ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl

All Implemented Interfaces:: org.springframework.beans.factory.InitializingBean, BaseDao<ExpressionExperiment>, BaseVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>, CachedFilteringDao<ExpressionExperiment>, CachedFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, CuratableDao<ExpressionExperiment>, ExpressionExperimentDao, FilteringDao<ExpressionExperiment>, FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

@Repository public class ExpressionExperimentDaoImpl extends AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject> implements ExpressionExperimentDao

Author:

pavlidis

See Also:

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Nested classes/interfaces inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
ExpressionExperimentDao.Identifiers
Field Summary

Fields inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
CURATION_DETAILS_ALIAS

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class ubic.gemma.persistence.service.AbstractDao
log

Fields inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao
FREE_TEXT, OBJECT_ALIAS, UNCATEGORIZED
Constructor Summary

Constructors

Constructor

Description

ExpressionExperimentDaoImpl(SessionFactory sessionFactory)
Method Summary

Modifier and Type

Method

Description

int

addRawDataVectors(ExpressionExperiment ee, QuantitationType newQt, Collection<RawExpressionDataVector> newVectors)

Add raw data vectors with the given quantitation type.

List<ExpressionExperiment>

browse(int start, int limit)

List<ExpressionExperiment>

browse(int start, int limit, String orderField, boolean descending)

protected void

configureFilterableProperties(AbstractFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>.FilterablePropertiesConfigurer configurer)

Register filterable properties.

long

countBioMaterials(Filters filters)

Count the number of biomaterials of datasets satisfying the given filters.

int

createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)

Add processed data vectors

void

createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)

Create a single-cell dimension for a given experiment.

void

deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)

Delete the given single-cell dimension.

protected ExpressionExperimentValueObject

doLoadValueObject(ExpressionExperiment entity)

Load a value object for a given entity.

Collection<Long>

filterByTaxon(Collection<Long> ids, Taxon taxon)

ExpressionExperiment

find(ExpressionExperiment entity)

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Collection<ExpressionExperiment>

findByAccession(String accession)

Collection<ExpressionExperiment>

findByAccession(DatabaseEntry accession)

Collection<ExpressionExperiment>

findByBibliographicReference(BibliographicReference bibRef)

ExpressionExperiment

findByBioAssay(BioAssay ba)

Collection<ExpressionExperiment>

findByBioMaterial(BioMaterial bm)

Map<ExpressionExperiment,Collection<BioMaterial>>

findByBioMaterials(Collection<BioMaterial> bms)

ExpressionExperiment

findByDesign(ExperimentalDesign ed)

ExpressionExperiment

findByDesignId(Long designId)

Collection<ExpressionExperiment>

findByExpressedGene(Gene gene, Double rank)

ExpressionExperiment

findByFactor(ExperimentalFactor ef)

Collection<ExpressionExperiment>

findByFactors(Collection<ExperimentalFactor> factors)

ExpressionExperiment

findByFactorValue(Long factorValueId)

ExpressionExperiment

findByFactorValue(FactorValue fv)

Collection<ExpressionExperiment>

findByFactorValueIds(Collection<Long> factorValueIds)

Collection<ExpressionExperiment>

findByFactorValues(Collection<FactorValue> fvs)

Collection<ExpressionExperiment>

findByGene(Gene gene)

uses GENE2CS table.

Collection<ExpressionExperiment>

findByName(String name)

ExpressionExperiment

findByQuantitationType(QuantitationType quantitationType)

ExpressionExperiment

findByShortName(String shortName)

Collection<ExpressionExperiment>

findByTaxon(Taxon taxon)

List<ExpressionExperiment>

findByUpdatedLimit(int limit)

List<ExpressionExperiment>

findByUpdatedLimit(Collection<Long> ids, int limit)

ExpressionExperiment

findOneByAccession(String accession)

ExpressionExperiment

findOneByName(String name)

Collection<ExpressionExperiment>

findUpdatedAfter(Date date)

Find experiments updated on or after a given date.

Map<Class<? extends Identifiable>,List<Characteristic>>

getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)

Obtain all annotations, grouped by applicable level.

Map<Long,Long>

getAnnotationCounts(Collection<Long> ids)

Map<Characteristic,Long>

getAnnotationsUsageFrequency(Collection<Long> eeIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, boolean includePredicates, boolean includeObjects)

We're making two assumptions: a dataset cannot have a characteristic more than once and a dataset cannot have the same characteristic at multiple levels to make counting more efficient.

Map<Characteristic,Long>

getAnnotationsUsageFrequencyInternal(Collection<Long> eeIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, boolean excludeCategoryOnly, Collection<String> retainedTermUris, String valueColumn, String valueUriColumn, boolean isCategorized)

Map<ArrayDesign,Long>

getArrayDesignsUsageFrequency(int maxResults)

Obtain dataset usage frequency by platform currently used.

Map<ArrayDesign,Long>

getArrayDesignsUsageFrequency(Collection<Long> eeIds, int maxResults)

Obtain dataset usage frequency by platform currently for the given dataset IDs.

Collection<ArrayDesign>

getArrayDesignsUsed(Collection<ExpressionExperiment> ees)

Collection<ArrayDesign>

getArrayDesignsUsed(ExpressionExperiment bas)

Collection<ArrayDesign>

getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)

Map<Long,Collection<AuditEvent>>

getAuditEvents(Collection<Long> ids)

BioAssayDimension

getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)

Retrieve a dimension for a given experiment and quantitation type.

BioAssayDimension

getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)

Retrieve a dimension for a given experiment and quantitation type.

BioAssayDimension

getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)

Obtain a bioassay dimension by ID.

Collection<BioAssayDimension>

getBioAssayDimensions(ExpressionExperiment expressionExperiment)

Collection<BioAssayDimension>

getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt)

Collection<BioAssayDimension>

getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)

Collection<BioAssayDimension>

getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)

Retrieve BioAssayDimension that are used by subsets of a given ExpressionExperiment.

List<Characteristic>

getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)

Obtain sample-level annotations.

List<Characteristic>

getBioMaterialAnnotations(ExpressionExperimentSubSet subset)

long

getBioMaterialCount(ExpressionExperiment expressionExperiment)

Map<Characteristic,Long>

getCategoriesUsageFrequency(Collection<Long> eeIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)

Characteristic

getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)

Obtain the characteristic at a given cell index.

Characteristic[]

getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)

List<CellLevelCharacteristics>

getCellLevelCharacteristics(ExpressionExperiment ee)

Obtain all cell-level characteristics from all single-cell dimensions.

List<CellLevelCharacteristics>

getCellLevelCharacteristics(ExpressionExperiment ee, Category category)

Obtain all cell-level characteristics from all single-cell dimensions matching the given category.

List<CellLevelCharacteristics>

getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)

CellLevelCharacteristics

getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)

Obtain a specific cell-level characteristic by ID.

CellLevelCharacteristics

getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)

List<CellLevelCharacteristics>

getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)

Category

getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)

Obtain the category of a cell-level characteristic.

Collection<CellLevelCharacteristics>

getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)

CellLevelCharacteristics

getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)

CellLevelCharacteristics

getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)

CellTypeAssignment

getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)

Obtain a cell type assignment by ID.

CellTypeAssignment

getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)

Obtain a cell type assignment by name.

Collection<CellTypeAssignment>

getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolName)

Collection<Protocol>

getCellTypeAssignmentProtocols()

Obtain all cell type assignment protocols currently used.

List<CellTypeAssignment>

getCellTypeAssignments(ExpressionExperiment ee)

List<CellTypeAssignment>

getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)

Collection<CellTypeAssignment>

getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)

CellTypeAssignment

getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)

Obtain a cell type assignment by ID without loading the indices.

CellTypeAssignment

getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)

Obtain a cell type assignment by name without loading the indices.

Characteristic

getCellTypeAt(CellTypeAssignment cta, int cellIndex)

Obtain the cell type at a given cell index.

Characteristic[]

getCellTypeAt(CellTypeAssignment cta, int startIndex, int endIndexExclusive)

List<Characteristic>

getCellTypes(ExpressionExperiment ee)

List<Characteristic>

getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)

Obtain experimental design-level annotations.

List<Characteristic>

getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)

Obtain experiment-level annotations.

Collection<ExpressionExperiment>

getExperimentsLackingPublications()

Collection<Characteristic>

getExperimentSubSetAnnotations(ExpressionExperiment ee)

Obtain the subset annotations.

Collection<ExpressionExperiment>

getExperimentsWithOutliers()

List<Statement>

getFactorValueAnnotations(ExpressionExperiment ee)

Obtain factor value-level annotations.

