Some Fixes for setting permisions on the current history when users login, and some preparation for the database update script.

lib/galaxy/app.py

@@ -26,7 +26,7 @@ class UniverseApplication( object ):
         self.model = galaxy.model.mapping.init( self.config.file_path,
                                                 db_url,
                                                 self.config.database_engine_options,
-                                                create_tables = True )
+                                                create_tables = self.config.database_create_tables )
         # Initialize the tools
         self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )
         #Load datatype converters

lib/galaxy/config.py

@@ -27,6 +27,7 @@ class Configuration( object ):
         self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root )
         self.database_connection =  kwargs.get( "database_connection", False )
         self.database_engine_options = get_database_engine_options( kwargs )                        
+        self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) )
         # Where dataset files are stored
         self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
         self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )

lib/galaxy/model/mapping.py

@@ -640,11 +640,8 @@ def db_next_hid( self ):
         raise
 
 History._next_hid = db_next_hid
-    
-def init( file_path, url, engine_options={}, create_tables=False ):
-    """Connect mappings to the database"""
-    # Connect dataset to the file path
-    Dataset.file_path = file_path
+
+def load_egg_for_url( url ):
     # Load the appropriate db module
     dialect = (url.split(':', 1))[0]
     try:
@@ -658,6 +655,13 @@ def init( file_path, url, engine_options={}, create_tables=False ):
     except KeyError:
         # Let this go, it could possibly work with db's we don't support
         log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
+
+def init( file_path, url, engine_options={}, create_tables=False ):
+    """Connect mappings to the database"""
+    # Connect dataset to the file path
+    Dataset.file_path = file_path
+    # Load the appropriate db module
+    load_egg_for_url( url )
     # Create the database engine
     engine = create_engine( url, **engine_options )
     # Connect the metadata to the database.
@@ -680,14 +684,11 @@ def init( file_path, url, engine_options={}, create_tables=False ):
     #load local galaxy security policy
     result.security_agent = GalaxyRBACAgent( result )
     # Create private roles if necessary.
-    if not result.Role.query().all():
-        for user in result.User.query().all():
-            role = Role( name = user.email, description = 'Private Role for ' + user.email, type = 'private' )
-            role.flush()
-            ura = UserRoleAssociation( user = user, role = role )
-            ura.flush()
-            dup = DefaultUserPermissions( user = user, action = result.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS.action, role = role )
-            dup.flush()
+    if create_tables: #This should be moved to the external update script
+        if not result.Role.query().all():
+            for user in result.User.query().all():
+                result.security_agent.create_private_user_role( user )
+                result.security_agent.user_set_default_permissions( user, history=True, dataset=True, bypass_manage_permission=True )
     return result
     
 def get_suite():

lib/galaxy/security/__init__.py

@@ -165,7 +165,7 @@ class GalaxyRBACAgent( RBACAgent ):
             else:
                 return None
         return role
-    def user_set_default_permissions( self, user, permissions = {}, history=False, dataset=False ):
+    def user_set_default_permissions( self, user, permissions = {}, history=False, dataset=False, bypass_manage_permission=False ):
         if user is None:
             return None
         if not permissions:
@@ -183,7 +183,7 @@ class GalaxyRBACAgent( RBACAgent ):
                 dup.flush()
         if history:
             for history in user.active_histories:
-                self.history_set_default_permissions( history, permissions=permissions, dataset=dataset )
+                self.history_set_default_permissions( history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission )
     def user_get_default_permissions( self, user ):
         perms = {}
         for action in self.get_actions():

lib/galaxy/web/controllers/user.py

@@ -157,7 +157,7 @@ class User( BaseController ):
                 user.flush()
                 trans.app.security_agent.create_private_user_role( user )
                 trans.handle_user_login( user )
-                trans.app.security_agent.user_set_default_permissions( user, history=True, dataset=True )
+                #trans.app.security_agent.user_set_default_permissions( user, history=True, dataset=True, bypass_manage_permission=True ) #This is taken care of by trans.handle_user_login
                 trans.log_event( "User created a new account" )
                 trans.log_event( "User logged in" )
                 #subscribe user to email list

lib/galaxy/web/framework/__init__.py

@@ -343,7 +343,7 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         if history.user is None:
             history.user = user
         self.galaxy_session.current_history = history
-        self.app.security_agent.history_set_default_permissions( history, dataset=True )
+        self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True )
         self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] )
         self.__update_session_cookie()
     def handle_user_logout( self ):

scripts/get_platforms.py

@@ -1,9 +1,12 @@
 #!/usr/bin/env python
 
-import sys
+import sys, os
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
-from eggs import get_full_platform, get_noplatform
+lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) )
+sys.path.append( lib )
+
+from galaxy.eggs import get_platform, get_noplatform
 print get_noplatform()
-print get_full_platform()
+print get_platform( platform=True )