From d294af4866849d3c0e78ddf6c26e141eb258ffd8 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 17 Sep 2014 01:33:17 -0400
Subject: [PATCH] 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 | 17 ++++++++++++-----
 scripts/manage_tools.py         |  2 +-
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index 59f31dcd4c4..0b399ac87fa 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/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' ]
diff --git a/scripts/manage_tools.py b/scripts/manage_tools.py
index 2f390096bd6..8187e75576c 100644
--- a/scripts/manage_tools.py
+++ b/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 )