Examples with WORKING org.hl7.fhir.dstu3.model.ListResource.ListMode.WORKING used on opensource projects

Example 1 with WORKING

use of org.hl7.fhir.dstu3.model.ListResource.ListMode.WORKING 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 2 with WORKING

use of org.hl7.fhir.dstu3.model.ListResource.ListMode.WORKING in project beneficiary-fhir-data by CMSgov.

the class R4ExplanationOfBenefitResourceProviderIT method assertEobEquals.

/**
 * Compares two ExplanationOfBenefit objects in detail while working around serialization issues
 * like comparing "0" and "0.0" or creation differences like using "Quantity" vs "SimpleQuantity"
 *
 * @param expected the expected
 * @param actual the actual
 */
private static void assertEobEquals(ExplanationOfBenefit expected, ExplanationOfBenefit actual) {
    // ID in the bundle will have `ExplanationOfBenefit/` in front, so make sure the last bit
    // matches up
    assertTrue(actual.getId().endsWith(expected.getId()));
    // Clean them out so we can do a deep compare later
    actual.setId("");
    expected.setId("");
    // If there are any contained resources, they might have lastupdate times in them too
    assertEquals(expected.getContained().size(), actual.getContained().size());
    for (int i = 0; i < expected.getContained().size(); i++) {
        Resource expectedContained = expected.getContained().get(i);
        Resource actualContained = actual.getContained().get(i);
        expectedContained.getMeta().setLastUpdated(null);
        actualContained.getMeta().setLastUpdated(null);
        // TODO: HAPI seems to be inserting the `#` in the ID of the contained element.
        // This is incorrect according to the FHIR spec:
        // https://build.fhir.org/references.html#contained
        // This works around that problem
        assertEquals("#" + expectedContained.getId(), actualContained.getId());
        expectedContained.setId("");
        actualContained.setId("");
    }
    // Dates are not easy to compare so just make sure they are there
    assertNotNull(actual.getMeta().getLastUpdated());
    // We compared all of meta that we care about so get it out of the way
    expected.getMeta().setLastUpdated(null);
    actual.getMeta().setLastUpdated(null);
    // Created is required, but can't be compared
    assertNotNull(actual.getCreated());
    expected.setCreated(null);
    actual.setCreated(null);
    // Extensions may have `valueMoney` elements
    assertEquals(expected.getExtension().size(), actual.getExtension().size());
    for (int i = 0; i < expected.getExtension().size(); i++) {
        Extension expectedEx = expected.getExtension().get(i);
        Extension actualEx = actual.getExtension().get(i);
        // We have to deal with Money objects separately
        if (expectedEx.hasValue() && expectedEx.getValue() instanceof Money) {
            assertTrue(actualEx.getValue() instanceof Money);
            assertCurrencyEquals((Money) expectedEx.getValue(), (Money) actualEx.getValue());
            // Now remove since we validated so we can compare the rest directly
            expectedEx.setValue(null);
            actualEx.setValue(null);
        }
    }
    // SupportingInfo can have `valueQuantity` that has the 0 vs 0.0 issue
    assertEquals(expected.getSupportingInfo().size(), actual.getSupportingInfo().size());
    for (int i = 0; i < expected.getSupportingInfo().size(); i++) {
        SupportingInformationComponent expectedSup = expected.getSupportingInfo().get(i);
        SupportingInformationComponent actualSup = actual.getSupportingInfo().get(i);
        // We have to deal with Money objects separately
        if (expectedSup.hasValueQuantity()) {
            assertTrue(actualSup.hasValueQuantity());
            assertEquals(expectedSup.getValueQuantity().getValue().floatValue(), actualSup.getValueQuantity().getValue().floatValue(), 0.0);
            // Now remove since we validated so we can compare the rest directly
            expectedSup.setValue(null);
            actualSup.setValue(null);
        }
    }
    // line items
    assertEquals(expected.getItem().size(), actual.getItem().size());
    for (int i = 0; i < expected.getItem().size(); i++) {
        ItemComponent expectedItem = expected.getItem().get(i);
        ItemComponent actualItem = actual.getItem().get(i);
        // Compare value directly because SimpleQuantity vs Quantity can't be compared
        assertEquals(expectedItem.getQuantity().getValue().floatValue(), actualItem.getQuantity().getValue().floatValue(), 0.0);
        expectedItem.setQuantity(null);
        actualItem.setQuantity(null);
        assertEquals(expectedItem.getAdjudication().size(), actualItem.getAdjudication().size());
        for (int j = 0; j < expectedItem.getAdjudication().size(); j++) {
            AdjudicationComponent expectedAdj = expectedItem.getAdjudication().get(j);
            AdjudicationComponent actualAdj = actualItem.getAdjudication().get(j);
            // Here is where we start getting into trouble with "0" vs "0.0", so we do this manually
            if (expectedAdj.hasAmount()) {
                assertNotNull(actualAdj.getAmount());
                assertCurrencyEquals(expectedAdj.getAmount(), actualAdj.getAmount());
            } else {
                // If expected doesn't have an amount, actual shouldn't
                assertFalse(actualAdj.hasAmount());
            }
            // We just checked manually, so null them out and check the rest of the fields
            expectedAdj.setAmount(null);
            actualAdj.setAmount(null);
        }
    }
    // Total has the same problem with values
    assertEquals(expected.getTotal().size(), actual.getTotal().size());
    for (int i = 0; i < expected.getTotal().size(); i++) {
        TotalComponent expectedTot = expected.getTotal().get(i);
        TotalComponent actualTot = actual.getTotal().get(i);
        if (expectedTot.hasAmount()) {
            assertNotNull(actualTot.getAmount());
            assertCurrencyEquals(expectedTot.getAmount(), actualTot.getAmount());
        } else {
            // If expected doesn't have an amount, actual shouldn't
            assertFalse(actualTot.hasAmount());
        }
        expectedTot.setAmount(null);
        actualTot.setAmount(null);
    }
    // Benefit Balance Financial components
    assertEquals(expected.getBenefitBalance().size(), actual.getBenefitBalance().size());
    for (int i = 0; i < expected.getBenefitBalance().size(); i++) {
        BenefitBalanceComponent expectedBen = expected.getBenefitBalance().get(i);
        BenefitBalanceComponent actualBen = actual.getBenefitBalance().get(i);
        assertEquals(expectedBen.getFinancial().size(), actualBen.getFinancial().size());
        for (int j = 0; j < expectedBen.getFinancial().size(); j++) {
            BenefitComponent expectedFinancial = expectedBen.getFinancial().get(j);
            BenefitComponent actualFinancial = actualBen.getFinancial().get(j);
            // Are we dealing with Money?
            if (expectedFinancial.hasUsedMoney()) {
                assertNotNull(actualFinancial.getUsedMoney());
                assertCurrencyEquals(expectedFinancial.getUsedMoney(), actualFinancial.getUsedMoney());
                // Clean up
                expectedFinancial.setUsed(null);
                actualFinancial.setUsed(null);
            }
        }
    }
    // As does payment
    if (expected.hasPayment()) {
        assertTrue(actual.hasPayment());
        assertCurrencyEquals(expected.getPayment().getAmount(), actual.getPayment().getAmount());
    } else {
        // If expected doesn't have an amount, actual shouldn't
        assertFalse(actual.hasPayment());
    }
    expected.getPayment().setAmount(null);
    actual.getPayment().setAmount(null);
    // Now for the grand finale, we can do an `equalsDeep` on the rest
    assertTrue(expected.equalsDeep(actual));
}

