Hello Zhaozhen,

this is a known problem. The shed_tool_conf.xml got moved along with other
configs into /config folder but unfortunately some tools stored the path
absolutely in the DB. You can use the following script (which you should
find in the Galaxy /scripts folder):
https://github.com/galaxyproject/galaxy/blob/dev/scripts/update_shed_config_path.py
to update your DB to have the correct path to the config.

Sorry for the inconvenience.

Martin, Galaxy Team


On Tue, Apr 7, 2015 at 10:16 AM 孙兆朕 <sunzzn...@163.com> wrote:

> Hi all,
>
> I want to update some of my tool plug-in and some problem shows, even if I
> updated my Galaxy instance to the latest. I suppose it is not related to
> the version of Galaxy.
>
> The problem occured when I used the administrator's panel and update my
> plug-in using the  "Get updates" option. The next page reports that an
> internal Server Error has occured and the update was not successful.  All
> the plug-in updates seems had the same problem.
>
> I checked the logs where I get the following message:
>
> CGI Variables
> -------------
>   CONTENT_LENGTH: '0'
>   HTTP_ACCEPT:
> 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
>   HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
>   HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
>   HTTP_CONNECTION: 'close'
>   HTTP_COOKIE:
> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
>   HTTP_HOST: '222.28.163.110'
>   HTTP_REFERER: '
> http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E
> .'
>   HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36
> (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
>   HTTP_X_FORWARDED_FOR: '222.28.170.89'
>   HTTP_X_FORWARDED_HOST: '222.28.163.110'
>   ORGINAL_HTTP_HOST: '127.0.0.1:8080'
>   ORGINAL_REMOTE_ADDR: '127.0.0.1'
>   PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
>   QUERY_STRING: 'tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> '
>   REMOTE_ADDR: '222.28.170.89'
>   REQUEST_METHOD: 'GET'
>   SERVER_NAME: '127.0.0.1'
>   SERVER_PORT: '8080'
>   SERVER_PROTOCOL: 'HTTP/1.0'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
>   is_api_request: False
>   paste.cookies: (<SimpleCookie:
> galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>,
> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object
> at 0xd888fd0>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0xdcf8650>
>   paste.parsed_querystring: ([('tool_shed_url', '
> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner',
> 'devteam'), ('changeset_revision', 'de11e1a921c4'),
> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')],
> 'tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> ')
>   paste.recursive.forward: <paste.recursive.Forwarder from />
>   paste.recursive.include: <paste.recursive.Includer from />
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
> />
>   paste.recursive.script_name: ''
>   paste.throw_errors: True
>   request_id: 'a12a5604dce911e4a05000215e543aa8'
>   webob._parsed_query_vars: (MultiDict([('tool_shed_url', '
> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner',
> 'devteam'), ('changeset_revision', 'de11e1a921c4'),
> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]),
> 'tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> ')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
> ----------------------------------------
> Exception happened during processing of request from ('127.0.0.1', 39438)
> Traceback (most recent call last):
>   File
> "/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
>     self.finish()
>   File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
>     self.wfile.flush()
>   File "/usr/lib64/python2.6/socket.py", line 303, in flush
>     self._sock.sendall(buffer(data, write_offset, buffer_size))
> error: [Errno 32] Broken pipe
> ----------------------------------------
> 222.28.170.89 - - [07/Apr/2015:13:47:59 +0800] "GET
> /admin_toolshed/update_to_changeset_revision?tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> HTTP/1.0" 500 - "
> http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E.";
> "Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36 (KHTML, like Gecko)
> Chrome/34.0.1847.116 Safari/537.36"
> Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no
> attribute 'get'
> URL:
