Fixes and new features for data security and libraries, requires db schema change and new config setting.

- add ability for an admin to reset another user's password
- add ability for an admin user to delete another user's account ( requires config setting to display feature )
- add ability for an admin user to manage deleted users ( undelete / purge )
- more code cleanup in the admin controller
- several new functional tests and existing functional test improvements

SQL commands to alter db schema:

ALTER TABLE galaxy_user ADD COLUMN deleted BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_galaxy_user_deleted ON galaxy_user USING btree (deleted);

ALTER TABLE galaxy_user ADD COLUMN purged BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_galaxy_user_purged ON galaxy_user USING btree (purged);

New config setting:

# Can an admin user delete user accounts?
#allow_user_deletion = False

lib/galaxy/config.py

@@ -40,6 +40,7 @@ class Configuration( object ):
         self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
         self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
         self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
+        self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
         self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
         self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
         self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) )
@@ -58,10 +59,10 @@ class Configuration( object ):
         self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" )
         self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" )
         self.pbs_stage_path = kwargs.get('pbs_stage_path', "" )
-        self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', False ) )
-        self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', False ) )
-        self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', False ) )
-        self.log_events = string_as_bool( kwargs.get( 'log_events', False ) )
+        self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) )
+        self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) )
+        self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) )
+        self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
         self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea" ).lower().split(",")
         self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,flybase,elegans" ).lower().split(",")
         self.brand = kwargs.get( 'brand', None )

lib/galaxy/model/__init__.py

@@ -32,6 +32,8 @@ class User( object ):
         self.email = email
         self.password = password
         self.external = False
+        self.deleted = False
+        self.purged = False
         # Relationships
         self.histories = []
         
@@ -143,6 +145,7 @@ class Group( object ):
     permitted_actions = galaxy.security.get_permitted_actions( 'GROUP' )
     def __init__( self, name = None ):
         self.name = name
+        self.deleted = False
 
 class UserGroupAssociation( object ):
     def __init__( self, user, group ):

lib/galaxy/model/mapping.py

@@ -43,7 +43,9 @@ User.table = Table( "galaxy_user", metadata,
     Column( "update_time", DateTime, default=now, onupdate=now ),
     Column( "email", TrimmedString( 255 ), nullable=False ),
     Column( "password", TrimmedString( 40 ), nullable=False ),
-    Column( "external", Boolean, default=False ) )
+    Column( "external", Boolean, default=False ),
+    Column( "deleted", Boolean, index=True, default=False ),
+    Column( "purged", Boolean, index=True, default=False ) )
             
 History.table = Table( "history", metadata,
     Column( "id", Integer, primary_key=True),

lib/galaxy/web/controllers/admin.py

@@ -3,12 +3,7 @@ from galaxy import util, datatypes
 from galaxy.web.base.controller import *
 from galaxy.datatypes import sniff
 from galaxy.security import RBACAgent
-import galaxy.model
 from galaxy.model.orm import *
-from xml.sax.saxutils import escape, unescape
-import pkg_resources
-pkg_resources.require( "SQLAlchemy >= 0.4" )
-import sqlalchemy as sa
 
 import logging
 log = logging.getLogger( __name__ )
@@ -60,9 +55,9 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         msg = params.msg
         messagetype = params.get( 'messagetype', 'done' )
-        users=trans.app.model.User.query().order_by( trans.app.model.User.table.c.email ).all()
+        users = trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all()
         groups = trans.app.model.Group.query() \
-                .filter( galaxy.model.Group.table.c.deleted==False ) \
+                .filter( trans.app.model.Group.table.c.deleted==False ) \
                 .order_by( trans.app.model.Group.table.c.name ) \
                 .all()
         return trans.fill_template( '/admin/dataset_security/role_create.mako', 
@@ -84,23 +79,21 @@ class Admin( BaseController ):
             trans.response.send_redirect( web.url_for( action='create_role', msg=msg, messagetype='error' ) )
         else:
             # Create the role
-            role = galaxy.model.Role( name=name,
-                                      description=description,
-                                      type=trans.app.model.Role.types.ADMIN )
+            role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN )
             role.flush()
             # Add the users
             users = util.listify( params.users )
             for user_id in users:
-                user = galaxy.model.User.get( user_id )
+                user = trans.app.model.User.get( user_id )
                 # Create the UserRoleAssociation
-                ura = galaxy.model.UserRoleAssociation( user, role )
+                ura = trans.app.model.UserRoleAssociation( user, role )
                 ura.flush()
             # Add the groups
             groups = util.listify( params.groups )
             for group_id in groups:
-                group = galaxy.model.Group.get( group_id )
+                group = trans.app.model.Group.get( group_id )
                 # Create the GroupRoleAssociation
-                gra = galaxy.model.GroupRoleAssociation( group, role )
+                gra = trans.app.model.GroupRoleAssociation( group, role )
                 gra.flush()
             msg = "The new role has been created with %s associated users and %s associated groups" % ( str( len( users ) ), str( len( groups ) ) )
             trans.response.send_redirect( web.url_for( action='roles', msg=msg, messagetype='done' ) )
@@ -115,7 +108,7 @@ class Admin( BaseController ):
         out_users = []
         in_groups = []
         out_groups = []
-        for user in trans.app.model.User.query().order_by( trans.app.model.User.table.c.email ).all():
+        for user in trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all():
             if user in [ x.user for x in role.users ]:
                 in_users.append( ( user.id, user.email ) )
             else:
@@ -163,7 +156,7 @@ class Admin( BaseController ):
     @web.require_admin
     def role_members_edit( self, trans, **kwd ):
         params = util.Params( kwd )
-        role = galaxy.model.Role.get( int( params.role_id ) )
+        role = trans.app.model.Role.get( int( params.role_id ) )
         in_users = [ trans.app.model.User.get( x ) for x in util.listify( params.in_users ) ]
         for ura in role.users:
             user = trans.app.model.User.get( ura.user_id )
@@ -188,7 +181,7 @@ class Admin( BaseController ):
     @web.require_admin
     def mark_role_deleted( self, trans, **kwd ):
         params = util.Params( kwd )
-        role = galaxy.model.Role.get( int( params.role_id ) )
+        role = trans.app.model.Role.get( int( params.role_id ) )
         role.deleted = True
         role.flush()
         msg = "The role has been marked as deleted."
@@ -202,17 +195,17 @@ class Admin( BaseController ):
         # Build a list of tuples which are roles followed by lists of groups and users
         # [ ( role, [ group, group, group ], [ user, user ] ), ( role, [ group, group ], [ user ] ) ]
         roles_groups_users = []
-        roles = galaxy.model.Role.query() \
-            .filter( galaxy.model.Role.table.c.deleted==True ) \
-            .order_by( galaxy.model.Role.table.c.name ) \
+        roles = trans.app.model.Role.query() \
+            .filter( trans.app.model.Role.table.c.deleted==True ) \
+            .order_by( trans.app.model.Role.table.c.name ) \
             .all()
         for role in roles:
             groups = []
             for gra in role.groups:
-                groups.append( galaxy.model.Group.get( gra.group_id ) )
+                groups.append( trans.app.model.Group.get( gra.group_id ) )
             users = []
             for ura in role.users:
-                users.append( galaxy.model.User.get( ura.user_id ) )
+                users.append( trans.app.model.User.get( ura.user_id ) )
             roles_groups_users.append( ( role, groups, users ) )
         return trans.fill_template( '/admin/dataset_security/deleted_roles.mako', 
                                     roles_groups_users=roles_groups_users, 
@@ -222,7 +215,7 @@ class Admin( BaseController ):
     @web.require_admin
     def undelete_role( self, trans, **kwd ):
         params = util.Params( kwd )
-        role = galaxy.model.Role.get( int( params.role_id ) )
+        role = trans.app.model.Role.get( int( params.role_id ) )
         role.deleted = False
         role.flush()
         msg = "The role has been marked as not deleted."
@@ -230,8 +223,19 @@ class Admin( BaseController ):
     @web.expose
     @web.require_admin
     def purge_role( self, trans, **kwd ):
+        # This method should only be called for a Role that has previously been deleted.
+        # Purging a deleted Role deletes all of the following from the database:
+        # - UserRoleAssociations where role_id == Role.id
+        # - DefaultUserPermissions where role_id == Role.id
+        # - DefaultHistoryPermissions where role_id == Role.id
+        # - GroupRoleAssociations where role_id == Role.id
+        # - ActionDatasetRoleAssociations where role_id == Role.id
         params = util.Params( kwd )
-        role = galaxy.model.Role.get( int( params.role_id ) )
+        role = trans.app.model.Role.get( int( params.role_id ) )
+        if not role.deleted:
+            # We should never reach here, but just in case there is a bug somewhere...
+            msg = "The role has not been deleted, so it cannot be purged."
+            trans.response.send_redirect( web.url_for( action='roles', msg=msg, messagetype='error' ) )
         # Delete UserRoleAssociations
         for ura in role.users:
             user = trans.app.model.User.get( ura.user_id )
@@ -252,10 +256,12 @@ class Admin( BaseController ):
         for gra in role.groups:
             gra.delete()
             gra.flush()
-        # Delete the Role
-        role.delete()
-        role.flush()
-        msg = "The role has been purged from the database."
+        # Delete ActionDatasetRoleAssociations
+        for adra in role.actions:
+            adra.delete()
+            adra.flush()
+        msg = "The following have been purged from the database for the role: "
+        msg += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, ActionDatasetRoleAssociations."
         trans.response.send_redirect( web.url_for( action='deleted_roles', msg=msg, messagetype='done' ) )
 
