Package ubic.gemma.persistence.service.association.phenotype

Class PhenotypeAssociationDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl

All Implemented Interfaces:

PhenotypeAssociationDao, BaseDao<PhenotypeAssociation>

@Repository
public class PhenotypeAssociationDaoImpl
extends AbstractDao<PhenotypeAssociation>
implements PhenotypeAssociationDao

deals with all basic queries used by Neurocarta

Author:

Nicolas

Field Summary

Fields

Modifier and Type	Field	Description
static int	DEFAULT_PA_LIMIT

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

elementClass

Constructor Summary

Constructors

Constructor	Description
PhenotypeAssociationDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
Long	countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)	counts the evidence that from neurocarta that came from a specific MetaAnalysis
PhenotypeAssociation	find(PhenotypeAssociation 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<CharacteristicValueObject>	findEvidenceCategoryTerms()	find category terms currently used in the database by evidence
Collection<String>	findEvidenceOwners()	return the list of the owners that have evidence in the system
Collection<PhenotypeAssociation>	findEvidencesWithExternalDatabaseName(String externalDatabaseName, int limit, int start)	loads all evidences from a specific external database
Collection<PhenotypeAssociation>	findEvidencesWithoutExternalDatabaseName()	find all evidence that doesn't come from an external course
Collection<ExternalDatabase>	findExternalDatabasesWithEvidence()	Gets all External Databases that are used with evidence
Map<GeneValueObject,OntologyTerm>	findGenesForPhenotype(OntologyTerm term, Long taxon, boolean includeIEA)
Collection<GeneEvidenceValueObject>	findGenesWithPhenotypes(Set<String> phenotypeUris, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds)	Key method: find Genes link to a phenotype taking into account private and public evidence Here on the cases : 1- Admin - can see anything 2- user not logged in - only public data 3- user logged in only showing what he has read access - public, shared + owned 4- user logged in only showing what he has write access - owned.
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneId(Long geneId)	find all PhenotypeAssociation for a specific gene id
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneIdAndDatabases(Long geneId, Collection<Long> externalDatabaseIds)	find all PhenotypeAssociation for a specific gene id and external Databases ids
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)	find all PhenotypeAssociation for a specific NCBI id
Collection<PhenotypeAssociation>	findPhenotypeAssociationForGeneNCBI(Integer geneNCBI, Set<String> phenotype)	find all PhenotypeAssociation for a specific NCBI id and phenotypes valueUri
Collection<PhenotypeAssociation>	findPhenotypeAssociationWithIds(Collection<Long> paIds)	find PhenotypeAssociation satisfying the given filters: paIds, taxonId and limit
Collection<PhenotypeAssociation>	findPhenotypesForBibliographicReference(String pubMedID)	find PhenotypeAssociations associated with a BibliographicReference
Set<Long>	findPrivateEvidenceId(Long taxonId, int limit)
Map<String,Set<Integer>>	findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)	find all private phenotypes associated with genes on a specific taxon and containing the valuesUri
Map<String,Set<Integer>>	findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation)	find all public phenotypes associated with genes on a specific taxon and containing the valuesUri
PhenotypeAssociation	load(Long id)	Loads the entity with given id from the persistent storage.
Collection<PhenotypeValueObject>	loadAllNeurocartaPhenotypes()	find all phenotypes in Neurocarta, this was requested by AspireBD
Set<String>	loadAllPhenotypesUri()	load all valueURI of Phenotype in the database
Collection<DifferentialExpressionEvidence>	loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId, int maxResults)
ExternalDatabaseStatisticsValueObject	loadStatisticsOnAllEvidence(String downloadFile)
Collection<ExternalDatabaseStatisticsValueObject>	loadStatisticsOnExternalDatabases(String downloadPath)
ExternalDatabaseStatisticsValueObject	loadStatisticsOnManualCuration(String downloadFile)
void	remove(PhenotypeAssociation entity)	Remove a persistent instance
int	removeAll()
void	removePhenotypePublication(PhenotypeAssociationPublication phenotypeAssociationPublication)	remove a PhenotypeAssociationPublication

