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Opened 5 years ago
Closed 4 years ago
#3967 closed defect (fixed)
Toolshed json parsing error and volume session-restore error
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-957.5.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /localhome/bscml/process/chx_TS_02_DS4/figure_models1.cxs format
> session
Log from Fri Nov 20 15:51:09 2020UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /localhome/bscml/process/chx_TS_02_DS4/figure_models1.cxs
Log from Fri Nov 20 15:28:35 2020 Startup Errors
---
bug | Error preloading available bundles:
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 12797 column 22
(char 453238)
File
"/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/json/decoder.py",
line 353, in raw_decode
obj, end = self.scan_once(s, idx)
See log for complete Python traceback.
note | Traceback (most recent call last):
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 360, in __init__
self.init_available_from_cache(logger)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 507, in
init_available_from_cache
abc.load_from_cache()
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/toolshed/available.py", line 70, in load_from_cache
data = json.load(f)
File
"/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/json/__init__.py",
line 296, in load
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
File
"/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/json/__init__.py",
line 348, in loads
return _default_decoder.decode(s)
File
"/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/json/decoder.py",
line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File
"/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/json/decoder.py",
line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 12797 column 22
(char 453238)
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 /localhome/bscml/process/chx_TS_02_DS4/figure_models.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot
grids = grid_data_from_state(data, gdcache, session, rfp)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/session.py", line 420, in grid_data_from_state
dpath = absolute_path(dstate.path, file_paths, base_path =
session.session_file_path)
AttributeError: 'dict' object has no attribute 'path'
opened ChimeraX session
> help help:quickstart
> help help:quickstart
> open /localhome/bscml/process/chx_TS_02_DS4/figure_models.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot
grids = grid_data_from_state(data, gdcache, session, rfp)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/session.py", line 420, in grid_data_from_state
dpath = absolute_path(dstate.path, file_paths, base_path =
session.session_file_path)
AttributeError: 'dict' object has no attribute 'path'
opened ChimeraX session
Traceback (most recent call last):
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 2069, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7f1bfae2bb50>
KeyError:
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
See log for complete Python traceback.
Traceback (most recent call last):
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 2069, in <lambda>
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
KeyError: <chimerax.help_viewer.tool.HelpUI object at 0x7f1bfae2bb50>
KeyError:
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 601, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
See log for complete Python traceback.
> open /localhome/bscml/process/chx_TS_02_DS4/figure_models.cxs
Unable to restore session, resetting.
Traceback (most recent call last):
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/session.py", line 219, in restore_snapshot
grids = grid_data_from_state(data, gdcache, session, rfp)
File "/localhome/bscml/software/chx/chimerax-1.1/lib/python3.7/site-
packages/chimerax/map/session.py", line 420, in grid_data_from_state
dpath = absolute_path(dstate.path, file_paths, base_path =
session.session_file_path)
AttributeError: 'dict' object has no attribute 'path'
opened ChimeraX session
> open /localhome/bscml/process/chx_TS_02_DS4/PM1.cmp
> /localhome/bscml/process/chx_TS_02_DS4/PM2.cmp
Opened PM1.cmp, grid size 351,194,89, pixel 3, shown at level 0.0115, step 1,
values float32
> volume #1.1 level 0.01329
> volume #1.1 level 0.004792
> volume #1.2 level 0.001259
> transparency #1 0
> save /localhome/bscml/process/chx_TS_02_DS4/figure_models1.cxs
opened ChimeraX session
> volume #1.1 level 0.002785
> volume #1.2 level 0.0001035
> save /localhom/bscml//process/chx_TS_02_DS4/figure_models1.cxs includeMaps
> true
[Errno 20] Not a directory: '/localhom/bscml//process/chx_TS_02_DS4'
> save /localhom/bscml/process/chx_TS_02_DS4/figure_models1.cxs includeMaps
> true
[Errno 20] Not a directory: '/localhom/bscml/process/chx_TS_02_DS4'
> save figure_models1.cxs includeMaps true
opened ChimeraX session
> open /localhome/bscml/process/chx_TS_02_DS4/fibrils_zone_range4.cmp
Opened fibrils_zone_range4.cmp, grid size 960,928,567, pixel 1, shown at step
1, values float32
> close #2
> open /localhome/bscml/process/chx_TS_02_DS4/fibrils_zone.cmp
Opened fibrils_zone.cmp, grid size 960,928,567, pixel 1, shown at step 1,
values float32
> open /localhome/bscml/process/chx_TS_02_DS4/fibrils_range3.cmp
Opened fibrils_range3.cmp, grid size 960,928,567, pixel 1, shown at step 1,
values float32
> volume #3 region 0,0,0,959,927,566 step 4
> volume #3 region 0,0,0,959,927,566 step 4
> volume #2 region 0,0,0,959,927,566 step 4
> volume #2 region 0,0,0,959,927,566 step 4
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> volume #2 level 3790
> volume #2 change image level 0,0 level 380.5,0.8 level 3805,1
> show #!3 models
> hide #!2 models
> volume #3 level 3790
> volume #3 change image level 0,0 level 380.4,0.8 level 3804,1
> open /localhome/bscml/process/chx_TS_02_DS4/fibrils_zone_range4.cmp
Opened fibrils_zone_range4.cmp, grid size 960,928,567, pixel 1, shown at step
1, values float32
> volume #4 region 0,0,0,959,927,566 step 4
> volume #4 region 0,0,0,959,927,566 step 4
> volume #4 level 3790
> volume #4 change image level 0,0 level 381.2,0.8 level 3812,1
> hide #!3 models
> volume #4 level 3783
> volume #4 level 3804
> volume #4 level 3783
> volume #4 level 3790
> volume #4 step 1
> hide #!4 models
> show #!3 models
> volume #3 step 1
> close session
OpenGL version: 3.3.0 NVIDIA 418.43
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 AMD Ryzen Threadripper 1950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125G 87G 750M 131M 37G 36G
Swap: 29G 0B 29G
Graphics:
0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)
Subsystem: PNY Device [196e:119e]
Kernel driver in use: nvidia
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-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 (6)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Various session-restore errors |
comment:2 by , 5 years ago
| Summary: | Various session-restore errors → Toolshed json parsing error and volume session-restore error |
|---|
comment:3 by , 5 years ago
comment:4 by , 5 years ago
Fixed the volume session restore. Made it properly open subsample data in different files. Also made saving a volume not change the file path for the volume GridData object.
comment:5 by , 5 years ago
| Cc: | removed |
|---|---|
| Owner: | changed from to |
Reassigning to Greg to look at Toolshed available bundles JSON error at top of log.
comment:6 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Something corrupted the avaailable.json file. Going to wait for another report for diving in.
Note:
See TracTickets
for help on using tickets.
The volume session restore error
AttributeError: 'dict' object has no attribute 'path'
is caused by a volume that has subsamples in different files. There is no obvious way to create a volume model with subsamples in different files in ChimeraX (although there was a Volume Viewer feature in Chimera 1 to do it). But there is a bug that allows it to be done. If you open a .cmap or .ims file those normally have subsamples in the same file. But if you then save as a .cmap file it changes the path for the full resolution data but not for the subsamples. Then you save a session and now the session uses subsamples from one file and full resolution from another file. But the session restore code is broken and won't restore subsamples from a different file.
First I need to fix the bug where saving a map changes the path but not the subsample paths. Then I should fix the session restore code.
I'm a bit baffled by why save changes the path. What if I save in a different format? Now the grid data for say an MRC file has a path to a .cmap file. If it then tried to reread the file say for different step size it would get an error. Try that. I think the right solution is save does not change the path of the currently opened volume.