feat: add germline diagnosis codes

src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java

@@ -103,6 +103,8 @@ public class DataCatalogueFactory {
                 return ConsentMvCatalogue.create(jdbcTemplate);
             } else if (c == ConsentMvVerlaufCatalogue.class) {
                 return ConsentMvVerlaufCatalogue.create(jdbcTemplate);
+            } else if (c == KeimbahndiagnoseCatalogue.class) {
+                return KeimbahndiagnoseCatalogue.create(jdbcTemplate);
             }
             throw new DataCatalogueCreationException(clazz);
         });

src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogue.java

@@ -0,0 +1,46 @@
+/*
+ * This file is part of mv64e-onkostar-data
+ *
+ * Copyright (C) 2025  Paul-Christian Volkmer
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+package dev.pcvolkmer.onco.datamapper.datacatalogues;
+
+import org.springframework.jdbc.core.JdbcTemplate;
+
+/**
+ * Load raw result sets from database table 'dk_dnpm_uf_keimbahndiagnose'
+ *
+ * @author Paul-Christian Volkmer
+ * @since 0.1
+ */
+public class KeimbahndiagnoseCatalogue extends AbstractSubformDataCatalogue {
+
+    private KeimbahndiagnoseCatalogue(JdbcTemplate jdbcTemplate) {
+        super(jdbcTemplate);
+    }
+
+    @Override
+    protected String getTableName() {
+        return "dk_dnpm_uf_keimbahndiagnose";
+    }
+
+    public static KeimbahndiagnoseCatalogue create(JdbcTemplate jdbcTemplate) {
+        return new KeimbahndiagnoseCatalogue(jdbcTemplate);
+    }
+
+}

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java

@@ -23,6 +23,7 @@ package dev.pcvolkmer.onco.datamapper.mapper;
 import dev.pcvolkmer.mv64e.mtb.*;
 import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.KeimbahndiagnoseCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue;
@@ -44,17 +45,20 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
     private final KpaCatalogue kpaCatalogue;
     private final TumorausbreitungCatalogue tumorausbreitungCatalogue;
     private final TumorgradingCatalogue tumorgradingCatalogue;
+    private final KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue;
     private final PropertyCatalogue propertyCatalogue;
 
     public KpaDiagnosisDataMapper(
             final KpaCatalogue kpaCatalogue,
             final TumorausbreitungCatalogue tumorausbreitungCatalogue,
             final TumorgradingCatalogue tumorgradingCatalogue,
+            final KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue,
             final PropertyCatalogue propertyCatalogue
     ) {
         this.kpaCatalogue = kpaCatalogue;
         this.tumorausbreitungCatalogue = tumorausbreitungCatalogue;
         this.tumorgradingCatalogue = tumorgradingCatalogue;
+        this.keimbahndiagnoseCatalogue = keimbahndiagnoseCatalogue;
         this.propertyCatalogue = propertyCatalogue;
     }
 
@@ -83,13 +87,12 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
                 .recordedOn(data.getDate("datumerstdiagnose"))
                 .topography(Coding.builder().code(data.getString("icdo3lokalisation")).build())
                 .type(getType(data))
-                // Nicht in Onkostar erfasst
-                //.germlineCodes()
                 .guidelineTreatmentStatus(
                         getMtbDiagnosisGuidelineTreatmentStatusCoding(data.getString("leitlinienstatus"), data.getInteger("leitlinienstatus_propcat_version"))
                 )
                 .grading(getGrading(id))
                 .staging(getStaging(id))
+                .germlineCodes(getGermlineCodes(id))
         ;
         return builder.build();
     }
@@ -172,6 +175,19 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
         return Staging.builder().history(all).build();
     }
 
