Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-08 Thread Nate Coraor 
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 
>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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Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-08 Thread Hans-Rudolf Hotz 

Hi

Don't use the '>' and '<'. That was just a sign to signal where to 
insert what.


Have you also looked at James' reply?


Regards, Hans

On 08/08/2012 01:51 AM, Kenneth Auerbach wrote:

Hi,

Now I'm using this database_connection in my universe_wsgi.ini file:

database_connection =
mysql://:@/?unix_socket=/var/run/mysqld/mysqld.sock


and I still get this:
-
linuxmint galaxy-galaxy-dist-ec29ce8e27a1 # sh run.sh
Traceback (most recent call last):
   File "./scripts/paster.py", line 34, in 
 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://:@/?unix_socket=/var/run/mysqld/mysqld.sock')

-
Any idea what the problem could be?
Thanks.

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Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-07 Thread Kenneth Auerbach 

Hi,

Now I'm using this database_connection in my universe_wsgi.ini file:

database_connection = 
mysql://:@/?unix_socket=/var/run/mysqld/mysqld.sock


and I still get this:
-
linuxmint galaxy-galaxy-dist-ec29ce8e27a1 # sh run.sh
Traceback (most recent call last):
  File "./scripts/paster.py", line 34, in 
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://:@/?unix_socket=/var/run/mysqld/mysqld.sock')

-
Any idea what the problem could be?
Thanks.
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Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-07 Thread James Taylor 
Quoting Kenneth Auerbach (2012-08-07 01:19:56)

> 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

Galaxy is failing to parse your config file. Do you actually have a
leading tab or space before database_connection? It needs to be removed. 

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Re: [galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-07 Thread Hans-Rudolf Hotz 


maybe you need to include username, password and host?

database_connection = 
mysql://:@/?unix_socket=/var/run/mysqld/mysqld.sock


Regards, Hans


On 08/07/2012 03:19 AM, Kenneth 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 
 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')

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