Class ExpressionExperimentReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentReadServiceImpl

All Implemented Interfaces:

ExpressionExperimentReadService

@Service("expressionExperimentReadService")
public class ExpressionExperimentReadServiceImpl
extends Object
implements ExpressionExperimentReadService

Implementation of ExpressionExperimentReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade ExpressionExperimentService interface — this class is unsecured at the AOP boundary on purpose, so that intra-gemma-core callers that hold an authenticated session can bypass duplicate ACL checks.

See Also:

• ExpressionExperimentService

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentReadServiceImpl(ExpressionExperimentDao expressionExperimentDao)

Method Summary

Modifier and Type	Method	Description
List<ExpressionExperiment>	browse(int start, int limit)
long	countBioMaterials(Filters filters)
long	countWithCache(Filters filters, Set<Long> extraIds)
boolean	existsByShortName(String shortName)
Collection<Long>	filter(String searchString)	returns ids of search results
Collection<Long>	filterByTaxon(Collection<Long> ids, Taxon taxon)
Collection<ExpressionExperiment>	findByAccession(String accession)
Collection<ExpressionExperiment>	findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	findByBibliographicReference(BibliographicReference bibRef)
ExpressionExperiment	findByBioAssay(BioAssay ba)
ExpressionExperiment	findByBioAssay(BioAssay ba, boolean includeSubSets)
Collection<ExpressionExperiment>	findByBioMaterial(BioMaterial bm)
Collection<ExpressionExperiment>	findByBioMaterial(BioMaterial bm, boolean includeSubSets)
Map<ExpressionExperiment, Collection<BioMaterial>>	findByBioMaterials(Collection<BioMaterial> biomaterials)
ExpressionExperiment	findByDesign(ExperimentalDesign ed)
ExpressionExperiment	findByDesignId(Long designId)
Collection<ExpressionExperiment>	findByExpressedGene(Gene gene, double rank)
ExpressionExperiment	findByFactor(ExperimentalFactor factor)
Collection<ExpressionExperiment>	findByFactors(Collection<ExperimentalFactor> factors)
ExpressionExperiment	findByFactorValue(FactorValue factorValue)
ExpressionExperiment	findByFactorValueId(Long factorValueId)
Collection<ExpressionExperiment>	findByFactorValueIds(Collection<Long> factorValueIds)
Collection<ExpressionExperiment>	findByFactorValues(Collection<FactorValue> factorValues)
Collection<ExpressionExperiment>	findByGene(Gene gene)
ExpressionExperiment	findByMeanVarianceRelation(MeanVarianceRelation mvr)
Collection<ExpressionExperiment>	findByName(String name)
ExpressionExperiment	findByQuantitationType(QuantitationType type)
ExpressionExperiment	findByShortName(String shortName)
ExpressionExperiment	findByShortNameAndThawLite(String shortName)
ExpressionExperiment	findByShortNameWithPrimaryPublication(String shortName)
Collection<ExpressionExperiment>	findByTaxon(Taxon taxon)
List<ExpressionExperiment>	findByUpdatedLimit(int limit)
Long	findIdByBioAssay(BioAssay ba, boolean includeSubSets)
Long	findIdByDesign(ExperimentalDesign design)
Long	findIdByFactor(ExperimentalFactor factor)
Long	findIdByFactorValue(FactorValue factorValue)
Long	findIdByMeanVarianceRelation(MeanVarianceRelation mvr)
Collection<Long>	findIdsByBioMaterial(BioMaterial bm, boolean includeSubSets)
ExpressionExperiment	findOneByAccession(String accession)
ExpressionExperiment	findOneByName(String name)
Collection<ExpressionExperiment>	findUpdatedAfter(Date date)
Map<Long,Long>	getAnnotationCountsByIds(Collection<Long> ids)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperiment expressionExperiment)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperiment expressionExperiment, boolean includeFreeText)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
List<ExpressionExperimentService.CharacteristicWithUsageStatisticsAndOntologyTerm>	getAnnotationsUsageFrequency(Filters filters, Set<Long> extraIds, String category, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, int minFrequency, Collection<String> retainedTermUris, int maxResults, boolean includePredicates, boolean includeObjects, long timeout, TimeUnit timeUnit)	If the term cannot be resolved via OntologyService.getTerm(String, long, TimeUnit), an attempt is done to resolve its category and assign it as its parent.
Map<ArrayDesign, Long>	getArrayDesignUsedOrOriginalPlatformUsageFrequency(Filters filters, Set<Long> extraIds, int maxResults)
long	getBioMaterialCount(ExpressionExperiment expressionExperiment)
Map<Characteristic, Long>	getCategoriesUsageFrequency(Filters filters, Set<Long> extraIds, Collection<String> excludedCategoryUris, Collection<String> excludedTermUris, Collection<String> retainedTermUris, int maxResults)
Filters	getEnhancedFilters(Filters f, Collection<OntologyTerm> mentionedTerms, Collection<OntologyTerm> inferredTerms, long timeout, TimeUnit timeUnit)
ExperimentalDesignValueObject	getExperimentalDesignValueObject(ExpressionExperiment ee)
Collection<ExpressionExperiment>	getExperimentsWithOutliers()
Map<Long,Date>	getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Date	getLastArrayDesignUpdate(ExpressionExperiment ee)
Map<Long, AuditEvent>	getLastLinkAnalysis(Collection<Long> ids)
Map<Long, AuditEvent>	getLastMissingValueAnalysis(Collection<Long> ids)
Map<Long, AuditEvent>	getLastProcessedDataUpdate(Collection<Long> ids)
Map<BioAssay,Long>	getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)
Map<Taxon,Long>	getPerTaxonCount()
Map<Long,Long>	getPopulatedFactorCounts(Collection<Long> ids)
Map<Long,Long>	getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)
long	getRawDataVectorCount(ExpressionExperiment ee)
Map<ExpressionExperiment, Collection<AuditEvent>>	getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Map<Taxon,Long>	getTaxaUsageFrequency(Filters filters, Set<Long> extraIds)
Taxon	getTaxon(ExpressionExperiment ee)	Included for cycle-break parity with the facade: the only read-method back-edge from ExpressionExperimentSetServiceImpl is getTaxon.
Map<TechnologyType, Long>	getTechnologyTypeUsageFrequency(Filters filters, Set<Long> extraIds)
SortedMap<String,String>	loadAllIdentifiersAndName(boolean includeNames)
Collection<ExpressionExperiment>	loadAllReferences()
ExpressionExperiment	loadAndThaw(Long id)
ExpressionExperiment	loadAndThawLite(Long id)
<T extends Exception> ExpressionExperiment	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier)
<T extends Exception> ExpressionExperiment	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
<T extends Exception> ExpressionExperiment	loadAndThawLiterOrFail(Long id, Function<String,T> exceptionSupplier)
ExpressionExperiment	loadAndThawLiteWithRefreshCacheMode(Long id)
<T extends Exception> ExpressionExperiment	loadAndThawOrFail(Long id, Function<String,T> exceptionSupplier)
Slice<ExpressionExperimentValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ExpressionExperimentValueObject>	loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ExpressionExperimentReadService.loadBlacklistedValueObjects(Filters, Sort, int, int).
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjects(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIds(Collection<Long> ids)
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsWithCache(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit)
List<ExpressionExperimentDao.Identifiers>	loadIdentifiers(Collection<Long> ids)	Resolve the short name and name of the given experiments, for callers that hold ids and need something a person can read.
List<Long>	loadIdsWithCache(Filters filters, Sort sort)
Collection<ExpressionExperiment>	loadLackingFactors()
Collection<ExpressionExperiment>	loadLackingTags()
ExpressionExperiment	loadReference(Long id)
Collection<ExpressionExperiment>	loadReferences(Collection<Long> ids)
List<Long>	loadTroubledIds()
List<ExpressionExperimentValueObject>	loadValueObjectsByIds(List<Long> ids, boolean maintainOrder)
List<ExpressionExperimentValueObject>	loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)
Slice<ExpressionExperimentValueObject>	loadValueObjectsWithCache(Filters filters, Sort sort, int offset, int limit)
ExpressionExperiment	loadWithAuditTrail(Long id)
ExpressionExperiment	loadWithCharacteristics(Long id)
ExpressionExperiment	loadWithMeanVarianceRelation(Long id)
ExpressionExperiment	loadWithPrimaryPublication(Long id)
ExpressionExperiment	loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)
ExpressionExperiment	reload(ExpressionExperiment ee)
ExpressionExperiment	thaw(ExpressionExperiment expressionExperiment)
ExpressionExperiment	thawBioAssays(ExpressionExperiment expressionExperiment)	Narrow thaw used by the /samples REST endpoint: initializes only the bioAssays collection and applies Thaws.thawBioAssay(BioAssay) to each assay (which warms the array design, original platform, and biomaterial-with-factor-values shape that BioAssayValueObject reads).
ExpressionExperiment	thawLite(ExpressionExperiment expressionExperiment)
ExpressionExperiment	thawLiter(ExpressionExperiment expressionExperiment)

