ubic.gemma.persistence.service.expression.experiment

Class ExpressionExperimentDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<C,VO>

ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl

All Implemented Interfaces:

BaseDao<ExpressionExperiment>, BaseVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>, BrowsingDao<ExpressionExperiment>, CuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>, ExpressionExperimentDao, FilteringDao<ExpressionExperiment>, FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

@Repository
public class ExpressionExperimentDaoImpl
extends AbstractCuratableDao<ExpressionExperiment,ExpressionExperimentValueObject>
implements ExpressionExperimentDao

Author:

pavlidis

See Also:

ExpressionExperiment

Nested Class Summary

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

AbstractQueryFilteringVoEnabledDao.QueryHint

Field Summary

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

REPORT_SLOW_QUERY_AFTER_MS

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

DEFAULT_BATCH_SIZE, elementClass, log

Fields inherited from interface ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDao

OBJECT_ALIAS

Constructor Summary

Constructors

Constructor and Description
ExpressionExperimentDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method and Description
List<ExpressionExperiment>	browse(int start, int limit)
List<ExpressionExperiment>	browse(int start, int limit, String orderField, boolean descending)
long	countNotTroubled()
long	countTroubledPlatforms(ExpressionExperiment ee) Count the number of distict platforms used that are troubled.
protected ExpressionExperimentValueObject	doLoadValueObject(ExpressionExperiment entity) Load a value object for a given entity.
Collection<Long>	filterByTaxon(Collection<Long> ids, Taxon taxon)
ExpressionExperiment	find(ExpressionExperiment entity) Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Collection<ExpressionExperiment>	findByAccession(DatabaseEntry accession)
Collection<ExpressionExperiment>	findByAccession(String accession)
Collection<ExpressionExperiment>	findByBibliographicReference(Long bibRefID)
ExpressionExperiment	findByBioAssay(BioAssay ba)
ExpressionExperiment	findByBioMaterial(BioMaterial bm)
Map<ExpressionExperiment,BioMaterial>	findByBioMaterials(Collection<BioMaterial> bms)
Collection<ExpressionExperiment>	findByExpressedGene(Gene gene, Double rank)
ExpressionExperiment	findByFactor(ExperimentalFactor ef)
ExpressionExperiment	findByFactorValue(FactorValue fv)
ExpressionExperiment	findByFactorValue(Long factorValueId)
Map<ExpressionExperiment,FactorValue>	findByFactorValues(Collection<FactorValue> fvs)
Collection<ExpressionExperiment>	findByGene(Gene gene)
ExpressionExperiment	findByQuantitationType(QuantitationType quantitationType)
Collection<ExpressionExperiment>	findByTaxon(Taxon taxon)
List<ExpressionExperiment>	findByUpdatedLimit(Collection<Long> ids, int limit)
List<ExpressionExperiment>	findByUpdatedLimit(int limit)
Collection<ExpressionExperiment>	findUpdatedAfter(Date date)
Map<Long,Long>	getAnnotationCounts(Collection<Long> ids)
Collection<? extends AnnotationValueObject>	getAnnotationsByBioMaterials(Long eeId)
Collection<? extends AnnotationValueObject>	getAnnotationsByFactorvalues(Long eeId)
Collection<ArrayDesign>	getArrayDesignsUsed(BioAssaySet bas)
Map<ArrayDesign,Collection<Long>>	getArrayDesignsUsed(Collection<Long> eeids)
Map<Long,Collection<AuditEvent>>	getAuditEvents(Collection<Long> ids)
Collection<BioAssayDimension>	getBioAssayDimensions(ExpressionExperiment expressionExperiment)
long	getBioMaterialCount(ExpressionExperiment expressionExperiment)
protected Query	getCountValueObjectsQuery(Filters filters) Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getLoadValueObjectsQuery(Filters, Sort, EnumSet).
long	getDesignElementDataVectorCount(ExpressionExperiment ee)
Collection<ExpressionExperiment>	getExperimentsLackingPublications()
Collection<ExpressionExperiment>	getExperimentsWithOutliers()
Map<Long,Date>	getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)
Date	getLastArrayDesignUpdate(ExpressionExperiment ee)
