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

Class GeneSetServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<GeneSet>

ubic.gemma.persistence.service.AbstractVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

ubic.gemma.persistence.service.genome.gene.GeneSetServiceImpl

All Implemented Interfaces:

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

@Service
@ParametersAreNonnullByDefault
public class GeneSetServiceImpl
extends AbstractVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>
implements GeneSetService

Service for managing gene sets

Author:

kelsey

Constructor Summary

Constructors

Constructor	Description
GeneSetServiceImpl(GeneSetDao voDao)

Method Summary

Modifier and Type	Method	Description
GeneSetValueObject	createDatabaseEntity(GeneSetValueObject geneSetVo)	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 object)
Collection<GeneValueObject>	getGenesInGroup(GeneSetValueObject object)	Get the gene value objects for the members of the group param
int	getSize(GeneSetValueObject object)
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
Collection<GeneSet>	loadAll(Taxon tax)
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)
DatabaseBackedGeneSetValueObject	loadValueObject(GeneSet geneSet)
DatabaseBackedGeneSetValueObject	loadValueObjectByIdLite(Long id)
List<DatabaseBackedGeneSetValueObject>	loadValueObjectsByIds(Collection<Long> ids)	Load value objects by a given collection of IDs.
List<DatabaseBackedGeneSetValueObject>	loadValueObjectsByIdsLite(Collection<Long> genesetIds)
Collection<GeneSet>	loadWithMembers(Collection<Long> ids)	Load the gene sets with their members initialized.
int	removeAll()
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 class ubic.gemma.persistence.service.AbstractVoEnabledService

loadAllValueObjects, loadValueObjectById, loadValueObjects

Methods inherited from class ubic.gemma.persistence.service.AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Methods inherited from interface ubic.gemma.persistence.service.genome.gene.GeneSetService

create, create, load, load, loadAll, loadAllValueObjects, loadOrFail, loadValueObjectById, loadValueObjects, remove, remove, remove, save, save, update, update

Constructor Details

GeneSetServiceImpl

@Autowired
public GeneSetServiceImpl(GeneSetDao voDao)

Method Details

loadWithMembers

@Transactional(readOnly=true)
public Collection<GeneSet> loadWithMembers(Collection<Long> ids)

Description copied from interface: GeneSetService

Load the gene sets with their members initialized.

Specified by:

loadWithMembers in interface GeneSetService

findByGene

@Transactional(readOnly=true)
public Collection<GeneSet> findByGene(Gene gene)

Description copied from interface: GeneSetService

Return all sets that contain the given gene. GeneSetDao

Specified by:

findByGene in interface GeneSetService

Parameters:

gene - gene

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadValueObject

@Transactional(readOnly=true)
public DatabaseBackedGeneSetValueObject loadValueObject(GeneSet geneSet)

Specified by:

loadValueObject in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Specified by:

loadValueObject in interface GeneSetService

Overrides:

loadValueObject in class AbstractVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)

loadValueObjectByIdLite

@Transactional(readOnly=true)
public DatabaseBackedGeneSetValueObject loadValueObjectByIdLite(Long id)

Specified by:

loadValueObjectByIdLite in interface GeneSetService

loadValueObjectsByIds

@Transactional(readOnly=true)
public List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIds(Collection<Long> ids)

Description copied from interface: BaseVoEnabledService

Load value objects by a given collection of IDs.

Specified by:

loadValueObjectsByIds in interface BaseVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Specified by:

loadValueObjectsByIds in interface GeneSetService

Overrides:

loadValueObjectsByIds in class AbstractVoEnabledService<GeneSet,DatabaseBackedGeneSetValueObject>

Parameters:

ids - ids

Returns:

gene set value object

loadValueObjectsByIdsLite

@Transactional(readOnly=true)
public List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIdsLite(Collection<Long> genesetIds)

Specified by:

loadValueObjectsByIdsLite in interface GeneSetService

findByName

@Transactional(readOnly=true)
public Collection<GeneSet> findByName(String name)

Specified by:

findByName in interface GeneSetService

Parameters:

name - name

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

findByName

@Transactional(readOnly=true)
public Collection<GeneSet> findByName(String name,
 Taxon taxon)

Specified by:

findByName in interface GeneSetService

Parameters:

name - name

taxon - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadAll

@Transactional(readOnly=true)
public Collection<GeneSet> loadAll(@Nullable
 Taxon tax)

Specified by:

loadAll in interface GeneSetService

Parameters:

tax - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadMyGeneSets

@Transactional(readOnly=true)
public Collection<GeneSet> loadMyGeneSets()

Description copied from interface: GeneSetService

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.

Specified by:

loadMyGeneSets in interface GeneSetService

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadMyGeneSets

@Transactional(readOnly=true)
public Collection<GeneSet> loadMyGeneSets(Taxon tax)

Specified by:

loadMyGeneSets in interface GeneSetService

Parameters:

tax - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

loadMySharedGeneSets

@Transactional(readOnly=true)
public Collection<GeneSet> loadMySharedGeneSets(Taxon tax)

Specified by:

loadMySharedGeneSets in interface GeneSetService

Parameters:

tax - taxon

Returns:

gene sets

See Also:

• GeneSetDao for security filtering

createDatabaseEntity

@Transactional
public GeneSetValueObject createDatabaseEntity(GeneSetValueObject geneSetVo)

Description copied from interface: GeneSetService

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

Specified by:

createDatabaseEntity in interface GeneSetService

Parameters:

geneSetVo - gene set value object

Returns:

value object converted from the newly created entity

findGeneSetsByGene

@Transactional(readOnly=true)
public Collection<GeneSetValueObject> findGeneSetsByGene(Long geneId)

Description copied from interface: GeneSetService

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

Specified by:

findGeneSetsByGene in interface GeneSetService

Parameters:

geneId - gene id

Returns:

collection of geneSetValueObject

updateDatabaseEntityNameDesc

@Transactional
public DatabaseBackedGeneSetValueObject updateDatabaseEntityNameDesc(DatabaseBackedGeneSetValueObject geneSetVO)

Description copied from interface: GeneSetService

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

Specified by:

updateDatabaseEntityNameDesc in interface GeneSetService

Parameters:

geneSetVO - gene set value object

Returns:

value objects for the updated entities

updateDatabaseEntityMembers

@Transactional
public void updateDatabaseEntityMembers(Long groupId,
 Collection<Long> geneIds)

Description copied from interface: GeneSetService

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.

Specified by:

updateDatabaseEntityMembers in interface GeneSetService

Parameters:

groupId - group id

geneIds - gene ids

updateDatabaseEntity

@Transactional
public Collection<DatabaseBackedGeneSetValueObject> updateDatabaseEntity(Collection<DatabaseBackedGeneSetValueObject> geneSetVos)

Description copied from interface: GeneSetService

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

Specified by:

updateDatabaseEntity in interface GeneSetService

Parameters:

geneSetVos - gene sets

Returns:

value objects for the updated entities

deleteDatabaseEntity

@Transactional
public void deleteDatabaseEntity(DatabaseBackedGeneSetValueObject geneSetVO)

Description copied from interface: GeneSetService

Security is handled within method, when the set is loaded

Specified by:

deleteDatabaseEntity in interface GeneSetService

Parameters:

geneSetVO - gene set VO

deleteDatabaseEntities

@Transactional
public void deleteDatabaseEntities(Collection<DatabaseBackedGeneSetValueObject> vos)

Description copied from interface: GeneSetService

Security is handled within method

Specified by:

deleteDatabaseEntities in interface GeneSetService

Parameters:

vos - gene set value objects

getUsersGeneGroups

@Transactional(readOnly=true)
public Collection<GeneSet> getUsersGeneGroups(boolean privateOnly,
 @Nullable
 Long taxonId,
 boolean sharedPublicOnly)

Specified by:

getUsersGeneGroups in interface GeneSetService

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

@Transactional(readOnly=true)
public Collection<DatabaseBackedGeneSetValueObject> getUsersGeneGroupsValueObjects(boolean privateOnly,
 Long taxonId)

Description copied from interface: GeneSetService

Returns just the current users gene sets

Specified by:

getUsersGeneGroupsValueObjects in interface GeneSetService

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

@Transactional(readOnly=true)
public Collection<GeneValueObject> getGenesInGroup(GeneSetValueObject object)

Description copied from interface: GeneSetService

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

Specified by:

getGenesInGroup in interface GeneSetService

Parameters:

object - can be just a wrapper to trigger security

Returns:

gene value object

getGeneIdsInGroup

@Transactional(readOnly=true)
public Collection<Long> getGeneIdsInGroup(GeneSetValueObject object)

Specified by:

getGeneIdsInGroup in interface GeneSetService

getSize

@Transactional(readOnly=true)
public int getSize(GeneSetValueObject object)

Specified by:

getSize in interface GeneSetService

findGeneSetsByName

@Transactional(readOnly=true)
public Collection<GeneSetValueObject> findGeneSetsByName(String query,
 @Nullable
 Long taxonId)
                                                  throws SearchException

Specified by:

findGeneSetsByName in interface GeneSetService

Parameters:

query - string to match to gene sets

taxonId - taxon id

Returns:

collection of GeneSetValueObjects that match name query

Throws:

SearchException

getTaxonVOforGeneSetVO

@Transactional(readOnly=true)
public TaxonValueObject getTaxonVOforGeneSetVO(SessionBoundGeneSetValueObject geneSetVO)

Description copied from interface: GeneSetService

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

Specified by:

getTaxonVOforGeneSetVO in interface GeneSetService

Parameters:

geneSetVO - gene set value object

Returns:

the taxon or null if the gene set param was null

getTaxon

@Transactional(readOnly=true)
public Taxon getTaxon(GeneSet geneSet)

Description copied from interface: GeneSetService

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

Specified by:

getTaxon in interface GeneSetService

Parameters:

geneSet - gene set

Returns:

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

getTaxa

@Transactional(readOnly=true)
public Set<Taxon> getTaxa(GeneSet geneSet)

Description copied from interface: GeneSetService

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

Specified by:

getTaxa in interface GeneSetService

removeAll

@Transactional
public int removeAll()

Specified by:

removeAll in interface GeneSetService