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

Example 1 with Reference

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

the class AppointmentResourceProvider method updateAppointment.

@Update
public MethodOutcome updateAppointment(@IdParam IdType appointmentId, @ResourceParam Appointment appointment) {
    MethodOutcome methodOutcome = new MethodOutcome();
    OperationOutcome operationalOutcome = new OperationOutcome();
    AppointmentDetail appointmentDetail = appointmentResourceConverterToAppointmentDetail(appointment);
    // URL ID and Resource ID must be the same
    if (!Objects.equals(appointmentId.getIdPartAsLong(), appointmentDetail.getId())) {
        operationalOutcome.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics("Id in URL (" + appointmentId.getIdPart() + ") should match Id in Resource (" + appointmentDetail.getId() + ")");
        methodOutcome.setOperationOutcome(operationalOutcome);
        return methodOutcome;
    }
    // Make sure there is an existing appointment to be amended
    AppointmentDetail oldAppointmentDetail = appointmentSearch.findAppointmentByID(appointmentId.getIdPartAsLong());
    if (oldAppointmentDetail == null) {
        operationalOutcome.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics("No appointment details found for ID: " + appointmentId.getIdPart());
        methodOutcome.setOperationOutcome(operationalOutcome);
        return methodOutcome;
    }
    String oldAppointmentVersionId = String.valueOf(oldAppointmentDetail.getLastUpdated().getTime());
    String newAppointmentVersionId = appointmentId.getVersionIdPart();
    if (newAppointmentVersionId != null && !newAppointmentVersionId.equalsIgnoreCase(oldAppointmentVersionId)) {
        throw new ResourceVersionConflictException("The specified version (" + newAppointmentVersionId + ") did not match the current resource version (" + oldAppointmentVersionId + ")");
    }
    // Determin if it is a cancel or an amend
    if (appointmentDetail.getCancellationReason() != null) {
        if (appointmentDetail.getCancellationReason().isEmpty()) {
            operationalOutcome.addIssue().setSeverity(IssueSeverity.ERROR).setDiagnostics("The cancellation reason can not be blank");
            methodOutcome.setOperationOutcome(operationalOutcome);
            return methodOutcome;
        }
        // This is a Cancellation - so copy across fields which can be
        // altered
        boolean cancelComparisonResult = compareAppointmentsForInvalidPropertyCancel(oldAppointmentDetail, appointmentDetail);
        if (cancelComparisonResult) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnclassifiedServerFailureException(400, "Invalid Appointment property has been amended (cancellation)"), SystemCode.BAD_REQUEST, IssueType.FORBIDDEN);
        }
        oldAppointmentDetail.setCancellationReason(appointmentDetail.getCancellationReason());
        String oldStatus = oldAppointmentDetail.getStatus();
        appointmentDetail = oldAppointmentDetail;
        appointmentDetail.setStatus("cancelled");
        if (!"cancelled".equalsIgnoreCase(oldStatus)) {
            for (Long slotId : appointmentDetail.getSlotIds()) {
                SlotDetail slotDetail = slotSearch.findSlotByID(slotId);
                // slotDetail.setAppointmentId(null);
                slotDetail.setFreeBusyType("FREE");
                slotDetail.setLastUpdated(new Date());
                slotStore.saveSlot(slotDetail);
            }
        }
    } else {
        if (appointment.getStatus().equals("cancelled")) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnclassifiedServerFailureException(400, "Appointment has been cancelled and cannot be amended"), SystemCode.BAD_REQUEST, IssueType.FORBIDDEN);
        }
        boolean amendComparisonResult = compareAppointmentsForInvalidPropertyAmend(appointmentDetail, oldAppointmentDetail);
        if (amendComparisonResult) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnclassifiedServerFailureException(403, "Invalid Appointment property has been amended"), SystemCode.BAD_REQUEST, IssueType.FORBIDDEN);
        }
        // This is an Amend
        oldAppointmentDetail.setComment(appointmentDetail.getComment());
        oldAppointmentDetail.setReasonCode(appointmentDetail.getReasonCode());
        oldAppointmentDetail.setDescription(appointmentDetail.getDescription());
        oldAppointmentDetail.setReasonDisplay(appointmentDetail.getReasonDisplay());
        oldAppointmentDetail.setTypeCode(appointmentDetail.getTypeCode());
        oldAppointmentDetail.setTypeDisplay(appointmentDetail.getTypeDisplay());
        appointmentDetail = oldAppointmentDetail;
    }
    List<SlotDetail> slots = new ArrayList<>();
    for (Long slotId : appointmentDetail.getSlotIds()) {
        SlotDetail slotDetail = slotSearch.findSlotByID(slotId);
        if (slotDetail == null) {
            throw new UnprocessableEntityException("Slot resource reference is not a valid resource");
        }
        slots.add(slotDetail);
    }
    // Update version and
    appointmentDetail.setLastUpdated(new Date());
    // lastUpdated timestamp
    appointmentDetail = appointmentStore.saveAppointment(appointmentDetail, slots);
    methodOutcome.setId(new IdDt("Appointment", appointmentDetail.getId()));
    methodOutcome.setResource(appointmentDetailToAppointmentResourceConverter(appointmentDetail));
    return methodOutcome;
}

