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

Example 41 with Specimen

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

the class RdfParser method composeMolecularSequence.

protected void composeMolecularSequence(Complex parent, String parentType, String name, MolecularSequence element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "MolecularSequence", name, element, index);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "MolecularSequence", "identifier", element.getIdentifier().get(i), i);
    if (element.hasTypeElement())
        composeEnum(t, "MolecularSequence", "type", element.getTypeElement(), -1);
    if (element.hasCoordinateSystemElement())
        composeInteger(t, "MolecularSequence", "coordinateSystem", element.getCoordinateSystemElement(), -1);
    if (element.hasPatient())
        composeReference(t, "MolecularSequence", "patient", element.getPatient(), -1);
    if (element.hasSpecimen())
        composeReference(t, "MolecularSequence", "specimen", element.getSpecimen(), -1);
    if (element.hasDevice())
        composeReference(t, "MolecularSequence", "device", element.getDevice(), -1);
    if (element.hasPerformer())
        composeReference(t, "MolecularSequence", "performer", element.getPerformer(), -1);
    if (element.hasQuantity())
        composeQuantity(t, "MolecularSequence", "quantity", element.getQuantity(), -1);
    if (element.hasReferenceSeq())
        composeMolecularSequenceMolecularSequenceReferenceSeqComponent(t, "MolecularSequence", "referenceSeq", element.getReferenceSeq(), -1);
    for (int i = 0; i < element.getVariant().size(); i++) composeMolecularSequenceMolecularSequenceVariantComponent(t, "MolecularSequence", "variant", element.getVariant().get(i), i);
    if (element.hasObservedSeqElement())
        composeString(t, "MolecularSequence", "observedSeq", element.getObservedSeqElement(), -1);
    for (int i = 0; i < element.getQuality().size(); i++) composeMolecularSequenceMolecularSequenceQualityComponent(t, "MolecularSequence", "quality", element.getQuality().get(i), i);
    if (element.hasReadCoverageElement())
        composeInteger(t, "MolecularSequence", "readCoverage", element.getReadCoverageElement(), -1);
    for (int i = 0; i < element.getRepository().size(); i++) composeMolecularSequenceMolecularSequenceRepositoryComponent(t, "MolecularSequence", "repository", element.getRepository().get(i), i);
    for (int i = 0; i < element.getPointer().size(); i++) composeReference(t, "MolecularSequence", "pointer", element.getPointer().get(i), i);
    for (int i = 0; i < element.getStructureVariant().size(); i++) composeMolecularSequenceMolecularSequenceStructureVariantComponent(t, "MolecularSequence", "structureVariant", element.getStructureVariant().get(i), i);
}

Example 42 with Specimen

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

the class RdfParser method composeImagingStudyImagingStudySeriesComponent.

protected void composeImagingStudyImagingStudySeriesComponent(Complex parent, String parentType, String name, ImagingStudy.ImagingStudySeriesComponent element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeBackboneElement(t, "series", name, element, index);
    if (element.hasUidElement())
        composeId(t, "ImagingStudy", "uid", element.getUidElement(), -1);
    if (element.hasNumberElement())
        composeUnsignedInt(t, "ImagingStudy", "number", element.getNumberElement(), -1);
    if (element.hasModality())
        composeCoding(t, "ImagingStudy", "modality", element.getModality(), -1);
    if (element.hasDescriptionElement())
        composeString(t, "ImagingStudy", "description", element.getDescriptionElement(), -1);
    if (element.hasNumberOfInstancesElement())
        composeUnsignedInt(t, "ImagingStudy", "numberOfInstances", element.getNumberOfInstancesElement(), -1);
    for (int i = 0; i < element.getEndpoint().size(); i++) composeReference(t, "ImagingStudy", "endpoint", element.getEndpoint().get(i), i);
    if (element.hasBodySite())
        composeCoding(t, "ImagingStudy", "bodySite", element.getBodySite(), -1);
    if (element.hasLaterality())
        composeCoding(t, "ImagingStudy", "laterality", element.getLaterality(), -1);
    for (int i = 0; i < element.getSpecimen().size(); i++) composeReference(t, "ImagingStudy", "specimen", element.getSpecimen().get(i), i);
    if (element.hasStartedElement())
        composeDateTime(t, "ImagingStudy", "started", element.getStartedElement(), -1);
    for (int i = 0; i < element.getPerformer().size(); i++) composeImagingStudyImagingStudySeriesPerformerComponent(t, "ImagingStudy", "performer", element.getPerformer().get(i), i);
    for (int i = 0; i < element.getInstance().size(); i++) composeImagingStudyImagingStudySeriesInstanceComponent(t, "ImagingStudy", "instance", element.getInstance().get(i), i);
}

Example 43 with Specimen

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

the class TurtleTests method test_specimen_example.

