Re: [galaxy-dev] upload error
Awesome. How is the upload behaving? Are you still having issues with it? M. On Sat, Mar 8, 2014 at 12:20 PM, ruiwang.sz wrote: > Hi John, > > Thanks for the note. Please see inline. > > On Fri, Mar 7, 2014 at 7:18 PM, John Chilton wrote: > >> Hmm... I am not certain but it sounds like the migration script ripped >> something out of your Galaxy tool panel that you did not want it to? This >> is unfortunate - but I don't think it would happen again now that the >> migration process is complete. Some future update to Galaxy may include >> additional migrations scripts but now that macs is out it won't ever be >> migrated again. imagine you can just update your tool_conf.xml file to >> point to your existing macs wrapper you set up manually and you can either >> leave the devteam version of macs in place or uninstall it if you prefer >> your own. Is it not this easy? >> > > Yes that's what I thought, but I was worrying that if I remove devteam > version of macs from the migrated_tool.conf, I might break something > potentially useful for galaxy. Mainly, I try not to manually change things > since that would not be maintainable over time. That's why I was asking how > to handle this properly. It's great to have your confirmation that it works > this way. :-) > > Thanks, > Rui > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] upload error
Hi John, Thanks for the note. Please see inline. On Fri, Mar 7, 2014 at 7:18 PM, John Chilton wrote: > Hmm... I am not certain but it sounds like the migration script ripped > something out of your Galaxy tool panel that you did not want it to? This > is unfortunate - but I don't think it would happen again now that the > migration process is complete. Some future update to Galaxy may include > additional migrations scripts but now that macs is out it won't ever be > migrated again. imagine you can just update your tool_conf.xml file to > point to your existing macs wrapper you set up manually and you can either > leave the devteam version of macs in place or uninstall it if you prefer > your own. Is it not this easy? > Yes that's what I thought, but I was worrying that if I remove devteam version of macs from the migrated_tool.conf, I might break something potentially useful for galaxy. Mainly, I try not to manually change things since that would not be maintainable over time. That's why I was asking how to handle this properly. It's great to have your confirmation that it works this way. :-) Thanks, Rui ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] upload error
Hi Rui,
Are you using the upload tool available in the tool panel under 'Get Data'
> 'Upload file from your computer'? Or the new upload dialog by clicking on
'Load Data'? Could you also please let me know if this error occurs always
or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM, ruiwang.sz wrote:
> Hi Guys,
>
> Our galaxy instance has been in use for a couple years but since Feb 2014
> it started to show us some weird behavior. Recently the upload function
> suddenly stopped working properly. We are getting messages like the
> following. I'm not sure if this only happens to us. If someone has seen
> this before, please give me some hints.
>
> P.S., I searched online and many says that this is because the browser
> does not wait till all the data from the server is received and closes the
> socket. However it happens both in firefox and chrome. I'm wondering if it
> is because galaxy has any change recently but when I do 'hg update stable'
> it reported that it is up to date.
>
> Thanks!
> Rui
>
> Error messages:
>
> Exception happened during processing of request from
> ('127.0.0.1'
>
> Exception happened during processing of request from (, 52259'127.0.0.1',
> 52260)
>
> Traceback (most recent call last):
>
> )
>
> Traceback (most recent call last):
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
>
>
> Exception happened during processing of request from
> (
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
> Exception happened during processing of request from'127.0.0.1' ,
> ('127.0.0.1'52264, 52262
>
> )
>
> Exception happened during processing of request from
> ('127.0.0.1'
>
> , )
>
> Traceback (most recent call last):
>
> Traceback (most recent call last):
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
> Exception happened during processing of request from 52261('127.0.0.1',
>
>
> )Exception happened during processing of request from
>
> Traceback (most recent call last):
>
> 52263('127.0.0.1')
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
> Traceback (most recent call last):
>
> , 52265)
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
> Traceback (most recent call last):
>
> File
> "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
> line 1068, in process_request_in_thread
>
> self.finish_request(request, client_address)
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> self.finish_request(request, client_address)
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> self.finish_request(request, client_address)
>
> self.finish_request(request, client_address)
>
> self.finish_request(request, client_address)
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> self.finish_request(request, client_address)
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> self.finish_request(request, client_address)
>
> File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
>
> 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET
> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root";
> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101
> Firefox/27.0"
>
> self.RequestHandlerClass(request, client_address, self)
>
> self.RequestHandlerClass(request, client_address, self)
>
> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
>
> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
>
> self.RequestHandlerClass(request, client_address, self)
>
> self.RequestHandlerClass(request, client_address, self)
>
> File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
>
> self.finish()
>
> self.RequestHandlerClass(request, client_address, self)
>
> self.finish()
>
> self.RequestHandlerClass(request, client_address, self)
>
> self.finish()
>
> File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
>
>
[galaxy-dev] upload error
Hi Guys,
Our galaxy instance has been in use for a couple years but since Feb 2014
it started to show us some weird behavior. Recently the upload function
suddenly stopped working properly. We are getting messages like the
following. I'm not sure if this only happens to us. If someone has seen
this before, please give me some hints.
