Incorporate latest grid features into managing users, groups and roles from the admin view.

2026-09-21 13:50:20 +08:00 · 2009-11-09 23:00:55 -05:00
parent 5371e0e6da
commit 00c3f84f40
19 changed files with 460 additions and 828 deletions
@@ -2,20 +2,31 @@ import string, sys
 from datetime import datetime, timedelta
 from galaxy import util, datatypes
 from galaxy.web.base.controller import *
+from galaxy.util.odict import odict
 from galaxy.model.orm import *
 from galaxy.web.framework.helpers import time_ago, iff, grids
 import logging
 log = logging.getLogger( __name__ )

+# States for passing messages
+SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
+
 class UserListGrid( grids.Grid ):
-    class EmailColumn( grids.GridColumn ):
+    class EmailColumn( grids.TextColumn ):
        def get_value( self, trans, grid, user ):
            return user.email
-    class UserNameColumn( grids.GridColumn ):
+    class UserNameColumn( grids.TextColumn ):
        def get_value( self, trans, grid, user ):
            if user.username:
                return user.username
            return 'not set'
+    class StatusColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, user ):
+            if user.purged:
+                return "purged"
+            elif user.deleted:
+                return "deleted"
+            return ""
    class GroupsColumn( grids.GridColumn ):
        def get_value( self, trans, grid, user ):
            if user.groups:
@@ -36,56 +47,242 @@ class UserListGrid( grids.Grid ):
            if user.galaxy_sessions:
                return self.format( user.galaxy_sessions[ 0 ].update_time )
            return 'never'
+    class DeletedColumn( grids.GridColumn ):
+       def get_accepted_filters( self ):
+           """ Returns a list of accepted filters for this column. """
+           accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" }
+           accepted_filters = []
+           for label, val in accepted_filter_labels_and_vals.items():
+               args = { self.key: val }
+               accepted_filters.append( grids.GridColumnFilter( label, args) )
+           return accepted_filters
+
    # Grid definition
    title = "Users"
    model_class = model.User
    template='/admin/user/grid.mako'
+    default_sort_key = "email"
    columns = [
-        EmailColumn( "Email", link=( lambda item: dict( operation="information", id=item.id ) ), attach_popup=True ),
-        UserNameColumn( "User Name", attach_popup=False ),
+        EmailColumn( "Email",
+                     key="email",
+                     model_class=model.User,
+                     link=( lambda item: dict( operation="information", id=item.id ) ),
+                     attach_popup=True,
+                     filterable="advanced" ),
+        UserNameColumn( "User Name",
+                        key="username",
+                        model_class=model.User,
+                        attach_popup=False,
+                        filterable="advanced" ),
        GroupsColumn( "Groups", attach_popup=False ),
        RolesColumn( "Roles", attach_popup=False ),
        ExternalColumn( "External", attach_popup=False ),
        LastLoginColumn( "Last Login", format=time_ago ),
-        # Valid for filtering but invisible
-        grids.GridColumn( "Deleted", key="deleted", visible=False )
+        StatusColumn( "Status", attach_popup=False ),
+        # Columns that are valid for filtering but are not visible.
+        DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search", 
+                                                cols_to_filter=[ columns[0], columns[1] ], 
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    global_actions = [
+        grids.GridAction( "Create new user", dict( controller='admin', action='users', operation='create' ) )
    ]
    operations = [
        grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False )
-        
    ]
    #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if 
    # the setting is False
    operations.append( grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) )
    operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) )
-    operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ) )
-    operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) )
+    operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) )
+    operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) )
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),
+        grids.GridColumnFilter( "Purged", args=dict( purged=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    default_filter = dict( email="All", username="All", deleted="False", purged="False" )
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def get_current_item( self, trans ):
+        return trans.user
+    def build_initial_query( self, session ):
+        return session.query( self.model_class )
+
+class RoleListGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, role ):
+            return role.name
+    class DescriptionColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, role ):
+            if role.description:
+                return role.description
+            return ''
+    class TypeColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, role ):
+            return role.type
+    class StatusColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, role ):
+            if role.deleted:
+                return "deleted"
+            return ""
+    class DeletedColumn( grids.GridColumn ):
+       def get_accepted_filters( self ):
+           """ Returns a list of accepted filters for this column. """
+           accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" }
+           accepted_filters = []
+           for label, val in accepted_filter_labels_and_vals.items():
+               args = { self.key: val }
+               accepted_filters.append( grids.GridColumnFilter( label, args) )
+           return accepted_filters
+    class GroupsColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, role ):
+            if role.groups:
+                return len( role.groups )
+            return 0
+    class UsersColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, role ):
+            if role.users:
+                return len( role.users )
+            return 0
+
+    # Grid definition
+    title = "Roles"
+    model_class = model.Role
+    template='/admin/dataset_security/role/grid.mako'
+    default_sort_key = "name"
+    columns = [
+        NameColumn( "Name",
+                    key="name",
+                    link=( lambda item: dict( controller="admin", action="role", id=item.id ) ),
+                    model_class=model.Role,
+                    attach_popup=True,
+                    filterable="advanced" ),
+        DescriptionColumn( "Description",
+                           key='description',
+                           model_class=model.Role,
+                           attach_popup=False,
+                           filterable="advanced" ),
+        TypeColumn( "Type",
+                    key='type',
+                    model_class=model.Role,
+                    attach_popup=False,
+                    filterable="advanced" ),
+        GroupsColumn( "Groups", attach_popup=False ),
+        UsersColumn( "Users", attach_popup=False ),
+        StatusColumn( "Status", attach_popup=False ),
+        # Columns that are valid for filtering but are not visible.
+        DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search", 
+                                                cols_to_filter=[ columns[0], columns[1], columns[2] ], 
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    global_actions = [
+        grids.GridAction( "Add new role", dict( controller='admin', action='roles', operation='create' ) )
+    ]
+    operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ),
+                   grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ),
+                   grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ]
    standard_filters = [
        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
    ]
-    default_filter = dict( deleted=False )
+    default_filter = dict( name="All", deleted="False", description="All", type="All" )
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
    def get_current_item( self, trans ):
-        return trans.user
+        return None
    def build_initial_query( self, session ):
        return session.query( self.model_class )
    def apply_default_filter( self, trans, query, **kwargs ):
-        email_filter = kwargs.get( "email_filter", None )
-        if email_filter:
-            if email_filter == 'all':
-                return query
-            else:
-                return query.filter( or_( trans.app.model.User.table.c.email.like( '%s' % email_filter.lower() + '%' ),
-                                          trans.app.model.User.table.c.email.like( '%s' % email_filter.upper() + '%' ) ) )
-        elif query.count() > 200:
-            return query.filter( or_( trans.app.model.User.table.c.email.like( 'A%' ),
-                                      trans.app.model.User.table.c.email.like( 'a%' ) ) )
-        return query
+        return query.filter( model.Role.type != model.Role.types.PRIVATE )
+
+class GroupListGrid( grids.Grid ):
+    class NameColumn( grids.TextColumn ):
+        def get_value( self, trans, grid, group ):
+            return group.name
+    class StatusColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, group ):
+            if group.deleted:
+                return "deleted"
+            return ""
+    class DeletedColumn( grids.GridColumn ):
+       def get_accepted_filters( self ):
+           """ Returns a list of accepted filters for this column. """
+           accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" }
+           accepted_filters = []
+           for label, val in accepted_filter_labels_and_vals.items():
+               args = { self.key: val }
+               accepted_filters.append( grids.GridColumnFilter( label, args) )
+           return accepted_filters
+    class RolesColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, group ):
+            if group.roles:
+                return len( group.roles )
+            return 0
+    class UsersColumn( grids.GridColumn ):
+        def get_value( self, trans, grid, group ):
+            if group.members:
+                return len( group.members )
+            return 0
+
+    # Grid definition
+    title = "Groups"
+    model_class = model.Group
+    template='/admin/dataset_security/group/grid.mako'
+    default_sort_key = "name"
+    columns = [
+        NameColumn( "Name",
+                    key="name",
+                    link=( lambda item: dict( controller="admin", action="group", id=item.id ) ),
+                    model_class=model.Group,
+                    attach_popup=True,
+                    filterable="advanced" ),
+        UsersColumn( "Users", attach_popup=False ),
+        RolesColumn( "Roles", attach_popup=False ),
+        StatusColumn( "Status", attach_popup=False ),
+        # Columns that are valid for filtering but are not visible.
