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

Example 76 with Immunization

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

the class RdfParser method composeImmunization.

protected void composeImmunization(Complex parent, String parentType, String name, Immunization element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeDomainResource(t, "Immunization", name, element, index);
    for (int i = 0; i < element.getIdentifier().size(); i++) composeIdentifier(t, "Immunization", "identifier", element.getIdentifier().get(i), i);
    if (element.hasStatusElement())
        composeCode(t, "Immunization", "status", element.getStatusElement(), -1);
    if (element.hasDateElement())
        composeDateTime(t, "Immunization", "date", element.getDateElement(), -1);
    if (element.hasVaccineCode())
        composeCodeableConcept(t, "Immunization", "vaccineCode", element.getVaccineCode(), -1);
    if (element.hasPatient())
        composeReference(t, "Immunization", "patient", element.getPatient(), -1);
    if (element.hasWasNotGivenElement())
        composeBoolean(t, "Immunization", "wasNotGiven", element.getWasNotGivenElement(), -1);
    if (element.hasReportedElement())
        composeBoolean(t, "Immunization", "reported", element.getReportedElement(), -1);
    if (element.hasPerformer())
        composeReference(t, "Immunization", "performer", element.getPerformer(), -1);
    if (element.hasRequester())
        composeReference(t, "Immunization", "requester", element.getRequester(), -1);
    if (element.hasEncounter())
        composeReference(t, "Immunization", "encounter", element.getEncounter(), -1);
    if (element.hasManufacturer())
        composeReference(t, "Immunization", "manufacturer", element.getManufacturer(), -1);
    if (element.hasLocation())
        composeReference(t, "Immunization", "location", element.getLocation(), -1);
    if (element.hasLotNumberElement())
        composeString(t, "Immunization", "lotNumber", element.getLotNumberElement(), -1);
    if (element.hasExpirationDateElement())
        composeDate(t, "Immunization", "expirationDate", element.getExpirationDateElement(), -1);
    if (element.hasSite())
        composeCodeableConcept(t, "Immunization", "site", element.getSite(), -1);
    if (element.hasRoute())
        composeCodeableConcept(t, "Immunization", "route", element.getRoute(), -1);
    if (element.hasDoseQuantity())
        composeQuantity(t, "Immunization", "doseQuantity", element.getDoseQuantity(), -1);
    for (int i = 0; i < element.getNote().size(); i++) composeAnnotation(t, "Immunization", "note", element.getNote().get(i), i);
    if (element.hasExplanation())
        composeImmunizationImmunizationExplanationComponent(t, "Immunization", "explanation", element.getExplanation(), -1);
    for (int i = 0; i < element.getReaction().size(); i++) composeImmunizationImmunizationReactionComponent(t, "Immunization", "reaction", element.getReaction().get(i), i);
    for (int i = 0; i < element.getVaccinationProtocol().size(); i++) composeImmunizationImmunizationVaccinationProtocolComponent(t, "Immunization", "vaccinationProtocol", element.getVaccinationProtocol().get(i), i);
}

Example 77 with Immunization

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

the class ProfileUtilitiesTests method execute.

public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
    System.out.println("loading context");
    context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation.zip"));
    comp = new ProfileComparer(context);
    compare("patient-daf-dafpatient.profile.xml", "patient-qicore-qicore-patient.profile.xml");
    compare("encounter-daf-dafencounter.profile.xml", "encounter-qicore-qicore-encounter.profile.xml");
    compare("substance-daf-dafsubstance.profile.xml", "substance-qicore-qicore-substance.profile.xml");
    compare("medication-daf-dafmedication.profile.xml", "medication-qicore-qicore-medication.profile.xml");
    compare("procedure-daf-dafprocedure.profile.xml", "procedure-qicore-qicore-procedure.profile.xml");
    compare("familymemberhistory-daf-daffamilymemberhistory.profile.xml", "familymemberhistory-qicore-qicore-familymemberhistory.profile.xml");
    compare("immunization-daf-dafimmunization.profile.xml", "immunization-qicore-qicore-immunization.profile.xml");
    compare("condition-daf-dafcondition.profile.xml", "condition-qicore-qicore-condition.profile.xml");
    compare("allergyintolerance-daf-dafallergyintolerance.profile.xml", "allergyintolerance-qicore-qicore-allergyintolerance.profile.xml");
    compare("medicationadministration-daf-dafmedicationadministration.profile.xml", "medicationadministration-qicore-qicore-medicationadministration.profile.xml");
    compare("medicationdispense-daf-dafmedicationdispense.profile.xml", "medicationdispense-qicore-qicore-medicationdispense.profile.xml");
    compare("medicationprescription-daf-dafmedicationprescription.profile.xml", "medicationprescription-qicore-qicore-medicationprescription.profile.xml");
    compare("medicationstatement-daf-dafmedicationstatement.profile.xml", "medicationstatement-qicore-qicore-medicationstatement.profile.xml");
    compare("observation-daf-smokingstatus-dafsmokingstatus.profile.xml", "observation-qicore-qicore-observation.profile.xml");
    compare("observation-daf-vitalsigns-dafvitalsigns.profile.xml", "observation-qicore-qicore-observation.profile.xml");
    // compare("observation-daf-results-dafresultobs.profile.xml", "observation-qicore-qicore-observation.profile.xml");
    // compare("diagnosticorder-daf-dafdiagnosticorder.profile.xml", "diagnosticorder-qicore-qicore-diagnosticorder.profile.xml");
    // compare("diagnosticreport-daf-dafdiagnosticreport.profile.xml", "diagnosticreport-qicore-qicore-diagnosticreport.profile.xml");
    System.out.println("processing output");
    for (ProfileComparison outcome : comp.getComparisons()) {
        if (outcome.getSubset() != null)
            new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")), outcome.getSubset());
        if (outcome.getSuperset() != null)
            new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
        System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and " + outcome.getRight().getUrl());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.INFORMATION)
            System.out.println(vm.summary());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.WARNING)
            System.out.println(vm.summary());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.ERROR)
            System.out.println(vm.summary());
        for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.FATAL)
            System.out.println(vm.summary());
        System.out.println("done. " + Integer.toString(outcome.getMessages().size()) + " messages");
        System.out.println("=================================================================");
    }
}

