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

Example 6 with Annotation

use of org.hl7.fhir.r4.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class R4CoverageResourceProvider method searchByBeneficiary.

/**
 * Adds support for the FHIR "search" operation for {@link Coverage}s, allowing users to search by
 * {@link Coverage#getBeneficiary()}.
 *
 * <p>The {@link Search} annotation indicates that this method supports the search operation.
 * There may be many different methods annotated with this {@link Search} annotation, to support
 * many different search criteria.
 *
 * @param beneficiary a {@link ReferenceParam} for the {@link Coverage#getBeneficiary()} to try
 *     and find matches for
 * @param startIndex an {@link OptionalParam} for the startIndex (or offset) used to determine
 *     pagination
 * @param lastUpdated an {@link OptionalParam} to filter the results based on the passed date
 *     range
 * @param requestDetails a {@link RequestDetails} containing the details of the request URL, used
 *     to parse out pagination values
 * @return Returns a {@link List} of {@link Coverage}s, which may contain multiple matching
 *     resources, or may also be empty.
 */
@Search
@Trace
public Bundle searchByBeneficiary(@RequiredParam(name = Coverage.SP_BENEFICIARY) @Description(shortDefinition = "The patient identifier to search for") ReferenceParam beneficiary, @OptionalParam(name = "startIndex") @Description(shortDefinition = "The offset used for result pagination") String startIndex, @OptionalParam(name = "_lastUpdated") @Description(shortDefinition = "Include resources last updated in the given range") DateRangeParam lastUpdated, RequestDetails requestDetails) {
    List<IBaseResource> coverages;
    try {
        Beneficiary beneficiaryEntity = findBeneficiaryById(beneficiary.getIdPart(), lastUpdated);
        if (!beneficiaryEntity.getBeneEnrollmentReferenceYear().isPresent()) {
            throw new ResourceNotFoundException("Cannot find coverage for non present enrollment year");
        }
        coverages = CoverageTransformerV2.transform(metricRegistry, beneficiaryEntity);
    } catch (NoResultException e) {
        coverages = new LinkedList<IBaseResource>();
    }
    OffsetLinkBuilder paging = new OffsetLinkBuilder(requestDetails, "/Coverage?");
    Operation operation = new Operation(Operation.Endpoint.V2_COVERAGE);
    operation.setOption("by", "beneficiary");
    operation.setOption("pageSize", paging.isPagingRequested() ? "" + paging.getPageSize() : "*");
    operation.setOption("_lastUpdated", Boolean.toString(lastUpdated != null && !lastUpdated.isEmpty()));
    operation.publishOperationName();
    // Add bene_id to MDC logs
    TransformerUtilsV2.logBeneIdToMdc(Arrays.asList(beneficiary.getIdPart()));
    return TransformerUtilsV2.createBundle(paging, coverages, loadedFilterManager.getTransactionTime());
}

Example 7 with Annotation

use of org.hl7.fhir.r4.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class R4ExplanationOfBenefitResourceProvider method read.

/**
 * Adds support for the FHIR "read" operation, for {@link ExplanationOfBenefit}s. The {@link Read}
 * annotation indicates that this method supports the read operation.
 *
 * <p>Read operations take a single parameter annotated with {@link IdParam}, and should return a
 * single resource instance.
 *
 * @param eobId The read operation takes one parameter, which must be of type {@link IdType} and
 *     must be annotated with the {@link IdParam} annotation.
 * @param requestDetails the request details for the read
 * @return Returns a resource matching the specified {@link IdDt}, or <code>null</code> if none
 *     exists.
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
@Read(version = false)
@Trace
public ExplanationOfBenefit read(@IdParam IdType eobId, RequestDetails requestDetails) {
    if (eobId == null)
        throw new IllegalArgumentException();
    if (eobId.getVersionIdPartAsLong() != null)
        throw new IllegalArgumentException();
    String eobIdText = eobId.getIdPart();
    if (eobIdText == null || eobIdText.trim().isEmpty())
        throw new IllegalArgumentException();
    Matcher eobIdMatcher = EOB_ID_PATTERN.matcher(eobIdText);
    if (!eobIdMatcher.matches())
        throw new IllegalArgumentException("Unsupported ID pattern: " + eobIdText);
    String eobIdTypeText = eobIdMatcher.group(1);
    Optional<ClaimTypeV2> eobIdType = ClaimTypeV2.parse(eobIdTypeText);
    if (!eobIdType.isPresent())
        throw new ResourceNotFoundException(eobId);
    String eobIdClaimIdText = eobIdMatcher.group(2);
    boolean includeTaxNumbers = returnIncludeTaxNumbers(requestDetails);
    Operation operation = new Operation(Operation.Endpoint.V2_EOB);
    operation.setOption("IncludeTaxNumbers", "" + includeTaxNumbers);
    operation.setOption("by", "id");
    operation.publishOperationName();
    Class<?> entityClass = eobIdType.get().getEntityClass();
    CriteriaBuilder builder = entityManager.getCriteriaBuilder();
    CriteriaQuery criteria = builder.createQuery(entityClass);
    Root root = criteria.from(entityClass);
    eobIdType.get().getEntityLazyAttributes().stream().forEach(a -> root.fetch(a));
    criteria.select(root);
    criteria.where(builder.equal(root.get(eobIdType.get().getEntityIdAttribute()), eobIdClaimIdText));
    Object claimEntity = null;
    Long eobByIdQueryNanoSeconds = null;
    Timer.Context timerEobQuery = metricRegistry.timer(MetricRegistry.name(getClass().getSimpleName(), "query", "eob_by_id")).time();
    try {
        claimEntity = entityManager.createQuery(criteria).getSingleResult();
    } catch (NoResultException e) {
        throw new ResourceNotFoundException(eobId);
    } finally {
        eobByIdQueryNanoSeconds = timerEobQuery.stop();
        TransformerUtilsV2.recordQueryInMdc("eob_by_id", eobByIdQueryNanoSeconds, claimEntity == null ? 0 : 1);
    }
    ExplanationOfBenefit eob = eobIdType.get().getTransformer().transform(metricRegistry, claimEntity, Optional.of(includeTaxNumbers));
    return eob;
}

