I'm making pretty good progress setting up our galaxy server, but have hit a snag. Since moving from an SQLite to a MySQL backend I'm getting an internal server error from the history panel on our galaxy instance. Running the galaxy server from a console gives me the following python traceback:
---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 60795) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 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 437, in handle_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py", line 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in replacement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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.
Having gone back to a stock configuration this error went away. Having reapplied all of my changes one at a time the one which causes the problem is disabling debug mode in universe_wsgi.ini. If I add
debug = False
to the config (removing the original), then I get the error below. If I leave debugging on then the histories work again.
Simon.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of simon andrews (BI) Sent: 30 July 2010 15:44 To: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] Server error from history view
I'm making pretty good progress setting up our galaxy server, but have hit a snag. Since moving from an SQLite to a MySQL backend I'm getting an internal server error from the history panel on our galaxy instance. Running the galaxy server from a console gives me the following python traceback:
---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 60795) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 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 437, in handle_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py", line 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in replacement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Simon,
The problem that was masking real exceptions when debug mode was *off* is now fixed in galaxy-central. Thus, you should see a real exception in the logs if you try again. If you test this, could you let us know what the exception is? It is very odd that you don't see any exception in the UI when debug is on. It might be occurring in an asynchronous 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. Having reapplied all of my changes one at a time the one which causes the problem is disabling debug mode in universe_wsgi.ini. If I add
debug = False
to the config (removing the original), then I get the error below. If I leave debugging on then the histories work again.
Simon.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu ] On Behalf Of simon andrews (BI) Sent: 30 July 2010 15:44 To: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] Server error from history view
I'm making pretty good progress setting up our galaxy server, but have hit a snag. Since moving from an SQLite to a MySQL backend I'm getting an internal server error from the history panel on our galaxy instance. Running the galaxy server from a console gives me the following python traceback:
Exception happened during processing of request from ('127.0.0.1', 60795) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 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 437, in handle_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/ middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/ errormiddleware.py", line 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in replacement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On 4 Aug 2010, at 20:18, James Taylor wrote:
Hi Simon,
The problem that was masking real exceptions when debug mode was *off* is now fixed in galaxy-central. Thus, you should see a real exception in the logs if you try again. If you test this, could you let us know what the exception is?
Since I'm running galaxy-dist at the moment can I selectively pull stuff from galaxy-central or should I set up a parallel install to debug this further?
Cheers
Simon.
It is very odd that you don't see any exception in the UI when debug is on. It might be occurring in an asynchronous 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. Having reapplied all of my changes one at a time the one which causes the problem is disabling debug mode in universe_wsgi.ini. If I add
debug = False
to the config (removing the original), then I get the error below. If I leave debugging on then the histories work again.
Simon.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu ] On Behalf Of simon andrews (BI) Sent: 30 July 2010 15:44 To: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] Server error from history view
I'm making pretty good progress setting up our galaxy server, but have hit a snag. Since moving from an SQLite to a MySQL backend I'm getting an internal server error from the history panel on our galaxy instance. Running the galaxy server from a console gives me the following python traceback:
Exception happened during processing of request from ('127.0.0.1', 60795) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 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 437, in handle_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/ middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/ errormiddleware.py", line 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in replacement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
If you want you can pull changes from central, and when you update dist the revisions will be properly recognized (so you will eventually return to dist automatically as dist moves up). However, it would be much safer to set up a parallel install.
On Aug 5, 2010, at 7:51 AM, simon andrews (BI) wrote:
Since I'm running galaxy-dist at the moment can I selectively pull stuff from galaxy-central or should I set up a parallel install to debug this further?
James,
Sorry to take so long to follow up on this. I've installed an instance of galaxy_central and have replicated the problem I had in galaxy_dist. I get the same internal server error in the history view and the backtrace I get in the console is below.
I hope this is a little more informative in getting to the bottom of this problem. As before, the error only occurrs when debugging is disabled. With debugging enabled the server runs normally.
Simon.
