Class ExpressionAnalysisResultSetDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

ubic.gemma.persistence.service.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, AnalysisResultSetDao<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet>, ExpressionAnalysisResultSetDao, BaseDao<ExpressionAnalysisResultSet>, BaseVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>, FilteringDao<ExpressionAnalysisResultSet>, FilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

@Repository
public class ExpressionAnalysisResultSetDaoImpl
extends AbstractCriteriaFilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>
implements ExpressionAnalysisResultSetDao

Author:

Paul

Nested Class Summary

Nested classes/interfaces inherited from class AbstractCriteriaFilteringVoEnabledDao

AbstractCriteriaFilteringVoEnabledDao.CriteriaContext<T,R>

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 AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Constructor Summary

Constructors

Constructor	Description
ExpressionAnalysisResultSetDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
protected void	configureFilterableProperties(AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>.FilterablePropertiesConfigurer configurer)	Register filterable properties.
long	countResults(ExpressionAnalysisResultSet ears)	Count the number of results in a given result set.
long	countResults(ExpressionAnalysisResultSet ears, double threshold)	Count the number of results in a given result set below a given corrected P-value threshold.
ExpressionAnalysisResultSet	create(ExpressionAnalysisResultSet entity)	Create an entity in the persistent storage.
protected DifferentialExpressionAnalysisResultSetValueObject	doLoadValueObject(ExpressionAnalysisResultSet entity)	Load a value object for a given entity.
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, Cursor cursor, int limit)	Cursor-paged counterpart to ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort): keyset pagination over the result sets associated to a set of BioAssaySet and external database entries, always sorted by ascending id.
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> databaseEntries, Filters filters, int offset, int limit, Sort sort)	Retrieve result sets associated to a set of BioAssaySet and external database entries.
Baseline	getBaseline(ExpressionAnalysisResultSet ears)	Retrieve the baseline for the given result set.
Map<@MayBeUninitialized ExpressionAnalysisResultSet, Baseline>	getBaselinesForInteractions(Collection<@MayBeUninitialized ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)	Retrieve baselines for all the given result sets representing factor interactions.
Map<Long,Baseline>	getBaselinesForInteractionsByIds(Collection<Long> ids, boolean initializeFactorValues)	Retrieve baselines using result set IDs representing factor interactions.
Map<Long, DiffExResultSetSummaryValueObject.Prefetch>	getPrefetchForVo(Collection<Long> ids)	Batch-fetch the experimentalFactors + baselineGroup associations of the given result sets in two queries (one per association, to avoid MultipleBagFetchException and Cartesian explosion on a multi-row join), and return a map keyed by result-set id.
Histogram	loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)	Obtain the stored histogram of the P-value distribution for a given result set.
Map<Long, Set<Gene>>	loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)	Load a DifferentialExpressionAnalysisResult to Gene multi-map.
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet entity, boolean includeFactorValuesInContrasts, boolean queryGenesByResult, boolean includeTaxonInGenes)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithAnalysisAndExperimentAnalyzed(Long id)	Load a result set with its analysis and the analysis' experimentAnalyzed fully initialized, in a single round-trip.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id, double threshold, int offset, int limit)	Load a slice of an analysis result set with a corrected P-value threshold.
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long id, int offset, int limit)	Load a slice of an analysis result set.
protected void	postProcessValueObjects(List<DifferentialExpressionAnalysisResultSetValueObject> differentialExpressionAnalysisResultSetValueObjects)	Post-process VOs in bulk.
void	remove(ExpressionAnalysisResultSet entity)	Remove a persistent entity.
void	thaw(ExpressionAnalysisResultSet ears)	Initialize the analysis and subset factor vale.
void	thawAll(Collection<ExpressionAnalysisResultSet> ears)	Batch counterpart to ExpressionAnalysisResultSetDao.thaw(ExpressionAnalysisResultSet) for a whole page of result sets.

Methods inherited from class AbstractCriteriaFilteringVoEnabledDao

count, getFilteringCriteria, load, load, loadIds, loadValueObjects, loadValueObjects

Methods inherited from class AbstractFilteringVoEnabledDao

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

Methods inherited from class AbstractVoEnabledDao

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class AbstractDao

countAll, create, find, 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, find, 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 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

ExpressionAnalysisResultSetDaoImpl

@Autowired
public ExpressionAnalysisResultSetDaoImpl(SessionFactory sessionFactory)

Method Details

create

public ExpressionAnalysisResultSet create(ExpressionAnalysisResultSet entity)

Description copied from interface: BaseDao

Create an entity in the persistent storage.

Specified by:

create in interface BaseDao<ExpressionAnalysisResultSet>

Overrides:

create in class AbstractDao<ExpressionAnalysisResultSet>

Parameters:

entity - the entity to create

Returns:

the persistent version of the entity

See Also:

• Session.persist(Object)

remove

public void remove(ExpressionAnalysisResultSet entity)

Description copied from interface: BaseDao

Remove a persistent entity.

