Fails to start on Windows 10, corrupted ui preference file

[joseph.chamieh@…]

ChimeraX fails to start on Windows 10 due to a corrupted ui preferences file. Not sure how this can happen, but we should definitely catch errors parsing preference files and then just ignore the preference file and issue an error dialog about the corrupted file, but still start. Probably also the code should rename the corrupted file, for instance, ui-1 to ui-1.corrupted and ask the user in the error message to submit a bug report and attach the renamed file.

Begin forwarded message:

From: "Joseph Chamieh"
Subject: RE: [chimerax-users] ChimeraX troubleshooting
Date: June 17, 2020 at 2:03:57 PM PDT
To: "'Tom Goddard'"
Cc: <chimerax-users@…>

Dear Tom
Thank you for your answer, this is the result of what you asked for:

C:\>"C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug
C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses

import imp, sys, os

Traceback (most recent call last):

File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193, in _run_module_as_main

"main", mod_spec)

File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85, in _run_code

exec(code, run_globals)

File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 895, in <module>

exit_code = init(sys.argv)

File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\ChimeraX_main.py", line 502, in init

sess.ui = ui_class(sess)

File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\ui\gui.py", line 110, in init

self.settings = UI_Settings(session, "ui")

File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\settings.py", line 165, in init

ConfigFile.init(self, session, tool_name, version=version)

File "C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\configfile.py", line 289, in init

self._config.read(self._filename, encoding='utf-8')

File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 696, in read

self._read(fp, filename)

File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 1079, in _read

raise MissingSectionHeaderError(fpname, lineno, line)

configparser.MissingSectionHeaderError: File contains no section headers.
file: 'C:
Users
Joseph
AppData
Local
UCSF
ChimeraX
ui-1', line: 1
'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'

I remain at your disposal for any further information
Best regards
Joseph

[Tom Goddard]

Same bug reported as #3346 involving corrupted ModelPanel preferences file.

[joseph.chamieh@…]

Dear all,
Please find attached the ui-1 file 
Best regards
Joseph

_____________________________________________________________________
Joseph Chamieh, PhD, HDR
Institut des Biomolécules Max Mousseron, UMR CNRS 5247, 
Université de Montpellier, 
Place Eugène Bataillon, case courrier 1706,
F-34095 Montpellier Cedex 5, France
Phone: +33 4 67 14 39 20
Fax: +33 4 67 63 10 46
http://www.dsbc.univ-montp2.fr/recherche_en.html
http://orcid.org/0000-0003-4209-1337
______________________________________________________________________


-----Message d'origine-----
De : ChimeraX [mailto:ChimeraX-bugs-admin@cgl.ucsf.edu] 
Envoyé : Wednesday, June 17, 2020 11:25 PM
À : undisclosed-recipients:
Cc : chimera-programmers@cgl.ucsf.edu; gregc@cgl.ucsf.edu; joseph.chamieh@umontpellier.fr
Objet : [ChimeraX] #3414: Fails to start on Windows 10, corrupted ui preference file

#3414: Fails to start on Windows 10, corrupted ui preference file
------------------------------+---------------------------------
 Reporter:  joseph.chamieh@…  |               Owner:  Greg Couch
     Type:  defect            |              Status:  assigned
 Priority:  moderate          |           Milestone:
Component:  Core              |             Version:
 Keywords:                    |          Blocked By:
 Blocking:                    |  Notify when closed:
 Platform:  all               |             Project:  ChimeraX
------------------------------+---------------------------------
 ChimeraX fails to start on Windows 10 due to a corrupted ui preferences  file.  Not sure how this can happen, but we should definitely catch errors  parsing preference files and then just ignore the preference file and  issue an error dialog about the corrupted file, but still start.  Probably  also the code should rename the corrupted file, for instance, ui-1 to  ui-1.corrupted and ask the user in the error message to submit a bug  report and attach the renamed file.

 Begin forwarded message:

 From: "Joseph Chamieh"
 Subject: RE: [chimerax-users] ChimeraX troubleshooting
 Date: June 17, 2020 at 2:03:57 PM PDT
 To: "'Tom Goddard'"
 Cc: <chimerax-users@cgl.ucsf.edu>

 Dear Tom
 Thank you for your answer, this is the result of what you asked for:

 C:\>"C:\Program Files\ChimeraX 1.0\bin\ChimeraX-console.exe" --debug  C:\Program Files\ChimeraX 1.0\bin\lib\site-
 packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is  deprecated in favour of importlib; see the module's documentation for  alternative uses
   import imp, sys, os
 Traceback (most recent call last):
   File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 193, in  _run_module_as_main
     "__main__", mod_spec)
   File "C:\Program Files\ChimeraX 1.0\bin\lib\runpy.py", line 85, in  _run_code
     exec(code, run_globals)
   File "C:\Program Files\ChimeraX 1.0\bin\lib\site-  packages\ChimeraX_main.py", line 895, in <module>
     exit_code = init(sys.argv)
   File "C:\Program Files\ChimeraX 1.0\bin\lib\site-  packages\ChimeraX_main.py", line 502, in init
     sess.ui = ui_class(sess)
   File "C:\Program Files\ChimeraX 1.0\bin\lib\site-  packages\chimerax\ui\gui.py", line 110, in __init__
     self.settings = UI_Settings(session, "ui")
   File "C:\Program Files\ChimeraX 1.0\bin\lib\site-  packages\chimerax\core\settings.py", line 165, in __init__
     ConfigFile.__init__(self, session, tool_name, version=version)
   File "C:\Program Files\ChimeraX 1.0\bin\lib\site-  packages\chimerax\core\configfile.py", line 289, in __init__
     self._config.read(self._filename, encoding='utf-8')
   File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 696,  in read
     self._read(fp, filename)
   File "C:\Program Files\ChimeraX 1.0\bin\lib\configparser.py", line 1079,  in _read
     raise MissingSectionHeaderError(fpname, lineno, line)
 configparser.MissingSectionHeaderError: File contains no section headers.
 file: 'C:\\Users\\Joseph\\AppData\\Local\\UCSF\\ChimeraX\\ui-1', line: 1  '\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00'

 I remain at your disposal for any further information  Best regards  Joseph

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3414>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

ui-1​

[joseph.chamieh@…]

Added by email2trac

[Tom Goddard]

ui-1 contains 46 zero bytes. Usually this is a short text file of about that length. Maybe the buffer values were somehow set to zero before being written.