Remove temporary config changes (rolling deployment chore)

[colleenXu]

Often, we use temporary overrides or other config adjustments to handle the staggered deployment of features (Dev -> CI -> Test -> Prod). We direct BTE to use updated/changed SmartAPI yamls.

Once the features are deployed to Prod (on all instances), we have a chore to remove them:

• make the changes into the default
  • merge the SmartAPI yaml changes to the master branch (registered yamls)
  • for TRAPI updates, update the registered yaml to latest TRAPI + all server urls. Then delete the temporary registrations used in the exclusions
• remove the temporary overrides or other config adjustments
• put into the next deployment cycle

We can't remove SmartAPI yaml branches used for the temporary overrides until the overrides have been removed from all instances.

[colleenXu]

For the current Translator Sprint (2/Octopus):

• We have SmartAPI overrides for biolink-4/treats-refactor and source_record_urls
• We have SmartAPI exclusions for the temporary TRAPI 1.5 registrations

[colleenXu]

Update: sprint 2/Octopus has deployed to Prod.

We've decided to add this chore to Eel ~the patch we're doing to Octopus~ with this PR https://github.com/biothings/bte-server/pull/30:

• removing the SmartAPI exclusions for the temporary TRAPI 1.5 registrations. Those temporary registrations have already been deleted.
• removing SmartAPI overrides for treats-refactor/biolink-4. Can use the registered yamls, which have been updated (Service-Provider-only, text-mining targeted)
• removing SmartAPI overrides for the new source_record_urls feature
  • Registered yamls for BioThings BindingDB and MyGene have been updated
  • DIDN'T UPDATE BioThings PFOCR YET. We need to wait until Eel ~the Octopus patch~ is released to all instances because it has code for handling the multiple urls in the PFOCR situation

EDIT: Done 7/31. Once the patch is deployed on all instances, then I can merge this PR to update BioThings PFOCR's registered yaml (which all instances will be using): https://github.com/NCATS-Tangerine/translator-api-registry/pull/153

[tokebe]

Eel changes deployed to Prod, resetting tracking label.

[colleenXu]

@tokebe

If we do any hot-fixes/ CI -> Test deployments for this last sprint / end of phase, can we include https://github.com/biothings/bte-server/pull/51?

It's fine to do because I've already merged the PFOCR yaml update to master. So these changes are live on all instances already. See more notes in https://github.com/biothings/biothings_explorer/issues/882#issuecomment-2445867781

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Documenting our decision on the other overrides...

We agreed to keep the overrides for "removing clinical trial operations" for this phase:

• we can't merge the yaml changes early - because then Prod will be affected and lose all clinical trial data
• we don't know if they'll still want us to use Multiomics CTKP exclusively for clinical trials data next phase. Once we know, then we can decide to merge the yaml changes or not.