+        DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
+    ]
+    columns.append( grids.MulticolFilterColumn( "Search", 
+                                                cols_to_filter=[ columns[0], columns[1], columns[2] ], 
+                                                key="free-text-search",
+                                                visible=False,
+                                                filterable="standard" ) )
+    global_actions = [
+        grids.GridAction( "Add new group", dict( controller='admin', action='groups', operation='create' ) )
+    ]
+    operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ),
+                   grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ),
+                   grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ]
+    standard_filters = [
+        grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
+        grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
+        grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
+    ]
+    default_filter = dict( name="All", deleted="False" )
+    num_rows_per_page = 50
+    preserve_state = False
+    use_paging = True
+    def get_current_item( self, trans ):
+        return None
+    def build_initial_query( self, session ):
+        return session.query( self.model_class )

 class Admin( BaseController ):
    
    user_list_grid = UserListGrid()
+    role_list_grid = RoleListGrid()
+    group_list_grid = GroupListGrid()
    
    @web.expose
    @web.require_admin
@@ -117,17 +314,23 @@ class Admin( BaseController ):
    # Galaxy Role Stuff
    @web.expose
    @web.require_admin
-    def roles( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        roles = trans.sa_session.query( trans.app.model.Role ).filter( and_( trans.app.model.Role.table.c.deleted==False,
-                                                                             trans.app.model.Role.table.c.type != trans.app.model.Role.types.PRIVATE ) ) \
-                                                              .order_by( trans.app.model.Role.table.c.name )
-        return trans.fill_template( '/admin/dataset_security/roles.mako',
-                                    roles=roles,
-                                    msg=msg,
-                                    messagetype=messagetype )
+    def roles( self, trans, **kwargs ):
+        if 'operation' in kwargs:
+            operation = kwargs['operation'].lower()
+            if operation == "roles":
+                return self.role( trans, **kwargs )
+            if operation == "create":
+                return self.create_role( trans, **kwargs )
+            if operation == "delete":
+                return self.mark_role_deleted( trans, **kwargs )
+            if operation == "undelete":
+                return self.undelete_role( trans, **kwargs )
+            if operation == "purge":
+                return self.purge_role( trans, **kwargs )
+            if operation == "manage users & groups":
+                return self.role( trans, **kwargs )
+        # Render the list view
+        return self.role_list_grid( trans, **kwargs )
    @web.expose
    @web.require_admin
    def create_role( self, trans, **kwd ):
@@ -164,7 +367,7 @@ class Admin( BaseController ):
                    ( group.name, role.name, len( in_users ), len( in_groups ) )
                else:
                    msg = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) )
-                trans.response.send_redirect( web.url_for( controller='admin', action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
+                trans.response.send_redirect( web.url_for( controller='admin', action='roles', message=util.sanitize_text( msg ), status='done' ) )
            trans.response.send_redirect( web.url_for( controller='admin', action='create_role', msg=util.sanitize_text( msg ), messagetype='error' ) )
        out_users = []
        for user in trans.sa_session.query( trans.app.model.User ) \
@@ -176,7 +379,7 @@ class Admin( BaseController ):
                                     .filter( trans.app.model.Group.table.c.deleted==False ) \
                                     .order_by( trans.app.model.Group.table.c.name ):
            out_groups.append( ( group.id, group.name ) )
-        return trans.fill_template( '/admin/dataset_security/role_create.mako',
+        return trans.fill_template( '/admin/dataset_security/role/role_create.mako',
                                    in_users=[],
                                    out_users=out_users,
                                    in_groups=[],
@@ -189,7 +392,7 @@ class Admin( BaseController ):
        params = util.Params( kwd )
        msg = util.restore_text( params.get( 'msg', ''  ) )
        messagetype = params.get( 'messagetype', 'done' )
-        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
+        role = get_role( trans, params.id )
        if params.get( 'role_members_edit_button', False ):
            in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ]
            for ura in role.users:
@@ -210,7 +413,7 @@ class Admin( BaseController ):
            trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups )
            trans.sa_session.refresh( role )
            msg = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) )
-            trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype=messagetype ) )
+            trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status=messagetype ) )
        elif params.get( 'rename', False ):
            if params.rename == 'submitted':
                old_name = role.name
@@ -218,17 +421,17 @@ class Admin( BaseController ):
                new_description = util.restore_text( params.description )
                if not new_name:
                    msg = 'Enter a valid name'
-                    return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype='error' )
+                    return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' )
                elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first():
                    msg = 'A role with that name already exists'
-                    return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype='error' )
+                    return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' )
                else:
                    role.name = new_name
                    role.description = new_description
                    role.flush()
                    msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name )
-                    return trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
-            return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype=messagetype )
+                    return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status='done' ) )
+            return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype=messagetype )
        in_users = []
        out_users = []
        in_groups = []
@@ -273,7 +476,7 @@ class Admin( BaseController ):
                    library_dataset_actions[ library ][ folder_path ].append( dp.action )
                except:
                    library_dataset_actions[ library ][ folder_path ] = [ dp.action ]
-        return trans.fill_template( '/admin/dataset_security/role.mako',
+        return trans.fill_template( '/admin/dataset_security/role/role.mako',
                                    role=role,
                                    in_users=in_users,
                                    out_users=out_users,
@@ -286,33 +489,20 @@ class Admin( BaseController ):
    @web.require_admin
    def mark_role_deleted( self, trans, **kwd ):
        params = util.Params( kwd )
-        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
+        role = get_role( trans, params.id )
        role.deleted = True
        role.flush()
-        msg = "Role '%s' has been marked as deleted." % role.name
-        trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def deleted_roles( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        roles = trans.sa_session.query( trans.app.model.Role ) \
-                                .filter( trans.app.model.Role.table.c.deleted==True ) \
-                                .order_by( trans.app.model.Role.table.c.name )
-        return trans.fill_template( '/admin/dataset_security/deleted_roles.mako', 
-                                    roles=roles, 
-                                    msg=msg,
-                                    messagetype=messagetype )
+        message = "Role '%s' has been marked as deleted." % role.name
+        trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) )
    @web.expose
    @web.require_admin
    def undelete_role( self, trans, **kwd ):
        params = util.Params( kwd )
-        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
+        role = get_role( trans, params.id )
        role.deleted = False
        role.flush()
-        msg = "Role '%s' has been marked as not deleted." % role.name
-        trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
+        message = "Role '%s' has been marked as not deleted." % role.name
+        trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) )
    @web.expose
    @web.require_admin
    def purge_role( self, trans, **kwd ):
@@ -324,11 +514,10 @@ class Admin( BaseController ):
        # - GroupRoleAssociations where role_id == Role.id
        # - DatasetPermissionss where role_id == Role.id
        params = util.Params( kwd )
-        role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) )
+        role = get_role( trans, params.id )
        if not role.deleted:
-            # We should never reach here, but just in case there is a bug somewhere...
-            msg = "Role '%s' has not been deleted, so it cannot be purged." % role.name
-            trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='error' ) )
+            message = "Role '%s' has not been deleted, so it cannot be purged." % role.name
+            trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='error' ) )
        # Delete UserRoleAssociations
        for ura in role.users:
            user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id )
@@ -353,54 +542,60 @@ class Admin( BaseController ):
        for dp in role.dataset_actions:
            trans.sa_session.delete( dp )
            dp.flush()
-        msg = "The following have been purged from the database for role '%s': " % role.name
-        msg += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss."
-        trans.response.send_redirect( web.url_for( action='deleted_roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
+        message = "The following have been purged from the database for role '%s': " % role.name
+        message += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss."
