Class ArrayDesignReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignReadServiceImpl

All Implemented Interfaces:

ArrayDesignReadService

@Service("arrayDesignReadService")
public class ArrayDesignReadServiceImpl
extends Object
implements ArrayDesignReadService

Implementation of ArrayDesignReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade ArrayDesignService 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:

• ArrayDesignService

Constructor Summary

Constructors

Constructor	Description
ArrayDesignReadServiceImpl(ArrayDesignDao arrayDesignDao, AuditEventDao auditEventDao)

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 ArrayDesignReadService.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)

Methods inherited from class Object

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

Constructor Details

ArrayDesignReadServiceImpl

@Autowired
public ArrayDesignReadServiceImpl(ArrayDesignDao arrayDesignDao,
 AuditEventDao auditEventDao)

Method Details

loadAllGenericGenePlatforms

@Transactional(readOnly=true)
public Collection<ArrayDesign> loadAllGenericGenePlatforms()

Specified by:

loadAllGenericGenePlatforms in interface ArrayDesignReadService

loadAndThaw

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

Specified by:

loadAndThaw in interface ArrayDesignReadService

loadAndThawLiteOrFail

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

Specified by:

loadAndThawLiteOrFail in interface ArrayDesignReadService

Throws:

T

loadWithAuditTrail

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

Specified by:

loadWithAuditTrail in interface ArrayDesignReadService

findByAlternateName

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByAlternateName(String queryString)

Specified by:

findByAlternateName in interface ArrayDesignReadService

findOneByAlternateName

@Transactional(readOnly=true)
public ArrayDesign findOneByAlternateName(String name)

Specified by:

findOneByAlternateName in interface ArrayDesignReadService

findByManufacturer

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByManufacturer(String searchString)

Specified by:

findByManufacturer in interface ArrayDesignReadService

findByName

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

Specified by:

findByName in interface ArrayDesignReadService

findByCompositeSequenceName

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByCompositeSequenceName(String name)

Specified by:

findByCompositeSequenceName in interface ArrayDesignReadService

findOneByName

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

Specified by:

findOneByName in interface ArrayDesignReadService

findByShortName

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

Specified by:

findByShortName in interface ArrayDesignReadService

findByTaxon

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

Specified by:

findByTaxon in interface ArrayDesignReadService

getAlignments

@Transactional(readOnly=true)
public Map<CompositeSequence, Collection<BlatResult>> getAlignments(ArrayDesign arrayDesign)

Specified by:

getAlignments in interface ArrayDesignReadService

getAllAssociatedBioAssays

@Transactional(readOnly=true)
public Collection<BioAssay> getAllAssociatedBioAssays(ArrayDesign arrayDesign)

Specified by:

getAllAssociatedBioAssays in interface ArrayDesignReadService

getBioSequences

@Transactional(readOnly=true)
public Map<CompositeSequence, BioSequence> getBioSequences(ArrayDesign arrayDesign)

Specified by:

getBioSequences in interface ArrayDesignReadService

getGenes

@Transactional(readOnly=true)
public Collection<Gene> getGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

getGenes in interface ArrayDesignReadService

getGenesByCompositeSequence

@Transactional(readOnly=true)
public Map<CompositeSequence, Set<Gene>> getGenesByCompositeSequence(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

getGenesByCompositeSequence in interface ArrayDesignReadService

getGenesByCompositeSequence

@Transactional(readOnly=true)
public Map<CompositeSequence, Set<Gene>> getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign,
 boolean useGene2Cs)

Specified by:

getGenesByCompositeSequence in interface ArrayDesignReadService

countCompositeSequences

@Transactional(readOnly=true)
public long countCompositeSequences(ArrayDesign arrayDesign)

Specified by:

countCompositeSequences in interface ArrayDesignReadService

getCompositeSequences

@Transactional(readOnly=true)
public Collection<CompositeSequence> getCompositeSequences(ArrayDesign arrayDesign)

Specified by:

getCompositeSequences in interface ArrayDesignReadService

getCompositeSequences

@Transactional(readOnly=true)
public Collection<CompositeSequence> getCompositeSequences(ArrayDesign arrayDesign,
 int limit,
 int offset)

Specified by:

getCompositeSequences in interface ArrayDesignReadService

getExpressionExperiments

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getExpressionExperiments(ArrayDesign arrayDesign)

Specified by:

getExpressionExperiments in interface ArrayDesignReadService

countExpressionExperiments

@Transactional(readOnly=true)
public long countExpressionExperiments(ArrayDesign arrayDesign)

Specified by:

countExpressionExperiments in interface ArrayDesignReadService

getLastGeneMapping

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

Specified by:

getLastGeneMapping in interface ArrayDesignReadService

getLastRepeatAnalysis

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

Specified by:

getLastRepeatAnalysis in interface ArrayDesignReadService

getLastSequenceAnalysis

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

Specified by:

getLastSequenceAnalysis in interface ArrayDesignReadService

getLastSequenceUpdate

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

Specified by:

getLastSequenceUpdate in interface ArrayDesignReadService

getPerTaxonCount

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

Specified by:

getPerTaxonCount in interface ArrayDesignReadService

getSwitchedExperiments

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getSwitchedExperiments(ArrayDesign arrayDesign)