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ExpressionExperimentReadServiceImpl

@Autowired
public ExpressionExperimentReadServiceImpl(ExpressionExperimentDao expressionExperimentDao)

Method Details

loadReference

@Nonnull
@Transactional(readOnly=true)
public ExpressionExperiment loadReference(Long id)

Specified by:

loadReference in interface ExpressionExperimentReadService

loadReferences

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> loadReferences(Collection<Long> ids)

Specified by:

loadReferences in interface ExpressionExperimentReadService

loadAllReferences

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> loadAllReferences()

Specified by:

loadAllReferences in interface ExpressionExperimentReadService

loadWithAuditTrail

@Transactional(readOnly=true)
public ExpressionExperiment loadWithAuditTrail(Long id)

Specified by:

loadWithAuditTrail in interface ExpressionExperimentReadService

loadTroubledIds

@Transactional(readOnly=true)
public List<Long> loadTroubledIds()

Specified by:

loadTroubledIds in interface ExpressionExperimentReadService

loadIdentifiers

@Transactional(readOnly=true)
public List<ExpressionExperimentDao.Identifiers> loadIdentifiers(Collection<Long> ids)

Description copied from interface: ExpressionExperimentReadService

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

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

Specified by:

loadIdentifiers in interface ExpressionExperimentReadService

See Also:

• ExpressionExperimentDao.loadIdentifiers(Collection)

loadAllIdentifiersAndName

@Transactional(readOnly=true)
public SortedMap<String,String> loadAllIdentifiersAndName(boolean includeNames)

Specified by:

loadAllIdentifiersAndName in interface ExpressionExperimentReadService

reload

@Transactional(readOnly=true)
public ExpressionExperiment reload(ExpressionExperiment ee)

Specified by:

reload in interface ExpressionExperimentReadService

loadWithPrimaryPublication

@Transactional(readOnly=true)
public ExpressionExperiment loadWithPrimaryPublication(Long id)

Specified by:

loadWithPrimaryPublication in interface ExpressionExperimentReadService

loadWithPrimaryPublicationAndOtherRelevantPublications

@Transactional(readOnly=true)
public ExpressionExperiment loadWithPrimaryPublicationAndOtherRelevantPublications(Long id)

Specified by:

loadWithPrimaryPublicationAndOtherRelevantPublications in interface ExpressionExperimentReadService

loadWithMeanVarianceRelation

@Transactional(readOnly=true)
public ExpressionExperiment loadWithMeanVarianceRelation(Long id)

Specified by:

loadWithMeanVarianceRelation in interface ExpressionExperimentReadService

loadWithCharacteristics

@Transactional(readOnly=true)
public ExpressionExperiment loadWithCharacteristics(Long id)

Specified by:

loadWithCharacteristics in interface ExpressionExperimentReadService

loadAndThaw

@Transactional(readOnly=true)
public ExpressionExperiment loadAndThaw(Long id)

Specified by:

loadAndThaw in interface ExpressionExperimentReadService

loadAndThawLite

@Transactional(readOnly=true)
public ExpressionExperiment loadAndThawLite(Long id)

Specified by:

loadAndThawLite in interface ExpressionExperimentReadService

loadAndThawLiteWithRefreshCacheMode

@Transactional(readOnly=true)
public ExpressionExperiment loadAndThawLiteWithRefreshCacheMode(Long id)

Specified by:

loadAndThawLiteWithRefreshCacheMode in interface ExpressionExperimentReadService

loadAndThawOrFail

@Transactional(readOnly=true)
public <T extends Exception> ExpressionExperiment loadAndThawOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                             throws T

Specified by:

loadAndThawOrFail in interface ExpressionExperimentReadService

Throws:

T

loadAndThawLiteOrFail

@Transactional(readOnly=true)
public <T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier,
 String message)
                                                                 throws T

Specified by:

loadAndThawLiteOrFail in interface ExpressionExperimentReadService

Throws:

T

loadAndThawLiteOrFail

@Transactional(readOnly=true)
public <T extends Exception> ExpressionExperiment loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                                 throws T

