Package ubic.gemma.persistence.service.expression.arrayDesign

Class ArrayDesignDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<ArrayDesign>

ubic.gemma.persistence.service.AbstractVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<ArrayDesign,ArrayDesignValueObject>

ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseDao<ArrayDesign>, BaseVoEnabledDao<ArrayDesign,ArrayDesignValueObject>, CachedFilteringDao<ArrayDesign>, CachedFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>, CuratableDao<ArrayDesign>, ArrayDesignDao, FilteringDao<ArrayDesign>, FilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

@Repository
public class ArrayDesignDaoImpl
extends AbstractCuratableDao<ArrayDesign,ArrayDesignValueObject>
implements ArrayDesignDao

Author:

pavlidis

See Also:

• ArrayDesign

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Field Summary

Fields inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

CURATION_DETAILS_ALIAS

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

REPORT_SLOW_QUERY_AFTER_MS

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

log

Fields inherited from interface ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao

OBJECT_ALIAS

Constructor Summary

Constructors

Constructor	Description
ArrayDesignDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
void	addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
protected void	configureFilterableProperties(AbstractFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>.FilterablePropertiesConfigurer configurer)	Register filterable properties.
long	countBioSequences(ArrayDesign arrayDesign)
long	countBlatResults(ArrayDesign arrayDesign)
long	countCompositeSequences(ArrayDesign arrayDesign)
long	countCompositeSequencesWithBioSequences()
long	countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)
long	countCompositeSequencesWithBlatResults()
long	countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)
long	countCompositeSequencesWithGenes(boolean useGene2Cs)
long	countCompositeSequencesWithGenes(Collection<ArrayDesign> arrayDesigns, boolean useGene2Cs)
long	countCompositeSequencesWithGenes(ArrayDesign arrayDesign, boolean useGene2Cs)
long	countExpressionExperiments(ArrayDesign arrayDesign)	Obtain the number of associated expression experiments.
long	countGenes(boolean useGene2Cs)
long	countGenes(ArrayDesign arrayDesign, boolean useGene2Cs)
long	countSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Count the number of switched ExpressionExperiment from a given platform.
void	deleteAlignmentData(ArrayDesign arrayDesign)
void	deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	deleteGeneProductAssociations(ArrayDesign arrayDesign)
protected ArrayDesignValueObject	doLoadValueObject(ArrayDesign ad)	Loads a single value objects for the given array design.
ArrayDesign	find(ArrayDesign entity)	Does a look-up for the given entity in the persistent storage, usually looking for a specific identifier if Identifiable.getId() is set or a business key.
Collection<ArrayDesign>	findByAlternateName(String queryString)
Collection<ArrayDesign>	findByCompositeSequenceName(String name)
Collection<ArrayDesign>	findByManufacturer(String queryString)
Collection<ArrayDesign>	findByName(String name)
ArrayDesign	findByShortName(String shortName)
Collection<ArrayDesign>	findByTaxon(Taxon taxon)
ArrayDesign	findOneByAlternateName(String name)
ArrayDesign	findOneByName(String name)
Collection<BioAssay>	getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Map<Long,Collection<AuditEvent>>	getAuditEvents(Collection<Long> ids)
Map<CompositeSequence,BioSequence>	getBioSequences(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	getExpressionExperiments(ArrayDesign arrayDesign)
protected Query	getFilteringCountQuery(Filters filters)	Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
protected Query	getFilteringIdQuery(Filters filters, Sort sort)	Produce a query that will be used to retrieve IDs of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
protected Query	getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving value objects after applying a set of filters and a given ordering.
Collection<Gene>	getGenes(ArrayDesign arrayDesign, boolean useGene2Cs)	Obtain all the genes associated to the platform.
Map<CompositeSequence,Set<Gene>>	getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesigns, boolean useGene2Cs)
Map<CompositeSequence,Set<Gene>>	getGenesByCompositeSequence(ArrayDesign arrayDesign, boolean useGene2Cs)	Obtain all the genes associated to the platform organized by corresponding design elements.
Map<Taxon,Long>	getPerTaxonCount()
Collection<ExpressionExperiment>	getSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
Collection<Taxon>	getTaxaFromBioSequences(ArrayDesign arrayDesign)	Obtain all the taxa associated to the BioSequence of the given platform.
protected void	initializeCachedFilteringResult(ArrayDesign ad)	Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
Map<Long,Boolean>	isMerged(Collection<Long> ids)
Map<Long,Boolean>	isMergee(Collection<Long> ids)
Map<Long,Boolean>	isSubsumed(Collection<Long> ids)
Map<Long,Boolean>	isSubsumer(Collection<Long> ids)
Map<CompositeSequence,Collection<BlatResult>>	loadAlignments(ArrayDesign arrayDesign)
Collection<ArrayDesign>	loadAllGenericGenePlatforms()
Slice<ArrayDesignValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Collection<CompositeSequence>	loadCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
List<ArrayDesignValueObject>	loadValueObjectsForEE(Long eeId)
protected void	postProcessValueObjects(List<ArrayDesignValueObject> results)	Post-process VOs in bulk.
void	remove(ArrayDesign arrayDesign)	Remove a persistent entity.
void	removeBiologicalCharacteristics(ArrayDesign arrayDesign)
protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder	resolveFilterablePropertyMeta(String propertyName)	Obtain various meta-information used to infer what to use in a Filter or Sort.
void	thaw(ArrayDesign arrayDesign)	Thaw the given platform as per ArrayDesignDao.thawLite(ArrayDesign) with its probes and genes.
void	thawCompositeSequences(ArrayDesign arrayDesign)	Only thaw the design elements of a given platform.
void	thawLite(ArrayDesign arrayDesign)	Lightly thaw the given platform.
boolean	updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)

