id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3213 REST: broken pipe g.m.carstairs@… Conrad Huang "On May 14, 2020, at 8:07 AM, Mungo Carstairs (Staff) wrote: Hi Elaine, I hope you are all well over there. Our group is able to carry on working from home more or less as normal (and we got a release of Jalview out 3 weeks ago!). I see ChimeraX 1.0 is due out very soon - looking forward to that as I'm sure you are. We are keen to put out a pre-release of Jalview with ChimeraX as soon as possible thereafter. The issue in this email trail remains open - at least up to ChimeraX 0.91. (I need to update my OSX from 1.12. ChimeraX 0.93 wouldn't launch - said it requires 1.13+ contrary to the documentation at http://www.rbvi.ucsf.edu/chimerax/download.html.) Has anyone had a change to look at it? Thanks and best wishes, Mungo 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 www.compbio.dundee.ac.uk g.m.carstairs@dundee.ac.uk We're Scottish University of the Year again! The Times / Sunday Times Good University Guide 2016 and 2017 From: Mungo Carstairs (Staff) Sent: 07 February 2020 09:44 To: Elaine Meng Subject: Re: [chimerax-users] ChimeraX and REST service interoperation Hi Elaine, No, not yet, still puzzled by this one. Nothing very urgent though, I hope you all keep well! Maybe I need to track down the equivalent code (Jetty server??) in Cytoscape to see how it is done there. Best, Mungo 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 www.compbio.dundee.ac.uk g.m.carstairs@dundee.ac.uk We're Scottish University of the Year again! The Times / Sunday Times Good University Guide 2016 and 2017 From: Elaine Meng Sent: 06 February 2020 21:48 To: Mungo Carstairs (Staff) Cc: Elaine Meng ; Eric Pettersen Subject: Re: [chimerax-users] ChimeraX and REST service interoperation Hi Mungo, Did Conrad ever respond to your latest query? I’m sorry if he hasn’t… he has been away from work sick this week. Maybe next week I will be able remind him in person. Apologies, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 24, 2020, at 7:13 AM, Mungo Carstairs (Staff) wrote: Hello Conrad, I tried recoding so the response is sent to the REST request before making a new request to it. I'm still getting the same timeout and stack trace (give or take port numbers). One thing that looks curious: The port number (if that is what it is) in the Chimera log message (after Jalview sends info selection level residue) Exception happened during processing of request from ('127.0.0.1', 50285) doesn't match that of the Jalview REST server as specified in the earlier command info notify start selection jalview prefix SelectionChanged urlhttp://localhost:50108/jalview/chimera2 Does that give any clue? For what it's worth, ChimeraX Preferences | Web Access does not have any proxy settings. thanks Mungo 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 www.compbio.dundee.ac.uk g.m.carstairs@dundee.ac.uk We're Scottish University of the Year again! The Times / Sunday Times Good University Guide 2016 and 2017 From: Conrad Huang Sent: 21 January 2020 20:28 To: Mungo Carstairs (Staff) ; chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ChimeraX and REST service interoperation 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 *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 www.compbio.dundee.ac.uk g.m.carstairs@dundee.ac.uk University of Dundee Facebook University of Dundee Twitter University of Dundee LinkedIn University of Dundee YouTube University of Dundee Instagram University of Dundee Snapchat *We're Scottish University of the Year again!* 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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users The University of Dundee is a registered Scottish Charity, No: SC015096" defect closed moderate 1.0 General Controls fixed all ChimeraX