Opened 6 years ago

Closed 6 years ago

#2707 closed defect (can't reproduce)

Problem showing Toolbar help: failed to load external entity

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Help System Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> RSR10_model_fit_into_20191115_sharpened_map_1.3295angpix_for_figures.cxs

Summary of feedback from opening
RSR10_model_fit_into_20191115_sharpened_map_1.3295angpix_for_figures.cxs  
---  
warning | Unable to restore "SchemesManager" object  
  
opened ChimeraX session  

> show #!2 models

> hide #!2 models

> windowsize 800 1200

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show cartoons

> hide atoms

> select /I:186

21 atoms, 23 bonds, 1 model selected  

> select /J:14

20 atoms, 21 bonds, 1 model selected  

> select up

8077 atoms, 9060 bonds, 1 model selected  

> show sel atoms

> hide sel cartoons

> select clear

> show #!1 models

> volume #1 level 6.24

> select #1

2 models selected  

> ~select #1

Nothing selected  

> select #2

18364 atoms, 19524 bonds, 2 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> select #2

18364 atoms, 19524 bonds, 2 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> select #2

18364 atoms, 19524 bonds, 2 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> select #1

2 models selected  

> ~select #1

Nothing selected  

> select #2/U

607 atoms, 616 bonds, 1 model selected  

> view sel

> ~select

Nothing selected  

> hide #!1 models

> nucleotides fill

> style nucleic stick

Changed 8077 atom styles  

> ui favorite true Toolbar

> help help:user/tools/Toolbar.html

Traceback (most recent call last):  
File
"/Users/zhoub2/Applications/ChimeraX-0.91.app/Contents/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 261, in interceptRequest  
self._callback(info)  
File
"/Users/zhoub2/Applications/ChimeraX-0.91.app/Contents/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 150, in intercept  
return self._intercept_cb(request_info, *args)  
File
"/Users/zhoub2/Applications/ChimeraX-0.91.app/Contents/lib/python3.7/site-
packages/chimerax/help_viewer/tool.py", line 95, in link_clicked  
new_path = _generate_index(path, self.session.logger)  
File
"/Users/zhoub2/Applications/ChimeraX-0.91.app/Contents/lib/python3.7/site-
packages/chimerax/help_viewer/cmd.py", line 121, in _generate_index  
html = lxml.html.parse(source)  
File
"/Users/zhoub2/Applications/ChimeraX-0.91.app/Contents/lib/python3.7/site-
packages/lxml/html/__init__.py", line 939, in parse  
return etree.parse(filename_or_url, parser, base_url=base_url, **kw)  
File "src/lxml/etree.pyx", line 3467, in lxml.etree.parse  
File "src/lxml/parser.pxi", line 1839, in lxml.etree._parseDocument  
File "src/lxml/parser.pxi", line 1865, in lxml.etree._parseDocumentFromURL  
File "src/lxml/parser.pxi", line 1769, in lxml.etree._parseDocFromFile  
File "src/lxml/parser.pxi", line 1163, in
lxml.etree._BaseParser._parseDocFromFile  
File "src/lxml/parser.pxi", line 601, in
lxml.etree._ParserContext._handleParseResultDoc  
File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult  
File "src/lxml/parser.pxi", line 638, in lxml.etree._raiseParseError  
OSError: Error reading file '/share/docs/user/index.html': failed to load
external entity "/share/docs/user/index.html"  
  
OSError: Error reading file '/share/docs/user/index.html': failed to load
external entity "/share/docs/user/index.html"  
  
File "src/lxml/parser.pxi", line 638, in lxml.etree._raiseParseError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (4)

comment:1 by Eric Pettersen, 6 years ago

Component: UnassignedHelp System
Owner: set to Greg Couch
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionProblem showing Toolbar help: failed to load external entity

comment:2 by Greg Couch, 6 years ago

How easy is this for you to reproduce? Does it matter if you type:

help help:user/tools/Toolbar.html

or use the context menu over the toolbar to bring its help?

comment:3 by Eric Pettersen, 6 years ago

Greg, there is no 'reporter' for this ticket.

--Eric

comment:4 by Greg Couch, 6 years ago

Resolution: can't reproduce
Status: assignedclosed

Whoops :-). Can't reproduce this bug.

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