Examples with Annotation org.hl7.fhir.r5.model.Annotation used on opensource projects

Example 66 with Annotation

use of org.hl7.fhir.r5.model.Annotation in project clinical_quality_language by cqframework.

the class Cql2ElmVisitor method processTags.

private void processTags(ParseTree tree, Object o) {
    if (libraryBuilder.isCompatibleWith("1.5")) {
        if (o instanceof Element) {
            Element element = (Element) o;
            if (!(tree instanceof cqlParser.LibraryContext)) {
                if (element instanceof UsingDef || element instanceof IncludeDef || element instanceof CodeSystemDef || element instanceof ValueSetDef || element instanceof CodeDef || element instanceof ConceptDef || element instanceof ParameterDef || element instanceof ContextDef || element instanceof ExpressionDef) {
                    List<Tag> tags = getTags(tree);
                    if (tags != null && tags.size() > 0) {
                        Annotation a = getAnnotation(element);
                        if (a == null) {
                            a = buildAnnotation();
                            element.getAnnotation().add(a);
                        }
                        // tags, and there is currently nothing that would add tags other than being processed from comments
                        if (a.getT().size() == 0) {
                            a.getT().addAll(tags);
                        }
                    }
                }
            } else {
                if (libraryInfo.getDefinition() != null && libraryInfo.getHeaderInterval() != null) {
                    List<Tag> tags = getTags(libraryInfo.getHeader());
                    if (tags != null && tags.size() > 0) {
                        Annotation a = getAnnotation(libraryBuilder.getLibrary());
                        if (a == null) {
                            a = buildAnnotation();
                            libraryBuilder.getLibrary().getAnnotation().add(a);
                        }
                        a.getT().addAll(tags);
                    }
                }
            }
        }
    }
}

Example 67 with Annotation

use of org.hl7.fhir.r5.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class PatientResourceProvider 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.V1_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 = TransformerUtils.createBundle(paging, patients, loadedFilterManager.getTransactionTime());
    return bundle;
}

Example 68 with Annotation

use of org.hl7.fhir.r5.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class R4ExplanationOfBenefitResourceProvider method findByPatient.

/**
 * Adds support for the FHIR "search" operation for {@link ExplanationOfBenefit}s, allowing users
 * to search by {@link ExplanationOfBenefit#getPatient()}.
 *
 * <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 patient a {@link ReferenceParam} for the {@link ExplanationOfBenefit#getPatient()} to
 *     try and find matches for {@link ExplanationOfBenefit}s
 * @param type a list of {@link ClaimTypeV2} to include in the result. Defaults to all types.
 * @param startIndex an {@link OptionalParam} for the startIndex (or offset) used to determine
 *     pagination
 * @param excludeSamhsa an {@link OptionalParam} that, if <code>"true"</code>, will use {@link
 *     R4EobSamhsaMatcher} to filter out all SAMHSA-related claims from the results
 * @param lastUpdated an {@link OptionalParam} that specifies a date range for the lastUpdated
 *     field.
 * @param serviceDate an {@link OptionalParam} that specifies a date range for {@link
 *     ExplanationOfBenefit}s that completed
 * @param requestDetails a {@link RequestDetails} containing the details of the request URL, used
 *     to parse out pagination values
 * @return Returns a {@link Bundle} of {@link ExplanationOfBenefit}s, which may contain multiple
 *     matching resources, or may also be empty.
 */
@Search
@Trace
public Bundle findByPatient(@RequiredParam(name = ExplanationOfBenefit.SP_PATIENT) @Description(shortDefinition = "The patient identifier to search for") ReferenceParam patient, @OptionalParam(name = "type") @Description(shortDefinition = "A list of claim types to include") TokenAndListParam type, @OptionalParam(name = "startIndex") @Description(shortDefinition = "The offset used for result pagination") String startIndex, @OptionalParam(name = "excludeSAMHSA") @Description(shortDefinition = "If true, exclude all SAMHSA-related resources") String excludeSamhsa, @OptionalParam(name = "_lastUpdated") @Description(shortDefinition = "Include resources last updated in the given range") DateRangeParam lastUpdated, @OptionalParam(name = "service-date") @Description(shortDefinition = "Include resources that completed in the given range") DateRangeParam serviceDate, RequestDetails requestDetails) {
    /*
     * startIndex is an optional parameter here because it must be declared in the
     * event it is passed in. However, it is not being used here because it is also
     * contained within requestDetails and parsed out along with other parameters
     * later.
     */
    String beneficiaryId = patient.getIdPart();
    Set<ClaimTypeV2> claimTypes = parseTypeParam(type);
    OffsetLinkBuilder paging = new OffsetLinkBuilder(requestDetails, "/ExplanationOfBenefit?");
    boolean includeTaxNumbers = returnIncludeTaxNumbers(requestDetails);
    Operation operation = new Operation(Operation.Endpoint.V2_EOB);
    operation.setOption("by", "patient");
    operation.setOption("IncludeTaxNumbers", "" + includeTaxNumbers);
    operation.setOption("types", (claimTypes.size() == ClaimTypeV2.values().length) ? "*" : claimTypes.stream().sorted(Comparator.comparing(ClaimTypeV2::name)).collect(Collectors.toList()).toString());
    operation.setOption("pageSize", paging.isPagingRequested() ? "" + paging.getPageSize() : "*");
    operation.setOption("_lastUpdated", Boolean.toString(lastUpdated != null && !lastUpdated.isEmpty()));
    operation.setOption("service-date", Boolean.toString(serviceDate != null && !serviceDate.isEmpty()));
    operation.publishOperationName();
    List<IBaseResource> eobs = new ArrayList<IBaseResource>();
    // Optimize when the lastUpdated parameter is specified and result set is empty
    if (loadedFilterManager.isResultSetEmpty(beneficiaryId, lastUpdated)) {
        return TransformerUtilsV2.createBundle(paging, eobs, loadedFilterManager.getTransactionTime());
    }
    /*
     * The way our JPA/SQL schema is setup, we have to run a separate search for
     * each claim type, then combine the results. It's not super efficient, but it's
     * also not so inefficient that it's worth fixing.
     */
    if (claimTypes.contains(ClaimTypeV2.CARRIER)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.CARRIER, findClaimTypeByPatient(ClaimTypeV2.CARRIER, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.DME)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.DME, findClaimTypeByPatient(ClaimTypeV2.DME, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.HHA)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.HHA, findClaimTypeByPatient(ClaimTypeV2.HHA, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.HOSPICE)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.HOSPICE, findClaimTypeByPatient(ClaimTypeV2.HOSPICE, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.INPATIENT)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.INPATIENT, findClaimTypeByPatient(ClaimTypeV2.INPATIENT, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.OUTPATIENT)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.OUTPATIENT, findClaimTypeByPatient(ClaimTypeV2.OUTPATIENT, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.PDE)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.PDE, findClaimTypeByPatient(ClaimTypeV2.PDE, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (claimTypes.contains(ClaimTypeV2.SNF)) {
        eobs.addAll(transformToEobs(ClaimTypeV2.SNF, findClaimTypeByPatient(ClaimTypeV2.SNF, beneficiaryId, lastUpdated, serviceDate), Optional.of(includeTaxNumbers)));
    }
    if (Boolean.parseBoolean(excludeSamhsa)) {
        filterSamhsa(eobs);
    }
    eobs.sort(R4ExplanationOfBenefitResourceProvider::compareByClaimIdThenClaimType);
    // Add bene_id to MDC logs
    TransformerUtilsV2.logBeneIdToMdc(Arrays.asList(beneficiaryId));
    return TransformerUtilsV2.createBundle(paging, eobs, loadedFilterManager.getTransactionTime());
}

