Opened 7 years ago

Closed 6 years ago

#1840 closed defect (fixed)

Session restore with BILD objects: Unable to restore objects of AtomicShapeDrawing class

Reported by: kovacs.bertalan@… Owned by: Greg Couch
Priority: normal Milestone: 1.0
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-47-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.8 (2018-12-17)
Description
Unable to save chimerax session or render png image file from the attached BILD file. 

Log:
Startup Messages  
---  
note | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 338, in __init__  
self.init_available_from_cache(logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 445, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 270, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-12-17)  
How to cite UCSF ChimeraX  

> open c1.0_drawing.bild

Opened BILD data containing 14 objects  

> save session "/HDD/Dokumentumok/PhD/PROJECTS/tandem
PDZ/analyses/15_redo_evaluation/fit_tandem_ensembles/fit_to_template/explicit_analyses/ligand_alignment/session.cxs"

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 791, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 564, in file_save_cb  
self.save_dialog.display(self, session)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
fmt.save(session, filename)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
return self._save(session, filename)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
run(session, "save session %s" % quote_if_necessary(filename))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 917, in save_session  
save(session, filename, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/io.py",
line 198, in export  
result = self.export_func(session, path, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 730, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 500, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 265, in process  
return copy_state(data, convert=self._add_obj)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 174, in copy_state  
return _copy(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 168, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 168, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 172, in _copy  
return convert(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of AtomicShapeDrawing class in
ChimeraX-Atomic bundle because the class name is not listed in the name to
class table for session restore  
  
RuntimeError: Unable to restore objects of AtomicShapeDrawing class in
ChimeraX-Atomic bundle because the class name is not listed in the name to
class table for session restore  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  

> save session "/HDD/Dokumentumok/PhD/PROJECTS/tandem
PDZ/analyses/15_redo_evaluation/fit_tandem_ensembles/fit_to_template/explicit_analyses/ligand_alignment/session.cxs"

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 791, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py",
line 564, in file_save_cb  
self.save_dialog.display(self, session)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
fmt.save(session, filename)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
return self._save(session, filename)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
run(session, "save session %s" % quote_if_necessary(filename))  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 917, in save_session  
save(session, filename, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/io.py",
line 198, in export  
result = self.export_func(session, path, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 730, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 500, in save  
mgr.discovery(self._state_containers)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 265, in process  
return copy_state(data, convert=self._add_obj)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 174, in copy_state  
return _copy(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 161, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 168, in _copy  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 168, in <listcomp>  
items = [_copy(o) for o in data]  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/state.py", line 172, in _copy  
return convert(data)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 240, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
RuntimeError: Unable to restore objects of AtomicShapeDrawing class in
ChimeraX-Atomic bundle because the class name is not listed in the name to
class table for session restore  
  
RuntimeError: Unable to restore objects of AtomicShapeDrawing class in
ChimeraX-Atomic bundle because the class name is not listed in the name to
class table for session restore  
  
File "/usr/lib/ucsf-chimerax/lib/python3.6/site-
packages/chimerax/core/session.py", line 142, in from_obj  
(obj_cls.__name__, bundle_info.name))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 18.2.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) 
OpenGL vendor: Intel Open Source Technology Center
File attachment: c1.0_drawing.bild

c1.0_drawing.bild​

Attachments (1)

c1.0_drawing.bild​ (1.4 KB ) - added by kovacs.bertalan@… 7 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by kovacs.bertalan@…, 7 years ago

Attachment: c1.0_drawing.bild​ added

Added by email2trac

comment:1 by pett, 7 years ago

Component: Unassigned → Depiction
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session restore with BILD objects: Unable to restore objects of AtomicShapeDrawing class

comment:2 by pett, 7 years ago

Milestone: → 1.0

comment:3 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Make AtomicShapeDrawings saveable in sessions.

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