+        trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) )

    # Galaxy Group Stuff
    @web.expose
    @web.require_admin
-    def groups( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        groups = trans.sa_session.query( trans.app.model.Group ) \
-                                 .filter( trans.app.model.Group.table.c.deleted==False ) \
-                                 .order_by( trans.app.model.Group.table.c.name )
-        return trans.fill_template( '/admin/dataset_security/groups.mako', 
-                                    groups=groups, 
-                                    msg=msg,
-                                    messagetype=messagetype )
+    def groups( self, trans, **kwargs ):
+        if 'operation' in kwargs:
+            operation = kwargs['operation'].lower()
+            if operation == "groups":
+                return self.group( trans, **kwargs )
+            if operation == "create":
+                return self.create_group( trans, **kwargs )
+            if operation == "delete":
+                return self.mark_group_deleted( trans, **kwargs )
+            if operation == "undelete":
+                return self.undelete_group( trans, **kwargs )
+            if operation == "purge":
+                return self.purge_group( trans, **kwargs )
+            if operation == "manage users & roles":
+                return self.group( trans, **kwargs )
+        # Render the list view
+        return self.group_list_grid( trans, **kwargs )
    @web.expose
    @web.require_admin
    def group( self, trans, **kwd ):
        params = util.Params( kwd )
        msg = util.restore_text( params.get( 'msg', ''  ) )
        messagetype = params.get( 'messagetype', 'done' )
-        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
+        group = get_group( trans, params.id )
        if params.get( 'group_roles_users_edit_button', False ):
            in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.in_roles ) ]
            in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ]
            trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=in_roles, users=in_users )
            trans.sa_session.refresh( group )
            msg += "Group '%s' has been updated with %d associated roles and %d associated users" % ( group.name, len( in_roles ), len( in_users ) )
-            trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype=messagetype ) )
+            trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status=messagetype ) )
        if params.get( 'rename', False ):
            if params.rename == 'submitted':
                old_name = group.name
                new_name = util.restore_text( params.name )
                if not new_name:
                    msg = 'Enter a valid name'
-                    return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype='error' )
+                    return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' )
                elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first():
                    msg = 'A group with that name already exists'
-                    return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype='error' )
+                    return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' )
                else:
                    group.name = new_name
                    group.flush()
                    msg = "Group '%s' has been renamed to '%s'" % ( old_name, new_name )
                    return trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
-            return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype=messagetype )
+            return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype=messagetype )
        in_roles = []
        out_roles = []
        in_users = []
@@ -420,7 +615,7 @@ class Admin( BaseController ):
            else:
                out_users.append( ( user.id, user.email ) )
        msg += 'Group %s is currently associated with %d roles and %d users' % ( group.name, len( in_roles ), len( in_users ) )
-        return trans.fill_template( '/admin/dataset_security/group.mako',
+        return trans.fill_template( '/admin/dataset_security/group/group.mako',
                                    group=group,
                                    in_roles=in_roles,
                                    out_roles=out_roles,
@@ -455,7 +650,7 @@ class Admin( BaseController ):
                    gra = trans.app.model.GroupRoleAssociation( group, role )
                    gra.flush()
                msg = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_users ), len( in_roles ) )
-                trans.response.send_redirect( web.url_for( controller='admin', action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
+                trans.response.send_redirect( web.url_for( controller='admin', action='groups', message=util.sanitize_text( msg ), status='done' ) )
            trans.response.send_redirect( web.url_for( controller='admin', action='create_group', msg=util.sanitize_text( msg ), messagetype='error' ) )
        out_users = []
        for user in trans.sa_session.query( trans.app.model.User ) \
@@ -467,7 +662,7 @@ class Admin( BaseController ):
                                    .filter( trans.app.model.Role.table.c.deleted==False ) \
                                    .order_by( trans.app.model.Role.table.c.name ):
            out_roles.append( ( role.id, role.name ) )
-        return trans.fill_template( '/admin/dataset_security/group_create.mako',
+        return trans.fill_template( '/admin/dataset_security/group/group_create.mako',
                                    in_users=[],
                                    out_users=out_users,
                                    in_roles=[],
@@ -478,44 +673,31 @@ class Admin( BaseController ):
    @web.require_admin
    def mark_group_deleted( self, trans, **kwd ):
        params = util.Params( kwd )
-        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
+        group = get_group( trans, params.id )
        group.deleted = True
        group.flush()
        msg = "Group '%s' has been marked as deleted." % group.name
-        trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def deleted_groups( self, trans, **kwd ):
-        params = util.Params( kwd )
-        msg = util.restore_text( params.get( 'msg', ''  ) )
-        messagetype = params.get( 'messagetype', 'done' )
-        groups = trans.sa_session.query( trans.app.model.Group ) \
-                                 .filter( trans.app.model.Group.table.c.deleted==True ) \
-                                 .order_by( trans.app.model.Group.table.c.name )
-        return trans.fill_template( '/admin/dataset_security/deleted_groups.mako', 
-                                    groups=groups, 
-                                    msg=msg,
-                                    messagetype=messagetype )
+        trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) )
    @web.expose
    @web.require_admin
    def undelete_group( self, trans, **kwd ):
        params = util.Params( kwd )
-        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
+        group = get_group( trans, params.id )
        group.deleted = False
        group.flush()
        msg = "Group '%s' has been marked as not deleted." % group.name
-        trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
+        trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) )
    @web.expose
    @web.require_admin
    def purge_group( self, trans, **kwd ):
        # This method should only be called for a Group that has previously been deleted.
        # Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations.
        params = util.Params( kwd )
-        group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) )
+        group = get_group( trans, params.id )
        if not group.deleted:
            # We should never reach here, but just in case there is a bug somewhere...
            msg = "Group '%s' has not been deleted, so it cannot be purged." % group.name
-            trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='error' ) )
+            trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='error' ) )
        # Delete UserGroupAssociations
        for uga in group.users:
            trans.sa_session.delete( uga )
@@ -525,8 +707,8 @@ class Admin( BaseController ):
            trans.sa_session.delete( gra )
            gra.flush()
        # Delete the Group
-        msg = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group.name
-        trans.response.send_redirect( web.url_for( action='deleted_groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
+        message = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group.name
+        trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) )

    # Galaxy User Stuff
    @web.expose
@@ -645,11 +827,12 @@ class Admin( BaseController ):
            message = "No user ids received for deleting"
            trans.response.send_redirect( web.url_for( action='users', message=message, status='error' ) )
        ids = util.listify( id )
+        message = "Deleted %d users: " % len( ids )
        for user_id in ids:
            user = get_user( trans, user_id )
            user.deleted = True
            user.flush()
-        message = "Deleted %d users" % len( ids )
+            message += " %s " % user.email
        trans.response.send_redirect( web.url_for( action='users', message=util.sanitize_text( message ), status='done' ) )
    @web.expose
    @web.require_admin
@@ -660,13 +843,15 @@ class Admin( BaseController ):
            trans.response.send_redirect( web.url_for( action='users', message=message, status='error' ) )
        ids = util.listify( id )
        count = 0
+        undeleted_users = ""
        for user_id in ids:
            user = get_user( trans, user_id )
            if user.deleted:
                user.deleted = False
                user.flush()
                count += 1
-        message = "Undeleted %d users" % count
+                undeleted_users += " %s" % user.email
+        message = "Undeleted %d users: %s" % ( count, undeleted_users )
        trans.response.send_redirect( web.url_for( action='users',
                                                   message=util.sanitize_text( message ),
                                                   status='done' ) )
@@ -691,6 +876,7 @@ class Admin( BaseController ):
                                                       message=util.sanitize_text( message ),
                                                       status='error' ) )
        ids = util.listify( id )
+        message = "Purged %d users: " % len( ids )
        for user_id in ids:
            user = get_user( trans, user_id )
            if not user.deleted:
@@ -726,7 +912,7 @@ class Admin( BaseController ):
            # Purge the user
            user.purged = True
            user.flush()
-        message = "Purged %d users" % len( ids )
+            message += "%s " % user.email
        trans.response.send_redirect( web.url_for( controller='admin',
                                                   action='users',
                                                   message=util.sanitize_text( message ),
@@ -750,6 +936,8 @@ class Admin( BaseController ):
                return self.create_new_user( trans, **kwargs )
            if operation == "information":
                return self.user_info( trans, **kwargs )
+            if operation == "manage roles & groups":
+                return self.user( trans, **kwargs )
        # Render the list view
        return self.user_list_grid( trans, **kwargs )
    @web.expose
@@ -774,6 +962,14 @@ class Admin( BaseController ):
                                                          admin_view=True, **kwd ) )
    @web.expose
    @web.require_admin
+    def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ):
+        """Return autocomplete data for user emails"""
+        ac_data = ""
+        for user in trans.sa_session.query( User ).filter_by( deleted=False ).filter( func.lower( User.email ).like( q.lower() + "%" ) ):
+            ac_data = ac_data + user.email + "\n"
+        return ac_data
+    @web.expose
+    @web.require_admin
    def user( self, trans, **kwd ):
        user_id = kwd.get( 'id', None )
        message = ''
@@ -932,5 +1128,21 @@ def get_user( trans, id ):
    id = trans.security.decode_id( id )
    user = trans.sa_session.query( model.User ).get( id )
    if not user:
-        err+msg( "User not found" )
+        return trans.show_error_message( "User not found for id (%s)" % str( id ) )
    return user
+def get_role( trans, id ):
+    """Get a Role from the database by id."""
+    # Load user from database
+    id = trans.security.decode_id( id )
+    role = trans.sa_session.query( model.Role ).get( id )
+    if not role:
+        return trans.show_error_message( "Role not found for id (%s)" % str( id ) )
+    return role
+def get_group( trans, id ):
+    """Get a Group from the database by id."""
