use of org.hl7.fhir.dstu3.model.Extension in project gpconnect-demonstrator by nhsconnect.
the class SlotResourceProvider method slotDetailToSlotResourceConverter.
private Slot slotDetailToSlotResourceConverter(SlotDetail slotDetail) {
Slot slot = new Slot();
Date lastUpdated = slotDetail.getLastUpdated() == null ? new Date() : slotDetail.getLastUpdated();
String resourceId = String.valueOf(slotDetail.getId());
String versionId = String.valueOf(lastUpdated.getTime());
IdType id = new IdType(resourceId);
slot.setId(id);
slot.getMeta().setVersionId(versionId);
slot.getMeta().addProfile(SystemURL.SD_GPC_SLOT);
slot.setSchedule(new Reference("Schedule/" + slotDetail.getScheduleReference()));
slot.setStart(slotDetail.getStartDateTime());
slot.setEnd(slotDetail.getEndDateTime());
// #218 Date time formats
slot.getStartElement().setPrecision(TemporalPrecisionEnum.SECOND);
slot.getEndElement().setPrecision(TemporalPrecisionEnum.SECOND);
switch(slotDetail.getFreeBusyType().toLowerCase(Locale.UK)) {
case "free":
slot.setStatus(SlotStatus.FREE);
break;
default:
slot.setStatus(SlotStatus.BUSY);
break;
}
String deliveryChannelCode = slotDetail.getDeliveryChannelCode();
ArrayList<Extension> al = new ArrayList<>();
if (deliveryChannelCode != null && !deliveryChannelCode.trim().isEmpty()) {
Extension deliveryChannelExtension = new Extension(SystemURL.SD_EXTENSION_GPC_DELIVERY_CHANNEL, new CodeType(deliveryChannelCode));
al.add(deliveryChannelExtension);
}
slot.setExtension(al);
// 1.2.7 add slot type description as service type
slot.addServiceType(new CodeableConcept().setText(slotDetail.getTypeDisply()));
return slot;
}
use of org.hl7.fhir.dstu3.model.Extension in project gpconnect-demonstrator by nhsconnect.
the class WarningCodeExtHelper method addWarningCodeExtensions.
/**
* confidential items are per record but the other two are global values per
* patient
*
* @param warningCodes
* @param list
* @param patientRepository
* @param medicationStatementRepository
* @param structuredAllergySearch
*/
public static void addWarningCodeExtensions(Set<String> warningCodes, ListResource list, PatientRepository patientRepository, MedicationStatementRepository medicationStatementRepository, StructuredAllergySearch structuredAllergySearch) {
String NHS = list.getSubject().getIdentifier().getValue();
PatientEntity patientEntity = patientRepository.findByNhsNumber(NHS);
List<MedicationStatementEntity> medicationStatements = medicationStatementRepository.findByPatientId(patientEntity.getId());
for (MedicationStatementEntity medicationStatement : medicationStatements) {
setFlags(medicationStatement.getWarningCode());
}
List<StructuredAllergyIntoleranceEntity> allergies = structuredAllergySearch.getAllergyIntollerence(NHS);
for (StructuredAllergyIntoleranceEntity allergy : allergies) {
setFlags(allergy.getWarningCode());
}
// check medication_statements for either of the global flags
if (dataInTransit) {
warningCodes.add(DATA_IN_TRANSIT);
}
if (dataAwaitingFiling) {
warningCodes.add(DATA_AWAITING_FILING);
}
StringBuilder sb = new StringBuilder();
warningCodes.forEach(warningCode -> {
if (warningCode != null) {
String warningCodeDisplay = "";
Annotation annotation = new Annotation();
switch(warningCode) {
case CONFIDENTIAL_ITEMS:
warningCodeDisplay = "Confidential Items";
// #266
annotation.setText(CONFIDENTIAL_ITEMS_NOTE);
// list.addNote(annotation);
sb.append("\r\n").append(annotation.getText());
break;
case DATA_IN_TRANSIT:
warningCodeDisplay = "Data in Transit";
Calendar cal = new GregorianCalendar();
Date now = new Date();
cal.setTime(now);
// a week before now
cal.add(Calendar.DAY_OF_YEAR, -7);
// #266
annotation.setText(String.format(DATA_IN_TRANSIT_NOTE, DATE_FORMAT.format(cal.getTime())));
// list.addNote(annotation);
sb.append("\r\n").append(annotation.getText());
break;
case DATA_AWAITING_FILING:
warningCodeDisplay = "Data Awaiting Filing";
// #266
annotation.setText(DATA_AWAITING_FILING_NOTE);
// list.addNote(annotation);
sb.append("\r\n").append(annotation.getText());
break;
default:
break;
}
// #182
Extension warningExt = new Extension(SystemURL.WARNING_CODE, new CodeType(warningCode));
list.addExtension(warningExt);
}
});
// cardinality of note 0..1 #266
if (sb.length() > 0) {
Annotation annotation = null;
if (list.getNote().size() > 0) {
annotation = list.getNote().get(0);
annotation.setText(annotation.getText());
annotation.setText(annotation.getText() + sb.toString());
} else {
annotation = new Annotation();
list.addNote(annotation);
annotation.setText(sb.toString().replaceFirst("^\r\n", ""));
}
}
}
use of org.hl7.fhir.dstu3.model.Extension in project gpconnect-demonstrator by nhsconnect.
the class MedicationStatementResourceProvider method getMedicationStatementResource.
