2:44 p.m.
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.
10:56 a.m.
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(a)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(a)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(a)lists.bx.psu.edu
http://lists.bx.psu.edu/listinfo/galaxy-dev
7:18 p.m.
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(a)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(a)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(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
11:51 a.m.
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(a)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(a)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(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
1:59 p.m.
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?
3:08 p.m.
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(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*
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(a)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(a)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(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
11:56 a.m.
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(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*
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(a)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(a)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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6 comments
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participants (2)
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James Taylor -
simon andrews (BI)