+    # Load user from database
+    id = trans.security.decode_id( id )
+    group = trans.sa_session.query( model.Group ).get( id )
+    if not group:
+        return trans.show_error_message( "Group not found for id (%s)" % str( id ) )
+    return group
@@ -1,101 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-## Render a row
-<%def name="render_row( group, ctr, anchored, curr_anchor )">
-    %if ctr % 2 == 1:
-        <tr class="odd_row">
-    %else:
-        <tr>
-    %endif
-        <td>
-            ${group.name}
-            <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-            <div popupmenu="group-${group.id}-popup">
-                <a class="action-button" href="${h.url_for( action='undelete_group', group_id=group.id )}">Undelete</a>
-                <a class="action-button" href="${h.url_for( action='purge_group', group_id=group.id )}">Purge</a>
-            </div>
-        </td>
-        <td>
-            ${len( group.members )}
-        </td>
-        <td>
-            ${len( group.roles )}
-            %if not anchored:
-                <a name="${curr_anchor}"></a>
-                <div style="float: right;"><a href="#TOP">top</a></div>
-            %endif
-        </td>
-    </tr>
-</%def>
-
-<a name="TOP"><h2>Deleted Groups</h2></a>
-
-%if msg:
-    ${render_msg( msg, messagetype )}
-%endif
-
-## TODO: make this a grid
-
-%if not groups:
-    There are no deleted Galaxy groups
-%else:
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <% 
-            render_quick_find = groups.count() > 200
-            ctr = 0
-        %>
-        %if render_quick_find:
-            <%
-                anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
-                anchor_loc = 0
-                anchored = False
-                curr_anchor = 'A'
-            %>
-            <tr style="background: #EEE">
-                <td colspan="3" style="text-align: center; border-bottom: 1px solid #D8B365">
-                    Jump to letter:
-                    %for a in anchors:
-                        | <a href="#${a}">${a}</a>
-                    %endfor
-                </td>
-            </tr>
-        %endif
-        <tr class="header">
-            <td>Name</td>
-            <td>Users</td>
-            <td>Roles</td>
-        </tr>
-        %for ctr, group in enumerate( groups ):
-            %if render_quick_find and not group.name.upper().startswith( curr_anchor ):
-                <% anchored = False %>
-            %endif
-            %if render_quick_find and group.name.upper().startswith( curr_anchor ):
-                %if not anchored:
-                    ${render_row( group, ctr, anchored, curr_anchor )}
-                    <% anchored = True %>
-                %else:
-                    ${render_row( group, ctr, anchored, curr_anchor )}
-                %endif
-            %elif render_quick_find:
-                %for anchor in anchors[ anchor_loc: ]:
-                    %if group.name.upper().startswith( anchor ):
-                        %if not anchored:
-                            <% curr_anchor = anchor %>
-                            ${render_row( group, ctr, anchored, curr_anchor )}
-                            <%  anchored = True %>
-                        %else:
-                            ${render_row( group, ctr, anchored, curr_anchor )}
-                        %endif
-                        <% 
-                            anchor_loc = anchors.index( anchor )
-                            break 
-                        %>
-                    %endif
-                %endfor
-            %else:
-                ${render_row( group, ctr, True, '' )}
-            %endif
-        %endfor
-    </table>
-%endif
@@ -1,103 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-## Render a row
-<%def name="render_row( role, ctr, anchored, curr_anchor )">
-    %if ctr % 2 == 1:
-        <tr class="odd_row">
-    %else:
-        <tr>
-    %endif
-        <td>
-            ${role.name}
-            <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-            <div popupmenu="role-${role.id}-popup">
-                <a class="action-button" href="${h.url_for( action='undelete_role', role_id=role.id )}">Undelete</a>
-                <a class="action-button" href="${h.url_for( action='purge_role', role_id=role.id )}">Purge</a>
-            </div>
-        </td>
-        <td>${role.description}</td>
-        <td>${role.type}</td>
-        <td>
-            ${len( role.users )}
-        </td>
-        <td>
-            ${len( role.groups )}
-            %if not anchored:
-                <a name="${curr_anchor}"></a>
-                <div style="float: right;"><a href="#TOP">top</a></div>
-            %endif
-        </td>
-    </tr>
-</%def>
-
-<a name="TOP"><h2>Deleted Roles</h2></a>
-
-%if msg:
-    ${render_msg( msg, messagetype )}
-%endif
-
-%if not roles:
-    There are no deleted Galaxy roles
-%else:
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <% 
-            render_quick_find = roles.count() > 200
-            ctr = 0
-        %>
-        %if render_quick_find:
-            <%
-                anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
-                anchor_loc = 0
-                anchored = False
-                curr_anchor = 'A'
-            %>
-            <tr style="background: #EEE">
-                <td colspan="3" style="text-align: center; border-bottom: 1px solid #D8B365">
-                    Jump to letter:
-                    %for a in anchors:
-                        | <a href="#${a}">${a}</a>
-                    %endfor
-                </td>
-            </tr>
-        %endif
-        <tr class="header">
-            <td>Name</td>
-            <td>Description</td>
-            <td>Type</td>
-            <td>Users</td>
-            <td>Groups</td>
-        </tr>
-        %for ctr, role in enumerate( roles ):
-            %if render_quick_find and not role.name.upper().startswith( curr_anchor ):
-                <% anchored = False %>
-            %endif
-            %if render_quick_find and role.name.upper().startswith( curr_anchor ):
-                %if not anchored:
-                    ${render_row( role, ctr, anchored, curr_anchor )}
-                    <% anchored = True %>
-                %else:
-                    ${render_row( role, ctr, anchored, curr_anchor )}
-                %endif
-            %elif render_quick_find:
-                %for anchor in anchors[ anchor_loc: ]:
-                    %if role.name.upper().startswith( anchor ):
-                        %if not anchored:
-                            <% curr_anchor = anchor %>
-                            ${render_row( role, ctr, anchored, curr_anchor )}
-                            <%  anchored = True %>
-                        %else:
-                            ${render_row( role, ctr, anchored, curr_anchor )}
-                        %endif
-                        <% 
-                            anchor_loc = anchors.index( anchor )
-                            break 
-                        %>
-                    %endif
-                %endfor
-            %else:
-                ${render_row( role, ctr, True, '' )}
-            %endif
-        %endfor
-    </table>
-%endif
@@ -0,0 +1 @@
+<%inherit file="/grid_base.mako"/>
@@ -24,7 +24,7 @@
            </div>
            <div class="form-row">
                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="hidden" name="group_id" value="${group.id}"/>
+                    <input type="hidden" name="id" value="${ trans.security.encode_id( group.id )}"/>
                </div>
                <div style="clear: both"></div>
            </div>
@@ -1,107 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-## Render a row
-<%def name="render_row( group, ctr, anchored, curr_anchor )">
-    %if ctr % 2 == 1:
-        <tr class="odd_row">
-    %else:
-        <tr>
-    %endif
-        <td>
-            <a href="${h.url_for( controller='admin', action='group', group_id=group.id )}">${group.name}</a>
-            <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-            <div popupmenu="group-${group.id}-popup">
-                <a class="action-button" href="${h.url_for( controller='admin', action='group', rename=True, group_id=group.id )}">Rename this group</a>
-                <a class="action-button" href="${h.url_for( controller='admin', action='group', group_id=group.id )}">Change associated users and roles</a>
-                <a class="action-button" href="${h.url_for( controller='admin', action='mark_group_deleted', group_id=group.id )}">Mark group deleted</a>
-            </div>
-        </td>
-        <td>
-            ${len( group.members )}
-        </td>
-        <td>
-            ${len( group.roles )}
-            %if not anchored:
-                <a name="${curr_anchor}"></a>
-                <div style="float: right;"><a href="#TOP">top</a></div>
-            %endif
-        </td>
-    </tr>
-</%def>
-
-<a name="TOP"><h2>Groups</h2></a>
-
-<ul class="manage-table-actions">
-    <li><a class="action-button" href="${h.url_for( controller='admin', action='create_group' )}">Create a new group</a></li>
-    <li><a class="action-button" href="${h.url_for( controller='admin', action='deleted_groups' )}">Manage deleted groups</a></li>
-</ul>
-
-%if msg:
-    ${render_msg( msg, messagetype )}
-%endif
-
-## TODO: make this a grid
-
-%if not groups:
-    There are no Galaxy groups
-%else:
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <% 
-            render_quick_find = groups.count() > 200
-            ctr = 0
-        %>
-        %if render_quick_find:
-            <%
-                anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
-                anchor_loc = 0
-                anchored = False
-                curr_anchor = 'A'
-            %>
-            <tr style="background: #EEE">
-                <td colspan="3" style="border-bottom: 1px solid #D8B365; text-align: center;">
-                    Jump to letter:
-                    %for a in anchors:
-                        | <a href="#${a}">${a}</a>
-                    %endfor
-                </td>
-            </tr>
-        %endif
-        <tr class="header">
-            <td>Name</td>
-            <td>Users</td>
-            <td>Roles</td>
-        </tr>
-        %for ctr, group in enumerate( groups ):
-            %if render_quick_find and not group.name.upper().startswith( curr_anchor ):
-                <% anchored = False %>
-            %endif
-            %if render_quick_find and group.name.upper().startswith( curr_anchor ):
-                %if not anchored:
-                    ${render_row( group, ctr, anchored, curr_anchor )}
-                    <% anchored = True %>
-                %else:
-                    ${render_row( group, ctr, anchored, curr_anchor )}
-                %endif
-            %elif render_quick_find:
-                %for anchor in anchors[ anchor_loc: ]:
-                    %if group.name.upper().startswith( anchor ):
-                        %if not anchored:
-                            <% curr_anchor = anchor %>
-                            ${render_row( group, ctr, anchored, curr_anchor )}
-                            <%  anchored = True %>
-                        %else:
-                            ${render_row( group, ctr, anchored, curr_anchor )}
-                        %endif
-                        <% 
-                            anchor_loc = anchors.index( anchor )
-                            break 
-                        %>
-                    %endif
-                %endfor
-            %else:
-                ${render_row( group, ctr, True, '' )}
-            %endif
-        %endfor
-    </table>
-%endif
@@ -0,0 +1 @@
+<%inherit file="/grid_base.mako"/>
@@ -31,7 +31,7 @@
            </div>
            <div class="form-row">
                <div style="float: left; width: 250px; margin-right: 10px;">
-                    <input type="hidden" name="role_id" value="${role.id}"/>
+                    <input type="hidden" name="id" value="${trans.security.encode_id( role.id )}"/>
                </div>
                <div style="clear: both"></div>
            </div>
@@ -1,109 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-## Render a row
-<%def name="render_row( role, ctr, anchored, curr_anchor )">
-    %if ctr % 2 == 1:
-        <tr class="odd_row">
-    %else:
-        <tr>
-    %endif
-        <td>
-            <a href="${h.url_for( controller='admin', action='role', role_id=role.id )}">${role.name}</a>
-            <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-            <div popupmenu="role-${role.id}-popup">
-                <a class="action-button" href="${h.url_for( controller='admin', action='role', rename=True, role_id=role.id )}">Rename this role</a>
-                <a class="action-button" href="${h.url_for( controller='admin', action='role', role_id=role.id )}">Change associated users and groups</a>
