pcvolkmer/mv64e-onkostar-data
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feat: use patient id, not patients database id

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This commit is contained in:
Paul-Christian Volkmer
2025-07-04 00:03:58 +02:00
parent ce3df8da5e
commit 3e5c2cbb80
39 changed files with 102 additions and 142 deletions
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17
src/main/java/dev/pcvolkmer/onco/datamapper/ResultSet.java
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@@ -20,6 +20,7 @@
package dev.pcvolkmer.onco.datamapper;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
import java.time.LocalDate;
@@ -62,6 +63,22 @@ public class ResultSet {
return procedureId;
}
/**
* Get the id
*
* @return The procedures id
*/
public Reference getPatientReference() {
if (this.getString("patienten_id") == null) {
throw new DataAccessException("No patient id found");
}
return Reference.builder()
.id(this.getString("patienten_id"))
// Use "Patient" since Onkostar only provides patient data
.type("Patient")
.build();
}
/**
* Get column value as String and cast value if possible
*

3
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/AbstractDataCatalogue.java
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@@ -53,7 +53,8 @@ public abstract class AbstractDataCatalogue implements DataCatalogue {
public ResultSet getById(int id) {
var result = this.jdbcTemplate.queryForList(
String.format(
"SELECT * FROM %s JOIN prozedur ON (prozedur.id = %s.id) WHERE geloescht = 0 AND prozedur.id = ?",
"SELECT patient.patienten_id, %s.*, prozedur.* FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND prozedur.id = ?",
getTableName(),
getTableName(),
getTableName()
),

3
src/main/java/dev/pcvolkmer/onco/datamapper/datacatalogues/AbstractSubformDataCatalogue.java
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@@ -49,7 +49,8 @@ public abstract class AbstractSubformDataCatalogue extends AbstractDataCatalogue
public List<ResultSet> getAllByParentId(int id) {
return this.jdbcTemplate.queryForList(
String.format(
"SELECT * FROM %s JOIN prozedur ON (prozedur.id = %s.id) WHERE geloescht = 0 AND hauptprozedur_id = ?",
"SELECT patient.patienten_id, %s.*, prozedur.* FROM %s JOIN prozedur ON (prozedur.id = %s.id) JOIN patient ON (patient.id = prozedur.patient_id) WHERE geloescht = 0 AND hauptprozedur_id = ?",
getTableName(),
getTableName(),
getTableName()
),

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungProzedurDataMapper.java
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@@ -32,8 +32,6 @@ import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map diagnosis data from database table 'dk_dnpm_einzelempfehlung'
*
@@ -50,7 +48,7 @@ public class EinzelempfehlungProzedurDataMapper extends AbstractEinzelempfehlung
protected ProcedureRecommendation map(ResultSet resultSet) {
var resultBuilder = ProcedureRecommendation.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
// TODO Fix id?
.reason(Reference.builder().id(resultSet.getString("id")).build())
.issuedOn(resultSet.getDate("datum"))

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungStudieDataMapper.java
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@@ -28,8 +28,6 @@ import dev.pcvolkmer.onco.datamapper.datacatalogues.EinzelempfehlungCatalogue;
import java.util.List;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map diagnosis data from database table 'dk_dnpm_einzelempfehlung'
*
@@ -46,7 +44,7 @@ public class EinzelempfehlungStudieDataMapper extends AbstractEinzelempfehlungDa
protected MtbStudyEnrollmentRecommendation map(ResultSet resultSet) {
return MtbStudyEnrollmentRecommendation.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
// TODO Fix id?
.reason(Reference.builder().id(resultSet.getString("id")).build())
.issuedOn(resultSet.getDate("datum"))

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungWirkstoffDataMapper.java
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@@ -30,8 +30,6 @@ import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map diagnosis data from database table 'dk_dnpm_einzelempfehlung'
*
@@ -54,7 +52,7 @@ public class EinzelempfehlungWirkstoffDataMapper extends AbstractEinzelempfehlun
protected MtbMedicationRecommendation map(ResultSet resultSet) {
var resultBuilder = MtbMedicationRecommendation.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
// TODO Fix id?
.reason(Reference.builder().id(resultSet.getString("id")).build())
.issuedOn(resultSet.getDate("datum"))

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java
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@@ -32,8 +32,6 @@ import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map diagnosis data from database table 'dk_dnpm_kpa'
*
@@ -72,7 +70,7 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
var builder = MtbDiagnosis.builder();
builder
.id(data.getString("id"))
.patient(getPatientReference(data.getString("patient_id")))
.patient(data.getPatientReference())
.code(
Coding.builder()
.code(data.getString("icd10"))

6
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaEcogDataMapper.java
View File

@@ -32,8 +32,6 @@ import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_ecog'
*
@@ -49,7 +47,7 @@ public class KpaEcogDataMapper extends AbstractSubformDataMapper<PerformanceStat
/**
* Loads and maps Prozedur related by database id
*
* @param id The database id of the procedure data set
* @param id The patient id of the procedure data set
* @return The loaded data set
*/
@Override
@@ -72,7 +70,7 @@ public class KpaEcogDataMapper extends AbstractSubformDataMapper<PerformanceStat
var builder = PerformanceStatus.builder();
builder
.id(resultSet.getId().toString())
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.effectiveDate(resultSet.getDate("datum"))
.value(getEcogCoding(resultSet.getString("ecog")))
;

