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fixes for neuromorpho interface #148

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fixes for neuromorpho interface #148

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jakobtroidl
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This PR fixes errors in the navis neuromorpho interface. It seems like one of the URLs was deprecated, so I added the new, up-to-date one (http://cng.gmu.edu:8080/). Also, get_neuron previously threw an SSL error when requesting .swc files from the neuromorpho server. I added a workaround that pulls the files using pycurl, which works more reliably.

@schlegelp
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Thanks! This has been a thorn in my side for a while.

I had some local changes sitting around where I used resp = requests.get(url, verify=False) to work around the SSL certificate issue. Have you considered using that instead of pycurl? I'm a bit reluctant to add another dependency if not absolutely necessary.

I would also suggest being transparent about switching off verification. For e.g. you could have verification on by default and catch the SSL error adding a note that users can call the function with get_neuron(x, verify_ssl=False) to work around it but at their own risk.

Thoughts?

@jakobtroidl
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I agree that resp = requests.get(url, verify=False) would be the more elegant solution. It was also my first choice, but it doesn't seem to resolve the issue (see minimal reproducer below). That's why I went with pycurl. Maybe I am doing something wrong...

import requests
url = "https://neuromorpho.org/dableFiles/nathans/CNG%20version/skin2-10x-7.CNG.swc"
response = requests.get(url, verify=False)

throws the following error

Traceback (most recent call last):
  File "/Users/jakobtroidl/Desktop/navis/venv/lib/python3.9/site-packages/urllib3/connectionpool.py", line 467, in _make_request
    self._validate_conn(conn)
  File "/Users/jakobtroidl/Desktop/navis/venv/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1099, in _validate_conn
    conn.connect()
  File "/Users/jakobtroidl/Desktop/navis/venv/lib/python3.9/site-packages/urllib3/connection.py", line 653, in connect
    sock_and_verified = _ssl_wrap_socket_and_match_hostname(
  File "/Users/jakobtroidl/Desktop/navis/venv/lib/python3.9/site-packages/urllib3/connection.py", line 806, in _ssl_wrap_socket_and_match_hostname
    ssl_sock = ssl_wrap_socket(
  File "/Users/jakobtroidl/Desktop/navis/venv/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 465, in ssl_wrap_socket
    ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
  File "/Users/jakobtroidl/Desktop/navis/venv/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 509, in _ssl_wrap_socket_impl
    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
  File "/usr/local/Cellar/python@3.9/3.9.18/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 501, in wrap_socket
    return self.sslsocket_class._create(
  File "/usr/local/Cellar/python@3.9/3.9.18/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 1074, in _create
    self.do_handshake()
  File "/usr/local/Cellar/python@3.9/3.9.18/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 1343, in do_handshake
    self._sslobj.do_handshake()
ssl.SSLError: [SSL: DH_KEY_TOO_SMALL] dh key too small (_ssl.c:1129)

Additionally, this seems to work without SSL errors but returns the wrong string.

import requests
url = "http://cng.gmu.edu:8080/dableFiles/nathans/CNG%20version/skin2-10x-7.CNG.swc"
response = requests.get(url)
print(response.text)

returns

<html><head><title>Apache Tomcat/7.0.54 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 404 - /dableFiles/nathans/CNG%20version/skin2-10x-7.CNG.swc</h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u>/dableFiles/nathans/CNG%20version/skin2-10x-7.CNG.swc</u></p><p><b>description</b> <u>The requested resource is not available.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.54</h3></body></html>

I agree that the user should explicitly set disabling verification. I am happy to update my code after we decide which route to take.

@schlegelp
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FWIW I managed to find a workaround for requests:

import requests
requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += 'DEFAULT:!DH'
url = "https://neuromorpho.org/dableFiles/nathans/CNG%20version/skin2-10x-7.CNG.swc"
response = requests.get(url, verify=False)

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2 participants
@jakobtroidl @schlegelp