Great! that fixed the issue On Fri, Aug 26, 2016 at 10:20 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
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/galaxyproje ct/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/gala >>> xy2/lib/galaxy/util/pastescript/serve.py", line 1061, in run >>> invoke(command, command_name, options, args[1:]) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/util/pastescript/serve.py", line 1067, in invoke >>> exit_code = runner.run(args) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/util/pastescript/serve.py", line 223, in run >>> result = self.command() >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/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/gala >>> xy2/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in loadapp >>> return loadobj(APP, uri, name=name, **kw) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/util/pastescript/loadwsgi.py", line 317, in loadobj >>> return context.create() >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/util/pastescript/loadwsgi.py", line 755, in create >>> return self.object_type.invoke(self) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/util/pastescript/loadwsgi.py", line 274, in invoke >>> filtered = context.next_context.create() >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/util/pastescript/loadwsgi.py", line 755, in create >>> return self.object_type.invoke(self) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/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/gala >>> xy2/lib/galaxy/util/pastescript/loadwsgi.py", line 94, in fix_call >>> val = callable(*args, **kw) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in >>> app_factory >>> return paste_app_factory( global_conf, **kwargs ) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/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/gala >>> xy2/lib/galaxy/web/framework/webapp.py", line 115, in >>> add_ui_controllers >>> module = import_module( module_name ) >>> File "/opt/rh/python27/root/usr/lib >>> 64/python2.7/importlib/__init__.py", line 37, in import_module >>> __import__(name) >>> File "/remote/home/galaxyd/tmp/gala >>> xy2/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/ >> > >