-                <a class="action-button" href="${h.url_for( controller='admin', action='mark_role_deleted', role_id=role.id )}">Mark role deleted</a>
-            </div>
-        </td>
-        <td>${role.description}</td>
-        <td>${role.type}</td>
-        <td>
-            ${len( role.users )}
-        </td>
-        <td>
-            ${len( role.groups )}
-            %if not anchored:
-                <a name="${curr_anchor}"></a>
-                <div style="float: right;"><a href="#TOP">top</a></div>
-            %endif
-        </td>
-    </tr>
-</%def>
-
-<a name="TOP"><h2>Roles</h2></a>
-
-<ul class="manage-table-actions">
-    <li><a class="action-button" href="${h.url_for( controller='admin', action='create_role' )}">Create a new role</a></li>
-    <li><a class="action-button" href="${h.url_for( controller='admin', action='deleted_roles' )}">Manage deleted roles</a></li>
-</ul>
-
-%if msg:
-    ${render_msg( msg, messagetype )}
-%endif
-
-%if not roles:
-    There are no non-private Galaxy roles
-%else:
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <% 
-            render_quick_find = roles.count() > 200
-            ctr = 0
-        %>
-        %if render_quick_find:
-            <%
-                anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
-                anchor_loc = 0
-                anchored = False
-                curr_anchor = 'A'
-            %>
-            <tr style="background: #EEE">
-                <td colspan="4" style="text-align: center; border-bottom: 1px solid #D8B365">
-                    Jump to letter:
-                    %for a in anchors:
-                        | <a href="#${a}">${a}</a>
-                    %endfor
-                </td>
-            </tr>
-        %endif
-        <tr class="header">
-            <td>Name</td>
-            <td>Description</td>
-            <td>Type</td>
-            <td>Users</td>
-            <td>Groups</td>
-        </tr>
-        %for ctr, role in enumerate( roles ):
-            %if render_quick_find and not role.name.upper().startswith( curr_anchor ):
-                <% anchored = False %>
-            %endif
-            %if render_quick_find and role.name.upper().startswith( curr_anchor ):
-                %if not anchored:
-                    ${render_row( role, ctr, anchored, curr_anchor )}
-                    <% anchored = True %>
-                %else:
-                    ${render_row( role, ctr, anchored, curr_anchor )}
-                %endif
-            %elif render_quick_find:
-                %for anchor in anchors[ anchor_loc: ]:
-                    %if role.name.upper().startswith( anchor ):
-                        %if not anchored:
-                            <% curr_anchor = anchor %>
-                            ${render_row( role, ctr, anchored, curr_anchor )}
-                            <% anchored = True %>
-                        %else:
-                            ${render_row( role, ctr, anchored, curr_anchor )}
-                        %endif
-                        <% 
-                            anchor_loc = anchors.index( anchor )
-                            break 
-                        %>
-                    %endif
-                %endfor
-            %else:
-                ${render_row( role, ctr, True, '' )}
-            %endif
-        %endfor
-    </table>
-%endif
@@ -1,224 +1 @@
-<%inherit file="/base.mako"/>
-<%def name="title()">${grid.title}</%def>
-<% from galaxy import util %>
-
-%if message:
-    <p>
-        <div class="${message_type}message transient-message">${util.restore_text( message )}</div>
-        <div style="clear: both"></div>
-    </p>
-%endif
-
-<%def name="javascripts()">
-    ${parent.javascripts()}
-    ${h.js("jquery.autocomplete", "autocomplete_tagging" )}
-    <script type="text/javascript">        
-        ## TODO: generalize and move into galaxy.base.js
-        $(document).ready(function() {
-            $(".grid").each( function() {
-                var grid = this;
-                var checkboxes = $(this).find("input.grid-row-select-checkbox");
-                var update = $(this).find( "span.grid-selected-count" );
-                $(checkboxes).each( function() {
-                    $(this).change( function() {
-                        var n = $(checkboxes).filter("[checked]").size();
-                        update.text( n );
-                    });
-                })
-            });
-        });
-        ## Can this be moved into base.mako?
-        %if refresh_frames:
-            %if 'masthead' in refresh_frames:            
-                ## Refresh masthead == user changes (backward compatibility)
-                if ( parent.user_changed ) {
-                    %if trans.user:
-                        parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} );
-                    %else:
-                        parent.user_changed( null, false );
-                    %endif
-                }
-            %endif
-            %if 'history' in refresh_frames:
-                if ( parent.frames && parent.frames.galaxy_history ) {
-                    parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}";
-                    if ( parent.force_right_panel ) {
-                        parent.force_right_panel( 'show' );
-                    }
-                }
-            %endif
-            %if 'tools' in refresh_frames:
-                if ( parent.frames && parent.frames.galaxy_tools ) {
-                    parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}";
-                    if ( parent.force_left_panel ) {
-                        parent.force_left_panel( 'show' );
-                    }
-                }
-            %endif
-        %endif
-    </script>
-</%def>
-
-<%def name="stylesheets()">
-    ${h.css( "base", "autocomplete_tagging" )}
-    <style>
-        ## Not generic to all grids -- move to base?
-        .count-box {
-            min-width: 1.1em;
-            padding: 5px;
-            border-width: 1px;
-            border-style: solid;
-            text-align: center;
-            display: inline-block;
-        }
-    </style>
-</%def>
-
-%if grid.standard_filters:
-    <div class="grid-header">
-        <h2>${grid.title}</h2>
-        <span class="title">Filter:</span>
-        %for i, filter in enumerate( grid.standard_filters ):
-            %if i > 0:    
-                <span>|</span>
-            %endif
-            <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>
-        %endfor
-    </div>
-%endif
-
-<ul class="manage-table-actions">
-    <li><a class="action-button" href="${h.url_for( controller='admin', action='users', operation='create' )}">Create a new user</a></li>
-</ul>
-
-%if query.count() == 0:
-    No users were returned for the current query.  Click the Show all users button or a letter below.
-%endif:
-<%
-    letters = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
-%>
-<div class="toolFormBody">
-    <div class="form-row">
-        <a class="action-button" href="${h.url_for( controller='admin', action='users', email_filter='all' )}"><span>Show all users</span></a>
-        <div class="toolParamHelp" style="clear: both;">
-            Default behavior is displaying only users whose email begins with 'a' if there are more than 200 total users
-        </div>
-    </div>
-    <div class="form-row">
-        <label>Show only users whose email starts with:</label>
-        %for letter in letters:
-            | <a href="${h.url_for( controller='admin', action='users', email_filter=letter )}">${letter}</a>
-        %endfor
-        <div style="clear: both"></div>
-    </div>
-    <form name="user_actions" action="${url()}" method="post">
-        <table class="grid">
-            <thead>
-                <tr>
-                    <th></th>
-                    %for column in grid.columns:
-                        %if column.visible:
-                            <%
-                                href = ""
-                                extra = ""
-                                if column.sortable:
-                                    if sort_key == column.key:
-                                        if sort_order == "asc":
-                                            href = url( sort=( "-" + column.key ) )
-                                            extra = "&darr;"
-                                        else:
-                                            href = url( sort=( column.key ) )
-                                            extra = "&uarr;"
-                                    else:
-                                        href = url( sort=column.key )
-                            %>
-                            <th\
-                            %if column.ncells > 1:
-                                colspan="${column.ncells}"
-                            %endif
-                            >
-                                %if href:
-                                    <a href="${href}">${column.label}</a>
-                                %else:
-                                    ${column.label}
-                                %endif
-                                <span>${extra}</span>
-                            </th>
-                        %endif
-                    %endfor
-                    <th></th>
-                </tr>
-            </thead>
-            <tbody>
-                %for i, item in enumerate( query ):
-                    <tr \
-                    %if current_item == item:
-                        class="current" \
-                    %endif
-                    > 
-                        ## Item selection column
-                        <td style="width: 1.5em;">
-                            <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" />
-                        </td>
-                        ## Data columns
-                        %for column in grid.columns:
-                            %if column.visible:
-                                <%
-                                    # Link
-                                    link = column.get_link( trans, grid, item )
-                                    if link:
-                                        href = url( **link )
-                                    else:
-                                        href = None
-                                    # Value (coerced to list so we can loop)
-                                    value = column.get_value( trans, grid, item )
-                                    if column.ncells == 1:
-                                        value = [ value ]
-                                %>
-                                %for cellnum, v in enumerate( value ):
-                                    <%
-                                        # Attach popup menu?
-                                        if column.attach_popup and cellnum == 0:
-                                            extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>&#9660;</span></a>' % i
-                                        else:
-                                            extra = ""
-                                    %>
-                                    %if href:                    
-                                        <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td>
-                                    %else:
-                                        <td >${v}${extra}</td>
-                                    %endif    
-                                %endfor
-                            %endif
-                        %endfor
-                        ## Actions column
-                        <td>
-                            <div popupmenu="grid-${i}-popup">
-                                %for operation in grid.operations:
-                                    %if operation.allowed( item ) and operation.allow_popup:
-                                        <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a>
-                                    %endif
-                                %endfor
-                            </div>
-                        </td>
-                    </tr>
-                %endfor
-            </tbody>
-            %if grid.operations:
-                <tfoot>
-                    <tr>
-                        <td></td>
-                        <td colspan="100">
-                            For <span class="grid-selected-count"></span> selected users:
-                            %for operation in grid.operations:
-                                %if operation.allow_multiple:
-                                    <input type="submit" name="operation" value="${operation.label}" class="action-button">
-                                %endif
-                            %endfor
-                        </td>
-                    </tr>
-                </tfoot>
-            %endif
-        </table>
-    </form>
-</div>
+<%inherit file="/grid_base.mako"/>
@@ -1,5 +1,6 @@
 <%!
