taverna-player 0.1.0 → 0.2.0

data/.gitignore

@@ -7,7 +7,7 @@ test/dummy/log/*.log
 test/dummy/tmp/
 test/dummy/.sass-cache
 test/dummy/public/system/
-test/dummy/config/initializers/taverna_player.rb
+test/dummy/config/initializers/taverna_server.rb
 
 *~
 rdoc/

data/CHANGES.rdoc

@@ -0,0 +1,18 @@
+= Changes log for Taverna Player
+
+== Version 0.2.0
+
+* [TAV-461] Remove unique_id from the interaction table.
+* [TAV-353] Optimize table indexing.
+* [TAV-353] Set inverse relationships in the models.
+* [TAV-353] Remove unused Paperclip columns.
+* [TAV-462] Separate out the config for Taverna Server.
+* [TAV-463] Serialize metadata field on input port.
+* [TAV-464] Allow RunPort model to be overridden.
+* [TAV-464] Allow overriding of Input and Output models.
+
+== About this CHANGES file
+
+This file is, at least in part, generated by the following command:
+
+ $ git log --pretty=format:"* %s" --reverse --no-merges <commit-hash>..

data/README.rdoc

@@ -6,6 +6,7 @@ URL::         http://www.taverna.org.uk
 Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
 Copyright::   (c) 2013 The University of Manchester, UK
 
+{<img src="https://badge.fury.io/rb/taverna-player.png" alt="Gem Version" />}[http://badge.fury.io/rb/taverna-player]
 {<img src="https://codeclimate.com/github/myGrid/taverna-player.png" />}[https://codeclimate.com/github/myGrid/taverna-player]
 
 == Synopsis
@@ -37,12 +38,12 @@ And run the <tt>bundle install</tt> command to install it.
 Next you need to run the install generator:
  rails generate taverna_player:install
 
-This installs an initializer (into your application's
-<tt>config/initializers</tt> directory) which describes all of Taverna Player's
-configuration options and there are some things that MUST be configured before
-it will work - see below for more information. The install generator also
-prints out a list of other steps for setting up Taverna Player; these are
-repeated and detailed below.
+This installs two initializer files (into your application's
+<tt>config/initializers</tt> directory) which describe all of Taverna Player's
+configuration options; there are some things that MUST be configured before it
+will work - see below for more information. The install generator also prints
+out a list of other steps for setting up Taverna Player; these are repeated
+and detailed below.
 
 == Running Taverna Player
 
@@ -652,6 +653,8 @@ In no particular order:
 * Comprehensive Taverna Server administration panel. This would allow admin
   users to view and manage runs directly on the Taverna Server along with
   other such admin tasks.
+* I18n support.
+* oEmbed support (see http://oembed.com/ for more details).
 
 == Support
 

data/Rakefile

@@ -32,6 +32,7 @@ RDoc::Task.new(:rdoc) do |rdoc|
   rdoc.options << "--tab-width=2"
 
   files = [
+    "CHANGES.rdoc",
     "README.rdoc",
     "LICENCE.rdoc",
     "app/helpers/taverna_player/application_helper.rb",

data/app/helpers/taverna_player/runs_helper.rb

@@ -15,7 +15,7 @@ module TavernaPlayer
 
     def interaction_redirect(interaction)
       if interaction.page_uri.blank?
-        run_url(interaction.run) + "/interaction/#{interaction.unique_id}"
+        run_url(interaction.run) + "/interaction/#{interaction.serial}"
       else
         interaction.page_uri
       end

data/app/models/taverna_player/interaction.rb

@@ -12,12 +12,11 @@
 
 module TavernaPlayer
   class Interaction < ActiveRecord::Base
-    attr_accessible :displayed, :feed_reply, :page, :replied, :unique_id
+    attr_accessible :displayed, :feed_reply, :page, :replied
 
-    belongs_to :run, :class_name => "TavernaPlayer::Run"
+    belongs_to :run, :class_name => "TavernaPlayer::Run",
+      :inverse_of => :interactions
 
-    validates_presence_of :unique_id
-    validates_uniqueness_of :unique_id
     validates_presence_of :serial
     validates_uniqueness_of :serial, :scope => :run_id,
       :message => "Interaction serial number should be unique for a run"

data/app/models/taverna_player/run_port.rb

@@ -18,131 +18,59 @@ module TavernaPlayer
   #
   # A port can hold either a text value or a file.
   class RunPort < ActiveRecord::Base
+    include TavernaPlayer::Concerns::Models::RunPort
 
