Examples with Reference org.hl7.fhir.r4.model.Reference used on opensource projects

Example 11 with Reference

use of org.hl7.fhir.r4.model.Reference in project gpconnect-demonstrator by nhsconnect.

the class PatientResourceProvider method StructuredRecordOperation.

@Operation(name = GET_STRUCTURED_RECORD_OPERATION_NAME)
public Bundle StructuredRecordOperation(@ResourceParam Parameters params) throws FHIRException {
    Bundle structuredBundle = new Bundle();
    Boolean getAllergies = false;
    Boolean includeResolved = false;
    Boolean getMedications = false;
    Boolean includePrescriptionIssues = false;
    Period medicationPeriod = null;
    String NHS = getNhsNumber(params);
    PatientDetails patientDetails = patientSearch.findPatient(NHS);
    // see https://nhsconnect.github.io/gpconnect/accessrecord_structured_development_retrieve_patient_record.html#error-handling
    if (patientDetails == null || patientDetails.isSensitive() || patientDetails.isDeceased() || !patientDetails.isActive()) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(new ResourceNotFoundException("No patient details found for patient ID: " + NHS), SystemCode.PATIENT_NOT_FOUND, IssueType.NOTFOUND);
    }
    if (NHS.equals(patientNoconsent)) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(new ForbiddenOperationException("No patient consent to share for patient ID: " + NHS), SystemCode.NO_PATIENT_CONSENT, IssueType.FORBIDDEN);
    }
    operationOutcome = null;
    for (ParametersParameterComponent param : params.getParameter()) {
        if (validateParametersName(param.getName())) {
            if (param.getName().equals(SystemConstants.INCLUDE_ALLERGIES)) {
                getAllergies = true;
                if (param.getPart().isEmpty()) {
                    // addWarningIssue(param, IssueType.REQUIRED, "Miss parameter part : " + SystemConstants.INCLUDE_RESOLVED_ALLERGIES);
                    throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Miss parameter : " + SystemConstants.INCLUDE_RESOLVED_ALLERGIES), SystemCode.INVALID_PARAMETER, IssueType.REQUIRED);
                }
                boolean includeResolvedParameterPartPresent = false;
                for (ParametersParameterComponent paramPart : param.getPart()) {
                    if (paramPart.getName().equals(SystemConstants.INCLUDE_RESOLVED_ALLERGIES)) {
                        if (paramPart.getValue() instanceof BooleanType) {
                            includeResolved = Boolean.valueOf(paramPart.getValue().primitiveValue());
                            includeResolvedParameterPartPresent = true;
                        } else {
                            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Miss parameter : " + SystemConstants.INCLUDE_RESOLVED_ALLERGIES), SystemCode.INVALID_PARAMETER, IssueType.REQUIRED);
                        }
                    } else {
                        addWarningIssue(param, paramPart, IssueType.NOTSUPPORTED);
                    // throw OperationOutcomeFactory.buildOperationOutcomeException(
                    // new UnprocessableEntityException("Incorrect parameter passed : " + paramPart.getName()),
                    // SystemCode.INVALID_PARAMETER, IssueType.INVALID);
                    }
                }
                if (!includeResolvedParameterPartPresent) {
                    throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Miss parameter : " + SystemConstants.INCLUDE_RESOLVED_ALLERGIES), SystemCode.INVALID_PARAMETER, IssueType.REQUIRED);
                }
            }
            if (param.getName().equals(SystemConstants.INCLUDE_MEDICATION)) {
                getMedications = true;
                boolean isIncludedPrescriptionIssuesExist = false;
                for (ParametersParameterComponent paramPart : param.getPart()) {
                    if (paramPart.getName().equals(SystemConstants.INCLUDE_PRESCRIPTION_ISSUES)) {
                        if (paramPart.getValue() instanceof BooleanType) {
                            includePrescriptionIssues = Boolean.valueOf(paramPart.getValue().primitiveValue());
