Interface ExpressionExperimentReadService

All Known Implementing Classes:

ExpressionExperimentReadServiceImpl

public interface ExpressionExperimentReadService

Thin read-only retrieval service for ExpressionExperiment.

Phase 1 of the ExpressionExperimentService decomposition (strangler fig). This service houses the pure-retrieval "bucket A" methods: load/find/exists/thaw helpers that delegate directly to ExpressionExperimentDao with no orchestration of write-side collaborators.

Callers should generally keep using ExpressionExperimentService as the facade — the facade delegates to this service. Direct injection is appropriate where a class would otherwise create a Spring dependency cycle through the heavier facade (e.g. ExpressionExperimentSetService, SampleCoexpressionAnalysisService).

ACL / @Secured annotations live on ExpressionExperimentService (the caller-facing facade interface); enforcement happens at the facade proxy boundary.

See Also:

• ExpressionExperimentService

Method Summary

Modifier and Type	Method	Description
List<ExpressionExperiment>	browse(int start, int limit)
long	countBioMaterials(Filters filters)
long	countWithCache(Filters filters, Set<Long> extraIds)
boolean	existsByShortName(String shortName)
Collection<Long>	filter(String searchString)
Collection<Long>	filterByTaxon(Collection<Long> ids, Taxon taxon)
Collection<ExpressionExperiment>	findByAccession(String accession)
Collection<ExpressionExperiment>	findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	findByBibliographicReference(BibliographicReference bibRef)
ExpressionExperiment	findByBioAssay(BioAssay ba)
ExpressionExperiment	findByBioAssay(BioAssay ba, boolean includeSubSets)
Collection<ExpressionExperiment>	findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Map<ExpressionExperiment, Collection<BioMaterial>>	findByBioMaterials(Collection<BioMaterial> biomaterials)
ExpressionExperiment	findByDesign(ExperimentalDesign ed)
ExpressionExperiment	findByDesignId(Long designId)
Collection<ExpressionExperiment>	findByExpressedGene(Gene gene, double rank)
ExpressionExperiment	findByFactor(ExperimentalFactor factor)
Collection<ExpressionExperiment>	findByFactors(Collection<ExperimentalFactor> factors)
ExpressionExperiment	findByFactorValue(FactorValue factorValue)
ExpressionExperiment	findByFactorValueId(Long factorValueId)
Collection<ExpressionExperiment>	findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	findByGene(Gene gene)
ExpressionExperiment	findByMeanVarianceRelation(MeanVarianceRelation mvr)
Collection<ExpressionExperiment>	findByName(String name)
ExpressionExperiment	findByQuantitationType(QuantitationType type)
ExpressionExperiment	findByShortName(String shortName)
ExpressionExperiment	findByShortNameAndThawLite(String shortName)
ExpressionExperiment	findByShortNameWithPrimaryPublication(String shortName)
Collection<ExpressionExperiment>	findByTaxon(Taxon taxon)
List<ExpressionExperiment>	findByUpdatedLimit(int limit)
Long	findIdByBioAssay(BioAssay ba, boolean includeSubSets)
Long	findIdByDesign(ExperimentalDesign design)
Long	findIdByFactor(ExperimentalFactor factor)
Long	findIdByFactorValue(FactorValue factorValue)
Long	findIdByMeanVarianceRelation(MeanVarianceRelation mvr)
Collection<Long>	findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
ExpressionExperiment	findOneByAccession(String accession)
ExpressionExperiment	findOneByName(String name)
Collection<ExpressionExperiment>	findUpdatedAfter(Date date)
Map<Long,Long>	getAnnotationCountsByIds(Collection<Long> ids)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	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>	getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)
long	getBioMaterialCount(ExpressionExperiment expressionExperiment)
Map<Characteristic, Long>	getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Filters	getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
ExperimentalDesignValueObject	getExperimentalDesignValueObject(ExpressionExperiment ee)
Collection<ExpressionExperiment>	getExperimentsWithOutliers()
Map<Long,Date>	getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Date	getLastArrayDesignUpdate(ExpressionExperiment ee)
Map<Long, AuditEvent>	getLastLinkAnalysis(Collection<Long> ids)
