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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Taverna player usage
Date Thu, 02 Jul 2015 16:18:34 GMT
Thanks for describing what you did to start the Taverna Player. I have
copied Finn Bacall who has been maintaining it.

Just to have a try, you could also use these two Docker images:


docker run --name taverna -p 8080:8080 -d stain/taverna-server
docker run --name taverna-portal --link taverna:taverna -p 3000:3000
-d fbacall/taverna-player-portal

That will start up this portal on http://localhost:3000/ - linked to
http://localhost:8080/

... however it gives the same NotIdentifiedByImageMagickError.

In the log I get:

I, [2015-07-02T16:07:50.952952 #1]  INFO -- : Command :: file -b
--mime '/tmp/image_35283445860253326820150702-1-go20s8'
I, [2015-07-02T16:07:50.965587 #1]  INFO -- : Command :: identify
-format '%wx%h,%[exif:orientation]'
'/tmp/2c3f3120c2ed474472b4efe085057bd820150702-1-1quss2a[0]'
2>/dev/null
I, [2015-07-02T16:07:51.036714 #1]  INFO -- : [paperclip] An error was
received while processing:
#<Paperclip::Errors::NotIdentifiedByImageMagickError:
Paperclip::Errors::NotIdentifiedByImageMagickError>
I, [2015-07-02T16:07:51.036971 #1]  INFO -- : Command :: identify
-format '%wx%h,%[exif:orientation]'
'/tmp/2c3f3120c2ed474472b4efe085057bd820150702-1-1quss2a[0]'
2>/dev/null
I, [2015-07-02T16:07:51.094239 #1]  INFO -- : [paperclip] An error was
received while processing:
#<Paperclip::Errors::NotIdentifiedByImageMagickError:
Paperclip::Errors::NotIdentifiedByImageMagickError>


yet identify works in the shell:


root@da925ce1ee9b:/taverna-player-portal/log# identify -format
'%wx%h,%[exif:orientation]'
'/tmp/2c3f3120c2ed474472b4efe085057bd820150702-1-1quss2a[0]'
2>/dev/null ; echo
1890x301,


2c3f3120c2ed474472b4efe085057bd820150702 is a dot file of the t2flow.



Any idea, Finn?

On 2 July 2015 at 14:27, divzee Chandrashakher <divzeeblog@gmail.com> wrote:
> Hi Denis,
>
> Thank you for your step-wise instructions. I installed ruby 2.1.6 and
> followed the steps. But still I couldn't succeed (see below from A to F). I
> am thinking of writing simple web page that uses restful api of taverna
> server to execute workflows. Its a pity that there is no easy/simple guide
> for taverna beginners to install server and portal. I believe this might
> slow down user's adoption of taverna.
>
> A. "rake setup" did not work.
> [admin@localhost taverna-player-portal-master]$ rake setup
> rake aborted!
> Don't know how to build task 'setup'
>
> (See full trace by running task with --trace)
>
> B. So I simply invoked "rake". But it threw error which is something to do
> with paperclip (Diagram Paperclip::Errors::NotIdentifiedByImageMagickError)
> [admin@localhost taverna-player-portal-master]$ rake
> [Coveralls] Set up the SimpleCov formatter.
> [Coveralls] Using SimpleCov's 'rails' settings.
> DEPRECATION WARNING: superclass_delegating_accessor is deprecated and will
> be removed from Rails 5.0 (use class_attribute instead). (called from <top
> (required)> at
> /home/admin/01_Installations/taverna-player-portal-master/test/performance/authorization_test.rb:4)
> Run options: --seed 3155
>
> # Running:
>
> ....EEE.EEEEEEEEE.EEEEE.EFEEEEEEEEFEE...
>
> Finished in 4.373955s, 9.1450 runs/s, 3.8866 assertions/s.
>
>   1) Error:
> TavernaPlayer::RunsControllerTest#test_should_get_edit_form_if_admin:
> ActiveRecord::RecordInvalid: Validation failed: Diagram
> Paperclip::Errors::NotIdentifiedByImageMagickError, Diagram
> Paperclip::Errors::NotIdentifiedByImageMagickError
>     test/controllers/taverna_player/runs_controller_test.rb:43:in `block in
> <class:RunsControllerTest>'
>
> (output cut)
>
> 30) Error:
> WorkflowsTest#test_filters_out_non-visible_workflows:
> ActiveRecord::RecordInvalid: Validation failed: Diagram
> Paperclip::Errors::NotIdentifiedByImageMagickError, Diagram
> Paperclip::Errors::NotIdentifiedByImageMagickError
>     test/models/workflows_test.rb:22:in `block in <class:WorkflowsTest>'
>
> 40 runs, 17 assertions, 2 failures, 28 errors, 0 skips
> [Coveralls] Outside the CI environment, not sending data.
> [admin@localhost taverna-player-portal-master]$
>
>
> C. accessing portal via http://localhost:3000 asked me to run the following
> command. so I executed it
> [admin@localhost taverna-player-portal-master]$ bin/rake db:migrate
> RAILS_ENV=development
>
> D. Started server again
> [admin@localhost taverna-player-portal-master]$ bin/rails s
> => Booting WEBrick
> => Rails 4.2.1 application starting in development on http://localhost:3000
> => Run `rails server -h` for more startup options
> => Ctrl-C to shutdown server
> [2015-07-01 23:26:46] INFO  WEBrick 1.3.1
> [2015-07-01 23:26:46] INFO  ruby 2.1.6 (2015-04-13) [x86_64-linux]
> [2015-07-01 23:26:46] INFO  WEBrick::HTTPServer#start: pid=12947 port=3000
>
> E. from another console started job worker
> [admin@localhost taverna-player-portal-master]$ bin/rake jobs:work
> [Worker(host:localhost.localdomain pid:13058)] Starting job worker
>
> F. I could see the portal home page. Registered and logged in to upload
> taverna workflow. But this step failed with the following error
>
> 2 errors prohibited this workflow from being saved:
>
>     Diagram Paperclip::Errors::NotIdentifiedByImageMagickError
>     Diagram Paperclip::Errors::NotIdentifiedByImageMagickError
>
> Thanks
> Rakesh
>
> On Sun, Jun 28, 2015 at 11:42 AM, Denis Karyakin <samhane.me@gmail.com>
> wrote:
>>
>> Hello,
>> Taverna-player - only middleware for run workflows in Taverna Server. I am
>> not so long ago work with taverna, so more experienced members can correct
>> me.
>>
>> For run workflows you can use taverna-player-portal. For get this
>> application go to https://github.com/myGrid/taverna-player-portal and
>> download zip archive or clone git repository.
>> You should have installed ruby 2.1.6 version.
>>
>> Copy file
>> `taverna-player-portal/config/initializers/taverna_server.rb.example` to
>> `taverna-player-portal/config/initializers/taverna_server.rb` and modify
>> server_address to your server url.
>>
>> After this go to folder taverna-player-portal and run following commands:
>> rake setup - for install dependencies and  create database
>> rails s - for start rails server with UI
>> rake jobs:work - for start queues server, that will be control run
>> workflow in Taverna Server.
>>
>> Now you can go to url localhost:3000 for upload and run workflows
>>
>>
>> 2015-06-28 1:23 GMT+03:00 divzee Chandrashakher <divzeeblog@gmail.com>:
>>>
>>> Hi,
>>>
>>> I am newbie to Taverna. I could install Taverna Server (v 2.5.4) and
>>> Taverna player (v 0.11.0) in CentOS Virtual machine. For player
>>> installation, I followed the tutorial at
>>>
>>> http://mygrid.github.io/taverna-player/0.11.0/
>>>
>>> 1. In the above link, under "Essential (required) configuration", I am
>>> not able to understand the following snippet to be included in
>>> taverna_player.rb
>>>
>>> config.workflow_model_proxy("Workflow") do |proxy|
>>>   proxy.file_method_name = :file_name
>>> end
>>>
>>> Shall i simply copy the above lines to taverna_player.rb file? I don't
>>> know ruby much.
>>>
>>> 2. I am using the 'dummy' rails application that is available within the
>>> taverna_player gem installtion folder to test the server & player
>>> installation. I configured the taverna_server.rb to point to my server
>>> installation.
>>>
>>> Server
>>> http://localhost:8080/ts254/
>>> ---  works fine. prints the taverna help page
>>>
>>> Player (started the rails server)
>>> http://localhost:3000/
>>>
>>> The above url displays the following error:
>>> Couldn't find TavernaPlayer::Workflow with id=3
>>>
>>> I'm have no clue how id gets the value 3. I am not able to understand
>>> where the workflows are stored and how the taverna player can request the
>>> server to execute a particular workflow from the pool of workflows. Please
>>> help me.
>>>
>>> Thanks in advance
>>> Rakesh
>>>
>>>
>>>
>>
>
>
>
> --
> Divya C
> www.dealbitte.com
> Ideas for smart shopping



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718

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