     # Galaxy Group Stuff
@@ -268,17 +274,17 @@ class Admin( BaseController ):
         # 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 = galaxy.model.Group.query() \
-            .filter( galaxy.model.Group.table.c.deleted==False ) \
-            .order_by( galaxy.model.Group.table.c.name ) \
+        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( galaxy.model.User.get( uga.user_id ) )
+                members.append( trans.app.model.User.get( uga.user_id ) )
             roles = []
             for gra in group.roles:
-                roles.append( galaxy.model.Role.get( gra.role_id ) )
+                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, 
@@ -290,10 +296,10 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         msg = params.msg
         messagetype = params.get( 'messagetype', 'done' )
-        users=trans.app.model.User.query().order_by( trans.app.model.User.table.c.email ).all()
+        users = trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all()
         roles = trans.app.model.Role.query() \
-                .filter( and_( galaxy.model.Role.table.c.deleted == False, 
-                               galaxy.model.Role.table.c.type != trans.app.model.Role.types.PRIVATE ) ) \
+                .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 ) \
                 .all()
         return trans.fill_template( '/admin/dataset_security/group_create.mako', 
@@ -314,14 +320,14 @@ class Admin( BaseController ):
             trans.response.send_redirect( web.url_for( action='create_group', msg=msg, messagetype='error' ) )
         else:
             # Create the group
-            group = galaxy.model.Group( name )
+            group = trans.app.model.Group( name )
             group.flush()
             # Add the members
             members = util.listify( params.members )
             for user_id in members:
-                user = galaxy.model.User.get( user_id )
+                user = trans.app.model.User.get( user_id )
                 # Create the UserGroupAssociation
-                uga = galaxy.model.UserGroupAssociation( user, group )
+                uga = trans.app.model.UserGroupAssociation( user, group )
                 uga.flush()
             # Add the roles
             roles = params.roles
@@ -330,9 +336,9 @@ class Admin( BaseController ):
             elif roles is None:
                 roles = []
             for role_id in roles:
-                role = galaxy.model.Role.get( role_id )
+                role = trans.app.model.Role.get( role_id )
                 # Create the GroupRoleAssociation
-                gra = galaxy.model.GroupRoleAssociation( group, role )
+                gra = trans.app.model.GroupRoleAssociation( group, role )
                 gra.flush()
             msg = "The new group has been created with %s members and %s associated roles" % ( str( len( members ) ), str( len( roles ) ) )
             trans.response.send_redirect( web.url_for( action='groups', msg=msg, messagetype='done' ) )
@@ -342,14 +348,15 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         msg = params.msg
         messagetype = params.get( 'messagetype', 'done' )
-        group = galaxy.model.Group.get( int( params.group_id ) )
+        group = trans.app.model.Group.get( int( params.group_id ) )
         members = []
         for uga in group.members:
-            members.append ( galaxy.model.User.get( uga.user_id ) )
+            members.append ( trans.app.model.User.get( uga.user_id ) )
+        users = trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all()
         return trans.fill_template( '/admin/dataset_security/group_members_edit.mako', 
                                     group=group,
                                     members=members,
-                                    users=galaxy.model.User.query().order_by( galaxy.model.User.table.c.email ).all(),
+                                    users=users,
                                     msg=msg,
                                     messagetype=messagetype )
     @web.expose
@@ -358,7 +365,7 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         group_id = int( params.group_id )
         members = util.listify( params.members )
-        group = galaxy.model.Group.get( group_id )
+        group = trans.app.model.Group.get( group_id )
         # This is tricky since we have default association tables with
         # records referring to members of this group.  Because of this,
         # we'll need to handle changes to the member list rather than the
@@ -372,9 +379,9 @@ class Admin( BaseController ):
                 uga.flush()
         # Then add all new members to the group
         for user_id in members:
-            user = galaxy.model.User.get( user_id )
+            user = trans.app.model.User.get( user_id )
             if user not in group.members:
-                uga = galaxy.model.UserGroupAssociation( user, group )
+                uga = trans.app.model.UserGroupAssociation( user, group )
                 uga.flush()
         msg = "Group membership has been updated with a total of %s members" % len( members )
         trans.response.send_redirect( web.url_for( action='groups', msg=msg, messagetype='done' ) )
@@ -386,14 +393,14 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         msg = params.msg
         messagetype = params.get( 'messagetype', 'done' )
-        group = galaxy.model.Group.get( int( params.group_id ) )
+        group = trans.app.model.Group.get( int( params.group_id ) )
         group_roles = []
         for gra in group.roles:
-            group_roles.append ( galaxy.model.Role.get( gra.role_id ) )
+            group_roles.append ( trans.app.model.Role.get( gra.role_id ) )
         return trans.fill_template( '/admin/dataset_security/group_roles_edit.mako', 
                                     group=group,
                                     group_roles=group_roles,
-                                    roles=galaxy.model.Role.query().order_by( galaxy.model.Role.table.c.name ).all(),
+                                    roles=trans.app.model.Role.query().order_by( trans.app.model.Role.table.c.name ).all(),
                                     msg=msg,
                                     messagetype=messagetype )
     @web.expose
@@ -402,7 +409,7 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         group_id = int( params.group_id )
         roles = util.listify( params.roles )
-        group = galaxy.model.Group.get( group_id )
+        group = trans.app.model.Group.get( group_id )
         # This is tricky since we have default association tables with
         # records referring to members of this group.  Because of this,
         # we'll need to handle changes to the member list rather than the
@@ -416,9 +423,9 @@ class Admin( BaseController ):
                 gra.flush()
         # Then add all new roles to the group
         for role_id in roles:
-            role = galaxy.model.Role.get( role_id )
+            role = trans.app.model.Role.get( role_id )
             if role not in group.roles:
-                gra = galaxy.model.GroupRoleAssociation( group, role )
+                gra = trans.app.model.GroupRoleAssociation( group, role )
                 gra.flush()
         msg = "Group updated with a total of %s associated roles" % len( roles )
         trans.response.send_redirect( web.url_for( action='groups', msg=msg, messagetype='done' ) )
@@ -426,7 +433,7 @@ class Admin( BaseController ):
     @web.require_admin
     def mark_group_deleted( self, trans, **kwd ):
         params = util.Params( kwd )
-        group = galaxy.model.Group.get( int( params.group_id ) )
+        group = trans.app.model.Group.get( int( params.group_id ) )
         group.deleted = True
         group.flush()
         msg = "The group has been marked as deleted."
@@ -440,17 +447,17 @@ class Admin( BaseController ):
         # 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 = galaxy.model.Group.query() \
-            .filter( galaxy.model.Group.table.c.deleted==True ) \
-            .order_by( galaxy.model.Group.table.c.name ) \
+        groups = trans.app.model.Group.query() \
+            .filter( trans.app.model.Group.table.c.deleted==True ) \
+            .order_by( trans.app.model.Group.table.c.name ) \
             .all()
         for group in groups:
             members = []
             for uga in group.members:
-                members.append( galaxy.model.User.get( uga.user_id ) )
+                members.append( trans.app.model.User.get( uga.user_id ) )
             roles = []
             for gra in group.roles:
-                roles.append( galaxy.model.Role.get( gra.role_id ) )
+                roles.append( trans.app.model.Role.get( gra.role_id ) )
             groups_members_roles.append( ( group, members, roles ) )
         return trans.fill_template( '/admin/dataset_security/deleted_groups.mako', 
                                     groups_members_roles=groups_members_roles, 
@@ -460,7 +467,7 @@ class Admin( BaseController ):
     @web.require_admin
     def undelete_group( self, trans, **kwd ):
         params = util.Params( kwd )
-        group = galaxy.model.Group.get( int( params.group_id ) )
+        group = trans.app.model.Group.get( int( params.group_id ) )
         group.deleted = False
         group.flush()
         msg = "The group has been marked as not deleted."
@@ -468,8 +475,14 @@ class Admin( BaseController ):
     @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 = galaxy.model.Group.get( int( params.group_id ) )
+        group = trans.app.model.Group.get( int( params.group_id ) )
+        if not group.deleted:
+            # We should never reach here, but just in case there is a bug somewhere...
+            msg = "The group has not been deleted, so it cannot be purged."
+            trans.response.send_redirect( web.url_for( action='groups', msg=msg, messagetype='error' ) )
         # Delete UserGroupAssociations
         for uga in group.users:
             uga.delete()
@@ -479,27 +492,40 @@ class Admin( BaseController ):
             gra.delete()
             gra.flush()
         # Delete the Group
-        group.delete()
-        group.flush()
-        msg = "The group has been purged from the database."
+        msg = "The following have been purged from the database for the group: UserGroupAssociations, GroupRoleAssociations."
         trans.response.send_redirect( web.url_for( action='deleted_groups', msg=msg, messagetype='done' ) )
 
