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Merge pull request #386 from ehrbase/refactor_gecco_diagnose
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Refactor gecco diagnose
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@SevKohler
SevKohler authored Jul 12, 2021
2 parents 064067b + 391ff48 commit 6fc5f04
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Showing 35 changed files with 3,731 additions and 3,780 deletions.
4 changes: 2 additions & 2 deletions ...ase/fhirbridge/ehr/converter/specific/geccodiagnose/AusgeschlosseneDiagnoseConverter.java
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Expand Up @@ -11,11 +11,11 @@ public class AusgeschlosseneDiagnoseConverter extends EntryEntityConverter<Condi
@Override
protected AusgeschlosseneDiagnoseEvaluation convertInternal(Condition resource) {
AusgeschlosseneDiagnoseEvaluation ausgeschlosseneDiagnose = new AusgeschlosseneDiagnoseEvaluation();
ausgeschlosseneDiagnose.setAussageUeberDenAusschlussDefiningCode(AussageUeberDenAusschlussDefiningCode.KNOWN_ABSENT_QUALIFIER_VALUE);
ausgeschlosseneDiagnose.setAussageUeberDenAusschluss(DvCodedTextParser.parseDefiningCode(AussageUeberDenAusschlussDefiningCode.KNOWN_ABSENT_QUALIFIER_VALUE));
Coding problem = resource.getCode().getCoding().get(0);
if (problem.getSystem().equals(CodeSystem.SNOMED.getUrl()) &&
GeccoDiagnoseCodeDefiningCodeMaps.getProblemDiagnoseMap().containsKey(problem.getCode())) {
ausgeschlosseneDiagnose.setProblemDiagnoseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getProblemDiagnoseMap().get(problem.getCode()));
ausgeschlosseneDiagnose.setProblemDiagnose(DvCodedTextParser.parseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getProblemDiagnoseMap().get(problem.getCode())));
}
return ausgeschlosseneDiagnose;
}
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26 changes: 26 additions & 0 deletions ...n/java/org/ehrbase/fhirbridge/ehr/converter/specific/geccodiagnose/DvCodedTextParser.java
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@@ -0,0 +1,26 @@
package org.ehrbase.fhirbridge.ehr.converter.specific.geccodiagnose;

import com.nedap.archie.rm.datatypes.CodePhrase;
import com.nedap.archie.rm.datavalues.DvCodedText;
import com.nedap.archie.rm.support.identification.TerminologyId;
import org.ehrbase.client.classgenerator.EnumValueSet;
import org.ehrbase.fhirbridge.ehr.converter.specific.CodeSystem;
import org.hl7.fhir.r4.model.Coding;
import java.util.Optional;

public class DvCodedTextParser {

public static DvCodedText parseDefiningCode(EnumValueSet enumValueSet){
return new DvCodedText(enumValueSet.getValue(), new CodePhrase(new TerminologyId(enumValueSet.getTerminologyId(), ""), enumValueSet.getCode()));
}

public static Optional<DvCodedText> parseFHIRCoding(Coding coding){
if(coding.hasDisplay() && coding.hasSystem() && coding.hasCode() && coding.getSystem().equals(CodeSystem.SNOMED.getUrl())){
return Optional.of(new DvCodedText(coding.getDisplay(), new CodePhrase(new TerminologyId("SNOMED Clinical Terms", ""), coding.getCode())));
}else if (coding.hasCode() && coding.getSystem().equals(CodeSystem.SNOMED.getUrl())){
return Optional.of(new DvCodedText("", new CodePhrase(new TerminologyId("SNOMED Clinical Terms", ""), coding.getCode())));
}else{
return Optional.empty();
}
}
}
2 changes: 1 addition & 1 deletion ...se/fhirbridge/ehr/converter/specific/geccodiagnose/GECCODiagnoseCompositionConverter.java
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Expand Up @@ -33,7 +33,7 @@ public GECCODiagnoseComposition convertInternal(@NonNull Condition resource) {
private void mapCategoryCoding(Condition resource, GECCODiagnoseComposition composition) {
Coding categoryCoding = resource.getCategory().get(0).getCoding().get(0);
if (categoryCoding.getSystem().equals(CodeSystem.SNOMED.getUrl()) && GeccoDiagnoseCodeDefiningCodeMaps.getKategorieMap().containsKey(categoryCoding.getCode())) {
composition.setKategorieDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getKategorieMap().get(categoryCoding.getCode()));
composition.setKategorie(DvCodedTextParser.parseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getKategorieMap().get(categoryCoding.getCode())));
} else {
throw new UnprocessableEntityException("Category has either no or an unsupported SNOMED code");
}
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10 changes: 0 additions & 10 deletions ...se/fhirbridge/ehr/converter/specific/geccodiagnose/GeccoDiagnoseCodeDefiningCodeMaps.java
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Expand Up @@ -2,7 +2,6 @@

