taverna-player 0.8.0 → 0.9.0

data/lib/generators/taverna_player/models_generator.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -19,8 +19,8 @@ module TavernaPlayer
         "customization."
 
       def copy_models
-        ["run.rb", "run_port.rb"].each do |file|
-          copy_file file, "app/models/taverna_player/#{file}"
+        %w(run run_port workflow).each do |file|
+          copy_file "#{file}.rb", "app/models/taverna_player/#{file}.rb"
         end
       end
     end

data/lib/generators/templates/callbacks/worker_callbacks.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -11,21 +11,21 @@
 #------------------------------------------------------------------------------
 
 def player_pre_run_callback(run)
-  w = Workflow.find(run.workflow_id)
+  w = TavernaPlayer::Workflow.find(run.workflow_id)
   puts "Pre-run callback called for run '#{run.name}' of workflow '#{w.id}'"
 end
 
 def player_post_run_callback(run)
-  w = Workflow.find(run.workflow_id)
+  w = TavernaPlayer::Workflow.find(run.workflow_id)
   puts "Post-run callback called for run '#{run.name}' of workflow '#{w.id}'"
 end
 
 def player_run_cancelled_callback(run)
-  w = Workflow.find(run.workflow_id)
+  w = TavernaPlayer::Workflow.find(run.workflow_id)
   puts "Run-cancelled callback called for run '#{run.name}' of workflow '#{w.id}'"
 end
 
 def player_run_failed_callback(run)
-  w = Workflow.find(run.workflow_id)
+  w = TavernaPlayer::Workflow.find(run.workflow_id)
   puts "Run-failed callback called for run '#{run.name}' of workflow '#{w.id}'"
 end

data/{test/dummy/app → lib/generators/templates}/controllers/workflows_controller.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -10,8 +10,11 @@
 # Author: Robert Haines
 #------------------------------------------------------------------------------
 
-class WorkflowsController < ApplicationController
-  def index
-    @workflows = Workflow.all
+module TavernaPlayer
+  class WorkflowsController < TavernaPlayer::ApplicationController
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Controllers::WorkflowsController
+
+    # Extend the WorkflowsController here.
   end
 end

data/{test/dummy/test/functional/workflows_controller_test.rb → lib/generators/templates/models/workflow.rb}

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -10,12 +10,11 @@
 # Author: Robert Haines
 #------------------------------------------------------------------------------
 
-require 'test_helper'
+module TavernaPlayer
+  class Workflow < ActiveRecord::Base
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Models::Workflow
 
-class WorkflowsControllerTest < ActionController::TestCase
-  test "should get index" do
-    get :index
-    assert_response :success
+    # Extend the Workflow model here.
   end
-
 end

data/lib/generators/templates/player_initializer.rb

@@ -2,10 +2,11 @@
 
 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.workflow_model_proxy("Workflow") do |proxy|
+  # This can be set to the name of a workflow model class in the main
+  # application and the listed methods should also be mapped if necessary. The
+  # default behaviour is to use the Workflow model provided by Taverna Player.
+  config.workflow_model_proxy = "TavernaPlayer::Workflow"
+  #config.workflow_model_proxy("TavernaPlayer::Workflow") do |proxy|
     # This is the method that returns the name of the workflow file. Your
     # model MUST provide this otherwise a workflow cannot be run.
     #proxy.file_method_name = :file

data/lib/taverna-player.rb

@@ -33,10 +33,14 @@ module TavernaPlayer
   mattr_accessor :server_address, :server_password, :server_username
 
   # This should be set to the name of the workflow model class in the main
-  # application via the workflow_model_proxy method below.
+  # application via the workflow_model_proxy method below. Defaults to the
+  # internal Taverna Player Workflow model (TavernaPlayer::Workflow).
   mattr_reader :workflow_proxy
+  @@workflow_proxy =
+    ModelProxy.new("TavernaPlayer::Workflow", [:file, :title, :inputs])
 
