Has anyone actually *tested* mysql as the database backend recently?

It won't work with the current logic in lib/galaxy/model/mapping.py fixed in this revision

(Note the wierd traceback below - looking in build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py on a linux box!?)


[rerla@hg rgalaxy_svn]$ sh run.sh
Architecture appears to be linux-x86_64 UCS4
python path: /home/rerla/rgalaxy_svn/lib:/home/rerla/rgalaxy_svn/eggs/UCS4:/home/rerla/rgalaxy_svn/eggs
python path is: /home/rerla/rgalaxy_svn/scripts, /usr/local/lib/python2.4/site-packages/setuptools-0.6c6-py2.4.egg, /home/rerla/rgalaxy_svn/lib,
/home/rerla/rgalaxy_svn/eggs/UCS4/Cheetah-1.0-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4/bx_python-0.5.0_dev-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/pysqlite-2.3.5_3.4.2_static-py2.4-linux-x86_64.egg,
/home/rerla/rgalaxy_svn/eggs/UCS4/psycopg2-2.0.6_8.2.4_static-py2.4-linux-x86_64.egg, /home/rerla/rgalaxy_svn/eggs/UCS4,
/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/Paste-1.0-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Routes-1.6.3-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/flup-0.5.dev_r2311-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/docutils-0.4-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/elementtree-1.2.6_20050316-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/WebHelpers-0.2-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/simplejson-1.4-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Mako-0.1.8-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/Beaker-0.5-py2.4.egg,
/home/rerla/rgalaxy_svn/eggs/MyghtyUtils-0.52-py2.4.egg, /home/rerla/rgalaxy_svn/eggs/SQLAlchemy-0.3.11-py2.4.egg, /home/rerla/rgalaxy_svn/eggs,
/usr/local/lib/python24.zip, /usr/local/lib/python2.4, /usr/local/lib/python2.4/plat-linux2, /usr/local/lib/python2.4/lib-tk,
/usr/local/lib/python2.4/lib-dynload, /usr/local/lib/python2.4/site-packages, /usr/local/lib/python2.4/site-packages/Numeric,
/usr/local/lib/python2.4/site-packages/PIL
Traceback (most recent call last):
  File "./scripts/paster.py", line 7, in ?
    command.run()
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 76, in run
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 115, in invoke
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/command.py", line 210, in run
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 184, in command
  File "/home/rerla/rgalaxy_svn/eggs/PasteScript-1.0-py2.4.egg/paste/script/serve.py", line 204, in loadapp
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 193, in loadapp
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 214, in loadobj
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 596, in create
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/loadwsgi.py", line 99, in invoke
  File "/home/rerla/rgalaxy_svn/eggs/PasteDeploy-1.0-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call
  File "/home/rerla/rgalaxy_svn/lib/galaxy/web/buildapp.py", line 56, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/home/rerla/rgalaxy_svn/lib/galaxy/app.py", line 23, in __init__
    create_tables = True )
  File "/home/rerla/rgalaxy_svn/lib/galaxy/model/mapping.py", line 297, in init
    metadata.create_all()
  File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1238, in create_all
  File "build/bdist.macosx-10.3-fat/egg/sqlalchemy/schema.py", line 1274, in _get_engine
sqlalchemy.exceptions.InvalidRequestError: This SchemaItem is not connected to any Engine or Connection.

lib/galaxy/model/mapping.py

@@ -273,8 +273,9 @@ def init( file_path, url, **kwargs ):
                 table.columns['create_time'].type = TIMESTAMP()
             if table.columns.has_key( "update_time" ):
                 table.columns['update_time'].type = TIMESTAMP()
+        metadata.connect( url, **kwargs )
     # Connect the metadata to the database. 
-    elif url.startswith( "postgresql:///" ):
+    elif url.startswith( "postgresql:///" ): 
         import psycopg
         try:
             dbconn = url.split('///')
@@ -290,6 +291,7 @@ def init( file_path, url, **kwargs ):
             log.exception( "error connecting to database using connection: '%s'." % url )
             metadata.connect( url, **kwargs )
     else:
+        print '### connecting non-postgresql/mysql url=',url
         metadata.connect( url, **kwargs )
     ## metadata.engine.echo = True
     # Create tables if needed