Package ubic.gemma.persistence.service.genome.gene

Interface GeneSetService

All Superinterfaces:

BaseImmutableService<GeneSet>, BaseReadOnlyService<GeneSet>, BaseService<GeneSet>, BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

All Known Implementing Classes:

GeneSetServiceImpl

@ParametersAreNonnullByDefault
public interface GeneSetService
extends BaseService<GeneSet>, BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Service for managing gene sets

Author:

kelsey, paul

Method Summary

Modifier and Type	Method	Description
Collection<GeneSet>	create(Collection<GeneSet> sets)	Creates all the given entities in a persistent storage
GeneSet	create(GeneSet geneset)	Creates the given entity in the persistent storage.
GeneSetValueObject	createDatabaseEntity(GeneSetValueObject gsvo)	create an entity in the database based on the value object parameter
void	deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject> vos)	Security is handled within method
void	deleteDatabaseEntity(DatabaseBackedGeneSetValueObject geneSetVO)	Security is handled within method, when the set is loaded
Collection<GeneSet>	findByGene(Gene gene)	Return all sets that contain the given gene.
Collection<GeneSet>	findByName(String name)
Collection<GeneSet>	findByName(String name, Taxon taxon)
Collection<GeneSetValueObject>	findGeneSetsByGene(Long geneId)	Given a Gemma Gene Id, find all the gene groups it is a member of (filtering is handled when gene sets are loaded)
Collection<GeneSetValueObject>	findGeneSetsByName(String query, Long taxonId)
Collection<Long>	getGeneIdsInGroup(GeneSetValueObject geneSetVO)
Collection<GeneValueObject>	getGenesInGroup(GeneSetValueObject object)	Get the gene value objects for the members of the group param
int	getSize(GeneSetValueObject geneSetVO)
Set<Taxon>	getTaxa(GeneSet geneSet)	Obtain all the taxa for the members of a given gene set.
Taxon	getTaxon(GeneSet geneSet)	get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
TaxonValueObject	getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject geneSetVO)	get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes
Collection<GeneSet>	getUsersGeneGroups(boolean privateOnly, Long taxonId, boolean sharedPublicOnly)
Collection<DatabaseBackedGeneSetValueObject>	getUsersGeneGroupsValueObjects(boolean privateOnly, Long taxonId)	Returns just the current users gene sets
GeneSet	load(Long id)	Loads object with given ID.
Collection<GeneSet>	load(Collection<Long> ids)	Loads objects with given ids.
Collection<GeneSet>	loadAll()	Loads all the entities of specific type.
Collection<GeneSet>	loadAll(Taxon tax)
List<DatabaseBackedGeneSetValueObject>	loadAllValueObjects()	Loads value objects representing all the entities of specific type.
Collection<GeneSet>	loadMyGeneSets()	Returns the GeneSets for the currently logged in User - i.e, ones for which the current user has specific read permissions on (as opposed to data sets which are public).
Collection<GeneSet>	loadMyGeneSets(Taxon tax)
Collection<GeneSet>	loadMySharedGeneSets(Taxon tax)
GeneSet	loadOrFail(Long id)	Convenience for running BaseReadOnlyService.load(Long) and checking if the result is null.
DatabaseBackedGeneSetValueObject	loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	loadValueObjectById(Long entityId)
DatabaseBackedGeneSetValueObject	loadValueObjectByIdLite(Long id)
List<DatabaseBackedGeneSetValueObject>	loadValueObjects(Collection<GeneSet> entities)	Loads value objects for all given entities.
List<DatabaseBackedGeneSetValueObject>	loadValueObjectsByIds(Collection<Long> ids)	Ids of member genes will be filled in
List<DatabaseBackedGeneSetValueObject>	loadValueObjectsByIdsLite(Collection<Long> geneSetIds)
Collection<GeneSet>	loadWithMembers(Collection<Long> ids)	Load the gene sets with their members initialized.
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<GeneSet> entities)	Removes all the given entities from persistent storage.
void	remove(GeneSet entity)	Removes the given entity from the persistent storage.
int	removeAll()
Collection<GeneSet>	save(Collection<GeneSet> entities)
GeneSet	save(GeneSet entity)
void	update(Collection<GeneSet> entities)	Updates all entities in the given collection in the persistent storage.
void	update(GeneSet entity)	Updates the given entity in the persistent storage.
Collection<DatabaseBackedGeneSetValueObject>	updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)	AJAX Updates the database entity (permission permitting) with the fields of the param value object
void	updateDatabaseEntityMembers(Long groupId, Collection<Long> geneIds)	Updates the database record for the param gene set value object (permission permitting) with the members specified of the set, not the name or description etc.
DatabaseBackedGeneSetValueObject	updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)	AJAX Updates the database entity (permission permitting) with the name and description fields of the param value object

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

findOrCreate

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

countAll, find, findOrFail, getElementClass, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Method Details

loadWithMembers

Collection<GeneSet> loadWithMembers(Collection<Long> ids)

Load the gene sets with their members initialized.

create

@Secured("GROUP_USER")
Collection<GeneSet> create(Collection<GeneSet> sets)

Description copied from interface: BaseImmutableService

Creates all the given entities in a persistent storage

Specified by:

create in interface BaseImmutableService<GeneSet>

Parameters:

sets - the entities to be created.