Example 2 with Reference

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

the class MedicationAdministrationResourceProvider method getMedicationAdministrationsForPatientId.

@Search
public List<MedicationAdministration> getMedicationAdministrationsForPatientId(@RequiredParam(name = "patient") String patientId) {
    ArrayList<MedicationAdministration> medicationAdministrations = new ArrayList<>();
    List<MedicationAdministrationDetail> medicationAdministrationDetailList = medicationAdministrationSearch.findMedicationAdministrationForPatient(Long.parseLong(patientId));
    if (medicationAdministrationDetailList != null && !medicationAdministrationDetailList.isEmpty()) {
        for (MedicationAdministrationDetail medicationAdministrationDetail : medicationAdministrationDetailList) {
            MedicationAdministration medicationAdministration = new MedicationAdministration();
            String resourceId = String.valueOf(medicationAdministrationDetail.getId());
            String versionId = String.valueOf(medicationAdministrationDetail.getLastUpdated().getTime());
            String resourceType = medicationAdministration.getResourceType().toString();
            IdType id = new IdType(resourceType, resourceId, versionId);
            medicationAdministration.setId(id);
            medicationAdministration.getMeta().setVersionId(versionId);
            medicationAdministration.getMeta().setLastUpdated(medicationAdministrationDetail.getLastUpdated());
            medicationAdministration.addDefinition(new Reference("Patient/" + medicationAdministrationDetail.getPatientId()));
            medicationAdministration.addDefinition(new Reference("Practitioner/" + medicationAdministrationDetail.getPractitionerId()));
            medicationAdministration.setPrescription(new Reference("MedicationOrder/" + medicationAdministrationDetail.getPrescriptionId()));
            medicationAdministration.setEffective(new DateType(medicationAdministrationDetail.getAdministrationDate()));
            medicationAdministration.setMedication(new Reference("Medication/" + medicationAdministrationDetail.getMedicationId()));
            medicationAdministrations.add(medicationAdministration);
        }
    }
    return medicationAdministrations;
}

Example 3 with Reference

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

the class MedicationOrderResourceProvider method medicationOrderDetailsToMedicationOrderResourceConverter.

