Package ubic.gemma.persistence.service.genome.taxon

Interface TaxonService

All Superinterfaces:

BaseImmutableService<Taxon>, BaseReadOnlyService<Taxon>, BaseVoEnabledService<Taxon,TaxonValueObject>, FilteringService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>

All Known Implementing Classes:

TaxonServiceImpl

public interface TaxonService
extends BaseImmutableService<Taxon>, FilteringVoEnabledService<Taxon,TaxonValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Taxon	findByCommonName(String commonName)
Taxon	findByNcbiId(Integer ncbiId)
Taxon	findByScientificName(String scientificName)
Taxon	findOrCreate(Taxon taxon)	Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<TaxonValueObject>	getTaxaWithArrays()
Collection<TaxonValueObject>	getTaxaWithDatasets()
Collection<TaxonValueObject>	getTaxaWithGenes()
Collection<Taxon>	loadAllTaxaWithGenes()
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<Taxon> entities)	Removes all the given entities from persistent storage.
void	remove(Taxon taxon)	Removes the given entity from the persistent storage.
void	updateGenesUsable(Taxon taxon, boolean isGenesUsable)

Methods inherited from interface ubic.gemma.persistence.service.BaseImmutableService

create, create

Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService

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

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.FilteringService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

Methods inherited from interface ubic.gemma.persistence.service.FilteringVoEnabledService

loadValueObjects, loadValueObjects

Method Detail

findByCommonName

Taxon findByCommonName(String commonName)

findByScientificName

Taxon findByScientificName(String scientificName)

findByNcbiId

Taxon findByNcbiId(Integer ncbiId)

findOrCreate

@Secured("GROUP_USER")
Taxon findOrCreate(Taxon taxon)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<Taxon>

Parameters:

taxon - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

remove

@Secured("GROUP_USER")
void remove(Collection<Taxon> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<Taxon>

Parameters:

entities - the entities to be removed.

remove

@Secured("GROUP_ADMIN")
void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<Taxon>

Parameters:

id - the ID of entity to be removed.

remove

@Secured("GROUP_USER")
void remove(Taxon taxon)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<Taxon>

Parameters:

taxon - the entity to be removed.

loadAllTaxaWithGenes

Collection<Taxon> loadAllTaxaWithGenes()

Returns:

Taxon that have genes loaded into Gemma and that should be used

getTaxaWithGenes

Collection<TaxonValueObject> getTaxaWithGenes()

Returns:

Taxon that have genes loaded into Gemma and that should be used

getTaxaWithDatasets

Collection<TaxonValueObject> getTaxaWithDatasets()

Returns:

collection of taxa that have expression experiments available.

getTaxaWithArrays

Collection<TaxonValueObject> getTaxaWithArrays()

Returns:

List of taxa with array designs in gemma

updateGenesUsable

void updateGenesUsable(Taxon taxon,
                       boolean isGenesUsable)