Examples with Annotation org.hl7.cql_annotations.r1.Annotation used on opensource projects

Example 16 with Annotation

use of org.hl7.cql_annotations.r1.Annotation in project quality-measure-and-cohort-service by Alvearie.

the class R4ParameterDefinitionWithDefaultToCohortParameterConverterTest method testAnnotation__shouldThrowException.

@Test(expected = UnsupportedFhirTypeException.class)
public void testAnnotation__shouldThrowException() {
    ParameterDefinition parameterDefinition = getBaseParameterDefinition("Annotation");
    Annotation fhirValue = new Annotation();
    parameterDefinition.addExtension(CDMConstants.PARAMETER_DEFAULT_URL, fhirValue);
    R4ParameterDefinitionWithDefaultToCohortParameterConverter.toCohortParameter(parameterDefinition);
}

Example 17 with Annotation

use of org.hl7.cql_annotations.r1.Annotation in project summary-care-record-api by NHSDigital.

the class DeviceMapper method mapDevice.

public Device mapDevice(Node deviceHl7) {
    Device deviceFhir = new Device();
    deviceFhir.setId(randomUUID());
    xmlUtils.getOptionalValueByXPath(deviceHl7, ID_EXTENSION_XPATH).ifPresent(id -> deviceFhir.addIdentifier().setValue(id));
    xmlUtils.detachOptionalNodeByXPath(deviceHl7, CODE_ELEMENT_XPATH).ifPresent(code -> deviceFhir.setType(new CodeableConcept(new Coding().setCode(xmlUtils.getValueByXPath(code, CODE_ATTRIBUTE_XPATH)).setDisplay(xmlUtils.getValueByXPath(code, CODE_DISPLAY_XPATH)))));
    addName(deviceHl7, deviceFhir, NAME_XPATH, OTHER);
    addName(deviceHl7, deviceFhir, MANUFACTURER_MODE_NAME_XPATH, MANUFACTURERNAME);
    xmlUtils.detachOptionalNodeByXPath(deviceHl7, DESCRIPTION_XPATH).ifPresent(descNode -> deviceFhir.addNote(new Annotation().setText(descNode.getTextContent())));
    xmlUtils.detachOptionalNodeByXPath(deviceHl7, SOFTWARE_NAME_XPATH).ifPresent(software -> deviceFhir.addVersion(new DeviceVersionComponent().setValue(software.getTextContent())));
    return deviceFhir;
}

Example 18 with Annotation

use of org.hl7.cql_annotations.r1.Annotation 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 19 with Annotation

use of org.hl7.cql_annotations.r1.Annotation in project openmrs-module-fhir2 by openmrs.

the class AllergyIntoleranceTranslatorImplTest method toOpenmrsType_shouldTranslateNoteToComment.

@Test
public void toOpenmrsType_shouldTranslateNoteToComment() {
    AllergyIntolerance allergyIntolerance = new AllergyIntolerance();
    allergyIntolerance.addNote(new Annotation().setText("Test Allergy"));
    allergyIntoleranceTranslator.toOpenmrsType(omrsAllergy, allergyIntolerance);
    assertThat(omrsAllergy, notNullValue());
    assertThat(omrsAllergy.getComment(), equalTo("Test Allergy"));
}

Example 20 with Annotation

use of org.hl7.cql_annotations.r1.Annotation in project openmrs-module-fhir2 by openmrs.

the class AllergyIntoleranceTranslatorImpl method toFhirResource.

@Override
public AllergyIntolerance toFhirResource(@Nonnull Allergy omrsAllergy) {
    notNull(omrsAllergy, "The Allergy object should not be null");
    AllergyIntolerance allergy = new AllergyIntolerance();
    allergy.setId(omrsAllergy.getUuid());
    if (omrsAllergy.getAllergen() != null) {
        allergy.addCategory(categoryTranslator.toFhirResource(omrsAllergy.getAllergen().getAllergenType()));
    }
    allergy.setClinicalStatus(setClinicalStatus(omrsAllergy.getVoided()));
    allergy.setVerificationStatus(new CodeableConcept().setText("Confirmed").addCoding(new Coding(FhirConstants.ALLERGY_INTOLERANCE_VERIFICATION_STATUS_SYSTEM_URI, "confirmed", "Confirmed")));
    allergy.setPatient(patientReferenceTranslator.toFhirResource(omrsAllergy.getPatient()));
    allergy.setRecorder(practitionerReferenceTranslator.toFhirResource(omrsAllergy.getCreator()));
    allergy.setRecordedDate(omrsAllergy.getDateCreated());
    allergy.getMeta().setLastUpdated(omrsAllergy.getDateChanged());
    allergy.setType(AllergyIntolerance.AllergyIntoleranceType.ALLERGY);
    allergy.addNote(new Annotation().setText(omrsAllergy.getComment()));
    allergy.setCriticality(criticalityTranslator.toFhirResource(severityTranslator.toFhirResource(omrsAllergy.getSeverity())));
    allergy.addReaction(reactionComponentTranslator.toFhirResource(omrsAllergy));
    allergy.setCode(allergy.getReactionFirstRep().getSubstance());
    allergy.addContained(provenanceTranslator.getCreateProvenance(omrsAllergy));
    allergy.addContained(provenanceTranslator.getUpdateProvenance(omrsAllergy));
    return allergy;
}