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

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, loadAll, loadReference, loadReference, remove, remove, save, save, update, update

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.BaseDao

countAll, create, create, findOrCreate, getElementClass, getIdentifierPropertyName, load, loadAll, loadReference, loadReference, remove, remove, save, save, update, update

Field Detail

DEFAULT_PA_LIMIT

public static final int DEFAULT_PA_LIMIT

See Also:

Constant Field Values

Constructor Detail

PhenotypeAssociationDaoImpl

@Autowired
public PhenotypeAssociationDaoImpl(SessionFactory sessionFactory)

Method Detail

load

public PhenotypeAssociation load(Long id)

Description copied from interface: BaseDao

Loads the entity with given id from the persistent storage.

Specified by:

load in interface BaseDao<PhenotypeAssociation>

Overrides:

load in class AbstractDao<PhenotypeAssociation>

Parameters:

id - the id of entity to load.

Returns:

the entity with given ID, or null if such entity does not exist or if the passed ID was null

See Also:

Session.get(Class, Serializable)

find

public PhenotypeAssociation find(PhenotypeAssociation 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<PhenotypeAssociation>

Overrides:

find in class AbstractDao<PhenotypeAssociation>

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.

countEvidenceWithGeneDifferentialExpressionMetaAnalysis

public Long countEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId)

counts the evidence that from neurocarta that came from a specific MetaAnalysis

Specified by:

countEvidenceWithGeneDifferentialExpressionMetaAnalysis in interface PhenotypeAssociationDao

Parameters:

geneDifferentialExpressionMetaAnalysisId - id

Returns:

count of the evidence that from neurocarta that came from a specific MetaAnalysis

findEvidenceCategoryTerms

public Collection<CharacteristicValueObject> findEvidenceCategoryTerms()

find category terms currently used in the database by evidence

Specified by:

findEvidenceCategoryTerms in interface PhenotypeAssociationDao

Returns:

category terms currently used in the database by evidence

findEvidenceOwners

public Collection<String> findEvidenceOwners()

return the list of the owners that have evidence in the system

Specified by:

findEvidenceOwners in interface PhenotypeAssociationDao

Returns:

the list of the owners that have evidence in the system

findEvidencesWithExternalDatabaseName

public Collection<PhenotypeAssociation> findEvidencesWithExternalDatabaseName(String externalDatabaseName,
                                                                              int limit,
                                                                              int start)

loads all evidences from a specific external database

Specified by:

findEvidencesWithExternalDatabaseName in interface PhenotypeAssociationDao

Parameters:

externalDatabaseName - external database name

limit - limit

start - start

Returns:

all evidences from a specific external database

findEvidencesWithoutExternalDatabaseName

public Collection<PhenotypeAssociation> findEvidencesWithoutExternalDatabaseName()

find all evidence that doesn't come from an external course

Specified by:

findEvidencesWithoutExternalDatabaseName in interface PhenotypeAssociationDao

Returns:

all evidence that doesn't come from an external course

findExternalDatabasesWithEvidence

public Collection<ExternalDatabase> findExternalDatabasesWithEvidence()

Gets all External Databases that are used with evidence

Specified by:

findExternalDatabasesWithEvidence in interface PhenotypeAssociationDao

Returns:

all External Databases that are used with evidence

findGenesForPhenotype

public Map<GeneValueObject,OntologyTerm> findGenesForPhenotype(OntologyTerm term,
                                                                     Long taxon,
                                                                     boolean includeIEA)

Specified by:

findGenesForPhenotype in interface PhenotypeAssociationDao

Parameters:

term - term

taxon - taxon

includeIEA - if false, electronic annotations will be omitted

Returns:

map of gene value objects to the exact phenotype the gene was annotated to. (gives no indication of 'bag of terms')

findGenesWithPhenotypes

public Collection<GeneEvidenceValueObject> findGenesWithPhenotypes(Set<String> phenotypeUris,
                                                                   @Nullable
                                                                   Taxon taxon,
                                                                   boolean showOnlyEditable,
                                                                   @Nullable
                                                                   Collection<Long> externalDatabaseIds)

Key method: find Genes link to a phenotype taking into account private and public evidence Here on the cases :

• 1- Admin - can see anything
• 2- user not logged in - only public data
• 3- user logged in only showing what he has read access - public, shared + owned
• 4- user logged in only showing what he has write access - owned.

