pcvolkmer/mv64e-onkostar-data
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feat: add Histologie and related specimens

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Paul-Christian Volkmer
2025-07-06 17:27:43 +02:00
parent 37c553a34e
commit 4f82993431
4 changed files with 153 additions and 15 deletions
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11
README.md
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@@ -47,11 +47,11 @@ var jsonResult = Converter.toJsonString(
| ECOG-Verlauf | ✅ | |
| Tumor-Proben | ⛅ | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (1) |
| vorherige Molekular-Diagnostik | ✅ | |
| Histologie-Berichte | ⌛ | Aktuell in Arbeit |
| Histologie-Berichte | ✅ | Hinweis (2) |
| 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) |
| NGS-Berichte | ⛅ | Best effort: Formular OS.Molekulargenetik erfüllt nicht alle Anforderungen (3) |
| MTB-Beschlüsse | ✅ | Stützende molekulare Alteration(en) für einfache Variante und CNV (4) |
| Follow-Up Verlauf | | |
| Antrag Kostenübernahme | | |
| Antwort Kostenübernahme | | |
@@ -61,9 +61,10 @@ var jsonResult = Converter.toJsonString(
### Hinweise
1. Nicht alle möglichen Ausprägungen in `OS.Molekulargenetik` vorhanden.
2. Aktuell nicht alle Angaben effektiv im Formular `OS.Molekulargenetik` wie gefordert angebbar.
2. Aktuell wird die Version der Morphologie nicht mit exportiert, nur der Wert.
3. Aktuell nicht alle Angaben effektiv im Formular `OS.Molekulargenetik` wie gefordert angebbar.
Hinweis: Tumorzellgehalt-Methode problematisch, wenn auch im NGS-Bericht histologisch festgestellt.
3. Implementierung des Mappings von HGNC-Symbol (Gen-Name) zu HGNC-ID über enthaltene Gen-Liste.
4. Implementierung des Mappings von HGNC-Symbol (Gen-Name) zu HGNC-ID über enthaltene Gen-Liste.
## Enthaltene Liste mit Genen

118
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaHistologieDataMapper.java Normal file
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@@ -0,0 +1,118 @@
/*
* 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.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.HistologieCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.MolekulargenetikCatalogue;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_vorbefunde'
*
* @author Paul-Christian Volkmer
* @since 0.1
*/
public class KpaHistologieDataMapper extends AbstractSubformDataMapper<HistologyReport> {
private final MolekulargenetikCatalogue molekulargenetikCatalogue;
private final PropertyCatalogue propertyCatalogue;
public KpaHistologieDataMapper(
final HistologieCatalogue catalogue,
final MolekulargenetikCatalogue molekulargenetikCatalogue,
final PropertyCatalogue propertyCatalogue
) {
super(catalogue);
this.molekulargenetikCatalogue = molekulargenetikCatalogue;
this.propertyCatalogue = propertyCatalogue;
}
/**
* Loads and maps Prozedur related by database id
*
* @param id The database id of the procedure data set
* @return The loaded data set
*/
@Override
public HistologyReport getById(final int id) {
var data = catalogue.getById(id);
return this.map(data);
}
@Override
public List<HistologyReport> getByParentId(final int parentId) {
return catalogue.getAllByParentId(parentId)
.stream()
.map(this::map)
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
@Override
protected HistologyReport map(final ResultSet resultSet) {
var builder = HistologyReport.builder();
var osMolGen = molekulargenetikCatalogue.getById(resultSet.getInteger("histologie"));
if (null != osMolGen) {
builder
.id(resultSet.getId().toString())
.patient(resultSet.getPatientReference())
.issuedOn(resultSet.getDate("erstellungsdatum"))
.specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
.results(
HistologyReportResults.builder()
.tumorCellContent(
TumorCellContent.builder()
.id(resultSet.getId().toString())
.patient(resultSet.getPatientReference())
.specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
.value(resultSet.getLong("tumorzellgehalt"))
// Nicht in OS.Molekulargenetik
//.method()
.build()
)
.tumorMorphology(
TumorMorphology.builder()
.id(resultSet.getId().toString())
.patient(resultSet.getPatientReference())
.specimen(Reference.builder().id(osMolGen.getId().toString()).type("Specimen").build())
.value(Coding.builder().code(resultSet.getString("morphologie")).build())
.build()
)
.build()
)
;
return builder.build();
}
return null;
}
}

