Opened 5 years ago

Closed 5 years ago

#4318 closed defect (duplicate)

Toolshed using internal UI API

Reported by: sofeaarina@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-42-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
just installed and got this error

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 223, in install  
self.cancel()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2137, in float_changed  
self.main_window._float_changed(self.tool_window, floating)  
AttributeError: 'NoneType' object has no attribute '_float_changed'  
  
AttributeError: 'NoneType' object has no attribute '_float_changed'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2137, in float_changed  
self.main_window._float_changed(self.tool_window, floating)  
  
See log for complete Python traceback.  
  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 223, in install  
self.cancel()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 223, in install  
self.cancel()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 223, in install  
self.cancel()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  

> open /home/sofea/3cxn_clean.pdb

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/toolshed_utils/tool.py", line 115, in cancel  
self.session.ui.main_window.close_request(self.tool_window)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.toolshed_utils.tool.UpdateTool object at 0x7f183ac0dc50>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 601, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 20.2.6
OpenGL renderer: Mesa DRI Intel(R) HD Graphics 4400 (HSW GT2)
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: Hewlett-Packard
Model: HP EliteBook Folio 1040 G1
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-4310U CPU @ 2.00GHz
Cache Size: 3072 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          7.7Gi       3.3Gi       273Mi       1.0Gi       4.1Gi       3.0Gi
	Swap:         2.0Gi        10Mi       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Haswell-ULT Integrated Graphics Controller [8086:0a16] (rev 0b)	
	DeviceName: 32	
	Subsystem: Hewlett-Packard Company Haswell-ULT Integrated Graphics Controller [103c:213e]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by pett, 5 years ago

Cc: pett added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Toolshed using internal UI API

comment:2 by pett, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Hi Sofea,

Thanks for reporting this error. The packages you were trying to install were in fact successfully installed, and the error you encountered was an unrelated bug that happens as the Updates tool window closes, so you can safely ignore it and continue using ChimeraX without any issues.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.