                            isIncludedPrescriptionIssuesExist = true;
                        }
                    } else if (paramPart.getName().equals(SystemConstants.MEDICATION_SEARCH_FROM_DATE) && paramPart.getValue() instanceof DateType) {
                        DateType startDateDt = (DateType) paramPart.getValue();
                        medicationPeriod = new Period();
                        medicationPeriod.setStart(startDateDt.getValue());
                        medicationPeriod.setEnd(null);
                        String startDate = startDateDt.asStringValue();
                        if (!validateStartDateParamAndEndDateParam(startDate, null)) {
                        // addWarningIssue(param, paramPart, IssueType.INVALID, "Invalid date used");
                        }
                    } else {
                        addWarningIssue(param, paramPart, IssueType.NOTSUPPORTED);
                    // throw OperationOutcomeFactory.buildOperationOutcomeException(
                    // new UnprocessableEntityException("Incorrect parameter passed : " + paramPart.getName()),
                    // SystemCode.INVALID_PARAMETER, IssueType.INVALID);
                    }
                }
                if (!isIncludedPrescriptionIssuesExist) {
                    // # 1.2.6 now defaults to true if not provided
                    includePrescriptionIssues = true;
                }
            }
        } else {
            // invalid parameter
            addWarningIssue(param, IssueType.NOTSUPPORTED);
        }
    }
    // for parameter
    // Add Patient
    Patient patient = patientDetailsToPatientResourceConverter(patientDetails);
    if (patient.getIdentifierFirstRep().getValue().equals(NHS)) {
        structuredBundle.addEntry().setResource(patient);
    }
    // Organization from patient
    Set<String> orgIds = new HashSet<>();
    orgIds.add(patientDetails.getManagingOrganization());
    // Practitioner from patient
    Set<String> practitionerIds = new HashSet<>();
    List<Reference> practitionerReferenceList = patient.getGeneralPractitioner();
    practitionerReferenceList.forEach(practitionerReference -> {
        String[] pracRef = practitionerReference.getReference().split("/");
        if (pracRef.length > 1) {
            practitionerIds.add(pracRef[1]);
        }
    });
    if (getAllergies) {
        structuredBundle = structuredAllergyIntoleranceBuilder.buildStructuredAllergyIntolerence(NHS, practitionerIds, structuredBundle, includeResolved);
    }
    if (getMedications) {
        structuredBundle = populateMedicationBundle.addMedicationBundleEntries(structuredBundle, patientDetails, includePrescriptionIssues, medicationPeriod, practitionerIds, orgIds);
    }
    // Add all practitioners and practitioner roles
    for (String practitionerId : practitionerIds) {
        Practitioner pracResource = practitionerResourceProvider.getPractitionerById(new IdType(practitionerId));
        structuredBundle.addEntry().setResource(pracResource);
        List<PractitionerRole> practitionerRoleList = practitionerRoleResourceProvider.getPractitionerRoleByPracticionerId(new IdType(practitionerId));
        for (PractitionerRole role : practitionerRoleList) {
            String[] split = role.getOrganization().getReference().split("/");
            orgIds.add(split[1]);
            structuredBundle.addEntry().setResource(role);
        }
    }
    // Add all organizations
    for (String orgId : orgIds) {
        OrganizationDetails organizationDetails = organizationSearch.findOrganizationDetails(new Long(orgId));
        Organization organization = organizationResourceProvider.convertOrganizationDetailsToOrganization(organizationDetails);
        structuredBundle.addEntry().setResource(organization);
    }
    structuredBundle.setType(BundleType.COLLECTION);
    structuredBundle.getMeta().addProfile(SystemURL.SD_GPC_STRUCTURED_BUNDLE);
    if (operationOutcome != null) {
        structuredBundle.addEntry().setResource(operationOutcome);
    } else {
        removeDuplicateResources(structuredBundle);
    }
    return structuredBundle;
}

