taverna-player 0.5.0 → 0.6.0

data/taverna_player.gemspec

@@ -34,19 +34,21 @@ Gem::Specification.new do |s|
   s.test_files  = `git ls-files -- test/*`.split("\n")
 
   s.add_dependency "rails", "~> 3.2.12"
-  s.add_dependency "jquery-rails", "~> 3.0.4"
-  s.add_dependency "paperclip", "~> 3.4.1"
+  s.add_dependency "jquery-rails", "~> 3.0"
+  s.add_dependency "paperclip", "~> 4.1"
   s.add_dependency "t2-server", "~> 1.0.0"
-  s.add_dependency "delayed_job_active_record", "~> 0.4.3"
+  s.add_dependency "delayed_job_active_record", "~> 4.0"
   s.add_dependency "daemons", "~> 1.1.9"
   s.add_dependency "rubyzip", "~> 0.9.9"
-  s.add_dependency "coderay", "~> 1.0.9"
+  s.add_dependency "coderay", "~> 1.1"
   s.add_dependency "rails_autolink", "~> 1.1.0"
   s.add_dependency "require_all", "~> 1.3.1"
-  s.add_dependency "jbuilder", "~> 1.5.2"
+  s.add_dependency "jbuilder", "~> 2.0"
   s.add_dependency "pmrpc-rails", "~> 1.0.0"
 
   s.add_development_dependency "sqlite3"
+  s.add_development_dependency "coveralls"
+  s.add_development_dependency "flexmock", "~> 1.3"
 
   s.require_path = "lib"
 end

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

@@ -14,5 +14,5 @@
 
 <h2>An embedded workflow</h2>
 <div>
-  <iframe src="<%= new_embedded_run_url(3) %>&input=10" width="100%" height="500px"></iframe>
+  <iframe src="<%= new_embedded_run_url(3) %>&input[input]=10" width="100%" height="500px"></iframe>
 </div>

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

@@ -28,7 +28,8 @@
 		<%= link_to "Home", main_app.root_path %> |
 		<%= link_to "Workflows", main_app.workflows_path %> |
 		<%= link_to "Runs", taverna_player.runs_path %> |
-		<%= link_to "Service Credentials", taverna_player.service_credentials_path %>
+		<%= link_to "Service Credentials", taverna_player.service_credentials_path %> |
+		<%= link_to "Job Queue", taverna_player.job_queue_path %>
 	</p>
 
 	<p id="notice"><%= notice %></p>

data/test/dummy/config/application.rb

@@ -25,6 +25,7 @@ module Dummy
     # config.time_zone = 'Central Time (US & Canada)'
 
     # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+    I18n.enforce_available_locales = true
     # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
     # config.i18n.default_locale = :de
 

data/test/dummy/config/initializers/taverna_player.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.
 #
@@ -13,9 +13,14 @@
 # Taverna Player configuration
 
 TavernaPlayer.setup do |config|
-  config.workflow_model_proxy("Workflow")
+  config.workflow_model_proxy("Workflow") do |proxy|
+    proxy.file_method_name = :file
+  end
   config.user_model_proxy = "User"
-  config.current_user_callback = :user_one
+  config.current_user_callback = Proc.new { User.find(1) }
+
+  # Move admin resources into their own namespace.
+  config.admin_scope = "admin"
 
   # Callbacks to be run at various points during a workflow run.
   require "callbacks"

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

@@ -0,0 +1,36 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+en:
+  taverna_player:
+    status:
+      pending: "Queued!"
+      pre-callback: "Running pre-run tasks"
+      connect: "Connecting to Taverna Server"
+      full: "Server full - please wait; run will start soon"
+      initialized: "Initializing new workflow run"
+      inputs: "Uploading run inputs"
+      start: "Starting run"
+      busy: "Server busy - please wait; run will start soon"
+      running: "Running!"
+      interact: "Waiting for user input"
+      outputs: "Gathering run outputs and log"
+      post-callback: "Running post-run tasks"
+      finished: "Finished!"
+      cancel: "Cancelling"
+      cancel-callback: "Running post-cancel tasks"
+      cancelled: "Cancelled!"
+      timeout: "Run execution timed out"
+      fail-callback: "Running post-failure tasks"
+      failed: "Failed!"
+    errors:
+      invalid-parent: "Parents must have lower ids than their children"

data/test/dummy/db/migrate/20140226143013_change_taverna_player_runs_status_message_to_use_keys.taverna_player.rb

