[galaxy-dev] [hg] galaxy 2374: Display only the number of associations on the...

29 Apr 2009

details:   http://www.bx.psu.edu/hg/galaxy/rev/d0c905db68db
changeset: 2374:d0c905db68db
user:      Greg Von Kuster <greg@bx.psu.edu>
date:      Mon Apr 27 16:03:44 2009 -0400
description:
Display only the number of associations on the main users, groups, roles pages rather than the associated objects - much faster display times.  Also a tweek to my last fix for the column_maker tool.

6 file(s) affected in this change:

lib/galaxy/web/controllers/admin.py
templates/admin/dataset_security/groups.mako
templates/admin/dataset_security/roles.mako
templates/admin/dataset_security/users.mako
test/base/twilltestcase.py
tools/stats/column_maker.py

diffs (483 lines):

diff -r 22118cf46b0a -r d0c905db68db lib/galaxy/web/controllers/admin.py

--- a/lib/galaxy/web/controllers/admin.py	Mon Apr 27 13:33:47 2009 -0400
+++ b/lib/galaxy/web/controllers/admin.py	Mon Apr 27 16:03:44 2009 -0400
@@ -280,23 +280,12 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        # Build a list of tuples which are groups followed by lists of members and roles
-        # [ ( group, [ member, member, member ], [ role, role ] ), ( group, [ member, member ], [ role ] ) ]
-        groups_members_roles = []
         groups = trans.app.model.Group.query() \
             .filter( trans.app.model.Group.table.c.deleted==False ) \
             .order_by( trans.app.model.Group.table.c.name ) \
             .all()
-        for group in groups:
-            members = []
-            for uga in group.members:
-                members.append( trans.app.model.User.get( uga.user_id ) )
-            roles = []
-            for gra in group.roles:
-                roles.append( trans.app.model.Role.get( gra.role_id ) )
-            groups_members_roles.append( ( group, members, roles ) )
         return trans.fill_template( '/admin/dataset_security/groups.mako', 
-                                    groups_members_roles=groups_members_roles, 
+                                    groups=groups, 
                                     msg=msg,
                                     messagetype=messagetype )
     @web.expose
@@ -647,20 +636,9 @@
         params = util.Params( kwd )
         msg = util.restore_text( params.get( 'msg', ''  ) )
         messagetype = params.get( 'messagetype', 'done' )
-        # Build a list of tuples which are users followed by lists of groups and roles
-        # [ ( user, [ group, group, group ], [ role, role ] ), ( user, [ group, group ], [ role ] ) ]
-        users_groups_roles = []
         users = trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all()
-        for user in users:
-            groups = []
-            for uga in user.groups:
-                groups.append( trans.app.model.Group.get( uga.group_id ) )
-            roles = []
-            for ura in user.non_private_roles:
-                roles.append( trans.app.model.Role.get( ura.role_id ) )
-            users_groups_roles.append( ( user, groups, roles ) )
         return trans.fill_template( '/admin/dataset_security/users.mako',
-                                    users_groups_roles=users_groups_roles,
+                                    users=users,
                                     allow_user_deletion=trans.app.config.allow_user_deletion,
                                     msg=msg,
                                     messagetype=messagetype )
@@ -702,91 +680,6 @@
                                     out_groups=out_groups,
                                     msg=msg,
                                     messagetype=messagetype )
-    # Utility methods to enable removal of associations - redirects are key
-    @web.expose
-    @web.require_admin
-    def remove_group_from_role( self, trans, **kwd ):
-        params = util.Params( kwd )
-        group_id = int( params.group_id )
-        group = trans.app.model.Group.get( group_id )
-        role_id = int( params.role_id )
-        role = trans.app.model.Role.get( role_id )
-        gra = trans.app.model.GroupRoleAssociation.filter( and_( trans.app.model.GroupRoleAssociation.table.c.group_id==group_id,
-                                                                 trans.app.model.GroupRoleAssociation.table.c.role_id==role_id ) ).first()
