Hi Mathieu,

As I mentioned in my previous email, here is the select that is needed.  I need to see the values of all columns for the mothur_toolsuite row.

select * from tool_shed_repository where name = 'mothur_toolsuite';


On Nov 13, 2012, at 7:33 AM, Mathieu Bahin wrote:

Hi Greg !

Running the sql command, I got that (actually, it's 'mothur_toolsuite' so I change a bit the request but it is not deleted):

mysql> select name from tool_shed_repository;

+--------------------+
| name                 |
+--------------------+
| mothur_toolsuite   |
| protk              |
| roche454_toolsuite |
| toolfactory        |
+--------------------+
4 rows in set (0.00 sec)


The mothur entries in 'shed_tool_conf.xml' file and the mothur repository are still existing.

Cheers,
Mathieu Bahin



De: "Greg Von Kuster" <greg@bx.psu.edu>
À: "Mathieu Bahin" <mathieu.bahin@irisa.fr>
Cc: "Galaxy Dev" <galaxy-dev@bx.psu.edu>
Envoyé: Lundi 12 Novembre 2012 22:18:05
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError

Hi Mathieu,

It's pretty difficult to tell you where to start looking within your environment for the cause of the problem.

You mentioned that you attempted to uninstall the repository name mothur from you local Galaxy instance, and that action produced this problem.  What is the result of running the following sql command in your db?

select * from tool_shed_repository where name = 'mothur';

Also, have the entries for the mothur tools been eliminated from your shed_tool_conf.xml file?

How about the install directory for the mothur repository?  Has is been removed from disk?

Greg Von Kuster


On Nov 12, 2012, at 10:57 AM, Mathieu Bahin wrote:

Hi Greg,

I kind of forgot a maybe interesting information. We found this message at the end of the paster.log :

Exception happened during processing of request from ('127.0.0.1', 55428)
Traceback (most recent call last):
  File "/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1053, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 323, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 641, in __init__
    self.finish()
  File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 694, in finish
    self.wfile.flush()
  File "/local/python/2.7-bis/lib/python2.7/socket.py", line 301, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe

Cheers,
Mathieu

De: "Mathieu Bahin" <mathieu.bahin@irisa.fr>
À: "Greg Von Kuster" <greg@bx.psu.edu>
Cc: galaxy-dev@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 15:54:35
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError

Hi again,

I got this with "hg heads" :

changeset:   7986:12fcd068b12e
tag:         tip
user:        Daniel Blankenberg <dan@bx.psu.edu>
date:        Thu Oct 18 11:22:12 2012 -0400
summary:     Do not hide failed datasets with HideDatasetAction post job action.

changeset:   7152:ffc20445b35e
branch:      split_blast2
parent:      7058:22f545c0d412
user:        Dannon Baker <dannonbaker@me.com>
date:        Wed Apr 18 07:59:38 2012 -0400
summary:     Branch close.

changeset:   7151:c94957ac5454
branch:      workflow_import_menu_api
parent:      6834:1a3d01b09f7a
user:        Dannon Baker <dannonbaker@me.com>
date:        Wed Mar 21 09:50:44 2012 -0400
summary:     Branch close for pull request.

changeset:   7150:314a10ae112d
branch:      split_blast
parent:      6757:ebf65c0b1e26
user:        Dannon Baker <dannonbaker@me.com>
date:        Tue Feb 28 12:32:54 2012 -0500
summary:     Close split_blast branch

changeset:   7149:1327f2219423
branch:      meme_requirement_on_fimo
parent:      6662:8ba74c17e809
user:        Daniel Blankenberg <dan@bx.psu.edu>
date:        Fri Feb 03 11:15:29 2012 -0500
summary:     close branch
--------------------------------------------------------

And I got this with the debug at :

JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 65522)

