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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 Identifiable,S extends 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 Identifiable,S extends FilteringService<T>> - Class in ubic.gemma.rest.util.args

AbstractEntityArgService(S) - Constructor for class ubic.gemma.rest.util.args.AbstractEntityArgService

AbstractEntityArrayArg<O extends Identifiable,S extends 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

AbstractFactorValueValueObjectSerializer<T> - Class in ubic.gemma.rest.serializers

Base serializer for FactorValue VOs.

AbstractFactorValueValueObjectSerializer(Class<T>) - Constructor for class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer

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

ASC - ubic.gemma.rest.util.args.SortArg.Sort.Direction

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

authorities() - Method in annotation type ubic.gemma.rest.annotations.CacheControl

Authorities to whom this cache directive applies.

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() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext

CONJUNCTION(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.FilterContext

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

DESC - ubic.gemma.rest.util.args.SortArg.Sort.Direction

destroy() - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider

disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext

disjunction() - Method in class ubic.gemma.rest.util.args.FilterArgParser

disjunction(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext

DISJUNCTION - Static variable in class ubic.gemma.rest.util.args.FilterArgLexer

DISJUNCTION - Static variable 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 Identifiable,S extends 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

FactorValueBasicValueObjectSerializer - Class in ubic.gemma.rest.serializers

FactorValueBasicValueObjectSerializer() - Constructor for class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer

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.

FactorValueValueObjectSerializer - Class in ubic.gemma.rest.serializers

FactorValueValueObjectSerializer() - Constructor for class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer

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 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.

getDatasetHasBatchInformation(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(QueryArg, 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(QueryArg, FilterArg<ExpressionExperiment>, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject>, LimitArg, Integer, String, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, 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(QueryArg, FilterArg<ExpressionExperiment>, LimitArg, StringArrayArg, Boolean, StringArrayArg, Boolean, Boolean, Boolean) - Method in class ubic.gemma.rest.DatasetsWebService

getDatasetsPlatformsUsageStatistics(QueryArg, FilterArg<ExpressionExperiment>, LimitArg) - Method in class ubic.gemma.rest.DatasetsWebService

getDatasetsTaxaUsageStatistics(QueryArg, 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(AbstractEntityArg<?, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService

getEntities(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService

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

getEntity(QuantitationTypeArg<?>, ExpressionExperiment, Class<? extends DesignElementDataVector>) - Method in class ubic.gemma.rest.util.args.QuantitationTypeArgService

getEntityWithContrastsAndResults(ExpressionAnalysisResultSetService) - Method in class ubic.gemma.rest.util.args.ExpressionAnalysisResultSetArg

getEntityWithPlatform(CompositeSequenceArg<?>, ArrayDesign) - Method in class ubic.gemma.rest.util.args.CompositeSequenceArgService

getEntityWithTaxon(GeneService, Taxon) - Method in class ubic.gemma.rest.util.args.GeneEnsemblIdArg

getEntityWithTaxon(GeneService, Taxon) - Method in class ubic.gemma.rest.util.args.GeneSymbolArg

getEntityWithTaxon(GeneArg<?>, Taxon) - Method in class ubic.gemma.rest.util.args.GeneArgService

getErrors() - Method in class ubic.gemma.rest.util.WellComposedErrorBody

Used by JSON Serializer.

getExcludedUris(StringArrayArg, boolean, boolean) - Method in class ubic.gemma.rest.util.args.DatasetArgService

Obtain a list of exclude URIs from an argument containing excluded URIs.

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

getFilters(AbstractEntityArg<A, T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService

getFilters(AbstractEntityArg<A, T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService

getFilters(AbstractEntityArg<A, Taxon, TaxonService>) - Method in class ubic.gemma.rest.util.args.TaxonArgService

getFilters(AbstractEntityArrayArg<T, S>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService

getFilters(AbstractEntityArrayArg<T, S>) - Method in interface ubic.gemma.rest.util.args.EntityArgService

getFilters(FilterArg<T>) - Method in class ubic.gemma.rest.util.args.AbstractEntityArgService

getFilters(FilterArg<T>) - Method in interface ubic.gemma.rest.util.args.EntityArgService

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

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

getIdsForSearchQuery(QueryArg) - Method in class ubic.gemma.rest.util.args.DatasetArgService

Shortcut for extracting the result IDs from DatasetArgService.getResultsForSearchQuery(QueryArg, Highlighter).

getIdsForSearchQuery(QueryArg, Map<Long, Double>) - Method in class ubic.gemma.rest.util.args.DatasetArgService

Shortcut for extracting the result IDs and scores from DatasetArgService.getResultsForSearchQuery(QueryArg, Highlighter).

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(QueryArg, 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(DatasetArg<?>) - Method in class ubic.gemma.rest.util.args.DatasetArgService

Retrieves the Platforms of the Dataset that this argument represents.

getPlatforms(FilterArg<ArrayDesign>, OffsetArg, LimitArg, SortArg<ArrayDesign>) - Method in class ubic.gemma.rest.PlatformsWebService

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.

getResponseBuilder(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper

getResponseBuilder(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper

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.

getResultsForSearchQuery(QueryArg, Highlighter) - Method in class ubic.gemma.rest.util.args.DatasetArgService

Obtain the search results for a given query and highlighter.

