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BAH-4029 | adding better logs in cases of outside range values or invalid values for coded answers #269

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Jul 19, 2024
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BAH-4029 | adding better logs in cases of outside range values or invalid values for coded answers #269

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BAH-4029 | Logging better logs in cases of outside range values or in…
angshu Jul 18, 2024
4cfbb74
BAH-4029 | minor improvement - adding a gaurd clause to check if conc…
angshu Jul 18, 2024
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27 changes: 25 additions & 2 deletions ...i/src/main/java/org/openmrs/module/bahmniemrapi/laborder/mapper/LabOrderResultMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.openmrs.Concept;
import org.openmrs.ConceptNumeric;
import org.openmrs.Obs;
import org.openmrs.Order;
import org.openmrs.api.APIException;
Expand All @@ -14,13 +15,15 @@

import java.text.ParseException;
import java.util.Date;
import java.util.Optional;

import static org.apache.commons.lang3.StringUtils.isEmpty;
import static org.apache.commons.lang3.StringUtils.isNotBlank;

@Component
public class LabOrderResultMapper {
private static final Log log = LogFactory.getLog(LabOrderResultMapper.class);
private static final String EMPTY_STRING = "";
public static final String LAB_RESULT = "LAB_RESULT";
public static final String LAB_ABNORMAL = "LAB_ABNORMAL";
public static final String LAB_MINNORMAL = "LAB_MINNORMAL";
Expand Down Expand Up @@ -72,13 +75,14 @@ private Obs newResultObs(Order testOrder, Date obsDate, Concept concept, LabOrde
obs.setConcept(concept);
obs.setOrder(testOrder);
obs.setObsDatetime(obsDate);
String accessionUuid = Optional.ofNullable(labOrderResult.getAccessionUuid()).orElseGet(() -> Optional.ofNullable(obs.getOrder()).map(Order::getAccessionNumber).orElse(EMPTY_STRING));
if (concept.getDatatype().getHl7Abbreviation().equals("CWE")) {
String resultUuid = labOrderResult.getResultUuid();
Concept conceptAnswer = isEmpty(resultUuid) ? null : conceptService.getConceptByUuid(resultUuid);
obs.setValueCoded(conceptAnswer);
if (conceptAnswer == null) {
log.warn(String.format("Concept is not available in OpenMRS for ConceptUuid : [%s] , In Accession : [%s]"
, resultUuid,labOrderResult.getAccessionUuid()));
log.error(String.format("Concept [%s] does not not have coded answer with ConceptUuid [%s] in OpenMRS, In Accession [%s]",
obs.getConcept().getName(), resultUuid, accessionUuid));
return null;
}
return obs;
Expand All @@ -88,9 +92,28 @@ private Obs newResultObs(Order testOrder, Date obsDate, Concept concept, LabOrde
return null;
}
obs.setValueAsString(labOrderResult.getResult());
checkResultRangesForAbsolutes(obs, accessionUuid);
return obs;
}

/**
* This method just logs error if the results are out of absolute ranges. This will be errored out (ValidationException)
* by openmrs by the {@link org.openmrs.validator.ObsValidator} during save
*/
private void checkResultRangesForAbsolutes(Obs obs, String accessionUuid) {
if (obs.getConcept().isNumeric()) {
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if (obs.getValueNumeric() != null) {
ConceptNumeric cn = (ConceptNumeric) obs.getConcept();
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if (cn.getHiAbsolute() != null && cn.getHiAbsolute() < obs.getValueNumeric()) {
log.error(String.format("Test results for [%s] is beyond the absolute high range, in Accession [%s]", cn.getName(), accessionUuid));
}
if (cn.getLowAbsolute() != null && cn.getLowAbsolute() > obs.getValueNumeric()) {
log.error(String.format("Test results for [%s] is beyond the absolute low range, in Accession [%s]", cn.getName(), accessionUuid));
}
}
}
}

private Concept getConceptByName(String conceptName) {
return conceptService.getConceptByName(conceptName);
}
Expand Down
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