Examples with FINAL org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL used on opensource projects

Example 1 with FINAL

use of org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL in project loinc2hpo by monarch-initiative.

the class CodeSystemInternal method init.

@Override
protected void init() {
    final Coding BELOWNORMAL = new Coding(INTERNALSYSTEM, "L", "below normal range");
    final Coding NORMAL = new Coding(INTERNALSYSTEM, "N", "within normal range");
    final Coding ABOVENORMAL = new Coding(INTERNALSYSTEM, "H", "above normal range");
    final Coding ABSENCE = new Coding(INTERNALSYSTEM, "NP", "not present");
    final Coding PRESENCE = new Coding(INTERNALSYSTEM, "P", "present");
    final Coding UNKNOWN = new Coding(INTERNALSYSTEM, "unknown", "unknown");
    codes.put(BELOWNORMAL.getCode(), BELOWNORMAL);
    codes.put(NORMAL.getCode(), NORMAL);
    codes.put(ABOVENORMAL.getCode(), ABOVENORMAL);
    codes.put(ABSENCE.getCode(), ABSENCE);
    codes.put(PRESENCE.getCode(), PRESENCE);
    codes.put(UNKNOWN.getCode(), UNKNOWN);
}

Example 2 with FINAL

use of org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL in project gpconnect-demonstrator by nhsconnect.

the class AppointmentResourceProvider method updateAppointment.

