Package ubic.gemma.persistence.service.expression.bioAssay

Interface BioAssayService

All Superinterfaces:

BaseImmutableService<BioAssay>, BaseReadOnlyService<BioAssay>, BaseService<BioAssay>, BaseVoEnabledService<BioAssay,BioAssayValueObject>

All Known Implementing Classes:

BioAssayServiceImpl

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

Author:

kelsey

Method Summary

Modifier and Type	Method	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.
Filter	getFilter(String property, Filter.Operator operator, String value)
Filter	getFilter(String property, Filter.Operator operator, Collection<String> values)
Set<String>	getFilterableProperties()
String	getFilterablePropertyDescription(String property)
Class<?>	getFilterablePropertyType(String property)
Sort	getSort(String property, Sort.Direction direction)
BioAssay	load(Long id)	Loads object with given ID.
Collection<BioAssay>	load(Collection<Long> ids)	Loads objects with given ids.
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.
Collection<BioAssay>	thaw(Collection<BioAssay> bioAssays)
BioAssay	thaw(BioAssay bioAssay)
void	update(BioAssay bioAssay)	Updates the given entity in the persistent storage.

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

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

addBioMaterialAssociation

@PreAuthorize("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({"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({"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({"GROUP_USER","AFTER_ACL_READ"})
BioAssay findOrCreate(BioAssay bioAssay)

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<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("GROUP_USER")
BioAssay create(BioAssay bioAssay)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<BioAssay>

Parameters:

bioAssay - 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<BioAssay> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<BioAssay>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

load

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

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<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({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssay> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<BioAssay>

Returns:

collection of all entities currently available in the persistent storage.

remove

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

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<BioAssay>

Parameters:

bioAssay - the entity to be removed.

update

@Secured({"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({"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

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
BioAssay thaw(BioAssay bioAssay)

thaw

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

loadValueObjects

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

getFilterableProperties

Set<String> getFilterableProperties()

See Also:

FilteringDao.getFilterableProperties()

getFilterablePropertyType

Class<?> getFilterablePropertyType(String property)

See Also:

FilteringDao.getFilterablePropertyType(String)

getFilterablePropertyDescription

@Nullable
String getFilterablePropertyDescription(String property)

See Also:

FilteringDao.getFilterablePropertyDescription(String)

getFilter

Filter getFilter(String property,
                 Filter.Operator operator,
                 String value)
          throws IllegalArgumentException

Throws:

IllegalArgumentException

See Also:

FilteringDao.getFilterableProperties()

getFilter

Filter getFilter(String property,
                 Filter.Operator operator,
                 Collection<String> values)
          throws IllegalArgumentException

Throws:

IllegalArgumentException

See Also:

FilteringDao.getFilter(String, Filter.Operator, Collection)

getSort

Sort getSort(String property,
             @Nullable
             Sort.Direction direction)
      throws IllegalArgumentException

Throws:

IllegalArgumentException

See Also:

FilteringDao.getSort(String, Sort.Direction)