Thanks Nate, it's much appreciated.  I'm glad I was able to help out a bit, just sorry I wasn't able to provide a complete fix (though maybe that's for the best if there is a rewrite underway).


Nate Coraor wrote:

Hi Lance,

I'm rewriting much of this code, I should have all of it committed (including this fix) some time this week.  Thanks for figuring out exactly what's going on here.


On Jan 18, 2013, at 5:28 PM, Lance Parsons wrote:

Just an update on this issue. Upon further investigation, it looks like the dynamic job runner code in commit 6f3b4e8 broke this. I haven't been able to parse through everything going on yet to propose a fix, but I've discovered two things:

1) Moving the self.__clear_user_job_count() call outside of the if block, does indeed fix that issue
2) Fixing that leads the __check_user_jobs method to fail since it does not check `self.track_jobs_in_database`, but instead assumes that jobs are in the database, resulting in a different exception regarding invalid columns.

Lance Parsons wrote:

I submitted a trello "ticket" [( regarding this, but wanted to make sure I brought it to someone's attention (it's causing me some queue issues with my instance of galaxy).

When registered_user_job_limit and anonymous_user_job_limit are set in universe.wsgi jobs cannot be run, instead the following error occurs: ERROR 2012-12-04 12:44:51,869 failure running job 22396
Traceback (most recent call last):
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/", line 183, in __monitor_step
    job_state = self.__check_if_ready_to_run( job )
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/", line 253, in __check_if_ready_to_run
    state = self.__check_user_jobs( job )
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/", line 274, in __check_user_jobs
    if not self.user_job_count:
AttributeError: 'JobHandlerQueue' object has no attribute 'user_job_count'

Commenting out the lines for registered_user_job_limit and anonymous_user_job_limit in universe.wsgi allows job to be queue one again.
It looks like this is due to the fact that `self.__clear_user_job_count()` on line 159 of `` is only called when jobs are tracked in the database. If jobs are not tracked in the database (as in my case), the error occurs. Perhaps the fix would be to simply move the call outside the `if` block.

It appears this was broken in the 2012-11-13 revision (73e05bc).

Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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