@@ -0,0 +1,20 @@
+# This migration comes from taverna_player (originally 20140226135723)
+class ChangeTavernaPlayerRunsStatusMessageToUseKeys < ActiveRecord::Migration
+  def up
+    rename_column :taverna_player_runs, :status_message, :status_message_key
+
+    TavernaPlayer::Run.all.each do |run|
+      run.status_message_key = run.saved_state
+      run.save
+    end
+  end
+
+  def down
+    rename_column :taverna_player_runs, :status_message_key, :status_message
+
+    TavernaPlayer::Run.all.each do |run|
+      run.status_message = run.saved_state.capitalize
+      run.save
+    end
+  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 => 20131127172420) do
+ActiveRecord::Schema.define(:version => 20140226143013) do
 
   create_table "delayed_jobs", :force => true do |t|
     t.integer  "priority",   :default => 0
@@ -66,21 +66,21 @@ ActiveRecord::Schema.define(:version => 20131127172420) do
 
   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.string   "status_message"
+    t.integer  "workflow_id",                               :null => false
+    t.datetime "created_at",                                :null => false
+    t.datetime "updated_at",                                :null => false
+    t.string   "status_message_key"
     t.string   "results_file_name"
     t.integer  "results_file_size"
-    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.integer  "log_file_size"
-    t.string   "name",              :default => "None"
+    t.string   "name",               :default => "None"
     t.integer  "delayed_job_id"
     t.text     "failure_message"
     t.integer  "parent_id"

data/test/dummy/lib/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.
 #
@@ -29,7 +29,3 @@ def player_run_failed_callback(run)
   w = Workflow.find(run.workflow_id)
   puts "Run-failed callback called for run '#{run.name}' of workflow '#{w.id}'"
 end
-
-def user_one
-  User.find(1)
-end

