predict-drug-target API results in internal server error

[micheldumontier]

@vemonet

running /predict-drug-target at https://predict-drug-target.137.120.31.160.nip.io/docs#/

with

{
"subjects": ["PUBCHEM.COMPOUND:5329102"]
}

yields an Internal Server Error

did this service ever work? or ideas about what could be happening? thanks!

[vemonet]

This is the API deployed from the GPU server workspace container, it was more for faster training and testing, the idea was to import the prediction endpoint in translator-openpredict, so we don't need to maintain 5 different APIs, and the underlying trained model was not stable (once boost, once random forest), so there might be change to do in the predict function: https://github.com/MaastrichtU-IDS/predict-drug-target/blob/main/src/predict_drug_target/predict.py

Also checking if the pretrained model file loaded for prediction is were the code expects it to be

Checkout the docker compose logs for more details on the error normally

[micheldumontier]

@vemonet thanks for the info!

@ensaremirerol can you check the docker logs?

[ensaremirerol]

Pydantic throws validation error when parsing the Response Object

predict-drug-target-api-1  | INFO:     172.19.0.6:49168 - "POST /predict-drug-target HTTP/1.1" 500 Internal Server Error
predict-drug-target-api-1  | 2024-06-05 14:38:36,180 ERROR: [h11_impl:run_asgi] Exception in ASGI application
predict-drug-target-api-1  | Traceback (most recent call last):
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/anyio/streams/memory.py", line 98, in receive
predict-drug-target-api-1  |     return self.receive_nowait()
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/anyio/streams/memory.py", line 93, in receive_nowait
predict-drug-target-api-1  |     raise WouldBlock
predict-drug-target-api-1  | anyio.WouldBlock
predict-drug-target-api-1  |
predict-drug-target-api-1  | During handling of the above exception, another exception occurred:
predict-drug-target-api-1  |
predict-drug-target-api-1  | Traceback (most recent call last):
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/base.py", line 78, in call_next
predict-drug-target-api-1  |     message = await recv_stream.receive()
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/anyio/streams/memory.py", line 118, in receive
predict-drug-target-api-1  |     raise EndOfStream
predict-drug-target-api-1  | anyio.EndOfStream
predict-drug-target-api-1  |
predict-drug-target-api-1  | During handling of the above exception, another exception occurred:
predict-drug-target-api-1  |
predict-drug-target-api-1  | Traceback (most recent call last):
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/uvicorn/protocols/http/h11_impl.py", line 408, in run_asgi
predict-drug-target-api-1  |     result = await app(  # type: ignore[func-returns-value]
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
predict-drug-target-api-1  |     return await self.app(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/fastapi/applications.py", line 292, in __call__
predict-drug-target-api-1  |     await super().__call__(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/applications.py", line 122, in __call__
predict-drug-target-api-1  |     await self.middleware_stack(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/errors.py", line 184, in __call__
predict-drug-target-api-1  |     raise exc
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/errors.py", line 162, in __call__
predict-drug-target-api-1  |     await self.app(scope, receive, _send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/base.py", line 108, in __call__
predict-drug-target-api-1  |     response = await self.dispatch_func(request, call_next)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/trapi_predict_kit/trapi.py", line 221, in add_process_time_header
predict-drug-target-api-1  |     response = await call_next(request)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/base.py", line 84, in call_next
predict-drug-target-api-1  |     raise app_exc
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/base.py", line 70, in coro
predict-drug-target-api-1  |     await self.app(scope, receive_or_disconnect, send_no_error)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/cors.py", line 91, in __call__
predict-drug-target-api-1  |     await self.simple_response(scope, receive, send, request_headers=headers)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/cors.py", line 146, in simple_response
predict-drug-target-api-1  |     await self.app(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/exceptions.py", line 79, in __call__
predict-drug-target-api-1  |     raise exc
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/middleware/exceptions.py", line 68, in __call__
predict-drug-target-api-1  |     await self.app(scope, receive, sender)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/fastapi/middleware/asyncexitstack.py", line 20, in __call__
predict-drug-target-api-1  |     raise e
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/fastapi/middleware/asyncexitstack.py", line 17, in __call__
predict-drug-target-api-1  |     await self.app(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/routing.py", line 718, in __call__
predict-drug-target-api-1  |     await route.handle(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/routing.py", line 276, in handle
predict-drug-target-api-1  |     await self.app(scope, receive, send)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/starlette/routing.py", line 66, in app
predict-drug-target-api-1  |     response = await func(request)
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/fastapi/routing.py", line 291, in app
predict-drug-target-api-1  |     content = await serialize_response(
predict-drug-target-api-1  |   File "/usr/local/lib/python3.10/dist-packages/fastapi/routing.py", line 154, in serialize_response
predict-drug-target-api-1  |     raise ResponseValidationError(
predict-drug-target-api-1  | fastapi.exceptions.ResponseValidationError: 1 validation errors:
predict-drug-target-api-1  |   {'loc': ('response',), 'msg': 'value is not a valid dict', 'type': 'type_error.dict'}
predict-drug-target-api-1  |

I have no clue where this exceptions starts but I would start checking from the end of that function.

Also maybe casting result to its data object might be a good idea in terms of logging

result_dict = {"hits": scores_list, "count": len(scores_list)}
try:
   result_model = PredictOutput(**result_dict)
except ValidationError as e:
   # Logging - print the dict for debugging
except e:
   # For other exceptions