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

getSort(SortArg<ExpressionExperiment>) - Method in class ubic.gemma.rest.util.args.DatasetArgService

getStatus() - Method in class ubic.gemma.rest.util.WellComposedErrorBody

getStatus(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper

Translate the exception to an HTTP Response.Status.

getStatus(Throwable) - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper

getStatus(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper

getStatus(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper

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

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() - Method in class ubic.gemma.rest.util.args.QueryArg

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(NotFoundException) - Method in class ubic.gemma.rest.providers.NotFoundExceptionMapper

getWellComposedErrorBody(MalformedArgException) - Method in class ubic.gemma.rest.providers.MalformedArgExceptionMapper

GoogleAnalytics4Provider - Class in ubic.gemma.rest.analytics.ga4

Implementation of the AnalyticsProvider interface for Google Analytics 4 collect API.

GoogleAnalytics4Provider(String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider

GoogleAnalytics4Provider(RestTemplate, String, String) - Constructor for class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider

Create a new Google Analytics 4 provider.

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 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

IN() - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionOperatorContext

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

isPrivate() - Method in annotation type ubic.gemma.rest.annotations.CacheControl

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>, String, 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

Represents a payload with a limited number of results.

LimitedResponseDataObject(List<T>, String, 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(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper

Indicate if the given exception should be logged.

logException(Throwable) - Method in class ubic.gemma.rest.providers.UnhandledExceptionMapper

logException(WebApplicationException) - Method in class ubic.gemma.rest.providers.WebApplicationExceptionMapper

logException(AuthenticationException) - Method in class ubic.gemma.rest.providers.AuthenticationExceptionMapper

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) - Constructor for exception ubic.gemma.rest.util.MalformedArgException

MalformedArgException(String, Throwable) - 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.

maxAge() - Method in annotation type ubic.gemma.rest.annotations.CacheControl

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(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.AnalyticsRequestEventListener

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

QuantitationTypeArgService - Class in ubic.gemma.rest.util.args

QuantitationTypeArgService(QuantitationTypeService) - Constructor for class ubic.gemma.rest.util.args.QuantitationTypeArgService

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

QueriedAndFilteredResponseDataObject<T> - Class in ubic.gemma.rest.util

QueriedAndFilteredResponseDataObject(List<T>, String, Filters, String[], Sort) - Constructor for class ubic.gemma.rest.util.QueriedAndFilteredResponseDataObject

queryAndFilter(List<T>, String, Filters, String[], Sort) - Static method in class ubic.gemma.rest.util.Responder

queryAndPaginate(Slice<T>, String, Filters, String[]) - Static method in class ubic.gemma.rest.util.Responder

QueryArg - Class in ubic.gemma.rest.util.args

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(QueryArg, 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 SearchWebService.search(QueryArg, TaxonArg, PlatformArg, List, LimitArg, ExcludeArg)'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() - Method in class ubic.gemma.rest.util.args.FilterArgParser

scalar() - Method in class ubic.gemma.rest.util.args.FilterArgParser.SubClauseContext

scalar(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.CollectionContext

ScalarContext(ParserRuleContext, int) - Constructor for class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext

search(QueryArg, 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 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, String...) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider

Publish an event without specifying a date.

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, Date, Map<String, String>) - Method in interface ubic.gemma.rest.analytics.AnalyticsProvider

Publish an event.

sendEvent(String, Date, Map<String, String>) - Method in class ubic.gemma.rest.analytics.ga4.GoogleAnalytics4Provider

serialize(FactorValueBasicValueObject, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.FactorValueBasicValueObjectSerializer

serialize(FactorValueValueObject, JsonGenerator, SerializerProvider) - Method in class ubic.gemma.rest.serializers.FactorValueValueObjectSerializer

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 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 - Static variable in class ubic.gemma.rest.util.args.FilterArgParser

STRING() - Method in class ubic.gemma.rest.util.args.FilterArgParser.ScalarContext

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() - Method in class ubic.gemma.rest.util.args.FilterArgParser

subClause(int) - Method in class ubic.gemma.rest.util.args.FilterArgParser.ClauseContext

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(JsonMappingException) - Method in class ubic.gemma.rest.providers.JsonMappingExceptionMapper

toResponse(E) - Method in class ubic.gemma.rest.providers.AbstractExceptionMapper

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.serializers - package ubic.gemma.rest.serializers

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

value() - Method in annotation type ubic.gemma.rest.annotations.CacheControls

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 class ubic.gemma.rest.util.args.QueryArg

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.

writeCharacteristics(Long, Collection<StatementValueObject>, JsonGenerator) - Method in class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer

writeStatements(Long, Collection<StatementValueObject>, JsonGenerator) - Method in class ubic.gemma.rest.serializers.AbstractFactorValueValueObjectSerializer

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

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