Index (Gemma REST 1.30.0 API)

A C D E F G I J L M N O P Q R S T U V W _

A

AbstractArg<T> - Class in ubic.gemma.rest.util.args: 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).
AbstractArg(T) - Constructor for class ubic.gemma.rest.util.args.AbstractArg: Constructor for well-formed value.
AbstractArrayArg<T> - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an array.
AbstractArrayArg(List<T>) - Constructor for class ubic.gemma.rest.util.args.AbstractArrayArg
AbstractEntityArg<T,O extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<O>> - Class in ubic.gemma.rest.util.args: Interface representing and API call argument that can represent various identifiers of different types.
AbstractEntityArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArg
AbstractEntityArgService<T extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<T>> - Class in ubic.gemma.rest.util.args
AbstractEntityArgService(S) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArgService
AbstractEntityArrayArg<O extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<O>> - Class in ubic.gemma.rest.util.args
AbstractEntityArrayArg(Class<? extends AbstractEntityArg>, List<String>) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArrayArg
AbstractExceptionMapper<E extends Throwable> - Class in ubic.gemma.rest.providers
AbstractExceptionMapper() - Constructor for class ubic.gemma.rest.providers.AbstractExceptionMapper
acceptsJson(HttpHeaders) - Static method in class ubic.gemma.rest.util.ExceptionMapperUtils
AccessDeniedExceptionMapper - Class in ubic.gemma.rest.providers: Map Spring Security's AccessDeniedException to a 403 Forbidden response.
AccessDeniedExceptionMapper() - Constructor for class ubic.gemma.rest.providers.AccessDeniedExceptionMapper
addErrorsField(String, String) - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Adds a new field into the errors array property.
addExceptionFields(WellComposedErrorBody, Throwable) - Static method in class ubic.gemma.rest.util.WellComposedErrorBody: Adds descriptive values from the throwable object to the instance of WellComposedErrorBody.
afterPropertiesSet() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
AnalysisResultSetsWebService - Class in ubic.gemma.rest: Endpoint for AnalysisResultSet
AnalysisResultSetsWebService() - Constructor for class ubic.gemma.rest.AnalysisResultSetsWebService
AnalyticsApplicationEventListener - Class in ubic.gemma.rest.providers: Register AnalyticsRequestEventListener
AnalyticsApplicationEventListener() - Constructor for class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
AnalyticsProvider - Interface in ubic.gemma.rest.analytics: Interface for analytics providers.
AnalyticsRequestEventListener - Class in ubic.gemma.rest.providers: Request event listener that publishes an event when a request is finished.
AnalyticsRequestEventListener(String, Date, AnalyticsProvider) - Constructor for class ubic.gemma.rest.providers.AnalyticsRequestEventListener
AnnotationSearchResultValueObject() - Constructor for class ubic.gemma.rest.AnnotationsWebService.AnnotationSearchResultValueObject
AnnotationsWebService - Class in ubic.gemma.rest: RESTful interface for annotations.
AnnotationsWebService() - Constructor for class ubic.gemma.rest.AnnotationsWebService: Required by spring
AnnotationsWebService(OntologyService, SearchService, CharacteristicService, ExpressionExperimentService, DatasetArgService, TaxonArgService) - Constructor for class ubic.gemma.rest.AnnotationsWebService: Constructor for service autowiring
AnnotationsWebService.AnnotationSearchResultValueObject - Class in ubic.gemma.rest
AnnotationWithUsageStatisticsValueObject(Characteristic, Long, Set<DatasetsWebService.OntologyTermValueObject>) - Constructor for class ubic.gemma.rest.DatasetsWebService.AnnotationWithUsageStatisticsValueObject
ApiInfoValueObject(String, OpenAPI, URI, List<ExternalDatabaseValueObject>) - Constructor for class ubic.gemma.rest.RootWebService.ApiInfoValueObject
Arg<T> - Interface in ubic.gemma.rest.util.args
ArgUtils - Class in ubic.gemma.rest.util: Utilities for working with Arg.
ArgUtils() - Constructor for class ubic.gemma.rest.util.ArgUtils
aroundWriteTo(WriterInterceptorContext) - Method in class ubic.gemma.rest.providers.CacheControlHeaderDecorator
aroundWriteTo(WriterInterceptorContext) - Method in class ubic.gemma.rest.providers.GzipHeaderDecorator
ArrayDesignWithUsageStatisticsValueObject(ArrayDesignValueObject, Long, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject
AuthenticationBasedUserIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy for the user ID that uses the authentication object from the SecurityContextHolder.
AuthenticationBasedUserIdRetrievalStrategy(AuthenticationTrustResolver) - Constructor for class ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy
AuthenticationExceptionMapper - Class in ubic.gemma.rest.providers: Handles Spring Security AuthenticationException by producing a 403 Forbidden response.
AuthenticationExceptionMapper() - Constructor for class ubic.gemma.rest.providers.AuthenticationExceptionMapper

C

CacheControl - Annotation Type in ubic.gemma.rest.annotations
CacheControlHeaderDecorator - Class in ubic.gemma.rest.providers
CacheControlHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.CacheControlHeaderDecorator
CacheControls - Annotation Type in ubic.gemma.rest.annotations
CategoryWithUsageStatisticsValueObject() - Constructor for class ubic.gemma.rest.DatasetsWebService.CategoryWithUsageStatisticsValueObject
channelNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
checkEntity(AbstractEntityArg<?, T, S>, T) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Checks whether the given object is null, and throws an appropriate exception if necessary.
clause() - Method in class ubic.gemma.rest.util.args.FilterArgParser
clause() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
clause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
ClauseContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
ClientIdRetrievalStrategy - Interface in ubic.gemma.rest.analytics.ga4: Strategy for retrieving a client ID.
collection() - Method in class ubic.gemma.rest.util.args.FilterArgParser
collection() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
CollectionContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
collectionOperator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
CollectionOperatorContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
commence(HttpServletRequest, HttpServletResponse, AuthenticationException) - Method in class ubic.gemma.rest.security.RestAuthEntryPoint
CompositeClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Composite strategy for retrieving client ID.
CompositeClientIdRetrievalStrategy(List<ClientIdRetrievalStrategy>) - Constructor for class ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy
CompositeSequenceArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Composite Sequence arguments.
CompositeSequenceArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArg
CompositeSequenceArgService - Class in ubic.gemma.rest.util.args
CompositeSequenceArgService(CompositeSequenceService) - Constructor for class ubic.gemma.rest.util.args.CompositeSequenceArgService
CompositeSequenceArrayArg - Class in ubic.gemma.rest.util.args
CompositeSequenceIdArg - Class in ubic.gemma.rest.util.args: Composite Sequence argument for CS ID.
CompositeSequenceNameArg - Class in ubic.gemma.rest.util.args: Composite Sequence argument for CS name.
CONJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
CONJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
CONJUNCTION(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
CONJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
contextDestroyed(ServletContextEvent) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolverRegistrationListener
contextInitialized(ServletContextEvent) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolverRegistrationListener
CorsFilter - Class in ubic.gemma.rest.servlet: Filter for adding CORS headers to the RESTful API responses.
CorsFilter() - Constructor for class ubic.gemma.rest.servlet.CorsFilter
CustomModelResolver - Class in ubic.gemma.rest.swagger.resolver: Resolve Arg parameters' schema.
CustomModelResolver(ObjectMapper, SearchService) - Constructor for class ubic.gemma.rest.swagger.resolver.CustomModelResolver
CustomModelResolverRegistrationListener - Class in ubic.gemma.rest.swagger.resolver: Registers our customized ModelResolver.
CustomModelResolverRegistrationListener() - Constructor for class ubic.gemma.rest.swagger.resolver.CustomModelResolverRegistrationListener

D

DatabaseEntryArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for DatabaseEntry API.
DatabaseEntryArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArg
DatabaseEntryArgService - Class in ubic.gemma.rest.util.args
DatabaseEntryArgService(DatabaseEntryService) - Constructor for class ubic.gemma.rest.util.args.DatabaseEntryArgService
DatabaseEntryArrayArg - Class in ubic.gemma.rest.util.args
DatabaseEntryIdArg - Class in ubic.gemma.rest.util.args: Long argument type for DatabaseEntry API, referencing the Taxon ID.
DatabaseEntryStringArg - Class in ubic.gemma.rest.util.args: String argument type for DatabaseEntry API, Can also be null.
DatasetArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for dataset (ExpressionExperiment) API.
DatasetArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.DatasetArg
DatasetArgService - Class in ubic.gemma.rest.util.args
DatasetArgService(ExpressionExperimentService, SearchService, ArrayDesignService, BioAssayService, OutlierDetectionService) - Constructor for class ubic.gemma.rest.util.args.DatasetArgService
DatasetArrayArg - Class in ubic.gemma.rest.util.args
DatasetIdArg - Class in ubic.gemma.rest.util.args: Long argument type for dataset API, referencing the Dataset ID.
DatasetIdArg(long) - Constructor for class ubic.gemma.rest.util.args.DatasetIdArg
DatasetStringArg - Class in ubic.gemma.rest.util.args: String argument type for dataset API, referencing the Dataset short name.
DatasetsWebService - Class in ubic.gemma.rest: RESTful interface for datasets.
DatasetsWebService() - Constructor for class ubic.gemma.rest.DatasetsWebService
DatasetsWebService.AnnotationWithUsageStatisticsValueObject - Class in ubic.gemma.rest: This is an aggregated entity across value URI and value, thus the id and objectClass are omitted.
DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.CategoryWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.ExpressionExperimentWithSearchResultValueObject - Class in ubic.gemma.rest
DatasetsWebService.OntologyTermValueObject - Class in ubic.gemma.rest
DatasetsWebService.TaxonWithUsageStatisticsValueObject - Class in ubic.gemma.rest
DatasetsWebService.UsageStatistics - Interface in ubic.gemma.rest
decodeCompressedArg(String) - Static method in class ubic.gemma.rest.util.ArgUtils: Decode a base64-encoded gzip-compressed argument.
DEFAULT_REQUEST_HEADER - Static variable in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
destroy() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
disjunction(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser
DISJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
DISJUNCTION() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
DisjunctionContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.CorsFilter
doFilterInternal(HttpServletRequest, HttpServletResponse, FilterChain) - Method in class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter

E

enterClause(FilterArgParser.ClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.clause().
enterClause(FilterArgParser.ClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.clause().
enterCollection(FilterArgParser.CollectionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.collection().
enterCollection(FilterArgParser.CollectionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.collection().
enterCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.collectionOperator().
enterCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.collectionOperator().
enterDisjunction(FilterArgParser.DisjunctionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.disjunction().
enterDisjunction(FilterArgParser.DisjunctionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.disjunction().
enterEveryRule(ParserRuleContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
enterFilter(FilterArgParser.FilterContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.filter().
enterFilter(FilterArgParser.FilterContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.filter().
enterOperator(FilterArgParser.OperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.operator().
enterOperator(FilterArgParser.OperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.operator().
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
enterRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
enterScalar(FilterArgParser.ScalarContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.scalar().
enterScalar(FilterArgParser.ScalarContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.scalar().
enterSubClause(FilterArgParser.SubClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Enter a parse tree produced by FilterArgParser.subClause().
enterSubClause(FilterArgParser.SubClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Enter a parse tree produced by FilterArgParser.subClause().
EntityArgService<T extends ubic.gemma.model.common.Identifiable,S extends ubic.gemma.persistence.service.FilteringService<T>> - Interface in ubic.gemma.rest.util.args: Bridges Arg operating on entities with their corresponding FilteringService.
entityArgValueOf(Class<? extends AbstractEntityArg<?, T, S>>, String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Invoke either a static valueOf method or a suitable constructor to instantiate the argument.
EntityNotFoundException - Exception in ubic.gemma.rest.util
EntityNotFoundException(String) - Constructor for exception ubic.gemma.rest.util.EntityNotFoundException
EntityNotFoundExceptionMapper - Class in ubic.gemma.rest.providers: Deprecated.
EntityNotFoundExceptionMapper() - Constructor for class ubic.gemma.rest.providers.EntityNotFoundExceptionMapper: Deprecated.
EOF() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
EQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
EQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
EQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
ERROR_MSG - Static variable in class ubic.gemma.rest.util.args.AbstractArrayArg
ExceptionMapperUtils - Class in ubic.gemma.rest.util
ExceptionMapperUtils() - Constructor for class ubic.gemma.rest.util.ExceptionMapperUtils
ExcludeArg<T> - Class in ubic.gemma.rest.util.args
exitClause(FilterArgParser.ClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.clause().
exitClause(FilterArgParser.ClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.clause().
exitCollection(FilterArgParser.CollectionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.collection().
exitCollection(FilterArgParser.CollectionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.collection().
exitCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.collectionOperator().
exitCollectionOperator(FilterArgParser.CollectionOperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.collectionOperator().
exitDisjunction(FilterArgParser.DisjunctionContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.disjunction().
exitDisjunction(FilterArgParser.DisjunctionContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.disjunction().
exitEveryRule(ParserRuleContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
exitFilter(FilterArgParser.FilterContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.filter().
exitFilter(FilterArgParser.FilterContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.filter().
exitOperator(FilterArgParser.OperatorContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.operator().
exitOperator(FilterArgParser.OperatorContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.operator().
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
exitRule(ParseTreeListener) - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
exitScalar(FilterArgParser.ScalarContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.scalar().
exitScalar(FilterArgParser.ScalarContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.scalar().
exitSubClause(FilterArgParser.SubClauseContext) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener: Exit a parse tree produced by FilterArgParser.subClause().
exitSubClause(FilterArgParser.SubClauseContext) - Method in interface ubic.gemma.rest.util.args.FilterArgListener: Exit a parse tree produced by FilterArgParser.subClause().
ExpLevelConsolidationArg - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be one of the expression level consolidation options.
ExpressionAnalysisResultSetArg - Class in ubic.gemma.rest.util.args: Represents an expression analysis result set identifier.
ExpressionAnalysisResultSetArgService - Class in ubic.gemma.rest.util.args
ExpressionAnalysisResultSetArgService(ExpressionAnalysisResultSetService) - Constructor for class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArgService
ExpressionExperimentWithSearchResultValueObject(ExpressionExperimentValueObject, SearchResult<ExpressionExperiment>) - Constructor for class ubic.gemma.rest.DatasetsWebService.ExpressionExperimentWithSearchResultValueObject

F

FactorValueArg<A> - Class in ubic.gemma.rest.util.args: Represents an API arguments that maps to a FactorValue by its ID or name.
FactorValueArg(String, Class<A>, A) - Constructor for class ubic.gemma.rest.util.args.FactorValueArg
FactorValueArrayArg - Class in ubic.gemma.rest.util.args
FactorValueArrayArg(List<String>) - Constructor for class ubic.gemma.rest.util.args.FactorValueArrayArg
FactorValueIdArg - Class in ubic.gemma.rest.util.args: Maps a long identifier to a FactorValue.
FactorValueIdArg(long) - Constructor for class ubic.gemma.rest.util.args.FactorValueIdArg
FactorValueValueArg - Class in ubic.gemma.rest.util.args: Deprecated.
FactorValueValueArg(String) - Constructor for class ubic.gemma.rest.util.args.FactorValueValueArg: Deprecated.
filter() - Method in class ubic.gemma.rest.util.args.FilterArgParser
filter(List<T>, Filters) - Static method in class ubic.gemma.rest.util.Responder: Produce a FilteredResponseDataObject for a given filtered List.
FilterArg<O extends ubic.gemma.model.common.Identifiable> - Class in ubic.gemma.rest.util.args: Represent a filter argument designed to generate a Filters from user input.
FilterArg.Filter - Class in ubic.gemma.rest.util.args: Represents the internal value of a FilterArg.
FilterArgBaseListener - Class in ubic.gemma.rest.util.args: 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.
FilterArgBaseListener() - Constructor for class ubic.gemma.rest.util.args.FilterArgBaseListener
FilterArgLexer - Class in ubic.gemma.rest.util.args
FilterArgLexer(CharStream) - Constructor for class ubic.gemma.rest.util.args.FilterArgLexer
FilterArgListener - Interface in ubic.gemma.rest.util.args: This interface defines a complete listener for a parse tree produced by FilterArgParser.
FilterArgParser - Class in ubic.gemma.rest.util.args
FilterArgParser(TokenStream) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser
FilterArgParser.ClauseContext - Class in ubic.gemma.rest.util.args
FilterArgParser.CollectionContext - Class in ubic.gemma.rest.util.args
FilterArgParser.CollectionOperatorContext - Class in ubic.gemma.rest.util.args
FilterArgParser.DisjunctionContext - Class in ubic.gemma.rest.util.args
FilterArgParser.FilterContext - Class in ubic.gemma.rest.util.args
FilterArgParser.OperatorContext - Class in ubic.gemma.rest.util.args
FilterArgParser.ScalarContext - Class in ubic.gemma.rest.util.args
FilterArgParser.SubClauseContext - Class in ubic.gemma.rest.util.args
FilterContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
FilteredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredAndPaginatedResponseDataObject(Slice<T>, Filters, String[]) - Constructor for class ubic.gemma.rest.util.FilteredAndPaginatedResponseDataObject
FilteredResponseDataObject<T> - Class in ubic.gemma.rest.util
FilteredResponseDataObject(List<T>, Filters) - Constructor for class ubic.gemma.rest.util.FilteredResponseDataObject
findCandidateGenesInTaxon(TaxonArg<?>, StringArrayArg, Boolean) - Method in class ubic.gemma.rest.TaxaWebService: Deprecated.

G

GE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
GE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
GE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
GeneAnyIdArg<T> - Class in ubic.gemma.rest.util.args: Base class for GeneArg representing any of the identifiers of a Gene.
GeneAnyIdArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.GeneAnyIdArg
GeneArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Gene API.
GeneArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.GeneArg
GeneArgService - Class in ubic.gemma.rest.util.args
GeneArgService(GeneService, PhenotypeAssociationManagerService, GeneOntologyService) - Constructor for class ubic.gemma.rest.util.args.GeneArgService
GeneArrayArg - Class in ubic.gemma.rest.util.args
GeneEnsemblIdArg - Class in ubic.gemma.rest.util.args: Long argument type for Gene API, referencing the Gene Ensembl ID.
GeneNcbiIdArg - Class in ubic.gemma.rest.util.args: Long argument type for Gene API, referencing the Gene NCBI ID.
GeneSymbolArg - Class in ubic.gemma.rest.util.args: String argument type for Gene API.
GeneWebService - Class in ubic.gemma.rest: RESTful interface for genes.
GeneWebService() - Constructor for class ubic.gemma.rest.GeneWebService: Required by spring
GeneWebService(GeneService, CompositeSequenceService, GeneCoexpressionSearchService, GeneArgService) - Constructor for class ubic.gemma.rest.GeneWebService: Constructor for service autowiring
GEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
GEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
GEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
get() - Method in class ubic.gemma.rest.analytics.ga4.AuthenticationBasedUserIdRetrievalStrategy
get() - Method in interface ubic.gemma.rest.analytics.ga4.ClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.CompositeClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy
get() - Method in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
get() - Method in interface ubic.gemma.rest.analytics.ga4.UserIdRetrievalStrategy
getAnnotations(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getApiInfo(HttpServletRequest, ServletConfig) - Method in class ubic.gemma.rest.RootWebService: Returns an object with API information.
getArgsByPropertyName(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService: Given a AbstractEntityArrayArg, construct a mapping of properties it refers to values those properties are allowed to take in a filter.
getArgsByPropertyName(AbstractEntityArrayArg<Taxon, TaxonService>) - Method in class ubic.gemma.rest.util.args.TaxonArgService
getATN() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getATN() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getBlacklistedDatasets(FilterArg<ExpressionExperiment>, SortArg<ExpressionExperiment>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService: Browse blacklisted datasets.
getBlacklistedPlatforms(FilterArg<ArrayDesign>, SortArg<ArrayDesign>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService
getChannelNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getCode() - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Used by JSON Serializer.
getContext(Class<?>) - Method in class ubic.gemma.rest.providers.ObjectMapperResolver
getData() - Method in class ubic.gemma.rest.util.ResponseDataObject
getDatasetAnnotations(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the annotations for the given dataset.
getDatasetDesign(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the design for the given dataset.
getDatasetDifferentialExpression(DatasetArrayArg, Long, Double, LimitArg, Boolean, ExpLevelConsolidationArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of genes highly expressed in the given component on given datasets.
getDatasetDifferentialExpressionAnalyses(DatasetArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the differential analysis results for the given dataset.
getDatasetDifferentialExpressionAnalysesResultSets(DatasetArg<?>, HttpServletRequest) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the result sets of all the differential expression analyses of a dataset.
getDatasetExpression(DatasetArg<?>, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the data for the given dataset.
getDatasetExpressionForGenes(DatasetArrayArg, GeneArrayArg, Boolean, ExpLevelConsolidationArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of given genes on given datasets.
getDatasetExpressionPca(DatasetArrayArg, Integer, LimitArg, Boolean, ExpLevelConsolidationArg) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the expression levels of genes highly expressed in the given component on given datasets.
getDatasetHasBatch(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Returns true if the experiment has had batch information successfully filled in.
getDatasetPlatforms(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves platforms for the given dataset.
getDatasetProcessedExpression(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve processed expression data.
getDatasetQuantitationTypes(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve all available quantitation types for a dataset.
getDatasetRawExpression(DatasetArg<?>, QuantitationTypeArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieve raw expression data.
getDatasets(String, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSamples(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the samples for the given dataset.
getDatasetsAnnotationsUsageStatistics(String, FilterArg<ExpressionExperiment>, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject>, LimitArg, Integer, String, StringArrayArg, StringArrayArg, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsByIds(DatasetArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves all datasets matching the given identifiers.
getDatasetsCategoriesUsageStatistics(String, FilterArg<ExpressionExperiment>, StringArrayArg, StringArrayArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsPlatformsUsageStatistics(String, FilterArg<ExpressionExperiment>, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetsTaxaUsageStatistics(String, FilterArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService
getDatasetSvd(DatasetArg<?>) - Method in class ubic.gemma.rest.DatasetsWebService: Retrieves the design for the given dataset.
getElementClass() - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getElementClass() - Method in interface ubic.gemma.rest.util.args.EntityArgService
getElements(PlatformArg<?>, int, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Retrieves the Elements of the Platform that this argument represents.
getEntities(AbstractEntityArg<?, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntities(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntities(AbstractEntityArg<?, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getEntities(AbstractEntityArrayArg<T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getEntity(AbstractEntityArg<?, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getEntity(AbstractEntityArg<?, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getEntityForExpressionExperimentAndDataVectorType(ExpressionExperiment, Class<? extends DesignElementDataVector>, QuantitationTypeService) - Method in class ubic.gemma.rest.util.args.QuantitationTypeArg
getEntityForExpressionExperimentAndDataVectorType(ExpressionExperiment, Class<? extends DesignElementDataVector>, QuantitationTypeService) - Method in class ubic.gemma.rest.util.args.QuantitationTypeByIdArg
getEntityForExpressionExperimentAndDataVectorType(ExpressionExperiment, Class<? extends DesignElementDataVector>, QuantitationTypeService) - Method in class ubic.gemma.rest.util.args.QuantitationTypeByNameArg
getEntityWithContrastsAndResults(ExpressionAnalysisResultSetService) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg
getEntityWithPlatform(CompositeSequenceArg<?>, ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgService
getEntityWithTaxon(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService
getEntityWithTaxon(GeneService, Taxon) - Method in class ubic.gemma.rest.util.args.GeneEnsemblIdArg
getEntityWithTaxon(GeneService, Taxon) - Method in class ubic.gemma.rest.util.args.GeneSymbolArg
getErrors() - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Used by JSON Serializer.
getExperiments(PlatformArg<?>, int, int) - Method in class ubic.gemma.rest.util.args.PlatformArgService: Retrieves the Datasets of the Platform that this argument represents.
getFilterableProperties() - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterableProperties() - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyAllowedValues(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyAllowedValues(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyConfigAttributes(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyConfigAttributes(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyDescription(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyDescription(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyIsUsingSubquery(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyIsUsingSubquery(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyResolvableAllowedValuesLabels(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterablePropertyType(String) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilterablePropertyType(String) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilterForSearchQuery(String, Highlighter, List<SearchResult<ExpressionExperiment>>) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Obtain a Filter for the result of a ExpressionExperiment search.
getFilterForSearchQuery(String) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFilters(AbstractEntityArg<A, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(FilterArg<T>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getFilters(FilterArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFilters(FilterArg<ExpressionExperiment>, Collection<OntologyTerm>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getFilters(AbstractEntityArg<A, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilters(AbstractEntityArrayArg<T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilters(FilterArg<T>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getFilters(AbstractEntityArg<A, Taxon, TaxonService>) - Method in class ubic.gemma.rest.util.args.TaxonArgService
getGeneEvidence(GeneArg<?>) - Method in class ubic.gemma.rest.GeneWebService: Deprecated.
getGeneEvidence(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Deprecated.
getGeneGeneCoexpression(GeneArg<?>, GeneArg<?>, LimitArg, Integer) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the coexpression of two given genes.
getGeneGoTerms(GeneArg<?>) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the GO terms of the given gene.
getGeneLocation(GeneArg<?>) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns all known locations of the gene(s) that this GeneArg represents.
getGeneLocation(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns all known locations of the gene that this GeneArg represents.
getGeneLocations(GeneArg<?>) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the physical location of the given gene.
getGeneLocationsInTaxon(TaxonArg<?>, GeneArg<?>) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves gene location for the gene on the given taxon.
getGeneProbes(GeneArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves the probes (composite sequences) with this gene.
getGenes(GeneArrayArg) - Method in class ubic.gemma.rest.GeneWebService: Retrieves all genes matching the identifier.
getGenesEvidenceInTaxon(TaxonArg<?>, GeneArg<?>) - Method in class ubic.gemma.rest.TaxaWebService: Deprecated.
getGenesOnChromosome(TaxonArg<?>, String, String, long, int) - Method in class ubic.gemma.rest.util.args.TaxonArgService: Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.
getGenesOnTaxon(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService
getGoTerms(GeneArg<?>) - Method in class ubic.gemma.rest.util.args.GeneArgService: Returns GO terms for the gene that this GeneArg represents.
getGrammarFileName() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getGrammarFileName() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getMessage() - Method in class ubic.gemma.rest.util.WellComposedErrorBody: Used by JSON Serializer.
getModeNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getMyself() - Method in class ubic.gemma.rest.RootWebService: Retrieve user information for the current user.
getNumberOfDatasets(String, FilterArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.DatasetsWebService
getNumberOfExpressionExperiments() - Method in interface ubic.gemma.rest.DatasetsWebService.UsageStatistics
getNumberOfPlatforms(FilterArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService
getNumberOfResultSets(FilterArg<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService
getOpenApi(ServletConfig) - Static method in class ubic.gemma.rest.util.OpenApiUtils: Obtain the OpenAPI definition for this RESTful API.
getPhenotypeDumps() - Method in class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Finds all dumps.
getPhenotypeEvidence(String, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Finds all evidence with the given external database name.
getPlatformAnnotations(PlatformArg<?>) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the annotation file for the given platform.
getPlatformDatasets(PlatformArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves experiments in the given platform.
getPlatformElement(PlatformArg<?>, CompositeSequenceArrayArg, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves composite sequences (elements) of the given platform.
getPlatformElementGenes(PlatformArg<?>, CompositeSequenceArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the genes on the given platform element.
getPlatformElements(PlatformArg<?>, OffsetArg, LimitArg) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves the composite sequences (elements) for the given platform.
getPlatformFilter() - Method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
getPlatforms(FilterArg<ArrayDesign>, OffsetArg, LimitArg, SortArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService
getPlatforms(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieves the Platforms of the Dataset that this argument represents.
getPlatformsByIds(PlatformArrayArg, FilterArg<ArrayDesign>, OffsetArg, LimitArg, SortArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService: Retrieves all datasets matching the given identifiers.
getQuantitationTypes(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService: Retrieve a dataset with quantitation type initialized.
getResultSet(ExpressionAnalysisResultSetArg, Boolean) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve a AnalysisResultSet given its identifier.
getResultSetAsTsv(ExpressionAnalysisResultSetArg) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve an AnalysisResultSet in a tabular format.
getResultSets(DatasetArrayArg, DatabaseEntryArrayArg, FilterArg<ExpressionAnalysisResultSet>, OffsetArg, LimitArg, SortArg<ExpressionAnalysisResultSet>) - Method in class ubic.gemma.rest.AnalysisResultSetsWebService: Retrieve all AnalysisResultSet matching a set of criteria.
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.DisjunctionContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
getRuleIndex() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
getRuleNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getRuleNames() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getSamples(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService
getSearchSettings() - Method in class ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
getSerializedATN() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getSerializedATN() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getSort(SortArg<T>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService
getSort(SortArg<T>) - Method in interface ubic.gemma.rest.util.args.EntityArgService
getStatus(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Translate the exception to an HTTP Response.Status.
getStatus(AccessDeniedException) - Method in class ubic.gemma.rest.providers.AccessDeniedExceptionMapper
getStatus(AuthenticationException) - Method in class ubic.gemma.rest.providers.AuthenticationExceptionMapper
getStatus(EntityNotFoundException) - Method in class ubic.gemma.rest.providers.EntityNotFoundExceptionMapper: Deprecated.
getStatus(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper
getStatus(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper
getStatus(Throwable) - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper
getStatus(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper
getStatus() - Method in class ubic.gemma.rest.util.WellComposedErrorBody
getTaxa() - Method in class ubic.gemma.rest.TaxaWebService: Lists all available taxa.
getTaxaByIds(TaxonArrayArg) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves single taxon based on the given identifier.
getTaxonDatasets(TaxonArg<?>, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<Taxon>) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves datasets for the given taxon.
getTaxonGenes(TaxonArg<?>, GeneArg<?>) - Method in class ubic.gemma.rest.TaxaWebService: Retrieves genes matching the identifier on the given taxon.
getTaxonGenesOverlappingChromosome(TaxonArg<?>, String, String, Long, Integer) - Method in class ubic.gemma.rest.TaxaWebService: Finds genes overlapping a given region.
getTaxonPhenotypes(TaxonArg<?>, Boolean, Boolean) - Method in class ubic.gemma.rest.TaxaWebService: Loads all phenotypes for the given taxon.
getTokenNames() - Method in class ubic.gemma.rest.util.args.FilterArgLexer: Deprecated.
getTokenNames() - Method in class ubic.gemma.rest.util.args.FilterArgParser: Deprecated.
getUser(String) - Method in class ubic.gemma.rest.RootWebService: Retrieve user information.
getValue() - Method in class ubic.gemma.rest.util.args.AbstractArg: Obtain the value represented by this argument.
getValue() - Method in interface ubic.gemma.rest.util.args.Arg: Obtain the value represented by this argument.
getValue() - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit ensuring that it is smaller than LimitArg.MAXIMUM
getValue(Integer) - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit and ensure it is smaller than a given maximum.
getValueNoMaximum() - Method in class ubic.gemma.rest.util.args.LimitArg: Obtain the value of the limit, explicitly disregarding the maximum defined by LimitArg.MAXIMUM.
getValueObjects(GeneArg<?>) - Method in class ubic.gemma.rest.util.args.GeneArgService
getVocabulary() - Method in class ubic.gemma.rest.util.args.FilterArgLexer
getVocabulary() - Method in class ubic.gemma.rest.util.args.FilterArgParser
getWellComposedErrorBody(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Obtain a WellComposedErrorBody for the exception.
getWellComposedErrorBody(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper
getWellComposedErrorBody(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper
GoogleAnalytics4Provider - Class in ubic.gemma.rest.analytics.ga4: Implementation of the AnalyticsProvider interface for Google Analytics 4 collect API.
GoogleAnalytics4Provider(RestTemplate, ScheduledExecutorService, String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Create a new Google Analytics 4 provider.
GoogleAnalytics4Provider(String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
GroupedResponseDataObject<T> - Class in ubic.gemma.rest.util
GroupedResponseDataObject(List<T>, String[], Sort) - Constructor for class ubic.gemma.rest.util.GroupedResponseDataObject
GZIP - Annotation Type in ubic.gemma.rest.annotations: Used to annotate endpoints that will have their payload compressed with GZIPOutputStream unconditionally.
GzipHeaderDecorator - Class in ubic.gemma.rest.providers: Automagically add the Content-Encoding: gzip header to endpoints annotated with GZIP.
GzipHeaderDecorator() - Constructor for class ubic.gemma.rest.providers.GzipHeaderDecorator

