NCATSTranslator / ReasonerAPI

NCATS Biomedical Translator Reasoners Standard API
35 stars 28 forks source link

Refactor of source retrieval provenance model #388

Closed mbrush closed 1 year ago

mbrush commented 1 year ago

Adding RetrievalSource object (and a reference to it form Edge) to support richer representations of retrieval provenance per #369.

edeutsch commented 1 year ago

super-fussy yamllint is still unhappy with this PR:

  875:26    error    trailing spaces  (trailing-spaces)

  877:63    error    trailing spaces  (trailing-spaces)

  878:71    error    trailing spaces  (trailing-spaces)

  879:68    error    trailing spaces  (trailing-spaces)

  881:26    error    trailing spaces  (trailing-spaces)

  1197:72   error    trailing spaces  (trailing-spaces)

  1199:61   error    trailing spaces  (trailing-spaces)

  1201:18   error    trailing spaces  (trailing-spaces)

  1204:74   error    trailing spaces  (trailing-spaces)

  1209:23   error    trailing spaces  (trailing-spaces)

  1212:71   error    trailing spaces  (trailing-spaces)

  1214:70   error    trailing spaces  (trailing-spaces)

  1222:17   error    trailing spaces  (trailing-spaces)

  1224:26   error    trailing spaces  (trailing-spaces)

  1225:68   error    trailing spaces  (trailing-spaces)

  1226:73   error    trailing spaces  (trailing-spaces)

  1227:76   error    trailing spaces  (trailing-spaces)

  1228:73   error    trailing spaces  (trailing-spaces)

  1229:75   error    trailing spaces  (trailing-spaces)

  1231:73   error    trailing spaces  (trailing-spaces)

  1232:69   error    trailing spaces  (trailing-spaces)

  1238:1    error    syntax error: found unexpected end of stream (syntax)
edeutsch commented 1 year ago

Automatic checks are still failing. I think the problem is that on line 1124 there is an unclosed quote

edeutsch commented 1 year ago

The automatic build is still failing. The goal would be to ensure that the automatic validation passes. yamllint is now happy but there are multiple OpenAPI schema violations. I think the easiest way to debug your yaml is to paste the entire yaml document in https://editor.swagger.io/ (after clearing the current content) That interface is pretty good about showing you the schema problems.

sierra-moxon commented 1 year ago

I fixed the tests for this change in PR #393, this PR could be closed in favor of that one (it was easier to collaborate on a new branch in this repo, then try to fix this off of a fork of your fork off of Richard's fork @mbrush :) ).

mbrush commented 1 year ago

Replaced with PR #393 (in which @sierra-moxon fixed syntax errors that were causing test failures, and made resourceRole an object to reference so that it can leverage biolink enums)