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Hello Conrad,</div>
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<br>
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I tried recoding so the response is sent to the REST request before making a new request to it.</div>
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I'm still getting the same timeout and stack trace (give or take port numbers).</div>
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<br>
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One thing that looks curious:</div>
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The port number (if that is what it is) in the Chimera log message (after Jalview sends <span style="font-family: "Courier New", monospace; font-size: 11pt;">info selection level residue</span>)</div>
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<span style="font-family: "Courier New", monospace; font-size: medium; display: inline !important;">Exception happened during processing of request from ('127.0.0.1', 50285)</span><br>
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doesn't match that of the Jalview REST server as specified in the earlier command</div>
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<span style="font-family: "Courier New", monospace;">info notify start selection jalview prefix SelectionChanged url
</span><a href="http://localhost:50108/jalview/chimera2"><span style="font-family: "Courier New", monospace;">http://localhost:50108/jalview/chimera2</span></a><br>
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<br>
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Does that give any clue?</div>
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For what it's worth, ChimeraX Preferences | Web Access does not have any proxy settings.</div>
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<br>
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thanks</div>
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<br>
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Mungo</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Conrad Huang <conrad@cgl.ucsf.edu><br>
<b>Sent:</b> 21 January 2020 20:28<br>
<b>To:</b> Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk>; chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] ChimeraX and REST service interoperation</font>
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<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi, Mungo.<br>
<br>
I believe ChimeraX is still waiting a response to the "SelectionChanged" <br>
GET request. It's supposed to be a REST transaction, which I had <br>
assumed would be quick, so it is reading directly from the network <br>
connection rather than doing it in a separate thread. (The response is <br>
discarded, so it doesn't matter what gets sent back. Just something to <br>
confirm that the transaction is complete.)<br>
<br>
Conrad<br>
<br>
On 1/16/2020 3:02 AM, Mungo Carstairs (Staff) wrote:<br>
> Hi,<br>
> <br>
> With your helpful hints, I have a version of Jalview interacting with <br>
> ChimeraX in the same way it can already with Chimera, over the REST <br>
> interface.<br>
> Functionality includes loading structures, aligning, colouring, raising <br>
> labels on structure on mouseover in Jalview, and exchange of residue <br>
> features/attributes.<br>
> <br>
> I have just one interaction not working yet: highlighting residues in <br>
> Jalview when a selection is made in ChimeraX.<br>
> - Jalview starts listening for ChimeraX selections with (e.g.)<br>
> <br>
> info notify start selection jalview prefix SelectionChanged url <br>
> <a href="http://localhost:49981/jalview/chimera1">http://localhost:49981/jalview/chimera1</a><br>
> <br>
> - user makes a selection in ChimeraX<br>
> - ChimeraX sends <br>
> GET?chimerax_notification=SelectionChangedselection+changed<br>
> - Jalview send 'info selection level residue'<br>
> - no response / timeout; ChimeraX log reports 'broken pipe error'<br>
> <br>
> Exception happened during processing of request from ('127.0.0.1', 50714)<br>
> Traceback (most recent call last):<br>
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 316, <br>
> in _handle_request_noblock<br>
> self.process_request(request, client_address)<br>
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 347, <br>
> in process_request<br>
> self.finish_request(request, client_address)<br>
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 360, <br>
> in finish_request<br>
> self.RequestHandlerClass(request, client_address, self)<br>
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 720, <br>
> in __init__<br>
> self.handle()<br>
> File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 426, in <br>
> handle<br>
> self.handle_one_request()<br>
> File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 414, in <br>
> handle_one_request<br>
> method()<br>
> File <br>
> "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py",
<br>
> line 97, in do_GET<br>
> self._run(args)<br>
> File <br>
> "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py",
<br>
> line 174, in _run<br>
> self.wfile.write(data)<br>
> File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 799, <br>
> in write<br>
> self._sock.sendall(b)<br>
> BrokenPipeError: [Errno 32] Broken pipe<br>
> <br>
> NB this is all before a response has been sent to the 'SelectionChanged' <br>
> message.<br>
> Any idea what the problem is here please?<br>
> Do I need to reply to the first message before sending another?<br>
> The same mechanism does work ok with Chimera.<br>
> <br>
> Thanks,<br>
> <br>
> Mungo<br>
> <br>
> p.s. I noticed the 'listinfo' command (undocumented) seems to behave <br>
> like 'info'. Should I continue to use 'list' or switch to 'info'?<br>
> <br>
> *<br>
> <br>
> <br>
> Email signature<br>
> University of Dundee shield logo <<a href="http://uod.ac.uk/sig-home">http://uod.ac.uk/sig-home</a>>
<br>
> <br>
> *Mungo Carstairs*<br>
> Jalview Computational Scientist<br>
> <br>
> The Barton Group<br>
> Division of Computational Biology<br>
> <br>
> School of Life Sciences<br>
> <br>
> University of Dundee, Dundee, Scotland, UK<br>
> <br>
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