use of org.hl7.fhir.r4b.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);
}
}
}
}
}
}
use of org.hl7.fhir.r4b.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;
}
use of org.hl7.fhir.r4b.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());
}
use of org.hl7.fhir.r4b.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;
}
use of org.hl7.fhir.r4b.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;
}
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