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From Stian Soiland-Reyes <st...@apache.org>
Subject Re: Taverna player usage
Date Mon, 06 Jul 2015 17:19:58 GMT
(Forwarding to list on behalf of Finn)

On 2 July 2015 at 18:27, Finn Bacall <finn.bacall@manchester.ac.uk> wrote:
> Hi all,
>
> It seems this issue is caused by a missing dependency: "ghostscript"
>
> Installing this via apt-get, or using the latest docker image (when it has
> finished building [1]) should fix this issue.
>
> Cheers,
>
> Finn
>
> [1]
> https://registry.hub.docker.com/u/fbacall/taverna-player-portal/builds_history/226759/
>
>
>
> On 02/07/2015 17:18, Stian Soiland-Reyes wrote:
>>
>> 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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