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While attempting to fix another issue, I noticed this in the logs:
[2024-09-19 11:21:53 +0200] [9] [ERROR] Exception in ASGI application + Exception Group Traceback (most recent call last): | File "/usr/local/lib/python3.11/site-packages/starlette/_utils.py", line 87, in collapse_excgroups | yield | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/base.py", line 190, in __call__ | async with anyio.create_task_group() as task_group: | File "/usr/local/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 678, in __aexit__ | raise BaseExceptionGroup( | ExceptionGroup: unhandled errors in a TaskGroup (1 sub-exception) +-+---------------- 1 ---------------- | Traceback (most recent call last): | File "/usr/local/lib/python3.11/site-packages/uvicorn/protocols/http/httptools_impl.py", line 411, in run_asgi | result = await app( # type: ignore[func-returns-value] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/uvicorn/middleware/proxy_headers.py", line 69, in __call__ | return await self.app(scope, receive, send) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/fastapi/applications.py", line 1054, in __call__ | await super().__call__(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/applications.py", line 123, in __call__ | await self.middleware_stack(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/errors.py", line 186, in __call__ | raise exc | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/errors.py", line 164, in __call__ | await self.app(scope, receive, _send) | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/base.py", line 189, in __call__ | with collapse_excgroups(): | File "/usr/local/lib/python3.11/contextlib.py", line 158, in __exit__ | self.gen.throw(typ, value, traceback) | File "/usr/local/lib/python3.11/site-packages/starlette/_utils.py", line 93, in collapse_excgroups | raise exc | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/base.py", line 191, in __call__ | response = await self.dispatch_func(request, call_next) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/home/worker/app/genotype_api/api/middleware.py", line 12, in dispatch | response = await call_next(request) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/base.py", line 165, in call_next | raise app_exc | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/base.py", line 151, in coro | await self.app(scope, receive_or_disconnect, send_no_error) | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/cors.py", line 93, in __call__ | await self.simple_response(scope, receive, send, request_headers=headers) | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/cors.py", line 148, in simple_response | await self.app(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/middleware/exceptions.py", line 65, in __call__ | await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app | raise exc | File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app | await app(scope, receive, sender) | File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 756, in __call__ | await self.middleware_stack(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 776, in app | await route.handle(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 297, in handle | await self.app(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 77, in app | await wrap_app_handling_exceptions(app, request)(scope, receive, send) | File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app | raise exc | File "/usr/local/lib/python3.11/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app | await app(scope, receive, sender) | File "/usr/local/lib/python3.11/site-packages/starlette/routing.py", line 72, in app | response = await func(request) | ^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/fastapi/routing.py", line 278, in app | raw_response = await run_endpoint_function( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/fastapi/routing.py", line 193, in run_endpoint_function | return await run_in_threadpool(dependant.call, **values) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool | return await anyio.to_thread.run_sync(func, *args) | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/anyio/to_thread.py", line 56, in run_sync | return await get_async_backend().run_sync_in_worker_thread( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread | return await future | ^^^^^^^^^^^^ | File "/usr/local/lib/python3.11/site-packages/anyio/_backends/_asyncio.py", line 851, in run | result = context.run(func, *args) | ^^^^^^^^^^^^^^^^^^^^^^^^ | File "/home/worker/app/genotype_api/api/endpoints/samples.py", line 178, in match | return sample_service.get_match_results( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/home/worker/app/genotype_api/services/endpoint_services/sample_service.py", line 111, in get_match_results | matches: list[MatchResult] = MatchGenotypeService.get_matches( | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | File "/home/worker/app/genotype_api/services/match_genotype_service/match_genotype.py", line 19, in get_matches | genotype_pairs = zip(genotype.genotypes, sample_analysis.genotypes) | ^^^^^^^^^^^^^^^^^^^^^^^^^ | AttributeError: 'NoneType' object has no attribute 'genotypes' +------------------------------------
which seems to be related to MatchGenoTypeService in genotype-api/genotype_api/services/match_genotype_service/match_genotype.py
MatchGenoTypeService
genotype-api/genotype_api/services/match_genotype_service/match_genotype.py
This happens when trying to Find matches: https://cigrid.scilifelab.se/genotype/samples/ACC15622A20. Here is the error message:
The text was updated successfully, but these errors were encountered:
No branches or pull requests
While attempting to fix another issue, I noticed this in the logs:
which seems to be related to
MatchGenoTypeService
ingenotype-api/genotype_api/services/match_genotype_service/match_genotype.py
This happens when trying to Find matches: https://cigrid.scilifelab.se/genotype/samples/ACC15622A20. Here is the error message:
The text was updated successfully, but these errors were encountered: