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 KusterOn Nov 12, 2012, at 4:56 AM, Mathieu Bahin wrote:And here is the paster...<paster.log>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 : JSONDecodeErrorHi 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 BahinDe: "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 KusterOn Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote:Hi,<07.png>___________________________________________________________
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
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