Search in sources :

Example 1 with RequestHeaders

use of gov.cms.bfd.server.war.commons.RequestHeaders in project beneficiary-fhir-data by CMSgov.

the class PatientResourceProvider method read.

/**
 * Adds support for the FHIR "read" operation, for {@link Patient}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 patientId The read operation takes one parameter, which must be of type {@link IdType}
 *     and must be annotated with the {@link IdParam} annotation.
 * @param requestDetails a {@link RequestDetails} containing the details of the request URL, used
 *     to parse out pagination values
 * @return Returns a resource matching the specified {@link IdDt}, or <code>null</code> if none
 *     exists.
 */
@Read(version = false)
@Trace
public Patient read(@IdParam IdType patientId, RequestDetails requestDetails) {
    if (patientId == null)
        throw new IllegalArgumentException();
    if (patientId.getVersionIdPartAsLong() != null)
        throw new IllegalArgumentException();
    String beneIdText = patientId.getIdPart();
    if (beneIdText == null || beneIdText.trim().isEmpty())
        throw new IllegalArgumentException();
    RequestHeaders requestHeader = RequestHeaders.getHeaderWrapper(requestDetails);
    Operation operation = new Operation(Operation.Endpoint.V1_PATIENT);
    operation.setOption("by", "id");
    // there is another method with exclude list: requestHeader.getNVPairs(<excludeHeaders>)
    requestHeader.getNVPairs().forEach((n, v) -> operation.setOption(n, v.toString()));
    operation.publishOperationName();
    CriteriaBuilder builder = entityManager.getCriteriaBuilder();
    CriteriaQuery<Beneficiary> criteria = builder.createQuery(Beneficiary.class);
    Root<Beneficiary> root = criteria.from(Beneficiary.class);
    root.fetch(Beneficiary_.skippedRifRecords, JoinType.LEFT);
    if (requestHeader.isHICNinIncludeIdentifiers())
        root.fetch(Beneficiary_.beneficiaryHistories, JoinType.LEFT);
    if (requestHeader.isMBIinIncludeIdentifiers())
        root.fetch(Beneficiary_.medicareBeneficiaryIdHistories, JoinType.LEFT);
    criteria.select(root);
    criteria.where(builder.equal(root.get(Beneficiary_.beneficiaryId), beneIdText));
    Beneficiary beneficiary = null;
    Long beneByIdQueryNanoSeconds = null;
    Timer.Context timerBeneQuery = metricRegistry.timer(MetricRegistry.name(getClass().getSimpleName(), "query", "bene_by_id")).time();
    try {
        beneficiary = entityManager.createQuery(criteria).getSingleResult();
    } catch (NoResultException e) {
        throw new ResourceNotFoundException(patientId);
    } finally {
        beneByIdQueryNanoSeconds = timerBeneQuery.stop();
        TransformerUtils.recordQueryInMdc(String.format("bene_by_id.include_%s", String.join("_", (List<String>) requestHeader.getValue(HEADER_NAME_INCLUDE_IDENTIFIERS))), beneByIdQueryNanoSeconds, beneficiary == null ? 0 : 1);
    }
    // Null out the unhashed HICNs if we're not supposed to be returning them
    if (!requestHeader.isHICNinIncludeIdentifiers()) {
        beneficiary.setHicnUnhashed(Optional.empty());
    }
    // Null out the unhashed MBIs if we're not supposed to be returning
    if (!requestHeader.isMBIinIncludeIdentifiers()) {
        beneficiary.setMedicareBeneficiaryId(Optional.empty());
    }
    // Add bene_id to MDC logs
    TransformerUtils.logBeneIdToMdc(Arrays.asList(beneIdText));
    Patient patient = BeneficiaryTransformer.transform(metricRegistry, beneficiary, requestHeader);
    return patient;
}
Also used : CriteriaBuilder(javax.persistence.criteria.CriteriaBuilder) Patient(org.hl7.fhir.dstu3.model.Patient) Operation(gov.cms.bfd.server.war.Operation) NoResultException(javax.persistence.NoResultException) Timer(com.codahale.metrics.Timer) RequestHeaders(gov.cms.bfd.server.war.commons.RequestHeaders) ResourceNotFoundException(ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException) Beneficiary(gov.cms.bfd.model.rif.Beneficiary) Read(ca.uhn.fhir.rest.annotation.Read) Trace(com.newrelic.api.agent.Trace)