Example 12 with Reference

use of org.hl7.fhir.r4.model.Reference in project gpconnect-demonstrator by nhsconnect.

the class MedicationRequestResourceProvider method getMedicationRequestFromDetail.

private MedicationRequest getMedicationRequestFromDetail(MedicationRequestDetail requestDetail) {
    MedicationRequest medicationRequest = new MedicationRequest();
    medicationRequest.setId(requestDetail.getId().toString());
    List<Identifier> identifiers = new ArrayList<>();
    Identifier identifier = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(requestDetail.getGuid());
    identifiers.add(identifier);
    medicationRequest.setIdentifier(identifiers);
    medicationRequest.setMeta(new Meta().addProfile(SystemURL.SD_GPC_MEDICATION_REQUEST));
    setBasedOnReferences(medicationRequest, requestDetail);
    if (requestDetail.getPrescriptionTypeCode().contains("repeat")) {
        medicationRequest.setGroupIdentifier(new Identifier().setValue(requestDetail.getGroupIdentifier()));
    }
    try {
        medicationRequest.setStatus(MedicationRequestStatus.fromCode(requestDetail.getStatusCode()));
    } catch (FHIRException e) {
        throw new UnprocessableEntityException(e.getMessage());
    }
    try {
        medicationRequest.setIntent(MedicationRequestIntent.fromCode(requestDetail.getIntentCode()));
    } catch (FHIRException e) {
        throw new UnprocessableEntityException(e.getMessage());
    }
    if (requestDetail.getMedicationId() != null) {
        medicationRequest.setMedication(new Reference(new IdType("Medication", requestDetail.getMedicationId())));
    }
    if (requestDetail.getPatientId() != null) {
        medicationRequest.setSubject(new Reference(new IdType("Patient", requestDetail.getPatientId())));
    }
    if (requestDetail.getAuthorisingPractitionerId() != null) {
        medicationRequest.setRecorder(new Reference(new IdType("Practitioner", requestDetail.getAuthorisingPractitionerId())));
    }
    if (requestDetail.getPriorMedicationRequestId() != null) {
        medicationRequest.setPriorPrescription(new Reference(new IdType("MedicationRequest", requestDetail.getPriorMedicationRequestId())));
    }
    medicationRequest.setAuthoredOn(requestDetail.getAuthoredOn());
    medicationRequest.setDispenseRequest(getDispenseRequestComponent(requestDetail));
    // medicationRequest.setRequester(getRequesterComponent(requestDetail)); //TODO - spec needs to clarify whether this should be populated or not
    setReasonCodes(medicationRequest, requestDetail);
    setNotes(medicationRequest, requestDetail);
    if (medicationRequest.getIntent() != MedicationRequestIntent.ORDER) {
        setRepeatInformation(medicationRequest, requestDetail);
    }
    setPrescriptionType(medicationRequest, requestDetail);
    setStatusReason(medicationRequest, requestDetail);
    String dosageInstructionText = requestDetail.getDosageText();
    medicationRequest.addDosageInstruction(new Dosage().setText(dosageInstructionText == null || dosageInstructionText.trim().isEmpty() ? NO_INFORMATION_AVAILABLE : dosageInstructionText).setPatientInstruction(requestDetail.getDosageInstructions()));
    return medicationRequest;
}

Example 13 with Reference

use of org.hl7.fhir.r4.model.Reference 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;
}

Example 14 with Reference

use of org.hl7.fhir.r4.model.Reference in project bunsen by cerner.

the class TestData method newCondition.

/**
 * Returns a FHIR Condition for testing purposes.
 */
public static Condition newCondition() {
    Condition condition = new Condition();
    // Condition based on example from FHIR:
    // https://www.hl7.org/fhir/condition-example.json.html
    condition.setId("Condition/example");
    condition.setLanguage("en_US");
    // Narrative text
    Narrative narrative = new Narrative();
    narrative.setStatusAsString("generated");
    narrative.setDivAsString("This data was generated for test purposes.");
    XhtmlNode node = new XhtmlNode();
    node.setNodeType(NodeType.Text);
    node.setValue("Severe burn of left ear (Date: 24-May 2012)");
    condition.setText(narrative);
    condition.setSubject(new Reference("Patient/example").setDisplay("Here is a display for you."));
    condition.setVerificationStatus(Condition.ConditionVerificationStatus.CONFIRMED);
    // Condition code
    CodeableConcept code = new CodeableConcept();
    code.addCoding().setSystem("http://snomed.info/sct").setCode("39065001").setDisplay("Severe");
    condition.setSeverity(code);
    // Severity code
    CodeableConcept severity = new CodeableConcept();
    severity.addCoding().setSystem("http://snomed.info/sct").setCode("24484000").setDisplay("Burn of ear").setUserSelected(true);
    condition.setSeverity(severity);
    // Onset date time
    DateTimeType onset = new DateTimeType();
    onset.setValueAsString("2012-05-24");
    condition.setOnset(onset);
    return condition;
}

Example 15 with Reference

use of org.hl7.fhir.r4.model.Reference in project bunsen by cerner.

the class TestData method newMedRequest.

/**
 * Returns a FHIR medication request for testing purposes.
 */
public static MedicationRequest newMedRequest() {
    MedicationRequest medReq = new MedicationRequest();
    medReq.setId("test-med");
    // Medication code
    CodeableConcept med = new CodeableConcept();
    med.addCoding().setSystem("http://www.nlm.nih.gov/research/umls/rxnorm").setCode("582620").setDisplay("Nizatidine 15 MG/ML Oral Solution [Axid]");
    med.setText("Nizatidine 15 MG/ML Oral Solution [Axid]");
    medReq.setMedication(med);
    Annotation annotation = new Annotation();
    annotation.setText("Test medication note.");
    annotation.setAuthor(new Reference("Provider/example").setDisplay("Example provider."));
    medReq.addNote(annotation);
    return medReq;
}