Specified by:

loadAndThawLiteOrFail in interface ExpressionExperimentReadService

Throws:

T

loadAndThawLiterOrFail

@Transactional(readOnly=true)
public <T extends Exception> ExpressionExperiment loadAndThawLiterOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                                  throws T

Specified by:

loadAndThawLiterOrFail in interface ExpressionExperimentReadService

Throws:

T

findByAccession

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)

Specified by:

findByAccession in interface ExpressionExperimentReadService

findByAccession

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByAccession(String accession)

Specified by:

findByAccession in interface ExpressionExperimentReadService

findOneByAccession

@Transactional(readOnly=true)
public ExpressionExperiment findOneByAccession(String accession)

Specified by:

findOneByAccession in interface ExpressionExperimentReadService

findByBibliographicReference

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByBibliographicReference(BibliographicReference bibRef)

Specified by:

findByBibliographicReference in interface ExpressionExperimentReadService

findByBioAssay

@Transactional(readOnly=true)
public ExpressionExperiment findByBioAssay(BioAssay ba)

Specified by:

findByBioAssay in interface ExpressionExperimentReadService

findByBioAssay

@Transactional(readOnly=true)
public ExpressionExperiment findByBioAssay(BioAssay ba,
 boolean includeSubSets)

Specified by:

findByBioAssay in interface ExpressionExperimentReadService

findIdByBioAssay

@Transactional(readOnly=true)
public Long findIdByBioAssay(BioAssay ba,
 boolean includeSubSets)

Specified by:

findIdByBioAssay in interface ExpressionExperimentReadService

findByBioMaterial

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm)

Specified by:

findByBioMaterial in interface ExpressionExperimentReadService

findByBioMaterial

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByBioMaterial(BioMaterial bm,
 boolean includeSubSets)

Specified by:

findByBioMaterial in interface ExpressionExperimentReadService

findIdsByBioMaterial

@Transactional(readOnly=true)
public Collection<Long> findIdsByBioMaterial(BioMaterial bm,
 boolean includeSubSets)

Specified by:

findIdsByBioMaterial in interface ExpressionExperimentReadService

findByBioMaterials

@Transactional(readOnly=true)
public Map<ExpressionExperiment, Collection<BioMaterial>> findByBioMaterials(Collection<BioMaterial> biomaterials)

Specified by:

findByBioMaterials in interface ExpressionExperimentReadService

findByExpressedGene

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByExpressedGene(Gene gene,
 double rank)

Specified by:

findByExpressedGene in interface ExpressionExperimentReadService

findByDesign

@Transactional(readOnly=true)
public ExpressionExperiment findByDesign(ExperimentalDesign ed)

Specified by:

findByDesign in interface ExpressionExperimentReadService

findIdByDesign

@Transactional(readOnly=true)
public Long findIdByDesign(ExperimentalDesign design)

Specified by:

findIdByDesign in interface ExpressionExperimentReadService

findByDesignId

@Transactional(readOnly=true)
public ExpressionExperiment findByDesignId(Long designId)

Specified by:

findByDesignId in interface ExpressionExperimentReadService

findByFactor

@Transactional(readOnly=true)
public ExpressionExperiment findByFactor(ExperimentalFactor factor)

Specified by:

findByFactor in interface ExpressionExperimentReadService

findIdByFactor

@Transactional(readOnly=true)
public Long findIdByFactor(ExperimentalFactor factor)

Specified by:

findIdByFactor in interface ExpressionExperimentReadService

findByFactors

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByFactors(Collection<ExperimentalFactor> factors)

Specified by:

findByFactors in interface ExpressionExperimentReadService

findByFactorValue

@Transactional(readOnly=true)
public ExpressionExperiment findByFactorValue(FactorValue factorValue)

Specified by:

findByFactorValue in interface ExpressionExperimentReadService

findIdByFactorValue

@Transactional(readOnly=true)
public Long findIdByFactorValue(FactorValue factorValue)

Specified by:

findIdByFactorValue in interface ExpressionExperimentReadService

findByFactorValueId

@Transactional(readOnly=true)
public ExpressionExperiment findByFactorValueId(Long factorValueId)

Specified by:

findByFactorValueId in interface ExpressionExperimentReadService

findByFactorValues

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByFactorValues(Collection<FactorValue> factorValues)

