[ChimeraX 1.6.1] The log class seems to be not functioning, in the generic linux 64-bit 9 May 2023 release.

[Chung-Han.Tsai@…]

Hi Dear ChimeraX team,

I would like to report a bug that shows in my terminal when opening up the latest production release of ChimeraX 1.6.1 (Generic Linux 64-bit 9 May 2023)

Could you kindly help me look into this? The Log class seems to be not functioning. It wouldn't allow me to report bug from ChimeraX directly as well. The log windows is not showing.
Thank you so much.

Regards,
Chung-Han.
-

The terminal log is as the following, relating to the Log class:

[ct0651@gadi-analysis-01 chimerax-1.6.1]$ ls
ChimeraX  bin  chimerax  etc  include  lib  share
[ct0651@gadi-analysis-01 chimerax-1.6.1]$ ./chimerax
NOTE: available bundle cache has not been initialized yet
NOTE: Traceback (most recent call last):
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 560, in start_tool
    ti = api._api_caller.start_tool(api, session, self, tool_info)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1269, in start_tool
    return cls._get_func(api, "start_tool")(session, ti.name)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/log/__init__.py", line 39, in start_tool
    return cmd.get_singleton(session, create=True)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/log/cmd.py", line 19, in get_singleton
    return tools.get_singleton(session, Log, 'Log', create=create)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton
    tinst = tool_class(session, tool_name, **kw)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/log/tool.py", line 161, in __init__
    from chimerax.ui.widgets import ChimeraXHtmlView
ImportError: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets'
(/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/__init__.py)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/tools.py", line 394, in start_tools
    bi.start_tool(session, tool_name)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool
    raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:
cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets'
(/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/__init__.py)


BUG: Tool "Log" failed to start:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:
cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets'
(/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/ui/widgets/__init__.py)

File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 567, in start_tool
raise ToolshedError(

 _See log for complete Python traceback._


NOTE: UCSF ChimeraX version: 1.6.1 (2023-05-09)
NOTE: © 2016-2023 Regents of the University of California.  All rights reserved.
NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html)

NOTE: Traceback (most recent call last):
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke
    return self._func(self._name, data)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/bug_reporter/crash_report.py", line 127, in
_delayed_register_log_recorder
    _register_log_recorder(session)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/bug_reporter/crash_report.py", line 161, in
_register_log_recorder
    log.record_to_file(log_file)
  File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/log/tool.py", line 397, in record_to_file
    self._log_to_file(self.page_source)
AttributeError: 'Log' object has no attribute 'page_source'


BUG: Error processing trigger "new frame":
AttributeError: 'Log' object has no attribute 'page_source'

File "/g/data/yt35/applications/viz/chimerax-1.6.1/lib/python3.9/site-
packages/chimerax/log/tool.py", line 397, in record_to_file
self._log_to_file(self.page_source)

 _See log for complete Python traceback._


NOTE: Updating list of available bundles failed: Internal Server Error
NOTE: [toolshed cache](help:user/commands/toolshed.html#cache)

[toolshed cache](cxcmd:toolshed cache)

Toolshed cache: /jobfs/84242512.gadi-pbs/.cache/ChimeraX/1.6/toolshed
NOTE: [ui tool show](help:user/commands/ui.html#tool-show) Log

[ui tool show Log](cxcmd:ui tool show Log)







Chung-Han Tsai
Data Analytics Engineer
Centre for Advanced Microscopy
The Australian National University<https://www.anu.edu.au/> | Microscopy Australia<https://micro.org.au/>

The Australian National University
131 Garran Road, Acton ACT 2601, AUSTRALIA
T: + 61 2 6125 8917
chung-han.tsai@anu.edu.au<mailto:chung-han.tsai@anu.edu.au>
https://microscopy.anu.edu.au/

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ChimeraX_error_self.page_source.png​

[Chung-Han.Tsai@…]

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[Eric Pettersen]

The ChimeraXHtmlView import seems to be guarded by a qt_have_web_engine() call, which must be returning False.

[goddard@…]

The generic Linux ChimeraX build often has problems because the Linux system does not have the needed libraries to run the Qt window toolkit, especially the HTML panes like the Log, file history thumbnails overlaying the graphics, and help viewer.  You should certainly use the Ubuntu or Redhat ChimeraX versions if you can since those packages list the needed system libraries and assure that they are installed.  What Linux distribution are you using?  If you have to use the generic Linux version you will need to try to find which system libraries are missing and install them on your system.  You may be able to get an error message that says what library is missing my starting the Python included in ChimeraX (in the bin directory) and then typing "import PyQt6.QWebEngineWidgets".  This will likely fail and may tell you which system library it failed to find that is needed by Qt.

Our servers and email and ChimeraX bug tracking are currently down due to a server upgrade in progress.  So it may take a while before we get your email replies and respond to them.