Ok, thanks for the response!
On 6 November 2012 12:50, Dannon Baker dannonbaker@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 < juanramongvallinas@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/9d6a61f060d359a0289b3163990f...
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)
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: