Class ExpressionExperimentSetServiceImpl
java.lang.Object
ubic.gemma.persistence.service.AbstractService<ExpressionExperimentSet>
ubic.gemma.persistence.service.AbstractVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>
ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentSetServiceImpl
- All Implemented Interfaces:
BaseImmutableService<ExpressionExperimentSet>, BaseReadOnlyService<ExpressionExperimentSet>, BaseService<ExpressionExperimentSet>, BaseVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>, ExpressionExperimentSetService
@Service
public class ExpressionExperimentSetServiceImpl
extends AbstractVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>
implements ExpressionExperimentSetService
Spring Service base class for
ubic.gemma.model.analysis.expression.ExpressionExperimentSetService,
provides access to all services and entities referenced by this service.- See Also:
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Field Summary
Fields inherited from class AbstractService
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Constructor Summary
ConstructorsConstructorDescriptionExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao expressionExperimentSetDao, ExpressionExperimentService expressionExperimentService) -
Method Summary
Modifier and TypeMethodDescriptionfind(BioAssaySet bioAssaySet) findByName(String name) security at DAO levelfindIds(BioAssaySet bioAssaySet) security at DAO levelGet the (security-filtered) list of experiments in a set.Get the member experiment value objects for the set id; security filtered.initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon) Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.".booleanisAutomaticallyGenerated(String experimentSetDescription) Determines if set was automatically generated by matching the description to that used in ubic.gemma.core.analysis.expression .coexpression.ExpressionExperimentSetService.AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTIONSecurity at DAO level.loadAllExperimentSetValueObjects(boolean loadEEIds) Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()loadMySetValueObjects(boolean loadEEIds) load the user's setsloadValueObjectById(Long id, boolean loadEEIds) Get a value object for the id param.loadValueObjectsByIds(Collection<Long> eeSetIds) Load value objects by a given collection of IDs.intRemove an experiment from all sets it is in.thaw(ExpressionExperimentSet expressionExperimentSet) voidupdate(Collection<ExpressionExperimentSet> entities) Updates all entities in the given collection in the persistent storage.voidupdate(ExpressionExperimentSet expressionExperimentSet) Updates the given entity in the persistent storage.Methods inherited from class AbstractVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjectsMethods inherited from class AbstractService
countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, streamAll, streamAllMethods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface BaseImmutableService
create, findOrCreate, remove, removeMethods inherited from interface BaseReadOnlyService
countAll, find, findOrFail, getElementClass, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAllMethods inherited from interface BaseService
save, saveMethods inherited from interface BaseVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjects
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Constructor Details
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ExpressionExperimentSetServiceImpl
@Autowired public ExpressionExperimentSetServiceImpl(ExpressionExperimentSetDao expressionExperimentSetDao, ExpressionExperimentService expressionExperimentService)
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Method Details
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find
@Transactional(readOnly=true) public Collection<ExpressionExperimentSet> find(BioAssaySet bioAssaySet) - Specified by:
findin interfaceExpressionExperimentSetService
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findByName
Description copied from interface:ExpressionExperimentSetServicesecurity at DAO level- Specified by:
findByNamein interfaceExpressionExperimentSetService- Parameters:
name- name- Returns:
- collection of ee sets
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findIds
Description copied from interface:ExpressionExperimentSetServicesecurity at DAO level- Specified by:
findIdsin interfaceExpressionExperimentSetService- Parameters:
bioAssaySet- BA set- Returns:
- collection of IDs
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getExperimentsInSet
Description copied from interface:ExpressionExperimentSetServiceGet the (security-filtered) list of experiments in a set.- Specified by:
getExperimentsInSetin interfaceExpressionExperimentSetService- Parameters:
id- id- Returns:
- collection of ees
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getExperimentValueObjectsInSet
@Transactional(readOnly=true) public Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id) Description copied from interface:ExpressionExperimentSetServiceGet the member experiment value objects for the set id; security filtered.- Specified by:
getExperimentValueObjectsInSetin interfaceExpressionExperimentSetService- Parameters:
id- id- Returns:
- value objects or an empty set
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initAutomaticallyGeneratedExperimentSet
public ExpressionExperimentSet initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon) Instantiate non-persistent experiment set with description = "Automatically generated for ## EEs.". Mostly for use in Gene2GenePopulationServiceImpl.intializeNewAnalysis(Collection, Taxon, Collection, String, int). By convention, these sets should not be modifiable.- Specified by:
initAutomaticallyGeneratedExperimentSetin interfaceExpressionExperimentSetService
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isAutomaticallyGenerated
@Transactional(readOnly=true) public boolean isAutomaticallyGenerated(String experimentSetDescription) Determines if set was automatically generated by matching the description to that used in ubic.gemma.core.analysis.expression .coexpression.ExpressionExperimentSetService.AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION- Specified by:
isAutomaticallyGeneratedin interfaceExpressionExperimentSetService- Returns:
- true if the set was automatically generated, false otherwise
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loadAllExperimentSetsWithTaxon
@Transactional(readOnly=true) public Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()Description copied from interface:ExpressionExperimentSetServiceSecurity at DAO level.- Specified by:
loadAllExperimentSetsWithTaxonin interfaceExpressionExperimentSetService- Returns:
- ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.