15
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MolekulargenetikToSpecimenDataMapper.java
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@@ -21,7 +21,6 @@
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.*;
@@ -43,6 +42,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
private final ReevaluationCatalogue reevaluationCatalogue;
private final EinzelempfehlungCatalogue einzelempfehlungCatalogue;
private final VorbefundeCatalogue vorbefundeCatalogue;
private final HistologieCatalogue histologieCatalogue;
public MolekulargenetikToSpecimenDataMapper(
final MolekulargenetikCatalogue molekulargenetikCatalogue,
@@ -50,7 +50,8 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
final RebiopsieCatalogue rebiopsieCatalogue,
final ReevaluationCatalogue reevaluationCatalogue,
final EinzelempfehlungCatalogue einzelempfehlungCatalogue,
final VorbefundeCatalogue vorbefundeCatalogue
final VorbefundeCatalogue vorbefundeCatalogue,
final HistologieCatalogue histologieCatalogue
) {
this.molekulargenetikCatalogue = molekulargenetikCatalogue;
this.therapieplanCatalogue = therapieplanCatalogue;
@@ -58,6 +59,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
this.reevaluationCatalogue = reevaluationCatalogue;
this.einzelempfehlungCatalogue = einzelempfehlungCatalogue;
this.vorbefundeCatalogue = vorbefundeCatalogue;
this.histologieCatalogue = histologieCatalogue;
}
/**
@@ -136,6 +138,15 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
.collect(Collectors.toList())
);
// Histologie
osMolGen.addAll(
histologieCatalogue.getAllByParentId(kpaId).stream()
.map(rs -> rs.getInteger("histologie"))
.map(molekulargenetikCatalogue::getById)
.map(ResultSet::getId)
.collect(Collectors.toList())
);
return osMolGen.stream()
.filter(Objects::nonNull)
.distinct()

24
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MtbDataMapper.java
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@@ -21,7 +21,6 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.Mtb;
import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
@@ -121,7 +120,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
catalogueFactory.catalogue(RebiopsieCatalogue.class),
catalogueFactory.catalogue(ReevaluationCatalogue.class),
einzelempfehlungCatalogue,
catalogueFactory.catalogue(VorbefundeCatalogue.class)
catalogueFactory.catalogue(VorbefundeCatalogue.class),
catalogueFactory.catalogue(HistologieCatalogue.class)
);
var kpaMolekulargenetikDataMapper = new KpaMolekulargenetikDataMapper(molekulargenetikCatalogue, catalogueFactory.catalogue(MolekulargenuntersuchungCatalogue.class), propertyCatalogue);
@@ -132,6 +132,12 @@ public class MtbDataMapper implements DataMapper<Mtb> {
propertyCatalogue
);
var kpaHistologieDataMapper = new KpaHistologieDataMapper(
catalogueFactory.catalogue(HistologieCatalogue.class),
molekulargenetikCatalogue,
propertyCatalogue
);
var resultBuilder = Mtb.builder();
try {
@@ -152,6 +158,8 @@ public class MtbDataMapper implements DataMapper<Mtb> {
.familyMemberHistories(verwandteDataMapper.getByParentId(kpaId))
// Vorbefunde
.priorDiagnosticReports(kpaVorbefundeDataMapper.getByParentId(kpaId))
// Histologie-Berichte
.histologyReports(kpaHistologieDataMapper.getByParentId(kpaId))
// DNPM Therapieplan
.carePlans(
therapieplanCatalogue
@@ -161,14 +169,14 @@ public class MtbDataMapper implements DataMapper<Mtb> {
)
// Tumorproben
.specimens(
molekulargenetikToSpecimenDataMapper.getAllByKpaId(
kpaId,
Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
)
molekulargenetikToSpecimenDataMapper.getAllByKpaId(
kpaId,
Reference.builder().id(diagnosis.getId()).type("MTBDiagnosis").build()
)
)
// NGS Berichte
.ngsReports(
kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
kpaMolekulargenetikDataMapper.getAllByKpaId(kpaId)
)
;
@@ -195,7 +203,7 @@ public class MtbDataMapper implements DataMapper<Mtb> {
* Loads and maps a Mtb file using the patient id and tumor id
*
* @param patientId The patients id (not database id)
* @param tumorId The tumor identification
* @param tumorId The tumor identification
* @return The loaded Mtb file
*/
public Mtb getLatestByPatientIdAndTumorId(String patientId, int tumorId) {