I

IN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
IN() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext
IN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
init() - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
init() - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
initFilterBean() - Method in class ubic.gemma.rest.servlet.CorsFilter

J

JacksonConfig - Class in ubic.gemma.rest.util: Configure the various beans injected in Swagger's components relating to Jackson's JSON serialization.
JacksonConfig() - Constructor for class ubic.gemma.rest.util.JacksonConfig
JsonMappingExceptionMapper - Class in ubic.gemma.rest.providers: Mapper that creates a well composed error body response out of a JsonMappingException.
JsonMappingExceptionMapper() - Constructor for class ubic.gemma.rest.providers.JsonMappingExceptionMapper

L

LE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
LEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
LIKE - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
LIKE() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
limit(List<T>, Filters, String[], Sort, Integer) - Static method in class ubic.gemma.rest.util.Responder
LimitArg - Class in ubic.gemma.rest.util.args: Argument used to represent a limit.
LimitedResponseDataObject<T> - Class in ubic.gemma.rest.util: Represent limit results.
LimitedResponseDataObject(List<T>, Filters, String[], Sort, Integer) - Constructor for class ubic.gemma.rest.util.LimitedResponseDataObject
load(Filters, Sort, int, int) - Method in interface ubic.gemma.rest.util.Responder.FilterMethod
log - Static variable in class ubic.gemma.rest.TaxaWebService
logException() - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper: Indicate if the exception should be logged.
logException() - Method in class ubic.gemma.rest.providers.AuthenticationExceptionMapper
logException() - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper

M

MalformedArgException - Exception in ubic.gemma.rest.util: Specialized error for malformed Arg The recommended HTTP status for this exception is 400 Bad Request.
MalformedArgException(String, Throwable) - Constructor for exception ubic.gemma.rest.util.MalformedArgException
MalformedArgException(String) - Constructor for exception ubic.gemma.rest.util.MalformedArgException
MalformedArgException(Throwable) - Constructor for exception ubic.gemma.rest.util.MalformedArgException
MalformedArgExceptionMapper - Class in ubic.gemma.rest.providers
MalformedArgExceptionMapper() - Constructor for class ubic.gemma.rest.providers.MalformedArgExceptionMapper
MAX_CLAUSES - Static variable in class ubic.gemma.rest.util.args.FilterArg: Maximum number of clauses that can appear in a filter expression.
MAX_SEARCH_RESULTS - Static variable in class ubic.gemma.rest.SearchWebService: Maximum number of search results.
MAXIMUM - Static variable in class ubic.gemma.rest.util.args.LimitArg: This is the default maximum used for LimitArg.getValue().
MediaTypeUtils - Class in ubic.gemma.rest.util: Utilities for MediaType.
MediaTypeUtils() - Constructor for class ubic.gemma.rest.util.MediaTypeUtils
MetricsApplicationEventListener - Class in ubic.gemma.rest.providers
MetricsApplicationEventListener() - Constructor for class ubic.gemma.rest.providers.MetricsApplicationEventListener
modeNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer

N

NEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
NEQ - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
NEQ() - Method in class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext
NotFoundExceptionMapper - Class in ubic.gemma.rest.providers: This mapper ensures that raised NotFoundException throughout the API contain well-formed ResponseErrorObject entity.
NotFoundExceptionMapper() - Constructor for class ubic.gemma.rest.providers.NotFoundExceptionMapper

O

objectMapper() - Method in class ubic.gemma.rest.util.JacksonConfig: Mapper used to generate JSON payloads from the REST API.
ObjectMapperResolver - Class in ubic.gemma.rest.providers
ObjectMapperResolver() - Constructor for class ubic.gemma.rest.providers.ObjectMapperResolver
OffsetArg - Class in ubic.gemma.rest.util.args: Argument used to represent an offset.
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
onEvent(RequestEvent) - Method in class ubic.gemma.rest.providers.AnalyticsRequestEventListener
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
onEvent(ApplicationEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionEventListener
onEvent(RequestEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionLogger
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.AnalyticsApplicationEventListener
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.MetricsApplicationEventListener
onRequest(RequestEvent) - Method in class ubic.gemma.rest.providers.RequestExceptionEventListener
OntologyTermValueObject(OntologyTerm, Set<DatasetsWebService.OntologyTermValueObject>) - Constructor for class ubic.gemma.rest.DatasetsWebService.OntologyTermValueObject
OpenApiUtils - Class in ubic.gemma.rest.util: Utilities for interacting with OpenAPI at runtime.
OpenApiUtils() - Constructor for class ubic.gemma.rest.util.OpenApiUtils
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
operator() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
OperatorContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.OperatorContext

P

paginate(Slice<T>, String[]) - Static method in class ubic.gemma.rest.util.Responder: Produce a PaginatedResponseDataObject for a given unfiltered Slice.
paginate(Slice<T>, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responder: Produce a FilteredAndPaginatedResponseDataObject for a given Slice
paginate(Responder.FilterMethod<T>, Filters, String[], Sort, int, int) - Static method in class ubic.gemma.rest.util.Responder: Paginate using an arbitrary filtering method.
PaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util: Represents paginated results with offset and limit.
PaginatedResponseDataObject(Slice<T>, String[]) - Constructor for class ubic.gemma.rest.util.PaginatedResponseDataObject
PhenotypeWebService - Class in ubic.gemma.rest: Deprecated.
PhenotypeWebService() - Constructor for class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Required by spring
PhenotypeWebService(PhenotypeAssociationManagerService) - Constructor for class ubic.gemma.rest.PhenotypeWebService: Deprecated.

Constructor for service autowiring
PlatformArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for dataset (ExpressionExperiment) API.
PlatformArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.PlatformArg
PlatformArgService - Class in ubic.gemma.rest.util.args
PlatformArgService(ArrayDesignService, ExpressionExperimentService, CompositeSequenceService) - Constructor for class ubic.gemma.rest.util.args.PlatformArgService
PlatformArrayArg - Class in ubic.gemma.rest.util.args
PlatformIdArg - Class in ubic.gemma.rest.util.args: Long argument type for platform API, referencing the platform ID.
PlatformStringArg - Class in ubic.gemma.rest.util.args: String argument type for platform API, referencing the Platform short name.
PlatformsWebService - Class in ubic.gemma.rest: RESTful interface for platforms.
PlatformsWebService() - Constructor for class ubic.gemma.rest.PlatformsWebService: Required by spring
PlatformsWebService(GeneService, ArrayDesignService, CompositeSequenceService, ArrayDesignAnnotationService, PlatformArgService, CompositeSequenceArgService) - Constructor for class ubic.gemma.rest.PlatformsWebService: Constructor for service autowiring
PROPERTY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
PROPERTY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
PROPERTY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
PROPERTY() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext

Q

QuantitationTypeArg<T> - Class in ubic.gemma.rest.util.args
QuantitationTypeArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArg
QuantitationTypeByIdArg - Class in ubic.gemma.rest.util.args
QuantitationTypeByNameArg - Class in ubic.gemma.rest.util.args
QueriedAndFilteredAndPaginatedResponseDataObject<T> - Class in ubic.gemma.rest.util
QueriedAndFilteredAndPaginatedResponseDataObject(Slice<T>, String, Filters, String[]) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredAndPaginatedResponseDataObject
queryAndPaginate(Slice<T>, String, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responder
QUOTED_STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
QUOTED_STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
QUOTED_STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext

R

RequestAttributesBasedClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy that retrieves and store client IDs in the RequestAttributes.
RequestAttributesBasedClientIdRetrievalStrategy() - Constructor for class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy
RequestExceptionEventListener - Class in ubic.gemma.rest.providers: Listen and dispatch ApplicationEvent.
RequestExceptionEventListener() - Constructor for class ubic.gemma.rest.providers.RequestExceptionEventListener
RequestExceptionLogger - Class in ubic.gemma.rest.providers: Log request exceptions.
RequestExceptionLogger() - Constructor for class ubic.gemma.rest.providers.RequestExceptionLogger
RequestHeaderBasedClientIdRetrievalStrategy - Class in ubic.gemma.rest.analytics.ga4: Strategy that retrieves the client ID in a request header.
RequestHeaderBasedClientIdRetrievalStrategy() - Constructor for class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy
resolve(AnnotatedType, ModelConverterContext, Iterator<ModelConverter>) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolveAllowableValues(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver: Resolves allowed values for the SearchWebService.search(String, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg) resultTypes argument.
resolveDescription(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
resolveExtensions(Annotated, Annotation[], Schema) - Method in class ubic.gemma.rest.swagger.resolver.CustomModelResolver
respond(T) - Static method in class ubic.gemma.rest.util.Responder: Produce a ResponseDataObject that wraps the given argument.
Responder - Class in ubic.gemma.rest.util: Handles setting of the response status code and composing a proper payload structure.
Responder() - Constructor for class ubic.gemma.rest.util.Responder
Responder.FilterMethod<T> - Interface in ubic.gemma.rest.util: A functional interface matching the signature of a paginating service method.
ResponseDataObject<T> - Class in ubic.gemma.rest.util: Wrapper for a non-error response payload compliant with the Google JSON style-guide
ResponseDataObject(T) - Constructor for class ubic.gemma.rest.util.ResponseDataObject
ResponseErrorObject - Class in ubic.gemma.rest.util: Wrapper for an error response payload compliant with the Google JSON style-guide
ResponseErrorObject(WellComposedErrorBody, OpenAPI) - Constructor for class ubic.gemma.rest.util.ResponseErrorObject
RestapidocsIndexRewriteFilter - Class in ubic.gemma.rest.servlet: Rewrites the path to the index file.
RestapidocsIndexRewriteFilter() - Constructor for class ubic.gemma.rest.servlet.RestapidocsIndexRewriteFilter
RestAuthEntryPoint - Class in ubic.gemma.rest.security: Implementation of AuthenticationEntryPoint for the RESTful API to handle authentication.
RestAuthEntryPoint(ObjectMapper) - Constructor for class ubic.gemma.rest.security.RestAuthEntryPoint
RESULT_TYPES_SCHEMA_NAME - Static variable in class ubic.gemma.rest.SearchWebService: Name used in the OpenAPI schema to identify result types as per #search(String, TaxonArg, PlatformArg, List, LimitArg, StringArrayArg)'s fourth argument.
RootWebService - Class in ubic.gemma.rest: Handles calls to the root API url and user info api
RootWebService() - Constructor for class ubic.gemma.rest.RootWebService
RootWebService.ApiInfoValueObject - Class in ubic.gemma.rest
RootWebService.UserValueObject - Class in ubic.gemma.rest
RULE_clause - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_collection - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_collectionOperator - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_disjunction - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_filter - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_operator - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_scalar - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
RULE_subClause - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
ruleNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
ruleNames - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

S

scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
scalar(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser
scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
ScalarContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
search(String, TaxonArg<?>, PlatformArg<?>, List<String>, LimitArg, ExcludeArg<SearchResult<?>>) - Method in class ubic.gemma.rest.SearchWebService: Search everything subject to taxon and platform constraints.
searchAnnotations(StringArrayArg) - Method in class ubic.gemma.rest.AnnotationsWebService: Does a search for annotation tags based on the given string.
searchAnnotationsByPathQuery(StringArrayArg) - Method in class ubic.gemma.rest.AnnotationsWebService
searchDatasets(StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService: Does a search for datasets containing characteristics matching the given string.
searchDatasetsByQueryInPath(StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService
SearchResultsResponseDataObject(List<SearchWebService.SearchResultValueObject<?>>, SearchWebService.SearchSettingsValueObject) - Constructor for class ubic.gemma.rest.SearchWebService.SearchResultsResponseDataObject
SearchResultValueObject(SearchResult<T>) - Constructor for class ubic.gemma.rest.SearchWebService.SearchResultValueObject
SearchSettingsValueObject(SearchSettings) - Constructor for class ubic.gemma.rest.SearchWebService.SearchSettingsValueObject
searchTaxonDatasets(TaxonArg<?>, StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService: Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
searchTaxonDatasetsByQueryInPath(TaxonArg<?>, StringArrayArg, FilterArg<ExpressionExperiment>, OffsetArg, LimitArg, SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.AnnotationsWebService
SearchWebService - Class in ubic.gemma.rest: Provides search capabilities to the RESTful API.
SearchWebService() - Constructor for class ubic.gemma.rest.SearchWebService
SearchWebService.SearchResultsResponseDataObject - Class in ubic.gemma.rest
SearchWebService.SearchResultValueObject<T extends ubic.gemma.model.IdentifiableValueObject<?>> - Class in ubic.gemma.rest: Representation of SearchResult for the RESTful API.
SearchWebService.SearchSettingsValueObject - Class in ubic.gemma.rest: Represents search settings for the RESTful API.
sendEvent(String, Date, Map<String, String>) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event.
sendEvent(String, Date, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event with additional parameters expressed as a sequence of keys and values.
sendEvent(String, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider: Publish an event without specifying a date.
sendEvent(String, Date, Map<String, String>) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider
service - Variable in class ubic.gemma.rest.util.args.AbstractEntityArgService
ServletUtils - Class in ubic.gemma.rest.util
ServletUtils() - Constructor for class ubic.gemma.rest.util.ServletUtils
setAllowCredentials(boolean) - Method in class ubic.gemma.rest.servlet.CorsFilter: Indicate if the credentials (i.e.
setAllowedHeaders(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed headers by a CORS request.
setAllowedMethods(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed methods by a CORS request.
setAllowedOrigins(String) - Method in class ubic.gemma.rest.servlet.CorsFilter: Set the allowed origins of a CORS request.
setAttribute(String) - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy: Set the attribute to retrieve to obtain the client ID.
setClientIdRetrievalStrategy(ClientIdRetrievalStrategy) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Set the strategy used to retrieve client IDs.
setDebug(boolean) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Enable the debug mode.
setPlatform(ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg
setPollingIntervalMillis(long) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Interval at which events are polled and flushed.
setRequestHeader(String) - Method in class ubic.gemma.rest.analytics.ga4.RequestHeaderBasedClientIdRetrievalStrategy: Set the request header used for retrieving the client ID.
setResolutionMillis(long) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Time resolution for regrouping events in the same batch.
setScope(int) - Method in class ubic.gemma.rest.analytics.ga4.RequestAttributesBasedClientIdRetrievalStrategy: Set the scope to use for retrieving and storing the client ID.
setServletConfig(ServletConfig) - Method in class ubic.gemma.rest.security.RestAuthEntryPoint
setUserIdRetrievalStrategy(UserIdRetrievalStrategy) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider: Set the strategy used to retrieve user IDs.
SortArg<O extends ubic.gemma.model.common.Identifiable> - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an integer.
SortArg.Sort - Class in ubic.gemma.rest.util.args
SortArg.Sort.Direction - Enum in ubic.gemma.rest.util.args
SortValueObject - Class in ubic.gemma.rest.util: Represents Sort as part of a PaginatedResponseDataObject.
SortValueObject(Sort) - Constructor for class ubic.gemma.rest.util.SortValueObject
splitAndTrim(String) - Static method in class ubic.gemma.rest.util.args.AbstractArrayArg: Split a string by the ',' comma character and trim the resulting pieces.
STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext
STRING - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
StringArrayArg - Class in ubic.gemma.rest.util.args: Class representing an API argument that should be an array of Strings.
subClause() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
subClause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext
subClause() - Method in class ubic.gemma.rest.util.args.FilterArgParser
SubClauseContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext
summarizeRequest(HttpServletRequest) - Static method in class ubic.gemma.rest.util.ServletUtils: Summarize a HttpServletRequest in a single line format.
swaggerObjectMapper() - Method in class ubic.gemma.rest.util.JacksonConfig: This is the ObjectMapper used by Swagger to generate the /openapi.json endpoint.

T

T__0 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__0 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
T__1 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__1 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
T__2 - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
T__2 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
TaxaWebService - Class in ubic.gemma.rest: RESTful interface for taxa.
TaxaWebService() - Constructor for class ubic.gemma.rest.TaxaWebService: Required by spring
TaxaWebService(TaxonService, ExpressionExperimentService, PhenotypeAssociationManagerService, TaxonArgService, DatasetArgService, GeneArgService) - Constructor for class ubic.gemma.rest.TaxaWebService: Constructor for service autowiring
TaxonArg<T> - Class in ubic.gemma.rest.util.args: Mutable argument type base class for Taxon API
TaxonArg(String, Class<T>, T) - Constructor for class ubic.gemma.rest.util.args.TaxonArg
TaxonArgService - Class in ubic.gemma.rest.util.args
TaxonArgService(TaxonService, ChromosomeService, GeneService) - Constructor for class ubic.gemma.rest.util.args.TaxonArgService
TaxonArrayArg - Class in ubic.gemma.rest.util.args
TaxonIdArg - Class in ubic.gemma.rest.util.args: Long argument type for taxon API, referencing the Taxon ID.
TaxonNameArg - Class in ubic.gemma.rest.util.args: String argument type for taxon API, referencing the Taxon scientific name or common name.
TaxonNcbiIdArg - Class in ubic.gemma.rest.util.args: Long argument type for taxon API, referencing the Taxon ID.
TaxonWithUsageStatisticsValueObject(Taxon, Long) - Constructor for class ubic.gemma.rest.DatasetsWebService.TaxonWithUsageStatisticsValueObject
TEXT_TAB_SEPARATED_VALUES_UTF8 - Static variable in class ubic.gemma.rest.util.MediaTypeUtils
TEXT_TAB_SEPARATED_VALUES_UTF8_TYPE - Static variable in class ubic.gemma.rest.util.MediaTypeUtils
tokenNames - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer: Deprecated.
Use FilterArgLexer.VOCABULARY instead.
tokenNames - Static variable in class ubic.gemma.rest.util.args.FilterArgParser: Deprecated.
Use FilterArgParser.VOCABULARY instead.
toResponse(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper
toResponse(JsonMappingException) - Method in class ubic.gemma.rest.providers.JsonMappingExceptionMapper
toString() - Method in class ubic.gemma.rest.util.args.AbstractArg

U

ubic.gemma.rest - package ubic.gemma.rest
ubic.gemma.rest.analytics - package ubic.gemma.rest.analytics
ubic.gemma.rest.analytics.ga4 - package ubic.gemma.rest.analytics.ga4
ubic.gemma.rest.annotations - package ubic.gemma.rest.annotations
ubic.gemma.rest.providers - package ubic.gemma.rest.providers
ubic.gemma.rest.security - package ubic.gemma.rest.security
ubic.gemma.rest.servlet - package ubic.gemma.rest.servlet
ubic.gemma.rest.swagger.resolver - package ubic.gemma.rest.swagger.resolver
ubic.gemma.rest.util - package ubic.gemma.rest.util
ubic.gemma.rest.util.args - package ubic.gemma.rest.util.args
UnhandledExceptionMapper - Class in ubic.gemma.rest.providers: Render unhandled exceptions.
UnhandledExceptionMapper() - Constructor for class ubic.gemma.rest.providers.UnhandledExceptionMapper
UserIdRetrievalStrategy - Interface in ubic.gemma.rest.analytics.ga4: Strategy for retrieving a user ID.
UserValueObject(User, String) - Constructor for class ubic.gemma.rest.RootWebService.UserValueObject

V

valueOf(String) - Static method in class ubic.gemma.rest.util.args.CompositeSequenceArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.CompositeSequenceArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatabaseEntryArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatabaseEntryArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatasetArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.DatasetArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExcludeArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExpLevelConsolidationArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FactorValueArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FactorValueArrayArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.FilterArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.GeneArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.GeneArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.LimitArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.OffsetArg
valueOf(String) - Static method in class ubic.gemma.rest.util.args.PlatformArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.PlatformArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.QuantitationTypeArg
valueOf(String) - Static method in enum ubic.gemma.rest.util.args.SortArg.Sort.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.SortArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.StringArrayArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.TaxonArg: Used by RS to parse value of request parameters.
valueOf(String) - Static method in class ubic.gemma.rest.util.args.TaxonArrayArg: Used by RS to parse value of request parameters.
values() - Static method in enum ubic.gemma.rest.util.args.SortArg.Sort.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
visitErrorNode(ErrorNode) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
visitTerminal(TerminalNode) - Method in class ubic.gemma.rest.util.args.FilterArgBaseListener
VOCABULARY - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
VOCABULARY - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

W

WebApplicationExceptionMapper - Class in ubic.gemma.rest.providers: Map WebApplicationException so that it always expose a ResponseErrorObject entity.
WebApplicationExceptionMapper() - Constructor for class ubic.gemma.rest.providers.WebApplicationExceptionMapper
WellComposedErrorBody - Class in ubic.gemma.rest.util: Object acting as a payload for the ResponseErrorObject.
WellComposedErrorBody(Response.Status, String) - Constructor for class ubic.gemma.rest.util.WellComposedErrorBody: Creates a new well composed error body that can be used as a payload for a GemmaApiException, or ResponseErrorObject.
WS - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
WS - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

_

_ATN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_ATN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
_decisionToDFA - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_decisionToDFA - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
_serializedATN - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_serializedATN - Static variable in class ubic.gemma.rest.util.args.FilterArgParser
_sharedContextCache - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer
_sharedContextCache - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

A C D E F G I J L M N O P Q R S T U V W _