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&mes....' 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&a...' 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&a...') 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&a...') 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&a... HTTP/1.0" 500 - "http://222.28.163.110/admin_toolshed/browse_repositories?status=done&mes...." "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_... 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&mes....' 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&a...' 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&a...') 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&a...') wsgi process: 'Multithreaded' ------------------------------------------------------------
Could you please give me some advise to figure out where the problem is and how to fix it? Thanks,
Zhaozhen