Methods inherited from class ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao

addEventsToMap, addNonTroubledFilter, distinctIfNecessary, formNativeNonTroubledClause, formNonTroubledClause, groupByIfNecessary, loadTroubledIds, updateCurationDetailsFromAuditEvent

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

count, countWithCache, getEntityTransformer, getValueObjectTransformer, load, load, loadIds, loadIdsWithCache, loadValueObjects, loadValueObjects, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

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

afterPropertiesSet, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyMeta, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, resolveFilterablePropertyMeta

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

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

countAll, create, create, findByProperty, findByPropertyIn, findIdByProperty, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao

countAll, create, create, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

countWithCache, loadIdsWithCache, loadWithCache, loadWithCache

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

loadValueObjectsWithCache, loadValueObjectsWithCache

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao

loadTroubledIds, updateCurationDetailsFromAuditEvent

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Details

ArrayDesignDaoImpl

@Autowired
public ArrayDesignDaoImpl(SessionFactory sessionFactory)

Method Details

loadAllGenericGenePlatforms

public Collection<ArrayDesign> loadAllGenericGenePlatforms()

Specified by:

loadAllGenericGenePlatforms in interface ArrayDesignDao

addProbes

public void addProbes(ArrayDesign arrayDesign,
 Collection<CompositeSequence> newProbes)

Specified by:

addProbes in interface ArrayDesignDao

deleteAlignmentData

public void deleteAlignmentData(ArrayDesign arrayDesign)

Specified by:

deleteAlignmentData in interface ArrayDesignDao

deleteGeneProductAlignmentAssociations

public void deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)

Specified by:

deleteGeneProductAlignmentAssociations in interface ArrayDesignDao

deleteGeneProductAnnotationAssociations

public void deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)

Specified by:

deleteGeneProductAnnotationAssociations in interface ArrayDesignDao

loadBlacklistedValueObjects

public Slice<ArrayDesignValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Specified by:

loadBlacklistedValueObjects in interface ArrayDesignDao

deleteGeneProductAssociations

public void deleteGeneProductAssociations(ArrayDesign arrayDesign)