-    MAXIMUM_DATABASE_VALUE_SIZE = 255  # :nodoc:
-
-    self.inheritance_column = "port_type"
-
-    belongs_to :run, :class_name => "TavernaPlayer::Run"
-
-    validates_presence_of :name
-    validates_uniqueness_of :name, :scope => [:run_id, :port_type]
-
-    attr_accessible :depth, :file, :name, :value
-
-    has_attached_file :file,
-      :path => File.join(TavernaPlayer.file_store, ":class/:attachment/:id/:filename"),
-      :url => :file_url_via_run,
-      :default_url => ""
-
-    default_scope order("lower(name) ASC")
-
-    # If there is both a value and a file, then prefer the file. If the file
-    # is changed, delete the value. This must be run before "process_value"!
-    before_save :delete_value, :if => :file_file_name_changed?
-
-    # Overflow the value into a file if it is too big. Don't try to process
-    # the value if the file has changed. This must run after "delete_value"!
-    before_save :process_value, :if => :value_changed?, :unless => :file_file_name_changed?
-
+    ##
+    # :method: display_name
     # :call-seq:
     #   display_name -> string
     #
     # Convert this port's name to a more presentable form. In practice this
     # means converting underscores (_) to spaces, while preserving case.
-    def display_name
-      name.gsub('_', ' ')
-    end
 
+    ##
+    # :method: value_preview
     # :call-seq:
     #   value_preview -> string
     #
     # Show up to the first 256 characters of the port's value. This returns
     # nil if the port has a file instead of a value.
-    def value_preview
-      self[:value]
-    end
 
+    ##
+    # :method: value
     # :call-seq:
     #   value -> string
     #
     # Return the value held in this port if there is one.
-    def value
-      v = self[:value]
-      if !v.blank? && !file.path.blank?
-        File.read(file.path)
-      else
-        v
-      end
-    end
-
-    private
-
-    def delete_value
-      self[:value] = nil
-    end
-
-    # If the value is too big to fit in the database then overflow it into a
-    # file.
-    def process_value
-      v = self[:value]
-
-      if !v.blank? && v.size > MAXIMUM_DATABASE_VALUE_SIZE
-        self[:value] = v[0...MAXIMUM_DATABASE_VALUE_SIZE]
-        save_value_to_file(v)
-      else
-        self.file = nil unless file.path.blank?
-      end
-    end
-
-    def save_value_to_file(v)
-      Dir.mktmpdir("#{id}", Rails.root.join("tmp")) do |tmp_dir|
-        tmp_file_name = File.join(tmp_dir, "#{name}.txt")
-
-        File.write(tmp_file_name, v.force_encoding("UTF-8"))
-
-        self.file = File.new(tmp_file_name)
-      end
-    end
-  end
-
-  # This class represents a workflow input port.
-  class RunPort::Input < RunPort
-
-    private
-
-    def file_url_via_run
-      "/runs/#{run_id}/input/#{name}"
-    end
-  end
-
-  # This class represents a workflow output port.
-  class RunPort::Output < RunPort
-
-    attr_accessible :metadata
-
-    serialize :metadata
-
-    private
-
-    def file_url_via_run
-      "/runs/#{run_id}/output/#{name}"
-    end
-
-    public
 
     ##
     # :method: metadata
     # :call-seq:
     #   metadata -> hash
     #
-    # Get the size and type metadata for this output port in a Hash. For a
-    # list output it might look like this:
+    # Get the size and type metadata for this port in a Hash. For a list it
+    # might look like this:
     #
     #  {
     #    :size => [12, 36509],
     #    :type => ["text/plain", "image/png"]
     #  }
+    #
+    # <b>Note:</b> By default Taverna Player only uses this field on outputs.
+    # It is provided as a field for inputs too as a convenience for
+    # implementors and for possible future use.
+
+  end
 
+  # This class represents a workflow input port. All functionality is provided
+  # by the RunPort superclass.
+  class RunPort::Input < RunPort
+    include TavernaPlayer::Concerns::Models::Input
+  end
+
+  # This class represents a workflow output port. All functionality is
+  # provided by the RunPort superclass.
+  class RunPort::Output < RunPort
+    include TavernaPlayer::Concerns::Models::Output
   end
 end

data/app/views/taverna_player/runs/_interaction.html.erb

@@ -20,7 +20,7 @@
       pmrpc.register({
         publicProcedureName : "reply",
         procedure : function(status, results) {
-          interaction_reply('<%= "#{run_url(run)}/interaction/#{interaction.unique_id}" %>', status, results);
+          interaction_reply('<%= "#{run_url(run)}/interaction/#{interaction.serial}" %>', status, results);
           return "OK";
         }
       });

data/app/views/taverna_player/runs/show.json.jbuilder

@@ -18,7 +18,6 @@ end
 
 unless @interaction.nil?
   json.interaction do
-    json.id @interaction.unique_id
     json.serial @interaction.serial
     json.uri interaction_redirect(@interaction)
   end

data/config/routes.rb

@@ -24,8 +24,8 @@ TavernaPlayer::Engine.routes.draw do
       end
 
       scope "interaction" do
-        get ":int_id", :action => "read_interaction"
-        post ":int_id", :action => "write_interaction"
+        get ":serial", :action => "read_interaction"
+        post ":serial", :action => "write_interaction"
       end
     end
   end

data/db/migrate/20131126175424_remove_unique_id_from_taverna_player_interactions.rb

