[not43s]

Update xCRG pin which includes changes for sqlite schema changes.

Related GitHub issues here:
* #2889
* #2891

This was brought up in discussion at AHM (2026-09-30), documented here.

Other notes:

• There is another open PR to test xCRG (here); that one will likely be closed in lieu of this PR being merged.
• We are pinning commit on dev branch, but we are close to a proper xCRG release on pypi (hopefully soon); and so commit pinning ought to go away shortly anyway.

[not43s]

/deploy

[github-actions]

Preview pytest

Build: update-xcrg-pin @ 2fb4c0d

Container: rtx_pr_2897

pytest: 176 passed, 1 failed, 144 skipped in 139.35s (0:02:19)

failed tests and last 80 lines

FAILED test_ARAX_expand.py::test_input_curie_remapping - KeyError: 'n0'

--- last 80 lines of output ---

2026-09-30T18:50:02.942690 INFO: (174) [] Examine input Query for needed information for dispatch
2026-09-30T18:50:02.942727 INFO: (174) [] Found input processing plan. Sending to the ProcessingPlanExecutor
2026-09-30T18:50:02.942749 DEBUG: (174) [] Entering execute_processing_plan
2026-09-30T18:50:02.942800 DEBUG: (174) [] Connecting to ResponseCache
2026-09-30T18:50:02.960852 DEBUG: (174) [] Creating ARAXMessenger instance
2026-09-30T18:50:02.960921 DEBUG: (174) [] No starting messages were referenced. Will start with a blank template Message
2026-09-30T18:50:02.960946 INFO: (174) [] Creating an empty template TRAPI Response
2026-09-30T18:50:02.963009 DEBUG: (174) [] Found actions
2026-09-30T18:50:02.963055 INFO: (174) [] Parsing input actions list
2026-09-30T18:50:02.963078 DEBUG: (174) [] Parsing action: add_qnode(key=n0, ids=KEGG.COMPOUND:C00022)
2026-09-30T18:50:02.963126 DEBUG: (174) [] Parsing action: add_qnode(key=n1, categories=biolink:Protein)
2026-09-30T18:50:02.963164 DEBUG: (174) [] Parsing action: add_qedge(key=e01, subject=n0, object=n1)
2026-09-30T18:50:02.963202 DEBUG: (174) [] Parsing action: expand(kp=infores:retriever)
2026-09-30T18:50:02.963236 DEBUG: (174) [] Parsing action: return(message=true, store=false)
2026-09-30T18:50:02.963278: DEBUG: In BiolinkHelper init
2026-09-30T18:50:02.965084: DEBUG: Loading pickle file: /mnt/data/orangeboard/production/RTX/code/ARAX/BiolinkHelper/biolink_model_4.2.5.yaml
2026-09-30T18:50:02.966539 INFO: (174) [] Processing action 'add_qnode' with parameters {'key': 'n0', 'ids': 'KEGG.COMPOUND:C00022'}
2026-09-30T18:50:02.966588 INFO: (174) [] Adding a QueryNode to Message with input parameters {'key': 'n0', 'ids': 'KEGG.COMPOUND:C00022', 'name': None, 'categories': None, 'is_set': None, 'option_group_id': None}
2026-09-30T18:50:02.966932 DEBUG: (174) [] Looking up ids ['KEGG.COMPOUND:C00022'] in NodeSynonymizer
2026-09-30T18:50:02.984044 INFO: (174) [] Processing action 'add_qnode' with parameters {'key': 'n1', 'categories': 'biolink:Protein'}
2026-09-30T18:50:02.984119 INFO: (174) [] Adding a QueryNode to Message with input parameters {'key': 'n1', 'ids': None, 'name': None, 'categories': 'biolink:Protein', 'is_set': None, 'option_group_id': None}
2026-09-30T18:50:02.984473 INFO: (174) [] Processing action 'add_qedge' with parameters {'key': 'e01', 'subject': 'n0', 'object': 'n1'}
2026-09-30T18:50:02.984516 INFO: (174) [] Adding a QueryEdge to Message with parameters {'key': 'e01', 'subject': 'n0', 'object': 'n1', 'predicates': None, 'option_group_id': None, 'exclude': None}
2026-09-30T18:50:02.984558 INFO: (174) [] Processing action 'expand' with parameters {'kp': 'infores:retriever'}
2026-09-30T18:50:02.984714 DEBUG: (174) [] Loading cached Smart API and meta map info
2026-09-30T18:50:02.986514: DEBUG: In BiolinkHelper init
2026-09-30T18:50:02.988367: DEBUG: Loading pickle file: /mnt/data/orangeboard/production/RTX/code/ARAX/BiolinkHelper/biolink_model_4.2.5.yaml