-    from galaxy.model import History, HistoryDatasetAssociation
+    from galaxy.model import History, HistoryDatasetAssociation, User, Role, Group
+    import galaxy.util
    def inherit(context):
        if context.get('use_panels'):
            return '/base_panels.mako'
@@ -11,7 +12,7 @@
 ## Render the grid's basic elements. Each of these elements can be subclassed.
 %if message:
    <p>
-        <div class="${message_type}message transient-message">${message}</div>
+        <div class="${message_type}message transient-message">${util.restore_text( message )}</div>
        <div style="clear: both"></div>
    </p>
 %endif
@@ -303,6 +304,12 @@ ${self.grid_table()}
                    items_plural = "histories"
                elif grid.model_class == HistoryDatasetAssociation:
                     items_plural = "datasets"
+                elif grid.model_class == User:
+                    items_plural = "users"
+                elif grid.model_class == Role:
+                    items_plural = "roles"
+                elif grid.model_class == Group:
+                    items_plural = "groups"
            %>
            %if num_pages > 1:
                <tr>
@@ -672,7 +672,8 @@ class TwillTestCase( unittest.TestCase ):
        self.check_page_for_string( "The user information has been updated with the changes." )
        for value in info_values:
            self.check_page_for_string( value )
-    def user_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id=2 ): # role.id = 2 is Private Role for test2@bx.psu.edu 
+    def user_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id='2' ):
+        # role.id = 2 is Private Role for test2@bx.psu.edu 
        # NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value 
        # in each select list or twill throws an exception, which is: ParseError: OPTION outside of SELECT
        # Due to this bug, we'll bypass visiting the page, and simply pass the permissions on to the 
@@ -921,6 +922,7 @@ class TwillTestCase( unittest.TestCase ):
    # Tests associated with users
    def create_new_account_as_admin( self, email='test4@bx.psu.edu', password='testuser' ):
        """Create a new account for another user"""
+        # TODO: fix this so that it uses the form rather than the following URL.
        self.home()
        self.visit_url( "%s/user/create?admin_view=True&email=%s&password=%s&confirm=%s&create_user_button=Submit&subscribe=False" \
                        % ( self.url, email, password, password ) )
@@ -983,7 +985,13 @@ class TwillTestCase( unittest.TestCase ):
        self.home()

    # Tests associated with roles
-    def create_role( self, name='Role One', description="This is Role One", in_user_ids=[], in_group_ids=[], create_group_for_role='no', private_role='' ):
+    def create_role( self,
+                     name='Role One',
+                     description="This is Role One",
+                     in_user_ids=[],
+                     in_group_ids=[],
+                     create_group_for_role='no',
+                     private_role='' ):
        """Create a new role"""
        url = "%s/admin/create_role?create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) )
        if in_user_ids:
@@ -1017,7 +1025,7 @@ class TwillTestCase( unittest.TestCase ):
    def rename_role( self, role_id, name='Role One Renamed', description='This is Role One Re-described' ):
        """Rename a role"""
        self.home()
-        self.visit_url( "%s/admin/role?rename=True&role_id=%s" % ( self.url, role_id ) )
+        self.visit_url( "%s/admin/role?rename=True&id=%s" % ( self.url, role_id ) )
        self.check_page_for_string( 'Change role name and description' )
        tc.fv( "1", "name", name )
        tc.fv( "1", "description", description )
@@ -1026,28 +1034,28 @@ class TwillTestCase( unittest.TestCase ):
    def mark_role_deleted( self, role_id, role_name ):
        """Mark a role as deleted"""
        self.home()
-        self.visit_url( "%s/admin/mark_role_deleted?role_id=%s" % ( self.url, role_id ) )
+        self.visit_url( "%s/admin/roles?operation=delete&id=%s" % ( self.url, role_id ) )
        check_str = "Role '%s' has been marked as deleted" % role_name
        self.check_page_for_string( check_str )
        self.home()
    def undelete_role( self, role_id, role_name ):
        """Undelete an existing role"""
        self.home()
-        self.visit_url( "%s/admin/undelete_role?role_id=%s" % ( self.url, role_id ) )
+        self.visit_url( "%s/admin/roles?operation=undelete&id=%s" % ( self.url, role_id ) )
        check_str = "Role '%s' has been marked as not deleted" % role_name
        self.check_page_for_string( check_str )
        self.home()
    def purge_role( self, role_id, role_name ):
        """Purge an existing role"""
        self.home()
-        self.visit_url( "%s/admin/purge_role?role_id=%s" % ( self.url, role_id ) )
+        self.visit_url( "%s/admin/roles?operation=purge&id=%s" % ( self.url, role_id ) )
        check_str = "The following have been purged from the database for role '%s': " % role_name
        check_str += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss."
        self.check_page_for_string( check_str )
        self.home()
    def associate_users_and_groups_with_role( self, role_id, role_name, user_ids=[], group_ids=[] ):
        self.home()
-        url = "%s/admin/role?role_id=%s&role_members_edit_button=Save" % ( self.url, role_id )
+        url = "%s/admin/role?id=%s&role_members_edit_button=Save" % ( self.url, role_id )
        if user_ids:
            url += "&in_users=%s" % ','.join( user_ids )
        if group_ids:
@@ -1076,14 +1084,14 @@ class TwillTestCase( unittest.TestCase ):
    def rename_group( self, group_id, name='Group One Renamed' ):
        """Rename a group"""
        self.home()
-        self.visit_url( "%s/admin/group?rename=True&group_id=%s" % ( self.url, group_id ) )
+        self.visit_url( "%s/admin/group?rename=True&id=%s" % ( self.url, group_id ) )
        self.check_page_for_string( 'Change group name' )
        tc.fv( "1", "name", name )
        tc.submit( "rename_group_button" )
        self.home()
    def associate_users_and_roles_with_group( self, group_id, group_name, user_ids=[], role_ids=[] ):
        self.home()
-        url = "%s/admin/group?group_id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id )
+        url = "%s/admin/group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id )
        if user_ids:
            url += "&in_users=%s" % ','.join( user_ids )
        if role_ids:
@@ -1095,21 +1103,21 @@ class TwillTestCase( unittest.TestCase ):
    def mark_group_deleted( self, group_id, group_name ):
        """Mark a group as deleted"""
        self.home()
-        self.visit_url( "%s/admin/mark_group_deleted?group_id=%s" % ( self.url, group_id ) )
+        self.visit_url( "%s/admin/groups?operation=delete&id=%s" % ( self.url, group_id ) )
        check_str = "Group '%s' has been marked as deleted" % group_name
        self.check_page_for_string( check_str )
        self.home()
    def undelete_group( self, group_id, group_name ):
        """Undelete an existing group"""
        self.home()
-        self.visit_url( "%s/admin/undelete_group?group_id=%s" % ( self.url, group_id ) )
+        self.visit_url( "%s/admin/groups?operation=undelete&id=%s" % ( self.url, group_id ) )
        check_str = "Group '%s' has been marked as not deleted" % group_name
        self.check_page_for_string( check_str )
        self.home()
    def purge_group( self, group_id, group_name ):
        """Purge an existing group"""
        self.home()
-        self.visit_url( "%s/admin/purge_group?group_id=%s" % ( self.url, group_id ) )
+        self.visit_url( "%s/admin/groups?operation=purge&id=%s" % ( self.url, group_id ) )
        check_str = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group_name
        self.check_page_for_string( check_str )
        self.home()
@@ -780,8 +780,8 @@ class TestHistory( TwillTestCase ):
        self.delete_history( id=self.security.encode_id( history4.id ) )
        self.delete_history( id=self.security.encode_id( history5.id ) )
        # Eliminate Sharing role for: test@bx.psu.edu, test2@bx.psu.edu
-        self.mark_role_deleted( str( sharing_role.id ), sharing_role.name )
-        self.purge_role( str( sharing_role.id ), sharing_role.name )
+        self.mark_role_deleted( self.security.encode_id( sharing_role.id ), sharing_role.name )
+        self.purge_role( self.security.encode_id( sharing_role.id ), sharing_role.name )
        # Manually delete the sharing role from the database
        sa_session.refresh( sharing_role )
        sa_session.delete( sharing_role )
@@ -327,8 +327,12 @@ class TestSecurityAndLibraries( TwillTestCase ):
        name = 'Role One'
        description = "This is Role Ones description"
        user_ids=[ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ]
-        self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=[],
-                          create_group_for_role='yes', private_role=admin_user.email )
+        self.create_role( name=name,
+                          description=description,
+                          in_user_ids=user_ids,
+                          in_group_ids=[],
+                          create_group_for_role='yes',
+                          private_role=admin_user.email )
        # Get the role object for later tests
        global role_one
        role_one = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first()
@@ -352,13 +356,13 @@ class TestSecurityAndLibraries( TwillTestCase ):
        # Rename the role
        rename = "Role One's been Renamed"
        redescription="This is Role One's Re-described"
-        self.rename_role( str( role_one.id ), name=rename, description=redescription )
+        self.rename_role( self.security.encode_id( role_one.id ), name=rename, description=redescription )
        self.home()
        self.visit_page( 'admin/roles' )
