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refactor: separate usage of study enrollment

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This commit is contained in:
Paul-Christian Volkmer
2025-06-30 00:46:07 +02:00
parent 070ac3c2ab
commit d53c2074e4
9 changed files with 228 additions and 64 deletions
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20
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/AbstractEinzelempfehlungDataMapper.java
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@ -4,6 +4,7 @@ import dev.pcvolkmer.mv64e.mtb.*;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.EinzelempfehlungCatalogue;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Objects;
@ -18,6 +19,25 @@ public abstract class AbstractEinzelempfehlungDataMapper<T> extends AbstractSubf
super(einzelempfehlungCatalogue);
}
protected RecommendationPriorityCoding getRecommendationPriorityCoding(String code, int version) {
if (code == null || !Arrays.stream(RecommendationPriorityCodingCode.values()).map(RecommendationPriorityCodingCode::toValue).collect(Collectors.toSet()).contains(code)) {
return null;
}
var resultBuilder = RecommendationPriorityCoding.builder()
.system("dnpm-dip/recommendation/priority");
try {
resultBuilder
.code(RecommendationPriorityCodingCode.forValue(code))
.display(code);
} catch (IOException e) {
return null;
}
return resultBuilder.build();
}
protected LevelOfEvidence getLevelOfEvidence(ResultSet resultSet) {
if (resultSet == null) {
return null;

64
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungProzedurDataMapper.java
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@ -1,14 +1,15 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.*;
import dev.pcvolkmer.mv64e.mtb.MtbProcedureRecommendationCategoryCoding;
import dev.pcvolkmer.mv64e.mtb.MtbProcedureRecommendationCategoryCodingCode;
import dev.pcvolkmer.mv64e.mtb.ProcedureRecommendation;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.EinzelempfehlungCatalogue;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
@ -27,26 +28,33 @@ public class EinzelempfehlungProzedurDataMapper extends AbstractEinzelempfehlung
@Override
protected ProcedureRecommendation map(ResultSet resultSet) {
return ProcedureRecommendation.builder()
var resultBuilder = ProcedureRecommendation.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
// TODO Fix id?
.reason(Reference.builder().id(resultSet.getString("id")).build())
.issuedOn(resultSet.getDate("datum"))
.priority(
getRecommendationPriorityCoding(
resultSet.getString("evidenzlevel"),
resultSet.getInteger("evidenzlevel_propcat_version")
)
)
.code(
getMtbProcedureRecommendationCategoryCoding(
resultSet.getString("art_der_therapie"),
resultSet.getInteger("art_der_therapie_propcat_version")
)
)
.levelOfEvidence(getLevelOfEvidence(resultSet))
.build();
.levelOfEvidence(getLevelOfEvidence(resultSet));
if (null != resultSet.getString("evidenzlevel")) {
resultBuilder.priority(
getRecommendationPriorityCoding(
resultSet.getString("evidenzlevel"),
resultSet.getInteger("evidenzlevel_propcat_version")
)
);
}
if (null != resultSet.getString("art_der_therapie")) {
resultBuilder.code(
getMtbProcedureRecommendationCategoryCoding(
resultSet.getString("art_der_therapie"),
resultSet.getInteger("art_der_therapie_propcat_version")
)
);
}
return resultBuilder.build();
}
@Override
@ -60,29 +68,11 @@ public class EinzelempfehlungProzedurDataMapper extends AbstractEinzelempfehlung
.stream()
// Filter Prozedurempfehlung (Weitere Empfehlungen)
.filter(it -> it.getString("art_der_therapie") != null && !it.getString("art_der_therapie").isBlank())
.filter(it -> "sonstige".equals(it.getString("empfehlungskategorie")))
.map(this::map)
.collect(Collectors.toList());
}
private RecommendationPriorityCoding getRecommendationPriorityCoding(String code, int version) {
if (code == null || !Arrays.stream(RecommendationPriorityCodingCode.values()).map(RecommendationPriorityCodingCode::toValue).collect(Collectors.toSet()).contains(code)) {
return null;
}
var resultBuilder = RecommendationPriorityCoding.builder()
.system("dnpm-dip/recommendation/priority");
try {
resultBuilder
.code(RecommendationPriorityCodingCode.forValue(code))
.display(code);
} catch (IOException e) {
return null;
}
return resultBuilder.build();
}
private MtbProcedureRecommendationCategoryCoding getMtbProcedureRecommendationCategoryCoding(String code, int version) {
if (code == null || !Arrays.stream(MtbProcedureRecommendationCategoryCodingCode.values()).map(MtbProcedureRecommendationCategoryCodingCode::toValue).collect(Collectors.toSet()).contains(code)) {
return null;

60
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungStudieDataMapper.java Normal file
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@ -0,0 +1,60 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.MtbStudyEnrollmentRecommendation;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.ResultSet;
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'
*
* @author Paul-Christian Volkmer
* @since 0.1
*/
public class EinzelempfehlungStudieDataMapper extends AbstractEinzelempfehlungDataMapper<MtbStudyEnrollmentRecommendation> {
public EinzelempfehlungStudieDataMapper(EinzelempfehlungCatalogue einzelempfehlungCatalogue) {
super(einzelempfehlungCatalogue);
}
@Override
protected MtbStudyEnrollmentRecommendation map(ResultSet resultSet) {
return MtbStudyEnrollmentRecommendation.builder()
.id(resultSet.getString("id"))
.patient(getPatientReference(resultSet.getString("patient_id")))
// TODO Fix id?
.reason(Reference.builder().id(resultSet.getString("id")).build())
.issuedOn(resultSet.getDate("datum"))
.priority(
getRecommendationPriorityCoding(
resultSet.getString("evidenzlevel"),
resultSet.getInteger("evidenzlevel_propcat_version")
)
)
.medication(JsonToMedicationMapper.map(resultSet.getString("wirkstoffe_json")))
.levelOfEvidence(getLevelOfEvidence(resultSet))
.study(JsonToStudyMapper.map(resultSet.getString("studien_alle_json")))
.build();
}
@Override
public MtbStudyEnrollmentRecommendation getById(int id) {
return this.map(this.catalogue.getById(id));
}
@Override
public List<MtbStudyEnrollmentRecommendation> getByParentId(final int parentId) {
return catalogue.getAllByParentId(parentId)
.stream()
// Filter Wirkstoffempfehlung (Systemische Therapie)
.filter(it -> "studie".equals(it.getString("empfehlungskategorie")))
.map(this::map)
.collect(Collectors.toList());
}
}

29
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/EinzelempfehlungWirkstoffDataMapper.java
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@ -1,14 +1,10 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.MtbMedicationRecommendation;
import dev.pcvolkmer.mv64e.mtb.RecommendationPriorityCoding;
import dev.pcvolkmer.mv64e.mtb.RecommendationPriorityCodingCode;
import dev.pcvolkmer.mv64e.mtb.Reference;
import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.EinzelempfehlungCatalogue;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
@ -55,28 +51,13 @@ public class EinzelempfehlungWirkstoffDataMapper extends AbstractEinzelempfehlun
return catalogue.getAllByParentId(parentId)
.stream()
// Filter Wirkstoffempfehlung (Systemische Therapie)
.filter(it -> it.getString("art_der_therapie") == null || it.getString("art_der_therapie").isBlank() )
.filter(it -> it.getString("art_der_therapie") == null
|| it.getString("art_der_therapie").isBlank())
.filter(it -> it.getString("empfehlungskategorie") == null
|| it.getString("empfehlungskategorie").isBlank()
|| "systemisch".equals(it.getString("empfehlungskategorie")))
.map(this::map)
.collect(Collectors.toList());
}
private RecommendationPriorityCoding getRecommendationPriorityCoding(String code, int version) {
if (code == null || !Arrays.stream(RecommendationPriorityCodingCode.values()).map(RecommendationPriorityCodingCode::toValue).collect(Collectors.toSet()).contains(code)) {
return null;
}
var resultBuilder = RecommendationPriorityCoding.builder()
.system("dnpm-dip/recommendation/priority");
try {
resultBuilder
.code(RecommendationPriorityCodingCode.forValue(code))
.display(code);
} catch (IOException e) {
return null;
}
return resultBuilder.build();
}
}

81
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/JsonToStudyMapper.java Normal file
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@ -0,0 +1,81 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import com.fasterxml.jackson.annotation.JsonAlias;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import dev.pcvolkmer.mv64e.mtb.StudyReference;
import dev.pcvolkmer.mv64e.mtb.StudySystem;
import dev.pcvolkmer.onco.datamapper.exceptions.DataAccessException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
/**
* Maps JSON strings used in form into DNPM study
*
* @author Paul-Christian Volkmer
* @since 0.1
*/
public class JsonToStudyMapper {
private JsonToStudyMapper() {
// intentionally left empty
}
public static List<StudyReference> map(String studyJson) {
if (studyJson == null) {
return List.of();
}
try {
return new ObjectMapper().readValue(studyJson, new TypeReference<List<Studie>>() {
}).stream()
.map(studie -> StudyReference.builder()
.id(studie.id)
.system(getStudySystem(studie.system))
.type("Study")
.build()
)
.collect(Collectors.toList());
} catch (Exception e) {
throw new DataAccessException(String.format("Cannot map medication for %s", studyJson));
}
}
private static StudySystem getStudySystem(String code) {
if (code == null || !Arrays.stream(StudySystem.values()).map(StudySystem::toValue).collect(Collectors.toSet()).contains(code)) {
return null;
}
try {
return StudySystem.valueOf(code);
} catch (IllegalArgumentException e) {
return null;
}
}
@JsonIgnoreProperties(ignoreUnknown = true)
private static class Studie {
@JsonAlias("nct")
private String id;
private String system;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getSystem() {
return system;
}
public void setSystem(String system) {
this.system = system;
}
}
}

