Examples with DateTimeType org.hl7.fhir.r5.model.DateTimeType used on opensource projects

Example 76 with DateTimeType

use of org.hl7.fhir.r5.model.DateTimeType in project gpconnect-demonstrator by nhsconnect.

the class StructuredAllergyIntoleranceBuilder method buildStructuredAllergyIntolerence.

public Bundle buildStructuredAllergyIntolerence(String NHS, Set<String> practitionerIds, Bundle bundle, Boolean includedResolved) {
    List<StructuredAllergyIntoleranceEntity> allergyData = structuredAllergySearch.getAllergyIntollerence(NHS);
    ListResource activeList = initiateListResource(NHS, ACTIVE_ALLERGIES_DISPLAY, allergyData);
    ListResource resolvedList = initiateListResource(NHS, RESOLVED_ALLERGIES_DISPLAY, allergyData);
    // This is patient 5 example 2 only
    if (allergyData.size() == 1 && allergyData.get(0).getClinicalStatus().equals(SystemConstants.NO_KNOWN)) {
        StructuredAllergyIntoleranceEntity noKnownAllergy = allergyData.get(0);
        // #214 had incorrect code and value for no known allergies
        CodeableConcept noKnownAllergies = createCoding(SystemURL.VS_LIST_EMPTY_REASON_CODE, NO_CONTENT_RECORDED, NO_CONTENT_RECORDED_DISPLAY);
        noKnownAllergies.setText("No Known Allergies");
        // activeList.setEmptyReason(noKnownAllergies);
        // see spec example 2 no known allergies positively asserted
        Reference patient = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyData.get(0).getPatientRef());
        String noKnownAllergyId = noKnownAllergy.getGuid();
        Reference allergyIntolerance = new Reference("AllergyIntolerance/" + noKnownAllergyId);
        Resource noKnownAllergyResource = createNoKnownAllergy(noKnownAllergy);
        activeList.setSubject(patient);
        // reference to AllergyIntolerance item
        activeList.addEntry().setItem(allergyIntolerance);
        activeList.setOrderedBy(createCoding(SystemURL.CS_LIST_ORDER, "event-date", "Sorted by Event Date"));
        bundle.addEntry().setResource(activeList);
        bundle.addEntry().setResource(noKnownAllergyResource);
        if (includedResolved) {
            resolvedList.setSubject(patient);
            resolvedList.setEmptyReason(noKnownAllergies);
            bundle.addEntry().setResource(resolvedList);
        }
        return bundle;
    }
    for (StructuredAllergyIntoleranceEntity allergyIntoleranceEntity : allergyData) {
        AllergyIntolerance allergyIntolerance = new AllergyIntolerance();
        allergyIntolerance.setOnset(new DateTimeType(allergyIntoleranceEntity.getOnSetDateTime()));
        allergyIntolerance.setMeta(createMeta(SystemURL.SD_CC_ALLERGY_INTOLERANCE));
        allergyIntolerance.setId(allergyIntoleranceEntity.getId().toString());
        List<Identifier> identifiers = new ArrayList<>();
        Identifier identifier1 = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(allergyIntoleranceEntity.getGuid());
        identifiers.add(identifier1);
        allergyIntolerance.setIdentifier(identifiers);
        if (allergyIntoleranceEntity.getClinicalStatus().equals(SystemConstants.ACTIVE)) {
            allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
        } else {
            allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.RESOLVED);
        }
        if (allergyIntoleranceEntity.getCategory().equals(SystemConstants.MEDICATION)) {
            allergyIntolerance.addCategory(AllergyIntoleranceCategory.MEDICATION);
        } else {
            allergyIntolerance.addCategory(AllergyIntoleranceCategory.ENVIRONMENT);
        }
        allergyIntolerance.setVerificationStatus(AllergyIntoleranceVerificationStatus.UNCONFIRMED);
        // CODE
        codeableConceptBuilder.addConceptCode(SystemConstants.SNOMED_URL, allergyIntoleranceEntity.getConceptCode(), allergyIntoleranceEntity.getConceptDisplay()).addDescription(allergyIntoleranceEntity.getDescCode(), allergyIntoleranceEntity.getDescDisplay()).addTranslation(allergyIntoleranceEntity.getCodeTranslationRef());
        allergyIntolerance.setCode(codeableConceptBuilder.build());
        codeableConceptBuilder.clear();
        allergyIntolerance.setAssertedDate(allergyIntoleranceEntity.getAssertedDate());
        Reference patient = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyIntoleranceEntity.getPatientRef());
