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 AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Nested classes/interfaces inherited from interface FilteringDao

FilteringDao.ConjunctSpec

Field Summary

Fields inherited from class AbstractCuratableDao

CURATION_DETAILS_ALIAS

Fields inherited from class AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class AbstractDao

log

Fields inherited from interface 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 org.hibernate.query.Query	getFilteringCountQuery(Filters filters)
protected org.hibernate.query.Query	getFilteringIdQuery(Filters filters, Sort sort)
protected org.hibernate.query.Query	getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving filtered entities or VOs after applying filters and 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 TypedResultTransformer<ArrayDesignValueObject>	getValueObjectTransformer()
protected void	initializeCachedFilteringResult(ArrayDesign ad)	Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from cache.
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()
Map<Long, ArrayDesign>	loadAsMap(Collection<Long> ids)	Load a batch of ArrayDesigns by ID and return them keyed by ID for O(1) per-id lookup.
Slice<ArrayDesignValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
CursorPage<ArrayDesignValueObject>	loadBlacklistedValueObjectsByCursor(Filters filters, Sort sort, Cursor cursor, int limit)	Cursor-mode counterpart to ArrayDesignDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted platforms, applying the same shortName/accession blacklist filter that the offset-mode variant composes — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.
Collection<CompositeSequence>	loadCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
List<ArrayDesignValueObject>	loadOriginalPlatformValueObjectsForEE(Long eeId)	Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.
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 AbstractCuratableDao

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

Methods inherited from class AbstractQueryFilteringVoEnabledDao

count, countWithCache, getEntityTransformer, getQueryCacheRegion, load, load, loadIds, loadIdsWithCache, loadValueObjects, loadValueObjects, loadValueObjectsByCursor, loadValueObjectsByCursorWithCache, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

Methods inherited from class AbstractFilteringVoEnabledDao

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

Methods inherited from class AbstractVoEnabledDao

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class 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 Object

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

Methods inherited from interface BaseDao

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

Methods inherited from interface BaseVoEnabledDao

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface CachedFilteringDao

countWithCache, loadIdsWithCache, loadWithCache, loadWithCache

Methods inherited from interface CachedFilteringVoEnabledDao

loadValueObjectsWithCache, loadValueObjectsWithCache

Methods inherited from interface CuratableDao

loadTroubledIds, updateCurationDetailsFromAuditEvent

Methods inherited from interface FilteringDao

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

Methods inherited from interface FilteringVoEnabledDao

loadValueObjects, loadValueObjects, loadValueObjectsByCursor

Constructor Details

ArrayDesignDaoImpl

@Autowired
public ArrayDesignDaoImpl(SessionFactory sessionFactory)

Method Details

loadAsMap

public Map<Long, ArrayDesign> loadAsMap(Collection<Long> ids)

Description copied from interface: ArrayDesignDao

Load a batch of ArrayDesigns by ID and return them keyed by ID for O(1) per-id lookup. Issues a single WHERE id IN (...) fetch (delegating to the base DAO's BaseDao.load(Collection)), then collects to a map.

Use this in place of N×Session.get(ArrayDesign.class, id) loop patterns — see round-2 perf probe finding #8 (PERF_PROBE_REPORT_ROUND2.md): 20 sequential PK lookups (~138 ms each on the prod tunnel) cost ~2,766 ms, vs ~121 ms for a single batched fetch.

The returned map preserves no ordering. The base loader fetches the AD root entity only — lazy collections (e.g. designElements, compositeSequences) are NOT initialised; callers that need them must thaw explicitly to avoid a secondary N+1.

Specified by:

loadAsMap in interface ArrayDesignDao

Parameters:

ids - platform IDs to load; an empty collection returns an empty map

Returns:

a map of id → ArrayDesign for every id that resolved to a row

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

loadBlacklistedValueObjectsByCursor

public CursorPage<ArrayDesignValueObject> loadBlacklistedValueObjectsByCursor(@Nullable
 Filters filters,
 Sort sort,
 @Nullable
 Cursor cursor,
 int limit)

Description copied from interface: ArrayDesignDao

Cursor-mode counterpart to ArrayDesignDao.loadBlacklistedValueObjects(Filters, Sort, int, int): keyset pagination over the blacklisted platforms, applying the same shortName/accession blacklist filter that the offset-mode variant composes — see CURSOR_PAGINATION_STEP1_PLAN.md step 1h.

Specified by:

loadBlacklistedValueObjectsByCursor 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>

getValueObjectTransformer

protected TypedResultTransformer<ArrayDesignValueObject> getValueObjectTransformer()

Overrides:

getValueObjectTransformer in class AbstractQueryFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

loadValueObjectsForEE

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

Specified by:

loadValueObjectsForEE in interface ArrayDesignDao

loadOriginalPlatformValueObjectsForEE

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

Description copied from interface: ArrayDesignDao

Load the platforms a dataset was ORIGINALLY submitted on, before any platform switch.

A dataset can have more than one — its assays need not have come from a single submitted platform. A platform recorded as an original that is ALSO the one in use is a no-op switch and is left out, so an unswitched dataset answers with an empty list rather than echoing its current platform. That is the same rule the details VO applies, kept identical so the two cannot drift into disagreeing.

Specified by:

loadOriginalPlatformValueObjectsForEE in interface ArrayDesignDao

See Also:

• ArrayDesignDao.loadValueObjectsForEE(Long)

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 org.hibernate.query.Query getFilteringQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query for retrieving filtered entities or VOs after applying filters and ordering.

The query is expected to return a List of O. Implementations that return tuples should also override AbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().

Specified by:

getFilteringQuery in class AbstractQueryFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

initializeCachedFilteringResult

protected void initializeCachedFilteringResult(ArrayDesign ad)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from cache. Lazy-loaded relations fetched by the filtering query must be initialized here so that VOs populated from the second-level cache have the expected fields.

Specified by:

initializeCachedFilteringResult in class AbstractQueryFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

getFilteringIdQuery

protected org.hibernate.query.Query getFilteringIdQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Overrides:

getFilteringIdQuery in class AbstractQueryFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

getFilteringCountQuery

protected org.hibernate.query.Query getFilteringCountQuery(@Nullable
 Filters filters)

Overrides:

getFilteringCountQuery in class AbstractQueryFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

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)