List<Statement>

getFactorValueAnnotations(ExpressionExperimentSubSet subset)

Obtain factor value-level annotations for a given subset.

protected Query

getFilteringCountQuery(Filters filters)

Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

protected Query

getFilteringIdQuery(Filters filters, Sort sort)

Produce a query that will be used to retrieve IDs of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

protected Query

getFilteringQuery(Filters filters, Sort sort)

Produce a query for retrieving value objects after applying a set of filters and a given ordering.

Collection<Gene>

getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)

Obtain genes used by the processed vectors of this dataset.

Map<Long,Date>

getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)

Date

getLastArrayDesignUpdate(ExpressionExperiment ee)

Map<QuantitationType,Collection<RawExpressionDataVector>>

getMissingValueVectors(ExpressionExperiment ee)

Obtain the missing value vectors for a given experiment.

Map<BioAssay,Long>

getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)

long

getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)

Obtain the number of non-zeroes.

Map<BioAssay,Long>

getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)

Obtain the number of non-zeroes by sample.

long

getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)

Obtain the number of single-cell vectors for a given QT.

Map<ArrayDesign,Long>

getOriginalPlatformsUsageFrequency(int maxResults)

Obtain dataset usage frequency by original platforms.

Map<ArrayDesign,Long>

getOriginalPlatformsUsageFrequency(Collection<Long> eeIds, int maxResults)

Obtain dataset usage frequency by platform currently for the given dataset IDs.

Map<Taxon,Long>

getPerTaxonCount()

Obtain the count of distinct experiments per taxon.

Map<Taxon,Long>

getPerTaxonCount(Collection<Long> ids)

Obtain the count of distinct experiments per taxon for experiments with the given IDs.

Map<Long,Long>

getPopulatedFactorCounts(Collection<Long> ids)

Map<Long,Long>

getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)

CellTypeAssignment

getPreferredCellTypeAssignment(ExpressionExperiment ee)

Obtain the preferred assignment of the preferred single-cell vectors.

CellTypeAssignment

getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)

Obtain the preferred assignment for the given quantitation type.

CellTypeAssignment

getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)

Obtain the preferred assignment for the given quantitation type without loading the indices.

QuantitationType

getPreferredQuantitationType(ExpressionExperiment ee)

Obtain the preferred quantitation type for the raw vectors, if available.

Collection<RawExpressionDataVector>

getPreferredRawDataVectors(ExpressionExperiment ee)

Obtain the preferred raw data vectors for a given experiment.

SingleCellDimension

getPreferredSingleCellDimension(ExpressionExperiment ee)

Obtain the preferred single-cell dimension, that is the dimension associated to the preferred set of single-cell vectors.

SingleCellDimension

getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)

SingleCellDimension

getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)

Load a single-cell dimension without its cell IDs.

QuantitationType

getPreferredSingleCellQuantitationType(ExpressionExperiment ee)

Obtain the preferred quantitation type for single-cell data, if available.

Collection<ProcessedExpressionDataVector>

getProcessedDataVectors(ExpressionExperiment ee)

Retrieve the processed vector for an experiment.

Collection<ProcessedExpressionDataVector>

getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)

Retrieve a slice of processed vectors for an experiment.

QuantitationType

getProcessedQuantitationType(ExpressionExperiment ee)

Obtain the quantitation type for the processed vectors, if available.

Map<QuantitationType,Long>

getQuantitationTypeCount(ExpressionExperiment ee)

long

getRawDataVectorCount(ExpressionExperiment ee)

Collection<RawExpressionDataVector>

getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)

Obtain a slice of the raw vectors for a given experiment and QT.

Collection<RawExpressionDataVector>

getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)

Obtain raw vectors for a given experiment and QT.

Map<ExpressionExperiment,Collection<AuditEvent>>

getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)

List<SingleCellExpressionDataVector>

getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)

Obtain a set of single-cell data vectors for the given quantitation type.

List<SingleCellExpressionDataVector>

getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeCellIds, boolean includeData, boolean includeDataIndices)

Obtain a set of single-cell data vectors for the given quantitation type.

SingleCellExpressionDataVector

getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)

SingleCellDimension

getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)

Obtain the single-cell dimension used by a specific QT.

List<SingleCellDimension>

getSingleCellDimensions(ExpressionExperiment ee)

Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.

List<SingleCellDimension>

getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)

Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.

List<SingleCellDimension>

getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)

SingleCellDimension

getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)

Load a single-cell dimension used by a specific QT without its cell IDs.

SingleCellDimension

getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)

List<QuantitationType>

getSingleCellQuantitationTypes(ExpressionExperiment ee)

Obtain a list of single-cell QTs.

ExpressionExperimentSubSet

getSubSetById(ExpressionExperiment ee, Long subSetId)

Collection<ExpressionExperimentSubSet>

getSubSets(ExpressionExperiment expressionExperiment)

Collection<ExpressionExperimentSubSet>

getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)

Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>

getSubSetsByDimension(ExpressionExperiment expressionExperiment)

Map<ExpressionExperiment,Taxon>

getTaxa(Collection<ExpressionExperiment> ees)

Taxon

getTaxon(ExpressionExperiment ee)

Determine the taxon for a given experiment or subset.

Map<TechnologyType,Long>

getTechnologyTypeUsageFrequency()

Obtain the dataset usage frequency by technology type.

Map<TechnologyType,Long>

getTechnologyTypeUsageFrequency(Collection<Long> eeIds)

Obtain the dataset usage frequency by technology type for the given dataset IDs.

protected TypedResultTransformer<ExpressionExperimentValueObject>

getValueObjectTransformer()

Obtain a value object transformer for the results of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

boolean

hasProcessedExpressionData(ExpressionExperiment ee)

Test if the dataset has preferred expression data vectors.

boolean

hasSingleCellQuantitationTypes(ExpressionExperiment ee)

Indicate if the given experiment has single-cell quantitation types.

protected void

initializeCachedFilteringResult(ExpressionExperiment ee)

Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.

ExpressionExperiment

load(Long id, CacheMode cacheMode)

Load an experiment by ID with a specific cache mode.

List<ExpressionExperimentDao.Identifiers>

loadAllIdentifiers()

Load all possible identifiers for all experiments.

Slice<ExpressionExperimentValueObject>

loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)

Slice<ExpressionExperimentDetailsValueObject>

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

Special method for front-end access.

List<ExpressionExperimentDetailsValueObject>

loadDetailsValueObjectsByIds(Collection<Long> ids)

Like ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.

List<ExpressionExperimentDetailsValueObject>

loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)

Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.

Slice<ExpressionExperimentDetailsValueObject>

loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)

Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.

Collection<ExpressionExperiment>

loadLackingFactors()

Collection<ExpressionExperiment>

loadLackingTags()

List<ExpressionExperimentValueObject>

loadValueObjects(Filters filters, Sort sort)

Load VOs with minimal ordering and filtering.

Slice<ExpressionExperimentValueObject>

loadValueObjects(Filters filters, Sort sort, int offset, int limit)

Load VOs with ordering, filtering and offset/limit.

List<ExpressionExperiment>

loadWithRelationsAndCache(List<Long> ids)

Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).

protected void

postProcessValueObjects(List<ExpressionExperimentValueObject> results)

Post-process VOs in bulk.

void

remove(ExpressionExperiment ee)

Remove a persistent instance

int

removeAllRawDataVectors(ExpressionExperiment ee)

Remove all raw data vectors.

int

removeAllSingleCellDataVectors(ExpressionExperiment ee)

Remove all single-cell data vectors and their quantitation types.

int

removeProcessedDataVectors(ExpressionExperiment ee)

Remove processed data vectors.

int

removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)

Remove raw data vectors for a given quantitation type.

int

removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean deleteQt)

Remove the given single-cell data vectors.

int

replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)

Replace processed data vectors.

int

replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)

Replace raw data vectors for a given quantitation type.

protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder

resolveFilterablePropertyMeta(String propertyName)

Checks for special properties that are allowed to be referenced on certain objects.

Stream<String>

streamCellIds(SingleCellDimension dimension, boolean createNewSession)

Stream the cell IDs of a dimension.

Stream<Characteristic>

streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)

Stream<Characteristic>

streamCellTypes(CellTypeAssignment cta, boolean createNewSession)

Stream<SingleCellExpressionDataVector>

streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)

Obtain a stream over the vectors for a given QT.

Stream<SingleCellExpressionDataVector>

streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)

void

thaw(ExpressionExperiment expressionExperiment)

Thaw everything.

void

thawLite(ExpressionExperiment ee)

Thaw experiment metadata and bioassays.

void

thawLiter(ExpressionExperiment expressionExperiment)

Thaw experiment metadata.

