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

Class BioMaterialServiceImpl

java.lang.Object

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

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>, SecurableBaseImmutableService<BioMaterial>, SecurableBaseReadOnlyService<BioMaterial>, SecurableBaseService<BioMaterial>, SecurableBaseVoEnabledService<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, CharacteristicService characteristicService)

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)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
Collection<BioMaterial>	findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial.
Collection<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)
<T extends Exception> BioMaterial	loadAndThawOrFail(Long bmId, Function<String,T> exceptionSupplier, String message)
void	removeCharacteristics(BioMaterial bm, Collection<Characteristic> characteristicsToRemove)	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, loadOrFail, loadOrFail, remove, remove, save, save, streamAll, streamAll, 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.BaseReadOnlyService

countAll, getElementClass, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, create, findOrCreate, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Constructor Details

BioMaterialServiceImpl

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

Method Details

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

findSubBioMaterials

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

Specified by:

findSubBioMaterials in interface BioMaterialService

See Also:

• BioMaterialDao.findSubBioMaterials(BioMaterial, boolean)

findSiblings

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

Description copied from interface: BioMaterialService

Find the siblings of a given biomaterial.

Specified by:

findSiblings in interface BioMaterialService

findByExperiment

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

Specified by:

findByExperiment in interface BioMaterialService

findByFactor

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

Specified by:

findByFactor in interface BioMaterialService

loadAndThawOrFail

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

Specified by:

loadAndThawOrFail in interface BioMaterialService

Throws:

T

getExpressionExperiments

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

Specified by:

getExpressionExperiments 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

Parameters:

d2fv - map of dates to factor values

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)

removeCharacteristics

@Transactional
public void removeCharacteristics(BioMaterial bm,
 Collection<Characteristic> characteristicsToRemove)

Description copied from interface: BioMaterialService

Remove the given characteristic from the given biomaterial

Specified by:

removeCharacteristics in interface BioMaterialService