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Diagnosis Mapper

This Java class is used to map diagnosis data from an encounter CSV row to the Bahmni diagnosis request format. It takes the diagnosis data from the row, checks if it matches a concept, and sets the diagnosis on the request as either coded or free text. It also sets other fields like order, certainty and date on the diagnosis request object.

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nicolethomson2020
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19 views2 pages

Diagnosis Mapper

This Java class is used to map diagnosis data from an encounter CSV row to the Bahmni diagnosis request format. It takes the diagnosis data from the row, checks if it matches a concept, and sets the diagnosis on the request as either coded or free text. It also sets other fields like order, certainty and date on the diagnosis request object.

Uploaded by

nicolethomson2020
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
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package org.bahmni.module.admin.

observation;

import org.apache.commons.lang.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.bahmni.csv.KeyValue;
import org.bahmni.module.admin.csv.models.EncounterRow;
import org.openmrs.Concept;
import org.openmrs.api.ConceptService;
import org.openmrs.module.bahmniemrapi.diagnosis.contract.BahmniDiagnosisRequest;
import org.openmrs.module.emrapi.diagnosis.Diagnosis;
import org.openmrs.module.emrapi.encounter.domain.EncounterTransaction;
import org.openmrs.module.emrapi.encounter.exception.ConceptNotFoundException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;

import java.text.ParseException;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;

@Component(value = "adminDiagnosisMapper")
public class DiagnosisMapper {

private static final Logger log = LogManager.getLogger(DiagnosisMapper.class);

private final ConceptCache conceptCache;

@Autowired
public DiagnosisMapper(ConceptService conceptService) {
this.conceptCache = new ConceptCache(conceptService);
}

public List<BahmniDiagnosisRequest> getBahmniDiagnosis(EncounterRow


encounterRow) throws ParseException {
List<BahmniDiagnosisRequest> bahmniDiagnoses = new ArrayList<>();
if (encounterRow.hasDiagnoses()) {
Date encounterDate = encounterRow.getEncounterDate();
for (KeyValue uniqueDiagnosisKeyValue : encounterRow.diagnosesRows) {
String diagnosis = uniqueDiagnosisKeyValue.getValue();
if (StringUtils.isNotBlank(diagnosis)) {
BahmniDiagnosisRequest bahmniDiagnosisRequest =
createDiagnosis(encounterDate, diagnosis);
bahmniDiagnoses.add(bahmniDiagnosisRequest);
}
}
}
return bahmniDiagnoses;
}

private BahmniDiagnosisRequest createDiagnosis(Date encounterDate, String


diagnosis) throws ParseException {
Concept obsConcept = getConcept(diagnosis);

BahmniDiagnosisRequest bahmniDiagnosisRequest = new


BahmniDiagnosisRequest();
bahmniDiagnosisRequest.setOrder(String.valueOf(Diagnosis.Order.PRIMARY));

bahmniDiagnosisRequest.setCertainty(String.valueOf(Diagnosis.Certainty.CONFIRMED));
bahmniDiagnosisRequest.setDiagnosisDateTime(encounterDate);

if (obsConcept == null) {
bahmniDiagnosisRequest.setFreeTextAnswer(diagnosis);
} else {
EncounterTransaction.Concept diagnosisConcept = new
EncounterTransaction.Concept(obsConcept.getUuid(), obsConcept.getName().getName());
bahmniDiagnosisRequest.setCodedAnswer(diagnosisConcept);
}

return bahmniDiagnosisRequest;
}

protected Concept getConcept(String diagnosis) {


try {
return conceptCache.getConcept(diagnosis);
} catch (ConceptNotFoundException cnfe) {
log.error(cnfe.getMessage() + " Setting it as free text answer", cnfe);
return null;
}
}
}

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