Package ubic.gemma.persistence.service.expression.bioAssay

Class BioAssayServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<BioAssay>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<BioAssay,BioAssayValueObject>

ubic.gemma.persistence.service.expression.bioAssay.BioAssayServiceImpl

All Implemented Interfaces:

BaseImmutableService<BioAssay>, BaseReadOnlyService<BioAssay>, BaseService<BioAssay>, BaseVoEnabledService<BioAssay,BioAssayValueObject>, BioAssayService, FilteringService<BioAssay>, FilteringVoEnabledService<BioAssay,BioAssayValueObject>

@Service
public class BioAssayServiceImpl
extends AbstractFilteringVoEnabledService<BioAssay,BioAssayValueObject>
implements BioAssayService

Author:

pavlidis, keshav, joseph

See Also:

• BioAssayService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
BioAssayServiceImpl(BioAssayDao bioAssayDao, BioMaterialDao bioMaterialDao, ArrayDesignDao arrayDesignDao)

Method Summary

Modifier and Type	Method	Description
void	addBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Associates a bioMaterial with a specified bioAssay.
Collection<BioAssayDimension>	findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs
Collection<BioAssay>	findByAccession(String accession)
BioAssay	findByShortName(String shortName)
Collection<BioAssay>	findSiblings(BioAssay bioAssay)
Collection<BioAssay>	findSubBioAssays(BioAssay bioAssay, boolean direct)
Collection<BioAssaySet>	getBioAssaySets(BioAssay bioAssay)	Obtain all the BioAssaySet that contain the given BioAssay.
List<BioAssayValueObject>	loadValueObjects(Collection<BioAssay> entities, Map<BioAssay,BioAssay> assay2sourceAssayMap, boolean basic, boolean allFactorValues)
void	removeBioMaterialAssociation(BioAssay bioAssay, BioMaterial bioMaterial)	Removes the association between a specific bioMaterial and a bioAssay.
Collection<BioAssay>	thaw(Collection<BioAssay> bioAssays)
BioAssay	thaw(BioAssay ba)

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, streamAll, streamAll, 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.BaseImmutableService

create, remove, remove

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

countAll, find, findOrFail, getElementClass, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

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

save, save, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.expression.bioAssay.BioAssayService

create, findOrCreate, load, load, loadAll, remove, update

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

Constructor Details

BioAssayServiceImpl

@Autowired
public BioAssayServiceImpl(BioAssayDao bioAssayDao,
 BioMaterialDao bioMaterialDao,
 ArrayDesignDao arrayDesignDao)

Method Details

addBioMaterialAssociation

@Transactional
public void addBioMaterialAssociation(BioAssay bioAssay,
 BioMaterial bioMaterial)

Description copied from interface: BioAssayService

Associates a bioMaterial with a specified bioAssay.

Specified by:

addBioMaterialAssociation in interface BioAssayService

Parameters:

bioAssay - bio assay

bioMaterial - bio material

findBioAssayDimensions

@Transactional(readOnly=true)
public Collection<BioAssayDimension> findBioAssayDimensions(BioAssay bioAssay)

Description copied from interface: BioAssayService

Locate all BioAssayDimensions in which the selected BioAssay occurs

Specified by:

findBioAssayDimensions in interface BioAssayService

Parameters:

bioAssay - bio assay

Returns:

bio assay dimensions

See Also:

• BioAssayService.findBioAssayDimensions(BioAssay)

findByShortName

@Transactional(readOnly=true)
public BioAssay findByShortName(String shortName)

Specified by:

findByShortName in interface BioAssayService

findByAccession

@Transactional(readOnly=true)
public Collection<BioAssay> findByAccession(String accession)

Specified by:

findByAccession in interface BioAssayService

Parameters:

accession - eg GSM12345.

Returns:

BioAssays that match based on the plain accession (unconstrained by ExternalDatabase).

findSubBioAssays

@Transactional(readOnly=true)
public Collection<BioAssay> findSubBioAssays(BioAssay bioAssay,
 boolean direct)

Specified by:

findSubBioAssays in interface BioAssayService

See Also:

• BioMaterialService.findSubBioMaterials(BioMaterial, boolean)

findSiblings

@Transactional(readOnly=true)
public Collection<BioAssay> findSiblings(BioAssay bioAssay)

Specified by:

findSiblings in interface BioAssayService

getBioAssaySets

@Transactional(readOnly=true)
public Collection<BioAssaySet> getBioAssaySets(BioAssay bioAssay)

Description copied from interface: BioAssayService

Obtain all the BioAssaySet that contain the given BioAssay.

Specified by:

getBioAssaySets in interface BioAssayService

removeBioMaterialAssociation

@Transactional
public void removeBioMaterialAssociation(BioAssay bioAssay,
 BioMaterial bioMaterial)

Description copied from interface: BioAssayService

Removes the association between a specific bioMaterial and a bioAssay.

Specified by:

removeBioMaterialAssociation in interface BioAssayService

Parameters:

bioAssay - bio assay

bioMaterial - bio material

See Also:

• BioAssayService.removeBioMaterialAssociation(BioAssay, ubic.gemma.model.expression.biomaterial.BioMaterial)

thaw

@Transactional(readOnly=true)
public BioAssay thaw(BioAssay ba)

Specified by:

thaw in interface BioAssayService

thaw

@Transactional(readOnly=true)
public Collection<BioAssay> thaw(Collection<BioAssay> bioAssays)

Specified by:

thaw in interface BioAssayService

loadValueObjects

@Transactional(readOnly=true)
public List<BioAssayValueObject> loadValueObjects(Collection<BioAssay> entities,
 @Nullable
 Map<BioAssay,BioAssay> assay2sourceAssayMap,
 boolean basic,
 boolean allFactorValues)

Specified by:

loadValueObjects in interface BioAssayService

See Also:

• BioAssayDao.loadValueObjects(Collection, Map, Map, boolean, boolean)