Hi Conrad,


I will see if I can change to POST.

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.


Thanks,


Mungo


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Mungo Carstairs
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The Barton Group
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www.compbio.dundee.ac.uk 
g.m.carstairs@dundee.ac.uk
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From: Conrad Huang <conrad@cgl.ucsf.edu>
Sent: 04 February 2019 21:21:12
To: Mungo Carstairs (Staff); chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Help: 'broken pipe' error
 
Hi, Mungo.

I tried using the RESTserver on a recent daily build, and it opening
4zhp worked fine.  Since RESTserver hasn't changed in a very long time,
I suspect the results would be the same with 1.13.

The way I tested it is to start the RESTserver in Chimera, and then go
to a browser to visit "http://localhost:PORT/static/cmdline.html" where
PORT is the port number reported in the Reply Log.  A form is displayed
in the browser and I type in "open cifID:4zhp", which runs the command
and displays Chimera messages in the browser rather than the Reply Log.

I did notice that your tests show messages like:

> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 -

whereas mine show:

> 127.0.0.1 - - [04/Feb/2019 12:02:46] "POST /run HTTP/1.1" 200 -

That looks to me like you are sending requests using http GET, whereas
my tests are using POST.  It /shouldn't/ make any difference, but would
it be possible for you to test using POST to send requests to Chimera
instead of GET?

Conrad

On 2/1/2019 2:43 AM, Mungo Carstairs (Staff) wrote:
> Hi there,
>
>
> I'm experimenting with Jalview /as Javascript/ talking to Chimera over
> the latter's REST server.
>
> The first few 'list models' commands work fine, but when I send a
> command 'open cifID:4zhp' I (usually but not always) get an error
> '[Errno 32] Broken Pipe' in Chimera. Is there a clue in the stack traces
> below as to the reason for this? Thanks.
>
>
> Chimera 1.12 (build 41481) on OSX Sierra 10.12.6.
>
>
> REST server on host 127.0.0.1 port 53135
> 127.0.0.1 - - [01/Feb/2019 10:06:14] "GET
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=open%20cifID%3A4zhp HTTP/1.1" 200 -
> Traceback (most recent call last):
>    File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py",
> line 50, in _checkThread
>      callable()
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 83, in run
>      _run(q, h, args)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 163, in _run
>      replyobj.error(str(v) + '\n')
>    File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line
> 637, in error
>      _replyStack[-1].error(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 184, in writeLine
>      self.write(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 191, in write
>      self.f.write(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 328, in write
>      self.flush()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 307, in flush
>      self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
> thread callback:
> error: [Errno 32] Broken pipe
>
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 307, in flush
>      self._sock.sendall(view[write_offset:write_offset+buffer_size])
>
> See reply log for Python traceback.
>
>
> ----------------------------------------
> Exception happened during processing of request from ('127.0.0.1', 53326)
> Traceback (most recent call last):
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 295, in _handle_request_noblock
>      self.process_request(request, client_address)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 321, in process_request
>      self.finish_request(request, client_address)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 334, in finish_request
>      self.RequestHandlerClass(request, client_address, self)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 657, in __init__
>      self.finish()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 716, in finish
>      self.wfile.close()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 283, in close
>      self.flush()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 307, in flush
>      self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
> ----------------------------------------
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=list%20model%20spec%20%230%20attribute%20color HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=list%20residues%20spec%20%230 HTTP/1.1" 200 -
> Traceback (most recent call last):
>    File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/threadq.py",
> line 50, in _checkThread
>      callable()
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 83, in run
>      _run(q, h, args)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 159, in _run
>      chimera.runCommand(cmd)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line
> 2750, in runCommand
>      makeCommand(*args, **kw)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line
> 69, in makeCommand
>      f(c, args)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/ChimeraExtension.py",
> line 20, in command
>      self.module("cmdline").process(cmdName, args)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line
> 12, in process
>      doList(args)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line
> 543, in doList
>      doExtensionFunc(func, otherArgs, **kwargs)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/Midas/midas_text.py", line
> 451, in doExtensionFunc
>      extFunc(*tuple(processedArgs), **kw)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/ListInfo/cmdline.py", line
> 192, in listr
>      replyobj.info(info)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/replyobj.py", line
> 625, in info
>      _replyStack[-1].info(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 202, in message
>      self.writeLine(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 184, in writeLine
>      self.write(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/share/RESTServer/__init__.py",
> line 191, in write
>      self.f.write(s)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 328, in write
>      self.flush()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 307, in flush
>      self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
> thread callback:
> error: [Errno 32] Broken pipe
>
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 307, in flush
>      self._sock.sendall(view[write_offset:write_offset+buffer_size])
>
> See reply log for Python traceback.
>
>
> ----------------------------------------
> Exception happened during processing of request from ('127.0.0.1', 53329)
> Traceback (most recent call last):
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 295, in _handle_request_noblock
>      self.process_request(request, client_address)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 321, in process_request
>      self.finish_request(request, client_address)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 334, in finish_request
>      self.RequestHandlerClass(request, client_address, self)
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 657, in __init__
>      self.finish()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/SocketServer.py",
> line 716, in finish
>      self.wfile.close()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 283, in close
>      self.flush()
>    File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/socket.py",
> line 307, in flush
>      self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
> ----------------------------------------
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET /run?command=focus HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:03] "GET
> /run?command=list%20models%20type%20molecule HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET
> /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -
> 127.0.0.1 - - [01/Feb/2019 10:32:05] "GET
> /run?command=color%20%238db520%20%230%3A2-98.A HTTP/1.1" 200 -
>
>
> 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@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>
>
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