Uses of Class
ubic.gemma.persistence.util.Filters

Packages that use Filters

Package	Description
ubic.gemma.persistence.service
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.expression.arrayDesign
ubic.gemma.persistence.service.expression.designElement
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.taxon
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util
ubic.gemma.rest.util.args

Uses of Filters in ubic.gemma.persistence.service

Methods in ubic.gemma.persistence.service with parameters of type Filters

Modifier and Type	Method	Description
long	AbstractCriteriaFilteringVoEnabledDao.count(Filters filters)
long	AbstractFilteringVoEnabledService.count(Filters filters)
final long	AbstractNoopFilteringVoEnabledDao.count(Filters filters)
long	AbstractQueryFilteringVoEnabledDao.count(Filters filters)
long	FilteringDao.count(Filters filters)	Count VOs matching the given filters.
long	FilteringService.count(Filters filters)
long	AbstractQueryFilteringVoEnabledDao.countWithCache(Filters filters)
long	CachedFilteringDao.countWithCache(Filters filters)
protected org.hibernate.query.Query<?>	AbstractQueryFilteringVoEnabledDao.getFilteringCountQuery(Filters filters)
protected <T> AbstractCriteriaFilteringVoEnabledDao.CriteriaContext<T,O>	AbstractCriteriaFilteringVoEnabledDao.getFilteringCriteria(jakarta.persistence.criteria.CriteriaBuilder cb, Class<T> resultType, Filters filters)	Build a CriteriaQuery of the given result type rooted at the element class and apply the filter restriction.
protected org.hibernate.query.Query<?>	AbstractQueryFilteringVoEnabledDao.getFilteringIdQuery(Filters filters, Sort sort)
protected abstract org.hibernate.query.Query<?>	AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving filtered entities or VOs after applying filters and ordering.
List<O>	AbstractCriteriaFilteringVoEnabledDao.load(Filters filters, Sort sort)
Slice<O>	AbstractCriteriaFilteringVoEnabledDao.load(Filters filters, Sort sort, int offset, int limit)
List<O>	AbstractFilteringVoEnabledService.load(Filters filters, Sort sort)
Slice<O>	AbstractFilteringVoEnabledService.load(Filters filters, Sort sort, int offset, int limit)
final List<O>	AbstractNoopFilteringVoEnabledDao.load(Filters filters, Sort sort)
final Slice<O>	AbstractNoopFilteringVoEnabledDao.load(Filters filters, Sort sort, int offset, int limit)
List<O>	AbstractQueryFilteringVoEnabledDao.load(Filters filters, Sort sort)
Slice<O>	AbstractQueryFilteringVoEnabledDao.load(Filters filters, Sort sort, int offset, int limit)
List<O>	FilteringDao.load(Filters filters, Sort sort)	Load entities matching the given filters.
Slice<O>	FilteringDao.load(Filters filters, Sort sort, int offset, int limit)	Load a slice of entities matching the given filters.
List<O>	FilteringService.load(Filters filters, Sort sort)
Slice<O>	FilteringService.load(Filters filters, Sort sort, int offset, int limit)
List<Long>	AbstractCriteriaFilteringVoEnabledDao.loadIds(Filters filters, Sort sort)
List<Long>	AbstractFilteringVoEnabledService.loadIds(Filters filters, Sort sort)
final List<Long>	AbstractNoopFilteringVoEnabledDao.loadIds(Filters filters, Sort sort)
List<Long>	AbstractQueryFilteringVoEnabledDao.loadIds(Filters filters, Sort sort)
List<Long>	FilteringDao.loadIds(Filters filters, Sort sort)	Load IDs of entities matching the given filters.
List<Long>	FilteringService.loadIds(Filters filters, Sort sort)
List<Long>	AbstractQueryFilteringVoEnabledDao.loadIdsWithCache(Filters filters, Sort sort)
List<Long>	CachedFilteringDao.loadIdsWithCache(Filters filters, Sort sort)
List<VO>	AbstractCriteriaFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort)
Slice<VO>	AbstractCriteriaFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
List<VO>	AbstractFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort)
Slice<VO>	AbstractFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
final List<VO>	AbstractNoopFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort)
final Slice<VO>	AbstractNoopFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
List<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort)
Slice<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
List<VO>	FilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort)	Load VOs with minimal ordering and filtering.
Slice<VO>	FilteringVoEnabledDao.loadValueObjects(Filters filters, Sort sort, int offset, int limit)	Load VOs with ordering, filtering and offset/limit.
List<VO>	FilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort)
Slice<VO>	FilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<VO>	AbstractFilteringVoEnabledService.loadValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
default CursorPage<VO>	FilteringVoEnabledDao.loadValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Load VOs by keyset (cursor) pagination.
default CursorPage<VO>	FilteringVoEnabledService.loadValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Keyset (cursor) pagination — service-layer pass-through to FilteringVoEnabledDao.loadValueObjectsByCursor(Filters, Sort, Cursor, int).
CursorPage<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjectsByCursorWithCache(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-paged sister of AbstractQueryFilteringVoEnabledDao.loadValueObjectsWithCache(Filters, Sort, int, int).
List<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort)
Slice<VO>	AbstractQueryFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
List<VO>	CachedFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort)
Slice<VO>	CachedFilteringVoEnabledDao.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
List<O>	AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters filters, Sort sort)
Slice<O>	AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters filters, Sort sort, int offset, int limit)
List<O>	CachedFilteringDao.loadWithCache(Filters filters, Sort sort)
Slice<O>	CachedFilteringDao.loadWithCache(Filters filters, Sort sort, int offset, int limit)

