Fix SQLAlchemy 2.x subquery deprecation warnings in controllers

[DhanushVarma-2]

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{pull request content here}
Several controllers were passing SQLAlchemy Subquery objects directly to .in_(), which triggers a deprecation warning in SQLAlchemy 2.x. This fix explicitly calls .select() on the subquery before passing it to .in_() across mod_sample, mod_test, mod_ci, and mod_customized. All 416 tests pass after the fix.

[canihavesomecoffee]

Please fix the pycodestyle errors and rebase.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

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[DhanushVarma-2]

Please fix the pycodestyle errors and rebase.

@canihavesomecoffee Rebased on master, resolved conflicts, and fixed the pycodestyle error.
Ready for another look.