protected Query	getLoadValueObjectsQuery(Filters filters, Sort sort, EnumSet<AbstractQueryFilteringVoEnabledDao.QueryHint> hints) Produce a query for retrieving value objects after applying a set of filters and a given ordering.
QuantitationType	getMaskedPreferredQuantitationType(ExpressionExperiment ee) Obtain the masked preferred quantitation type, if available.
Map<Taxon,Long>	getPerTaxonCount()
Map<Long,Long>	getPopulatedFactorCounts(Collection<Long> ids)
Map<Long,Long>	getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)
QuantitationType	getPreferredQuantitationType(ExpressionExperiment ee) Obtain the preferred quantitation type, if available.
Map<QuantitationType,Long>	getQuantitationTypeCount(ExpressionExperiment ee)
Collection<QuantitationType>	getQuantitationTypes(ExpressionExperiment expressionExperiment)
Collection<QuantitationType>	getQuantitationTypes(ExpressionExperiment expressionExperiment, ArrayDesign arrayDesign)
Map<ExpressionExperiment,Collection<AuditEvent>>	getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)
Collection<ExpressionExperimentSubSet>	getSubSets(ExpressionExperiment expressionExperiment)
<T extends BioAssaySet> Map<T,Taxon>	getTaxa(Collection<T> bioAssaySets)
Taxon	getTaxon(BioAssaySet ee)
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjects(Filters filters, Sort sort, int offset, int limit) This is a specialized flavour of ExpressionExperimentDao.loadDetailsValueObjects(Filters, Sort, int, int) for detailed EE VOs.
List<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIds(@NonNull Collection<Long> ids) Like ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection, Taxon, Sort, int, int), but returning a list.
Slice<ExpressionExperimentDetailsValueObject>	loadDetailsValueObjectsByIds(Collection<Long> ids, Taxon taxon, Sort sort, int offset, int limit) Special method for front-end access.
Collection<ExpressionExperiment>	loadLackingFactors()
Collection<ExpressionExperiment>	loadLackingTags()
List<ExpressionExperimentValueObject>	loadValueObjectsPreFilter(Filters filters, Sort sort) Load VOs with minimal ordering and filtering.
Slice<ExpressionExperimentValueObject>	loadValueObjectsPreFilter(Filters filters, Sort sort, int offset, int limit) Load VOs with ordering, filtering and offset/limit.
protected ExpressionExperimentValueObject	processLoadValueObjectsQueryResult(Object result) Process a result from Hibernate into a value object.
void	remove(ExpressionExperiment ee) Remove a persistent instance
void	thaw(ExpressionExperiment expressionExperiment)
void	thawBioAssays(ExpressionExperiment expressionExperiment)
void	thawForFrontEnd(ExpressionExperiment expressionExperiment)
void	thawWithoutVectors(ExpressionExperiment ee)
MeanVarianceRelation	updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
int	updateTroubledByArrayDesign(ArrayDesign arrayDesign, boolean troubled) Update the troubled status of all experiments using a given platform.

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

addEventsToMap, addNonTroubledFilter, create, findByName, findByShortName

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

getObjectAlias, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

doLoadValueObjects

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

countAll, create, createInBatch, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, flush, getElementClass, getSessionFactory, load, load, loadAll, remove, remove, removeAllInBatch, removeInBatch, save, save, saveInBatch, update, update, updateInBatch

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.expression.experiment.ExpressionExperimentDao

loadValueObjectsByIds

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

findByName, findByShortName

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

getElementClass, getObjectAlias

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects

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

countAll, create, create, createInBatch, findOrCreate, load, load, loadAll, remove, remove, removeAllInBatch, removeInBatch, save, save, saveInBatch, update, update, updateInBatch