Example 8 with Annotation

use of org.hl7.fhir.r4.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class R4PatientResourceProvider method searchByIdentifier.

/**
 * Adds support for the FHIR "search" operation for {@link Patient}s, allowing users to search by
 * {@link Patient#getIdentifier()}. Specifically, the following criteria are supported:
 *
 * <p>Searches that don't match one of the above forms are not supported.
 *
 * <p>The {@link Search} annotation indicates that this method supports the search operation.
 * There may be many different methods annotated with this {@link Search} annotation, to support
 * many different search criteria.
 *
 * @param identifier an {@link Identifier} {@link TokenParam} for the {@link
 *     Patient#getIdentifier()} to try and find a matching {@link Patient} for
 * @param startIndex an {@link OptionalParam} for the startIndex (or offset) used to determine
 *     pagination
 * @param lastUpdated an {@link OptionalParam} to filter the results based on the passed date
 *     range
 * @param requestDetails a {@link RequestDetails} containing the details of the request URL, used
 *     to parse out pagination values
 * @return Returns a {@link List} of {@link Patient}s, which may contain multiple matching
 *     resources, or may also be empty.
 */
@Search
@Trace
public Bundle searchByIdentifier(@RequiredParam(name = Patient.SP_IDENTIFIER) @Description(shortDefinition = "The patient identifier to search for") TokenParam identifier, @OptionalParam(name = "startIndex") @Description(shortDefinition = "The offset used for result pagination") String startIndex, @OptionalParam(name = "_lastUpdated") @Description(shortDefinition = "Include resources last updated in the given range") DateRangeParam lastUpdated, RequestDetails requestDetails) {
    if (identifier.getQueryParameterQualifier() != null) {
        throw new InvalidRequestException("Unsupported query parameter qualifier: " + identifier.getQueryParameterQualifier());
    }
    if (!SUPPORTED_HASH_IDENTIFIER_SYSTEMS.contains(identifier.getSystem()))
        throw new InvalidRequestException("Unsupported identifier system: " + identifier.getSystem());
    RequestHeaders requestHeader = RequestHeaders.getHeaderWrapper(requestDetails);
    Operation operation = new Operation(Operation.Endpoint.V2_PATIENT);
    operation.setOption("by", "identifier");
    requestHeader.getNVPairs().forEach((n, v) -> operation.setOption(n, v.toString()));
    operation.setOption("_lastUpdated", Boolean.toString(lastUpdated != null && !lastUpdated.isEmpty()));
    operation.publishOperationName();
    List<IBaseResource> patients;
    try {
        Patient patient;
        switch(identifier.getSystem()) {
            case TransformerConstants.CODING_BBAPI_BENE_MBI_HASH:
                patient = queryDatabaseByMbiHash(identifier.getValue(), requestHeader);
                break;
            case TransformerConstants.CODING_BBAPI_BENE_HICN_HASH:
            case TransformerConstants.CODING_BBAPI_BENE_HICN_HASH_OLD:
                patient = queryDatabaseByHicnHash(identifier.getValue(), requestHeader);
                break;
            default:
                throw new InvalidRequestException("Unsupported identifier system: " + identifier.getSystem());
        }
        patients = QueryUtils.isInRange(patient.getMeta().getLastUpdated().toInstant(), lastUpdated) ? Collections.singletonList(patient) : Collections.emptyList();
    } catch (NoResultException e) {
        patients = new LinkedList<>();
    }
    OffsetLinkBuilder paging = new OffsetLinkBuilder(requestDetails, "/Patient?");
    return TransformerUtilsV2.createBundle(paging, patients, loadedFilterManager.getTransactionTime());
}

Example 9 with Annotation

use of org.hl7.fhir.r4.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class R4PatientResourceProvider method searchByLogicalId.

/**
 * Adds support for the FHIR "search" operation for {@link Patient}s, allowing users to search by
 * {@link Patient#getId()}.
 *
 * <p>The {@link Search} annotation indicates that this method supports the search operation.
 * There may be many different methods annotated with this {@link Search} annotation, to support
 * many different search criteria.
 *
 * @param logicalId a {@link TokenParam} (with no system, per the spec) for the {@link
 *     Patient#getId()} to try and find a matching {@link Patient} for
 * @param startIndex an {@link OptionalParam} for the startIndex (or offset) used to determine
 *     pagination
 * @param lastUpdated an {@link OptionalParam} to filter the results based on the passed date
 *     range
 * @param requestDetails a {@link RequestDetails} containing the details of the request URL, used
 *     to parse out pagination values
 * @return Returns a {@link List} of {@link Patient}s, which may contain multiple matching
 *     resources, or may also be empty.
 */
@Search
@Trace
public Bundle searchByLogicalId(@RequiredParam(name = Patient.SP_RES_ID) @Description(shortDefinition = "The patient identifier to search for") TokenParam logicalId, @OptionalParam(name = "startIndex") @Description(shortDefinition = "The offset used for result pagination") String startIndex, @OptionalParam(name = "_lastUpdated") @Description(shortDefinition = "Include resources last updated in the given range") DateRangeParam lastUpdated, RequestDetails requestDetails) {
    if (logicalId.getQueryParameterQualifier() != null)
        throw new InvalidRequestException("Unsupported query parameter qualifier: " + logicalId.getQueryParameterQualifier());
    if (logicalId.getSystem() != null && !logicalId.getSystem().isEmpty())
        throw new InvalidRequestException("Unsupported query parameter system: " + logicalId.getSystem());
    if (logicalId.getValueNotNull().isEmpty())
        throw new InvalidRequestException("Unsupported query parameter value: " + logicalId.getValue());
    List<IBaseResource> patients;
    if (loadedFilterManager.isResultSetEmpty(logicalId.getValue(), lastUpdated)) {
        patients = Collections.emptyList();
    } else {
        try {
            patients = Optional.of(read(new IdType(logicalId.getValue()), requestDetails)).filter(p -> QueryUtils.isInRange(p.getMeta().getLastUpdated().toInstant(), lastUpdated)).map(p -> Collections.singletonList((IBaseResource) p)).orElse(Collections.emptyList());
        } catch (ResourceNotFoundException e) {
            patients = Collections.emptyList();
        }
    }
    /*
     * Publish the operation name. Note: This is a bit later than we'd normally do this, as we need
     * to override the operation name that was published by the possible call to read(...), above.
     */
    RequestHeaders requestHeader = RequestHeaders.getHeaderWrapper(requestDetails);
    Operation operation = new Operation(Operation.Endpoint.V2_PATIENT);
    operation.setOption("by", "id");
    // track all api hdrs
    requestHeader.getNVPairs().forEach((n, v) -> operation.setOption(n, v.toString()));
    operation.setOption("_lastUpdated", Boolean.toString(lastUpdated != null && !lastUpdated.isEmpty()));
    operation.publishOperationName();
    OffsetLinkBuilder paging = new OffsetLinkBuilder(requestDetails, "/Patient?");
    Bundle bundle = TransformerUtilsV2.createBundle(paging, patients, loadedFilterManager.getTransactionTime());
    return bundle;
}

Example 10 with Annotation

use of org.hl7.fhir.r4.model.Annotation in project kindling by HL7.

the class Publisher method stripXsd.

private InputStream stripXsd(InputStream source) throws Exception {
    byte[] src = IOUtils.toByteArray(source);
    try {
        byte[] xslt = IOUtils.toByteArray(new FileInputStream(Utilities.path(page.getFolders().rootDir, "implementations", "xmltools", "AnnotationStripper.xslt")));
        String scrs = new String(src);
        String xslts = new String(xslt);
        return new ByteArrayInputStream(XsltUtilities.transform(new HashMap<String, byte[]>(), src, xslt));
    } catch (Exception e) {
        if (web) {
            e.printStackTrace();
            throw e;
        } else
            return new ByteArrayInputStream(src);
    }
// DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
// factory.setNamespaceAware(false);
// DocumentBuilder builder = factory.newDocumentBuilder();
// Document doc = builder.parse(source);
// stripElement(doc.getDocumentElement(), "annotation");
// TransformerFactory transformerFactory = TransformerFactory.newInstance();
// Transformer transformer = transformerFactory.newTransformer();
// ByteArrayOutputStream bo = new ByteArrayOutputStream();
// DOMSource src = new DOMSource(doc);erent
// StreamResult streamResult =  new StreamResult(bo);
// transformer.transform(src, streamResult);
// bo.close();
// return new ByteArrayInputStream(bo.toByteArray());
}