   # :call-seq:
+  #   workflow_model_proxy = workflow_class
   #   workflow_model_proxy(workflow_class) {|proxy| ...}
   #
   # Set up a proxy to the main application's workflow model. The class name
@@ -48,6 +52,12 @@ module TavernaPlayer
     yield @@workflow_proxy if block_given?
   end
 
+  # :stopdoc:
+  def self.workflow_model_proxy=(workflow_class)
+    TavernaPlayer.workflow_model_proxy(workflow_class)
+  end
+  # :startdoc:
+
   # This should be set to the name of the user model class in the main
   # application via the user_model_proxy method below. Defaults to nil.
   mattr_reader :user_proxy

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

@@ -45,7 +45,7 @@ module TavernaPlayer
           end
 
           def find_workflow
-            @workflow = TavernaPlayer.workflow_proxy.class_name.find(params[:workflow_id])
+            @workflow = TavernaPlayer.workflow_proxy.class_const.find(params[:workflow_id])
           end
 
           def find_port

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

@@ -0,0 +1,41 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 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 Controllers
+      module WorkflowsController
+
+        extend ActiveSupport::Concern
+
+        included do
+          respond_to :html, :json
+
+          before_filter :find_workflows, :only => :index
+
+          private
+
+          def find_workflows
+            @workflows = Workflow.all
+          end
+
+        end # included
+
+        # GET /workflows
+        def index
+
+        end
+
+      end
+    end
+  end
+end

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

@@ -24,10 +24,10 @@ module TavernaPlayer
 
           # Each run is spawned from a workflow. This provides the link to the
           # workflow model in the parent app, whatever it calls its model.
-          belongs_to :workflow, :class_name => TavernaPlayer.workflow_proxy.class_name.to_s
+          belongs_to :workflow, :class_name => TavernaPlayer.workflow_proxy.class_name
 
           unless TavernaPlayer.user_proxy.nil?
-            belongs_to :user, :class_name => TavernaPlayer.user_proxy.class_name.to_s
+            belongs_to :user, :class_name => TavernaPlayer.user_proxy.class_name
           end
 
           has_many :inputs, :class_name => "TavernaPlayer::RunPort::Input",
@@ -85,6 +85,7 @@ module TavernaPlayer
           after_create :populate_child_inputs, :if => :has_parent?
           after_create :enqueue
           before_destroy :complete?
+          after_destroy :destroy_failed_delayed_jobs
 
           private
 
@@ -110,7 +111,14 @@ module TavernaPlayer
           def enqueue
             worker = TavernaPlayer::Worker.new(self)
             job = Delayed::Job.enqueue worker, :queue => TavernaPlayer.job_queue_name
-            update_attributes(:delayed_job => job, :status_message_key => "pending")
+
+            self.delayed_job = job
+            self.status_message_key = "pending"
+            save
+          end
+
+          def destroy_failed_delayed_jobs
+            delayed_job.destroy unless delayed_job.nil?
           end
 
         end # included
@@ -137,22 +145,25 @@ module TavernaPlayer
         #
         # See the note above about the :cancelled state.
         def cancel
-          return if complete?
+          return unless incomplete?
 
-          # If the run has a delayed job (still) and it hasn't been locked yet
-          # then we just remove it from the queue directly and mark the run as
-          # cancelled.
+          # Set the stop flag for all cases.
+          self.stop = true
+
+          # If the run has a delayed job and it hasn't been locked yet, or it
+          # has failed, then we just remove it from the queue directly and
+          # mark the run as cancelled.
           unless delayed_job.nil?
             delayed_job.with_lock do
-              if delayed_job.locked_by.nil?
+              if delayed_job.locked_by.nil? || !delayed_job.failed_at.nil?
                 delayed_job.destroy
-                update_attribute(:saved_state, "cancelled")
-                update_attribute(:status_message_key, "cancelled")
+                self.state = :cancelled
+                self.status_message_key = "cancelled"
               end
             end
           end
 
-          update_attribute(:stop, true)
+          save
         end
 
         # Return state as a symbol. If a run is running, but has been asked to
@@ -181,6 +192,14 @@ module TavernaPlayer
           I18n.t("taverna_player.status.#{key}")
         end
 
