Hi Jeremy,

I was able to reproduce the error on the public Galaxy server. I shared the 
history with you (jeremy.goe...@emory.edu). It's named "export history to file 
bug".

Thanks.
Sarah


----- Original Message -----
From: "Sarah Diehl" <di...@immunbio.mpg.de>
To: "Jeremy Goecks" <jeremy.goe...@emory.edu>
Cc: "galaxy-dev@lists.bx.psu.edu List" <galaxy-dev@lists.bx.psu.edu>
Sent: Wednesday, May 9, 2012 11:40:50 AM
Subject: Re: [galaxy-dev] Error when exporting history to file

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
>>>> ___________________________________________________________
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