import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.KategorieDefiningCode;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.NameDerKoerperstelleDefiningCode;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.NameDesProblemsDerDiagnoseDefiningCode;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.ProblemDiagnoseDefiningCode;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.SchweregradDefiningCode;

Expand All @@ -13,7 +12,6 @@ class GeccoDiagnoseCodeDefiningCodeMaps {

private static final Map<String, KategorieDefiningCode> kategorieMap = new HashMap<>();
private static final Map<String, ProblemDiagnoseDefiningCode> problemDiagnoseMap = new HashMap<>();
private static final Map<String, NameDesProblemsDerDiagnoseDefiningCode> nameDesProblemDiagnoseMap = new HashMap<>();
private static final Map<String, NameDerKoerperstelleDefiningCode> koerperstelleMap = new HashMap<>();
private static final Map<String, SchweregradDefiningCode> schweregradMap = new HashMap<>();

Expand All @@ -26,10 +24,6 @@ class GeccoDiagnoseCodeDefiningCodeMaps {
problemDiagnoseMap.put(problem.getCode(), problem);
}

for (NameDesProblemsDerDiagnoseDefiningCode problem : NameDesProblemsDerDiagnoseDefiningCode.values()) {
nameDesProblemDiagnoseMap.put(problem.getCode(), problem);
}

for (NameDerKoerperstelleDefiningCode koerperstelleDefiningCode : NameDerKoerperstelleDefiningCode.values()) {
koerperstelleMap.put(koerperstelleDefiningCode.getCode(), koerperstelleDefiningCode);
}
Expand All @@ -47,10 +41,6 @@ static Map<String, ProblemDiagnoseDefiningCode> getProblemDiagnoseMap() {
return problemDiagnoseMap;
}

static Map<String, NameDesProblemsDerDiagnoseDefiningCode> getNameDesProblemDiagnoseMap() {
return nameDesProblemDiagnoseMap;
}

static Map<String, NameDerKoerperstelleDefiningCode> getKoerperstelleMap() {
return koerperstelleMap;
}
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4 changes: 2 additions & 2 deletions ...hirbridge/ehr/converter/specific/geccodiagnose/UnbekannteDiagnoseEvaluationConverter.java
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Expand Up @@ -12,7 +12,7 @@ public class UnbekannteDiagnoseEvaluationConverter extends EntryEntityConverter<
@Override
protected UnbekannteDiagnoseEvaluation convertInternal(Condition condition) {
UnbekannteDiagnoseEvaluation unbekannteDiagnose = new UnbekannteDiagnoseEvaluation();
unbekannteDiagnose.setAussageUeberDieFehlendeInformationDefiningCode(AussageUeberDieFehlendeInformationDefiningCode.UNKNOWN_QUALIFIER_VALUE);
unbekannteDiagnose.setAussageUeberDieFehlendeInformation(DvCodedTextParser.parseDefiningCode(AussageUeberDieFehlendeInformationDefiningCode.UNKNOWN_QUALIFIER_VALUE));
mapProblem(condition, unbekannteDiagnose);

