Bug report : JSONDecodeError
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
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:
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: <blockquote> 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/ </blockquote>
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
<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:
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.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:
<paster.log>
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
<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:
<paster.log>
participants (2)
-
Greg Von Kuster -
Mathieu Bahin