pcvolkmer/mv64e-onkostar-data
1
0
Fork 0
mirror of https://github.com/pcvolkmer/mv64e-onkostar-data.git synced 2025-09-13 07:52:52 +00:00
Code Activity

feat: add Vorbefunde mapper

Browse Source
This commit is contained in:
Paul-Christian Volkmer
2025-07-06 16:10:35 +02:00
parent 8db5abe9b7
commit 21ce6f3185
6 changed files with 182 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
README.md
View File

@@ -46,10 +46,10 @@ var jsonResult = Converter.toJsonString(
| Leitlinien-Prozeduren | ✅ | Siehe auch: https://github.com/dnpm-dip/mtb-model/issues/9 |
| ECOG-Verlauf | ✅ | |
| Tumor-Proben | ⛅ | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (1) |
| vorherige Molekular-Diagnostik | ⌛ | Aktuell in Arbeit |
| vorherige Molekular-Diagnostik | ✅ | |
| Histologie-Berichte | ⌛ | Aktuell in Arbeit |
| IHC-Berichte | | |
| MSI-Befunde | | |
| IHC-Berichte | ⌛ | Aktuell in Arbeit |
| MSI-Befunde | ⌛ | Aktuell in Arbeit |
| NGS-Berichte | ⛅ | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (2) |
| MTB-Beschlüsse | ✅ | Stützende molekulare Alteration(en) für einfache Variante und CNV (3) |
| Follow-Up Verlauf | | |

4
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/VorbefundeCatalogue.java
View File

@@ -23,7 +23,7 @@ package dev.pcvolkmer.onco.datamapper.datacatalogues;
import org.springframework.jdbc.core.JdbcTemplate;
/**
* Load raw result sets from database table 'dk_dnpm_uf_vorbefunde'
* Load raw result sets from database table 'dk_dnpm_vorbefunde'
*
* @author Paul-Christian Volkmer
* @since 0.1
@@ -36,7 +36,7 @@ public class VorbefundeCatalogue extends AbstractSubformDataCatalogue {
@Override
protected String getTableName() {
return "dk_dnpm_uf_vorbefunde";
return "dk_dnpm_vorbefunde";
}
public static VorbefundeCatalogue create(JdbcTemplate jdbcTemplate) {

40
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaVorbefundeDataMapper.java
View File

@@ -20,10 +20,14 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
import dev.pcvolkmer.mv64e.mtb.*;
import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.EcogCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.VorbefundeCatalogue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
@@ -35,8 +39,11 @@ import java.util.stream.Collectors;
*/
public class KpaVorbefundeDataMapper extends AbstractSubformDataMapper<PriorDiagnosticReport> {
public KpaVorbefundeDataMapper(final EcogCatalogue catalogue) {
private final PropertyCatalogue propertyCatalogue;
public KpaVorbefundeDataMapper(final VorbefundeCatalogue catalogue, PropertyCatalogue propertyCatalogue) {
super(catalogue);
this.propertyCatalogue = propertyCatalogue;
}
/**
@@ -65,11 +72,36 @@ public class KpaVorbefundeDataMapper extends AbstractSubformDataMapper<PriorDiag
builder
.id(resultSet.getId().toString())
.patient(resultSet.getPatientReference())
.issuedOn(resultSet.getDate("datum"))
.results(List.of(resultSet.getString("ecog")))
.issuedOn(resultSet.getDate("erstellungsdatum"))
.specimen(Reference.builder().id(resultSet.getString("befundnummer")).type("Specimen").build())
.type(
getMolecularDiagnosticReportCoding(
resultSet.getString("artderdiagnostik"),
resultSet.getInteger("artderdiagnostik_propcat_version")
)
)
.results(List.of(
resultSet.getString("ergebnisse")
))
;
return builder.build();
}
private MolecularDiagnosticReportCoding getMolecularDiagnosticReportCoding(String value, int version) {
if (value == null || !Arrays.stream(MolecularDiagnosticReportCodingCode.values()).map(MolecularDiagnosticReportCodingCode::toValue).collect(Collectors.toSet()).contains(value)) {
return null;
}
var resultBuilder = MolecularDiagnosticReportCoding.builder()
.display(propertyCatalogue.getByCodeAndVersion(value, version).getShortdesc());
try {
resultBuilder.code(MolecularDiagnosticReportCodingCode.forValue(value));
} catch (IOException e) {
return null;
}
return resultBuilder.build();
}
}

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java
View File

@@ -126,6 +126,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
var kpaVorbefundeDataMapper = new KpaVorbefundeDataMapper(catalogueFactory.catalogue(VorbefundeCatalogue.class), propertyCatalogue);
var resultBuilder = Mtb.builder();
try {
@@ -144,6 +146,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
.guidelineTherapies(therapielinieMapper.getByParentId(kpaId))
.performanceStatus(ecogMapper.getByParentId(kpaId))
.familyMemberHistories(verwandteDataMapper.getByParentId(kpaId))
// Vorbefunde
.priorDiagnosticReports(kpaVorbefundeDataMapper.getByParentId(kpaId))
// DNPM Therapieplan
.carePlans(
therapieplanCatalogue

6
src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/VorbefundeCatalogueTest.java
View File