MeanVarianceRelation

updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)

void

updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)

Update a single-cell dimensino for a given experiment.

Methods inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao
addEventsToMap, addNonTroubledFilter, distinctIfNecessary, formNativeNonTroubledClause, formNonTroubledClause, groupByIfNecessary, loadTroubledIds, updateCurationDetailsFromAuditEvent

Methods inherited from class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
count, countWithCache, getEntityTransformer, load, load, loadIds, loadIdsWithCache, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao
afterPropertiesSet, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyMeta, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, resolveFilterablePropertyMeta

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractDao
countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.CachedFilteringDao
countWithCache, loadIdsWithCache, loadWithCache, loadWithCache

Methods inherited from interface ubic.gemma.persistence.service.CachedFilteringVoEnabledDao
loadValueObjectsWithCache, loadValueObjectsWithCache

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao
loadTroubledIds, updateCurationDetailsFromAuditEvent

Methods inherited from interface ubic.gemma.persistence.service.FilteringDao
count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

Constructor Details
- ExpressionExperimentDaoImpl
  
  @Autowired public ExpressionExperimentDaoImpl(SessionFactory sessionFactory)
Method Details
- load
  
  public ExpressionExperiment load(Long id, CacheMode cacheMode)
  
  Description copied from interface: ExpressionExperimentDao
  
  Load an experiment by ID with a specific cache mode.
  The cache mode will be effective for the remainder of the Hibernate session.
  
  Specified by:
  
  load in interface ExpressionExperimentDao
- loadAllIdentifiers
  
  public List<ExpressionExperimentDao.Identifiers> loadAllIdentifiers()
  
  Description copied from interface: ExpressionExperimentDao
  
  Load all possible identifiers for all experiments.
  
  Specified by:
  
  loadAllIdentifiers in interface ExpressionExperimentDao
- browse
  
  public List<ExpressionExperiment> browse(int start, int limit)
  
  Specified by:
  
  browse in interface BrowsingDao<ExpressionExperiment>
- browse
  
  public List<ExpressionExperiment> browse(int start, int limit, String orderField, boolean descending)
  
  Specified by:
  
  browse in interface BrowsingDao<ExpressionExperiment>
- filterByTaxon
  
  public Collection<Long> filterByTaxon(@Nullable Collection<Long> ids, Taxon taxon)
  
  Specified by:
  
  filterByTaxon in interface ExpressionExperimentDao
- findByShortName
  
  public ExpressionExperiment findByShortName(String shortName)
  
  Specified by:
  
  findByShortName in interface ExpressionExperimentDao
- findByName
  
  public Collection<ExpressionExperiment> findByName(String name)
  
  Specified by:
  
  findByName in interface ExpressionExperimentDao
- findOneByName
  
  public ExpressionExperiment findOneByName(String name)
  
  Specified by:
  
  findOneByName in interface ExpressionExperimentDao
- find
  
  public ExpressionExperiment find(ExpressionExperiment entity)
  
  Description copied from interface: BaseDao
  
  Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
  
  Specified by:
  
  find in interface BaseDao<ExpressionExperiment>
  
  Overrides:
  
  find in class AbstractDao<ExpressionExperiment>
  
  Parameters:
  
  entity - the entity to look for.
  
  Returns:
  
  an entity that was found in the persistent storage, or null if no such entity was found.
- findByAccession
  
  public Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)
  
  Specified by:
  
  findByAccession in interface ExpressionExperimentDao
- findByAccession
  
  public Collection<ExpressionExperiment> findByAccession(String accession)
  
  Specified by:
  
  findByAccession in interface ExpressionExperimentDao
- findOneByAccession
  
  @Nullable public ExpressionExperiment findOneByAccession(String accession)
  
  Specified by:
  
  findOneByAccession in interface ExpressionExperimentDao
- findByBibliographicReference
  
  public Collection<ExpressionExperiment> findByBibliographicReference(BibliographicReference bibRef)
  
  Specified by:
  
  findByBibliographicReference in interface ExpressionExperimentDao
- findByBioAssay
  
  public ExpressionExperiment findByBioAssay(BioAssay ba)
  
  Specified by:
  
  findByBioAssay in interface ExpressionExperimentDao
- findByBioMaterial
  
  public Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm)
  
  Specified by:
  
  findByBioMaterial in interface ExpressionExperimentDao
- findByBioMaterials
  
  public Map<ExpressionExperiment,Collection<BioMaterial>> findByBioMaterials(Collection<BioMaterial> bms)
  
  Specified by:
  
  findByBioMaterials in interface ExpressionExperimentDao
- findByExpressedGene
  
  public Collection<ExpressionExperiment> findByExpressedGene(Gene gene, Double rank)
  
  Specified by:
  
  findByExpressedGene in interface ExpressionExperimentDao
- findByDesign
  
  public ExpressionExperiment findByDesign(ExperimentalDesign ed)
  
  Specified by:
  
  findByDesign in interface ExpressionExperimentDao
- findByDesignId
  
  public ExpressionExperiment findByDesignId(Long designId)
  
  Specified by:
  
  findByDesignId in interface ExpressionExperimentDao
- findByFactor
  
  public ExpressionExperiment findByFactor(ExperimentalFactor ef)
  
  Specified by:
  
  findByFactor in interface ExpressionExperimentDao
- findByFactors
  
  public Collection<ExpressionExperiment> findByFactors(Collection<ExperimentalFactor> factors)
  
  Specified by:
  
  findByFactors in interface ExpressionExperimentDao
- findByFactorValue
  
  public ExpressionExperiment findByFactorValue(FactorValue fv)
  
  Specified by:
  
  findByFactorValue in interface ExpressionExperimentDao
- findByFactorValue
  
  public ExpressionExperiment findByFactorValue(Long factorValueId)
  
  Specified by:
  
  findByFactorValue in interface ExpressionExperimentDao
- findByFactorValues
  
  public Collection<ExpressionExperiment> findByFactorValues(Collection<FactorValue> fvs)
  
  Specified by:
  
  findByFactorValues in interface ExpressionExperimentDao
- findByFactorValueIds
  
  public Collection<ExpressionExperiment> findByFactorValueIds(Collection<Long> factorValueIds)
  
  Specified by:
  
  findByFactorValueIds in interface ExpressionExperimentDao
- findByGene
  
  public Collection<ExpressionExperiment> findByGene(Gene gene)
  
  uses GENE2CS table.
  
  Specified by:
  
  findByGene in interface ExpressionExperimentDao
- findByQuantitationType
  
  public ExpressionExperiment findByQuantitationType(QuantitationType quantitationType)
  
  Specified by:
  
  findByQuantitationType in interface ExpressionExperimentDao
- findByTaxon
  
  public Collection<ExpressionExperiment> findByTaxon(Taxon taxon)
  
  Specified by:
  
  findByTaxon in interface ExpressionExperimentDao
- findByUpdatedLimit
  
  public List<ExpressionExperiment> findByUpdatedLimit(Collection<Long> ids, int limit)
  
  Specified by:
  
  findByUpdatedLimit in interface ExpressionExperimentDao
- findByUpdatedLimit
  
  public List<ExpressionExperiment> findByUpdatedLimit(int limit)
  
  Specified by:
  
  findByUpdatedLimit in interface ExpressionExperimentDao
- findUpdatedAfter
  
  public Collection<ExpressionExperiment> findUpdatedAfter(@Nullable Date date)
  
  Description copied from interface: ExpressionExperimentDao
  
  Find experiments updated on or after a given date.
  
  Specified by:
  
  findUpdatedAfter in interface ExpressionExperimentDao
- getAnnotationCounts
  
  public Map<Long,Long> getAnnotationCounts(Collection<Long> ids)
  
  Specified by:
  
  getAnnotationCounts in interface ExpressionExperimentDao
- getAllAnnotations
  
  public Map<Class<? extends Identifiable>,List<Characteristic>> getAllAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain all annotations, grouped by applicable level.
  
  Specified by:
  
  getAllAnnotations in interface ExpressionExperimentDao
  
  Parameters:
  
  useEe2c - use the EXPRESSION_EXPERIMENT2CHARACTERISTIC table to retrieve annotations
- getExperimentAnnotations
  
  public List<Characteristic> getExperimentAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain experiment-level annotations.
  