Specified by:

findByFactorValues in interface ExpressionExperimentReadService

findByFactorValueIds

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByFactorValueIds(Collection<Long> factorValueIds)

Specified by:

findByFactorValueIds in interface ExpressionExperimentReadService

findByGene

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByGene(Gene gene)

Specified by:

findByGene in interface ExpressionExperimentReadService

findByName

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByName(String name)

Specified by:

findByName in interface ExpressionExperimentReadService

findOneByName

@Transactional(readOnly=true)
public ExpressionExperiment findOneByName(String name)

Specified by:

findOneByName in interface ExpressionExperimentReadService

findByQuantitationType

@Transactional(readOnly=true)
public ExpressionExperiment findByQuantitationType(QuantitationType type)

Specified by:

findByQuantitationType in interface ExpressionExperimentReadService

findByShortName

@Transactional(readOnly=true)
public ExpressionExperiment findByShortName(String shortName)

Specified by:

findByShortName in interface ExpressionExperimentReadService

findByShortNameWithPrimaryPublication

@Transactional(readOnly=true)
public ExpressionExperiment findByShortNameWithPrimaryPublication(String shortName)

Specified by:

findByShortNameWithPrimaryPublication in interface ExpressionExperimentReadService

findByShortNameAndThawLite

@Transactional(readOnly=true)
public ExpressionExperiment findByShortNameAndThawLite(String shortName)

Specified by:

findByShortNameAndThawLite in interface ExpressionExperimentReadService

findByTaxon

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface ExpressionExperimentReadService

findByUpdatedLimit

@Transactional(readOnly=true)
public List<ExpressionExperiment> findByUpdatedLimit(int limit)

Specified by:

findByUpdatedLimit in interface ExpressionExperimentReadService

findUpdatedAfter

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> findUpdatedAfter(Date date)

Specified by:

findUpdatedAfter in interface ExpressionExperimentReadService

findByMeanVarianceRelation

@Transactional(readOnly=true)
public ExpressionExperiment findByMeanVarianceRelation(MeanVarianceRelation mvr)

Specified by:

findByMeanVarianceRelation in interface ExpressionExperimentReadService

findIdByMeanVarianceRelation

@Transactional(readOnly=true)
public Long findIdByMeanVarianceRelation(MeanVarianceRelation mvr)

Specified by:

findIdByMeanVarianceRelation in interface ExpressionExperimentReadService

existsByShortName

@Transactional(readOnly=true)
public boolean existsByShortName(String shortName)

Specified by:

existsByShortName in interface ExpressionExperimentReadService

loadLackingFactors

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> loadLackingFactors()

Specified by:

loadLackingFactors in interface ExpressionExperimentReadService

loadLackingTags

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> loadLackingTags()

Specified by:

loadLackingTags in interface ExpressionExperimentReadService

thaw

@Transactional(readOnly=true)
public ExpressionExperiment thaw(ExpressionExperiment expressionExperiment)

Specified by:

thaw in interface ExpressionExperimentReadService

thawLite

@Transactional(readOnly=true)
public ExpressionExperiment thawLite(ExpressionExperiment expressionExperiment)

Specified by:

thawLite in interface ExpressionExperimentReadService

thawLiter

@Transactional(readOnly=true)
public ExpressionExperiment thawLiter(ExpressionExperiment expressionExperiment)

Specified by:

thawLiter in interface ExpressionExperimentReadService

thawBioAssays

@Transactional(readOnly=true)
public ExpressionExperiment thawBioAssays(ExpressionExperiment expressionExperiment)

Description copied from interface: ExpressionExperimentReadService

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

Specified by:

thawBioAssays in interface ExpressionExperimentReadService

getTaxon

@Transactional(readOnly=true)
public Taxon getTaxon(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentReadService

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

Specified by:

getTaxon in interface ExpressionExperimentReadService

browse

@Transactional(readOnly=true)
public List<ExpressionExperiment> browse(int start,
 int limit)

Specified by:

browse in interface ExpressionExperimentReadService

filter

@Transactional(readOnly=true)
public Collection<Long> filter(String searchString)
                        throws SearchException

returns ids of search results

Specified by:

filter in interface ExpressionExperimentReadService

Returns:

collection of ids or an empty collection

Throws:

SearchException

filterByTaxon

@Transactional(readOnly=true)
public Collection<Long> filterByTaxon(Collection<Long> ids,
 Taxon taxon)

Specified by:

filterByTaxon in interface ExpressionExperimentReadService

getAnnotationCountsByIds

@Transactional(readOnly=true)
public Map<Long,Long> getAnnotationCountsByIds(Collection<Long> ids)

Specified by:

getAnnotationCountsByIds in interface ExpressionExperimentReadService

getExperimentalDesignValueObject

@Transactional(readOnly=true)
public ExperimentalDesignValueObject getExperimentalDesignValueObject(ExpressionExperiment ee)

Specified by:

getExperimentalDesignValueObject in interface ExpressionExperimentReadService

getAnnotations

@Transactional(readOnly=true)
public Set<AnnotationValueObject> getAnnotations(ExpressionExperiment expressionExperiment)

Specified by:

getAnnotations in interface ExpressionExperimentReadService

getAnnotations

@Transactional(readOnly=true)
public Set<AnnotationValueObject> getAnnotations(ExpressionExperiment expressionExperiment,
 boolean includeFreeText)

Specified by:

getAnnotations in interface ExpressionExperimentReadService

Parameters:

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

getAnnotations

@Transactional(readOnly=true)
public Set<AnnotationValueObject> getAnnotations(ExpressionExperimentSubSet ee)

Specified by:

getAnnotations in interface ExpressionExperimentReadService

getAnnotations

@Transactional(readOnly=true)
public Set<AnnotationValueObject> getAnnotations(ExpressionExperimentSubSet ee,
 boolean includeFreeText)

Specified by:

getAnnotations in interface ExpressionExperimentReadService

See Also:

• ExpressionExperimentReadService.getAnnotations(ExpressionExperiment, boolean)

getEnhancedFilters

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

Specified by:

getEnhancedFilters in interface ExpressionExperimentReadService

Throws:

TimeoutException

getNumberOfDesignElementsPerSample

@Transactional(readOnly=true)
public Map<BioAssay,Long> getNumberOfDesignElementsPerSample(ExpressionExperiment expressionExperiment)

Specified by:

getNumberOfDesignElementsPerSample in interface ExpressionExperimentReadService

loadIdsWithCache

@Transactional(readOnly=true)
public List<Long> loadIdsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Specified by:

loadIdsWithCache in interface ExpressionExperimentReadService

countWithCache

@Transactional(readOnly=true)
public long countWithCache(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds)

Specified by:

countWithCache in interface ExpressionExperimentReadService

loadValueObjectsWithCache

@Transactional(readOnly=true)
public Slice<ExpressionExperimentValueObject> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Specified by:

loadValueObjectsWithCache in interface ExpressionExperimentReadService

getCategoriesUsageFrequency

@Transactional(readOnly=true)
public 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)

Specified by:

getCategoriesUsageFrequency in interface ExpressionExperimentReadService

getAnnotationsUsageFrequency

@Transactional(readOnly=true)
public 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

If the term cannot be resolved via OntologyService.getTerm(String, long, TimeUnit), an attempt is done to resolve its category and assign it as its parent. This handles free-text terms that lack a value URI.

Specified by:

getAnnotationsUsageFrequency in interface ExpressionExperimentReadService

Throws:

TimeoutException

getTechnologyTypeUsageFrequency

@Transactional(readOnly=true)
public Map<TechnologyType, Long> getTechnologyTypeUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds)

Specified by:

getTechnologyTypeUsageFrequency in interface ExpressionExperimentReadService

getArrayDesignUsedOrOriginalPlatformUsageFrequency

@Transactional(readOnly=true)
public Map<ArrayDesign, Long> getArrayDesignUsedOrOriginalPlatformUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds,
 int maxResults)

Specified by:

getArrayDesignUsedOrOriginalPlatformUsageFrequency in interface ExpressionExperimentReadService

getTaxaUsageFrequency

@Transactional(readOnly=true)
public Map<Taxon,Long> getTaxaUsageFrequency(@Nullable
 Filters filters,
 @Nullable
 Set<Long> extraIds)

Specified by:

getTaxaUsageFrequency in interface ExpressionExperimentReadService

getBioMaterialCount

@Transactional(readOnly=true)
public long getBioMaterialCount(ExpressionExperiment expressionExperiment)

Specified by:

getBioMaterialCount in interface ExpressionExperimentReadService

getRawDataVectorCount

@Transactional(readOnly=true)
public long getRawDataVectorCount(ExpressionExperiment ee)

Specified by:

getRawDataVectorCount in interface ExpressionExperimentReadService

getExperimentsWithOutliers

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getExperimentsWithOutliers()

Specified by:

getExperimentsWithOutliers in interface ExpressionExperimentReadService

getLastArrayDesignUpdate

@Transactional(readOnly=true)
public Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)

Specified by:

getLastArrayDesignUpdate in interface ExpressionExperimentReadService

getLastArrayDesignUpdate

@Transactional(readOnly=true)
public Date getLastArrayDesignUpdate(ExpressionExperiment ee)

Specified by:

getLastArrayDesignUpdate in interface ExpressionExperimentReadService

getLastLinkAnalysis

@Transactional(readOnly=true)
public Map<Long, AuditEvent> getLastLinkAnalysis(Collection<Long> ids)

Specified by:

getLastLinkAnalysis in interface ExpressionExperimentReadService

getLastMissingValueAnalysis

@Transactional(readOnly=true)
public Map<Long, AuditEvent> getLastMissingValueAnalysis(Collection<Long> ids)

Specified by:

getLastMissingValueAnalysis in interface ExpressionExperimentReadService

getLastProcessedDataUpdate

@Transactional(readOnly=true)
public Map<Long, AuditEvent> getLastProcessedDataUpdate(Collection<Long> ids)

Specified by:

getLastProcessedDataUpdate in interface ExpressionExperimentReadService

getPerTaxonCount

@Transactional(readOnly=true)
public Map<Taxon,Long> getPerTaxonCount()

Specified by:

getPerTaxonCount in interface ExpressionExperimentReadService

getPopulatedFactorCounts

@Transactional(readOnly=true)
public Map<Long,Long> getPopulatedFactorCounts(Collection<Long> ids)

Specified by:

getPopulatedFactorCounts in interface ExpressionExperimentReadService

getPopulatedFactorCountsExcludeBatch

@Transactional(readOnly=true)
public Map<Long,Long> getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)

Specified by:

getPopulatedFactorCountsExcludeBatch in interface ExpressionExperimentReadService

getSampleRemovalEvents

@Transactional(readOnly=true)
public Map<ExpressionExperiment, Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)

Specified by:

getSampleRemovalEvents in interface ExpressionExperimentReadService

loadDetailsValueObjects

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

Specified by:

loadDetailsValueObjects in interface ExpressionExperimentReadService

loadDetailsValueObjectsWithCache

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

Specified by:

loadDetailsValueObjectsWithCache in interface ExpressionExperimentReadService

loadDetailsValueObjectsByIds

@Transactional(readOnly=true)
public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(Collection<Long> ids)

Specified by:

loadDetailsValueObjectsByIds in interface ExpressionExperimentReadService

loadDetailsValueObjectsByIdsWithCache

@Transactional(readOnly=true)
public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIdsWithCache(Collection<Long> ids)

Specified by:

loadDetailsValueObjectsByIdsWithCache in interface ExpressionExperimentReadService

loadBlacklistedValueObjects

@Transactional(readOnly=true)
public Slice<ExpressionExperimentValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Specified by:

loadBlacklistedValueObjects in interface ExpressionExperimentReadService

loadBlacklistedValueObjectsByCursor

@Transactional(readOnly=true)
public CursorPage<ExpressionExperimentValueObject> loadBlacklistedValueObjectsByCursor(@Nullable
 Filters filters,
 Sort sort,
 @Nullable
 Cursor cursor,
 int limit)

Description copied from interface: ExpressionExperimentReadService

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

Specified by:

loadBlacklistedValueObjectsByCursor in interface ExpressionExperimentReadService

See Also:

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

loadValueObjectsByIdsWithRelationsAndCache

@Transactional(readOnly=true)
public List<ExpressionExperimentValueObject> loadValueObjectsByIdsWithRelationsAndCache(List<Long> ids)

Specified by:

loadValueObjectsByIdsWithRelationsAndCache in interface ExpressionExperimentReadService

loadValueObjectsByIds

@Transactional(readOnly=true)
public List<ExpressionExperimentValueObject> loadValueObjectsByIds(List<Long> ids,
 boolean maintainOrder)

Specified by:

loadValueObjectsByIds in interface ExpressionExperimentReadService

countBioMaterials

@Transactional(readOnly=true)
public long countBioMaterials(@Nullable
 Filters filters)

Specified by:

countBioMaterials in interface ExpressionExperimentReadService