Uses of Filters in ubic.gemma.persistence.service.analysis.expression.diff

Methods in ubic.gemma.persistence.service.analysis.expression.diff with parameters of type Filters

Modifier and Type	Method	Description
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, Cursor cursor, int limit)	Cursor-paged counterpart to ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort): keyset pagination over the result sets associated to a set of BioAssaySet and external database entries, always sorted by ascending id.
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDaoImpl.findByBioAssaySetInAndDatabaseEntryInByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, Cursor cursor, int limit)
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, Cursor cursor, int limit)	Cursor-paged counterpart to ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort).
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetServiceImpl.findByBioAssaySetInAndDatabaseEntryInByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, Cursor cursor, int limit)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)	Retrieve result sets associated to a set of BioAssaySet and external database entries.
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetDaoImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetServiceImpl.findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)

Uses of Filters in ubic.gemma.persistence.service.common.auditAndSecurity

Methods in ubic.gemma.persistence.service.common.auditAndSecurity with parameters of type Filters

Modifier and Type	Method	Description
List<C>	SecurableFilteringVoEnabledService.load(Filters filters, Sort sort)
Slice<C>	SecurableFilteringVoEnabledService.load(Filters filters, Sort sort, int offset, int limit)
List<Long>	SecurableFilteringVoEnabledService.loadIds(Filters filters, Sort sort)
List<VO>	SecurableFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort)
Slice<VO>	SecurableFilteringVoEnabledService.loadValueObjects(Filters filters, Sort sort, int offset, int limit)

Uses of Filters in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Methods in ubic.gemma.persistence.service.common.auditAndSecurity.curation with parameters of type Filters

Modifier and Type	Method	Description
protected void	AbstractCuratableDao.addNonTroubledFilter(Filters filters, String objectAlias)	Restrict results to non-troubled curatable entities for callers who do not curate.

