Hi Dannon, Thanks for the fast reply
On 5 February 2013 14:49, Dannon Baker <dannonba...@me.com> wrote: > Hi Eric, The threading.Thread issue indicated below has been fixed (the changeset is > already available in galaxy-dist) and isn't eclipse-centric. > Ok somehow I didn't get this update from https://bitbucket.org/galaxy/galaxy-dist even today. > From eclipse, how are you launching galaxy? > I installed a Mercurial plugin in Eclipse, checked out from ' https://bitbucket.org/galaxy/galaxy-dist"; ran ./run.sh one time to download the Eggs necessary, installed the eggs in my eclipse PYTHONPATH and put paster.py serve universe_wsgi.ini in a run configuration. The running of galaxy works nicely, my logs are handled by Eclipse and breakpointing works. So I was quite happy with everything, until I asked PyDev for a Code analysis. It turns out that PyDev did not understand the Bunch() classes like "model.Job.states.QUEUED", but also functions in classes that don't have self as a variable or udefined variables that are called. Probably in real life this is not a big problem, because galaxy is running quite flawlessly, so maybe I just misconfigured PyDev. Because of this I was curious if more people tried the "Eclipse way" or maybe another IDE with debugging enabled. Because I think an IDE can be a great advantage over text-editor developing. > > Personally for debugging I've found it easier to use the debugging > middleware for anything that happens inside a web transaction (sometimes > intentionally raising an exception just to kick out to it), and a simple > addition of 'import pdb; pdb.set_trace()' for creating breakpoints that I > can work through via pdb in the terminal. > Yeah maybe it's better just to debug this way but it feels a bit low tech with all the nice PyDev features in Eclipse. Thanks again, Eric > -Dannon > > > On Feb 5, 2013, at 5:29 AM, Eric Kuyt <eric.ku...@wur.nl> wrote: > > > Hi All, > > > > I am Running my local galaxy instance in Eclipse - pydev to make > debugging somewhat easier, but now I run into loads of Code errors. It > seems that pydev doesn't understand the Bunch() Class frequently used in > Galaxy. > > > > But also code errors that maybe could be fixed. such as: > > > > lib/galaxy/jobs/runner/lwr.py:232 > > > > #worker = threading.Thread( ( name="LwrJobRunner.thread-%d" % i ), # > target=self.run_next ) > > --> > > #worker = threading.Thread( name="LwrJobRunner.thread-%d" % i , > #target=self.run_next ) > > > > Are these real errors or am I doing something wrong. > > > > Is there anyone with more experience in running Galaxy from within > Eclipse? > > > > Thanks, > > > > Eric > > > > > > > > ___________________________________________________________ > > 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/ > > > >
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