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<p style="margin-top:0;margin-bottom:0">Hi Conrad,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I will see if I can change to POST.</p>
<p style="margin-top:0;margin-bottom:0">To explain a bit: Jalview (Java) application uses POST, we now have a Javascript version which for the moment is limited to sending GET requests, so I tweaked the code for that. I will see if I can persuade it to fake
a POST instead and let you know what I find.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Mungo</p>
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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> 04 February 2019 21:21:12<br>
<b>To:</b> Mungo Carstairs (Staff); chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Help: 'broken pipe' error</font>
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<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi, Mungo.<br>
<br>
I tried using the RESTserver on a recent daily build, and it opening <br>
4zhp worked fine. Since RESTserver hasn't changed in a very long time, <br>
I suspect the results would be the same with 1.13.<br>
<br>
The way I tested it is to start the RESTserver in Chimera, and then go <br>
to a browser to visit "<a href="http://localhost:PORT/static/cmdline.html">http://localhost:PORT/static/cmdline.html</a>" where
<br>
PORT is the port number reported in the Reply Log. A form is displayed <br>
in the browser and I type in "open cifID:4zhp", which runs the command <br>
and displays Chimera messages in the browser rather than the Reply Log.<br>
<br>
I did notice that your tests show messages like:<br>
<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 -<br>
<br>
whereas mine show:<br>
<br>
> 127.0.0.1 - - [04/Feb/2019 12:02:46] "POST /run HTTP/1.1" 200 -<br>
<br>
That looks to me like you are sending requests using http GET, whereas <br>
my tests are using POST. It /shouldn't/ make any difference, but would <br>
it be possible for you to test using POST to send requests to Chimera <br>
instead of GET?<br>
<br>
Conrad<br>
<br>
On 2/1/2019 2:43 AM, Mungo Carstairs (Staff) wrote:<br>
> Hi there,<br>
> <br>
> <br>
> I'm experimenting with Jalview /as Javascript/ talking to Chimera over <br>
> the latter's REST server.<br>
> <br>
> The first few 'list models' commands work fine, but when I send a <br>
> command 'open cifID:4zhp' I (usually but not always) get an error <br>
> '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces <br>
> below as to the reason for this? Thanks.<br>
> <br>
> <br>
> Chimera 1.12 (build 41481) on OSX Sierra 10.12.6.<br>
> <br>
> <br>
> REST server on host 127.0.0.1 port 53135<br>
> 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET <br>
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 -<br>
> Traceback (most recent call last):<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", <br>
> line 50, in _checkThread<br>
> callable()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 83, in run<br>
> _run(q, h, args)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 163, in _run<br>
> replyobj.error(str(v) + '\n')<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line <br>
> 637, in error<br>
> _replyStack[-1].error(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 184, in writeLine<br>
> self.write(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 191, in write<br>
> self.f.write(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 328, in write<br>
> self.flush()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 307, in flush<br>
> self._sock.sendall(view[write_offset:write_offset+buffer_size])<br>
> error: [Errno 32] Broken pipe<br>
> thread callback:<br>
> error: [Errno 32] Broken pipe<br>
> <br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 307, in flush<br>
> self._sock.sendall(view[write_offset:write_offset+buffer_size])<br>
> <br>
> See reply log for Python traceback.<br>
> <br>
> <br>
> ----------------------------------------<br>
> Exception happened during processing of request from ('127.0.0.1', 53326)<br>
> Traceback (most recent call last):<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 295, in _handle_request_noblock<br>
> self.process_request(request, client_address)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 321, in process_request<br>
> self.finish_request(request, client_address)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 334, in finish_request<br>
> self.RequestHandlerClass(request, client_address, self)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 657, in __init__<br>
> self.finish()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 716, in finish<br>
> self.wfile.close()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 283, in close<br>
> self.flush()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 307, in flush<br>
> self._sock.sendall(view[write_offset:write_offset+buffer_size])<br>
> error: [Errno 32] Broken pipe<br>
> ----------------------------------------<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 -<br>
> Traceback (most recent call last):<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py", <br>
> line 50, in _checkThread<br>
> callable()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 83, in run<br>
> _run(q, h, args)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 159, in _run<br>
> chimera.runCommand(cmd)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line <br>
> 2750, in runCommand<br>
> makeCommand(*args, **kw)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line <br>
> 69, in makeCommand<br>
> f(c, args)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py",
<br>
> line 20, in command<br>
> self.module("cmdline").process(cmdName, args)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line <br>
> 12, in process<br>
> doList(args)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line <br>
> 543, in doList<br>
> doExtensionFunc(func, otherArgs, **kwargs)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line <br>
> 451, in doExtensionFunc<br>
> extFunc(*tuple(processedArgs), **kw)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line <br>
> 192, in listr<br>
> replyobj.info(info)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line <br>
> 625, in info<br>
> _replyStack[-1].info(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 202, in message<br>
> self.writeLine(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 184, in writeLine<br>
> self.write(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py", <br>
> line 191, in write<br>
> self.f.write(s)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 328, in write<br>
> self.flush()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 307, in flush<br>
> self._sock.sendall(view[write_offset:write_offset+buffer_size])<br>
> error: [Errno 32] Broken pipe<br>
> thread callback:<br>
> error: [Errno 32] Broken pipe<br>
> <br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 307, in flush<br>
> self._sock.sendall(view[write_offset:write_offset+buffer_size])<br>
> <br>
> See reply log for Python traceback.<br>
> <br>
> <br>
> ----------------------------------------<br>
> Exception happened during processing of request from ('127.0.0.1', 53329)<br>
> Traceback (most recent call last):<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 295, in _handle_request_noblock<br>
> self.process_request(request, client_address)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 321, in process_request<br>
> self.finish_request(request, client_address)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 334, in finish_request<br>
> self.RequestHandlerClass(request, client_address, self)<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 657, in __init__<br>
> self.finish()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py", <br>
> line 716, in finish<br>
> self.wfile.close()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 283, in close<br>
> self.flush()<br>
> File <br>
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py", <br>
> line 307, in flush<br>
> self._sock.sendall(view[write_offset:write_offset+buffer_size])<br>
> error: [Errno 32] Broken pipe<br>
> ----------------------------------------<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET <br>
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET <br>
> /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -<br>
> 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET <br>
> /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -<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>
> <a href="http://www.jalview.org">www.jalview.org</a> <<a href="http://www.jalview.org">http://www.jalview.org</a>><br>
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