Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

#1395 closed defect (fixed)

Sequence session-restore failure: get_class() missing 1 required positional argument: 'logger'

Reported by: pascal.albanese@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-10-20)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-10-20)  
How to cite UCSF ChimeraX  

open D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs

open D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs

Summary of feedback from opening D:/UTRECHT_MS/Xlink_results/TL183/Docking.cxs  
---  
error | Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 590, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\tool.py", line 574, in restore_snapshot  
inst.seq_canvas.restore_state(session, data['seq canvas'])  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1085, in restore_state  
header_class = bundle.get_class(class_name)  
TypeError: get_class() missing 1 required positional argument: 'logger'  
  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 542, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2563, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 577, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 815, in open  
    session.restore(stream, path=path, resize_window=resize_window)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 596, in restore  
    self.reset()  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 410, in reset  
    sm.reset_state(container, self)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 576, in reset_state  
    for pbg in list(self.group_map.values()):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
    raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 229, in _actually_resize  
    self._reformat()  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 995, in _reformat  
    self.label_width, self.font_pixels, self.numbering_widths,
self.letter_gaps())  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 1566, in __init__  
    self.layout_lines(alignment.seqs, self.normal_label_color)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2208, in layout_lines  
    self._layout_line(line, label_color, bli, end)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2158, in _layout_line  
    font=self._label_font(line))  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2098, in _label_font  
    if self.has_associated_structures(line):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2036, in has_associated_structures  
    and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\seq-
view\seq_canvas.py", line 2036, in <listcomp>  
    and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 66, in get_attr  
    raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 66, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

open D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs format session

open D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs format session

Summary of feedback from opening D:\UTRECHT_MS\Xlink_results\TL183\Docking.cxs  
---  
error | Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 562, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 410, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 576, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 529, in customEvent  
    func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 278, in defer  
    cxcmd(session, topic)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 374, in cxcmd  
    run(session, cmd)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2563, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 110, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 577, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 815, in open  
    session.restore(stream, path=path, resize_window=resize_window)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 596, in restore  
    self.reset()  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 410, in reset  
    sm.reset_state(container, self)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 576, in reset_state  
    for pbg in list(self.group_map.values()):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 39, in __getattr__  
    return look_in_class._attr_registration.get_attr(attr_name)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
    raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\attr_registration.py", line 64, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 388.75
OpenGL renderer: GeForce 940M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (4)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Sequence session-restore failure: get_class() missing 1 required positional argument: 'logger'

comment:2 by Eric Pettersen, 7 years ago

Resolution: → fixed
Status: accepted → closed

Pushed a fix; can't test until #1397 fixed

comment:3 by Eric Pettersen, 7 years ago

Needed an additional fix. Your session should restore in tomorrow's build. Sorry for the inconvenience.

--Eric

in reply to:  4 ; comment:4 by pascal.albanese@…, 7 years ago 

Thanks!

Il giorno mer 31 ott 2018 alle 23:25 ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> ha scritto:
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