ubic.gemma.persistence.service.expression.bioAssay

Interface BioAssayService

All Superinterfaces:

BaseService<BioAssay>, BaseVoEnabledService<BioAssay,BioAssayValueObject>, FilteringService<BioAssay>

All Known Implementing Classes:

BioAssayServiceImpl

@Service
public interface BioAssayService
extends BaseVoEnabledService<BioAssay,BioAssayValueObject>, FilteringService<BioAssay>

Author:

kelsey

Method Summary

Modifier and Type	Method and Description
void	addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial) Associates a bioMaterial with a specified bioAssay.
BioAssay	create(BioAssay bioAssay) Creates the given entity in the persistent storage.
Collection<BioAssayDimension>	findBioAssayDimensions(BioAssay bioAssay) Locate all BioAssayDimensions in which the selected BioAssay occurs
Collection<BioAssay>	findByAccession(String accession)
BioAssay	findOrCreate(BioAssay bioAssay) Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<BioAssay>	load(Collection<Long> ids) Loads objects with given ids.
BioAssay	load(Long id) Loads object with given ID.
Collection<BioAssay>	loadAll() Loads all the entities of specific type.
List<BioAssayValueObject>	loadValueObjects(Collection<BioAssay> entities, boolean basic)
void	remove(BioAssay bioAssay) Removes the given entity from the persistent storage.
void	removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial) Removes the association between a specific bioMaterial and a bioAssay.
void	thaw(BioAssay bioAssay)
Collection<BioAssay>	thaw(Collection<BioAssay> bioAssays)
void	update(BioAssay bioAssay) Updates the given entity in the persistent storage.

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

getObjectFilter, getObjectFilter, getSort

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

countAll, create, find, findOrFail, loadOrFail, remove, remove, removeAll, save, save, update

Method Detail

addBioMaterialAssociation

@PreAuthorize(value="hasPermission(#bioAssay, \'write\') or hasPermission(#bioAssay, \'administration\')")
void addBioMaterialAssociation(BioAssay bioAssay,
                                                                                                                                          BioMaterial bioMaterial)

Associates a bioMaterial with a specified bioAssay.

Parameters:

bioAssay - bio assay

bioMaterial - bio material

findBioAssayDimensions

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Locate all BioAssayDimensions in which the selected BioAssay occurs

Parameters:

bioAssay - bio assay

Returns:

bio assay dimensions

findByAccession

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> findByAccession(String accession)

Parameters:

accession - eg GSM12345.

Returns:

BioAssays that match based on the plain accession (unconstrained by ExternalDatabase).

findOrCreate

@Secured(value={"GROUP_USER","AFTER_ACL_READ"})
BioAssay findOrCreate(BioAssay bioAssay)

Description copied from interface: BaseService

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

Specified by:

findOrCreate in interface BaseService<BioAssay>

Parameters:

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

Returns:

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

create

@Secured(value="GROUP_USER")
BioAssay create(BioAssay bioAssay)

Description copied from interface: BaseService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseService<BioAssay>

Parameters:

bioAssay - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

load

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

Description copied from interface: BaseService

Loads objects with given ids.

Specified by:

load in interface BaseService<BioAssay>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

load

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
BioAssay load(Long id)

Description copied from interface: BaseService

Loads object with given ID.

Specified by:

load in interface BaseService<BioAssay>

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(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> loadAll()

Description copied from interface: BaseService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseService<BioAssay>

Returns:

collection of all entities currently available in the persistent storage.

remove

@Secured(value={"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(BioAssay bioAssay)

Description copied from interface: BaseService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseService<BioAssay>

Parameters:

bioAssay - the entity to be removed.

update

@Secured(value={"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(BioAssay bioAssay)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<BioAssay>

Parameters:

bioAssay - the entity to be updated.

removeBioMaterialAssociation

@Secured(value={"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeBioMaterialAssociation(BioAssay bioAssay,
                                                                                      BioMaterial bioMaterial)

Removes the association between a specific bioMaterial and a bioAssay.

Parameters:

bioAssay - bio assay

bioMaterial - bio material

thaw

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
void thaw(BioAssay bioAssay)

thaw

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> thaw(Collection<BioAssay> bioAssays)

loadValueObjects

List<BioAssayValueObject> loadValueObjects(Collection<BioAssay> entities,
                                           boolean basic)