Uses of Filters in ubic.gemma.persistence.service.expression.arrayDesign

Methods in ubic.gemma.persistence.service.expression.arrayDesign with parameters of type Filters

Modifier and Type	Method	Description
long	ArrayDesignReadService.countWithCache(Filters filters)
long	ArrayDesignReadServiceImpl.countWithCache(Filters filters)
long	ArrayDesignService.countWithCache(Filters filters)
long	ArrayDesignServiceImpl.countWithCache(Filters filters)
protected org.hibernate.query.Query	ArrayDesignDaoImpl.getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query	ArrayDesignDaoImpl.getFilteringIdQuery(Filters filters, Sort sort)
protected org.hibernate.query.Query	ArrayDesignDaoImpl.getFilteringQuery(Filters filters, Sort sort)
Slice<ArrayDesignValueObject>	ArrayDesignDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignReadService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ArrayDesignValueObject>	ArrayDesignService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)	No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.
Slice<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ArrayDesignValueObject>	ArrayDesignDao.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted platforms, applying the same shortName/accession blacklist filter that the offset-mode variant composes — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
CursorPage<ArrayDesignValueObject>	ArrayDesignDaoImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ArrayDesignValueObject>	ArrayDesignReadService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ArrayDesignValueObject>	ArrayDesignService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignService.loadBlacklistedValueObjects(Filters, Sort, int, int) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
CursorPage<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
Collection<ArrayDesignValueObject>	ArrayDesignReadService.loadValueObjectsWithCache(Filters filters, Sort sort)
Collection<ArrayDesignValueObject>	ArrayDesignReadServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort)
Collection<ArrayDesignValueObject>	ArrayDesignService.loadValueObjectsWithCache(Filters filters, Sort sort)
Collection<ArrayDesignValueObject>	ArrayDesignServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort)

Uses of Filters in ubic.gemma.persistence.service.expression.designElement

Methods in ubic.gemma.persistence.service.expression.designElement with parameters of type Filters

Modifier and Type	Method	Description
protected org.hibernate.query.Query	CompositeSequenceDaoImpl.getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query	CompositeSequenceDaoImpl.getFilteringIdQuery(Filters filters, Sort sort)
protected org.hibernate.query.Query	CompositeSequenceDaoImpl.getFilteringQuery(Filters filters, Sort sort)

Uses of Filters in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return Filters

Modifier and Type	Method	Description
Filters	ExpressionExperimentReadService.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
Filters	ExpressionExperimentReadServiceImpl.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
Filters	ExpressionExperimentService.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)	Perform various transformation to the provided filters to enhance it.
Filters	ExpressionExperimentServiceImpl.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type Filters