@@ -0,0 +1,11 @@
+class RemoveUniqueIdFromTavernaPlayerInteractions < ActiveRecord::Migration
+  def up
+    remove_index :taverna_player_interactions, :unique_id
+    remove_column :taverna_player_interactions, :unique_id
+  end
+
+  def down
+    add_column :taverna_player_interactions, :unique_id, :string
+    add_index :taverna_player_interactions, :unique_id
+  end
+end

data/db/migrate/20131127162157_add_indexes_where_missing.rb

@@ -0,0 +1,12 @@
+class AddIndexesWhereMissing < ActiveRecord::Migration
+  def change
+    add_index :taverna_player_interactions, [:run_id, :serial]
+    add_index :taverna_player_interactions, [:run_id, :replied]
+
+    add_index :taverna_player_run_ports, [:run_id, :name]
+
+    add_index :taverna_player_runs, :user_id
+    add_index :taverna_player_runs, :workflow_id
+    add_index :taverna_player_runs, :parent_id
+  end
+end

data/db/migrate/20131127163438_remove_run_id_index_from_taverna_player_runs.rb

@@ -0,0 +1,9 @@
+class RemoveRunIdIndexFromTavernaPlayerRuns < ActiveRecord::Migration
+  def up
+    remove_index :taverna_player_runs, :run_id
+  end
+
+  def down
+    add_index :taverna_player_runs, :run_id
+  end
+end

data/db/migrate/20131127171823_remove_unused_paperclip_columns.rb

@@ -0,0 +1,17 @@
+class RemoveUnusedPaperclipColumns < ActiveRecord::Migration
+  def up
+    remove_column :taverna_player_runs, :results_content_type
+    remove_column :taverna_player_runs, :results_updated_at
+
+    remove_column :taverna_player_runs, :log_content_type
+    remove_column :taverna_player_runs, :log_updated_at
+  end
+
+  def down
+    add_column :taverna_player_runs, :log_updated_at, :datetime
+    add_column :taverna_player_runs, :log_content_type, :string
+
+    add_column :taverna_player_runs, :results_updated_at, :datetime
+    add_column :taverna_player_runs, :results_content_type, :string
+  end
+end

data/lib/generators/taverna_player/install_generator.rb

@@ -15,11 +15,14 @@ module TavernaPlayer
     class InstallGenerator < Rails::Generators::Base
       source_root File.expand_path("../../templates", __FILE__)
 
-      desc "Creates a Taverna Player initializer"
+      desc "Creates Taverna Player initializers"
 
-      def copy_initializer
-        copy_file "initializer.rb",
-          "config/initializers/taverna_player.rb.example"
+      def copy_initializers
+        copy_file "player_initializer.rb",
+          "config/initializers/taverna_player.rb"
+
+        copy_file "server_initializer.rb",
+          "config/initializers/taverna_server.example.rb"
       end
 
       def show_readme

data/lib/generators/taverna_player/models_generator.rb

@@ -19,8 +19,9 @@ module TavernaPlayer
         "customization."
 
       def copy_models
-        copy_file "run.rb",
-          "app/models/taverna_player/run.rb"
+        ["run.rb", "run_port.rb", "input.rb", "output.rb"].each do |file|
+          copy_file file, "app/models/taverna_player/#{file}"
+        end
       end
     end
   end

data/lib/generators/templates/ReadMe.txt

@@ -1,14 +1,19 @@
 
 ==============================================================================
 
-An example initializer has been installed to:
+Two initializers have been installed to:
 
-  config/initializers/taverna_player.rb.example
+  config/initializers/taverna_player.rb
+  config/initializers/taverna_server.example.rb
 
-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:
+The first is general configuration for Taverna Player and it is safe to commit
+this to your repository. The second is configuration specific to your Taverna
+Server instance and should not be commited to your repository. Please look
+through these files and make any alterations as required. BEFORE you configure
+the Taverna Server URI and login information in taverna_server.example.rb copy
+this file to:
 
-  config/initializers/taverna_player.rb
+  config/initializers/taverna_server.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

data/lib/generators/templates/models/input.rb

@@ -0,0 +1,20 @@
+#------------------------------------------------------------------------------
+# 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 Input < ActiveRecord::Base
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Models::Input
+
+    # Extend the Input model here.
+  end
+end

data/lib/generators/templates/models/output.rb

@@ -0,0 +1,20 @@
+#------------------------------------------------------------------------------
+# 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 Output < ActiveRecord::Base
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Models::Output
+
+    # Extend the Output model here.
+  end
+end

data/lib/generators/templates/models/run_port.rb

@@ -0,0 +1,20 @@
+#------------------------------------------------------------------------------
+# 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 RunPort < ActiveRecord::Base
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Models::RunPort
+
+    # Extend the RunPort model here.
+  end
+end

data/lib/generators/templates/{initializer.rb → player_initializer.rb}

@@ -38,26 +38,6 @@ TavernaPlayer.setup do |config|
   # in the main app. For Devise this would be :current_user. Defaults to nil.
   #config.current_user_callback = nil
 