@@ -62,7 +62,7 @@ class VorbefundeCatalogueTest {
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
assertThat(captor.getValue())
.isEqualTo("SELECT patient.patienten_id, dk_dnpm_uf_vorbefunde.*, prozedur.* FROM dk_dnpm_uf_vorbefunde JOIN prozedur ON (prozedur.id = dk_dnpm_uf_vorbefunde.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?");
.isEqualTo("SELECT patient.patienten_id, dk_dnpm_vorbefunde.*, prozedur.* FROM dk_dnpm_vorbefunde JOIN prozedur ON (prozedur.id = dk_dnpm_vorbefunde.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?");
}
@Test
@@ -77,7 +77,7 @@ class VorbefundeCatalogueTest {
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
assertThat(captor.getValue())
.isEqualTo("SELECT patient.patienten_id, dk_dnpm_uf_vorbefunde.*, prozedur.* FROM dk_dnpm_uf_vorbefunde JOIN prozedur ON (prozedur.id = dk_dnpm_uf_vorbefunde.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
.isEqualTo("SELECT patient.patienten_id, dk_dnpm_vorbefunde.*, prozedur.* FROM dk_dnpm_vorbefunde JOIN prozedur ON (prozedur.id = dk_dnpm_vorbefunde.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?");
}
@Test
@@ -95,7 +95,7 @@ class VorbefundeCatalogueTest {
verify(this.jdbcTemplate).queryForList(captor.capture(), anyInt());
assertThat(captor.getValue())
.isEqualTo("SELECT feldname, feldwert FROM dk_dnpm_uf_vorbefunde_merkmale WHERE eintrag_id = ?");
.isEqualTo("SELECT feldname, feldwert FROM dk_dnpm_vorbefunde_merkmale WHERE eintrag_id = ?");
}
@Test

134
src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaVorbefundeDataMapperTest.java Normal file
View File

@@ -0,0 +1,134 @@
/*
* 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.MolecularDiagnosticReportCoding;
import dev.pcvolkmer.mv64e.mtb.MolecularDiagnosticReportCodingCode;
import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.VorbefundeCatalogue;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import java.time.Instant;
import java.util.Date;
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.when;
@ExtendWith(MockitoExtension.class)
class KpaVorbefundeDataMapperTest {
VorbefundeCatalogue catalogue;
PropertyCatalogue propertyCatalogue;
KpaVorbefundeDataMapper dataMapper;
@BeforeEach
void setUp(
@Mock VorbefundeCatalogue catalogue,
@Mock PropertyCatalogue propertyCatalogue
) {
this.catalogue = catalogue;
this.propertyCatalogue = propertyCatalogue;
this.dataMapper = new KpaVorbefundeDataMapper(catalogue, propertyCatalogue);
}
@Test
void shouldMapResultSet(@Mock ResultSet resultSet) {
Map<String, Object> testData = Map.of(
"id", "1",
"patienten_id", "42",
"erstellungsdatum", new java.sql.Date(Date.from(Instant.parse("2000-07-06T12:00:00Z")).getTime()),
"befundnummer", "X/2025/1234",
"ergebnisse", "Befundtext",
"artderdiagnostik", "panel",
"artderdiagnostik_propcat_version", "1234"
);
doAnswer(invocationOnMock -> Reference.builder().id(testData.get("patienten_id").toString()).type("Patient").build())
.when(resultSet).getPatientReference();
doAnswer(invocationOnMock -> {
var columnName = invocationOnMock.getArgument(0, String.class);
return testData.get(columnName);
}).when(resultSet).getDate(anyString());
doAnswer(invocationOnMock -> {
var columnName = invocationOnMock.getArgument(0, String.class);
return testData.get(columnName);
}).when(resultSet).getString(anyString());
when(resultSet.getId()).thenReturn(1);
doAnswer(invocationOnMock -> List.of(resultSet))
.when(catalogue)
.getAllByParentId(anyInt());
doAnswer(invocationOnMock -> {
var testPropertyData = Map.of(
"panel", new PropertyCatalogue.Entry("panel", "Panel", "Panel")
);
var code = invocationOnMock.getArgument(0, String.class);
return testPropertyData.get(code);
}
).when(propertyCatalogue).getByCodeAndVersion(anyString(), anyInt());
var actualList = this.dataMapper.getByParentId(1);
assertThat(actualList).hasSize(1);
var actual = actualList.get(0);
assertThat(actual).isInstanceOf(PriorDiagnosticReport.class);
assertThat(actual.getId()).isEqualTo("1");
assertThat(actual.getPatient())
.isEqualTo(Reference.builder()
.id("42")
.type("Patient")
.build()
);
assertThat(actual.getIssuedOn())
.isEqualTo(new java.sql.Date(Date.from(Instant.parse("2000-07-06T12:00:00Z")).getTime()));
assertThat(actual.getSpecimen())
.isEqualTo(Reference.builder()
.id("X/2025/1234")
.type("Specimen")
.build()
);
assertThat(actual.getType())
.isEqualTo(MolecularDiagnosticReportCoding.builder()
.code(MolecularDiagnosticReportCodingCode.PANEL)
.display("Panel")
.build()
);
}
}