Example 3 with WORKING

use of org.hl7.fhir.dstu3.model.ListResource.ListMode.WORKING in project beneficiary-fhir-data by CMSgov.

the class R4ExplanationOfBenefitResourceProviderIT method searchForEobsIncludeTaxNumbersHandling.

/**
 * Verifies that {@link
 * gov.cms.bfd.server.war.r4.providers.ExplanationOfBenefitResourceProvider#findByPatient(ca.uhn.fhir.rest.param.ReferenceParam)}
 * handles the {@link ExplanationOfBenefitResourceProvider#HEADER_NAME_INCLUDE_TAX_NUMBERS} header
 * properly.
 *
 * @throws FHIRException (indicates test failure)
 */
// TODO: Fix this test .. it isn't working. Tax number is not showing up.
@Test
public void searchForEobsIncludeTaxNumbersHandling() throws FHIRException {
    List<Object> loadedRecords = ServerTestUtils.get().loadData(Arrays.asList(StaticRifResourceGroup.SAMPLE_A.getResources()));
    IGenericClient fhirClient = ServerTestUtils.get().createFhirClientV2();
    Beneficiary beneficiary = loadedRecords.stream().filter(r -> r instanceof Beneficiary).map(r -> (Beneficiary) r).findFirst().get();
    CarrierClaim carrierClaim = loadedRecords.stream().filter(r -> r instanceof CarrierClaim).map(r -> (CarrierClaim) r).findFirst().get();
    DMEClaim dmeClaim = loadedRecords.stream().filter(r -> r instanceof DMEClaim).map(r -> (DMEClaim) r).findFirst().get();
    Bundle searchResults;
    ExplanationOfBenefit carrierEob;
    ExplanationOfBenefit dmeEob;
    // Run the search without requesting tax numbers.
    searchResults = fhirClient.search().forResource(ExplanationOfBenefit.class).where(ExplanationOfBenefit.PATIENT.hasId(TransformerUtilsV2.buildPatientId(beneficiary))).returnBundle(Bundle.class).execute();
    assertNotNull(searchResults);
    // Verify that tax numbers aren't present for carrier claims.
    carrierEob = filterToClaimType(searchResults, ClaimTypeV2.CARRIER).get(0);
    assertNull(TransformerTestUtilsV2.findCareTeamEntryForProviderTaxNumber(carrierClaim.getLines().get(0).getProviderTaxNumber(), carrierEob.getCareTeam()));
    // Verify that tax numbers aren't present for DME claims.
    dmeEob = filterToClaimType(searchResults, ClaimTypeV2.DME).get(0);
    assertNull(TransformerTestUtilsV2.findCareTeamEntryForProviderTaxNumber(dmeClaim.getLines().get(0).getProviderTaxNumber(), dmeEob.getCareTeam()));
    RequestHeaders requestHeader = RequestHeaders.getHeaderWrapper(CommonHeaders.HEADER_NAME_INCLUDE_TAX_NUMBERS, "true");
    fhirClient = ServerTestUtils.get().createFhirClientWithHeadersV2(requestHeader);
    searchResults = fhirClient.search().forResource(ExplanationOfBenefit.class).where(ExplanationOfBenefit.PATIENT.hasId(TransformerUtilsV2.buildPatientId(beneficiary))).returnBundle(Bundle.class).execute();
    assertNotNull(searchResults);
}

