Hi Jeremy,
I'm using galaxy-dist, but it's quite possible that I'm a version or two
behind. I'm not yet able to reproduce the problem on the public server,
but I'm still missing some steps from the input to the problematic
dataset. I'll get back to you if I'm able to reproduce it or if it still
persist when I have updated our Galaxy server.
Thanks for your help!
Best regards,
Sarah
On 05/09/2012 02:09 AM, Jeremy Goecks wrote:
Sarah,
I'm not able to reproduce your issue using galaxy-central. This could mean that
this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist
yet—it appears you are using galaxy-dist—or there's other information needed to
reproduce this issue. A couple more questions:
Are you using galaxy-dist?
Can you reproduce the issue on our public server using the problematic dataset
and/or workflow?
Thanks,
J.
On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5
with flavor: Numerical sort
everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks,
J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 -
"http://galaxy.immunbio.mpg.de/"; "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24)
Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24"
Error -<type
'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at
0x8ba67d0> is not JSON serializable
URL: http://galaxy.immunbio.mpg.de/history/export_archive
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line
80 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in
__call__
body = method( trans, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in
export_archive
history_exp_tool.execute( trans, incoming = params, set_output_hid = True )
File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute
return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid, history=history, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line
106 in execute
include_deleted=incoming[ 'include_deleted' ] )
File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in
setup_job
jobs_attrs_out.write( to_json_string( jobs_attrs,
cls=HistoryDatasetAssociationEncoder ) )
File
'/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py',
line 268 in dumps
File
'/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
line 214 in encode
File
'/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
line 282 in iterencode
File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in
default
return simplejson.JSONEncoder.default( self, obj )
File
'/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
line 190 in default
TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0>
is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty
history and I can still not export this history to a file. This file doesn't
have any special characters in either its name, info or annotation. I can't
find anything special about this file...
Any help is greatly appreciated!
Best regards,
Sarah
___________________________________________________________
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/
___________________________________________________________
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/
___________________________________________________________
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/
