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

Interface ExpressionExperimentService

All Superinterfaces:

BaseImmutableService<ExpressionExperiment>, BaseReadOnlyService<ExpressionExperiment>, BaseService<ExpressionExperiment>, BaseVoEnabledService<ExpressionExperiment,ExpressionExperimentValueObject>, FilteringService<ExpressionExperiment>, FilteringVoEnabledService<ExpressionExperiment,ExpressionExperimentValueObject>, SecurableBaseImmutableService<ExpressionExperiment>, SecurableBaseReadOnlyService<ExpressionExperiment>, SecurableBaseService<ExpressionExperiment>, SecurableBaseVoEnabledService<ExpressionExperiment,ExpressionExperimentValueObject>, SecurableFilteringVoEnabledService<ExpressionExperiment,ExpressionExperimentValueObject>

All Known Implementing Classes:

ExpressionExperimentServiceImpl

public interface ExpressionExperimentService
extends SecurableBaseService<ExpressionExperiment>, SecurableFilteringVoEnabledService<ExpressionExperiment,ExpressionExperimentValueObject>

Author:

kelsey

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static final class	ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm

Field Summary

Fields

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

Method Summary

Modifier and Type	Method	Description
void	addCharacteristic(ExpressionExperiment ee, Characteristic vc)	Will add the vocab characteristic to the expression experiment and persist the changes.
ExperimentalFactor	addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
FactorValue	addFactorValue(ExpressionExperiment ee, FactorValue fv)
void	addFactorValues(ExpressionExperiment ee, Map<BioMaterial,FactorValue> fvs)	Intended with the case of a continuous factor being added.
int	addRawDataVectors(ExpressionExperiment eeToUpdate, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Used when we want to add data for a quantitation type.
List<ExpressionExperiment>	browse(int start, int limit)
long	countBioMaterials(Filters filters)
long	countWithCache(Filters filters, Set<Long> extraIds)
int	createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Create a new set of processed vectors for an experiment.
Collection<Long>	filter(String searchString)	returns ids of search results.
Collection<Long>	filterByTaxon(Collection<Long> ids, Taxon taxon)	Remove IDs of Experiments that are not from the given taxon.
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> biomaterials)
ExpressionExperiment	findByDesign(ExperimentalDesign ed)
ExpressionExperiment	findByDesignId(Long designId)
Collection<ExpressionExperiment>	findByExpressedGene(Gene gene, double rank)
ExpressionExperiment	findByFactor(ExperimentalFactor factor)
Collection<ExpressionExperiment>	findByFactors(Collection<ExperimentalFactor> factors)
ExpressionExperiment	findByFactorValue(Long factorValueId)
ExpressionExperiment	findByFactorValue(FactorValue factorValue)
Collection<ExpressionExperiment>	findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	findByGene(Gene gene)
Collection<ExpressionExperiment>	findByName(String name)
ExpressionExperiment	findByQuantitationType(QuantitationType type)
ExpressionExperiment	findByShortName(String shortName)
ExpressionExperiment	findByShortNameAndThawLite(String shortName)
Collection<ExpressionExperiment>	findByTaxon(Taxon taxon)
List<ExpressionExperiment>	findByUpdatedLimit(int limit)
ExpressionExperiment	findOneByAccession(String accession)
ExpressionExperiment	findOneByName(String name)
Collection<ExpressionExperiment>	findUpdatedAfter(Date date)
Map<Long,Long>	getAnnotationCountsByIds(Collection<Long> ids)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperiment ee)	Retrieve annotations for a given experiment.
Set<AnnotationValueObject>	getAnnotations(ExpressionExperimentSubSet ee)	Retrieve annotations for a given experiment subset.
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	getAnnotationsUsageFrequency(Filters filters, Set<Long> extraIds, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, int minFrequency, Collection<String> retainedTermUris, int maxResults, boolean includePredicates, boolean includeObjects, long timeout, TimeUnit timeUnit)	Obtain annotation usage frequency for datasets matching the given filters.
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperiment expressionExperiment)
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Collection<ArrayDesign>	getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType)	Obtain a collection of ArrayDesign used by a specific set of vectors.
Map<ArrayDesign,Long>	getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)	Calculate the usage frequency of platforms by the datasets matching the provided filters.
BioAssayDimension	getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)
BioAssayDimension	getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId)	Find a BioAssayDimension by ID.
BioAssayDimension	getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)	Retrieve all the dimensions that are linked to the subsets of the given experiment.
Collection<BioAssayDimension>	getBioAssayDimensionsWithAssays(ExpressionExperiment ee, QuantitationType qt)	Obtain all BioAssayDimensions with their assays initialized as per Thaws.thawBioAssay(BioAssay) associated to a particular QuantitationType.
long	getBioMaterialCount(ExpressionExperiment expressionExperiment)
Map<Characteristic,Long>	getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)	Obtain category usage frequency for datasets matching the given filter.
Filters	getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)	Perform various transformation to the provided filters to enhance it.
Collection<ExpressionExperiment>	getExperimentsLackingPublications()
Collection<ExpressionExperiment>	getExperimentsWithOutliers()
Collection<Gene>	getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)	Retrieve the genes used by the preferred vectors of this experiment.
Map<Long,Date>	getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Date	getLastArrayDesignUpdate(ExpressionExperiment expressionExperiment)
Map<Long,AuditEvent>	getLastLinkAnalysis(Collection<Long> ids)
Map<Long,AuditEvent>	getLastMissingValueAnalysis(Collection<Long> ids)
Map<Long,AuditEvent>	getLastProcessedDataUpdate(Collection<Long> ids)
Map<BioAssay,Long>	getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)	Obtain the number of design elements for the platform of each bioassay in the given experiment.
Map<Taxon,Long>	getPerTaxonCount()
