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.
> 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
> > 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
> > Thanks,
> > Eric
> > ___________________________________________________________
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