  Specified by:
  
  getExperimentAnnotations in interface ExpressionExperimentDao
  
  Parameters:
  
  useEe2c - use the EXPRESSION_EXPERIMENTE2CHARACTERISTIC table, TableMaintenanceUtil
- getExperimentSubSetAnnotations
  
  public Collection<Characteristic> getExperimentSubSetAnnotations(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the subset annotations.
  
  Specified by:
  
  getExperimentSubSetAnnotations in interface ExpressionExperimentDao
- getBioMaterialAnnotations
  
  public List<Characteristic> getBioMaterialAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain sample-level annotations.
  This uses the EE2C table under the hood.
  
  Specified by:
  
  getBioMaterialAnnotations in interface ExpressionExperimentDao
- getBioMaterialAnnotations
  
  public List<Characteristic> getBioMaterialAnnotations(ExpressionExperimentSubSet subset)
  
  Specified by:
  
  getBioMaterialAnnotations in interface ExpressionExperimentDao
- getExperimentalDesignAnnotations
  
  public List<Characteristic> getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment, boolean useEe2c)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain experimental design-level annotations.
  This is equivalent to the subject components of ExpressionExperimentDao.getFactorValueAnnotations(ExpressionExperiment) for now, but other annotations from the experimental design might be included in the future.
  
  Specified by:
  
  getExperimentalDesignAnnotations in interface ExpressionExperimentDao
- getFactorValueAnnotations
  
  public List<Statement> getFactorValueAnnotations(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain factor value-level annotations.
  
  Specified by:
  
  getFactorValueAnnotations in interface ExpressionExperimentDao
- getFactorValueAnnotations
  
  public List<Statement> getFactorValueAnnotations(ExpressionExperimentSubSet subset)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain factor value-level annotations for a given subset.
  
  Specified by:
  
  getFactorValueAnnotations in interface ExpressionExperimentDao
- getCategoriesUsageFrequency
  
  public Map<Characteristic,Long> getCategoriesUsageFrequency(@Nullable Collection<Long> eeIds, @Nullable Collection<String> excludedCategoryUris, @Nullable Collection<String> excludedTermUris, @Nullable Collection<String> retainedTermUris, int maxResults)
  
  Specified by:
  
  getCategoriesUsageFrequency in interface ExpressionExperimentDao
- getAnnotationsUsageFrequency
  
  public Map<Characteristic,Long> getAnnotationsUsageFrequency(@Nullable Collection<Long> eeIds, @Nullable Class<? extends Identifiable> level, int maxResults, int minFrequency, @Nullable String category, @Nullable Collection<String> excludedCategoryUris, @Nullable Collection<String> excludedTermUris, @Nullable Collection<String> retainedTermUris, boolean includePredicates, boolean includeObjects)
  
  We're making two assumptions: a dataset cannot have a characteristic more than once and a dataset cannot have the same characteristic at multiple levels to make counting more efficient.
  
  Specified by:
  
  getAnnotationsUsageFrequency in interface ExpressionExperimentDao
  
  Parameters:
  
  eeIds - IDs of ExpressionExperiment to use for restricting annotations, or null to consider everything
  
  level - applicable annotation level, one of ExpressionExperiment, ExperimentalDesign or BioMaterial
  
  maxResults - maximum number of annotations to return, or -1 to return everything
  
  minFrequency - minimum usage frequency to be reported (0 effectively allows everything)
  
  category - a category URI or free text category to restrict the results to, or null to consider everything, empty string to consider uncategorized terms
  
  retainedTermUris - a collection of term to retain even if they don't meet the minimum frequency criteria
  
  includePredicates - include predicates
  
  includeObjects - include objects
- getAnnotationsUsageFrequencyInternal
  
  public Map<Characteristic,Long> getAnnotationsUsageFrequencyInternal(@Nullable Collection<Long> eeIds, @Nullable Class<? extends Identifiable> level, int maxResults, int minFrequency, @Nullable String category, @Nullable Collection<String> excludedCategoryUris, @Nullable Collection<String> excludedTermUris, boolean excludeCategoryOnly, @Nullable Collection<String> retainedTermUris, String valueColumn, String valueUriColumn, boolean isCategorized)
- getExperimentsLackingPublications
  
  public Collection<ExpressionExperiment> getExperimentsLackingPublications()
  
  Specified by:
  
  getExperimentsLackingPublications in interface ExpressionExperimentDao
- updateMeanVarianceRelation
  
  public MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
  
  Specified by:
  
  updateMeanVarianceRelation in interface ExpressionExperimentDao
- countBioMaterials
  
  public long countBioMaterials(@Nullable Filters filters)
  
  Description copied from interface: ExpressionExperimentDao
  
  Count the number of biomaterials of datasets satisfying the given filters.
  The result is stored in the standard query cache.
  
  Specified by:
  
  countBioMaterials in interface ExpressionExperimentDao
- getArrayDesignsUsed
  
  public Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment bas)
  
  Specified by:
  
  getArrayDesignsUsed in interface ExpressionExperimentDao
- getArrayDesignsUsed
  
  public Collection<ArrayDesign> getArrayDesignsUsed(Collection<ExpressionExperiment> ees)
  
  Specified by:
  
  getArrayDesignsUsed in interface ExpressionExperimentDao
- getArrayDesignsUsed
  
  public Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> dataVectorType)
  
  Specified by:
  
  getArrayDesignsUsed in interface ExpressionExperimentDao
- getGenesUsedByPreferredVectors
  
  public Collection<Gene> getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain genes used by the processed vectors of this dataset.
  
  Specified by:
  
  getGenesUsedByPreferredVectors in interface ExpressionExperimentDao
- getTechnologyTypeUsageFrequency
  
  public Map<TechnologyType,Long> getTechnologyTypeUsageFrequency()
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the dataset usage frequency by technology type.
  If a dataset was switched to a platform of a different technology type, it is counted toward both.
  
  Specified by:
  
  getTechnologyTypeUsageFrequency in interface ExpressionExperimentDao
- getTechnologyTypeUsageFrequency
  
  public Map<TechnologyType,Long> getTechnologyTypeUsageFrequency(Collection<Long> eeIds)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the dataset usage frequency by technology type for the given dataset IDs.
  Note: No ACL filtering is performed.
  Specified by:
  
  getTechnologyTypeUsageFrequency in interface ExpressionExperimentDao
  
  See Also:
  
  ExpressionExperimentDao.getTechnologyTypeUsageFrequency()
- getArrayDesignsUsageFrequency
  
  public Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(int maxResults)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain dataset usage frequency by platform currently used.
  Note that a dataset counts toward all the platforms mentioned through its BioAssay.
  This method uses ACLs and the troubled status to only displays the counts of datasets the current user is entitled to see. Only administrator can see troubled platforms.
  
  Specified by:
  
  getArrayDesignsUsageFrequency in interface ExpressionExperimentDao
- getArrayDesignsUsageFrequency
  
  public Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(Collection<Long> eeIds, int maxResults)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain dataset usage frequency by platform currently for the given dataset IDs.
  Note: no ACL filtering is performed. Only administrator can see troubled platforms.
  Specified by:
  
  getArrayDesignsUsageFrequency in interface ExpressionExperimentDao
  
  See Also:
  
  ExpressionExperimentDao.getArrayDesignsUsageFrequency(int)
- getOriginalPlatformsUsageFrequency
  
  public Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(int maxResults)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain dataset usage frequency by original platforms.
  Note that a dataset counts toward all the platforms mentioned through its BioAssay. Datasets whose platform hasn't been switched (i.e. the original is the same as the current one) are ignored.
  This method uses ACLs and the troubled status to only displays the counts of datasets the current user is entitled to see. Only administrators can see troubled platforms.
  
  Specified by:
  
  getOriginalPlatformsUsageFrequency in interface ExpressionExperimentDao
- getOriginalPlatformsUsageFrequency
  
  public Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(Collection<Long> eeIds, int maxResults)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain dataset usage frequency by platform currently for the given dataset IDs.
  Note: no ACL filtering is performed. Only administrators can see troubled platforms.
  Specified by:
  
  getOriginalPlatformsUsageFrequency in interface ExpressionExperimentDao
  
  See Also:
  
  ExpressionExperimentDao.getOriginalPlatformsUsageFrequency(int)
- getAuditEvents
  
  public Map<Long,Collection<AuditEvent>> getAuditEvents(Collection<Long> ids)
  
  Specified by:
  
  getAuditEvents in interface ExpressionExperimentDao
- getBioAssayDimensions
  
  public Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment)
  
  Specified by:
  
  getBioAssayDimensions in interface ExpressionExperimentDao
- getBioAssayDimensionsFromSubSets
  
  public Collection<BioAssayDimension> getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)
  
  Description copied from interface: ExpressionExperimentDao
  
  Retrieve BioAssayDimension that are used by subsets of a given ExpressionExperiment.
  This covers cases where BAs in a subset are not the same as the BAs in the experiment such as for single-cell data where we use sub-assays.
  