        allergyIntolerance.setPatient(patient);
        Annotation noteAnnotation = new Annotation(new StringType(allergyIntoleranceEntity.getNote()));
        allergyIntolerance.setNote(Collections.singletonList(noteAnnotation));
        AllergyIntoleranceReactionComponent reaction = new AllergyIntoleranceReactionComponent();
        // MANIFESTATION
        List<CodeableConcept> theManifestation = new ArrayList<>();
        codeableConceptBuilder.addConceptCode(SystemConstants.SNOMED_URL, allergyIntoleranceEntity.getManifestationCoding(), allergyIntoleranceEntity.getManifestationDisplay()).addDescription(allergyIntoleranceEntity.getManifestationDescCoding(), allergyIntoleranceEntity.getManifestationDescDisplay()).addTranslation(allergyIntoleranceEntity.getManTranslationRef());
        theManifestation.add(codeableConceptBuilder.build());
        codeableConceptBuilder.clear();
        reaction.setManifestation(theManifestation);
        reaction.setDescription(allergyIntoleranceEntity.getNote());
        // SEVERITY
        try {
            reaction.setSeverity(AllergyIntoleranceSeverity.fromCode(allergyIntoleranceEntity.getSeverity()));
        } catch (FHIRException e) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Unknown severity: " + allergyIntoleranceEntity.getSeverity()), SystemCode.INVALID_RESOURCE, IssueType.INVALID);
        }
        // EXPOSURE
        CodeableConcept exposureRoute = new CodeableConcept();
        reaction.setExposureRoute(exposureRoute);
        allergyIntolerance.addReaction(reaction);
        // RECORDER
        final Reference refValue = new Reference();
        final Identifier identifier = new Identifier();
        final String recorder = allergyIntoleranceEntity.getRecorder();
        // This is just an example to demonstrate using Reference element instead of Identifier element
        if (recorder.equals(patient2NhsNo.trim())) {
            Reference rec = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyIntoleranceEntity.getPatientRef());
            allergyIntolerance.setRecorder(rec);
        } else if (patientRepository.findByNhsNumber(recorder) != null) {
            identifier.setSystem(SystemURL.ID_NHS_NUMBER);
            identifier.setValue(recorder);
            refValue.setIdentifier(identifier);
            allergyIntolerance.setRecorder(refValue);
        } else if (practitionerSearch.findPractitionerByUserId(recorder) != null) {
            refValue.setReference("Practitioner/" + recorder);
            allergyIntolerance.setRecorder(refValue);
            practitionerIds.add(recorder);
        }
        // CLINICAL STATUS
        List<Extension> extensions = new ArrayList<>();
        if (allergyIntolerance.getClinicalStatus().getDisplay().contains("Active")) {
            listResourceBuilder(activeList, allergyIntolerance, false);
            bundle.addEntry().setResource(allergyIntolerance);
        } else if (allergyIntolerance.getClinicalStatus().getDisplay().equals("Resolved") && includedResolved.equals(true)) {
            listResourceBuilder(resolvedList, allergyIntolerance, true);
            allergyIntolerance.setLastOccurrence(allergyIntoleranceEntity.getEndDate());
            final Extension allergyEndExtension = createAllergyEndExtension(allergyIntoleranceEntity);
            extensions.add(allergyEndExtension);
        }
        if (!extensions.isEmpty()) {
            allergyIntolerance.setExtension(extensions);
        }
        // ASSERTER
        Reference asserter = allergyIntolerance.getAsserter();
        if (asserter != null && asserter.getReference() != null && asserter.getReference().startsWith("Practitioner")) {
            String[] split = asserter.getReference().split("/");
            practitionerIds.add(split[1]);
        }
    }
    if (!activeList.hasEntry()) {
        addEmptyListNote(activeList);
        addEmptyReasonCode(activeList);
    }
    bundle.addEntry().setResource(activeList);
    if (includedResolved && !resolvedList.hasEntry()) {
        addEmptyListNote(resolvedList);
        addEmptyReasonCode(resolvedList);
    }
    if (includedResolved) {
        bundle.addEntry().setResource(resolvedList);
    }
    return bundle;
}