-  # Taverna Server configuration information. The poll interval is in seconds
-  # and sets how often the server will be polled for updates by each worker.
-  # The retry interval is also in seconds and sets how long a worker will wait
-  # before trying to start a run if the server is initially busy.
-  config.server_address = "http://localhost:8080/taverna"
-  config.server_username = "taverna"
-  config.server_password = "taverna"
-  config.server_poll_interval = 5
-  config.server_retry_interval = 10
-
-  # Taverna Server connection configuration.
-  #config.server_connection[:verify_peer] = true
-  #config.server_connection[:ca_file] = "/etc/certs/my-cert.crt"
-  #config.server_connection[:ca_path] = "/etc/certs/"
-  #config.server_connection[:client_certificate] = "client-cert.crt"
-  #config.server_connection[:client_password] = "P@5$w0Rd!"
-  #config.server_connection[:ssl_version] = :TLSv1
-  #config.server_connection[:open_timeout] = 10
-  #config.server_connection[:read_timeout] = 10
-
   # Where to store files created by workflow runs. Should be fully qualified
   # or use :rails_root for the root directory of your application.
   #config.file_store = ":rails_root/public/system"

data/lib/generators/templates/server_initializer.rb

@@ -0,0 +1,24 @@
+# Taverna Player Server configuration
+
+TavernaPlayer.setup do |config|
+
+  # Taverna Server configuration information. The poll interval is in seconds
+  # and sets how often the server will be polled for updates by each worker.
+  # The retry interval is also in seconds and sets how long a worker will wait
+  # before trying to start a run if the server is initially busy.
+  config.server_address = "http://localhost:8080/taverna"
+  config.server_username = "taverna"
+  config.server_password = "taverna"
+  config.server_poll_interval = 5
+  config.server_retry_interval = 10
+
+  # Taverna Server connection configuration.
+  #config.server_connection[:verify_peer] = true
+  #config.server_connection[:ca_file] = "/etc/certs/my-cert.crt"
+  #config.server_connection[:ca_path] = "/etc/certs/"
+  #config.server_connection[:client_certificate] = "client-cert.crt"
+  #config.server_connection[:client_password] = "P@5$w0Rd!"
+  #config.server_connection[:ssl_version] = :TLSv1
+  #config.server_connection[:open_timeout] = 10
+  #config.server_connection[:read_timeout] = 10
+end

data/lib/taverna_player/concerns/controllers/runs_controller.rb

@@ -66,7 +66,7 @@ module TavernaPlayer
           end
 
           def find_interaction
-            @interaction = Interaction.find_by_unique_id(params[:int_id])
+            @interaction = Interaction.find_by_run_id_and_serial(@run.id, params[:serial])
           end
 
           # Read the data from the results zip file.

data/lib/taverna_player/concerns/models/input_port.rb

@@ -0,0 +1,34 @@
+#------------------------------------------------------------------------------
+# 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 Concerns
+    module Models
+      module Input
+
+        extend ActiveSupport::Concern
+
+        included do
+          belongs_to :run, :class_name => "TavernaPlayer::Run",
+            :inverse_of => :inputs
+
+          private
+
+          def file_url_via_run
+            "/runs/#{run_id}/input/#{name}"
+          end
+        end # included
+
+      end
+    end
+  end
+end

data/lib/taverna_player/concerns/models/output_port.rb

@@ -0,0 +1,34 @@
+#------------------------------------------------------------------------------
+# 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 Concerns
+    module Models
+      module Output
+
+        extend ActiveSupport::Concern
+
+        included do
+          belongs_to :run, :class_name => "TavernaPlayer::Run",
+            :inverse_of => :outputs
+
+          private
+
+          def file_url_via_run
+            "/runs/#{run_id}/output/#{name}"
+          end
+        end # included
+
+      end
+    end
+  end
+end

data/lib/taverna_player/concerns/models/run.rb

@@ -31,18 +31,20 @@ module TavernaPlayer
           end
 
           has_many :inputs, :class_name => "TavernaPlayer::RunPort::Input",
-            :dependent => :destroy
+            :inverse_of => :run, :dependent => :destroy
           has_many :outputs, :class_name => "TavernaPlayer::RunPort::Output",
-            :dependent => :destroy
+            :inverse_of => :run, :dependent => :destroy
           has_many :interactions, :class_name => "TavernaPlayer::Interaction",
-            :dependent => :destroy
+            :inverse_of => :run, :dependent => :destroy
           belongs_to :delayed_job, :class_name => "::Delayed::Job"
 
