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

Class BioAssayServiceImpl

java.lang.Object

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

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)
List<BioAssayValueObject>	loadValueObjects(Collection<BioAssay> entities, boolean basic)
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 bioAssay)

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, 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

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 Detail

BioAssayServiceImpl

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

Method Detail

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)

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).

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 bioAssay)

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,
                                                  boolean basic)

Specified by:

loadValueObjects in interface BioAssayService