Example 2 with RequestHeaders

use of gov.cms.bfd.server.war.commons.RequestHeaders in project beneficiary-fhir-data by CMSgov.

the class PatientResourceProvider 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:
 *
 * <ul>
 *   <li>Matching a {@link Beneficiary#getHicn()} hash value: when {@link TokenParam#getSystem()}
 *       matches one of the {@link #SUPPORTED_HASH_IDENTIFIER_SYSTEMS} entries.
 * </ul>
 *
 * <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.V1_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_HICN_HASH:
            case TransformerConstants.CODING_BBAPI_BENE_HICN_HASH_OLD:
                patient = queryDatabaseByHicnHash(identifier.getValue(), requestHeader);
                break;
            case TransformerConstants.CODING_BBAPI_BENE_MBI_HASH:
                patient = queryDatabaseByMbiHash(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?");
    Bundle bundle = TransformerUtils.createBundle(paging, patients, loadedFilterManager.getTransactionTime());
    return bundle;
}
Also used : OffsetLinkBuilder(gov.cms.bfd.server.war.commons.OffsetLinkBuilder) Bundle(org.hl7.fhir.dstu3.model.Bundle) Patient(org.hl7.fhir.dstu3.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 3 with RequestHeaders

use of gov.cms.bfd.server.war.commons.RequestHeaders in project beneficiary-fhir-data by CMSgov.

the class BeneficiaryTransformerV2Test method shouldMatchAddressWithAddrHeader.

/**
 * Verifies that {@link gov.cms.bfd.server.war.r4.providers.BeneficiaryTransformerV2} works
 * correctly when passed a {@link Beneficiary} with includeAddressFields header values.
 */
@Test
public void shouldMatchAddressWithAddrHeader() {
    RequestHeaders reqHdr = getRHwithIncldAddrFldHdr("true");
    createPatient(reqHdr);
    assertNotNull(patient);
    List<Address> addrList = patient.getAddress();
    assertEquals(1, addrList.size());
    assertEquals(6, addrList.get(0).getLine().size());
    Address compare = new Address();
    compare.setPostalCode("12345");
    compare.setState("MO");
    compare.setCity("PODUNK");
    ArrayList<StringType> lineList = new ArrayList<>(Arrays.asList(new StringType("204 SOUTH ST"), new StringType("7560 123TH ST"), new StringType("SURREY"), new StringType("DAEJEON SI 34867"), new StringType("COLOMBIA"), new StringType("SURREY")));
    compare.setLine(lineList);
    assertTrue(compare.equalsDeep(addrList.get(0)));
}
Also used : Address(org.hl7.fhir.r4.model.Address) StringType(org.hl7.fhir.r4.model.StringType) ArrayList(java.util.ArrayList) RequestHeaders(gov.cms.bfd.server.war.commons.RequestHeaders) Test(org.junit.jupiter.api.Test)

Example 4 with RequestHeaders

use of gov.cms.bfd.server.war.commons.RequestHeaders 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 5 with RequestHeaders

use of gov.cms.bfd.server.war.commons.RequestHeaders 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)

Aggregations

RequestHeaders (gov.cms.bfd.server.war.commons.RequestHeaders)31 Beneficiary (gov.cms.bfd.model.rif.Beneficiary)28 Patient (org.hl7.fhir.dstu3.model.Patient)20 Test (org.junit.jupiter.api.Test)18 TransformerConstants (gov.cms.bfd.server.war.commons.TransformerConstants)17 Arrays (java.util.Arrays)17 List (java.util.List)17 Collectors (java.util.stream.Collectors)17 InvalidRequestException (ca.uhn.fhir.rest.server.exceptions.InvalidRequestException)13 ResourceNotFoundException (ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException)13 MetricRegistry (com.codahale.metrics.MetricRegistry)13 BeneficiaryHistory (gov.cms.bfd.model.rif.BeneficiaryHistory)13 CommonHeaders (gov.cms.bfd.server.war.commons.CommonHeaders)13 Optional (java.util.Optional)13 ArrayList (java.util.ArrayList)12 StaticRifResourceGroup (gov.cms.bfd.model.rif.samples.StaticRifResourceGroup)8 ServerTestUtils (gov.cms.bfd.server.war.ServerTestUtils)8 Assertions.assertEquals (org.junit.jupiter.api.Assertions.assertEquals)8 IGenericClient (ca.uhn.fhir.rest.client.api.IGenericClient)7 CcwCodebookVariable (gov.cms.bfd.model.codebook.data.CcwCodebookVariable)7