Opened 3 years ago
Closed 3 years ago
#7170 closed defect (fixed)
Session restore: decompression failure
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | 1.5 |
Component: | Sessions | Version: | |
Keywords: | Cc: | Tom Goddard, Eric Pettersen | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Opening the file (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/ykulathu/Downloads/Ligase_fitted.cxs Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 284, in event _open_dropped_file(self.session, event.file()) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1945, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Applications/ChimeraX-1.4.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 "/Applications/ChimeraX-1.4.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 "/Applications/ChimeraX-1.4.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 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 458, in collated_open return remember_data_format() File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py", line 26, in open return cxs_open(session, data, **kw) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 641, in restore use_pickle = stream.peek(1)[0] != ord(b'#') IndexError: index out of range Populating font family aliases took 845 ms. Replace uses of missing font family ".AppleSystemUIFont" with one that exists to avoid this cost. IndexError: index out of range File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 641, in restore use_pickle = stream.peek(1)[0] != ord(b'#') See log for complete Python traceback. > open /Users/ykulathu/Downloads/Ligase_fitted.cxs Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 284, in event _open_dropped_file(self.session, event.file()) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1945, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 38, in run results = command.run(text, log=log, return_json=return_json) File "/Applications/ChimeraX-1.4.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 "/Applications/ChimeraX-1.4.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 "/Applications/ChimeraX-1.4.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 "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 193, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 458, in collated_open return remember_data_format() File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/open_command/cmd.py", line 428, in remember_data_format models, status = func(*func_args, **func_kw) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py", line 26, in open return cxs_open(session, data, **kw) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 1001, in open session.restore(stream, path=path, resize_window=resize_window) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 641, in restore use_pickle = stream.peek(1)[0] != ord(b'#') IndexError: index out of range IndexError: index out of range File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 641, in restore use_pickle = stream.peek(1)[0] != ord(b'#') See log for complete Python traceback. > open /Users/ykulathu/Downloads/Ligase_fitted.cxs Unable to restore session, resetting. Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py", line 705, in restore data = fdeserialize(stream) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/serialize.py", line 70, in msgpack_deserialize return next(stream) File "msgpack/_unpacker.pyx", line 544, in msgpack._cmsgpack.Unpacker.__next__ File "msgpack/_unpacker.pyx", line 478, in msgpack._cmsgpack.Unpacker._unpack File "msgpack/_unpacker.pyx", line 444, in msgpack._cmsgpack.Unpacker.read_from_file File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/lz4/frame/__init__.py", line 651, in read return self._buffer.read(size) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/_compression.py", line 68, in readinto data = self.read(len(byte_view)) File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/_compression.py", line 99, in read raise EOFError("Compressed file ended before the " EOFError: Compressed file ended before the end-of-stream marker was reached opened ChimeraX session Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/volume_viewer.py", line 1530, in <lambda> QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50)) RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/volume_viewer.py", line 1530, in QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50)) See log for complete Python traceback. OpenGL version: 4.1 ATI-4.6.21 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0) Software: System Software Overview: System Version: macOS 11.6.4 (20G417) Kernel Version: Darwin 20.6.0 Time since boot: 10:24 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 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 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0
Change History (5)
comment:1 by , 3 years ago
Cc: | added |
---|---|
Component: | Unassigned → Sessions |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Session restore: decompression failure |
comment:2 by , 3 years ago
I think these error messages mean the session file you tried to open
/Users/ykulathu/Downloads/Ligase_fitted.cxs
is empty or truncated. Maybe you were in the process of downloading it but the download did not complete before you tried to open it. The person this ticket is assigned to is out for 3 weeks.
comment:3 by , 3 years ago
Milestone: | → 1.5 |
---|
Just a quick note before completely going on vacation.
This is consistent with trying to open an empty session file. We will improve the code to report that fact instead of giving a traceback.
comment:4 by , 3 years ago
Status: | assigned → accepted |
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Reported by Yogesh Kulathu