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" <g...@bx.psu.edu>
> À: "Mathieu Bahin" <mathieu.ba...@irisa.fr>
> Cc: "Galaxy Dev" <galaxy-...@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.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
> >
>
> > > ----- Mail original -----
> >
>
> > > > 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...
> > > >
> > >
> >
>
> > > > > ----- Mail original -----
> > > >
> > >
> >
>
> > > > > > 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
> > > > >
> > > >
> > >
> >
>
> > > > > > ----- Mail original -----
> > > > >
> > > >
> > >
> >
>
> > > > > > > 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>
> > > >
> > >
> >
>___________________________________________________________
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