fetch timeout

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-30)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.92 (2020-01-30)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2og3

Traceback (most recent call last):  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 44, in open  
db_models, status = _fetch_from_database(session, db_id, db_name, db_format,
name, ignore_cache, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 153, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 438, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 501, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 383, in fetch_cb  
return fetch_shim(session, identifier, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 381, in fetch_shim  
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 46, in fetch_from_database  
return fetcher(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 315, in fetch_mmcif  
cache, ignore_cache=ignore_cache)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 69, in fetch_file  
check_certificates=check_certificates, name=name, timeout=timeout)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 142, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.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
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.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
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 543, in _open  
'_open', req)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1345, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 1320, in do_open  
r = h.getresponse()  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1336, in getresponse  
response.begin()  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 306, in begin  
version, status, reason = self._read_status()  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 267, in _read_status  
line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 589, in readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
socket.timeout: timed out  
  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/1B20BCCB-9199-4BB3-A310-A642D1247DA0/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 589, in readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-10.36.30
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

[Eric Pettersen]

Duplicate of #3439