Re: [galaxy-dev] Think I found a bug

7 Nov 2012

      It should have been fixed yesterday - if a job is running locally and the user cancels it, then the 
job will be stopped immediately. 

Thanks, Juan! 

-Scott 

----- Original Message -----
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Ok, thanks for the response!
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On 6 November 2012 12:50, Dannon Baker < dannonbaker@me.com > wrote:
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Hi Juan,

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Thanks for reporting this, it is indeed a bug. The fix below isn't
quite correct (if there is an external metadata job, we do actually
want to terminate it) but I'll take care of it.

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For reporting bugs in the future, certainly feel free to message
this
list or you can also file an issue using
http://galaxyproject.org/trello

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Thanks!

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-Dannon

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On Nov 6, 2012, at 11:54 AM, Juan González-Vallinas <
juanramongvallinas@gmail.com > wrote:

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Hi galaxy devs,
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We are in the final stages of deploying a new Galaxy instance. We
downloaded the galaxy-dist version a month ago aprox. We realized
that, when launching a job and deleting it in the middle of the
execution (hitting the Delete button in the history bar) will
output the following error in the logger:
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galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job
45:
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galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45
in local runner
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galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in
monitor_step
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Traceback (most recent call last):
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File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py",
line
298, in monitor
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self.monitor_step()
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File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py",
line
341, in monitor_step
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self.dispatcher.stop( job )
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File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py",
line
438, in stop
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self.job_runners[runner_name].stop_job( job )
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File
"/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 180, in stop_job
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if job.get_external_output_metadata():
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AttributeError: 'Job' object has no attribute
'get_external_output_metadata'
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By copying the definition of get_external_output_data from the
Task
class into the Job class, we fixed the problem and now the jobs
are terminated successfully. This is the code I added:
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class Job( object ):
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def get_external_output_metadata( self ):
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return None
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In this file:
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https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f...
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Do you think this fix is correct, or is it a potential problem?
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Also, sorry I sent you through this channel, I couldn't find the
way of reporting this on BitBucket.
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Regards,
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--
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Juan González-Vallinas
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PhD Student
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Regulatory Genomics Group
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Research Unit in Biomedical Informatics (GRIB)
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Universitat Pompeu Fabra (UPF)
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Barcelona
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Spain
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(Currently @ UPenn)
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Re: [galaxy-dev] Think I found a bug

Scott McManus