Class FactorValueReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.FactorValueReadServiceImpl

All Implemented Interfaces:

FactorValueReadService

@Service("factorValueReadService")
public class FactorValueReadServiceImpl
extends Object
implements FactorValueReadService

Implementation of FactorValueReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade FactorValueService interface — this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• FactorValueService

Constructor Summary

Constructors

Constructor	Description
FactorValueReadServiceImpl(FactorValueDao factorValueDao)

Method Summary

Modifier and Type	Method	Description
Collection<FactorValue>	findByValueStartingWith(String valuePrefix, int maxResults)
Map<FactorValue, Characteristic>	getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)	Return the experimental factor categories of the given factor values.
Map<FactorValue, ExpressionExperiment>	getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)	Return the ExpressionExperiment that owns each of the given factor values.
Slice<FactorValue>	loadAll(int offset, int limit)
Collection<Long>	loadAllIds()
Slice<Long>	loadAllIds(int offset, int limit)
Map<Long,Integer>	loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)
Collection<FactorValue>	loadIgnoreAcls(Set<Long> ids)	Load FactorValues by IDs, ignoring ACLs.
FactorValue	loadWithExperimentalFactor(Long id)	Load a FactorValue by id and eagerly initialize its experimental factor.
<T extends Exception> FactorValue	loadWithExperimentalFactorOrFail(Long id, Function<String,T> exceptionSupplier)	Load a FactorValue with an initialized experimental factor, or throw the supplied exception if no such factor value exists.
FactorValue	loadWithOldStyleCharacteristics(Long id, boolean readOnly)

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

FactorValueReadServiceImpl

@Autowired
public FactorValueReadServiceImpl(FactorValueDao factorValueDao)

Method Details

loadWithExperimentalFactor

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

Description copied from interface: FactorValueReadService

Load a FactorValue by id and eagerly initialize its experimental factor.

Specified by:

loadWithExperimentalFactor in interface FactorValueReadService

loadWithExperimentalFactorOrFail

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

Description copied from interface: FactorValueReadService

Load a FactorValue with an initialized experimental factor, or throw the supplied exception if no such factor value exists.

Specified by:

loadWithExperimentalFactorOrFail in interface FactorValueReadService

Throws:

T

getExperimentalFactorCategoriesIgnoreAcls

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

Description copied from interface: FactorValueReadService

Return the experimental factor categories of the given factor values.

Specified by:

getExperimentalFactorCategoriesIgnoreAcls in interface FactorValueReadService

See Also:

• FactorValueDao.getExperimentalFactorCategories(Collection)

getExpressionExperimentsIgnoreAcls

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

Description copied from interface: FactorValueReadService

Return the ExpressionExperiment that owns each of the given factor values.

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

Specified by:

getExpressionExperimentsIgnoreAcls in interface FactorValueReadService

See Also:

• FactorValueDao.getExpressionExperimentsIgnoreAcls(Collection)

loadWithOldStyleCharacteristics

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

Specified by:

loadWithOldStyleCharacteristics in interface FactorValueReadService

See Also:

• FactorValueDao.loadWithOldStyleCharacteristics(Long, boolean)

loadIdsWithNumberOfOldStyleCharacteristics

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

Specified by:

loadIdsWithNumberOfOldStyleCharacteristics in interface FactorValueReadService

See Also:

• FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set)

loadIgnoreAcls

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

Description copied from interface: FactorValueReadService

Load FactorValues by IDs, ignoring ACLs.

Specified by:

loadIgnoreAcls in interface FactorValueReadService

loadAll

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

Specified by:

loadAll in interface FactorValueReadService

See Also:

• FactorValueDao.loadAll(int, int)

loadAllIds

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

Specified by:

loadAllIds in interface FactorValueReadService

See Also:

• FactorValueDao.loadAllIds()

loadAllIds

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

Specified by:

loadAllIds in interface FactorValueReadService

See Also:

• FactorValueDao.loadAllIds(int, int)

findByValueStartingWith

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

Specified by:

findByValueStartingWith in interface FactorValueReadService

See Also:

• FactorValueDao.findByValueStartingWith(String, int)