[chimerax-users] ChimeraX and REST service interoperation

Fri Jan 24 07:13:58 PST 2020

Hello Conrad,

I tried recoding so the response is sent to the REST request before making a new request to it.
I'm still getting the same timeout and stack trace (give or take port numbers).

One thing that looks curious:
The port number (if that is what it is) in the Chimera log message (after Jalview sends info selection level residue)
Exception happened during processing of request from ('127.0.0.1', 50285)
doesn't match that of the Jalview REST server as specified in the earlier command
info notify start selection jalview prefix SelectionChanged url http://localhost:50108/jalview/chimera2

Does that give any clue?
For what it's worth, ChimeraX Preferences | Web Access does not have any proxy settings.

thanks

Mungo

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org<http://www.jalview.org>

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________________________________
From: Conrad Huang <conrad at cgl.ucsf.edu>
Sent: 21 January 2020 20:28
To: Mungo Carstairs (Staff) <g.m.carstairs at dundee.ac.uk>; chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] ChimeraX and REST service interoperation

Hi, Mungo.

I believe ChimeraX is still waiting a response to the "SelectionChanged"
GET request.  It's supposed to be a REST transaction, which I had
assumed would be quick, so it is reading directly from the network
connection rather than doing it in a separate thread.  (The response is
discarded, so it doesn't matter what gets sent back.  Just something to
confirm that the transaction is complete.)

Conrad

On 1/16/2020 3:02 AM, Mungo Carstairs (Staff) wrote:
> Hi,
>
> With your helpful hints, I have a version of Jalview interacting with
> ChimeraX in the same way it can already with Chimera, over the REST
> interface.
> Functionality includes loading structures, aligning, colouring, raising
> labels on structure on mouseover in Jalview, and exchange of residue
> features/attributes.
>
> I have just one interaction not working yet: highlighting residues in
> Jalview when a selection is made in ChimeraX.
>   - Jalview starts listening for ChimeraX selections with (e.g.)
>
>    info notify start selection jalview prefix SelectionChanged url
> http://localhost:49981/jalview/chimera1
>
>   - user makes a selection in ChimeraX
>   - ChimeraX sends
> GET?chimerax_notification=SelectionChangedselection+changed
>   - Jalview send 'info selection level residue'
>   - no response / timeout; ChimeraX log reports 'broken pipe error'
>
> Exception happened during processing of request from ('127.0.0.1', 50714)
> Traceback (most recent call last):
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 316,
> in _handle_request_noblock
> self.process_request(request, client_address)
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 347,
> in process_request
> self.finish_request(request, client_address)
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 360,
> in finish_request
> self.RequestHandlerClass(request, client_address, self)
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 720,
> in __init__
> self.handle()
> File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 426, in
> handle
> self.handle_one_request()
> File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 414, in
> handle_one_request
> method()
> File
> "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py",
> line 97, in do_GET
> self._run(args)
> File
> "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py",
> line 174, in _run
> self.wfile.write(data)
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 799,
> in write
> self._sock.sendall(b)
> BrokenPipeError: [Errno 32] Broken pipe
>
> NB this is all before a response has been sent to the 'SelectionChanged'
> message.
> Any idea what the problem is here please?
> Do I need to reply to the first message before sending another?
> The same mechanism does work ok with Chimera.
>
> Thanks,
>
> Mungo
>
> p.s. I noticed the 'listinfo' command (undocumented) seems to behave
> like 'info'. Should I continue to use 'list' or switch to 'info'?
>
>   *
>
>
> Email signature
> University of Dundee shield logo <http://uod.ac.uk/sig-home>
>
> *Mungo Carstairs*
> Jalview Computational Scientist
>
> The Barton Group
> Division of Computational Biology
>
> School of Life Sciences
>
> University of Dundee, Dundee, Scotland, UK
>
> www.jalview.org<http://www.jalview.org> <http://www.jalview.org>
>
> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> <http://www.compbio.dundee.ac.uk>
> g.m.carstairs at dundee.ac.uk <mailto:g.m.carstairs at dundee.ac.uk>
>
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