Opened 5 years ago

Closed 5 years ago

#4228 closed defect (duplicate)

IHM: cached zip file corrupted

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7639 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
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 pdbdev:00000010

Summary of feedback from opening 00000010 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
zipfile.BadZipFile: File is not a zip file  
  
zipfile.BadZipFile: File is not a zip file  
  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:00000010

Summary of feedback from opening 00000010 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
zipfile.BadZipFile: File is not a zip file  
  
zipfile.BadZipFile: File is not a zip file  
  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7639
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Pro
OS: Microsoft Windows 10 家庭版 (Build 18363)
Memory: 8,507,518,976
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7300U CPU @ 2.60GHz"
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-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
    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: 1.18.5+mkl
    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: 1.4.1
    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
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → IHM: cached zip file corrupted

comment:2 by Eric Pettersen, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #4229

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