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
- Author:
- kelsey
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic final class -
Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionvoidWill add the vocab characteristic to the expression experiment and persist the changes.addFactor(ExpressionExperiment ee, ExperimentalFactor factor) voidIntended with the case of a continuous factor being added.intaddRawDataVectors(ExpressionExperiment eeToUpdate, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors) Used when we want to add data for a quantitation type.browse(int start, int limit) longcountBioMaterials(Filters filters) longcountWithCache(Filters filters, Set<Long> extraIds) intcreateProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors) Create a new set of processed vectors for an experiment.returns ids of search results.filterByTaxon(Collection<Long> ids, Taxon taxon) Remove IDs of Experiments that are not from the given taxon.findByAccession(String accession) findByAccession(DatabaseEntry accession) findByBioMaterials(Collection<BioMaterial> biomaterials) findByDesignId(Long designId) findByExpressedGene(Gene gene, double rank) findByFactor(ExperimentalFactor factor) findByFactors(Collection<ExperimentalFactor> factors) findByFactorValue(Long factorValueId) findByFactorValue(FactorValue factorValue) findByFactorValueIds(Collection<Long> factorValueIds) findByFactorValues(Collection<FactorValue> factorValues) findByGene(Gene gene) findByName(String name) findByShortName(String shortName) findByShortNameAndThawLite(String shortName) findByTaxon(Taxon taxon) findByUpdatedLimit(int limit) findOneByAccession(String accession) findOneByName(String name) findUpdatedAfter(Date date) Retrieve annotations for a given experiment.Retrieve annotations for a given experiment subset.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.getArrayDesignsUsed(ExpressionExperiment expressionExperiment) Obtain a collection ofArrayDesignused by a specific set of vectors.getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType) Obtain a collection ofArrayDesignused by a specific set of vectors.getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults) Calculate the usage frequency of platforms by the datasets matching the provided filters.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType) getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId) Find aBioAssayDimensionby ID.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType) getBioAssayDimensions(ExpressionExperiment expressionExperiment) getBioAssayDimensionsFromSubSets(ExpressionExperiment expressionExperiment) Retrieve all the dimensions that are linked to the subsets of the given experiment.Obtain allBioAssayDimensions with their assays initialized as perThaws.thawBioAssay(BioAssay)associated to a particularQuantitationType.longgetBioMaterialCount(ExpressionExperiment expressionExperiment) 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.getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit) Perform various transformation to the provided filters to enhance it.getGenesUsedByPreferredVectors(ExpressionExperiment experimentConstraint) Retrieve the genes used by the preferred vectors of this experiment.getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments) getLastArrayDesignUpdate(ExpressionExperiment expressionExperiment) getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment) Obtain the number of design elements for the platform of each bioassay in the given experiment.Iterates over the quantitation types for a given expression experiment and returns the preferred quantitation types.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays) getQuantitationTypes(ExpressionExperiment expressionExperiment) Retrieve all the quantitation types used by the given expression experiment.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension) Retrieve all the quantitation types used by the given experiment and dimension.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType) Map<Class<? extends DataVector>, Set<QuantitationType>> getQuantitationTypeValueObjects(ExpressionExperiment expressionExperiment) Load allQuantitationTypeassociated to an expression experiment as VOs.longgetRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt) getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments) getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId) Obtain a particular subset by ID.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension) Obtain the subsets for a particular dimension.getSubSetsByDimension(ExpressionExperiment expressionExperiment) Obtain all the subsets organized by dimension for a given dataset.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment) Obtain all the subsets organized by dimension for a given dataset.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension) Reconstitute the FV to subset mapping for a given experiment.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension) Reconstitute the FV to subset mapping for a given experiment and factor.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension) Reconstitute the FV to subset mapping for a given experiment and factor.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment) Obtain all the subsets for a given dataset.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension) Obtain the subsets for a particular dimension.Obtain all the subsets for a given dataset.Return the taxon for each of the given experiments.getTaxaUsageFrequency(Filters filters, Set<Long> extraIds) Calculate the usage frequency of taxa by the datasets matching the provided filters.getTaxon(ExpressionExperiment expressionExperiment) Returns the taxon of the given experiment or subset.getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds) booleanTest if the given experiment has processed data vectors.booleanisBlackListed(String geoAccession) booleanisRNASeq(ExpressionExperiment expressionExperiment) booleanIndicate if the given experiment is a single-cell experiment.booleanisTroubled(ExpressionExperiment expressionExperiment) Check if the dataset is either troubled or uses a troubled platform.loadAllIdentifiersAndName(boolean includeNames) Load all possible identifiers for experiments.Load references for all experiments.loadAndThaw(Long id) Load an experiment and thaw it as perthaw(ExpressionExperiment).loadAndThawLite(Long id) <T extends Exception>
ExpressionExperimentloadAndThawLiteOrFail(Long id, Function<String, T> exceptionSupplier) <T extends Exception>
ExpressionExperimentloadAndThawLiteOrFail(Long id, Function<String, T> exceptionSupplier, String message) Load an experiment and thaw it as perthawLite(ExpressionExperiment)or fail with the supplied exception and message.<T extends Exception>
ExpressionExperimentloadAndThawLiterOrFail(Long id, Function<String, T> exceptionSupplier) Load an experiment without cache and thaw it as perthaw(ExpressionExperiment)withCacheMode.REFRESH.<T extends Exception>