Map<Long, AuditEvent>	getLastMissingValueAnalysis(Collection<Long> ids)
Map<Long, AuditEvent>	getLastProcessedDataUpdate(Collection<Long> ids)
Map<BioAssay,Long>	getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<Taxon,Long>	getPerTaxonCount()
Map<Long,Long>	getPopulatedFactorCounts(Collection<Long> ids)
Map<Long,Long>	getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)
long	getRawDataVectorCount(ExpressionExperiment ee)
Map<ExpressionExperiment, Collection<AuditEvent>>	getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<Taxon,Long>	getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)
Taxon	getTaxon(ExpressionExperiment expressionExperiment)	Included for cycle-break parity with the facade: the only read-method back-edge from ExpressionExperimentSetServiceImpl is getTaxon.
Map<TechnologyType, Long>	getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
SortedMap<String,String>	loadAllIdentifiersAndName(boolean includeNames)
Collection<ExpressionExperiment>	loadAllReferences()
ExpressionExperiment	loadAndThaw(Long id)
ExpressionExperiment	loadAndThawLite(Long id)
<T extends Exception> ExpressionExperiment	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
<T extends Exception> ExpressionExperiment	loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
ExpressionExperiment	loadAndThawLiteWithRefreshCacheMode(Long id)
<T extends Exception> ExpressionExperiment	loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)
Slice<ExpressionExperimentValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ExpressionExperimentValueObject>	loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to loadBlacklistedValueObjects(Filters, Sort, int, int).
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIds(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<ExpressionExperimentDao.Identifiers>	loadIdentifiers(Collection<Long> ids)	Resolve the short name and name of the given experiments, for callers that hold ids and need something a person can read.
List<Long>	loadIdsWithCache(Filters filters, Sort sort)
Collection<ExpressionExperiment>	loadLackingFactors()
Collection<ExpressionExperiment>	loadLackingTags()
ExpressionExperiment	loadReference(Long id)
Collection<ExpressionExperiment>	loadReferences(Collection<Long> ids)
List<Long>	loadTroubledIds()
List<ExpressionExperimentValueObject>	loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)
List<ExpressionExperimentValueObject>	loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)
Slice<ExpressionExperimentValueObject>	loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
ExpressionExperiment	loadWithAuditTrail(Long id)
ExpressionExperiment	loadWithCharacteristics(Long id)
ExpressionExperiment	loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	loadWithPrimaryPublication(Long id)
ExpressionExperiment	loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	reload(ExpressionExperiment ee)
ExpressionExperiment	thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	thawBioAssays(ExpressionExperiment expressionExperiment)	Narrow thaw used by the /samples REST endpoint: initializes only the bioAssays collection and applies Thaws.thawBioAssay(BioAssay) to each assay (which warms the array design, original platform, and biomaterial-with-factor-values shape that BioAssayValueObject reads).
ExpressionExperiment	thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	thawLiter(ExpressionExperiment expressionExperiment)

Method Details

loadReference

@Nonnull
ExpressionExperiment loadReference(Long id)

loadReferences

Collection<ExpressionExperiment> loadReferences(Collection<Long> ids)

loadAllReferences

Collection<ExpressionExperiment> loadAllReferences()

loadWithAuditTrail

@Nullable
ExpressionExperiment loadWithAuditTrail(Long id)

loadTroubledIds

List<Long> loadTroubledIds()

loadAllIdentifiersAndName

SortedMap<String,String> loadAllIdentifiersAndName(boolean includeNames)

loadIdentifiers

List<ExpressionExperimentDao.Identifiers> loadIdentifiers(Collection<Long> ids)

Resolve the short name and name of the given experiments, for callers that hold ids and need something a person can read.

ACL-filtered: an id the caller cannot read is absent from the result rather than throwing, so a caller labelling a list it was handed cannot learn about a dataset it could not otherwise see.