URL: http://dev-galaxy.genouest.org/admin_toolshed/browse_repositories
File '/opt/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__
  environ, self.app)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output
  app_iter = application(environ, replacement_start_response)
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__
  return self.app( environ, start_response )
File '/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__
  body = method( trans, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 203 in decorator
  return func( self, trans, *args, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 381 in browse_repositories
  return self.installed_repository_grid( trans, **kwd )
File '/opt/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 277 in __call__
  kwargs=kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 765 in fill_template
  return self.fill_template_mako( filename, **kwargs )
File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 776 in fill_template_mako
  return template.render( **data )
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render
  return runtime._render(self, self.callable_, args, data)
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render
  **_kwargs_for_callable(callable_, data))
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context
  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File '/opt/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template
  callable_(context, *args, **kwargs)
File '/opt/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body
  __M_writer(unicode(next.body()))
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 119 in render_body
  __M_writer(unicode(self.grid_body( grid )))
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 784 in render_grid_body
  __M_writer(unicode(self.make_grid( grid )))
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 813 in render_make_grid
  __M_writer(unicode(self.render_grid_table( grid, show_item_checkboxes )))
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 762 in render_render_grid_table
  __M_writer(unicode(render_grid_table_body_contents( grid, show_item_checkboxes )))
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 658 in render_grid_table_body_contents
  return render_render_grid_table_body_contents(context,grid,show_item_checkboxes)
File '/opt/galaxy-dist/database/compiled_templates/grid_base.mako.py', line 281 in render_render_grid_table_body_contents
  for i, item in enumerate( query ):
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1422 in instances
  rows = [process[0](context, row) for row in fetch]
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 2032 in main
  return _instance(row, None)
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py', line 1729 in _instance
  populate_state(state, dict_, row, isnew, only_load_props)
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/mapper.py', line 1614 in populate_state
  populator(state, dict_, row, isnew=isnew, **flags)
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/strategies.py', line 120 in new_execute
  dict_[key] = row[col]
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 1348 in __getitem__
  return self.__parent._get_col(self.__row, key)
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 1620 in _get_col
  return processor(row[index])
File '/opt/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/types.py', line 284 in process
  return self.process_result_value(impl_processor(value), dialect)
File '/opt/galaxy-dist/lib/galaxy/model/custom_types.py', line 50 in process_result_value
  return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) )
File '/opt/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 402 in decode
File '/opt/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/decoder.py', line 418 in raw_decode
JSONDecodeError: Unterminated string starting at: line 1 column 65522 (char 65522)
----------------------------------------------

I hope this can help you find the problem !

Thanks,
Mathieu




De: "Greg Von Kuster" <greg@bx.psu.edu>
À: "Mathieu Bahin" <mathieu.bahin@irisa.fr>
Cc: galaxy-dev@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 12:33:10
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError

Hi Matthiew,

Can you clarify the version of Galaxy you are using?  What is the result of typing "hg heads" in your Galaxy installation directory?

ALso, I noticed the following in your paster log:

----------------------------------------
131.254.16.26 - - [12/Nov/2012:10:52:26 +0200] "GET /admin_toolshed/browse_repositories HTTP/1.1" 500 - "http://dev-galaxy.genouest.org/admin" "Mozilla/5.0 (X11; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0"

Directing your browser to the URL in the "Debug at" address will provide a stack trace of the exception thrown due to the problem.  What is this this complete stack trace?

Thanks,

Greg Von Kuster


On Nov 12, 2012, at 4:56 AM, Mathieu Bahin wrote:

And here is the paster...

De: "Mathieu Bahin" <mathieu.bahin@irisa.fr>
À: "Greg Von Kuster" <greg@bx.psu.edu>
Cc: galaxy-dev@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 10:54:21
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError

Hi Greg !

Thanks for the quick answer.

I am using the 7720 parent version but I keep it up-to-date without any problems.
Enclosed you'll find the 'paster.log' file generated when I start Galaxy and try to access the manage installed tool shed repositories page.

Cheers,
Mathieu Bahin

De: "Greg Von Kuster" <greg@bx.psu.edu>
À: "Mathieu Bahin" <mathieu.bahin@irisa.fr>
Cc: galaxy-dev@bx.psu.edu
Envoyé: Vendredi 9 Novembre 2012 19:28:09
Objet: Re: [galaxy-dev] Bug report : JSONDecodeError

Hello Mathieu,

What version of Galaxy are you running?  Also, I cannot read the stack trace from your pasted image, so can you send a text version of the complete stack trace from your paster log?

Thanks,

Greg Von Kuster



On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote:

Hi,

I am using my own Galaxy instance and I had a problem removing a tool from the tool shed : mothur.
The installation was ok and I the mothur tool running without any problem. But when I tried to uninstall the tool, I get an error (screenshot enclosed). And I get the same every time I try to go on the 'Manage tool shed repositories' in the Admin panel.

I have tried to rebuilt the eggs and to restart Galaxy basically. Actually, I don't really understand the error message.

Cheers,
Mathieu Bahin
<07.png>___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/



<paster.log>