taverna-player 0.1.0

data/test/dummy/config/environment.rb

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+# Load the rails application
+require File.expand_path('../application', __FILE__)
+
+# Initialize the rails application
+Dummy::Application.initialize!

data/test/dummy/config/environments/development.rb

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+Dummy::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # In the development environment your application's code is reloaded on
+  # every request. This slows down response time but is perfect for development
+  # since you don't have to restart the web server when you make code changes.
+  config.cache_classes = false
+
+  # Log error messages when you accidentally call methods on nil.
+  config.whiny_nils = true
+
+  # Show full error reports and disable caching
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Don't care if the mailer can't send
+  config.action_mailer.raise_delivery_errors = false
+
+  # Print deprecation notices to the Rails logger
+  config.active_support.deprecation = :log
+
+  # Only use best-standards-support built into browsers
+  config.action_dispatch.best_standards_support = :builtin
+
+  # Raise exception on mass assignment protection for Active Record models
+  config.active_record.mass_assignment_sanitizer = :strict
+
+  # Log the query plan for queries taking more than this (works
+  # with SQLite, MySQL, and PostgreSQL)
+  config.active_record.auto_explain_threshold_in_seconds = 0.5
+
+  # Do not compress assets
+  config.assets.compress = false
+
+  # Expands the lines which load the assets
+  config.assets.debug = true
+end

data/test/dummy/config/environments/production.rb

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+Dummy::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # Code is not reloaded between requests
+  config.cache_classes = true
+
+  # Full error reports are disabled and caching is turned on
+  config.consider_all_requests_local       = false
+  config.action_controller.perform_caching = true
+
+  # Disable Rails's static asset server (Apache or nginx will already do this)
+  config.serve_static_assets = false
+
+  # Compress JavaScripts and CSS
+  config.assets.compress = true
+
+  # Don't fallback to assets pipeline if a precompiled asset is missed
+  config.assets.compile = false
+
+  # Generate digests for assets URLs
+  config.assets.digest = true
+
+  # Defaults to nil and saved in location specified by config.assets.prefix
+  # config.assets.manifest = YOUR_PATH
+
+  # Specifies the header that your server uses for sending files
+  # config.action_dispatch.x_sendfile_header = "X-Sendfile" # for apache
+  # config.action_dispatch.x_sendfile_header = 'X-Accel-Redirect' # for nginx
+
+  # Force all access to the app over SSL, use Strict-Transport-Security, and use secure cookies.
+  # config.force_ssl = true
+
+  # See everything in the log (default is :info)
+  # config.log_level = :debug
+
+  # Prepend all log lines with the following tags
+  # config.log_tags = [ :subdomain, :uuid ]
+
+  # Use a different logger for distributed setups
+  # config.logger = ActiveSupport::TaggedLogging.new(SyslogLogger.new)
+
+  # Use a different cache store in production
+  # config.cache_store = :mem_cache_store
+
+  # Enable serving of images, stylesheets, and JavaScripts from an asset server
+  # config.action_controller.asset_host = "http://assets.example.com"
+
+  # Precompile additional assets (application.js, application.css, and all non-JS/CSS are already added)
+  # config.assets.precompile += %w( search.js )
+
+  # Disable delivery errors, bad email addresses will be ignored
+  # config.action_mailer.raise_delivery_errors = false
+
+  # Enable threaded mode
+  # config.threadsafe!
+
+  # Enable locale fallbacks for I18n (makes lookups for any locale fall back to
+  # the I18n.default_locale when a translation can not be found)
+  config.i18n.fallbacks = true
+
+  # Send deprecation notices to registered listeners
+  config.active_support.deprecation = :notify
+
+  # Log the query plan for queries taking more than this (works
+  # with SQLite, MySQL, and PostgreSQL)
+  # config.active_record.auto_explain_threshold_in_seconds = 0.5
+end

data/test/dummy/config/environments/test.rb

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+Dummy::Application.configure do
+  # Settings specified here will take precedence over those in config/application.rb
+
+  # The test environment is used exclusively to run your application's
+  # test suite. You never need to work with it otherwise. Remember that
+  # your test database is "scratch space" for the test suite and is wiped
+  # and recreated between test runs. Don't rely on the data there!
+  config.cache_classes = true
+
+  # Configure static asset server for tests with Cache-Control for performance
+  config.serve_static_assets = true
+  config.static_cache_control = "public, max-age=3600"
+
+  # Log error messages when you accidentally call methods on nil
+  config.whiny_nils = true
+
+  # Show full error reports and disable caching
+  config.consider_all_requests_local       = true
+  config.action_controller.perform_caching = false
+
+  # Raise exceptions instead of rendering exception templates
+  config.action_dispatch.show_exceptions = false
+
+  # Disable request forgery protection in test environment
+  config.action_controller.allow_forgery_protection    = false
+
+  # Tell Action Mailer not to deliver emails to the real world.
+  # The :test delivery method accumulates sent emails in the
+  # ActionMailer::Base.deliveries array.
+  config.action_mailer.delivery_method = :test
+
+  # Raise exception on mass assignment protection for Active Record models
+  config.active_record.mass_assignment_sanitizer = :strict
+
+  # Print deprecation notices to the stderr
+  config.active_support.deprecation = :stderr
+end

