Package ubic.gemma.web.controller.genome.gene

Class GeneSetController

  • @Controller
@RequestMapping("/geneSet")
public class GeneSetController
extends Object
    Exposes GeneSetServices methods over ajax. Some methods take and return collections to be compatible with Store interfaces (which, as of May 2014, we do not use)
    Author:
    kelsey

    • Method Summary

      All Methods Instance Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject addSessionGroup​(ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject gsvo, Boolean modificationBased)
      * AJAX adds the gene group to the session, used by SessionGeneGroupStore and SessionDatasetGroupStore sets the groups taxon value and reference.
      Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> addSessionGroups​(Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> geneSetVos, Boolean modificationBased)
      Deprecated. 
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> addUserAndSessionGroups​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> geneSetVos)
      AJAX adds the gene group to the session
      String canCurrentUserEditGroup​(ubic.gemma.model.genome.gene.GeneSetValueObject gsvo)
      AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> create​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> geneSetVos)
      AJAX create an entities in the database based on the value objects passed in
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> findGeneSetsByGene​(Long geneId)
      Given a Gemma Gene Id will find all gene groups that the current user is allowed to use
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> findGeneSetsByName​(String query, Long taxonId)  
      Collection<Long> getGeneIdsInGroup​(Long groupId)
      AJAX
      Collection<ubic.gemma.model.genome.gene.GeneValueObject> getGenesInGroup​(Long groupId, Integer limit)
      AJAX If the current user has access to given gene group, will return the gene value objects in the gene group
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> getUserAndSessionGeneGroups​(boolean privateOnly, Long taxonId)
      AJAX Returns the current users gene sets as well as their session gene sets
      Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> getUserSessionGeneGroups​(boolean privateOnly, Long taxonId)
      AJAX Returns just the current users gene sets
      Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> getUsersGeneGroups​(boolean privateOnly, Long taxonId)
      AJAX Returns just the current users gene sets
      ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject load​(Long id)
      AJAX - load with the IDs filled in
      Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> remove​(Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> vos)
      AJAX Given a valid gene group will remove it from db (if the user has permissons to do so).
      Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> removeSessionGroups​(Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> vos)
      Deprecated. 
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> removeUserAndSessionGroups​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> vos)
      AJAX Given valid gene groups will remove them from the session or the database appropriately.
      org.springframework.web.servlet.ModelAndView showGeneSet​(Long id)
      If the current user has access to given gene group will return the gene ids in the gene group;
      Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> update​(Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> geneSetVos)
      AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
      void updateMembers​(Long groupId, Collection<Long> geneIds)
      AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
      ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject updateNameDesc​(ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject geneSetVO)
      AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
      ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject updateSessionGroup​(ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject vos)
      AJAX updates a session group
      Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> updateSessionGroups​(Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> vos)
      Deprecated. 
      Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> updateUserAndSessionGroups​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> vos)
      AJAX Updates the session group and user database groups.

    • Constructor Detail

      • GeneSetController

        public GeneSetController()

    • Method Detail

      • addSessionGroups

        @Deprecated
public Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> addSessionGroups​(Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> geneSetVos,
                                                                                                Boolean modificationBased)
        Deprecated.
        AJAX adds the gene group to the session, used by SessionGeneGroupStore and SessionDatasetGroupStore sets the groups taxon value and reference.
        Parameters:
        geneSetVos - 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.genome.gene.SessionBoundGeneSetValueObject addSessionGroup​(ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject gsvo,
                                                                                   Boolean modificationBased)
        * AJAX adds the gene group to the session, used by SessionGeneGroupStore and SessionDatasetGroupStore sets the groups taxon value and reference.
        Parameters:
        gsvo - gsvo
        modificationBased - whether the set was modified by the user
        Returns:
        gene set vo

      • addUserAndSessionGroups

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> addUserAndSessionGroups​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> geneSetVos)
        AJAX adds the gene group to the session
        Parameters:
        geneSetVos - value object constructed on the client.
        Returns:
        id of the new gene group

      • canCurrentUserEditGroup

        public String canCurrentUserEditGroup​(ubic.gemma.model.genome.gene.GeneSetValueObject gsvo)
        AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
        Parameters:
        gsvo - gsvo
        Returns:
        string

      • create

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> create​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> geneSetVos)
        AJAX create an entities in the database based on the value objects passed in
        Parameters:
        geneSetVos - value objects constructed on the client.
        Returns:
        value objects converted from the newly created entities

      • findGeneSetsByGene

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> findGeneSetsByGene​(Long geneId)
        Given a Gemma Gene Id will find all gene groups that the current user is allowed to use
        Parameters:
        geneId - gene id
        Returns:
        collection of geneSetValueObject

      • findGeneSetsByName

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> findGeneSetsByName​(String query,
                                                                                      Long taxonId)
        Parameters:
        query - string to match to a gene set.
        taxonId - taxon id
        Returns:
        collection of GeneSetValueObject

      • getGenesInGroup

        public Collection<ubic.gemma.model.genome.gene.GeneValueObject> getGenesInGroup​(Long groupId,
                                                                                Integer limit)
        AJAX If the current user has access to given gene group, will return the gene value objects in the gene group
        Parameters:
        groupId - group id
        limit - if greater than zero, limit to how many genes are returned (for previews)
        Returns:
        gene vos

      • getGeneIdsInGroup

        public Collection<Long> getGeneIdsInGroup​(Long groupId)
        AJAX
        Parameters:
        groupId - group id
        Returns:
        ids of genes in the gene set.

      • getUserAndSessionGeneGroups

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> getUserAndSessionGeneGroups​(boolean privateOnly,
                                                                                               Long taxonId)
        AJAX Returns the current users gene sets as well as their session gene sets
        Parameters:
        privateOnly - private only
        taxonId - if non-null, restrict the groups by ones which have genes in the given taxon.
        Returns:
        gene set vos

      • getUserSessionGeneGroups

        public Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> getUserSessionGeneGroups​(boolean privateOnly,
                                                                                                        Long taxonId)
        AJAX Returns just the current users gene sets
        Parameters:
        privateOnly - private only
        taxonId - if non-null, restrict the groups by ones which have genes in the given taxon.
        Returns:
        gene set vos

      • getUsersGeneGroups

        public Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> getUsersGeneGroups​(boolean privateOnly,
                                                                                                    Long taxonId)
        AJAX Returns just the current users gene sets
        Parameters:
        privateOnly - private only
        taxonId - if non-null, restrict the groups by ones which have genes in the given taxon.
        Returns:
        gene set vos

      • load

        public ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject load​(Long id)
        AJAX - load with the IDs filled in
        Parameters:
        id - id
        Returns:
        gene set vos

      • remove

        public Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> remove​(Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> vos)
        AJAX Given a valid gene group will remove it from db (if the user has permissons to do so).
        Parameters:
        vos - vos
        Returns:
        gene set vos

      • removeSessionGroups

        @Deprecated
public Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> removeSessionGroups​(Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> vos)
        Deprecated.
        AJAX Given a valid gene group will remove it from the session.
        Parameters:
        vos - vos
        Returns:
        gene set vos

      • removeUserAndSessionGroups

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> removeUserAndSessionGroups​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> vos)
        AJAX Given valid gene groups will remove them from the session or the database appropriately.
        Parameters:
        vos - vos
        Returns:
        gene set vos

      • showGeneSet

        @RequestMapping(value="/showGeneSet.html",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView showGeneSet​(@RequestParam("id")
                                                                Long id)
        If the current user has access to given gene group will return the gene ids in the gene group;

      • update

        public Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> update​(Collection<ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject> geneSetVos)
        AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
        Parameters:
        geneSetVos - vos
        Returns:
        gene set vos

      • updateMembers

        public void updateMembers​(Long groupId,
                          Collection<Long> geneIds)
        AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice. Cannot update name or description, just members
        Parameters:
        groupId - id of the gene set being updated
        geneIds - gene ids

      • updateNameDesc

        public ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject updateNameDesc​(ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject geneSetVO)
        AJAX Updates the given gene group (permission permitting) with the given list of geneIds Will not allow the same gene to be added to the gene set twice.
        Parameters:
        geneSetVO - gene set vos
        Returns:
        gene set vo

      • updateSessionGroups

        @Deprecated
public Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> updateSessionGroups​(Collection<ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject> vos)
        Deprecated.
        AJAX Updates the session group.
        Parameters:
        vos - vos
        Returns:
        gene set vos

      • updateSessionGroup

        public ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject updateSessionGroup​(ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject vos)
        AJAX updates a session group
        Parameters:
        vos - vos
        Returns:
        gene set vo

      • updateUserAndSessionGroups

        public Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> updateUserAndSessionGroups​(Collection<ubic.gemma.model.genome.gene.GeneSetValueObject> vos)
        AJAX Updates the session group and user database groups.
        Parameters:
        vos - vos
        Returns:
        gene set vos