Fix instance data links

[kltm]

Also see #491 (previous PR) and #492 (issue)

[kltm]

Tests are run with npm run tests in javascript/npm/amigo2-instance-data.

[kltm]

Sadly, failing as we (I) cowboy coded the fix to PANTHER yesterday.

[kltm]

@nathandunn Could you pull javascript/lib/amigo/linker.js.tests from the PR--that is actually the wrong library/file. I'm making the corrections in the right place.

[kltm]

@nathandunn For this test, there is still a problem:

      AssertionError: linker: wb gene: expected 'http://www.wormbase.org/db/gene/gene?name=WBGene00003001' to equal 'http://www.wormbase.org/get?name=WBGene00003001&class=Gene'

[kltm]

@nathandunn Could you also remove external/db-xrefs.yaml ? This is an offline backup and I'll update that now separately on master. No relation to anything on this ticket.

[kltm]

@nathandunn I merged back with master after copying from upstream and your external/db-xrefs.yaml is still off--that shouldn't be correct. What other changes were you making that are not reflected upstream?

[nathandunn]

@kltm Fortuitious . . I'll fix and add one more type

[kltm]

Fix in the upstream, yes?

[nathandunn]

is it just a fix in db-xrefs.yaml . ? or do I need to fix it in the tets as well

[kltm]

All data is derived from the upstream db-xrefs.yaml (the copy in external/db-xrefs.yaml is a backup in case the internet of borked and rarely used), so all fixes must start there. If there is a change necessary in the tests, that is done in javascript/npm/amigo2-instance-data/tests/linker.tests.js . I believe the changes in javascript/lib/amigo/linker.js.tests should be removed (that is something of a holdover and not related to the code we publish).

[nathandunn]

@kltm Is there a way to run the tests directly? Make changes to db-xrefs, etc. ? It looks like its running the linker tests off of the old db-xrefs.yaml defintion

[nathandunn]

@kltm Where is the upstream file located?

[kltm]

@nathandunn

Sorry, I though you were clear what the db-xrefs.yaml upstream was from our conversations over the last couple of days. To reiterate: all metadata is derived from geneontology/go-site. In this case: https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml . If it doesn't happen in master on go-site, it didn't happen. The file external/db-xrefs.yaml is an offline backup that is not realistically every used; it was strange times when that backup was added.

Tests are run as: #493 (comment)

A description of the release process is: https://github.com/geneontology/amigo#releases . The install step is what grabs the new upstream and compiles it into JavaScript.

[nathandunn]

I updated the tests to reflect transgenes