Example 4 with WORKING

use of org.hl7.fhir.dstu3.model.ListResource.ListMode.WORKING in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7EventTypeFHIRConversionTest method validate_evn_segment_no_period_override.

@Test
void validate_evn_segment_no_period_override() {
    String hl7message = "MSH|^~\\&|||||||ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r" + // + "EVN||||7525||20210319134735|\r"  // TODO, not working with this value
    "EVN||||O||20210319134735|\r" + "PV1|1|I||R|||||||||R|1||||||||||||||||||||||||||||||200603150624|200603150625|||||||";
    String json = ftv.convert(hl7message, OPTIONS);
    assertThat(json).isNotBlank();
    FHIRContext context = new FHIRContext();
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    // Find the encounter from the FHIR bundle.
    List<Resource> encounterResource = e.stream().filter(v -> ResourceType.Encounter == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(encounterResource).hasSize(1);
    Encounter encounter = (Encounter) encounterResource.get(0);
    // ENV.4 is used for reasonCode
    List<CodeableConcept> reasonCodes = encounter.getReasonCode();
    assertEquals(1, reasonCodes.size());
    CodeableConcept encounterReason = encounter.getReasonCodeFirstRep();
    Coding encounterReasonCoding = encounterReason.getCodingFirstRep();
    // assertThat(encounterReasonCoding.getCode()).isEqualTo("7525");  // TODO, should be able to use user-defined values
    assertThat(encounterReasonCoding.getCode()).isEqualTo("O");
    // EVN.6 is used for start period if there is no PV1.44 but since we have a
    // PV1.44 it should use that not EVN.6
    Base period = encounter.getNamedProperty("period").getValues().get(0);
    String startPeriod = period.getNamedProperty("start").getValues().get(0).toString();
    // And use PV1.45 for end period.
    String endPeriod = period.getNamedProperty("end").getValues().get(0).toString();
    assertThat(startPeriod).isEqualTo("DateTimeType[2006-03-15T06:24:00+08:00]");
    assertThat(endPeriod).isEqualTo("DateTimeType[2006-03-15T06:25:00+08:00]");
}

Example 5 with WORKING

use of org.hl7.fhir.dstu3.model.ListResource.ListMode.WORKING in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7EventTypeFHIRConversionTest method validate_evn_segment.

@Test
void validate_evn_segment() {
    String hl7message = "MSH|^~\\&|||||||ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r" + // + "EVN||||851||20210319134735|\r"  // TODO, not working with this value
    "EVN||||O||20210319134735|\r" + "PV1|1|I||R|||||||||R|1||||||||||||||||||||||||||||||||||||||";
    String json = ftv.convert(hl7message, OPTIONS);
    assertThat(json).isNotBlank();
    FHIRContext context = new FHIRContext(true, false);
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    // Find the encounter from the FHIR bundle.
    List<Resource> encounterResource = e.stream().filter(v -> ResourceType.Encounter == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(encounterResource).hasSize(1);
    Encounter encounter = (Encounter) encounterResource.get(0);
    // ENV.4 is used for reasonCode
    List<CodeableConcept> reasonCodes = encounter.getReasonCode();
    assertEquals(1, reasonCodes.size());
    CodeableConcept encounterReason = encounter.getReasonCodeFirstRep();
    Coding encounterReasonCoding = encounterReason.getCodingFirstRep();
    // assertThat(encounterReasonCoding.getCode()).isEqualTo("851");  // TODO, should be able to use user-defined values
    assertThat(encounterReasonCoding.getCode()).isEqualTo("O");
    // EVN.6 is used for start period (with no end) if there is no PV1.44
    Base period = encounter.getNamedProperty("period").getValues().get(0);
    String startPeriod = period.getNamedProperty("start").getValues().get(0).toString();
    int endPeriodSize = period.getNamedProperty("end").getValues().size();
    assertThat(startPeriod).isEqualTo("DateTimeType[2021-03-19T13:47:35+08:00]");
    assertThat(endPeriodSize).isZero();
}