2026-09-30T18:50:02.989889 DEBUG: (174) [] Saving original query graph (has qnodes {'n1', 'n0'} and qedges {'e01'})..
2026-09-30T18:50:02.990228 DEBUG: (174) [] Applying Expand to Message with parameters {'kp': ['infores:retriever'], 'edge_key': ['e01'], 'node_key': [], 'prune_threshold': None, 'kp_timeout': None, 'return_minimal_metadata': False}
2026-09-30T18:50:02.990273 DEBUG: (174) [] for qnode n0 which is specified by id ['KEGG.COMPOUND:C00022'], setting categories to None
2026-09-30T18:50:02.990298 DEBUG: (174) [] for qnode n1 which is specified by categories ['biolink:Protein'], applying conflations
2026-09-30T18:50:02.990345 DEBUG: (174) [] For qnode n1, conflated categories are: ['biolink:Protein', 'biolink:Gene']
2026-09-30T18:50:02.990366 DEBUG: (174) [] Making sure QG only uses canonical predicates
2026-09-30T18:50:02.990676 DEBUG: (174) [] Query graph for this Expand() call is: {'nodes': {'n0': {'ids': ['KEGG.COMPOUND:C00022'], 'categories': None, 'is_set': False, 'set_id': None, 'set_interpretation': None, 'constraints': [], 'option_group_id': None}, 'n1': {'ids': None, 'categories': ['biolink:Protein', 'biolink:Gene'], 'is_set': False, 'set_id': None, 'set_interpretation': None, 'constraints': [], 'option_group_id': None}}, 'edges': {'e01': {'knowledge_type': None, 'predicates': ['biolink:related_to'], 'subject': 'n0', 'object': 'n1', 'attribute_constraints': [], 'qualifier_constraints': [], 'exclude': False, 'option_group_id': None}}}
2026-09-30T18:50:02.990723 INFO: (174) [] Expanding qedge e01 in lookup fashion
2026-09-30T18:50:02.990976 DEBUG: (174) [] Modified QG for this qedge is (n0:None ['KEGG.COMPOUND:C00022'])-['biolink:related_to']-(n1:['biolink:Protein', 'biolink:Gene'])
2026-09-30T18:50:02.991013 DEBUG: (174) [] For e01, pre-prune threshold is 500
2026-09-30T18:50:02.991045 DEBUG: (174) [] Will use asyncio to run KP queries concurrently
2026-09-30T18:50:02.991276 INFO: (174) [] Expanding qedge e01 using infores:retriever
2026-09-30T18:50:02.991552 DEBUG: (174) [] infores:retriever: Qnodes with an implied parent query ID are: {'n0': 'KEGG.COMPOUND:C00022'}
2026-09-30T18:50:02.991584 DEBUG: (174) [] Verifying that infores:retriever can answer this kind of one-hop query
2026-09-30T18:50:02.992132 DEBUG: (174) [] Sending NodeSynonymizer.get_canonical_curies() a list of 1 curies
2026-09-30T18:50:03.016529 DEBUG: (174) [] Got response back from NodeSynonymizer
2026-09-30T18:50:03.016604 WARNING: (174) [] NodeSynonymizer did not recognize: {'KEGG.COMPOUND:C00022'}
2026-09-30T18:50:03.016913 INFO: (174) [] For query to infores:retriever, set body.parameters.tiers to [0]
2026-09-30T18:50:03.017009 DEBUG: (174) [] infores:retriever: Sending query to infores:retriever API (https://retriever.ci.transltr.io) with timeout=120
*** Looking for pre-existing query_url=https://retriever.ci.transltr.io/query, query_object={'message': {'query_graph': {'nodes': {'n0': {'ids': ['KEGG.COMPOUND:C00022'], 'is_set': False}, 'n1': {'categories': ['biolink:Gene', 'biolink:Protein'], 'is_set': True}}, 'edges': {'e01': {'predicates': ['biolink:related_to'], 'subject': 'n0', 'object': 'n1', 'exclude': False}}}}, 'submitter': 'infores:arax', 'parameters': {'tiers': [0]}} which yields query_hash=9a5b539cbfc430343428b63cc55cfbb243a4d20574d0da377e2f233e647b4f23
*** Planning to write a cache entry for query_url=https://retriever.ci.transltr.io/query, query_object={'message': {'query_graph': {'nodes': {'n0': {'ids': ['KEGG.COMPOUND:C00022'], 'is_set': False}, 'n1': {'categories': ['biolink:Gene', 'biolink:Protein'], 'is_set': True}}, 'edges': {'e01': {'predicates': ['biolink:related_to'], 'subject': 'n0', 'object': 'n1', 'exclude': False}}}}, 'submitter': 'infores:arax', 'parameters': {'tiers': [0]}} which yields query_hash=9a5b539cbfc430343428b63cc55cfbb243a4d20574d0da377e2f233e647b4f23
2026-09-30T18:50:03.076271 DEBUG: (174) [] infores:retriever: No 'results' were returned.