+    private List<Coding> getGermlineCodes(final int id) {
+        return keimbahndiagnoseCatalogue.getAllByParentId(id).stream()
+                .map(it ->
+                        Coding.builder()
+                                .code(it.getString("icd10"))
+                                .system("http://fhir.de/CodeSystem/bfarm/icd-10-gm")
+                                .display(propertyCatalogue.getByCodeAndVersion(it.getString("icd10"), it.getInteger("icd10_propcat_version")).getShortdesc())
+                                .version(propertyCatalogue.getByCodeAndVersion(it.getString("icd10"), it.getInteger("icd10_propcat_version")).getVersionDescription())
+                                .build()
+                )
+                .collect(Collectors.toList());
+    }
+
     private Type getType(final ResultSet resultSet) {
         var diagnosisCoding = MtbDiagnosisCoding.builder();
         var code = resultSet.getString("diagnosetyp");

src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java

@@ -85,6 +85,7 @@ public class MtbDataMapper implements DataMapper<Mtb> {
                 kpaCatalogue,
                 catalogueFactory.catalogue(TumorausbreitungCatalogue.class),
                 catalogueFactory.catalogue(TumorgradingCatalogue.class),
+                catalogueFactory.catalogue(KeimbahndiagnoseCatalogue.class),
                 propertyCatalogue
         );
         var mtbEpisodeDataMapper = new MtbEpisodeDataMapper(kpaCatalogue, propertyCatalogue);

src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogueTest.java

@@ -0,0 +1,126 @@
+/*
+ * This file is part of mv64e-onkostar-data
+ *
+ * Copyright (C) 2025  Paul-Christian Volkmer
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+package dev.pcvolkmer.onco.datamapper.datacatalogues;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Mock;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.springframework.jdbc.core.JdbcTemplate;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.ArgumentMatchers.anyInt;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.Mockito.*;
+
+@ExtendWith(MockitoExtension.class)
+class KeimbahndiagnoseCatalogueTest {
+
+    JdbcTemplate jdbcTemplate;
+    KeimbahndiagnoseCatalogue catalogue;
+
+    @BeforeEach
+    void setUp(@Mock JdbcTemplate jdbcTemplate) {
+        this.jdbcTemplate = jdbcTemplate;
+        this.catalogue = KeimbahndiagnoseCatalogue.create(jdbcTemplate);
+    }
+
+    @Test
+    void shouldUseCorrectQuery(@Mock Map<String, Object> resultSet) {
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        this.catalogue.getById(1);
+
+        var captor = ArgumentCaptor.forClass(String.class);
+        verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
+
+        assertThat(captor.getValue())
+                .isEqualTo("SELECT patient.patienten_id, dk_dnpm_uf_keimbahndiagnose.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_uf_keimbahndiagnose JOIN prozedur ON (prozedur.id = dk_dnpm_uf_keimbahndiagnose.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?");
+    }
+
+    @Test
+    void shouldUseCorrectSubformQuery(@Mock Map<String, Object> resultSet) {
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        this.catalogue.getAllByParentId(1);
+
+        var captor = ArgumentCaptor.forClass(String.class);
+        verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
+
+        assertThat(captor.getValue())
+                .isEqualTo("SELECT patient.patienten_id, dk_dnpm_uf_keimbahndiagnose.*, prozedur.patient_id, prozedur.hauptprozedur_id FROM dk_dnpm_uf_keimbahndiagnose JOIN prozedur ON (prozedur.id = dk_dnpm_uf_keimbahndiagnose.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
+    }
+
+    @Test
+    void shouldUseCorrectMerkmalQuery(@Mock Map<String, Object> resultSet) {
+        when(resultSet.get(anyString()))
+                .thenReturn(Map.of("feldname", "name", "feldwert", "wert"));
+
+        doAnswer(invocationOnMock -> List.of(resultSet))
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        this.catalogue.getMerkmaleById(1);
+
+        var captor = ArgumentCaptor.forClass(String.class);
+        verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
+
+        assertThat(captor.getValue())
+                .isEqualTo("SELECT feldname, feldwert FROM dk_dnpm_uf_keimbahndiagnose_merkmale WHERE eintrag_id = ?");
+    }
+
+    @Test
+    void shouldUseMerkmalList() {
+        doAnswer(invocationOnMock -> {
+            var sql = invocationOnMock.getArgument(0, String.class);
+            ArrayList<Map<String, Object>> result = new ArrayList<>();
+            if (sql.startsWith("SELECT feldname")) {
+                result.add(Map.of("feldname", "name", "feldwert", "wert1"));
+                result.add(Map.of("feldname", "name", "feldwert", "wert2"));
+            } else {
+                var map = new HashMap<String, Object>();
+                map.put("id", 1);
+                map.put("name", "x");
+                result.add(map);
+            }
+            return result;
+        })
+                .when(jdbcTemplate)
+                .queryForList(anyString(), anyInt());
+
+        var result = this.catalogue.getById(1);
+
+        assertThat(result.getInteger("id")).isEqualTo(1);
+        assertThat(result.getMerkmalList("name")).isEqualTo(List.of("wert1", "wert2"));
+    }
+
+}

