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 -
 |
Mungo Carstairs
The Barton Group School of Life Sciences University of Dundee, Dundee, Scotland, UK |
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