Hey Eric,

Odd - is MSI still using tool runner URLs in universe_wsgi.ini or have
you guys transitioned to job_conf.xml. If you are using a job_conf.xml
file - out of curiosity are you explicitly declaring an XML encoding
at the top of it? Not that this would be the wrong thing to do - I am
just trying to understand why you guys are the first to encounter this
bug.

Regardless, does this hack get you anywhere?

https://gist.github.com/jmchilton/9353654

-John


On Tue, Mar 4, 2014 at 12:46 PM, Eric Badger <bad...@msi.umn.edu> wrote:
> Hi there,
>
> I've run into an issue with the pbs runner involving pbs server name
> strings becoming 'unicode' rather than 'str'. The pbs_python lib can't
> pass unicode strings down to the C library, which results in this
> failure:
>
> https://gist.github.com/anonymous/9352218
>
> The very top line of log output in the above gist is due to a line I added to
> runners/pbs.py:
>
> https://gist.github.com/anonymous/9352101#file-pbs-py-L16
>
> I can reproduce this as follows:
>
> 1. Start a job using pbs runner.
> 2. While the job is still running, restart galaxy.
> 3. Error now appears in the logs.
>
> It seems that this is happening because, when deserializing
> job.destination_params from the database, the strings are converted to
> unicode. The jobs in this state are effectively stuck, since galaxy
> can't connect to check on their status.
>
> I'm not sure where the best place to address this would be; thoughts?
>
> This is on an up to date galaxy-dist with Torque 2.5.13.
>
> Thanks,
> Eric
>
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