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Siva Reddy | BS-7 | Diagnosis Save (#189)
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* Siva Reddy | BS-7 | Changes for saving a concept

* Siva Reddy | BS-7 | Tests for Diagnosis Concept Presave Command

* Siva Reddy | BS-7 | Support for multiple locales

* Siva Reddy | BS-7 | Updating artefact name

* Siva Reddy | BS-7 | Minor code fixes

* Siva Reddy | BS-7 | Incorporating PR comments
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@sivareddyp
sivareddyp committed Mar 31, 2023
1 parent 1910e85 commit 6fc2729
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16 changes: 16 additions & 0 deletions bahmni-emr-api/pom.xml
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<groupId>org.bahmni.module</groupId>
<artifactId>bahmni-commons-api</artifactId>
</dependency>
<dependency>
<groupId>org.bahmni.module</groupId>
<artifactId>fhir-ts-services-int-api</artifactId>
<version>${terminologyServices.version}</version>
</dependency>
<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>fhir2-api</artifactId>
<version>${openmrs.fhir2.version}</version>
</dependency>
<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>webservices.rest-omod-common</artifactId>
<version>${openMRSWebServicesVersion}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.openmrs.web</groupId>
<artifactId>openmrs-web</artifactId>
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181 changes: 181 additions & 0 deletions ...emrapi/encountertransaction/command/impl/BahmniDiagnosisAnswerConceptSaveCommandImpl.java
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package org.openmrs.module.bahmniemrapi.encountertransaction.command.impl;

import org.apache.commons.lang.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.openmrs.Concept;
import org.openmrs.ConceptClass;
import org.openmrs.ConceptDatatype;
import org.openmrs.ConceptMap;
import org.openmrs.ConceptMapType;
import org.openmrs.ConceptName;
import org.openmrs.ConceptReferenceTerm;
import org.openmrs.ConceptSource;
import org.openmrs.api.APIException;
import org.openmrs.api.AdministrationService;
import org.openmrs.api.ConceptService;
import org.openmrs.api.context.Context;
import org.openmrs.module.bahmniemrapi.diagnosis.contract.BahmniDiagnosisRequest;
import org.openmrs.module.bahmniemrapi.encountertransaction.command.EncounterDataPreSaveCommand;
import org.openmrs.module.bahmniemrapi.encountertransaction.contract.BahmniEncounterTransaction;
import org.openmrs.module.fhir2.api.FhirConceptSourceService;
import org.bahmni.module.fhirterminologyservices.api.TerminologyLookupService;
import org.openmrs.module.emrapi.EmrApiProperties;
import org.openmrs.module.emrapi.encounter.domain.EncounterTransaction;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.stereotype.Component;

import java.util.Collection;
import java.util.List;
import java.util.Optional;

@Component
public class BahmniDiagnosisAnswerConceptSaveCommandImpl implements EncounterDataPreSaveCommand {

private AdministrationService adminService;

private ConceptService conceptService;

private EmrApiProperties emrApiProperties;

private TerminologyLookupService terminologyLookupService;

private FhirConceptSourceService fhirConceptSourceService;

private static Logger logger = LogManager.getLogger(BahmniDiagnosisAnswerConceptSaveCommandImpl.class);

public static final String CONCEPT_CLASS_DIAGNOSIS = "Diagnosis";

public static final String CONCEPT_DATATYPE_NA = "N/A";

public static final String DEFAULT_CONCEPT_SET_FOR_DIAGNOSIS_CONCEPT = "Unclassified";

public static final String GP_DEFAULT_CONCEPT_SET_FOR_DIAGNOSIS_CONCEPT_UUID = "bahmni.diagnosisSetForNewDiagnosisConcepts";

private static final String TERMINOLOGY_SERVER_CODED_ANSWER_DELIMITER = "/";

@Autowired
public BahmniDiagnosisAnswerConceptSaveCommandImpl(@Qualifier("adminService") AdministrationService administrationService, ConceptService conceptService,
EmrApiProperties emrApiProperties, TerminologyLookupService terminologyLookupService,
FhirConceptSourceService fhirConceptSourceService) {
this.adminService = administrationService;
this.conceptService = conceptService;
this.emrApiProperties = emrApiProperties;
this.terminologyLookupService = terminologyLookupService;
this.fhirConceptSourceService = fhirConceptSourceService;
}

@Override
public BahmniEncounterTransaction update(BahmniEncounterTransaction bahmniEncounterTransaction) {
List<BahmniDiagnosisRequest> bahmniDiagnoses = bahmniEncounterTransaction.getBahmniDiagnoses();
bahmniDiagnoses.stream().forEach(this::updateDiagnosisAnswerConceptUuid);
return bahmniEncounterTransaction;
}

@Override
public Object postProcessBeforeInitialization(Object bean, String beanName) throws BeansException {
return bean;
}