Constructor Detail

ExpressionExperimentDaoImpl

@Autowired
public ExpressionExperimentDaoImpl(SessionFactory sessionFactory)

Method Detail

browse

public List<ExpressionExperiment> browse(int start,
                                         int limit)

Specified by:

browse in interface BrowsingDao<ExpressionExperiment>

browse

public List<ExpressionExperiment> browse(int start,
                                         int limit,
                                         String orderField,
                                         boolean descending)

Specified by:

browse in interface BrowsingDao<ExpressionExperiment>

countNotTroubled

public long countNotTroubled()

Specified by:

countNotTroubled in interface ExpressionExperimentDao

filterByTaxon

public Collection<Long> filterByTaxon(@Nullable
                                      Collection<Long> ids,
                                      Taxon taxon)

Specified by:

filterByTaxon in interface ExpressionExperimentDao

find

public ExpressionExperiment find(ExpressionExperiment entity)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<ExpressionExperiment>

Overrides:

find in class AbstractDao<ExpressionExperiment>

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.

findByAccession

public Collection<ExpressionExperiment> findByAccession(DatabaseEntry accession)

Specified by:

findByAccession in interface ExpressionExperimentDao

findByAccession

public Collection<ExpressionExperiment> findByAccession(String accession)

Specified by:

findByAccession in interface ExpressionExperimentDao

findByBibliographicReference

public Collection<ExpressionExperiment> findByBibliographicReference(Long bibRefID)

Specified by:

findByBibliographicReference in interface ExpressionExperimentDao

findByBioAssay

public ExpressionExperiment findByBioAssay(BioAssay ba)

Specified by:

findByBioAssay in interface ExpressionExperimentDao

findByBioMaterial

public ExpressionExperiment findByBioMaterial(BioMaterial bm)

Specified by:

findByBioMaterial in interface ExpressionExperimentDao

findByBioMaterials

public Map<ExpressionExperiment,BioMaterial> findByBioMaterials(Collection<BioMaterial> bms)

Specified by:

findByBioMaterials in interface ExpressionExperimentDao

findByExpressedGene

public Collection<ExpressionExperiment> findByExpressedGene(Gene gene,
                                                            Double rank)

Specified by:

findByExpressedGene in interface ExpressionExperimentDao

findByFactor

public ExpressionExperiment findByFactor(ExperimentalFactor ef)

Specified by:

findByFactor in interface ExpressionExperimentDao

findByFactorValue

public ExpressionExperiment findByFactorValue(FactorValue fv)

Specified by:

findByFactorValue in interface ExpressionExperimentDao

findByFactorValue

public ExpressionExperiment findByFactorValue(Long factorValueId)

Specified by:

findByFactorValue in interface ExpressionExperimentDao

findByFactorValues

public Map<ExpressionExperiment,FactorValue> findByFactorValues(Collection<FactorValue> fvs)

Specified by:

findByFactorValues in interface ExpressionExperimentDao

findByGene

public Collection<ExpressionExperiment> findByGene(Gene gene)

Specified by:

findByGene in interface ExpressionExperimentDao

findByQuantitationType

public ExpressionExperiment findByQuantitationType(QuantitationType quantitationType)

Specified by:

findByQuantitationType in interface ExpressionExperimentDao

findByTaxon

public Collection<ExpressionExperiment> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface ExpressionExperimentDao

findByUpdatedLimit

public List<ExpressionExperiment> findByUpdatedLimit(Collection<Long> ids,
                                                     int limit)

Specified by:

findByUpdatedLimit in interface ExpressionExperimentDao

findByUpdatedLimit

public List<ExpressionExperiment> findByUpdatedLimit(int limit)

Specified by:

findByUpdatedLimit in interface ExpressionExperimentDao

findUpdatedAfter

public Collection<ExpressionExperiment> findUpdatedAfter(@Nullable
                                                         Date date)

Specified by:

findUpdatedAfter in interface ExpressionExperimentDao

getAnnotationCounts

public Map<Long,Long> getAnnotationCounts(Collection<Long> ids)

