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 I'm responsible for Bio-Linux which currently ships with an out-of-date and slightly flakey galaxy, but I'm working to fix that.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 patches. 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 ./run.sh (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 -- 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 http://nebc.nerc.ac.uk +44 1491 69 2705 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
