20260621 Tier-0 graph rollout: for mid-summer deployment

[saramsey]

• Build database file curie_to_pmids_v1.0_tier0-MMDDYYYY.sqlite (assignee: @hodgesf; subissue: ) (build script: build_ngd_database.py)
• Build database file autocomplete_v1.0_tier0-MMDDYYYY.sqlite (assignee: @hodgesf; subissue: ) (build script: create_load_db.py)
• Build database file tier0-info-for-overlay_v1.0_tier0-MMDDYYYY.sqlite (assignee: @hodgesf; subissue: ) (build script: generate_sqlite.py)
• Build database file curie_ngd_v1.0_tier0-MMDDYYYY.sqlite (assignee: @mohsenht; subissue: )
• Build database file ExplainableDTD_v1.0_tier0-MMDDYYYY-all_with_paths.db (assignee: @chunyuma; subissue: )
• gandalf_mmap tarball refresh work. Work with PSU team on this. (assignee: @mohsenht; subissue: )
• Update ARAX config_dbs.json for the new database files. (assignee: @bazarkua; subissue: )
• Update ARAX_database_manager.py for the new database files. (assignee: @bazarkua; subissue: )
• Stage all rebuilt Tier0 KG-based ARAX database files on the following servers: (assignee: @hodgesf; subissue: )
  • team-expander-USERNAME@sftp.transltr.io
  • ARAX-databases.rtx.ai
  • arax.ncats.io
  • CICD.rtx.ai
• Trigger a Test Build of issue-XXXX branch on cicd.rtx.ai; verify pytests are all passing (assignee: @bazarkua; subissue: )
• Attempt to merge master branch into issue-XXXX branch (assignee: @hodgesf; subissue: )
• Test the newly merged issue-XXXX branch (assignee: @bazarkua; subissue: )
  • Run pytest suite on a development machine
  • Run ARAX flask server on a development machine; run all four example queries and inspect both the results and the TRAPI message logs
  • Install the code on arax.ncats.io/test and re-test there (check STDERR and make sure the Background Tasker is working)
• Tag head of master branch with the previous Tier0 version in case quick reverting is needed. (pre 20260621)
• Merge of the issue-XXXX branch to master; (assignee: @hodgesf; subissue: ) (ideally, the following people would concur that we are ready, before we do this):
  • @hodgesf
  • @bazarkua
  • @saramsey
  • @dkoslicki
  • @edeutsch
• Roll out the new master branch to arax.ncats.io/test and re-test everything (pytest, flask application, etc.)
• Test ARAX in ITRB CI to see if the auto-deployment worked
• Roll out the new master branch progressively to different arax.ncats.io endpoints, leaving at least one legacy endpoint

PLEASE UPDATE THE SPREADSHEET WITH THE STATUS OF YOUR TASKS TO HELP WITH ASYNC COORDINATION.

For detailed guidance on how to complete the above steps, reference the Rollout Procedure Wiki

[saramsey]

I have created an issue branch (issue-2812) for this work, off of the master branch.

[saramsey]

Currently blocked waiting for the new Tier0 graph