Uses of Class
ubic.gemma.rest.util.args.LimitArg

Packages that use LimitArg

Package	Description
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of LimitArg in ubic.gemma.rest

Methods in ubic.gemma.rest with parameters of type LimitArg

Modifier and Type	Method	Description
Object	DatasetsWebService.getBlacklistedDatasets(FilterArg<ExpressionExperiment> filterArg, SortArg<ExpressionExperiment> sortArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg)	Browse blacklisted datasets.
Object	PlatformsWebService.getBlacklistedPlatforms(FilterArg<ArrayDesign> filter, SortArg<ArrayDesign> sort, OffsetArg offset, LimitArg limit, CursorArg cursorArg)
Object	DatasetsWebService.getDatasetAuditEvents(DatasetArg<?> datasetArg, CursorArg cursorArg, LimitArg limitArg, boolean compact, boolean excludeEmpty)
ResponseDataObject<List<DifferentialExpressionAnalysisValueObject>>	DatasetsWebService.getDatasetDifferentialExpressionAnalyses(DatasetArg<?> datasetArg, OffsetArg offsetArg, LimitArg limitArg, boolean includeAssays)	Retrieves the differential analysis results for the given dataset.
DatasetsWebService.QueriedAndFilteredAndInferredAndPaginatedResponseDataObject<DatasetsWebService.ExpressionExperimentWithSearchResultValueObject>	DatasetsWebService.getDatasets(QueryArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, SortArg<ExpressionExperiment> sortArg)
Object	DatasetsWebService.getDatasetSamples(DatasetArg<?> datasetArg, QuantitationTypeArg<?> quantitationTypeArg, boolean useProcessedQuantitationType, CursorArg cursorArg, LimitArg limitArg, ExcludeArg<BioAssayValueObject> excludeArg, boolean includePredictedOutliers)	Retrieves the samples for the given dataset.
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<DatasetsWebService.AnnotationWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsAnnotationsUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filter, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject> exclude, LimitArg limitArg, Integer minFrequency, String category, StringArrayArg excludedCategoryUris, Boolean excludeFreeTextCategories, StringArrayArg excludedTermUris, Boolean excludeFreeTextTerms, Boolean excludeUncategorizedTerms, Boolean retainMentionedTerms, Boolean includePredicates, Boolean includeObjects)
Object	DatasetsWebService.getDatasetsByIds(DatasetArrayArg datasetsArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort, CursorArg cursorArg)	Retrieves all datasets matching the given identifiers.
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<DatasetsWebService.CategoryWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsCategoriesUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filter, LimitArg limit, StringArrayArg excludedCategoryUris, Boolean excludeFreeTextCategories, StringArrayArg excludedTermUris, Boolean excludeFreeTextTerms, Boolean excludeUncategorizedTerms, Boolean retainMentionedTerms)
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsDifferentialExpression(DatasetArrayArg datasets, Long diffExSet, Double threshold, LimitArg limit, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, Boolean precise)	Retrieves the expression levels of genes highly expressed in the given component on given datasets.
Object	DatasetsWebService.getDatasetsDifferentialExpressionAnalysisResultsForGene(GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, jakarta.ws.rs.core.HttpHeaders headers)	Obtain differential expression analysis results for a given gene.
Object	DatasetsWebService.getDatasetsDifferentialExpressionAnalysisResultsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offsetArg, LimitArg limitArg, Double threshold, jakarta.ws.rs.core.HttpHeaders headers)	Obtain differential expression analysis results for a given gene in a given taxon.
Object	DatasetsWebService.getDatasetsExpressionLevelsForGene(GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, CursorArg cursorArg, Boolean precise)	Retrieve the expression levels of a given gene across all datasets.
Object	DatasetsWebService.getDatasetsExpressionLevelsForGeneInTaxon(TaxonArg<?> taxonArg, GeneArg<?> geneArg, QueryArg queryArg, FilterArg<ExpressionExperiment> filterArg, OffsetArg offsetArg, LimitArg limitArg, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, CursorArg cursorArg, Boolean precise)	Retrieve the expression levels of a given gene and taxon across all datasets.
