pcvolkmer/mv64e-onkostar-data
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feat: add util method to create patient reference

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This commit is contained in:
Paul-Christian Volkmer
2025-06-22 15:31:54 +02:00
parent e848752e45
commit 684c866b97
8 changed files with 55 additions and 16 deletions
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4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapper.java
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@ -12,6 +12,8 @@ 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'
*
@ -50,7 +52,7 @@ public class KpaDiagnosisDataMapper implements DataMapper<MtbDiagnosis> {
var builder = MtbDiagnosis.builder();
builder
.id(data.getString("id"))
.patient(Reference.builder().id(data.getString("patient_id")).build())
.patient(getPatientReference(data.getString("patient_id")))
.code(
Coding.builder()
.code(data.getString("icd10"))

11
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaEcogDataMapper.java
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@ -3,7 +3,6 @@ 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.Reference;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.EcogCatalogue;
@ -13,6 +12,8 @@ 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'
*
@ -51,13 +52,7 @@ public class KpaEcogDataMapper extends AbstractSubformDataMapper<PerformanceStat
var builder = PerformanceStatus.builder();
builder
.id(resultSet.getProcedureId().toString())
.patient(
Reference.builder()
.id(resultSet.getString("patient_id"))
// Use "Patient" since Onkostar only provides patient data
.type("Patient")
.build()
)
.patient(getPatientReference(resultSet.getString("patient_id")))
.effectiveDate(resultSet.getDate("datum"))
.value(getEcogCoding(resultSet.getString("ecog")))
;

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaProzedurDataMapper.java
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@ -7,6 +7,8 @@ import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.ProzedurCatalogue;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_uf_prozedur'
*
@ -42,7 +44,7 @@ public class KpaProzedurDataMapper extends AbstractKpaTherapieverlaufDataMapper<
var builder = OncoProcedure.builder();
builder
.id(resultSet.getString("id"))
.patient(Reference.builder().id(resultSet.getString("patient_id")).build())
.patient(getPatientReference(resultSet.getString("patient_id")))
.basedOn(Reference.builder().id(diseases.get(0).getDiseaseId().toString()).build())
.recordedOn(resultSet.getDate("erfassungsdatum"))
.therapyLine(resultSet.getLong("therapielinie"))

4
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/KpaTherapielinieDataMapper.java
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@ -7,6 +7,8 @@ import dev.pcvolkmer.onco.datamapper.PropertyCatalogue;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.TherapielinieCatalogue;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
/**
* Mapper class to load and map prozedur data from database table 'dk_dnpm_therapielinie'
*
@ -42,7 +44,7 @@ public class KpaTherapielinieDataMapper extends AbstractKpaTherapieverlaufDataMa
var builder = MtbSystemicTherapy.builder();
builder
.id(resultSet.getString("id"))
.patient(Reference.builder().id(resultSet.getString("patient_id")).build())
.patient(getPatientReference(resultSet.getString("patient_id")))
.basedOn(Reference.builder().id(diseases.get(0).getDiseaseId().toString()).build())
.recordedOn(resultSet.getDate("erfassungsdatum"))
.therapyLine(resultSet.getLong("therapielinie"))

30
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MapperUtils.java Normal file
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@ -0,0 +1,30 @@
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();
}
}

6
src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaDiagnosisDataMapperTest.java
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@ -1,6 +1,7 @@
package dev.pcvolkmer.onco.datamapper.mapper;
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.KpaCatalogue;
@ -67,13 +68,16 @@ class KpaDiagnosisDataMapperTest {
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");
}
private static Map<String, Object> testData() {
return Map.of(
"id", "1",
"icd10", "F79.9"
"icd10", "F79.9",
"patient_id", "42"
);
}

6
src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaProzedurDataMapperTest.java
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@ -42,7 +42,6 @@ class KpaProzedurDataMapperTest {
@Test
void shouldMapResultSet(@Mock ResultSet resultSet) {
var testData = Map.of(
"erkrankung.id", "1",
"id", "1",
"beginn", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
"ende", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
@ -51,7 +50,8 @@ class KpaProzedurDataMapperTest {
"status", "stopped",
"statusgrund", "patient-death",
"therapielinie", 1L,
"typ", "surgery"
"typ", "surgery",
"patient_id", "42"
);
doAnswer(invocationOnMock -> {
@ -99,6 +99,8 @@ class KpaProzedurDataMapperTest {
var actual = actualList.get(0);
assertThat(actual).isInstanceOf(OncoProcedure.class);
assertThat(actual.getId()).isEqualTo("1");
assertThat(actual.getPatient())
.isEqualTo(Reference.builder().id("42").type("Patient").build());
assertThat(actual.getPeriod()).isEqualTo(
PeriodDate.builder()
.start(Date.from(Instant.parse("2000-01-01T12:00:00Z")))

6
src/test/java/dev/pcvolkmer/onco/datamapper/mapper/KpaTherapielinieDataMapperTest.java
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@ -42,7 +42,6 @@ class KpaTherapielinieDataMapperTest {
@Test
void shouldMapResultSet(@Mock ResultSet resultSet) {
var testData = Map.of(
"erkrankung.id", "1",
"id", "1",
"beginn", new java.sql.Date(Date.from(Instant.parse("2000-01-01T12:00:00Z")).getTime()),
"ende", new java.sql.Date(Date.from(Instant.parse("2024-06-19T12:00:00Z")).getTime()),
@ -50,7 +49,8 @@ class KpaTherapielinieDataMapperTest {
"intention", "S",
"status", "stopped",
"statusgrund", "patient-death",
"therapielinie", 1L
"therapielinie", 1L,
"patient_id", "42"
);
doAnswer(invocationOnMock -> {
@ -99,6 +99,8 @@ class KpaTherapielinieDataMapperTest {
.isInstanceOf(MtbSystemicTherapy.class);
assertThat(actual.getId())
.isEqualTo("1");
assertThat(actual.getPatient())
.isEqualTo(Reference.builder().id("42").type("Patient").build());
assertThat(actual.getPeriod())
.isEqualTo(
PeriodDate.builder()