Specified by:

remove in interface BaseDao<ExpressionAnalysisResultSet>

Overrides:

remove in class AbstractDao<ExpressionAnalysisResultSet>

Parameters:

entity - the entity to be removed

loadWithAnalysisAndExperimentAnalyzed

@Nullable
public ExpressionAnalysisResultSet loadWithAnalysisAndExperimentAnalyzed(Long id)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a result set with its analysis and the analysis' experimentAnalyzed fully initialized, in a single round-trip. Avoids the sequential lazy-init chain that thaw() does — the dominant cost on the /datasets/{id}/expressions/differential endpoint over a high-latency DB link.

Specified by:

loadWithAnalysisAndExperimentAnalyzed in interface ExpressionAnalysisResultSetDao

loadWithResultsAndContrasts

public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id)

Description copied from interface: ExpressionAnalysisResultSetDao

Load an analysis result set with its all of its associated results.

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetDao

Parameters:

id - the ID of the analysis result set

Returns:

the analysis result set with its associated results, or null if not found

loadWithResultsAndContrasts

public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id,
 int offset,
 int limit)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a slice of an analysis result set.

Results are sorted by ascending correct P-value.

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetDao

Parameters:

offset - an offset of results to load

limit - a limit of results to load, or -1 to load all results starting at offset

See Also:

• ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long)

loadWithResultsAndContrasts

public ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long id,
 double threshold,
 int offset,
 int limit)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a slice of an analysis result set with a corrected P-value threshold.

Important note: when using a threshold, results with null P-values will not be included, thus setting the threshold to 1.0 is not equivalent to ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long, int, int).

Specified by:

loadWithResultsAndContrasts in interface ExpressionAnalysisResultSetDao

Parameters:

threshold - corrected P-value maximum threshold (inclusive)

canDelete

public boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

canDelete in interface ExpressionAnalysisResultSetDao

findByBioAssaySetInAndDatabaseEntryInLimit

public Slice<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInLimit(@Nullable
 Collection<BioAssaySet> bioAssaySets,
 @Nullable
 Collection<DatabaseEntry> databaseEntries,
 @Nullable
 Filters filters,
 int offset,
 int limit,
 @Nullable
 Sort sort)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve result sets associated to a set of BioAssaySet and external database entries.

Specified by:

findByBioAssaySetInAndDatabaseEntryInLimit in interface ExpressionAnalysisResultSetDao

Parameters:

bioAssaySets - related BioAssaySet, or any if null

databaseEntries - related external identifier associated to the BioAssaySet, or any if null

filters - filters for restricting results

limit - maximum number of results to return

sort - field and direction by which the collection is ordered

findByBioAssaySetInAndDatabaseEntryInByCursor

public CursorPage<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInByCursor(@Nullable
 Collection<BioAssaySet> bioAssaySets,
 @Nullable
 Collection<DatabaseEntry> databaseEntries,
 @Nullable
 Filters filters,
 @Nullable
 Cursor cursor,
 int limit)

Description copied from interface: ExpressionAnalysisResultSetDao

Cursor-paged counterpart to ExpressionAnalysisResultSetDao.findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort): keyset pagination over the result sets associated to a set of BioAssaySet and external database entries, always sorted by ascending id.

Single-component id-asc sort only — see CURSOR_PAGINATION_STEP1_PLAN.md step 1i (compound sorts deferred pending the indexed-column audit, recce sec. 3.4). When cursor is non-null the cursor's sortSpec must equal "+id" and its key tuple must be a single numeric id.

Specified by:

findByBioAssaySetInAndDatabaseEntryInByCursor in interface ExpressionAnalysisResultSetDao

Parameters:

bioAssaySets - related BioAssaySet, or any if null

databaseEntries - related external identifier associated to the BioAssaySet, or any if null

filters - filters for restricting results

cursor - decoded cursor (forward or backward) for keyset pagination, or null for the first page

limit - maximum number of results to return

postProcessValueObjects

protected void postProcessValueObjects(List<DifferentialExpressionAnalysisResultSetValueObject> differentialExpressionAnalysisResultSetValueObjects)

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<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

thaw

public void thaw(ExpressionAnalysisResultSet ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Initialize the analysis and subset factor vale.

Specified by:

thaw in interface ExpressionAnalysisResultSetDao

thawAll

public void thawAll(Collection<ExpressionAnalysisResultSet> ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Batch counterpart to ExpressionAnalysisResultSetDao.thaw(ExpressionAnalysisResultSet) for a whole page of result sets.

Initializes the same set of lazy associations as the single-element form (analysis, analysis.experimentAnalyzed, analysis.subsetFactorValue (+EF), experimentalFactors, baselineGroup (+EF)) but issues a small fixed number of queries across the whole collection instead of 5-7 sequential Hibernate.initialize round-trips per row. Idempotent and safe to call with an empty or null collection (no-op).

Specified by:

thawAll in interface ExpressionAnalysisResultSetDao

countResults

public long countResults(ExpressionAnalysisResultSet ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Count the number of results in a given result set.

Specified by:

countResults in interface ExpressionAnalysisResultSetDao

countResults

public long countResults(ExpressionAnalysisResultSet ears,
 double threshold)

Description copied from interface: ExpressionAnalysisResultSetDao

Count the number of results in a given result set below a given corrected P-value threshold.