Specified by:

findGenesWithPhenotypes in interface PhenotypeAssociationDao

Parameters:

phenotypeUris - phenotype value uri

taxon - taxon

showOnlyEditable - show only editable

externalDatabaseIds - external db ids

Returns:

Genes link to a phenotype

findPhenotypeAssociationForGeneId

public Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneId(Long geneId)

find all PhenotypeAssociation for a specific gene id

Specified by:

findPhenotypeAssociationForGeneId in interface PhenotypeAssociationDao

Parameters:

geneId - gene id

Returns:

all PhenotypeAssociation for a specific gene id

findPhenotypeAssociationForGeneIdAndDatabases

public Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneIdAndDatabases(Long geneId,
                                                                                      @Nullable
                                                                                      Collection<Long> externalDatabaseIds)

find all PhenotypeAssociation for a specific gene id and external Databases ids

Specified by:

findPhenotypeAssociationForGeneIdAndDatabases in interface PhenotypeAssociationDao

Parameters:

geneId - gene id

externalDatabaseIds - external db ids

Returns:

all PhenotypeAssociation for a specific gene id and external Databases ids

findPhenotypeAssociationForGeneNCBI

public Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneNCBI(Integer geneNCBI)

find all PhenotypeAssociation for a specific NCBI id

Specified by:

findPhenotypeAssociationForGeneNCBI in interface PhenotypeAssociationDao

Parameters:

geneNCBI - gene ncbi id

Returns:

all PhenotypeAssociation for a specific NCBI id

findPhenotypeAssociationForGeneNCBI

public Collection<PhenotypeAssociation> findPhenotypeAssociationForGeneNCBI(Integer geneNCBI,
                                                                            Set<String> phenotype)

find all PhenotypeAssociation for a specific NCBI id and phenotypes valueUri

Specified by:

findPhenotypeAssociationForGeneNCBI in interface PhenotypeAssociationDao

Parameters:

geneNCBI - gene ncbi id

phenotype - phenotype

Returns:

all PhenotypeAssociation for a specific NCBI id and phenotypes valueUri

findPhenotypeAssociationWithIds

public Collection<PhenotypeAssociation> findPhenotypeAssociationWithIds(Collection<Long> paIds)

find PhenotypeAssociation satisfying the given filters: paIds, taxonId and limit

Specified by:

findPhenotypeAssociationWithIds in interface PhenotypeAssociationDao

Parameters:

paIds - ids

Returns:

PhenotypeAssociations satisfying the given filters: ids, taxonId and limit

findPhenotypesForBibliographicReference

public Collection<PhenotypeAssociation> findPhenotypesForBibliographicReference(String pubMedID)

find PhenotypeAssociations associated with a BibliographicReference

Specified by:

findPhenotypesForBibliographicReference in interface PhenotypeAssociationDao

Parameters:

pubMedID - pumbed id

Returns:

PhenotypeAssociations associated with a BibliographicReference

findPrivateEvidenceId

public Set<Long> findPrivateEvidenceId(@Nullable
                                       Long taxonId,
                                       int limit)

Specified by:

findPrivateEvidenceId in interface PhenotypeAssociationDao

Parameters:

taxonId - taxon id

limit - limit

Returns:

private evidence id that the user can modify or owns

findPrivatePhenotypesGenesAssociations

public Map<String,Set<Integer>> findPrivatePhenotypesGenesAssociations(@Nullable
                                                                             Taxon taxon,
                                                                             @Nullable
                                                                             Set<String> valuesUri,
                                                                             boolean showOnlyEditable,
                                                                             @Nullable
                                                                             Collection<Long> externalDatabaseIds,
                                                                             boolean noElectronicAnnotation)

find all private phenotypes associated with genes on a specific taxon and containing the valuesUri