2026-09-30T18:50:03.076373 INFO: (174) [] infores:retriever: Query for edge e01 completed (no answers)
2026-09-30T18:50:03.076404 INFO: (174) [] infores:retriever: checking unbound nodes and edges in result; number of unbound nodes: 0; number of unbound edges: 0
2026-09-30T18:50:03.076823 DEBUG: (174) [] Got answers from all KPs; merging them into one KG
2026-09-30T18:50:03.076955 DEBUG: (174) [] Merging answer into Message.KnowledgeGraph
2026-09-30T18:50:03.077326 DEBUG: (174) [] Sending NodeSynonymizer.get_canonical_curies() a list of 1 curies
2026-09-30T18:50:03.113374 DEBUG: (174) [] Got response back from NodeSynonymizer
2026-09-30T18:50:03.113447 WARNING: (174) [] NodeSynonymizer did not recognize: {'KEGG.COMPOUND:C00022'}
2026-09-30T18:50:03.113705 DEBUG: (174) [] After merging KPs' answers, total KG counts are: no answers
2026-09-30T18:50:03.113754 DEBUG: (174) [] After merging KPs' answers, total aux graphs are: 0
2026-09-30T18:50:03.113781 DEBUG: (174) [] Handling any knowledge source constraints
2026-09-30T18:50:03.113808 DEBUG: (174) [] KP allowlist is None, denylist is set()
2026-09-30T18:50:03.113832 DEBUG: (174) [] Pruning any paths that are now dead ends (with help of Resultify)
2026-09-30T18:50:03.114247 DEBUG: (174) [] Calling Resultify from Expand..
2026-09-30T18:50:03.114288 DEBUG: (174) [] KG node count: 0; KG edge count: 0
2026-09-30T18:50:03.114326 DEBUG: (174) [] Expanded qedges are {'e01'}, expanded qnodes are {'n1', 'n0'}; will resultify only this sub-QG
2026-09-30T18:50:03.114358 DEBUG: (174) [] Non-kryptonite qedges are {'e01'}, non-kryptonite qnodes are {'n1', 'n0'}.
2026-09-30T18:50:03.114402 DEBUG: (174) [] Grabbing only required portion of QG
2026-09-30T18:50:03.114545 DEBUG: (174) [] Required qnodes are {'n1', 'n0'}, required qedges are {'e01'}
2026-09-30T18:50:03.114591 DEBUG: (174) [] KG does not fulfill the (required portion of the) QG. Unfulfilled qnodes: {'n1', 'n0'}. Unfulfilled qedges: {'e01'}.
2026-09-30T18:50:03.114617 WARNING: (174) [] no results returned; empty knowledge graph
2026-09-30T18:50:03.114638 DEBUG: (174) [] num nodes in kg_bound: 0
2026-09-30T18:50:03.114657 DEBUG: (174) [] num edges in kg_bound: 0
2026-09-30T18:50:03.114686 DEBUG: (174) [] After removing dead-end paths, KG counts are: no answers
2026-09-30T18:50:03.114746 WARNING: (174) [] No paths were found in any KPs satisfying qedge {'e01'}.
2026-09-30T18:50:03.115473 INFO: (174) [] Processing action 'return' with parameters {'message': 'true', 'store': 'false'}
2026-09-30T18:50:03.115505 DEBUG: (174) [] Calling ResultTransformer; number of results is: 0
2026-09-30T18:50:03.115528 DEBUG: (174) [] Results have been transformed; number of results is: 0
2026-09-30T18:50:03.115557 INFO: (174) [] Processing is complete and resulted in 0 results.
=========================== short test summary info ============================
FAILED test_ARAX_expand.py::test_input_curie_remapping - KeyError: 'n0'
====== 1 failed, 176 passed, 144 skipped, 1 warning in 139.35s (0:02:19) =======

[2026-09-30T18:52:04Z] wrote the status page /var/www/arax-preview/index.html

Workflow run

[github-actions]

Preview live queries

Build: update-xcrg-pin @ 2fb4c0d

Endpoint: https://cicd.rtx.ai/2897/api/arax/v1.4/query

#	query	HTTP	s	results	KG nodes/edges	status
Example 1	interacts_with (CHEBI:46195)	200	1.93	58	59/132	Success
Example 2	treats inferred (MONDO:0015564)	200	13.40	117	224/1536	Success
Example 3	affects qualified (NCBIGene:1576)	200	3.56	500	506/1963	Success
Pathfinder	pathfinder (MONDO:0005011 to MONDO:0005180)	200	116.96	1	254/2401	Success
[2026-09-30T18:54:30Z] wrote the status page /var/www/arax-preview/index.html

Workflow run

[github-actions]

ARAX preview

🧹 ARAX preview for this PR was removed.