Map<Long,Long>	getPopulatedFactorCounts(Collection<Long> ids)
Map<Long,Long>	getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)
Optional<QuantitationType>	getPreferredQuantitationType(ExpressionExperiment ee)	Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.
Optional<Collection<ProcessedExpressionDataVector>>	getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<QuantitationType>	getProcessedQuantitationType(ExpressionExperiment ee)
Map<QuantitationType,Long>	getQuantitationTypeCount(ExpressionExperiment ee)
Collection<QuantitationType>	getQuantitationTypes(ExpressionExperiment expressionExperiment)	Retrieve all the quantitation types used by the given expression experiment.
Collection<QuantitationType>	getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Retrieve all the quantitation types used by the given experiment and dimension.
Collection<QuantitationType>	getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)
Map<Class<? extends DataVector>,Set<QuantitationType>>	getQuantitationTypesByVectorType(ExpressionExperiment ee)
Collection<QuantitationTypeValueObject>	getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)	Load all QuantitationType associated to an expression experiment as VOs.
long	getRawDataVectorCount(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Map<ExpressionExperiment,Collection<AuditEvent>>	getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
ExpressionExperimentSubSet	getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID.
Collection<ExpressionExperimentSubSet>	getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	getSubSetsByDimension(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<ExperimentalFactor,Map<FactorValue,ExpressionExperimentSubSet>>	getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment.
Map<FactorValue,ExpressionExperimentSubSet>	getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<FactorValue,ExpressionExperimentSubSet>	getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Collection<ExpressionExperimentSubSet>	getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset.
Map<ExpressionExperiment,Taxon>	getTaxa(Collection<ExpressionExperiment> ees)	Return the taxon for each of the given experiments.
Map<Taxon,Long>	getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)	Calculate the usage frequency of taxa by the datasets matching the provided filters.
Taxon	getTaxon(ExpressionExperiment expressionExperiment)	Returns the taxon of the given experiment or subset.
Map<TechnologyType,Long>	getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
boolean	hasProcessedExpressionData(ExpressionExperiment ee)	Test if the given experiment has processed data vectors.
boolean	isBlackListed(String geoAccession)
boolean	isRNASeq(ExpressionExperiment expressionExperiment)
boolean	isSingleCell(ExpressionExperiment ee)	Indicate if the given experiment is a single-cell experiment.
Boolean	isSuitableForDEA(ExpressionExperiment ee)
boolean	isTroubled(ExpressionExperiment expressionExperiment)	Check if the dataset is either troubled or uses a troubled platform.
SortedMap<String,String>	loadAllIdentifiersAndName(boolean includeNames)	Load all possible identifiers for experiments.
Collection<ExpressionExperiment>	loadAllReferences()	Load references for all experiments.
ExpressionExperiment	loadAndThaw(Long id)	Load an experiment and thaw it as per thaw(ExpressionExperiment).
ExpressionExperiment	loadAndThawLite(Long id)
<T extends Exception> ExpressionExperiment	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)	Load an experiment and thaw it as per thawLite(ExpressionExperiment) or fail with the supplied exception and message.
<T extends Exception> ExpressionExperiment	loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
ExpressionExperiment	loadAndThawLiteWithRefreshCacheMode(Long id)	Load an experiment without cache and thaw it as per thaw(ExpressionExperiment) with CacheMode.REFRESH.
<T extends Exception> ExpressionExperiment	loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)	Load an experiment and thaw it as per thawLite(ExpressionExperiment) or fail with the supplied exception and message.
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)
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIds(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<Long>	loadIdsWithCache(Filters filters, Sort sort)
Collection<ExpressionExperiment>	loadLackingFactors()
Collection<ExpressionExperiment>	loadLackingTags()
ExpressionExperiment	loadReference(Long id)
Collection<ExpressionExperiment>	loadReferences(Collection<Long> ids)	Load references for the given experiment IDs.
List<Long>	loadTroubledIds()	Load troubled experiment IDs.
List<ExpressionExperimentValueObject>	loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)	Variant of BaseVoEnabledService.loadValueObjectsByIds(Collection) that preserve its input order.
List<ExpressionExperimentValueObject>	loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)	Load VOs for the given dataset IDs and initialize their relations like SecurableFilteringVoEnabledService.load(Filters, Sort).
Slice<ExpressionExperimentValueObject>	loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
ExpressionExperiment	loadWithAuditTrail(Long id)	Load an experiment with its audit trail initialized.
ExpressionExperiment	loadWithCharacteristics(Long id)
ExpressionExperiment	loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	loadWithPrimaryPublication(Long id)
ExpressionExperiment	loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	reload(ExpressionExperiment ee)
int	removeAllRawDataVectors(ExpressionExperiment ee)
int	removeProcessedDataVectors(ExpressionExperiment ee)	Remove the processed data vectors for the given experiment.
int	removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
int	removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)	Used when we are replacing data, such as when converting an experiment from one platform to another.
int	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Replace the processed data vectors for the given experiment.
int	replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors)
ExpressionExperiment	thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	thawLiter(ExpressionExperiment expressionExperiment)
MeanVarianceRelation	updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
void	updateQuantitationType(ExpressionExperiment ee, QuantitationType qt)	Update a quantitation type.

