Fix unit tests broken by the transition to TRAPI 1.6.0 in kp_info_cacher (which means Expand uses Retriever)

[saramsey]

@edeutsch I could use your help reviewing this PR. This is for issue #2712, the broken unit tests in ARAX master branch since the transition to ARAX only talking to TRAPI 1.6.0 KPs.

[edeutsch]

This looks excellent to me, except that one test is still failing for me:

$ pytest -v test_ARAX_workflows.py::test_FET_example_3
...
>       assert response.status == 'OK'
E       AssertionError: assert 'ERROR' == 'OK'
E         
E         - OK
E         + ERROR

test_ARAX_workflows.py:254: AssertionError

[saramsey]

I will work on that. Also I will add the old tests in an archive folder, this same PR.

[saramsey]

Hmm, test test_ARAX_workflows.py::test_FET_example_3 seems to work for me:

@edeutsch can you please run this command, wherever you were running your tests? (assuming your shell is bash):

pytest -vv -s --cache-clear test/test_ARAX_workflows.py::test_FET_example_3 2>output.log 1>&2

and post output.log as an upload to this PR?

[Copilot]

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Updates ARAX’s test harness and query expansion utilities to work with TRAPI 1.6.0-era KPs (notably infores:retriever), aiming to restore passing unit tests on master after the KP transition.

Changes:

• Adds pytest.ini configuration to exclude legacy/slow/unrelated test directories from default pytest discovery.
• Updates many unit tests and workflow examples to use infores:retriever and updated curies/predicates/categories aligned with TRAPI 1.6.0 expectations.
• Refactors portions of Expand/Filter_KG logic for TRAPI 1.6.0 structures (qnode_keys/qedge_keys handling, subclass edge handling, KP selection).

Reviewed changes

Copilot reviewed 32 out of 32 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
pytest.ini	Excludes legacy/archived and non-unit-test dirs from pytest discovery.
notes/arax-maintenance-sop.md	Updates unit-test run instructions and expected test counts.
code/code-archive/old-arax-tests/test_ARAX_translate.py	Adds archived legacy translate tests (now excluded by pytest.ini).
code/code-archive/old-arax-tests/test_ARAX_synonymizer.py	Adds archived legacy synonymizer tests (now excluded by pytest.ini).
code/code-archive/old-arax-tests/test_ARAX_standup_queries.py	Adds archived legacy standup workflow tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_ranker.py	Adds archived legacy ranker tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_query.py	Adds archived legacy query tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_messenger.py	Adds archived legacy messenger tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_json_queries.py	Adds archived legacy JSON query tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_infer.py	Adds archived legacy infer tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_filter_results.py	Adds archived legacy filter_results tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_filter_kg.py	Adds archived legacy filter_kg tests (now excluded).
code/code-archive/old-arax-tests/test_ARAX_connect.py	Adds archived legacy connect tests (now excluded).
code/code-archive/old-arax-tests/conftest.py	Adds archived legacy pytest config/markers (now excluded).
code/ARAX/test/test_ARAX_workflows.py	Updates workflow tests to use infores:retriever and revised categories/predicates.
code/ARAX/test/test_ARAX_translate.py	Updates translate tests (curies + allowlists) for infores:retriever.
code/ARAX/test/test_ARAX_resultify.py	Updates resultify tests to use infores:retriever and revises some test queries.
code/ARAX/test/test_ARAX_overlay.py	Updates overlay tests (categories/predicates/KP) for TRAPI 1.6.0 behavior.
code/ARAX/test/test_ARAX_json_queries.py	Updates JSON workflow tests to infores:retriever and revised expectations.
code/ARAX/test/test_ARAX_filter_results.py	Updates filter_results tests to infores:retriever.
code/ARAX/test/test_ARAX_filter_kg.py	Updates filter_kg tests to infores:retriever and revised expected error codes.
code/ARAX/test/test_ARAX_expand.py	Updates expand tests to infores:retriever, adjusts curies, removes single-node tests.
code/ARAX/ARAXQuery/Filter_KG/remove_edges.py	Improves robustness around missing qnode_keys/qedge_keys, adds logging, refactors locals.
code/ARAX/ARAXQuery/Expand/trapi_querier.py	Adjusts QG↔KG mapping behavior, attribute handling, and subclass edge parent-node sourcing.
code/ARAX/ARAXQuery/Expand/kp_selector.py	Tweaks KP selection defaults and refines CURIE conversion logic/order.
code/ARAX/ARAXQuery/Expand/kp_info_cacher.py	Fixes a debug-log typo.
code/ARAX/ARAXQuery/ARAX_filter_kg.py	Makes allowable-parameter computation tolerant of missing qnode_keys/qedge_keys.
code/ARAX/ARAXQuery/ARAX_expander.py	Changes post-processing expectations for KP outputs; refactors/limits single-node expansion.

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[saramsey]

@bazarkua can you get Copilot to re-review this PR, after commit 02df4b6?

[Copilot]

Pull request overview

Copilot reviewed 32 out of 32 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (3)

pytest.ini:1

• norecursedirs is doing a lot of heavy lifting to restrict collection, including excluding at least one source directory (code/ARAX/ARAXQuery/Overlay). A more maintainable approach is typically to set testpaths = code/ARAX/test (and optionally python_files = test_*.py) so pytest only collects intended unit tests, without needing to keep an expanding exclude list. This reduces the chance of accidentally excluding legitimate tests or masking new test directories.
  notes/arax-maintenance-sop.md:1
• The SOP hardcodes an exact expected unit test count in multiple places (now two different numbers appear in the same doc). This tends to go stale and causes confusion when tests are added/removed. Consider rephrasing to avoid exact counts (e.g., “All standard unit tests should pass”) or centralizing the number in one place.
  notes/arax-maintenance-sop.md:1
• The SOP hardcodes an exact expected unit test count in multiple places (now two different numbers appear in the same doc). This tends to go stale and causes confusion when tests are added/removed. Consider rephrasing to avoid exact counts (e.g., “All standard unit tests should pass”) or centralizing the number in one place.

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[saramsey]

OK, all the pytests are passing (both on my MBP and on arax.ncats.io/devED), and I believe I have address Copilot's concerns with the last few commits. All three Example queries and the example Pathfinder query are running fine, on my MBP and on arax.ncats.io/devED.

@edeutsch @bazarkua @dkoslicki what do you think? OK to merge to master?

[saramsey]

The red "x" for the Test Build is (I think) because it is running the pytests for the code in the master branch, which (obviously) is not working. That's literally the point of this issue.

[saramsey]

I think I just initiated a Test Build from the issue-2712 branch:
https://github.com/RTXteam/RTX/actions/runs/23969548433

[saramsey]

OK, to get the Test Build to actually check out the issue-2712 branch on cicd.rtx.ai, I had to actually modify the CICD-Dockerfile, which is a bit inelegant, but it will have to do for now. Test Build is currently running.

[saramsey]

OK, as you can see, the Test Build passed. I'm pasting a screencap of it here, because as soon as I revert commit 50b7bc4, the Test Build that is kicked off will not pass anymore (because the CICD-Dockerfile clones the master branch RTX.git code). But trust me, it passed!

[edeutsch]

thank you, Steve!