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

Interface ExpressionExperimentSetService

    • Field Detail

      • AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION

        static final String AUTOMATICALLY_GENERATED_EXPERIMENT_GROUP_DESCRIPTION
        See Also:
        Constant Field Values

    • Method Detail

      • load

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_READ"})
ExpressionExperimentSet load​(Long id)
        Description copied from interface: BaseService
        Loads object with given ID.
        Specified by:
        load in interface BaseService<ExpressionExperimentSet>
        Parameters:
        id - the ID of entity to be loaded.
        Returns:
        the entity with matching ID, or null if the entity does not exist or if the passed ID was null

      • deleteDatabaseEntity

        void deleteDatabaseEntity​(ExpressionExperimentSetValueObject eesvo)
        Security is handled within method, when the set is loaded
        Parameters:
        eesvo - ee value object

      • 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

        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

        @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

      • updateDatabaseEntity

        void updateDatabaseEntity​(ExpressionExperimentSetValueObject eesvo)
        Update corresponding entity based on value object
        Parameters:
        eesvo - ee value object

      • updateDatabaseEntityMembers

        void updateDatabaseEntityMembers​(Long groupId,
                                 Collection<Long> eeIds)
        Updates the database record for the param experiment set value object (permission permitting) with the members specified of the set, not the name or description etc.
        Parameters:
        eeIds - ee ids
        groupId - group id

      • updateDatabaseEntityNameDesc

        ExpressionExperimentSetValueObject updateDatabaseEntityNameDesc​(ExpressionExperimentSetValueObject eeSetVO,
                                                                boolean loadEEIds)
        Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
        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.
        eeSetVO - ee set value object
        Returns:
        ee vo