Class FactorValueServiceImpl
- java.lang.Object
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- ubic.gemma.persistence.service.AbstractService<O>
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- ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<FactorValue,FactorValueValueObject>
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- ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl
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- 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
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Field Summary
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Fields inherited from class ubic.gemma.persistence.service.AbstractService
log
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Constructor Summary
Constructors Constructor Description FactorValueServiceImpl(ExpressionExperimentService expressionExperimentService, AuditTrailService auditTrailService, AuditEventService auditEventService, FactorValueDao factorValueDao, StatementDao statementDao)
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Method Summary
All Methods Instance Methods Concrete Methods Deprecated Methods 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)
Deprecated.Map<Long,Integer>
loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)
Deprecated.FactorValue
loadWithExperimentalFactor(Long id)
FactorValue
loadWithExperimentalFactorOrFail(Long id)
Load aFactorValue
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 perFactorValueService.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, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds
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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, update, update
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService
create, create, remove
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Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll, find, findOrFail, getElementClass, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail
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Methods inherited from interface ubic.gemma.persistence.service.BaseService
save, save
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds
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Methods inherited from interface ubic.gemma.persistence.service.expression.experiment.FactorValueService
findOrCreate, load, update, update
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Methods inherited from interface ubic.gemma.persistence.service.FilteringService
count, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds
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Methods inherited from interface ubic.gemma.persistence.service.FilteringVoEnabledService
loadValueObjects, loadValueObjects
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Constructor Detail
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FactorValueServiceImpl
@Autowired public FactorValueServiceImpl(ExpressionExperimentService expressionExperimentService, AuditTrailService auditTrailService, AuditEventService auditEventService, FactorValueDao factorValueDao, StatementDao statementDao)
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Method Detail
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loadWithExperimentalFactor
@Transactional(readOnly=true) public FactorValue loadWithExperimentalFactor(Long id)
- Specified by:
loadWithExperimentalFactor
in interfaceFactorValueService
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loadWithExperimentalFactorOrFail
@Transactional(readOnly=true) public FactorValue loadWithExperimentalFactorOrFail(Long id)
Description copied from interface:FactorValueService
Load aFactorValue
with an initialized experimental factor or fail.- Specified by:
loadWithExperimentalFactorOrFail
in interfaceFactorValueService
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loadWithOldStyleCharacteristics
@Deprecated @Transactional(readOnly=true) public FactorValue loadWithOldStyleCharacteristics(Long id, boolean readOnly)
Deprecated.Description copied from interface:FactorValueService
Load aFactorValue
along with its old-style characteristics.- Specified by:
loadWithOldStyleCharacteristics
in interfaceFactorValueService
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loadIdsWithNumberOfOldStyleCharacteristics
@Deprecated @Transactional(readOnly=true) public Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)
Deprecated.- Specified by:
loadIdsWithNumberOfOldStyleCharacteristics
in interfaceFactorValueService
- See Also:
FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set)
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findByValue
@Deprecated @Transactional(readOnly=true) public Collection<FactorValue> findByValue(String valuePrefix)
Deprecated.- Specified by:
findByValue
in interfaceFactorValueService
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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 interfaceFactorValueService
- Parameters:
factorValue
- the factor value to add the statement tostatement
- the statement to be created and added to the factor value- Returns:
- the created statement
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saveStatement
@Transactional public Statement saveStatement(FactorValue fv, Statement statement)
Description copied from interface:FactorValueService
Create a given statement as perFactorValueService.createStatement(FactorValue, Statement)
if it is transient, otherwise update an existing statement.- Specified by:
saveStatement
in interfaceFactorValueService
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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 interfaceFactorValueService
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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 interfaceFactorValueService
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remove
@Transactional public void remove(FactorValue entity)
Description copied from interface:BaseImmutableService
Removes the given entity from the persistent storage.- Specified by:
remove
in interfaceBaseImmutableService<FactorValue>
- Specified by:
remove
in interfaceFactorValueService
- Overrides:
remove
in classAbstractService<FactorValue>
- Parameters:
entity
- the entity to be removed.
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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 interfaceBaseImmutableService<FactorValue>
- Overrides:
remove
in classAbstractService<FactorValue>
- Parameters:
entities
- the entities to be removed.
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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 interfaceFactorValueService
- Parameters:
factorValue
- a factor value to mark as needs attentionnote
- note to use for theFactorValueNeedsAttentionEvent
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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 interfaceFactorValueService
- Parameters:
factorValue
- a factor value whose needs flag will be clearednote
- a note to use for theDoesNotNeedAttentionEvent
if the dataset does not need attention for any other reason.
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