taverna-player 0.1.0

data/script/delayed_job

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+#!/usr/bin/env ruby
+
+require File.expand_path(File.join(File.dirname(__FILE__), '..', 'config', 'environment'))
+require 'delayed/command'
+Delayed::Command.new(ARGV).daemonize

data/script/rails

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+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+ENGINE_ROOT = File.expand_path('../..', __FILE__)
+ENGINE_PATH = File.expand_path('../../lib/taverna_player/engine', __FILE__)
+
+require 'rails/all'
+require 'rails/engine/commands'

data/taverna_player.gemspec

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+$:.push File.expand_path("../lib", __FILE__)
+
+require "taverna_player/version"
+
+Gem::Specification.new do |s|
+  s.name        = "taverna-player"
+  s.version     = TavernaPlayer::VERSION
+  s.authors     = ["Robert Haines"]
+  s.email       = ["support@mygrid.org.uk"]
+  s.homepage    = "http://www.taverna.org.uk"
+  s.summary     = "Taverna Player is a rails plugin to run Taverna Workflows."
+  s.description = "Taverna Player runs Taverna Workflows using Taverna Server."
+  s.license     = "BSD"
+
+  s.files       = `git ls-files`.split("\n")
+  s.test_files  = `git ls-files -- test/*`.split("\n")
+
+  s.add_dependency "rails", "~> 3.2.12"
+  s.add_dependency "jquery-rails", "~> 3.0.4"
+  s.add_dependency "paperclip", "~> 3.4.1"
+  s.add_dependency "t2-server", "~> 1.0.0"
+  s.add_dependency "delayed_job_active_record", "~> 0.4.3"
+  s.add_dependency "daemons", "~> 1.1.9"
+  s.add_dependency "rubyzip", "~> 0.9.9"
+  s.add_dependency "coderay", "~> 1.0.9"
+  s.add_dependency "rails_autolink", "~> 1.1.0"
+  s.add_dependency "require_all", "~> 1.3.1"
+  s.add_dependency "jbuilder", "~> 1.5.2"
+  s.add_dependency "pmrpc-rails", "~> 1.0.0"
+
+  s.add_development_dependency "sqlite3"
+
+  s.require_path = "lib"
+end

data/test/dummy/Rakefile

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+#!/usr/bin/env rake
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+require File.expand_path('../config/application', __FILE__)
+
+Dummy::Application.load_tasks

data/test/dummy/app/assets/javascripts/application.js

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+// This is a manifest file that'll be compiled into application.js, which will include all the files
+// listed below.
+//
+// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
+// or vendor/assets/javascripts of plugins, if any, can be referenced here using a relative path.
+//
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// the compiled file.
+//
+// WARNING: THE FIRST BLANK LINE MARKS THE END OF WHAT'S TO BE PROCESSED, ANY BLANK LINE SHOULD
+// GO AFTER THE REQUIRES BELOW.
+//
+//= require jquery
+//= require jquery_ujs
+//= require taverna_player/application
+//= require_tree .

data/test/dummy/app/assets/stylesheets/application.css

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+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, vendor/assets/stylesheets,
+ * or vendor/assets/stylesheets of plugins, if any, can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the top of the
+ * compiled file, but it's generally better to create a new file per style scope.
+ *
+ *= require_self
+ *= require_tree .
+ *= require taverna_player/application
+ */

data/test/dummy/app/controllers/application_controller.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+class ApplicationController < ActionController::Base
+  protect_from_forgery
+end

data/test/dummy/app/controllers/home_controller.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+class HomeController < ApplicationController
+  def index
+  end
+end

data/test/dummy/app/controllers/taverna_player/runs_controller.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class RunsController < TavernaPlayer::ApplicationController
+    include TavernaPlayer::Concerns::Controllers::RunsController
+
+    before_filter :override, :only => :index
+
+    private
+
+    def override
+      @override = true
+    end
+  end
+end

