Hi Zhaozhen, the --config_file argument needs to point to galaxy.ini config so the script can load the database.
Galaxy continues to support Python 2.6 and 2.7, I am sorry that this script required 2.7 (or you could `pip install argparse`) - we will look into improving it. Martin, Galaxy Team On Wed, Apr 8, 2015 at 4:09 AM 孙兆朕 <sunzzn...@163.com> wrote: > Hi Martin, > > Thanks for the advise. It helped a lot for me to figure out where the > problem is. However, there were still error messages there. > I tried to run the update_shed_config_path.py script under the /script > folder. At first it says there was no module named argparse, then I found > out it was the python version problem, which required python 2.7+. Then I > updated my python. Then there was another error said there was no module > named galaxy.model.tool_shed_install. Then I tried harder, and found out > that it was the path problem. I figured out the sys path was in the above > folder. Then I copied and pasted the update_shed_config_path.py to the > parent folder and seemed solved the problem. Then I run > the update_shed_config_path.py and the command somehow run for a while, > with the error message No module named _sqlite3. It must be the DB > versions and plug-ins, then I fixed the DB. Then finally there came the > following message: > > usage: update_shed_config_path.py [-h] --config_file CONFIG_FILE --from > BAD_FILENAME --to GOOD_FILENAME [--force] > update_shed_config_path.py: error: argument --config_file is required > > I run the command line in: python2.7 update_shed_config_path.py > I wonder if I need some more input for the command line or something? > By the way, I hope there would be some advise for the new Galaxy > administrtators to know their Python should be 2.7+ and file path issues. > When I started to deploy Galaxy last year, the requirement in the web page > was Python 2.5 or something lower than 2.6 I used. I think that message > need to be updated as well. > Thanks in advance, > > Yours, > > Zhaozhen > > > > > argparse > > > At 2015-04-07 22:43:50, "Martin Čech" <mar...@bx.psu.edu> wrote: > > 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 >> >> >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >
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