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
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.
BioMaterial	create(BioMaterial bioMaterial)	Creates the given entity in the persistent storage.
Collection<BioMaterial>	findByExperiment(ExpressionExperiment experiment)
Collection<BioMaterial>	findByFactor(ExperimentalFactor experimentalFactor)
BioMaterial	findOrCreate(BioMaterial bioMaterial)	Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<BioMaterial>	findSiblings(BioMaterial bioMaterial)	Find the siblings of a given biomaterial.
Collection<BioMaterial>	findSubBioMaterials(BioMaterial bioMaterial, boolean direct)
String	getBioMaterialIdList(Collection<BioMaterial> bioMaterials)
Map<BioMaterial,Map<BioAssay,ExpressionExperiment>>	getExpressionExperiments(BioMaterial bm)
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.
void	removeCharacteristic(BioMaterial bm, Characteristic vc)	Remove the given characteristic from the given biomaterial
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, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

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 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)

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.

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_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)

addCharacteristic

void addCharacteristic(BioMaterial bm,
 Characteristic vc)

Will persist the give vocab characteristic to the given biomaterial

See Also:

• ExpressionExperimentService.addCharacteristic(ExpressionExperiment, Characteristic)

removeCharacteristic

void removeCharacteristic(BioMaterial bm,
 Characteristic vc)

Remove the given characteristic from the given biomaterial

Throws:

IllegalArgumentException - if the characteristic does not belong to the biomaterial