data/test/dummy/config/initializers/backtrace_silencers.rb

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+# Be sure to restart your server when you modify this file.
+
+# You can add backtrace silencers for libraries that you're using but don't wish to see in your backtraces.
+# Rails.backtrace_cleaner.add_silencer { |line| line =~ /my_noisy_library/ }
+
+# You can also remove all the silencers if you're trying to debug a problem that might stem from framework code.
+# Rails.backtrace_cleaner.remove_silencers!

data/test/dummy/config/initializers/inflections.rb

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+# Be sure to restart your server when you modify this file.
+
+# Add new inflection rules using the following format
+# (all these examples are active by default):
+# ActiveSupport::Inflector.inflections do |inflect|
+#   inflect.plural /^(ox)$/i, '\1en'
+#   inflect.singular /^(ox)en/i, '\1'
+#   inflect.irregular 'person', 'people'
+#   inflect.uncountable %w( fish sheep )
+# end
+#
+# These inflection rules are supported but not enabled by default:
+# ActiveSupport::Inflector.inflections do |inflect|
+#   inflect.acronym 'RESTful'
+# end

data/test/dummy/config/initializers/mime_types.rb

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+# Be sure to restart your server when you modify this file.
+
+# Add new mime types for use in respond_to blocks:
+# Mime::Type.register "text/richtext", :rtf
+# Mime::Type.register_alias "text/html", :iphone

data/test/dummy/config/initializers/secret_token.rb

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+# Be sure to restart your server when you modify this file.
+
+# Your secret key for verifying the integrity of signed cookies.
+# If you change this key, all old signed cookies will become invalid!
+# Make sure the secret is at least 30 characters and all random,
+# no regular words or you'll be exposed to dictionary attacks.
+Dummy::Application.config.secret_token = '72d3482fd1fd11dea077d471511ffc0e69c9305e4d981d91cb9688d6eb25b05263d1c46b80b14b4fbf7c7ecf2e6ea20374ef4833e8518554007a259f588e9042'

data/test/dummy/config/initializers/session_store.rb

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+# Be sure to restart your server when you modify this file.
+
+Dummy::Application.config.session_store :cookie_store, :key => '_dummy_session'
+
+# Use the database for sessions instead of the cookie-based default,
+# which shouldn't be used to store highly confidential information
+# (create the session table with "rails generate session_migration")
+# Dummy::Application.config.session_store :active_record_store

data/test/dummy/config/initializers/taverna_player.example.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
+#------------------------------------------------------------------------------
+
+# Taverna Player configuration
+
+TavernaPlayer.setup do |config|
+  # This should be set to the name of the workflow model class in the main
+  # application and the listed methods should also be mapped if necessary.
+  config.workflow_model_proxy("Workflow")
+
+  config.user_model_proxy = "User"
+  config.current_user_callback = :user_one
+
+  # Taverna Server configuration information. The poll interval is in seconds.
+  config.server_address = "https://example.com:8443/tavserv"
+  config.server_username = "taverna"
+  config.server_password = "taverna"
+  config.server_poll_interval = 1
+  config.server_retry_interval = 10
+
+  # Taverna Server connection configuration.
+  config.server_connection[:open_timeout] = 10
+
+  # Callbacks to be run at various points during a workflow run.
+  require "callbacks"
+
+  config.pre_run_callback = :player_pre_run_callback
+  config.post_run_callback = :player_post_run_callback
+  config.run_cancelled_callback = :player_run_cancelled_callback
+  config.run_failed_callback = :player_run_failed_callback
+end

data/test/dummy/config/initializers/wrap_parameters.rb

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+# Be sure to restart your server when you modify this file.
+#
+# This file contains settings for ActionController::ParamsWrapper which
+# is enabled by default.
+
+# Enable parameter wrapping for JSON. You can disable this by setting :format to an empty array.
+ActiveSupport.on_load(:action_controller) do
+  wrap_parameters :format => [:json]
+end
+
+# Disable root element in JSON by default.
+ActiveSupport.on_load(:active_record) do
+  self.include_root_in_json = false
+end

data/test/dummy/config/locales/en.yml

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+# Sample localization file for English. Add more files in this directory for other locales.
+# See https://github.com/svenfuchs/rails-i18n/tree/master/rails%2Flocale for starting points.
+
+en:
+  hello: "Hello world"

data/test/dummy/config/routes.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
+#------------------------------------------------------------------------------
+
+Rails.application.routes.draw do
+
+  root :to => "home#index"
+
+  resources :workflows, :only => :index do
+    resources :runs, :controller => "TavernaPlayer::Runs", :except => :edit
+  end
+
+  mount TavernaPlayer::Engine, :at => "/"
+end