Example 78 with Immunization

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

the class RdfParser method composeImmunizationImmunizationPerformerComponent.

protected void composeImmunizationImmunizationPerformerComponent(Complex parent, String parentType, String name, Immunization.ImmunizationPerformerComponent element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeBackboneElement(t, "performer", name, element, index);
    if (element.hasFunction())
        composeCodeableConcept(t, "Immunization", "function", element.getFunction(), -1);
    if (element.hasActor())
        composeReference(t, "Immunization", "actor", element.getActor(), -1);
}

Example 79 with Immunization

use of org.hl7.fhir.r4.model.Immunization in project eCRNow by drajer-health.

the class CdaImmunizationGenerator method generateImmunizationSection.

public static String generateImmunizationSection(R4FhirData data, LaunchDetails details) {
    StringBuilder sb = new StringBuilder(2000);
    List<Immunization> imms = data.getImmunizations();
    if (imms != null && !imms.isEmpty()) {
        // Generate the component and section end tags
        sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.COMP_EL_NAME));
        sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.SECTION_EL_NAME));
        sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_SEC_TEMPLATE_ID));
        sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_SEC_TEMPLATE_ID, CdaGeneratorConstants.IMMUNIZATION_SEC_TEMPLATE_ID_EXT));
        sb.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.CODE_EL_NAME, CdaGeneratorConstants.IMMUNIZATION_SEC_CODE, CdaGeneratorConstants.LOINC_CODESYSTEM_OID, CdaGeneratorConstants.LOINC_CODESYSTEM_NAME, CdaGeneratorConstants.IMMUNIZATION_SEC_NAME));
        // add Title
        sb.append(CdaGeneratorUtils.getXmlForText(CdaGeneratorConstants.TITLE_EL_NAME, CdaGeneratorConstants.IMMUNIZATION_SEC_TITLE));
        // add Narrative Text
        sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TEXT_EL_NAME));
        // Create Table Header.
        List<String> list = new ArrayList<>();
        list.add(CdaGeneratorConstants.IMM_TABLE_COL_1_TITLE);
        list.add(CdaGeneratorConstants.IMM_TABLE_COL_2_TITLE);
        sb.append(CdaGeneratorUtils.getXmlForTableHeader(list, CdaGeneratorConstants.TABLE_BORDER, CdaGeneratorConstants.TABLE_WIDTH));
        // add Table Body
        sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TABLE_BODY_EL_NAME));
        // add Body Rows
        int rowNum = 1;
        for (Immunization imm : imms) {
            String medDisplayName = CdaGeneratorConstants.UNKNOWN_VALUE;
            if (imm.getVaccineCode() != null && imm.getVaccineCode().getCodingFirstRep() != null && !StringUtils.isEmpty(imm.getVaccineCode().getCodingFirstRep().getDisplay())) {
                medDisplayName = imm.getVaccineCode().getCodingFirstRep().getDisplay();
            }
            String dt = null;
            if (imm.getOccurrenceDateTimeType() != null) {
                dt = imm.getOccurrenceDateTimeType().getValue().toString();
            }
            Map<String, String> bodyvals = new LinkedHashMap<>();
            bodyvals.put(CdaGeneratorConstants.IMM_TABLE_COL_1_BODY_CONTENT, medDisplayName);
            bodyvals.put(CdaGeneratorConstants.IMM_TABLE_COL_2_BODY_CONTENT, dt);
            sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
            // TODO: ++rowNum or rowNum++
            ++rowNum;
        }
        sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TABLE_BODY_EL_NAME));
        // End Table.
        sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TABLE_EL_NAME));
        sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TEXT_EL_NAME));
        for (Immunization imm : imms) {
            // add the Entries.
            sb.append(CdaGeneratorUtils.getXmlForActEntry(CdaGeneratorConstants.TYPE_CODE_DEF));
            // add the immunization Act
            if (imm.getStatus() != ImmunizationStatus.COMPLETED) {
                sb.append(CdaGeneratorUtils.getXmlForActWithNegationInd(CdaGeneratorConstants.MED_ACT_EL_NAME, CdaGeneratorConstants.MED_CLASS_CODE, CdaGeneratorConstants.MOOD_CODE_DEF, "true", true));
            } else {
                sb.append(CdaGeneratorUtils.getXmlForActWithNegationInd(CdaGeneratorConstants.MED_ACT_EL_NAME, CdaGeneratorConstants.MED_CLASS_CODE, CdaGeneratorConstants.MOOD_CODE_DEF, "false", true));