ExpressionExperimentloadAndThawOrFail(Long id, Function<String, T> exceptionSupplier) Load an experiment and thaw it as perthawLite(ExpressionExperiment)or fail with the supplied exception and message.loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit) loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) loadIdsWithCache(Filters filters, Sort sort) loadReference(Long id) loadReferences(Collection<Long> ids) Load references for the given experiment IDs.Load troubled experiment IDs.loadValueObjectsByIds(List<Long> ids, boolean maintainOrder) Variant ofBaseVoEnabledService.loadValueObjectsByIds(Collection)that preserve its input order.Load VOs for the given dataset IDs and initialize their relations likeSecurableFilteringVoEnabledService.load(Filters, Sort).loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit) Load an experiment with its audit trail initialized.intintRemove the processed data vectors for the given experiment.intintremoveRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension) intUsed when we are replacing data, such as when converting an experiment from one platform to another.intreplaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors) Replace the processed data vectors for the given experiment.intreplaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors) thaw(ExpressionExperiment expressionExperiment) thawLite(ExpressionExperiment expressionExperiment) thawLiter(ExpressionExperiment expressionExperiment) voidUpdate a quantitation type.Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll, getElementClass, loadOrFail, loadOrFailMethods inherited from interface ubic.gemma.persistence.service.FilteringService
count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubqueryMethods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService
create, create, findOrCreate, remove, remove, removeMethods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService
find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAllMethods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService
save, save, update, updateMethods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIdsMethods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService
load, load, loadIds, loadValueObjects, loadValueObjects
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Field Details
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FREE_TEXT
Special indicator for free-text terms.- See Also:
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UNCATEGORIZED
Special indicator for uncategorized terms.- See Also:
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Method Details
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loadReference
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loadReferences
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
Load troubled experiment IDs.- See Also:
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loadAllIdentifiersAndName
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
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reload
- See Also:
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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.
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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:
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getRawDataVectors
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt) - See Also:
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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
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replaceRawDataVectors
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) int replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors) - See Also:
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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- experimentvectors- If they are from more than one platform, that will be dealt with.- Returns:
- the number of vectors replaced
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removeAllRawDataVectors
- See Also:
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removeRawDataVectors
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) int removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt) - See Also:
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removeRawDataVectors
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) int removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension) - See Also:
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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:
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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:
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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:
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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:
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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:
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browse
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) List<ExpressionExperiment> browse(int start, int limit) -
filter
returns ids of search results.- Parameters:
searchString- search string- Returns:
- collection of ids or an empty collection.
- Throws:
SearchException
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filterByTaxon
Remove IDs of Experiments that are not from the given taxon.- Parameters:
ids- collection to purge.taxon- taxon to retain.- Returns:
- purged IDs.
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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 TLoad an experiment and thaw it as perthawLite(ExpressionExperiment)or fail with the supplied exception and message.- Throws:
T
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loadAndThawLiteOrFail
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) <T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id, Function<String, T> exceptionSupplier) throws T- Throws:
T
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loadAndThawLiterOrFail
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) <T extends Exception> ExpressionExperiment loadAndThawLiterOrFail(Long id, Function<String, T> exceptionSupplier) throws T- Throws:
T
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loadAndThaw
@Nullable @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) ExpressionExperiment loadAndThaw(Long id) Load an experiment and thaw it as perthaw(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 perthaw(ExpressionExperiment)withCacheMode.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.
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loadAndThawOrFail
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) <T extends Exception> ExpressionExperiment loadAndThawOrFail(Long id, Function<String, T> exceptionSupplier) throws TLoad an experiment and thaw it as perthawLite(ExpressionExperiment)or fail with the supplied exception and message.- Throws:
T
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loadIdsWithCache
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countWithCache
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loadValueObjectsWithCache
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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.