  Specified by:
  
  getBioAssayDimensionsFromSubSets in interface ExpressionExperimentDao
- getBioAssayDimensions
  
  public Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt)
  
  Specified by:
  
  getBioAssayDimensions in interface ExpressionExperimentDao
- getBioAssayDimensions
  
  public Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
  
  Specified by:
  
  getBioAssayDimensions in interface ExpressionExperimentDao
- getBioAssayDimension
  
  public BioAssayDimension getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
  
  Description copied from interface: ExpressionExperimentDao
  
  Retrieve a dimension for a given experiment and quantitation type.
  
  Specified by:
  
  getBioAssayDimension in interface ExpressionExperimentDao
  
  Parameters:
  
  dataVectorType - the type of data vectors to consider, this is necessary because otherwise all the vector tables would have to be looked at. If you do nto know the type of vector, use ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment, QuantitationType).
- getBioAssayDimension
  
  public BioAssayDimension getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Retrieve a dimension for a given experiment and quantitation type.
  
  Specified by:
  
  getBioAssayDimension in interface ExpressionExperimentDao
- getBioAssayDimensionById
  
  public BioAssayDimension getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a bioassay dimension by ID.
  
  Specified by:
  
  getBioAssayDimensionById in interface ExpressionExperimentDao
- getBioMaterialCount
  
  public long getBioMaterialCount(ExpressionExperiment expressionExperiment)
  
  Specified by:
  
  getBioMaterialCount in interface ExpressionExperimentDao
- getRawDataVectorCount
  
  public long getRawDataVectorCount(ExpressionExperiment ee)
  
  Specified by:
  
  getRawDataVectorCount in interface ExpressionExperimentDao
  
  Parameters:
  
  ee - the expression experiment
  
  Returns:
  
  count of RAW vectors.
- getExperimentsWithOutliers
  
  public Collection<ExpressionExperiment> getExperimentsWithOutliers()
  
  Specified by:
  
  getExperimentsWithOutliers in interface ExpressionExperimentDao
- getLastArrayDesignUpdate
  
  public Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
  
  Specified by:
  
  getLastArrayDesignUpdate in interface ExpressionExperimentDao
- getLastArrayDesignUpdate
  
  public Date getLastArrayDesignUpdate(ExpressionExperiment ee)
  
  Specified by:
  
  getLastArrayDesignUpdate in interface ExpressionExperimentDao
- getPerTaxonCount
  
  public Map<Taxon,Long> getPerTaxonCount()
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the count of distinct experiments per taxon.
  Experiments are filtered by ACLs and troubled experiments are only visible to administrators.
  
  Specified by:
  
  getPerTaxonCount in interface ExpressionExperimentDao
- getPerTaxonCount
  
  public Map<Taxon,Long> getPerTaxonCount(Collection<Long> ids)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the count of distinct experiments per taxon for experiments with the given IDs.
  Experiments are not filtered by ACLs and toubled experiments are only visible to administrators.
  
  Specified by:
  
  getPerTaxonCount in interface ExpressionExperimentDao
- getPopulatedFactorCounts
  
  public Map<Long,Long> getPopulatedFactorCounts(Collection<Long> ids)
  
  Specified by:
  
  getPopulatedFactorCounts in interface ExpressionExperimentDao
- getPopulatedFactorCountsExcludeBatch
  
  public Map<Long,Long> getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)
  
  Specified by:
  
  getPopulatedFactorCountsExcludeBatch in interface ExpressionExperimentDao
- getQuantitationTypeCount
  
  public Map<QuantitationType,Long> getQuantitationTypeCount(ExpressionExperiment ee)
  
  Specified by:
  
  getQuantitationTypeCount in interface ExpressionExperimentDao
- getPreferredSingleCellQuantitationType
  
  public QuantitationType getPreferredSingleCellQuantitationType(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred quantitation type for single-cell data, if available.
  
  Specified by:
  
  getPreferredSingleCellQuantitationType in interface ExpressionExperimentDao
- getPreferredQuantitationType
  
  public QuantitationType getPreferredQuantitationType(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred quantitation type for the raw vectors, if available.
  
  Specified by:
  
  getPreferredQuantitationType in interface ExpressionExperimentDao
- getProcessedQuantitationType
  
  public QuantitationType getProcessedQuantitationType(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the quantitation type for the processed vectors, if available.
  
  Specified by:
  
  getProcessedQuantitationType in interface ExpressionExperimentDao
- hasProcessedExpressionData
  
  public boolean hasProcessedExpressionData(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Test if the dataset has preferred expression data vectors.
  
  Specified by:
  
  hasProcessedExpressionData in interface ExpressionExperimentDao
- getSampleRemovalEvents
  
  public Map<ExpressionExperiment,Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
  
  Specified by:
  
  getSampleRemovalEvents in interface ExpressionExperimentDao
- getSubSets
  
  public Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment)
  
  Specified by:
  
  getSubSets in interface ExpressionExperimentDao
- getSubSets
  
  public Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)
  
  Specified by:
  
  getSubSets in interface ExpressionExperimentDao
- getSubSetsByDimension
  
  public Map<BioAssayDimension,Set<ExpressionExperimentSubSet>> getSubSetsByDimension(ExpressionExperiment expressionExperiment)
  
  Specified by:
  
  getSubSetsByDimension in interface ExpressionExperimentDao
- getSubSetById
  
  public ExpressionExperimentSubSet getSubSetById(ExpressionExperiment ee, Long subSetId)
  
  Specified by:
  
  getSubSetById in interface ExpressionExperimentDao
- getTaxa
  
  public Map<ExpressionExperiment,Taxon> getTaxa(Collection<ExpressionExperiment> ees)
  
  Specified by:
  
  getTaxa in interface ExpressionExperimentDao
- getTaxon
  
  public Taxon getTaxon(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Determine the taxon for a given experiment or subset.
  
  Specified by:
  
  getTaxon in interface ExpressionExperimentDao
  
  Returns:
  
  a unique taxon for the dataset, or null if no taxon could be determined
- loadWithRelationsAndCache
  
  public List<ExpressionExperiment> loadWithRelationsAndCache(List<Long> ids)
  
  Description copied from interface: ExpressionExperimentDao
  
  Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).
  
  Specified by:
  
  loadWithRelationsAndCache in interface ExpressionExperimentDao
- loadDetailsValueObjects
  
  public Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjects(@Nullable Collection<Long> ids, @Nullable Taxon taxon, @Nullable Sort sort, int offset, int limit)
  
  Description copied from interface: ExpressionExperimentDao
  
  Special method for front-end access. This is partly redundant with FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int); however, it fills in more information, returns ExpressionExperimentDetailsValueObject
  
  Specified by:
  
  loadDetailsValueObjects in interface ExpressionExperimentDao
  
  Parameters:
  
  ids - only list specific ids, or null to ignore
  
  taxon - only list EEs in the specified taxon, or null to ignore
  
  sort - the field to order the results by.
  
  offset - offset
  
  limit - maximum number of results to return
  
  Returns:
  
  a list of EE details VOs representing experiments matching the given arguments.
- loadDetailsValueObjectsByIdsWithCache
  
  public Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(@Nullable Collection<Long> ids, @Nullable Taxon taxon, @Nullable Sort sort, int offset, int limit)
  
  Description copied from interface: ExpressionExperimentDao
  
  Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
  
  Specified by:
  
  loadDetailsValueObjectsByIdsWithCache in interface ExpressionExperimentDao
- loadDetailsValueObjectsByIds
  
  public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(Collection<Long> ids)
  
  Description copied from interface: ExpressionExperimentDao
  
  Like ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
  
  Specified by:
  
  loadDetailsValueObjectsByIds in interface ExpressionExperimentDao
- loadDetailsValueObjectsByIdsWithCache
  
  public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
  
  Description copied from interface: ExpressionExperimentDao
  
  Flavour of ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection), but using the query cache.
  