@Test
public void test_specimen_example() throws FileNotFoundException, IOException, Exception {
    System.out.println("specimen-example.ttl");
    new Turtle().parse(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\specimen-example.ttl"));
}

Example 44 with Specimen

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

the class RdfParser method composeServiceRequest.

protected void composeServiceRequest(Complex parent, String parentType, String name, ServiceRequest element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "ServiceRequest", name, element, index);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "ServiceRequest", "identifier", element.getIdentifier().get(i), i);
    for (int i = 0; i < element.getInstantiatesCanonical().size(); i++) composeCanonical(t, "ServiceRequest", "instantiatesCanonical", element.getInstantiatesCanonical().get(i), i);
    for (int i = 0; i < element.getInstantiatesUri().size(); i++) composeUri(t, "ServiceRequest", "instantiatesUri", element.getInstantiatesUri().get(i), i);
    for (int i = 0; i < element.getBasedOn().size(); i++) composeReference(t, "ServiceRequest", "basedOn", element.getBasedOn().get(i), i);
    for (int i = 0; i < element.getReplaces().size(); i++) composeReference(t, "ServiceRequest", "replaces", element.getReplaces().get(i), i);
    if (element.hasRequisition())
        composeIdentifier(t, "ServiceRequest", "requisition", element.getRequisition(), -1);
    if (element.hasStatusElement())
        composeEnum(t, "ServiceRequest", "status", element.getStatusElement(), -1);
    if (element.hasIntentElement())
        composeEnum(t, "ServiceRequest", "intent", element.getIntentElement(), -1);
    for (int i = 0; i < element.getCategory().size(); i++) composeCodeableConcept(t, "ServiceRequest", "category", element.getCategory().get(i), i);
    if (element.hasPriorityElement())
        composeEnum(t, "ServiceRequest", "priority", element.getPriorityElement(), -1);
    if (element.hasDoNotPerformElement())
        composeBoolean(t, "ServiceRequest", "doNotPerform", element.getDoNotPerformElement(), -1);
    if (element.hasCode())
        composeCodeableConcept(t, "ServiceRequest", "code", element.getCode(), -1);
    for (int i = 0; i < element.getOrderDetail().size(); i++) composeCodeableConcept(t, "ServiceRequest", "orderDetail", element.getOrderDetail().get(i), i);
    if (element.hasQuantity())
        composeType(t, "ServiceRequest", "quantity", element.getQuantity(), -1);
    if (element.hasSubject())
        composeReference(t, "ServiceRequest", "subject", element.getSubject(), -1);
    if (element.hasEncounter())
        composeReference(t, "ServiceRequest", "encounter", element.getEncounter(), -1);
    if (element.hasOccurrence())
        composeType(t, "ServiceRequest", "occurrence", element.getOccurrence(), -1);
    if (element.hasAsNeeded())
        composeType(t, "ServiceRequest", "asNeeded", element.getAsNeeded(), -1);
    if (element.hasAuthoredOnElement())
        composeDateTime(t, "ServiceRequest", "authoredOn", element.getAuthoredOnElement(), -1);
    if (element.hasRequester())
        composeReference(t, "ServiceRequest", "requester", element.getRequester(), -1);
    if (element.hasPerformerType())
        composeCodeableConcept(t, "ServiceRequest", "performerType", element.getPerformerType(), -1);
    for (int i = 0; i < element.getPerformer().size(); i++) composeReference(t, "ServiceRequest", "performer", element.getPerformer().get(i), i);
    for (int i = 0; i < element.getLocationCode().size(); i++) composeCodeableConcept(t, "ServiceRequest", "locationCode", element.getLocationCode().get(i), i);
    for (int i = 0; i < element.getLocationReference().size(); i++) composeReference(t, "ServiceRequest", "locationReference", element.getLocationReference().get(i), i);
    for (int i = 0; i < element.getReasonCode().size(); i++) composeCodeableConcept(t, "ServiceRequest", "reasonCode", element.getReasonCode().get(i), i);
    for (int i = 0; i < element.getReasonReference().size(); i++) composeReference(t, "ServiceRequest", "reasonReference", element.getReasonReference().get(i), i);
    for (int i = 0; i < element.getInsurance().size(); i++) composeReference(t, "ServiceRequest", "insurance", element.getInsurance().get(i), i);
    for (int i = 0; i < element.getSupportingInfo().size(); i++) composeReference(t, "ServiceRequest", "supportingInfo", element.getSupportingInfo().get(i), i);
    for (int i = 0; i < element.getSpecimen().size(); i++) composeReference(t, "ServiceRequest", "specimen", element.getSpecimen().get(i), i);
    for (int i = 0; i < element.getBodySite().size(); i++) composeCodeableConcept(t, "ServiceRequest", "bodySite", element.getBodySite().get(i), i);
    for (int i = 0; i < element.getNote().size(); i++) composeAnnotation(t, "ServiceRequest", "note", element.getNote().get(i), i);
    if (element.hasPatientInstructionElement())
        composeString(t, "ServiceRequest", "patientInstruction", element.getPatientInstructionElement(), -1);
    for (int i = 0; i < element.getRelevantHistory().size(); i++) composeReference(t, "ServiceRequest", "relevantHistory", element.getRelevantHistory().get(i), i);
}