/**
 * amend or cancel an existing appointment
 *
 * @param appointmentId
 * @param appointment Resource
 * @param theRequest required to access the interaction id
 * @return MethodOutcome
 */
@Update
public MethodOutcome updateAppointment(@IdParam IdType appointmentId, @ResourceParam Appointment appointment, HttpServletRequest theRequest) {
    MethodOutcome methodOutcome = new MethodOutcome();
    OperationOutcome operationalOutcome = new OperationOutcome();
    AppointmentDetail appointmentDetail = appointmentResourceConverterToAppointmentDetail(appointment);
    Meta meta = appointment.getMeta();
    final List<UriType> profiles = meta.getProfile();
    // #203 validations
    VC.execute(new VC[] { new VC(() -> profiles.isEmpty(), () -> "Meta element must be present in Appointment"), new VC(() -> !profiles.get(0).getValue().equalsIgnoreCase(SD_GPC_APPOINTMENT), // what to do if > 1 meta profile element?
    () -> "Meta.profile " + profiles.get(0).getValue() + " is not equal to " + SD_GPC_APPOINTMENT), // #203
    new VC(() -> !appointment.getReason().isEmpty(), () -> "Appointment reason shouldn't be provided!"), new VC(() -> !appointment.getSpecialty().isEmpty(), () -> "Appointment speciality shouldn't be provided!"), // new VC(() -> !appointment.getServiceType().isEmpty(), () -> "Appointment service type shouldn't be provided!"),
    new VC(() -> !appointment.getAppointmentType().isEmpty(), () -> "Appointment type shouldn't be provided!"), new VC(() -> !appointment.getIndication().isEmpty(), () -> "Appointment indication shouldn't be provided!"), new VC(() -> !appointment.getSupportingInformation().isEmpty(), () -> "Appointment supporting information shouldn't be provided!"), new VC(() -> !appointment.getIncomingReferral().isEmpty(), () -> "Appointment incoming referral shouldn't be provided!") });
    // 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;
    }
    // 1.2.7 set the old service type and service category for comparison with incoming update/cancel content values
    SlotDetail slotDetail1 = slotSearch.findSlotByID(oldAppointmentDetail.getSlotIds().get(0));
    oldAppointmentDetail.setServiceType(slotDetail1.getTypeDisply());
    ScheduleDetail scheduleDetail = scheduleSearch.findScheduleByID(slotDetail1.getScheduleReference());
    oldAppointmentDetail.setServiceCategory(scheduleDetail.getTypeDescription());
    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 + ")");
    }
    // check for absolute reference #200
    Iterator<AppointmentParticipantComponent> iter = appointment.getParticipant().iterator();
    while (iter.hasNext()) {
        AppointmentParticipantComponent participant = iter.next();
        if (participant.getActor() != null) {
            checkReferenceIsRelative(participant.getActor().getReference());
        }
    }
    String interactionId = theRequest.getHeader(SSP_INTERACTIONID);
    // Determine if it is a cancel or an amend. This was previously a check for the presence of a cancellation reason
    // but that is not sufficient. We can sefely assume that the interaction id is populated at this point.
    AppointmentOperation appointmentOperation = null;
    final AppointmentDetail fAppointmentDetail = appointmentDetail;
    switch(interactionId) {
        case REST_CANCEL_APPOINTMENT:
            appointmentOperation = AppointmentOperation.CANCEL;
            // added at 1.2.2
            VC.execute(new VC[] { new VC(() -> appointment.getStatus() != AppointmentStatus.CANCELLED, () -> "Status must be \"cancelled\""), // #203
            new VC(() -> isInThePast(fAppointmentDetail.getStartDateTime()), () -> "The cancellation start date cannot be in the past"), new VC(() -> fAppointmentDetail.getCancellationReason() == null, () -> "The cancellation reason must be provided"), // no point in this since fhir forbids empty elements
            new VC(() -> fAppointmentDetail.getCancellationReason().isEmpty(), () -> "The cancellation reason can not be blank") });
            validateAppointmentExtensions(appointment, profiles, appointmentOperation);
            // #172
            String appointmentType = appointment.getAppointmentType().getText();
            if (appointmentType != null) {
                throwUnprocessableEntity422_InvalidResourceException("The appointment type cannot be updated on a cancellation");
            }
            // This is a Cancellation - so copy across fields which can be
            // altered
            List cancelComparisonResult = compareAppointmentsForInvalidProperty(AppointmentOperation.CANCEL, oldAppointmentDetail, appointmentDetail);
            if (cancelComparisonResult.size() > 0) {
                throwUnprocessableEntity422_InvalidResourceException("Invalid Appointment property has been amended (cancellation) " + cancelComparisonResult);
            }
            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);
