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> |
Class representing an API argument that should be an array.
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| AbstractEntityArg<T,O extends Identifiable,S extends FilteringService<O>> |
Interface representing and API call argument that can represent various identifiers of different types.
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| AbstractEntityArgService<T extends Identifiable,S extends FilteringService<T>> |
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| AbstractEntityArrayArg<O extends Identifiable,S extends FilteringService<O>> |
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| AbstractExceptionMapper<E extends Throwable> |
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| AbstractFactorValueValueObjectSerializer<T> |
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| AccessDeniedExceptionMapper |
Map Spring Security's AccessDeniedException to a 403 Forbidden response.
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| AnalysisResultSetsWebService |
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| AnalyticsApplicationEventListener |
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| AnalyticsProvider |
Interface for analytics providers.
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| AnalyticsRequestEventListener |
Request event listener that publishes an event when a request is finished.
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| AnnotationsWebService |
RESTful interface for annotations.
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| AnnotationsWebService.AnnotationSearchResultValueObject |
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| Arg<T> |
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| ArgUtils |
Utilities for working with Arg. |
| AuthenticationBasedUserIdRetrievalStrategy |
Strategy for the user ID that uses the authentication object from the SecurityContextHolder.
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| AuthenticationExceptionMapper |
Handles Spring Security AuthenticationException by producing a 403 Forbidden response.
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| CacheControl |
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| CacheControlHeaderDecorator |
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| CacheControls |
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| ClientIdRetrievalStrategy |
Strategy for retrieving a client ID.
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| CompositeClientIdRetrievalStrategy |
Composite strategy for retrieving client ID.
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| CompositeSequenceArg<T> |
Mutable argument type base class for Composite Sequence arguments.
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| CompositeSequenceArgService |
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| CompositeSequenceArrayArg |
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| CompositeSequenceIdArg |
Composite Sequence argument for CS ID.
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| CompositeSequenceNameArg |
Composite Sequence argument for CS name.
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| CorsFilter |
Filter for adding CORS headers to the RESTful API responses.
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| CustomModelResolver |
Resolve Arg parameters' schema. |
| CustomModelResolverRegistrationListener |
Registers our customized ModelResolver.
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| DatabaseEntryArg<T> |
Mutable argument type base class for DatabaseEntry API.
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| DatabaseEntryArgService |
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| DatabaseEntryArrayArg |
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| DatabaseEntryIdArg |
Long argument type for DatabaseEntry API, referencing the Taxon ID.
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| DatabaseEntryStringArg |
String argument type for DatabaseEntry API, Can also be null.
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| DatasetArg<T> |
Mutable argument type base class for dataset (ExpressionExperiment) API.
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| DatasetArgService |
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| DatasetArrayArg |
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| DatasetIdArg |
Long argument type for dataset API, referencing the Dataset ID.
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| DatasetStringArg |
String argument type for dataset API, referencing the Dataset short name.
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| DatasetsWebService |
RESTful interface for datasets.
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| DatasetsWebService.AnnotationWithUsageStatisticsValueObject |
This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
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| DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject |
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| DatasetsWebService.CategoryWithUsageStatisticsValueObject |
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| DatasetsWebService.ExpressionExperimentWithSearchResultValueObject |
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| DatasetsWebService.OntologyTermValueObject |
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| DatasetsWebService.TaxonWithUsageStatisticsValueObject |
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| DatasetsWebService.UsageStatistics |
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| EntityArgService<T extends Identifiable,S extends FilteringService<T>> |
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| EntityNotFoundException |
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| EntityNotFoundExceptionMapper |
Deprecated. |
| ExceptionMapperUtils |
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| ExcludeArg<T> |
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| ExpLevelConsolidationArg |
Class representing an API argument that should be one of the expression level consolidation options.
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| ExpressionAnalysisResultSetArg |
Represents an expression analysis result set identifier.
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| ExpressionAnalysisResultSetArgService |
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| FactorValueArg<A> |
Represents an API arguments that maps to a FactorValue by its ID or name. |
| FactorValueArrayArg |
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| FactorValueBasicValueObjectSerializer |
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| FactorValueIdArg |
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| FactorValueValueArg |
Deprecated. |
| FactorValueValueObjectSerializer |
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| FilterArg<O extends 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 |
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| FilterArgParser.ClauseContext |
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| FilterArgParser.CollectionContext |
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| FilterArgParser.CollectionOperatorContext |
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| FilterArgParser.DisjunctionContext |
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| FilterArgParser.FilterContext |
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| FilterArgParser.OperatorContext |
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| FilterArgParser.ScalarContext |
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| FilterArgParser.SubClauseContext |
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| FilteredAndPaginatedResponseDataObject<T> |
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| FilteredResponseDataObject<T> |
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| GeneAnyIdArg<T> |
Base class for GeneArg representing any of the identifiers of a Gene.
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| GeneArg<T> |
Mutable argument type base class for Gene API.
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| GeneArgService |
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| GeneArrayArg |
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| GeneEnsemblIdArg |
Long argument type for Gene API, referencing the Gene Ensembl ID.
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| GeneNcbiIdArg |
Long argument type for Gene API, referencing the Gene NCBI ID.
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| GeneSymbolArg |
String argument type for Gene API.
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| 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 GZIPOutputStream
unconditionally. |
| GzipHeaderDecorator |
Automagically add the Content-Encoding: gzip header to endpoints annotated with GZIP. |
| JacksonConfig |
Configure the various beans injected in Swagger's components relating to Jackson's JSON serialization.
|
| JsonMappingExceptionMapper |
Mapper that creates a well composed error body response out of a JsonMappingException.
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| LimitArg |
Argument used to represent a limit.
|
| LimitedResponseDataObject<T> |
Represents a payload with a limited number of results.
|
| MalformedArgException |
Specialized error for malformed Arg
The recommended HTTP status for this exception is 400 Bad Request. |
| MalformedArgExceptionMapper |
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| MediaTypeUtils |
Utilities for MediaType.
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| MetricsApplicationEventListener |
|
| NotFoundExceptionMapper |
This mapper ensures that raised NotFoundException throughout the API contain well-formed ResponseErrorObject
entity. |
| ObjectMapperResolver |
|
| OffsetArg |
Argument used to represent an offset.
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| OpenApiUtils |
Utilities for interacting with OpenAPI at runtime.
|
| PaginatedResponseDataObject<T> |
Represents paginated results with offset and limit.
|
| PhenotypeWebService |
Deprecated. |
| PlatformArg<T> |
Mutable argument type base class for dataset (ExpressionExperiment) API.
|
| PlatformArgService |
|
| PlatformArrayArg |
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| PlatformIdArg |
Long argument type for platform API, referencing the platform ID.
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| PlatformStringArg |
String argument type for platform API, referencing the Platform short name.
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| PlatformsWebService |
RESTful interface for platforms.
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| QuantitationTypeArg<T> |
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| QuantitationTypeArgService |
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| QuantitationTypeByIdArg |
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| QuantitationTypeByNameArg |
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| QueriedAndFilteredAndPaginatedResponseDataObject<T> |
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| QueriedAndFilteredResponseDataObject<T> |
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| QueryArg |
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| RequestAttributesBasedClientIdRetrievalStrategy |
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| RequestExceptionEventListener |
Listen and dispatch ApplicationEvent.
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| RequestExceptionLogger |
Log request exceptions.
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| RequestHeaderBasedClientIdRetrievalStrategy |
Strategy that retrieves the client ID in a request header.
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| Responder |
Handles setting of the response status code and composing a proper payload structure.
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| Responder.FilterMethod<T> |
A functional interface matching the signature of a paginating service method.
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| ResponseDataObject<T> |
|
| ResponseErrorObject |
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| 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 IdentifiableValueObject<?>> |
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| ServletUtils |
|
| SortArg<O extends Identifiable> |
Class representing an API argument that should be an integer.
|
| SortArg.Sort |
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| SortArg.Sort.Direction |
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| SortValueObject |
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| 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.
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| WebApplicationExceptionMapper |
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| WellComposedErrorBody |
Object acting as a payload for the ResponseErrorObject.
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