Interface ArrayDesignReadService

All Known Implementing Classes:

ArrayDesignReadServiceImpl

public interface ArrayDesignReadService

Thin read-only retrieval service for ArrayDesign.

Phase 3 of the ArrayDesignService decomposition (strangler fig). This service houses the pure-retrieval methods: load/find/count/get/thaw/audit-event lookups that delegate directly to ArrayDesignDao (and AuditEventDao for the getLastXxx methods) with no orchestration of write-side collaborators.

Callers should generally keep using ArrayDesignService as the facade — the facade delegates here. Direct injection is appropriate where a class would otherwise create a Spring dependency cycle through the heavier facade.

ACL / @Secured annotations live on ArrayDesignService (the caller-facing facade interface); enforcement happens at the facade proxy boundary. Methods on this interface are unsecured at the AOP layer on purpose — intra-core callers that hold an authenticated session can bypass duplicate ACL checks.

See Also:

• ArrayDesignService

Method Summary

Modifier and Type	Method	Description
long	countBioSequences(ArrayDesign arrayDesign)
long	countBlatResults(ArrayDesign arrayDesign)
long	countCompositeSequences(ArrayDesign arrayDesign)
long	countCompositeSequencesWithBioSequences()
long	countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)
long	countCompositeSequencesWithBlatResults()
long	countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)
long	countCompositeSequencesWithGenes(boolean useGene2Cs)
long	countCompositeSequencesWithGenes(ArrayDesign arrayDesign, boolean useGene2Cs)
long	countExpressionExperiments(ArrayDesign arrayDesign)
long	countGenes(boolean useGene2Cs)
long	countGenes(ArrayDesign arrayDesign, boolean useGene2Cs)
long	countSwitchedExpressionExperiments(ArrayDesign id)
long	countWithCache(Filters filters)
Collection<ArrayDesign>	findByAlternateName(String queryString)
Collection<ArrayDesign>	findByCompositeSequenceName(String name)
Collection<ArrayDesign>	findByManufacturer(String searchString)
Collection<ArrayDesign>	findByName(String name)
ArrayDesign	findByShortName(String shortName)
Collection<ArrayDesign>	findByTaxon(Taxon taxon)
ArrayDesign	findOneByAlternateName(String name)
ArrayDesign	findOneByName(String name)
Map<CompositeSequence, Collection<BlatResult>>	getAlignments(ArrayDesign arrayDesign)
Collection<BioAssay>	getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Map<CompositeSequence, BioSequence>	getBioSequences(ArrayDesign arrayDesign)
Collection<CompositeSequence>	getCompositeSequences(ArrayDesign arrayDesign)
Collection<CompositeSequence>	getCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
Collection<ExpressionExperiment>	getExpressionExperiments(ArrayDesign arrayDesign)
Collection<Gene>	getGenes(ArrayDesign arrayDesign, boolean useGene2Cs)
Map<CompositeSequence, Set<Gene>>	getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign, boolean useGene2Cs)
Map<CompositeSequence, Set<Gene>>	getGenesByCompositeSequence(ArrayDesign arrayDesign, boolean useGene2Cs)
Map<Long, AuditEvent>	getLastGeneMapping(Collection<Long> ids)
Map<Long, AuditEvent>	getLastRepeatAnalysis(Collection<Long> ids)
Map<Long, AuditEvent>	getLastSequenceAnalysis(Collection<Long> ids)
Map<Long, AuditEvent>	getLastSequenceUpdate(Collection<Long> ids)
Map<Taxon,Long>	getPerTaxonCount()
Collection<ExpressionExperiment>	getSwitchedExperiments(ArrayDesign arrayDesign)
Collection<Taxon>	getTaxaFromBioSequences(ArrayDesign arrayDesign)
Map<Long,Boolean>	isMerged(Collection<Long> ids)
Map<Long,Boolean>	isMergee(Collection<Long> ids)
Map<Long,Boolean>	isSubsumed(Collection<Long> ids)
Map<Long,Boolean>	isSubsumer(Collection<Long> ids)
Collection<ArrayDesign>	loadAllGenericGenePlatforms()
ArrayDesign	loadAndThaw(Long id)
<T extends Exception> ArrayDesign	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)
Slice<ArrayDesignValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ArrayDesignValueObject>	loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to loadBlacklistedValueObjects(Filters, Sort, int, int).
List<ArrayDesignValueObject>	loadOriginalPlatformValueObjectsForEE(Long eeId)	Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
List<ArrayDesignValueObject>	loadValueObjectsForEE(Long eeId)
Collection<ArrayDesignValueObject>	loadValueObjectsWithCache(Filters filters, Sort sort)
ArrayDesign	loadWithAuditTrail(Long id)
Collection<ArrayDesign>	thaw(Collection<ArrayDesign> aas)
ArrayDesign	thaw(ArrayDesign arrayDesign)
Collection<ArrayDesign>	thawCompositeSequences(Collection<ArrayDesign> ads)
ArrayDesign	thawCompositeSequences(ArrayDesign arrayDesign)
Collection<ArrayDesign>	thawLite(Collection<ArrayDesign> arrayDesigns)
ArrayDesign	thawLite(ArrayDesign arrayDesign)

Method Details

loadAllGenericGenePlatforms

Collection<ArrayDesign> loadAllGenericGenePlatforms()

loadAndThaw

@Nullable
ArrayDesign loadAndThaw(Long id)

loadAndThawLiteOrFail

<T extends Exception> ArrayDesign loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier,
 String message)
                                                 throws T

