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

Class ExpressionExperimentSetServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl

All Implemented Interfaces:

BaseImmutableService<ExpressionExperimentSet>, BaseReadOnlyService<ExpressionExperimentSet>, BaseService<ExpressionExperimentSet>, BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>, SecurableBaseImmutableService<ExpressionExperimentSet>, SecurableBaseReadOnlyService<ExpressionExperimentSet>, SecurableBaseService<ExpressionExperimentSet>, SecurableBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>, ExpressionExperimentSetService

@Service
public class ExpressionExperimentSetServiceImpl
extends AbstractVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
implements ExpressionExperimentSetService

Spring Service base class for ubic.gemma.model.analysis.expression.ExpressionExperimentSetService, provides access to all services and entities referenced by this service.

See Also:

• ExpressionExperimentSetService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao expressionExperimentSetDao, ExpressionExperimentService expressionExperimentService)

Method Summary

Modifier and Type	Method	Description
Collection<ExpressionExperimentSet>	find(ExpressionExperiment ee)
Collection<ExpressionExperimentSet>	findByAccession(String accession)
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)	Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.".
boolean	isAutomaticallyGenerated(String experimentSetDescription)	Determines if set was automatically generated by matching the description to that used in ubic.gemma.core.analysis.expression .coexpression.ExpressionExperimentSetService.AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
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.
int	removeFromSets(ExpressionExperiment bas)	Remove an experiment from all sets it is in.
ExpressionExperimentSet	thaw(ExpressionExperimentSet expressionExperimentSet)
void	update(Collection<ExpressionExperimentSet> entities)
void	update(ExpressionExperimentSet expressionExperimentSet)

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

loadAllValueObjects, loadValueObject, 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, save, save, streamAll, streamAll

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.BaseReadOnlyService

countAll, getElementClass, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, create, findOrCreate, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjects

Constructor Details

ExpressionExperimentSetServiceImpl

@Autowired
public ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao expressionExperimentSetDao,
 ExpressionExperimentService expressionExperimentService)

Method Details

find

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSet> find(ExpressionExperiment ee)

Specified by:

find in interface ExpressionExperimentSetService

findByName

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

Description copied from interface: ExpressionExperimentSetService

security at DAO level

Specified by:

findByName in interface ExpressionExperimentSetService

Parameters:

name - name

Returns:

collection of ee sets

findByAccession

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSet> findByAccession(String accession)

Specified by:

findByAccession in interface ExpressionExperimentSetService

findIds

@Transactional(readOnly=true)
public Collection<Long> findIds(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentSetService

security at DAO level

Specified by:

findIds in interface ExpressionExperimentSetService

Parameters:

ee - BA set

Returns:

collection of IDs

getExperimentsInSet

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getExperimentsInSet(Long id)

Description copied from interface: ExpressionExperimentSetService

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

Specified by:

getExperimentsInSet in interface ExpressionExperimentSetService

Parameters:

id - id

Returns:

collection of ees

getExperimentValueObjectsInSet

@Transactional(readOnly=true)
public Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)

Description copied from interface: ExpressionExperimentSetService

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

Specified by:

getExperimentValueObjectsInSet in interface ExpressionExperimentSetService

Parameters:

id - id

Returns:

value objects or an empty set

initAutomaticallyGeneratedExperimentSet

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

Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.". Mostly for use in Gene2GenePopulationServiceImpl.intializeNewAnalysis(Collection, Taxon, Collection, String, int). By convention, these sets should not be modifiable.

Specified by:

initAutomaticallyGeneratedExperimentSet in interface ExpressionExperimentSetService

isAutomaticallyGenerated

@Transactional(readOnly=true)
public boolean isAutomaticallyGenerated(String experimentSetDescription)

Determines if set was automatically generated by matching the description to that used in ubic.gemma.core.analysis.expression .coexpression.ExpressionExperimentSetService.AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION

Specified by:

isAutomaticallyGenerated in interface ExpressionExperimentSetService

Returns:

true if the set was automatically generated, false otherwise

loadAllExperimentSetsWithTaxon

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()

Description copied from interface: ExpressionExperimentSetService

Security at DAO level.

Specified by:

loadAllExperimentSetsWithTaxon in interface ExpressionExperimentSetService

Returns:

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

loadAllExperimentSetValueObjects

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSetValueObject> loadAllExperimentSetValueObjects(boolean loadEEIds)

Description copied from interface: ExpressionExperimentSetService

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

Specified by:

loadAllExperimentSetValueObjects in interface ExpressionExperimentSetService

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

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSetValueObject> loadMySetValueObjects(boolean loadEEIds)

Description copied from interface: ExpressionExperimentSetService

load the user's sets

Specified by:

loadMySetValueObjects in interface ExpressionExperimentSetService

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

@Transactional(readOnly=true)
public ExpressionExperimentSetValueObject loadValueObjectById(Long id,
 boolean loadEEIds)

Description copied from interface: ExpressionExperimentSetService

Get a value object for the id param.

Specified by:

loadValueObjectById in interface ExpressionExperimentSetService

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

@Transactional(readOnly=true)
public ExpressionExperimentSetValueObject loadValueObjectById(Long id)

Specified by:

loadValueObjectById in interface BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

Specified by:

loadValueObjectById in interface SecurableBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

Overrides:

loadValueObjectById in class AbstractVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

See Also:

• BaseVoEnabledDao.loadValueObjectById(Long)

loadValueObjectsByIds

@Transactional(readOnly=true)
public 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>

Specified by:

loadValueObjectsByIds in interface SecurableBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

Overrides:

loadValueObjectsByIds in class AbstractVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

thaw

@Transactional(readOnly=true)
public ExpressionExperimentSet thaw(ExpressionExperimentSet expressionExperimentSet)

Specified by:

thaw in interface ExpressionExperimentSetService

update

@Transactional
public void update(ExpressionExperimentSet expressionExperimentSet)

Specified by:

update in interface BaseService<ExpressionExperimentSet>

Specified by:

update in interface SecurableBaseService<ExpressionExperimentSet>

Overrides:

update in class AbstractService<ExpressionExperimentSet>

See Also:

• BaseDao.update(Identifiable)

update

@Transactional
public void update(Collection<ExpressionExperimentSet> entities)

Specified by:

update in interface BaseService<ExpressionExperimentSet>

Specified by:

update in interface SecurableBaseService<ExpressionExperimentSet>

Overrides:

update in class AbstractService<ExpressionExperimentSet>

See Also:

• BaseDao.update(Collection)

removeFromSets

@Transactional
public int removeFromSets(ExpressionExperiment bas)

Description copied from interface: ExpressionExperimentSetService

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.

Specified by:

removeFromSets in interface ExpressionExperimentSetService

Returns:

the number of sets this experiment was removed from