data/test/dummy/db/migrate/20130314103555_create_workflows.rb

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+class CreateWorkflows < ActiveRecord::Migration
+  def change
+    create_table :workflows do |t|
+      t.string :title
+      t.string :author
+      t.text :description
+      t.string :file
+
+      t.timestamps
+    end
+  end
+end

data/test/dummy/db/migrate/20130318141557_create_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130313105546)
+class CreateTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    create_table :taverna_player_runs do |t|
+      t.string :run_id
+      t.string :state, :default => "pending", :null => false
+      t.datetime :create_time
+      t.datetime :start_time
+      t.datetime :finish_time
+      t.integer :workflow_id, :null => false
+
+      t.timestamps
+    end
+
+    add_index :taverna_player_runs, :run_id
+  end
+end

data/test/dummy/db/migrate/20130318141558_create_taverna_player_run_ports.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130315163019)
+class CreateTavernaPlayerRunPorts < ActiveRecord::Migration
+  def change
+    create_table :taverna_player_run_ports do |t|
+      t.string :name
+      t.string :value
+      t.string :file
+      t.string :port_type
+      t.references :run
+
+      t.timestamps
+    end
+
+    add_index :taverna_player_run_ports, :run_id
+  end
+end

data/test/dummy/db/migrate/20130318173013_add_attachment_file_to_taverna_player_run_ports.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130318170744)
+class AddAttachmentFileToTavernaPlayerRunPorts < ActiveRecord::Migration
+  def change
+    remove_column :taverna_player_run_ports, :file
+    add_attachment :taverna_player_run_ports, :file
+  end
+end

data/test/dummy/db/migrate/20130319183816_create_delayed_jobs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130319183634)
+class CreateDelayedJobs < ActiveRecord::Migration
+  def self.up
+    create_table :delayed_jobs, :force => true do |table|
+      table.integer  :priority, :default => 0      # Allows some jobs to jump to the front of the queue
+      table.integer  :attempts, :default => 0      # Provides for retries, but still fail eventually.
+      table.text     :handler                      # YAML-encoded string of the object that will do work
+      table.text     :last_error                   # reason for last failure (See Note below)
+      table.datetime :run_at                       # When to run. Could be Time.zone.now for immediately, or sometime in the future.
+      table.datetime :locked_at                    # Set when a client is working on this object
+      table.datetime :failed_at                    # Set when all retries have failed (actually, by default, the record is deleted instead)
+      table.string   :locked_by                    # Who is working on this object (if locked)
+      table.string   :queue                        # The name of the queue this job is in
+      table.timestamps
+    end
+
+    add_index :delayed_jobs, [:priority, :run_at], :name => 'delayed_jobs_priority'
+  end
+
+  def self.down
+    drop_table :delayed_jobs
+  end
+end

data/test/dummy/db/migrate/20130320102635_add_status_message_to_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130320102600)
+class AddStatusMessageToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :status_message, :string
+  end
+end

data/test/dummy/db/migrate/20130321161859_add_depth_and_metadata_to_taverna_player_run_ports.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130321100110)
+class AddDepthAndMetadataToTavernaPlayerRunPorts < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_run_ports, :depth, :integer, :default => 0
+    add_column :taverna_player_run_ports, :metadata, :text
+  end
+end

data/test/dummy/db/migrate/20130704100146_add_attachment_results_to_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130704095504)
+class AddAttachmentResultsToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_attachment :taverna_player_runs, :results
+  end
+end

data/test/dummy/db/migrate/20130705142816_add_embedded_to_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130705142704)
+class AddEmbeddedToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :embedded, :boolean, :default => false
+  end
+end

data/test/dummy/db/migrate/20130714142144_create_taverna_player_interactions.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130714140911)
+class CreateTavernaPlayerInteractions < ActiveRecord::Migration
+  def change
+    create_table :taverna_player_interactions do |t|
+      t.string :uri
+      t.boolean :replied, :default => false
+      t.references :run
+
+      t.timestamps
+    end
+
+    add_index :taverna_player_interactions, :run_id
+  end
+end

data/test/dummy/db/migrate/20130717084809_add_proxy_to_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130717083653)
+class AddProxyToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :proxy_notifications, :string
+    add_column :taverna_player_runs, :proxy_interactions, :string
+  end
+end

data/test/dummy/db/migrate/20130718102707_add_stop_to_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130717155415)
+class AddStopToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :stop, :boolean, :default => false
+  end
+end

data/test/dummy/db/migrate/20130811204449_add_attachment_log_to_taverna_player_runs.taverna_player.rb

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+# This migration comes from taverna_player (originally 20130811152840)
+class AddAttachmentLogToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_attachment :taverna_player_runs, :log
+  end
+end