Modifier and Type	Method	Description
long	ExpressionExperimentDao.countBioMaterials(Filters filters)	Count the number of biomaterials of datasets satisfying the given filters.
long	ExpressionExperimentDaoImpl.countBioMaterials(Filters filters)
long	ExpressionExperimentReadService.countBioMaterials(Filters filters)
long	ExpressionExperimentReadServiceImpl.countBioMaterials(Filters filters)
long	ExpressionExperimentService.countBioMaterials(Filters filters)
long	ExpressionExperimentServiceImpl.countBioMaterials(Filters filters)
long	ExpressionExperimentReadService.countWithCache(Filters filters, Set<Long> extraIds)
long	ExpressionExperimentReadServiceImpl.countWithCache(Filters filters, Set<Long> extraIds)
long	ExpressionExperimentService.countWithCache(Filters filters, Set<Long> extraIds)	Count the number of experiments that match the given filters.
long	ExpressionExperimentServiceImpl.countWithCache(Filters filters, Set<Long> extraIds)
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	ExpressionExperimentReadService.getAnnotationsUsageFrequency(Filters filters, Set<Long> extraIds, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, int minFrequency, Collection<String> retainedTermUris, int maxResults, boolean includePredicates, boolean includeObjects, long timeout, TimeUnit timeUnit)
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	ExpressionExperimentReadServiceImpl.getAnnotationsUsageFrequency(Filters filters, Set<Long> extraIds, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, int minFrequency, Collection<String> retainedTermUris, int maxResults, boolean includePredicates, boolean includeObjects, long timeout, TimeUnit timeUnit)	If the term cannot be resolved via OntologyService.getTerm(String, long, TimeUnit), an attempt is done to resolve its category and assign it as its parent.
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	ExpressionExperimentService.getAnnotationsUsageFrequency(Filters filters, Set<Long> extraIds, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, int minFrequency, Collection<String> retainedTermUris, int maxResults, boolean includePredicates, boolean includeObjects, long timeout, TimeUnit timeUnit)	Obtain annotation usage frequency for datasets matching the given filters.
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	ExpressionExperimentServiceImpl.getAnnotationsUsageFrequency(Filters filters, Set<Long> extraIds, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, int minFrequency, Collection<String> retainedTermUris, int maxResults, boolean includePredicates, boolean includeObjects, long timeout, TimeUnit timeUnit)
Map<ArrayDesign, Long>	ExpressionExperimentReadService.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)
Map<ArrayDesign, Long>	ExpressionExperimentReadServiceImpl.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)
Map<ArrayDesign, Long>	ExpressionExperimentService.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)	Calculate the usage frequency of platforms by the datasets matching the provided filters.
Map<ArrayDesign, Long>	ExpressionExperimentServiceImpl.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)
Map<Characteristic, Long>	ExpressionExperimentReadService.getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Map<Characteristic, Long>	ExpressionExperimentReadServiceImpl.getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Map<Characteristic, Long>	ExpressionExperimentService.getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)	Obtain category usage frequency for datasets matching the given filter.
Map<Characteristic, Long>	ExpressionExperimentServiceImpl.getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Filters	ExpressionExperimentReadService.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
Filters	ExpressionExperimentReadServiceImpl.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
Filters	ExpressionExperimentService.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)	Perform various transformation to the provided filters to enhance it.
Filters	ExpressionExperimentServiceImpl.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
protected org.hibernate.query.Query	ExpressionExperimentDaoImpl.getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query	ExpressionExperimentDaoImpl.getFilteringIdQuery(Filters filters, Sort sort)
protected org.hibernate.query.Query	ExpressionExperimentDaoImpl.getFilteringQuery(Filters filters, Sort sort)
Map<Taxon,Long>	ExpressionExperimentReadService.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)
Map<Taxon,Long>	ExpressionExperimentReadServiceImpl.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)
Map<Taxon,Long>	ExpressionExperimentService.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)	Calculate the usage frequency of taxa by the datasets matching the provided filters.
Map<Taxon,Long>	ExpressionExperimentServiceImpl.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)
Map<TechnologyType, Long>	ExpressionExperimentReadService.getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
Map<TechnologyType, Long>	ExpressionExperimentReadServiceImpl.getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
Map<TechnologyType, Long>	ExpressionExperimentService.getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
Map<TechnologyType, Long>	ExpressionExperimentServiceImpl.getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDao.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentDao.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted-experiment view.
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentService.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)
List<Long>	ExpressionExperimentReadService.loadIdsWithCache(Filters filters, Sort sort)
List<Long>	ExpressionExperimentReadServiceImpl.loadIdsWithCache(Filters filters, Sort sort)
List<Long>	ExpressionExperimentService.loadIdsWithCache(Filters filters, Sort sort)
List<Long>	ExpressionExperimentServiceImpl.loadIdsWithCache(Filters filters, Sort sort)
List<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentDaoImpl.loadValueObjects(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentReadServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentService.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
Slice<ExpressionExperimentValueObject>	ExpressionExperimentServiceImpl.loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
List<ExpressionExperiment>	ExpressionExperimentDao.loadWithCache(Filters filters, Sort sort)

Uses of Filters in ubic.gemma.persistence.service.genome

Methods in ubic.gemma.persistence.service.genome with parameters of type Filters

Modifier and Type	Method	Description
protected org.hibernate.query.Query	GeneDaoImpl.getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query	GeneDaoImpl.getFilteringQuery(Filters filters, Sort sort)

Uses of Filters in ubic.gemma.persistence.service.genome.taxon

Methods in ubic.gemma.persistence.service.genome.taxon with parameters of type Filters