ResponseDataObject<List<ExperimentExpressionLevelsValueObject>>	DatasetsWebService.getDatasetsExpressionPca(DatasetArrayArg datasets, Integer component, LimitArg limit, Boolean keepNonSpecific, ExpLevelConsolidationArg consolidate, Boolean precise)	Retrieves the expression levels of genes highly expressed in the given component on given datasets.
DatasetsWebService.QueriedAndFilteredAndInferredAndLimitedResponseDataObject<DatasetsWebService.ArrayDesignWithUsageStatisticsValueObject>	DatasetsWebService.getDatasetsPlatformsUsageStatistics(QueryArg query, FilterArg<ExpressionExperiment> filter, LimitArg limit)
Object	DatasetsWebService.getDatasetSubSetSamples(DatasetArg<?> datasetArg, Long subSetId, CursorArg cursorArg, LimitArg limitArg, boolean includePredictedOutliers)	Retrieves the samples of a specific subset of a dataset.
Object	DatasetsWebService.getDatasetTickets(DatasetArg<?> datasetArg, CursorArg cursorArg, LimitArg limitArg)
PaginatedResponseDataObject<ExpressionExperimentSetValueObject>	ExperimentSetsWebService.getExperimentSets(boolean mine, String query, boolean includeMembers, OffsetArg offsetArg, LimitArg limitArg)
Object	GeneWebService.getGeneProbes(GeneArg<?> geneArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg, boolean summary)	Retrieves the probes (composite sequences) with this gene.
Object	GeneWebService.getGenes(OffsetArg offsetArg, LimitArg limitArg, CursorArg cursorArg)
PaginatedResponseDataObject<GeneValueObject>	GoTermsWebService.getGenesByGoTerm(String termUri, TaxonArg<?> taxonArg, OffsetArg offsetArg, LimitArg limitArg, boolean propagate, int maxTerms)	Reverse lookup: genes annotated with the given GO term.
PaginatedResponseDataObject<GroupsWebService.GroupSummaryValueObject>	GroupsWebService.getGroups(String query, OffsetArg offsetArg, LimitArg limitArg)	List groups (paginated; offset/limit).
Object	PlatformsWebService.getPlatformDatasets(PlatformArg<?> platformArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg)	Retrieves experiments in the given platform.
Object	PlatformsWebService.getPlatformElement(PlatformArg<?> platformArg, CompositeSequenceArrayArg probesArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg, boolean withSequence, boolean withGenes)	Retrieves composite sequences (elements) of the given platform.
Object	PlatformsWebService.getPlatformElementGenes(PlatformArg<?> platformArg, CompositeSequenceArg<?> probeArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg)	Retrieves the genes on the given platform element.
Object	PlatformsWebService.getPlatformElements(PlatformArg<?> platformArg, OffsetArg offset, LimitArg limit, CursorArg cursorArg, boolean withSequence, boolean withGenes, QueryArg geneQuery, FilterArg<CompositeSequence> filter)	Retrieves the composite sequences (elements) for the given platform.
Object	PlatformsWebService.getPlatforms(FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort, CursorArg cursorArg, boolean withGeneCounts)
Object	PlatformsWebService.getPlatformsByIds(PlatformArrayArg platformsArg, FilterArg<ArrayDesign> filter, OffsetArg offset, LimitArg limit, SortArg<ArrayDesign> sort, CursorArg cursorArg, boolean withGeneCounts)	Retrieves all datasets matching the given identifiers.
Object	PlatformsWebService.getPlatformTickets(PlatformArg<?> platformArg, CursorArg cursorArg, LimitArg limitArg)	Retrieves the open curation tickets for a given platform.
Object	AnalysisResultSetsWebService.getResultSet(ExpressionAnalysisResultSetArg analysisResultSet, Double threshold, OffsetArg offsetArg, LimitArg limitArg, Boolean includeFactorValuesInContrasts, Boolean includeTaxonInGenes, Boolean excludeResults, jakarta.ws.rs.core.HttpHeaders headers)	Retrieve a AnalysisResultSet given its identifier.
Object	AnalysisResultSetsWebService.getResultSets(DatasetArrayArg datasets, DatabaseEntryArrayArg databaseEntries, FilterArg<ExpressionAnalysisResultSet> filters, OffsetArg offset, LimitArg limit, SortArg<ExpressionAnalysisResultSet> sort, CursorArg cursorArg)	Retrieve all AnalysisResultSet matching a set of criteria.
PaginatedResponseDataObject<DatasetsWebService.StaleDatasetValueObject>	DatasetsWebService.getStaleDatasets(OffsetArg offset, LimitArg limit)	The datasets that owe pipeline work: every dataset with at least one stale step, and which steps those are.