                }
            }
            break;
        case REST_UPDATE_APPOINTMENT:
            appointmentOperation = AppointmentOperation.AMEND;
            VC.execute(new VC[] { new VC(() -> appointment.getStatus() != AppointmentStatus.BOOKED, () -> "Status must be \"booked\""), // this subsumes #161 which only inhibited amendment of the cancellation reason in an amend
            new VC(() -> fAppointmentDetail.getCancellationReason() != null, () -> "Cannot amend cancellation reason in appointment amend"), // added at 1.2.2
            new VC(() -> isInThePast(fAppointmentDetail.getStartDateTime()), () -> "The appointment amend start date cannot be in the past") });
            List amendComparisonResult = compareAppointmentsForInvalidProperty(AppointmentOperation.AMEND, oldAppointmentDetail, appointmentDetail);
            if (amendComparisonResult.size() > 0) {
                throwUnprocessableEntity422_InvalidResourceException("Invalid Appointment property has been amended " + amendComparisonResult);
            }
            validateAppointmentExtensions(appointment, profiles, appointmentOperation);
            // This is an Amend
            oldAppointmentDetail.setComment(appointmentDetail.getComment());
            oldAppointmentDetail.setDescription(appointmentDetail.getDescription());
            appointmentDetail = oldAppointmentDetail;
            break;
        default:
            System.err.println("AppointmentResourceProvider.updateAppointment Unhandled interaction id  " + interactionId);
    }
    // we'll get the delivery channel from the slot
    String deliveryChannel = null;
    String practitionerRoleCode = null;
    String practitionerRoleDisplay = null;
    ScheduleDetail schedule = null;
    // Common to both Update and cancel
    // slots valid?
    List<SlotDetail> slots = new ArrayList<>();
    for (Long slotId : appointmentDetail.getSlotIds()) {
        SlotDetail slotDetail = slotSearch.findSlotByID(slotId);
        if (slotDetail == null) {
            throwUnprocessableEntity422_InvalidResourceException("Slot resource reference is not a valid resource");
        }
        if (deliveryChannel == null) {
            deliveryChannel = slotDetail.getDeliveryChannelCode();
        }
        if (schedule == null) {
            // load the schedule so we can get the Practitioner ID
            schedule = scheduleSearch.findScheduleByID(slotDetail.getScheduleReference());
        }
        if (practitionerRoleDisplay == null) {
            practitionerRoleDisplay = schedule.getPractitionerRoleDisplay();
            practitionerRoleCode = schedule.getPractitionerRoleCode();
        }
        slots.add(slotDetail);
    }
    validateUpdateExtensions(deliveryChannel, practitionerRoleDisplay, practitionerRoleCode, appointment.getExtension());
    // dates valid?
    // #203
    Date firstSlotStart = slots.get(0).getStartDateTime();
    Date lastSlotEnd = slots.get(slots.size() - 1).getEndDateTime();
    // need to insert a colon in the timezone string
    String firstSlotStartStr = TIMESTAMP_FORMAT.format(firstSlotStart).replaceFirst("([0-9]{2})([0-9]{2})$", "$1:$2");
    String lastSlotEndStr = TIMESTAMP_FORMAT.format(lastSlotEnd).replaceFirst("([0-9]{2})([0-9]{2})$", "$1:$2");
    VC.execute(new VC[] { new VC(() -> appointment.getStart().compareTo(firstSlotStart) != 0, () -> String.format("Start date '%s' must match start date of first slot '%s'", appointment.getStart(), firstSlotStart)), new VC(() -> appointment.getEnd().compareTo(lastSlotEnd) != 0, () -> String.format("End date '%s' must match end date of last slot '%s'", appointment.getEnd(), lastSlotEnd)), // #218 strings should match exactly
    new VC(() -> !appointment.getStartElement().getValueAsString().equals(firstSlotStartStr), () -> String.format("Start date '%s' must lexically match start date of first slot '%s'", appointment.getStartElement().getValueAsString(), firstSlotStartStr)), new VC(() -> !appointment.getEndElement().getValueAsString().equals(lastSlotEndStr), () -> String.format("End date '%s' must lexically match end date of last slot '%s'", appointment.getEndElement().getValueAsString(), lastSlotEndStr)), new VC(() -> appointment.getSlot().size() != slots.size(), () -> String.format("Slot count mismatch %d provided appointment has %d", appointment.getSlot().size(), slots.size())) });
    // check the slots match
    HashSet<String> hs = new HashSet<>();
    for (SlotDetail slotDetail : slots) {
        hs.add("Slot/" + slotDetail.getId());
    }
    for (Reference reference : appointment.getSlot()) {
        if (!hs.contains(reference.getReference())) {
            throwUnprocessableEntity422_InvalidResourceException(String.format("Provided slot id %s does not exist in booked appointment", reference.getReference()));
        }
    }
    // 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 3 with FINAL