Modifier and Type	Method	Description
protected org.hibernate.query.Query<?>	TaxonDaoImpl.getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query<?>	TaxonDaoImpl.getFilteringQuery(Filters filters, Sort sort)

Uses of Filters in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util that return Filters

Modifier and Type	Method	Description
<T> Filters	Filters.and(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Collection<T> requiredValues)	Add a new clause of one explicit clause with a collection right hand side to to the conjunction.
<T> Filters	Filters.and(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Collection<T> requiredValues, String originalProperty)
<T> Filters	Filters.and(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, T requiredValue)	Add a clause of one explicit clause to the conjunction.
<T> Filters	Filters.and(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, T requiredValue, String originalProperty)
<T> Filters	Filters.and(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Subquery requiredValues)
<T> Filters	Filters.and(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Subquery requiredValues, String originalProperty)
Filters	Filters.and(Filter... filters)	Add a clause of one or more Filter sub-clauses to the conjunction.
Filters	Filters.and(Filters filters)	Add all the clauses of another filter to this.
Filters	Filters.FiltersClauseBuilder.build()
static <T> Filters	Filters.by(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Collection<T> requiredValue)
static <T> Filters	Filters.by(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Collection<T> requiredValue, String originalProperty)
static <T> Filters	Filters.by(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, T requiredValue)	Create a singleton Filters from an explicit clause.
static <T> Filters	Filters.by(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, T requiredValue, String originalProperty)
static <T> Filters	Filters.by(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Subquery requiredValue)
static <T> Filters	Filters.by(String objectAlias, String propertyName, Class<T> propertyType, Filter.Operator operator, Subquery requiredValue, String originalProperty)
static Filters	Filters.by(Filter... subClauses)	Create a singleton Filters from a Filter.
static Filters	Filters.by(Filters filters)	Copy constructor.
static Filters	Filters.empty()	Create an empty filter.

Methods in ubic.gemma.persistence.util with parameters of type Filters

Modifier and Type	Method	Description
static void	FilterQueryUtils.addRestrictionParameters(org.hibernate.query.Query query, Filters filters)	Adds all parameters contained in the filters argument to the query by calling Query.setParameter(String, Object) or Query.setParameterList(String, Collection) as needed.
Filters	Filters.and(Filters filters)	Add all the clauses of another filter to this.
static Filters	Filters.by(Filters filters)	Copy constructor.
static boolean	FiltersUtils.containsAnyAlias(Filters filters, Sort sort, String... aliases)	Check if an alias is mentioned in a set of Filter.
static jakarta.persistence.criteria.Predicate	FilterJpaUtils.formRestrictionClause(jakarta.persistence.criteria.CriteriaBuilder cb, jakarta.persistence.criteria.CommonAbstractCriteria query, jakarta.persistence.criteria.Root<?> root, Filters filters)	Build a JPA Predicate from a Filters (a conjunction of disjunctions).
static jakarta.persistence.criteria.Predicate	FilterJpaUtils.formRestrictionClause(jakarta.persistence.criteria.CriteriaBuilder cb, jakarta.persistence.criteria.CommonAbstractCriteria query, jakarta.persistence.criteria.Root<?> root, Filters filters, Map<String,String> aliasPrefixes)	Variant of FilterJpaUtils.formRestrictionClause(CriteriaBuilder, CommonAbstractCriteria, Root, Filters) that honours a registered objectAlias → dotted-prefix map so alias-prefixed paths (e.g.
static jakarta.persistence.criteria.Predicate	FilterJpaUtils.formRestrictionClause(jakarta.persistence.criteria.CriteriaBuilder cb, jakarta.persistence.criteria.Root<?> root, Filters filters)	Deprecated. prefer FilterJpaUtils.formRestrictionClause(CriteriaBuilder, CommonAbstractCriteria, Root, Filters) so inSubquery filters can resolve.
static String	FilterQueryUtils.formRestrictionClause(Filters filters)	Creates a CNF restriction clause from the given Filters list.

