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From divzee Chandrashakher <divzeeb...@gmail.com>
Subject Re: Taverna player usage
Date Thu, 02 Jul 2015 13:27:21 GMT
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
Run options: --seed 3155

# Running:


Finished in 4.373955s, 9.1450 runs/s, 3.8866 assertions/s.

  1) Error:
ActiveRecord::RecordInvalid: Validation failed: Diagram
Paperclip::Errors::NotIdentifiedByImageMagickError, Diagram
    test/controllers/taverna_player/runs_controller_test.rb:43:in `block in

(output cut)

30) Error:
ActiveRecord::RecordInvalid: Validation failed: Diagram
Paperclip::Errors::NotIdentifiedByImageMagickError, Diagram
    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

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


On Sun, Jun 28, 2015 at 11:42 AM, Denis Karyakin <samhane.me@gmail.com>

> 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
*Ideas for smart shopping*

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