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

Interface ExpressionExperimentSetService

    • Method Detail

      • 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

      • findIds

        Collection<Long> findIds​(BioAssaySet bioAssaySet)
        security at DAO level
        Parameters:
        bioAssaySet - 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

      • 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

      • removeFromSets

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_EDIT"})
int removeFromSets​(BioAssaySet 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