Thanks, Peter! I'll get to it this afternoon EDT.

-Scott

----- Original Message -----
> On Thu, Oct 18, 2012 at 5:19 PM, Scott McManus
> <scottmcma...@gatech.edu> wrote:
> >
> > Hey Peter-
> >
> > Thanks - I'll look into it. If you're able to reproduce the problem
> > easily
> > and wouldn't mind crafting a pull request, then it would be much
> > appreciated. Otherwise I'll put this on my to-do list to be done
> > soon.
> > I or someone else may want to revisit the exception handling to
> > prevent
> > that from happening.
> >
> > Thanks!
> >
> > -Scott
> 
> OK then:
> https://bitbucket.org/galaxy/galaxy-central/pull-request/78/avoid-stall-when-merging-zero-files-fao/diff
> 
> I can explain what was happening: We had a mount problem. The
> Galaxy server could talk to SGE and submit jobs, but when the
> jobs came to run the mount providing their home directory and
> the Galaxy file system was down, so they failed. Naturally this
> meant Galaxy got no output files back.
> 
> Reading the code, you deliberately attempt to merge any files
> present (e.g. if 9 out of 10 come back). That does make sense
> as it could be instructive (as long as it is flagged as an error,
> which doesn't seem to be happening).
> 
> I think getting zero files back from the split-jobs ought to be an
> error condition. In fact, failing to get all the expected sub-files
> back should also be an error condition (although it is still nice
> to do the merge so the user can see the partial output).
> 
> I think a little re-factoring might be needed to treat these
> explicitly as errors.
> 
> Regards,
> 
> Peter
> 
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