Re: [galaxy-dev] Server error from history view

10 Aug 2010

      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.
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