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Example 6 with Annotation

use of org.hl7.fhir.dstu2016may.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());
}
Also used : OffsetLinkBuilder(gov.cms.bfd.server.war.commons.OffsetLinkBuilder) NoResultException(javax.persistence.NoResultException) Operation(gov.cms.bfd.server.war.Operation) IBaseResource(org.hl7.fhir.instance.model.api.IBaseResource) ResourceNotFoundException(ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException) LinkedList(java.util.LinkedList) Beneficiary(gov.cms.bfd.model.rif.Beneficiary) Trace(com.newrelic.api.agent.Trace) Search(ca.uhn.fhir.rest.annotation.Search)

Example 7 with Annotation

use of org.hl7.fhir.dstu2016may.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;
}
Also used : CriteriaBuilder(javax.persistence.criteria.CriteriaBuilder) Root(javax.persistence.criteria.Root) Matcher(java.util.regex.Matcher) CriteriaQuery(javax.persistence.criteria.CriteriaQuery) Operation(gov.cms.bfd.server.war.Operation) NoResultException(javax.persistence.NoResultException) ExplanationOfBenefit(org.hl7.fhir.r4.model.ExplanationOfBenefit) Timer(com.codahale.metrics.Timer) ResourceNotFoundException(ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException) Read(ca.uhn.fhir.rest.annotation.Read) Trace(com.newrelic.api.agent.Trace)

Example 8 with Annotation

use of org.hl7.fhir.dstu2016may.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());
}
Also used : OffsetLinkBuilder(gov.cms.bfd.server.war.commons.OffsetLinkBuilder) Patient(org.hl7.fhir.r4.model.Patient) InvalidRequestException(ca.uhn.fhir.rest.server.exceptions.InvalidRequestException) Operation(gov.cms.bfd.server.war.Operation) NoResultException(javax.persistence.NoResultException) RequestHeaders(gov.cms.bfd.server.war.commons.RequestHeaders) IBaseResource(org.hl7.fhir.instance.model.api.IBaseResource) LinkedList(java.util.LinkedList) Trace(com.newrelic.api.agent.Trace) Search(ca.uhn.fhir.rest.annotation.Search)