P.S., I searched online and many says that this is because the browser does
not wait till all the data from the server is received and closes the
socket. However it happens both in firefox and chrome. I'm wondering if it
is because galaxy has any change recently but when I do 'hg update stable'
it reported that it is up to date.
Thanks!
Rui
Error messages:
Exception happened during processing of request from
('127.0.0.1'
Exception happened during processing of request from (, 52259'127.0.0.1',
52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from
(
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from'127.0.0.1' ,
('127.0.0.1'52264, 52262
)
Exception happened during processing of request from
('127.0.0.1'
, )
Traceback (most recent call last):
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Exception happened during processing of request from 52261('127.0.0.1',
)Exception happened during processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Traceback (most recent call last):
, 52265)
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
self.finish_request(request, client_address)
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101
Firefox/27.0"
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
self.RequestHandlerClass(request, client_address, self)
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__
self.finish()
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finis
Re: [galaxy-dev] upload error in the local instance of galaxy
Brad Langhorst wrote:
> On 10/19/11 3:09 AM, "Amit Anand" wrote:
>
> > Hi,
> >
> > I have just installed a local instance of galaxy. Though I am not too
> > familiar
> > with unix, I preferred a local instance because of large amount of data I
> > have
> > to process. However, I am unable to upload a file more that 2 GB in size,
> > the
> > error log is pased below
> >
> Hi anand:
> It¹s not possible to upoad such big files.
> You need to use FTP or local file import methods to do that.
>
> See:
> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
> ?highlight=%28import%29
>
>
> Brad
> >
> >
You probably also need to set:
debug = False
use_interactive = False
In universe_wsgi.ini
> >
> > 127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index
> > HTTP/1.1"
> > 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1"; "Mozilla/5.0
> > (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2"
> > Debug at: http://127.0.0.1:8080/_debug/view/1319007854
> >
> >
> > Exception happened during processing of request from ('127.0.0.1', 61099)
> > Traceback (most recent call last):
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> > er.py", line 1053, in process_request_in_thread
> > self.finish_request(request, client_address)
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.
> > py", line 322, in finish_request
> > self.RequestHandlerClass(request, client_address, self)
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.
> > py", line 617, in __init__
> > self.handle()
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> > er.py", line 432, in handle
> > BaseHTTPRequestHandler.handle(self)
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServe
> > r.py", line 329, in handle
> > self.handle_one_request()
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> > er.py", line 427, in handle_one_request
> > self.wsgi_execute()
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> > er.py", line 287, in wsgi_execute
> > self.wsgi_start_response)
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.p
> > y", line 202, in __call__
> > return app(environ, start_response)
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xfo
> > rwardedhost.py", line 21, in __call__
> > return self.app( environ, start_response )
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/
> > deploy/config.py", line 164, in __call__
> > app_iter = self.application(environ, start_response)
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/tra
> > nslogger.py", line 68, in __call__
> > return self.application(environ, replacement_start_response)
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e
> > valexception/middleware.py", line 226, in __call__
> > return self.respond(environ, start_response)
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e
> > valexception/middleware.py", line 399, in respond
> > if self.xmlhttp_key in req.params:
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init
> > __.py", line 900, in params
> > params = self.str_params
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init
> > __.py", line 892, in str_params
> > return NestedMultiDict(self.str_GET, self.str_POST)
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init
> > __.py", line 818, in str_POST
> > keep_blank_values=True)
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
> > line
> > 508, in __init__
> > self.read_multi(environ, keep_blank_values, strict_parsing)
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
> > line
> > 632, in read_multi
> > environ, keep_blank_values, strict_parsing)
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
> > line
> > 510, in __init__
> > self.read_single()
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
> > line
> > 647, in read_single
> > self.read_lines()
> > File
> > "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py",
> > line
> > 253, in read_lines
> > self.read_lines_to_outerboundary()
> > File
> > "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
Re: [galaxy-dev] upload error in the local instance of galaxy
On 10/19/11 3:09 AM, "Amit Anand" wrote:
> Hi,
>
> I have just installed a local instance of galaxy. Though I am not too familiar
> with unix, I preferred a local instance because of large amount of data I have
> to process. However, I am unable to upload a file more that 2 GB in size, the
> error log is pased below
>
Hi anand:
It¹s not possible to upoad such big files.