Throws:

T

loadWithAuditTrail

@Nullable
ArrayDesign loadWithAuditTrail(Long id)

findByAlternateName

Collection<ArrayDesign> findByAlternateName(String queryString)

findOneByAlternateName

@Nullable
ArrayDesign findOneByAlternateName(String name)

findByManufacturer

Collection<ArrayDesign> findByManufacturer(String searchString)

findByName

Collection<ArrayDesign> findByName(String name)

findByCompositeSequenceName

Collection<ArrayDesign> findByCompositeSequenceName(String name)

findOneByName

@Nullable
ArrayDesign findOneByName(String name)

findByShortName

@Nullable
ArrayDesign findByShortName(String shortName)

findByTaxon

Collection<ArrayDesign> findByTaxon(Taxon taxon)

getAlignments

Map<CompositeSequence, Collection<BlatResult>> getAlignments(ArrayDesign arrayDesign)

getAllAssociatedBioAssays

Collection<BioAssay> getAllAssociatedBioAssays(ArrayDesign arrayDesign)

getBioSequences

Map<CompositeSequence, BioSequence> getBioSequences(ArrayDesign arrayDesign)

getGenes

Collection<Gene> getGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

getGenesByCompositeSequence

Map<CompositeSequence, Set<Gene>> getGenesByCompositeSequence(ArrayDesign arrayDesign,
 boolean useGene2Cs)

getGenesByCompositeSequence

Map<CompositeSequence, Set<Gene>> getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign,
 boolean useGene2Cs)

countCompositeSequences

long countCompositeSequences(ArrayDesign arrayDesign)

getCompositeSequences

Collection<CompositeSequence> getCompositeSequences(ArrayDesign arrayDesign)

getCompositeSequences

Collection<CompositeSequence> getCompositeSequences(ArrayDesign arrayDesign,
 int limit,
 int offset)

getExpressionExperiments

Collection<ExpressionExperiment> getExpressionExperiments(ArrayDesign arrayDesign)

countExpressionExperiments

long countExpressionExperiments(ArrayDesign arrayDesign)

getLastGeneMapping

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

getLastRepeatAnalysis

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

getLastSequenceAnalysis

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

getLastSequenceUpdate

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

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

getSwitchedExperiments

Collection<ExpressionExperiment> getSwitchedExperiments(ArrayDesign arrayDesign)

countSwitchedExpressionExperiments

long countSwitchedExpressionExperiments(ArrayDesign id)

getTaxaFromBioSequences

Collection<Taxon> getTaxaFromBioSequences(ArrayDesign arrayDesign)

loadBlacklistedValueObjects

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

loadBlacklistedValueObjectsByCursor

CursorPage<ArrayDesignValueObject> loadBlacklistedValueObjectsByCursor(@Nullable
 Filters filters,
 Sort sort,
 @Nullable
 Cursor cursor,
 int limit)

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

See Also:

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

loadValueObjectsWithCache

Collection<ArrayDesignValueObject> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

countWithCache

long countWithCache(@Nullable
 Filters filters)

isMerged

Map<Long,Boolean> isMerged(Collection<Long> ids)

isMergee

Map<Long,Boolean> isMergee(Collection<Long> ids)

isSubsumed

Map<Long,Boolean> isSubsumed(Collection<Long> ids)

isSubsumer

Map<Long,Boolean> isSubsumer(Collection<Long> ids)

loadValueObjectsForEE

List<ArrayDesignValueObject> loadValueObjectsForEE(Long eeId)

loadOriginalPlatformValueObjectsForEE

List<ArrayDesignValueObject> loadOriginalPlatformValueObjectsForEE(Long eeId)

Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.

A dataset can have more than one — its assays need not have come from a single submitted platform. A platform recorded as an original that is ALSO the one in use is a no-op switch and is left out, so an unswitched dataset answers with an empty list rather than echoing its current platform. That is the same rule the details VO applies, kept identical so the two cannot drift into disagreeing.

See Also:

• loadValueObjectsForEE(Long)

countCompositeSequencesWithBioSequences

long countCompositeSequencesWithBioSequences()

countCompositeSequencesWithBlatResults

long countCompositeSequencesWithBlatResults()

countCompositeSequencesWithGenes

long countCompositeSequencesWithGenes(boolean useGene2Cs)

countGenes

long countGenes(boolean useGene2Cs)

countBioSequences

long countBioSequences(ArrayDesign arrayDesign)

countBlatResults

long countBlatResults(ArrayDesign arrayDesign)

countCompositeSequencesWithBioSequences

long countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)

countCompositeSequencesWithBlatResults

long countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)

countCompositeSequencesWithGenes

long countCompositeSequencesWithGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

countGenes

long countGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

thaw

@CheckReturnValue
ArrayDesign thaw(ArrayDesign arrayDesign)

thaw

@CheckReturnValue
Collection<ArrayDesign> thaw(Collection<ArrayDesign> aas)

thawCompositeSequences

@CheckReturnValue
ArrayDesign thawCompositeSequences(ArrayDesign arrayDesign)

thawCompositeSequences

@CheckReturnValue
Collection<ArrayDesign> thawCompositeSequences(Collection<ArrayDesign> ads)

thawLite

@CheckReturnValue
ArrayDesign thawLite(ArrayDesign arrayDesign)

thawLite

@CheckReturnValue
Collection<ArrayDesign> thawLite(Collection<ArrayDesign> arrayDesigns)