return unbekannteDiagnose;
Expand All @@ -22,7 +22,7 @@ private void mapProblem(Condition condition, UnbekannteDiagnoseEvaluation unbeka
for(Coding coding : condition.getCode().getCoding()){
if (coding.getSystem().equals(CodeSystem.SNOMED.getUrl()) &&
GeccoDiagnoseCodeDefiningCodeMaps.getProblemDiagnoseMap().containsKey(coding.getCode())) {
unbekannteDiagnose.setUnbekannteDiagnoseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getProblemDiagnoseMap().get(coding.getCode()));
unbekannteDiagnose.setUnbekannteDiagnose(DvCodedTextParser.parseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getProblemDiagnoseMap().get(coding.getCode())));
}
}
}
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17 changes: 11 additions & 6 deletions ...irbridge/ehr/converter/specific/geccodiagnose/VorliegendeDiagnoseEvaluationConverter.java
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Expand Up @@ -6,6 +6,8 @@
import org.ehrbase.fhirbridge.ehr.converter.specific.CodeSystem;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.KoerperstelleCluster;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.VorliegendeDiagnoseEvaluation;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.VorliegendeDiagnoseNameDesProblemsDerDiagnoseChoice;
import org.ehrbase.fhirbridge.ehr.opt.geccodiagnosecomposition.definition.VorliegendeDiagnoseNameDesProblemsDerDiagnoseDvCodedText;
import org.hl7.fhir.r4.model.Annotation;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Condition;
Expand Down Expand Up @@ -61,7 +63,7 @@ private void mapSeverity(Condition condition, VorliegendeDiagnoseEvaluation vorl

private void convertSevertiy(Coding coding, VorliegendeDiagnoseEvaluation vorliegendeDiagnose) {
if (coding.getSystem().equals(CodeSystem.SNOMED.getUrl()) && GeccoDiagnoseCodeDefiningCodeMaps.getSchweregradMap().containsKey(coding.getCode())) {
vorliegendeDiagnose.setSchweregradDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getSchweregradMap().get(coding.getCode()));
vorliegendeDiagnose.setSchweregrad(DvCodedTextParser.parseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getSchweregradMap().get(coding.getCode())));
isEmpty = false;
} else {
throw new UnprocessableEntityException("Severity contains either a wrong code or code system.");
Expand All @@ -73,7 +75,7 @@ private void mapBodySite(Condition condition, VorliegendeDiagnoseEvaluation vorl
for (Coding bodySite : condition.getBodySite().get(0).getCoding()) {
if (bodySite.getSystem().equals(CodeSystem.SNOMED.getUrl()) && GeccoDiagnoseCodeDefiningCodeMaps.getKoerperstelleMap().containsKey(bodySite.getCode())) {
KoerperstelleCluster korperstelleCluster = new KoerperstelleCluster();
korperstelleCluster.setNameDerKoerperstelleDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getKoerperstelleMap().get(bodySite.getCode()));
korperstelleCluster.setNameDerKoerperstelle(DvCodedTextParser.parseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getKoerperstelleMap().get(bodySite.getCode())));
addKoerperstelleCluster(korperstelleCluster, vorliegendeDiagnose);
isEmpty = false;
} else {
Expand All @@ -94,10 +96,13 @@ private void addKoerperstelleCluster(KoerperstelleCluster korperstelleCluster, V

private void mapNameDesProblemsDerDiagnose(Condition condition, VorliegendeDiagnoseEvaluation vorliegendeDiagnose) {
for (Coding coding : condition.getCode().getCoding()) {
if (coding.getSystem().equals(CodeSystem.SNOMED.getUrl()) &&
GeccoDiagnoseCodeDefiningCodeMaps.getNameDesProblemDiagnoseMap().containsKey(coding.getCode())) {
vorliegendeDiagnose.setNameDesProblemsDerDiagnoseDefiningCode(GeccoDiagnoseCodeDefiningCodeMaps.getNameDesProblemDiagnoseMap().get(coding.getCode()));
isEmpty = false;
if (coding.getSystem().equals(CodeSystem.SNOMED.getUrl())) {
if(DvCodedTextParser.parseFHIRCoding(coding).isPresent()){
VorliegendeDiagnoseNameDesProblemsDerDiagnoseDvCodedText vorliegendeDiagnoseNameDesProblemsDerDiagnoseDvCodedText = new VorliegendeDiagnoseNameDesProblemsDerDiagnoseDvCodedText();
vorliegendeDiagnoseNameDesProblemsDerDiagnoseDvCodedText.setNameDesProblemsDerDiagnose(DvCodedTextParser.parseFHIRCoding(coding).get());
vorliegendeDiagnose.setNameDesProblemsDerDiagnose(vorliegendeDiagnoseNameDesProblemsDerDiagnoseDvCodedText);
isEmpty = false;
}
}
}
}
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