data/test/dummy/app/controllers/taverna_player/service_credentials_controller.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  class ServiceCredentialsController < TavernaPlayer::ApplicationController
+    include TavernaPlayer::Concerns::Controllers::ServiceCredentialsController
+
+    before_filter :override, :only => :index
+
+    private
+
+    def override
+      @override = true
+    end
+  end
+end

data/test/dummy/app/controllers/workflows_controller.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+class WorkflowsController < ApplicationController
+  def index
+    @workflows = Workflow.all
+  end
+end

data/test/dummy/app/models/user.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+class User < ActiveRecord::Base
+  attr_accessible :email, :name
+end

data/test/dummy/app/models/workflow.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+class Workflow < ActiveRecord::Base
+  attr_accessible :author, :description, :file, :title
+
+  has_many :runs, :class_name => "TavernaPlayer::Run"
+
+  def inputs
+    workflow = File.open(file)
+    model = T2Flow::Parser.new.parse(workflow)
+
+    result = []
+    model.sources.each do |i|
+      description = i.descriptions.nil? ? "" : i.descriptions.join
+      example = i.example_values.nil? ? "" : i.example_values.join
+      result << { :name => i.name, :description => description,
+        :example => example }
+    end
+
+    result
+  end
+end

data/test/dummy/app/views/home/index.html.erb

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+<%
+  # Copyright (c) 2013 The University of Manchester, UK.
+  #
+  # BSD Licenced. See LICENCE.rdoc for details.
+  #
+  # Taverna Player was developed in the BioVeL project, funded by the European
+  # Commission 7th Framework Programme (FP7), through grant agreement
+  # number 283359.
+  #
+  # Author: Robert Haines
+%>
+
+<h1>Home#index</h1>
+
+<h2>An embedded workflow</h2>
+<div>
+  <iframe src="<%= new_embedded_run_url(3) %>&input=10" width="100%" height="500px"></iframe>
+</div>

data/test/dummy/app/views/layouts/application.html.erb

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+<%
+  # Copyright (c) 2013 The University of Manchester, UK.
+  #
+  # BSD Licenced. See LICENCE.rdoc for details.
+  #
+  # Taverna Player was developed in the BioVeL project, funded by the European
+  # Commission 7th Framework Programme (FP7), through grant agreement
+  # number 283359.
+  #
+  # Author: Robert Haines
+%>
+
+<!DOCTYPE html>
+<html>
+<head>
+  <title>Dummy</title>
+  <%= stylesheet_link_tag    "application", :media => "all" %>
+  <%= javascript_include_tag "application" %>
+  <%= csrf_meta_tags %>
+</head>
+<body>
+
+	<p>
+		DUMMY PORTAL HEADER
+
+		<br />
+
+		<%= link_to "Home", main_app.root_path %> |
+		<%= link_to "Workflows", main_app.workflows_path %> |
+		<%= link_to "Runs", taverna_player.runs_path %> |
+		<%= link_to "Service Credentials", taverna_player.service_credentials_path %>
+	</p>
+
+	<p id="notice"><%= notice %></p>
+
+	<%= yield %>
+
+	<p>
+		DUMMY PORTAL FOOTER
+	</p>
+
+</body>
+</html>

data/test/dummy/app/views/workflows/index.html.erb

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+<%
+  # Copyright (c) 2013 The University of Manchester, UK.
+  #
+  # BSD Licenced. See LICENCE.rdoc for details.
+  #
+  # Taverna Player was developed in the BioVeL project, funded by the European
+  # Commission 7th Framework Programme (FP7), through grant agreement
+  # number 283359.
+  #
+  # Author: Robert Haines
+%>
+
+<h1>Workflows</h1>
+
+<table>
+  <tr>
+    <th>Workflow</th>
+    <th>Title</th>
+    <th>Author</th>
+    <th>Description</th>
+    <th colspan="2">Action</th>
+  </tr>
+
+<% @workflows.each do |w| %>
+  <tr>
+    <td><%= w.id %></td>
+    <td><%= w.title%></td>
+    <td><%= w.author %></td>
+    <td><%= w.description %></td>
+    <td><%= link_to "List runs of this workflow", workflow_runs_path(w)%></td>
+    <td><%= link_to "Run this workflow", new_workflow_run_path(w) %></td>
+  </tr>
+<% end %>
+
+</table>

