Set Library Permissions

[mira-miracoli]

I added a tool to set the permissions of ALL datasets in a given data library (in folders and subfolders) at once to the given roles.
It is a workaround for one point of this Issue, I created.

Usage:

usage: set_library_permissions [-h] [-v] [-g GALAXY] [-u USER] [-p PASSWORD] [-a API_KEY] [--library LIBRARY] [--roles ROLES]

Currently the default loglevel is INFO. I don't have experience with this so please tell me if I should change it.

[hexylena]

Some small review comments, this will be really nice to have :)

[hexylena]

looks great with the new progress bar, fantastic!

[hexylena]

looks good to me! great work @mira-miracoli

[mira-miracoli]

Thank you for your reviews and suggestions @hexylena :)

[hexylena]

Sorry @mira-miracoli, the linter has some additional requests for you to re-order the imports and add whitespace here and there to make it happy.

[hexylena]

Traceback (most recent call last):
  File "/home/runner/work/ephemeris/ephemeris/.tox/py36-integration/bin/shed-tools", line 8, in <module>
    sys.exit(main())
 ...
  File "/home/runner/work/ephemeris/ephemeris/.tox/py36-integration/lib/python3.6/site-packages/bioblend/galaxyclient.py", line 266, in key
    headers = self.json_headers.copy()
AttributeError: 'GalaxyInstance' object has no attribute 'json_headers'

that looks unrelated, but not sure what's causing that

[mira-miracoli]

I saw it failing in the actions before, I don't know if it is a issue related to my code

[mira-miracoli]

Shall I change something or can we merge it?

[hexylena]

@nsoranzo any ideas about this error?

[nsoranzo]

That error was fixed in commit galaxyproject/bioblend@22f2d89 , which was first released in BioBlend v0.17.0 . That release also dropped support for Python 3.6 (EOL for almost a year now), which is the version used in the tests.
So my suggestion would be to update the GitHub workflows to use Python 3.7 .

[nsoranzo]

You may also want to add a python_requires (e.g. https://github.com/galaxyproject/gravity/blob/main/setup.py#L39 ) which is metadata used by PyPI and pip.

[hexylena]

Looks good to me.

Someone with more privileges than me (@mvdbeek?) will need to change the branch protection requirements to now depend on the update test names since their name includes the python version.

[natefoo]

Someone with more privileges than me (@mvdbeek?) will need to change the branch protection requirements to now depend on the update test names since their name includes the python version.

Got it

[mvdbeek]

Thanks @mira-miracoli and reviewers, very cool work!