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

countAll, getElementClass, loadOrFail, loadOrFail

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, create, findOrCreate, remove, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService

load, load, loadIds, loadValueObjects, loadValueObjects

Field Details

FREE_TEXT

static final String FREE_TEXT

Special indicator for free-text terms.

See Also:

• ExpressionExperimentDao.FREE_TEXT

UNCATEGORIZED

static final String UNCATEGORIZED

Special indicator for uncategorized terms.

See Also:

• ExpressionExperimentDao.UNCATEGORIZED

Method Details

loadReference

@Nonnull
ExpressionExperiment loadReference(Long id)

loadReferences

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

Load references for the given experiment IDs.

loadAllReferences

Collection<ExpressionExperiment> loadAllReferences()

Load references for all experiments.

References are pre-filtered for ACLs as per SecurableFilteringVoEnabledService.loadIds(Filters, Sort).

loadWithAuditTrail

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment loadWithAuditTrail(Long id)

Load an experiment with its audit trail initialized.

loadTroubledIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<Long> loadTroubledIds()

Load troubled experiment IDs.

See Also:

• CuratableDao.loadTroubledIds()

loadAllIdentifiersAndName

SortedMap<String,String> loadAllIdentifiersAndName(boolean includeNames)

Load all possible identifiers for experiments.

Parameters:

includeNames - if true, include experiment names as possible identifier

Returns:

a mapping of candidate identifier to experiment name

reload

ExpressionExperiment reload(ExpressionExperiment ee)

See Also:

• invalid reference

  ExpressionExperimentDao#reload(Object)

addFactor

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
ExperimentalFactor addFactor(ExpressionExperiment ee,
 ExperimentalFactor factor)

addFactorValue

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
FactorValue addFactorValue(ExpressionExperiment ee,
 FactorValue fv)

Parameters:

ee - experiment.

fv - must already have the experimental factor filled in.

addFactorValues

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void addFactorValues(ExpressionExperiment ee,
 Map<BioMaterial,FactorValue> fvs)

Intended with the case of a continuous factor being added.

getRawDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

See Also:

• ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment, QuantitationType)

getRawDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType qt)

See Also:

• ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment, List, QuantitationType)

addRawDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int addRawDataVectors(ExpressionExperiment eeToUpdate,
 QuantitationType quantitationType,
 Collection<RawExpressionDataVector> newVectors)

Used when we want to add data for a quantitation type. Does not remove any existing vectors.

Parameters:

eeToUpdate - experiment to be updated.

newVectors - vectors to be added.

