Registration code not handling some date formats

[rk97@…]

The following bug report has been submitted:
Platform:        Linux-4.17.0-9-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.8 (2018-09-01)
Description
The current version of chimerax deas not recognize "common" extensions of *.pdb1 and *.ent. Files with these extension were recognized by previous versions of chimerax software. It would be great if this functionality (i.e. the ability to read files with pdb1 and ent extensions) was restored. 

Log:
Startup Messages  
---  
warning | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/info.py", line 411, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/toolshed/__init__.py", line 1198, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/nag.py", line 29, in nag  
_check_usage(session)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/nag.py", line 167, in _check_usage  
usage = _get_usage()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/registration/nag.py", line 204, in _get_usage  
usage["dates"].append(datetime.strptime(value, TimeFormat))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/_strptime.py", line 565, in
_strptime_datetime  
tt, fraction = _strptime(data_string, format)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/_strptime.py", line 362, in
_strptime  
(data_string, format))  
ValueError: time data 'Tue Jan 30 11:47:14 2018' does not match format '%a %b
%d %H:%M:%S %Y'  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-09-01)  
How to cite UCSF ChimeraX  

open /home/rajmund/Downloads/pdb5v8m.ent

Unrecognized file suffix '.ent'  

open /home/rajmund/Desktop/3w1k.pdb1

Unrecognized file suffix '.pdb1'  

Unrecognized file suffix '.pdb1'  

open /home/rajmund/Desktop/3w1k.pdb1

Unrecognized file suffix '.pdb1'  

open /home/rajmund/Downloads/pdb5v8m.ent

Unrecognized file suffix '.ent'  

open /home/rajmund/Desktop/3w1k.pdb1

Unrecognized file suffix '.pdb1'  

Unrecognized file suffix '.pdb1'  




OpenGL version: 3.3.0 NVIDIA 390.87
OpenGL renderer: GeForce GTX 970/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: 3k3a.pdb1

3k3a.pdb1​

[rk97@…]

Added by email2trac

[Eric Pettersen]

Thanks for reporting this. We hadn't noticed that the ability to open those files had been lost during some code reorganization. The fix will be in the next daily build.

The log included with your bug report indicates another error, so I will be changing this ticket to one describing that error.

[Conrad Huang]

This is very odd. When I try parsing the same date string using the same code I do not get an error:

>>> x = datetime.strptime("Tue Jan 30 11:47:14 2018", "%a %b %d %H:%M:%S %Y")
>>> x
datetime.datetime(2018, 1, 30, 11, 47, 14)

The only thing I can think of is that the locale has changed and the day or month abbreviation no longer matches what is in the usage file. Can you please send me two items:

• the file named "preregistration" in the directory reported by the ChimeraX command:

  info path user unversioned data
  

• the output of the Unix command:

  printenv
  

Thanks.

[rk97@…]

Dear conrad,

I am sending the "preregistration" file (attached to this message), as well as the ptintenv output as you requested in your message.

Best regards
Rajmund Kazmierkiewicz


W dniu 2018-09-11 23:14:55 użytkownik ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> napisał:

preregistration​

printenv.out​

[rk97@…]

Added by email2trac

[rk97@…]

Added by email2trac

[Conrad Huang]

Hmm. I'm stuck. The preregistration file works fine on my machine, and changing the locale (language and language conventions) made no difference on our Linux machine. Do you get that traceback every time ChimeraX starts? If so, can you try removing the preregistration file and running ChimeraX again to see if the problem continues to happen? Thanks.

[rk97@…]

Dear conrad

I did remove preregistration and chimerax starts without any complains (at least I do not see any comment in the terminal when I start chimerax in the command line). It still does not open *.pdb1 and *.ent files.

Best regards
Rajmund Kazmierkiewicz 

W dniu 2018-09-12 23:37:25 użytkownik ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> napisał:

[Conrad Huang]

Can you please try the current daily build?  Yesterday's build failed 
and therefore did not pick up the fix.

Conrad

On 9/13/2018 12:45 AM, rk97 wrote:

[Conrad Huang]

Fixed in 0062071d.