> http://222.28.163.110/admin_toolshed/update_to_changeset_revision?tool_shed_url=https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
> line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
> line 84 in __call__
>   return self.application(environ, start_response)
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
> line 633 in __call__
>   return self.application(environ, start_response)
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 133 in __call__
>   return self.handle_request( environ, start_response )
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/base.py',
> line 191 in handle_request
>   body = method( trans, **kwargs )
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/web/framework/decorators.py',
> line 87 in decorator
>   return func( self, trans, *args, **kwargs )
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
> line 1954 in update_to_changeset_revision
>   persist=True )
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py',
> line 31 in __init__
>   metadata_dict=metadata_dict, user=None )
> File
> '/share/apps/galaxy/Galaxy_Test2015/galaxy-dist/lib/tool_shed/metadata/metadata_generator.py',
> line 60 in __init__
>   self.metadata_dict = { 'shed_config_filename' :
> self.shed_config_dict.get( 'config_filename', None ) }
> AttributeError: 'NoneType' object has no attribute 'get'
>
>
> CGI Variables
> -------------
>   CONTENT_LENGTH: '0'
>   HTTP_ACCEPT:
> 'text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
>   HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
>   HTTP_ACCEPT_LANGUAGE: 'zh-CN,zh;q=0.8'
>   HTTP_CONNECTION: 'close'
>   HTTP_COOKIE:
> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'
>   HTTP_HOST: '222.28.163.110'
>   HTTP_REFERER: '
> http://222.28.163.110/admin_toolshed/browse_repositories?status=done&message=The+status+has+not+changed+in+the+tool+shed+for+repository+%3Cb%3Eblast_datatypes%3C%2Fb%3E
> .'
>   HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 5.1) AppleWebKit/537.36
> (KHTML, like Gecko) Chrome/34.0.1847.116 Safari/537.36'
>   HTTP_X_FORWARDED_FOR: '222.28.170.89'
>   HTTP_X_FORWARDED_HOST: '222.28.163.110'
>   ORGINAL_HTTP_HOST: '127.0.0.1:8080'
>   ORGINAL_REMOTE_ADDR: '127.0.0.1'
>   PATH_INFO: '/admin_toolshed/update_to_changeset_revision'
>   QUERY_STRING: 'tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> '
>   REMOTE_ADDR: '222.28.170.89'
>   REQUEST_METHOD: 'GET'
>   SERVER_NAME: '127.0.0.1'
>   SERVER_PORT: '8080'
>   SERVER_PROTOCOL: 'HTTP/1.0'
>
>
> WSGI Variables
> --------------
>   application: <paste.recursive.RecursiveMiddleware object at 0xd888510>
>   is_api_request: False
>   paste.cookies: (<SimpleCookie:
> galaxysession='c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424'>,
> 'galaxysession=c6ca0ddb55be603a23b93349895e875da395c1164de6cfc693d5dd79dc3d9d2edcd8d527c7310424')
>   paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>   paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object
> at 0xd888fd0>
>   paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> 0xdcf8650>
>   paste.parsed_querystring: ([('tool_shed_url', '
> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner',
> 'devteam'), ('changeset_revision', 'de11e1a921c4'),
> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')],
> 'tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> ')
>   paste.recursive.forward: <paste.recursive.Forwarder from />
>   paste.recursive.include: <paste.recursive.Includer from />
>   paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from
> />
>   paste.recursive.script_name: ''
>   paste.throw_errors: True
>   request_id: 'a58bb404dce911e481c700215e543aa8'
>   webob._parsed_query_vars: (MultiDict([('tool_shed_url', '
> https://toolshed.g2.bx.psu.edu/'), ('name', 'blast_datatypes'), ('owner',
> 'devteam'), ('changeset_revision', 'de11e1a921c4'),
> ('latest_changeset_revision', '5482a8cd0f36'), ('latest_ctx_rev', '10')]),
> 'tool_shed_url=
> https://toolshed.g2.bx.psu.edu/&name=blast_datatypes&owner=devteam&changeset_revision=de11e1a921c4&latest_changeset_revision=5482a8cd0f36&latest_ctx_rev=10
> ')
>   wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
> Could you please give me some advise to figure out where the problem is
> and how to fix it?
>
> Thanks,
>
>
> Zhaozhen
>
>
>
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