@Override
public Object postProcessAfterInitialization(Object bean, String beanName) throws BeansException {
return bean;
}

private void updateDiagnosisAnswerConceptUuid(BahmniDiagnosisRequest bahmniDiagnosis) {
EncounterTransaction.Concept codedAnswer = bahmniDiagnosis.getCodedAnswer();
if (codedAnswer != null && codedAnswer.getUuid() != null) {
String codedAnswerUuidWithSystem = codedAnswer.getUuid();
int conceptCodeIndex = codedAnswerUuidWithSystem.lastIndexOf(TERMINOLOGY_SERVER_CODED_ANSWER_DELIMITER);
boolean isConceptFromTerminologyServer = conceptCodeIndex > -1 ? true : false;
if (isConceptFromTerminologyServer) {
String diagnosisConceptSystem = codedAnswerUuidWithSystem.substring(0, conceptCodeIndex);
String diagnosisConceptReferenceTermCode = codedAnswerUuidWithSystem.substring(conceptCodeIndex + 1);
updateDiagnosisAnswerConceptUuid(codedAnswer, diagnosisConceptReferenceTermCode, diagnosisConceptSystem);
}
}
}

private void updateDiagnosisAnswerConceptUuid(EncounterTransaction.Concept codedAnswer, String diagnosisConceptReferenceTermCode, String diagnosisConceptSystem) {
Optional<ConceptSource> conceptSourceByUrl = fhirConceptSourceService.getConceptSourceByUrl(diagnosisConceptSystem);
ConceptSource conceptSource = conceptSourceByUrl.isPresent() ? conceptSourceByUrl.get() : null;
if (conceptSource == null) {
logger.error("Concept Source " + diagnosisConceptSystem + " not found");
throw new APIException("Concept Source " + diagnosisConceptSystem + " not found");
}
Concept existingDiagnosisAnswerConcept = conceptService.getConceptByMapping(diagnosisConceptReferenceTermCode, conceptSource.getName());
if (existingDiagnosisAnswerConcept == null) {
Concept newDiagnosisAnswerConcept = createNewDiagnosisConcept(diagnosisConceptReferenceTermCode, conceptSource);
codedAnswer.setUuid(newDiagnosisAnswerConcept.getUuid());
addNewDiagnosisConceptToDiagnosisSet(newDiagnosisAnswerConcept);
} else {
ConceptName answerConceptNameInUserLocale = existingDiagnosisAnswerConcept.getFullySpecifiedName(Context.getLocale());
if (answerConceptNameInUserLocale == null) {
updateExistingConcept(existingDiagnosisAnswerConcept, diagnosisConceptReferenceTermCode);
}
codedAnswer.setUuid(existingDiagnosisAnswerConcept.getUuid());
}
}

private Concept createNewDiagnosisConcept(String conceptReferenceTermCode, ConceptSource conceptSource) {
Concept concept = getConcept(conceptReferenceTermCode);
addConceptMap(concept, conceptSource, conceptReferenceTermCode);
conceptService.saveConcept(concept);
return concept;
}

private void updateExistingConcept(Concept existingDiagnosisAnswerConcept, String conceptReferenceTermCode) {
Concept conceptInUserLocale = getConcept(conceptReferenceTermCode);
conceptInUserLocale.getNames(Context.getLocale()).stream().forEach(conceptName -> existingDiagnosisAnswerConcept.addName(conceptName));
conceptService.saveConcept(existingDiagnosisAnswerConcept);
}


private Concept getConcept(String referenceCode) {
Concept concept = terminologyLookupService.getConcept(referenceCode, Context.getLocale().getLanguage());
ConceptClass diagnosisConceptClass = conceptService.getConceptClassByName(CONCEPT_CLASS_DIAGNOSIS);
concept.setConceptClass(diagnosisConceptClass);

ConceptDatatype diagnosisConceptDataType = conceptService.getConceptDatatypeByName(CONCEPT_DATATYPE_NA);
concept.setDatatype(diagnosisConceptDataType);

return concept;
}

private void addConceptMap(Concept concept, ConceptSource conceptSource, String conceptReferenceTermCode) {
ConceptMap conceptMap = getConceptMap(concept.getName().getName(), conceptReferenceTermCode, conceptSource);
Collection<ConceptMap> conceptMappings = concept.getConceptMappings();
conceptMappings.add(conceptMap);
concept.setConceptMappings(conceptMappings);
}

private ConceptMap getConceptMap(String name, String conceptReferenceTermCode, ConceptSource conceptSource) {
ConceptReferenceTerm conceptReferenceTerm = new ConceptReferenceTerm(conceptSource, conceptReferenceTermCode, name);
ConceptMapType sameAsConceptMapType = conceptService.getConceptMapTypeByUuid(ConceptMapType.SAME_AS_MAP_TYPE_UUID);
ConceptMap conceptMap = new ConceptMap(conceptReferenceTerm, sameAsConceptMapType);
return conceptMap;
}

private void addNewDiagnosisConceptToDiagnosisSet(Concept diagnosisConcept) {
String diagnosisSetForNewConcepts = adminService.getGlobalProperty(GP_DEFAULT_CONCEPT_SET_FOR_DIAGNOSIS_CONCEPT_UUID);
Concept diagnosisConceptSet = null;
if (StringUtils.isNotBlank(diagnosisSetForNewConcepts)) {
diagnosisConceptSet = conceptService.getConceptByUuid(diagnosisSetForNewConcepts);
} else {
Collection<Concept> diagnosisSets = emrApiProperties.getDiagnosisSets();
Optional<Concept> optionalConcept = diagnosisSets.stream().filter(c -> c.getName().getName().equals(DEFAULT_CONCEPT_SET_FOR_DIAGNOSIS_CONCEPT) && !c.getRetired()).findFirst();
if (optionalConcept.isPresent()) {
diagnosisConceptSet = optionalConcept.get();
}
}
if (diagnosisConceptSet == null) {
logger.error("Concept Set " + DEFAULT_CONCEPT_SET_FOR_DIAGNOSIS_CONCEPT + " not found");
throw new APIException("Concept Set " + DEFAULT_CONCEPT_SET_FOR_DIAGNOSIS_CONCEPT + " not found");
}

diagnosisConceptSet.addSetMember(diagnosisConcept);
conceptService.saveConcept(diagnosisConceptSet);
}
}
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