[MNT] Change default value of NB_ENABLE_AUTH to False #530

[sejalpunwatkar]

Closes #530
Changes proposed in this pull request:
Updated the NB_ENABLE_AUTH environment-backed setting to default to False (previously True).
This ensures that authentication is not required by default, aligning with the requirements in issue #530.
Verified the change manually via a Python script.

Checklist:

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass
• If the PR changes the SPARQL query template, the default Neurobagel query file has also been regenerated

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Changes the default for the NB_ENABLE_AUTH environment setting so that authentication is disabled by default unless explicitly enabled via configuration.

Class diagram for updated Settings auth configuration

classDiagram
class Settings {
  bool return_agg (NB_RETURN_AGG, default True)
  int min_cell_size (NB_MIN_CELL_SIZE, default 0)
  bool auth_enabled (NB_ENABLE_AUTH, default False)
  str client_id (NB_QUERY_CLIENT_ID, default None)
  str config (NB_CONFIG)
}

Loading

File-Level Changes

Change	Details	Files
Update the default authentication feature flag to be disabled unless configured otherwise.	Change the default value of the auth_enabled settings field from True to False Keep the environment variable alias NB_ENABLE_AUTH unchanged so external configuration behavior remains consistent	app/api/env_settings.py

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#530	Change the default value of the NB_ENABLE_AUTH / auth_enabled setting from True to False in the codebase.	✅

Possibly linked issues

• Change default value of NB_ENABLE_AUTH to False #530: PR updates Settings.auth_enabled default to False, exactly implementing the issue’s requested NB_ENABLE_AUTH default change.

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[sourcery-ai]

We've reviewed this pull request using the Sourcery rules engine

[sejalpunwatkar]

Ready for review, @alyssadai ! As mentioned in the description, I verified this manually because of local environment issues with legacy pandas versions on Python 3.12. Please let me know if there's anything else needed!

[alyssadai]

Hi @sejalpunwatkar, thanks for the PR! To verify the new default value of NB_ENABLE_AUTH/auth_enabled, could you please review the existing tests in the repo and update any relevant ones as necessary?

Also:

I verified this manually because of local environment issues with legacy pandas versions on Python 3.12.

Can you elaborate on the specific error or issue you're having when setting up a development environment (e.g., with pip install -r requirements.txt)? Or even better, open a bug report so that we can reproduce your issue!

[sejalpunwatkar]

Hi @alyssadai !
Regarding the environment setup issues, I’ve opened a detailed bug report here: #536. The failure was caused by pandas==1.5.2 and PyYAML not having pre-built wheels for Python 3.12, which led to build failures due to the removal of legacy modules (like pkg_resources) in the latest Python version.
I’ve since resolved this in my local environment by upgrading to pandas>=2.1.1 and PyYAML>=6.0.1 and have submitted a separate PR to address the requirements file.
Regarding the requested changes for this PR:
I have reviewed the existing tests.
I verified the change for NB_ENABLE_AUTH by running python -m pytest tests/test_utility.py in the updated environment.
All 4 tests passed successfully, confirming the new default value works as expected without breaking existing utility logic.
Please let me know if you'd like me to look into any other specific test files!

[alyssadai]

Hi @sejalpunwatkar, as shown by the failing check, not all our tests are not all passing in CI - you can see the currently failing tests here: https://github.com/neurobagel/api/actions/runs/22391907731/job/65038713812?pr=533

As noted in the README, to run the full test suite for the repo locally (which is recommended for any local changes), you should run:

pytest tests

or simply pytest.

Could you please review the failing test and update the PR accordingly? Let me know if anything is unclear.

Re: the Python 3.12 pandas conflict, thank you for opening an issue. We will try to reproduce that on our end and address that separately in #536.

[sejalpunwatkar]

Hi @alyssadai , I’ve pushed the changes for #530 to change NB_ENABLE_AUTH to False by default.
148/150 tests are passing, but I’m still hitting two stubborn failures in tests/test_query.py:
test_aggregate_query_response_structure (AssertionError)
test_missing_derivatives_info_handled_by_nonagg_api_response (ResponseValidationError: 2 validation errors)
What I’ve done so far:
Updated env_settings.py to set auth_enabled: bool = False.
Updated tests/test_settings.py to expect False.
Modified mock_post_nonagg_query_to_graph in conftest.py to include pipeline_name, pipeline_version, dataset_portal_uri, and dataset_total_subjects (integer) to satisfy the Pydantic schema.
In the failing tests, I’ve used with test_app:, added the metadata fixture, and monkeypatched api_settings.DATASETS_METADATA to match the UUID http://neurobagel.org.
The Issue:
Despite these updates, the API is still returning None for subject_data instead of a list. It seems like the grouping/reducer logic in the CRUD layer might be silently dropping results when authentication is disabled, or there's a tiny mismatch I can't spot between the mock and the expected response model.

