Opened 7 months ago

Closed 7 months ago

#17158 closed defect (duplicate)

Web services down

Reported by: julio.bonilla@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Web Services Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202503210042 (2025-03-21 00:42:17 UTC)
Description
I have been trying to blast proteins sequences, several of them in the past 2 days and the problem persists. I have installed the daily build. The following error occurs:

blastprotein MTVNISYLTDMDGVLIREGDMIPGADRFLHALVHNDIEFMVLTNNSIFTPRDLSARLRSSGLDIPPERIWTSATATAHFLKSQVSEGTAYVVGESGLTTALHTAGWILTDSNPEFVVLGETRTYSFEAITTAINLILGGARFICTNPDVTGPSPTGILPATGSVAALITAATGAEPYYIGKPNPVMMRSALNTIGAHSEHTVMIGDRMDTDVISGLEAGMRTVLVKSGISNEAEIRRYPFRPTMVVDSIADIAERWDDPFGDGSFQVPDHAEQDAEQDAEQN database pdb cutoff 1e-3 matrix BLOSUM80 maxSeqs 100 version None name bp2
Exception in thread Thread-50 (_run_function): Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 1038, in _bootstrap_inner self.run() File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\core\tasks.py", line 300, in _run_function func(*args, **kw) File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-packages\chimerax\webservices\cxservices_job.py", line 156, in run reason = json.loads(e.body)["description"] ^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\__init__.py", line 346, in loads return _default_decoder.decode(s) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

Log:
UCSF ChimeraX version: 1.10.dev202503210042 (2025-03-21)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open q8fnj4 format uniprot fromDatabase uniprot

Summary of feedback from opening q8fnj4 fetched from uniprot  
---  
notes | <urllib.request.Request object at 0x000001D9EF6DA290>  
UniProt identifier q8fnj4 maps to entry Q8FNJ4  
Alignment identifier is q8fnj4  
  
Opened UniProt q8fnj4  

> open q8fnj4 format uniprot fromDatabase uniprot

Summary of feedback from opening q8fnj4 fetched from uniprot  
---  
notes | <urllib.request.Request object at 0x000001D9EED87CD0>  
UniProt identifier q8fnj4 maps to entry Q8FNJ4  
Destroying pre-existing alignment with identifier q8fnj4  
Alignment identifier is q8fnj4  
  
Opened UniProt q8fnj4  

> open q8fnj4 format uniprot fromDatabase uniprot

Summary of feedback from opening q8fnj4 fetched from uniprot  
---  
notes | <urllib.request.Request object at 0x000001D9EEDD7CD0>  
UniProt identifier q8fnj4 maps to entry Q8FNJ4  
Destroying pre-existing alignment with identifier q8fnj4  
Alignment identifier is q8fnj4  
  
Opened UniProt q8fnj4  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2496, in <lambda>  
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\ui\gui.py", line 817, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
KeyError: None  
  
KeyError: None  
  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\ui\gui.py", line 817, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open q8fnj4 format uniprot fromDatabase uniprot

Summary of feedback from opening q8fnj4 fetched from uniprot  
---  
notes | <urllib.request.Request object at 0x000001D9C1686590>  
UniProt identifier q8fnj4 maps to entry Q8FNJ4  
Destroying pre-existing alignment with identifier q8fnj4  
Alignment identifier is q8fnj4  
  
Opened UniProt q8fnj4  

> blastprotein q8fnj4:1 database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp1

Exception in thread Thread-34 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py",
line 1038, in _bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py",
line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\core\tasks.py", line 300, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 156, in run  
reason = json.loads(e.body)["description"]  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX
1.10.dev202503210042\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\decoder.py",
line 355, in raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  

> ui tool show "Blast Protein"

> blastprotein
> MTVNISYLTDMDGVLIREGDMIPGADRFLHALVHNDIEFMVLTNNSIFTPRDLSARLRSSGLDIPPERIWTSATATAHFLKSQVSEGTAYVVGESGLTTALHTAGWILTDSNPEFVVLGETRTYSFEAITTAINLILGGARFICTNPDVTGPSPTGILPATGSVAALITAATGAEPYYIGKPNPVMMRSALNTIGAHSEHTVMIGDRMDTDVISGLEAGMRTVLVKSGISNEAEIRRYPFRPTMVVDSIADIAERWDDPFGDGSFQVPDHAEQDAEQDAEQN
> database pdb cutoff 1e-3 matrix BLOSUM80 maxSeqs 100 version None name bp2

Exception in thread Thread-50 (_run_function):  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py",
line 1038, in _bootstrap_inner  
self.run()  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\threading.py",
line 975, in run  
self._target(*self._args, **self._kwargs)  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\core\tasks.py", line 300, in _run_function  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\site-
packages\chimerax\webservices\cxservices_job.py", line 156, in run  
reason = json.loads(e.body)["description"]  
^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX
1.10.dev202503210042\bin\Lib\json\\__init__.py", line 346, in loads  
return _default_decoder.decode(s)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\decoder.py",
line 337, in decode  
obj, end = self.raw_decode(s, idx=_w(s, 0).end())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.dev202503210042\bin\Lib\json\decoder.py",
line 355, in raw_decode  
raise JSONDecodeError("Expecting value", s, err.value) from None  
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)  




OpenGL version: 3.3.0 - Build 31.0.101.4887
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: es_EC.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: HP
Model: HP ProBook 450 15.6 inch G10 Notebook PC
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,794,292,224
MaxProcessMemory: 137,438,953,344
CPU: 12 13th Gen Intel(R) Core(TM) i7-1355U
OSLanguage: es-ES

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.0
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503210042
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.44
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.7.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.7
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 310
    pyzmq: 26.3.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Web Services
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Web services down

comment:2 by Eric Pettersen, 7 months ago

Resolution: → duplicate
Status: assigned → closed

Adding reporter to the main ticket we have open for this.

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