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.ba...@irisa.fr>
> À: "Greg Von Kuster" <g...@bx.psu.edu>
> Cc: galaxy-...@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 <d...@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 <dannonba...@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 <dannonba...@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 <dannonba...@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 <d...@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" <g...@bx.psu.edu>
> À: "Mathieu Bahin" <mathieu.ba...@irisa.fr>
> Cc: galaxy-...@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"
> Debug at: http://dev-galaxy.genouest.org/_debug/view/1352713905
> 
> 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.ba...@irisa.fr>
> À: "Greg Von Kuster" <g...@bx.psu.edu>
> Cc: galaxy-...@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" <g...@bx.psu.edu>
> À: "Mathieu Bahin" <mathieu.ba...@irisa.fr>
> Cc: galaxy-...@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>
> 
> 
> 
> 

___________________________________________________________
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/

Reply via email to