Fixed in galaxy-central changeset cc70c3dcd6f7

Sarah, thanks for taking the time to reproduce on the public server.

Best,
J.

On May 10, 2012, at 10:17 AM, Sarah Diehl wrote:

> 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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> 
> 
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