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feat: initial support for NGS reports

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This commit is contained in:
Paul-Christian Volkmer
2025-07-05 13:32:31 +02:00
parent a711b391bb
commit 433dbbc188
9 changed files with 377 additions and 30 deletions
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2
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/DataCatalogueFactory.java
View File

@@ -93,6 +93,8 @@ public class DataCatalogueFactory {
return EinzelempfehlungCatalogue.create(jdbcTemplate);
} else if (c == MolekulargenetikCatalogue.class) {
return MolekulargenetikCatalogue.create(jdbcTemplate);
} else if (c == MolekulargenuntersuchungCatalogue.class) {
return MolekulargenuntersuchungCatalogue.create(jdbcTemplate);
} else if (c == RebiopsieCatalogue.class) {
return RebiopsieCatalogue.create(jdbcTemplate);
} else if (c == ReevaluationCatalogue.class) {

57
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/MolekulargenetikCatalogue.java
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@@ -20,15 +20,19 @@
package dev.pcvolkmer.onco.datamapper.datacatalogues;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import org.springframework.jdbc.core.JdbcTemplate;
import java.util.List;
import java.util.stream.Collectors;
/**
* Load raw result sets from database table 'dk_molekulargenetik'
*
* @author Paul-Christian Volkmer
* @since 0.1
*/
public class MolekulargenetikCatalogue extends AbstractSubformDataCatalogue {
public class MolekulargenetikCatalogue extends AbstractDataCatalogue {
private MolekulargenetikCatalogue(JdbcTemplate jdbcTemplate) {
super(jdbcTemplate);
@@ -43,4 +47,55 @@ public class MolekulargenetikCatalogue extends AbstractSubformDataCatalogue {
return new MolekulargenetikCatalogue(jdbcTemplate);
}
/**
* Get procedure IDs by related Therapieplan procedure id
* Related form references in Einzelempfehlung, Rebiopsie, Reevaluation
*
* @param therapieplanId The procedure id
* @return The procedure ids
*/
public List<Integer> getByTherapieplanId(int therapieplanId) {
return this.jdbcTemplate.queryForList(
"SELECT DISTINCT ref_molekulargenetik FROM dk_dnpm_uf_einzelempfehlung JOIN prozedur ON (prozedur.id = dk_dnpm_uf_einzelempfehlung.id) "
+ " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id = ? "
+ " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_rebiopsie JOIN prozedur ON (prozedur.id = dk_dnpm_uf_rebiopsie.id) "
+ " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id = ? "
+ " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_reevaluation JOIN prozedur ON (prozedur.id = dk_dnpm_uf_reevaluation.id) "
+ " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id = ?;"
,
therapieplanId,
therapieplanId,
therapieplanId)
.stream()
.map(ResultSet::from)
.map(rs -> rs.getInteger("ref_molekulargenetik"))
.collect(Collectors.toList());
}
/**
* Get procedure IDs used in related KPA/Therapieplan procedures
* Related form references in Einzelempfehlung, Rebiopsie, Reevaluation
*
* @param kpaId The procedure id
* @return The procedure ids
*/
public List<Integer> getIdsByKpaId(int kpaId) {
return this.jdbcTemplate.queryForList(
"SELECT DISTINCT ref_molekulargenetik FROM dk_dnpm_uf_einzelempfehlung JOIN prozedur ON (prozedur.id = dk_dnpm_uf_einzelempfehlung.id) "
+ " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id IN (SELECT id FROM dk_dnpm_therapieplan WHERE ref_dnpm_klinikanamnese = ?) "
+ " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_rebiopsie JOIN prozedur ON (prozedur.id = dk_dnpm_uf_rebiopsie.id) "
+ " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id IN (SELECT id FROM dk_dnpm_therapieplan WHERE ref_dnpm_klinikanamnese = ?) "
+ " UNION SELECT ref_molekulargenetik FROM dk_dnpm_uf_reevaluation JOIN prozedur ON (prozedur.id = dk_dnpm_uf_reevaluation.id) "
+ " WHERE ref_molekulargenetik IS NOT NULL AND hauptprozedur_id IN (SELECT id FROM dk_dnpm_therapieplan WHERE ref_dnpm_klinikanamnese = ?);"
,
kpaId,
kpaId,
kpaId)
.stream()
.map(ResultSet::from)
.map(rs -> rs.getInteger("ref_molekulargenetik"))
.distinct()
.collect(Collectors.toList());
}
}