Returns:

the number of added vectors

replaceRawDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int replaceRawDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<RawExpressionDataVector> vectors)

See Also:

• ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection)

replaceAllRawDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int replaceAllRawDataVectors(ExpressionExperiment ee,
 Collection<RawExpressionDataVector> vectors)

Used when we are replacing data, such as when converting an experiment from one platform to another. Examples would be exon array or RNA-seq data sets, or other situations where we are replacing data. Does not take care of computing the processed data vectors, but it does clear them out.

Parameters:

ee - experiment

vectors - If they are from more than one platform, that will be dealt with.

Returns:

the number of vectors replaced

removeAllRawDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int removeAllRawDataVectors(ExpressionExperiment ee)

See Also:

• ExpressionExperimentDao.removeAllRawDataVectors(ExpressionExperiment)

removeRawDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

See Also:

• ExpressionExperimentDao.removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean)

removeRawDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 boolean keepDimension)

See Also:

• ExpressionExperimentDao.removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean)

getProcessedDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<Collection<ProcessedExpressionDataVector>> getProcessedDataVectors(ExpressionExperiment ee)

Returns:

a collection of processed data vectors for the given experiment and list of assays, or Optional.empty() if there are no processed vectors

See Also:

• ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment)

getProcessedDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<Collection<ProcessedExpressionDataVector>> getProcessedDataVectors(ExpressionExperiment ee,
 List<BioAssay> assays)

Returns:

a collection of processed data vectors for the given experiment and list of assays, or Optional.empty() if there are no processed vectors

See Also:

• ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment, List)

createProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int createProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

Create a new set of processed vectors for an experiment.

You might actually want to use ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment, boolean, boolean) as this method is fairly low-level.

See Also:

• ExpressionExperimentDao.createProcessedDataVectors(ExpressionExperiment, Collection)

replaceProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int replaceProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

Replace the processed data vectors for the given experiment.

You might actually want to use ProcessedExpressionDataVectorService.replaceProcessedDataVectors(ExpressionExperiment, Collection, boolean) (ExpressionExperiment)}. as this method is fairly low-level.

See Also:

• ExpressionExperimentDao.replaceProcessedDataVectors(ExpressionExperiment, Collection)

removeProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int removeProcessedDataVectors(ExpressionExperiment ee)

Remove the processed data vectors for the given experiment.

You might actually want to use ProcessedExpressionDataVectorService.removeProcessedDataVectors(ExpressionExperiment). as this method is fairly low-level.

See Also:

• ExpressionExperimentDao.removeProcessedDataVectors(ExpressionExperiment)

browse

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
List<ExpressionExperiment> browse(int start,
 int limit)

filter

Collection<Long> filter(String searchString)
                 throws SearchException

returns ids of search results.

Parameters:

searchString - search string

Returns:

collection of ids or an empty collection.

Throws:

SearchException

filterByTaxon

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

Remove IDs of Experiments that are not from the given taxon.

Parameters:

ids - collection to purge.

taxon - taxon to retain.

Returns:

purged IDs.

loadWithCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment loadWithCharacteristics(Long id)

loadAndThawLiteOrFail

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier,
 String message)
                                                          throws T

Load an experiment and thaw it as per thawLite(ExpressionExperiment) or fail with the supplied exception and message.

Throws:

T

loadAndThawLiteOrFail

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                          throws T

Throws:

T

loadAndThawLiterOrFail

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> ExpressionExperiment loadAndThawLiterOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                           throws T

Throws:

T

loadAndThaw

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment loadAndThaw(Long id)

Load an experiment and thaw it as per thaw(ExpressionExperiment).

loadAndThawLite

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment loadAndThawLite(Long id)

loadAndThawLiteWithRefreshCacheMode

@Nullable
@Secured({"GROUP_ADMIN","AFTER_ACL_READ"})
ExpressionExperiment loadAndThawLiteWithRefreshCacheMode(Long id)

Load an experiment without cache and thaw it as per thaw(ExpressionExperiment) with CacheMode.REFRESH.

This has the side effect of refreshing the cache with the latest data. Since this can be expensive, only administrators are allowed to do this.

loadAndThawOrFail

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> ExpressionExperiment loadAndThawOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                      throws T

Load an experiment and thaw it as per thawLite(ExpressionExperiment) or fail with the supplied exception and message.