Specified by:

countResults in interface ExpressionAnalysisResultSetDao

getBaseline

public Baseline getBaseline(ExpressionAnalysisResultSet ears)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve the baseline for the given result set.

Factor values are always initialized.

Specified by:

getBaseline in interface ExpressionAnalysisResultSetDao

Returns:

a baseline, or null if none could be determined for the given result set

getBaselinesForInteractions

public Map<@MayBeUninitialized ExpressionAnalysisResultSet, Baseline> getBaselinesForInteractions(Collection<@MayBeUninitialized ExpressionAnalysisResultSet> resultSets,
 boolean initializeFactorValues)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve baselines for all the given result sets representing factor interactions.

Specified by:

getBaselinesForInteractions in interface ExpressionAnalysisResultSetDao

Parameters:

initializeFactorValues - whether to initialize factor values

getBaselinesForInteractionsByIds

public Map<Long,Baseline> getBaselinesForInteractionsByIds(Collection<Long> ids,
 boolean initializeFactorValues)

Description copied from interface: ExpressionAnalysisResultSetDao

Retrieve baselines using result set IDs representing factor interactions.

Specified by:

getBaselinesForInteractionsByIds in interface ExpressionAnalysisResultSetDao

Parameters:

initializeFactorValues - whether to initialize factor values

loadPvalueDistribution

public Histogram loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)

Description copied from interface: ExpressionAnalysisResultSetDao

Obtain the stored histogram of the P-value distribution for a given result set.

Read straight out of the PVALUE_DISTRIBUTION row hanging off the result set; nothing is aggregated. DifferentialExpressionAnalyzerServiceImpl#addPvalueDistribution writes it at analysis time with 100 fixed-width bins over [0, 1] of the RAW p-values, so bin i covers (i/100, (i+1)/100] and bin 0 also holds 0.0. There is no stored corrected-p-value histogram.

Specified by:

loadPvalueDistribution in interface ExpressionAnalysisResultSetDao

Returns:

the stored histogram, or null when PVALUE_DISTRIBUTION_FK is null

configureFilterableProperties

protected void configureFilterableProperties(AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>.FilterablePropertiesConfigurer configurer)

Description copied from class: AbstractFilteringVoEnabledDao

Register filterable properties.

Overrides:

configureFilterableProperties in class AbstractFilteringVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

doLoadValueObject

protected DifferentialExpressionAnalysisResultSetValueObject doLoadValueObject(ExpressionAnalysisResultSet 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, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

loadValueObjectWithResults

public DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet entity,
 boolean includeFactorValuesInContrasts,
 boolean queryGenesByResult,
 boolean includeTaxonInGenes)

Description copied from interface: ExpressionAnalysisResultSetDao

Load an analysis result set with its all of its associated results.

Specified by:

loadValueObjectWithResults in interface ExpressionAnalysisResultSetDao

Parameters:

includeFactorValuesInContrasts - include complete FV in the contrasts, only IDs are displayed if false

queryGenesByResult - query genes by results instead of result set, this is considerably faster if the results are sliced (i.e. from ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long, int, int))

includeTaxonInGenes - include complete taxon in the contrasts, only the ID is displayed if false

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)
• ExpressionAnalysisResultSetDao.loadResultToGenesMap(ExpressionAnalysisResultSet, boolean)

loadResultToGenesMap

public Map<Long, Set<Gene>> loadResultToGenesMap(ExpressionAnalysisResultSet resultSet,
 boolean queryByResult)

Description copied from interface: ExpressionAnalysisResultSetDao

Load a DifferentialExpressionAnalysisResult to Gene multi-map.

This is much faster than navigating through the probe's alignments, transcripts and then genes as it uses the internal GENE2CS table described in TableMaintenanceUtil.updateGene2CsEntries().

Note: Not all probes have associated genes, so you should use Map.getOrDefault(Object, Object) with an empty collection to handle this case.

Specified by:

loadResultToGenesMap in interface ExpressionAnalysisResultSetDao

Parameters:

queryByResult - query by results instead of result set, this is considerably faster if the results are sliced (i.e. from ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long, int, int))

getPrefetchForVo

public Map<Long, DiffExResultSetSummaryValueObject.Prefetch> getPrefetchForVo(Collection<Long> ids)

Description copied from interface: ExpressionAnalysisResultSetDao

Batch-fetch the experimentalFactors + baselineGroup associations of the given result sets in two queries (one per association, to avoid MultipleBagFetchException and Cartesian explosion on a multi-row join), and return a map keyed by result-set id.

Consumed by the findByExperimentIds VO enrichment path so the per-row DiffExResultSetSummaryValueObject ctor can skip three sequential Hibernate.initialize round-trips on a warm cache.

Returns an empty map if ids is empty. Result-sets missing from the result (e.g. concurrently deleted) are simply absent from the map; the caller should fall back to the lazy-load path for those.

Specified by:

getPrefetchForVo in interface ExpressionAnalysisResultSetDao

Parameters:

ids - the result-set ids to prefetch

Returns:

map from result-set id to DiffExResultSetSummaryValueObject.Prefetch