50
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/MolekulargenuntersuchungCatalogue.java Normal file
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@@ -0,0 +1,50 @@
/*
* 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 dev.pcvolkmer.onco.datamapper.ResultSet;
import org.springframework.jdbc.core.JdbcTemplate;
import java.util.List;
import java.util.stream.Collectors;
/**
* Load raw result sets from database table 'dk_molekulargenuntersuchung'
*
* @author Paul-Christian Volkmer
* @since 0.1
*/
public class MolekulargenuntersuchungCatalogue extends AbstractSubformDataCatalogue {
private MolekulargenuntersuchungCatalogue(JdbcTemplate jdbcTemplate) {
super(jdbcTemplate);
}
@Override
protected String getTableName() {
return "dk_molekulargenuntersuchung";
}
public static MolekulargenuntersuchungCatalogue create(JdbcTemplate jdbcTemplate) {
return new MolekulargenuntersuchungCatalogue(jdbcTemplate);
}
}

9
src/main/java/dev/pcvolkmer/onco/datamapper/genes/GeneUtils.java
View File

@@ -20,6 +20,7 @@
package dev.pcvolkmer.onco.datamapper.genes;
import dev.pcvolkmer.mv64e.mtb.Coding;
import org.apache.commons.csv.CSVFormat;
import java.io.IOException;
@@ -48,6 +49,14 @@ public class GeneUtils {
return genes().stream().filter(gene -> gene.getSymbol().equalsIgnoreCase(symbol)).findFirst();
}
public static Coding toCoding(Gene gene) {
return Coding.builder()
.code(gene.getHgncId())
.display(gene.getSymbol())
.system("https://www.genenames.org/")
.build();
}
private static List<Gene> genes() {
var result = new ArrayList<Gene>();

15
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/JsonToMolAltVarianteMapper.java
View File

@@ -23,7 +23,6 @@ package dev.pcvolkmer.onco.datamapper.mapper;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import dev.pcvolkmer.mv64e.mtb.Coding;
import dev.pcvolkmer.mv64e.mtb.GeneAlterationReference;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
@@ -53,19 +52,11 @@ public class JsonToMolAltVarianteMapper {
}).stream()
.map(variante -> {
var resultBuilder = GeneAlterationReference.builder();
GeneUtils.findBySymbol(variante.getGen()).ifPresent(gene -> {
resultBuilder
.gene(
Coding.builder()
.code(gene.getHgncId())
.display(gene.getSymbol())
.system("https://www.genenames.org/")
.build()
)
GeneUtils.findBySymbol(variante.getGen()).ifPresent(gene -> resultBuilder
.gene(GeneUtils.toCoding(gene))
.variant(
Reference.builder().id(variante.id).type("Variant").build()
);
});
));
return resultBuilder.build();
})
.collect(Collectors.toList());

166
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaMolekulargenetikDataMapper.java Normal file
View File