Example 77 with DateTimeType

use of org.hl7.fhir.r5.model.DateTimeType in project gpconnect-demonstrator by nhsconnect.

the class PatientResourceProvider method patientDetailsToMinimalPatient.

private Patient patientDetailsToMinimalPatient(PatientDetails patientDetails) throws FHIRException {
    Patient patient = new Patient();
    Date lastUpdated = patientDetails.getLastUpdated() == null ? new Date() : patientDetails.getLastUpdated();
    String resourceId = String.valueOf(patientDetails.getId());
    String versionId = String.valueOf(lastUpdated.getTime());
    String resourceType = patient.getResourceType().toString();
    IdType id = new IdType(resourceType, resourceId, versionId);
    patient.setId(id);
    patient.getMeta().setVersionId(versionId);
    patient.getMeta().setLastUpdated(lastUpdated);
    patient.getMeta().addProfile(SystemURL.SD_GPC_PATIENT);
    Identifier patientNhsNumber = new Identifier().setSystem(SystemURL.ID_NHS_NUMBER).setValue(patientDetails.getNhsNumber());
    Extension extension = createCodingExtension("01", "Number present and verified", SystemURL.CS_CC_NHS_NUMBER_VERIF, SystemURL.SD_CC_EXT_NHS_NUMBER_VERIF);
    patientNhsNumber.addExtension(extension);
    patient.addIdentifier(patientNhsNumber);
    patient.setBirthDate(patientDetails.getDateOfBirth());
    String gender = patientDetails.getGender();
    if (gender != null) {
        patient.setGender(AdministrativeGender.fromCode(gender.toLowerCase(Locale.UK)));
    }
    Date registrationEndDateTime = patientDetails.getRegistrationEndDateTime();
    Date registrationStartDateTime = patientDetails.getRegistrationStartDateTime();
    Extension regDetailsExtension = new Extension(SystemURL.SD_EXTENSION_CC_REG_DETAILS);
    Period registrationPeriod = new Period().setStart(registrationStartDateTime).setEnd(registrationEndDateTime);
    Extension regPeriodExt = new Extension(SystemURL.SD_CC_EXT_REGISTRATION_PERIOD, registrationPeriod);
    regDetailsExtension.addExtension(regPeriodExt);
    String registrationStatusValue = patientDetails.getRegistrationStatus();
    patient.setActive(ACTIVE_REGISTRATION_STATUS.equals(registrationStatusValue) || null == registrationStatusValue);
    String registrationTypeValue = patientDetails.getRegistrationType();
    if (registrationTypeValue != null) {
        Coding regTypeCode = new Coding();
        regTypeCode.setCode(registrationTypeValue);
        // Should always be Temporary
        regTypeCode.setDisplay("Temporary");
        regTypeCode.setSystem(SystemURL.CS_REGISTRATION_TYPE);
        CodeableConcept regTypeConcept = new CodeableConcept();
        regTypeConcept.addCoding(regTypeCode);
        Extension regTypeExt = new Extension(SystemURL.SD_CC_EXT_REGISTRATION_TYPE, regTypeConcept);
        regDetailsExtension.addExtension(regTypeExt);
    }
    patient.addExtension(regDetailsExtension);
    String maritalStatus = patientDetails.getMaritalStatus();
    if (maritalStatus != null) {
        CodeableConcept marital = new CodeableConcept();
        Coding maritalCoding = new Coding();
        maritalCoding.setSystem(SystemURL.VS_CC_MARITAL_STATUS);
        maritalCoding.setCode(patientDetails.getMaritalStatus());
        maritalCoding.setDisplay("Married");
        marital.addCoding(maritalCoding);
        patient.setMaritalStatus(marital);
    }
    patient.setMultipleBirth(patientDetails.isMultipleBirth());
    if (patientDetails.isDeceased()) {
        DateTimeType decesed = new DateTimeType(patientDetails.getDeceased());
        patient.setDeceased(decesed);
    }
    return patient;
}

