StarMap: 'NoneType' object has no attribute 'strip'

[scluo@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.7.dev202307150241 (2023-07-15 02:41:29 UTC)
Description
I got this problem when I want to lauhch the Starmap on chimeraX

Log:
UCSF ChimeraX version: 1.7.dev202307150241 (2023-07-15)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_StarMap-1.2.15-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 23.2  
[notice] To update, run: ChimeraX.exe -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing e:\download\chimerax_starmap-1.2.15-py3-none-any.whl  
Requirement already satisfied: pyparsing in c:\users\chimerax\bin\lib\site-
packages (from ChimeraX-StarMap==1.2.15) (3.1.0)  
Collecting pyqtgraph  
Using cached pyqtgraph-0.13.3-py3-none-any.whl (960 kB)  
Requirement already satisfied: ChimeraX-Core>=1.4 in
c:\users\chimerax\bin\lib\site-packages (from ChimeraX-StarMap==1.2.15)
(1.7.dev202307150241)  
Requirement already satisfied: numpy>=1.20.0 in
c:\users\chimerax\bin\lib\site-packages (from pyqtgraph->ChimeraX-
StarMap==1.2.15) (1.23.5)  
Installing collected packages: pyqtgraph, ChimeraX-StarMap  
Successfully installed ChimeraX-StarMap-1.2.15 pyqtgraph-0.13.3  
\---  

Successfully installed ChimeraX-StarMap-1.2.15 pyqtgraph-0.13.3  
Installed ChimeraX-StarMap (1.2.15)  

> ui tool show StarMap

> starting StarMap 1.2.15  
> use command <stmhelp show> for the StarMap manual  
Traceback (most recent call last):  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py",
line 560, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1271, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\starmap\\__init__.py", line 39, in start_tool  
check_config()  
File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\starmap\config.py", line 285, in check_config  
check_rosetta_cmd()  
File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\starmap\config.py", line 224, in check_rosetta_cmd  
ROSETTA_SCRIPTS_CMD = rosetta_cmd_location(ROSETTA_SCRIPTS_CMD) or
ROSETTA_SCRIPTS_CMD  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\starmap\config.py", line 111, in rosetta_cmd_location  
if platform.system() == "Windows" and not wsl_check_distribution():  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\starmap\config.py", line 78, in wsl_check_distribution  
diststr = wsl_find_location(' --status')  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User1\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\starmap\config.py", line 70, in wsl_find_location  
return str(output.strip())  
^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'strip'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 1715,
in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\run.py",
line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\ui\cmd.py", line 219,
in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py",
line 567, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool StarMap in
bundle ChimeraX-StarMap:  
'NoneType' object has no attribute 'strip'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool StarMap in
bundle ChimeraX-StarMap:  
'NoneType' object has no attribute 'strip'  
  
File "C:\Users\ChimeraX\bin\Lib\site-packages\chimerax\core\toolshed\info.py",
line 567, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  
Exception in thread Thread-4 (_readerthread):  
Traceback (most recent call last):  
File "C:\Users\ChimeraX\bin\Lib\threading.py", line 1038, in _bootstrap_inner  
self.run()  
File "C:\Users\ChimeraX\bin\Lib\threading.py", line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Users\ChimeraX\bin\Lib\subprocess.py", line 1552, in _readerthread  
buffer.append(fh.read())  
^^^^^^^^^  
UnicodeDecodeError: 'cp950' codec can't decode byte 0x97 in position 11:
illegal multibyte sequence  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GT 730/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: zh_TW.cp950
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7090
OS: Microsoft Windows 10 專業版 (Build 19044)
Memory: 16,887,386,112
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700 @ 2.50GHz
OSLanguage: zh-TW

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307150241
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.30.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.41.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.4
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8
    WMI: 1.5.1

[wolfgang.lugmayr@…]

Hi,

this bug is related to the Windows Subsystem for Linux which is needed by StarMap to run Rosetta or MEDIC.