Throws:

T

loadIdsWithCache

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

countWithCache

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

loadValueObjectsWithCache

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Slice<ExpressionExperimentValueObject> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadWithPrimaryPublication

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment loadWithPrimaryPublication(Long id)

loadWithPrimaryPublicationAndOtherRelevantPublications

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)

loadWithMeanVarianceRelation

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment loadWithMeanVarianceRelation(Long id)

findByAccession

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)

Parameters:

accession - accession

Returns:

Experiments which have the given accession. There can be more than one, because one GEO accession can result in multiple experiments in Gemma.

findByAccession

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByAccession(String accession)

findOneByAccession

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment findOneByAccession(String accession)

findByBibliographicReference

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByBibliographicReference(BibliographicReference bibRef)

Parameters:

bibRef - bibliographic reference

Returns:

a collection of EE that have that reference that BibliographicReference

findByBioAssay

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByBioAssay(BioAssay ba)

Parameters:

ba - bio material

Returns:

experiment the given bioassay is associated with

findByBioMaterial

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm)

Parameters:

bm - bio material

Returns:

experiment the given biomaterial is associated with

findByBioMaterials

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Map<ExpressionExperiment,Collection<BioMaterial>> findByBioMaterials(Collection<BioMaterial> biomaterials)

findByExpressedGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByExpressedGene(Gene gene,
 double rank)

Parameters:

gene - gene

rank - rank

Returns:

a collection of expression experiment ids that express the given gene above the given expression level

findByDesign

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByDesign(ExperimentalDesign ed)

findByDesignId

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByDesignId(Long designId)

findByFactor

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByFactor(ExperimentalFactor factor)

findByFactors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByFactors(Collection<ExperimentalFactor> factors)

findByFactorValue

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByFactorValue(FactorValue factorValue)

findByFactorValue

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByFactorValue(Long factorValueId)

findByFactorValues

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByFactorValues(Collection<FactorValue> factorValues)

findByFactorValueIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByFactorValueIds(Collection<Long> factorValueIds)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByGene(Gene gene)

Parameters:

gene - gene

Returns:

a collection of expression experiments that have an AD that detects the given Gene (ie a probe on the AD hybridizes to the given Gene)

findByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByName(String name)

findOneByName

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment findOneByName(String name)

findByQuantitationType

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment findByQuantitationType(QuantitationType type)

findByShortName

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment findByShortName(String shortName)

findByShortNameAndThawLite

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ_QUIET"})
ExpressionExperiment findByShortNameAndThawLite(String shortName)

findByTaxon

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findByTaxon(Taxon taxon)

findByUpdatedLimit

@Secured({"GROUP_AGENT","AFTER_ACL_COLLECTION_READ"})
List<ExpressionExperiment> findByUpdatedLimit(int limit)

findUpdatedAfter

@Secured({"GROUP_AGENT","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> findUpdatedAfter(Date date)

getAnnotationCountsByIds

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

Parameters:

ids - ids

Returns:

the map of ids to number of terms associated with each expression experiment.

getAnnotations

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Set<AnnotationValueObject> getAnnotations(ExpressionExperiment ee)

Retrieve annotations for a given experiment.

The following are included:

• Experiment-level tags
• Experimental design tags
• Sample-level tags

getAnnotations

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Set<AnnotationValueObject> getAnnotations(ExpressionExperimentSubSet ee)

Retrieve annotations for a given experiment subset.

The following are included:

• Experiment-level tags
• Subset-level tags
• Experimental design tags minus the subset factor
• Sample-level tags for the samples within the subset

getEnhancedFilters

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

Perform various transformation to the provided filters to enhance it.

• rewrite clauses over objects and predicates to include second/third, etc... predicates/objects
• apply ontological inference to augment a filter with additional terms.

Parameters:

mentionedTerms - if non-null, all the terms explicitly mentioned in the filters are added to the collection.

inferredTerms - if non-null, all the terms inferred from those mentioned in the filters are added to the collection

Throws:

TimeoutException

getNumberOfDesignElementsPerSample

Map<BioAssay,Long> getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)

Obtain the number of design elements for the platform of each bioassay in the given experiment.

getCategoriesUsageFrequency

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

Obtain category usage frequency for datasets matching the given filter.

Parameters:

filters - filters restricting the terms to a given set of datasets

excludedCategoryUris - ensure that the given category URIs are excluded

excludedTermUris - ensure that the given term URIs and their sub-terms (as per subClassOf relation) are excluded; this requires relevant ontologies to be loaded in OntologyService.

retainedTermUris - ensure that the given terms are retained (overrides any exclusion from minFrequency and excludedTermUris)

maxResults - maximum number of results to return

getAnnotationsUsageFrequency

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

Obtain annotation usage frequency for datasets matching the given filters.

Terms may originate from the experiment tags, experimental design or samples.

