Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#9648 closed defect (not a bug)

Web service failure

Reported by: debbie.shalev@… Owned by: pett
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-10-10.0.22621
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
I tried to blast a chain within a PDB file (3qbt) and both Chimera and ChimeraX complained... Thanks! 

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/WORK/2023 Benny
> Aroeti/Rab8-EspH/esph_rab8a_unrelaxed_rank_1_model_3.pdb"

Chain information for esph_rab8a_unrelaxed_rank_1_model_3.pdb #1  
---  
Chain | Description  
B | No description available  
C | No description available  
  

> ui tool show "Blast Protein"

> blastprotein /C database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 641, in
http_response  
'http', request, response, code, msg, hdrs)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 563, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 503, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 755, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 641, in
http_response  
'http', request, response, code, msg, hdrs)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 503, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 1:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 629, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 69, in on_finish  
out = self.get_stdout()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 274, in get_stdout  
return self.get_file("stdout.txt")  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  

> close session

> open 3qbt

Summary of feedback from opening 3qbt fetched from pdb  
---  
notes | Fetching compressed mmCIF 3qbt from
http://files.rcsb.org/download/3qbt.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
Fetching CCD GNP from http://ligand-expo.rcsb.org/reports/G/GNP/GNP.cif  
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif  
  
3qbt title:  
Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp [more info...]  
  
Chain information for 3qbt #1  
---  
Chain | Description  
A C E G | Ras-related protein Rab-8A  
B D F H | Inositol polyphosphate 5-phosphatase OCRL-1  
  
Non-standard residues in 3qbt #1  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
SO4 — sulfate ion  
  
3qbt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> ui tool show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 67, in open  
return self.u2open(u2request)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 132, in u2open  
return url.open(u2request, timeout=tm)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 641, in
http_response  
'http', request, response, code, msg, hdrs)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 563, in
error  
result = self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 503, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 755, in
http_error_302  
return self.parent.open(new, timeout=req.timeout)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 531, in
open  
response = meth(req, response)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 641, in
http_response  
'http', request, response, code, msg, hdrs)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 569, in
error  
return self._call_chain(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 503, in
_call_chain  
result = func(*args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\urllib\request.py", line 649, in
http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tasks.py", line 196, in _run_thread  
self.run(*args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\tasks.py", line 283, in run  
self.launch(*args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 121, in launch  
self._suds = Client(self.service_url + "?wsdl")  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\client.py",
line 115, in __init__  
self.wsdl = reader.open(url)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\reader.py",
line 150, in open  
d = self.fn(url, self.options)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\wsdl.py", line
136, in __init__  
d = reader.open(url)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\reader.py",
line 74, in open  
d = self.download(url)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\suds\reader.py",
line 92, in download  
fp = self.options.transport.open(Request(url))  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\https.py", line 62, in open  
return HttpTransport.open(self, request)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
Exception in thread 2:  
suds.transport.TransportError: HTTP Error 404: Not Found  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\suds\transport\http.py", line 69, in open  
raise TransportError(str(e), e.code, e.fp)  
  
See log for complete Python traceback.  
  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 629, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 69, in on_finish  
out = self.get_stdout()  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 274, in get_stdout  
return self.get_file("stdout.txt")  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\webservices\opal_job.py", line 258, in get_file  
url = self._status_url + '/' + filename  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 512.72
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: G3 3590
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,195,800,064
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    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: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (4)

comment:1 by pett, 2 years ago

Component: Unassigned → Web Services
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Web service failure

comment:2 by pett, 2 years ago

Resolution: → not a bug
Status: accepted → closed

Hi Debbie,

The way that Chimera and ChimeraX communicate with their backend servers that provide the Blast web service changed about 3 months ago. You need to get newer versions of the programs in order to run Blast.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by debbie.shalev@…, 2 years ago 

Thank you so very much!

On Mon, Aug 28, 2023 at 9:30 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>
>
>

comment:4 by pett, 2 years ago

Happy to help!

--Eric

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