[Bio-linux-dev] BL-6 Galaxy history export error

[Tim Booth]

Hi Simon,

It looks at first glance like a Galaxy bug, but as you say it could also
be something in the packaging if, say, Galaxy is failing to read or
write a file and not trapping that error correctly.

I'm going to give you a cop-out answer - I have a half-done updated
Galaxy package which I'll get back to working on after I'm done with
Qiime.  Maybe if Galaxy is updated the problem will go away!

Cheers,

TIM

On Wed, 2012-08-15 at 14:59 +0100, Wagstaff, Simon wrote:
> Hi Tim,
> 
> I'm running a local installation of Galaxy on BL-6. On the 'analyze
> data' page, when I go to the history pane and drop down the options
> menu to 'export to file' I get the error pasted below:
> 
> This doesn't happen with all histories - this particular one is a
> large RNASeq workflow (100+ steps).
> 
>  
> 
> I can't see this error on the Galaxy so I've reported it here in the
> first instance in case it's a packaging issue.
> 
>  
> 
> With Thanks,
> 
>  
> 
> Simon
> 
> 
> Error Traceback:
> View as:  Interactive  |  Text  |  XML (full) 
> 
> ⇝AttributeError: 'NoneType' object has no attribute 'hid'
> 
> URL: http://localhost:8080/history/export_archive
> 
> Module weberror.evalexception.middleware:364 in respond        view
> >> app_iter= self.application(environ,detect_start_response)
> 
> Module paste.debug.prints:98 in __call__        view
> >> environ,self.app)
> 
> Module paste.wsgilib:539 in intercept_output        view
> >> app_iter= application(environ,replacement_start_response)
> 
> Module paste.recursive:80 in __call__        view
> >> returnself.application(environ,start_response)
> 
> Module paste.httpexceptions:632 in __call__        view
> >> returnself.application(environ,start_response)
> 
> Module galaxy.web.framework.base:160 in __call__        view
> >> body= method(trans,**kwargs)
> 
> Module galaxy.web.controllers.history:679 in export_archive
> view
> >> history_exp_tool.execute(trans,incoming= params,set_output_hid=
> True)
> 
> Module galaxy.tools:1661 in execute        view
> >> returnself.tool_action.execute(self,trans,incoming=incoming,set_output_hid=set_output_hid,history=history,**kwargs)
> 
> Module galaxy.tools.actions.history_imp_exp:108 in execute        view
> >> include_deleted=incoming['include_deleted'] )
> 
> Module galaxy.tools.imp_exp:419 in setup_job        view
> >> input_datasets= [ assoc.dataset.hidforassocinjob.input_datasets]
> 
> AttributeError: 'NoneType' object has no attribute 'hid'
> 
>  
> 
>  
> 
> *****************************************
> Dr. Simon Wagstaff
> Liverpool School of Tropical Medicine
> Pembroke Place
> Liverpool
> L3 5QA UK
> Tel: +44-151-705-3164
> Fax: +44-151-705-3371
> email: simonw at liv.ac.uk
> 
> http://venoms.liv.ac.uk
> ***************************************** 
> 
>  
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705
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