Examples with CodedEntry uk.nhs.adaptors.scr.mappings.from.hl7.common.CodedEntry used on opensource projects

Example 1 with CodedEntry

use of uk.nhs.adaptors.scr.mappings.from.hl7.common.CodedEntry in project summary-care-record-api by NHSDigital.

the class DiagnosisMapper method map.

@SneakyThrows
public List<Resource> map(Node document) {
    var resources = new ArrayList<Resource>();
    NodeList pertinentNodes = xmlUtils.getNodeListByXPath(document, PERTINENT_CRET_BASE_PATH);
    for (int i = 0; i < pertinentNodes.getLength(); i++) {
        Node pertinentCREType = xmlUtils.getNodeAndDetachFromParent(pertinentNodes, i);
        var pertinentCRETypeCode = xmlUtils.getValueByXPath(pertinentCREType, PERTINENT_CODE_CODE_XPATH);
        var pertinentCRETypeDisplay = xmlUtils.getValueByXPath(pertinentCREType, PERTINENT_CODE_DISPLAY_XPATH);
        NodeList diagnosisNodes = xmlUtils.getNodeListByXPath(pertinentCREType, DIAGNOSIS_BASE_PATH);
        for (int j = 0; j < diagnosisNodes.getLength(); j++) {
            Node node = xmlUtils.getNodeAndDetachFromParent(diagnosisNodes, j);
            CodedEntry entry = codedEntryMapper.getCommonCodedEntryValues(node);
            if (COVID_19_ENTRIES.contains(entry.getCodeValue())) {
                var pertinentSupportingInfo = xmlUtils.getOptionalValueByXPath(node, DIAGNOSIS_PERTINENT_SUPPORTING_INFO_XPATH);
                var condition = new Condition();
                condition.setId(entry.getId());
                condition.addIdentifier().setValue(entry.getId());
                condition.setCode(new CodeableConcept().addCoding(new Coding().setCode(entry.getCodeValue()).setSystem(SNOMED_SYSTEM).setDisplay(entry.getCodeDisplay())));
                setConditionStatus(condition, entry.getStatus());
                condition.addCategory(new CodeableConcept(new Coding().setSystem(SNOMED_SYSTEM).setCode(pertinentCRETypeCode).setDisplay(pertinentCRETypeDisplay)));
                if (entry.getEffectiveTimeHigh().isPresent()) {
                    condition.setOnset(entry.getEffectiveTimeLow().get());
                    condition.setAbatement(entry.getEffectiveTimeHigh().get());
                } else {
                    condition.setOnset(entry.getEffectiveTimeLow().get());
                }
                resources.add(condition);
                pertinentSupportingInfo.map(value -> new Annotation().setText(value)).ifPresent(condition::addNote);
                xmlUtils.getNodesByXPath(node, DIAGNOSIS_PERTINENT_FINDINGS_XPATH).stream().map(it -> xmlUtils.getValueByXPath(it, DIAGNOSIS_PERTINENT_FINDING_ID_XPATH)).map(it -> new Reference(new Observation().setId(it))).map(reference -> new Condition.ConditionEvidenceComponent().addDetail(reference)).forEach(condition::addEvidence);
                mapEncounter(node, condition, resources);
            }
        }
    }
    return resources;
}

Example 2 with CodedEntry

use of uk.nhs.adaptors.scr.mappings.from.hl7.common.CodedEntry in project summary-care-record-api by NHSDigital.

the class FindingMapper method mapObservation.

private void mapObservation(ArrayList<Resource> resources, String creTypeCode, String creTypeDisplay, Node node) {
    CodedEntry entry = codedEntryMapper.getCommonCodedEntryValues(node);
    if (SARS_COV_2_CODE.equals(entry.getCodeValue())) {
        var effectiveTimeCentre = xmlUtils.getOptionalValueByXPath(node, EFFECTIVE_TIME_CENTRE_XPATH).map(it -> parseDate(it, DateTimeType.class));
        var observation = new Observation();
        observation.setId(entry.getId());
        observation.setMeta(new Meta().addProfile(UK_CORE_OBSERVATION_META));
        observation.addIdentifier(new Identifier().setValue(entry.getId()));
        observation.setCode(new CodeableConcept().addCoding(new Coding().setCode(entry.getCodeValue()).setSystem(SNOMED_SYSTEM).setDisplay(entry.getCodeDisplay())));
        observation.setStatus(mapStatus(entry.getStatus()));
        if (entry.getEffectiveTimeLow().isPresent() || entry.getEffectiveTimeHigh().isPresent()) {
            var period = new Period();
            entry.getEffectiveTimeLow().ifPresent(period::setStartElement);
            entry.getEffectiveTimeHigh().ifPresent(period::setEndElement);
            observation.setEffective(period);
        } else {
            effectiveTimeCentre.ifPresent(observation::setEffective);
        }
        observation.addCategory(new CodeableConcept(new Coding().setSystem(SNOMED_SYSTEM).setCode(creTypeCode).setDisplay(creTypeDisplay)));
        mapEncounter(node, observation, resources);
        resources.add(observation);
    }
}