Thanks for the bug report. I have fixed this problem here (https://github.com/galaxyproject/planemo/commit/a32d082eeee0a6b856d8d15c9619...) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue. -John On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

Hi Alexander,

I have opend an issue: https://github.com/galaxyproject/planemo/issues/240

Thanks for reporting, Bjoern

Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel:

...

Hi,

I'm running:

planemo shed_update --check_diff --shed_target toolshed

and get a python error message (see below).

shed_diff and shed_lint are working fine. planemo, version 0.12.2

Best, Alexander

Traceback (most recent call last):

...

File "/usr/local/bin/planemo", line 11, in <module> sys.exit(planemo()) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 664, in __call__ return self.main(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 644, in main rv = self.invoke(ctx) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 991, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 837, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 464, in invoke return callback(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args[1:], **kwargs) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 464, in invoke return callback(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/planemo/commands/cmd_shed_update.py", line 52, in cli tsi = shed.tool_shed_client(ctx, **kwds) File "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", line 331, in tool_shed_client key = prop("key") File "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", line 323, in prop return kwds.get("shed_%s" % key, None) or shed_config.get(key, None) AttributeError: 'NoneType' object has no attribute 'get'

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Do you have a ~/.planemo.yml file? I think probably yes based on the previous exception. Can you replace passwords and keys with XXXX and send me a copy of that as well as the command-line that produced the above output? -John On Mon, Jun 29, 2015 at 12:05 PM, Alexander Vowinkel <vowinkel.alexander@gmail.com> wrote:

Thanks,

now I get the following directly after the diff output:

...

Could not update stacks object of type 'NoneType' has no len()

/usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning)

/usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) Repository metadata updated. Failed to update a repository.

What does that mean?

Best, Alexander

2015-06-29 10:41 GMT-05:00 John Chilton <jmchilton@gmail.com>:

...

Thanks for the bug report. I have fixed this problem here

(https://github.com/galaxyproject/planemo/commit/a32d082eeee0a6b856d8d15c9619...) and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue.

-John

On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

...

Hi Alexander,

I have opend an issue: https://github.com/galaxyproject/planemo/issues/240

Thanks for reporting, Bjoern

Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel:

...

Hi,

I'm running:

planemo shed_update --check_diff --shed_target toolshed

and get a python error message (see below).

shed_diff and shed_lint are working fine. planemo, version 0.12.2

Best, Alexander

Traceback (most recent call last):

...

File "/usr/local/bin/planemo", line 11, in <module> sys.exit(planemo()) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 664, in __call__ return self.main(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 644, in main rv = self.invoke(ctx) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 991, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 837, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 464, in invoke return callback(*args, **kwargs) File "/usr/local/lib/python2.7/dist-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args[1:], **kwargs) File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 464, in invoke return callback(*args, **kwargs) File

"/usr/local/lib/python2.7/dist-packages/planemo/commands/cmd_shed_update.py", line 52, in cli tsi = shed.tool_shed_client(ctx, **kwds) File "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", line 331, in tool_shed_client key = prop("key") File "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", line 323, in prop return kwds.get("shed_%s" % key, None) or shed_config.get(key, None) AttributeError: 'NoneType' object has no attribute 'get'

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Ay shit. Just realized during looking at it the third time: Someone forgot to uncomment the key line o_o' 2015-06-29 16:21 GMT-05:00 Alexander Vowinkel <vowinkel.alexander@gmail.com> :

Here they are:

~/.planemo.yml: http://pastebin.com/nWdT6ybx Command-Log: http://pastebin.com/baBmrD8d

2015-06-29 15:23 GMT-05:00 John Chilton <jmchilton@gmail.com>:

...

Do you have a ~/.planemo.yml file? I think probably yes based on the previous exception. Can you replace passwords and keys with XXXX and send me a copy of that as well as the command-line that produced the above output?

-John

On Mon, Jun 29, 2015 at 12:05 PM, Alexander Vowinkel <vowinkel.alexander@gmail.com> wrote:

...

Thanks,

now I get the following directly after the diff output:

...

Could not update stacks object of type 'NoneType' has no len()

/usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768:

...

InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning)

/usr/local/lib/python2.7/dist-packages/requests/packages/urllib3/connectionpool.py:768:

...

InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.org/en/latest/security.html InsecureRequestWarning) Repository metadata updated. Failed to update a repository.

What does that mean?

Best, Alexander

2015-06-29 10:41 GMT-05:00 John Chilton <jmchilton@gmail.com>:

...

Thanks for the bug report. I have fixed this problem here

(

https://github.com/galaxyproject/planemo/commit/a32d082eeee0a6b856d8d15c9619... )

...

and released a new version of planemo (0.13.0) with fix. Hopefully you will get a better error message after the upgrade if there is still a configuration issue.

-John

On Sat, Jun 27, 2015 at 6:32 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:

...

Hi Alexander,

I have opend an issue: https://github.com/galaxyproject/planemo/issues/240

Thanks for reporting, Bjoern

Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel:

...

Hi,

I'm running:

planemo shed_update --check_diff --shed_target toolshed

and get a python error message (see below).

shed_diff and shed_lint are working fine. planemo, version 0.12.2

Best, Alexander

Traceback (most recent call last): > File "/usr/local/bin/planemo", line 11, in <module> > sys.exit(planemo()) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line > 664, > in __call__ > return self.main(*args, **kwargs) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line > 644, > in main > rv = self.invoke(ctx) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line > 991, > in invoke > return _process_result(sub_ctx.command.invoke(sub_ctx)) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line > 837, > in invoke > return ctx.invoke(self.callback, **ctx.params) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line > 464, > in invoke > return callback(*args, **kwargs) > File "/usr/local/lib/python2.7/dist-packages/click/decorators.py", > line > 64, in new_func > return ctx.invoke(f, obj, *args[1:], **kwargs) > File "/usr/local/lib/python2.7/dist-packages/click/core.py", line > 464, > in invoke > return callback(*args, **kwargs) > File > > "/usr/local/lib/python2.7/dist-packages/planemo/commands/cmd_shed_update.py", > line 52, in cli > tsi = shed.tool_shed_client(ctx, **kwds) > File > "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", > line 331, in tool_shed_client > key = prop("key") > File > "/usr/local/lib/python2.7/dist-packages/planemo/shed/__init__.py", > line 323, in prop > return kwds.get("shed_%s" % key, None) or shed_config.get(key, > None) > AttributeError: 'NoneType' object has no attribute 'get'

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___________________________________________________________ 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/