Opened 4 years ago

Closed 4 years ago

#5040 closed defect (can't reproduce)

SSL failure during registration attempt

Reported by: noreng.sigrid@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Infrastructure Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
note | Updating list of available bundles failed: [SSL:
CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate
in certificate chain (_ssl.c:1076)  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1319, in do_open  
encode_chunked=req.has_header('Transfer-encoding'))  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1422, in connect  
server_hostname=server_hostname)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 423, in wrap_socket  
session=session  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 870, in _create  
self.do_handshake()  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 1139, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: self signed certificate in certificate chain (_ssl.c:1076)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in customEvent  
func(*args, **kw)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/gui.py", line 67, in handle_scheme  
self.session.ui.thread_safe(self._register, url)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 342, in thread_safe  
func(*args, **kw)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/gui.py", line 121, in _register  
join_announcements=values["join_announcements"])  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/cmd.py", line 76, in register  
funding, funding_other, comment)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/cmd.py", line 123, in _get_registration  
with urlopen(RegistrationURL, urlencode(params).encode()) as f:  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1362, in https_open  
context=self._context, check_hostname=self._check_hostname)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1076)>  
  
urllib.error.URLError:  
  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1319, in do_open  
encode_chunked=req.has_header('Transfer-encoding'))  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1422, in connect  
server_hostname=server_hostname)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 423, in wrap_socket  
session=session  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 870, in _create  
self.do_handshake()  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 1139, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: self signed certificate in certificate chain (_ssl.c:1076)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in customEvent  
func(*args, **kw)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/gui.py", line 67, in handle_scheme  
self.session.ui.thread_safe(self._register, url)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 342, in thread_safe  
func(*args, **kw)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/gui.py", line 121, in _register  
join_announcements=values["join_announcements"])  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/cmd.py", line 76, in register  
funding, funding_other, comment)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/cmd.py", line 123, in _get_registration  
with urlopen(RegistrationURL, urlencode(params).encode()) as f:  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1362, in https_open  
context=self._context, check_hostname=self._check_hostname)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1076)>  
  
urllib.error.URLError:  
  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1319, in do_open  
encode_chunked=req.has_header('Transfer-encoding'))  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1422, in connect  
server_hostname=server_hostname)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 423, in wrap_socket  
session=session  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 870, in _create  
self.do_handshake()  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py",
line 1139, in do_handshake  
self._sslobj.do_handshake()  
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: self signed certificate in certificate chain (_ssl.c:1076)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in customEvent  
func(*args, **kw)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/gui.py", line 67, in handle_scheme  
self.session.ui.thread_safe(self._register, url)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 342, in thread_safe  
func(*args, **kw)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/gui.py", line 121, in _register  
join_announcements=values["join_announcements"])  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/cmd.py", line 76, in register  
funding, funding_other, comment)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/registration/cmd.py", line 123, in _get_registration  
with urlopen(RegistrationURL, urlencode(params).encode()) as f:  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 525, in open  
response = self._open(req, data)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1362, in https_open  
context=self._context, check_hostname=self._check_hostname)  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed: self signed certificate in certificate chain
(_ssl.c:1076)>  
  
urllib.error.URLError:  
  
File
"/Users/norengs/Desktop/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1321, in do_open  
raise URLError(err)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.21
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Infrastructure
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SSL failure during registration attempt


comment:2 by Greg Couch, 4 years ago

Status: assigned → feedback

Why are you running ChimeraX 0.93? ChimeraX 1.2 is available, you will like the improvements. So please update and let us know if the problem persists.

If it does persists, then my guess is that this bug might be because of the configuration of your company's firewall. So try the new version first. If it still happens, you can turn off getting information about bundle updates by going to Favorites / Settings... dialog. And changing the Toolshed Update Interval to Never. That is not an option with 0.93.

comment:3 by Greg Couch, 4 years ago

Resolution: → can't reproduce
Status: feedback → closed

Unable to reproduce.

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