Specified by:

deleteGeneProductAssociations in interface ArrayDesignDao

findByShortName

public ArrayDesign findByShortName(String shortName)

Specified by:

findByShortName in interface ArrayDesignDao

findByName

public Collection<ArrayDesign> findByName(String name)

Specified by:

findByName in interface ArrayDesignDao

findOneByName

public ArrayDesign findOneByName(String name)

Specified by:

findOneByName in interface ArrayDesignDao

findByCompositeSequenceName

public Collection<ArrayDesign> findByCompositeSequenceName(String name)

Specified by:

findByCompositeSequenceName in interface ArrayDesignDao

find

public ArrayDesign find(ArrayDesign entity)

Description copied from interface: BaseDao

Does a look-up for the given entity in the persistent storage, usually looking for a specific identifier if Identifiable.getId() is set or a business key.

Specified by:

find in interface BaseDao<ArrayDesign>

Overrides:

find in class AbstractDao<ArrayDesign>

Parameters:

entity - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

findByAlternateName

public Collection<ArrayDesign> findByAlternateName(String queryString)

Specified by:

findByAlternateName in interface ArrayDesignDao

findOneByAlternateName

@Nullable
public ArrayDesign findOneByAlternateName(String name)

Specified by:

findOneByAlternateName in interface ArrayDesignDao

findByManufacturer

public Collection<ArrayDesign> findByManufacturer(String queryString)

Specified by:

findByManufacturer in interface ArrayDesignDao

findByTaxon

public Collection<ArrayDesign> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface ArrayDesignDao

getAllAssociatedBioAssays

public Collection<BioAssay> getAllAssociatedBioAssays(ArrayDesign arrayDesign)

Specified by:

getAllAssociatedBioAssays in interface ArrayDesignDao

getAuditEvents

public Map<Long,Collection<AuditEvent>> getAuditEvents(Collection<Long> ids)

Specified by:

getAuditEvents in interface ArrayDesignDao

getBioSequences

public Map<CompositeSequence,BioSequence> getBioSequences(ArrayDesign arrayDesign)

Specified by:

getBioSequences in interface ArrayDesignDao

getGenes

public Collection<Gene> getGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Description copied from interface: ArrayDesignDao

Obtain all the genes associated to the platform.

Specified by:

getGenes in interface ArrayDesignDao

getGenesByCompositeSequence

public Map<CompositeSequence,Set<Gene>> getGenesByCompositeSequence(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Description copied from interface: ArrayDesignDao

Obtain all the genes associated to the platform organized by corresponding design elements.

Specified by:

getGenesByCompositeSequence in interface ArrayDesignDao

getGenesByCompositeSequence

public Map<CompositeSequence,Set<Gene>> getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesigns,
 boolean useGene2Cs)

Specified by:

getGenesByCompositeSequence in interface ArrayDesignDao

getExpressionExperiments

public Collection<ExpressionExperiment> getExpressionExperiments(ArrayDesign arrayDesign)

Specified by:

getExpressionExperiments in interface ArrayDesignDao

countExpressionExperiments

public long countExpressionExperiments(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignDao

Obtain the number of associated expression experiments.

This is much faster than looking up the size of ArrayDesignDao.getExpressionExperiments(ArrayDesign).

Specified by:

countExpressionExperiments in interface ArrayDesignDao

See Also:

• ArrayDesignDao.getExpressionExperiments(ArrayDesign)

getPerTaxonCount

public Map<Taxon,Long> getPerTaxonCount()

Specified by:

getPerTaxonCount in interface ArrayDesignDao

getSwitchedExpressionExperiments

public Collection<ExpressionExperiment> getSwitchedExpressionExperiments(ArrayDesign arrayDesign)

Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.

Specified by:

getSwitchedExpressionExperiments in interface ArrayDesignDao

Parameters:

arrayDesign - a platform for which the statistic is computed

Returns:

collection of experiment IDs.

countSwitchedExpressionExperiments

public long countSwitchedExpressionExperiments(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignDao

Count the number of switched ExpressionExperiment from a given platform.

