On Dec 18, 2012, at 12:05 PM, "Ganote, Carrie L" <cgan...@iu.edu> wrote:

> Hi all,
> 
> Right now I have drmaa running with Torque.  I have a virtual machine with 
> Galaxy installed on it, a filesystem mounted on the virtual machine that 
> holds the dataset info, and a cluster that runs big jobs and also has access 
> to the mounted filesystem.  When running Galaxy as a real user, I get an 
> error because the real user has no pwd listing in the virtual machine.  In 
> this entry there is mention of galaxy_user.username; where is that and how is 
> it populated?  I use kerberos to authenticate through apache.
> 
> Any clues appreciated!
> 
> Here's the dump:
> galaxy.jobs ERROR 2012-12-18 11:29:01,871 (989) Failed to change ownership of 
> /Filesystem/job_working_directory/000/989, making world-writable instead
> Traceback (most recent call last):
>   File "/Prefix/galaxy-dist/lib/galaxy/jobs/__init__.py", line 893, in 
> change_ownership_for_run
>     self._change_ownership( self.user_system_pwent[0], str( 
> self.user_system_pwent[3] ) )
> TypeError: 'NoneType' object is unsubscriptable
> galaxy.jobs.runners.drmaa ERROR 2012-12-18 11:29:01,928 Uncaught exception 
> queueing job
> Traceback (most recent call last):
>   File "/Prefix/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 145, in 
> run_next
>     self.queue_job( obj )
>   File "/Prefix/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 237, in 
> queue_job
>     log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( 
> galaxy_id_tag, job_wrapper.user_system_pwent[0], 
> job_wrapper.user_system_pwent[2] ) )
> TypeError: 'NoneType' object is unsubscriptable
> 
> Carrie Ganote

Hi Carrie,

I run a crontab job every 5 minutes that repopulates the galaxy database with 
the real user names we use instead of the email style user names by updating 
the galaxy_user.username column.

Then, I patch jobs/__init__.py as follows:

#                self.__user_system_pwent = pwd.getpwnam( 
job.user.email.split('@')[0] )
                self.__user_system_pwent = pwd.getpwnam( job.user.username )

Regards,

Alex 

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