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Clinical-Genomics / preClinVar

A ClinVar API submission helper written in FastAPI
MIT License
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Error in csv_2_json while reading csv files #42

Closed northwestwitch closed 1 year ago

northwestwitch commented 1 year ago 
INFO:     2022-11-14 15:18:29,246 : 130.237.250.5:0 - "POST /csv_2_json HTTP/1.0" 500
[2022-11-14 15:18:29 +0100] [4] [ERROR] Exception in ASGI application
Traceback (most recent call last):
File "/home/worker/app/preClinVar/csv_parser.py", line 226, in csv_lines
next(csvreader)  # skip header
File "/usr/local/lib/python3.8/csv.py", line 111, in __next__
row = next(self.reader)
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/worker/venv/lib/python3.8/site-packages/uvicorn/protocols/http/h11_impl.py", line 403, in run_asgi
result = await app(self.scope, self.receive, self.send)
File "/home/worker/venv/lib/python3.8/site-packages/uvicorn/middleware/proxy_headers.py", line 78, in __call__
return await self.app(scope, receive, send)
File "/home/worker/venv/lib/python3.8/site-packages/fastapi/applications.py", line 269, in __call__
await super().__call__(scope, receive, send)
File "/home/worker/venv/lib/python3.8/site-packages/starlette/applications.py", line 124, in __call__
await self.middleware_stack(scope, receive, send)
File "/home/worker/venv/lib/python3.8/site-packages/starlette/middleware/errors.py", line 184, in __call__
raise exc
File "/home/worker/venv/lib/python3.8/site-packages/starlette/middleware/errors.py", line 162, in __call__
await self.app(scope, receive, _send)
File "/home/worker/venv/lib/python3.8/site-packages/starlette/exceptions.py", line 93, in __call__
raise exc
File "/home/worker/venv/lib/python3.8/site-packages/starlette/exceptions.py", line 82, in __call__
await self.app(scope, receive, sender)
File "/home/worker/venv/lib/python3.8/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
raise e
File "/home/worker/venv/lib/python3.8/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
await self.app(scope, receive, send)
File "/home/worker/venv/lib/python3.8/site-packages/starlette/routing.py", line 670, in __call__
await route.handle(scope, receive, send)
File "/home/worker/venv/lib/python3.8/site-packages/starlette/routing.py", line 266, in handle
await self.app(scope, receive, send)
File "/home/worker/venv/lib/python3.8/site-packages/starlette/routing.py", line 65, in app
response = await func(request)
File "/home/worker/venv/lib/python3.8/site-packages/fastapi/routing.py", line 227, in app
raw_response = await run_endpoint_function(
File "/home/worker/venv/lib/python3.8/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
return await dependant.call(**values)
File "/home/worker/app/preClinVar/main.py", line 93, in csv_2_json
file_lines = await csv_lines(file)
RuntimeError: coroutine raised StopIteration
[hiseq.clinical@cg-vm1 ~]$
northwestwitch commented 1 year ago

Check here: https://stackoverflow.com/questions/19205807/stopiteration-error-in-pythoncode-while-reading-csv-data