Which Windows 7, 10, 11 is used? I need this to examine and reproduce the plugin error.

Can you also please open the Windows cmd.exe or the PowerShell and type:
wsl --status

And attach the result of this command to this ticket?

Thanks & cheers,
Wolfgang




----- Original Message -----
From: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
To: "starmap" <starmap@marlovitslab.org>, scluo@gate.sinica.edu.tw
Sent: Monday, 17 July, 2023 20:25:01
Subject: Re: [ChimeraX] #9380: StarMap: 'NoneType' object has no attribute 'strip' (was: ChimeraX bug report submission)

#9380: StarMap: 'NoneType' object has no attribute 'strip'
----------------------------------+------------------------------
          Reporter:  scluo@\u2026      |      Owner:  Wolfgang Lugmayr
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+------------------------------
Changes (by pett):

 * component:  Unassigned => Third Party
 * owner:  (none) => Wolfgang Lugmayr
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => assigned
 * summary:  ChimeraX bug report submission => StarMap: 'NoneType' object
     has no attribute 'strip'

[wolfgang.lugmayr@…]

Hi,

the original error message by the reporter was by calling
wsl --status
Error code: Wsl/WSL_E_WSL_OPTIONAL_COMPONENT_REQUIRED.

On all out test machines it returns an empty string if WSL was not installed yet.
Once WSL was successful installed it returns the default distribution name.

Could you please confirm that after 'wsl --install' the error has gone?

Meanwhile i improved the result check and print the messages of this command also in the ChimeraX log window.
This includes fixing the NoneType error. The fix is in StarMap v1.2.16+

I am not sure if I should make an extra toolshed release immediately for it, since I cannot influence the WSL installation process. I can only print more hints and updated the manual. Showing the StarMap manual already works when its installed but not opened.

Cheers,
Wolfgang

----- Original Message -----
From: "Wolfgang Lugmayr" <wolfgang.lugmayr@cssb-hamburg.de>
To: "chimerax-bugs" <ChimeraX-bugs@cgl.ucsf.edu>
Cc: "starmap" <starmap@marlovitslab.org>, "scluo" <scluo@gate.sinica.edu.tw>
Sent: Tuesday, 18 July, 2023 10:55:09
Subject: Re: [ChimeraX] #9380: StarMap: 'NoneType' object has no attribute 'strip' (was: ChimeraX bug report submission)

Hi,

this bug is related to the Windows Subsystem for Linux which is needed by StarMap to run Rosetta or MEDIC.

Which Windows 7, 10, 11 is used? I need this to examine and reproduce the plugin error.

Can you also please open the Windows cmd.exe or the PowerShell and type:
wsl --status

And attach the result of this command to this ticket?

Thanks & cheers,
Wolfgang




----- Original Message -----
From: "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu>
To: "starmap" <starmap@marlovitslab.org>, scluo@gate.sinica.edu.tw
Sent: Monday, 17 July, 2023 20:25:01
Subject: Re: [ChimeraX] #9380: StarMap: 'NoneType' object has no attribute 'strip' (was: ChimeraX bug report submission)

#9380: StarMap: 'NoneType' object has no attribute 'strip'
----------------------------------+------------------------------
          Reporter:  scluo@\u2026      |      Owner:  Wolfgang Lugmayr
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+------------------------------
Changes (by pett):

 * component:  Unassigned => Third Party
 * owner:  (none) => Wolfgang Lugmayr
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => assigned
 * summary:  ChimeraX bug report submission => StarMap: 'NoneType' object
     has no attribute 'strip'

[Eric Pettersen]

Hi Wolfgang,

Whether to update immediately is obviously up to you. If it were me in this case, if there were other changes that would be occurring soon-ish I might wait to batch this with those, but if it was probably going to be awhile before the next version I'd just go ahead and push out these changes.

--Eric

[Eric Pettersen]

Fixed in starmap 1.2.17