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higlass / higlass-docker

Builds a docker container wrapping higlass-server and higlass-client in nginx
MIT License
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higlass-manage start raises error ValueError: invalid literal for int() with base 16: b'' #169

Open enjras opened 3 years ago

enjras commented 3 years ago

I just installed higlass, but if I try to start working with it by typing higlass-manage start, the following error is raised:

`Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 697, in _update_chunk_length self.chunk_left = int(line, 16) ValueError: invalid literal for int() with base 16: b''

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 438, in _error_catcher yield File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 764, in read_chunked self._update_chunk_length() File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 701, in _update_chunk_length raise InvalidChunkLength(self, line) urllib3.exceptions.InvalidChunkLength: InvalidChunkLength(got length b'', 0 bytes read)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/requests/models.py", line 753, in generate for chunk in self.raw.stream(chunk_size, decode_content=True): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 572, in stream for line in self.read_chunked(amt, decode_content=decode_content): File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 793, in read_chunked self._original_response.close() File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/contextlib.py", line 135, in exit self.gen.throw(type, value, traceback) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py", line 455, in _error_catcher raise ProtocolError("Connection broken: %r" % e, e) urllib3.exceptions.ProtocolError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))`

I obtain similar problems by trying to ingest a bedfile.

Any help is very much appreciated!

pkerpedjiev commented 3 years ago

Hi! Could you take a look at the solution here and see if it helps?

https://github.com/higlass/higlass-manage/issues/67

enjras commented 3 years ago

I'm not so sure, in that solution, you suggested to go to the application settings, clear the cookies and reinstall urllib3. I apologize if the question is stupid, but it is not clear to me which application you are referring to.

pkerpedjiev commented 3 years ago

Oh, I'm sorry. You don't have to reinstall urllib3. Just go to your browser's developer tools.

image

Go to application:

image

And then under cookies remove the one for localhost (not shown in the screenshot but it should be there for you):

image

enjras commented 3 years ago

I think I solved the problem by modyifing the file response.py as you suggested. I was able to find it at the path: /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/urllib3/response.py

Thank you so much!

enjras commented 3 years ago

btw if I went through the developer tools (thanks for explaining there weren't cookies for the localhost)