Clean up deprecated KG2 code, in light of Plover2.0

[amykglen]

created the branch kg2cleanup for this - plan is to do all work in this branch, and then only merge it to master after ITRB has already deleted their KG2 instances

code to cleanup:

• make the cicd instance query the dev Plover2.0 KG2 instead of its own self-hosted KG2
• update the KG2 rollout issue template
• update the Dockerfile that cicd.rtx.ai uses - either make cicd.rtx.ai use the ARAX Dockerfile, or remove KG2 portions from MergedDockerfile? @sundareswarpullela will tackle this
• remove the KG2 flask server directory: https://github.com/RTXteam/RTX/tree/master/code/UI/OpenAPI/python-flask-server/KG2 (note that we still need a yaml file for the KG2 smartapi registration, but that doesn't live in this directory - it's here)
• get rid of mode == "rtxkg2" code in Expand
• remove kg2_querier.py (verify pathfinder and other modules are no longer using)
  • remove usages of KG2Querier in ARAX_expander.py
  • looks like Pathfinder and CRG are using it - check with Mohsen/Kevin about this
  • @mohsenht will remove related code from pathfinder on Nov. 20
  • @kvnthomas98 will remove related code from CRG on Nov. 20
• in KG2c build, don't create/upload the meta KG anymore (automatically provided by Plover)
• update ARAX's node/edge decoration - should we still be doing this? Plover2.0 returns all attributes... do we still want to decorate other KPs' nodes/edges?
• remove the 'force_local' mechanism from ARAX_expander (no longer relevant)
• Update example here: https://github.com/RTXteam/RTX/blob/master/code/ARAX/Examples/kg2_api_example.py
• Remove all the KG2 UI components and Apache configs and symlinks
• Delete DockerBuild/kg2-config.js?
• Delete KG2-Dockerfile?

other things to update:

• update hard-coded kg2 links on this page https://github.com/NCATSTranslator/Translator-All/wiki/KG2
• update hard-coded kg2 links on this page https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/architecture/kp/rtx-kg2/?h=rtx
  • made a PR to do this (NCATSTranslator/TranslatorTechnicalDocumentation@4cc25ac)
• update Plover wiki details about how to do Plover dev work
• update our spreadsheet on ARAX, KG2, and Plover instances
• look for any other hard-coded KG2 urls in wikis/documentation
• update ARAX wiki with new info on Plover URL override, remove KG2 url override info
• update/remove the KG2 watchdog? @edeutsch

deployment plan:

• @edeutsch will turn off all arax.ncats.io/kg2* endpoints the week of Nov. 11 and verify
• notify Translator community that KG2 URLs are changing (SmartAPI reg will be updated accordingly, but just a heads up for anyone with hard-coded URLs)
• ask ITRB to remove all kg2.x.transltr.io instances on Friday Nov. 15 (after the ITRB PROD deployment is done on Thurs Nov. 14 and verified working)
• after ITRB has removed their kg2 instances, we can merge kg2cleanup into master (pending testing)

please add anything else as you think of it!

[edeutsch]

Thank you @amykglen, this is really great and thorough!

[amykglen]

so I updated the URLs on this wiki page: https://github.com/NCATSTranslator/Translator-All/wiki/KG2

which I think is what is used to populate this documentation page: https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/architecture/kp/rtx-kg2/?h=rtx

but the latter hasn't shown the updates yet - not sure how that works or how often it's run... anyone know about that?

[amykglen]

hey @sundareswarpullela - thanks for your work on the Dockerfiles for this issue. wondering - in the kg2cleanup branch, can we delete the KG2-Dockerfile?