Interface ArrayDesignDao

All Superinterfaces:

BaseDao<ArrayDesign>, BaseVoEnabledDao<ArrayDesign, ArrayDesignValueObject>, CachedFilteringDao<ArrayDesign>, CachedFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>, CuratableDao<ArrayDesign>, FilteringDao<ArrayDesign>, FilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

All Known Implementing Classes:

ArrayDesignDaoImpl

@Repository
public interface ArrayDesignDao
extends CuratableDao<ArrayDesign>, CachedFilteringVoEnabledDao<ArrayDesign, ArrayDesignValueObject>

Created by tesarst on 13/03/17. ArrayDesignDao interface

Nested Class Summary

Nested classes/interfaces inherited from interface FilteringDao

FilteringDao.ConjunctSpec

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OBJECT_ALIAS

Method Summary

Modifier and Type	Method	Description
void	addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
long	countBioSequences(ArrayDesign arrayDesign)
long	countBlatResults(ArrayDesign arrayDesign)
long	countCompositeSequences(ArrayDesign id)
long	countCompositeSequencesWithBioSequences()
long	countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)
long	countCompositeSequencesWithBlatResults()
long	countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)
long	countCompositeSequencesWithGenes(boolean useGene2Cs)
long	countCompositeSequencesWithGenes(Collection<ArrayDesign> arrayDesign, 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)
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)
Collection<Gene>	getGenes(ArrayDesign arrayDesign, boolean useGene2Cs)	Obtain all the genes associated to the platform.
Map<CompositeSequence, Set<Gene>>	getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign, 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)	Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.
Collection<Taxon>	getTaxaFromBioSequences(ArrayDesign arrayDesign)	Obtain all the taxa associated to the BioSequence of the given platform.
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 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)
void	removeBiologicalCharacteristics(ArrayDesign arrayDesign)
void	thaw(ArrayDesign arrayDesign)	Thaw the given platform as per 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 interface BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, 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

Field Details

OBJECT_ALIAS

static final String OBJECT_ALIAS

See Also:

• Constant Field Values

Method Details

loadAsMap

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. 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.

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

Collection<ArrayDesign> loadAllGenericGenePlatforms()

addProbes

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

deleteAlignmentData

void deleteAlignmentData(ArrayDesign arrayDesign)

deleteGeneProductAssociations

void deleteGeneProductAssociations(ArrayDesign arrayDesign)

findByShortName

@Nullable
ArrayDesign findByShortName(String shortName)

findByName

Collection<ArrayDesign> findByName(String name)

findOneByName

@Nullable
ArrayDesign findOneByName(String name)

findByCompositeSequenceName

Collection<ArrayDesign> findByCompositeSequenceName(String name)

findByAlternateName

Collection<ArrayDesign> findByAlternateName(String queryString)

findOneByAlternateName

@Nullable
ArrayDesign findOneByAlternateName(String name)

findByManufacturer

Collection<ArrayDesign> findByManufacturer(String queryString)

findByTaxon

Collection<ArrayDesign> findByTaxon(Taxon taxon)

getAllAssociatedBioAssays

Collection<BioAssay> getAllAssociatedBioAssays(ArrayDesign arrayDesign)

getAuditEvents

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

getBioSequences

Map<CompositeSequence, BioSequence> getBioSequences(ArrayDesign arrayDesign)

countBioSequences

long countBioSequences(ArrayDesign arrayDesign)

getGenes

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

Obtain all the genes associated to the platform.

countGenes

long countGenes(boolean useGene2Cs)

countGenes

long countGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

getGenesByCompositeSequence

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

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

getGenesByCompositeSequence

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

getExpressionExperiments

Collection<ExpressionExperiment> getExpressionExperiments(ArrayDesign arrayDesign)

countExpressionExperiments

long countExpressionExperiments(ArrayDesign arrayDesign)

Obtain the number of associated expression experiments.

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

See Also:

• getExpressionExperiments(ArrayDesign)

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

getSwitchedExpressionExperiments

Collection<ExpressionExperiment> getSwitchedExpressionExperiments(ArrayDesign arrayDesign)

Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.

If you only need to count them, consider using the more performant countSwitchedExpressionExperiments(ArrayDesign) instead.

countSwitchedExpressionExperiments

long countSwitchedExpressionExperiments(ArrayDesign arrayDesign)

Count the number of switched ExpressionExperiment from a given platform.

See Also:

• getSwitchedExpressionExperiments(ArrayDesign)

getTaxaFromBioSequences

Collection<Taxon> getTaxaFromBioSequences(ArrayDesign arrayDesign)

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

isMerged

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

isMergee

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

isSubsumed

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

isSubsumer

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

loadAlignments

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

loadCompositeSequences

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

loadValueObjectsForEE

List<ArrayDesignValueObject> loadValueObjectsForEE(Long eeId)

loadOriginalPlatformValueObjectsForEE

List<ArrayDesignValueObject> loadOriginalPlatformValueObjectsForEE(Long eeId)

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.

See Also:

• loadValueObjectsForEE(Long)

countCompositeSequencesWithBioSequences

long countCompositeSequencesWithBioSequences()

countCompositeSequencesWithBlatResults

long countCompositeSequencesWithBlatResults()

countCompositeSequencesWithGenes

long countCompositeSequencesWithGenes(boolean useGene2Cs)

countBlatResults

long countBlatResults(ArrayDesign arrayDesign)

countCompositeSequences

long countCompositeSequences(ArrayDesign id)

countCompositeSequencesWithBioSequences

long countCompositeSequencesWithBioSequences(ArrayDesign arrayDesign)

countCompositeSequencesWithBlatResults

long countCompositeSequencesWithBlatResults(ArrayDesign arrayDesign)

countCompositeSequencesWithGenes

long countCompositeSequencesWithGenes(ArrayDesign arrayDesign,
 boolean useGene2Cs)

countCompositeSequencesWithGenes

long countCompositeSequencesWithGenes(Collection<ArrayDesign> arrayDesign,
 boolean useGene2Cs)

removeBiologicalCharacteristics

void removeBiologicalCharacteristics(ArrayDesign arrayDesign)

thawLite

void thawLite(ArrayDesign arrayDesign)

Lightly thaw the given platform.

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

thaw

void thaw(ArrayDesign arrayDesign)

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

thawCompositeSequences

void thawCompositeSequences(ArrayDesign arrayDesign)

Only thaw the design elements of a given platform.

updateSubsumingStatus

boolean updateSubsumingStatus(ArrayDesign candidateSubsumer,
 ArrayDesign candidateSubsumee)

deleteGeneProductAlignmentAssociations

void deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)

deleteGeneProductAnnotationAssociations

void deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)

loadBlacklistedValueObjects

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

loadBlacklistedValueObjectsByCursor

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

Cursor-mode counterpart to 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.