Opened 18 months ago
Last modified 18 months ago
#14977 accepted defect
Toolshed updates: IndexError: tuple index out of range
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Tool Shed | Version: | |
Keywords: | Cc: | Eric Pettersen | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Not sure what happened here. I just started ChimeraX and a few seconds later it spontaneously produced this error while I was in the process of typing an open command in the command-line. Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Traceback (most recent call last): File "/Users/goddard/Desktop/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/gui.py", line 719, in customEvent func(*args, **kw) File "/Users/goddard/Desktop/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/tool.py", line 29, in show return UpdateTool(session, "Update Bundles", dialog_type) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/goddard/Desktop/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/tool.py", line 125, in __init__ self._fill_updates() File "/Users/goddard/Desktop/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/tool.py", line 194, in _fill_updates ([], installed_version, available.synopsis, available.categories[0])) ~~~~~~~~~~~~~~~~~~~~^^^ IndexError: tuple index out of range IndexError: tuple index out of range File "/Users/goddard/Desktop/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/toolshed_utils/tool.py", line 194, in _fill_updates ([], installed_version, available.synopsis, available.categories[0])) ~~~~~~~~~~~~~~~~~~~~^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 2 hours, 32 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiobotocore: 2.12.2 aiohttp: 3.9.3 aioitertools: 0.11.0 aiosignal: 1.3.1 alabaster: 0.7.16 alphashape: 1.3.1 appdirs: 1.4.4 appnope: 0.1.3 asciitree: 0.3.3 asttokens: 2.4.1 attrs: 23.2.0 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 botocore: 1.34.51 build: 0.10.0 certifi: 2022.12.7 cffi: 1.16.0 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.3 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NIHPresets: 1.1.15 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OME-Zarr: 0.5.2 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-TetraScapeCommand: 0.1 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 click: 8.1.7 click-log: 0.4.0 cloudpickle: 3.0.0 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cryptography: 42.0.5 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 dask: 2024.4.1 debugpy: 1.8.0 decorator: 5.1.1 distributed: 2024.4.1 docutils: 0.19 executing: 2.0.1 fasteners: 0.19 filelock: 3.9.0 fonttools: 4.47.2 frozenlist: 1.4.1 fsspec: 2024.3.1 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imageio: 2.34.0 imagesize: 1.4.1 importlib-metadata: 7.1.0 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jmespath: 1.0.1 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 lazy-loader: 0.4 line-profiler: 4.0.2 locket: 1.0.0 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 multidict: 6.0.5 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numcodecs: 0.12.1 numexpr: 2.8.8 numpy: 1.25.1 ome-zarr: 0.8.3 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 partd: 1.4.1 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pycparser: 2.22 pydicom: 2.3.0 Pygments: 2.16.1 pynmrstar: 3.3.2 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 pyspnego: 0.10.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 PyYAML: 6.0.1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 Rtree: 1.1.0 s3fs: 2024.3.1 scikit-image: 0.22.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 shapely: 2.0.2 six: 1.16.0 smbprotocol: 1.13.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tblib: 3.0.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 toolz: 0.12.1 tornado: 6.4 traitlets: 5.9.0 trimesh: 4.0.10 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.0.7 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 wrapt: 1.16.0 yarl: 1.9.4 zarr: 2.17.2 zict: 3.0.0 zipp: 3.18.1
Change History (8)
comment:1 by , 18 months ago
Cc: | added |
---|---|
Component: | Unassigned → Tool Shed |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Toolshed updates: IndexError: tuple index out of range |
comment:2 by , 18 months ago
Status: | assigned → accepted |
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comment:3 by , 18 months ago
Actually, but is in 1.8 daily too. The bug is that the category for the OME_Zarr bundle is missing. Not sure why yet.
comment:4 by , 18 months ago
The OME-Zarr bundle info is missing the categories for the bundle. So in the bundle_info.xml file, it doesn't have any categories listed for the bundle. And so when ChimeraX asks for a list of the available bundles, the bundle comes without any categories. It's a bug that the toolshed accepted the submission. But the workaround will be to place the bundle in General category.
comment:5 by , 18 months ago
If you want Utz Ermel to update the OMEZarr bundle to add a category, he is very responsive. This may help ChimeraX 1.7 users if you intend to put your fix in ChimeraX. But if the fix is on the server side then Utz doesn't need to do anything.
comment:7 by , 18 months ago
New copick bundle has the same problem.
Fixed the immediate problem with:
. activate.sh ./manage.py dbshell MariaDB [cxtoolshed]> select id from apps_app where name = 'chimeraxomezarr'; MariaDB [cxtoolshed]> select id from apps_release where app_id = 534; MariaDB [cxtoolshed]> insert into apps_releasemetadata (release_id, type, name, `key`, `value`) values (1148, "bundle", "ChimeraX_OME_Zarr", "categories", "Volume Data");
And changed ChimeraX daily build to assume bundles are in the General category if no categories are present.
Long term solution is to reject uploads of bundles without categories. That will fix the problem for older versions of ChimeraX tool.
comment:8 by , 18 months ago
Related: the fix to #15048 makes it a build error to omit a category for TOML bundles
Reproduced with "toolshed update all" in ChimeraX 1.7. Works in 1.8 daily build.