Examples with DateTime org.hl7.elm.r1.DateTime used on opensource projects

Example 1 with DateTime

use of org.hl7.elm.r1.DateTime in project beneficiary-fhir-data by CMSgov.

the class BeneficiaryTransformerV2 method transform.

/**
 * @param beneficiary the CCW {@link Beneficiary} to transform
 * @param requestHeader {@link RequestHeaders} the holder that contains all supported resource
 *     request headers
 * @return a FHIR {@link Patient} resource that represents the specified {@link Beneficiary}
 */
private static Patient transform(Beneficiary beneficiary, RequestHeaders requestHeader) {
    Objects.requireNonNull(beneficiary);
    Patient patient = new Patient();
    /*
     * Notify end users when they receive Patient records impacted by
     * https://jira.cms.gov/browse/BFD-1566. See the documentation on
     * LoadAppOptions.isFilteringNonNullAndNon2022Benes() for details.
     */
    if (!beneficiary.getSkippedRifRecords().isEmpty()) {
        patient.getMeta().addTag(TransformerConstants.CODING_SYSTEM_BFD_TAGS, TransformerConstants.CODING_BFD_TAGS_DELAYED_BACKDATED_ENROLLMENT, TransformerConstants.CODING_BFD_TAGS_DELAYED_BACKDATED_ENROLLMENT_DISPLAY);
    }
    // Required values not directly mapped
    patient.getMeta().addProfile(ProfileConstants.C4BB_PATIENT_URL);
    patient.setId(beneficiary.getBeneficiaryId());
    // BENE_ID => patient.identifier
    TransformerUtilsV2.addIdentifierSlice(patient, TransformerUtilsV2.createCodeableConcept(TransformerConstants.CODING_SYSTEM_HL7_IDENTIFIER_TYPE, null, TransformerConstants.PATIENT_MB_ID_DISPLAY, "MB"), Optional.of(beneficiary.getBeneficiaryId()), Optional.of(TransformerConstants.CODING_BBAPI_BENE_ID));
    // Unhashed MBI
    if (beneficiary.getMedicareBeneficiaryId().isPresent()) {
        Period mbiPeriod = new Period();
        if (beneficiary.getMbiEffectiveDate().isPresent()) {
            TransformerUtilsV2.setPeriodStart(mbiPeriod, beneficiary.getMbiEffectiveDate().get());
        }
        if (beneficiary.getMbiObsoleteDate().isPresent()) {
            TransformerUtilsV2.setPeriodEnd(mbiPeriod, beneficiary.getMbiObsoleteDate().get());
        }
        addUnhashedIdentifier(patient, beneficiary.getMedicareBeneficiaryId().get(), TransformerConstants.CODING_BBAPI_MEDICARE_BENEFICIARY_ID_UNHASHED, TransformerUtilsV2.createIdentifierCurrencyExtension(CurrencyIdentifier.CURRENT), mbiPeriod);
    }
    // Add lastUpdated
    TransformerUtilsV2.setLastUpdated(patient, beneficiary.getLastUpdated());
    /**
     * The following logic attempts to distill {@link MedicareBeneficiaryIdHistory} data into only
     * those records which have an endDate present. This is due to the fact that it includes the
     * CURRENT MBI record which was handle previously. Also, the {@link
     * MedicareBeneficiaryIdHistory} table appears to contain spurious records with the only
     * difference is the generated surrogate key identifier.
     */
    if (requestHeader.isMBIinIncludeIdentifiers()) {
        HashMap<LocalDate, MedicareBeneficiaryIdHistory> mbiHistMap = new HashMap<LocalDate, MedicareBeneficiaryIdHistory>();
        for (MedicareBeneficiaryIdHistory mbiHistory : beneficiary.getMedicareBeneficiaryIdHistories()) {
            // and will have been previously provided as the CURRENT rcd.
            if (mbiHistory.getMbiEndDate().isPresent()) {
                mbiHistMap.put(mbiHistory.getMbiEndDate().get(), mbiHistory);
            }
            // would come in ascending order, so any rcd would have a later
            // update date than prev rcd.
            TransformerUtilsV2.updateMaxLastUpdated(patient, mbiHistory.getLastUpdated());
        }
        if (mbiHistMap.size() > 0) {
            Extension historicalIdentifier = TransformerUtilsV2.createIdentifierCurrencyExtension(CurrencyIdentifier.HISTORIC);
            for (MedicareBeneficiaryIdHistory mbi : mbiHistMap.values()) {
                addUnhashedIdentifier(patient, mbi.getMedicareBeneficiaryId().get(), TransformerConstants.CODING_BBAPI_MEDICARE_BENEFICIARY_ID_UNHASHED, historicalIdentifier, null);
            }
        }
    }
    // support header includeAddressFields from downstream components e.g. BB2
    // per requirement of BFD-379, BB2 always send header includeAddressFields = False
    Boolean addrHdrVal = requestHeader.getValue(R4PatientResourceProvider.HEADER_NAME_INCLUDE_ADDRESS_FIELDS);
    if (addrHdrVal != null && addrHdrVal) {
        patient.addAddress().setState(beneficiary.getStateCode()).setPostalCode(beneficiary.getPostalCode()).setCity(beneficiary.getDerivedCityName().orElse(null)).addLine(beneficiary.getDerivedMailingAddress1().orElse(null)).addLine(beneficiary.getDerivedMailingAddress2().orElse(null)).addLine(beneficiary.getDerivedMailingAddress3().orElse(null)).addLine(beneficiary.getDerivedMailingAddress4().orElse(null)).addLine(beneficiary.getDerivedMailingAddress5().orElse(null)).addLine(beneficiary.getDerivedMailingAddress6().orElse(null));