           # A run can have children, which are runs.
           # A run can have a parent, which is another run.
           has_many :children, :class_name => "TavernaPlayer::Run",
-            :foreign_key => "parent_id", :dependent => :nullify
-          belongs_to :parent, :class_name => "TavernaPlayer::Run"
+            :foreign_key => "parent_id", :inverse_of => :parent,
+            :dependent => :nullify
+          belongs_to :parent, :class_name => "TavernaPlayer::Run",
+            :inverse_of => :children
 
           accepts_nested_attributes_for :inputs
 

data/lib/taverna_player/concerns/models/run_port.rb

@@ -0,0 +1,99 @@
+#------------------------------------------------------------------------------
+# 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 Concerns
+    module Models
+      module RunPort
+
+        extend ActiveSupport::Concern
+
+        included do
+
+          MAXIMUM_DATABASE_VALUE_SIZE = 255
+
+          self.inheritance_column = "port_type"
+
+          validates_presence_of :name
+          validates_uniqueness_of :name, :scope => [:run_id, :port_type]
+
+          attr_accessible :depth, :file, :metadata, :name, :value
+
+          serialize :metadata
+
+          has_attached_file :file,
+            :path => File.join(TavernaPlayer.file_store, ":class/:attachment/:id/:filename"),
+            :url => :file_url_via_run,
+            :default_url => ""
+
+          default_scope order("lower(name) ASC")
+
+          # If there is both a value and a file, then prefer the file. If the
+          # file is changed, delete the value. This must be run before
+          # "process_value"!
+          before_save :delete_value, :if => :file_file_name_changed?
+
+          # Overflow the value into a file if it is too big. Don't try to
+          # process the value if the file has changed. This must run after
+          # "delete_value"!
+          before_save :process_value, :if => :value_changed?,
+            :unless => :file_file_name_changed?
+
+          private
+
+          def delete_value
+            self[:value] = nil
+          end
+
+          # If the value is too big to fit in the database then overflow it
+          # into a file.
+          def process_value
+            v = self[:value]
+
+            if !v.blank? && v.size > MAXIMUM_DATABASE_VALUE_SIZE
+              self[:value] = v[0...MAXIMUM_DATABASE_VALUE_SIZE]
+              save_value_to_file(v)
+            else
+              self.file = nil unless file.path.blank?
+            end
+          end
+
+          def save_value_to_file(v)
+            Dir.mktmpdir("#{id}", Rails.root.join("tmp")) do |tmp_dir|
+              tmp_file_name = File.join(tmp_dir, "#{name}.txt")
+
+              File.write(tmp_file_name, v.force_encoding("UTF-8"))
+
+              self.file = File.new(tmp_file_name)
+            end
+          end
+
+        end # included
+
+        def display_name
+          name.gsub('_', ' ')
+        end
+
+        def value_preview
+          self[:value]
+        end
+
+        def value
+          v = self[:value]
+
+          (!v.blank? && !file.path.blank?) ? File.read(file.path) : v
+        end
+
+      end
+    end
+  end
+end

data/lib/taverna_player/version.rb

@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end

data/lib/taverna_player/worker.rb

@@ -116,7 +116,7 @@ module TavernaPlayer
             if @run.has_parent?
               next if note.has_reply?
               int = Interaction.find_by_run_id_and_serial(@run.parent_id, note.serial)
-              new_int = Interaction.find_or_initialize_by_run_id_and_unique_id_and_serial(@run.id, note.id, note.serial)
+              new_int = Interaction.find_or_initialize_by_run_id_and_serial(@run.id, note.serial)
               if new_int.new_record?
                 note.reply(int.feed_reply, int.data)
                 new_int.displayed = true
@@ -127,7 +127,7 @@ module TavernaPlayer
               end
             else
               waiting = true unless note.has_reply?
-              int = Interaction.find_or_initialize_by_run_id_and_unique_id_and_serial(@run.id, note.id, note.serial)
+              int = Interaction.find_or_initialize_by_run_id_and_serial(@run.id, note.serial)
 
               # Need to catch this here in case some other process has replied.
               if note.has_reply? && !int.replied?

data/taverna_player.gemspec

@@ -21,7 +21,13 @@ Gem::Specification.new do |s|
   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.description = "Taverna Player is a Ruby on Rails plugin to run Taverna "\
+    "Workflows using Taverna Server. Taverna Player surfaces a workflow in "\
+    "three ways: As a Web interface in the browser; As an embeddable widget "\
+    "to be included in any other Web page; As a REST-based Web Service. All "\
+    "three modes provide functionality to fully configure a workflow’s "\
+    "inputs; run the workflow on a Taverna Server; collect workflow outputs, "\
+    "logs and messages; and present the results in an appropriate manner."
   s.license     = "BSD"
 
   s.files       = `git ls-files`.split("\n")

data/test/dummy/config/initializers/{taverna_player.example.rb → taverna_player.rb}

@@ -13,23 +13,10 @@
 # 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"
 

data/test/dummy/config/initializers/taverna_server.example.rb

@@ -0,0 +1,26 @@
+#------------------------------------------------------------------------------
+# 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 Server configuration
+
+TavernaPlayer.setup do |config|
+
+  # 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
+end

data/test/dummy/db/migrate/20131126175640_remove_unique_id_from_taverna_player_interactions.taverna_player.rb

