Hi All,

Some of the developers will know me already but it's my first time being
properly on this list as I'm now working concertedly on Galaxy.  I'm
responsible for Bio-Linux which currently ships with an out-of-date and
slightly flakey galaxy, but I'm working to fix that.

I've hit a problem.  This may or may not be the same as the issue seen
by Luobin Yang.

When uploading a file, no job appears in the right-hand panel.  If I
click refresh I might see a job but it stays in the blue "Dataset is
uploading" state forever.

I'm working on packaging Galaxy for Debian/Ubuntu/Bio-Linux,
specifically Ubuntu 12.04 LTS (python 2.7.3).  To rearrange Galaxy into
something that resembles a Debian package takes a lot of tinkering and
I've patched a few bits of the code, so when uploads started freezing
like this I assumed it was something I'd done and started reverting

But it turns out I can trigger this problem on a pristine download of
the latest server release (20130926 from Bitbucket).  All I do is:

grab and unpack latest version
python ./scripts/fetch_eggs.py -c universe_wsgi.ini.sample
python ./scripts/fetch_eggs.py -c universe_wsgi.ini.sample -e psycopg2
(note - I'm not actually using Posgres in this case and I'm assuming
this is irrelevant but reporting for completenes)
mkdir eggs-cache ; export PYTHON_EGG_CACHE=`pwd`/eggs-cache
(wait for SQLite DB to build)
Ctrl-C, ./run.sh, test, Ctrl-C, ./run.sh, test,  etc...

After a few restarts the problem occurs.  Failing that, it seems I can
make failure more likely by tarring up the whole directory and untarring
it again.  I suspect all this is doing is affecting the disk cache
timing and thus triggering some underlying race condition.

Once the server is started, behaviour is apparently consistent - ie. all
uploads either fail or all work.  Other tasks seem to work, so long as
they don't depend on the stalled uploads, but I've only tried a couple
of these (just a basic "select first lines").

I'm now convinced there is some sort of race condition on start-up that
is responsible.  On my DEB package it fails like this all the time, but
an issue is clearly there in the unmolested code, just rarer.

I don't mind getting into the code to try and debug this but I don't
know where to start, even with the source code docs and my rapidly
increasing Python-fu.  Trying to fathom the interactions between the
threads and the browser and the SQLAlchemy layer I either need a good
outline document or a developer to hold my hand for a bit.  Can someone
help me out with this one?

Thanks in advance,


Tim Booth <tbo...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

+44 1491 69 2705

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