    } else {
        patient.addAddress().setState(beneficiary.getStateCode()).setPostalCode(beneficiary.getPostalCode());
    }
    if (beneficiary.getBirthDate() != null) {
        patient.setBirthDate(TransformerUtilsV2.convertToDate(beneficiary.getBirthDate()));
    }
    // "Patient.deceased[x]": ["boolean", "dateTime"],
    if (beneficiary.getBeneficiaryDateOfDeath().isPresent()) {
        patient.setDeceased(new DateTimeType(TransformerUtilsV2.convertToDate(beneficiary.getBeneficiaryDateOfDeath().get()), TemporalPrecisionEnum.DAY));
    } else {
        patient.setDeceased(new BooleanType(false));
    }
    char sex = beneficiary.getSex();
    if (sex == Sex.MALE.getCode())
        patient.setGender((AdministrativeGender.MALE));
    else if (sex == Sex.FEMALE.getCode())
        patient.setGender((AdministrativeGender.FEMALE));
    else
        patient.setGender((AdministrativeGender.UNKNOWN));
    if (beneficiary.getRace().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.RACE, beneficiary.getRace().get()));
        // for race category, v2 will just treat all race codes as Unknown (UNK);
        // thus we'll simply pass in the Unknown race code .
        RaceCategory raceCategory = TransformerUtilsV2.getRaceCategory('0');
        Extension raceChildOMBExt1 = new Extension().setValue(new Coding().setCode(raceCategory.toCode()).setSystem(raceCategory.getSystem()).setDisplay(raceCategory.getDisplay())).setUrl("ombCategory");
        Extension raceChildOMBExt2 = new Extension().setValue(new StringType().setValue(raceCategory.getDisplay())).setUrl("text");
        Extension parentOMBRace = new Extension().setUrl(TransformerConstants.CODING_RACE_US);
        parentOMBRace.addExtension(raceChildOMBExt1);
        parentOMBRace.addExtension(raceChildOMBExt2);
        patient.addExtension(parentOMBRace);
    }
    HumanName name = patient.addName().addGiven(beneficiary.getNameGiven()).setFamily(beneficiary.getNameSurname()).setUse(HumanName.NameUse.USUAL);
    if (beneficiary.getNameMiddleInitial().isPresent()) {
        name.addGiven(String.valueOf(beneficiary.getNameMiddleInitial().get()));
    }
    // The reference year of the enrollment data
    if (beneficiary.getBeneEnrollmentReferenceYear().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionDate(CcwCodebookVariable.RFRNC_YR, beneficiary.getBeneEnrollmentReferenceYear()));
    }
    // Monthly Medicare-Medicaid dual eligibility codes
    if (beneficiary.getMedicaidDualEligibilityJanCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_01, beneficiary.getMedicaidDualEligibilityJanCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityFebCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_02, beneficiary.getMedicaidDualEligibilityFebCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityMarCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_03, beneficiary.getMedicaidDualEligibilityMarCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityAprCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_04, beneficiary.getMedicaidDualEligibilityAprCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityMayCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_05, beneficiary.getMedicaidDualEligibilityMayCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityJunCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_06, beneficiary.getMedicaidDualEligibilityJunCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityJulCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_07, beneficiary.getMedicaidDualEligibilityJulCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityAugCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_08, beneficiary.getMedicaidDualEligibilityAugCode()));
    }
    if (beneficiary.getMedicaidDualEligibilitySeptCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_09, beneficiary.getMedicaidDualEligibilitySeptCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityOctCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_10, beneficiary.getMedicaidDualEligibilityOctCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityNovCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_11, beneficiary.getMedicaidDualEligibilityNovCode()));
    }
    if (beneficiary.getMedicaidDualEligibilityDecCode().isPresent()) {
        patient.addExtension(TransformerUtilsV2.createExtensionCoding(patient, CcwCodebookVariable.DUAL_12, beneficiary.getMedicaidDualEligibilityDecCode()));
    }
    // Last Updated => Patient.meta.lastUpdated
    TransformerUtilsV2.setLastUpdated(patient, beneficiary.getLastUpdated());
    return patient;
}

