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,