Opened 5 years ago

Closed 5 years ago

#3213 closed defect (fixed)

REST: broken pipe

Reported by: g.m.carstairs@… Owned by: Conrad Huang
Priority: moderate Milestone: 1.0
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

On May 14, 2020, at 8:07 AM, Mungo Carstairs (Staff) <g.m.carstairs@…> 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@…

We're Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: Mungo Carstairs (Staff) <g.m.carstairs@…>
Sent: 07 February 2020 09:44
To: Elaine Meng <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@…

We're Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: Elaine Meng <meng@…>
Sent: 06 February 2020 21:48
To: Mungo Carstairs (Staff) <g.m.carstairs@…>
Cc: Elaine Meng <meng@…>; Eric Pettersen <pett@…>
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) <g.m.carstairs@…> 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@…

We're Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: Conrad Huang <conrad@…>
Sent: 21 January 2020 20:28
To: Mungo Carstairs (Staff) <g.m.carstairs@…>; chimerax-users@… <chimerax-users@…>
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'?

*

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*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>
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Change History (4)

comment:1 by Conrad Huang, 5 years ago

Status: assigned → feedback

Hi, Mungo.

My apologies for the lack of progress. I started work on another project and somehow this ticket got lost in my mailbox.

I've made a change to the "info notification" code so that the network connection is made in a separate thread. This may help depending on how the JalView-ChimeraX communications code is structured. The change should be in tomorrow's candidate build (chimerax-rc built 2020-05-19). Can you please give that a try and see if it makes any difference.

If not, can you tell what I need to replicate the problem? Software version, data files, commands to execute, etc. Thanks.

Conrad

in reply to:  2 ; comment:2 by g.m.carstairs@…, 5 years ago 

Hi Conrad,

Thanks for the update. I will give that a try - but first I need to update from OSX 10.12 to something more current!
Will let you know if that helps as soon as I can.

Best regards,

Mungo



[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>

[University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw>  [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li>  [University of Dundee YouTube] <http://uod.ac.uk/sig-yt>  [University of Dundee Instagram] <http://uod.ac.uk/sig-ig>  [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc>
We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 18 May 2020 20:26
Cc: conrad@cgl.ucsf.edu <conrad@cgl.ucsf.edu>; Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk>
Subject: Re: [ChimeraX] #3213: REST: broken pipe

#3213: REST: broken pipe
---------------------------------------+--------------------------
          Reporter:  g.m.carstairs@…   |      Owner:  Conrad Huang
              Type:  defect            |     Status:  feedback
          Priority:  moderate          |  Milestone:  1.0
         Component:  General Controls  |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------------
Changes (by Conrad Huang):

 * status:  assigned => feedback


Comment:

 Hi, Mungo.

 My apologies for the lack of progress.  I started work on another project
 and somehow this ticket got lost in my mailbox.

 I've made a change to the "info notification" code so that the network
 connection is made in a separate thread.  This may help depending on how
 the JalView-ChimeraX communications code is structured.  The change should
 be in tomorrow's candidate build (chimerax-rc built 2020-05-19).  Can you
 please give that a try and see if it makes any difference.

 If not, can you tell what I need to replicate the problem?  Software
 version, data files, commands to execute, etc.  Thanks.

 Conrad

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3213#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

The University of Dundee is a registered Scottish Charity, No: SC015096

in reply to:  3 ; comment:3 by g.m.carstairs@…, 5 years ago 

Hello Conrad,

I just tried that (ChimeraX-1.0-rc-2020.05.21) and it works perfectly!

Result: selections made in ChimeraX can be highlighted in a mapped Jalview alignment (same as in Chimera).

Many thanks!

Best regards,

Mungo



[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>

[University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw>  [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li>  [University of Dundee YouTube] <http://uod.ac.uk/sig-yt>  [University of Dundee Instagram] <http://uod.ac.uk/sig-ig>  [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc>
We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 19 May 2020 08:56
To: conrad@cgl.ucsf.edu <conrad@cgl.ucsf.edu>; Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk>
Subject: Re: [ChimeraX] #3213: REST: broken pipe

#3213: REST: broken pipe
---------------------------------------+--------------------------
          Reporter:  g.m.carstairs@…   |      Owner:  Conrad Huang
              Type:  defect            |     Status:  feedback
          Priority:  moderate          |  Milestone:  1.0
         Component:  General Controls  |    Version:
        Resolution:                    |   Keywords:
        Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
           Project:  ChimeraX          |
---------------------------------------+--------------------------

Comment (by g.m.carstairs@…):

 {{{
 Hi Conrad,

 Thanks for the update. I will give that a try - but first I need to update
 from OSX 10.12 to something more current!
 Will let you know if that helps as soon as I can.

 Best regards,

 Mungo



 [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<http://www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk>>
 g.m.carstairs@dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk>

 [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of
 Dundee Twitter] <http://uod.ac.uk/sig-tw>  [University of Dundee LinkedIn]
 <http://uod.ac.uk/sig-li>  [University of Dundee YouTube]
 <http://uod.ac.uk/sig-yt>  [University of Dundee Instagram]
 <http://uod.ac.uk/sig-ig>  [University of Dundee Snapchat]
 <http://uod.ac.uk/sig-sc>
 We're Scottish University of the Year again!<http://uod.ac.uk/sig-
 strapline>
 The Times / Sunday Times Good University Guide 2016 and 2017
 ________________________________
 From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
 Sent: 18 May 2020 20:26
 Cc: conrad@cgl.ucsf.edu <conrad@cgl.ucsf.edu>; Mungo Carstairs (Staff)
 <g.m.carstairs@dundee.ac.uk>
 Subject: Re: [ChimeraX] #3213: REST: broken pipe

 #3213: REST: broken pipe
 ---------------------------------------+--------------------------
           Reporter:  g.m.carstairs@…   |      Owner:  Conrad Huang
               Type:  defect            |     Status:  feedback
           Priority:  moderate          |  Milestone:  1.0
          Component:  General Controls  |    Version:
         Resolution:                    |   Keywords:
         Blocked By:                    |   Blocking:
 Notify when closed:                    |   Platform:  all
            Project:  ChimeraX          |
 ---------------------------------------+--------------------------
 Changes (by Conrad Huang):

  * status:  assigned => feedback


 Comment:

  Hi, Mungo.

  My apologies for the lack of progress.  I started work on another project
  and somehow this ticket got lost in my mailbox.

  I've made a change to the "info notification" code so that the network
  connection is made in a separate thread.  This may help depending on how
  the JalView-ChimeraX communications code is structured.  The change
 should
  be in tomorrow's candidate build (chimerax-rc built 2020-05-19).  Can you
  please give that a try and see if it makes any difference.

  If not, can you tell what I need to replicate the problem?  Software
  version, data files, commands to execute, etc.  Thanks.

  Conrad

 --
 Ticket URL:
 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3213#comment:1>
 ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
 ChimeraX Issue Tracker

 The University of Dundee is a registered Scottish Charity, No: SC015096
 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3213#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

The University of Dundee is a registered Scottish Charity, No: SC015096

comment:4 by Conrad Huang, 5 years ago

Resolution: → fixed
Status: feedback → closed

The fix worked!

Note: See TracTickets for help on using tickets.