data/test/dummy/config.ru

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+# This file is used by Rack-based servers to start the application.
+
+require ::File.expand_path('../config/environment',  __FILE__)
+run Dummy::Application

data/test/dummy/config/application.rb

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+require File.expand_path('../boot', __FILE__)
+
+require 'rails/all'
+
+Bundler.require
+
+module Dummy
+  class Application < Rails::Application
+    # Settings in config/environments/* take precedence over those specified here.
+    # Application configuration should go into files in config/initializers
+    # -- all .rb files in that directory are automatically loaded.
+
+    # Custom directories with classes and modules you want to be autoloadable.
+    # config.autoload_paths += %W(#{config.root}/extras)
+
+    # Only load the plugins named here, in the order given (default is alphabetical).
+    # :all can be used as a placeholder for all plugins not explicitly named.
+    # config.plugins = [ :exception_notification, :ssl_requirement, :all ]
+
+    # Activate observers that should always be running.
+    # config.active_record.observers = :cacher, :garbage_collector, :forum_observer
+
+    # Set Time.zone default to the specified zone and make Active Record auto-convert to this zone.
+    # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
+    # config.time_zone = 'Central Time (US & Canada)'
+
+    # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+    # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
+    # config.i18n.default_locale = :de
+
+    # Configure the default encoding used in templates for Ruby 1.9.
+    config.encoding = "utf-8"
+
+    # Configure sensitive parameters which will be filtered from the log file.
+    config.filter_parameters += [:password]
+
+    # Enable escaping HTML in JSON.
+    config.active_support.escape_html_entities_in_json = true
+
+    # Use SQL instead of Active Record's schema dumper when creating the database.
+    # This is necessary if your schema can't be completely dumped by the schema dumper,
+    # like if you have constraints or database-specific column types
+    # config.active_record.schema_format = :sql
+
+    # Enforce whitelist mode for mass assignment.
+    # This will create an empty whitelist of attributes available for mass-assignment for all models
+    # in your app. As such, your models will need to explicitly whitelist or blacklist accessible
+    # parameters by using an attr_accessible or attr_protected declaration.
+    config.active_record.whitelist_attributes = true
+
+    # Enable the asset pipeline
+    config.assets.enabled = true
+
+    # Version of your assets, change this if you want to expire all your assets
+    config.assets.version = '1.0'
+  end
+end
+

data/test/dummy/config/boot.rb

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+require 'rubygems'
+gemfile = File.expand_path('../../../../Gemfile', __FILE__)
+
+if File.exist?(gemfile)
+  ENV['BUNDLE_GEMFILE'] = gemfile
+  require 'bundler'
+  Bundler.setup
+end
+
+$:.unshift File.expand_path('../../../../lib', __FILE__)

data/test/dummy/config/database.yml

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+# SQLite version 3.x
+#   gem install sqlite3
+#
+#   Ensure the SQLite 3 gem is defined in your Gemfile
+#   gem 'sqlite3'
+development:
+  adapter: sqlite3
+  database: db/development.sqlite3
+  pool: 5
+  timeout: 5000
+
+# Warning: The database defined as "test" will be erased and
+# re-generated from your development database when you run "rake".
+# Do not set this db to the same as development or production.
+test:
+  adapter: sqlite3
+  database: db/test.sqlite3
+  pool: 5
+  timeout: 5000
+
+production:
+  adapter: sqlite3
+  database: db/production.sqlite3
+  pool: 5
+  timeout: 5000