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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
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findByBioAssay
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"}) ExpressionExperiment findByBioAssay(BioAssay ba) - Parameters:
ba- bio material- Returns:
- experiment the given bioassay is associated with
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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
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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- generank- rank- Returns:
- a collection of expression experiment ids that express the given gene above the given expression level
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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)
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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
- Parameters:
ids- ids- Returns:
- the map of ids to number of terms associated with each expression experiment.
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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
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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
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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
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getNumberOfDesignElementsPerSample
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 datasetsexcludedCategoryUris- ensure that the given category URIs are excludedexcludedTermUris- ensure that the given term URIs and their sub-terms (as persubClassOfrelation) are excluded; this requires relevant ontologies to be loaded inOntologyService.retainedTermUris- ensure that the given terms are retained (overrides any exclusion from minFrequency and excludedTermUris)maxResults- maximum number of results to return
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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 datasetscategory- a category to restrict annotations to, or null to include all categoriesexcludedCategoryUris- ensure that the given category URIs are excludedexcludedTermUris- ensure that the given term URIs and their sub-terms (as persubClassOfrelation) are excluded; this requires relevant ontologies to be loaded inOntologyService.minFrequency- minimum occurrences of a term to be included in the resultsretainedTermUris- ensure that the given terms are retained (overrides any exclusion from minFrequency and excludedTermUris)maxResults- maximum number of results to returnincludePredicates-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:
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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.
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getArrayDesignsUsed
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt) Obtain a collection ofArrayDesignused by a specific set of vectors.The type of vectors is inferred.
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getArrayDesignsUsed
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Collection<ArrayDesign> getArrayDesignsUsed(ExpressionExperiment ee, QuantitationType qt, Class<? extends DataVector> vectorType) Obtain a collection ofArrayDesignused 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
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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 perSecurableFilteringVoEnabledService.load(Filters, Sort, int, int)maxResults- the maximum of results, or unlimited if less than 1
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getTaxaUsageFrequency
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:
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getBioAssayDimensions
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment) - Parameters:
expressionExperiment- experiment- Returns:
- the BioAssayDimensions for the study.
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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 allBioAssayDimensions with their assays initialized as perThaws.thawBioAssay(BioAssay)associated to a particularQuantitationType.In some special edge cases, a
QuantitationTypemay have more than oneBioAssayDimension. -
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 aBioAssayDimensionby 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.
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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.
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getLastLinkAnalysis
- 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.
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getLastMissingValueAnalysis
- 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.
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getLastProcessedDataUpdate
- 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.
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getPerTaxonCount
- Returns:
- counts of expression experiments grouped by taxon
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getPopulatedFactorCounts
- Parameters:
ids- ids- Returns:
- map of ids to how many factor values the experiment has, counting only factor values which are associated with biomaterials.
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getPopulatedFactorCountsExcludeBatch
- 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
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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
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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
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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:
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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 allQuantitationTypeassociated to an expression experiment as VOs.- See Also:
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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.
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getSubSetsByFactorValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) Map<ExperimentalFactor,Map<FactorValue, getSubSetsByFactorValueExpressionExperimentSubSet>> (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.
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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
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).
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isSingleCell
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.
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isRNASeq
- Parameters:
expressionExperiment- ee- Returns:
- true if this experiment was run on a sequencing-based platform.
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isTroubled
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:
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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
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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 likeSecurableFilteringVoEnabledService.load(Filters, Sort).The order of VOs is preserved.
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loadValueObjectsByIds
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"}) List<ExpressionExperimentValueObject> loadValueObjectsByIds(List<Long> ids, boolean maintainOrder) Variant ofBaseVoEnabledService.loadValueObjectsByIds(Collection)that preserve its input order.- Parameters:
ids- ids to loadmaintainOrder- If true, order of valueObjects returned will correspond to order of ids passed in.- Returns:
- value objects
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addCharacteristic
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.
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thaw
@CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) ExpressionExperiment thaw(ExpressionExperiment expressionExperiment) - See Also:
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thawLiter
@CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) ExpressionExperiment thawLiter(ExpressionExperiment expressionExperiment) - See Also:
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thawLite
@CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) ExpressionExperiment thawLite(ExpressionExperiment expressionExperiment) - See Also:
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isBlackListed
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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.
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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)
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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.
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updateMeanVarianceRelation
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"}) MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr) -
countBioMaterials
- See Also:
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