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>, SecurableBaseImmutableService<FactorValue>, SecurableBaseReadOnlyService<FactorValue>, SecurableBaseService<FactorValue>, SecurableBaseVoEnabledService<FactorValue,FactorValueValueObject>, SecurableFilteringVoEnabledService<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(FactorValueDao factorValueDao, StatementDao statementDao)

Method Summary

Modifier and Type	Method	Description
Statement	createStatement(FactorValue factorValue, Statement statement)	Create a given statement and add it to the given factor value.
Collection<FactorValue>	findByValueStartingWith(String valuePrefix, int maxResults)	Deprecated.
Map<FactorValue,Characteristic>	getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)	Obtain the categories of the given factor values.
Map<FactorValue,ExpressionExperiment>	getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	For efficiency, only the ID, short name and name of the EEs are populated.
Slice<FactorValue>	loadAll(int offset, int limit)	Load a slice of FactorValues.
Collection<Long>	loadAllIds()	Load all factor value IDs.
Slice<Long>	loadAllIds(int offset, int limit)	Load a slice of the factor values IDs.
Map<Long,Integer>	loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)	Deprecated.
Collection<FactorValue>	loadIgnoreAcls(Set<Long> ids)	Load FactorValues by IDs, ignoring ACLs.
FactorValue	loadWithExperimentalFactor(Long id)
<T extends Exception> FactorValue	loadWithExperimentalFactorOrFail(Long id, Function<String,T> exceptionSupplier)	Load a FactorValue with an initialized experimental factor or fail.
FactorValue	loadWithOldStyleCharacteristics(Long id, boolean readOnly)	Deprecated.
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, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, 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, 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.BaseReadOnlyService

countAll, getElementClass, loadOrFail, loadOrFail

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery

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

create, create, findOrCreate, 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, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

load, load, loadIds, loadValueObjects, loadValueObjects

Constructor Details

FactorValueServiceImpl

@Autowired
public FactorValueServiceImpl(FactorValueDao factorValueDao,
 StatementDao statementDao)

Method Details

loadWithExperimentalFactor

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

Specified by:

loadWithExperimentalFactor in interface FactorValueService

loadWithExperimentalFactorOrFail

@Nonnull
@Transactional(readOnly=true)
public <T extends Exception> FactorValue loadWithExperimentalFactorOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                                   throws T

Description copied from interface: FactorValueService

Load a FactorValue with an initialized experimental factor or fail.

Specified by:

loadWithExperimentalFactorOrFail in interface FactorValueService

Throws:

T

getExperimentalFactorCategoriesIgnoreAcls

@Transactional(readOnly=true)
public Map<FactorValue,Characteristic> getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)

Description copied from interface: FactorValueService

Obtain the categories of the given factor values.

This can be used as a lightweight alternative to loading the full experimental factor.

Specified by:

getExperimentalFactorCategoriesIgnoreAcls in interface FactorValueService

getExpressionExperimentsIgnoreAcls

@Transactional(readOnly=true)
public Map<FactorValue,ExpressionExperiment> getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)

Description copied from interface: FactorValueService

For efficiency, only the ID, short name and name of the EEs are populated.

Specified by:

getExpressionExperimentsIgnoreAcls 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)

loadIgnoreAcls

@Transactional(readOnly=true)
public Collection<FactorValue> loadIgnoreAcls(Set<Long> ids)

Description copied from interface: FactorValueService

Load FactorValues by IDs, ignoring ACLs.

Specified by:

loadIgnoreAcls in interface FactorValueService

loadAll

@Transactional(readOnly=true)
public Slice<FactorValue> loadAll(int offset,
 int limit)

Description copied from interface: FactorValueService

Load a slice of FactorValues.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

loadAll in interface FactorValueService

See Also:

• FactorValueDao.loadAll(int, int)

loadAllIds

@Transactional(readOnly=true)
public Collection<Long> loadAllIds()

Description copied from interface: FactorValueService

Load all factor value IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

loadAllIds in interface FactorValueService

See Also:

• FactorValueDao.loadAllIds()

loadAllIds

@Transactional(readOnly=true)
public Slice<Long> loadAllIds(int offset,
 int limit)

Description copied from interface: FactorValueService

Load a slice of the factor values IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

loadAllIds in interface FactorValueService

See Also:

• FactorValueDao.loadAllIds(int, int)

findByValueStartingWith

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

Deprecated.

Description copied from interface: FactorValueService

Find factor values by their value using a prefix match.

Results are filtered by ACL on the owning ExpressionExperiment.

Specified by:

findByValueStartingWith in interface FactorValueService

See Also:

• FactorValueDao.findByValueStartingWith(String, int)

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 SecurableBaseImmutableService<FactorValue>

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>

Specified by:

remove in interface SecurableBaseImmutableService<FactorValue>

Overrides:

remove in class AbstractService<FactorValue>

Parameters:

entities - the entities to be removed.