Examples with Time org.hl7.elm.r1.Time used on opensource projects

Example 1 with Time

use of org.hl7.elm.r1.Time 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;
}

Example 2 with Time

use of org.hl7.elm.r1.Time in project beneficiary-fhir-data by CMSgov.

the class HospiceClaimTransformer method transform.

/**
 * @param metricRegistry the {@link MetricRegistry} to use
 * @param claim the CCW {@link HospiceClaim} to transform
 * @param includeTaxNumbers whether or not to include tax numbers in the result (see {@link
 *     ExplanationOfBenefitResourceProvider#HEADER_NAME_INCLUDE_TAX_NUMBERS}, defaults to <code>
 *     false</code>)
 * @return a FHIR {@link ExplanationOfBenefit} resource that represents the specified {@link
 *     HospiceClaim}
 */
@Trace
static ExplanationOfBenefit transform(MetricRegistry metricRegistry, Object claim, Optional<Boolean> includeTaxNumbers) {
    Timer.Context timer = metricRegistry.timer(MetricRegistry.name(HospiceClaimTransformer.class.getSimpleName(), "transform")).time();
    if (!(claim instanceof HospiceClaim))
        throw new BadCodeMonkeyException();
    ExplanationOfBenefit eob = transformClaim((HospiceClaim) claim);
    timer.stop();
    return eob;
}

Example 3 with Time

use of org.hl7.elm.r1.Time in project beneficiary-fhir-data by CMSgov.

the class InpatientClaimTransformer method transform.

/**
 * @param metricRegistry the {@link MetricRegistry} to use
 * @param claim the CCW {@link InpatientClaim} to transform
 * @param includeTaxNumbers whether or not to include tax numbers in the result (see {@link
 *     ExplanationOfBenefitResourceProvider#HEADER_NAME_INCLUDE_TAX_NUMBERS}, defaults to <code>
 *     false</code>)
 * @return a FHIR {@link ExplanationOfBenefit} resource that represents the specified {@link
 *     InpatientClaim}
 */
@Trace
static ExplanationOfBenefit transform(MetricRegistry metricRegistry, Object claim, Optional<Boolean> includeTaxNumbers) {
    Timer.Context timer = metricRegistry.timer(MetricRegistry.name(InpatientClaimTransformer.class.getSimpleName(), "transform")).time();
    if (!(claim instanceof InpatientClaim))
        throw new BadCodeMonkeyException();
    ExplanationOfBenefit eob = transformClaim((InpatientClaim) claim);
    timer.stop();
    return eob;
}

Example 4 with Time

use of org.hl7.elm.r1.Time in project beneficiary-fhir-data by CMSgov.

the class PatientResourceProvider method queryDatabaseByHash.

