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

Class FactorValueServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<FactorValue,FactorValueValueObject>

ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl

All Implemented Interfaces:

BaseImmutableService<FactorValue>, BaseReadOnlyService<FactorValue>, BaseService<FactorValue>, BaseVoEnabledService<FactorValue,FactorValueValueObject>, FactorValueService, FilteringService<FactorValue>, FilteringVoEnabledService<FactorValue,FactorValueValueObject>

@Service
public class FactorValueServiceImpl
extends AbstractFilteringVoEnabledService<FactorValue,FactorValueValueObject>
implements FactorValueService

Spring Service base class for FactorValueService, provides access to all services and entities referenced by this service.

Author:

pavlidis, keshav

See Also:

• FactorValueService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
FactorValueServiceImpl(ExpressionExperimentService expressionExperimentService, AuditTrailService auditTrailService, AuditEventService auditEventService, FactorValueDao factorValueDao, StatementDao statementDao)

Method Summary

Modifier and Type	Method	Description
void	clearNeedsAttentionFlag(FactorValue factorValue, String note)	Clear a needs attention flag on a given factor value.
Statement	createStatement(FactorValue factorValue, Statement statement)	Create a given statement and add it to the given factor value.
Collection<FactorValue>	findByValue(String valuePrefix, int maxResults)	Deprecated.
Map<Long,Integer>	loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)	Deprecated.
FactorValue	loadWithExperimentalFactor(Long id)
FactorValue	loadWithExperimentalFactorOrFail(Long id)	Load a FactorValue with an initialized experimental factor or fail.
FactorValue	loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
void	markAsNeedsAttention(FactorValue factorValue, String note)	Mark a given factor value as needs attention.
void	remove(Collection<FactorValue> entities)	Removes all the given entities from persistent storage.
void	remove(FactorValue entity)	Removes the given entity from the persistent storage.
void	removeStatement(FactorValue fv, Statement statement)	Remove a statement from a factor value.
Statement	saveStatement(FactorValue fv, Statement statement)	Create a given statement as per FactorValueService.createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.
Statement	saveStatementIgnoreAcl(FactorValue fv, Statement statement)	Save a statement ignoring ACLs.

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds

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, 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

create, create, remove

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

countAll, find, findOrFail, getElementClass, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

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

save, save

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

findOrCreate, load, update, update

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Details

FactorValueServiceImpl

@Autowired
public FactorValueServiceImpl(ExpressionExperimentService expressionExperimentService,
 AuditTrailService auditTrailService,
 AuditEventService auditEventService,
 FactorValueDao factorValueDao,
 StatementDao statementDao)

Method Details

loadWithExperimentalFactor

@Transactional(readOnly=true)
public FactorValue loadWithExperimentalFactor(Long id)

Specified by:

loadWithExperimentalFactor in interface FactorValueService

loadWithExperimentalFactorOrFail

@Transactional(readOnly=true)
public FactorValue loadWithExperimentalFactorOrFail(Long id)

Description copied from interface: FactorValueService

Load a FactorValue with an initialized experimental factor or fail.

Specified by:

loadWithExperimentalFactorOrFail in interface FactorValueService

loadWithOldStyleCharacteristics

@Deprecated
@Transactional(readOnly=true)
public FactorValue loadWithOldStyleCharacteristics(Long id,
 boolean readOnly)

Deprecated.

Description copied from interface: FactorValueService

Load a FactorValue along with its old-style characteristics.

Specified by:

loadWithOldStyleCharacteristics in interface FactorValueService

loadIdsWithNumberOfOldStyleCharacteristics

@Deprecated
@Transactional(readOnly=true)
public Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)

Deprecated.

Specified by:

loadIdsWithNumberOfOldStyleCharacteristics in interface FactorValueService

See Also:

• FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set)

findByValue

@Deprecated
@Transactional(readOnly=true)
public Collection<FactorValue> findByValue(String valuePrefix,
 int maxResults)

Deprecated.

Specified by:

findByValue in interface FactorValueService

createStatement

@Transactional
public Statement createStatement(FactorValue factorValue,
 Statement statement)

Description copied from interface: FactorValueService

Create a given statement and add it to the given factor value.

Specified by:

createStatement in interface FactorValueService

Parameters:

factorValue - the factor value to add the statement to

statement - the statement to be created and added to the factor value

Returns:

the created statement

saveStatement

@Transactional
public Statement saveStatement(FactorValue fv,
 Statement statement)

Description copied from interface: FactorValueService

Create a given statement as per FactorValueService.createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.

Specified by:

saveStatement in interface FactorValueService

saveStatementIgnoreAcl

@Transactional
public Statement saveStatementIgnoreAcl(FactorValue fv,
 Statement statement)

Description copied from interface: FactorValueService

Save a statement ignoring ACLs.

This requires the GROUP_ADMIN authority.

Specified by:

saveStatementIgnoreAcl in interface FactorValueService

removeStatement

@Transactional
public void removeStatement(FactorValue fv,
 Statement statement)

Description copied from interface: FactorValueService

Remove a statement from a factor value.

Specified by:

removeStatement in interface FactorValueService

remove

@Transactional
public void remove(FactorValue entity)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<FactorValue>

Specified by:

remove in interface FactorValueService

Overrides:

remove in class AbstractService<FactorValue>

Parameters:

entity - the entity to be removed.

remove

@Transactional
public void remove(Collection<FactorValue> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<FactorValue>

Overrides:

remove in class AbstractService<FactorValue>

Parameters:

entities - the entities to be removed.

markAsNeedsAttention

@Transactional
public void markAsNeedsAttention(FactorValue factorValue,
 String note)

Description copied from interface: FactorValueService

Mark a given factor value as needs attention.

Specified by:

markAsNeedsAttention in interface FactorValueService

Parameters:

factorValue - a factor value to mark as needs attention

note - note to use for the FactorValueNeedsAttentionEvent

clearNeedsAttentionFlag

@Transactional
public void clearNeedsAttentionFlag(FactorValue factorValue,
 String note)

Description copied from interface: FactorValueService

Clear a needs attention flag on a given factor value.

Specified by:

clearNeedsAttentionFlag in interface FactorValueService

Parameters:

factorValue - a factor value whose needs flag will be cleared

note - a note to use for the DoesNotNeedAttentionEvent if the dataset does not need attention for any other reason.