src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java

@@ -24,6 +24,7 @@ import dev.pcvolkmer.mv64e.mtb.MtbDiagnosis;
 import dev.pcvolkmer.mv64e.mtb.Reference;
 import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
 import dev.pcvolkmer.onco.datamapper.ResultSet;
+import dev.pcvolkmer.onco.datamapper.datacatalogues.KeimbahndiagnoseCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorausbreitungCatalogue;
 import dev.pcvolkmer.onco.datamapper.datacatalogues.TumorgradingCatalogue;
@@ -34,6 +35,7 @@ import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 
 import javax.sql.DataSource;
+import java.util.List;
 import java.util.Map;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -47,6 +49,7 @@ class KpaDiagnosisDataMapperTest {
     KpaCatalogue kpaCatalogue;
     TumorausbreitungCatalogue tumorausbreitungCatalogue;
     TumorgradingCatalogue tumorgradingCatalogue;
+    KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue;
     PropertyCatalogue propertyCatalogue;
 
     KpaDiagnosisDataMapper dataMapper;
@@ -56,13 +59,21 @@ class KpaDiagnosisDataMapperTest {
             @Mock KpaCatalogue kpaCatalogue,
             @Mock TumorausbreitungCatalogue tumorausbreitungCatalogue,
             @Mock TumorgradingCatalogue tumorgradingCatalogue,
+            @Mock KeimbahndiagnoseCatalogue keimbahndiagnoseCatalogue,
             @Mock PropertyCatalogue propertyCatalogue
     ) {
         this.kpaCatalogue = kpaCatalogue;
         this.tumorausbreitungCatalogue = tumorausbreitungCatalogue;
         this.tumorgradingCatalogue = tumorgradingCatalogue;
+        this.keimbahndiagnoseCatalogue = keimbahndiagnoseCatalogue;
         this.propertyCatalogue = propertyCatalogue;
-        this.dataMapper = new KpaDiagnosisDataMapper(kpaCatalogue, tumorausbreitungCatalogue, tumorgradingCatalogue, propertyCatalogue);
+        this.dataMapper = new KpaDiagnosisDataMapper(
+                kpaCatalogue,
+                tumorausbreitungCatalogue,
+                tumorgradingCatalogue,
+                keimbahndiagnoseCatalogue,
+                propertyCatalogue
+        );
     }
 
     @Test
@@ -88,12 +99,27 @@ class KpaDiagnosisDataMapperTest {
                 new PropertyCatalogue.Entry("C00.0", "Bösartige Neubildung: Äußere Oberlippe", "Bösartige Neubildung: Äußere Oberlippe")
         ).when(propertyCatalogue).getByCodeAndVersion(anyString(), anyInt());
 
+        doAnswer(invocationOnMock ->
+                List.of(
+                        ResultSet.from(
+                                Map.of(
+                                        "id", 1,
+                                        "icd10", "C00.0",
+                                        "icd10_propcat_version", 42
+                                )
+                        )
+                )
+        ).when(keimbahndiagnoseCatalogue).getAllByParentId(anyInt());
+
         var actual = this.dataMapper.getById(1);
         assertThat(actual).isInstanceOf(MtbDiagnosis.class);
         assertThat(actual.getId()).isEqualTo("1");
         assertThat(actual.getPatient())
                 .isEqualTo(Reference.builder().id("42").type("Patient").build());
         assertThat(actual.getCode().getCode()).isEqualTo("F79.9");
+
+        assertThat(actual.getGermlineCodes()).hasSize(1);
+        assertThat(actual.getGermlineCodes().get(0).getCode()).isEqualTo("C00.0");
     }
 
     private static Map<String, Object> testData() {