Example 78 with DateTimeType

use of org.hl7.fhir.r5.model.DateTimeType in project hapi-fhir-jpaserver-starter by hapifhir.

the class ElasticsearchLastNR4IT method testLastN.

@Test
void testLastN() throws IOException, InterruptedException {
    Thread.sleep(2000);
    Patient pt = new Patient();
    pt.addName().setFamily("Lastn").addGiven("Arthur");
    IIdType id = ourClient.create().resource(pt).execute().getId().toUnqualifiedVersionless();
    Observation obs = new Observation();
    obs.getSubject().setReferenceElement(id);
    String observationCode = "testobservationcode";
    String codeSystem = "http://testobservationcodesystem";
    obs.getCode().addCoding().setCode(observationCode).setSystem(codeSystem);
    obs.setValue(new StringType(observationCode));
    Date effectiveDtm = new GregorianCalendar().getTime();
    obs.setEffective(new DateTimeType(effectiveDtm));
    obs.getCategoryFirstRep().addCoding().setCode("testcategorycode").setSystem("http://testcategorycodesystem");
    IIdType obsId = ourClient.create().resource(obs).execute().getId().toUnqualifiedVersionless();
    myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
    Parameters output = ourClient.operation().onType(Observation.class).named("lastn").withParameter(Parameters.class, "max", new IntegerType(1)).andParameter("subject", new StringType("Patient/" + id.getIdPart())).execute();
    Bundle b = (Bundle) output.getParameter().get(0).getResource();
    assertEquals(1, b.getTotal());
    assertEquals(obsId, b.getEntry().get(0).getResource().getIdElement().toUnqualifiedVersionless());
}

Example 79 with DateTimeType

use of org.hl7.fhir.r5.model.DateTimeType in project synthea by synthetichealth.

the class FhirStu3 method medicationAdministration.

/**
 * Add a MedicationAdministration if needed for the given medication.
 *
 * @param rand Source of randomness to use when generating ids etc
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication, MedicationRequest medicationRequest) {
    MedicationAdministration medicationResource = new MedicationAdministration();
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    medicationResource.setEffective(new DateTimeType(new Date(medication.start)));
    medicationResource.setStatus(MedicationAdministrationStatus.fromCode("completed"));
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        MedicationAdministrationDosageComponent dosage = new MedicationAdministrationDosageComponent();
        // as_needed is true if present
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            dosage.setDose((SimpleQuantity) dose);
            if (rxInfo.has("instructions")) {
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    dosage.setText(instruction.get("display").getAsString());
                }
            }
        }
        medicationResource.setDosage(dosage);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            if (entry.getResource().fhirType().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                Coding coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.addReasonReference().setReference(entry.getFullUrl());
                }
            }
        }
    }
    BundleEntryComponent medicationAdminEntry = newEntry(rand, bundle, medicationResource);
    return medicationAdminEntry;
}

Example 80 with DateTimeType

use of org.hl7.fhir.r5.model.DateTimeType in project clinical_quality_language by cqframework.

the class DataRequirementsProcessor method toFhirValue.