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loadAllExperimentSetValueObjects
@Transactional(readOnly=true) public Collection<ExpressionExperimentSetValueObject> loadAllExperimentSetValueObjects(boolean loadEEIds) Description copied from interface:ExpressionExperimentSetServiceSecurity filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()- Specified by:
loadAllExperimentSetValueObjectsin interfaceExpressionExperimentSetService- Parameters:
loadEEIds- whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.- Returns:
- ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.
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loadMySetValueObjects
@Transactional(readOnly=true) public Collection<ExpressionExperimentSetValueObject> loadMySetValueObjects(boolean loadEEIds) Description copied from interface:ExpressionExperimentSetServiceload the user's sets- Specified by:
loadMySetValueObjectsin interfaceExpressionExperimentSetService- Parameters:
loadEEIds- whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.- Returns:
- colelction of EE set VOs
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loadValueObjectById
@Transactional(readOnly=true) public ExpressionExperimentSetValueObject loadValueObjectById(Long id, boolean loadEEIds) Description copied from interface:ExpressionExperimentSetServiceGet a value object for the id param.- Specified by:
loadValueObjectByIdin interfaceExpressionExperimentSetService- Parameters:
id- IDloadEEIds- whether the returned value object should have the ExpressionExperimentIds collection populated. This might be a useful information, but loading the IDs takes slightly longer, so for larger amount of EESets this might want to be avoided.- Returns:
- null if id doesn't match an experiment set
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loadValueObjectById
@Transactional(readOnly=true) public ExpressionExperimentSetValueObject loadValueObjectById(Long id) - Specified by:
loadValueObjectByIdin interfaceBaseVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>- Specified by:
loadValueObjectByIdin interfaceExpressionExperimentSetService- Overrides:
loadValueObjectByIdin classAbstractVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>- See Also:
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loadValueObjectsByIds
@Transactional(readOnly=true) public List<ExpressionExperimentSetValueObject> loadValueObjectsByIds(Collection<Long> eeSetIds) Description copied from interface:BaseVoEnabledServiceLoad value objects by a given collection of IDs.- Specified by:
loadValueObjectsByIdsin interfaceBaseVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>- Specified by:
loadValueObjectsByIdsin interfaceExpressionExperimentSetService- Overrides:
loadValueObjectsByIdsin classAbstractVoEnabledService<ExpressionExperimentSet, ExpressionExperimentSetValueObject>
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thaw
@Transactional(readOnly=true) public ExpressionExperimentSet thaw(ExpressionExperimentSet expressionExperimentSet) - Specified by:
thawin interfaceExpressionExperimentSetService
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update
Description copied from interface:BaseServiceUpdates the given entity in the persistent storage.- Specified by:
updatein interfaceBaseService<ExpressionExperimentSet>- Specified by:
updatein interfaceExpressionExperimentSetService- Overrides:
updatein classAbstractService<ExpressionExperimentSet>- Parameters:
expressionExperimentSet- the entity to be updated.- See Also:
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update
Description copied from interface:BaseServiceUpdates all entities in the given collection in the persistent storage.- Specified by:
updatein interfaceBaseService<ExpressionExperimentSet>- Overrides:
updatein classAbstractService<ExpressionExperimentSet>- Parameters:
entities- the entities to be updated.
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removeFromSets
Description copied from interface:ExpressionExperimentSetServiceRemove an experiment from all sets it is in.Using this allows one to bypass the requirement of "owning edit rights" on the set as long as the current user has the right to edit the experiment itself.
If a set ends-up empty as a result, it is removed as well.
- Specified by:
removeFromSetsin interfaceExpressionExperimentSetService- Returns:
- the number of sets this experiment was removed from
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