Class BioMaterialReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.biomaterial.BioMaterialReadServiceImpl

All Implemented Interfaces:

BioMaterialReadService

@Service("bioMaterialReadService")
public class BioMaterialReadServiceImpl
extends Object
implements BioMaterialReadService

Implementation of BioMaterialReadService.

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

• BioMaterialService

Constructor Summary

Constructors

Constructor	Description
BioMaterialReadServiceImpl(BioMaterialDao bioMaterialDao)

Method Summary

Modifier and Type	Method	Description
BioMaterial	copy(BioMaterial bioMaterial)	Copy a BioMaterial.
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial (other direct sub-materials of the same source).
Collection<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Map<BioMaterial, Map<BioAssay, ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)	Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.
<T extends Exception> BioMaterial	loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)	Load a BioMaterial by ID and thaw it eagerly, or throw the supplied exception if no such biomaterial exists.
Collection<BioMaterial>	thaw(Collection<BioMaterial> bioMaterials)	Thaw a collection of BioMaterial for full traversal.
BioMaterial	thaw(BioMaterial bioMaterial)	Thaw a single BioMaterial for full traversal.

Methods inherited from class Object

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

Constructor Details

BioMaterialReadServiceImpl

@Autowired
public BioMaterialReadServiceImpl(BioMaterialDao bioMaterialDao)

Method Details

copy

@Transactional(readOnly=true)
public BioMaterial copy(BioMaterial bioMaterial)

Description copied from interface: BioMaterialReadService

Copy a BioMaterial.

Specified by:

copy in interface BioMaterialReadService

See Also:

• BioMaterialDao.copy(BioMaterial)

findSubBioMaterials

@Transactional(readOnly=true)
public Collection<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

Specified by:

findSubBioMaterials in interface BioMaterialReadService

See Also:

• BioMaterialDao.findSubBioMaterials(BioMaterial, boolean)

findSiblings

@Transactional(readOnly=true)
public Collection<BioMaterial> findSiblings(BioMaterial bioMaterial)

Description copied from interface: BioMaterialReadService

Find the siblings of a given biomaterial (other direct sub-materials of the same source).

Specified by:

findSiblings in interface BioMaterialReadService

findByExperiment

@Transactional(readOnly=true)
public Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

Specified by:

findByExperiment in interface BioMaterialReadService

See Also:

• BioMaterialDao.findByExperiment(ExpressionExperiment)

findByFactor

@Transactional(readOnly=true)
public Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

Specified by:

findByFactor in interface BioMaterialReadService

See Also:

• BioMaterialDao.findByFactor(ExperimentalFactor)

loadAndThawOrFail

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

Description copied from interface: BioMaterialReadService

Load a BioMaterial by ID and thaw it eagerly, or throw the supplied exception if no such biomaterial exists.

Specified by:

loadAndThawOrFail in interface BioMaterialReadService

Throws:

T

getExpressionExperiments

@Transactional(readOnly=true)
public Map<BioMaterial, Map<BioAssay, ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

Description copied from interface: BioMaterialReadService

Return the ExpressionExperiment occurrences of a given biomaterial, organized by BioAssay.

Specified by:

getExpressionExperiments in interface BioMaterialReadService

See Also:

• BioMaterialDao.getExpressionExperiments(BioMaterial)

thaw

@Transactional(readOnly=true)
public BioMaterial thaw(BioMaterial bioMaterial)

Description copied from interface: BioMaterialReadService

Thaw a single BioMaterial for full traversal.

Specified by:

thaw in interface BioMaterialReadService

thaw

@Transactional(readOnly=true)
public Collection<BioMaterial> thaw(Collection<BioMaterial> bioMaterials)

Description copied from interface: BioMaterialReadService

Thaw a collection of BioMaterial for full traversal.

Specified by:

thaw in interface BioMaterialReadService