See Also:

• ExpressionExperimentDao.loadIdentifiers(Collection)

reload

ExpressionExperiment reload(ExpressionExperiment ee)

loadWithPrimaryPublication

@Nullable
ExpressionExperiment loadWithPrimaryPublication(Long id)

loadWithPrimaryPublicationAndOtherRelevantPublications

@Nullable
ExpressionExperiment loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)

loadWithMeanVarianceRelation

@Nullable
ExpressionExperiment loadWithMeanVarianceRelation(Long id)

loadWithCharacteristics

@Nullable
ExpressionExperiment loadWithCharacteristics(Long id)

loadAndThaw

@Nullable
ExpressionExperiment loadAndThaw(Long id)

loadAndThawLite

@Nullable
ExpressionExperiment loadAndThawLite(Long id)

loadAndThawLiteWithRefreshCacheMode

@Nullable
ExpressionExperiment loadAndThawLiteWithRefreshCacheMode(Long id)

loadAndThawOrFail

<T extends Exception> ExpressionExperiment loadAndThawOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                      throws T

Throws:

T

loadAndThawLiteOrFail

<T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier,
 String message)
                                                          throws T

Throws:

T

loadAndThawLiteOrFail

<T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                          throws T

Throws:

T

loadAndThawLiterOrFail

<T extends Exception> ExpressionExperiment loadAndThawLiterOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                           throws T

Throws:

T

findByAccession

Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)

findByAccession

Collection<ExpressionExperiment> findByAccession(String accession)

findOneByAccession

@Nullable
ExpressionExperiment findOneByAccession(String accession)

findByBibliographicReference

Collection<ExpressionExperiment> findByBibliographicReference(BibliographicReference bibRef)

findByBioAssay

ExpressionExperiment findByBioAssay(BioAssay ba)

findByBioAssay

ExpressionExperiment findByBioAssay(BioAssay ba,
 boolean includeSubSets)

findIdByBioAssay

@Nullable
Long findIdByBioAssay(BioAssay ba,
 boolean includeSubSets)

findByBioMaterial

Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm)

findByBioMaterial

Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm,
 boolean includeSubSets)

findIdsByBioMaterial

Collection<Long> findIdsByBioMaterial(BioMaterial bm,
 boolean includeSubSets)

findByBioMaterials

Map<ExpressionExperiment, Collection<BioMaterial>> findByBioMaterials(Collection<BioMaterial> biomaterials)

findByExpressedGene

Collection<ExpressionExperiment> findByExpressedGene(Gene gene,
 double rank)

findByDesign

@Nullable
ExpressionExperiment findByDesign(ExperimentalDesign ed)

findIdByDesign

@Nullable
Long findIdByDesign(ExperimentalDesign design)

findByDesignId

@Nullable
ExpressionExperiment findByDesignId(Long designId)

findByFactor

@Nullable
ExpressionExperiment findByFactor(ExperimentalFactor factor)

findIdByFactor

@Nullable
Long findIdByFactor(ExperimentalFactor factor)

findByFactors

Collection<ExpressionExperiment> findByFactors(Collection<ExperimentalFactor> factors)

findByFactorValue

@Nullable
ExpressionExperiment findByFactorValue(FactorValue factorValue)

findIdByFactorValue

@Nullable
Long findIdByFactorValue(FactorValue factorValue)

findByFactorValueId

@Nullable
ExpressionExperiment findByFactorValueId(Long factorValueId)

findByFactorValues

Collection<ExpressionExperiment> findByFactorValues(Collection<FactorValue> factorValues)

findByFactorValueIds

Collection<ExpressionExperiment> findByFactorValueIds(Collection<Long> factorValueIds)

findByGene

Collection<ExpressionExperiment> findByGene(Gene gene)

findByName

Collection<ExpressionExperiment> findByName(String name)

findOneByName

@Nullable
ExpressionExperiment findOneByName(String name)