private MedicationRequest medicationOrderDetailsToMedicationOrderResourceConverter(MedicationOrderDetails medicationOrderDetails) {
    MedicationRequest medicationOrder = new MedicationRequest();
    String resourceId = String.valueOf(medicationOrderDetails.getId());
    String versionId = String.valueOf(medicationOrderDetails.getLastUpdated().getTime());
    String resourceType = medicationOrder.getResourceType().toString();
    IdType id = new IdType(resourceType, resourceId, versionId);
    medicationOrder.setId(id);
    medicationOrder.getMeta().setVersionId(versionId);
    medicationOrder.getMeta().setLastUpdated(medicationOrderDetails.getLastUpdated());
    switch(medicationOrderDetails.getOrderStatus().toLowerCase(Locale.UK)) {
        case "active":
            medicationOrder.setStatus(MedicationRequestStatus.ACTIVE);
            break;
        case "completed":
            medicationOrder.setStatus(MedicationRequestStatus.COMPLETED);
            break;
        case "draft":
            medicationOrder.setStatus(MedicationRequestStatus.DRAFT);
            break;
        case "entered_in_error":
            medicationOrder.setStatus(MedicationRequestStatus.ENTEREDINERROR);
            break;
        case "on_hold":
            medicationOrder.setStatus(MedicationRequestStatus.ONHOLD);
            break;
        case "stopped":
            medicationOrder.setStatus(MedicationRequestStatus.STOPPED);
            break;
    }
    if (medicationOrderDetails.getPatientId() != null) {
        medicationOrder.setSubject(new Reference("Patient/" + medicationOrderDetails.getPatientId()));
    } else {
        medicationOrder.setSubject(new Reference());
    }
    medicationOrder.setRecorder(new Reference("Practitioner/" + medicationOrderDetails.getAutherId()));
    medicationOrder.setMedication(new Reference("Medication/" + medicationOrderDetails.getMedicationId()));
    medicationOrder.addDosageInstruction().setText(medicationOrderDetails.getDosageText());
    MedicationRequestDispenseRequestComponent dispenseRequest = new MedicationRequestDispenseRequestComponent();
    dispenseRequest.addExtension(new Extension(SystemURL.SD_EXTENSION_MEDICATION_QUANTITY_TEXT, new StringDt(medicationOrderDetails.getDispenseQuantityText())));
    dispenseRequest.addExtension(new Extension(SystemURL.SD_EXTENSION_PERSCRIPTION_REPEAT_REVIEW_DATE, new DateTimeDt(medicationOrderDetails.getDispenseReviewDate())));
    dispenseRequest.setId("Medication/" + medicationOrderDetails.getDispenseMedicationId());
    dispenseRequest.setNumberOfRepeatsAllowed(medicationOrderDetails.getDispenseRepeatsAllowed());
    medicationOrder.setDispenseRequest(dispenseRequest);
    return medicationOrder;
}

Example 4 with Reference

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

the class PatientResourceProvider method setStaticPatientData.

private Patient setStaticPatientData(Patient patient) {
    patient.setLanguage(("en-GB"));
    patient.addExtension(createCodingExtension("CG", "Greek Cypriot", SystemURL.CS_CC_ETHNIC_CATEGORY, SystemURL.SD_CC_EXT_ETHNIC_CATEGORY));
    patient.addExtension(createCodingExtension("SomeSnomedCode", "Some Snomed Code", SystemURL.CS_CC_RELIGIOUS_AFFILI, SystemURL.SD_CC_EXT_RELIGIOUS_AFFILI));
    patient.addExtension(new Extension(SystemURL.SD_PATIENT_CADAVERIC_DON, new BooleanType(false)));
    patient.addExtension(createCodingExtension("H", "UK Resident", SystemURL.CS_CC_RESIDENTIAL_STATUS, SystemURL.SD_CC_EXT_RESIDENTIAL_STATUS));
    patient.addExtension(createCodingExtension("3", "To pay hotel fees only", SystemURL.CS_CC_TREATMENT_CAT, SystemURL.SD_CC_EXT_TREATMENT_CAT));
    Extension nhsCommExtension = new Extension();
    nhsCommExtension.setUrl(SystemURL.SD_CC_EXT_NHS_COMMUNICATION);
    nhsCommExtension.addExtension(createCodingExtension("en", "English", SystemURL.CS_CC_HUMAN_LANG, SystemURL.SD_CC_EXT_COMM_LANGUAGE));
    nhsCommExtension.addExtension(new Extension(SystemURL.SD_CC_COMM_PREFERRED, new BooleanType(false)));
    nhsCommExtension.addExtension(createCodingExtension("RWR", "Received written", SystemURL.CS_CC_LANG_ABILITY_MODE, SystemURL.SD_CC_MODE_OF_COMM));
    nhsCommExtension.addExtension(createCodingExtension("E", "Excellent", SystemURL.CS_CC_LANG_ABILITY_PROFI, SystemURL.SD_CC_COMM_PROFICIENCY));
    nhsCommExtension.addExtension(new Extension(SystemURL.SD_CC_INTERPRETER_REQUIRED, new BooleanType(false)));
    patient.addExtension(nhsCommExtension);
    Identifier localIdentifier = new Identifier();
    localIdentifier.setUse(IdentifierUse.USUAL);
    localIdentifier.setSystem(SystemURL.ID_LOCAL_PATIENT_IDENTIFIER);
    localIdentifier.setValue("123456");
    CodeableConcept liType = new CodeableConcept();
    Coding liTypeCoding = new Coding();
    liTypeCoding.setCode("EN");
    liTypeCoding.setDisplay("Employer number");
    liTypeCoding.setSystem(SystemURL.VS_IDENTIFIER_TYPE);
    liType.addCoding(liTypeCoding);
    localIdentifier.setType(liType);
    localIdentifier.setAssigner(new Reference("Organization/1"));
    patient.addIdentifier(localIdentifier);
    Calendar calendar = Calendar.getInstance();
    calendar.set(2017, 1, 1);
    DateTimeDt endDate = new DateTimeDt(calendar.getTime());
    calendar.set(2016, 1, 1);
    DateTimeDt startDate = new DateTimeDt(calendar.getTime());
    Period pastPeriod = new Period().setStart(calendar.getTime()).setEnd(calendar.getTime());
    patient.addName().setFamily("AnotherOfficialFamilyName").addGiven("AnotherOfficialGivenName").setUse(NameUse.OFFICIAL).setPeriod(pastPeriod);
    patient.addName().setFamily("AdditionalFamily").addGiven("AdditionalGiven").setUse(NameUse.TEMP);
    patient.addTelecom(staticElHelper.getValidTelecom());
    patient.addAddress(staticElHelper.getValidAddress());
    return patient;
}

Example 5 with Reference

use of org.hl7.fhir.r5.model.Reference in project loinc2hpo by monarch-initiative.

the class ObservationAnalysisFromQnValue method getHPOforObservation.

@Override
public HpoTermId4LoincTest getHPOforObservation() throws ReferenceNotFoundException, AmbiguousReferenceException, UnrecognizedCodeException {
    HpoTermId4LoincTest hpoTermId4LoincTest = null;
    // find applicable reference range
    List<Observation.ObservationReferenceRangeComponent> references = this.references.stream().filter(p -> withinAgeRange(p)).collect(Collectors.toList());
    if (references.size() < 1) {
        throw new ReferenceNotFoundException();
    } else if (references.size() == 1) {
        Observation.ObservationReferenceRangeComponent targetReference = references.get(0);
        double low = targetReference.hasLow() ? targetReference.getLow().getValue().doubleValue() : Double.MIN_VALUE;
        double high = targetReference.hasHigh() ? targetReference.getHigh().getValue().doubleValue() : Double.MAX_VALUE;
        double observed = valueQuantity.getValue().doubleValue();
        Loinc2HPOCodedValue result;
        if (observed < low) {
            result = Loinc2HPOCodedValue.fromCode("L");
        } else if (observed > high) {
            result = Loinc2HPOCodedValue.fromCode("H");
        } else {
            result = Loinc2HPOCodedValue.fromCode("N");
        }
        Code resultCode = Code.getNewCode().setSystem(Loinc2HPOCodedValue.CODESYSTEM).setCode(result.toCode());
        hpoTermId4LoincTest = annotationMap.get(loincId).loincInterpretationToHPO(resultCode);
    } else if (references.size() == 2) {
        // what does it mean with multiple references
        throw new AmbiguousReferenceException();
    } else if (references.size() == 3) {
    // it can happen when there is actually one range but coded in three ranges
    // e.g. normal 20-30
    // in this case, one range ([20, 30]) is sufficient;
    // however, it is written as three ranges: ( , 20) [20, 30] (30, )
    // We should handle this case
    } else {
        throw new AmbiguousReferenceException();
    }
    // if we can still not find an answer, it is probably that we did not have the annotation
    if (hpoTermId4LoincTest == null)
        throw new UnrecognizedCodeException();
    return hpoTermId4LoincTest;
}