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

11 Aug 2010

      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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