Opened 5 years ago

Closed 5 years ago

#3778 closed defect (fixed)

Segger: Attempted to add model mask.seg #2 to scene twice

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-48-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Openning .seg file returns the error: "ValueError: Attempted to add model mask.seg #2 to scene twice"

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 266, in _strptime  
month = _months.index(month_name)  
ValueError: tuple.index(x): x not in tuple  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 38, in nag  
_check_usage(session)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage  
usage = _get_usage()  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 228, in _get_usage  
usage["dates"].append(_strptime(value))  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 275, in _strptime  
raise ValueError("time data does not match format")  
ValueError: time data does not match format  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/davidherreros/mask.seg format segger

Summary of feedback from opening /home/davidherreros/mask.seg  
---  
note | Showing 4 region surfaces  
  
Traceback (most recent call last):  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent  
func(*args, **kw)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 188, in provider_open  
session.models.add(opened_models)  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/models.py", line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
ValueError: Attempted to add model mask.seg #2 to scene twice  
  
ValueError: Attempted to add model mask.seg #2 to scene twice  
  
File
"/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/models.py", line 641, in add  
raise ValueError('Attempted to add model %s to scene twice' % model)  
  
See log for complete Python traceback.  
  
Showing mask.seg - 4 regions, 4 surfaces  

> ui tool show Shell

/home/davidherreros/scipion3/software/em/chimerax-1.1/lib/python3.7/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  




OpenGL version: 3.3.0 NVIDIA 450.66
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware m15 R2
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        6.7G        4.1G        405M        4.6G        8.0G
	Swap:          5.6G          0B        5.6G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:3e9b]	
	Subsystem: Dell Device [1028:093b]	
	Kernel driver in use: i915
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: 1.6.1
    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: 1.0
    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-ScipionExtensions: 1.2
    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 (5)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Segger: Attempted to add model mask.seg #2 to scene twice

Reported by David Herreros

comment:2 by Tom Goddard, 5 years ago

Cc: gregdp@… added

I was able to reproduce your problem opening mask.seg. Somehow the code ends up trying to open a model twice. Should be easy to fix. Possibly older ChimeraX 1.0 will open the file. In 1.1 I added more code to check that duplicate models were not mistakenly opened.

This ticket also showed the registration code failed. That will also need fixing.

comment:3 by Tom Goddard, 5 years ago

Fixed opening of .seg file. Code was trying to add the segmentation model to the session twice.

Need to look at registration error next.

comment:4 by Tom Goddard, 5 years ago

The error at startup is caused by a bug in the registration code. I made a new ticket for that #3785. The problem is the format of dates in the preregistration file where ChimeraX tracks how many times the program has been used so it can ask you to register after 15 days of use. The simplest fix for that error is to delete the preregistration file. To find where that file is on your system use ChimeraX command

info path user unversioned config

and it will report the path in the Log.

comment:5 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed reading .seg file.

Registration error on start up is ticket #3785.

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