Package ubic.gemma.persistence.service.expression.experiment

Interface ExpressionExperimentSetService

All Superinterfaces:

BaseImmutableService<ExpressionExperimentSet>, BaseReadOnlyService<ExpressionExperimentSet>, BaseService<ExpressionExperimentSet>, BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

All Known Implementing Classes:

ExpressionExperimentSetServiceImpl

public interface ExpressionExperimentSetService
extends BaseService<ExpressionExperimentSet>, BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

Author:

paul

Method Summary

Modifier and Type	Method	Description
ExpressionExperimentSet	create(ExpressionExperimentSet expressionExperimentSet)	Creates the given entity in the persistent storage.
Collection<ExpressionExperimentSet>	find(ExpressionExperiment ee)
Collection<ExpressionExperimentSet>	findByName(String name)	security at DAO level
Collection<Long>	findIds(ExpressionExperiment ee)	security at DAO level
Collection<ExpressionExperiment>	getExperimentsInSet(Long id)	Get the (security-filtered) list of experiments in a set.
Collection<ExpressionExperimentDetailsValueObject>	getExperimentValueObjectsInSet(Long id)	Get the member experiment value objects for the set id; security filtered.
ExpressionExperimentSet	initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)
boolean	isAutomaticallyGenerated(String experimentSetDescription)
ExpressionExperimentSet	load(Long id)	Loads object with given ID.
Collection<ExpressionExperimentSet>	load(Collection<Long> ids)	Loads objects with given ids.
Collection<ExpressionExperimentSet>	loadAll()	Loads all the entities of specific type.
Collection<ExpressionExperimentSet>	loadAllExperimentSetsWithTaxon()	Security at DAO level.
Collection<ExpressionExperimentSetValueObject>	loadAllExperimentSetValueObjects(boolean loadEEIds)	Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()
Collection<ExpressionExperimentSetValueObject>	loadMySetValueObjects(boolean loadEEIds)	load the user's sets
ExpressionExperimentSetValueObject	loadValueObjectById(Long id)
ExpressionExperimentSetValueObject	loadValueObjectById(Long id, boolean loadEEIds)	Get a value object for the id param.
List<ExpressionExperimentSetValueObject>	loadValueObjectsByIds(Collection<Long> eeSetIds)	Load value objects by a given collection of IDs.
void	remove(ExpressionExperimentSet expressionExperimentSet)	Removes the given entity from the persistent storage.
int	removeFromSets(ExpressionExperiment bas)	Remove an experiment from all sets it is in.
ExpressionExperimentSet	thaw(ExpressionExperimentSet set)
void	update(ExpressionExperimentSet expressionExperimentSet)	Updates the given entity in the persistent storage.

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

create, findOrCreate, 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, loadValueObjects

Method Details

create

@Secured("GROUP_USER")
ExpressionExperimentSet create(ExpressionExperimentSet expressionExperimentSet)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<ExpressionExperimentSet>

Parameters:

expressionExperimentSet - 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<ExpressionExperimentSet> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<ExpressionExperimentSet>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

load

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

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<ExpressionExperimentSet>

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<ExpressionExperimentSet> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<ExpressionExperimentSet>

Returns:

collection of all entities currently available in the persistent storage.

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(ExpressionExperimentSet expressionExperimentSet)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<ExpressionExperimentSet>

Parameters:

expressionExperimentSet - the entity to be removed.

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(ExpressionExperimentSet expressionExperimentSet)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<ExpressionExperimentSet>

Parameters:

expressionExperimentSet - the entity to be updated.

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSet> find(ExpressionExperiment ee)

findByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSet> findByName(String name)

security at DAO level

Parameters:

name - name

Returns:

collection of ee sets

findIds

Collection<Long> findIds(ExpressionExperiment ee)

security at DAO level

Parameters:

ee - BA set

Returns:

collection of IDs

getExperimentsInSet

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperiment> getExperimentsInSet(Long id)

Get the (security-filtered) list of experiments in a set.

Parameters:

id - id

Returns:

collection of ees

getExperimentValueObjectsInSet

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)

Get the member experiment value objects for the set id; security filtered.

Parameters:

id - id

Returns:

value objects or an empty set

initAutomaticallyGeneratedExperimentSet

ExpressionExperimentSet initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments,
 Taxon taxon)

isAutomaticallyGenerated

boolean isAutomaticallyGenerated(String experimentSetDescription)

loadAllExperimentSetsWithTaxon

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()

Security at DAO level.

Returns:

ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.

loadAllExperimentSetValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Collection<ExpressionExperimentSetValueObject> loadAllExperimentSetValueObjects(boolean loadEEIds)

Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()

Parameters:

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.

loadMySetValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Collection<ExpressionExperimentSetValueObject> loadMySetValueObjects(boolean loadEEIds)

load the user's sets

Parameters:

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

colelction of EE set VOs

loadValueObjectById

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
ExpressionExperimentSetValueObject loadValueObjectById(Long id,
 boolean loadEEIds)

Get a value object for the id param.

Parameters:

id - ID

loadEEIds - whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.

Returns:

null if id doesn't match an experiment set

loadValueObjectById

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
ExpressionExperimentSetValueObject loadValueObjectById(Long id)

Specified by:

loadValueObjectById in interface BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

See Also:

• BaseVoEnabledDao.loadValueObjectById(Long)

loadValueObjectsByIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<ExpressionExperimentSetValueObject> loadValueObjectsByIds(Collection<Long> eeSetIds)

Description copied from interface: BaseVoEnabledService

Load value objects by a given collection of IDs.

Specified by:

loadValueObjectsByIds in interface BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
ExpressionExperimentSet thaw(ExpressionExperimentSet set)

removeFromSets

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_EDIT"})
int removeFromSets(ExpressionExperiment bas)

Remove an experiment from all sets it is in.

Using this allows one to bypass the requirement of "owning edit rights" on the set as long as the current user has the right to edit the experiment itself.

If a set ends-up empty as a result, it is removed as well.

Returns:

the number of sets this experiment was removed from