Hi John,
I did as you suggested wiping out galaxy's .venv folder.
And restoring requirements.txt as in gthub.
The results where quite interesting.
The planemo test ran fine.
planemo test --galaxy_root=/home/christian/galaxy_new columns.xml
(As long as there is no .venv folder in Galaxy)
===
However then I started and stopped the galaxy server using
sh run.sh
The exact same planemo test than FAILED.
Full output attached but key lines are:
unctional_tests.py ERROR 2015-11-23 08:43:42,227 Failure running tests
Traceback (most recent call last):
File "./scripts/functional_tests.py", line 494, in main
success = _run_functional_test( )
File "./scripts/functional_tests.py", line 443, in _run_functional_test
import functional.test_toolbox
File "/home/christian/galaxy_new/test/functional/test_toolbox.py", line 3, in
<module>
from base.twilltestcase import TwillTestCase
File "/home/christian/galaxy_new/test/base/twilltestcase.py", line 21, in
<module>
import twill
ImportError: No module named twill
functional_tests.py INFO 2015-11-23 08:43:42,227 Shutting down
===
I then added the four lines to requirements,txt
Ran sh run.sh again
Full output attached.
But key lines are:
Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64))
Collecting twill==1.8.0 (from -r requirements.txt (line 67))
/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90:
InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3
from configuring SSL appropriately and may cause certain SSL connections to fail. For more
information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformw....
InsecurePlatformWarning
/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90:
InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3
from configuring SSL appropriately and may cause certain SSL connections to fail. For more
information, see
https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformw....
InsecurePlatformWarning
Using cached twill-1.8.0.tar.gz
Collecting lxml==3.5.0 (from -r requirements.txt (line 68))
Using cached lxml-3.5.0.tar.gz
Collecting cssselect==0.9.1 (from -r requirements.txt (line 69))
Using cached cssselect-0.9.1.tar.gz
Collecting NoseHTML==0.4.2 (from -r requirements.txt (line 70)
Using cached NoseHTML-0.4.2-py2-none-any.whl
Installing collected packages: twill, lxml, cssselect, NoseHTML
Running setup.py install for twill
Running setup.py install for lxml
Running setup.py install for cssselectt
Successfully installed NoseHTML-0.4.2 cssselect-0.9.1 lxml-3.5.0 twill-1.8.0
Activating virtualenv at /home/christian/galaxy_new/.venv
No handlers could be found for logger "galaxy.config"
I then reran planemo and it worked fine.
===
So it looks like if galaxy does not have a .venv to use planemo runs fine
But if there is a galaxy .venv Planemo uses that one and fails on missing reguirements.
Unless these are added in.
====
While this indicates that the issue is not directly with Planemo is is worrying that
Plnemo will not run against a galaxy instance that has been used.
Christian
University of Manchester
PS. Twill and the other missing requirements have been installed on my machine
________________________________________
From: John Chilton [jmchilton(a)gmail.com]
Sent: Friday, November 20, 2015 5:19 PM
To: Christian Brenninkmeijer
Cc: Peter Cock; galaxy-dev(a)lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
DVCSs are weird - 1aecca7889681ad9518e26e2a62b470809d2cdd1 is a single
commit that is in dev from a week ago but its parent is from dev on
October 11 (that is when the branch was forked). So it actually
doesn't have the recent huge switch from eggs to wheels that broken
everything.
For instance, the following file in the commit still references Galaxy
eggs:
https://github.com/galaxyproject/galaxy/blob/1aecca7889681ad9518e26e2a62b...
I guess what I am saying is I suspect this actually broke when we
merged 428 (
https://github.com/galaxyproject/galaxy/pull/428) closer
to the end of October.
Anyway, if you have virtualenv than I am fairly stumped. Can you wipe
out Galaxy's virtualenv and show me the full output of running planemo
test.
-John
On Fri, Nov 20, 2015 at 1:30 PM, Christian Brenninkmeijer
<christian.brenninkmeijer(a)manchester.ac.uk> wrote:
I was referring to Galaxy's requirements .txt
This appears to be an issue with changes made to galaxy last weekend.
The very same Planemo work with
commit 1aecca7889681ad9518e26e2a62b470809d2cdd1
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: Sat Nov 14 23:56:19 2015 +0100
But fails at or BEFORE
commit b19e71ec465c7145840acf684f8f09eeebb99b5a
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: Mon Nov 16 14:57:53 2015 +0000
Christian
________________________________________
From: Peter Cock [p.j.a.cock(a)googlemail.com]
Sent: Friday, November 20, 2015 12:41 PM
To: Christian Brenninkmeijer
Cc: John Chilton; galaxy-dev(a)lists.galaxyproject.org
Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
Which file are you looking at? There is no nose entry here:
https://github.com/galaxyproject/planemo/blob/master/requirements.txt
Perhaps a more recent version of nose is needed?
Peter
On Fri, Nov 20, 2015 at 11:51 AM, Christian Brenninkmeijer
<christian.brenninkmeijer(a)manchester.ac.uk> wrote:
> Hi Peter/ John
> requirementx.txt already includes the latest version of nose
>
> nose==1.3.7
>
> It is nose that is complaining it does not like the sys,args passed in by
FunctionalTest.py
>
> Christian
>
> ________________________________________
> From: Peter Cock [p.j.a.cock(a)googlemail.com]
> Sent: Friday, November 20, 2015 11:30 AM
> To: Christian Brenninkmeijer; John Chilton
> Cc: galaxy-dev(a)lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Unable to up Planemo against latest dev
>
> On Fri, Nov 20, 2015 at 9:59 AM, Christian Brenninkmeijer
> <christian.brenninkmeijer(a)manchester.ac.uk> wrote:
>> Hi All,
>>
>> I am unable to run Planemo against the latest dev branch.
>>
>> 1. import twill error
>>
>> I was able to fix this by adding to requirements.txt
>> twill==1.8.0
>> lxml==3.5.0
>> cssselect==0.9.1
>>
>> But then I get
>>
>> functional_tests.py: error: no such option: --with-nosehtml
>> functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests
>> Traceback (most recent call last):
>> ...
>> SystemExit: 2
>
> That's not a very helpful error, is it? It reminds me of a missing
> dependency / installation problem I had long ago when first
> setting up TravisCI to run Galaxy tool tests:
>
>
https://github.com/peterjc/pico_galaxy/commit/c8265f4a42caf62eb3bc8b36b47...
>
> @John: My guess is we need to add "nose" to planemo's requirements.txt
> to ensure this gets installed automatically?
>
> Peter