@@ -0,0 +1,166 @@
/*
* 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.mapper;
import dev.pcvolkmer.mv64e.mtb.*;
import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
import dev.pcvolkmer.onco.datamapper.genes.GeneUtils;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
/**
* Mapper class to load and map prozedur data from database table 'dk_molekulargenetik'
*
* @author Paul-Christian Volkmer
* @since 0.1
*/
public class KpaMolekulargenetikDataMapper implements DataMapper<SomaticNgsReport> {
private final MolekulargenetikCatalogue catalogue;
private final MolekulargenuntersuchungCatalogue untersuchungCatalogue;
public KpaMolekulargenetikDataMapper(
final MolekulargenetikCatalogue catalogue,
final MolekulargenuntersuchungCatalogue untersuchungCatalogue,
final PropertyCatalogue propertyCatalogue
) {
this.catalogue = catalogue;
this.untersuchungCatalogue = untersuchungCatalogue;
}
/**
* Loads and maps Prozedur related by database id
*
* @param id The database id of the procedure data set
* @return The loaded Procedure
*/
@Override
public SomaticNgsReport getById(final int id) {
var data = catalogue.getById(id);
var builder = SomaticNgsReport.builder();
builder
.id(data.getString("id"))
.patient(data.getPatientReference())
.issuedOn(data.getDate("datum"))
.specimen(Reference.builder().id(data.getString("einsendenummer")).type("Specimen").build())
.results(this.getNgsReportResults(id))
;
return builder.build();
}
/**
* Loads and maps all Prozedur related by KPA database id
*
* @param kpaId The database id of the KPA procedure data set
* @return The loaded Procedures
*/
public List<SomaticNgsReport> getAllByKpaId(final int kpaId) {
return this.catalogue.getIdsByKpaId(kpaId).stream()
.distinct()
.map(this::getById)
.collect(Collectors.toList());
}
private NgsReportResults getNgsReportResults(int id) {
var subforms = this.untersuchungCatalogue.getAllByParentId(id);
var resultBuilder = NgsReportResults.builder();
resultBuilder.simpleVariants(
subforms.stream()
// P => Einfache Variante
.filter(subform -> "P".equals(subform.getString("ergebnis")))
.map(subform -> {
final var geneOptional = GeneUtils.findBySymbol(subform.getString("untersucht"));
if (geneOptional.isEmpty()) {
return null;
}
final var snvBuilder = Snv.builder()
.id(subform.getString("id"))
.patient(subform.getPatientReference())
.gene(GeneUtils.toCoding(geneOptional.get()))
.exonId(subform.getString("exon"))
.dnaChange(subform.getString("cdnanomenklatur"))
.proteinChange(subform.getString("proteinebenenomenklatur"));
if (null != subform.getLong("allelfrequenz")) {
snvBuilder.allelicFrequency(subform.getLong("allelfrequenz"));
}
if (null != subform.getLong("evreaddepth")) {
snvBuilder.readDepth(subform.getLong("evreaddepth"));
}
geneOptional.get().getSingleChromosomeInPropertyForm().ifPresent(snvBuilder::chromosome);
return snvBuilder.build();
})
.collect(Collectors.toList())
);
resultBuilder.copyNumberVariants(
subforms.stream()
.filter(subform -> "CNV".equals(subform.getString("ergebnis")))
.map(subform -> {
final var geneOptional = GeneUtils.findBySymbol(subform.getString("untersucht"));
if (geneOptional.isEmpty()) {
return null;
}
final var reportedAffectedGenes = new ArrayList<String>();
reportedAffectedGenes.add(subform.getString("untersucht"));
// Weitere betroffene Gene aus Freitextfeld?
if (null != subform.getString("cnvbetroffenegene")) {
reportedAffectedGenes.addAll(
Arrays.stream(subform.getString("cnvbetroffenegene").split("\\s")).collect(Collectors.toList())
);
}
final var cnvBuilder = Cnv.builder()
.id(subform.getString("id"))
.patient(subform.getPatientReference())
.reportedAffectedGenes(
reportedAffectedGenes.stream()
.distinct()
.map(GeneUtils::findBySymbol)
.filter(Optional::isPresent)
.map(gene -> GeneUtils.toCoding(gene.get()))
.collect(Collectors.toList())
)
.totalCopyNumber(subform.getLong("cnvtotalcn"));
geneOptional.get().getSingleChromosomeInPropertyForm().ifPresent(cnvBuilder::chromosome);
return cnvBuilder.build();
})
.collect(Collectors.toList())
);
return resultBuilder.build();
}
}

7
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java
View File

@@ -124,6 +124,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
propertyCatalogue
);
var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
var resultBuilder = Mtb.builder();
try {
@@ -156,6 +158,11 @@ public class MtbDataMapper implements DataMapper<Mtb> {
Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
)
)
// NGS Berichte
.ngsReports(
kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
)
;
} catch (DataAccessException e) {
logger.error("Error while getting Mtb.", e);

15
src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/MolekulargenetikCatalogueTest.java
View File

@@ -64,19 +64,4 @@ class MolekulargenetikCatalogueTest {
.isEqualTo("SELECT patient.patienten_id, dk_molekulargenetik.*, prozedur.* FROM dk_molekulargenetik JOIN prozedur ON (prozedur.id = dk_molekulargenetik.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_molekulargenetik.*, prozedur.* FROM dk_molekulargenetik JOIN prozedur ON (prozedur.id = dk_molekulargenetik.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
}
}

82
src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/MolekulargenuntersuchungCatalogueTest.java Normal file
View File

@@ -0,0 +1,82 @@
/*
* 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.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.doAnswer;
import static org.mockito.Mockito.verify;
@ExtendWith(MockitoExtension.class)
class MolekulargenuntersuchungCatalogueTest {
JdbcTemplate jdbcTemplate;
MolekulargenuntersuchungCatalogue catalogue;
@BeforeEach
void setUp(@Mock JdbcTemplate jdbcTemplate) {
this.jdbcTemplate = jdbcTemplate;
this.catalogue = MolekulargenuntersuchungCatalogue.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_molekulargenuntersuchung.*, prozedur.* FROM dk_molekulargenuntersuchung JOIN prozedur ON (prozedur.id = dk_molekulargenuntersuchung.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_molekulargenuntersuchung.*, prozedur.* FROM dk_molekulargenuntersuchung JOIN prozedur ON (prozedur.id = dk_molekulargenuntersuchung.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
}
}