Uses of Filters in ubic.gemma.rest

Constructors in ubic.gemma.rest with parameters of type Filters

Modifier	Constructor	Description
	FilteredAndInferredAndCursorPaginatedResponseDataObject(CursorPage<T> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	FilteredAndInferredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject(CursorPage<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	FilteredAndInferredAndPaginatedResponseDataObject(Slice<T> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	FilteredAndInferredAndPaginatedResponseDataObjectExpressionExperimentValueObject(Slice<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObject(CursorPage<T> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndCursorPaginatedResponseDataObjectExperimentExpressionLevelsValueObject(CursorPage<ExperimentExpressionLevelsValueObject> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndLimitedResponseDataObject(List<T> payload, String query, Filters filters, String[] groupBy, Sort sort, Integer limit, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndPaginatedResponseDataObject(Slice<T> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultByGeneValueObject(Slice<DatasetsWebService.DifferentialExpressionAnalysisResultByGeneValueObject> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredAndPaginatedResponseDataObjectExperimentExpressionLevelsValueObject(Slice<ExperimentExpressionLevelsValueObject> payload, String query, Filters filters, String[] groupBy, Collection<OntologyTerm> inferredTerms)
	QueriedAndFilteredAndInferredResponseDataObject(List<T> payload, String query, Filters filters, String[] groupBy, Sort sort, Collection<OntologyTerm> inferredTerms)

Uses of Filters in ubic.gemma.rest.util

Methods in ubic.gemma.rest.util with parameters of type Filters

Modifier and Type	Method	Description
static <T> QueriedAndFilteredResponseDataObject<T>	Responders.all(List<T> payload, String query, Filters filters, String[] groupBy, Sort sort)
static <T> FilteredResponseDataObject<T>	Responders.all(List<T> payload, Filters filters, String[] groupBy, Sort sort)	Produce all results.
Slice<T>	Responders.FilterMethod.load(Filters filters, Sort sort, int offset, int limit)
static <T> QueriedAndFilteredAndPaginatedResponseDataObject<T>	Responders.paginate(Slice<T> payload, String query, Filters filters, String[] groupBy)	Paginate results with a filter and a full-text query.
static <T> FilteredAndPaginatedResponseDataObject<T>	Responders.paginate(Slice<T> payload, Filters filters, String[] groupBy)	Paginate results with a filter.
static <T> FilteredAndPaginatedResponseDataObject<T>	Responders.paginate(Responders.FilterMethod<T> filterMethod, Filters filters, String[] groupBy, Sort sort, int offset, int limit)	Paginate results with a filter using a callback to produce the payload.
static <T> FilteredAndLimitedResponseDataObject<T>	Responders.top(List<T> payload, Filters filters, String[] groupBy, Sort sort, Integer limit)	Produce top results.

Constructors in ubic.gemma.rest.util with parameters of type Filters

Modifier	Constructor	Description
	FilteredAndCursorPaginatedResponseDataObject(CursorPage<T> payload, Filters filters, String[] groupBy)
	FilteredAndCursorPaginatedResponseDataObjectArrayDesignValueObject(CursorPage<ArrayDesignValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndCursorPaginatedResponseDataObjectCompositeSequenceValueObject(CursorPage<CompositeSequenceValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndCursorPaginatedResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject(CursorPage<DifferentialExpressionAnalysisResultSetValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndCursorPaginatedResponseDataObjectExpressionExperimentValueObject(CursorPage<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndCursorPaginatedResponseDataObjectGeneValueObject(CursorPage<GeneValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndLimitedResponseDataObject(List<T> payload, Filters filters, String[] groupBy, Sort sort, Integer limit)
	FilteredAndPaginatedResponseDataObject(Slice<T> payload, Filters filters, String[] groupBy)
	FilteredAndPaginatedResponseDataObjectArrayDesignValueObject(Slice<ArrayDesignValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndPaginatedResponseDataObjectCompositeSequenceValueObject(Slice<CompositeSequenceValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndPaginatedResponseDataObjectDifferentialExpressionAnalysisResultSetValueObject(Slice<DifferentialExpressionAnalysisResultSetValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndPaginatedResponseDataObjectExpressionExperimentValueObject(Slice<ExpressionExperimentValueObject> payload, Filters filters, String[] groupBy)
	FilteredAndPaginatedResponseDataObjectGeneValueObject(Slice<GeneValueObject> payload, Filters filters, String[] groupBy)
	FilteredResponseDataObject(List<T> payload, Filters filters, String[] groupBy, Sort sort)
	QueriedAndFilteredAndCursorPaginatedResponseDataObject(CursorPage<T> payload, String query, Filters filters, String[] groupBy)
	QueriedAndFilteredAndLimitedResponseDataObject(List<T> payload, String query, Filters filters, String[] groupBy, Sort sort, Integer limit)
	QueriedAndFilteredAndPaginatedResponseDataObject(Slice<T> payload, String query, Filters filters, String[] groupBy)
	QueriedAndFilteredResponseDataObject(List<T> payload, String query, Filters filters, String[] groupBy, Sort sort)

