All Classes Interface Summary Class Summary Enum Summary Exception Summary Annotation Types Summary
| Class |
Description |
| AbstractArg<T> |
Base class for non Object-specific functionality argument types, that can be malformed on input (E.g an argument
representing a number was a non-numeric string in the request).
|
| AbstractArrayArg<T> |
Represents a comma-delimited array API argument.
|
| AbstractEntityArg<T,O extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<O>> |
Interface representing and API call argument that can represent various identifiers of different types.
|
| AbstractEntityArgService<T extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<T>> |
|
| AbstractEntityArrayArg<O extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<O>> |
|
| AbstractExceptionMapper<E extends Throwable> |
|
| AbstractFactorValueValueObjectSerializer<T extends ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject> |
Base serializer for FactorValue VOs.
|
| AbstractGzipHeaderDecorator |
Base class for decorators that handle the GZIP annotation. |
| AccessDeniedExceptionMapper |
Map Spring Security's AccessDeniedException to a 403 Forbidden response.
|
| AnalysisResultSetsWebService |
Endpoint for AnalysisResultSet
|
| AnalysisResultSetsWebService.PaginatedResultsResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject |
|
| AnalyticsApplicationEventListener |
|
| AnalyticsProvider |
Interface for analytics providers.
|
| AnalyticsRequestEventListener |
Request event listener that publishes an event when a request is finished.
|
| AnnotationsWebService |
RESTful interface for annotations.
|
| AnnotationsWebService.AnnotationSearchResultValueObject |
|
| Arg<T> |
|
| ArgUtils |
Utilities for working with Arg. |
| AuthenticationBasedUserIdRetrievalStrategy |
Strategy for the user ID that uses the authentication object from the SecurityContextHolder.
|
| AuthenticationExceptionMapper |
Handles Spring Security AuthenticationException by producing a 403 Forbidden response.
|
| BuildInfoValueObject |
|
| CacheControl |
|
| CacheControlHeaderDecorator |
|
| CacheControls |
|
| ClientIdRetrievalStrategy |
Strategy for retrieving a client ID.
|
| CompositeClientIdRetrievalStrategy |
Composite strategy for retrieving client ID.
|
| CompositeSequenceArg<T> |
Mutable argument type base class for Composite Sequence arguments.
|
| CompositeSequenceArgService |
|
| CompositeSequenceArrayArg |
|
| CompositeSequenceIdArg |
Composite Sequence argument for CS ID.
|
| CompositeSequenceNameArg |
Composite Sequence argument for CS name.
|
| CorsFilter |
Filter for adding CORS headers to the RESTful API responses.
|
| CustomModelResolver |
Resolve Arg parameters' schema. |
| DatabaseEntryArg<T> |
Mutable argument type base class for DatabaseEntry API.
|
| DatabaseEntryArgService |
|
| DatabaseEntryArrayArg |
|
| DatabaseEntryIdArg |
Long argument type for DatabaseEntry API, referencing the Taxon ID.
|
| DatabaseEntryStringArg |
String argument type for DatabaseEntry API, Can also be null.
|
| DatasetArg<T> |
Mutable argument type base class for dataset (ExpressionExperiment) API.
|
| DatasetArgService |
|
| DatasetArrayArg |
|
| DatasetIdArg |
Long argument type for dataset API, referencing the Dataset ID.
|
| DatasetStringArg |
String argument type for dataset API, referencing the Dataset short name.
|
| DatasetsWebService |
RESTful interface for datasets.
|
| DatasetsWebService.AnnotationWithUsageStatisticsValueObject |
This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
|
| DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject |
|
| DatasetsWebService.BatchConfoundValueObject |
|
| DatasetsWebService.BatchEffectStatisticsValueObject |
|
| DatasetsWebService.BatchInformationValueObject |
|
| DatasetsWebService.CategoryWithUsageStatisticsValueObject |
|
| DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject |
|
| DatasetsWebService.ExpressionExperimentSubSetGroupValueObject |
A group of subsets, logically organized by a BioAssayDimension.
|
| DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject |
|
| DatasetsWebService.ExpressionExperimentSubSetWithGroupsValueObject |
|
| DatasetsWebService.ExpressionExperimentWithSearchResultValueObject |
|
| DatasetsWebService.FilteredAndInferredAndPaginatedResponseDataObject<T> |
|
| DatasetsWebService.OntologyTermValueObject |
|
| DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<T> |
|
| DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<T> |
|
| DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject |
|
| DatasetsWebService.QueriedAndFilteredAndInferredResponseDataObject<T> |
|
| DatasetsWebService.ResponseDataObjectCellTypeAssignmentValueObject |
|
| DatasetsWebService.ResponseDataObjectExpressionExperimentValueObject |
|
| DatasetsWebService.ResponseDataObjectListCellLevelCharacteristicsValueObject |
|
| DatasetsWebService.ResponseDataObjectSingleCellDimensionValueObject |
|
| DatasetsWebService.SimpleSVDValueObject |
|
| DatasetsWebService.TaxonWithUsageStatisticsValueObject |
|
| DatasetsWebService.UsageStatistics |
|
| EntityArgService<T extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<T>> |
Bridges Arg operating on entities with their corresponding FilteringService. |
| EntityNotFoundException |
|
| ExcludeArg<T> |
|
| ExpLevelConsolidationArg |
Class representing an API argument that should be one of the expression level consolidation options.
|
| ExpressionAnalysisResultSetArg |
Represents an expression analysis result set identifier.
|
| ExpressionAnalysisResultSetArgService |
|
| FactorValueArg<A> |
Represents an API arguments that maps to a FactorValue by its ID or name.
|
| FactorValueBasicValueObjectSerializer |
|
| FactorValueIdArg |
Maps a long identifier to a FactorValue.
|
| FactorValueValueArg |
Deprecated. |
| FactorValueValueObjectSerializer |
Deprecated. |
| FilterArg<O extends ubic.gemma.model.common.Identifiable> |
Represent a filter argument designed to generate a Filters from user input.
|
| FilterArg.Filter |
Represents the internal value of a FilterArg. |
| FilterArgBaseListener |
This class provides an empty implementation of FilterArgListener,
which can be extended to create a listener which only needs to handle a subset
of the available methods. |
| FilterArgLexer |
|
| FilterArgListener |
This interface defines a complete listener for a parse tree produced by
FilterArgParser. |
| FilterArgParser |
|
| FilterArgParser.ClauseContext |
|
| FilterArgParser.CollectionContext |
|
| FilterArgParser.CollectionOperatorContext |
|
| FilterArgParser.DisjunctionContext |
|
| FilterArgParser.FilterContext |
|
| FilterArgParser.OperatorContext |
|
| FilterArgParser.PredicateContext |
|
| FilterArgParser.QuantifierContext |
|
| FilterArgParser.ScalarContext |
|
| FilterArgParser.SubClauseContext |
|
| FilteredAndLimitedResponseDataObject<T> |
|
| FilteredAndPaginatedResponseDataObject<T> |
|
| FilteredResponseDataObject<T> |
|
| GeneArg<T> |
Mutable argument type base class for Gene API.
|
| GeneArgService |
|
| GeneArrayArg |
|
| GeneEnsemblIdArg |
Long argument type for Gene API, referencing the Gene Ensembl ID.
|
| GeneNcbiIdArg |
Long argument type for Gene API, referencing the Gene NCBI ID.
|
| GeneSymbolArg |
String argument type for Gene API.
|
| GeneWebService |
RESTful interface for genes.
|
| GoogleAnalytics4Provider |
Implementation of the AnalyticsProvider interface for Google Analytics 4 collect API. |
| GZIP |
Used to annotate endpoints that will have their payload compressed with gzip unconditionally.
|
| GzipHeaderDecorator |
Automagically add the Content-Encoding: gzip header to endpoints annotated with GZIP. |
| GzipHeaderDecoratorAfterGZipEncoder |
Adds a Content-Encoding: gzip after the context has been intercepted by GZipEncoder.
|
| JacksonConfig |
Configuration for JSON serialization with Jackson.
|
| LimitArg |
Argument used to represent a limit.
|
| LocationType |
|
| LockedPathProvider |
Write a LockedPath to a message body and ensure that the lock is released.