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

@@ -29,8 +29,6 @@ import dev.pcvolkmer.onco.datamapper.datacatalogues.ProzedurCatalogue;
import java.util.List;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_prozedur'
*
@@ -66,7 +64,7 @@ public class KpaProzedurDataMapper extends AbstractKpaTherapieverlaufDataMapper<
var builder = OncoProcedure.builder();
builder
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.basedOn(Reference.builder().id(diseases.get(0).getString("id")).build())
.recordedOn(resultSet.getDate("erfassungsdatum"))
.therapyLine(resultSet.getLong("therapielinie"))

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

@@ -29,8 +29,6 @@ import dev.pcvolkmer.onco.datamapper.datacatalogues.TherapielinieCatalogue;
import java.util.List;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_therapielinie'
*
@@ -66,7 +64,7 @@ public class KpaTherapielinieDataMapper extends AbstractKpaTherapieverlaufDataMa
var builder = MtbSystemicTherapy.builder();
builder
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.basedOn(
Reference.builder()
.id(resultSet.getString("ref_einzelempfehlung"))

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

@@ -29,8 +29,6 @@ import dev.pcvolkmer.onco.datamapper.datacatalogues.VerwandteCatalogue;
import java.util.Arrays;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_verwandte'
*
@@ -60,7 +58,7 @@ public class KpaVerwandteDataMapper extends AbstractSubformDataMapper<FamilyMemb
var builder = FamilyMemberHistory.builder();
builder
.id(resultSet.getId().toString())
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.relationship(
getFamilyMemberHistoryRelationshipTypeCoding(resultSet.getString("verwandtschaftsgrad"))
)

10
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaVorbefundeDataMapper.java
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@@ -20,21 +20,13 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.EcogCoding;
import dev.pcvolkmer.mv64e.mtb.EcogCodingCode;
import dev.pcvolkmer.mv64e.mtb.PerformanceStatus;
import dev.pcvolkmer.mv64e.mtb.PriorDiagnosticReport;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.EcogCatalogue;
import java.io.IOException;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_vorbefunde'
*
@@ -72,7 +64,7 @@ public class KpaVorbefundeDataMapper extends AbstractSubformDataMapper<PriorDiag
var builder = PriorDiagnosticReport.builder();
builder
.id(resultSet.getId().toString())
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.issuedOn(resultSet.getDate("datum"))
.results(List.of(resultSet.getString("ecog")))
;

50
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MapperUtils.java
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@@ -1,50 +0,0 @@
/*
* 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.Reference;
import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
/**
* Utility methods to be used in mappers
*/
public class MapperUtils {
private MapperUtils() {
}
/**
* Get Patient Reference based on default column name 'patient_id'
*
* @return The patient reference
*/
public static Reference getPatientReference(String patientId) {
if (patientId == null) {
throw new DataAccessException("No patient id found");
}
return Reference.builder()
.id(patientId)
// Use "Patient" since Onkostar only provides patient data
.type("Patient")
.build();
}
}

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MolekulargenetikToSpecimenDataMapper.java
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@@ -29,8 +29,6 @@ import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map patient data from database table 'dk_molekulargenetik'
*
@@ -76,7 +74,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
var builder = TumorSpecimen.builder();
builder
.id(data.getString("id"))
.patient(getPatientReference(data.getString("patient_id")))
.patient(data.getPatientReference())
.type(getTumorSpecimenCoding(data.getString("materialfixierung")))
.collection(getCollection(data))
// TODO add diagnosis later

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

@@ -28,8 +28,6 @@ import dev.pcvolkmer.onco.datamapper.datacatalogues.KpaCatalogue;
import java.util.List;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map patient data from database table 'dk_dnpm_kpa'
*
@@ -63,7 +61,7 @@ public class MtbEpisodeDataMapper implements DataMapper<MtbEpisodeOfCare> {
var builder = MtbEpisodeOfCare.builder();
builder
.id(kpaData.getString("id"))
.patient(getPatientReference(kpaData.getString("patient_id")))
.patient(kpaData.getPatientReference())
.diagnoses(
List.of(
Reference.builder()

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

@@ -22,15 +22,16 @@ 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.datacatalogues.EinzelempfehlungCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.RebiopsieCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.ReevaluationCatalogue;
import dev.pcvolkmer.onco.datamapper.datacatalogues.TherapieplanCatalogue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map patient data from database table 'dk_dnpm_therapieplan'
*
@@ -78,7 +79,7 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
var builder = MtbCarePlan.builder();
builder
.id(therapieplanData.getString("id"))
.patient(getPatientReference(therapieplanData.getString("patient_id")))
.patient(therapieplanData.getPatientReference())
.issuedOn(therapieplanData.getDate("datum"))
.histologyReevaluationRequests(getHistologyReevaluationRequests(id))
.rebiopsyRequests(
@@ -125,7 +126,7 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
builder.geneticCounselingRecommendation(
GeneticCounselingRecommendation.builder()
.id(therapieplanData.getString("id"))
.patient(getPatientReference(therapieplanData.getString("patient_id")))
.patient(therapieplanData.getPatientReference())
.issuedOn(therapieplanData.getDate("datum_tk_humangenber"))
.reason(
getGeneticCounselingRecommendationReasonCoding(
@@ -177,7 +178,7 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
.map(resultSet ->
RebiopsyRequest.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.issuedOn(resultSet.getDate("datum"))
.tumorEntity(diagnosisReference)
.build()
@@ -190,7 +191,7 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
.map(resultSet ->
HistologyReevaluationRequest.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
.patient(resultSet.getPatientReference())
.issuedOn(resultSet.getDate("datum"))
.specimen(Reference.builder().id(resultSet.getString("ref_molekulargenetik")).build())
.build()