Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5081 closed defect (can't reproduce)

Blast protein: Internal Server Error

Reported by: goddard@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc: Scooter Morris
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108190418 (2021-08-19 04:18:32 UTC)
Description
Blast REST service is giving a server error.  Opened 3dwt and used Tools / Sequence / Blast Protein to blast PDB.  Tried other structures, all fail.  Tried blasting alphafold, same failure.  Seems the server is broken.

Log:
UCSF ChimeraX version: 1.3.dev202108190418 (2021-08-19)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3dwt format mmcif fromDatabase pdb

3dwt title:  
Structure of CabBCII-10 nanobody [more info...]  
  
Chain information for 3dwt #1  
---  
Chain | Description  
A B C D E F G H | cAbBCII-10  
  
Non-standard residues in 3dwt #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3dwt 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  
5| author_and_software_defined_assembly  
6| author_and_software_defined_assembly  
7| author_and_software_defined_assembly  
8| author_and_software_defined_assembly  
  

> ui tool show "Blast Protein"

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

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 331, in interceptRequest  
self._callback(info)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 92, in _intercept  
return interceptor(request_info, *args)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 374, in thread_safe  
func(*args, **kw)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/tool.py", line 109, in handle_scheme  
self.blast(url)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/tool.py", line 195, in blast  
run(self.session, cmd)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/cmd.py", line 55, in blastprotein  
BlastProteinJob(session, chain.ungapped(), chain_spec,  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/job.py", line 158, in BlastProteinJob  
return ServiceMap[service](session, seq, atomspec, **kw)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/job.py", line 146, in __init__  
self.start("blast", params)  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 62, in start  
self.job_id = self.api.job_id().job_id  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 650, in job_id  
(data) = self.job_id_with_http_info(**kwargs) # noqa: E501  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 702, in job_id_with_http_info  
return self.api_client.call_api(  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 233, in GET  
return self.request("GET", url,  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 227, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (500)  
Reason: Internal Server Error  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 20 Aug 2021 03:07:19
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Content-Length': '617',
'Connection': 'close', 'Content-Type': 'text/html; charset=iso-8859-1'})  
HTTP response body: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">  
<html><head>  
<title>500 Internal Server Error</title>  
</head><body>  
<h1>Internal Server Error</h1>  
<p>The server encountered an internal error or  
misconfiguration and was unable to complete  
your request.</p>  
<p>Please contact the server administrator at  
root@localhost to inform them of the time this error occurred,  
and the actions you performed just before this error.</p>  
<p>More information about this error may be available  
in the server error log.</p>  
<hr>  
<address>Apache/2.4.6 (CentOS) Server at webservices.rbvi.ucsf.edu Port
80</address>  
</body></html>  
  
  
  
cxservices.rest.ApiException: (500)  
Reason: Internal Server Error  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 20 Aug 2021 03:07:19
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Content-Length': '617',
'Connection': 'close', 'Content-Type': 'text/html; charset=iso-8859-1'})  
HTTP response body:  
  
500 Internal Server Error  
  

# Internal Server Error

  

The server encountered an internal error or  
misconfiguration and was unable to complete  
your request.

  

Please contact the server administrator at  
root@localhost to inform them of the time this error occurred,  
and the actions you performed just before this error.

  

More information about this error may be available  
in the server error log.

  

* * *

  
Apache/2.4.6 (CentOS) Server at webservices.rbvi.ucsf.edu Port 80  
  
  
  
  
File "/Users/goddard/Desktop/ChimeraX Aug 19
2021.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 227, in request  
raise ApiException(http_resp=r)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1030)
      Kernel Version: Darwin 19.6.0
      Time since boot: 91 days 1:08

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    charset-normalizer: 2.0.4
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.28.1
    ChimeraX-AtomicLibrary: 4.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    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: 1.4
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202108190418
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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: 1.1
    ChimeraX-Hbonds: 2.1.1
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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
    ChimeraX-MDcrds: 2.5
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.3
    ChimeraX-ModelPanel: 1.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6
    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: 2.1
    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.2
    ChimeraX-Shape: 1.0.1
    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
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.11.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0.1
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    distlib: 0.3.1
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    imagesize: 1.2.0
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    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Tom Goddard, 4 years ago

Cc: Scooter Morris added
Component: Unassigned → Sequence
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Blast protein: Internal Server Error

comment:2 by Zach Pearson, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Restarted webservices at some point between this being opened and me seeing it. Tested the commands from the log and the service was working.

in reply to:  3 ; comment:3 by goddard@…, 4 years ago 

Thanks!  If the blast REST service goes haywire again we'll need to figure out what is going on before this ChimeraX with blast rest gets into too many hands and users start complaining.
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