Package ubic.gemma.persistence.service.expression.experiment

Interface ExpressionExperimentDao

All Superinterfaces:

BaseDao<ExpressionExperiment>, BaseVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>, CachedFilteringDao<ExpressionExperiment>, CachedFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, CuratableDao<ExpressionExperiment>, FilteringDao<ExpressionExperiment>, FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

All Known Implementing Classes:

ExpressionExperimentDaoImpl

public interface ExpressionExperimentDao
extends CuratableDao<ExpressionExperiment>, CachedFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>

Created by tesarst on 13/03/17.

Author:

tesarst

Field Summary

Fields

Modifier and Type	Field	Description
static String	FREE_TEXT	Special indicator for free-text terms.
static String	OBJECT_ALIAS
static String	UNCATEGORIZED	Special indicator for an uncategorized term.

Method Summary

Modifier and Type	Method	Description
long	countBioMaterials(Filters filters)	Count the number of biomaterials of datasets satisfying the given filters.
Collection<Long>	filterByTaxon(Collection<Long> ids, Taxon taxon)
Collection<ExpressionExperiment>	findByAccession(String accession)
Collection<ExpressionExperiment>	findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	findByBibliographicReference(Long bibRefID)
ExpressionExperiment	findByBioAssay(BioAssay ba)
ExpressionExperiment	findByBioMaterial(BioMaterial bm)
Map<ExpressionExperiment,BioMaterial>	findByBioMaterials(Collection<BioMaterial> bms)
ExpressionExperiment	findByDesign(ExperimentalDesign ed)
Collection<ExpressionExperiment>	findByExpressedGene(Gene gene, Double rank)
ExpressionExperiment	findByFactor(ExperimentalFactor ef)
ExpressionExperiment	findByFactorValue(Long factorValueId)
ExpressionExperiment	findByFactorValue(FactorValue fv)
Map<ExpressionExperiment,FactorValue>	findByFactorValues(Collection<FactorValue> fvs)
Collection<ExpressionExperiment>	findByGene(Gene gene)
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)
Collection<ExpressionExperiment>	findUpdatedAfter(Date date)
Map<Class<? extends Identifiable>,List<Characteristic>>	getAllAnnotations(ExpressionExperiment expressionExperiment)	Obtain all annotations, grouped by applicable level.
Map<Long,Long>	getAnnotationCounts(Collection<Long> ids)
Collection<? extends AnnotationValueObject>	getAnnotationsByBioMaterials(Long eeId)
Collection<? extends AnnotationValueObject>	getAnnotationsByFactorValues(Long eeId)
Map<Characteristic,Long>	getAnnotationsUsageFrequency(Collection<Long> expressionExperimentIds, Class<? extends Identifiable> level, int maxResults, int minFrequency, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris)	Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.
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.
Map<ArrayDesign,Collection<Long>>	getArrayDesignsUsed(Collection<Long> eeids)
Collection<ArrayDesign>	getArrayDesignsUsed(BioAssaySet bas)
Map<Long,Collection<AuditEvent>>	getAuditEvents(Collection<Long> ids)
Collection<BioAssayDimension>	getBioAssayDimensions(ExpressionExperiment expressionExperiment)
List<Characteristic>	getBioMaterialAnnotations(ExpressionExperiment expressionExperiment)	Obtain sample-level annotations.
long	getBioMaterialCount(ExpressionExperiment expressionExperiment)
Map<Characteristic,Long>	getCategoriesUsageFrequency(Collection<Long> eeIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
long	getDesignElementDataVectorCount(ExpressionExperiment ee)
List<Characteristic>	getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment)	Obtain experimental design-level annotations.
List<Characteristic>	getExperimentAnnotations(ExpressionExperiment expressionExperiment)	Obtain experiment-level annotations.
Collection<ExpressionExperiment>	getExperimentsLackingPublications()
Collection<ExpressionExperiment>	getExperimentsWithOutliers()
Map<Long,Date>	getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Date	getLastArrayDesignUpdate(ExpressionExperiment ee)
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)
QuantitationType	getPreferredQuantitationType(ExpressionExperiment ee)	Obtain the preferred quantitation type, if available.
Map<QuantitationType,Long>	getQuantitationTypeCount(ExpressionExperiment ee)
Collection<QuantitationType>	getQuantitationTypes(ExpressionExperiment expressionExperiment)
Map<ExpressionExperiment,Collection<AuditEvent>>	getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Collection<ExpressionExperimentSubSet>	getSubSets(ExpressionExperiment expressionExperiment)
<T extends BioAssaySet> Map<T,Taxon>	getTaxa(Collection<T> bioAssaySets)
Taxon	getTaxon(BioAssaySet ee)
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.
boolean	hasProcessedExpressionData(ExpressionExperiment ee)	Test if the dataset has preferred expression data vectors.
BioAssaySet	loadBioAssaySet(Long id)
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 loadDetailsValueObjects(Collection, Taxon, Sort, int, int), but returning a list.
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)	Flavour of loadDetailsValueObjectsByIds(Collection), but using the query cache.
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)	Flavour of loadDetailsValueObjectsByIds(Collection), but using the query cache.
Collection<ExpressionExperiment>	loadLackingFactors()
Collection<ExpressionExperiment>	loadLackingTags()
List<ExpressionExperiment>	loadWithRelationsAndCache(List<Long> ids)	Load datasets by IDs with the same relation as CachedFilteringDao.loadWithCache(Filters, Sort).
void	thaw(ExpressionExperiment expressionExperiment)
void	thawBioAssays(ExpressionExperiment expressionExperiment)
void	thawForFrontEnd(ExpressionExperiment expressionExperiment)
void	thawWithoutVectors(ExpressionExperiment expressionExperiment)
MeanVarianceRelation	updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)

