Fix scripts that use galaxy.model.orm.scripts' get_config method to find either config/galaxy.ini or universe_wsgi.ini. For the tool_shed database it'll find either config/tool_shed.ini or tool_shed_wsgi.ini. Also re-fix the unit test.

Database and tool migrations won't work if you use galaxy.ini.sample. Perhaps it should automatically try appending .sample? Or we should really be encouraging people to use the config file properly.

lib/galaxy/model/orm/scripts.py

@@ -18,7 +18,7 @@ import pkg_resources
 
 log = logging.getLogger( __name__ )
 
-DEFAULT_CONFIG_FILE = 'galaxy.ini'
+DEFAULT_CONFIG_FILE = 'config/galaxy.ini'
 DEFAULT_CONFIG_PREFIX = ''
 DEFAULT_DATABASE = 'galaxy'
 
@@ -26,17 +26,20 @@ DATABASE = {
     "galaxy":
         {
             'repo': 'lib/galaxy/model/migrate',
+            'old_config_file': 'universe_wsgi.ini',
             'default_sqlite_file': './database/universe.sqlite',
         },
     "tool_shed":
         {
             'repo':  'lib/galaxy/webapps/tool_shed/model/migrate',
             'config_file': 'config/tool_shed.ini',
+            'old_config_file': 'tool_shed_wsgi.ini',
             'default_sqlite_file': './database/community.sqlite',
         },
     "install":
         {
             'repo': 'lib/galaxy/model/tool_shed_install/migrate',
+            'old_config_file': 'universe_wsgi.ini',
             'config_prefix': 'install_',
             'default_sqlite_file': './database/install.sqlite',
         },
@@ -58,13 +61,16 @@ def require_dialect_egg( db_url ):
         log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
 
 
-def read_config_file_arg( argv, default ):
+def read_config_file_arg( argv, default, old_default ):
     if '-c' in argv:
         pos = argv.index( '-c' )
         argv.pop(pos)
         config_file = argv.pop( pos )
     else:
-        config_file = default
+        if not os.path.exists( default ) and os.path.exists( old_default ):
+            config_file = old_default
+        else:
+            config_file = default
     return config_file
 
 
@@ -74,11 +80,12 @@ def get_config( argv, cwd=None ):
 
     >>> from tempfile import mkdtemp
     >>> config_dir = mkdtemp()
+    >>> os.makedirs(os.path.join(config_dir, 'config'))
     >>> def write_ini(path, property, value):
     ...     p = SafeConfigParser()
     ...     p.add_section('app:main')
     ...     p.set('app:main', property, value)
-    ...     with open(os.path.join(config_dir, path), 'w') as f: p.write(f)
+    ...     with open(os.path.join(config_dir, 'config', path), 'w') as f: p.write(f)
     >>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1')
     >>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir)
     >>> config['repo']
@@ -98,7 +105,7 @@ def get_config( argv, cwd=None ):
         database = 'galaxy'
     database_defaults = DATABASE[ database ]
 
-    config_file = read_config_file_arg( argv, database_defaults.get( 'config_file', DEFAULT_CONFIG_FILE ) )
+    config_file = read_config_file_arg( argv, database_defaults.get( 'config_file', DEFAULT_CONFIG_FILE ), database_defaults.get( 'old_config_file' ) )
     repo = database_defaults[ 'repo' ]
     config_prefix = database_defaults.get( 'config_prefix', DEFAULT_CONFIG_PREFIX )
     default_sqlite_file = database_defaults[ 'default_sqlite_file' ]

scripts/manage_tools.py

@@ -22,7 +22,7 @@ from galaxy.model.orm.scripts import read_config_file_arg
 
 log = logging.getLogger( __name__ )
 
-config_file = read_config_file_arg( sys.argv, 'config/galaxy.ini' )
+config_file = read_config_file_arg( sys.argv, 'config/galaxy.ini', 'universe_wsgi.ini' )
 if not os.path.exists( config_file ):
     print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
     sys.exit( 1 )