Specified by:

getAnnotationCounts in interface ExpressionExperimentDao

getAnnotationsByBioMaterials

public Collection<? extends AnnotationValueObject> getAnnotationsByBioMaterials(Long eeId)

Specified by:

getAnnotationsByBioMaterials in interface ExpressionExperimentDao

getAnnotationsByFactorvalues

public Collection<? extends AnnotationValueObject> getAnnotationsByFactorvalues(Long eeId)

Specified by:

getAnnotationsByFactorvalues in interface ExpressionExperimentDao

getExperimentsLackingPublications

public Collection<ExpressionExperiment> getExperimentsLackingPublications()

Specified by:

getExperimentsLackingPublications in interface ExpressionExperimentDao

updateTroubledByArrayDesign

public int updateTroubledByArrayDesign(ArrayDesign arrayDesign,
                                       boolean troubled)

Description copied from interface: ExpressionExperimentDao

Update the troubled status of all experiments using a given platform.

Specified by:

updateTroubledByArrayDesign in interface ExpressionExperimentDao

Returns:

the number of expression experiments marked or unmarked as troubled

countTroubledPlatforms

public long countTroubledPlatforms(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentDao

Count the number of distict platforms used that are troubled.

Specified by:

countTroubledPlatforms in interface ExpressionExperimentDao

updateMeanVarianceRelation

public MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
                                                       MeanVarianceRelation mvr)

Specified by:

updateMeanVarianceRelation in interface ExpressionExperimentDao

getArrayDesignsUsed

public Collection<ArrayDesign> getArrayDesignsUsed(BioAssaySet bas)

Specified by:

getArrayDesignsUsed in interface ExpressionExperimentDao

getArrayDesignsUsed

public Map<ArrayDesign,Collection<Long>> getArrayDesignsUsed(Collection<Long> eeids)

Specified by:

getArrayDesignsUsed in interface ExpressionExperimentDao

getAuditEvents

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

Specified by:

getAuditEvents in interface ExpressionExperimentDao

getBioAssayDimensions

public Collection<BioAssayDimension> getBioAssayDimensions(ExpressionExperiment expressionExperiment)

Specified by:

getBioAssayDimensions in interface ExpressionExperimentDao

getBioMaterialCount

public long getBioMaterialCount(ExpressionExperiment expressionExperiment)

Specified by:

getBioMaterialCount in interface ExpressionExperimentDao

getDesignElementDataVectorCount

public long getDesignElementDataVectorCount(ExpressionExperiment ee)

Specified by:

getDesignElementDataVectorCount in interface ExpressionExperimentDao

Parameters:

ee - the expression experiment

Returns:

count of RAW vectors.

getExperimentsWithOutliers

public Collection<ExpressionExperiment> getExperimentsWithOutliers()

Specified by:

getExperimentsWithOutliers in interface ExpressionExperimentDao

getLastArrayDesignUpdate

public Map<Long,Date> getLastArrayDesignUpdate(Collection<ExpressionExperiment> expressionExperiments)

Specified by:

getLastArrayDesignUpdate in interface ExpressionExperimentDao

getLastArrayDesignUpdate

public Date getLastArrayDesignUpdate(ExpressionExperiment ee)

Specified by:

getLastArrayDesignUpdate in interface ExpressionExperimentDao

getPerTaxonCount

public Map<Taxon,Long> getPerTaxonCount()

Specified by:

getPerTaxonCount in interface ExpressionExperimentDao

getPopulatedFactorCounts

public Map<Long,Long> getPopulatedFactorCounts(Collection<Long> ids)

Specified by:

getPopulatedFactorCounts in interface ExpressionExperimentDao

getPopulatedFactorCountsExcludeBatch

public Map<Long,Long> getPopulatedFactorCountsExcludeBatch(Collection<Long> ids)

Specified by:

getPopulatedFactorCountsExcludeBatch in interface ExpressionExperimentDao

getQuantitationTypeCount

public Map<QuantitationType,Long> getQuantitationTypeCount(ExpressionExperiment ee)