The implementation uses a denormalized table for associating EEs to characteristics which is not always in sync if new terms are attached.

Parameters:

filters - filters restricting the terms to a given set of datasets

category - a category to restrict annotations to, or null to include all categories

excludedCategoryUris - ensure that the given category URIs are excluded

excludedTermUris - ensure that the given term URIs and their sub-terms (as per subClassOf relation) are excluded; this requires relevant ontologies to be loaded in OntologyService.

minFrequency - minimum occurrences of a term to be included in the results

retainedTermUris - ensure that the given terms are retained (overrides any exclusion from minFrequency and excludedTermUris)

maxResults - maximum number of results to return

includePredicates -

includeObjects -

Returns:

mapping annotations grouped by category and term (URI or value if null) to their number of occurrences in the matched datasets and ordered in descending number of associated experiments

Throws:

TimeoutException

See Also:

• ExpressionExperimentDao.getAnnotationsUsageFrequency(Collection, Class, int, int, String, Collection, Collection, Collection, boolean, boolean)

getArrayDesignsUsed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - experiment

Returns:

a collection of ArrayDesigns referenced by any of the BioAssays that make up the given ExpressionExperiment.

getArrayDesignsUsed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee,
 QuantitationType qt)

Obtain a collection of ArrayDesign used by a specific set of vectors.

The type of vectors is inferred.

See Also:

• getArrayDesignsUsed(ExpressionExperiment, QuantitationType, Class)

getArrayDesignsUsed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee,
 QuantitationType qt,
 Class<? extends DataVector> vectorType)

Obtain a collection of ArrayDesign used by a specific set of vectors.

getGenesUsedByPreferredVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<Gene> getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint)

Retrieve the genes used by the preferred vectors of this experiment.

getTechnologyTypeUsageFrequency

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

getArrayDesignUsedOrOriginalPlatformUsageFrequency

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

Calculate the usage frequency of platforms by the datasets matching the provided filters.

Parameters:

filters - a set of filters to be applied as per SecurableFilteringVoEnabledService.load(Filters, Sort, int, int)

maxResults - the maximum of results, or unlimited if less than 1

getTaxaUsageFrequency

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

Calculate the usage frequency of taxa by the datasets matching the provided filters.

If no filters are supplied (either being null or empty), the getPerTaxonCount() fast path is used.

See Also:

• getPerTaxonCount()

getBioAssayDimensions

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - experiment

Returns:

the BioAssayDimensions for the study.

getBioAssayDimensionsFromSubSets

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioAssayDimension> getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment)

Retrieve all the dimensions that are linked to the subsets of the given experiment.

getBioAssayDimension

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioAssayDimension getBioAssayDimension(ExpressionExperiment ee,
 QuantitationType qt,
 Class<? extends BulkExpressionDataVector> dataVectorType)

getBioAssayDimension

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioAssayDimension getBioAssayDimension(ExpressionExperiment ee,
 QuantitationType qt)

getBioAssayDimensionsWithAssays

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioAssayDimension> getBioAssayDimensionsWithAssays(ExpressionExperiment ee,
 QuantitationType qt)

Obtain all BioAssayDimensions with their assays initialized as per Thaws.thawBioAssay(BioAssay) associated to a particular QuantitationType.

In some special edge cases, a QuantitationType may have more than one BioAssayDimension.

getBioAssayDimensionById

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioAssayDimension getBioAssayDimensionById(ExpressionExperiment ee,
 Long dimensionId,
 Class<? extends BulkExpressionDataVector> dataVectorType)

getBioAssayDimensionById

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioAssayDimension getBioAssayDimensionById(ExpressionExperiment ee,
 Long dimensionId)

Find a BioAssayDimension by ID.

This is less efficient than getBioAssayDimensionById(ExpressionExperiment, Long, Class) because all bulk vector types need to be inspected.

getBioMaterialCount

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long getBioMaterialCount(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - experiment

Returns:

the amount of biomaterials associated with the given expression experiment.

getRawDataVectorCount

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long getRawDataVectorCount(ExpressionExperiment ee)

getExperimentsWithOutliers

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> getExperimentsWithOutliers()

getLastArrayDesignUpdate

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)

getLastArrayDesignUpdate

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Date getLastArrayDesignUpdate(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - experiment

Returns:

the date of the last time any of the array designs associated with this experiment were updated.

getLastLinkAnalysis

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

Parameters:

ids - ids

Returns:

AuditEvents of the latest link analyses for the specified expression experiment ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.

getLastMissingValueAnalysis

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

Parameters:

ids - ids

Returns:

