On Aug 6, 2012, at 9:17 PM, Kenneth R. Auerbach wrote:

> Hello,
> 
> Galaxy runs fine 'out of the box' with the default universe_wsgi.ini 
> initialization file. But when I change the "database_connection" statement to 
> connect to my MySql database, I get the errors below. Can you please tell 
> what the problem is?  Thanks!
> 
> -Wolf.
> 
> 
> Modification to universe_wsgi.ini file:
> ------------------------------------
> #database_connection = 
> sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
> 
> database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock
> -------------------------------------
> 
> Then when I type "sh run.sh" I get this:
> 
> ---------
> wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh
> Traceback (most recent call last):
>  File "./scripts/paster.py", line 34, in <module>
>    command.run()
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
>  line 84, in run
>    invoke(command, command_name, options, args[1:])
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
>  line 123, in invoke
>    exit_code = runner.run(args)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
>  line 218, in run
>    result = self.command()
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
>  line 276, in command
>    relative_to=base, global_conf=vars)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
>  line 313, in loadapp
>    **kw)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 204, in loadapp
>    return loadobj(APP, uri, name=name, **kw)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 224, in loadobj
>    global_conf=global_conf)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 248, in loadcontext
>    global_conf=global_conf)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 278, in _loadconfig
>    return loader.get_context(object_type, name, global_conf)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 413, in get_context
>    section)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 458, in _context_from_explicit
>    value = import_string(found_expr)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
>  line 18, in import_string
>    return pkg_resources.EntryPoint.parse("x="+s).load(False)
>  File 
> "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py", 
> line 1997, in parse
>    src
> ValueError: ("EntryPoint must be in 'name=module:attrs [extras]' format", 
> 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = 
> mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock')

Hi Wolf,

It looks like the 'paste.app_factory' option was somehow messed up.  Can you 
double check that it looks like:

paste.app_factory = galaxy.web.buildapp:app_factory

And is the only 'paste.app_factory' entry in your config file?

--nate

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