#15004 closed defect (limitation)

ArtiaX dependency not installed

Reported by: johutchings@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Tool Shed Version:
Keywords: Cc: Utz Ermel
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-14.2-arm64-arm-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Installed latest ArtiaX using toolshed. 
Error recieved when launching ArtiaX.

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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/__init__.py",
line 120, in run_provider  
from .toolbar import run_provider  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/toolbar/__init__.py", line 3, in <module>  
from .toolbar import *  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/toolbar/toolbar.py", line 4, in <module>  
from ..particle.ParticleList import delete_selected_particles,
invert_selection  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/__init__.py", line 2, in <module>  
from .ParticleList import ParticleList  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/particle/ParticleList.py", line 19, in <module>  
from ..io.ParticleData import ParticleData  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/io/__init__.py",
line 7, in <module>  
from .Copick import CopickParticleData  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/io/Copick/__init__.py", line 3, in <module>  
from .CopickParticleData import COPICK_FORMAT  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in <module>  
import pydantic  
ModuleNotFoundError: No module named 'pydantic'  
  
ModuleNotFoundError: No module named 'pydantic'  
  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in  
import pydantic  
  
See log for complete Python traceback.  
  

> artiax start

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/__init__.py",
line 121, in run_provider  
run_provider(session, name)  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/toolbar/toolbar.py", line 71, in run_provider  
run(session, what)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/cmd/cmd.py",
line 36, in artiax_start  
get_singleton(session)  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/cmd/cmd.py",
line 24, in get_singleton  
from ..tool import ArtiaXUI  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/tool.py", line
29, in <module>  
from .ArtiaX import (  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/ArtiaX.py", line
14, in <module>  
from .io import open_particle_list, save_particle_list, get_fmt_aliases  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-packages/chimerax/artiax/io/__init__.py",
line 7, in <module>  
from .Copick import CopickParticleData  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/io/Copick/__init__.py", line 3, in <module>  
from .CopickParticleData import COPICK_FORMAT  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in <module>  
import pydantic  
ModuleNotFoundError: No module named 'pydantic'  
  
ModuleNotFoundError: No module named 'pydantic'  
  
File "/Users/joshuahutchings/Library/Application
Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/artiax/io/Copick/CopickParticleData.py", line 6, in  
import pydantic  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3
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: MacBook Pro
      Model Identifier: Mac15,3
      Model Number: Z1C80001JLL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2 (23C64)
      Kernel Version: Darwin 23.2.0
      Time since boot: 25 days, 5 hours, 20 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.4.5
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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-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
    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-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
    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: 1.5.13
    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-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    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: 1.12.3
    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-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    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
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    geomdl: 5.3.1
    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
    imagesize: 1.4.1
    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
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    pandas: 2.1.4
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    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
    pydicom: 2.3.0
    Pygments: 2.16.1
    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
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    starfile: 0.5.4
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (6)

comment:1 by pett, 18 months ago

Cc: Utz Ermel added
Component: UnassignedTool Shed
Owner: set to Greg Couch
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionArtiaX dependency not installed

pydantic is listed in the ArtiaX dependencies, but seemingly wasn't installed. Maybe the ArtiaX wheel was directly pip installed?

Reported by Josh Hutchings

comment:2 by Greg Couch, 18 months ago

How did you install ArtiaX?

comment:3 by Utz Ermel, 18 months ago

Hi Greg and Josh, 

I had encountered the same thing when I initially added the pydantic requirement, but wasn\u2019t able to reproduce it anymore later on, so thought it was a fluke.

This should do the trick for a fix: 
1. toolshed uninstall artiax
2. Restart ChimeraX
3. toolshed reload available
4. toolshed install artiax

Completely reinstalling seems to add the additional requirements. This may be a bug during bundle installation? 

Best,
Utz


comment:4 by Greg Couch, 18 months ago

If you add a dependency to a bundle, then you need to increase the version number for the new dependency to be picked up. Or, as you appear to have discovered, if the version number doesn't change, uninstall the existing version first.

Does that scenario match what you experienced?

comment:5 by Utz Ermel, 18 months ago

I believe I did increase the version from 0.4.2 to 0.4.3 when I added the pydantic requirement (see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_FrangakisLab_ArtiaX_compare_v0.4.2...v0.4.3&d=DwIFaQ&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=CKzZmwKi9_YVvHng-0ezdJFE-0MROfpdFWLsI4CZgtQ&m=3XVJPF1pP0vkMWgJNgCutuW5Z4eLLOKEyq82SMG0V35J78G6vZ2ZCyeHInIVuRrf&s=SKZve1BsLMpZtHOdCO5560KaRAPOT3lB0nbSmGAVgrw&e= ). 

Do I need to do a minor (or even major) version increase when I add requirements? 

That would be an easy fix. 

comment:6 by Greg Couch, 18 months ago

Resolution: limitation
Status: assignedclosed

Any version number change should work. ChimeraX uses pip to install dependencies, and there is no option to only update the dependencies of the bundle/wheel that is being forcibly reinstalled.

It is easy to forget to change the version number while developing a bundle. Especially if you have already changed the version number for the next release, installed that, and then decide to add a dependency, but don't change the version number again.

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