public MedicationStatement getMedicationStatementResource(MedicationStatementDetail statementDetail) {
MedicationStatement medicationStatement = new MedicationStatement();
medicationStatement.setId(statementDetail.getId().toString());
List<Identifier> identifiers = new ArrayList<>();
Identifier identifier = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(statementDetail.getGuid());
identifiers.add(identifier);
medicationStatement.setIdentifier(identifiers);
medicationStatement.setMeta(new Meta().addProfile(SystemURL.SD_GPC_MEDICATION_STATEMENT));
medicationStatement.addExtension(new Extension(SystemURL.SD_CC_EXT_MEDICATION_STATEMENT_LAST_ISSUE, new DateTimeType(statementDetail.getLastIssueDate(), TemporalPrecisionEnum.DAY)));
if (statementDetail.getMedicationRequestPlanId() != null) {
medicationStatement.addBasedOn(new Reference(new IdType("MedicationRequest", statementDetail.getMedicationRequestPlanId())));
}
try {
medicationStatement.setStatus(MedicationStatementStatus.fromCode(statementDetail.getStatusCode()));
} catch (FHIRException e) {
throw new UnprocessableEntityException(e.getMessage());
}
if (statementDetail.getMedicationId() != null) {
medicationStatement.setMedication(new Reference(new IdType("Medication", statementDetail.getMedicationId())));
}
medicationStatement.setEffective(new Period().setStart(statementDetail.getStartDate()).setEnd(statementDetail.getEndDate()));
medicationStatement.setDateAsserted(statementDetail.getDateAsserted());
if (statementDetail.getPatientId() != null)
medicationStatement.setSubject(new Reference(new IdType("Patient", statementDetail.getPatientId())));
try {
medicationStatement.setTaken(statementDetail.getTakenCode() != null ? MedicationStatementTaken.fromCode(statementDetail.getTakenCode()) : MedicationStatementTaken.UNK);
} catch (FHIRException e) {
throw new UnprocessableEntityException(e.getMessage());
}
setReasonCodes(medicationStatement, statementDetail);
setNotes(medicationStatement, statementDetail);
String dosageText = statementDetail.getDosageText();
medicationStatement.addDosage(new Dosage().setText(dosageText == null || dosageText.trim().isEmpty() ? NO_INFORMATION_AVAILABLE : dosageText).setPatientInstruction(statementDetail.getDosagePatientInstruction()));
String prescribingAgency = statementDetail.getPrescribingAgency();
if (prescribingAgency != null && !prescribingAgency.trim().isEmpty()) {
String prescribingAgencyDisplay = "";
if (prescribingAgency.equalsIgnoreCase("prescribed-at-gp-practice")) {
prescribingAgencyDisplay = "Prescribed at GP practice";
} else if (prescribingAgency.equalsIgnoreCase("prescribed-by-another-organisation")) {
prescribingAgencyDisplay = "Prescribed by another organisation";
}
Coding coding = new Coding(SystemURL.CS_CC_PRESCRIBING_AGENCY_STU3, prescribingAgency, prescribingAgencyDisplay);
CodeableConcept codeableConcept = new CodeableConcept().addCoding(coding);
medicationStatement.addExtension(new Extension(SystemURL.SD_EXTENSION_CC_PRESCRIBING_AGENCY, codeableConcept));
}
// #281 1.2.5 add dosageLastChanged
Date dosageLastChanged = statementDetail.getDosageLastChanged();
if (dosageLastChanged != null) {
medicationStatement.addExtension(new Extension(SystemURL.SD_EXTENSION_CC_DOSAGE_LAST_CHANGED, new DateTimeType(dosageLastChanged)));
}
return medicationStatement;
}
use of org.hl7.fhir.dstu3.model.Extension 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.dstu3.model.Extension in project gpconnect-demonstrator by nhsconnect.
the class StructuredAllergyIntoleranceBuilder method createNoKnownAllergy.
/**
* This relates to the positively asserted this patient has no know
* allergies as opposed to the the negatively asserted no allergies recorded
* patient 5 example 2 from the spec
*
* @param allergyIntoleranceEntity object from the db
* @return the allergy intolerance resource
*/
private AllergyIntolerance createNoKnownAllergy(StructuredAllergyIntoleranceEntity allergyIntoleranceEntity) {
AllergyIntolerance allergyIntolerance = new AllergyIntolerance();
allergyIntolerance.setId(allergyIntoleranceEntity.getGuid());
allergyIntolerance.setAssertedDate(allergyIntoleranceEntity.getAssertedDate());
// db has clinical status of "no known" which is not a valid value
allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
allergyIntolerance.setVerificationStatus(AllergyIntoleranceVerificationStatus.valueOf(allergyIntoleranceEntity.getVerificationStatus().toUpperCase()));
allergyIntolerance.setType(AllergyIntoleranceType.ALLERGY);
CodeableConcept codeableConcept = new CodeableConcept();
Coding coding = new Coding();
coding.setDisplay(allergyIntoleranceEntity.getConceptDisplay());
// That's as in db under concept code 716186003
coding.setCode(allergyIntoleranceEntity.getConceptCode());
coding.setSystem(SystemConstants.SNOMED_URL);
Extension extension = new Extension(SystemURL.SD_EXT_SCT_DESC_ID);
// 3305010017
extension.addExtension("descriptionId", new StringType(allergyIntoleranceEntity.getDescCode()));
// NKA - No known allergy
extension.addExtension("descriptionDisplay", new StringType(allergyIntoleranceEntity.getDescDisplay()));
coding.addExtension(extension);
codeableConcept.addCoding(coding);
allergyIntolerance.setCode(codeableConcept);
return allergyIntolerance;
}
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