Specified by:

getSwitchedExperiments in interface ArrayDesignReadService

countSwitchedExpressionExperiments

@Transactional(readOnly=true)
public long countSwitchedExpressionExperiments(ArrayDesign id)

Specified by:

countSwitchedExpressionExperiments in interface ArrayDesignReadService

getTaxaFromBioSequences

@Transactional(readOnly=true)
public Collection<Taxon> getTaxaFromBioSequences(ArrayDesign arrayDesign)

Specified by:

getTaxaFromBioSequences in interface ArrayDesignReadService

loadBlacklistedValueObjects

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

Specified by:

loadBlacklistedValueObjects in interface ArrayDesignReadService

loadBlacklistedValueObjectsByCursor

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

Description copied from interface: ArrayDesignReadService

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

Specified by:

loadBlacklistedValueObjectsByCursor in interface ArrayDesignReadService

See Also:

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

loadValueObjectsWithCache

@Transactional(readOnly=true)
public Collection<ArrayDesignValueObject> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Specified by:

loadValueObjectsWithCache in interface ArrayDesignReadService

countWithCache

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

Specified by:

countWithCache in interface ArrayDesignReadService

isMerged

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

Specified by:

isMerged in interface ArrayDesignReadService

isMergee

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

Specified by:

isMergee in interface ArrayDesignReadService

isSubsumed

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

Specified by:

isSubsumed in interface ArrayDesignReadService

isSubsumer

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

Specified by:

isSubsumer in interface ArrayDesignReadService

loadValueObjectsForEE

@Transactional(readOnly=true)
public List<ArrayDesignValueObject> loadValueObjectsForEE(Long eeId)

Specified by:

loadValueObjectsForEE in interface ArrayDesignReadService

loadOriginalPlatformValueObjectsForEE

@Transactional(readOnly=true)
public List<ArrayDesignValueObject> loadOriginalPlatformValueObjectsForEE(Long eeId)

Description copied from interface: ArrayDesignReadService

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.

Specified by:

loadOriginalPlatformValueObjectsForEE in interface ArrayDesignReadService

See Also:

• ArrayDesignReadService.loadValueObjectsForEE(Long)

countCompositeSequencesWithBioSequences

@Transactional(readOnly=true)
public long countCompositeSequencesWithBioSequences()

Specified by:

countCompositeSequencesWithBioSequences in interface ArrayDesignReadService

countCompositeSequencesWithBlatResults

@Transactional(readOnly=true)
public long countCompositeSequencesWithBlatResults()

Specified by:

countCompositeSequencesWithBlatResults in interface ArrayDesignReadService

countCompositeSequencesWithGenes

@Transactional(readOnly=true)
public long countCompositeSequencesWithGenes(boolean useGene2Cs)

Specified by:

countCompositeSequencesWithGenes in interface ArrayDesignReadService

countGenes

@Transactional(readOnly=true)
public long countGenes(boolean useGene2Cs)

Specified by:

countGenes in interface ArrayDesignReadService

countBioSequences

@Transactional(readOnly=true)
public long countBioSequences(ArrayDesign arrayDesign)

Specified by:

countBioSequences in interface ArrayDesignReadService

countBlatResults

@Transactional(readOnly=true)
public long countBlatResults(ArrayDesign arrayDesign)

Specified by:

countBlatResults in interface ArrayDesignReadService

countCompositeSequencesWithBioSequences

@Transactional(readOnly=true)
public long countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)

Specified by:

countCompositeSequencesWithBioSequences in interface ArrayDesignReadService

countCompositeSequencesWithBlatResults

@Transactional(readOnly=true)
public long countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)

Specified by:

countCompositeSequencesWithBlatResults in interface ArrayDesignReadService

countCompositeSequencesWithGenes

@Transactional(readOnly=true)
public long countCompositeSequencesWithGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

countCompositeSequencesWithGenes in interface ArrayDesignReadService

countGenes

@Transactional(readOnly=true)
public long countGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

countGenes in interface ArrayDesignReadService

thaw

@Transactional(readOnly=true)
public ArrayDesign thaw(ArrayDesign arrayDesign)

Specified by:

thaw in interface ArrayDesignReadService

thaw

@Transactional(readOnly=true)
public Collection<ArrayDesign> thaw(Collection<ArrayDesign> aas)

Specified by:

thaw in interface ArrayDesignReadService

thawCompositeSequences

@Transactional(readOnly=true)
public ArrayDesign thawCompositeSequences(ArrayDesign arrayDesign)

Specified by:

thawCompositeSequences in interface ArrayDesignReadService

thawCompositeSequences

@Transactional(readOnly=true)
public Collection<ArrayDesign> thawCompositeSequences(Collection<ArrayDesign> ads)

Specified by:

thawCompositeSequences in interface ArrayDesignReadService

thawLite

@Transactional(readOnly=true)
public ArrayDesign thawLite(ArrayDesign arrayDesign)

Specified by:

thawLite in interface ArrayDesignReadService

thawLite

@Transactional(readOnly=true)
public Collection<ArrayDesign> thawLite(Collection<ArrayDesign> arrayDesigns)

Specified by:

thawLite in interface ArrayDesignReadService