ubic.gemma.persistence.service.expression.experiment

Interface ExpressionExperimentSetService

All Superinterfaces:

BaseService<ExpressionExperimentSet>, BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

All Known Implementing Classes:

ExpressionExperimentSetServiceImpl

public interface ExpressionExperimentSetService
extends BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

Author:

paul

Field Summary

Fields

Modifier and Type	Field and Description
static String	AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION

Method Summary

Modifier and Type	Method and Description
ExpressionExperimentSet	create(ExpressionExperimentSet expressionExperimentSet) Creates the given entity in the persistent storage.
ExpressionExperimentSet	createFromValueObject(ExpressionExperimentSetValueObject eesvo)
void	deleteDatabaseEntity(ExpressionExperimentSetValueObject eesvo) Security is handled within method, when the set is loaded
Collection<ExpressionExperimentSet>	find(BioAssaySet bioAssaySet)
Collection<ExpressionExperimentSet>	findByName(String name) security at DAO level
Collection<Long>	findIds(BioAssaySet bioAssaySet) 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)
Collection<ExpressionExperimentSet>	load(Collection<Long> ids) Loads objects with given ids.
ExpressionExperimentSet	load(Long id) Loads object with given ID.
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.
void	thaw(ExpressionExperimentSet set)
void	update(ExpressionExperimentSet expressionExperimentSet) Updates the given entity in the persistent storage.
void	updateDatabaseEntity(ExpressionExperimentSetValueObject eesvo) Update corresponding entity based on value object
void	updateDatabaseEntityMembers(Long groupId, Collection<Long> eeIds) Updates the database record for the param experiment set value object (permission permitting) with the members specified of the set, not the name or description etc.
ExpressionExperimentSetValueObject	updateDatabaseEntityNameDesc(ExpressionExperimentSetValueObject eeSetVO, boolean loadEEIds) Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.

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

loadAllValueObjects, loadValueObject, loadValueObjects

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

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

Field Detail

AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION

static final String AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION

See Also:

Constant Field Values

Method Detail

create

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

Description copied from interface: BaseService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseService<ExpressionExperimentSet>

Parameters:

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

Description copied from interface: BaseService

Loads objects with given ids.

Specified by:

load in interface BaseService<ExpressionExperimentSet>

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"})
ExpressionExperimentSet load(Long id)

Description copied from interface: BaseService

Loads object with given ID.

Specified by:

load in interface BaseService<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(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSet> loadAll()

Description copied from interface: BaseService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseService<ExpressionExperimentSet>

Returns:

collection of all entities currently available in the persistent storage.

remove

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

Description copied from interface: BaseService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseService<ExpressionExperimentSet>

Parameters:

expressionExperimentSet - the entity to be removed.

update

@Secured(value={"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.

createFromValueObject

@Secured(value="GROUP_USER")
ExpressionExperimentSet createFromValueObject(ExpressionExperimentSetValueObject eesvo)

deleteDatabaseEntity

void deleteDatabaseEntity(ExpressionExperimentSetValueObject eesvo)

Security is handled within method, when the set is loaded

Parameters:

eesvo - ee value object

find

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<ExpressionExperimentSet> find(BioAssaySet bioAssaySet)

findByName

Collection<ExpressionExperimentSet> findByName(String name)

security at DAO level

Parameters:

name - name

Returns:

collection of ee sets

findIds

Collection<Long> findIds(BioAssaySet bioAssaySet)

security at DAO level

Parameters:

bioAssaySet - BA set

Returns:

collection of IDs

getExperimentsInSet

@Secured(value={"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(value={"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

Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()

Security at DAO level.

Returns:

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

loadAllExperimentSetValueObjects

@Secured(value={"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(value={"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(value={"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

updateDatabaseEntity

void updateDatabaseEntity(ExpressionExperimentSetValueObject eesvo)

Update corresponding entity based on value object

Parameters:

eesvo - ee value object

updateDatabaseEntityMembers

void updateDatabaseEntityMembers(Long groupId,
                                 Collection<Long> eeIds)

Updates the database record for the param experiment set value object (permission permitting) with the members specified of the set, not the name or description etc.

Parameters:

eeIds - ee ids

groupId - group id

updateDatabaseEntityNameDesc

ExpressionExperimentSetValueObject updateDatabaseEntityNameDesc(ExpressionExperimentSetValueObject eeSetVO,
                                                                boolean loadEEIds)

Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.

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.

eeSetVO - ee set value object

Returns:

ee vo

loadValueObjectById

@Secured(value={"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(value={"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

void thaw(ExpressionExperimentSet set)