Package ubic.gemma.web.controller.expression.experiment

Class ExpressionExperimentSetController

  • @Controller
@RequestMapping("/expressionExperimentSet")
public class ExpressionExperimentSetController
extends BaseController
    For fetching and manipulating ExpressionExperimentSets. Methods take collections to be compatible with Store interfaces.
    Author:
    paul

    • Constructor Detail

      • ExpressionExperimentSetController

        public ExpressionExperimentSetController()

    • Method Detail

      • addSessionGroups

        @Deprecated
public Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> addSessionGroups​(Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> eeSetVos,
                                                                                                                          Boolean modificationBased)
        Deprecated.
        AJAX adds the Expression Experiment group to the session
        Parameters:
        eeSetVos - value object constructed on the client.
        modificationBased - whether the set was modified by the user
        Returns:
        collection of added session groups (with updated reference.id etc)

      • addSessionGroup

        public ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject addSessionGroup​(ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject eesvo,
                                                                                                             Boolean modificationBased)
        AJAX adds the Expression Experiment group to the session

      • addUserAndSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> addUserAndSessionGroups​(Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> sets)
        AJAX adds the experiment group to the session
        Returns:
        the new gene groups

      • canCurrentUserEditGroup

        public String canCurrentUserEditGroup​(ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject eesvo)
        AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed

      • create

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> create​(Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> entities)

      • getExperimentsInSet

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject> getExperimentsInSet​(Long groupId,
                                                                                                                     Integer limit)
        Parameters:
        limit - to return only up to a given number of experiments, e.g. for a preview of the set.

      • load

        public ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject load​(Long id)
        AJAX
        Parameters:
        id - of the set
        Returns:
        the ExpressionExperimentSetValueObject for the id param
        Throws:
        IllegalArgumentException - if the id param is null
        org.springframework.security.access.AccessDeniedException - if the id param is not null but the loading function returns a null value

      • loadAll

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> loadAll()
        AJAX returns all available sets that have a taxon value (so not really all) sets can have *any* number of experiments
        Returns:
        all available sets that have a taxon value

      • loadAllSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> loadAllSessionGroups()
        AJAX
        Returns:
        all available session backed sets

      • loadAllUserAndSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> loadAllUserAndSessionGroups()
        AJAX
        Returns:
        all available sets from db and also session backed sets

      • loadAllUserOwnedAndSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> loadAllUserOwnedAndSessionGroups()
        AJAX
        Returns:
        all available sets that have a taxon value from db and also session backed sets

      • loadByName

        public ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject loadByName​(String name)

      • remove

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> remove​(Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> entities)
        Returns:
        the entities which were removed.

      • removeSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> removeSessionGroups​(Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> vos)
        AJAX Given a valid experiment group will remove it from the session.

      • removeUserAndSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> removeUserAndSessionGroups​(Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> vos)
        AJAX Given valid experiment groups will remove them from the session or the database appropriately.

      • showExpressionExperimentSet

        @RequestMapping(value="/showExpressionExperimentSet.html",
                method=GET)
public ModelAndView showExpressionExperimentSet​(javax.servlet.http.HttpServletRequest request,
                                                javax.servlet.http.HttpServletResponse response)

      • update

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> update​(Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> entities)
        Returns:
        the entities which were updated (even if they weren't actually updated)

      • updateMembers

        public String updateMembers​(Long groupId,
                            Collection<Long> eeIds)
        AJAX Updates the given group (permission permitting) with the given list of memberIds. Will not allow the same experiment to be added to the set twice. Will not update name or description, just members.
        Parameters:
        groupId - id of the gene set being updated
        Returns:
        error message or null if no errors

      • updateNameDesc

        public ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject updateNameDesc​(ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject eeSetVO)
        AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
        Parameters:
        eeSetVO - the value object that represents the database record to update
        Returns:
        a value object for the updated set

      • updateSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> updateSessionGroups​(Collection<ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject> vos)
        AJAX Updates the session group.

      • updateUserAndSessionGroups

        public Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> updateUserAndSessionGroups​(Collection<ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject> vos)
        AJAX Updates the session group and user database groups.