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/

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/

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/

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/ >> > >