Example 9 with Annotation

use of org.hl7.fhir.dstu2016may.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;
}
Also used : IdParam(ca.uhn.fhir.rest.annotation.IdParam) Arrays(java.util.Arrays) PatientLinkBuilder(gov.cms.bfd.server.war.commons.PatientLinkBuilder) Description(ca.uhn.fhir.model.api.annotation.Description) Identifier(org.hl7.fhir.r4.model.Identifier) NoResultException(javax.persistence.NoResultException) StringUtils(org.apache.commons.lang3.StringUtils) BigDecimal(java.math.BigDecimal) DateRangeParam(ca.uhn.fhir.rest.param.DateRangeParam) Predicate(javax.persistence.criteria.Predicate) IResourceProvider(ca.uhn.fhir.rest.server.IResourceProvider) IBaseResource(org.hl7.fhir.instance.model.api.IBaseResource) Map(java.util.Map) CriteriaBuilder(javax.persistence.criteria.CriteriaBuilder) JoinType(javax.persistence.criteria.JoinType) BeneficiaryHistory(gov.cms.bfd.model.rif.BeneficiaryHistory) LoadedFilterManager(gov.cms.bfd.server.war.commons.LoadedFilterManager) Patient(org.hl7.fhir.r4.model.Patient) SingularAttribute(javax.persistence.metamodel.SingularAttribute) CriteriaQuery(javax.persistence.criteria.CriteriaQuery) IdDt(ca.uhn.fhir.model.primitive.IdDt) InvalidRequestException(ca.uhn.fhir.rest.server.exceptions.InvalidRequestException) BeneficiaryMonthly_(gov.cms.bfd.model.rif.BeneficiaryMonthly_) QueryHints(org.hibernate.jpa.QueryHints) Collectors(java.util.stream.Collectors) BeneficiaryMonthly(gov.cms.bfd.model.rif.BeneficiaryMonthly) Objects(java.util.Objects) Beneficiary(gov.cms.bfd.model.rif.Beneficiary) List(java.util.List) BeneficiaryHistory_(gov.cms.bfd.model.rif.BeneficiaryHistory_) TransformerConstants(gov.cms.bfd.server.war.commons.TransformerConstants) Year(java.time.Year) LocalDate(java.time.LocalDate) Timer(com.codahale.metrics.Timer) Optional(java.util.Optional) OptionalParam(ca.uhn.fhir.rest.annotation.OptionalParam) QueryUtils(gov.cms.bfd.server.war.commons.QueryUtils) Trace(com.newrelic.api.agent.Trace) HashMap(java.util.HashMap) RequestHeaders(gov.cms.bfd.server.war.commons.RequestHeaders) TypedQuery(javax.persistence.TypedQuery) Beneficiary_(gov.cms.bfd.model.rif.Beneficiary_) ArrayList(java.util.ArrayList) RequiredParam(ca.uhn.fhir.rest.annotation.RequiredParam) Inject(javax.inject.Inject) Strings(com.google.common.base.Strings) RequestDetails(ca.uhn.fhir.rest.api.server.RequestDetails) Search(ca.uhn.fhir.rest.annotation.Search) CcwCodebookVariable(gov.cms.bfd.model.codebook.data.CcwCodebookVariable) ResourceNotFoundException(ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException) CommonHeaders(gov.cms.bfd.server.war.commons.CommonHeaders) LinkedList(java.util.LinkedList) Root(javax.persistence.criteria.Root) Read(ca.uhn.fhir.rest.annotation.Read) OffsetLinkBuilder(gov.cms.bfd.server.war.commons.OffsetLinkBuilder) MetricRegistry(com.codahale.metrics.MetricRegistry) Operation(gov.cms.bfd.server.war.Operation) EntityManager(javax.persistence.EntityManager) PersistenceContext(javax.persistence.PersistenceContext) IdType(org.hl7.fhir.r4.model.IdType) TokenParam(ca.uhn.fhir.rest.param.TokenParam) Component(org.springframework.stereotype.Component) MDC(org.slf4j.MDC) YearMonth(java.time.YearMonth) Bundle(org.hl7.fhir.r4.model.Bundle) Collections(java.util.Collections) OffsetLinkBuilder(gov.cms.bfd.server.war.commons.OffsetLinkBuilder) Bundle(org.hl7.fhir.r4.model.Bundle) InvalidRequestException(ca.uhn.fhir.rest.server.exceptions.InvalidRequestException) Operation(gov.cms.bfd.server.war.Operation) IBaseResource(org.hl7.fhir.instance.model.api.IBaseResource) ResourceNotFoundException(ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException) RequestHeaders(gov.cms.bfd.server.war.commons.RequestHeaders) IdType(org.hl7.fhir.r4.model.IdType) Trace(com.newrelic.api.agent.Trace) Search(ca.uhn.fhir.rest.annotation.Search)

Example 10 with Annotation

use of org.hl7.fhir.dstu2016may.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());
}
Also used : ByteArrayInputStream(java.io.ByteArrayInputStream) LinkedHashMap(java.util.LinkedHashMap) HashMap(java.util.HashMap) CSFileInputStream(org.hl7.fhir.utilities.CSFileInputStream) FileInputStream(java.io.FileInputStream) TransformerException(javax.xml.transform.TransformerException) IOException(java.io.IOException) FHIRException(org.hl7.fhir.exceptions.FHIRException) FileNotFoundException(java.io.FileNotFoundException) UnsupportedEncodingException(java.io.UnsupportedEncodingException)

Aggregations

NotImplementedException (org.apache.commons.lang3.NotImplementedException)14 Trace (com.newrelic.api.agent.Trace)13 Operation (gov.cms.bfd.server.war.Operation)13 IBaseResource (org.hl7.fhir.instance.model.api.IBaseResource)12 Annotation (org.hl7.fhir.r4.model.Annotation)12 NoResultException (javax.persistence.NoResultException)11 ResourceNotFoundException (ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException)9 Annotation (org.hl7.fhir.dstu3.model.Annotation)9 Search (ca.uhn.fhir.rest.annotation.Search)8 OffsetLinkBuilder (gov.cms.bfd.server.war.commons.OffsetLinkBuilder)8 XhtmlNode (org.hl7.fhir.utilities.xhtml.XhtmlNode)8 Read (ca.uhn.fhir.rest.annotation.Read)7 Beneficiary (gov.cms.bfd.model.rif.Beneficiary)7 Patient (org.hl7.fhir.dstu3.model.Patient)7 ArrayList (java.util.ArrayList)6 List (java.util.List)6 Collectors (java.util.stream.Collectors)6 CodeableConcept (org.hl7.fhir.r4.model.CodeableConcept)6 Resource (org.hl7.fhir.r4.model.Resource)6 Test (org.junit.jupiter.api.Test)6