ERROR: Tool "Command Line Interface" failed to start

[michaelclark@…]

Hello ChimeraX team,
I am using chimerax0.6 via SBGRID distribution on a CentOS7 machine and
experienced a crash. After restarting computer and relaunching chimerax,
the command line interface does not load. The standard output upon
launching the program is below. Is there an easy fix to get the command
line back?
Thanks,
Michael

Traceback (most recent call last):
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/toolshed/info.py", line 485, in start_tool
    ti = api._api_caller.start_tool(api, session, self, tool_info)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/toolshed/__init__.py", line 965, in start_tool
    return cls._get_func(api, "start_tool")(session, ti.name)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/cmd_line/__init__.py", line 22, in start_tool
    return CommandLine.get_singleton(session)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/cmd_line/tool.py", line 226, in get_singleton
    return tools.get_singleton(session, CommandLine, 'Command Line
Interface', **kw)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/tools.py", line 214, in get_singleton
    tinst = tool_class(session, tool_name, **kw)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/cmd_line/tool.py", line 32, in __init__
    self.history_dialog = _HistoryDialog(self)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/cmd_line/tool.py", line 263, in __init__
    self.history = FIFOHistory(self.NUM_REMEMBERED, controller.session,
"command line")
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/history.py", line 139, in __init__
    obj = self._history.load()
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/history.py", line 96, in load
    return json.load(f)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/json/__init__.py",
line 299, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook,
**kw)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/json/__init__.py",
line 354, in loads
    return _default_decoder.decode(s)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/json/decoder.py",
line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/json/decoder.py",
line 357, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/tools.py", line 422, in start_tools
    bi.start_tool(session, tool_name)
  File "/programs/x86_64-linux/chimerax/0.6/lib/python3.6/
site-packages/chimerax/core/toolshed/info.py", line 491, in start_tool
    "start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name,
self.name, str(e)))
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Command
Line Interface in bundle ChimeraX-CommandLine:
Expecting value: line 1 column 1 (char 0)
Tool "Command Line Interface" failed to start

[Eric Pettersen]

Hi Michael,
To remedy your problem remove this file:

~/.local/share/ChimeraX/command line

I will try to make ChimeraX more robust in the face of a corrupted command-ine-history file. Thanks for reporting the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Eric Pettersen]

Catch the JSON decode error (due to the corrupted file) and treat the history as empty instead of throwing the error.