Transition fisher_exact_test.py away from using KG2/PloverDB internally

[saramsey]

You might think that with commit 83ed888, ARAX no longer at query time would query KG2/PloverDB, and that it would instead always query infores:retriever. For the most part, it does. But not entirely.

I discovered that fisher_exact_test.py still queries KG2/PloverDB, here:

RTX/code/ARAX/ARAXQuery/Overlay/fisher_exact_test.py

Lines 489 to 510 in 7b5ed40

	else:
	infores_key = "infores:rtx-kg2"
	from ARAX_expander import ARAXExpander
	expander = ARAXExpander()
	query_graph_builtin = {'nodes':
	{'FET_n00':
	{'ids': node_curie,
	'is_set': False},
	'FET_n01':
	{'categories': [adjacent_type],
	'is_set': False}},
	'edges':
	{'FET_e00':
	{'subject': 'FET_n00',
	'object': 'FET_n01',
	'predicates': [rel_type]}
	}}
	query_graph = QueryGraph.from_dict(query_graph_builtin)
	from kp_selector import KPSelector
	kp_selector = KPSelector(kg2_mode=True,
	log=self.response)
	kp_selector.kp_urls = {infores_key: RTX_CONFIG.plover_url}

Note the use of kg2_mode=True.

I just noticed this today, when debugging the dreaded test_ARAX_workflows.py::test_FET_example_3 unit test.

I think at some point we will want to transition to using the Tier0 graph, somehow, for fisher_exct_test.py.

[saramsey]

I've tagged the folks who I hope will jump in on the discussion. But all are welcome to discuss!

[saramsey]

I suppose the default plan is eventually we will just pivot to having fisher_exact_test.py query Tier0/PloverDB

[saramsey]

The good news is that, not counting ARAX_query.py and unit tests, the only place other than fisher_exact_test.py that seems to use ARAXExpander is ARAX_resultify.py.

[saramsey]

In terms of prioritization, @dkoslicki indicated this could be something to implement in Summer 2026.