Specified by:

countSwitchedExpressionExperiments in interface ArrayDesignDao

See Also:

• ArrayDesignDao.getSwitchedExpressionExperiments(ArrayDesign)

getTaxaFromBioSequences

public Collection<Taxon> getTaxaFromBioSequences(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignDao

Obtain all the taxa associated to the BioSequence of the given platform.

Specified by:

getTaxaFromBioSequences in interface ArrayDesignDao

isMerged

public Map<Long,Boolean> isMerged(Collection<Long> ids)

Specified by:

isMerged in interface ArrayDesignDao

isMergee

public Map<Long,Boolean> isMergee(Collection<Long> ids)

Specified by:

isMergee in interface ArrayDesignDao

isSubsumed

public Map<Long,Boolean> isSubsumed(Collection<Long> ids)

Specified by:

isSubsumed in interface ArrayDesignDao

isSubsumer

public Map<Long,Boolean> isSubsumer(Collection<Long> ids)

Specified by:

isSubsumer in interface ArrayDesignDao

loadAlignments

public Map<CompositeSequence,Collection<BlatResult>> loadAlignments(ArrayDesign arrayDesign)

Specified by:

loadAlignments in interface ArrayDesignDao

loadCompositeSequences

public Collection<CompositeSequence> loadCompositeSequences(ArrayDesign arrayDesign,
 int limit,
 int offset)

Specified by:

loadCompositeSequences in interface ArrayDesignDao

doLoadValueObject

protected ArrayDesignValueObject doLoadValueObject(ArrayDesign ad)

Loads a single value objects for the given array design.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

Parameters:

ad - the array design to be converted to a value object

Returns:

a value object with properties of the given array design.

postProcessValueObjects

protected void postProcessValueObjects(List<ArrayDesignValueObject> results)

Description copied from class: AbstractVoEnabledDao

Post-process VOs in bulk.

Use this as an opportunity to load extra informations that could not be populated in the initial AbstractVoEnabledDao.doLoadValueObject(Identifiable) or AbstractVoEnabledDao.doLoadValueObjects(Collection)

Overrides:

postProcessValueObjects in class AbstractVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

loadValueObjectsForEE

public List<ArrayDesignValueObject> loadValueObjectsForEE(@Nullable
 Long eeId)

Specified by:

loadValueObjectsForEE in interface ArrayDesignDao

countCompositeSequencesWithBioSequences

public long countCompositeSequencesWithBioSequences()

Specified by:

countCompositeSequencesWithBioSequences in interface ArrayDesignDao

countCompositeSequencesWithBlatResults

public long countCompositeSequencesWithBlatResults()

Specified by:

countCompositeSequencesWithBlatResults in interface ArrayDesignDao

countCompositeSequencesWithGenes

public long countCompositeSequencesWithGenes(boolean useGene2Cs)

Specified by:

countCompositeSequencesWithGenes in interface ArrayDesignDao

countGenes

public long countGenes(boolean useGene2Cs)

Specified by:

countGenes in interface ArrayDesignDao

countBioSequences

public long countBioSequences(ArrayDesign arrayDesign)

Specified by:

countBioSequences in interface ArrayDesignDao

countBlatResults

public long countBlatResults(ArrayDesign arrayDesign)

Specified by:

countBlatResults in interface ArrayDesignDao

countCompositeSequences

public long countCompositeSequences(ArrayDesign arrayDesign)

Specified by:

countCompositeSequences in interface ArrayDesignDao

countCompositeSequencesWithBioSequences

public long countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)

Specified by:

countCompositeSequencesWithBioSequences in interface ArrayDesignDao

countCompositeSequencesWithBlatResults

public long countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)

Specified by:

countCompositeSequencesWithBlatResults in interface ArrayDesignDao

countCompositeSequencesWithGenes

public long countCompositeSequencesWithGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

countCompositeSequencesWithGenes in interface ArrayDesignDao

countCompositeSequencesWithGenes

public long countCompositeSequencesWithGenes(Collection<ArrayDesign> arrayDesigns,
 boolean useGene2Cs)

Specified by:

countCompositeSequencesWithGenes in interface ArrayDesignDao

countGenes

public long countGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

countGenes in interface ArrayDesignDao

remove

public void remove(ArrayDesign arrayDesign)

Description copied from interface: BaseDao

Remove a persistent entity.