            }
            sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_ACTIVITY_TEMPLATE_ID));
            sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_ACTIVITY_TEMPLATE_ID, CdaGeneratorConstants.IMMUNIZATION_ACTIVITY_TEMPLATE_ID_EXT));
            sb.append(CdaGeneratorUtils.getXmlForII(details.getAssigningAuthorityId(), imm.getId()));
            // set status code
            sb.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.STATUS_CODE_EL_NAME, CdaGeneratorConstants.COMPLETED_STATUS));
            // Set up Effective Time for start and End time.
            if (imm.getOccurrenceDateTimeType() != null) {
                logger.debug("Date Value = {}", imm.getOccurrenceDateTimeType().getValue());
                sb.append(CdaFhirUtilities.getDateTimeTypeXml(imm.getOccurrenceDateTimeType(), CdaGeneratorConstants.EFF_TIME_EL_NAME));
            } else {
                sb.append(CdaGeneratorUtils.getXmlForNullEffectiveTime(CdaGeneratorConstants.EFF_TIME_EL_NAME, CdaGeneratorConstants.NF_NI));
            }
            // add the consumable presentation.
            sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.CONSUMABLE_EL_NAME));
            sb.append(CdaGeneratorUtils.getXmlForStartElementWithClassCode(CdaGeneratorConstants.MAN_PROD_EL_NAME, CdaGeneratorConstants.MANU_CLASS_CODE));
            sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_MEDICATION_INFORMATION));
            sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_MEDICATION_INFORMATION, CdaGeneratorConstants.IMMUNIZATION_MEDICATION_INFORMATION_EXT));
            sb.append(CdaGeneratorUtils.getXmlForIIUsingGuid());
            sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.MANU_MAT_EL_NAME));
            List<CodeableConcept> cds = new ArrayList<>();
            cds.add(imm.getVaccineCode());
            String codeXml = CdaFhirUtilities.getCodeableConceptXmlForCodeSystem(cds, CdaGeneratorConstants.CODE_EL_NAME, false, CdaGeneratorConstants.FHIR_CVX_URL, false);
            if (!codeXml.isEmpty()) {
                sb.append(codeXml);
            } else {
                sb.append(CdaFhirUtilities.getCodeableConceptXml(cds, CdaGeneratorConstants.CODE_EL_NAME, false));
            }
            sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.MANU_MAT_EL_NAME));
            sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.MAN_PROD_EL_NAME));
            sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.CONSUMABLE_EL_NAME));
            // End Tags for Entries
            sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.MED_ACT_EL_NAME));
            sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.ENTRY_EL_NAME));
        }
        // Complete the section end tags.
        sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.SECTION_EL_NAME));
        sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.COMP_EL_NAME));
    } else {
        sb.append(generateEmptyImmunizations());
    }
    return sb.toString();
}

Example 80 with Immunization

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

the class ImmunizationMapper method mapImmunization.

private Immunization mapImmunization(RCMRMT030101UK04EhrComposition ehrComposition, RCMRMT030101UK04ObservationStatement observationStatement, Patient patientResource, List<Encounter> encounterList, String practiseCode) {
    Immunization immunization = new Immunization();
    var id = observationStatement.getId().getRoot();
    var practitioner = ParticipantReferenceUtil.getParticipantReference(observationStatement.getParticipant(), ehrComposition);
    var encounter = getEncounterReference(encounterList, ehrComposition.getId());
    immunization.setMeta(generateMeta(META_PROFILE));
    immunization.addIdentifier(buildIdentifier(id, practiseCode));
    immunization.addExtension(createVaccineProcedureExtension(observationStatement));
    immunization.addExtension(createRecordedTimeExtension(ehrComposition));
    immunization.setEncounter(encounter).addPractitioner(new ImmunizationPractitionerComponent(practitioner)).setStatus(ImmunizationStatus.COMPLETED).setNotGiven(false).setPrimarySource(false).setPatient(new Reference(patientResource)).setId(id);
    buildNote(observationStatement).forEach(immunization::addNote);
    setDateFields(immunization, observationStatement);
    return immunization;
}