Class BioAssayReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.bioAssay.BioAssayReadServiceImpl

All Implemented Interfaces:

BioAssayReadService

@Service("bioAssayReadService")
public class BioAssayReadServiceImpl
extends Object
implements BioAssayReadService

Implementation of BioAssayReadService.

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

See Also:

• BioAssayService

Constructor Summary

Constructors

Constructor	Description
BioAssayReadServiceImpl(BioAssayDao bioAssayDao, ArrayDesignDao arrayDesignDao, BioMaterialReadService bioMaterialReadService)

Method Summary

Modifier and Type	Method	Description
Collection<BioAssayDimension>	findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs.
Collection<BioAssay>	findByAccession(String accession)
BioAssay	findByShortName(String shortName)
Collection<BioAssay>	findSiblings(BioAssay bioAssay)
Collection<BioAssay>	findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssaySet>	getBioAssaySets(BioAssay bioAssay)	Obtain all the BioAssaySet that contain the given BioAssay.
List<BioAssayValueObject>	loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
CursorPage<BioAssayValueObject>	loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
Collection<BioAssay>	thaw(Collection<BioAssay> bioAssays)
BioAssay	thaw(BioAssay ba)

Methods inherited from class Object

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

Constructor Details

BioAssayReadServiceImpl

@Autowired
public BioAssayReadServiceImpl(BioAssayDao bioAssayDao,
 ArrayDesignDao arrayDesignDao,
 BioMaterialReadService bioMaterialReadService)

Method Details

findBioAssayDimensions

@Transactional(readOnly=true)
public Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Description copied from interface: BioAssayReadService

Locate all BioAssayDimensions in which the selected BioAssay occurs.

Specified by:

findBioAssayDimensions in interface BioAssayReadService

findByShortName

@Nullable
@Transactional(readOnly=true)
public BioAssay findByShortName(String shortName)

Specified by:

findByShortName in interface BioAssayReadService

findByAccession

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

Specified by:

findByAccession in interface BioAssayReadService

Parameters:

accession - eg GSM12345.

Returns:

BioAssays that match based on the plain accession (unconstrained by ExternalDatabase).

findSubBioAssays

@Transactional(readOnly=true)
public Collection<BioAssay> findSubBioAssays(BioAssay bioAssay,
 boolean direct)

Specified by:

findSubBioAssays in interface BioAssayReadService

findSiblings

@Transactional(readOnly=true)
public Collection<BioAssay> findSiblings(BioAssay bioAssay)

Specified by:

findSiblings in interface BioAssayReadService

getBioAssaySets

@Transactional(readOnly=true)
public Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)

Description copied from interface: BioAssayReadService

Obtain all the BioAssaySet that contain the given BioAssay.

Specified by:

getBioAssaySets in interface BioAssayReadService

thaw

@Transactional(readOnly=true)
public BioAssay thaw(BioAssay ba)

Specified by:

thaw in interface BioAssayReadService

thaw

@Transactional(readOnly=true)
public Collection<BioAssay> thaw(Collection<BioAssay> bioAssays)

Specified by:

thaw in interface BioAssayReadService

loadValueObjects

@Transactional(readOnly=true)
public List<BioAssayValueObject> loadValueObjects(Collection<BioAssay> entities,
 @Nullable
 Map<BioAssay,BioAssay> assay2sourceAssayMap,
 boolean basic,
 boolean allFactorValues)

Specified by:

loadValueObjects in interface BioAssayReadService

See Also:

• BioAssayDao.loadValueObjects(Collection, Map, Map, boolean, boolean)

loadValueObjectsByCursorForExpressionExperiment

@Transactional(readOnly=true)
public CursorPage<BioAssayValueObject> loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment ee,
 @Nullable
 Cursor cursor,
 int limit)

Specified by:

loadValueObjectsByCursorForExpressionExperiment in interface BioAssayReadService

See Also:

• BioAssayDao.loadValueObjectsByCursorForExpressionExperiment(ExpressionExperiment, Cursor, int)

loadValueObjectsByCursorForSubSet

@Transactional(readOnly=true)
public CursorPage<BioAssayValueObject> loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset,
 @Nullable
 Cursor cursor,
 int limit)

Specified by:

loadValueObjectsByCursorForSubSet in interface BioAssayReadService

See Also:

• BioAssayDao.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet, Cursor, int)