private DataType toFhirValue(ElmRequirementsContext context, Expression value) {
    if (value == null) {
        return null;
    }
    if (value instanceof Interval) {
        // TODO: Handle lowclosed/highclosed
        return new Period().setStartElement(toFhirDateTimeValue(context, ((Interval) value).getLow())).setEndElement(toFhirDateTimeValue(context, ((Interval) value).getHigh()));
    } else if (value instanceof Literal) {
        if (context.getTypeResolver().isDateTimeType(value.getResultType())) {
            return new DateTimeType(((Literal) value).getValue());
        } else if (context.getTypeResolver().isDateType(value.getResultType())) {
            return new DateType(((Literal) value).getValue());
        } else if (context.getTypeResolver().isIntegerType(value.getResultType())) {
            return new IntegerType(((Literal) value).getValue());
        } else if (context.getTypeResolver().isDecimalType(value.getResultType())) {
            return new DecimalType(((Literal) value).getValue());
        } else if (context.getTypeResolver().isStringType(value.getResultType())) {
            return new StringType(((Literal) value).getValue());
        }
    } else if (value instanceof DateTime) {
        DateTime dateTime = (DateTime) value;
        return new DateTimeType(toDateTimeString(toFhirValue(context, dateTime.getYear()), toFhirValue(context, dateTime.getMonth()), toFhirValue(context, dateTime.getDay()), toFhirValue(context, dateTime.getHour()), toFhirValue(context, dateTime.getMinute()), toFhirValue(context, dateTime.getSecond()), toFhirValue(context, dateTime.getMillisecond()), toFhirValue(context, dateTime.getTimezoneOffset())));
    } else if (value instanceof org.hl7.elm.r1.Date) {
        org.hl7.elm.r1.Date date = (org.hl7.elm.r1.Date) value;
        return new DateType(toDateString(toFhirValue(context, date.getYear()), toFhirValue(context, date.getMonth()), toFhirValue(context, date.getDay())));
    } else if (value instanceof Start) {
        DataType operand = toFhirValue(context, ((Start) value).getOperand());
        if (operand != null) {
            Period period = (Period) operand;
            return period.getStartElement();
        }
    } else if (value instanceof End) {
        DataType operand = toFhirValue(context, ((End) value).getOperand());
        if (operand != null) {
            Period period = (Period) operand;
            return period.getEndElement();
        }
    } else if (value instanceof ParameterRef) {
        if (context.getTypeResolver().isIntervalType(value.getResultType())) {
            Extension e = toExpression(context, (ParameterRef) value);
            org.hl7.cql.model.DataType pointType = ((IntervalType) value.getResultType()).getPointType();
            if (context.getTypeResolver().isDateTimeType(pointType) || context.getTypeResolver().isDateType(pointType)) {
                Period period = new Period();
                period.addExtension(e);
                return period;
            } else if (context.getTypeResolver().isQuantityType(pointType) || context.getTypeResolver().isIntegerType(pointType) || context.getTypeResolver().isDecimalType(pointType)) {
                Range range = new Range();
                range.addExtension(e);
                return range;
            } else {
                throw new IllegalArgumentException(String.format("toFhirValue not implemented for interval of %s", pointType.toString()));
            }
        } else // Boolean, Integer, Decimal, String, Quantity, Date, DateTime, Time, Coding, CodeableConcept
        if (context.getTypeResolver().isBooleanType(value.getResultType())) {
            BooleanType result = new BooleanType();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isIntegerType(value.getResultType())) {
            IntegerType result = new IntegerType();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isDecimalType(value.getResultType())) {
            DecimalType result = new DecimalType();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isQuantityType(value.getResultType())) {
            Quantity result = new Quantity();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isCodeType(value.getResultType())) {
            Coding result = new Coding();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isConceptType(value.getResultType())) {
            CodeableConcept result = new CodeableConcept();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isDateType(value.getResultType())) {
            DateType result = new DateType();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isDateTimeType(value.getResultType())) {
            DateTimeType result = new DateTimeType();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else if (context.getTypeResolver().isTimeType(value.getResultType())) {
            TimeType result = new TimeType();
            result.addExtension(toExpression(context, (ParameterRef) value));
            return result;
        } else {
            throw new IllegalArgumentException(String.format("toFhirValue not implemented for parameter of type %s", value.getResultType().toString()));
        }
    }
    throw new IllegalArgumentException(String.format("toFhirValue not implemented for %s", value.getClass().getSimpleName()));
}