Swagger UI does not submit HTTP request to API server

[eecavanna]

At least for some endpoints (all that I've tried so far), Swagger UI is not submitting the HTTP request to the API server. Instead, an error about data validation is appearing in the JS console. Here's a screenshot showing the error.

Background:

• nmdc-runtime was updated earlier today to use a version of FastAPI that works around yesterday's Swagger UI issue. As a result, that Swagger UI problem stopped affecting us and we were able to access previously-inaccessible sections of the Swagger UI. The web page isn't hanging anymore.
• That nmdc-runtime update seems to have introduced this new issue (see introductory paragraph above) affecting Swagger UI usage.

More details are on Slack, at: https://nmdc-group.slack.com/archives/C05EFGHCYRH/p1698791445508619

[eecavanna]

While creating this Issue, I wanted to cite a version number of nmdc-runtime. Since it currently doesn't have version numbers (see related ticket), I will cite the commit hash instead.

Here's the commit hash where this issue is present: f097bdd

[dwinston]

I suspect this is an outcome of point 9 from #337 (comment). That is, a pydantic field specification like filter: Optional[str] no longer means a field is optional. For pydantic V2, one needs to specify e.g. filter: Optional[str] = None. The first form now (in pydantic V2) seems to mean "this field is required, and its value may be a str or the value None".

[dwinston]

I will first try to use the bump-pydantic tool to migrate, i.e. close #339. If this exercise proves nontrivial, I will revert to 46d6543 and try to pin fastapi as fastapi>=0.104.1 and also pin pydantic as pydantic<2.0.0.