implement workaround for permission error when copying read-only files that have extended attributes set and using Python 3.6

[jfgrimm]

Ran into this issue like this, when configuring EasyBuild with read-only-installdir:

== 2024-09-16 13:26:56,117 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Failed to copy file /mnt/scratch/users/jfg508/eb/software/EasyBuild/4.9.2/lib/python3.6/site-packages/easybuild/easyblocks/e/easybuildmeta.py to /tmp/eb-l7y97vxy/reprod_20240916132656_823857/easyblocks/easybuildmeta.py: [Errno 13] Permission denied: '/tmp/eb-l7y97vxy/reprod_20240916132656_823857/easyblocks/easybuildmeta.py' (at easybuild/tools/filetools.py:2437 in copy_file)

Having taken a closer look, it seems that on our system shutil.copy2() spits out a PermissionError when the file to be copied is read-only. However, the copy still succeeds (and has the correct contents).

[ocaisa]

I think this is the real problem that I thought I was solving with #4604

[ocaisa]

To me this now looks good, but can we add a test for it? It may not be very thorough, but you should just be able to create a file, change the permissions to read-only and then attempt a copy. I don't know if that is guaranteed to hit the LoC, but it is worth a shot. Should be a variation on

easybuild-framework/test/framework/filetools.py

Lines 1805 to 1810 in f7035e9

	testdir = os.path.dirname(os.path.abspath(__file__))
	toy_ec = os.path.join(testdir, 'easyconfigs', 'test_ecs', 't', 'toy', 'toy-0.0.eb')
	target_path = os.path.join(self.test_prefix, 'toy.eb')
	ft.copy_file(toy_ec, target_path)
	self.assertExists(target_path)
	self.assertTrue(ft.read_file(toy_ec) == ft.read_file(target_path))

[jfgrimm]

I have traced the underlying issue to: https://bugs.python.org/issue24538

So this should only appear in python < 3.7

[jfgrimm]

since the _copyxattr issue is filesystem-dependent, and the issue was fixed in python 3.7+, I don't know that it's of much value adding a test?

[ocaisa]

Like everything, this was more work than it seemed initially!

[jfgrimm]

@ocaisa I've pushed another commit (or two) that actually use the upstream approach to ensure the extended attributes are truly copied as well. A cleaner fix imo

[ocaisa]

Ha, this is correct but quite confusing (add=False means remove the permissions)

[jfgrimm]

yeah, hence the comment at the top of that block
it's not the most intuitive that add=False removes the permissions

[boegel]

Should we open an issue to improve the API of adjust_permissions in EasyBuild 5.0?

stale

[boegel]

There really should be a dedicated test that verifies whether the changes indeed fix the problem at hand.

I puzzled one together, see jfgrimm#1

Unless I'm misunderstanding something, the extra test shows the fix isn't fully working as designed yet, since it fails on Python 3.6.8 in RHEL8...

[boegel]

This part doesn't make sense to me, I think it should be removed...

If we give up here if the source file is read-only, then why bother with the attempt to fix the issue when using Python 3.6 via shutil._copyxattr below?

[boegel]

Discussed with @jfgrimm in Slack, the condition is wrong here, should be if os.stat...

Also, it makes more sense to me to check whether the target file is read-only or not?

Fixed in jfgrimm#1