+        def pending?
+          state == :pending
+        end
+
+        def initialized?
+          state == :initialized
+        end
+
         def running?
           state == :running
         end
@@ -205,10 +224,19 @@ module TavernaPlayer
           state == :failed
         end
 
-        # This is used as a catch-all for finished, cancelled, failed and
-        # timeout
+        def job_failed?
+          !delayed_job.nil? && !delayed_job.failed_at.nil?
+        end
+
+        # This is used as a catch-all for pending?, initialized? and running?
+        def incomplete?
+          running? || pending? || initialized?
+        end
+
+        # This is used as a catch-all for finished, cancelled, failed,
+        # job_failed? and timeout
         def complete?
-          finished? || cancelled? || failed? || timeout?
+          finished? || cancelled? || failed? || job_failed? || timeout?
         end
 
         def has_parent?

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

@@ -103,7 +103,8 @@ module TavernaPlayer
             md = metadata
             md = Hash.new if md.nil?
             md[field] = value
-            update_attribute(:metadata, md)
+            self.metadata = md
+            save
           end
 
         end # included

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

@@ -0,0 +1,44 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 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 Workflow
+
+        extend ActiveSupport::Concern
+
+        included do
+          attr_accessible :author, :description, :file, :title
+
+          has_many :runs, :class_name => "TavernaPlayer::Run"
+        end # included
+
+        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
+    end
+  end
+end

data/lib/taverna_player/model_proxy.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -15,21 +15,27 @@ module TavernaPlayer
     attr_reader :class_name
 
     def initialize(class_name, method_names = [])
-      if class_name.is_a?(String)
-        begin
-          @class_name = Object.const_get(class_name)
-        rescue NameError
-          @class_name = class_name.constantize
-        end
-      end
+      @class_name = root_name(class_name.to_s)
 
       method_names.each do |name|
         add_method(name.to_sym)
       end
     end
 
+    def class_const
+      @const ||= begin
+                   Object.const_get(@class_name)
+                 rescue NameError
+                   @class_name.constantize
+                 end
+    end
+
     private
 
+    def root_name(name)
+      name.start_with?("::") ? name : "::#{name}"
+    end
+
     def add_method(name)
       setter = "#{name}_method_name=".to_sym
       mapper = name

data/lib/taverna_player/version.rb

@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.8.0"
+  VERSION = "0.9.0"
 end

data/taverna_player.gemspec

@@ -36,6 +36,7 @@ Gem::Specification.new do |s|
   s.add_dependency "rails", "~> 3.2.12"
   s.add_dependency "jquery-rails", "~> 3.0"
   s.add_dependency "paperclip", "~> 4.1"
+  s.add_dependency "taverna-t2flow", "~> 0.5.1"
   s.add_dependency "t2-server", "~> 1.1"
   s.add_dependency "delayed_job_active_record", "~> 4.0"
   s.add_dependency "daemons", "~> 1.1.9"

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

@@ -26,7 +26,7 @@
 		<br />
 
 		<%= link_to "Home", main_app.root_path %> |
-		<%= link_to "Workflows", main_app.workflows_path %> |
+		<%= link_to "Workflows", taverna_player.workflows_path %> |
 		<%= link_to "Runs", taverna_player.runs_path %> |
 		<%= link_to "Service Credentials", taverna_player.service_credentials_path %> |
 		<%= link_to "Job Queue", taverna_player.job_queue_path %>

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

@@ -13,11 +13,8 @@
 # Taverna Player configuration
 
 TavernaPlayer.setup do |config|
-  config.workflow_model_proxy("Workflow") do |proxy|
-    proxy.file_method_name = :file
-  end
   config.user_model_proxy = "User"
-  config.current_user_callback = Proc.new { User.find(1) }
+  config.current_user_callback = Proc.new { User.first }
 
   # Move admin resources into their own namespace.
   config.admin_scope = "admin"

data/test/dummy/config/routes.rb

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2013 The University of Manchester, UK.
+# Copyright (c) 2013, 2014 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -11,12 +11,6 @@
 #------------------------------------------------------------------------------
 
 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