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

Interface FactorValueService

All Superinterfaces:

BaseImmutableService<FactorValue>, BaseReadOnlyService<FactorValue>, BaseService<FactorValue>, BaseVoEnabledService<FactorValue,FactorValueValueObject>, FilteringService<FactorValue>, FilteringVoEnabledService<FactorValue,FactorValueValueObject>, SecurableBaseImmutableService<FactorValue>, SecurableBaseReadOnlyService<FactorValue>, SecurableBaseService<FactorValue>, SecurableBaseVoEnabledService<FactorValue,FactorValueValueObject>, SecurableFilteringVoEnabledService<FactorValue,FactorValueValueObject>

All Known Implementing Classes:

FactorValueServiceImpl

public interface FactorValueService
extends SecurableBaseService<FactorValue>, SecurableFilteringVoEnabledService<FactorValue,FactorValueValueObject>

Author:

kelsey

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. because FactorValue.getValue() is 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. do not use, this is only for migrating old-style characteristics to statements and will be removed
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. do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
void	removeStatement(FactorValue fv, Statement c)	Remove a statement from a factor value.
Statement	saveStatement(FactorValue fv, Statement statement)	Create a given statement as per createStatement(FactorValue, Statement) if it is transient, otherwise update an existing statement.
Statement	saveStatementIgnoreAcl(FactorValue fv, Statement statement)	Deprecated. do not use this, it is meant for FactorValue migration only

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, remove, 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

Method Details

loadIgnoreAcls

Collection<FactorValue> loadIgnoreAcls(Set<Long> ids)

Load FactorValues by IDs, ignoring ACLs.

loadAll

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Slice<FactorValue> loadAll(int offset,
 int limit)

Load a slice of FactorValues.

Results are filtered by ACL on the owning ExpressionExperiment.

See Also:

• FactorValueDao.loadAll(int, int)

loadAllIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Collection<Long> loadAllIds()

Load all factor value IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

See Also:

• FactorValueDao.loadAllIds()

loadAllIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Slice<Long> loadAllIds(int offset,
 int limit)

Load a slice of the factor values IDs.

Results are filtered by ACL on the owning ExpressionExperiment.

See Also:

• FactorValueDao.loadAllIds(int, int)

findByValueStartingWith

@Deprecated
@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Collection<FactorValue> findByValueStartingWith(String valuePrefix,
 int maxResults)

Deprecated.

because FactorValue.getValue() is deprecated

Find factor values by their value using a prefix match.

Results are filtered by ACL on the owning ExpressionExperiment.

See Also:

• FactorValueDao.findByValueStartingWith(String, int)

loadWithExperimentalFactor

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
FactorValue loadWithExperimentalFactor(Long id)

loadWithExperimentalFactorOrFail

@Nonnull
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
<T extends Exception> FactorValue loadWithExperimentalFactorOrFail(Long id,
 Function<String,T> exceptionSupplier)
                                                            throws T

Load a FactorValue with an initialized experimental factor or fail.

Throws:

T

getExperimentalFactorCategoriesIgnoreAcls

Map<FactorValue,Characteristic> getExperimentalFactorCategoriesIgnoreAcls(Collection<FactorValue> factorValues)

Obtain the categories of the given factor values.

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

getExpressionExperimentsIgnoreAcls

Map<FactorValue,ExpressionExperiment> getExpressionExperimentsIgnoreAcls(Collection<FactorValue> factorValues)

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

loadWithOldStyleCharacteristics

@Nullable
@Deprecated
@Secured("GROUP_ADMIN")
FactorValue loadWithOldStyleCharacteristics(Long id,
 boolean readOnly)

Deprecated.

do not use this, it is only meant for the purpose of migrating old-style characteristics to statements

Load a FactorValue along with its old-style characteristics.

loadIdsWithNumberOfOldStyleCharacteristics

@Deprecated
@Secured("GROUP_ADMIN")
Map<Long,Integer> loadIdsWithNumberOfOldStyleCharacteristics(Set<Long> excludedIds)

Deprecated.

do not use, this is only for migrating old-style characteristics to statements and will be removed

See Also:

• FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set)

createStatement

@CheckReturnValue
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Statement createStatement(FactorValue factorValue,
 Statement statement)

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

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

Throws:

IllegalArgumentException - if the statement already exists

saveStatement

@CheckReturnValue
@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
Statement saveStatement(FactorValue fv,
 Statement statement)

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

saveStatementIgnoreAcl

@Deprecated
@CheckReturnValue
@Secured("GROUP_ADMIN")
Statement saveStatementIgnoreAcl(FactorValue fv,
 Statement statement)

Deprecated.

do not use this, it is meant for FactorValue migration only

Save a statement ignoring ACLs.

This requires the GROUP_ADMIN authority.

removeStatement

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeStatement(FactorValue fv,
 Statement c)

Remove a statement from a factor value.