  Specified by:
  
  loadDetailsValueObjectsByIdsWithCache in interface ExpressionExperimentDao
- loadBlacklistedValueObjects
  
  public Slice<ExpressionExperimentValueObject> loadBlacklistedValueObjects(@Nullable Filters filters, @Nullable Sort sort, int offset, int limit)
  
  Specified by:
  
  loadBlacklistedValueObjects in interface ExpressionExperimentDao
- loadLackingFactors
  
  public Collection<ExpressionExperiment> loadLackingFactors()
  
  Specified by:
  
  loadLackingFactors in interface ExpressionExperimentDao
- loadLackingTags
  
  public Collection<ExpressionExperiment> loadLackingTags()
  
  Specified by:
  
  loadLackingTags in interface ExpressionExperimentDao
- doLoadValueObject
  
  protected ExpressionExperimentValueObject doLoadValueObject(ExpressionExperiment entity)
  
  Description copied from class: AbstractVoEnabledDao
  
  Load a value object for a given entity.
  This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.
  
  Specified by:
  
  doLoadValueObject in class AbstractVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
- postProcessValueObjects
  
  protected void postProcessValueObjects(List<ExpressionExperimentValueObject> results)
  
  Description copied from class: AbstractVoEnabledDao
  
  Post-process VOs in bulk.
  Use this as an opportunity to load extra informations that could not be populated in the initial AbstractVoEnabledDao.doLoadValueObject(Identifiable) or AbstractVoEnabledDao.doLoadValueObjects(Collection)
  
  Overrides:
  
  postProcessValueObjects in class AbstractVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
- loadValueObjects
  
  public List<ExpressionExperimentValueObject> loadValueObjects(@Nullable Filters filters, @Nullable Sort sort)
  
  Description copied from interface: FilteringVoEnabledDao
  
  Load VOs with minimal ordering and filtering.
  Use this as an alternative to FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int) if you do not intend to provide pagination capabilities.
  Specified by:
  
  loadValueObjects in interface FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  Overrides:
  
  loadValueObjects in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  See Also:
  
  FilteringDao.load(Filters, Sort)
  
  FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)
- loadValueObjects
  
  public Slice<ExpressionExperimentValueObject> loadValueObjects(@Nullable Filters filters, @Nullable Sort sort, int offset, int limit)
  
  Description copied from interface: FilteringVoEnabledDao
  
  Load VOs with ordering, filtering and offset/limit.
  Consider using FilteringDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode) to produce the filters and sort safely from user input.
  Specified by:
  
  loadValueObjects in interface FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  Overrides:
  
  loadValueObjects in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  Parameters:
  
  filters - filters applied on the search. The properties mentioned in the Filter must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".
  
  sort - an object property and direction to order by. This property must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".
  
  offset - an offset from which entities are retrieved when sorted according to the sort argument, or 0 to ignore
  
  limit - a limit on the number of returned results, or -1 to ignore
  
  Returns:
  
  a slice of the relevant data
  
  See Also:
  
  FilteringDao.load(Filters, Sort, int, int)
- getValueObjectTransformer
  
  protected TypedResultTransformer<ExpressionExperimentValueObject> getValueObjectTransformer()
  
  Description copied from class: AbstractQueryFilteringVoEnabledDao
  
  Obtain a value object transformer for the results of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
  By default, it will process the first element of the tuple with AbstractVoEnabledDao.doLoadValueObjects(Collection) and then post-process the resulting VOs with AbstractVoEnabledDao.postProcessValueObjects(List).
  
  Overrides:
  
  getValueObjectTransformer in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
- remove
  
  public void remove(ExpressionExperiment ee)
  
  Description copied from interface: BaseDao
  
  Remove a persistent instance
  
  Specified by:
  
  remove in interface BaseDao<ExpressionExperiment>
  
  Overrides:
  
  remove in class AbstractDao<ExpressionExperiment>
  
  Parameters:
  
  ee - the entity to be removed
- thaw
  
  public void thaw(ExpressionExperiment expressionExperiment)
  
  Description copied from interface: ExpressionExperimentDao
  
  Thaw everything.
  Includes ExpressionExperimentDao.thawLite(ExpressionExperiment) and raw/processed vectors.
  Does not include single-cell vectors.
  
  Specified by:
  
  thaw in interface ExpressionExperimentDao
- thawLite
  
  public void thawLite(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Thaw experiment metadata and bioassays.
  Include ExpressionExperimentDao.thawLiter(ExpressionExperiment) and bioassays.
  
  Specified by:
  
  thawLite in interface ExpressionExperimentDao
- thawLiter
  
  public void thawLiter(ExpressionExperiment expressionExperiment)
  
  Description copied from interface: ExpressionExperimentDao
  
  Thaw experiment metadata.
  
  Specified by:
  
  thawLiter in interface ExpressionExperimentDao
- getSingleCellDimensions
  
  public List<SingleCellDimension> getSingleCellDimensions(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
  
  Specified by:
  
  getSingleCellDimensions in interface ExpressionExperimentDao
- getSingleCellDimensionsWithoutCellIds
  
  public List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
  Cell IDs are not loaded.
  
  Specified by:
  
  getSingleCellDimensionsWithoutCellIds in interface ExpressionExperimentDao
- getSingleCellDimensionsWithoutCellIds
  
  public List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
  
  Specified by:
  
  getSingleCellDimensionsWithoutCellIds in interface ExpressionExperimentDao
- getSingleCellDimension
  
  public SingleCellDimension getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the single-cell dimension used by a specific QT.
  
  Specified by:
  
  getSingleCellDimension in interface ExpressionExperimentDao
- getSingleCellDimensionWithoutCellIds
  
  public SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Load a single-cell dimension used by a specific QT without its cell IDs.
  
  Specified by:
  
  getSingleCellDimensionWithoutCellIds in interface ExpressionExperimentDao
- getSingleCellDimensionWithoutCellIds
  
  public SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
  
  Specified by:
  
  getSingleCellDimensionWithoutCellIds in interface ExpressionExperimentDao
- getPreferredSingleCellDimension
  
  public SingleCellDimension getPreferredSingleCellDimension(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred single-cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
  
  Specified by:
  
  getPreferredSingleCellDimension in interface ExpressionExperimentDao
- getPreferredSingleCellDimensionWithoutCellIds
  
  public SingleCellDimension getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Load a single-cell dimension without its cell IDs.
  
  Specified by:
  
  getPreferredSingleCellDimensionWithoutCellIds in interface ExpressionExperimentDao
- getPreferredSingleCellDimensionsWithoutCellIds
  
  public SingleCellDimension getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
  
  Specified by:
  
  getPreferredSingleCellDimensionsWithoutCellIds in interface ExpressionExperimentDao
- createSingleCellDimension
  
  public void createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
  
  Description copied from interface: ExpressionExperimentDao
  
  Create a single-cell dimension for a given experiment.
  
  Specified by:
  
  createSingleCellDimension in interface ExpressionExperimentDao
- updateSingleCellDimension
  
  public void updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
  
  Description copied from interface: ExpressionExperimentDao
  
  Update a single-cell dimensino for a given experiment.
  
  Specified by:
  
  updateSingleCellDimension in interface ExpressionExperimentDao
- deleteSingleCellDimension
  
  public void deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
  
  Description copied from interface: ExpressionExperimentDao
  
  Delete the given single-cell dimension.
  
  Specified by:
  
  deleteSingleCellDimension in interface ExpressionExperimentDao
- streamCellIds
  
  public Stream<String> streamCellIds(SingleCellDimension dimension, boolean createNewSession)
  
  Description copied from interface: ExpressionExperimentDao
  
  Stream the cell IDs of a dimension.
  
  Specified by:
  
  streamCellIds in interface ExpressionExperimentDao
  
  Parameters:
  
  createNewSession - create a new session held by the stream, allowing to use the stream beyond the lifetime current session. If you set this to true, make absolutely sure that the resulting stream is closed.
  
  Returns:
  
  a stream of cell IDs, or null if the dimension is not found
- streamCellTypes
  
  public Stream<Characteristic> streamCellTypes(CellTypeAssignment cta, boolean createNewSession)
  
  Specified by:
  
  streamCellTypes in interface ExpressionExperimentDao
- getCellLevelCharacteristicsCategory
  
  public Category getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the category of a cell-level characteristic.
  This handles the case where the characteristics were not loaded (i.e. using ExpressionExperimentDao.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment, boolean, boolean, boolean, boolean, boolean, boolean)).
  
  Specified by:
  
  getCellLevelCharacteristicsCategory in interface ExpressionExperimentDao
- getCellTypeAt
  
  public Characteristic getCellTypeAt(CellTypeAssignment cta, int cellIndex)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the cell type at a given cell index.
  
  Specified by:
  
  getCellTypeAt in interface ExpressionExperimentDao
- getCellTypeAt
  
  public Characteristic[] getCellTypeAt(CellTypeAssignment cta, int startIndex, int endIndexExclusive)
  
  Specified by:
  
  getCellTypeAt in interface ExpressionExperimentDao
- getCellLevelCharacteristicAt
  
  public Characteristic getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the characteristic at a given cell index.
  
  Specified by:
  
  getCellLevelCharacteristicAt in interface ExpressionExperimentDao
- getCellLevelCharacteristicAt
  
  public Characteristic[] getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)
  
  Specified by:
  
  getCellLevelCharacteristicAt in interface ExpressionExperimentDao
- streamCellLevelCharacteristics
  
  public Stream<Characteristic> streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)
  
  Specified by:
  
  streamCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellTypeAssignments
  
  public List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment ee)
  
  Specified by:
  
  getCellTypeAssignments in interface ExpressionExperimentDao
- getCellTypeAssignments
  
  public List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
  
  Specified by:
  
  getCellTypeAssignments in interface ExpressionExperimentDao
- getCellTypeAssignmentsWithoutIndices
  
  public Collection<CellTypeAssignment> getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
  
  Specified by:
  
  getCellTypeAssignmentsWithoutIndices in interface ExpressionExperimentDao
- getPreferredCellTypeAssignment
  
  public CellTypeAssignment getPreferredCellTypeAssignment(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred assignment of the preferred single-cell vectors.
  
  Specified by:
  
  getPreferredCellTypeAssignment in interface ExpressionExperimentDao
- getPreferredCellTypeAssignment
  
  public CellTypeAssignment getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt) throws NonUniqueResultException
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred assignment for the given quantitation type.
  
  Specified by:
  
  getPreferredCellTypeAssignment in interface ExpressionExperimentDao
  
  Throws:
  
  NonUniqueResultException - if there are multiple preferred cell-type labellings
- getPreferredCellTypeAssignmentWithoutIndices
  
  public CellTypeAssignment getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt) throws NonUniqueResultException
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred assignment for the given quantitation type without loading the indices.
  
  Specified by:
  
  getPreferredCellTypeAssignmentWithoutIndices in interface ExpressionExperimentDao
  
  Throws:
  
  NonUniqueResultException - if there are multiple preferred cell-type labellings
- getCellTypeAssignment
  
  public CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a cell type assignment by ID.
  
  Specified by:
  
  getCellTypeAssignment in interface ExpressionExperimentDao
- getCellTypeAssignmentWithoutIndices
  
  public CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a cell type assignment by ID without loading the indices.
  
  Specified by:
  
  getCellTypeAssignmentWithoutIndices in interface ExpressionExperimentDao
- getCellTypeAssignment
  
  public CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a cell type assignment by name.
  
  Specified by:
  
  getCellTypeAssignment in interface ExpressionExperimentDao
- getCellTypeAssignmentProtocols
  
  public Collection<Protocol> getCellTypeAssignmentProtocols()
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain all cell type assignment protocols currently used.
  
  Specified by:
  
  getCellTypeAssignmentProtocols in interface ExpressionExperimentDao
- getCellTypeAssignmentByProtocol
  
  @Nullable public Collection<CellTypeAssignment> getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolName)
  
  Specified by:
  
  getCellTypeAssignmentByProtocol in interface ExpressionExperimentDao
- getCellTypeAssignmentWithoutIndices
  
  public CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a cell type assignment by name without loading the indices.
  
  Specified by:
  
  getCellTypeAssignmentWithoutIndices in interface ExpressionExperimentDao
- getCellLevelCharacteristics
  
  public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain all cell-level characteristics from all single-cell dimensions.
  
  Specified by:
  
  getCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellLevelCharacteristics
  
  public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain all cell-level characteristics from all single-cell dimensions matching the given category.
  
  Specified by:
  
  getCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellLevelCharacteristics
  
  public CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a specific cell-level characteristic by ID.
  When using this method, no CellTypeAssignment can be returned as those are stored in a different table.
  
  Specified by:
  
  getCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellLevelCharacteristics
  
  @Nullable public CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String clcName)
  
  Specified by:
  
  getCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellLevelCharacteristics
  
  public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
  
  Specified by:
  
  getCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellLevelCharacteristics
  
  public List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Category category)
  
  Specified by:
  
  getCellLevelCharacteristics in interface ExpressionExperimentDao
- getCellLevelCharacteristicsWithoutIndices
  
  public CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long clcId)
  
  Specified by:
  
  getCellLevelCharacteristicsWithoutIndices in interface ExpressionExperimentDao
- getCellLevelCharacteristicsWithoutIndices
  
  public CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
  
  Specified by:
  
  getCellLevelCharacteristicsWithoutIndices in interface ExpressionExperimentDao
- getCellLevelCharacteristicsWithoutIndices
  
  public Collection<CellLevelCharacteristics> getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
  
  Specified by:
  
  getCellLevelCharacteristicsWithoutIndices in interface ExpressionExperimentDao
- getCellTypes
  
  public List<Characteristic> getCellTypes(ExpressionExperiment ee)
  
  Specified by:
  
  getCellTypes in interface ExpressionExperimentDao
- getSingleCellQuantitationTypes
  
  public List<QuantitationType> getSingleCellQuantitationTypes(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a list of single-cell QTs.
  
  Specified by:
  
  getSingleCellQuantitationTypes in interface ExpressionExperimentDao
- hasSingleCellQuantitationTypes
  
  public boolean hasSingleCellQuantitationTypes(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Indicate if the given experiment has single-cell quantitation types.
  
  Specified by:
  
  hasSingleCellQuantitationTypes in interface ExpressionExperimentDao
- getSingleCellDataVectors
  
  public List<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a set of single-cell data vectors for the given quantitation type.
  
  Specified by:
  
  getSingleCellDataVectors in interface ExpressionExperimentDao
- getSingleCellDataVectors
  
  public List<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a set of single-cell data vectors for the given quantitation type.
  
  Specified by:
  
  getSingleCellDataVectors in interface ExpressionExperimentDao
- streamSingleCellDataVectors
  
  public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a stream over the vectors for a given QT.
  Specified by:
  
  streamSingleCellDataVectors in interface ExpressionExperimentDao
  
  Parameters:
  
  fetchSize - number of vectors to fetch at once
  
  createNewSession - create a new session held by the stream. If you set this to true, make absolutely sure that the resulting stream is closed because it is attached to a Session object.
  
  See Also:
  
  QueryUtils.stream(Query, Class, int, boolean, boolean)
- streamSingleCellDataVectors
  
  public Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, boolean includeCellIds, boolean includeData, boolean includeDataIndices)
  
  Specified by:
  
  streamSingleCellDataVectors in interface ExpressionExperimentDao
- getSingleCellDataVectorWithoutCellIds
  
  public SingleCellExpressionDataVector getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)
  
  Specified by:
  
  getSingleCellDataVectorWithoutCellIds in interface ExpressionExperimentDao
- getNumberOfSingleCellDataVectors
  
  public long getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the number of single-cell vectors for a given QT.
  
  Specified by:
  
  getNumberOfSingleCellDataVectors in interface ExpressionExperimentDao
- getNumberOfNonZeroes
  
  public long getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the number of non-zeroes.
  
  Specified by:
  
  getNumberOfNonZeroes in interface ExpressionExperimentDao
- getNumberOfNonZeroesBySample
  
  public Map<BioAssay,Long> getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the number of non-zeroes by sample.
  This is quite costly because the indices of each vector has to be examined.
  
  Specified by:
  
  getNumberOfNonZeroesBySample in interface ExpressionExperimentDao
- removeSingleCellDataVectors
  
  public int removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, boolean deleteQt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Remove the given single-cell data vectors.
  
  Specified by:
  
  removeSingleCellDataVectors in interface ExpressionExperimentDao
  
  Parameters:
  
  quantitationType - quantitation to remove
  
  deleteQt - if true, detach the QT from the experiment and delete it TODO: add a replaceSingleCellDataVectors to avoid needing this
- removeAllSingleCellDataVectors
  
  public int removeAllSingleCellDataVectors(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Remove all single-cell data vectors and their quantitation types.
  
  Specified by:
  
  removeAllSingleCellDataVectors in interface ExpressionExperimentDao
- getNumberOfDesignElementsPerSample
  
  public Map<BioAssay,Long> getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
  
  Specified by:
  
  getNumberOfDesignElementsPerSample in interface ExpressionExperimentDao
- getFilteringQuery
  
  protected Query getFilteringQuery(@Nullable Filters filters, @Nullable Sort sort)
  
  Description copied from class: AbstractQueryFilteringVoEnabledDao
  
  Produce a query for retrieving value objects after applying a set of filters and a given ordering.
  Note that if your implementation does not produce a List of AbstractQueryFilteringVoEnabledDao when Query.list() is invoked, you must override AbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().
  The make the cached query (i.e. AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters, Sort) behave the same, you also have to explicitly initialize any lazy relations in AbstractVoEnabledDao.doLoadValueObject(Identifiable) because the VO constructor will not initialize them.
  
  Specified by:
  
  getFilteringQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  Returns:
  
  a Query that produce a list of AbstractQueryFilteringVoEnabledDao
- initializeCachedFilteringResult
  
  protected void initializeCachedFilteringResult(ExpressionExperiment ee)
  
  Description copied from class: AbstractQueryFilteringVoEnabledDao
  
  Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
  Lazy-loaded relations that are fetched in AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) must be initialized manually in this method to ensure that the entity has all the expected fields if they are retrieved from the second-level cache.
  
  Specified by:
  
  initializeCachedFilteringResult in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
- getFilteringIdQuery
  
  protected Query getFilteringIdQuery(@Nullable Filters filters, @Nullable Sort sort)
  
  Description copied from class: AbstractQueryFilteringVoEnabledDao
  
  Produce a query that will be used to retrieve IDs of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
  
  Overrides:
  
  getFilteringIdQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
- getFilteringCountQuery
  
  protected Query getFilteringCountQuery(@Nullable Filters filters)
  
  Description copied from class: AbstractQueryFilteringVoEnabledDao
  
  Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
  
  Overrides:
  
  getFilteringCountQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  Returns:
  
  a Query which must return a single Long value
- configureFilterableProperties
  
  protected void configureFilterableProperties(AbstractFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>.FilterablePropertiesConfigurer configurer)
  
  Description copied from class: AbstractFilteringVoEnabledDao
  
  Register filterable properties.
  
  Overrides:
  
  configureFilterableProperties in class AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
- resolveFilterablePropertyMeta
  
  protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder resolveFilterablePropertyMeta(String propertyName)
  
  Checks for special properties that are allowed to be referenced on certain objects. E.g. characteristics on EEs. Obtain various meta-information used to infer what to use in a Filter or Sort.
  This is used by AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode).
  Include filtering by lastUpdated, troubled and needsAttention from the associated curation details.
  Overrides:
  
  resolveFilterablePropertyMeta in class AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
  
  See Also:
  
  AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String)
  
  AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, Collection)
  
  FilteringDao.getSort(String, Sort.Direction, Sort.NullMode)
- getRawDataVectors
  
  public Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain raw vectors for a given experiment and QT.
  This is preferable to using ExpressionExperiment.getRawExpressionDataVectors() as it only loads vectors relevant to the given QT.
  
  Specified by:
  
  getRawDataVectors in interface ExpressionExperimentDao
- getRawDataVectors
  
  public Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain a slice of the raw vectors for a given experiment and QT.
  
  Specified by:
  
  getRawDataVectors in interface ExpressionExperimentDao
- getPreferredRawDataVectors
  
  public Collection<RawExpressionDataVector> getPreferredRawDataVectors(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the preferred raw data vectors for a given experiment.
  
  Specified by:
  
  getPreferredRawDataVectors in interface ExpressionExperimentDao
- getMissingValueVectors
  
  public Map<QuantitationType,Collection<RawExpressionDataVector>> getMissingValueVectors(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Obtain the missing value vectors for a given experiment.
  
  Specified by:
  
  getMissingValueVectors in interface ExpressionExperimentDao
- addRawDataVectors
  
  public int addRawDataVectors(ExpressionExperiment ee, QuantitationType newQt, Collection<RawExpressionDataVector> newVectors)
  
  Description copied from interface: ExpressionExperimentDao
  
  Add raw data vectors with the given quantitation type.
  
  Specified by:
  
  addRawDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the number of raw data vectors created
- removeAllRawDataVectors
  
  public int removeAllRawDataVectors(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Remove all raw data vectors.
  All affected QTs are removed.
  
  Specified by:
  
  removeAllRawDataVectors in interface ExpressionExperimentDao
- removeRawDataVectors
  
  public int removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
  
  Description copied from interface: ExpressionExperimentDao
  
  Remove raw data vectors for a given quantitation type.
  Unused BioAssayDimension are removed unless keepDimension is set to true.
  
  Specified by:
  
  removeRawDataVectors in interface ExpressionExperimentDao
  
  Parameters:
  
  keepDimension - keep the BioAssayDimension if it is not used by any other vectors. Use this only if you intend to reuse the dimension for another set of vectors. Alternatively, ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) can be used.
  
  Returns:
  
  the number of removed raw vectors
- replaceRawDataVectors
  
  public int replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)
  
  Description copied from interface: ExpressionExperimentDao
  
  Replace raw data vectors for a given quantitation type.
  
  Specified by:
  
  replaceRawDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the number of replaced raw vectors
- getProcessedDataVectors
  
  public Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Retrieve the processed vector for an experiment.
  Unlike ExpressionExperiment.getProcessedExpressionDataVectors(), this is guaranteed to return only one set of vectors and will raise a NonUniqueResultException if there is more than one processed QTs.
  Specified by:
  
  getProcessedDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the processed vectors, or null if there are no processed vectors
  
  See Also:
  
  ExpressionExperimentDao.getProcessedQuantitationType(ExpressionExperiment)
- getProcessedDataVectors
  
  public Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
  
  Description copied from interface: ExpressionExperimentDao
  
  Retrieve a slice of processed vectors for an experiment.
  
  Specified by:
  
  getProcessedDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the processed vectors, or null if there are no processed vectors
- createProcessedDataVectors
  
  public int createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
  
  Description copied from interface: ExpressionExperimentDao
  
  Add processed data vectors
  The number of vectors ExpressionExperiment.getNumberOfDataVectors() is updated.
  
  Specified by:
  
  createProcessedDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the number of created processed vectors
- removeProcessedDataVectors
  
  public int removeProcessedDataVectors(ExpressionExperiment ee)
  
  Description copied from interface: ExpressionExperimentDao
  
  Remove processed data vectors.
  Their corresponding QT is detached from the experiment and removed. The number of vectors (i.e. ExpressionExperiment.getNumberOfDataVectors() is set to zero. Unused dimensions are removed.
  
  Specified by:
  
  removeProcessedDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the number of removed processed vectors
- replaceProcessedDataVectors
  
  public int replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
  
  Description copied from interface: ExpressionExperimentDao
  
  Replace processed data vectors.
  The QT is reused and the number of vectors ExpressionExperiment.getNumberOfDataVectors() is updated. Unused dimensions are removed.
  
  Specified by:
  
  replaceProcessedDataVectors in interface ExpressionExperimentDao
  
  Returns:
  
  the number of vectors replaced

Class ExpressionExperimentDaoImpl

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

Nested classes/interfaces inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Field Summary

Fields inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

Fields inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

Constructor Summary

Method Summary

Methods inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

Methods inherited from class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

Methods inherited from class java.lang.Object

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao

Methods inherited from interface ubic.gemma.persistence.service.CachedFilteringDao

Methods inherited from interface ubic.gemma.persistence.service.CachedFilteringVoEnabledDao

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao

Methods inherited from interface ubic.gemma.persistence.service.FilteringDao

Constructor Details

ExpressionExperimentDaoImpl

Method Details

load

loadAllIdentifiers

browse

browse

filterByTaxon

findByShortName

findByName

findOneByName

find

findByAccession

findByAccession

findOneByAccession

findByBibliographicReference

findByBioAssay

findByBioMaterial

findByBioMaterials

findByExpressedGene

findByDesign

findByDesignId

findByFactor

findByFactors

findByFactorValue

findByFactorValue

findByFactorValues

findByFactorValueIds

findByGene

findByQuantitationType

findByTaxon

findByUpdatedLimit

findByUpdatedLimit

findUpdatedAfter

getAnnotationCounts

getAllAnnotations

getExperimentAnnotations

getExperimentSubSetAnnotations

getBioMaterialAnnotations

getBioMaterialAnnotations

getExperimentalDesignAnnotations

getFactorValueAnnotations

getFactorValueAnnotations

getCategoriesUsageFrequency

getAnnotationsUsageFrequency

getAnnotationsUsageFrequencyInternal

getExperimentsLackingPublications

updateMeanVarianceRelation

countBioMaterials

getArrayDesignsUsed

getArrayDesignsUsed

getArrayDesignsUsed

getGenesUsedByPreferredVectors

getTechnologyTypeUsageFrequency

getTechnologyTypeUsageFrequency

getArrayDesignsUsageFrequency

getArrayDesignsUsageFrequency