Re: [galaxy-dev] Server error from history view
Yes, definitely using galaxy central. The command I used earlier today was: hg clone http://www.bx.psu.edu/hg/galaxy galaxy_central Do I need to do anything else to pull in your latest additions? Simon. -----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: 10 August 2010 16:14 To: simon andrews (BI) Subject: Re: [galaxy-dev] Server error from history view Hi Simon, it looks like you are still running an older revision there (paste translogger should no longer appear in the stack trace). I may have done something wrong, but just wanted to check first that you are sure this is from galaxy-central. Thanks! On Aug 10, 2010, at 11:08 AM, simon andrews (BI) wrote:
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
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
That url actually tracks galaxy-dist. You can clone central by doing: hg clone http://bitbucket.org/galaxy/galaxy-central Is there a documentation error somewhere pointing to that other url for central? Thanks! -- jt James Taylor Assistant Professor Department of Biology Department of Mathematics & Computer Science Emory University On Aug 10, 2010, at 12:06 PM, simon andrews (BI) wrote:
Yes, definitely using galaxy central. The command I used earlier today was:
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_central
Do I need to do anything else to pull in your latest additions?
Simon.
-----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: 10 August 2010 16:14 To: simon andrews (BI) Subject: Re: [galaxy-dev] Server error from history view
Hi Simon, it looks like you are still running an older revision there (paste translogger should no longer appear in the stack trace). I may have done something wrong, but just wanted to check first that you are sure this is from galaxy-central. Thanks!
On Aug 10, 2010, at 11:08 AM, simon andrews (BI) wrote:
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
_______________________________________________ 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 10 Aug 2010, at 17:14, James Taylor wrote:
That url actually tracks galaxy-dist. You can clone central by doing:
hg clone http://bitbucket.org/galaxy/galaxy-central
Is there a documentation error somewhere pointing to that other url for central? Thanks!
Ah right. It's not a documentation error, just me guessing mercurial syntax from the galaxy-dist example and getting it wrong. I'll do a pull from the correct repository and see what happens. Thanks Simon.
On Aug 10, 2010, at 12:06 PM, simon andrews (BI) wrote:
Yes, definitely using galaxy central. The command I used earlier today was:
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_central
Do I need to do anything else to pull in your latest additions?
Simon.
-----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: 10 August 2010 16:14 To: simon andrews (BI) Subject: Re: [galaxy-dev] Server error from history view
Hi Simon, it looks like you are still running an older revision there (paste translogger should no longer appear in the stack trace). I may have done something wrong, but just wanted to check first that you are sure this is from galaxy-central. Thanks!
On Aug 10, 2010, at 11:08 AM, simon andrews (BI) wrote:
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
_______________________________________________ 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
participants (2)
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James Taylor -
simon andrews (BI)