20260621 Tier-0 graph rollout on ARAX endpoints CATRAX#2832
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Pull request overview
Updates ARAX configuration and supporting tooling for the Tier-0 (20260621) graph/database rollout, along with test harness adjustments to manage known failing tests during deployment.
Changes:
- Point Tier-0 database configuration to the 20260621 dataset paths.
- Update NGD overlay build/audit tooling to use the renamed
stitchimport path and clarify related documentation. - Add pytest support for “broken” tests (skip by default unless opted-in), bump
catrax-pathfinder, and adjust ARAX pathfinder/connect behavior.
Reviewed changes
Copilot reviewed 12 out of 13 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| requirements.txt | Bumps catrax-pathfinder dependency version. |
| code/config_dbs.json | Updates Tier-0 database file locations to the 20260621 rollout paths. |
| code/ARAX/test/test_ARAX_workflows.py | Marks specific workflow tests as “broken” (now skipped by default). |
| code/ARAX/test/test_ARAX_resultify.py | Marks specific resultify tests as “broken” (now skipped by default). |
| code/ARAX/test/test_ARAX_overlay.py | Marks specific overlay tests as “broken” (now skipped by default). |
| code/ARAX/test/test_ARAX_filter_kg.py | Marks warnings-related test as “broken” (now skipped by default). |
| code/ARAX/test/test_ARAX_expand.py | Adjusts an XDTD test query and marks an issue test as “broken”. |
| code/ARAX/test/conftest.py | Adds --runbroken/--runonlybroken and implements default skipping for “broken” tests. |
| code/ARAX/ARAXQuery/Overlay/ngd/README.md | Updates docs to reflect stitch import path and package rename context. |
| code/ARAX/ARAXQuery/Overlay/ngd/build_ngd_database.py | Switches Babel resolver imports from stitch_proj to stitch. |
| code/ARAX/ARAXQuery/Overlay/ngd/audit_ngd_db.py | Switches Babel resolver imports to stitch and updates environment checks. |
| code/ARAX/ARAXQuery/Expand/kp_info_cacher.py | Adds special-casing for Retriever KP URL selection. |
| code/ARAX/ARAXQuery/ARAX_connect.py | Adjusts Pathfinder degree_threshold parameter. |
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| if kp_smart_api_registration["infores_name"] == "infores:retriever": | ||
| raw_url = "https://retriever.ci.transltr.io" | ||
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| "tier0_sqlite": "/translator/data/orangeboard/databases/tier0-20260621/tier0-info-for-overlay_v1.0_tier0-20260621.sqlite", | ||
| "kg2c_sqlite": "/translator/data/orangeboard/databases/tier0-20260621/tier0-info-for-overlay_v1.0_tier0-20260621.sqlite", | ||
| "fda_approved_drugs": "/translator/data/orangeboard/databases/tier0-20260408/fda_approved_drugs_v1.0.pickle", | ||
| "autocomplete": "/translator/data/orangeboard/databases/tier0-20260408/autocomplete_v1.0_tier0-20260408.sqlite", | ||
| "curie_to_pmids": "/translator/data/orangeboard/databases/tier0-20260408/curie_to_pmids_v1.0_tier0-20260408.sqlite", | ||
| "curie_ngd": "/translator/data/orangeboard/databases/tier0-20260408/curie_ngd_v1.0_tier0-20260408.sqlite", | ||
| "gandalf_mmap": "/translator/data/orangeboard/databases/tier0-20260408/gandalf_mmap_tier0-20260408.tar.gz", | ||
| "explainable_dtd_db": "/translator/data/orangeboard/databases/tier0-20260408/ExplainableDTD_v1.0_tier0-20260408-all_with_paths.db", | ||
| "autocomplete": "/translator/data/orangeboard/databases/tier0-20260621/autocomplete_v1.0_tier0-20260621.sqlite", | ||
| "curie_to_pmids": "/translator/data/orangeboard/databases/tier0-20260621/curie_to_pmids_v1.0_tier0-20260621.sqlite", |
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| if "broken" in item.keywords: | ||
| if not config.getoption("--runbroken") and not config.getoption("--runonlybroken"): | ||
| item.add_marker(skip_broken) | ||
| elif config.getoption("--runonlybroken"): | ||
| item.add_marker(skip_working) |
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| query = { | ||
| "nodes": { | ||
| "disease": { | ||
| "ids": ["MONDO:0015564"] | ||
| }, | ||
| "chemical": { | ||
| "ids": ["CHEBI:2659"] | ||
| "categories": ["biolink:ChemicalEntity"] | ||
| } |
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| if args.babel_db: | ||
| p(" [FAIL] stitch_proj — not installed (required for --babel-db)") | ||
| p(" [FAIL] stitch — not installed (required for --babel-db)") | ||
| ok = False | ||
| else: | ||
| p(" [ -- ] stitch_proj — not installed (not needed without --babel-db)") | ||
| p(" [ -- ] stitch — not installed (not needed without --babel-db)") |
edeutsch
approved these changes
Jul 1, 2026
Collaborator
Author
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The cause of failing build is a hard version conflict that the pathfinder bump on issue-2812 introduced: requirements.txt pins bmt==1.4.6 |
Collaborator
Author
|
Another issue found: |
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please see tracking issue #2812