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 6vyo

6vyo title:  
Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from
SARS coronavirus 2 [more info...]  
  
Chain information for 6vyo #1  
---  
Chain | Description  
A B C D | Nucleoprotein  
  
Non-standard residues in 6vyo #1  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
ZN — zinc ion  
  
  

Unknown command: bg color white  

Unknown command: background solid white  

> set bgColor white

> close session

> open "/Users/nli4519/Desktop/Nprotein CTD Temp/NTD images/NEW/6VYO - chain a
> ribbon structure for fig 1.cxs" format session

opened ChimeraX session  

> ~select

Nothing selected  

> open 2cjr

2cjr title:  
Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid
protein. [more info...]  
  
Chain information for 2cjr #2  
---  
Chain | Description  
A B C D E F G H | nucleocapsid protein  
  
2cjr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  
  

> hide #2

> show #2 ribbons

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2cjr, chain A (#2) with 6vyo, chain A (#1), sequence alignment
score = 20  
RMSD between 9 pruned atom pairs is 1.257 angstroms; (across all 20 pairs:
10.587)  
  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> view #1

> open 2ofz

Traceback (most recent call last):  
File
"/private/var/folders/25/3mqfjt_n7xx23gtwm4msfh108mfkxt/T/AppTranslocation/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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/B18486CF-D50C-417F-9CDE-
EAF1D0DA111A/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.

[pett]

Maybe the call to urlopen() should catch socket.timeout and issue an intelligible error message?

[Tom Goddard]

Fixed.

Catch socket.timeout during fetch and report a simple error message.
I was not able to test this, having no internet connection does not produce a timeout.