Example 2 with DateTime

use of org.hl7.elm.r1.DateTime in project kindling by HL7.

the class JsonLDDefinitionsGenerator method generate.

// private String genDate;
// private String version;
// private BuildWorkerContext workerContext;
public void generate(Definitions definitions, IniFile ini, String tmpResDir, String dstDir, String srcDir, FHIRVersion version, String genDate, BuildWorkerContext workerContext) throws Exception {
    // this.genDate = genDate;
    // this.version = version;
    // this.workerContext = workerContext;
    JsonObject defn = new JsonObject();
    JsonObject context = new JsonObject();
    defn.add("@context", context);
    defn.addProperty("@id", "http://hl7.org/fhir/");
    context.addProperty("fhir", "http://hl7.org/fhir/");
    context.addProperty("xsd", "http://www.w3.org/2001/XMLSchema#");
    // properties for primitives, helpers, format features
    addProperty(context, "value", "fhir:value", "xsd:string");
    addProperty(context, "decimal", "fhir:value", "xsd:decimal");
    addProperty(context, "integer", "fhir:value", "xsd:integer");
    if (!version.isR4B()) {
        addProperty(context, "integer64", "fhir:value", "xsd:string");
    }
    addProperty(context, "boolean", "fhir:value", "xsd:boolean");
    addProperty(context, "binary", "fhir:value", "xsd:base64Binary");
    addProperty(context, "date", "fhir:value", "xsd:date");
    addProperty(context, "dateTime", "fhir:value", "xsd:dateTime");
    addProperty(context, "gYearMonth", "fhir:value", "xsd:gYearMonth");
    addProperty(context, "gYear", "fhir:value", "xsd:gYear");
    addProperty(context, "link", "fhir:link", "@id");
    addProperty(context, "concept", "fhir:concept", "@id");
    addProperty(context, "index", "fhir:index", "xsd:integer");
    addProperty(context, "role", "fhir:nodeRole", "@id");
    // elements defined in FHIR:
    for (TypeRef tr : definitions.getKnownTypes()) {
        if (!definitions.hasPrimitiveType(tr.getName()) && !tr.getName().equals("SimpleQuantity") && !tr.getName().equals("MoneyQuantity")) {
            TypeDefn root = definitions.getElementDefn(tr.getName());
            new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root, version, genDate);
        }
    }
    List<String> names = new ArrayList<String>();
    names.addAll(definitions.getResources().keySet());
    names.addAll(definitions.getBaseResources().keySet());
    names.add("Parameters");
    Collections.sort(names);
    for (String name : names) {
        ResourceDefn root = definitions.getResourceByName(name);
        new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root.getRoot(), version, genDate);
    }
    save(defn, dstDir + "fhir.jsonld");
}

