Interface ExpressionExperimentSetService
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- 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
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Field Summary
Fields Modifier and Type Field Description static String
AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method 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 loadedCollection<ExpressionExperimentSet>
find(BioAssaySet bioAssaySet)
Collection<ExpressionExperimentSet>
findByName(String name)
security at DAO levelCollection<Long>
findIds(BioAssaySet bioAssaySet)
security at DAO levelCollection<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 setsExpressionExperimentSetValueObject
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.ExpressionExperimentSet
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 objectvoid
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.BaseImmutableService
create, findOrCreate, remove, remove
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Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll, find, findOrFail, getElementClass, loadOrFail, loadOrFail, loadOrFail, loadOrFail
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Methods inherited from interface ubic.gemma.persistence.service.BaseService
save, save, update
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjects
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Field Detail
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AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
static final String AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
- See Also:
- Constant Field Values
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Method Detail
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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 interfaceBaseImmutableService<ExpressionExperimentSet>
- Parameters:
expressionExperimentSet
- the entity to be created.- Returns:
- object referencing the persistent instance of the given entity.
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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 interfaceBaseReadOnlyService<ExpressionExperimentSet>
- Parameters:
ids
- the ids of objects to be loaded.- Returns:
- collection containing object with given IDs.
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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 interfaceBaseReadOnlyService<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
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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 interfaceBaseReadOnlyService<ExpressionExperimentSet>
- Returns:
- collection of all entities currently available in the persistent storage.
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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 interfaceBaseImmutableService<ExpressionExperimentSet>
- Parameters:
expressionExperimentSet
- the entity to be removed.
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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 interfaceBaseService<ExpressionExperimentSet>
- Parameters:
expressionExperimentSet
- the entity to be updated.
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createFromValueObject
@Secured("GROUP_USER") ExpressionExperimentSet createFromValueObject(ExpressionExperimentSetValueObject eesvo)
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deleteDatabaseEntity
void deleteDatabaseEntity(ExpressionExperimentSetValueObject eesvo)
Security is handled within method, when the set is loaded- Parameters:
eesvo
- ee value object
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find
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<ExpressionExperimentSet> find(BioAssaySet bioAssaySet)
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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
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findIds
Collection<Long> findIds(BioAssaySet bioAssaySet)
security at DAO level- Parameters:
bioAssaySet
- BA set- Returns:
- collection of IDs
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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
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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
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initAutomaticallyGeneratedExperimentSet
ExpressionExperimentSet initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)
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isAutomaticallyGenerated
boolean isAutomaticallyGenerated(String experimentSetDescription)
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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.
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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.
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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
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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
- IDloadEEIds
- 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
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updateDatabaseEntity
void updateDatabaseEntity(ExpressionExperimentSetValueObject eesvo)
Update corresponding entity based on value object- Parameters:
eesvo
- ee value object
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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 idsgroupId
- group id
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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
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loadValueObjectById
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"}) ExpressionExperimentSetValueObject loadValueObjectById(Long id)
- Specified by:
loadValueObjectById
in interfaceBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
- See Also:
BaseVoEnabledDao.loadValueObjectById(Long)
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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 interfaceBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
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thaw
@CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) ExpressionExperimentSet thaw(ExpressionExperimentSet set)
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