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

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

browse, browse

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

updateCurationDetailsFromAuditEvent

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

count, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Field Detail

OBJECT_ALIAS

static final String OBJECT_ALIAS

See Also:

Constant Field Values

FREE_TEXT

static final String FREE_TEXT

Special indicator for free-text terms.

Free-text terms or categories have a null URI and a non-empty label.

UNCATEGORIZED

static final String UNCATEGORIZED

Special indicator for an uncategorized term.

Uncategorized terms (or the uncategorized category) has both null URI and label.

Method Detail

loadBioAssaySet

@Nullable
BioAssaySet loadBioAssaySet(Long id)

filterByTaxon

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

findByShortName

ExpressionExperiment findByShortName(String shortName)

findByName

Collection<ExpressionExperiment> findByName(String name)

findByAccession

Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)

findByAccession

Collection<ExpressionExperiment> findByAccession(String accession)

findByBibliographicReference

Collection<ExpressionExperiment> findByBibliographicReference(Long bibRefID)

findByBioAssay

ExpressionExperiment findByBioAssay(BioAssay ba)

findByBioMaterial

ExpressionExperiment findByBioMaterial(BioMaterial bm)

findByBioMaterials

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

findByExpressedGene

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

findByDesign

ExpressionExperiment findByDesign(ExperimentalDesign ed)

findByFactor

ExpressionExperiment findByFactor(ExperimentalFactor ef)

findByFactorValue

ExpressionExperiment findByFactorValue(FactorValue fv)

findByFactorValue

ExpressionExperiment findByFactorValue(Long factorValueId)

findByFactorValues

Map<ExpressionExperiment,FactorValue> findByFactorValues(Collection<FactorValue> fvs)

findByGene

Collection<ExpressionExperiment> findByGene(Gene gene)

findByQuantitationType

ExpressionExperiment findByQuantitationType(QuantitationType quantitationType)

findByTaxon

Collection<ExpressionExperiment> findByTaxon(Taxon taxon)

findByUpdatedLimit

List<ExpressionExperiment> findByUpdatedLimit(Collection<Long> ids,
                                              int limit)

findByUpdatedLimit

List<ExpressionExperiment> findByUpdatedLimit(int limit)

findUpdatedAfter

Collection<ExpressionExperiment> findUpdatedAfter(Date date)

getAnnotationCounts

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

getArrayDesignsUsed

Collection<ArrayDesign> getArrayDesignsUsed(BioAssaySet bas)

getArrayDesignsUsed

Map<ArrayDesign,Collection<Long>> getArrayDesignsUsed(Collection<Long> eeids)

getTechnologyTypeUsageFrequency

Map<TechnologyType,Long> getTechnologyTypeUsageFrequency()

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.

getTechnologyTypeUsageFrequency

Map<TechnologyType,Long> getTechnologyTypeUsageFrequency(Collection<Long> eeIds)

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

Note: No ACL filtering is performed.

See Also:

getTechnologyTypeUsageFrequency()

getArrayDesignsUsageFrequency

Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(int maxResults)

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.

getArrayDesignsUsageFrequency

Map<ArrayDesign,Long> getArrayDesignsUsageFrequency(Collection<Long> eeIds,
                                                          int maxResults)

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

Note: no ACL filtering is performed. Only administrator can see troubled platforms.

See Also:

getArrayDesignsUsageFrequency(int)

getOriginalPlatformsUsageFrequency

Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(int maxResults)

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.

getOriginalPlatformsUsageFrequency

Map<ArrayDesign,Long> getOriginalPlatformsUsageFrequency(Collection<Long> eeIds,
                                                               int maxResults)

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

Note: no ACL filtering is performed. Only administrators can see troubled platforms.