Returns:

collection of objects referencing the persistent instances of given entities.

create

@Secured("GROUP_USER")
GeneSet create(GeneSet geneset)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<GeneSet>

Parameters:

geneset - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

save

@Secured("GROUP_USER")
GeneSet save(GeneSet entity)

Specified by:

save in interface BaseService<GeneSet>

See Also:

• invalid reference

  BaseDao#save(Object)

save

@Secured("GROUP_USER")
Collection<GeneSet> save(Collection<GeneSet> entities)

Specified by:

save in interface BaseService<GeneSet>

See Also:

• BaseDao.save(Collection)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<GeneSet> findByGene(Gene gene)

Return all sets that contain the given gene. GeneSetDao

Parameters:

gene - gene

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadValueObject

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
DatabaseBackedGeneSetValueObject loadValueObject(GeneSet geneSet)

Specified by:

loadValueObject in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)

loadValueObjectById

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
DatabaseBackedGeneSetValueObject loadValueObjectById(Long entityId)

Specified by:

loadValueObjectById in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

See Also:

• BaseVoEnabledDao.loadValueObjectById(Long)

loadValueObjectByIdLite

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"})
DatabaseBackedGeneSetValueObject loadValueObjectByIdLite(Long id)

loadValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<DatabaseBackedGeneSetValueObject> loadValueObjects(Collection<GeneSet> entities)

Description copied from interface: BaseVoEnabledService

Loads value objects for all given entities.

Specified by:

loadValueObjects in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Parameters:

entities - the entities to be converted to value objects

Returns:

a collection of value objects representing he given entities.

loadValueObjectsByIds

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

Ids of member genes will be filled in

Specified by:

loadValueObjectsByIds in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Parameters:

ids - ids

Returns:

gene set value object

loadValueObjectsByIdsLite

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIdsLite(Collection<Long> geneSetIds)

loadAllValueObjects

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
List<DatabaseBackedGeneSetValueObject> loadAllValueObjects()

Description copied from interface: BaseVoEnabledService

Loads value objects representing all the entities of specific type.

Specified by:

loadAllValueObjects in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Returns:

a collection of value objects

findByName

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

Parameters:

name - name

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

findByName

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

Parameters:

name - name

taxon - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

load

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

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<GeneSet>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

loadOrFail

@Nonnull
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
GeneSet loadOrFail(Long id)
            throws NullPointerException

Description copied from interface: BaseReadOnlyService

Convenience for running BaseReadOnlyService.load(Long) and checking if the result is null.

Specified by:

loadOrFail in interface BaseReadOnlyService<GeneSet>

Parameters:

id - the ID used to retrieve the entity

Returns:

the entity as per BaseReadOnlyService.load(Long), never null

Throws:

NullPointerException - if the entity does not exist in the persistent storage

load

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

Description copied from interface: BaseReadOnlyService

Loads object with given ID.

Specified by:

load in interface BaseReadOnlyService<GeneSet>

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<GeneSet> loadAll()

Description copied from interface: BaseReadOnlyService

Loads all the entities of specific type.

Specified by:

loadAll in interface BaseReadOnlyService<GeneSet>

Returns:

collection of all entities currently available in the persistent storage.

loadAll

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<GeneSet> loadAll(@Nullable
 Taxon tax)

Parameters:

tax - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadMyGeneSets

@Secured({"GROUP_USER","AFTER_ACL_FILTER_MY_DATA"})
Collection<GeneSet> loadMyGeneSets()

Returns the GeneSets for the currently logged in User - i.e, ones for which the current user has specific read permissions on (as opposed to data sets which are public). Important: This method will return all gene sets if security is not enabled. Implementation note: Via a methodInvocationFilter. See AclAfterFilterCollectionForMyData for processConfigAttribute.

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadMyGeneSets

@Secured({"GROUP_USER","AFTER_ACL_FILTER_MY_DATA"})
Collection<GeneSet> loadMyGeneSets(Taxon tax)

Parameters:

tax - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadMySharedGeneSets

@Secured({"GROUP_USER","AFTER_ACL_FILTER_MY_PRIVATE_DATA"})
Collection<GeneSet> loadMySharedGeneSets(Taxon tax)

Parameters:

tax - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

createDatabaseEntity

GeneSetValueObject createDatabaseEntity(GeneSetValueObject gsvo)

create an entity in the database based on the value object parameter

Parameters:

gsvo - gene set value object

Returns:

value object converted from the newly created entity

findGeneSetsByGene

Collection<GeneSetValueObject> findGeneSetsByGene(Long geneId)

Given a Gemma Gene Id, find all the gene groups it is a member of (filtering is handled when gene sets are loaded)

Parameters:

geneId - gene id

Returns:

collection of geneSetValueObject

updateDatabaseEntityNameDesc

DatabaseBackedGeneSetValueObject updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)

AJAX Updates the database entity (permission permitting) with the name and description fields of the param value object

Parameters:

geneSetVO - gene set value object

Returns:

value objects for the updated entities

updateDatabaseEntityMembers

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

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

Parameters:

groupId - group id

geneIds - gene ids

updateDatabaseEntity

Collection<DatabaseBackedGeneSetValueObject> updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)

AJAX Updates the database entity (permission permitting) with the fields of the param value object

Parameters:

geneSetVos - gene sets

Returns:

value objects for the updated entities

deleteDatabaseEntity

void deleteDatabaseEntity(DatabaseBackedGeneSetValueObject geneSetVO)

Security is handled within method, when the set is loaded

Parameters:

geneSetVO - gene set VO

deleteDatabaseEntities

void deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject> vos)

Security is handled within method

Parameters:

vos - gene set value objects

getUsersGeneGroups

@Secured("GROUP_USER")
Collection<GeneSet> getUsersGeneGroups(boolean privateOnly,
 @Nullable
 Long taxonId,
 boolean sharedPublicOnly)

Parameters:

privateOnly - only return private sets owned by the user or private sets shared with the user

taxonId - if non-null, restrict the groups by ones which have genes in the given taxon (can be null)

sharedPublicOnly - if true, the only public sets returned will be those that are owned by the user or have been shared with the user. If param privateOnly is true, this will have no effect.

Returns:

all the gene sets user can see, with optional restrictions based on taxon and whether the set is public or private

getUsersGeneGroupsValueObjects

@Secured({"GROUP_USER","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Collection<DatabaseBackedGeneSetValueObject> getUsersGeneGroupsValueObjects(boolean privateOnly,
 Long taxonId)

Returns just the current users gene sets

Parameters:

privateOnly - only private

taxonId - if non-null, restrict the groups by ones which have genes in the given taxon.

Returns:

gene set value objects

getGenesInGroup

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<GeneValueObject> getGenesInGroup(GeneSetValueObject object)

Get the gene value objects for the members of the group param

Parameters:

object - can be just a wrapper to trigger security

Returns:

gene value object

getGeneIdsInGroup

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<Long> getGeneIdsInGroup(GeneSetValueObject geneSetVO)

getSize

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
int getSize(GeneSetValueObject geneSetVO)

findGeneSetsByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"})
Collection<GeneSetValueObject> findGeneSetsByName(String query,
 @Nullable
 Long taxonId)
                                           throws SearchException

Parameters:

query - string to match to gene sets

taxonId - taxon id

Returns:

collection of GeneSetValueObjects that match name query

Throws:

SearchException

getTaxonVOforGeneSetVO

TaxonValueObject getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject geneSetVO)

get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes

Parameters:

geneSetVO - gene set value object

Returns:

the taxon or null if the gene set param was null

getTaxon

@Nullable
Taxon getTaxon(GeneSet geneSet)

get the taxon for the gene set parameter, assumes that the taxon of the first gene will be representational of all the genes

Parameters:

geneSet - gene set

Returns:

a taxon, or null if the gene set has no member

getTaxa

Set<Taxon> getTaxa(GeneSet geneSet)

Obtain all the taxa for the members of a given gene set.

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(GeneSet entity)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<GeneSet>

Parameters:

entity - the entity to be updated.

update

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"})
void update(Collection<GeneSet> entities)

Description copied from interface: BaseService

Updates all entities in the given collection in the persistent storage.

Specified by:

update in interface BaseService<GeneSet>

Parameters:

entities - the entities to be updated.

remove

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void remove(GeneSet entity)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneSet>

Parameters:

entity - the entity to be removed.

remove

@Secured({"GROUP_USER","ACL_SECURABLE_COLLECTION_EDIT"})
void remove(Collection<GeneSet> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneSet>

Parameters:

entities - the entities to be removed.

remove

@Secured("GROUP_ADMIN")
void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<GeneSet>

Parameters:

id - the ID of entity to be removed.

removeAll

@Secured("GROUP_ADMIN")
int removeAll()