Swagger UI freezes when expanding specific endpoints

[turbomam]

@brynnz22 and I are having trouble just accessing the swagger interface for submitting a changesheet.

@dwinston or @eecavanna can you please look into this or delegate it to somebody else?

[eecavanna]

I'll start digging into this (as my highest priority) by 2:30pm PT. Thanks for bringing it to my/our attention.

[eecavanna]

Here's the URL of the web page in question: https://api.microbiomedata.org/docs

As of 2:37pm PT on Monday 10/31, it is loading OK for me in Brave browser Version 1.57.47 Chromium: 116.0.5845.96 (Official Build) (arm64).

I will check Rancher to see whether it was recently rebooted.

[eecavanna]

I confirmed, via Rancher, that neither pod rebooted within the last 7 days.

Next, I'll check the pods' container logs.

[eecavanna]

I think this is happening due to a bug in Swagger UI.

• Swagger UI v5.9.1 introduced a bug
  • The bug affects the expansion of sections describing endpoints whose schemas are large
• FastAPI v0.104.1 introduced a workaround for the bug
  • The workaround is to pin (i.e. lock) Swagger UI to version v5.9.0 until the upstream bug gets fixed
• nmdc-runtime currently uses FastAPI version 0.103.2
• I want to update nmdc-runtime to use FastAPI v0.104.1 so it gets this bugfix.

@dwinston, I've never updated the fastapi dependency of nmdc-runtime. Do you have a particular process for updating a core dependency like that?

https://github.com/microbiomedata/nmdc-runtime/blob/46d6543339d2436524475a624644652d901a6517/requirements/main.txt#L180C17-L181

[eecavanna]

More details are in this Slack thread.

[dwinston]

Thanks for the investigation, @eecavanna! I'll draft a PR for this.

[dwinston]

1. I first updated the dep in requirements/main.in:

# requirements/main.in
fastapi>=0.104.1 # Pins Swagger UI version to 5.9.0 temporarily to handle a bug crashing it in 5.9.1

2. I then ran make update to update requirements/main.txt.

3. Next, I ran make up-dev to rebuild containers using the latest requirements/main.txt.

4. ran docker compose logs -f fastapi and noticed this error:

fastapi  | pydantic.errors.PydanticUserError: If you use `@root_validator` with pre=False (the default) you MUST specify `skip_on_failure=True`. Note that `@root_validator` is deprecated and should be replaced with `@model_validator`.

5. Updated all @root_validator decorations as required (leaving refactoring to @model_validator to a later time / separate PR)

6. Re-ran make up-dev. Noticed another pydantic-upgrade error via docker compose logs -f fastapi:

fastapi  | TypeError: constr() got an unexpected keyword argument 'regex'

7. Ran a 'Replace in Files' process to take constr(regex= to constr(pattern= throughout the codebase (~10 instances) after jumping to and inspecting constr source (cmd+b in pycharm). Re-ran make up-dev. Another pydantic-upgrade error:

fastapi  |   File "/code/components/nmdc_runtime/workflow_execution_activity/spec.py", line 12, in <module>
fastapi  |     class ActivityTree(BaseModel):
fastapi  |   File "/usr/local/lib/python3.10/site-packages/pydantic/_internal/_model_construction.py", line 184, in __new__
fastapi  |     complete_model_class(
...
fastapi  |     raise PydanticSchemaGenerationError(
fastapi  | pydantic.errors.PydanticSchemaGenerationError: Unable to generate pydantic-core schema for <class 'nmdc_schema.nmdc.WorkflowExecutionActivityId'>. Set `arbitrary_types_allowed=True` in the model_config to ignore this error or implement `__get_pydantic_core_schema__` on your type to fully support it.

8. Added model_config = ConfigDict(arbitrary_types_allowed=True) to class. Noting here briefly that linkml-generated nmdc-schema clases may have an issue with pydantic v2. Re-ran stuff; Another pydantic-upgrade error:

fastapi  | pydantic_core._pydantic_core.ValidationError: 1 validation error for ObjectType
fastapi  | description
fastapi  |   Field required [type=missing,

9. It seems description: Optional[str] no longer means a field is optional. Changed all instances in codebase to description: Optional[str] = None. Re-ran make up-dev, and see "Application startup complete" via docker compose logs -f fastapi

10. confirmed that http://localhost:8000/docs#/metadata/submit_changesheet_metadata_changesheets_submit_postloads without issue.