/**
 * @param hash the {@link Beneficiary} hash value to match
 * @param hashType a string to represent the hash type (used for logging purposes)
 * @param requestHeader the {@link #RequestHeaders} where resource request headers are
 *     encapsulated
 * @param beneficiaryHashField the JPA location of the beneficiary hash field
 * @param beneficiaryHistoryHashField the JPA location of the beneficiary history hash field
 * @return a FHIR {@link Patient} for the CCW {@link Beneficiary} that matches the specified
 *     {@link Beneficiary} hash value
 * @throws NoResultException A {@link NoResultException} will be thrown if no matching {@link
 *     Beneficiary} can be found
 */
@Trace
private Patient queryDatabaseByHash(String hash, String hashType, SingularAttribute<Beneficiary, String> beneficiaryHashField, SingularAttribute<BeneficiaryHistory, String> beneficiaryHistoryHashField, RequestHeaders requestHeader) {
    if (hash == null || hash.trim().isEmpty())
        throw new IllegalArgumentException();
    /*
     * Beneficiaries' HICN/MBIs can change over time and those past HICN/MBIs may land in
     * BeneficiaryHistory records. Accordingly, we need to search for matching HICN/MBIs in both the
     * Beneficiary and the BeneficiaryHistory records.
     *
     * There's no sane way to do this in a single query with JPA 2.1, it appears: JPA doesn't
     * support UNIONs and it doesn't support subqueries in FROM clauses. That said, the ideal query
     * would look like this:
     *
     * SELECT * FROM ( SELECT DISTINCT "beneficiaryId" FROM "Beneficiaries" WHERE "hicn" =
     * :'hicn_hash' UNION SELECT DISTINCT "beneficiaryId" FROM "BeneficiariesHistory" WHERE "hicn" =
     * :'hicn_hash') AS matching_benes INNER JOIN "Beneficiaries" ON matching_benes."beneficiaryId"
     * = "Beneficiaries"."beneficiaryId" LEFT JOIN "BeneficiariesHistory" ON
     * "Beneficiaries"."beneficiaryId" = "BeneficiariesHistory"."beneficiaryId" LEFT JOIN
     * "MedicareBeneficiaryIdHistory" ON "Beneficiaries"."beneficiaryId" =
     * "MedicareBeneficiaryIdHistory"."beneficiaryId";
     *
     * ... with the returned columns and JOINs being dynamic, depending on IncludeIdentifiers.
     *
     * In lieu of that, we run two queries: one to find HICN/MBI matches in BeneficiariesHistory,
     * and a second to find BENE_ID or HICN/MBI matches in Beneficiaries (with all of their data, so
     * we're ready to return the result). This is bad and dumb but I can't find a better working
     * alternative.
     *
     * (I'll just note that I did also try JPA/Hibernate native SQL queries but couldn't get the
     * joins or fetch groups to work with them.)
     *
     * If we want to fix this, we need to move identifiers out entirely to separate tables:
     * BeneficiaryHicns and BeneficiaryMbis. We could then safely query these tables and join them
     * back to Beneficiaries (and hopefully the optimizer will play nice, too).
     */
    CriteriaBuilder builder = entityManager.getCriteriaBuilder();
    // First, find all matching hashes from BeneficiariesHistory.
    CriteriaQuery<String> beneHistoryMatches = builder.createQuery(String.class);
    Root<BeneficiaryHistory> beneHistoryMatchesRoot = beneHistoryMatches.from(BeneficiaryHistory.class);
    beneHistoryMatches.select(beneHistoryMatchesRoot.get(BeneficiaryHistory_.beneficiaryId));
    beneHistoryMatches.where(builder.equal(beneHistoryMatchesRoot.get(beneficiaryHistoryHashField), hash));
    List<String> matchingIdsFromBeneHistory = null;
    Long hicnsFromHistoryQueryNanoSeconds = null;
    Timer.Context beneHistoryMatchesTimer = metricRegistry.timer(MetricRegistry.name(getClass().getSimpleName(), "query", "bene_by_" + hashType, hashType + "s_from_beneficiarieshistory")).time();
    try {
        matchingIdsFromBeneHistory = entityManager.createQuery(beneHistoryMatches).getResultList();
    } finally {
        hicnsFromHistoryQueryNanoSeconds = beneHistoryMatchesTimer.stop();
        TransformerUtils.recordQueryInMdc("bene_by_" + hashType + "." + hashType + "s_from_beneficiarieshistory", hicnsFromHistoryQueryNanoSeconds, matchingIdsFromBeneHistory == null ? 0 : matchingIdsFromBeneHistory.size());
    }
    // Then, find all Beneficiary records that match the hash or those BENE_IDs.
    CriteriaQuery<Beneficiary> beneMatches = builder.createQuery(Beneficiary.class);
    Root<Beneficiary> beneMatchesRoot = beneMatches.from(Beneficiary.class);
    beneMatchesRoot.fetch(Beneficiary_.skippedRifRecords, JoinType.LEFT);
    if (requestHeader.isHICNinIncludeIdentifiers())
        beneMatchesRoot.fetch(Beneficiary_.beneficiaryHistories, JoinType.LEFT);
    if (requestHeader.isMBIinIncludeIdentifiers())
        beneMatchesRoot.fetch(Beneficiary_.medicareBeneficiaryIdHistories, JoinType.LEFT);
    beneMatches.select(beneMatchesRoot);
    Predicate beneHashMatches = builder.equal(beneMatchesRoot.get(beneficiaryHashField), hash);
    if (matchingIdsFromBeneHistory != null && !matchingIdsFromBeneHistory.isEmpty()) {
        Predicate beneHistoryHashMatches = beneMatchesRoot.get(Beneficiary_.beneficiaryId).in(matchingIdsFromBeneHistory);
        beneMatches.where(builder.or(beneHashMatches, beneHistoryHashMatches));
    } else {
        beneMatches.where(beneHashMatches);
    }
    List<Beneficiary> matchingBenes = Collections.emptyList();
    Long benesByHashOrIdQueryNanoSeconds = null;
    Timer.Context timerHicnQuery = metricRegistry.timer(MetricRegistry.name(getClass().getSimpleName(), "query", "bene_by_" + hashType, "bene_by_" + hashType + "_or_id")).time();
    try {
        matchingBenes = entityManager.createQuery(beneMatches).getResultList();
    } finally {
        benesByHashOrIdQueryNanoSeconds = timerHicnQuery.stop();
        TransformerUtils.recordQueryInMdc(String.format("bene_by_" + hashType + ".bene_by_" + hashType + "_or_id.include_%s", String.join("_", (List<String>) requestHeader.getValue(HEADER_NAME_INCLUDE_IDENTIFIERS))), benesByHashOrIdQueryNanoSeconds, matchingBenes.size());
    }
    // Then, if we found more than one distinct BENE_ID, or none, throw an error.
    long distinctBeneIds = matchingBenes.stream().map(Beneficiary::getBeneficiaryId).filter(Objects::nonNull).distinct().count();
    Beneficiary beneficiary = null;
    if (distinctBeneIds <= 0) {
        throw new NoResultException();
    } else if (distinctBeneIds > 1) {
        MDC.put("database_query.by_hash.collision.distinct_bene_ids", Long.toString(distinctBeneIds));
        throw new ResourceNotFoundException("By hash query found more than one distinct BENE_ID: " + Long.toString(distinctBeneIds));
    } else if (distinctBeneIds == 1) {
        beneficiary = matchingBenes.get(0);
    }
    // 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());
    }
    Patient patient = BeneficiaryTransformer.transform(metricRegistry, beneficiary, requestHeader);
    return patient;
}

Example 5 with Time

use of org.hl7.elm.r1.Time 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;
}