Interface ExpressionAnalysisResultSetService

All Superinterfaces:

AnalysisResultSetService<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet>, BaseReadOnlyService<ExpressionAnalysisResultSet>, BaseVoEnabledService<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>, FilteringService<ExpressionAnalysisResultSet>, FilteringVoEnabledService<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

All Known Implementing Classes:

ExpressionAnalysisResultSetServiceImpl

public interface ExpressionAnalysisResultSetService
extends AnalysisResultSetService<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet>, FilteringVoEnabledService<ExpressionAnalysisResultSet, DifferentialExpressionAnalysisResultSetValueObject>

🔒 The loaders below are ACL-guarded. Before that they were not, and GET /resultSets/{id} served the complete result set -- experimental design, factor values and per-probe results with genes -- to anonymous callers for experiments that GET /datasets/{id} correctly hides. The guards mirror DifferentialExpressionAnalysisService, which has always had them. A result set's ACL parent chain runs result set -> analysis -> experiment, so READ resolves against the owning experiment.

Method Summary

Modifier and Type	Method	Description
long	countResults(ExpressionAnalysisResultSet ears)
long	countResults(ExpressionAnalysisResultSet ears, double threshold)
CursorPage<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInByCursor(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, Cursor cursor, int limit)	Cursor-paged counterpart to findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort).
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Baseline	getBaseline(ExpressionAnalysisResultSet ears)
Map<@MayBeUninitialized ExpressionAnalysisResultSet, Baseline>	getBaselinesForInteractions(Set<@MayBeUninitialized ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<Long,Baseline>	getBaselinesForInteractionsByIds(Collection<Long> rsIds, boolean initializeFactorValues)
Histogram	loadPvalueDistribution(ExpressionAnalysisResultSet resulSet)
Map<Long, Set<Gene>>	loadResultIdToGenesMap(ExpressionAnalysisResultSet ears)
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet ears, boolean includeFactorValuesInContrasts, boolean queryByResult, boolean includeTaxonInGenes)
ExpressionAnalysisResultSet	loadWithAnalysis(Long id)
ExpressionAnalysisResultSet	loadWithExperimentAnalyzed(Long id)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value, int offset, int limit)
ExpressionAnalysisResultSet	thaw(ExpressionAnalysisResultSet e)

Methods inherited from interface BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface FilteringService

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

Methods inherited from interface FilteringVoEnabledService

loadValueObjects, loadValueObjects, loadValueObjectsByCursor

Method Details

loadWithAnalysis

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
ExpressionAnalysisResultSet loadWithAnalysis(Long id)

loadWithResultsAndContrasts

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value)

loadWithResultsAndContrasts

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value,
 int offset,
 int limit)

loadWithResultsAndContrasts

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value,
 double threshold,
 int offset,
 int limit)

countResults

long countResults(ExpressionAnalysisResultSet ears)

countResults

long countResults(ExpressionAnalysisResultSet ears,
 double threshold)

thaw

@CheckReturnValue
ExpressionAnalysisResultSet thaw(ExpressionAnalysisResultSet e)

loadWithExperimentAnalyzed

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
@PostAuthorize("returnObject == null or hasPermission(returnObject, 'READ') or hasPermission(returnObject, 'ADMINISTRATION')")
ExpressionAnalysisResultSet loadWithExperimentAnalyzed(Long id)

loadValueObjectWithResults

DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet ears,
 boolean includeFactorValuesInContrasts,
 boolean queryByResult,
 boolean includeTaxonInGenes)

loadResultIdToGenesMap

Map<Long, Set<Gene>> loadResultIdToGenesMap(ExpressionAnalysisResultSet ears)

findByBioAssaySetInAndDatabaseEntryInLimit

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

findByBioAssaySetInAndDatabaseEntryInByCursor

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

Cursor-paged counterpart to findByBioAssaySetInAndDatabaseEntryInLimit(Collection, Collection, Filters, int, int, Sort). Always sorts by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1i.

getBaseline

Baseline getBaseline(ExpressionAnalysisResultSet ears)

getBaselinesForInteractions

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

getBaselinesForInteractionsByIds

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

loadPvalueDistribution

@Nullable
Histogram loadPvalueDistribution(ExpressionAnalysisResultSet resulSet)