AuditEvents of the latest missing value analysis for the specified expression experiment ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.

getLastProcessedDataUpdate

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

Parameters:

ids - ids

Returns:

AuditEvents of the latest rank computation for the specified expression experiment ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

Returns:

counts of expression experiments grouped by taxon

getPopulatedFactorCounts

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

Parameters:

ids - ids

Returns:

map of ids to how many factor values the experiment has, counting only factor values which are associated with biomaterials.

getPopulatedFactorCountsExcludeBatch

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

Parameters:

ids - ids

Returns:

map of ids to how many factor values the experiment has, counting only factor values which are associated with biomaterials and only factors that aren't batch

getPreferredQuantitationType

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<QuantitationType> getPreferredQuantitationType(ExpressionExperiment ee)

Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.

Parameters:

ee - experiment

Returns:

quantitation types

getProcessedQuantitationType

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<QuantitationType> getProcessedQuantitationType(ExpressionExperiment ee)

hasProcessedExpressionData

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
boolean hasProcessedExpressionData(ExpressionExperiment ee)

Test if the given experiment has processed data vectors.

getQuantitationTypeCount

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<QuantitationType,Long> getQuantitationTypeCount(ExpressionExperiment ee)

Returns:

counts design element data vectors grouped by quantitation type

getQuantitationTypes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<QuantitationType> getQuantitationTypes(ExpressionExperiment expressionExperiment)

Retrieve all the quantitation types used by the given expression experiment.

See Also:

• QuantitationTypeDao.findByExpressionExperiment(ExpressionExperiment)

getQuantitationTypesByVectorType

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<Class<? extends DataVector>,Set<QuantitationType>> getQuantitationTypesByVectorType(ExpressionExperiment ee)

getQuantitationTypes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<QuantitationType> getQuantitationTypes(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Retrieve all the quantitation types used by the given experiment and dimension.

getQuantitationTypes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<QuantitationType> getQuantitationTypes(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension,
 Class<? extends BulkExpressionDataVector> dataVectorType)

getQuantitationTypeValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<QuantitationTypeValueObject> getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment)

Load all QuantitationType associated to an expression experiment as VOs.

See Also:

• getQuantitationTypes(ExpressionExperiment)

getSampleRemovalEvents

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_MAP_READ"})
Map<ExpressionExperiment,Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)

getSubSetsWithBioAssays

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ExpressionExperimentSubSet> getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)

Obtain all the subsets for a given dataset.

getSubSetsWithCharacteristics

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ExpressionExperimentSubSet> getSubSetsWithCharacteristics(ExpressionExperiment ee)

Obtain all the subsets for a given dataset.

Subsets characteristics are initialized and assays are thawed as per Thaws.thawBioAssay(BioAssay).

getSubSetsByDimension

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>> getSubSetsByDimension(ExpressionExperiment expressionExperiment)

Obtain all the subsets organized by dimension for a given dataset.

getSubSetsByDimensionWithBioAssays

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>> getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)

Obtain all the subsets organized by dimension for a given dataset.

Assays are thawed as per Thaws.thawBioAssay(BioAssay).

getSubSets

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Obtain the subsets for a particular dimension.

getSubSetsWithBioAssays

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ExpressionExperimentSubSet> getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Obtain the subsets for a particular dimension.

Assays are lightly thawed.

getSubSetsByFactorValue

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<ExperimentalFactor,Map<FactorValue,ExpressionExperimentSubSet>> getSubSetsByFactorValue(ExpressionExperiment expressionExperiment,
 BioAssayDimension dimension)

Reconstitute the FV to subset mapping for a given experiment.

This will generally return a single factor that was used for splitting the dataset. However, if there are confounding factors, those will be returned as well.

getSubSetsByFactorValue

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<FactorValue,ExpressionExperimentSubSet> getSubSetsByFactorValue(ExpressionExperiment expressionExperiment,
 ExperimentalFactor experimentalFactor,
 BioAssayDimension dimension)

Reconstitute the FV to subset mapping for a given experiment and factor.

getSubSetsByFactorValueWithCharacteristicsAndBioAssays

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<FactorValue,ExpressionExperimentSubSet> getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment,
 ExperimentalFactor experimentalFactor,
 BioAssayDimension dimension)

Reconstitute the FV to subset mapping for a given experiment and factor.

Subsets characteristics are initialized and assays are thawed as per Thaws.thawBioAssay(BioAssay).

getSubSetByIdWithCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ExpressionExperimentSubSet getSubSetByIdWithCharacteristics(ExpressionExperiment ee,
 Long subSetId)

getSubSetByIdWithCharacteristicsAndBioAssays

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ExpressionExperimentSubSet getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee,
 Long subSetId)

Obtain a particular subset by ID.

