Right - it is obviously not an XML encoding issue based on your
original e-mail. Sorry about that - still wish I understood why others
have not encountered this or when the regression was introduced.
Regardless - I have committed this patch to galaxy-central. Let me
know if there is anything else I can do.
On Tue, Mar 4, 2014 at 1:53 PM, Eric Badger <bad...@msi.umn.edu> wrote:
> Hey John,
> We're using job_conf.xml, which does not specify an encoding. It doesn't
> seem to be the XML parsing at issue; if you omit the restarting of
> galaxy step, jobs go through just fine. Only when galaxy is restarted
> while the job is running (and destination_params must therefore be
> reloaded) does the issue appear.
> The provided hack does the trick; I'd done up something similar myself
> but felt like I might've been going about it the wrong way. I'll forge
> ahead with it though if it looks to be the right way.
> I'm getting this, by the way, on a freshly cloned galaxy too, not just
> on the existing MSI instances.
> On Tue, Mar 04, 2014 at 01:30:00PM -0600, John Chilton wrote:
>> 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
>> Regardless, does this hack get you anywhere?
>> 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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