@@ -0,0 +1,12 @@
+# This migration comes from taverna_player (originally 20131126175424)
+class RemoveUniqueIdFromTavernaPlayerInteractions < ActiveRecord::Migration
+  def up
+    remove_index :taverna_player_interactions, :unique_id
+    remove_column :taverna_player_interactions, :unique_id
+  end
+
+  def down
+    add_column :taverna_player_interactions, :unique_id, :string
+    add_index :taverna_player_interactions, :unique_id
+  end
+end

data/test/dummy/db/migrate/20131127163538_add_indexes_where_missing.taverna_player.rb

@@ -0,0 +1,13 @@
+# This migration comes from taverna_player (originally 20131127162157)
+class AddIndexesWhereMissing < ActiveRecord::Migration
+  def change
+    add_index :taverna_player_interactions, [:run_id, :serial]
+    add_index :taverna_player_interactions, [:run_id, :replied]
+
+    add_index :taverna_player_run_ports, [:run_id, :name]
+
+    add_index :taverna_player_runs, :user_id
+    add_index :taverna_player_runs, :workflow_id
+    add_index :taverna_player_runs, :parent_id
+  end
+end

data/test/dummy/db/migrate/20131127163539_remove_run_id_index_from_taverna_player_runs.taverna_player.rb

@@ -0,0 +1,10 @@
+# This migration comes from taverna_player (originally 20131127163438)
+class RemoveRunIdIndexFromTavernaPlayerRuns < ActiveRecord::Migration
+  def up
+    remove_index :taverna_player_runs, :run_id
+  end
+
+  def down
+    add_index :taverna_player_runs, :run_id
+  end
+end

data/test/dummy/db/migrate/20131127172420_remove_unused_paperclip_columns.taverna_player.rb

@@ -0,0 +1,18 @@
+# This migration comes from taverna_player (originally 20131127171823)
+class RemoveUnusedPaperclipColumns < ActiveRecord::Migration
+  def up
+    remove_column :taverna_player_runs, :results_content_type
+    remove_column :taverna_player_runs, :results_updated_at
+
+    remove_column :taverna_player_runs, :log_content_type
+    remove_column :taverna_player_runs, :log_updated_at
+  end
+
+  def down
+    add_column :taverna_player_runs, :log_updated_at, :datetime
+    add_column :taverna_player_runs, :log_content_type, :string
+
+    add_column :taverna_player_runs, :results_updated_at, :datetime
+    add_column :taverna_player_runs, :results_content_type, :string
+  end
+end

data/test/dummy/db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended to check this file into your version control system.
 
-ActiveRecord::Schema.define(:version => 20131114130937) do
+ActiveRecord::Schema.define(:version => 20131127172420) do
 
   create_table "delayed_jobs", :force => true do |t|
     t.integer  "priority",   :default => 0
@@ -35,7 +35,6 @@ ActiveRecord::Schema.define(:version => 20131114130937) do
     t.datetime "created_at",                                        :null => false
     t.datetime "updated_at",                                        :null => false
     t.boolean  "displayed",                      :default => false
-    t.string   "unique_id"
     t.text     "page"
     t.string   "feed_reply"
     t.text     "data",       :limit => 16777215
@@ -43,8 +42,9 @@ ActiveRecord::Schema.define(:version => 20131114130937) do
     t.string   "page_uri"
   end
 
+  add_index "taverna_player_interactions", ["run_id", "replied"], :name => "index_taverna_player_interactions_on_run_id_and_replied"
+  add_index "taverna_player_interactions", ["run_id", "serial"], :name => "index_taverna_player_interactions_on_run_id_and_serial"
   add_index "taverna_player_interactions", ["run_id"], :name => "index_taverna_player_interactions_on_run_id"
-  add_index "taverna_player_interactions", ["unique_id"], :name => "index_taverna_player_interactions_on_unique_id"
 
   create_table "taverna_player_run_ports", :force => true do |t|
     t.string   "name"
@@ -61,36 +61,35 @@ ActiveRecord::Schema.define(:version => 20131114130937) do
     t.text     "metadata"
   end
 
+  add_index "taverna_player_run_ports", ["run_id", "name"], :name => "index_taverna_player_run_ports_on_run_id_and_name"
   add_index "taverna_player_run_ports", ["run_id"], :name => "index_taverna_player_run_ports_on_run_id"
 
   create_table "taverna_player_runs", :force => true do |t|
     t.string   "run_id"
-    t.string   "saved_state",          :default => "pending", :null => false
+    t.string   "saved_state",       :default => "pending", :null => false
     t.datetime "create_time"
     t.datetime "start_time"
     t.datetime "finish_time"
-    t.integer  "workflow_id",                                 :null => false
-    t.datetime "created_at",                                  :null => false
-    t.datetime "updated_at",                                  :null => false
+    t.integer  "workflow_id",                              :null => false
+    t.datetime "created_at",                               :null => false
+    t.datetime "updated_at",                               :null => false
     t.string   "status_message"
     t.string   "results_file_name"
-    t.string   "results_content_type"
     t.integer  "results_file_size"
-    t.datetime "results_updated_at"
-    t.boolean  "embedded",             :default => false
-    t.boolean  "stop",                 :default => false
+    t.boolean  "embedded",          :default => false
+    t.boolean  "stop",              :default => false
     t.string   "log_file_name"
-    t.string   "log_content_type"
     t.integer  "log_file_size"
-    t.datetime "log_updated_at"
-    t.string   "name",                 :default => "None"
+    t.string   "name",              :default => "None"
     t.integer  "delayed_job_id"
     t.text     "failure_message"
     t.integer  "parent_id"
     t.integer  "user_id"
   end
 
-  add_index "taverna_player_runs", ["run_id"], :name => "index_taverna_player_runs_on_run_id"
+  add_index "taverna_player_runs", ["parent_id"], :name => "index_taverna_player_runs_on_parent_id"
+  add_index "taverna_player_runs", ["user_id"], :name => "index_taverna_player_runs_on_user_id"
+  add_index "taverna_player_runs", ["workflow_id"], :name => "index_taverna_player_runs_on_workflow_id"
 
   create_table "taverna_player_service_credentials", :force => true do |t|
     t.string   "uri",         :null => false

data/test/fixtures/taverna_player/interactions.yml

@@ -11,21 +11,18 @@
 #------------------------------------------------------------------------------
 
 one:
-  unique_id: b6d0dad1-ef0a-436a-bd16-62f3fe767801
   serial: ask0
   replied: false
   displayed: false
   run_id: 4
 
 two:
-  unique_id: 602f98fc-f1b7-4fbd-9ee3-d4aa001492bb
   serial: Nested_workflow:Interaction0
   replied: true
   displayed: true
   run_id: 3
 
 three:
-  unique_id: 101d727f-31cf-4601-8c3c-9d936b9e6c5e
   serial: Nested_workflow:Interaction0
   replied: false
   displayed: true

data/test/fixtures/taverna_player/run_ports.yml

@@ -34,6 +34,7 @@ three:
   port_type: TavernaPlayer::RunPort::Input
   run_id: 3
   depth: 0
+  metadata: "---\n:size: 3\n:type: text/plain"
 
 four:
   id: 4

data/test/functional/taverna_player/runs_controller_test.rb

@@ -64,16 +64,16 @@ module TavernaPlayer
 
     test "should route to interaction write proxy" do
       assert_routing({ :method => "post",
-        :path => "/runs/1/interaction/#{@int.unique_id}" },
+        :path => "/runs/1/interaction/#{@int.serial}" },
         { :controller => "taverna_player/runs", :action => "write_interaction",
-          :id => "1", :int_id => @int.unique_id }, {}, {},
+          :id => "1", :serial => @int.serial }, {}, {},
         "Did not route correctly")
     end
 
     test "should route to interaction read proxy" do
-      assert_routing "/runs/1/interaction/#{@int.unique_id}",
+      assert_routing "/runs/1/interaction/#{@int.serial}",
         { :controller => "taverna_player/runs", :action => "read_interaction",
-          :id => "1", :int_id => @int.unique_id, }, {}, {},
+          :id => "1", :serial => @int.serial, }, {}, {},
         "Did not route correctly"
     end
 

data/test/unit/taverna_player/interaction_test.rb

@@ -14,21 +14,13 @@ require 'test_helper'
 
 module TavernaPlayer
   class InteractionTest < ActiveSupport::TestCase
-    test "should not save interaction without a unique_id" do
-      int = Interaction.new
-      int.serial = "ask0"
-      refute int.save, "Saved the interaction without a unique_id"
-    end
-
     test "should not save interaction without a serial number" do
       int = Interaction.new
-      int.unique_id = "af19046f-4614-44a7-ad83-f940cea63c4a"
       refute int.save, "Saved the interaction without a serial number"
     end
 
     test "should not allow two identical serial numbers for the same run" do
       int = Interaction.new
-      int.unique_id = "fdb30aed-96ac-4499-b8b6-0a11cf82ccee"
       int.serial = "ask0"
       int.run_id = 4
       refute int.save, "Saved the interaction with a non-unique serial number"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taverna-player
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-25 00:00:00.000000000 Z
+date: 2013-11-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -219,7 +219,12 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
-description: Taverna Player runs Taverna Workflows using Taverna Server.
+description: ! 'Taverna Player is a Ruby on Rails plugin to run Taverna Workflows
+  using Taverna Server. Taverna Player surfaces a workflow in three ways: As a Web
+  interface in the browser; As an embeddable widget to be included in any other Web
+  page; As a REST-based Web Service. All three modes provide functionality to fully
+  configure a workflow’s inputs; run the workflow on a Taverna Server; collect workflow
+  outputs, logs and messages; and present the results in an appropriate manner.'
 email:
 - support@mygrid.org.uk
 executables: []
@@ -227,6 +232,7 @@ extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- CHANGES.rdoc
 - Gemfile
 - LICENCE.rdoc
 - README.rdoc
@@ -300,6 +306,10 @@ files:
 - db/migrate/20131105115218_remove_proxy_from_taverna_player_runs.rb
 - db/migrate/20131105141934_change_taverna_player_interactions_output_value_column_name.rb
 - db/migrate/20131112165520_add_user_to_taverna_player_run.rb
+- db/migrate/20131126175424_remove_unique_id_from_taverna_player_interactions.rb
+- db/migrate/20131127162157_add_indexes_where_missing.rb
+- db/migrate/20131127163438_remove_run_id_index_from_taverna_player_runs.rb
+- db/migrate/20131127171823_remove_unused_paperclip_columns.rb
 - lib/generators/taverna_player/callbacks_generator.rb
 - lib/generators/taverna_player/controllers_generator.rb
 - lib/generators/taverna_player/install_generator.rb
@@ -312,14 +322,21 @@ files:
 - lib/generators/templates/callbacks/worker_callbacks.rb
 - lib/generators/templates/controllers/runs_controller.rb
 - lib/generators/templates/controllers/service_credentials_controller.rb
-- lib/generators/templates/initializer.rb
+- lib/generators/templates/models/input.rb
+- lib/generators/templates/models/output.rb
 - lib/generators/templates/models/run.rb
+- lib/generators/templates/models/run_port.rb
+- lib/generators/templates/player_initializer.rb
+- lib/generators/templates/server_initializer.rb
 - lib/tasks/delete-cancelled-runs.rake
 - lib/tasks/delete-old-embedded-runs.rake
 - lib/taverna-player.rb
 - lib/taverna_player/concerns/controllers/runs_controller.rb
 - lib/taverna_player/concerns/controllers/service_credentials_controller.rb
+- lib/taverna_player/concerns/models/input_port.rb
+- lib/taverna_player/concerns/models/output_port.rb
 - lib/taverna_player/concerns/models/run.rb
+- lib/taverna_player/concerns/models/run_port.rb
 - lib/taverna_player/engine.rb
 - lib/taverna_player/model_proxy.rb
 - lib/taverna_player/output_renderer.rb
@@ -355,7 +372,8 @@ files:
 - test/dummy/config/initializers/mime_types.rb
 - test/dummy/config/initializers/secret_token.rb
 - test/dummy/config/initializers/session_store.rb
-- test/dummy/config/initializers/taverna_player.example.rb
+- test/dummy/config/initializers/taverna_player.rb
+- test/dummy/config/initializers/taverna_server.example.rb
 - test/dummy/config/initializers/wrap_parameters.rb
 - test/dummy/config/locales/en.yml
 - test/dummy/config/routes.rb
@@ -386,6 +404,10 @@ files:
 - test/dummy/db/migrate/20131105142417_change_taverna_player_interactions_output_value_column_name.taverna_player.rb
 - test/dummy/db/migrate/20131112165815_add_user_to_taverna_player_run.taverna_player.rb
 - test/dummy/db/migrate/20131114130937_create_users.rb
+- test/dummy/db/migrate/20131126175640_remove_unique_id_from_taverna_player_interactions.taverna_player.rb
+- test/dummy/db/migrate/20131127163538_add_indexes_where_missing.taverna_player.rb
+- test/dummy/db/migrate/20131127163539_remove_run_id_index_from_taverna_player_runs.taverna_player.rb
+- test/dummy/db/migrate/20131127172420_remove_unused_paperclip_columns.taverna_player.rb
 - test/dummy/db/schema.rb
 - test/dummy/lib/callbacks.rb
 - test/dummy/log/.gitkeep
@@ -432,7 +454,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3245351155395870817
+      hash: 4535908520263145975
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -441,7 +463,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3245351155395870817
+      hash: 4535908520263145975
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.21
@@ -475,7 +497,8 @@ test_files:
 - test/dummy/config/initializers/mime_types.rb
 - test/dummy/config/initializers/secret_token.rb
 - test/dummy/config/initializers/session_store.rb
-- test/dummy/config/initializers/taverna_player.example.rb
+- test/dummy/config/initializers/taverna_player.rb
+- test/dummy/config/initializers/taverna_server.example.rb
 - test/dummy/config/initializers/wrap_parameters.rb
 - test/dummy/config/locales/en.yml
 - test/dummy/config/routes.rb
@@ -506,6 +529,10 @@ test_files:
 - test/dummy/db/migrate/20131105142417_change_taverna_player_interactions_output_value_column_name.taverna_player.rb
 - test/dummy/db/migrate/20131112165815_add_user_to_taverna_player_run.taverna_player.rb
 - test/dummy/db/migrate/20131114130937_create_users.rb
+- test/dummy/db/migrate/20131126175640_remove_unique_id_from_taverna_player_interactions.taverna_player.rb
+- test/dummy/db/migrate/20131127163538_add_indexes_where_missing.taverna_player.rb
+- test/dummy/db/migrate/20131127163539_remove_run_id_index_from_taverna_player_runs.taverna_player.rb
+- test/dummy/db/migrate/20131127172420_remove_unused_paperclip_columns.taverna_player.rb
 - test/dummy/db/schema.rb
 - test/dummy/lib/callbacks.rb
 - test/dummy/log/.gitkeep