[chimerax-users] ChimeraX and REST service interoperation

[Conrad Huang]

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>
> 
> 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>
> 
> University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of 
> Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn 
> <http://uod.ac.uk/sig-li> University of Dundee YouTube 
> <http://uod.ac.uk/sig-yt> University of Dundee Instagram 
> <http://uod.ac.uk/sig-ig> University of Dundee Snapchat 
> <http://uod.ac.uk/sig-sc>
> *We're Scottish University of the Year again!* 
> <http://uod.ac.uk/sig-strapline>
> The Times / Sunday Times Good University Guide 2016 and 2017
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>