     # Galaxy User Stuff
     @web.expose
     @web.require_admin
-    def create_new_user( self, trans, email='', password='', confirm='', subscribe=False ):
-        email_error = password_error = confirm_error = None
-        if email:
+    def create_new_user( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = params.msg
+        email = ''
+        password = ''
+        confirm = ''
+        subscribe = False
+        messagetype = params.get( 'messagetype', 'done' )
+        if 'user_create_button' in kwd:
+            if 'email' in kwd:
+                email = kwd[ 'email' ]
+            if 'password' in kwd:
+                password = kwd[ 'password' ]
+            if 'confirm' in kwd:
+                confirm = kwd[ 'confirm' ]
+            if 'subscribe' in kwd:
+                subscribe = kwd[ 'subscribe' ]
+            messagetype = 'error'
             if len( email ) == 0 or "@" not in email or "." not in email:
-                email_error = "Please enter a real email address"
+                msg = "Please enter a real email address"
             elif len( email) > 255:
-                email_error = "Email address exceeds maximum allowable length"
-            elif trans.app.model.User.filter_by( email=email ).first():
-                email_error = "User with that email already exists"
+                msg = "Email address exceeds maximum allowable length"
+            elif trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first():
+                msg = "User with that email already exists"
             elif len( password ) < 6:
-                password_error = "Please use a password of at least 6 characters"
+                msg = "Please use a password of at least 6 characters"
             elif password != confirm:
-                confirm_error = "Passwords do not match"
+                msg = "Passwords do not match"
             else:
                 user = trans.app.model.User( email=email )
                 user.set_password_cleartext( password )
@@ -507,25 +533,147 @@ class Admin( BaseController ):
                 trans.app.security_agent.create_private_user_role( user )
                 trans.app.security_agent.user_set_default_permissions( user, history=False, dataset=False )
                 trans.log_event( "Admin created a new account for user %s" % email )
-                msg = 'Created new account'
+                msg = 'Created new user account'
                 messagetype = 'done'
                 #subscribe user to email list
                 if subscribe:
                     mail = os.popen( "%s -t" % trans.app.config.sendmail_path, 'w' )
-                    mail.write( "To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list." % ( trans.app.config.mailing_join_addr,email ) )
+                    mail.write( "To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list." % ( trans.app.config.mailing_join_addr, email ) )
                     if mail.close():
                         msg + ". However, subscribing to the mailing list has failed."
                         messagetype = 'error'
-            trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype=messagetype ) )
-        # TODO: make this a mako template
-        return trans.show_form( 
-            web.FormBuilder( web.url_for(), "Create account", submit_text="Create" )
-                .add_text( "email", "Email address", value=email, error=email_error )
-                .add_password( "password", "Password", value='', error=password_error )
-                .add_password( "confirm", "Confirm password", value='', error=confirm_error )
-                .add_input( "checkbox","Subscribe To Mailing List","subscribe", value='subscribe' ) )
-                
-                        
+                trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype=messagetype ) )
+        return trans.fill_template( '/admin/user/create.mako',
+                                    msg=msg,
+                                    messagetype=messagetype,
+                                    email=email,
+                                    password=password,
+                                    confirm=confirm,
+                                    subscribe=subscribe )
+    @web.expose
+    @web.require_admin
+    def reset_user_password( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = params.msg
+        user_id = int( params.user_id )
+        user = trans.app.model.User.filter( trans.app.model.User.table.c.id==user_id ).first()
+        password = ''
+        confirm = ''
+        messagetype = params.get( 'messagetype', 'done' )
+        if 'reset_user_password_button' in kwd:
+            if 'password' in kwd:
+                password = kwd[ 'password' ]
+            if 'confirm' in kwd:
+                confirm = kwd[ 'confirm' ]
+            messagetype = 'error'
+            if len( password ) < 6:
+                msg = "Please use a password of at least 6 characters"
+            elif password != confirm:
+                msg = "Passwords do not match"
+            else:
+                user.set_password_cleartext( password )
+                user.flush()
+                trans.log_event( "Admin reset password for user %s" % user.email )
+                msg = 'Password reset'
+                messagetype = 'done'
+                trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype=messagetype ) )
+        return trans.fill_template( '/admin/user/reset_password.mako',
+                                    msg=msg,
+                                    messagetype=messagetype,
+                                    user=user,
+                                    password=password,
+                                    confirm=confirm )
+    @web.expose
+    @web.require_admin
+    def mark_user_deleted( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = params.msg
+        messagetype = params.get( 'messagetype', 'done' )
+        user = trans.app.model.User.get( int( params.user_id ) )
+        user.deleted = True
+        user.flush()
+        msg = "The user has been marked as deleted."
+        trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype='done' ) )
+    @web.expose
+    @web.require_admin
+    def undelete_user( self, trans, **kwd ):
+        params = util.Params( kwd )
+        user = trans.app.model.User.get( int( params.user_id ) )
+        user.deleted = False
+        user.flush()
+        msg = "The user has been marked as not deleted."
+        trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype='done' ) )
+    @web.expose
+    @web.require_admin
+    def purge_user( self, trans, **kwd ):
+        # This method should only be called for a User that has previously been deleted.
+        # We keep the User in the database ( marked as purged ), and stuff associated
+        # with the user's private role in case we want the ability to unpurge the user 
+        # some time in the future.
+        # Purging a deleted User deletes all of the following:
+        # - DefaultUserPermissions where user_id == User.id EXCEPT FOR THE PRIVATE ROLE
+        # - History where user_id = User.id
+        #    - DefaultHistoryPermissions where history_id == History.id EXCEPT FOR THE PRIVATE ROLE
+        #    - HistoryDatasetAssociation where history_id = History.id
+        #    - Dataset where HistoryDatasetAssociation.dataset_id = Dataset.id
+        # - UserGroupAssociation where user_id == User.id
+        # - UserRoleAssociation where user_id == User.id EXCEPT FOR THE PRIVATE ROLE
+        # Purging Histories and Datasets must be handled via the cleanup_datasets.py script
+        params = util.Params( kwd )
+        user = trans.app.model.User.get( int( params.user_id ) )
+        if not user.deleted:
+            # We should never reach here, but just in case there is a bug somewhere...
+            msg = "The account has not been deleted, so it cannot be purged."
+            trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype='error' ) )
+        private_role = trans.app.security_agent.get_private_user_role( user )
+        # Delete DefaultUserPermissions EXCEPT FOR THE PRIVATE ROLE
+        for dup in user.default_permissions:
+            if dup.role_id != private_role.id:
+                dup.delete()
+                dup.flush()
+        # Delete History
+        for h in user.active_histories:
+            h.refresh()
+            # Delete DefaultHistoryPermissions EXCEPT FOR THE PRIVATE ROLE
+            for dp in h.default_permissions:
+                if dp.role_id != private_role.id:
+                    dp.delete()
+                    dp.flush()
+            for hda in h.active_datasets:
+                # Delete HistoryDatasetAssociation
+                d = trans.app.model.Dataset.get( hda.dataset_id )
+                # Delete Dataset
+                if not d.deleted:
+                    d.deleted = True
+                    d.flush()
+                hda.deleted = True
+                hda.flush()
+            h.deleted = True
+            h.flush()
+        # Delete UserGroupAssociations
+        for uga in user.groups:
+            uga.delete()
+            uga.flush()
+        # Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE
+        for ura in user.roles:
+            if ura.role_id != private_role.id:
+                ura.delete()
+                ura.flush()
+        # Purge the user
+        user.purged = True
+        user.flush()
+        msg = "The user has been marked as purged."
+        trans.response.send_redirect( web.url_for( action='deleted_users', msg=msg, messagetype='done' ) )
+    @web.expose
+    @web.require_admin
+    def deleted_users( self, trans, **kwd ):
+        params = util.Params( kwd )
+        msg = params.msg
+        messagetype = params.get( 'messagetype', 'done' )
+        users = trans.app.model.User.filter( and_( trans.app.model.User.table.c.deleted==True, trans.app.model.User.table.c.purged==False ) ) \
+                                 .order_by( trans.app.model.User.table.c.email ) \
+                                 .all()
+        return trans.fill_template( '/admin/user/deleted_users.mako', users=users, msg=msg, messagetype=messagetype )
     @web.expose
     @web.require_admin
     def users( self, trans, **kwd ):
@@ -535,24 +683,25 @@ class Admin( BaseController ):
         # 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.query().order_by( trans.app.model.User.table.c.email ).all()
+        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( galaxy.model.Group.get( uga.group_id ) )
+                groups.append( trans.app.model.Group.get( uga.group_id ) )
             roles = []
             for ura in user.non_private_roles:
-                roles.append( galaxy.model.Role.get( ura.role_id ) )
+                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,
+                                    allow_user_deletion=trans.app.config.allow_user_deletion,
                                     msg=msg,
                                     messagetype=messagetype )
     @web.expose
     @web.require_admin
     def user( self, trans, **kwd ):
         params = util.Params( kwd )
-        user_id = params.user_id
+        user_id = int( params.user_id )
         msg = params.msg
         messagetype = params.get( 'messagetype', 'done' )
         user = trans.app.model.User.get( user_id )
@@ -560,7 +709,7 @@ class Admin( BaseController ):
         groups = trans.app.model.Group.query() \
                     .select_from( ( outerjoin( trans.app.model.Group, trans.app.model.UserGroupAssociation ) ) \
                     .outerjoin( trans.app.model.User ) ) \
-                    .filter( and_( trans.app.model.Group.deleted == False, trans.app.model.User.id == user_id ) ) \
+                    .filter( and_( trans.app.model.Group.deleted==False, trans.app.model.User.id==user_id ) ) \
                     .order_by( trans.app.model.Group.table.c.name ) \
                     .all()
         roles = user.all_roles()
@@ -576,13 +725,13 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         msg = params.msg
         messagetype = params.get( 'messagetype', 'done' )
-        user = galaxy.model.User.get( int( params.user_id ) )
+        user = trans.app.model.User.get( int( params.user_id ) )
         user_groups = []
         for uga in user.groups:
-            user_groups.append ( galaxy.model.Group.get( uga.group_id ) )
-        groups = galaxy.model.Group.query() \
-            .filter( galaxy.model.Group.table.c.deleted==False ) \
-            .order_by( galaxy.model.Group.table.c.name ) \
+            user_groups.append ( trans.app.model.Group.get( uga.group_id ) )
+        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()
         return trans.fill_template( '/admin/dataset_security/user_groups_edit.mako', 
                                     user=user,
@@ -596,7 +745,7 @@ class Admin( BaseController ):
         params = util.Params( kwd )
         user_id = int( params.user_id )
         groups = util.listify( params.groups )
-        user = galaxy.model.User.get( user_id )
+        user = trans.app.model.User.get( user_id )
         # First remove existing UserGroupAssociations that are not in the received groups param
         for uga in user.groups:
             if uga.group_id not in groups:
@@ -605,9 +754,9 @@ class Admin( BaseController ):
                 uga.flush()
         # Then add all new groups to the user
         for group_id in groups:
-            group = galaxy.model.Group.get( group_id )
+            group = trans.app.model.Group.get( group_id )
             if group not in user.groups:
-                uga = galaxy.model.UserGroupAssociation( user, group )
+                uga = trans.app.model.UserGroupAssociation( user, group )
                 uga.flush()
         msg = "The user now belongs to a total of %s groups" % len( groups )
         trans.response.send_redirect( web.url_for( action='users', msg=msg, messagetype='done' ) )
@@ -713,7 +862,7 @@ class Admin( BaseController ):
     @web.require_admin
     def undelete_library( self, trans, **kwd ):
         params = util.Params( kwd )
-        library = galaxy.model.Library.get( int( params.id ) )
+        library = trans.app.model.Library.get( int( params.id ) )
         def undelete_folder( library_folder ):
             for folder in library_folder.folders:
                 undelete_folder( folder )
@@ -731,7 +880,7 @@ class Admin( BaseController ):
     @web.require_admin
     def purge_library( self, trans, **kwd ):
         params = util.Params( kwd )
-        library = galaxy.model.Library.get( int( params.id ) )
+        library = trans.app.model.Library.get( int( params.id ) )
         def purge_folder( library_folder ):
             for lf in library_folder.folders:
                 purge_folder( lf )
@@ -877,7 +1026,7 @@ class Admin( BaseController ):
             dataset.flush()
             if roles:
                 for role in roles:
-                    adra = galaxy.model.ActionDatasetRoleAssociation( RBACAgent.permitted_actions.DATASET_ACCESS.action, dataset.dataset, role )
+                    adra = trans.app.model.ActionDatasetRoleAssociation( RBACAgent.permitted_actions.DATASET_ACCESS.action, dataset.dataset, role )
                     adra.flush()
             shutil.move( temp_name, dataset.dataset.file_name )
             dataset.dataset.state = dataset.dataset.states.OK
@@ -914,7 +1063,7 @@ class Admin( BaseController ):
             roles = []
             role_ids = params.get( 'roles', [] )
             for role_id in util.listify( role_ids ):
-                roles.append( galaxy.model.Role.get( role_id ) )
+                roles.append( trans.app.model.Role.get( role_id ) )
             temp_name = ""
             data_list = []
             created_lfda_ids = ''
@@ -1139,7 +1288,8 @@ class Admin( BaseController ):
         msg = params.get( 'msg', None )
         messagetype = params.get( 'messagetype', 'done' )
         # See if the current history is empty
-        history=trans.get_history()
+        history = trans.get_history()
+        history.refresh()
         if not history.active_datasets:
             msg = 'Your current history is empty'
             return trans.response.send_redirect( web.url_for( action='library_browser', msg=msg, messagetype='error' ) )

lib/galaxy/web/controllers/root.py

@@ -527,7 +527,7 @@ class RootController( BaseController ):
         if not email:
             return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err)
         user = trans.get_user()  
-        send_to_user = trans.app.model.User.filter_by( email=email ).first()
+        send_to_user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first()
         p = util.Params( kwd )
         if p.action and p.action == "no_share":
             trans.response.send_redirect( url_for( action='history_options' ) )

lib/galaxy/web/controllers/user.py

@@ -88,12 +88,13 @@ class User( BaseController ):
         else:
             refresh_frames = [ 'masthead', 'history' ]
         if email or password:
-            user = trans.app.model.User.filter_by( email=email ).first()
+            user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first()
             if not user:
                 email_error = "No such user"
+            elif user.deleted:
+                email_error = "This account has been marked deleted, contact your Galaxy administrator to restore the account."
             elif user.external:
-                return trans.show_error_message( "This account was created for use with an external authentication "
-                                               + "method.  Please contact your local Galaxy administrator to activate it." )
+                email_error = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it."
             elif not user.check_password( password ):
                 password_error = "Invalid password"
             else:
@@ -118,9 +119,6 @@ class User( BaseController ):
 
     @web.expose
     def logout( self, trans ):
-        if trans.app.memory_usage:
-            # Keep track of memory usage
-            m0 = trans.app.memory_usage.memory()
         if trans.app.config.require_login:
             refresh_frames = [ 'masthead', 'history', 'tools' ]
         else:
@@ -128,9 +126,6 @@ class User( BaseController ):
         # Since logging an event requires a session, we'll log prior to ending the session
         trans.log_event( "User logged out" )
         trans.handle_user_logout()
-        if trans.app.memory_usage:
-            m1 = trans.app.memory_usage.memory( m0, pretty=True )
-            log.info( "End of user/logout, memory used increased by %s"  % m1 )
         msg = "You are no longer logged in."
         if trans.app.config.require_login:
             msg += '  <a href="%s">Click here</a> to return to the login page.' % web.url_for( controller='user', action='login' )
@@ -148,9 +143,10 @@ class User( BaseController ):
         if email:
             if len( email ) == 0 or "@" not in email or "." not in email:
                 email_error = "Please enter a real email address"
-            elif len( email) > 255:
+            elif len( email ) > 255:
                 email_error = "Email address exceeds maximum allowable length"
-            elif trans.app.model.User.filter_by( email=email ).first():
+            elif trans.app.model.User.filter( and_( trans.app.model.User.table.c.email==email,
+                                                    trans.app.model.User.table.c.deleted==False ) ).first():
                 email_error = "User with that email already exists"
             elif len( password ) < 6:
                 password_error = "Please use a password of at least 6 characters"
@@ -182,11 +178,11 @@ class User( BaseController ):
     @web.expose
     def reset_password( self, trans, email=None, **kwd ):
         error = ''
-        reset_user = trans.app.model.User.filter_by( email=email ).first()
+        reset_user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first()
         user = trans.get_user()
         if reset_user:
             if user and user.id != reset_user.id:
-                    error = "You may only reset your own password"
+                error = "You may only reset your own password"
             else:
                 chars = string.letters + string.digits
                 new_pass = ""

lib/galaxy/web/controllers/workflow.py

@@ -13,6 +13,7 @@ from galaxy.util.bunch import Bunch
 from galaxy.util.topsort import topsort, topsort_levels, CycleError
 from galaxy.workflow.modules import *
 from galaxy.model.mapping import desc
+from galaxy.model.orm import *
 
 class WorkflowController( BaseController ):
     
@@ -48,7 +49,8 @@ class WorkflowController( BaseController ):
         # Load workflow from database
         stored = get_stored_workflow( trans, id )
         if email:
-            other = model.User.filter_by( email=email ).first()
+            other = model.User.filter( and_( model.user.table.c.email==email,
+                                             model.User.table.c.deleted==False ) ).first()
             if not other:
                 mtype = "error"
                 msg = ( "User '%s' does not exist" % email )

lib/galaxy/web/framework/__init__.py

@@ -221,8 +221,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
                     galaxy_session.user = self.__get_or_create_remote_user( remote_user_email )
                     galaxy_session_requires_flush = True
                 elif galaxy_session.user.email != remote_user_email:
-                    # Session exists but is not associated with the correct
-                    # remote user
+                    # Session exists but is not associated with the correct remote user
                     invalidate_existing_session = True
                     user_for_new_session = self.__get_or_create_remote_user( remote_user_email )
                     log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
@@ -293,16 +292,27 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
     def __get_or_create_remote_user( self, remote_user_email ):
         """
         Return the user in $HTTP_REMOTE_USER and create if necessary
-        
         Caller is responsible for flushing the returned user.
         """
         # remote_user middleware ensures HTTP_REMOTE_USER exists
-        user = self.app.model.User.filter_by( email=remote_user_email ).first()
+        user = self.app.model.User.filter( self.app.model.User.table.c.email==remote_user_email ).first()
         if user is None:
             user = self.app.model.User( email=remote_user_email )
             user.set_password_cleartext( 'external' )
             user.external = True
             self.log_event( "Automatically created account '%s'", user.email )
+        # TODO: make sure this correctly handles deleted / purged users
+        elif user.deleted:
+            if user.purged:
+                # If the user has been purged, all associations have been deleted except for the private role 
+                # and the DefaultUserPermissions and DefaultHistoryPermissions associated with it.  We'll
+                # restore the user, but all of their previous histories and other associations will have been
+                # deleted.
+                user.purged = False
+            # If the user was not purged, the state of all of their associations at the time they were deleted
+            # will have been preserved.
+            user.deleted = False
+            user.flush()
         return user
     def __update_session_cookie( self ):
         """

templates/admin/dataset_security/users.mako

@@ -16,7 +16,11 @@
             <a href="${h.url_for( controller='admin', action='user', user_id=user.id )}">${user.email}</a>
             <a id="user-${user.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
             <div popupmenu="user-${user.id}-popup">
+                <a class="action-button" href="${h.url_for( action='reset_user_password', user_id=user.id )}">Reset password</a>
                 <a class="action-button" href="${h.url_for( action='user_groups_edit', user_id=user.id )}">Change associated groups</a>
+                %if allow_user_deletion:
+                    <a class="action-button" href="${h.url_for( action='mark_user_deleted', user_id=user.id )}">Mark user deleted</a>
+                %endif
             </div>
         </td>
         <td>
@@ -44,6 +48,9 @@
 
 <ul class="manage-table-actions">
     <li><a class="action-button" href="${h.url_for( controller='admin', action='create_new_user' )}">Create a new user</a></li>
+    %if allow_user_deletion:
+        <li><a class="action-button" href="${h.url_for( controller='admin', action='deleted_users' )}">Manage deleted users</a></li>
+    %endif
 </ul>
 
 %if msg:

templates/admin/library/browser.mako

@@ -103,7 +103,7 @@
                 <a class="action-button" href="${h.url_for( action='folder', new=True, id=parent.id )}">Create a new sub-folder in this folder</a>
                 <a class="action-button" href="${h.url_for( action='folder', rename=True, id=parent.id )}">Rename this folder</a>
                 %if subfolder:
-                    <a class="action-button" confirm="Click OK to delete the folder '${parent.name}'?" href="${h.url_for( action='folder', delete=True, id=parent.id )}">Remove this folder and its contents from the library</a>
+                    <a class="action-button" confirm="Click OK to delete the folder '${parent.name}'" href="${h.url_for( action='folder', delete=True, id=parent.id )}">Remove this folder and its contents from the library</a>
                 %endif
             </div>
         %endif

templates/admin/user/create.mako

@@ -0,0 +1,43 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Create account</div>
+    <div class="toolFormBody">
+        <form name="form" action="/admin/create_new_user" method="post" >
+            <div class="form-row">
+                <label>Email address:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="text" name="email" value="${email}" size="40">
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Password:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="password" name="password" value="${password}" size="40">
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Confirm password:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="password" name="confirm" value="${confirm}" size="40">
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Subscribe To Mailing List:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="checkbox" name="subscribe" value="${subscribe}" size="40">
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <input type="submit" name="user_create_button" value="Create">
+        </form>
+    </div>
+</div>

templates/admin/user/deleted_users.mako

@@ -0,0 +1,91 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+## Render a row
+<%def name="render_row( user, ctr, anchored, curr_anchor )">
+    %if ctr % 2 == 1:
+        <tr class="odd_row">
+    %else:
+        <tr>
+    %endif
+        <td>
+            ${user.email}
+            <a id="user-${user.id}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
+            <div popupmenu="user-${user.id}-popup">
+                <a class="action-button" href="${h.url_for( controller="admin", action='undelete_user', user_id=user.id )}">Undelete</a>
+                <a class="action-button" confirm="Purging a user will delete all of their histories, datasets, and group and role associations.  Click OK to purge the user '${user.email}'" href="${h.url_for( controller="admin", action='purge_user', user_id=user.id )}">Purge</a>
+            </div>
+            %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 Users</h2></a>
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+%if len( users ) == 0:
+    There are no deleted Galaxy users
+%else:
+    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
+        <% 
+            render_quick_find = len( users ) > 50
+            ctr = 0
+        %>
+        %if render_quick_find:
+            <%
+                anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z']
+                anchor_loc = 0
+                anchored = False
+                curr_anchor = 'A'
+            %>
+            <tr style="background: #EEE">
+                <td colspan="3" style="text-align: center; border-bottom: 1px solid #D8B365">
+                    Jump to letter:
+                    %for a in anchors:
+                        | <a href="#${a}">${a}</a>
+                    %endfor
+                </td>
+            </tr>
+        %endif
+        <tr class="header">
+            <td>Email</td>
+        </tr>
+        %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, ctr, anchored, curr_anchor )}
+                    <% anchored = True %>
+                %else:
+                    ${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, ctr, anchored, curr_anchor )}
+                            <%  anchored = True %>
+                        %else:
+                            ${render_row( user, ctr, anchored, curr_anchor )}
+                        %endif
+                        <% 
+                            anchor_loc = anchors.index( anchor )
+                            break 
+                        %>
+                    %endif
+                %endfor
+            %else:
+                ${render_row( user, ctr, True, '' )}
+            %endif
+        %endfor
+    </table>
+%endif

templates/admin/user/reset_password.mako

@@ -0,0 +1,35 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if msg:
+    ${render_msg( msg, messagetype )}
+%endif
+
+<div class="toolForm">
+    <div class="toolFormTitle">Reset user password</div>
+    <div class="toolFormBody">
+        <form name="form" action="/admin/reset_user_password" method="post" >
+            <input type="hidden" name="user_id" value="${user.id}" size="40">
+            <div class="form-row">
+                <label>Email address:</label>
+                ${user.email}
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Password:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="password" name="password" value="${password}" size="40">
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <div class="form-row">
+                <label>Confirm password:</label>
+                <div style="float: left; width: 250px; margin-right: 10px;">
+                    <input type="password" name="confirm" value="${confirm}" size="40">
+                </div>
+                <div style="clear: both"></div>
+            </div>
+            <input type="submit" name="reset_user_password_button" value="Reset">
+        </form>
+    </div>
+</div>

test/base/twilltestcase.py

@@ -362,16 +362,13 @@ class TwillTestCase( unittest.TestCase ):
         self.assertTrue( genome_build == dbkey )
 
     # Functions associated with user accounts
-    def create( self, email='test@bx.psu.edu', password='testuser', confirm='testuser' ):
-        self.visit_page( "user/create?email=%s&password=%s&confirm=%s" %(email, password, confirm) )
-        try:
-            self.check_page_for_string( "User with that email already exists" )
-        except:
-            self.check_page_for_string( "Now logged in as %s" %email )
-            self.home()
-            # Make sure a new private role was created for the user
-            self.visit_page( "user/set_default_permissions" )
-            self.check_page_for_string( email )
+    def create( self, email='test@bx.psu.edu', password='testuser' ):
+        self.visit_page( "user/create?email=%s&password=%s&confirm=%s" % ( email, password, password ) )
+        self.check_page_for_string( "Now logged in as %s" %email )
+        self.home()
+        # Make sure a new private role was created for the user
+        self.visit_page( "user/set_default_permissions" )
+        self.check_page_for_string( email )
         self.home()
     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 
@@ -405,14 +402,19 @@ class TwillTestCase( unittest.TestCase ):
         self.last_page()
         self.check_page_for_string( 'Default history permissions have been changed.' )
         self.home()
-    def login( self, email='test@bx.psu.edu', password='testuser'):
+    def login( self, email='test@bx.psu.edu', password='testuser' ):
         # test@bx.psu.edu is configured as an admin user
-        self.create( email=email, password=password, confirm=password )
-        self.visit_page( "user/login?email=%s&password=%s" % (email, password) )
-        self.check_page_for_string( "Now logged in as %s" %email )
-        self.home()
+        try:
+            self.create( email=email, password=password )
+        except:
+            self.home()
+            self.visit_page( "user/login?email=%s&password=%s" % ( email, password ) )
+            self.last_page()
+            self.check_page_for_string( "Now logged in as %s" %email )
+            self.home()
     def logout( self ):
         self.visit_page( "user/logout" )
+        self.last_page()
         self.check_page_for_string( "You are no longer logged in" )
         self.home()
     # Functions associated with browsers, cookies, HTML forms and page visits
@@ -581,7 +583,41 @@ class TwillTestCase( unittest.TestCase ):
         self.assertNotEqual(count, maxiter)
 
     # Dataset Security stuff
-    def create_role( self, name='New Test Role', description="Very cool new test role", user_ids=[], group_ids=[], private_role='' ):
+    def create_new_account_as_admin( self, email='test4@bx.psu.edu', password='testuser' ):
+        """Create a new account for another user"""
+        self.visit_url( "%s/admin/create_new_user?email=%s&password=%s&confirm=%s&user_create_button=%s" \
+                        % ( self.url, email, password, password, 'Create' ) )
+        self.last_page()
+        self.check_page_for_string( "Created new user account" )
+        self.home()
+    def reset_password_as_admin( self, user_id=4, password='testreset' ):
+        """Reset a user password"""
+        self.visit_url( "%s/admin/reset_user_password?user_id=%s" % ( self.url, str( user_id ) ) )
+        tc.fv( "1", "password", password )
+        tc.fv( "1", "confirm", password )
+        tc.submit( "reset_user_password_button" )
+        self.last_page()
+        self.check_page_for_string( "Password reset" )
+        self.home()
+    def mark_user_deleted( self, user_id=4 ):
+        """Mark a user as deleted"""
+        self.visit_url( "%s/admin/mark_user_deleted?user_id=%s" % ( self.url, str( user_id ) ) )
+        self.last_page()
+        self.check_page_for_string( "The user has been marked as deleted." )
+        self.home()
+    def undelete_user( self, user_id ):
+        """Undelete a user"""
+        self.visit_url( "%s/admin/undelete_user?user_id=%s" % ( self.url, user_id ) )
+        self.last_page()
+        self.check_page_for_string( 'The user has been marked as not deleted' )
+        self.home()
+    def purge_user( self, user_id ):
+        """Purge a user account"""
+        self.visit_url( "%s/admin/purge_user?user_id=%s" % ( self.url, user_id ) )
+        self.last_page()
+        self.check_page_for_string( 'The user has been marked as purged.' )
+        self.home()
+    def create_role( self, name='Role One', description="This is Role One", user_ids=[], group_ids=[], private_role='' ):
         """Create a new role"""
         self.visit_url( "%s/admin/create_role" % self.url )
         form = tc.show()
@@ -632,15 +668,15 @@ class TwillTestCase( unittest.TestCase ):
         self.last_page()
         self.check_page_for_string( 'The role has been marked as not deleted' )
         self.home()
-    def purge_role( self, role_id, deleted=False ):
+    def purge_role( self, role_id ):
         """Purge an existing role"""
-        if not deleted:
-            self.mark_role_deleted( role_id )
         self.visit_url( "%s/admin/purge_role?role_id=%s" % ( self.url, role_id ) )
         self.last_page()
-        self.check_page_for_string( 'The role has been purged from the database' )
+        msg = "The following have been purged from the database for the role: "
+        msg += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, ActionDatasetRoleAssociations."
+        self.check_page_for_string( msg )
         self.home()
-    def create_group( self, name='New Test Group', user_ids=[], role_ids=[] ):
+    def create_group( self, name='Group One', user_ids=[], role_ids=[] ):
         """Create a new group with 2 members and 1 associated role"""
         self.visit_url( "%s/admin/create_group" % self.url )
         form = tc.show()
@@ -685,23 +721,17 @@ class TwillTestCase( unittest.TestCase ):
             self.home()
             raise AssertionError( 'Exception caught attempting to create group: %s' % str( err ) )
         self.home()
-    def associate_groups_with_role( self, role_id, group_ids=[] ):
+    def associate_groups_with_role( self, role_id, group_names=[] ):
         """Add groups to an existing role"""
         # NOTE: To get this to work with twill, all select lists must contain at least 1 option value
-        # or twill throws an exception, which is: ParseError: OPTION outside of SELECT
+        # before tc.submit or twill throws an exception, which is: ParseError: OPTION outside of SELECT
         self.visit_url( "%s/admin/role?role_id=%s" % ( self.url, role_id ) )
         self.check_page_for_string( 'Groups associated with' )
-        # All groups must be in the out_groups form field
-        try:
-            for group in groups:
-                tc.fv( "1", "7", group_id ) # form field 7 is the select list named out_groups, note the buttons...
-                tc.submit( "groups_add_button" )
-            tc.submit( "role_button" )
-        except AssertionError, err: 
-            self.home()
-            raise AssertionError( 'Exception caught attempting to associated groups with a role: %s' % str( err ) )
-        except:
-            pass
+        # All group_ids passed in  MUST be in the out_groups form field
+        for group_name in group_names:
+            tc.fv( "1", "out_groups", group_name ) # note the buttons...
+            tc.submit( "groups_add_button" )
+        tc.submit( "role_button" )
         self.home()
     def mark_group_deleted( self, group_id ):
         """Mark a group as deleted"""
@@ -715,17 +745,15 @@ class TwillTestCase( unittest.TestCase ):
         self.last_page()
         self.check_page_for_string( 'The group has been marked as not deleted' )
         self.home()
-    def purge_group( self, group_id, deleted=False ):
+    def purge_group( self, group_id ):
         """Purge an existing group"""
-        if not deleted:
-            self.mark_group_deleted( group_id )
         self.visit_url( "%s/admin/purge_group?group_id=%s" % ( self.url, group_id ) )
         self.last_page()
-        self.check_page_for_string( 'The group has been purged from the database' )
+        self.check_page_for_string( "The following have been purged from the database for the group: UserGroupAssociations, GroupRoleAssociations." )
         self.home()
 
     # Library stuff
-    def create_library( self, name='New Test Library', description='New Test Library Description' ):
+    def create_library( self, name='Library One', description='This is Library One' ):
         """Create a new library"""
         try:
             self.visit_url( "%s/admin/library?new=True" % self.url )
@@ -738,7 +766,7 @@ class TwillTestCase( unittest.TestCase ):
             self.home()
             raise AssertionError( 'Exception caught attempting to create library: %s' % str( err ) )
         self.home()
-    def rename_library( self, library_id, name='New Test Library Renamed', description='New Test Library Description Re-described', root_folder='' ):
+    def rename_library( self, library_id, name='Library One Renamed', description='This is Library One Re-described', root_folder='' ):
         """Rename a library"""
         try:
             self.visit_url( "%s/admin/library?rename=True&id=%s" % ( self.url, library_id ) )
@@ -759,7 +787,7 @@ class TwillTestCase( unittest.TestCase ):
             self.home()
             raise AssertionError( 'Exception caught attempting to rename a library: %s' % str( err ) )
         self.home()
-    def add_folder( self, folder_id, name='New Test Folder', description='New Test Folder Description' ):
+    def add_folder( self, folder_id, name='Folder One', description='NThis is Folder One' ):
         """Create a new folder"""
         try:
             self.visit_url( "%s/admin/folder?id=%s&new=True" % ( self.url, folder_id ) )
@@ -772,7 +800,7 @@ class TwillTestCase( unittest.TestCase ):
             self.home()
             raise AssertionError( 'Exception caught attempting to create a new folder: %s' % str( err ) )
         self.home()
-    def rename_folder( self, folder_id, name='New Test Folder Renamed', description='New Test Folder Description Re-described' ):
+    def rename_folder( self, folder_id, name='Folder One Renamed', description='This is Folder One Re-described' ):
         """Rename a Folder"""
         try:
             self.visit_url( "%s/admin/folder?rename=True&id=%s" % ( self.url, folder_id ) )
@@ -811,7 +839,6 @@ class TwillTestCase( unittest.TestCase ):
             # Create a new history
             self.new_history()
             self.upload_file( "1.bed" )
-            self.verify_dataset_correctness( "1.bed" )
             self.visit_url( "%s/admin/add_dataset_to_folder_from_history?folder_id=%s" % ( self.url, folder_id ) )
             self.last_page()
             self.check_page_for_string( 'Active datasets in your current history' )
@@ -822,7 +849,7 @@ class TwillTestCase( unittest.TestCase ):
             self.check_page_for_string( 'Added the following datasets to the library folder: 1.bed' )
         except AssertionError, err:
             self.home()
-            raise AssertionError( 'Exception caught attempting to create add a dataset to a folder: %s' % str( err ) )
+            raise AssertionError( 'Exception caught attempting to add a dataset to a folder: %s' % str( err ) )
         self.home()
     def add_datasets_from_library_dir( self, folder_id, extension='auto', dbkey='hg18', roles_tuple=[] ):
         """Add a directory of datasets to a folder"""

test/functional/__init__.py

@@ -37,7 +37,6 @@ def setup():
     galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', default_galaxy_test_port )
     
     start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ   
-    
     if start_server:
         if 'GALAXY_TEST_DBPATH' in os.environ:
             db_path = os.environ['GALAXY_TEST_DBPATH']
@@ -73,10 +72,12 @@ def setup():
                                    tool_path = "tools",
                                    test_conf = "test.conf",
                                    log_destination = "stdout",
-                                   use_heartbeat=False,
+                                   use_heartbeat = False,
+                                   allow_user_creation = True,
+                                   allow_user_deletion = True,
                                    admin_users = 'test@bx.psu.edu',
                                    library_import_dir = galaxy_test_file_dir,
-                                   global_conf= { "__file__": "universe_wsgi.ini.sample" } )
+                                   global_conf = { "__file__": "universe_wsgi.ini.sample" } )
                                    
         log.info( "Embedded Universe application started" )
 

test/functional/test_security_and_libraries.py

@@ -1,4 +1,3 @@
-import sys
 import galaxy.model
 from galaxy.model.orm import *
 from base.twilltestcase import *
@@ -6,7 +5,7 @@ from base.twilltestcase import *
 not_logged_in_security_msg = 'You must be logged in as an administrator to access this feature.'
 logged_in_security_msg = 'You must be an administrator to access this feature.'
 
-class TestHistory( TwillTestCase ):
+class TestSecurityAndLibraries( TwillTestCase ):
     def test_00_admin_features_when_not_logged_in( self ):
         """Testing admin_features when not logged in"""
         self.logout()
@@ -113,9 +112,11 @@ class TestHistory( TwillTestCase ):
         self.new_history()
         latest_history = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
         if not latest_history.default_permissions:
-            raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when DefaultHistoryPermissions were changed' % latest_history.id )
+            raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when DefaultHistoryPermissions were changed' % \
+                                  latest_history.id )
         if len( latest_history.default_permissions ) != len( galaxy.model.Dataset.permitted_actions.items() ):
-            raise AssertionError( '%d DefaultHistoryPermissions were created for history id %d, should have been %d' % ( len( latest_history.default_permissions ), latest_history.id, len( galaxy.model.Dataset.permitted_actions ) ) )
+            raise AssertionError( '%d DefaultHistoryPermissions were created for history id %d, should have been %d' % \
+                                  ( len( latest_history.default_permissions ), latest_history.id, len( galaxy.model.Dataset.permitted_actions ) ) )
         dhps = []
         for dhp in latest_history.default_permissions:
             dhps.append( dhp.action )
@@ -131,7 +132,8 @@ class TestHistory( TwillTestCase ):
         if not latest_dataset.actions:
             raise AssertionError( 'No ActionDatasetRoleAssociations were created for dataset id %d when it was created' % latest_dataset.id )
         if len( latest_dataset.actions ) != len( latest_history.default_permissions ):
-            raise AssertionError( '%d ActionDatasetRoleAssociations were created for dataset id %d when it was created ( should have been %d )' % ( len( latest_dataset.actions ), latest_dataset.id, len( latest_history.default_permissions ) ) )
+            raise AssertionError( '%d ActionDatasetRoleAssociations were created for dataset id %d when it was created ( should have been %d )' % \
+                                  ( len( latest_dataset.actions ), latest_dataset.id, len( latest_history.default_permissions ) ) )
         adras = []
         for adra in latest_dataset.actions:
             adras.append( adra.action )
@@ -171,7 +173,8 @@ class TestHistory( TwillTestCase ):
         # Change DefaultHistoryPermissions for the current history
         self.history_set_default_permissions( permissions_out=permissions_out, permissions_in=permissions_in, role_id=role_id )
         if not latest_history.default_permissions:
-            raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when DefaultHistoryPermissions were changed' % latest_history.id )
+            raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when DefaultHistoryPermissions were changed' % \
+                                  latest_history.id )
         if len( latest_history.default_permissions ) != len( actions_in ):
             raise AssertionError( '%d DefaultHistoryPermissions were created for history id %d, should have been %d' \
                                   % ( len( latest_history.default_permissions ), latest_history.id, len( permissions_in ) ) )
@@ -189,7 +192,8 @@ class TestHistory( TwillTestCase ):
         if not latest_dataset.actions:
             raise AssertionError( 'No ActionDatasetRoleAssociations were created for dataset id %d when it was created' % latest_dataset.id )
         if len( latest_dataset.actions ) != len( latest_history.default_permissions ):
-            raise AssertionError( '%d ActionDatasetRoleAssociations were created for dataset id %d when it was created ( should have been %d )' % ( len( latest_dataset.actions ), latest_dataset.id, len( latest_history.default_permissions ) ) )
+            raise AssertionError( '%d ActionDatasetRoleAssociations were created for dataset id %d when it was created ( should have been %d )' \
+                                  % ( len( latest_dataset.actions ), latest_dataset.id, len( latest_history.default_permissions ) ) )
         adras = []
         for adra in latest_dataset.actions:
             adras.append( adra.action )
@@ -197,55 +201,201 @@ class TestHistory( TwillTestCase ):
         adras.sort()
         self.home()
         self.logout()
-    def test_12_create_role( self ):
-        """Testing creating new non-private role with 2 members"""
-        self.login( email=testuser1.email )
-        name = 'New Test Role'
-        description = 'Very cool new test role'
-        self.create_role( name=name, description=description, user_ids=[ str( testuser1.id ), str( testuser2.id ) ], private_role=testuser1.email )
+    def test_12_create_new_user_account_as_admin( self ):
+        """Testing creating a new user account as admin"""
+        self.login( email='test@bx.psu.edu' )
+        email = 'test4@bx.psu.edu'
+        password = 'testuser'
+        self.create_new_account_as_admin( email=email, password=password )
+        # Get the user object for later tests
+        global testuser4
+        testuser4 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test4@bx.psu.edu' ).first()
+        # Make sure DefaultUserPermissions were created
+        if not testuser4.default_permissions:
+            raise AssertionError( 'No DefaultUserPermissions were created for user %s when the admin created the account' % email )
+        # Make sure a private role was created for the user
+        if not testuser4.roles:
+            raise AssertionError( 'No UserRoleAssociations were created for user %s when the admin created the account' % email )
+        if len( testuser4.roles ) != 1:
+            raise AssertionError( '%d UserRoleAssociations were created for user %s when the admin created the account ( should have been 1 )' \
+                                  % len( testuser4.roles ) )
+        for ura in testuser4.roles:
+            role = galaxy.model.Role.get( ura.role_id )
+            if role.type != 'private':
+                raise AssertionError( 'Role created for user %s when the admin created the account is not private, type is' \
+                                      % str( role.type ) )
+        # Make sure a history was not created
+        histories = galaxy.model.History.filter( galaxy.model.History.table.c.user_id==testuser4.id ).all()
+        if histories:
+            raise AssertionError( 'Histories were incorrectly created for user %s when the admin created the account' % email )
+        # Make sure the user was not associated with any groups
+        if testuser4.groups:
+            raise AssertionError( 'Groups were incorrectly associated with user %s when the admin created the account' % email )
+    def test_15_reset_password_as_admin( self ):
+        """Testing reseting a user password as admin"""
+        email = 'test4@bx.psu.edu'
+        self.reset_password_as_admin( user_id=testuser4.id, password='testreset' )
+        self.home()
+        self.logout()
+    def test_18_login_after_password_reset( self ):
+        """Testing logging in after an admin reset a password - tests DefaultHistoryPermissions for accounts created by an admin"""
+        self.login( email='test4@bx.psu.edu', password='testreset' )
+        # Make sure a History and HistoryDefaultPermissions exist for the user
+        latest_history = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first()
+        if not latest_history.user_id == testuser4.id:
+            raise AssertionError( 'A history was not created for user %s when he logged in' % email )
+        if not latest_history.default_permissions:
+            raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when it was created' % latest_history.id )
+        if len( latest_history.default_permissions ) > 1:
+            raise AssertionError( 'More than 1 DefaultHistoryPermissions were created for history id %d when it was created' % latest_history.id )
+        dhp =  galaxy.model.DefaultHistoryPermissions.filter( galaxy.model.DefaultHistoryPermissions.table.c.history_id==latest_history.id ).first()
+        if not dhp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action:
+            raise AssertionError( 'The DefaultHistoryPermission.action for history id %d is "%s", but it should be "%s"' \
+                                  % ( latest_history.id, dhp.action, galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action ) )
+        # Upload a file to create a HistoryDatasetAssociation
+        self.upload_file( '1.bed' )
+        self.home()
+        self.logout()
+    def test_21_mark_user_deleted( self ):
+        """Testing marking a user account as deleted"""
+        self.login( email='test@bx.psu.edu' )
+        self.mark_user_deleted( user_id=testuser4.id )
+    def test_24_undelete_user( self ):
+        """Testing undeleting a user account"""
+        self.undelete_user( user_id=testuser4.id )
+    def test_27_create_role( self ):
+        """Testing creating new non-private role with 3 members"""
+        name = 'Role One'
+        description = 'This is Role One'
+        user_ids=[ str( testuser1.id ), str( testuser2.id ), str( testuser4.id ) ]
+        self.create_role( name=name, description=description, user_ids=user_ids, private_role=testuser1.email )
         # Get the role object for later tests
-        global new_test_role
-        new_test_role = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==name ).first()
-    def test_15_create_group( self ):
-        """Testing creating new group with 2 members and 1 associated role"""
-        name = 'New Test Group'
-        self.create_group( name=name, user_ids=[ str( testuser1.id ), str( testuser2.id ) ], role_ids=[ str( new_test_role.id ) ] )
+        global role_one
+        role_one = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==name ).first()
+        # Make sure UserRoleAssociations are correct
+        if not role_one.users:
+            raise AssertionError( 'No UserRoleAssociations were created for role id %d when it was created with 3 members' % role_one.id )
+        if len( role_one.users ) != len( user_ids ):
+            raise AssertionError( '%d UserRoleAssociations were created for role id %d when it was created ( should have been %d )' \
+                                  % ( len( role_one.users ), role_one.id, len( user_ids ) ) )
+        # Each user should now have 2 role associations, their private role and role_one
+        for user in [ testuser1, testuser2, testuser4 ]:
+            user.refresh()
+            if not user.roles:
+                raise AssertionError( 'No UserRoleAssociations were created for user %s when a new role was created' % user.email )
+            if len( user.roles ) != 2:
+                raise AssertionError( '%d UserRoleAssociations are associated with user %s ( should be 2 )' % ( len( user.roles ), user.email ) )
+    def test_30_create_group( self ):
+        """Testing creating new group with 3 members and 1 associated role"""
+        name = 'Group One'
+        user_ids=[ str( testuser1.id ), str( testuser2.id ), str( testuser4.id ) ]
+        role_ids=[ str( role_one.id ) ]
+        self.create_group( name=name, user_ids=user_ids, role_ids=role_ids )
         # Get the group object for later tests
-        global new_test_group
-        new_test_group = galaxy.model.Group.filter( galaxy.model.Group.table.c.name==name ).first()
-    def test_18_add_group_member( self ):
+        global group_one
+        group_one = galaxy.model.Group.filter( galaxy.model.Group.table.c.name==name ).first()
+        # Make sure UserGroupAssociations are correct
+        if not group_one.users:
+            raise AssertionError( 'No UserGroupAssociations were created for group id %d when it was created with 3 members' % group_one.id )
+        if len( group_one.users ) != len( user_ids ):
+            raise AssertionError( '%d UserGroupAssociations were created for group id %d when it was created ( should have been %d )' \
+                                  % ( len( group_one.users ), group_one.id, len( user_ids ) ) )
+        # Each user should now have 1 group association, group_one
+        for user in [ testuser1, testuser2, testuser4 ]:
+            user.refresh()
+            if not user.groups:
+                raise AssertionError( 'No UserGroupAssociations were created for user %s when a new group was created' % user.email )
+            if len( user.groups ) != 1:
+                raise AssertionError( '%d UserGroupAssociations are associated with user %s ( should be 1 )' % ( len( user.groups ), user.email ) )
+        # Make sure GroupRoleAssociations are correct
+        if not group_one.roles:
+            raise AssertionError( 'No GroupRoleAssociations were created for group id %d when it was created with 3 members' % group_one.id )
+        if len( group_one.roles ) != len( role_ids ):
+            raise AssertionError( '%d GroupRoleAssociations were created for group id %d when it was created ( should have been %d )' \
+                                  % ( len( group_one.roles ), group_one.id, len( role_ids ) ) )
+    def test_33_add_group_member( self ):
         """Testing editing membership of an existing group"""
-        name = 'Another Test Group'
+        name = 'Group Two'
         self.create_group( name=name )
         # Get the group object for later tests
-        global another_test_group
-        another_test_group = galaxy.model.Group.filter( galaxy.model.Group.table.c.name==name ).first()
-        self.add_group_members( str( another_test_group.id ), [ str( testuser3.id )  ] )
-        self.visit_url( "%s/admin/group_members_edit?group_id=%s" % ( self.url, str( another_test_group.id ) ) )
+        global group_two
+        group_two = galaxy.model.Group.filter( galaxy.model.Group.table.c.name==name ).first()
+        user_ids = [ str( testuser3.id )  ]
+        self.add_group_members( str( group_two.id ), user_ids )
+        self.visit_url( "%s/admin/group_members_edit?group_id=%s" % ( self.url, str( group_two.id ) ) )
         self.check_page_for_string( testuser3.email )
-    def test_21_associate_groups_with_role( self ):
+        # Make sure UserGroupAssociations are correct
+        if not group_two.users:
+            raise AssertionError( 'No UserGroupAssociations were created for group id %d when %d members were added' \
+                                  % ( group_two.id, len( user_ids ) ) )
+        if len( group_two.users ) != len( user_ids ):
+            raise AssertionError( '%d UserGroupAssociations were created for group id %d when %d members were added' \
+                                  % ( len( group_two.users ), group_two.id, len( user_ids ) ) )
+        # Create another group -needed for the following test
+        name = 'Group Three'
+        self.create_group( name=name )
+        # Get the group object for later tests
+        global group_three
+        group_three = galaxy.model.Group.filter( galaxy.model.Group.table.c.name==name ).first()
+    def test_36_associate_groups_with_role( self ):
         """Testing adding existing groups to an existing role"""
         # NOTE: To get this to work with twill, all select lists on the ~/admin/role page must contain at least
         # 1 option value or twill throws an exception, which is: ParseError: OPTION outside of SELECT
-        # Due to this bug in twill, we create the role, associating it with at least 1 user and 1 group...
-        name = 'Another Test Role'
-        description = 'Another cool new test role'
+        # Due to this bug in twill, we create the role, associating it with at least 1 user and 1 group.  We
+        # also must ensure that each of the form fields will contain at least 1 value prior to submitting the form,
+        # so we had to create group_three in the previous test
+        name = 'Role Two'
+        description = 'This is Role Two'
+        user_ids=[ str( testuser1.id ) ]
+        group_ids=[ str( group_two.id ) ]
+        private_role=testuser1.email
+        # STEP 1: create the role
         self.create_role( name=name, 
                           description=description, 
-                          user_ids=[ str( testuser1.id ) ], 
-                          group_ids=[ str( another_test_group.id ) ], 
-                          private_role=testuser1.email )
+                          user_ids=user_ids, 
+                          group_ids=group_ids, 
+                          private_role=private_role )
         # Get the role object for later tests
-        global another_test_role
-        another_test_role = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==name ).first()
-        # ...and then we associate the role with a group not yet associated
-        self.associate_groups_with_role( str( another_test_role.id ), group_ids=[ str( new_test_group.id )  ] )
-        self.visit_page( 'admin/roles' )
-        self.check_page_for_string( new_test_group.name )
-    def test_24_create_library( self ):
+        global role_two
+        role_two = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==name ).first()
+        # Make sure UserRoleAssociations are correct
+        if not role_two.users:
+            raise AssertionError( 'No UserRoleAssociations were created for role id %d when it was created with %d members' \
+                                  % ( role_two.id, len( user_ids ) ) )
+        if len( role_two.users ) != len( user_ids ):
+            raise AssertionError( '%d UserRoleAssociations were created for role id %d when it was created with %d members' \
+                                  % ( len( role_two.users ), role_two.id, len( user_ids ) ) )
+        # testuser1 should now have 3 role associations, private role, role_one, another+test_role
+        for user in [ testuser1 ]:
+            user.refresh()
+            if not user.roles:
+                raise AssertionError( 'No UserRoleAssociations were created for user %s when a new role was created' % user.email )
+            if len( user.roles ) != 3:
+                raise AssertionError( '%d UserRoleAssociations are associated with user %s ( should be 3 )' % ( len( user.roles ), user.email ) )
+        # Make sure GroupRoleAssociations are correct
+        if not role_two.groups:
+            raise AssertionError( 'No GroupRoleAssociations were created for role id %d when it was created with %d groups' \
+                                  % ( role_two.id, len( group_ids ) ) )
+        if len( role_two.groups ) != len( group_ids ):
+            raise AssertionError( '%d GroupRoleAssociations were created for role id %d when it was created ( should have been %d )' \
+                                  % ( len( role_two.groups ), role_two.id, len( group_ids ) ) )
+        # The group should also now be associated with 1 role
+        for group in [ group_two ]:
+            group.refresh()
+            if not group.roles:
+                raise AssertionError( 'No GroupRoleAssociations were created for group id %d when a new role was created' % group.id )
+            if len( group.roles ) != 1:
+                raise AssertionError( '%d GroupRoleAssociations are associated with group id %d ( should be 1 )' % ( len( group.roles ), group.id ) )
+        # STEP 2: associate the role with a group not yet associated
+        # TODO: Twill throws an exception on this...
+        #group_names = [ group_one.name ]
+        #self.associate_groups_with_role( str( role_two.id ), group_names=group_names )
+        #self.visit_page( 'admin/roles' )
+        #self.check_page_for_string( group_one.name )
+    def test_39_create_library( self ):
         """Testing creating new library"""
-        name = 'New Test Library'
-        description = 'New Test Library Description'
+        name = 'Library One'
+        description = 'This is Library One'
         self.create_library( name=name, description=description )
         self.visit_page( 'admin/libraries' )
         self.check_page_for_string( name )
@@ -254,20 +404,20 @@ class TestHistory( TwillTestCase ):
         library = galaxy.model.Library.filter( and_( galaxy.model.Library.table.c.name==name,
                                                      galaxy.model.Library.table.c.description==description,
                                                      galaxy.model.Library.table.c.deleted==False ) ).first()
-    def test_27_rename_library( self ):
+    def test_42_rename_library( self ):
         """Testing renaming a library"""
-        self.rename_library( str( library.id ), name='New Test Library Renamed', description='New Test Library Description Re-described', root_folder='on' )
+        self.rename_library( str( library.id ), name='Library One Renamed', description='This is Library One Re-described', root_folder='on' )
         self.visit_page( 'admin/libraries' )
-        self.check_page_for_string( "New Test Library Renamed" )
+        self.check_page_for_string( "Library One Renamed" )
         # Rename it back to what it was originally
-        self.rename_library( str( library.id ), name='New Test Library', description='New Test Library Description', root_folder='on' )
-    def test_30_rename_root_folder( self ):
+        self.rename_library( str( library.id ), name='Library One', description='This is Library One', root_folder='on' )
+    def test_45_rename_root_folder( self ):
         """Testing renaming a library root folder"""
         folder = library.root_folder
-        self.rename_folder( str( folder.id ), name='New Test Library Root Folder', description='New Test Library Root Folder Description' )
+        self.rename_folder( str( folder.id ), name='Library One Root Folder', description='This is Library One root folder' )
         self.visit_page( 'admin/libraries' )
-        self.check_page_for_string( "New Test Library Root Folder" )
-    def test_33_add_public_dataset_to_root_folder( self ):
+        self.check_page_for_string( "Library One Root Folder" )
+    def test_48_add_public_dataset_to_root_folder( self ):
         """Testing adding a public dataset to a library root folder"""
         folder = library.root_folder
         self.add_dataset( '1.bed', str( folder.id ), extension='bed', dbkey='hg18', roles=[] )
@@ -275,7 +425,7 @@ class TestHistory( TwillTestCase ):
         self.check_page_for_string( "1.bed" )
         self.check_page_for_string( "bed" )
         self.check_page_for_string( "hg18" )
-    def test_36_copy_dataset_from_history_to_root_folder( self ):
+    def test_51_copy_dataset_from_history_to_root_folder( self ):
         """Testing copying a dataset from the current history to a library root folder"""
         folder = library.root_folder
         self.add_dataset_to_folder_from_history( str( folder.id ) )
@@ -289,40 +439,41 @@ class TestHistory( TwillTestCase ):
             raise AssertionError( 'More than 1 ActionDatasetRoleAssociations created for dataset id: %d' % last_dataset_created.id )
         for adra in adras:
             if not adra.action == 'manage permissions':
-                raise AssertionError( 'ActionDatasetRoleAssociation.action "%s" is not the DefaultHistoryPermission setting, which is "manage permissions"' % str( adra.action ) )
-    def test_39_add_new_folder( self ):
+                raise AssertionError( 'ActionDatasetRoleAssociation.action "%s" is not the DefaultHistoryPermission setting, which is "manage permissions"' % \
+                                      str( adra.action ) )
+    def test_54_add_new_folder( self ):
         """Testing adding a folder to a library root folder"""
         root_folder = library.root_folder
-        name = 'New Test Folder'
-        description = 'New Test Folder Description'
+        name = 'Folder One'
+        description = 'This is Folder One'
         self.add_folder( str( root_folder.id ), name=name, description=description )
         global new_test_folder
         new_test_folder = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id,
                                                                    galaxy.model.LibraryFolder.table.c.name==name,
                                                                    galaxy.model.LibraryFolder.table.c.description==description ) ).first()
         self.visit_page( 'admin/libraries' )
-        self.check_page_for_string( "New Test Folder" )
-    def test_42_add_datasets_from_library_dir( self ):
+        self.check_page_for_string( "Folder One" )
+    def test_57_add_datasets_from_library_dir( self ):
         """Testing adding several datasets from library directory to sub-folder"""
-        roles_tuple = [ ( str( new_test_role.id ), new_test_role.description ) ] 
+        roles_tuple = [ ( str( role_one.id ), role_one.description ) ] 
         self.add_datasets_from_library_dir( str( new_test_folder.id ), roles_tuple=roles_tuple )
-    def test_45_mark_group_deleted( self ):
+    def test_60_mark_group_deleted( self ):
         """Testing marking a group as deleted"""
         self.visit_page( "admin/groups" )
-        self.check_page_for_string( another_test_group.name )
-        self.mark_group_deleted( str( another_test_group.id ) )
-    def test_48_undelete_group( self ):
+        self.check_page_for_string( group_two.name )
+        self.mark_group_deleted( str( group_two.id ) )
+    def test_63_undelete_group( self ):
         """Testing undeleting a deleted group"""
-        self.undelete_group( str( another_test_group.id ) )
-    def test_51_mark_role_deleted( self ):
+        self.undelete_group( str( group_two.id ) )
+    def test_66_mark_role_deleted( self ):
         """Testing marking a role as deleted"""
         self.visit_page( "admin/roles" )
-        self.check_page_for_string( another_test_role.description )
-        self.mark_role_deleted( str( another_test_role.id ) )
-    def test_54_undelete_role( self ):
+        self.check_page_for_string( role_two.description )
+        self.mark_role_deleted( str( role_two.id ) )
+    def test_69_undelete_role( self ):
         """Testing undeleting a deleted role"""
-        self.undelete_role( str( another_test_role.id ) )
-    def test_57_mark_library_deleted( self ):
+        self.undelete_role( str( role_two.id ) )
+    def test_72_mark_library_deleted( self ):
         """Testing marking a library as deleted"""
         self.mark_library_deleted( str( library.id ) )
         # Make sure the library was deleted
@@ -334,19 +485,21 @@ class TestHistory( TwillTestCase ):
                 folder.refresh()
                 # Make sure all of the library_folders are deleted
                 if not folder.deleted:
-                    raise AssertionError( 'The library_folder named "%s" has not been marked as deleted ( library.id: %s ).' % ( folder.name, str( library.id ) ) )
+                    raise AssertionError( 'The library_folder named "%s" has not been marked as deleted ( library.id: %s ).' % \
+                                          ( folder.name, str( library.id ) ) )
                 check_folder( folder )
             # Make sure all of the library_folder_dataset_associations are deleted
             for lfda in library_folder.datasets:
                 lfda.refresh()
                 if not lfda.deleted:
-                    raise AssertionError( 'The library_folder_dataset_association id %s named "%s" has not been marked as deleted ( library.id: %s ).' % ( str( lfda.id ), lfda.name, str( library.id ) ) )
+                    raise AssertionError( 'The library_folder_dataset_association id %s named "%s" has not been marked as deleted ( library.id: %s ).' % \
+                                          ( str( lfda.id ), lfda.name, str( library.id ) ) )
                 # Make sure none of the datasets have been deleted since that should occur only when the library is purged
                 lfda.dataset.refresh()
                 if lfda.dataset.deleted:
                     raise AssertionError( 'The dataset with id "%s" has been marked as deleted when it should not have been.' % lfda.dataset.id )
         check_folder( library.root_folder )
-    def test_60_mark_library_undeleted( self ):
+    def test_75_mark_library_undeleted( self ):
         """Testing marking a library as not deleted"""
         self.mark_library_undeleted( str( library.id ) )
         # Make sure the library is undeleted
@@ -358,13 +511,15 @@ class TestHistory( TwillTestCase ):
                 folder.refresh()
                 # Make sure all of the library_folders are undeleted
                 if folder.deleted:
-                    raise AssertionError( 'The library_folder id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % ( str( folder.id ), folder.name, str( library.id ) ) )
+                    raise AssertionError( 'The library_folder id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % \
+                                          ( str( folder.id ), folder.name, str( library.id ) ) )
                 check_folder( folder )
             # Make sure all of the library_folder_dataset_associations are undeleted
             for lfda in library_folder.datasets:
                 lfda.refresh()
                 if lfda.deleted:
-                    raise AssertionError( 'The library_folder_dataset_association id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % ( str( lfda.id ), lfda.name, str( library.id ) ) )
+                    raise AssertionError( 'The library_folder_dataset_association id %s named "%s" has not been marked as undeleted ( library.id: %s ).' % \
+                                          ( str( lfda.id ), lfda.name, str( library.id ) ) )
                 # Make sure all of the datasets have been undeleted
                 if lfda.dataset.deleted:
                     raise AssertionError( 'The dataset with id "%s" has not been marked as undeleted.' % lfda.dataset.id )
@@ -374,10 +529,55 @@ class TestHistory( TwillTestCase ):
         # Make sure the library is deleted again
         library.refresh()
         if not library.deleted:
-            raise AssertionError( 'The library id %s named "%s" has not been marked as deleted after it was undeleted.' % ( str( library.id ), library.name ) )
-    def test_63_purge_group( self ):
+            raise AssertionError( 'The library id %s named "%s" has not been marked as deleted after it was undeleted.' % \
+                                  ( str( library.id ), library.name ) )
+    def test_78_purge_user( self ):
+        """Testing purging a user account"""
+        self.mark_user_deleted( user_id=testuser4.id )
+        self.purge_user( user_id=testuser4.id )
+        testuser4.refresh()
+        if not testuser4.purged:
+            raise AssertionError( 'User %s was not marked as purged.' % testuser4.email )
+        # Make sure DefaultUserPermissions deleted EXCEPT FOR THE PRIVATE ROLE
+        if len( testuser4.default_permissions ) != 1:
+            raise AssertionError( 'DefaultUserPermissions for user %s were not deleted.' % testuser4.email )
+        for dup in testuser4.default_permissions:
+            role = galaxy.model.Role.get( dup.role_id )
+            if role.type != 'private':
+                raise AssertionError( 'DefaultUserPermissions for user %s are not related with the private role.' % testuser4.email )
+        # Make sure History deleted
+        for history in testuser4.histories:
+            if not history.deleted:
+                raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( testuser4.email, hda.id ) )
+            # Make sure DefaultHistoryPermissions deleted EXCEPT FOR THE PRIVATE ROLE
+            if len( history.default_permissions ) != 1:
+                raise AssertionError( 'DefaultHistoryPermissions for history id %d were not deleted.' % history.id )
+            for dhp in history.default_permissions:
+                role = galaxy.model.Role.get( dhp.role_id )
+                if role.type != 'private':
+                    raise AssertionError( 'DefaultHistoryPermissions for history id %d are not related with the private role.' % history.id )
+            # Make sure HistoryDatasetAssociation deleted
+            for hda in history.datasets:
+                if not hda.deleted:
+                    raise AssertionError( 'HistoryDatasetAssociation id %d was not deleted.' % hda.id )
+                # Make sure Dataset deleted
+                d = galaxy.model.Dataset.filter( galaxy.model.Dataset.table.c.id==hda.dataset_id ).first()
+                if not d.deleted:
+                    raise AssertionError( 'Dataset id %d was not deleted.' % d.id )
+        # Make sure UserGroupAssociations deleted
+        if testuser4.groups:
+            raise AssertionError( 'User %s has active group id %d after their account was marked as purged.' % ( testuser4.email, uga.id ) )
+        # Make sure UserRoleAssociations deleted EXCEPT FOR THE PRIVATE ROLE
+        if len( testuser4.roles ) != 1:
+            raise AssertionError( 'UserRoleAssociations for user %s were not deleted.' % testuser4.email )
+        for ura in testuser4.roles:
+            role = galaxy.model.Role.get( ura.role_id )
+            if role.type != 'private':
+                raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % testuser4.email )
+    def test_81_purge_group( self ):
         """Testing purging a group"""
-        group_id = str( another_test_group.id )
+        group_id = str( group_two.id )
+        self.mark_group_deleted( group_id )
         self.purge_group( group_id )
         # Make sure there are no UserGroupAssociations
         uga = galaxy.model.UserGroupAssociation.filter( galaxy.model.UserGroupAssociation.table.c.group_id == group_id ).all()
@@ -387,10 +587,23 @@ class TestHistory( TwillTestCase ):
         gra = galaxy.model.GroupRoleAssociation.filter( galaxy.model.GroupRoleAssociation.table.c.group_id == group_id ).all()
         if gra:
             raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id )
-    def test_66_purge_role( self ):
+    def test_84_purge_role( self ):
         """Testing purging a role"""
-        role_id = str( another_test_role.id )
+        role_id = str( role_two.id )
+        self.mark_role_deleted( role_id )
         self.purge_role( role_id )
+        # Make sure there are no UserRoleAssociations
+        uras = galaxy.model.UserRoleAssociation.filter( galaxy.model.UserRoleAssociation.table.c.role_id == role_id ).all()
+        if uras:
+            raise AssertionError( "Purging the role did not delete the UserRoleAssociations for role_id '%s'" % role_id )
+        # Make sure there are no DefaultUserPermissions associated with the Role
+        dups = galaxy.model.DefaultUserPermissions.filter( galaxy.model.DefaultUserPermissions.table.c.role_id == role_id ).all()
+        if dups:
+            raise AssertionError( "Purging the role did not delete the DefaultUserPermissions for role_id '%s'" % role_id )
+        # Make sure there are no DefaultHistoryPermissions associated with the Role
+        dhps = galaxy.model.DefaultHistoryPermissions.filter( galaxy.model.DefaultHistoryPermissions.table.c.role_id == role_id ).all()
+        if dhps:
+            raise AssertionError( "Purging the role did not delete the DefaultHistoryPermissions for role_id '%s'" % role_id )
         # Make sure there are no GroupRoleAssociations
         gra = galaxy.model.GroupRoleAssociation.filter( galaxy.model.GroupRoleAssociation.table.c.role_id == role_id ).all()
         if gra:
@@ -399,7 +612,7 @@ class TestHistory( TwillTestCase ):
         adra = galaxy.model.ActionDatasetRoleAssociation.filter( galaxy.model.ActionDatasetRoleAssociation.table.c.role_id == role_id ).all()
         if adra:
             raise AssertionError( "Purging the role did not delete the ActionDatasetRoleAssociations for role_id '%s'" % role_id )
-    def test_69_purge_library( self ):
+    def test_87_purge_library( self ):
         """Testing purging a library"""
         self.purge_library( str( library.id ) )
         # Make sure the library was purged
@@ -417,10 +630,12 @@ class TestHistory( TwillTestCase ):
             for lfda in library_folder.datasets:
                 lfda.refresh()
                 if not lfda.deleted:
-                    raise AssertionError( 'The library_folder_dataset_association id %s named "%s" has not been marked as deleted.' % ( str( lfda.id ), lfda.name ) )
+                    raise AssertionError( 'The library_folder_dataset_association id %s named "%s" has not been marked as deleted.' % \
+                                          ( str( lfda.id ), lfda.name ) )
                 # Make sure all of the datasets have been deleted
                 dataset = lfda.dataset
                 dataset.refresh()
                 if not dataset.deleted:
-                    raise AssertionError( 'The dataset with id "%s" has not been marked as deleted when it should have been.' % str( lfda.dataset.id ) )
+                    raise AssertionError( 'The dataset with id "%s" has not been marked as deleted when it should have been.' % \
+                                          str( lfda.dataset.id ) )
         check_folder( library.root_folder )

universe_wsgi.ini.sample

@@ -141,6 +141,9 @@ use_interactive = True
 # Can users register new accounts?
 #allow_user_creation = True
 
+# Can an admin user delete user accounts?
+#allow_user_deletion = False
+
 # ---- Job Execution --------------------------------------------------------
 
 # Number of concurrent jobs to run (local job runner)