Object	TaxaWebService.getTaxonDatasets(TaxonArg<?> taxonArg, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort, CursorArg cursorArg)	Retrieves datasets for the given taxon.
Object	TaxaWebService.getTaxonGeneProbes(TaxonArg<?> taxonArg, GeneArg<?> geneArg, OffsetArg offsetArg, LimitArg limitArg, CursorArg cursorArg)
Object	TaxaWebService.getTaxonGenes(TaxonArg<?> taxonArg, OffsetArg offsetArg, LimitArg limitArg, CursorArg cursorArg)
Object	TicketsWebService.getTicketEvents(Long id, CursorArg cursorArg, LimitArg limitArg)	Retrieve only the event log for a ticket.
Object	TicketsWebService.getTickets(boolean openOnly, Long assigneeId, TicketPriority priority, TicketType type, TicketState state, TicketTargetType targetType, Date updatedSince, OffsetArg offsetArg, LimitArg limitArg, CursorArg cursorArg)	List tickets with optional filters and offset/limit or cursor pagination.
PaginatedResponseDataObject<WorkflowWebService.WorkflowQueueEntryResponse>	WorkflowWebService.getWorkflowQueue(String stateName, String datasetType, String datasetTypeLegacy, String assignee, Date since, OffsetArg offsetArg, LimitArg limitArg)	Curator worklist: datasets currently in a given workflow state.
PaginatedResponseDataObject<AnnotationSetsWebService.AnnotationSetSummaryResponse>	AnnotationSetsWebService.listAnnotationSetsAcross(String role, String source, String createdBy, String kind, String status, String datasetIds, OffsetArg offsetArg, LimitArg limitArg, String sort)	Cross-experiment list of annotation sets, paginated.
jakarta.ws.rs.core.Response	DatasetsWebService.refreshDatasetsAnnotations(QueryArg query, FilterArg<ExpressionExperiment> filter, ExcludeArg<DatasetsWebService.AnnotationWithUsageStatisticsValueObject> exclude, LimitArg limitArg, Integer minFrequency, String category, StringArrayArg excludedCategoryUris, Boolean excludeFreeTextCategories, StringArrayArg excludedTermUris, Boolean excludeFreeTextTerms, Boolean excludeUncategorizedTerms, Boolean retainMentionedTerms, Boolean includePredicates, Boolean includeObjects)
jakarta.ws.rs.core.Response	DatasetsWebService.refreshDatasetsPlatforms(QueryArg query, FilterArg<ExpressionExperiment> filter, LimitArg limit)
SearchWebService.SearchResultsResponseDataObject	SearchWebService.search(QueryArg query, DatasetArg<?> datasetArg, TaxonArg<?> taxonArg, PlatformArg<?> platformArg, List<String> resultTypes, LimitArg limit, ExcludeArg<SearchResult<?>> excludeArg, boolean useGeneOntology, boolean inferRelations)	Search everything subject to taxon and platform constraints.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasets(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)	Does a search for datasets containing characteristics matching the given string.
ResponseDataObject<List<DatasetsWebService.DatasetSearchHitValueObject>>	DatasetsWebService.searchDatasets(QueryArg query, LimitArg limit)	Deprecated. redundant with GET /datasets?query=... (the paginated catalogue runs the same search), which every known client uses instead — no caller of this endpoint was found across gemma-ui, gemma-curation-agents, or gemma.R.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchDatasetsByQueryInPath(StringArrayArg query, FilterArg<ExpressionExperiment> filterArg, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sortArg)
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasets(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)	Same as AnnotationsWebService.searchDatasets(StringArrayArg, FilterArg, OffsetArg, LimitArg, SortArg) but also filters by taxon.
QueriedAndFilteredAndPaginatedResponseDataObject<ExpressionExperimentValueObject>	AnnotationsWebService.searchTaxonDatasetsByQueryInPath(TaxonArg<?> taxonArg, StringArrayArg query, FilterArg<ExpressionExperiment> filter, OffsetArg offset, LimitArg limit, SortArg<ExpressionExperiment> sort)
ResponseDataObject<List<TicketSearchHitValueObject>>	TicketsWebService.searchTickets(String query, boolean openOnly, LimitArg limitArg)	Ticket picker: "choose a ticket by typing".

Uses of LimitArg in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return LimitArg

Modifier and Type	Method	Description
static LimitArg	LimitArg.valueOf(String s)