Package ubic.gemma.persistence.service.expression.experiment

Interface ExpressionExperimentSetService

All Superinterfaces:
BaseImmutableService<ExpressionExperimentSet>, BaseReadOnlyService<ExpressionExperimentSet>, BaseService<ExpressionExperimentSet>, BaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>, SecurableBaseImmutableService<ExpressionExperimentSet>, SecurableBaseReadOnlyService<ExpressionExperimentSet>, SecurableBaseService<ExpressionExperimentSet>, SecurableBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
All Known Implementing Classes:
ExpressionExperimentSetServiceImpl
public interface ExpressionExperimentSetService extends SecurableBaseService<ExpressionExperimentSet>, SecurableBaseVoEnabledService<ExpressionExperimentSet,ExpressionExperimentSetValueObject>
Author:
paul

  • Method Details

    • find

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<ExpressionExperimentSet> find(ExpressionExperiment ee)

    • findByName

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<ExpressionExperimentSet> findByName(String name)
      security at DAO level
      Parameters:
      name - name
      Returns:
      collection of ee sets

    • findByAccession

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<ExpressionExperimentSet> findByAccession(String accession)

    • findIds

      Collection<Long> findIds(ExpressionExperiment ee)
      security at DAO level
      Parameters:
      ee - BA set
      Returns:
      collection of IDs

    • getExperimentsInSet

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<ExpressionExperiment> getExperimentsInSet(Long id)
      Get the (security-filtered) list of experiments in a set.
      Parameters:
      id - id
      Returns:
      collection of ees

    • getExperimentValueObjectsInSet

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"}) Collection<ExpressionExperimentDetailsValueObject> getExperimentValueObjectsInSet(Long id)
      Get the member experiment value objects for the set id; security filtered.
      Parameters:
      id - id
      Returns:
      value objects or an empty set

    • initAutomaticallyGeneratedExperimentSet

      ExpressionExperimentSet initAutomaticallyGeneratedExperimentSet(Collection<ExpressionExperiment> expressionExperiments, Taxon taxon)

    • isAutomaticallyGenerated

      boolean isAutomaticallyGenerated(String experimentSetDescription)

    • loadAllExperimentSetsWithTaxon

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"}) Collection<ExpressionExperimentSet> loadAllExperimentSetsWithTaxon()
      Security at DAO level.
      Returns:
      ExpressionExperimentSets that have more than 1 experiment in them & have a taxon value.

    • loadAllExperimentSetValueObjects

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"}) Collection<ExpressionExperimentSetValueObject> loadAllExperimentSetValueObjects(boolean loadEEIds)
      Security filtering is handled by the call to load the set entities ubic.gemma.model.analysis.expression.ExpressionExperimentSetService.loadAllExperimentSetsWithTaxon()
      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.

    • loadMySetValueObjects

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_COLLECTION_READ"}) Collection<ExpressionExperimentSetValueObject> loadMySetValueObjects(boolean loadEEIds)
      load the user's sets
      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

    • loadValueObjectById

      @Nullable @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_READ"}) ExpressionExperimentSetValueObject loadValueObjectById(Long id, boolean loadEEIds)
      Get a value object for the id param.
      Parameters:
      id - ID
      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:
      null if id doesn't match an experiment set

    • thaw

      @CheckReturnValue @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"}) ExpressionExperimentSet thaw(ExpressionExperimentSet set)

    • removeFromSets

      @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_EDIT"}) int removeFromSets(ExpressionExperiment bas)
      Remove 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.

      Returns:
      the number of sets this experiment was removed from