condition/04c8f27ca021b8fd87ffd3abbde1f4b907bb3d6921fd61c5d4b9a0a756b8d110"
+    }
+  } ]
+}
diff --git a/...apObservation_withGivenObdsXml_shouldMatchSnapshot.diagnosis_unset.xml.approved.fhir.json b/...apObservation_withGivenObdsXml_shouldMatchSnapshot.diagnosis_unset.xml.approved.fhir.json
@@ -0,0 +1,51 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [ {
+    "fullUrl": "Condition/dd9844e53c6d877fb91a9059f1bc0a433e7e892cd272770caa84aad4e7b7189d",
+    "resource": {
+      "resourceType": "Condition",
+      "id": "dd9844e53c6d877fb91a9059f1bc0a433e7e892cd272770caa84aad4e7b7189d",
+      "meta": {
+        "source": "KR7X825X.ONKOSTAR:obds-to-fhir:0.0.0-test",
+        "profile": [ "http://dktk.dkfz.de/fhir/StructureDefinition/onco-core-Condition-Primaerdiagnose" ]
+      },
+      "code": {
+        "coding": [ {
+          "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+          "version": "2019",
+          "code": "C43.2"
+        } ]
+      },
+      "bodySite": [ {
+        "coding": [ {
+          "system": "http://dktk.dkfz.de/fhir/onco/core/CodeSystem/SeitenlokalisationCS",
+          "code": "L",
+          "display": "links"
+        }, {
+          "system": "http://snomed.info/sct",
+          "code": "7771000",
+          "display": "Left"
+        } ]
+      } ],
+      "subject": {
+        "reference": "Patient/19cc75fbfb51266ac0149828ae2f8522106e3ba176ceac2b40acb3cb1c9365f9",
+        "identifier": {
+          "type": {
+            "coding": [ {
+              "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
+              "code": "MR"
+            } ]
+          },
+          "system": "https://fhir.diz.uk-erlangen.de/identifiers/patient-id",
+          "value": "0001234567"
+        }
+      },
+      "onsetDateTime": "2019-08-21"
+    },
+    "request": {
+      "method": "PUT",
+      "url": "Condition/dd9844e53c6d877fb91a9059f1bc0a433e7e892cd272770caa84aad4e7b7189d"
+    }
+  } ]
+}
diff --git a/src/test/resources/diagnosis_set.xml b/src/test/resources/diagnosis_set.xml
@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ADT_GEKID xmlns="http://www.gekid.de/namespace" Schema_Version="2.2.3">
+   <Absender Absender_ID="KR7X825X" Software_ID="ONKOSTAR" Installations_ID="2030">
+      <Absender_Bezeichnung>UKI</Absender_Bezeichnung>
+      <Absender_Ansprechpartner>Chef</Absender_Ansprechpartner>
+      <Absender_Anschrift>Irgendwo-Straße 1, 12345 Phantasieland</Absender_Anschrift>
+   </Absender>
+   <Menge_Patient>
+      <Patient>
+         <Patienten_Stammdaten Patient_ID="0001234567">
+            <KrankenversichertenNr>privatversichert</KrankenversichertenNr>
+            <KrankenkassenNr>1234567890</KrankenkassenNr>
+            <Patienten_Nachname>TestpatientEnzensperger</Patienten_Nachname>
+            <Patienten_Titel></Patienten_Titel>
+            <Patienten_Vornamen>Horst</Patienten_Vornamen>
+            <Patienten_Geburtsname></Patienten_Geburtsname>
+            <Patienten_Geschlecht>M</Patienten_Geschlecht>
+            <Patienten_Geburtsdatum>01.01.1950</Patienten_Geburtsdatum>
+            <Menge_Adresse>
+               <Adresse>
+                  <Patienten_Strasse>Irgendwo-Straße 2</Patienten_Strasse>
+                  <Patienten_Hausnummer>2</Patienten_Hausnummer>
+                  <Patienten_Land>DE</Patienten_Land>
+                  <Patienten_PLZ>12345</Patienten_PLZ>
+                  <Patienten_Ort>Phantasieland</Patienten_Ort>
+               </Adresse>
+            </Menge_Adresse>
+         </Patienten_Stammdaten>
+         <Menge_Meldung>
+            <Meldung Meldung_ID="000000B2-KR7X825X" Melder_ID="KR7X825X">
+               <Meldedatum>30.01.2024</Meldedatum>
+               <Meldebegruendung>D</Meldebegruendung>
+               <Meldeanlass>histologie_zytologie</Meldeanlass>
+               <Tumorzuordnung Tumor_ID="1">
+                  <Primaertumor_ICD_Code>C43.2</Primaertumor_ICD_Code>
+                  <Primaertumor_ICD_Version>10 2019 GM</Primaertumor_ICD_Version>
+                  <Diagnosedatum>21.08.2019</Diagnosedatum>
+                  <Seitenlokalisation>L</Seitenlokalisation>
+               </Tumorzuordnung>
+               <Diagnose Tumor_ID="1">
+                  <Primaertumor_ICD_Code>C43.5</Primaertumor_ICD_Code>
+                  <Primaertumor_ICD_Version>10 2010 GM</Primaertumor_ICD_Version>
+                  <Primaertumor_Diagnosetext>Bösartiges Melanom des Rumpfes</Primaertumor_Diagnosetext>
+                  <Menge_Histologie>
+                     <Histologie Histologie_ID="1234567">
+                        <Tumor_Histologiedatum>21.08.2019</Tumor_Histologiedatum>
+                        <Histologie_EinsendeNr>p 21557-19</Histologie_EinsendeNr>
+                        <Morphologie_Code>8720/3</Morphologie_Code>
+                        <Morphologie_ICD_O_Version>33</Morphologie_ICD_O_Version>
+                     </Histologie>
+                  </Menge_Histologie>
+                  <Modul_Allgemein>
+                     <DatumStudienrekrutierung>
+                        <NU>N</NU>
+                     </DatumStudienrekrutierung>
+                  </Modul_Allgemein>
+                  <Anmerkung> *** Pathobericht</Anmerkung>
+               </Diagnose>
+               <Menge_Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Vorname</Art>
+                     <Wert>Sepp</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Nachname</Art>
+                     <Wert>Prof. Dr. Doof</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Titel</Art>
+                     <Wert>-</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Strasse</Art>
+                     <Wert>Irgendwo-Straße</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Hausnummer</Art>
+                     <Wert>1</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Ort</Art>
+                     <Wert>Phantasieland</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_PLZ</Art>
+                     <Wert>12345</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_Einrichtung</Art>
+                     <Wert>Prof. Dr. Doof, UKI, HG</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_BSNR</Art>
+                     <Wert>-</Wert>
+                  </Zusatzitem>
+                  <Zusatzitem>
+                     <Art>Einsender_LANR</Art>
+                     <Wert>-</Wert>
+                  </Zusatzitem>
+               </Menge_Zusatzitem>
+            </Meldung>
+         </Menge_Meldung>
+      </Patient>
+   </Menge_Patient>
+   <Menge_Melder>
+      <Melder Melder_ID="KR7X825X">
+         <Meldende_Stelle>KR7X825X</Meldende_Stelle>
+      </Melder>
+   </Menge_Melder>
+</ADT_GEKID>