error running kappy unit tests

[yarden]

Hi,

I just upgraded kappy, and when running one of kappy's unit tests, kappa_std.py, I get a series of permission denied errors that look like this:

======================================================================
ERROR: test_static_analyses (test_std.StdClientTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "KaSim/python/tests/util.py", line 159, in test_static_analyses
    runtime = self.getRuntime()
  File "KaSim/python/tests/test_std.py", line 16, in getRuntime
    return kappy.KappaStd(BIN_DIR)
  File "/Users/yarden/miniconda2/envs/py3/lib/python3.7/site-packages/kappy/kappa_std.py", line 61, in __init__
    stderr=subprocess.STDOUT)
  File "/Users/yarden/miniconda2/envs/py3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/Users/yarden/miniconda2/envs/py3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: '/Users/yarden/miniconda2/envs/py3/lib/python3.7/site-packages/kappy/bin/KappaSwitchman'
-------------------- >> begin captured stdout << ---------------------
Getting runtime...

--------------------- >> end captured stdout << ----------------------

----------------------------------------------------------------------
Ran 6 tests in 0.029s

FAILED (errors=5)

It sounds like something went wrong with the pip installation of kappy. All I did was pip install . in the KaSim/ directory, and it generated no error. I didn't install the package as root or anything like that, so I don't understand where the permission denied error is coming from.

This doesn't necessarily mean kappy is broken - normally I just feed it a URL/path to where KaSim binaries are and don't rely on the function to find agent binaries. Do these tests work for other people?

Thanks.

[veghp]

Hi @pirbo , thanks for writing kappy, it's very useful. We use it for topkappy and kappagate.

Has this issue been solved? There is a similar error (PermissionError) for KappaSwitchman. Please see CI outputs for detail: https://travis-ci.org/github/Edinburgh-Genome-Foundry/kappagate https://travis-ci.org/github/Edinburgh-Genome-Foundry/topkappy

The CI build worked with the previous release (v4.0.93), six days ago.

[pirbo]

So This is 2 different issue. In yarden case the problem was that I forgot to include the binary KappaSwitchman in kappy package and that has been solved.

I double check and KappaSwitchman IS included in the wheel of kappy.4.1.0 for python 3.6 so your case is sadly different and needs more investigation...

[pirbo]

OK I know why:

$ ls -l site-packages/kappy/bin/
total 37412
-rw-r--r-- 1 pirbo pirbo  7134032 sept. 17 19:11 KaMoHa
-rw-r--r-- 1 pirbo pirbo  8596984 sept. 17 19:11 KappaSwitchman
-rw-r--r-- 1 pirbo pirbo 13660472 sept. 17 19:11 KaSaAgent
-rw-r--r-- 1 pirbo pirbo  8908928 sept. 17 19:11 KaSimAgent

The binaries are installed without execution rights!!! Sights... Here we go for yet an other fight against setup.py in order to understand why...

[veghp]

Thank you for the quick reply! I re-ran the CI and the error is definitely gone, but unfortunately there is another one:

E               FileNotFoundError: [Errno 2] No such file or directory: '/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/bin/KappaSwitchman': '/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/bin/KappaSwitchman'

/opt/python/3.6.7/lib/python3.6/subprocess.py:1344: FileNotFoundError

More detail: https://travis-ci.org/github/Edinburgh-Genome-Foundry/topkappy

[pirbo]

Sorry. I set the git tag to the wrong commit :-( There is now a kappy.4.1.2 which should finally be OK... Hopefully!

[veghp]

Thank you, this solved the problem. However, there must have been changes to kappy functions as topkappy still won't run properly which I'll try and sort out. Thanks.