See Also:

getOriginalPlatformsUsageFrequency(int)

getAuditEvents

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

getBioAssayDimensions

Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment)

getBioMaterialCount

long getBioMaterialCount(ExpressionExperiment expressionExperiment)

getDesignElementDataVectorCount

long getDesignElementDataVectorCount(ExpressionExperiment ee)

getExperimentsWithOutliers

Collection<ExpressionExperiment> getExperimentsWithOutliers()

getLastArrayDesignUpdate

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

getLastArrayDesignUpdate

Date getLastArrayDesignUpdate(ExpressionExperiment ee)

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

Obtain the count of distinct experiments per taxon.

Experiments are filtered by ACLs and troubled experiments are only visible to administrators.

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount(Collection<Long> ids)

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.

getPopulatedFactorCounts

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

getPopulatedFactorCountsExcludeBatch

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

getQuantitationTypeCount

Map<QuantitationType,Long> getQuantitationTypeCount(ExpressionExperiment ee)

getQuantitationTypes

Collection<QuantitationType> getQuantitationTypes(ExpressionExperiment expressionExperiment)

getPreferredQuantitationType

@Nullable
QuantitationType getPreferredQuantitationType(ExpressionExperiment ee)

Obtain the preferred quantitation type, if available.

hasProcessedExpressionData

boolean hasProcessedExpressionData(ExpressionExperiment ee)

Test if the dataset has preferred expression data vectors.

getSampleRemovalEvents

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

getSubSets

Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment)

getTaxa

<T extends BioAssaySet> Map<T,Taxon> getTaxa(Collection<T> bioAssaySets)

getTaxon

Taxon getTaxon(BioAssaySet ee)

loadWithRelationsAndCache

List<ExpressionExperiment> loadWithRelationsAndCache(List<Long> ids)

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

loadDetailsValueObjects

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

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

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

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

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

loadDetailsValueObjectsByIds

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

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

loadDetailsValueObjectsByIdsWithCache

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

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

loadBlacklistedValueObjects

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

loadLackingFactors

Collection<ExpressionExperiment> loadLackingFactors()

loadLackingTags

Collection<ExpressionExperiment> loadLackingTags()

thaw

void thaw(ExpressionExperiment expressionExperiment)

thawWithoutVectors

void thawWithoutVectors(ExpressionExperiment expressionExperiment)

thawBioAssays

void thawBioAssays(ExpressionExperiment expressionExperiment)

thawForFrontEnd

void thawForFrontEnd(ExpressionExperiment expressionExperiment)

getAnnotationsByBioMaterials

Collection<? extends AnnotationValueObject> getAnnotationsByBioMaterials(Long eeId)

getAnnotationsByFactorValues

Collection<? extends AnnotationValueObject> getAnnotationsByFactorValues(Long eeId)

getAllAnnotations

Map<Class<? extends Identifiable>,List<Characteristic>> getAllAnnotations(ExpressionExperiment expressionExperiment)

Obtain all annotations, grouped by applicable level.

getExperimentAnnotations

List<Characteristic> getExperimentAnnotations(ExpressionExperiment expressionExperiment)

Obtain experiment-level annotations.

getBioMaterialAnnotations

List<Characteristic> getBioMaterialAnnotations(ExpressionExperiment expressionExperiment)

Obtain sample-level annotations.

getExperimentalDesignAnnotations

List<Characteristic> getExperimentalDesignAnnotations(ExpressionExperiment expressionExperiment)

Obtain experimental design-level annotations.

getCategoriesUsageFrequency

Map<Characteristic,Long> getCategoriesUsageFrequency(@Nullable
                                                           Collection<Long> eeIds,
                                                           @Nullable
                                                           Collection<String> excludedCategoryUris,
                                                           @Nullable
                                                           Collection<String> excludedTermUris,
                                                           @Nullable
                                                           Collection<String> retainedTermUris,
                                                           int maxResults)

getAnnotationsUsageFrequency

Map<Characteristic,Long> getAnnotationsUsageFrequency(@Nullable
                                                            Collection<Long> expressionExperimentIds,
                                                            @Nullable
                                                            Class<? extends Identifiable> level,
                                                            int maxResults,
                                                            int minFrequency,
                                                            @Nullable
                                                            String category,
                                                            @Nullable
                                                            Collection<String> excludedCategoryUris,
                                                            @Nullable
                                                            Collection<String> excludedTermUris,
                                                            @Nullable
                                                            Collection<String> retainedTermUris)

Obtain annotations usage frequency for a set of given ExpressionExperiment IDs.

This is meant as a counterpart to CharacteristicService.findExperimentsByUris(Collection, Taxon, int, boolean, boolean) to answer the reverse question: which annotations can be used to filter a given set of datasets?

Parameters:

expressionExperimentIds - 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

getExperimentsLackingPublications

Collection<ExpressionExperiment> getExperimentsLackingPublications()

updateMeanVarianceRelation

MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
                                                MeanVarianceRelation mvr)

countBioMaterials

long countBioMaterials(@Nullable
                       Filters filters)

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

The result is stored in the standard query cache.