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

Class ExpressionExperimentSetServiceImpl

java.lang.Object

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

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>, 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

Fields inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService

AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao expressionExperimentSetDao)

Method Summary

Modifier and Type	Method	Description
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)	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.
void	setExpressionExperimentService(ExpressionExperimentService expressionExperimentService)
void	setExpressionExperimentValueObjectHelper(ExpressionExperimentSetValueObjectHelper expressionExperimentValueObjectHelper)
void	setSecurityService(gemma.gsec.SecurityService securityService)
void	setTaxonService(TaxonService taxonService)
ExpressionExperimentSet	thaw(ExpressionExperimentSet expressionExperimentSet)
void	update(Collection<ExpressionExperimentSet> entities)	Updates all entities in the given collection in the persistent storage.
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)	update the members of the experiment set with the given ids
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 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, remove, remove, remove, save, save

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

create, findOrCreate, remove, remove

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

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

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

save, save

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

loadAllValueObjects, loadValueObject, loadValueObjects

Methods inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetService

create, load, load, loadAll, remove

Constructor Detail

ExpressionExperimentSetServiceImpl

@Autowired
public ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao expressionExperimentSetDao)

Method Detail

setSecurityService

@Autowired
public void setSecurityService(gemma.gsec.SecurityService securityService)

setExpressionExperimentService

@Autowired
public void setExpressionExperimentService(ExpressionExperimentService expressionExperimentService)

setTaxonService

@Autowired
public void setTaxonService(TaxonService taxonService)

setExpressionExperimentValueObjectHelper

@Autowired
public void setExpressionExperimentValueObjectHelper(ExpressionExperimentSetValueObjectHelper expressionExperimentValueObjectHelper)

createFromValueObject

@Transactional
public ExpressionExperimentSet createFromValueObject(ExpressionExperimentSetValueObject eesvo)

Specified by:

createFromValueObject in interface ExpressionExperimentSetService

deleteDatabaseEntity

@Transactional
public void deleteDatabaseEntity(ExpressionExperimentSetValueObject eesvo)

Description copied from interface: ExpressionExperimentSetService

Security is handled within method, when the set is loaded

Specified by:

deleteDatabaseEntity in interface ExpressionExperimentSetService

Parameters:

eesvo - ee value object

find

@Transactional(readOnly=true)
public Collection<ExpressionExperimentSet> find(BioAssaySet bioAssaySet)

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

findIds

@Transactional(readOnly=true)
public Collection<Long> findIds(BioAssaySet bioAssaySet)

Description copied from interface: ExpressionExperimentSetService

security at DAO level

Specified by:

findIds in interface ExpressionExperimentSetService

Parameters:

bioAssaySet - 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

updateDatabaseEntity

@Transactional
public void updateDatabaseEntity(ExpressionExperimentSetValueObject eesvo)

Description copied from interface: ExpressionExperimentSetService

Update corresponding entity based on value object

Specified by:

updateDatabaseEntity in interface ExpressionExperimentSetService

Parameters:

eesvo - ee value object

updateDatabaseEntityMembers

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

update the members of the experiment set with the given ids

Specified by:

updateDatabaseEntityMembers in interface ExpressionExperimentSetService

Parameters:

groupId - set to update

eeIds - new set member ids

updateDatabaseEntityNameDesc

@Transactional
public ExpressionExperimentSetValueObject updateDatabaseEntityNameDesc(ExpressionExperimentSetValueObject eeSetVO,
                                                                       boolean loadEEIds)

Description copied from interface: ExpressionExperimentSetService

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

Specified by:

updateDatabaseEntityNameDesc in interface ExpressionExperimentSetService

Parameters:

eeSetVO - ee set value object

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:

ee vo

loadValueObjectById

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

Specified by:

loadValueObjectById in interface BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>

Specified by:

loadValueObjectById in interface ExpressionExperimentSetService

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 ExpressionExperimentSetService

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)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<ExpressionExperimentSet>

Specified by:

update in interface ExpressionExperimentSetService

Overrides:

update in class AbstractService<ExpressionExperimentSet>

Parameters:

expressionExperimentSet - the entity to be updated.

See Also:

ExpressionExperimentSetService.update(ExpressionExperimentSet)

update

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

Description copied from interface: BaseService

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

Specified by:

update in interface BaseService<ExpressionExperimentSet>

Overrides:

update in class AbstractService<ExpressionExperimentSet>

Parameters:

entities - the entities to be updated.