|
| MalformedArgException |
Specialized error for malformed Arg
The recommended HTTP status for this exception is 400 Bad Request. |
| MalformedArgExceptionMapper |
|
| MediaTypeUtils |
Utilities for MediaType.
|
| MetricsApplicationEventListener |
|
| MexBundlerProvider |
|
| NotFoundExceptionMapper |
This mapper ensures that raised NotFoundException throughout the API contain well-formed ResponseErrorObject
entity. |
| ObjectMapperResolver |
|
| OffsetArg |
Argument used to represent an offset.
|
| OpenApiConfig |
|
| OpenApiFactory |
Factory for OpenAPI.
|
| OpenApiGzipHeaderDecorator |
Decorate the OpenAPI spec with a Content-Encoding: gzip header.
|
| OpenAPIVisitor |
Visits an OpenAPI specification and perform string value resolution.
|
| PaginatedResponseDataObject<T> |
Represents paginated results with offset and limit.
|
| PathProvider |
Allow for reading and writing Path objects. |
| PlatformArg<T> |
Mutable argument type base class for dataset (ExpressionExperiment) API.
|
| PlatformArgService |
|
| PlatformArrayArg |
|
| PlatformIdArg |
Long argument type for platform API, referencing the platform ID.
|
| PlatformStringArg |
String argument type for platform API, referencing the Platform short name.
|
| PlatformsWebService |
RESTful interface for platforms.
|
| QuantitationTypeArg<T> |
|
| QuantitationTypeArgService |
|
| QuantitationTypeByIdArg |
|
| QuantitationTypeByNameArg |
|
| QueriedAndFilteredAndLimitedResponseDataObject<T> |
Represents a payload with a limited number of results.
|
| QueriedAndFilteredAndPaginatedResponseDataObject<T> |
|
| QueriedAndFilteredResponseDataObject<T> |
|
| QueryArg |
|
| RequestAttributesBasedClientIdRetrievalStrategy |
Strategy that retrieves and store client IDs in the RequestAttributes.
|
| RequestExceptionLogger |
|
| RequestHeaderBasedClientIdRetrievalStrategy |
Strategy that retrieves the client ID in a request header.
|
| Responders |
Handles setting of the response status code and composing a proper payload structure.
|
| Responders.FilterMethod<T> |
A functional interface matching the signature of a paginating service method.
|
| ResponseDataObject<T> |
|
| ResponseErrorObject |
|
| RestapidocsIndexRewriteFilter |
Rewrites the path to the index file.
|
| RestAuthEntryPoint |
Implementation of AuthenticationEntryPoint for the RESTful API to handle authentication.
|
| RootWebService |
Handles calls to the root API url and user info api
|
| RootWebService.ApiInfoValueObject |
|
| RootWebService.UserValueObject |
|
| SearchWebService |
Provides search capabilities to the RESTful API.
|
| SearchWebService.SearchResultsResponseDataObject |
|
| SearchWebService.SearchResultValueObject<T extends ubic.gemma.model.common.IdentifiableValueObject<?>> |
Representation of SearchResult for the RESTful API.
|
| SortArg<O extends ubic.gemma.model.common.Identifiable> |
Represents an API argument for sorting.
|
| SortArg.Sort |
|
| SortArg.Sort.Direction |
|
| SortArg.Sort.NullMode |
|
| SortValueObject |
|
| StringArrayArg |
Class representing an API argument that should be an array of strings.
|
| TaxaWebService |
RESTful interface for taxa.
|
| TaxonArg<T> |
Mutable argument type base class for Taxon API
|
| TaxonArgService |
|
| TaxonArrayArg |
|
| TaxonIdArg |
Long argument type for taxon API, referencing the Taxon ID.
|
| TaxonNameArg |
String argument type for taxon API, referencing the Taxon scientific name or common name.
|
| TaxonNcbiIdArg |
Long argument type for taxon API, referencing the Taxon ID.
|
| UnhandledExceptionMapper |
Render unhandled exceptions.
|
| UserIdRetrievalStrategy |
Strategy for retrieving a user ID.
|
| WebApplicationExceptionMapper |
|
| WellComposedError |
|
| WellComposedErrorBody |
Object acting as a payload for the ResponseErrorObject.
|
| WellComposedWarning |
|