Specified by:

findPrivatePhenotypesGenesAssociations in interface PhenotypeAssociationDao

Parameters:

taxon - taxon

valuesUri - value uris

showOnlyEditable - show only editable

externalDatabaseIds - external db ids

noElectronicAnnotation - no electronic annotation

Returns:

ll private phenotypes associated with genes on a specific taxon and containing the valuesUri

findPublicPhenotypesGenesAssociations

public Map<String,Set<Integer>> findPublicPhenotypesGenesAssociations(@Nullable
                                                                            Taxon taxon,
                                                                            @Nullable
                                                                            Set<String> valuesUri,
                                                                            boolean showOnlyEditable,
                                                                            @Nullable
                                                                            Collection<Long> externalDatabaseIds,
                                                                            boolean noElectronicAnnotation)

find all public phenotypes associated with genes on a specific taxon and containing the valuesUri

Specified by:

findPublicPhenotypesGenesAssociations in interface PhenotypeAssociationDao

Parameters:

taxon - taxon

valuesUri - values uri

showOnlyEditable - show only editable

externalDatabaseIds - external database ids

noElectronicAnnotation - no electronic annotation

Returns:

all public phenotypes associated with genes on a specific taxon and containing the valuesUri

loadAllNeurocartaPhenotypes

public Collection<PhenotypeValueObject> loadAllNeurocartaPhenotypes()

find all phenotypes in Neurocarta, this was requested by AspireBD

Specified by:

loadAllNeurocartaPhenotypes in interface PhenotypeAssociationDao

Returns:

all phenotypes in Neurocarta

loadAllPhenotypesUri

public Set<String> loadAllPhenotypesUri()

load all valueURI of Phenotype in the database

Specified by:

loadAllPhenotypesUri in interface PhenotypeAssociationDao

Returns:

all valueURI of Phenotype in the database

loadEvidenceWithGeneDifferentialExpressionMetaAnalysis

public Collection<DifferentialExpressionEvidence> loadEvidenceWithGeneDifferentialExpressionMetaAnalysis(Long geneDifferentialExpressionMetaAnalysisId,
                                                                                                         int maxResults)

Specified by:

loadEvidenceWithGeneDifferentialExpressionMetaAnalysis in interface PhenotypeAssociationDao

Parameters:

geneDifferentialExpressionMetaAnalysisId - id

maxResults - max results

Returns:

a Collection for a geneDifferentialExpressionMetaAnalysisId if one exists (can be used to find the threshold and phenotypes for a GeneDifferentialExpressionMetaAnalysis)

loadStatisticsOnAllEvidence

public ExternalDatabaseStatisticsValueObject loadStatisticsOnAllEvidence(String downloadFile)

Specified by:

loadStatisticsOnAllEvidence in interface PhenotypeAssociationDao

Parameters:

downloadFile - path

Returns:

statistics all evidences

loadStatisticsOnExternalDatabases

public Collection<ExternalDatabaseStatisticsValueObject> loadStatisticsOnExternalDatabases(String downloadPath)

Specified by:

loadStatisticsOnExternalDatabases in interface PhenotypeAssociationDao

Parameters:

downloadPath - path

Returns:

all external databases statistics used in neurocarta

loadStatisticsOnManualCuration

public ExternalDatabaseStatisticsValueObject loadStatisticsOnManualCuration(String downloadFile)

Specified by:

loadStatisticsOnManualCuration in interface PhenotypeAssociationDao

Parameters:

downloadFile - file

Returns:

find statistics for manual curation (numGene, numPhenotypes, etc.)

removePhenotypePublication

public void removePhenotypePublication(PhenotypeAssociationPublication phenotypeAssociationPublication)

Description copied from interface: PhenotypeAssociationDao

remove a PhenotypeAssociationPublication

Specified by:

removePhenotypePublication in interface PhenotypeAssociationDao

Parameters:

phenotypeAssociationPublicationId - remove a PhenotypeAssociationPublication

removeAll

public int removeAll()

Specified by:

removeAll in interface PhenotypeAssociationDao

remove

public void remove(PhenotypeAssociation entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<PhenotypeAssociation>

Overrides:

remove in class AbstractDao<PhenotypeAssociation>

Parameters:

entity - the entity to be removed