Examples with Specimen org.hl7.fhir.r4.model.Specimen used on opensource projects

Example 46 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeSpecimen.

protected void composeSpecimen(Complex parent, String parentType, String name, Specimen element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "Specimen", name, element, index);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "Specimen", "identifier", element.getIdentifier().get(i), i);
    if (element.hasAccessionIdentifier())
        composeIdentifier(t, "Specimen", "accessionIdentifier", element.getAccessionIdentifier(), -1);
    if (element.hasStatusElement())
        composeEnum(t, "Specimen", "status", element.getStatusElement(), -1);
    if (element.hasType())
        composeCodeableConcept(t, "Specimen", "type", element.getType(), -1);
    if (element.hasSubject())
        composeReference(t, "Specimen", "subject", element.getSubject(), -1);
    if (element.hasReceivedTimeElement())
        composeDateTime(t, "Specimen", "receivedTime", element.getReceivedTimeElement(), -1);
    for (int i = 0; i < element.getParent().size(); i++) composeReference(t, "Specimen", "parent", element.getParent().get(i), i);
    for (int i = 0; i < element.getRequest().size(); i++) composeReference(t, "Specimen", "request", element.getRequest().get(i), i);
    if (element.hasCollection())
        composeSpecimenSpecimenCollectionComponent(t, "Specimen", "collection", element.getCollection(), -1);
    for (int i = 0; i < element.getProcessing().size(); i++) composeSpecimenSpecimenProcessingComponent(t, "Specimen", "processing", element.getProcessing().get(i), i);
    for (int i = 0; i < element.getContainer().size(); i++) composeSpecimenSpecimenContainerComponent(t, "Specimen", "container", element.getContainer().get(i), i);
    for (int i = 0; i < element.getNote().size(); i++) composeAnnotation(t, "Specimen", "note", element.getNote().get(i), i);
}

Example 47 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project nia-patient-switching-standard-adaptor by NHSDigital.

the class SpecimenMapperTest method testInvalidSpecimenIsNotMapped.

@Test
public void testInvalidSpecimenIsNotMapped() {
    RCMRMT030101UK04EhrExtract ehrExtract = unmarshallEhrExtract("specimen_invalid.xml");
    List<Specimen> specimenList = specimenMapper.mapSpecimen(ehrExtract, List.of(DIAGNOSTIC_REPORT_WITHOUT_SPECIMEN), PATIENT, PRACTICE_CODE);
    assertThat(specimenList).isEmpty();
}

Example 48 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project nia-patient-switching-standard-adaptor by NHSDigital.

the class SpecimenMapperTest method generateDiagnosticReportWithSpecimenReference.

private static DiagnosticReport generateDiagnosticReportWithSpecimenReference() {
    DiagnosticReport diagnosticReport = (DiagnosticReport) new DiagnosticReport().setId(DR_ID);
    List<Reference> specimen = List.of(new Reference(SPECIMEN_PREFIX + TEST_SPECIMEN_ID));
    diagnosticReport.setSpecimen(specimen);
    return diagnosticReport;
}

Example 49 with Specimen

use of org.hl7.fhir.r4.model.Specimen in project nia-patient-switching-standard-adaptor by NHSDigital.

the class SpecimenMapperTest method testSpecimenIsMapped.

@Test
public void testSpecimenIsMapped() {
    when(dateTimeMapper.mapDateTime(any())).thenCallRealMethod();
    RCMRMT030101UK04EhrExtract ehrExtract = unmarshallEhrExtract("specimen_valid.xml");
    List<Specimen> specimenList = specimenMapper.mapSpecimen(ehrExtract, List.of(DIAGNOSTIC_REPORT_WITH_SPECIMEN), PATIENT, PRACTICE_CODE);
    assertThat(specimenList).isNotEmpty();
    final Specimen specimen = specimenList.get(0);
    checkFixedValues(specimen);
    assertThat(specimen.getNote().get(0).getText()).isEqualTo(NOTE_TEXT);
    assertThat(specimen.getAccessionIdentifier().getValue()).isEqualTo(ACCESSION_IDENTIFIER_VALUE);
    assertThat(specimen.getType().getText()).isEqualTo(SPECIMEN_TYPE_TEXT);
    assertThat(specimen.getCollection().getCollected().toString()).isEqualTo(SPECIMEN_COLLECTED_DATETIME.toString());
}