Package ubic.gemma.persistence.service.expression.biomaterial

Class BioMaterialServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<O>

ubic.gemma.persistence.service.AbstractVoEnabledService<BioMaterial,BioMaterialValueObject>

ubic.gemma.persistence.service.expression.biomaterial.BioMaterialServiceImpl

All Implemented Interfaces:

BaseImmutableService<BioMaterial>, BaseReadOnlyService<BioMaterial>, BaseService<BioMaterial>, BaseVoEnabledService<BioMaterial,BioMaterialValueObject>, BioMaterialService

@Service
public class BioMaterialServiceImpl
extends AbstractVoEnabledService<BioMaterial,BioMaterialValueObject>
implements BioMaterialService

Author:

pavlidis, keshav

See Also:

BioMaterialService

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Constructor	Description
BioMaterialServiceImpl(BioMaterialDao bioMaterialDao, FactorValueDao factorValueDao, BioAssayDao bioAssayDao, ExperimentalFactorDao experimentalFactorDao)

Method Summary

Modifier and Type	Method	Description
void	addCharacteristic(BioMaterial bm, Characteristic vc)	Will persist the give vocab characteristic to the given biomaterial
<T> void	associateBatchFactor(Map<BioMaterial,T> descriptors, Map<T,FactorValue> d2fv)	Associate dates with bioassays and any new factors with the biomaterials.
BioMaterial	copy(BioMaterial bioMaterial)	Copies a bioMaterial.
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
String	getBioMaterialIdList(Collection<BioMaterial> bioMaterials)
ExpressionExperiment	getExpressionExperiment(Long id)
void	removeCharacteristic(BioMaterial bm, Characteristic characterId)	Remove the given characteristic from the given biomaterial
Collection<BioMaterial>	thaw(Collection<BioMaterial> bioMaterials)
BioMaterial	thaw(BioMaterial bioMaterial)
Collection<BioMaterial>	updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)	Update the biomaterials that are described by the given valueObjects.

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, update, update

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService

create, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, loadOrFail, loadOrFail, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.BaseService

save, save, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService

create, findOrCreate, load, load, loadAll, remove, update

Constructor Detail

BioMaterialServiceImpl

@Autowired
public BioMaterialServiceImpl(BioMaterialDao bioMaterialDao,
                              FactorValueDao factorValueDao,
                              BioAssayDao bioAssayDao,
                              ExperimentalFactorDao experimentalFactorDao)

Method Detail

copy

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

Description copied from interface: BioMaterialService

Copies a bioMaterial.

Specified by:

copy in interface BioMaterialService

Parameters:

bioMaterial - ba to copy

Returns:

the copy

findByExperiment

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

Specified by:

findByExperiment in interface BioMaterialService

getExpressionExperiment

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

Specified by:

getExpressionExperiment in interface BioMaterialService

thaw

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

Specified by:

thaw in interface BioMaterialService

thaw

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

Specified by:

thaw in interface BioMaterialService

updateBioMaterials

@Transactional
public Collection<BioMaterial> updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)

Description copied from interface: BioMaterialService

Update the biomaterials that are described by the given valueObjects. This is used to update experimental designs in particular.

Specified by:

updateBioMaterials in interface BioMaterialService

Parameters:

valueObjects - VOs

Returns:

the biomaterials that were modified.

associateBatchFactor

@Transactional
public <T> void associateBatchFactor(Map<BioMaterial,T> descriptors,
                                     Map<T,FactorValue> d2fv)

Description copied from interface: BioMaterialService

Associate dates with bioassays and any new factors with the biomaterials. Note we can have missing values.

Specified by:

associateBatchFactor in interface BioMaterialService

d2fv - map of dates to factor values

getBioMaterialIdList

public String getBioMaterialIdList(Collection<BioMaterial> bioMaterials)

Specified by:

getBioMaterialIdList in interface BioMaterialService

addCharacteristic

@Transactional
public void addCharacteristic(BioMaterial bm,
                              Characteristic vc)

Description copied from interface: BioMaterialService

Will persist the give vocab characteristic to the given biomaterial

Specified by:

addCharacteristic in interface BioMaterialService

See Also:

ExpressionExperimentService.addCharacteristic(ExpressionExperiment, Characteristic)

removeCharacteristic

public void removeCharacteristic(BioMaterial bm,
                                 Characteristic characterId)

Description copied from interface: BioMaterialService

Remove the given characteristic from the given biomaterial

Specified by:

removeCharacteristic in interface BioMaterialService