Ok, so it should be gone, I guess. Check 'git status', maybe it's just there as an untracked file (and if so, just rm it)? On Fri, Aug 26, 2016 at 12:55 PM, D K <danielfortin86@gmail.com> wrote:
Hi Dannon,
There's your commit where you describe removing it. So why is it still there if I did a git pull (did I do this incorrectly?)?
I did a "git log -- cloudlaunch.py" and got the following:
commit 303597e48a8503aac09c33910aa5482a374f06a1 Author: Dannon Baker <dannon.baker@gmail.com> Date: Wed Aug 12 14:17:44 2015 -0400
Remove old cloudlaunch in favor of https://github.com/ galaxyproject/cloudlaunch, at launch.usegalaxy.org
commit 6049a7446897baea74c33a5286b6c086c9da31a8 Author: Dannon Baker <dannon.baker@gmail.com> Date: Tue Jul 21 14:03:22 2015 -0400
Catch and return error message during key verification in cloudlaunch.
commit 09719b884806fe1da24b2f7be0f159f1d3b06d04 Author: dannon <dannon.baker@gmail.com> Date: Sat Mar 7 22:51:35 2015 -0500
Cleanup in pbed_to_lped converter . . .
On Fri, Aug 26, 2016 at 9:49 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Can you check the git log for that controller, to see how it got added back to, or remained in, the codebase?
On Fri, Aug 26, 2016, 12:40 PM D K <danielfortin86@gmail.com> wrote:
Hi Dannon,
Yes, the "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py" does still exist.
If it's relevant I did a:
git commit -a -m 'changes made locally prior to upgrade to 16.07' git pull origin master
I had to move the file "lib/galaxy/datatypes/checkers.py" but otherwise didn't get any other errors
On Fri, Aug 26, 2016 at 9:38 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Can you check to see if that file (/remote/home/galaxyd/tmp/gala xy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py) does still exist? If it does not, it may be a leftover .pyc file (which you can delete safely). If you'd like to just clean out *all* the compiled python (which is also safe), run something like ```find <galaxy/lib> -name "*.pyc" -delete```.
On Fri, Aug 26, 2016 at 12:35 PM, D K <danielfortin86@gmail.com> wrote:
I have modified some files in my own local galaxy commit (I think only the sniffers in lib/galaxy/datatypes)
On Fri, Aug 26, 2016 at 9:31 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hey DK,
The cloudlaunch controller was deprecated and should not be in 16.07. Is this a custom modification you have?
-Dannon
On Fri, Aug 26, 2016 at 12:30 PM, D K <danielfortin86@gmail.com> wrote:
> Hi Galaxy-devs, > > I just tried upgrading to 16.07 from 16.01 and get this error when > starting up: > > >> Traceback (most recent call last): >> File "./scripts/paster.py", line 26, in <module> >> serve.run() >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", >> line 1061, in run >> invoke(command, command_name, options, args[1:]) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", >> line 1067, in invoke >> exit_code = runner.run(args) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", >> line 223, in run >> result = self.command() >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/serve.py", >> line 639, in command >> app = loadapp( app_spec, name=app_name, relative_to=base, >> global_conf=vars) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 292, in loadapp >> return loadobj(APP, uri, name=name, **kw) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 317, in loadobj >> return context.create() >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 755, in create >> return self.object_type.invoke(self) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 274, in invoke >> filtered = context.next_context.create() >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 755, in create >> return self.object_type.invoke(self) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 191, in invoke >> return fix_call(context.object, context.global_conf, >> **context.local_conf) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/util/pastescript/loadwsgi.py", >> line 94, in fix_call >> val = callable(*args, **kw) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py", >> line 39, in app_factory >> return paste_app_factory( global_conf, **kwargs ) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/buildapp.py", >> line 76, in paste_app_factory >> webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', >> app ) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/web/framework/webapp.py", >> line 115, in add_ui_controllers >> module = import_module( module_name ) >> File "/opt/rh/python27/root/usr/lib64/python2.7/importlib/__init__.py", >> line 37, in import_module >> __import__(name) >> File "/remote/home/galaxyd/tmp/galaxy2/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", >> line 16, in <module> >> from galaxy.util.json import dumps >> ImportError: cannot import name dumps > > > Any suggestions? > > Thanks! > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >