[Midas] ParaView Web support for Midas

Zach Mullen zach.mullen at kitware.com
Wed Nov 6 19:28:16 EST 2013 

Did you get the latest nightly package, or a release package? You will need
to download the nightly one, since there have been Python API changes since
the most recent official release.


On Wed, Nov 6, 2013 at 7:25 PM, BRIAN E CHAPMAN <Brian.Chapman at utah.edu>wrote:

>  Looking at the paraview python source files
> ParaView-4.0.1-Linux-64bit/lib/paraview-4.0/site-packages/paraview/web.py,
> there is no “protocols” to import. Do we have a version mismatch between
> what Midas is expecting and the binary Paraview download?
>
>  Brian
>
>
>   From: Sebastien Jourdain <sebastien.jourdain at kitware.com>
> Date: Wednesday, November 6, 2013 at 12:02 PM
> To: Brian Chapman <brian.chapman at utah.edu>
> Cc: Zach Mullen <zach.mullen at kitware.com>, "midas at public.kitware.com" <
> midas at public.kitware.com>
>
> Subject: Re: [Midas] ParaView Web support for Midas
>
>   The issue might be related to the fact that you should add the "-f"
> argument to the command line as Jetty may think that the process is not
> started yet.
> The -f will force to flush the output of the python process. This was
> added lately to prevent the +++++ to show up when running from the command
> line.
>
>  Hope that helps.
>
>  Seb
>
>
> On Wed, Nov 6, 2013 at 11:56 AM, BRIAN E CHAPMAN <Brian.Chapman at utah.edu>wrote:
>
>> Progress but not quite there. I do now actually get an attempt to launch
>> Paraview but a timeout occurs:
>>
>> Starting ParaviewWeb instance
>>
>> Waiting for binding on port 9000...
>> Instance creation failed: Instance did not bind to port within 5 seconds.
>>
>> Log content: Traceback (most recent call last):
>> File "/usr/local/src/Midas3/modules/pvw/apps/midas.py", line 19, in
>> from paraview.web import protocols, wamp
>> ImportError: cannot import name protocols
>>
>>
>> I’ll have to check configuration this afternoon.
>>
>> Brian
>>
>>
>> On 11/6/13, 11:04 AM, "Zach Mullen" <zach.mullen at kitware.com> wrote:
>>
>> >Ok, good to know. I packaged up the correct www dir and attached it to
>> >this email, dump that directory into the module's public dir as a
>> >directory named "import" (apps, ext, and lib should be directly
>> >underneath import). That should hopefully fix the issue.
>> >
>> >Thanks,
>> >
>> >Zach
>> >
>> >On Wed, Nov 6, 2013 at 1:00 PM, BRIAN E CHAPMAN <Brian.Chapman at utah.edu>
>> >wrote:
>> >> Yes. I¹m using the packaged binary. I was having a difficult time
>> >>getting
>> >> Paraview to compile on my machine.
>> >>
>> >> Brian
>> >>
>> >> On 11/6/13, 10:56 AM, "Zach Mullen" <zach.mullen at kitware.com> wrote:
>> >>
>> >>>After looking into it, it looks like this is actually only the case
>> >>>with the packaged version of ParaView, not one built from source.
>> >>>Brian, are you using the downloaded paraview package or building from
>> >>>source?
>> >>>
>> >>>On Wed, Nov 6, 2013 at 7:10 AM, Zach Mullen <zach.mullen at kitware.com>
>> >>>wrote:
>> >>>> This is indeed the issue I discovered yesterday. Some files were
>> moved
>> >>>> within ParaView and it broke compatibility with the Midas plugin. I
>> >>>>should
>> >>>> have a fix committed to next branch this morning.
>> >>>>
>> >>>> Thanks,
>> >>>>
>> >>>> Zach
>> >>>>
>> >>>>
>> >>>> On Tue, Nov 5, 2013 at 11:32 PM, Patrick Reynolds
>> >>>> <patrick.reynolds at kitware.com> wrote:
>> >>>>>
>> >>>>> Brian,
>> >>>>>
>> >>>>> This looks like it could be related to the symbolic link of the
>> >>>>>vtkweb
>> >>>>> javascript. This may be related to an issue that Zach is tracking.
>> >>>>>
>> >>>>> --
>> >>>>> Patrick Reynolds
>> >>>>> Technical Leader
>> >>>>> Kitware, Inc.
>> >>>>> 919 869 8848
>> >>>>>
>> >>>>> On Tuesday, October 29, 2013 at 5:15 PM, BRIAN E CHAPMAN wrote:
>> >>>>>
>> >>>>> Patrick,
>> >>>>>
>> >>>>> I've been toggling the dynamic help and looking at the logs (apache
>> >>>>>and
>> >>>>> midas/log/dev.log). Here is what I am getting without and with
>> >>>>>dynamic
>> >>>>>help
>> >>>>> turned on
>> >>>>>
>> >>>>> Dynamic help off:
>> >>>>>
>> >>>>> [Tue Oct 29 15:06:08.706120 2013] [:error] [pid 25319] [client
>> >>>>> 155.100.62.145:54950] PHP Warning:  Unknown: function 'NULL' not
>> >>>>>found
>> >>>>>or
>> >>>>> invalid function name in Unknown on line 0,
>> >>>>> referer:http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
>> >>>>>
>> >>>>> 2013-10-29 17:06:08 WARN (4): URL:
>> >>>>>
>> >>>>>
>> http://155.100.62.142/midas/modules/pvw/public/import/lib/js/vtkweb-al
>> >>>>>l.
>> >>>>>min.js
>> >>>>> Server IP: 155.100.62.142
>> >>>>> Client IP: 155.100.62.145
>> >>>>> User agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5)
>> >>>>> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/30.0.1599.101
>> >>>>>Safari/537.36
>> >>>>> Server time: 2013-10-29 17:06:08
>> >>>>> RequestURI:
>> /midas/modules/pvw/public/import/lib/js/vtkweb-all.min.js
>> >>>>> Referer: http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
>> >>>>> <b>Message: Invalid controller specified (modules)</b>
>> >>>>>
>> >>>>> Trace:
>> >>>>> #0 /usr/local/src/Midas3/library/Zend/Controller/Front.php(954):
>> >>>>>
>>
>> >>>>>Zend_Controller_Dispatcher_Standard->dispatch(Object(Zend_Controller_R
>> >>>>>eq
>> >>>>>uest_Http),
>> >>>>> Object(Zend_Controller_Response_Http))
>> >>>>> #1
>> >>>>>
>>
>> >>>>>/usr/local/src/Midas3/library/Zend/Application/Bootstrap/Bootstrap.php
>> >>>>>(9
>> >>>>>7):
>> >>>>> Zend_Controller_Front->dispatch()
>> >>>>> #2 /usr/local/src/Midas3/library/Zend/Application.php(366):
>> >>>>> Zend_Application_Bootstrap_Bootstrap->run()
>> >>>>> #3 /usr/local/src/Midas3/index.php(73): Zend_Application->run()
>> >>>>> #4 {main}
>> >>>>>
>> >>>>> Request data: array (
>> >>>>>   'controller' => 'modules',
>> >>>>>   'action' => 'pvw',
>> >>>>>   'public' => 'import',
>> >>>>>   'lib' => 'js',
>> >>>>>   'module' => 'default',
>> >>>>> )
>> >>>>>
>> >>>>> Session data:
>> >>>>> Dao: __PHP_Incomplete_Class::__set_state(array(
>> >>>>>    '__PHP_Incomplete_Class_Name' => 'UserDao',
>> >>>>>    '_model' => 'User',
>> >>>>>    'key' => NULL,
>> >>>>>    '_key' => 'user_id',
>> >>>>>    'saved' => true,
>> >>>>>    'user_id' => '1',
>> >>>>>    'firstname' => 'Brian',
>> >>>>>    'lastname' => 'Chapman',
>> >>>>>    'email' => 'brian.chapman at utah.edu',
>> >>>>>    'thumbnail' => NULL,
>> >>>>>    'company' => NULL,
>> >>>>>    'hash_alg' => 'sha256',
>> >>>>>    'salt' => 'uirWyLLLBDcN9udgEy2o0ZwZulN17z8s',
>> >>>>>    'creation' => '2013-10-24 14:09:40',
>> >>>>>    'folder_id' => '1',
>> >>>>>    'admin' => '1',
>> >>>>>    'privacy' => '0',
>> >>>>>    'view' => '0',
>> >>>>>    'uuid' => '52696264c0b08ca6ba63fc546fe5b950545d654ae59cc',
>> >>>>>    'city' => '',
>> >>>>>    'country' => '',
>> >>>>>    'website' => '',
>> >>>>>    'biography' => '',
>> >>>>>    'dynamichelp' => '1',
>> >>>>> ))
>> >>>>>
>> >>>>> Last database query: SELECT `setting`.* FROM `setting` WHERE (name =
>> >>>>> 'temp_directory') AND (module = 'core') LIMIT 1
>> >>>>>
>> >>>>>
>> >>>>> Dynamic Help ON:
>> >>>>>
>> >>>>> [Tue Oct 29 15:10:44.885671 2013] [:error] [pid 25321] [client
>> >>>>> 155.100.62.145:55013] PHP Warning:  Unknown: function 'NULL' not
>> >>>>>found
>> >>>>>or
>> >>>>> invalid function name in Unknown on line 0,
>> >>>>> referer:http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
>> >>>>> [Tue Oct 29 15:10:44.894376 2013] [:error] [pid 25319] [client
>> >>>>> 155.100.62.145:55006] PHP Fatal error:
>> >>>>>AppController::isDynamicHelp(): The
>> >>>>> script tried to execute a method or access a property of an
>> >>>>>incomplete
>> >>>>> object. Please ensure that the class definition "UserDao"
>> >>>>>of
>> >>>>>the
>> >>>>> object you are trying to operate on was loaded _before_
>> unserialize()
>> >>>>>gets
>> >>>>> called or provide a __autoload() function to load the class
>> >>>>>definition
>> >>>>> in
>> >>>>> /usr/local/src/Midas3/core/AppController.php on line 424,
>> >>>>> referer:http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
>> >>>>>
>> >>>>> 2013-10-29 17:10:44 CRIT (2): Fatal Error: Array
>> >>>>> (
>> >>>>>     [type] => 1
>> >>>>>     [message] => AppController::isDynamicHelp(): The script tried to
>> >>>>> execute a method or access a property of an incomplete object.
>> Please
>> >>>>>ensure
>> >>>>> that the class definition "UserDao" of the object you are
>> >>>>>trying
>> >>>>> to operate on was loaded _before_ unserialize() gets called or
>> >>>>>provide
>> >>>>>a
>> >>>>> __autoload() function to load the class definition
>> >>>>>     [file] => /usr/local/src/Midas3/core/AppController.php
>> >>>>>     [line] => 424
>> >>>>>     [typeText] => E_ERROR
>> >>>>> )
>> >>>>>
>> >>>>>
>> >>>>> URL:
>> >>>>>
>> >>>>>
>> http://155.100.62.142/midas/modules/pvw/public/import/lib/js/vtkweb-al
>> >>>>>l.
>> >>>>>min.js
>> >>>>>
>> >>>>> Server IP: 155.100.62.142
>> >>>>> User agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5)
>> >>>>> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/30.0.1599.101
>> >>>>>Safari/537.36
>> >>>>> Server time: 2013-10-29 17:10:44
>> >>>>> Referer: http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
>> >>>>> Parameters (post): Array
>> >>>>> (
>> >>>>> )
>> >>>>> Parameters (get): Array
>> >>>>> (
>> >>>>> )
>> >>>>>
>> >>>>>
>> >>>>> Brian E. Chapman, Ph.D.
>> >>>>> Associate Professor
>> >>>>> Department of Radiology
>> >>>>> University of Utah
>> >>>>>
>> >>>>>
>> >>>>> From: Patrick Reynolds <patrick.reynolds at kitware.com>
>> >>>>> Date: Tuesday, October 29, 2013 1:28 PM
>> >>>>> To: Brian Chapman <Brian.Chapman at utah.edu>
>> >>>>> Cc: "midas at public.kitware.com" <midas at public.kitware.com>
>> >>>>> Subject: Re: [Midas] ParaView Web support for Midas
>> >>>>>
>> >>>>> Brian,
>> >>>>>
>> >>>>> Are you able to get to the admin page and disable dynamic help?
>> >>>>>
>> >>>>> That should yield an improved error message.
>> >>>>>
>> >>>>> --
>> >>>>> Patrick Reynolds
>> >>>>> Technical Leader
>> >>>>> Kitware, Inc.
>> >>>>> 919 869 8848
>> >>>>>
>> >>>>> On Thursday, October 24, 2013 at 6:58 PM, BRIAN E CHAPMAN wrote:
>> >>>>>
>> >>>>> Hi Zach, et al.,
>> >>>>>
>> >>>>> I'm making progress here. I looked at Sebastien's suggestion of
>> using
>> >>>>> VirtualGL but decided to go back and build a VM with X11 support.
>> >>>>>I've
>> >>>>>got
>> >>>>> Midas running and ParaView web configured as per the web site and
>> >>>>>Zach's
>> >>>>> instructions. When I got to view an object (a 3D CT stored in .mha
>> >>>>>format) I
>> >>>>> get a blank canvas with "Volume rendering: pe0017s4.mha" on the top
>> >>>>>and a
>> >>>>> bunch of control widgets on the right.
>> >>>>>
>> >>>>> When I look at the apache2 logs I see the following.
>> >>>>>
>> >>>>> acces.log: 111.222.33.444 - - [24/Oct/2013:16:38:02 -0600] "GET
>> >>>>> /midas/modules/pvw/public/import/lib/js/vtkweb-all.min.js HTTP/1.1"
>> >>>>>500 936
>> >>>>> "http://111.222.33.555/midas/pvw/paraview/volume?itemId=1"
>> >>>>>"Mozilla/5.0
>> >>>>> (X11; Ubuntu; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
>> >>>>>
>> >>>>> error.log [Thu Oct 24 16:38:02.468812 2013] [:error] [pid 7303]
>> >>>>>[client
>> >>>>> 111.222.33.444:34502] PHP Fatal error:
>> >>>>>AppController::isDynamicHelp(): The
>> >>>>> script tried to execute a method or access a property of an
>> >>>>>incomplete
>> >>>>> object. Please ensure that the class definition "UserDao"
>> >>>>>of
>> >>>>>the
>> >>>>> object you are trying to operate on was loaded _before_
>> unserialize()
>> >>>>>gets
>> >>>>> cal
>> >>>>>
>> >>>>> The midas log file is as follows:
>> >>>>>
>> >>>>> dev.log
>> >>>>> Referer: http://111.222.33.555/midas/pvw/paraview/volume?itemId=1
>> >>>>> Parameters (post): Array
>> >>>>> (
>> >>>>> )
>> >>>>> Parameters (get): Array
>> >>>>> (
>> >>>>> )
>> >>>>>
>> >>>>> Any ideas as to what is going wrong?
>> >>>>>
>> >>>>> Brian
>> >>>>>
>> >>>>> Brian E. Chapman, Ph.D.
>> >>>>> Associate Professor
>> >>>>> Department of Radiology
>> >>>>> University of Utah
>> >>>>>
>> >>>>>
>> >>>>> From: Zach Mullen <zach.mullen at kitware.com>
>> >>>>> Date: Thursday, October 17, 2013 11:54 AM
>> >>>>> To: Brian Chapman <Brian.Chapman at utah.edu>
>> >>>>> Cc: Patrick Reynolds <patrick.reynolds at kitware.com>,
>> >>>>> "midas at public.kitware.com" <midas at public.kitware.com>
>> >>>>> Subject: Re: [Midas] ParaView Web support for Midas
>> >>>>>
>> >>>>> Hi Brian,
>> >>>>>
>> >>>>> Answered your questions inline.
>> >>>>>
>> >>>>>
>> >>>>> On Thu, Oct 17, 2013 at 1:49 PM, BRIAN E CHAPMAN
>> >>>>><Brian.Chapman at utah.edu>
>> >>>>> wrote:
>> >>>>>
>> >>>>> Patrick,
>> >>>>>
>> >>>>> That saved a lot of time! A couple of dummy questions. In
>> >>>>> /var/www/midas/modules there is already a pvw directory. So where am
>> >>>>>I
>> >>>>> supposed to create the symbolic link to
>> >>>>>$PARAVIEW_ROOT/lib/paraview-4.0/www?
>> >>>>>
>> >>>>>
>> >>>>> You should create a symlink at
>> >>>>>/var/www/midas/modules/pvw/public/import,
>> >>>>> and it should point to the paraview-4.0/www dir.
>> >>>>>
>> >>>>>
>> >>>>> Also, just because I'm kind of dense, do I need to set the DISPLAY
>> >>>>> environment variable. The pop-up help says "If the DISPLAY env var
>> >>>>>should be
>> >>>>> setŠ" I don't know if it should be.
>> >>>>>
>> >>>>> It depends what environment you are running in. If you plan on
>> >>>>>running
>> >>>>> this headlessly as a server, you will probably need to set the
>> >>>>>environment
>> >>>>> variable. If you are running the server within an already existing X
>> >>>>> environment, you probably won't need to set it. If you open a
>> >>>>>terminal
>> >>>>>and
>> >>>>> type
>> >>>>>
>> >>>>> echo $DISPLAY
>> >>>>>
>> >>>>> It will show you the current value of your display ID.
>> >>>>>
>> >>>>>
>> >>>>> Finally, is there a tutorial or demo for the Midas/ParaView
>> >>>>>interface?
>> >>>>>
>> >>>>>
>> >>>>> We just finished transitioning the demo application to the latest
>> >>>>>version
>> >>>>> of ParaViewWeb. The demo of the old capabilities is here:
>> >>>>>
>> >>>>>
>> http://50.58.123.185/external/midas/visualize/paraview/volume?itemId=4
>> >>>>>4
>> >>>>>
>> >>>>> There isn't much currently in the way of developer-oriented
>> >>>>>documentation
>> >>>>> for the module; for that you might have to just consult us with your
>> >>>>> questions :)
>> >>>>>
>> >>>>> Thanks,
>> >>>>>
>> >>>>>
>> >>>>> Thanks for the help.
>> >>>>>
>> >>>>> Brian
>> >>>>>
>> >>>>>
>> >>>>> From: Patrick Reynolds <patrick.reynolds at kitware.com>
>> >>>>> Date: Thursday, October 17, 2013 11:12 AM
>> >>>>> To: Brian Chapman <Brian.Chapman at utah.edu>
>> >>>>> Cc: "midas at public.kitware.com" <midas at public.kitware.com>
>> >>>>> Subject: Re: [Midas] ParaView Web support for Midas
>> >>>>>
>> >>>>> Brian,
>> >>>>>
>> >>>>> You'll need to build Paraview Web from Source or download binaries.
>> >>>>>It
>> >>>>> comes with paraview, so you should be able to follow the
>> instructions
>> >>>>> stemming from this wiki page:
>> >>>>>
>> >>>>> http://www.paraview.org/Wiki/ParaViewWeb
>> >>>>>
>> >>>>> HTH.
>> >>>>>
>> >>>>> --
>> >>>>> Patrick Reynolds
>> >>>>> Technical Leader
>> >>>>> Kitware, Inc.
>> >>>>> 919 869 8848
>> >>>>>
>> >>>>> On Thursday, October 17, 2013 at 12:56 PM, BRIAN E CHAPMAN wrote:
>> >>>>>
>> >>>>> Hello Midas World,
>> >>>>>
>> >>>>> I'm trying to build an instance of Midas with ParaviewWeb enabled.
>> >>>>>I'm
>> >>>>> working on an Ubuntu 12.04 instance. Midas built fine, but I'm
>> >>>>>having a
>> >>>>> difficult time getting Paraview to build. Just curious if the
>> >>>>> paraview-python package that is available in the ubuntu distribution
>> >>>>>is
>> >>>>> sufficient for this purpose? If it is, curious about the details of
>> >>>>>the
>> >>>>> configuration for the instructions: "Make sure to symlink the www
>> >>>>>directory
>> >>>>> of your ParView build directoryŠ"
>> >>>>>
>> >>>>> I'm suspicious of the package since when I try to run pvpython I get
>> >>>>>an
>> >>>>> error:
>> >>>>>
>> >>>>> "Error converting executable file
>> "/usr/bin/../lib/paraview/pvpython"
>> >>>>>to
>> >>>>> real path: no such file or directory"
>> >>>>>
>> >>>>>
>> >>>>> Brian E. Chapman, Ph.D.
>> >>>>> Associate Professor
>> >>>>> Department of Radiology
>> >>>>> University of Utah
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> Midas mailing list
>> >>>>> Midas at public.kitware.com
>> >>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> Midas mailing list
>> >>>>> Midas at public.kitware.com
>> >>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Zach Mullen
>> >>>>> R & D Engineer
>> >>>>> Kitware Inc.
>> >>>>> 919-869-8858
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> --
>> >>>> Zach Mullen
>> >>>> R & D Engineer
>> >>>> Kitware Inc.
>> >>>> 919-869-8858
>> >>>
>> >>>
>> >>>
>> >>>--
>> >>>Zach Mullen
>> >>>R & D Engineer
>> >>>Kitware Inc.
>> >>>919-869-8858
>> >>
>> >
>> >
>> >
>> >--
>> >Zach Mullen
>> >R & D Engineer
>> >Kitware Inc.
>> >919-869-8858
>>
>> _______________________________________________
>> Midas mailing list
>> Midas at public.kitware.com
>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
>>
>
>


-- 
Zach Mullen
R & D Engineer
Kitware Inc.
919-869-8858
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