use of org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL in project gpconnect-demonstrator by nhsconnect.

the class GpConnectServerCapabilityStatementProvider method getServerConformance.

@Override
public CapabilityStatement getServerConformance(HttpServletRequest theRequest) {
    final boolean FROM_JSON = true;
    CapabilityStatement capabilityStatement = null;
    if (!FROM_JSON) {
        // Get the automatically generated statement
        capabilityStatement = super.getServerConformance(theRequest);
        // added at 1.2.2 force overwrite the default entries which are not correct
        for (CapabilityStatement.CapabilityStatementRestComponent st : capabilityStatement.getRest()) {
            for (CapabilityStatement.CapabilityStatementRestOperationComponent operation : st.getOperation()) {
                String opPlusDollar = "$" + operation.getName();
                switch(opPlusDollar) {
                    case REGISTER_PATIENT_OPERATION_NAME:
                        operation.getDefinition().setReference(OD_GPC_REGISTER_PATIENT);
                        break;
                    case GET_STRUCTURED_RECORD_OPERATION_NAME:
                        operation.getDefinition().setReference(OD_GPC_GET_STRUCTURED_RECORD);
                        break;
                }
            }
        }
    } else {
        try {
            // 1.2.6 #316
            String interactionId = theRequest.getHeader(SSP_INTERACTIONID);
            String capabilityFile = null;
            switch(interactionId) {
                case REST_READ_STRUCTURED_METADATA:
                    capabilityFile = "structured_capability.json";
                    break;
                default:
                    capabilityFile = "capability.json";
            }
            // read a json capability file
            String capabilityJson = new String(Files.readAllBytes(Paths.get(FhirRequestGenericIntercepter.getConfigPath() + "/" + capabilityFile)));
            FhirContext ctx = FhirContext.forDstu3();
            capabilityStatement = (CapabilityStatement) ctx.newJsonParser().parseResource(capabilityJson);
        } catch (IOException ex) {
            return null;
        }
    }
    // And add additional required information
    capabilityStatement.setVersion(SystemVariable.VERSION);
    capabilityStatement.setDescription("This server implements the GP Connect API version " + SystemVariable.VERSION);
    capabilityStatement.setName("GP Connect");
    capabilityStatement.setCopyright("Copyright NHS Digital 2018");
    capabilityStatement.getSoftware().setReleaseDate(Date.valueOf(LocalDate.parse("2017-09-27")));
    return capabilityStatement;
}

Example 4 with FINAL

use of org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL in project beneficiary-fhir-data by CMSgov.

the class TransformerUtils method addCareTeamPractitioner.

/**
 * Ensures that the specified {@link ExplanationOfBenefit} has the specified {@link
 * CareTeamComponent}, and links the specified {@link ItemComponent} to that {@link
 * CareTeamComponent} (via {@link ItemComponent#addCareTeamLinkId(int)}).
 *
 * @param eob the {@link ExplanationOfBenefit} that the {@link CareTeamComponent} should be part
 *     of
 * @param eobItem the {@link ItemComponent} that should be linked to the {@link CareTeamComponent}
 * @param practitionerIdSystem the {@link Identifier#getSystem()} of the practitioner to reference
 *     in {@link CareTeamComponent#getProvider()}
 * @param practitionerIdValue the {@link Identifier#getValue()} of the practitioner to reference
 *     in {@link CareTeamComponent#getProvider()}
 * @param careTeamRole the {@link ClaimCareteamrole} to use for the {@link
 *     CareTeamComponent#getRole()}
 * @return the {@link CareTeamComponent} that was created/linked
 */
static CareTeamComponent addCareTeamPractitioner(ExplanationOfBenefit eob, ItemComponent eobItem, String practitionerIdSystem, String practitionerIdValue, ClaimCareteamrole careTeamRole) {
    // Try to find a matching pre-existing entry.
    CareTeamComponent careTeamEntry = eob.getCareTeam().stream().filter(ctc -> ctc.getProvider().hasIdentifier()).filter(ctc -> practitionerIdSystem.equals(ctc.getProvider().getIdentifier().getSystem()) && practitionerIdValue.equals(ctc.getProvider().getIdentifier().getValue())).filter(ctc -> ctc.hasRole()).filter(ctc -> careTeamRole.toCode().equals(ctc.getRole().getCodingFirstRep().getCode()) && careTeamRole.getSystem().equals(ctc.getRole().getCodingFirstRep().getSystem())).findAny().orElse(null);
    // If no match was found, add one to the EOB.
    if (careTeamEntry == null) {
        careTeamEntry = eob.addCareTeam();
        careTeamEntry.setSequence(eob.getCareTeam().size() + 1);
        careTeamEntry.setProvider(createIdentifierReference(practitionerIdSystem, practitionerIdValue));
        CodeableConcept careTeamRoleConcept = createCodeableConcept(ClaimCareteamrole.OTHER.getSystem(), careTeamRole.toCode());
        careTeamRoleConcept.getCodingFirstRep().setDisplay(careTeamRole.getDisplay());
        careTeamEntry.setRole(careTeamRoleConcept);
    }
    // care team entry is at eob level so no need to create item link id
    if (eobItem == null) {
        return careTeamEntry;
    }
    // Link the EOB.item to the care team entry (if it isn't already).
    final int careTeamEntrySequence = careTeamEntry.getSequence();
    if (eobItem.getCareTeamLinkId().stream().noneMatch(id -> id.getValue() == careTeamEntrySequence)) {
        eobItem.addCareTeamLinkId(careTeamEntrySequence);
    }
    return careTeamEntry;
}