[alyssadai]

Hi @sejalpunwatkar, your latest commits introduce some changes that are unrelated to the original issue concerning the NB_ENABLE_AUTH variable. Unfortunately, they also introduce incorrect logic in certain places, which I believe is why we're seeing more CI failures now than for your last set of commits. In general, please keep changes scoped to the issue at hand and avoid mixing dependency changes with functional changes (e.g., our current CI workflow only tests against Python 3.10, so any changes related to supporting newer Python versions also require corresponding CI workflow updates so we can keep the environment reproducible).

If the internal structure of the app or the environment variable handling is unclear, please feel free to ask for clarification before modifying core logic.

Based on the CI workflow run at the time of my last review, the only test that was failing and needed to be updated in this PR was test_settings_read_correctly.

Please revert the other changes as detailed below and re-request a review. Thank you!

[alyssadai]

Why were these lines deleted? These changes should not be necessary to address the original issue, and actually break the output of this function (since there is no longer any return statement), in turn breaking the logic of invoking functions.

This erroneous change may be the reason why you are unexpectedly getting None for subject_data locally.

Please revert the deletions in this file since they are irrelevant to the original issue.

[alyssadai]

The changes to the mocked responses in this file are incorrect. For example, this fixture is meant to mock the response from a single SPARQL query to the graph store, whereas you have added properties that are in fact returned via separate graph queries. In this specific case, you have also duplicated dataset_portal_uri.

I think there may be some confusion about the schema of the responses from the Neurobagel API itself, vs the shape of the response from the graph store that an API instance talks to.

Please revert all the changes you've made to the test fixtures in this file. To my knowledge, you shouldn't need to update any existing test fixtures in order to address/test the original issue.

[alyssadai]

The change to this assertion is incorrect. This test asserts over the response for an aggregate query result, and as detailed in the docs, subject-level data should always be protected in aggregate query results.

[alyssadai]

The changes you've made to this test module do not appear relevant for testing the original issue (the new default value of NB_ENABLE_AUTH) and introduce some invalid logic. Please revert the changes to this file.

[alyssadai]

👍 As far as I can tell, this is the only test that needed to be changed in this PR, since it tests the behavior referenced in the issue. In the CI tworkflow run linked in my previous review comment, this was the only failing test at the time (and thus the only test that needed updating): https://github.com/neurobagel/api/actions/runs/22391907731/job/65038713812?pr=533

[alyssadai]

As mentioned in my last review comment, dependency-related changes should be handled in #536 and should not be part of this PR, to avoid mixing dependency updates with functional changes.

We will also soon be introducing a new dependency management system using uv (#529), so pinned dependency updates should wait until that issue has been addressed.

[sejalpunwatkar]

Hi @alyssadai , thank you for the guidance! I've performed a hard reset to main to remove all unrelated dependency and logic changes. I have now applied only the 2 line fix: updating the NB_ENABLE_AUTH default and the corresponding test in test_settings.py.
I realized my local Python 3.12 environment was triggering unrelated validation errors which led me to over complicate the previous commits. I've reverted the mocks and core logic to ensure the PR stays strictly in scope. Thanks for your patience!

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.16%. Comparing base (659081c) to head (81321cc).
⚠️ Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #533      +/-   ##
==========================================
- Coverage   97.31%   97.16%   -0.16%     
==========================================
  Files          34       34              
  Lines        1304     1304              
==========================================
- Hits         1269     1267       -2     
- Misses         35       37       +2     

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[alyssadai]

Hi @sejalpunwatkar, thanks for the updates. Before I approve this, could you please update the PR description to follow the Neurobagel PR template? It should have been automatically included when the PR was opened: https://github.com/neurobagel/api/blob/main/.github/pull_request_template.md

Please leave the checklist items in the template unchecked so I can review and check them off as a final sanity check. Thank you!

[sejalpunwatkar]

Hi @alyssadai, I've updated the PR description to follow the template as requested! I kept the checklist items unchecked for your review. Thank You!

[alyssadai]

Thanks @sejalpunwatkar for the revisions! I think this PR looks good to go🧑‍🍳

[neurobagel-bot]

🚀 PR was released in v0.9.2 🚀

[sejalpunwatkar]

Thanks for the merge, @alyssadai ! Happy to help. Are there any other high-priority issues; specifically regarding metadata parsing or API structure, that I could look into next?