taverna-player 0.1.0

data/db/migrate/20130714140911_create_taverna_player_interactions.rb

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+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/db/migrate/20130717083653_add_proxy_to_taverna_player_runs.rb

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+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/db/migrate/20130717155415_add_stop_to_taverna_player_runs.rb

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+class AddStopToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :stop, :boolean, :default => false
+  end
+end

data/db/migrate/20130811152840_add_attachment_log_to_taverna_player_runs.rb

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+class AddAttachmentLogToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_attachment :taverna_player_runs, :log
+  end
+end

data/db/migrate/20130811211725_change_taverna_player_runs_state_column.rb

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+class ChangeTavernaPlayerRunsStateColumn < ActiveRecord::Migration
+  def change
+    rename_column :taverna_player_runs, :state, :saved_state
+  end
+end

data/db/migrate/20130812155839_add_name_to_taverna_player_runs.rb

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+class AddNameToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :name, :string, :default => "None"
+  end
+end

data/db/migrate/20130918135348_create_taverna_player_service_credentials.rb

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+class CreateTavernaPlayerServiceCredentials < ActiveRecord::Migration
+  def change
+    create_table :taverna_player_service_credentials do |t|
+      t.string :uri, :null => false
+      t.string :name
+      t.text :description
+      t.string :login
+      t.string :password
+
+      t.timestamps
+    end
+
+    add_index :taverna_player_service_credentials, :uri
+  end
+end

data/db/migrate/20130919154200_add_displayed_to_taverna_player_interactions.rb

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+class AddDisplayedToTavernaPlayerInteractions < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_interactions, :displayed, :boolean, :default => false
+  end
+end

data/db/migrate/20131007153209_add_job_ref_to_taverna_player_runs.rb

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+class AddJobRefToTavernaPlayerRuns < ActiveRecord::Migration
+  def up
+    change_table :taverna_player_runs do |t|
+      t.references :delayed_job
+    end
+  end
+
+  def down
+    change_table :taverna_player_runs do |t|
+      t.remove :delayed_job_id
+    end
+  end
+end

data/db/migrate/20131010094537_add_reply_caching_to_taverna_player_interactions.rb

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+class AddReplyCachingToTavernaPlayerInteractions < ActiveRecord::Migration
+  def up
+    remove_column :taverna_player_interactions, :uri
+    add_column :taverna_player_interactions, :unique_id, :string
+    add_column :taverna_player_interactions, :page, :text
+    add_column :taverna_player_interactions, :feed_reply, :string
+    add_column :taverna_player_interactions, :output_value, :text, :limit => 16777215
+    add_index :taverna_player_interactions, :unique_id
+  end
+
+  def down
+    remove_index :taverna_player_interactions, :unique_id
+    remove_column :taverna_player_interactions, :output_value
+    remove_column :taverna_player_interactions, :feed_reply
+    remove_column :taverna_player_interactions, :page
+    remove_column :taverna_player_interactions, :unique_id
+    add_column :taverna_player_interactions, :uri, :string
+  end
+end

data/db/migrate/20131017141514_add_failure_message_to_taverna_player_run.rb

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+class AddFailureMessageToTavernaPlayerRun < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :failure_message, :text
+  end
+end

data/db/migrate/20131018152940_add_serial_number_to_taverna_player_interactions.rb

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+class AddSerialNumberToTavernaPlayerInteractions < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_interactions, :serial, :string
+  end
+end

data/db/migrate/20131018160715_add_parent_run_id_to_taverna_player_runs.rb

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+class AddParentRunIdToTavernaPlayerRuns < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :parent_id, :integer
+  end
+end

data/db/migrate/20131102113933_add_page_uri_to_taverna_player_interaction.rb

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+class AddPageUriToTavernaPlayerInteraction < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_interactions, :page_uri, :string
+  end
+end

data/db/migrate/20131105115218_remove_proxy_from_taverna_player_runs.rb

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+class RemoveProxyFromTavernaPlayerRuns < ActiveRecord::Migration
+  def up
+    remove_column :taverna_player_runs, :proxy_notifications
+    remove_column :taverna_player_runs, :proxy_interactions
+  end
+
+  def down
+    add_column :taverna_player_runs, :proxy_interactions, :string
+    add_column :taverna_player_runs, :proxy_notifications, :string
+  end
+end

data/db/migrate/20131105141934_change_taverna_player_interactions_output_value_column_name.rb

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+class ChangeTavernaPlayerInteractionsOutputValueColumnName < ActiveRecord::Migration
+  def change
+    rename_column :taverna_player_interactions, :output_value, :data
+  end
+end

data/db/migrate/20131112165520_add_user_to_taverna_player_run.rb

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+class AddUserToTavernaPlayerRun < ActiveRecord::Migration
+  def change
+    add_column :taverna_player_runs, :user_id, :integer
+  end
+end

data/lib/generators/taverna_player/callbacks_generator.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
+  module Generators
+    class CallbacksGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../templates/callbacks", __FILE__)
+
+      desc "Create some basic callbacks in 'lib/taverna_player_callbacks.rb'"
+
+      def copy_callbacks
+        copy_file "worker_callbacks.rb", "lib/taverna_player_callbacks.rb"
+      end
+    end
+  end
+end

data/lib/generators/taverna_player/controllers_generator.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
+  module Generators
+    class ControllersGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../templates/controllers", __FILE__)
+
+      desc "Copy the Taverna Player controllers into the main app for "\
+        "customization."
+
+      def copy_controllers
+        copy_file "runs_controller.rb",
+          "app/controllers/taverna_player/runs_controller.rb"
+
+        copy_file "service_credentials_controller.rb",
+          "app/controllers/taverna_player/service_credentials_controller.rb"
+      end
+    end
+  end
+end