You need to use FTP or local file import methods to do that.
See:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
?highlight=%28import%29
Brad
>
>
>
> 127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1"
> 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1"; "Mozilla/5.0
> (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2"
> Debug at: http://127.0.0.1:8080/_debug/view/1319007854
>
>
> Exception happened during processing of request from ('127.0.0.1', 61099)
> Traceback (most recent call last):
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> er.py", line 1053, in process_request_in_thread
> self.finish_request(request, client_address)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.
> py", line 322, in finish_request
> self.RequestHandlerClass(request, client_address, self)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.
> py", line 617, in __init__
> self.handle()
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> er.py", line 432, in handle
> BaseHTTPRequestHandler.handle(self)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServe
> r.py", line 329, in handle
> self.handle_one_request()
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> er.py", line 427, in handle_one_request
> self.wsgi_execute()
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> er.py", line 287, in wsgi_execute
> self.wsgi_start_response)
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.p
> y", line 202, in __call__
> return app(environ, start_response)
> File
> "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xfo
> rwardedhost.py", line 21, in __call__
> return self.app( environ, start_response )
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/
> deploy/config.py", line 164, in __call__
> app_iter = self.application(environ, start_response)
> File
> "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/tra
> nslogger.py", line 68, in __call__
> return self.application(environ, replacement_start_response)
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e
> valexception/middleware.py", line 226, in __call__
> return self.respond(environ, start_response)
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e
> valexception/middleware.py", line 399, in respond
> if self.xmlhttp_key in req.params:
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init
> __.py", line 900, in params
> params = self.str_params
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init
> __.py", line 892, in str_params
> return NestedMultiDict(self.str_GET, self.str_POST)
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init
> __.py", line 818, in str_POST
> keep_blank_values=True)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line
> 508, in __init__
> self.read_multi(environ, keep_blank_values, strict_parsing)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line
> 632, in read_multi
> environ, keep_blank_values, strict_parsing)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line
> 510, in __init__
> self.read_single()
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line
> 647, in read_single
> self.read_lines()
> File
> "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line
> 253, in read_lines
> self.read_lines_to_outerboundary()
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line
> 697, in read_lines_to_outerboundary
> line = self.fp.readline(1<<16)
> File
> "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
> er.py", line 467, in readline
> data = self.file.readline(self.length - self._consumed)
> File
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py",
> line 409, in readline
> bline = bu
[galaxy-dev] upload error in the local instance of galaxy
Hi,
I have just installed a local instance of galaxy. Though I am not too familiar
with unix, I preferred a local instance because of large amount of data I have
to process. However, I am unable to upload a file more that 2 GB in size, the
error log is pased below
127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1"
500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1"; "Mozilla/5.0
(Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2"
Debug at: http://127.0.0.1:8080/_debug/view/1319007854
Exception happened during processing of request from ('127.0.0.1', 61099)
Traceback (most recent call last):
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py",
line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py",
line 617, in __init__
self.handle()
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 432, in handle
BaseHTTPRequestHandler.handle(self)
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py",
line 329, in handle
self.handle_one_request()
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 427, in handle_one_request
self.wsgi_execute()
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 287, in wsgi_execute
self.wsgi_start_response)
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py",
line 202, in __call__
return app(environ, start_response)
File
"/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py",
line 164, in __call__
app_iter = self.application(environ, start_response)
File
"/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
line 68, in __call__
return self.application(environ, replacement_start_response)
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py",
line 226, in __call__
return self.respond(environ, start_response)
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py",
line 399, in respond
if self.xmlhttp_key in req.params:
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
line 900, in params
params = self.str_params
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
line 818, in str_POST
keep_blank_values=True)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
line 510, in __init__
self.read_single()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
line 647, in read_single
self.read_lines()
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py",
line 253, in read_lines
self.read_lines_to_outerboundary()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py",
line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
File
"/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 467, in readline
data = self.file.readline(self.length - self._consumed)
File
"/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py",
line 409, in readline
bline = buf.readline(size)
OverflowError: long int too large to convert to int
Please help me to fix this, the python version is 2.6.6. Thank you.
Sincerely,
Amit,
Germline biology group
Temasek Life Sciences Laboratory
Singapore
--
Amit Anand
Germ Line Biology Group
Temasek Life Sciences Laboratory
1, Research Link
National University of Singapore
Singapore, 117604
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