        self.check_page_for_string( rename )
        self.check_page_for_string( redescription )
        # Reset the role back to the original name and description
-        self.rename_role( str( role_one.id ), name=name, description=description )
+        self.rename_role( self.security.encode_id( role_one.id ), name=name, description=description )
    def test_050_create_group( self ):
        """Testing creating new group with 3 members and 1 associated role, then renaming it"""
        name = "Group One's Name"
@@ -384,12 +388,12 @@ class TestSecurityAndLibraries( TwillTestCase ):
                                  % ( len( group_one.roles ), group_one.id, len( role_ids ) ) )
        # Rename the group
        rename = "Group One's been Renamed"
-        self.rename_group( str( group_one.id ), name=rename, )
+        self.rename_group( self.security.encode_id( group_one.id ), name=rename, )
        self.home()
        self.visit_page( 'admin/groups' )
        self.check_page_for_string( rename )
        # Reset the group back to the original name
-        self.rename_group( str( group_one.id ), name=name )
+        self.rename_group( self.security.encode_id( group_one.id ), name=name )
    def test_055_add_members_and_role_to_group( self ):
        """Testing editing user membership and role associations of an existing group"""
        name = 'Group Two'
@@ -405,10 +409,12 @@ class TestSecurityAndLibraries( TwillTestCase ):
        if group_two.roles:
            raise AssertionError( '%d GroupRoleAssociations were created for group id %d when it was created ( should have been 0 )' \
                              % ( len( group_two.roles ), group_two.id ) )
-        group_two_id = str( group_two.id )
        user_ids = [ str( regular_user1.id )  ]
        role_ids = [ str( role_one.id ) ]
-        self.associate_users_and_roles_with_group( group_two.id, group_two.name, user_ids=user_ids, role_ids=role_ids )
+        self.associate_users_and_roles_with_group( self.security.encode_id( group_two.id ),
+                                                   group_two.name,
+                                                   user_ids=user_ids,
+                                                   role_ids=role_ids )
    def test_060_create_role_with_user_and_group_associations( self ):
        """Testing creating a role with user and group associations"""
        # NOTE: To get this to work with twill, all select lists on the ~/admin/role page must contain at least
@@ -421,7 +427,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
        group_ids=[ str( group_two.id ) ]
        private_role=admin_user.email
        # Create the role
-        self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=group_ids, private_role=private_role )
+        self.create_role( name=name,
+                          description=description,
+                          in_user_ids=user_ids,
+                          in_group_ids=group_ids,
+                          private_role=private_role )
        # Get the role object for later tests
        global role_two
        role_two = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first()
@@ -451,7 +461,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
        user_ids=[]
        group_ids=[]
        private_role=admin_user.email
-        self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=group_ids, private_role=private_role )
+        self.create_role( name=name,
+                          description=description,
+                          in_user_ids=user_ids,
+                          in_group_ids=group_ids,
+                          private_role=private_role )
        # Get the role object for later tests
        global role_three
        role_three = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first()
@@ -466,8 +480,11 @@ class TestSecurityAndLibraries( TwillTestCase ):
        for uga in admin_user.groups:
            group_ids.append( str( uga.group_id ) )
        check_str = "User '%s' has been updated with %d associated roles and %d associated groups" % ( admin_user.email, len( role_ids ), len( group_ids ) )
-        self.associate_roles_and_groups_with_user( self.security.encode_id( admin_user.id ), str( admin_user.email ),
-                                                   in_role_ids=role_ids, in_group_ids=group_ids, check_str=check_str )
+        self.associate_roles_and_groups_with_user( self.security.encode_id( admin_user.id ),
+                                                   str( admin_user.email ),
+                                                   in_role_ids=role_ids,
+                                                   in_group_ids=group_ids,
+                                                   check_str=check_str )
        sa_session.refresh( admin_user )
        # admin_user should now be associated with 4 roles: private, role_one, role_two, role_three
        if len( admin_user.roles ) != 4:
@@ -1374,7 +1391,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
        self.home()
        self.visit_url( '%s/admin/groups' % self.url )
        self.check_page_for_string( group_two.name )
-        self.mark_group_deleted( str( group_two.id ), group_two.name )
+        self.mark_group_deleted( self.security.encode_id( group_two.id ), group_two.name )
        sa_session.refresh( group_two )
        if not group_two.deleted:
            raise AssertionError( '%s was not correctly marked as deleted.' % group_two.name )
@@ -1386,7 +1403,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
    def test_175_undelete_group( self ):
        """Testing undeleting a deleted group"""
        # Logged in as admin_user
-        self.undelete_group( str( group_two.id ), group_two.name )
+        self.undelete_group( self.security.encode_id( group_two.id ), group_two.name )
        sa_session.refresh( group_two )
        if group_two.deleted:
            raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name )
@@ -1396,7 +1413,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
        self.home()
        self.visit_url( '%s/admin/roles' % self.url )
        self.check_page_for_string( role_two.name )
-        self.mark_role_deleted( str( role_two.id ), role_two.name )
+        self.mark_role_deleted( self.security.encode_id( role_two.id ), role_two.name )
        sa_session.refresh( role_two )
        if not role_two.deleted:
            raise AssertionError( '%s was not correctly marked as deleted.' % role_two.name )
@@ -1408,7 +1425,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
    def test_185_undelete_role( self ):
        """Testing undeleting a deleted role"""
        # Logged in as admin_user
-        self.undelete_role( str( role_two.id ), role_two.name )
+        self.undelete_role( self.security.encode_id( role_two.id ), role_two.name )
    def test_190_mark_dataset_deleted( self ):
        """Testing marking a library dataset as deleted"""
        # Logged in as admin_user
@@ -1541,59 +1558,57 @@ class TestSecurityAndLibraries( TwillTestCase ):
    def test_235_purge_group( self ):
        """Testing purging a group"""
        # Logged in as admin_user
-        group_id = str( group_two.id )
-        self.mark_group_deleted( group_id, group_two.name )
-        self.purge_group( group_id, group_two.name )
+        self.mark_group_deleted( self.security.encode_id( group_two.id ), group_two.name )
+        self.purge_group( self.security.encode_id( group_two.id ), group_two.name )
        # Make sure there are no UserGroupAssociations
        uga = sa_session.query( galaxy.model.UserGroupAssociation ) \
-                        .filter( galaxy.model.UserGroupAssociation.table.c.group_id == group_id ) \
+                        .filter( galaxy.model.UserGroupAssociation.table.c.group_id == group_two.id ) \
                        .first()
        if uga:
-            raise AssertionError( "Purging the group did not delete the UserGroupAssociations for group_id '%s'" % group_id )
+            raise AssertionError( "Purging the group did not delete the UserGroupAssociations for group_id '%s'" % group_two.id )
        # Make sure there are no GroupRoleAssociations
        gra = sa_session.query( galaxy.model.GroupRoleAssociation ) \
-                        .filter( galaxy.model.GroupRoleAssociation.table.c.group_id == group_id ) \
+                        .filter( galaxy.model.GroupRoleAssociation.table.c.group_id == group_two.id ) \
                        .first()
        if gra:
-            raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id )
+            raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_two.id )
        # Undelete the group for later test runs
-        self.undelete_group( group_id, group_two.name )
+        self.undelete_group( self.security.encode_id( group_two.id ), group_two.name )
    def test_240_purge_role( self ):
        """Testing purging a role"""
        # Logged in as admin_user
-        role_id = str( role_two.id )
-        self.mark_role_deleted( role_id, role_two.name )
-        self.purge_role( role_id, role_two.name )
+        self.mark_role_deleted( self.security.encode_id( role_two.id ), role_two.name )
+        self.purge_role( self.security.encode_id( role_two.id ), role_two.name )
        # Make sure there are no UserRoleAssociations
        uras = sa_session.query( galaxy.model.UserRoleAssociation ) \
-                         .filter( galaxy.model.UserRoleAssociation.table.c.role_id == role_id ) \
+                         .filter( galaxy.model.UserRoleAssociation.table.c.role_id == role_two.id ) \
                         .all()
        if uras:
-            raise AssertionError( "Purging the role did not delete the UserRoleAssociations for role_id '%s'" % role_id )
+            raise AssertionError( "Purging the role did not delete the UserRoleAssociations for role_id '%s'" % role_two.id )
        # Make sure there are no DefaultUserPermissions associated with the Role