Example 5 with FINAL

use of org.hl7.fhir.dstu3.model.Observation.ObservationStatus.FINAL in project beneficiary-fhir-data by CMSgov.

the class ExplanationOfBenefitResourceProvider method findClaimTypeByPatient.

/**
 * @param claimType the {@link ClaimType} to find
 * @param patientId the {@link Beneficiary#getBeneficiaryId()} to filter by
 * @param lastUpdated the update time to filter by
 * @return the matching claim/event entities
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
@Trace
private <T> List<T> findClaimTypeByPatient(ClaimType claimType, String patientId, DateRangeParam lastUpdated, DateRangeParam serviceDate) {
    CriteriaBuilder builder = entityManager.getCriteriaBuilder();
    CriteriaQuery criteria = builder.createQuery((Class) claimType.getEntityClass());
    Root root = criteria.from(claimType.getEntityClass());
    claimType.getEntityLazyAttributes().stream().forEach(a -> root.fetch(a));
    criteria.select(root).distinct(true);
    // Search for a beneficiary's records. Use lastUpdated if present
    Predicate wherePredicate = builder.equal(root.get(claimType.getEntityBeneficiaryIdAttribute()), patientId);
    if (lastUpdated != null && !lastUpdated.isEmpty()) {
        Predicate predicate = QueryUtils.createLastUpdatedPredicate(builder, root, lastUpdated);
        wherePredicate = builder.and(wherePredicate, predicate);
    }
    criteria.where(wherePredicate);
    List<T> claimEntities = null;
    Long eobsByBeneIdQueryNanoSeconds = null;
    Timer.Context timerEobQuery = metricRegistry.timer(MetricRegistry.name(metricRegistry.getClass().getSimpleName(), "query", "eobs_by_bene_id", claimType.name().toLowerCase())).time();
    try {
        claimEntities = entityManager.createQuery(criteria).getResultList();
    } finally {
        eobsByBeneIdQueryNanoSeconds = timerEobQuery.stop();
        TransformerUtils.recordQueryInMdc(String.format("eobs_by_bene_id.%s", claimType.name().toLowerCase()), eobsByBeneIdQueryNanoSeconds, claimEntities == null ? 0 : claimEntities.size());
    }
    if (claimEntities != null && serviceDate != null && !serviceDate.isEmpty()) {
        final Instant lowerBound = serviceDate.getLowerBoundAsInstant() != null ? serviceDate.getLowerBoundAsInstant().toInstant() : null;
        final Instant upperBound = serviceDate.getUpperBoundAsInstant() != null ? serviceDate.getUpperBoundAsInstant().toInstant() : null;
        final java.util.function.Predicate<LocalDate> lowerBoundCheck = lowerBound == null ? (date) -> true : (date) -> compareLocalDate(date, lowerBound.atZone(ZoneId.systemDefault()).toLocalDate(), serviceDate.getLowerBound().getPrefix());
        final java.util.function.Predicate<LocalDate> upperBoundCheck = upperBound == null ? (date) -> true : (date) -> compareLocalDate(date, upperBound.atZone(ZoneId.systemDefault()).toLocalDate(), serviceDate.getUpperBound().getPrefix());
        return claimEntities.stream().filter(entity -> lowerBoundCheck.test(claimType.getServiceEndAttributeFunction().apply(entity)) && upperBoundCheck.test(claimType.getServiceEndAttributeFunction().apply(entity))).collect(Collectors.toList());
    }
    return claimEntities;
}