2
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/MolekulargenetikToSpecimenDataMapper.java
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@ -6,6 +6,7 @@ import dev.pcvolkmer.onco.datamapper.ResultSet;
import dev.pcvolkmer.onco.datamapper.datacatalogues.*;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static dev.pcvolkmer.onco.datamapper.mapper.MapperUtils.getPatientReference;
@ -109,6 +110,7 @@ public class MolekulargenetikToSpecimenDataMapper implements DataMapper<TumorSpe
);
return osMolGen.stream()
.filter(Objects::nonNull)
.map(this::getById)
.peek(it -> it.setDiagnosis(diagnoseReferenz))
.collect(Collectors.toList());

5
src/main/java/dev/pcvolkmer/onco/datamapper/mapper/TherapieplanDataMapper.java
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@ -25,6 +25,7 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
private final EinzelempfehlungProzedurDataMapper einzelempfehlungProzedurDataMapper;
private final EinzelempfehlungWirkstoffDataMapper einzelempfehlungWirkstoffDataMapper;
private final EinzelempfehlungStudieDataMapper einzelempfehlungStudieDataMapper;
public TherapieplanDataMapper(
final TherapieplanCatalogue therapieplanCatalogue,
@ -36,6 +37,7 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
this.einzelempfehlungProzedurDataMapper = new EinzelempfehlungProzedurDataMapper(einzelempfehlungCatalogue);
this.einzelempfehlungWirkstoffDataMapper = new EinzelempfehlungWirkstoffDataMapper(einzelempfehlungCatalogue);
this.einzelempfehlungStudieDataMapper = new EinzelempfehlungStudieDataMapper(einzelempfehlungCatalogue);
}
/**
@ -53,11 +55,12 @@ public class TherapieplanDataMapper implements DataMapper<MtbCarePlan> {
.id(therapieplanData.getString("id"))
.patient(getPatientReference(therapieplanData.getString("patient_id")))
.issuedOn(therapieplanData.getDate("datum"))
.procedureRecommendations(einzelempfehlungProzedurDataMapper.getByParentId(id))
;
if (therapieplanData.isTrue("mit_einzelempfehlung")) {
builder.medicationRecommendations(einzelempfehlungWirkstoffDataMapper.getByParentId(id));
builder.procedureRecommendations(einzelempfehlungProzedurDataMapper.getByParentId(id));
builder.studyEnrollmentRecommendations(einzelempfehlungStudieDataMapper.getByParentId(id));
}
// Formularfeld "protokollauszug"

3
src/test/java/dev/pcvolkmer/onco/datamapper/datacatalogues/JsonToMedicationMapperTest.java → src/test/java/dev/pcvolkmer/onco/datamapper/mapper/JsonToMedicationMapperTest.java
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@ -1,7 +1,6 @@
package dev.pcvolkmer.onco.datamapper.datacatalogues;
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.RequestedMedicationSystem;
import dev.pcvolkmer.onco.datamapper.mapper.JsonToMedicationMapper;
import org.junit.jupiter.api.Test;
import static org.assertj.core.api.Assertions.assertThat;

28
src/test/java/dev/pcvolkmer/onco/datamapper/mapper/JsonToStudyMapperTest.java Normal file
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@ -0,0 +1,28 @@
package dev.pcvolkmer.onco.datamapper.mapper;
import dev.pcvolkmer.mv64e.mtb.StudySystem;
import org.junit.jupiter.api.Test;
import static org.assertj.core.api.Assertions.assertThat;
class JsonToStudyMapperTest {
// See example in: https://github.com/pcvolkmer/onkostar-plugin-dnpm/blob/master/sql/sql-queries.md
@Test
void shouldMapEinzelempfehlungJson() {
var json = "[\n" +
" {\"studie\":\"TestInhibitor\",\"system\":\"NCT\",\"id\":\"NCT12345678\",\"nct\":\"NCT12345678\",\"ort\":\"Teststadt\",\"internextern\":\"e\"}\n" +
"]";
var actual = JsonToStudyMapper.map(json);
assertThat(actual).hasSize(1);
var study = actual.get(0);
assertThat(study.getId()).isEqualTo("NCT12345678");
assertThat(study.getDisplay()).isNull();
assertThat(study.getSystem()).isEqualTo(StudySystem.NCT);
assertThat(study.getType()).isEqualTo("Study");
}
}