Example 69 with Annotation

use of org.hl7.fhir.r5.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class CoverageResourceProvider method read.

/**
 * Adds support for the FHIR "read" operation, for {@link Coverage}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 coverageId The read operation takes one parameter, which must be of type {@link IdType}
 *     and must be annotated with the {@link IdParam} annotation.
 * @return Returns a resource matching the specified {@link IdDt}, or <code>null</code> if none
 *     exists.
 */
@Read(version = false)
@Trace
public Coverage read(@IdParam IdType coverageId) {
    if (coverageId == null)
        throw new IllegalArgumentException();
    if (coverageId.getVersionIdPartAsLong() != null)
        throw new IllegalArgumentException();
    String coverageIdText = coverageId.getIdPart();
    if (coverageIdText == null || coverageIdText.trim().isEmpty())
        throw new IllegalArgumentException();
    Operation operation = new Operation(Operation.Endpoint.V1_COVERAGE);
    operation.setOption("by", "id");
    operation.publishOperationName();
    Matcher coverageIdMatcher = COVERAGE_ID_PATTERN.matcher(coverageIdText);
    if (!coverageIdMatcher.matches())
        throw new IllegalArgumentException("Unsupported ID pattern: " + coverageIdText);
    String coverageIdSegmentText = coverageIdMatcher.group(1);
    Optional<MedicareSegment> coverageIdSegment = MedicareSegment.selectByUrlPrefix(coverageIdSegmentText);
    if (!coverageIdSegment.isPresent())
        throw new ResourceNotFoundException(coverageId);
    String coverageIdBeneficiaryIdText = coverageIdMatcher.group(2);
    Beneficiary beneficiaryEntity;
    try {
        beneficiaryEntity = findBeneficiaryById(coverageIdBeneficiaryIdText, null);
        if (!beneficiaryEntity.getBeneEnrollmentReferenceYear().isPresent()) {
            throw new ResourceNotFoundException("Cannot find coverage for non present enrollment year");
        }
    } catch (NoResultException e) {
        throw new ResourceNotFoundException(new IdDt(Beneficiary.class.getSimpleName(), coverageIdBeneficiaryIdText));
    }
    Coverage coverage = CoverageTransformer.transform(metricRegistry, coverageIdSegment.get(), beneficiaryEntity);
    return coverage;
}

Example 70 with Annotation

use of org.hl7.fhir.r5.model.Annotation in project beneficiary-fhir-data by CMSgov.

the class ExplanationOfBenefitResourceProvider 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 a {@link RequestDetails} containing the details of the request URL, used
 *     to parse out header values
 * @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<ClaimType> eobIdType = ClaimType.parse(eobIdTypeText);
    Boolean includeTaxNumbers = returnIncludeTaxNumbers(requestDetails);
    if (!eobIdType.isPresent())
        throw new ResourceNotFoundException(eobId);
    String eobIdClaimIdText = eobIdMatcher.group(2);
    Operation operation = new Operation(Operation.Endpoint.V1_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();
        TransformerUtils.recordQueryInMdc("eob_by_id", eobByIdQueryNanoSeconds, claimEntity == null ? 0 : 1);
    }
    ExplanationOfBenefit eob = eobIdType.get().getTransformer().transform(metricRegistry, claimEntity, Optional.of(includeTaxNumbers));
    return eob;
}