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 -----
> Ok, thanks for the response!
> On 6 November 2012 12:50, Dannon Baker < dannonba...@me.com > wrote:
> > Hi Juan,
>
> > 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.
>
> > 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
>
> > Thanks!
>
> > -Dannon
>
> > On Nov 6, 2012, at 11:54 AM, Juan González-Vallinas <
> > juanramongvalli...@gmail.com > wrote:
>
> > > Hi galaxy devs,
>
> > >
>
> > > 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:
>
> > >
>
> > > galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job
> > > 45:
>
> > > galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45
> > > in local runner
>
> > > galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in
> > > monitor_step
>
> > > Traceback (most recent call last):
>
> > > File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py",
> > > line
> > > 298, in monitor
>
> > > self.monitor_step()
>
> > > File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py",
> > > line
> > > 341, in monitor_step
>
> > > self.dispatcher.stop( job )
>
> > > File "/usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py",
> > > line
> > > 438, in stop
>
> > > self.job_runners[runner_name].stop_job( job )
>
> > > File
> > > "/usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py",
> > > line 180, in stop_job
>
> > > if job.get_external_output_metadata():
>
> > > AttributeError: 'Job' object has no attribute
> > > 'get_external_output_metadata'
>
> > >
>
> > > 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:
>
> > >
>
> > > class Job( object ):
>
> > >
>
> > > ...
>
> > > def get_external_output_metadata( self ):
>
> > > return None
>
> > > ...
>
> > >
>
> > > In this file:
>
> > >
>
> > > https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f6a8ba122d253/lib/galaxy/__init__.py?at=default
>
> > >
>
> > > Do you think this fix is correct, or is it a potential problem?
>
> > >
>
> > > Also, sorry I sent you through this channel, I couldn't find the
> > > way of reporting this on BitBucket.
>
> > >
>
> > > Regards,
>
> > >
>
> > > --
>
> > > Juan González-Vallinas
>
> > > PhD Student
>
> > > Regulatory Genomics Group
>
> > > Research Unit in Biomedical Informatics (GRIB)
>
> > > Universitat Pompeu Fabra (UPF)
>
> > > Barcelona
>
> > > Spain
>
> > > (Currently @ UPenn)
>
> > >
>
> > > ___________________________________________________________
>
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>
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>
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>
> > >
>
> > > http://lists.bx.psu.edu/
>
> ___________________________________________________________
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