Specified by:

getQuantitationTypeCount in interface ExpressionExperimentDao

getQuantitationTypes

public Collection<QuantitationType> getQuantitationTypes(ExpressionExperiment expressionExperiment)

Specified by:

getQuantitationTypes in interface ExpressionExperimentDao

getQuantitationTypes

public Collection<QuantitationType> getQuantitationTypes(ExpressionExperiment expressionExperiment,
                                                         @Nullable
                                                         ArrayDesign arrayDesign)

Specified by:

getQuantitationTypes in interface ExpressionExperimentDao

getPreferredQuantitationType

public QuantitationType getPreferredQuantitationType(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentDao

Obtain the preferred quantitation type, if available.

Specified by:

getPreferredQuantitationType in interface ExpressionExperimentDao

getMaskedPreferredQuantitationType

public QuantitationType getMaskedPreferredQuantitationType(ExpressionExperiment ee)

Description copied from interface: ExpressionExperimentDao

Obtain the masked preferred quantitation type, if available.

Specified by:

getMaskedPreferredQuantitationType in interface ExpressionExperimentDao

getSampleRemovalEvents

public Map<ExpressionExperiment,Collection<AuditEvent>> getSampleRemovalEvents(Collection<ExpressionExperiment> expressionExperiments)

Specified by:

getSampleRemovalEvents in interface ExpressionExperimentDao

getSubSets

public Collection<ExpressionExperimentSubSet> getSubSets(ExpressionExperiment expressionExperiment)

Specified by:

getSubSets in interface ExpressionExperimentDao

getTaxa

public <T extends BioAssaySet> Map<T,Taxon> getTaxa(Collection<T> bioAssaySets)

Specified by:

getTaxa in interface ExpressionExperimentDao

getTaxon

public Taxon getTaxon(BioAssaySet ee)

Specified by:

getTaxon in interface ExpressionExperimentDao

loadDetailsValueObjects

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

Description copied from interface: ExpressionExperimentDao

This is a specialized flavour of ExpressionExperimentDao.loadDetailsValueObjects(Filters, Sort, int, int) for detailed EE VOs.

Specified by:

loadDetailsValueObjects in interface ExpressionExperimentDao

loadDetailsValueObjectsByIds

public Slice<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(@Nullable
                                                                                  Collection<Long> ids,
                                                                                  @Nullable
                                                                                  Taxon taxon,
                                                                                  @Nullable
                                                                                  Sort sort,
                                                                                  int offset,
                                                                                  int limit)

Description copied from interface: ExpressionExperimentDao

Special method for front-end access. This is partly redundant with loadValueObjectsPreFilter; however, it fills in more information, returns ExpressionExperimentDetailsValueObject

Specified by:

loadDetailsValueObjectsByIds in interface ExpressionExperimentDao

Parameters:

ids - only list specific ids, or null to ignore

taxon - only list EEs in the specified taxon, or null to ignore

sort - the field to order the results by.

offset - offset

limit - maximum number of results to return

Returns:

a list of EE details VOs representing experiments matching the given arguments.

loadDetailsValueObjectsByIds

public List<ExpressionExperimentDetailsValueObject> loadDetailsValueObjectsByIds(@NonNull
                                                                                 @NonNull Collection<Long> ids)

Description copied from interface: ExpressionExperimentDao

Like ExpressionExperimentDao.loadDetailsValueObjectsByIds(Collection, Taxon, Sort, int, int), but returning a list.

Specified by:

loadDetailsValueObjectsByIds in interface ExpressionExperimentDao

loadLackingFactors

public Collection<ExpressionExperiment> loadLackingFactors()

Specified by:

loadLackingFactors in interface ExpressionExperimentDao

loadLackingTags

public Collection<ExpressionExperiment> loadLackingTags()

Specified by:

loadLackingTags in interface ExpressionExperimentDao

doLoadValueObject

protected ExpressionExperimentValueObject doLoadValueObject(ExpressionExperiment entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, consider overriding AbstractVoEnabledDao.loadValueObject(Identifiable) or AbstractVoEnabledDao.loadValueObjects(Collection).