Subsets characteristics are initialized and assays are thawed as per Thaws.thawBioAssay(BioAssay).

getTaxa

Map<ExpressionExperiment,Taxon> getTaxa(Collection<ExpressionExperiment> ees)

Return the taxon for each of the given experiments.

getTaxon

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Taxon getTaxon(ExpressionExperiment expressionExperiment)

Returns the taxon of the given experiment or subset.

Parameters:

bioAssaySet - bioAssaySet.

Returns:

taxon, or null if the experiment taxon cannot be determined (i.e., if it has no samples).

isSingleCell

boolean isSingleCell(ExpressionExperiment ee)

Indicate if the given experiment is a single-cell experiment.

Gemma does not treat single-cell experiments differently from other experiments, so we need to rely on various aspect of the dataset to determine if it is a single-cell experiment.

isRNASeq

boolean isRNASeq(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - ee

Returns:

true if this experiment was run on a sequencing-based platform.

isTroubled

boolean isTroubled(ExpressionExperiment expressionExperiment)

Check if the dataset is either troubled or uses a troubled platform.

loadDetailsValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjects(Collection<Long> ids,
 @Nullable
 Taxon taxon,
 @Nullable
 Sort sort,
 int offset,
 int limit)

See Also:

• ExpressionExperimentDao.loadDetailsValueObjects(Collection, Taxon, Sort, int, int)

loadDetailsValueObjectsWithCache

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsWithCache(Collection<Long> ids,
 @Nullable
 Taxon taxon,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadDetailsValueObjectsByIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(Collection<Long> ids)

loadDetailsValueObjectsByIdsWithCache

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)

loadBlacklistedValueObjects

@Secured({"GROUP_ADMIN","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Slice<ExpressionExperimentValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

loadLackingFactors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> loadLackingFactors()

loadLackingTags

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> loadLackingTags()

loadValueObjectsByIdsWithRelationsAndCache

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<ExpressionExperimentValueObject> loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)

Load VOs for the given dataset IDs and initialize their relations like SecurableFilteringVoEnabledService.load(Filters, Sort).

The order of VOs is preserved.

loadValueObjectsByIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<ExpressionExperimentValueObject> loadValueObjectsByIds(List<Long> ids,
 boolean maintainOrder)

Variant of BaseVoEnabledService.loadValueObjectsByIds(Collection) that preserve its input order.

Parameters:

ids - ids to load

maintainOrder - If true, order of valueObjects returned will correspond to order of ids passed in.

Returns:

value objects

addCharacteristic

void addCharacteristic(ExpressionExperiment ee,
 Characteristic vc)

Will add the vocab characteristic to the expression experiment and persist the changes.

Parameters:

ee - the experiment to add the characteristics to.

vc - If the evidence code is null, it will be filled in with IC. A category and value must be provided.

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ExpressionExperiment thaw(ExpressionExperiment expressionExperiment)

See Also:

• ExpressionExperimentDao.thaw(ExpressionExperiment)

thawLiter

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ExpressionExperiment thawLiter(ExpressionExperiment expressionExperiment)

See Also:

• ExpressionExperimentDao.thawLiter(ExpressionExperiment)

thawLite

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ExpressionExperiment thawLite(ExpressionExperiment expressionExperiment)

See Also:

• ExpressionExperimentDao.thawLite(ExpressionExperiment)

isBlackListed

boolean isBlackListed(String geoAccession)

isSuitableForDEA

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Boolean isSuitableForDEA(ExpressionExperiment ee)

Returns:

true if the experiment is not explicitly marked as unsuitable for DEA; false otherwise.

getExperimentsLackingPublications

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ExpressionExperiment> getExperimentsLackingPublications()

Returns:

collection of GEO experiments which lack an association with a publication (non-GEO experiments will be ignored)

updateQuantitationType

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void updateQuantitationType(ExpressionExperiment ee,
 QuantitationType qt)

Update a quantitation type.

If the provided QT is preferred (i.e. either single-cell, raw or processed), all other QTs in the experiment for that type of vectors will be set to non-preferred.

See Also:

• QuantitationTypeService.update(QuantitationType)

updateMeanVarianceRelation

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
 MeanVarianceRelation mvr)

countBioMaterials

long countBioMaterials(@Nullable
 Filters filters)

See Also:

• ExpressionExperimentDao.countBioMaterials(Filters)