add back missing models to openapi.json

[korikuzma]

542 removed the models. we should look at a solution for adding these back. we may want to consider looking to see if there's an alternate way to compute the digests in vrs-python

[korikuzma]

Wanted to post original message from slack on 2/22

I was having an issue with our FastAPI endpoints only returning the minimal information needed to create a digest. We define the response_model as a Pydantic model.

For example, it would return:

{
  "variation": {
    "location": "t-3DrWALhgLdXHsupI-e-M00aL3HgK3y",
    "state": {
      "sequence": "E",
      "type": "LiteralSequenceExpression"
    },
    "type": "Allele"
  }
}

rather than the expected

{
  "variation": {
    "id": "ga4gh:VA.j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L",
    "type": "Allele",
    "digest": "j4XnsLZcdzDIYa5pvvXM7t1wn9OITr0L",
    "location": {
      "id": "ga4gh:SL.t-3DrWALhgLdXHsupI-e-M00aL3HgK3y",
      "type": "SequenceLocation",
      "digest": "t-3DrWALhgLdXHsupI-e-M00aL3HgK3y",
      "sequenceReference": {
        "type": "SequenceReference",
        "refgetAccession": "SQ.cQvw4UsHHRRlogxbWCB8W-mKD4AraM9y"
      },
      "start": 599,
      "end": 600
    },
    "state": {
      "type": "LiteralSequenceExpression",
      "sequence": "E"
    }
  }
}

I think this is because FastAPI sets the mode to json in this line: https://github.com/tiangolo/fastapi/blob/master/fastapi/encoders.py#L225

The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

A work around for this is to remove the response_model field from our FastAPI endpoints and return model.model_dump(exclude_none=True) directly.

[github-actions[bot]]

Closed by #571.