From simon.andrews@bbsrc.ac.uk Wed Aug 11 07:57:19 2010 From: "simon andrews (BI)" To: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Server error from history view Date: Wed, 11 Aug 2010 12:56:58 +0100 Message-ID: In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============4097210831447780311==" --===============4097210831447780311== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable This time I seem to have installed the correct branch and have a proper backt= race. The problem still only occurs when debugging is turned off. The serve= r runs as expected with debugging on. Simon. Error - : 'NoneType' object is not callable URL: http://bilin8/history File '/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py', = line 144 in __call__ app_iter =3D self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call= __ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in = __call__ return self.application(environ, start_response) File '/data/private/galaxy/galaxy_central/lib/galaxy/web/framework/base.py', = line 154 in __call__ return body( environ, start_response ) File '/data/private/galaxy/galaxy_central/lib/galaxy/web/framework/__init__.p= y', line 668 in render template.render_context( context ) File '/data/private/galaxy/galaxy_central/eggs/Mako-0.2.5-py2.6.egg/mako/temp= late.py', line 146 in render_context runtime._render_context(self, self.callable_, context, *args, **kwargs) File '/data/private/galaxy/galaxy_central/eggs/Mako-0.2.5-py2.6.egg/mako/runt= ime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=3Dargs, kwargs=3Dkwargs) File '/data/private/galaxy/galaxy_central/eggs/Mako-0.2.5-py2.6.egg/mako/runt= ime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/data/private/galaxy/galaxy_central/database/compiled_templates/root/hi= story.mako.py', line 55 in render_body __M_writer(u'\n\n\n\n\n\n') File '/data/private/galaxy/galaxy_central/lib/galaxy/web/framework/__init__.p= y', line 665 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=3D0.9,*/*;q= =3D0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=3D0.7,*;q=3D0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-gb,en;q=3D0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=3Dc6ca0ddb55be603a8abc406e6f60568a7e933b904c42f= 358288cd4cedc3eb8af70d77d4726332a17' HTTP_HOST: 'bilin8' HTTP_REFERER: 'http://bilin8/' HTTP_USER_AGENT: 'Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2.= 8) Gecko/20100722 Firefox/3.6.8' HTTP_X_FORWARDED_FOR: '149.155.147.76' HTTP_X_FORWARDED_HOST: 'bilin8' HTTP_X_FORWARDED_SERVER: 'bilin8.babraham.bbsrc.ac.uk' ORGINAL_HTTP_HOST: 'bilin8.babraham.bbsrc.ac.uk:8080' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/history' REMOTE_ADDR: '149.155.147.76' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- __file__: '/data/private/galaxy/galaxy_central/universe_wsgi.ini' debug: 'False' here: '/data/private/galaxy/galaxy_central' static_cache_time: '360' static_dir: '/data/private/galaxy/galaxy_central/static/' static_enabled: 'True' static_favicon_dir: '/data/private/galaxy/galaxy_central/static/favicon.ico' static_images_dir: '/data/private/galaxy/galaxy_central/static/images' static_scripts_dir: '/data/private/galaxy/galaxy_central/static/scripts/' static_style_dir: '/data/private/galaxy/galaxy_central/static/june_2007_sty= le/blue' use_interactive: 'True' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x56555d0> paste.cookies: (<SimpleCookie: galaxysession=3D'c6ca0ddb55be603a8abc406e6f6= 0568a7e933b904c42f358288cd4cedc3eb8af70d77d4726332a17'>, 'galaxysession=3Dc6c= a0ddb55be603a8abc406e6f60568a7e933b904c42f358288cd4cedc3eb8af70d77d4726332a17= ') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at = 0x55f1f50> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x1dfa= 790> 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 webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded' ------------------------------------------------------------ -----Original Message----- From: James Taylor [mailto:james(a)jamestaylor.org]=20 Sent: 04 August 2010 20:19 To: simon andrews (BI) Cc: galaxy-dev(a)bx.psu.edu Subject: Re: [galaxy-dev] Server error from history view Hi Simon, The problem that was masking real exceptions when debug mode was *off* =20 is now fixed in galaxy-central. Thus, you should see a real exception =20 in the logs if you try again. If you test this, could you let us know =20 what the exception is? It is very odd that you don't see any exception =20 in the UI when debug is on. It might be occurring in an asynchronous =20 request that is not visible or something else unusual. Thanks James -- jt James Taylor Assistant Professor Department of Biology Department of Mathematics & Computer Science Emory University On Aug 3, 2010, at 6:56 AM, simon andrews (BI) wrote: > Having gone back to a stock configuration this error went away. =20 > Having reapplied all of my changes one at a time the one which =20 > causes the problem is disabling debug mode in universe_wsgi.ini. If =20 > I add > > debug =3D False > > to the config (removing the original), then I get the error below. =20 > If I leave debugging on then the histories work again. > > Simon. > > -----Original Message----- > From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces(a)li= sts.bx.psu.edu=20 > ] On Behalf Of simon andrews (BI) > Sent: 30 July 2010 15:44 > To: galaxy-dev(a)bx.psu.edu > Subject: [galaxy-dev] Server error from history view > > I'm making pretty good progress setting up our galaxy server, but =20 > have hit a snag. Since moving from an SQLite to a MySQL backend I'm =20 > getting an internal server error from the history panel on our =20 > galaxy instance. Running the galaxy server from a console gives me =20 > the following python traceback: > > ---------------------------------------- > Exception happened during processing of request from ('127.0.0.1', =20 > 60795) > Traceback (most recent call last): > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line =20 > 1068, in process_request_in_thread > self.finish_request(request, client_address) > File "/usr/lib64/python2.6/SocketServer.py", line 320, in =20 > finish_request > self.RequestHandlerClass(request, client_address, self) > File "/usr/lib64/python2.6/SocketServer.py", line 615, in __init__ > self.handle() > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line =20 > 442, in handle > BaseHTTPRequestHandler.handle(self) > File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle > self.handle_one_request() > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line =20 > 437, in handle_one_request > self.wsgi_execute() > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line =20 > 287, in wsgi_execute > self.wsgi_start_response) > File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, =20 > in __call__ > return app(environ, start_response) > File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/=20 > middleware/xforwardedhost.py", line 21, in __call__ > return self.app( environ, start_response ) > File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", =20 > line 164, in __call__ > app_iter =3D self.application(environ, start_response) > File "/usr/lib/python2.6/site-packages/paste/translogger.py", line =20 > 68, in __call__ > return self.application(environ, replacement_start_response) > File "/usr/lib/python2.6/site-packages/paste/exceptions/=20 > errormiddleware.py", line 154, in __call__ > exc_info) > File "/usr/lib/python2.6/site-packages/paste/translogger.py", line =20 > 67, in replacement_start_response > return start_response(status, headers) > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line =20 > 166, in wsgi_start_response > assert 0, "Attempt to set headers a second time w/o an exc_info" > AssertionError: Attempt to set headers a second time w/o an exc_info > ---------------------------------------- > > Any ideas? > > Thanks > > Simon. > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev --===============4097210831447780311==--