-        gra.delete()
-        gra.flush()
-        msg = "Group '%s' removed from role '%s'" % ( group.name, role.name )
-        trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def remove_group_from_user( self, trans, **kwd ):
-        params = util.Params( kwd )
-        group_id = int( params.group_id )
-        group = trans.app.model.Group.get( group_id )
-        user_id = int( params.user_id )
-        user = trans.app.model.User.get( user_id )
-        uga = trans.app.model.UserGroupAssociation.filter( and_( trans.app.model.UserGroupAssociation.table.c.group_id==group_id,
-                                                                 trans.app.model.UserGroupAssociation.table.c.user_id==user_id ) ).first()
-        uga.delete()
-        uga.flush()
-        msg = "Group '%s' removed from user '%s'" % ( group.name, user.email )
-        trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def remove_role_from_group( self, trans, **kwd ):
-        params = util.Params( kwd )
-        role_id = int( params.role_id )
-        role = trans.app.model.Role.get( role_id )
-        group_id = int( params.group_id )
-        group = trans.app.model.Group.get( group_id )
-        gra = trans.app.model.GroupRoleAssociation.filter( and_( trans.app.model.GroupRoleAssociation.table.c.role_id==role_id,
-                                                                 trans.app.model.GroupRoleAssociation.table.c.group_id==group_id ) ).first()
-        gra.delete()
-        gra.flush()
-        msg = "Role '%s' removed from group '%s'" % ( role.name, group.name )
-        trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def remove_role_from_user( self, trans, **kwd ):
-        params = util.Params( kwd )
-        user_id = int( params.user_id )
-        user = trans.app.model.User.get( user_id )
-        role_id = int( params.role_id )
-        role = trans.app.model.Role.get( role_id )
-        ura = trans.app.model.UserRoleAssociation.filter( and_( trans.app.model.UserRoleAssociation.table.c.user_id==user_id,
-                                                                trans.app.model.UserRoleAssociation.table.c.role_id==role_id ) ).first()
-        ura.delete()
-        ura.flush()
-        msg = "Role '%s' removed from user '%s'" % ( role.name, user.email )
-        trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def remove_user_from_group( self, trans, **kwd ):
-        params = util.Params( kwd )
-        user_id = int( params.user_id )
-        user = trans.app.model.User.get( user_id )
-        group_id = int( params.group_id )
-        group = trans.app.model.Group.get( group_id )
-        uga = trans.app.model.UserGroupAssociation.filter( and_( trans.app.model.UserGroupAssociation.table.c.user_id==user_id,
-                                                                 trans.app.model.UserGroupAssociation.table.c.group_id==group_id ) ).first()
-        uga.delete()
-        uga.flush()
-        msg = "User '%s' removed from group '%s'" % ( user.email, group.name )
-        trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) )
-    @web.expose
-    @web.require_admin
-    def remove_user_from_role( self, trans, **kwd ):
-        params = util.Params( kwd )
-        user_id = int( params.user_id )
-        user = trans.app.model.User.get( user_id )
-        role_id = int( params.role_id )
-        role = trans.app.model.Role.get( role_id )
-        ura = trans.app.model.UserRoleAssociation.filter( and_( trans.app.model.UserRoleAssociation.table.c.user_id==user_id,
-                                                                trans.app.model.UserRoleAssociation.table.c.role_id==role_id ) ).first()
-        ura.delete()
-        ura.flush()
-        msg = "User '%s' removed from role '%s'" % ( user.email, role.name )
-        trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) )
 
     # Galaxy Library Stuff
     @web.expose
diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/groups.mako
--- a/templates/admin/dataset_security/groups.mako	Mon Apr 27 13:33:47 2009 -0400
+++ b/templates/admin/dataset_security/groups.mako	Mon Apr 27 16:03:44 2009 -0400
@@ -2,7 +2,7 @@
 <%namespace file="/message.mako" import="render_msg" />
 
