use of org.hl7.fhir.r4b.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;
}
use of org.hl7.fhir.r4b.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;
}
use of org.hl7.fhir.r4b.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());
}
use of org.hl7.fhir.r4b.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;
}
use of org.hl7.fhir.r4b.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()));
}
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