findByQuantitationType

ExpressionExperiment findByQuantitationType(QuantitationType type)

findByShortName

@Nullable
ExpressionExperiment findByShortName(String shortName)

findByShortNameWithPrimaryPublication

@Nullable
ExpressionExperiment findByShortNameWithPrimaryPublication(String shortName)

findByShortNameAndThawLite

@Nullable
ExpressionExperiment findByShortNameAndThawLite(String shortName)

findByTaxon

Collection<ExpressionExperiment> findByTaxon(Taxon taxon)

findByUpdatedLimit

List<ExpressionExperiment> findByUpdatedLimit(int limit)

findUpdatedAfter

Collection<ExpressionExperiment> findUpdatedAfter(Date date)

findByMeanVarianceRelation

@Nullable
ExpressionExperiment findByMeanVarianceRelation(MeanVarianceRelation mvr)

findIdByMeanVarianceRelation

@Nullable
Long findIdByMeanVarianceRelation(MeanVarianceRelation mvr)

existsByShortName

boolean existsByShortName(String shortName)

loadLackingFactors

Collection<ExpressionExperiment> loadLackingFactors()

loadLackingTags

Collection<ExpressionExperiment> loadLackingTags()

thaw

ExpressionExperiment thaw(ExpressionExperiment expressionExperiment)

thawLite

ExpressionExperiment thawLite(ExpressionExperiment expressionExperiment)

thawLiter

ExpressionExperiment thawLiter(ExpressionExperiment expressionExperiment)

thawBioAssays

ExpressionExperiment thawBioAssays(ExpressionExperiment expressionExperiment)

Narrow thaw used by the /samples REST endpoint: initializes only the bioAssays collection and applies Thaws.thawBioAssay(BioAssay) to each assay (which warms the array design, original platform, and biomaterial-with-factor-values shape that BioAssayValueObject reads). Skips the nine EE-level lazy collections warmed by thawLite(ExpressionExperiment) — publications, otherParts, factors, factor values, quantitation types, characteristics, accession, mean-variance, geeq, curationDetails — none of which the assay-VO ctor reads.

getTaxon

@Nullable
Taxon getTaxon(ExpressionExperiment expressionExperiment)

Included for cycle-break parity with the facade: the only read-method back-edge from ExpressionExperimentSetServiceImpl is getTaxon. Living on the read service breaks that dependency cycle.

browse

List<ExpressionExperiment> browse(int start,
 int limit)

filter

Collection<Long> filter(String searchString)
                 throws SearchException

Throws:

SearchException

filterByTaxon

Collection<Long> filterByTaxon(Collection<Long> ids,
 Taxon taxon)

getAnnotationCountsByIds

Map<Long,Long> getAnnotationCountsByIds(Collection<Long> ids)

getExperimentalDesignValueObject

@Nullable
ExperimentalDesignValueObject getExperimentalDesignValueObject(ExpressionExperiment ee)

getAnnotations

Set<AnnotationValueObject> getAnnotations(ExpressionExperiment expressionExperiment)

getAnnotations

Set<AnnotationValueObject> getAnnotations(ExpressionExperiment expressionExperiment,
 boolean includeFreeText)

Parameters:

includeFreeText - also return annotations that carry no ontology mapping — no category URI, no value URI, or neither. These are persisted like any other tag but are excluded by default, which is correct for the tag cloud and wrong for curation read-back: a caller that has just committed a free-text tag would otherwise read back nothing and be unable to tell a rejected write from a filtered read.

getAnnotations

Set<AnnotationValueObject> getAnnotations(ExpressionExperimentSubSet ee)

getAnnotations

Set<AnnotationValueObject> getAnnotations(ExpressionExperimentSubSet ee,
 boolean includeFreeText)

See Also:

• getAnnotations(ExpressionExperiment, boolean)

getEnhancedFilters

Filters getEnhancedFilters(Filters f,
 @Nullable
 Collection<OntologyTerm> mentionedTerms,
 @Nullable
 Collection<OntologyTerm> inferredTerms,
 long timeout,
 TimeUnit timeUnit)
                    throws TimeoutException