        dups = sa_session.query( galaxy.model.DefaultUserPermissions ) \
-                         .filter( galaxy.model.DefaultUserPermissions.table.c.role_id == role_id ) \
+                         .filter( galaxy.model.DefaultUserPermissions.table.c.role_id == role_two.id ) \
                         .all()
        if dups:
-            raise AssertionError( "Purging the role did not delete the DefaultUserPermissions for role_id '%s'" % role_id )
+            raise AssertionError( "Purging the role did not delete the DefaultUserPermissions for role_id '%s'" % role_two.id )
        # Make sure there are no DefaultHistoryPermissions associated with the Role
        dhps = sa_session.query( galaxy.model.DefaultHistoryPermissions ) \
-                         .filter( galaxy.model.DefaultHistoryPermissions.table.c.role_id == role_id ) \
+                         .filter( galaxy.model.DefaultHistoryPermissions.table.c.role_id == role_two.id ) \
                         .all()
        if dhps:
-            raise AssertionError( "Purging the role did not delete the DefaultHistoryPermissions for role_id '%s'" % role_id )
+            raise AssertionError( "Purging the role did not delete the DefaultHistoryPermissions for role_id '%s'" % role_two.id )
        # Make sure there are no GroupRoleAssociations
        gra = sa_session.query( galaxy.model.GroupRoleAssociation ) \
-                        .filter( galaxy.model.GroupRoleAssociation.table.c.role_id == role_id ) \
+                        .filter( galaxy.model.GroupRoleAssociation.table.c.role_id == role_two.id ) \
                        .first()
        if gra:
-            raise AssertionError( "Purging the role did not delete the GroupRoleAssociations for role_id '%s'" % role_id )
+            raise AssertionError( "Purging the role did not delete the GroupRoleAssociations for role_id '%s'" % role_two.id )
        # Make sure there are no DatasetPermissionss
        dp = sa_session.query( galaxy.model.DatasetPermissions ) \
-                       .filter( galaxy.model.DatasetPermissions.table.c.role_id == role_id ) \
+                       .filter( galaxy.model.DatasetPermissions.table.c.role_id == role_two.id ) \
                       .first()
        if dp:
-            raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id )
+            raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_two.id )
    def test_245_manually_unpurge_role( self ):
        """Testing manually un-purging a role"""
        # Logged in as admin_user
@@ -1601,7 +1616,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
        # TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call
        role_two.purged = False
        role_two.flush()
-        self.undelete_role( str( role_two.id ), role_two.name )
+        self.undelete_role( self.security.encode_id( role_two.id ), role_two.name )
    def test_250_purge_library( self ):
        """Testing purging a library"""
        # Logged in as admin_user
@@ -1815,8 +1830,8 @@ class TestSecurityAndLibraries( TwillTestCase ):
        # Eliminate all non-private roles
        ##################
        for role in [ role_one, role_two, role_three ]:
-            self.mark_role_deleted( str( role.id ), role.name )
-            self.purge_role( str( role.id ), role.name )
+            self.mark_role_deleted( self.security.encode_id( role.id ), role.name )
+            self.purge_role( self.security.encode_id( role.id ), role.name )
            # Manually delete the role from the database
            sa_session.refresh( role )
            sa_session.delete( role )
@@ -1825,8 +1840,8 @@ class TestSecurityAndLibraries( TwillTestCase ):
        # Eliminate all groups
        ##################
        for group in [ group_zero, group_one, group_two ]:
-            self.mark_group_deleted( str( group.id ), group.name )
-            self.purge_group( str( group.id ), group.name )
+            self.mark_group_deleted( self.security.encode_id( group.id ), group.name )
+            self.purge_group( self.security.encode_id( group.id ), group.name )
            # Manually delete the group from the database
            sa_session.refresh( group )
            sa_session.delete( group )
@@ -1846,7 +1861,6 @@ class TestSecurityAndLibraries( TwillTestCase ):
        # Change DefaultHistoryPermissions for regular_user1 back to the default
        permissions_in = [ 'DATASET_MANAGE_PERMISSIONS' ]
        permissions_out = [ 'DATASET_ACCESS' ]
-        role_id = str( regular_user1_private_role.id )
-        self.user_set_default_permissions( permissions_in=permissions_in, permissions_out=permissions_out, role_id=role_id )
+        self.user_set_default_permissions( permissions_in=permissions_in, permissions_out=permissions_out, role_id=str( regular_user1_private_role.id ) )
        self.logout()
        self.login( email=admin_user.email )
@@ -8,6 +8,7 @@
    <tool file="data_source/biomart.xml" />
    <tool file="data_source/gramene_mart.xml" />
    <tool file="data_source/flymine.xml" />
+    <tool file="data_source/eupathdb.xml" />
    <tool file="data_source/encode_db.xml" />
    <tool file="data_source/epigraph_import.xml" />
  </section>
@@ -27,6 +28,7 @@
    <tool file="filters/catWrapper.xml" />
    <tool file="filters/condense_characters.xml" />
    <tool file="filters/convert_characters.xml" />
+    <tool file="filters/mergeCols.xml" />
    <tool file="filters/CreateInterval.xml" />
    <tool file="filters/cutWrapper.xml" />
    <tool file="filters/changeCase.xml" />
@@ -34,15 +36,17 @@
    <tool file="filters/remove_beginning.xml" />
    <tool file="filters/headWrapper.xml" />
    <tool file="filters/tailWrapper.xml" />
+     <tool file="filters/trimmer.xml" />
  </section>
  <section name="Convert Formats" id="convert">
    <tool file="filters/bed2gff.xml" />
    <tool file="fasta_tools/fasta_to_tabular.xml" />
    <tool file="filters/gff2bed.xml" />
    <tool file="maf/maf_to_bed.xml" />
-    <tool file="maf/maf_to_interval.xml" />
+    <tool file="maf/maf_to_interval.xml" /> 
    <tool file="maf/maf_to_fasta.xml" />
    <tool file="fasta_tools/tabular_to_fasta.xml" />
+    <tool file="fastx_toolkit/fastq_to_fasta.xml" />
  </section>
  <section name="FASTA manipulation" id="fasta_manipulation">
    <tool file="fasta_tools/fasta_compute_length.xml" />
@@ -50,6 +54,9 @@
    <tool file="fasta_tools/fasta_concatenate_by_species.xml" />
    <tool file="fasta_tools/fasta_to_tabular.xml" />
    <tool file="fasta_tools/tabular_to_fasta.xml" />
+    <tool file="fastx_toolkit/fasta_formatter.xml" />
+    <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
+    <tool file="fastx_toolkit/fastx_collapser.xml" />
  </section>
  <section name="Filter and Sort" id="filter">
    <tool file="stats/filtering.xml" />
@@ -80,9 +87,7 @@
    <tool file="maf/maf_limit_size.xml"/>
    <tool file="maf/maf_by_block_number.xml"/>
    <tool file="maf/maf_filter.xml"/>
-    <!--    
    <tool file="maf/maf_reverse_complement.xml"/>
-    -->
  </section>
  <section name="Get Genomic Scores" id="scores">
    <tool file="stats/wiggle_to_simple.xml" />
@@ -90,7 +95,7 @@
    <tool file="extract/phastOdds/phastOdds_tool.xml" />
  </section>
  <section name="Operate on Genomic Intervals" id="bxops">
-  	<tool file="new_operations/intersect.xml" />  
+    <tool file="new_operations/intersect.xml" />  
    <tool file="new_operations/subtract.xml" />
    <tool file="new_operations/merge.xml" />
    <tool file="new_operations/concat.xml" />
@@ -147,12 +152,6 @@
    <tool file="taxonomy/lca.xml" />
    <tool file="taxonomy/poisson2test.xml" />
  </section>
-  <section name="Short Read Analysis" id="short_read_analysis">
-    <tool file="metag_tools/short_reads_figure_score.xml" />
-    <tool file="metag_tools/short_reads_trim_seq.xml" />
-    <tool file="metag_tools/megablast_wrapper.xml" />
-    <tool file="metag_tools/megablast_xml_parser.xml" /> 
-  </section>
  <section name="EMBOSS" id="EMBOSSLite">
    <tool file="emboss_5/emboss_antigenic.xml" />
    <tool file="emboss_5/emboss_backtranseq.xml" />
@@ -262,4 +261,37 @@
    <tool file="emboss_5/emboss_wordcount.xml" />
    <tool file="emboss_5/emboss_wordmatch.xml" /> 
  </section>
+  <label text="NGS Toolbox Beta" id="ngs" />
+  <section name="NGS: QC and manipulation" id="cshl_library_information">
+    <label text="Generic FASTQ data" id="fastq" />
+        <tool file="next_gen_conversion/fastq_gen_conv.xml" />
+        <tool file="fastx_toolkit/fastq_quality_converter.xml" />
+        <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
+        <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
+        <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
+        <tool file="metag_tools/split_paired_reads.xml" />
+    <label text="Roche-454 data" id="454" />
+        <tool file="metag_tools/short_reads_figure_score.xml" />
+        <tool file="metag_tools/short_reads_trim_seq.xml" />
+    <label text="AB-SOLiD data" id="solid" />
+        <tool file="next_gen_conversion/solid_to_fastq.xml" />
+        <tool file="solid_tools/solid_qual_stats.xml" />
+        <tool file="solid_tools/solid_qual_boxplot.xml" />
+  </section>
+  <section name="NGS: Mapping" id="solexa_tools">
+   <tool file="sr_mapping/bowtie_wrapper.xml" />
+   <tool file="sr_mapping/bwa_wrapper.xml" />
+  <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> -->
+   <tool file="metag_tools/megablast_wrapper.xml" />
+   <tool file="metag_tools/megablast_xml_parser.xml" />
+  </section>
+  <section name="NGS: SAM Tools" id="samtools">
+   <tool file="samtools/sam_bitwise_flag_filter.xml" />
+   <tool file="samtools/sam2interval.xml" />
+   <tool file="samtools/sam_to_bam.xml" />
+   <tool file="samtools/sam_merge.xml" />
+   <tool file="samtools/sam_pileup.xml" />
+   <tool file="samtools/pileup_parser.xml" />
+   <tool file="samtools/pileup_interval.xml" />
+  </section>
 </toolbox>