Specified by:

remove in interface BaseDao<ArrayDesign>

Overrides:

remove in class AbstractDao<ArrayDesign>

Parameters:

arrayDesign - the entity to be removed

removeBiologicalCharacteristics

public void removeBiologicalCharacteristics(ArrayDesign arrayDesign)

Specified by:

removeBiologicalCharacteristics in interface ArrayDesignDao

thawLite

public void thawLite(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignDao

Lightly thaw the given platform.

This includes all the to-one relations, but not the design elements.

Specified by:

thawLite in interface ArrayDesignDao

thaw

public void thaw(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignDao

Thaw the given platform as per ArrayDesignDao.thawLite(ArrayDesign) with its probes and genes.

Specified by:

thaw in interface ArrayDesignDao

thawCompositeSequences

public void thawCompositeSequences(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignDao

Only thaw the design elements of a given platform.

Specified by:

thawCompositeSequences in interface ArrayDesignDao

updateSubsumingStatus

public boolean updateSubsumingStatus(ArrayDesign candidateSubsumer,
 ArrayDesign candidateSubsumee)

Specified by:

updateSubsumingStatus in interface ArrayDesignDao

getFilteringQuery

protected Query getFilteringQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query for retrieving value objects after applying a set of filters and a given ordering.

Note that if your implementation does not produce a List of AbstractQueryFilteringVoEnabledDao when Query.list() is invoked, you must override AbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().

The make the cached query (i.e. AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters, Sort) behave the same, you also have to explicitly initialize any lazy relations in AbstractVoEnabledDao.doLoadValueObject(Identifiable) because the VO constructor will not initialize them.

Specified by:

getFilteringQuery in class AbstractQueryFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

Returns:

a Query that produce a list of AbstractQueryFilteringVoEnabledDao

initializeCachedFilteringResult

protected void initializeCachedFilteringResult(ArrayDesign ad)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.

Lazy-loaded relations that are fetched in AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) must be initialized manually in this method to ensure that the entity has all the expected fields if they are retrieved from the second-level cache.

Specified by:

initializeCachedFilteringResult in class AbstractQueryFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

getFilteringIdQuery

protected Query getFilteringIdQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query that will be used to retrieve IDs of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

Overrides:

getFilteringIdQuery in class AbstractQueryFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

getFilteringCountQuery

protected Query getFilteringCountQuery(@Nullable
 Filters filters)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

Overrides:

getFilteringCountQuery in class AbstractQueryFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

Returns:

a Query which must return a single Long value

configureFilterableProperties

protected void configureFilterableProperties(AbstractFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>.FilterablePropertiesConfigurer configurer)

Description copied from class: AbstractFilteringVoEnabledDao

Register filterable properties.

Overrides:

configureFilterableProperties in class AbstractCuratableDao<ArrayDesign,ArrayDesignValueObject>

resolveFilterablePropertyMeta

protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta.FilterablePropertyMetaBuilder resolveFilterablePropertyMeta(String propertyName)

Description copied from class: AbstractCuratableDao

Obtain various meta-information used to infer what to use in a Filter or Sort.

This is used by AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode).

Include filtering by lastUpdated, troubled and needsAttention from the associated curation details.

Overrides:

resolveFilterablePropertyMeta in class AbstractCuratableDao<ArrayDesign,ArrayDesignValueObject>

See Also:

• AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String)
• AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, Collection)
• FilteringDao.getSort(String, Sort.Direction, Sort.NullMode)