 ## Render a row
-<%def name="render_row( group, members, roles, ctr, anchored, curr_anchor )">
+<%def name="render_row( group, ctr, anchored, curr_anchor )">
     %if ctr % 2 == 1:
         <tr class="odd_row">
     %else:
@@ -18,34 +18,10 @@
             </div>
         </td>
         <td>
-            <ul>
-                %for user in members:
-                    <li>
-                        <a href="${h.url_for( controller='admin', action='user', user_id=user.id )}">${user.email}</a>
-                        <a id="user-${user.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                        <div popupmenu="user-${user.id}-popup">
-                            <a class="action-button" href="${h.url_for( controller='admin', action='remove_user_from_group', group_id=group.id, user_id=user.id )}">Remove user from group</a>
-                        </div>
-                    </li>
-                %endfor
-            </ul>
+            ${len( group.members )}
         </td>
         <td>
-            <ul>
-                %for role in roles:
-                    <li>
-                        %if not role.type == trans.app.model.Role.types.PRIVATE:
-                            <a href="${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;">▼</a>
-                            <div popupmenu="role-${role.id}-popup">
-                                <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_group', group_id=group.id, role_id=role.id )}">Remove role from group</a>
-                            </div>
-                        %else:
-                            ${role.name}
-                        %endif
-                    </li>
-                %endfor
-            </ul>
+            ${len( group.roles )}
             %if not anchored:
                 <a name="${curr_anchor}"></a>
                 <div style="float: right;"><a href="#TOP">top</a></div>
@@ -65,12 +41,12 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if len( groups_members_roles ) == 0:
+%if len( groups ) == 0:
     There are no Galaxy groups
 %else:
     <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
         <% 
-            render_quick_find = len( groups_members_roles ) > 50
+            render_quick_find = len( groups ) > 50
             ctr = 0
         %>
         %if render_quick_find:
@@ -91,34 +67,29 @@
         %endif
         <tr class="header">
             <td>Name</td>
-            <td>Associated Users</td>
-            <td>Associated Roles</td>
+            <td>Users</td>
+            <td>Roles</td>
         </tr>
-        %for ctr, group_tuple in enumerate( groups_members_roles ):
-            <%
-                group = group_tuple[0]
-                members = group_tuple[1]
-                roles = group_tuple[2]
-            %>
+        %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, members, roles, ctr, anchored, curr_anchor )}
+                    ${render_row( group, ctr, anchored, curr_anchor )}
                     <% anchored = True %>
                 %else:
-                    ${render_row( group, members, roles, ctr, anchored, curr_anchor )}
+                    ${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, members, roles, ctr, anchored, curr_anchor )}
+                            ${render_row( group, ctr, anchored, curr_anchor )}
                             <%  anchored = True %>
                         %else:
-                            ${render_row( group, members, roles, ctr, anchored, curr_anchor )}
+                            ${render_row( group, ctr, anchored, curr_anchor )}
                         %endif
                         <% 
                             anchor_loc = anchors.index( anchor )
@@ -127,7 +98,7 @@
                     %endif
                 %endfor
             %else:
-                ${render_row( group, members, roles, ctr, True, '' )}
+                ${render_row( group, ctr, True, '' )}
             %endif
         %endfor
     </table>
diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/roles.mako
--- a/templates/admin/dataset_security/roles.mako	Mon Apr 27 13:33:47 2009 -0400
+++ b/templates/admin/dataset_security/roles.mako	Mon Apr 27 16:03:44 2009 -0400
@@ -20,30 +20,10 @@
         <td>${role.description}</td>
         <td>${role.type}</td>
         <td>
-            <ul>
-                %for ura in role.users:
-                    <li>
-                        <a href="${h.url_for( controller='admin', action='user', user_id=ura.user.id )}">${ura.user.email}</a>
-                        <a id="user-${ura.user.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                        <div popupmenu="user-${ura.user.id}-popup">
-                            <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_user', role_id=role.id, user_id=ura.user.id )}">Remove user from role</a>
-                        </div>
-                    </li>
-                %endfor
-            </ul>
+            ${len( role.users )}
         </td>
         <td>
-            <ul>
-                %for gra in role.groups:
-                    <li>
-                        <a href="${h.url_for( controller='admin', action='group', group_id=gra.group.id )}">${gra.group.name}</a>
-                        <a id="group-${gra.group.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                        <div popupmenu="group-${gra.group.id}-popup">
-                            <a class="action-button" href="${h.url_for( controller='admin', action='remove_group_from_role', role_id=role.id, group_id=gra.group.id )}">Remove group from role</a>
-                        </div>
-                    </li>
-                %endfor
-            </ul>
+            ${len( role.groups )}
             %if not anchored:
                 <a name="${curr_anchor}"></a>
                 <div style="float: right;"><a href="#TOP">top</a></div>
@@ -91,8 +71,8 @@
             <td>Name</td>
             <td>Description</td>
             <td>Type</td>
-            <td>Associated Users</td>
-            <td>Associated Groups</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 ):
diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/users.mako
--- a/templates/admin/dataset_security/users.mako	Mon Apr 27 13:33:47 2009 -0400
+++ b/templates/admin/dataset_security/users.mako	Mon Apr 27 16:03:44 2009 -0400
@@ -2,7 +2,7 @@
 <%namespace file="/message.mako" import="render_msg" />
 
 ## Render a row
-<%def name="render_row( user, groups, roles, ctr, anchored, curr_anchor )">
+<%def name="render_row( user, ctr, anchored, curr_anchor )">
     %if ctr % 2 == 1:
         <tr class="odd_row">
     %else:
@@ -20,30 +20,10 @@
             </div>
         </td>
         <td>
-            <ul>
-                %for group in groups:
-                    <li>
-                        <a href="${h.url_for( controller='admin', action='group', group_id=group.id )}">${group.name}</a>
-                        <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">▼</a>
-                        <div popupmenu="group-${group.id}-popup">
-                            <a class="action-button" href="${h.url_for( controller='admin', action='remove_group_from_user', user_id=user.id, group_id=group.id )}">Remove group from user</a>
-                        </div>
-                    </li>
-                %endfor
-            </ul>
+            ${len( user.groups )}
         </td>
         <td>
-            <ul>
-                %for role in roles:
-                    <li>
-                        <a href="${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;">▼</a>
-                        <div popupmenu="role-${role.id}-popup">
-                            <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_user', user_id=user.id, role_id=role.id )}">Remove role from user</a>
-                        </div>
-                    </li>
-                %endfor
-            </ul>
+            ${len( user.roles )}
             %if not anchored:
                 <a name="${curr_anchor}"></a>
                 <div style="float: right;"><a href="#TOP">top</a></div>
@@ -65,12 +45,12 @@
     ${render_msg( msg, messagetype )}
 %endif
 
-%if len( users_groups_roles ) == 0:
+%if len( users ) == 0:
     There are no Galaxy users
 %else:
     <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
         <%
-            render_quick_find = len( users_groups_roles ) > 50
+            render_quick_find = len( users ) > 50
             ctr = 0
         %>
         %if render_quick_find:
@@ -91,34 +71,29 @@
         %endif
         <tr class="header">
             <td>Email</td>
-            <td>Associated Groups</td>
-            <td>Associated Roles</td>
+            <td>Groups</td>
+            <td>Roles</td>
         </tr>
-        %for ctr, user_tuple in enumerate( users_groups_roles ):
-            <%
-                user = user_tuple[0]
-                groups = user_tuple[1]
-                roles = user_tuple[2]
-            %>
+        %for ctr, user in enumerate( users ):
             %if render_quick_find and not user.email.upper().startswith( curr_anchor ):
                 <% anchored = False %>
             %endif
             %if render_quick_find and user.email.upper().startswith( curr_anchor ):
                 %if not anchored:
-                    ${render_row( user, groups, roles, ctr, anchored, curr_anchor )}
+                    ${render_row( user, ctr, anchored, curr_anchor )}
                     <% anchored = True %>
                 %else:
-                    ${render_row( user, groups, roles, ctr, anchored, curr_anchor )}
+                    ${render_row( user, ctr, anchored, curr_anchor )}
                 %endif
             %elif render_quick_find:   
                 %for anchor in anchors[ anchor_loc: ]:
                     %if user.email.upper().startswith( anchor ):
                         %if not anchored:
                             <% curr_anchor = anchor %>
-                            ${render_row( user, groups, roles, ctr, anchored, curr_anchor )}
+                            ${render_row( user, ctr, anchored, curr_anchor )}
                             <%  anchored = True %>
                         %else:
-                            ${render_row( user, groups, roles, ctr, anchored, curr_anchor )}
+                            ${render_row( user, ctr, anchored, curr_anchor )}
                         %endif
                         <% 
                             anchor_loc = anchors.index( anchor )
@@ -127,7 +102,7 @@
                     %endif
                 %endfor
             %else:
-                ${render_row( user, groups, roles, ctr, True, '' )}
+                ${render_row( user, ctr, True, '' )}
             %endif
         %endfor
     </table>
diff -r 22118cf46b0a -r d0c905db68db test/base/twilltestcase.py
--- a/test/base/twilltestcase.py	Mon Apr 27 13:33:47 2009 -0400
+++ b/test/base/twilltestcase.py	Mon Apr 27 16:03:44 2009 -0400
@@ -787,29 +787,6 @@
         self.check_page_for_string( check_str )
         self.home()
 
-    # Utility methods to test removal of associations
-    def remove_role_from_group( self, role_id, role_name, group_id, group_name ):
-        """Remove a role from a group"""
-        self.home()
-        self.visit_url( "%s/admin/remove_role_from_group?role_id=%s&group_id=%s" % ( self.url, role_id, group_id ) )
-        check_str = "Role '%s' removed from group '%s'" % ( role_name, group_name )
-        self.check_page_for_string( check_str )
-        self.home()
-    def remove_user_from_group( self, user_id, email, group_id, group_name ):
-        """Remove a user from a group"""
-        self.home()
-        self.visit_url( "%s/admin/remove_user_from_group?user_id=%s&group_id=%s" % ( self.url, user_id, group_id ) )
-        check_str = "User '%s' removed from group '%s'" % ( email, group_name )
-        self.check_page_for_string( check_str )
-        self.home()
-    def remove_user_from_role( self, user_id, email, role_id, role_name ):
-        """Remove a user from a role"""
-        self.home()
-        self.visit_url( "%s/admin/remove_user_from_role?user_id=%s&role_id=%s" % ( self.url, user_id, role_id ) )
-        check_str = "User '%s' removed from role '%s'" % ( email, role_name )
-        self.check_page_for_string( check_str )
-        self.home()
-
     # Library stuff
     def create_library( self, name='Library One', description='This is Library One' ):
         """Create a new library"""
diff -r 22118cf46b0a -r d0c905db68db tools/stats/column_maker.py
--- a/tools/stats/column_maker.py	Mon Apr 27 13:33:47 2009 -0400
+++ b/tools/stats/column_maker.py	Mon Apr 27 16:03:44 2009 -0400
@@ -13,10 +13,6 @@
     sys.stderr.write( msg )
     sys.exit()
 
-data_err = "This tool can only be used with tab-delimited data."
-columns_err = "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  "
-column_types_err = "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  "
-invalid_metadata_err = "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it.  "
 inp_file = sys.argv[1]
 out_file = sys.argv[2]
 expr = sys.argv[3]
@@ -24,16 +20,16 @@
 try:
     in_columns = int( sys.argv[5] )
 except:
-    stop_err( columns_err + data_err )
+    stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
 if in_columns < 2:
     # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
-    stop_err( columns_err + data_err )
+    stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
 try:
     in_column_types = sys.argv[6].split( ',' )
 except:
-    stop_err( column_types_err + data_err )
+    stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
 if len( in_column_types ) != in_columns:
-    stop_err( invalid_metadata_err + data_err )
+    stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
     
 # Unescape if input has been escaped
 mapped_str = {

    