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" 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 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 ----- Mail original -----
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
----- 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 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
----- 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: >
> > http://lists.bx.psu.edu/ >
<paster.log>
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" 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, Sorry for the mistake in the request, but I think that now we spotted the problem more precisely. When I install 'mothur_toolsuite', the 'metadata' field is set with a long JSON value (length > 68,000). We noticed that when suppressing the tool, this value is truncated around a length of 65,500. Only this value was altered in the row. This field's type is BLOB. Maybe this BLOB type is too short for that value but I don't understand why there is no problem when the tool is installed (and the row inserted). Cheers, Mathieu ----- Mail original -----
De: "Greg Von Kuster" <greg@bx.psu.edu> À: "Mathieu Bahin" <mathieu.bahin@irisa.fr> Cc: "Galaxy Dev" <galaxy-dev@bx.psu.edu> Envoyé: Mardi 13 Novembre 2012 14:29:39 Objet: Re: [galaxy-dev] Bug report : JSONDecodeError
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
----- Mail original -----
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
----- 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 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
----- 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" > > > > > >
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> <paster.log>
participants (2)
-
Greg Von Kuster -
Mathieu Bahin