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

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

Modifier and Type	Method	Description
Filters	PlatformArgService.getElementFilters(PlatformArg<?> arg, CompositeSequenceArrayArg probesArg)	Filters for the /{platform}/elements/{probes} endpoints: the platform scope AND the {probes} id/name set restriction.
<A> Filters	AbstractEntityArgService.getFilters(AbstractEntityArg<A,T,S> entityArg)
Filters	AbstractEntityArgService.getFilters(AbstractEntityArrayArg<T,S> entitiesArg)
Filters	AbstractEntityArgService.getFilters(FilterArg<T> filterArg)
Filters	DatasetArgService.getFilters(FilterArg<ExpressionExperiment> filterArg)
Filters	DatasetArgService.getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms)
Filters	DatasetArgService.getFilters(FilterArg<ExpressionExperiment> filterArg, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
<A> Filters	EntityArgService.getFilters(AbstractEntityArg<A,T,S> entityArg)	Translate the provided entity argument into a Filters.
Filters	EntityArgService.getFilters(AbstractEntityArrayArg<T,S> entitiesArg)	Translate the provided entity argument into a Filters.
Filters	EntityArgService.getFilters(FilterArg<T> filterArg)	Obtain a Filters from a filter argument.
<A> Filters	TaxonArgService.getFilters(AbstractEntityArg<A, Taxon, TaxonService> entityArg)

Methods in ubic.gemma.rest.util.args with parameters of type Filters

Modifier and Type	Method	Description
CursorPage<ExpressionExperimentValueObject>	DatasetArgService.getBlacklistedDatasetsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ArrayDesignValueObject>	PlatformArgService.getBlacklistedPlatformsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignService.loadBlacklistedValueObjects(Filters, Sort, int, int).
CursorPage<ExpressionExperimentValueObject>	DatasetArgService.getDatasetsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to SecurableFilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int).
Slice<CompositeSequenceValueObject>	PlatformArgService.getElements(PlatformArg<?> arg, Filters userFilters, Collection<Long> geneIds, int limit, int offset, boolean withSequence, boolean withGenes)	Widest offset-mode variant: user-supplied filter= conjunct on top of everything else.
CursorPage<CompositeSequenceValueObject>	PlatformArgService.getElementsByCursor(PlatformArg<?> arg, Filters userFilters, Collection<Long> geneIds, Cursor cursor, int limit, boolean withSequence, boolean withGenes)	Widest cursor-mode variant; see PlatformArgService.getElements(PlatformArg, Filters, Collection, int, int, boolean, boolean).
CursorPage<ArrayDesignValueObject>	PlatformArgService.getPlatformsByCursor(Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to SecurableFilteringVoEnabledService.loadValueObjects(Filters, Sort, int, int).
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	ExpressionAnalysisResultSetArgService.getResultSetsByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionAnalysisResultSetService.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort).