Continue flailing on environment variable configuraiton of Galaxy.

Expand variables earlier right in app_factory so middleware, etc... pick up defaults/overrrides.

In particular GALAXY_CONFIG_OVERRIDE_DEBUG should now work properly. GALAXY_CONFIG_DEBUG cannot be used because the sample config template overrides debug's default.

Thanks to Bjoern for the bug report.

lib/galaxy/config.py

@@ -13,7 +13,6 @@ import logging.config
 import ConfigParser
 from datetime import timedelta
 from galaxy.web.formatting import expand_pretty_datetime_format
-from galaxy.util.properties import load_app_properties
 from galaxy.util import string_as_bool
 from galaxy.util import listify
 from galaxy.util.dbkeys import GenomeBuilds
@@ -37,9 +36,6 @@ class Configuration( object ):
     deprecated_options = ( 'database_file', )
 
     def __init__( self, **kwargs ):
-        kwargs = load_app_properties(
-            kwds=kwargs
-        )
         self.config_dict = kwargs
         self.root = kwargs.get( 'root_dir', '.' )
 

lib/galaxy/webapps/galaxy/buildapp.py

@@ -19,6 +19,7 @@ import galaxy.web.framework
 import galaxy.web.framework.webapp
 from galaxy import util
 from galaxy.util import asbool
+from galaxy.util.properties import load_app_properties
 
 import logging
 log = logging.getLogger( __name__ )
@@ -31,6 +32,9 @@ def app_factory( global_conf, **kwargs ):
     """
     Return a wsgi application serving the root object
     """
+    kwargs = load_app_properties(
+        kwds=kwargs
+    )
     # Create the Galaxy application unless passed in
     if 'app' in kwargs:
         app = kwargs.pop( 'app' )