Examples with Bundle org.hl7.fhir.dstu3.model.Bundle used on opensource projects

Example 1 with Bundle

use of org.hl7.fhir.dstu3.model.Bundle in project loinc2hpo by monarch-initiative.

the class ObservationDownloader method find20CompleteRecordOfEachType.

static void find20CompleteRecordOfEachType() {
    int i = 0;
    Bundle bundle = client.search().forResource(Observation.class).prettyPrint().returnBundle(Bundle.class).execute();
    while (true) {
        for (Bundle.BundleEntryComponent bundleEntryComponent : bundle.getEntry()) {
            Observation observation = (Observation) bundleEntryComponent.getResource();
            if (isComplte(observation)) {
                String completeRecord = jsonParser.encodeResourceToString(observation);
                i++;
                System.out.println(i + ". Find a complete record: \n" + completeRecord);
            }
            ;
        }
        if (bundle.getLink(IBaseBundle.LINK_NEXT) != null) {
            bundle = client.loadPage().next(bundle).execute();
        } else {
            break;
        }
    }
}

Example 2 with Bundle

use of org.hl7.fhir.dstu3.model.Bundle in project bunsen by cerner.

the class FunctionsTest method bundleToJson.

@Test
public void bundleToJson() {
    String jsonBundle = Functions.toJsonBundle(conditions);
    Bundle bundle = (Bundle) CONTEXT.newJsonParser().parseResource(jsonBundle);
    Condition parsedCondition = (Condition) bundle.getEntryFirstRep().getResource();
    Assert.assertEquals(condition.getId(), parsedCondition.getId());
}

Example 3 with Bundle

use of org.hl7.fhir.dstu3.model.Bundle in project gpconnect-demonstrator by nhsconnect.

the class PatientResourceProvider method registerPatient.

@Operation(name = REGISTER_PATIENT_OPERATION_NAME)
public Bundle registerPatient(@ResourceParam Parameters params) {
    Patient registeredPatient = null;
    validateParameterNames(params, registerPatientParams);
    Patient unregisteredPatient = params.getParameter().stream().filter(param -> "registerPatient".equalsIgnoreCase(param.getName())).map(ParametersParameterComponent::getResource).map(Patient.class::cast).findFirst().orElse(null);
    String nnn = nhsNumber.fromPatientResource(unregisteredPatient);
    // if its patient 14 spoof not on PDS and return the required error
    if (nnn.equals(patientNotOnSpine)) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(new InvalidRequestException(String.format("Patient (NHS number - %s) not present on PDS", nnn)), SystemCode.INVALID_PATIENT_DEMOGRAPHICS, IssueType.INVALID);
    } else if (nnn.equals(patientSuperseded)) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(new InvalidRequestException(String.format("Patient (NHS number - %s) is superseded", nnn)), SystemCode.INVALID_NHS_NUMBER, IssueType.INVALID);
    }
    if (unregisteredPatient != null) {
        validatePatient(unregisteredPatient);
        // check if the patient already exists
        PatientDetails patientDetails = patientSearch.findPatient(nhsNumber.fromPatientResource(unregisteredPatient));
        if (patientDetails == null || IsInactiveTemporaryPatient(patientDetails)) {
            if (patientDetails == null) {
                patientDetails = registerPatientResourceConverterToPatientDetail(unregisteredPatient);
                patientStore.create(patientDetails);
            } else {
                // reactivate inactive non temporary patient
                patientDetails.setRegistrationStatus(ACTIVE_REGISTRATION_STATUS);
                updateAddressAndTelecom(unregisteredPatient, patientDetails);
                patientStore.update(patientDetails);
            }
            try {
                registeredPatient = patientDetailsToRegisterPatientResourceConverter(patientSearch.findPatient(unregisteredPatient.getIdentifierFirstRep().getValue()));
                addPreferredBranchSurgeryExtension(registeredPatient);
            } catch (FHIRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }
        } else if (patientDetails.isDeceased() || patientDetails.isSensitive()) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new InvalidRequestException(String.format("Patient (NHS number - %s) has invalid demographics", nnn)), SystemCode.INVALID_PATIENT_DEMOGRAPHICS, IssueType.INVALID);
        } else {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnclassifiedServerFailureException(409, String.format("Patient (NHS number - %s) already exists", nnn)), SystemCode.DUPLICATE_REJECTED, IssueType.INVALID);
        }
    } else {
        throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Patient record not found"), SystemCode.INVALID_PARAMETER, IssueType.INVALID);
    }
    Bundle bundle = new Bundle().setType(BundleType.SEARCHSET);
    bundle.getMeta().addProfile(SystemURL.SD_GPC_SRCHSET_BUNDLE);
    bundle.addEntry().setResource(registeredPatient);
    return bundle;
}

Example 4 with Bundle

use of org.hl7.fhir.dstu3.model.Bundle 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 5 with Bundle

use of org.hl7.fhir.dstu3.model.Bundle in project gpconnect-demonstrator by nhsconnect.

the class PopulateSlotBundle method addOrganisation.

/**
 * Add OrganizationResource to Bundle
 *
 * @param organization OrganizationDetails object to add to bundle
 * @param bundle Bundle Resource to add organisation to
 */
private void addOrganisation(OrganizationDetails organization, Bundle bundle) {
    BundleEntryComponent organizationEntry = new BundleEntryComponent();
    Long organizationId = organization.getId();
    OrganizationDetails organizationDetails = organizationSearch.findOrganizationDetails(organizationId);
    Organization organizationResource = organizationResourceProvider.convertOrganizationDetailsToOrganization(organizationDetails);
    organizationEntry.setResource(organizationResource);
    // #202 use full urls
    // #215 full url removed completely
    // organizationEntry.setFullUrl(serverBaseUrl + "Organization/" + organization.getId());
    bundle.addEntry(organizationEntry);
}