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

Interface BioMaterialService

All Superinterfaces:

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

All Known Implementing Classes:

BioMaterialServiceImpl

public interface BioMaterialService
extends BaseService<BioMaterial>, BaseVoEnabledService<BioMaterial,BioMaterialValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
<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.
BioMaterial	create(BioMaterial bioMaterial)	Creates the given entity in the persistent storage.
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	findByFactorValue(FactorValue fv)
BioMaterial	findOrCreate(BioMaterial bioMaterial)	Does a search for the entity in the persistent storage, and if not found, creates it.
String	getBioMaterialIdList(Collection<BioMaterial> bioMaterials)
ExpressionExperiment	getExpressionExperiment(Long id)
BioMaterial	load(Long id)	Loads object with given ID.
Collection<BioMaterial>	load(Collection<Long> ids)	Loads objects with given ids.
Collection<BioMaterial>	loadAll()	Loads all the entities of specific type.
void	remove(BioMaterial bioMaterial)	Removes the given entity from the persistent storage.
Collection<BioMaterial>	thaw(Collection<BioMaterial> bioMaterials)
BioMaterial	thaw(BioMaterial bioMaterial)
void	update(BioMaterial bioMaterial)	Updates the given entity in the persistent storage.
Collection<BioMaterial>	updateBioMaterials(Collection<BioMaterialValueObject> valueObjects)	Update the biomaterials that are described by the given valueObjects.

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

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

Method Detail

copy

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

Copies a bioMaterial.

Parameters:

bioMaterial - ba to copy

Returns:

the copy

findByExperiment

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

findByFactorValue

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioMaterial> findByFactorValue(FactorValue fv)

findOrCreate

@Secured({"GROUP_USER","AFTER_ACL_READ"})
BioMaterial findOrCreate(BioMaterial bioMaterial)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<BioMaterial>

Parameters:

bioMaterial - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

@Secured("GROUP_USER")
BioMaterial create(BioMaterial bioMaterial)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<BioMaterial>

Parameters:

bioMaterial - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioMaterial> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<BioMaterial>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
BioMaterial load(Long id)

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<BioMaterial>

Parameters:

id - the ID of entity to be loaded.

Returns:

the entity with matching ID, or null if the entity does not exist or if the passed ID was null

loadAll

@Secured({"GROUP_USER","AFTER_ACL_COLLECTION_READ"})
Collection<BioMaterial> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<BioMaterial>

Returns:

collection of all entities currently available in the persistent storage.

remove

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

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<BioMaterial>

Parameters:

bioMaterial - the entity to be removed.

update

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

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<BioMaterial>

Parameters:

bioMaterial - the entity to be updated.

getExpressionExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperiment getExpressionExperiment(Long id)

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_USER")
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

getBioMaterialIdList

String getBioMaterialIdList(Collection<BioMaterial> bioMaterials)