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

Interface BioMaterialService

All Superinterfaces:

BaseImmutableService<BioMaterial>, BaseReadOnlyService<BioMaterial>, BaseService<BioMaterial>, BaseVoEnabledService<BioMaterial,BioMaterialValueObject>, SecurableBaseImmutableService<BioMaterial>, SecurableBaseReadOnlyService<BioMaterial>, SecurableBaseService<BioMaterial>, SecurableBaseVoEnabledService<BioMaterial,BioMaterialValueObject>

All Known Implementing Classes:

BioMaterialServiceImpl

public interface BioMaterialService
extends SecurableBaseService<BioMaterial>, SecurableBaseVoEnabledService<BioMaterial,BioMaterialValueObject>

Author:

kelsey

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> vc)	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 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

Method Details

copy

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
BioMaterial copy(BioMaterial bioMaterial)

Copies a bioMaterial.

Parameters:

bioMaterial - ba to copy

Returns:

the copy

findSubBioMaterials

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findSubBioMaterials(BioMaterial bioMaterial,
 boolean direct)

See Also:

• BioMaterialDao.findSubBioMaterials(BioMaterial, boolean)

findSiblings

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findSiblings(BioMaterial bioMaterial)

Find the siblings of a given biomaterial.

findByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findByExperiment(ExpressionExperiment experiment)

findByFactor

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioMaterial> findByFactor(ExperimentalFactor experimentalFactor)

loadAndThawOrFail

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> BioMaterial loadAndThawOrFail(Long bmId,
 Function<String,T> exceptionSupplier,
 String message)
                                             throws T

Throws:

T

getExpressionExperiments

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_MAP_READ"})
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>> getExpressionExperiments(BioMaterial bm)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE__READ"})
BioMaterial thaw(BioMaterial bioMaterial)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioMaterial> thaw(Collection<BioMaterial> bioMaterials)

updateBioMaterials

@Secured("GROUP_ADMIN")
Collection<BioMaterial> updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)

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

Parameters:

valueObjects - VOs

Returns:

the biomaterials that were modified.

associateBatchFactor

@Secured("GROUP_ADMIN")
<T> void associateBatchFactor(Map<BioMaterial,T> descriptors,
 Map<T,FactorValue> d2fv)

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

Parameters:

d2fv - map of dates to factor values

addCharacteristic

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void addCharacteristic(BioMaterial bm,
 Characteristic vc)

Will persist the give vocab characteristic to the given biomaterial

See Also:

• ExpressionExperimentService.addCharacteristic(ExpressionExperiment, Characteristic)

removeCharacteristics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCharacteristics(BioMaterial bm,
 Collection<Characteristic> vc)

Remove the given characteristic from the given biomaterial

Throws:

IllegalArgumentException - if the characteristic does not belong to the biomaterial