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 ----- Mail original -----
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" 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...
----- Mail original -----
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
----- Mail original -----
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
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