Opened 5 years ago

Closed 5 years ago

#3736 closed defect (can't reproduce)

vr meeting: source code string cannot contain null bytes

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: VR Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.2.dev202009170327 (2020-09-17 03:27:25 UTC)
Description
Another error in VR.

Log:
UCSF ChimeraX version: 1.2.dev202009170327 (2020-09-17)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\data\sars-cov-2-pore\sars-pores.cxs
> format session

Log from Fri Sep 18 10:47:56 2020UCSF ChimeraX version: 1.2.dev202009020044
(2020-09-02)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/sars-cov-2-pore/emd_11514.map

Opened emd_11514.map, grid size 96,96,96, pixel 7.02, shown at level 3.21,
step 1, values float32  

> volume #1 level 2.022

> open /Users/goddard/ucsf/data/sars-cov-2-pore/models/QHD43415_3.pdb

Chain information for QHD43415_3.pdb #2  
---  
Chain | Description  
| No description available  
  

> rainbow #2

Drag select of 287 residues  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> select clear

> open /Users/goddard/ucsf/data/sars-cov-2-pore/F1.large.png

Opened multi-channel map F1.large.png, 3 channels, grid size 1280,639,1, pixel
1, shown at step 1, values uint8  

> volume #3.1 level 105,0 level 120,0.8 level 255,1

> volume #3.1 level 120,0.8 level 255,1 color red color red

> volume #3.1 level 0.4713,0 level 255,1

> volume #3.2 level 107,0 level 121.8,0.8 level 255,1

> volume #3.2 level 107,0 level 255,1 color lime color lime

> volume #3.2 level 0,0 level 255,1

> volume #3.3 level 86.99,0 level 103.8,0.8 level 255,1

> volume #3.3 level 86.99,0 level 255,1 color blue color blue

> volume #3.3 level 0,0 level 255,1

> select #3

7 models selected  

> select clear

> lighting full

> save sars-pores.cxs

opened ChimeraX session  

> meeting start

Meeting at DESKTOP-J8FC2Q4 or 192.168.0.2 port 52194  

> vr true

> lighting simple

started SteamVR rendering  
Connection accepted from 68.84.133.89 port 63633  
Connection accepted from 73.128.52.221 port 51497  
VR mode contour level  

> volume #1 level 3.22

> volume #1 level 3.058

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 294, in read_socket  
while self._message_received(socket):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 384, in _message_received  
msg = self._decode_socket_message(socket)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 450, in _decode_socket_message  
msg_data = ast.literal_eval(msg)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
ValueError: source code string cannot contain null bytes  
  
ValueError: source code string cannot contain null bytes  
  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 294, in read_socket  
while self._message_received(socket):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 384, in _message_received  
msg = self._decode_socket_message(socket)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 450, in _decode_socket_message  
msg_data = ast.literal_eval(msg)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
ValueError: source code string cannot contain null bytes  
  
ValueError: source code string cannot contain null bytes  
  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 294, in read_socket  
while self._message_received(socket):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 384, in _message_received  
msg = self._decode_socket_message(socket)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 450, in _decode_socket_message  
msg_data = ast.literal_eval(msg)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
ValueError: source code string cannot contain null bytes  
  
ValueError: source code string cannot contain null bytes  
  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 294, in read_socket  
while self._message_received(socket):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 384, in _message_received  
msg = self._decode_socket_message(socket)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 450, in _decode_socket_message  
msg_data = ast.literal_eval(msg)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
ValueError: source code string cannot contain null bytes  
  
ValueError: source code string cannot contain null bytes  
  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 294, in read_socket  
while self._message_received(socket):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 384, in _message_received  
msg = self._decode_socket_message(socket)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 450, in _decode_socket_message  
msg_data = ast.literal_eval(msg)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  

[deleted a bunch of these]

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 294, in read_socket  
while self._message_received(socket):  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 384, in _message_received  
msg = self._decode_socket_message(socket)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 450, in _decode_socket_message  
msg_data = ast.literal_eval(msg)  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 46, in
literal_eval  
node_or_string = parse(node_or_string, mode='eval')  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
File "<unknown>", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "", line 0  
  
^  
SyntaxError: unexpected EOF while parsing  
  
File "C:\Program Files\ChimeraX-Sep-17-2020\bin\lib\ast.py", line 35, in parse  
return compile(source, filename, mode, PyCF_ONLY_AST)  
  
See log for complete Python traceback.  
  

> select #1

2 models selected  

> select #3.1

2 models selected  

> select #3.1

2 models selected  

> select clear

> select clear

VR mode tape measure  

> marker delete #4

Deleted 4 markers  

> marker delete #4

Deleted 0 markers  

> marker delete #4

Deleted 2 markers  

> marker delete #4

Deleted 0 markers  

> vr false




OpenGL version: 3.3.0 NVIDIA 442.19
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z270X-Gaming K7
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 17,129,693,184
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz"
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: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    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: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202009170327
    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: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 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: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    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: 2.2.1
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    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: 1.3
    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
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    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: 1.19.2
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    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
    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
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → VR
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → vr meeting: source code string cannot contain null bytes

comment:2 by Tom Goddard, 5 years ago

Resolution: → can't reproduce
Status: assigned → closed

Added debugging to report the offending string containing a null byte so next time I can see how this happened.

The meeting command passes data between participants as utf-8 encoded string of a Python dictionary that can have strings, tuples, numbers, .... It passes repr(d).encode('utf-8') where d is the dictionary. Then it decodes the literal value with ast.literal_eval(s.decode('utf-8')). Somehow in this bug that string contained a null byte. I don't think the conversion of string to bytes with encode('utf-8') and then back from bytes to string with decode('utf-8') changed the string. So repr(d) somehow contained a null byte. Testing repr({'value': '\0'}) produces "{'value': '
x00'}" which has a backslash and x and two 0 characters and no null bytes. So it seems that repr() is supposed to produce valid literals which cannot contain null bytes. So I don't have a theory how a null byte got into the string.

Note: See TracTickets for help on using tickets.