data/lib/generators/taverna_player/install_generator.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
+  module Generators
+    class InstallGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../templates", __FILE__)
+
+      desc "Creates a Taverna Player initializer"
+
+      def copy_initializer
+        copy_file "initializer.rb",
+          "config/initializers/taverna_player.rb.example"
+      end
+
+      def show_readme
+        readme "ReadMe.txt" if behavior == :invoke
+      end
+    end
+  end
+end

data/lib/generators/taverna_player/job_generator.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
+  module Generators
+    class JobGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../../../script", __FILE__)
+
+      desc "Installs the delayed_job script, if required"
+
+      def copy_job_script
+        copy_file "delayed_job",
+          "script/delayed_job"
+      end
+    end
+  end
+end

data/lib/generators/taverna_player/models_generator.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
+  module Generators
+    class ModelsGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../templates/models", __FILE__)
+
+      desc "Copy the Taverna Player models into the main app for "\
+        "customization."
+
+      def copy_models
+        copy_file "run.rb",
+          "app/models/taverna_player/run.rb"
+      end
+    end
+  end
+end

data/lib/generators/taverna_player/renderers_generator.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
+  module Generators
+    class RenderersGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../templates/callbacks", __FILE__)
+
+      desc "Create some basic renderer callbacks in "\
+        "'lib/taverna_player_renderers.rb'"
+
+      def copy_callbacks
+        copy_file "render_callbacks.rb", "lib/taverna_player_renderers.rb"
+      end
+    end
+  end
+end

data/lib/generators/taverna_player/views_generator.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
+  module Generators
+    class ViewsGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../../../app/views", __FILE__)
+
+      desc "Copy the Taverna Player views and layouts into the main app for "\
+        "user customization."
+
+      def copy_views_and_layouts
+        directory "taverna_player", "app/views/taverna_player"
+        directory "layouts", "app/views/layouts"
+      end
+    end
+  end
+end

data/lib/generators/templates/ReadMe.txt

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+
+==============================================================================
+
+An example initializer has been installed to:
+
+  config/initializers/taverna_player.rb.example
+
+Please look through this file and make any alterations as required. BEFORE you
+configure the Taverna Server URI and login information copy this file to:
+
+  config/initializers/taverna_player.rb
+
+Then check the example file into your repository, add the non-example file to
+your version control ignore file (e.g. .gitignore) and then configure the
+sensitive Taverna Server information. This allows you to check in most of the
+Taverna Player configuration, leaving the sensitive parts out.
+
+In your application's install instructions remember to tell your users to copy
+the example initializer and configure their Taverna Server information.
+
+There is also some manual setup to do, if you haven't already done it:
+
+  1. Mount the Taverna Player engine in your config/routes.rb. For example:
+
+       mount TavernaPlayer::Engine, :at => "/"
+
+     You can also nest the Taverna Player runs resources within your workflows
+     resources if you wish, like this:
+
+       resources :workflows do
+         resources :runs, :controller => "TavernaPlayer::Runs",
+           :except => :edit
+       end
+
+     The runs resources in Taverna Player do not provide an edit view by
+     default so, unless you add it yourself by overriding the controller you
+     should add the :except clause to the routes.
+
+  2. Perform Taverna Player's migrations:
+
+       rake taverna_player:install:migrations
+       rake db:migrate
+
+  3. Make sure you have defined root_url to something in your config/routes.rb.
+     For example:
+
+       root :to => "home#index"
+
+  4. Add Taverna Player's assets to your application's manifests.
+     In app/assets/javascripts/application.js:
+
+       //= require taverna_player/application
+
+     In app/assets/stylesheets/application.css
+
+       *= require taverna_player/application
+
+     And everything should be found by the asset pipeline automatically.
+
+  5. Make sure you have flash messages in your main layout
+     (usually app/views/layouts/application.html.erb). For example:
+
+       <p class="notice"><%= notice %></p>
+       <p class="alert"><%= alert %></p>
+
+  6. Taverna Player uses delayed_job to run workflows on a Taverna Server. If
+     your application is not already using delayed_job then you can install
+     the delayed_job script in your "script" directory with:
+
+       rails generate taverna_player:job
+
+  7. Taverna Player comes with some very simple, unstyled views and layouts.
+     If you wish to override these with your own customized views you can copy
+     them into your application with:
+
+       rails generate taverna_player:views
+
+     The views are copied to the app/views/taverna_player directory so that
+     they take precedence over the default ones. You can delete any that you
+     do not need to customize but there are no penalties for leaving them
+     there.
+
+  8. If you need to override the Taverna Player controllers, to implement user
+     authorization for example, you can copy some customizable stubs with:
+
+       rails generate taverna_player:controllers
+
+     The stubs are copied to the app/controllers/taverna_player directory so
+     that they take precedence over the default ones. You can delete any that
+     you do not need to customize but there are no penalties for leaving them
+     there.
+
+  9. If you need to override the Taverna Player Run model, to add columns to
+     the table for example, you can copy a customizable stub with:
+
+       rails generate taverna_player:models
+
+     The stub is copied to the app/models/taverna_player directory so that it
+     takes precedence over the default one.
+
+ 10. If you want to use pre- and post-run callbacks you can setup some basic
+     stubs with:
+
+       rails generate taverna_player:callbacks
+
+     They will be saved to "lib/taverna_player_callbacks.rb". Don't forget to
+     then require and register them in the Taverna Player initializer.
+
+ 11. You can add to, or change, the workflow run outputs render methods to
+     better suit your particular application. To copy the defaults that
+     Taverna Player ships with into your application for customization run:
+
+       rails generate taverna_player:renderers
+
+     They will be saved to "lib/taverna_player_renderers.rb". Don't forget to
+     then require and register them in the Taverna Player initializer.
+
+==============================================================================