Exception happened during processing of request from ('149.155.147.76', 50098) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in pro cess_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 442, in hand le 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 437, in hand le_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi _execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_central/lib/galaxy/web/framework/middleware/ xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in _ _call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __ca ll__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py", l ine 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in repl acement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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 ----------------------------------------
-----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: 04 August 2010 20:19 To: simon andrews (BI) Cc: galaxy-dev@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* is now fixed in galaxy-central. Thus, you should see a real exception in the logs if you try again. If you test this, could you let us know what the exception is? It is very odd that you don't see any exception in the UI when debug is on. It might be occurring in an asynchronous 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. Having reapplied all of my changes one at a time the one which causes the problem is disabling debug mode in universe_wsgi.ini. If I add
debug = False
to the config (removing the original), then I get the error below. If I leave debugging on then the histories work again.
Simon.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu ] On Behalf Of simon andrews (BI) Sent: 30 July 2010 15:44 To: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] Server error from history view
I'm making pretty good progress setting up our galaxy server, but have hit a snag. Since moving from an SQLite to a MySQL backend I'm getting an internal server error from the history panel on our galaxy instance. Running the galaxy server from a console gives me the following python traceback:
Exception happened during processing of request from ('127.0.0.1', 60795) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 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 437, in handle_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/ middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/ errormiddleware.py", line 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in replacement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
This time I seem to have installed the correct branch and have a proper backtrace. The problem still only occurs when debugging is turned off. The server runs as expected with debugging on.
Simon.
Error - <type 'exceptions.TypeError'>: '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 = 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__.py', line 668 in render template.render_context( context ) File '/data/private/galaxy/galaxy_central/eggs/Mako-0.2.5-py2.6.egg/mako/template.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/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/data/private/galaxy/galaxy_central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/data/private/galaxy/galaxy_central/database/compiled_templates/root/history.mako.py', line 55 in render_body __M_writer(u'\n<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\n\n<html>\n\n<head>\n<title>') File '/data/private/galaxy/galaxy_central/lib/galaxy/web/framework/__init__.py', 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=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-gb,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a8abc406e6f60568a7e933b904c42f358288cd4cedc3eb8af70d77d4726332a17' 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_style/blue' use_interactive: 'True'
WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x56555d0> paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a8abc406e6f60568a7e933b904c42f358288cd4cedc3eb8af70d77d4726332a17'>, 'galaxysession=c6ca0ddb55be603a8abc406e6f60568a7e933b904c42f358288cd4cedc3eb8af70d77d4726332a17') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x55f1f50> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x1dfa790> 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@jamestaylor.org] Sent: 04 August 2010 20:19 To: simon andrews (BI) Cc: galaxy-dev@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* is now fixed in galaxy-central. Thus, you should see a real exception in the logs if you try again. If you test this, could you let us know what the exception is? It is very odd that you don't see any exception in the UI when debug is on. It might be occurring in an asynchronous 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. Having reapplied all of my changes one at a time the one which causes the problem is disabling debug mode in universe_wsgi.ini. If I add
debug = False
to the config (removing the original), then I get the error below. If I leave debugging on then the histories work again.
Simon.
-----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu ] On Behalf Of simon andrews (BI) Sent: 30 July 2010 15:44 To: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] Server error from history view
I'm making pretty good progress setting up our galaxy server, but have hit a snag. Since moving from an SQLite to a MySQL backend I'm getting an internal server error from the history panel on our galaxy instance. Running the galaxy server from a console gives me the following python traceback:
Exception happened during processing of request from ('127.0.0.1', 60795) Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 320, in 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 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 437, in handle_one_request self.wsgi_execute() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 287, in wsgi_execute self.wsgi_start_response) File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, in __call__ return app(environ, start_response) File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/ middleware/xforwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", line 164, in __call__ app_iter = self.application(environ, start_response) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/usr/lib/python2.6/site-packages/paste/exceptions/ errormiddleware.py", line 154, in __call__ exc_info) File "/usr/lib/python2.6/site-packages/paste/translogger.py", line 67, in replacement_start_response return start_response(status, headers) File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 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.
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James Taylor -
simon andrews (BI)