Throws:

TimeoutException

getNumberOfDesignElementsPerSample

Map<BioAssay,Long> getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)

loadIdsWithCache

List<Long> loadIdsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

countWithCache

long countWithCache(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds)

loadValueObjectsWithCache

Slice<ExpressionExperimentValueObject> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

getCategoriesUsageFrequency

Map<Characteristic, Long> getCategoriesUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds,
 @Nullable
 Collection<String> excludedCategoryUris,
 @Nullable
 Collection<String> excludedTermUris,
 @Nullable
 Collection<String> retainedTermUris,
 int maxResults)

getAnnotationsUsageFrequency

List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm> getAnnotationsUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds,
 @Nullable
 String category,
 @Nullable
 Collection<String> excludedCategoryUris,
 @Nullable
 Collection<String> excludedTermUris,
 int minFrequency,
 @Nullable
 Collection<String> retainedTermUris,
 int maxResults,
 boolean includePredicates,
 boolean includeObjects,
 long timeout,
 TimeUnit timeUnit)
                                                                                                         throws TimeoutException

Throws:

TimeoutException

getTechnologyTypeUsageFrequency

Map<TechnologyType, Long> getTechnologyTypeUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds)

getArrayDesignUsedOrOriginalPlatformUsageFrequency

Map<ArrayDesign, Long> getArrayDesignUsedOrOriginalPlatformUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds,
 int maxResults)

getTaxaUsageFrequency

Map<Taxon,Long> getTaxaUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds)

getBioMaterialCount

long getBioMaterialCount(ExpressionExperiment expressionExperiment)

getRawDataVectorCount

long getRawDataVectorCount(ExpressionExperiment ee)

getExperimentsWithOutliers

Collection<ExpressionExperiment> getExperimentsWithOutliers()

getLastArrayDesignUpdate

Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)

getLastArrayDesignUpdate

Date getLastArrayDesignUpdate(ExpressionExperiment ee)

getLastLinkAnalysis

Map<Long, AuditEvent> getLastLinkAnalysis(Collection<Long> ids)

getLastMissingValueAnalysis

Map<Long, AuditEvent> getLastMissingValueAnalysis(Collection<Long> ids)

getLastProcessedDataUpdate

Map<Long, AuditEvent> getLastProcessedDataUpdate(Collection<Long> ids)

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

getPopulatedFactorCounts

Map<Long,Long> getPopulatedFactorCounts(Collection<Long> ids)

getPopulatedFactorCountsExcludeBatch

Map<Long,Long> getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)

getSampleRemovalEvents

Map<ExpressionExperiment, Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)

loadDetailsValueObjects

Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjects(@Nullable
 Collection<Long> ids,
 @Nullable
 Taxon taxon,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadDetailsValueObjectsWithCache

Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsWithCache(Collection<Long> ids,
 @Nullable
 Taxon taxon,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadDetailsValueObjectsByIds

List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(Collection<Long> ids)

loadDetailsValueObjectsByIdsWithCache

List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)

loadBlacklistedValueObjects

Slice<ExpressionExperimentValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadBlacklistedValueObjectsByCursor

CursorPage<ExpressionExperimentValueObject> loadBlacklistedValueObjectsByCursor(@Nullable
 Filters filters,
 Sort sort,
 @Nullable
 Cursor cursor,
 int limit)

Cursor-mode counterpart to loadBlacklistedValueObjects(Filters, Sort, int, int).

See Also:

• ExpressionExperimentDao.loadBlacklistedValueObjectsByCursor(Filters, Sort, Cursor, int)

loadValueObjectsByIdsWithRelationsAndCache

List<ExpressionExperimentValueObject> loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)

loadValueObjectsByIds

List<ExpressionExperimentValueObject> loadValueObjectsByIds(List<Long> ids,
 boolean maintainOrder)

countBioMaterials

long countBioMaterials(@Nullable
 Filters filters)