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

loadValueObjectsPreFilter

public List<ExpressionExperimentValueObject> loadValueObjectsPreFilter(@Nullable
                                                                       Filters filters,
                                                                       @Nullable
                                                                       Sort sort)

Description copied from interface: FilteringVoEnabledDao

Load VOs with minimal ordering and filtering. Use this as an alternative to FilteringVoEnabledDao.loadValueObjectsPreFilter(Filters, Sort, int, int) if you do not intend to provide pagination capabilities.

Specified by:

loadValueObjectsPreFilter in interface FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

Overrides:

loadValueObjectsPreFilter in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

See Also:

FilteringVoEnabledDao.loadValueObjectsPreFilter(Filters, Sort, int, int)

loadValueObjectsPreFilter

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

Description copied from interface: FilteringVoEnabledDao

Load VOs with ordering, filtering and offset/limit. Consider using FilteringService.getObjectFilter(String, ObjectFilter.Operator, String) and FilteringService.getSort(String, Sort.Direction) to produce the object filters and sort safely from user input.

Specified by:

loadValueObjectsPreFilter in interface FilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

Overrides:

loadValueObjectsPreFilter in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

Parameters:

filters - filters applied on the search. The properties mentioned in the ObjectFilter must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".

sort - an object property and direction to order by. This property must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".

offset - an offset from which entities are retrieved when sorted according to the sort argument, or 0 to ignore

limit - a limit on the number of returned results, or -1 to ignore

Returns:

a slice of the relevant data

processLoadValueObjectsQueryResult

protected ExpressionExperimentValueObject processLoadValueObjectsQueryResult(Object result)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Process a result from Hibernate into a value object. The result is obtained from Query.list(). By default, it will cast the result into a O and then apply AbstractVoEnabledDao.doLoadValueObject(Identifiable) to obtain a value object.

Overrides:

processLoadValueObjectsQueryResult in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

Returns:

a value object, or null, and it will be ignored when constructing the Slice in AbstractQueryFilteringVoEnabledDao.loadValueObjectsPreFilter(Filters, Sort, int, int)

remove

public void remove(ExpressionExperiment ee)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<ExpressionExperiment>

Overrides:

remove in class AbstractDao<ExpressionExperiment>

Parameters:

ee - the entity to be removed

thaw

public void thaw(ExpressionExperiment expressionExperiment)

Specified by:

thaw in interface ExpressionExperimentDao

thawWithoutVectors

public void thawWithoutVectors(ExpressionExperiment ee)

Specified by:

thawWithoutVectors in interface ExpressionExperimentDao

thawBioAssays

public void thawBioAssays(ExpressionExperiment expressionExperiment)

Specified by:

thawBioAssays in interface ExpressionExperimentDao

thawForFrontEnd

public void thawForFrontEnd(ExpressionExperiment expressionExperiment)

Specified by:

thawForFrontEnd in interface ExpressionExperimentDao

getLoadValueObjectsQuery

protected Query getLoadValueObjectsQuery(@Nullable
                                         Filters filters,
                                         @Nullable
                                         Sort sort,
                                         EnumSet<AbstractQueryFilteringVoEnabledDao.QueryHint> hints)

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 O when Query.list() is invoked, you must override AbstractQueryFilteringVoEnabledDao.processLoadValueObjectsQueryResult(Object).

Specified by:

getLoadValueObjectsQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

Returns:

a Query that produce a list of O

getCountValueObjectsQuery

protected Query getCountValueObjectsQuery(@Nullable
                                          Filters filters)

Description copied from class: AbstractQueryFilteringVoEnabledDao

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

Overrides:

getCountValueObjectsQuery in class AbstractQueryFilteringVoEnabledDao<ExpressionExperiment,ExpressionExperimentValueObject>

Returns:

a Query which must return a single Long value