Open command with a directory when a file was expected

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle SEQCROW-1.5.10-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip available: 22.2.2 -> 22.3.1  
[notice] To update, run:
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/MacOS/ChimeraX
-m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing /Users/franktucci/Downloads/SEQCROW-1.5.10-py3-none-any.whl  
Requirement already satisfied: scipy in
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.5.10) (1.9.0)  
Requirement already satisfied: psutil in
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.5.10) (5.9.1)  
Collecting Send2Trash  
Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB)  
Requirement already satisfied: ChimeraX-Core<=1.6,>=1.2 in
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.5.10) (1.5)  
Requirement already satisfied: jinja2 in
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.5.10) (3.1.2)  
Requirement already satisfied: MarkupSafe>=2.0 in
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jinja2->SEQCROW==1.5.10) (2.1.1)  
Requirement already satisfied: numpy<1.25.0,>=1.18.5 in
/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from scipy->SEQCROW==1.5.10) (1.23.1)  
Installing collected packages: Send2Trash, SEQCROW  
Successfully installed SEQCROW-1.5.10 Send2Trash-1.8.0  
\---  

Successfully installed SEQCROW-1.5.10 Send2Trash-1.8.0  
Installed SEQCROW (1.5.10)  

> open /Users/franktucci/Downloads/j_63b86ed5d43bb/j_63b86ed5d43bb.pdb format
> pdb

Chain information for j_63b86ed5d43bb.pdb #1  
---  
Chain | Description  
A E I | No description available  
B F J | No description available  
C G K | No description available  
  

> preset "overall look" "publication 2 (depth-cued)"

Using preset: Overall Look / Publication 2 (Depth-Cued)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes f
    lighting depthCue t

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting simple

> hide atoms

> show cartoons

> open
> /Users/franktucci/Downloads/mole_channels_ADh02Cmt0GTFTGxQDfNAw_1_pdb/tunnels.pdb
> format pdb

Summary of feedback from opening
/Users/franktucci/Downloads/mole_channels_ADh02Cmt0GTFTGxQDfNAw_1_pdb/tunnels.pdb  
---  
warning | Ignored bad PDB record found on line 14  
REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA  
notes | Combining 2 symmetry atoms into TUN /H:40 X  
Combining 2 symmetry atoms into TUN /H:7 X  
Combining 2 symmetry atoms into TUN /H:21 X  
Combining 2 symmetry atoms into TUN /H:23 X  
Combining 2 symmetry atoms into TUN /H:37 X  
9 messages similar to the above omitted  
  

> select add #2

6485 atoms, 50 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 6485 atom styles  

> select subtract #2

Nothing selected  

> open j_63b86ed5d43bb.sphere.json format mole

No such file/path: j_63b86ed5d43bb.sphere.json  

> open /Users/franktucci/Downloads/j_63b86ed5d43bb
> (1)-1/j_63b86ed5d43bb.sphere.json format mole

Traceback (most recent call last):  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 192, in provider_open  
data = _get_stream(mgr, fi.file_name, data_format.encoding)  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 303, in _get_stream  
return io.open_input(path, encoding)  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/io/io.py", line 56, in open_input  
return open(fs_source, mode, encoding=encoding)  
IsADirectoryError: [Errno 21] Is a directory:
'/Users/franktucci/Downloads/j_63b86ed5d43bb'  
  
IsADirectoryError: [Errno 21] Is a directory:
'/Users/franktucci/Downloads/j_63b86ed5d43bb'  
  
File
"/private/var/folders/h9/hf4hwztj0w1gb6td3l814l2m0000gn/T/AppTranslocation/F3485690-584C-4F1E-9B4F-4FA3469A8849/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/io/io.py", line 56, in open_input  
return open(fs_source, mode, encoding=encoding)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.5.6
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 447.80.3.0.0
      OS Loader Version: 540.100.7~14
      SMC Version (system): 2.43f11

Software:

    System Software Overview:

      System Version: macOS 12.3 (21E230)
      Kernel Version: Darwin 21.4.0
      Time since boot: 3 days 23:58

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    Send2Trash: 1.8.0
    SEQCROW: 1.5.10
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Tom Goddard]

User tried to open a json MOLE file with a space in the path without quoting so the error said it failed because the user specified a directory instead of a file.

This failed in the open_command bundle before the MOLE file reader was even called. Probably the open_command code should give a simple error message "A directory <path> was specified when a file is required" instead of a traceback. Reassigning to Eric in case he wants to make that improvement.

[Eric Pettersen]

Not sure how this produced a traceback. For me (using "open /Users/pett format pdb") the IsADirectoryError gets caught as IOError (due to the aliasing to OSError in PEP 3151) and rethrown as a UserError. Nonetheless, I now also specifically catch IsADirectoryError in order to provide a better message to the user.

fix: ​https://github.com/RBVI/ChimeraX/commit/eea61748e7c33ca7371cacd299d2c40266d1c81a