Example 45 with Specimen

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

the class RdfParser method composeDiagnosticReport.

protected void composeDiagnosticReport(Complex parent, String parentType, String name, DiagnosticReport element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "DiagnosticReport", name, element, index);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "DiagnosticReport", "identifier", element.getIdentifier().get(i), i);
    for (int i = 0; i < element.getBasedOn().size(); i++) composeReference(t, "DiagnosticReport", "basedOn", element.getBasedOn().get(i), i);
    if (element.hasStatusElement())
        composeEnum(t, "DiagnosticReport", "status", element.getStatusElement(), -1);
    for (int i = 0; i < element.getCategory().size(); i++) composeCodeableConcept(t, "DiagnosticReport", "category", element.getCategory().get(i), i);
    if (element.hasCode())
        composeCodeableConcept(t, "DiagnosticReport", "code", element.getCode(), -1);
    if (element.hasSubject())
        composeReference(t, "DiagnosticReport", "subject", element.getSubject(), -1);
    if (element.hasEncounter())
        composeReference(t, "DiagnosticReport", "encounter", element.getEncounter(), -1);
    if (element.hasEffective())
        composeType(t, "DiagnosticReport", "effective", element.getEffective(), -1);
    if (element.hasIssuedElement())
        composeInstant(t, "DiagnosticReport", "issued", element.getIssuedElement(), -1);
    for (int i = 0; i < element.getPerformer().size(); i++) composeReference(t, "DiagnosticReport", "performer", element.getPerformer().get(i), i);
    for (int i = 0; i < element.getResultsInterpreter().size(); i++) composeReference(t, "DiagnosticReport", "resultsInterpreter", element.getResultsInterpreter().get(i), i);
    for (int i = 0; i < element.getSpecimen().size(); i++) composeReference(t, "DiagnosticReport", "specimen", element.getSpecimen().get(i), i);
    for (int i = 0; i < element.getResult().size(); i++) composeReference(t, "DiagnosticReport", "result", element.getResult().get(i), i);
    for (int i = 0; i < element.getImagingStudy().size(); i++) composeReference(t, "DiagnosticReport", "imagingStudy", element.getImagingStudy().get(i), i);
    for (int i = 0; i < element.getMedia().size(); i++) composeDiagnosticReportDiagnosticReportMediaComponent(t, "DiagnosticReport", "media", element.getMedia().get(i), i);
    if (element.hasConclusionElement())
        composeString(t, "DiagnosticReport", "conclusion", element.getConclusionElement(), -1);
    for (int i = 0; i < element.getConclusionCode().size(); i++) composeCodeableConcept(t, "DiagnosticReport", "conclusionCode", element.getConclusionCode().get(i), i);
    for (int i = 0; i < element.getPresentedForm().size(); i++) composeAttachment(t, "DiagnosticReport", "presentedForm", element.getPresentedForm().get(i), i);
}