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bihealth / sodar-server

SODAR: System for Omics Data Access and Retrieval
https://github.com/bihealth/sodar-server
MIT License
14 stars 3 forks source link

Upgrade to python-irodsclient v2.0.x #1944

Closed mikkonie closed 5 months ago

mikkonie commented 5 months ago

This was originally a part of #1930, but turns out the v2.x releases are breaking. Upgrading without code changes resulted in 600+ test cases failing.

I also need to ensure compatibility of the latest version with both iRODS v4.3 and v4.2. Otherwise this will be postponed into SODAR v1.0.

mikkonie commented 5 months ago

Looks like there are more access control changing shenaningans, at least:

SetAccessTask failed: 'iRODSSession' object has no attribute 'permissions'

Update: documentation says.. "<session>.permissions was removed in v2.0.0 in favor of <session>.acls."

mikkonie commented 5 months ago

Second problem solved: iRODSSession.acls does not return user objects if permissions are set using groups. Instead, we need to check group permissions manually in such cases.

mikkonie commented 5 months ago

Third issue: from python-irodsclient==1.1.9 onwards, logging has been changed or is broken. In my tests, I'm receiving a mountain of warnings and errors which are normally suppressed. These happen with expected cases, where e.g. access is supposed to be denied for a view. Example:

test_auth_disabled (irodsbackend.tests.test_views.TestLocalAuthAPIView)
Test auth with existing user and auth check disabled ... ERROR:django.request:Internal Server Error: /irodsbackend/api/auth
ok
test_auth_invalid_password (irodsbackend.tests.test_views.TestLocalAuthAPIView)
Test auth with invalid password ... WARNING:django.request:Unauthorized: /irodsbackend/api/auth
ok
test_auth_invalid_user (irodsbackend.tests.test_views.TestLocalAuthAPIView)
Test auth with invalid user ... WARNING:django.request:Unauthorized: /irodsbackend/api/auth
ok

This also occurs in views which are in no way connected to the python client and don't even initialize . I can't find anything referring such a change in the documentation.

I'll see if there is a way to suppress this redundant logging. If not, I'll contact iRODS support.

mikkonie commented 5 months ago

The logging issue was fixed by disabling propagate and setting disable_existing_loggers True.

The fact that python-irodsclient>=1.1.9 acts as a ancestor logger and logs everything seems like a bug. I have discussed this with iRODS support and they are aware of it.

mikkonie commented 5 months ago

Done.