Ensure that annotation searches are to the latest production set

[kltm]

Annotation search (and transfer) should be from the latest public version of GO, the same as AmiGO. Workbenches/companions should all be using (at this point) golr-aux.geneontology.io. (It would be nice if this was an environmental variable.)

Check current endpoint usage and update as necessary.

[vanaukenk]

Hi - anything to report on this? Thx.

[kltm]

Not yet. When work has started, I'll move it to "In progress".

[kltm]

A quick survey of URLs that seem to be in use across the systems:

• noctua-annotation-review:
  • ./src/@noctua.form/services/lookup.service.ts
    • http://golr.berkeleybop.org/
  • ./src/environments/environment.prod.ts
    • http://amigo-dev-golr.berkeleybop.org
    • http://noctua-golr.berkeleybop.org/
• simple-annoton-editor:
  • ./app/lookup.service.js
    • http://golr.berkeleybop.org/
• noctua (edited):
  • ./config/startup.yaml.production
    • http://amigo-dev-golr.berkeleybop.org/
    • http://noctua-golr.berkeleybop.org/

[kltm]

From discussion, there are only two locations that should be in use:

• For annotation information, etc., one of the production GOlrs should be used; in our case, let's try http://golr-aux.geneontology.io/solr/
• For entity information (ontology terms, annotatable GPs, etc.), we should be using a "NEO" load; which we have as http://noctua-golr.berkeleybop.org/

This is all well and good--I'll make changes in the base noctua configs and roll those out. @tmushayahama , you'll have to make the changes in the workbenches that you work on. That said, workbenches should probably not be maintaining their own variables in this case, but rather accepting them from the bootstrapping environment, as from https://github.com/geneontology/noctua/blob/master/workbenches/README.md#workbench-variables :

• global_golr_server
• global_golr_neo_server

This way, we do not need to coordinate changes, emergency server switches, etc., as they are all centrally controlled.

[kltm]

noctua-dev should now have the new configuration. After checking that noctua-dev has not caught fire, we can add this to the production instance.

[kltm]

Seems to work. Rolling it out to production.

[kltm]

Seems to work.

[kltm]

Remaining is to examine the separately developed workbenches (@tmushayahama )

[goodb]

Wondering if this is related. Should obsolete terms be showing up in the noctua type-ahead search? e.g. [GO:0043234] protein complex ?

[kltm]

@goodb Unrelated, but a good catch: http://noctua-amigo.berkeleybop.org/amigo/term/GO:0043234 All "NEO" autocompletes should have is_obsolete false pinned.