Example 3 with DateTime

use of org.hl7.elm.r1.DateTime in project kindling by HL7.

the class FhirTurtleGenerator method genPrimitiveType.

/* ==============================================
     Generators for various FHIR types
   * ============================================== */
/**
 * PrimitiveType Generator
 *
 * @param pt FHIR Primitive Type (e.g. int, string, dateTime)
 */
// Note: For unknown reasons, getPrimitives returns DefinedCodes, not PrimitiveTypes...
private void genPrimitiveType(DefinedCode pt) {
    String ptName = pt.getCode();
    FHIRResource ptRes = fact.fhir_class(ptName, "Primitive").addDefinition(pt.getDefinition());
    Resource rdfType = RDFTypeMap.xsd_type_for(ptName, owlTarget);
    if (rdfType != null)
        ptRes.restriction(fact.fhir_cardinality_restriction(value, fact.fhir_datatype(rdfType).resource, 1, 1));
}

Example 4 with DateTime

use of org.hl7.elm.r1.DateTime in project hl7v2-fhir-converter by LinuxForHealth.

the class InputTimeZoneIdTest method validateTimeZoneIdSettingViaOption.

@Test
void validateTimeZoneIdSettingViaOption() {
    // NOTE: This simple Condition (PRB) segment is used for testing time because it has both
    // standard DateTime conversions (abatementDateTime, recordedDate) and value conversions (extension).
    String hl7message = "MSH|^~\\&|||||20040629164652|1|PPR^PC1|331|P|2.3.1||\r" + "PID||||||||||||||||||||||||||||||\r" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\r" + // PRB.16 to onsetDateTime (check time ZoneId)
    "PRB|AD|20020202020000|K80.00^Cholelithiasis^I10|53956|||20070707070000||20090909090000|||||||20160616160000\r";
    // FIRST test with city based ZoneId passed through options
    ConverterOptions customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().withZoneIdText("America/Chicago").build();
    // "America/Chicago" will become -06:00 in winter (CST) -05:00 in spring/summer/fall (CDT).  This is expected.
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
    // Find the condition from the FHIR bundle.
    List<Resource> conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
    assertThat(conditionResource).hasSize(1);
    Condition condition = (Condition) conditionResource.get(0);
    // PRB.2 Chicago Central STANDARD Time
    assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00-06:00");
    // PRB.9 Chicago Central DAYLIGHT Time
    assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00-05:00");
    // PRB.16 Chicago CDT
    assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00-05:00");
    assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7 Chicago CDT
    "2007-07-07T07:00:00-05:00");
    // SECOND test with fixed ZoneId passed through options
    customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().withZoneIdText("+03:00").build();
    e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
    // Find the condition from the FHIR bundle.
    conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
    assertThat(conditionResource).hasSize(1);
    condition = (Condition) conditionResource.get(0);
    // PRB.2 fixed ZoneId
    assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00+03:00");
    // PRB.9
    assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00+03:00");
    // PRB.16
    assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00+03:00");
    assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7
    "2007-07-07T07:00:00+03:00");
    // THIRD test with no ZoneId passed through options, so it uses the config.properties ZoneId
    customOptionsWithTenant = new Builder().withValidateResource().withPrettyPrint().build();
    e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message, customOptionsWithTenant);
    // Find the condition from the FHIR bundle.
    conditionResource = ResourceUtils.getResourceList(e, ResourceType.Condition);
    assertThat(conditionResource).hasSize(1);
    condition = (Condition) conditionResource.get(0);
    // PRB.2 config.properties ZoneId
    assert (condition.getRecordedDateElement().getValueAsString()).contains("2002-02-02T02:00:00+08:00");
    // PRB.9
    assert (condition.getAbatementDateTimeType().getValueAsString()).contains("2009-09-09T09:00:00+08:00");
    // PRB.16
    assert (condition.getOnsetDateTimeType().getValueAsString()).contains("2016-06-16T16:00:00+08:00");
    assert (condition.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/condition-assertedDate").getValueAsPrimitive().getValueAsString()).contains(// PRB.7
    "2007-07-07T07:00:00+08:00");
}

Example 5 with DateTime

use of org.hl7.elm.r1.DateTime in project cqf-ruler by DBCG.

the class ActivityDefinitionApplyProvider method resolveActivityDefinition.

// For library use
public Resource resolveActivityDefinition(ActivityDefinition activityDefinition, String patientId, String practitionerId, String organizationId, RequestDetails theRequest) throws FHIRException {
    Resource result = newResource(activityDefinition.getKind().toCode());
    switch(result.fhirType()) {
        case "ServiceRequest":
            result = resolveServiceRequest(activityDefinition, patientId, practitionerId, organizationId);
            break;
        case "MedicationRequest":
            result = resolveMedicationRequest(activityDefinition, patientId);
            break;
        case "SupplyRequest":
            result = resolveSupplyRequest(activityDefinition, practitionerId, organizationId);
            break;
        case "Procedure":
            result = resolveProcedure(activityDefinition, patientId);
            break;
        case "DiagnosticReport":
            result = resolveDiagnosticReport(activityDefinition, patientId);
            break;
        case "Communication":
            result = resolveCommunication(activityDefinition, patientId);
            break;
        case "CommunicationRequest":
            result = resolveCommunicationRequest(activityDefinition, patientId);
            break;
        case "Task":
            result = resolveTask(activityDefinition, patientId);
            break;
    }
    for (ActivityDefinition.ActivityDefinitionDynamicValueComponent dynamicValue : activityDefinition.getDynamicValue()) {
        // ActivityDefinition apply operation does not fail.
        try {
            if (dynamicValue.getExpression() != null) {
                // Special case for setting a Patient reference
                if ("Patient".equals(dynamicValue.getExpression().getExpression())) {
                    this.modelResolver.setValue(result, dynamicValue.getPath(), new Reference(patientId));
                } else {
                    /*
						 * TODO: Passing the activityDefinition as context here because that's what will
						 * have the libraries, but perhaps the "context" here should be the result
						 * resource?
						 */
                    Object value = expressionEvaluation.evaluateInContext(activityDefinition, dynamicValue.getExpression().getExpression(), patientId, theRequest);
                    if (value != null) {
                        logger.debug("dynamicValue value: {}", value);
                        if (value instanceof Boolean) {
                            value = new BooleanType((Boolean) value);
                        } else if (value instanceof DateTime) {
                            value = Date.from(((DateTime) value).getDateTime().toInstant());
                        } else if (value instanceof String) {
                            value = new StringType((String) value);
                        }
                        this.modelResolver.setValue(result, dynamicValue.getPath(), value);
                    } else {
                        logger.warn("WARNING: ActivityDefinition has null value for path: {}", dynamicValue.getPath());
                    }
                }
            }
        } catch (Exception e) {
            logger.error("ERROR: ActivityDefinition dynamicValue {} could not be applied and threw exception {}", dynamicValue.getPath(), e.toString());
            logger.error(e.toString());
        }
    }
    return result;
}