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feat: add germline diagnosis codes

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This commit is contained in:
Paul-Christian Volkmer
2025-07-26 21:32:47 +02:00
parent a6ba6c54e2
commit ed1d6a9dab
6 changed files with 220 additions and 3 deletions
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2
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java
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@@ -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);
});

46
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogue.java Normal file
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@@ -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);
}
}

20
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java
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@@ -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");

1
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java
View File

@@ -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);

126
src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/KeimbahndiagnoseCatalogueTest.java Normal file
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@@ -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"));
}
}

28
src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java
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@@ -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() {