Opened 4 years ago

Closed 4 years ago

#4640 closed defect (fixed)

socket.timeout reporting fetch progress

Reported by: zzhang@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.3 (2021-05-13 06:57:20 UTC)
Description
Click on a link in the quickstart tutorial and then:

socket.timeout: timed out

File "D:\Program Files\ChimeraX 1.2.3\bin\lib\socket.py", line 669, in readinto
return self._sock.recv_into(b)

See log for complete Python traceback.

Log:
UCSF ChimeraX version: 1.2.3 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> open C:/Users/lenovo/AppData/Local/Temp/ChimeraX-pNGfad/shift.png

Opened multi-channel map shift.png as #1, 3 channels, grid size 256,256,1,
pixel 1, shown at step 1, values uint8  

> close #1

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html format "web fetch"
> fromDatabase https

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
note | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 319, in intercept  
chimerax_intercept(request_info, *args, session=self.session,  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 150, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 74, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 323, in chimerax.mmcif.mmcif.fetch_mmcif  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 86, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 199, in retrieve_url  
read_and_uncompress(response, f, name, content_length, logger)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 225, in read_and_uncompress  
read_and_report_progress(file_in, cdata, name, content_length, logger,
chunk_size)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 240, in read_and_report_progress  
bytes = file_in.read(chunk_size)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\http\client.py", line 458, in
read  
n = self.readinto(b)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\http\client.py", line 502, in
readinto  
n = self.fp.readinto(b)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
socket.timeout: timed out  
  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  

> open 2bbv

Summary of feedback from opening 2bbv fetched from pdb  
---  
note | Fetching compressed mmCIF 2bbv from
http://files.rcsb.org/download/2bbv.cif  
  
Traceback (most recent call last):  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 324, in interceptRequest  
self._callback(info)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 85, in _intercept  
return interceptor(request_info, *args)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 319, in intercept  
chimerax_intercept(request_info, *args, session=self.session,  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 453, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\gui.py", line 366, in thread_safe  
func(*args, **kw)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 444, in defer  
cxcmd(session, topic)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 462, in cxcmd  
run(session, cmd)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 150, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 74, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 323, in chimerax.mmcif.mmcif.fetch_mmcif  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 86, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 199, in retrieve_url  
read_and_uncompress(response, f, name, content_length, logger)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 225, in read_and_uncompress  
read_and_report_progress(file_in, cdata, name, content_length, logger,
chunk_size)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\site-
packages\chimerax\core\fetch.py", line 240, in read_and_report_progress  
bytes = file_in.read(chunk_size)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\http\client.py", line 458, in
read  
n = self.readinto(b)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\http\client.py", line 502, in
readinto  
n = self.fp.readinto(b)  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
socket.timeout: timed out  
  
socket.timeout: timed out  
  
File "D:\Program Files\ChimeraX 1.2.3\bin\lib\socket.py", line 669, in
readinto  
return self._sock.recv_into(b)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 388.59
OpenGL renderer: GeForce 940MX/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: INVA
OS: Microsoft Windows 10 家庭中文版 (Build 19041)
Memory: 4,141,621,248
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.3
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.4
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.0
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → socket.timeout reporting fetch progress

comment:2 by Tom Goddard, 4 years ago

ChimeraX was fetching PDB 2bbv at timed out. This is a rare situation -- apparently the PDB web site was not down but was simply hung and not responding for probably a minute so this unusual error was raised. ChimeraX should catch this and report the PDB is not responding. I am pretty sure if the PDB was simply down ChimeraX already gives a clear message like "PDB not responding" but we are not catching the timeout error.

comment:3 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made the code give a clear error message and no traceback on socket time out.

Note: See TracTickets for help on using tickets.