AlphaFold database settings should not update at startup

[goddard@…]

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
Was surprised to see this "fetching alphafold database settings" message on startup.  That should not happen except when you use the alphafold database.

Log:
Startup Messages  
---  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

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: MacBookPro18,2
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 13 days 1:59

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          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-ArtiaX: 0.1
    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-Clipper: 0.18.0
    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-ISOLDE: 1.4
    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
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    ChimeraX-MMTF: 2.1
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    ChimeraX-Neuron: 1.0
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    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
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    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
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    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-SelInspector: 1.0
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    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
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
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    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
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    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
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    decorator: 5.1.1
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    entrypoints: 0.4
    filelock: 3.4.2
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    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
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    line-profiler: 3.4.0
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    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
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    openvr: 1.16.802
    packaging: 21.0
    pandas: 1.4.3
    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
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    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
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    PyQt6-sip: 13.3.1
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    sphinxcontrib-devhelp: 1.0.2
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    starfile: 0.4.11
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    tinyarray: 1.2.4
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    wheel-filename: 1.3.0

[Tom Goddard]

I put in a print statement in the check for alphafold database updates and it is not called in ChimeraX 1.4 or the current build. Very few code paths get the alphafold database settings that invoke this check and I don't see any that could happen at start up. But I must be missing something.

[Tom Goddard]

It looks like only using the alphafold can call this code. So it is a mystery how it happens at startup. But I just started ChimeraX 1.4 on my Mac laptop again and it once again gave this fetching settings message. But the next time I start it does not give it. I think it must be related to periodic toolshed lookup at startup. Let me see if I can find the toolshed last lookup time stamp and reset it to get it to happen again and put in a line to print a traceback. If I can't I can just wait a day or two and then start 1.4 with that traceback code in. I don't use 1.4 very often, instead use daily build.

[Tom Goddard]

ISOLDE monkey-patching code calls the _alphafold_database_settings() to set the database version to 3 every time ChimeraX is started when the ISOLDE bundle custom init routine is called. That call causes the online version check.

  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021, in <module>
    exit_code = init(sys.argv)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 642, in init
    sess.toolshed.bootstrap_bundles(sess, opts.safe_mode)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 766, in bootstrap_bundles
    failed += self._init_custom(session)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 784, in _init_custom
    self._init_bundle_custom(session, bi, done, initializing, failed)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 805, in _init_bundle_custom
    bi.initialize(session)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 365, in initialize
    api._api_caller.initialize(api, session, self)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1278, in initialize
    return cls._get_func(api, "initialize")(session, bi)
  File "/Users/goddard/Library/Application Support/ChimeraX/1.4/site-packages/chimerax/isolde/__init__.py", line 65, in initialize
    alphafold_monkeypatch(session)
  File "/Users/goddard/Library/Application Support/ChimeraX/1.4/site-packages/chimerax/isolde/alphafold_patch.py", line 6, in alphafold_monkeypatch
    settings = _alphafold_database_settings(session)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/database.py", line 59, in _alphafold_database_settings
    _check_for_database_update(session, settings)
  File "/Users/goddard/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/alphafold/database.py", line 67, in _check_for_database_update
    traceback.print_stack()

[Tom Goddard]

It is not great to have ISOLDE doing stuff every time ChimeraX starts even when ISOLDE isn't even used in the session. Would have been better to only do this monkey patching once ISOLDE is actually used. But maybe the thinking was that the user would load AlphaFold database models before starting ISOLDE.

Little harm done, except me wasting time debugging cryptic startup messages. I expect ISOLDE for ChimeraX 1.5 won't have this monkey patching code so the problem will disappear.

[Tom Goddard]

This was tricky to debug because the stdout and stderr debugging I originally put in did not log anything because those messages were written at startup before the Log gui redirected stdout and stderr. So I only saw the messages by running ChimeraX from a shell with --debug.