data/test/fixtures/files/non-ascii.csv

@@ -0,0 +1,30 @@
+authorship,genusPart,infragenericEpithet,specificEpithet,infraspecificEpithet,nameComplete,uninomial,taxonName,occurrenceID,decimalLatitude,decimalLongitude,earliestDateCollected,latestDateCollected,coordinateUncertaintyInMeters,country,collector,fieldNotes,locality,maximumDepthInMeters,maximumElevationInMeters,minimumDepthInMeters,minimumElevationInMeters,value,dataProviderName,dataResourceName,dataResourceRights,dataResourceCitation
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286810,55.0315,8.428,2009-08-18,2009-08-18,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2009,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2009, doi:10.1594/PANGAEA.755038"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286812,55.0304,8.4339,2009-08-18,2009-08-18,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2009,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2009, doi:10.1594/PANGAEA.755038"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286811,55.0312,8.4314,2009-08-18,2009-08-18,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2009,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2009, doi:10.1594/PANGAEA.755038"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354288927,55.0312,8.4314,2010-08-10,2010-08-10,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2010,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2010, doi:10.1594/PANGAEA.755039"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354288926,55.0315,8.428,2010-08-10,2010-08-10,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2010,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2010, doi:10.1594/PANGAEA.755039"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354288929,55.0304,8.4339,2010-08-10,2010-08-10,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2010,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2010, doi:10.1594/PANGAEA.755039"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354288928,55.0368,8.4172,2010-08-10,2010-08-10,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2010,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2010, doi:10.1594/PANGAEA.755039"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354285291,55.0315,8.428,2007-08-21,2007-08-21,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2007,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2007, doi:10.1594/PANGAEA.755036"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354285292,55.0312,8.4314,2007-08-21,2007-08-21,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2007,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2007, doi:10.1594/PANGAEA.755036"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354285293,55.0304,8.4339,2007-08-21,2007-08-21,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2007,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2007, doi:10.1594/PANGAEA.755036"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286707,55.0312,8.4314,2008-08-01,2008-08-01,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2008,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2008, doi:10.1594/PANGAEA.755037"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286705,55.0304,8.4339,2008-08-01,2008-08-01,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2008,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2008, doi:10.1594/PANGAEA.755037"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286704,55.0315,8.428,2008-08-01,2008-08-01,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2008,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2008, doi:10.1594/PANGAEA.755037"
+,,,,,Crassostrea gigas,,Crassostrea gigas,354286706,55.0368,8.4172,2008-08-01,2008-08-01,,,,,,,,0,,,PANGAEA - Publishing Network for Geoscientific and Environmental Data,Abundance of macrobenthos organisms in the northern Wadden Sea in 2008,,"Buschbaum, Christian (2010): Abundance of macrobenthos organisms in the northern Wadden Sea in 2008, doi:10.1594/PANGAEA.755037"
+,,,gigas,,Crassostrea gigas,,Crassostrea gigas,675167609,58.447262,8.8255959,2009-04-25,2009-04-25,70,Norway,Olsen K.M.,,Flangeborgkilen ?��?�???��?�?��?��?��?????��?�?��?????��???�?��?�???��?�??��?��?��?????����?��?�???��?�??��?��?��?�???��?�??��?�?��?�???��?�?��?��?��?????��?�?�??��?????��???�?��?�???��?�??��?��?��????���??��?�???��?�?��?��?��?????��?�?�??��?????��???ᬨ�����Ƭ���?��?�,0,0,0,0,,"Natural History Museum, University of Oslo",BioFokus,,
+,,,gigas,,Crassostrea gigas,,Crassostrea gigas,675183925,58.624622,9.0724735,2010-07-14,2010-07-14,180,Norway,Olsen K.M.,,Engholmen ?��?�???��?�?��?��?��?????��?�?��?????��???�?��?�???��?�??��?��?��?????����?��?�???��?�??��?��?��?�???��?�??��?�?��?�???��?�?��?��?��?????��?�?�??��?????��???�?��?�???��?�??��?��?��????���??��?�???��?�?��?��?��?????��?�?�??��?????��???ᬨ�����Ƭ���?��?� Pollen p?��?�???��?�?��?��?��?????��?�?��?????��???�?��?�???��?�??��?��?��?�???��?�?��?�?�??��?�???��?�??��?��?��?�???��?�??��?�?��?�???��?�?��?��?��?????��?�?��?????��???�?��?�???��?�??��?��?��?????�����������Ƭ������� nordsiden,0,2,0,0,,"Natural History Museum, University of Oslo",BioFokus,,
+,,,gigas,,Crassostrea gigas,,Crassostrea gigas,675159927,58.624821,9.0718365,2009-06-02,2009-06-02,7,Norway,Monrad J.V.,,Engholmkilen ?��?�???��?�?��?��?��?????��?�?��?????��???�?��?�???��?�??��?��?��?????����?��?�???��?�??��?��?��?�???��?�??��?�?��?�???��?�?��?��?��?????��?�?�??��?????��???�?��?�???��?�??��?��?��????���??��?�???��?�?��?��?��?????��?�?�??��?????��???ᬨ�����Ƭ���?��?� Der veien slutter ved Nordmannsvik og Engholmkilen,0,0,0,0,,"Natural History Museum, University of Oslo",BioFokus,,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251587382,54.42686225641775,-3.57473127238348,1994-11-30,1994-11-30,70.7,GB,Ian Killeen;Shelagh Smith,,"Nethertown,  6km north of Sellafield,Cumbria.",,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251577332,51.780431971927264,1.0374767507215295,,,707,GB,Pam Wilson;Peter Wilson,,Colne point Nature Reserve Essex,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,323579489,49.251403,-2.115802,1998-09-10,1998-09-10,70.7,,Ian Killeen;Jan Light,,Bonne Nuit Bay,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251581774,51.74780687224405,0.9048652323607271,1997-09-15,1997-09-15,707,GB,Pam Wilson;Peter Wilson,,Bradwell on sea Essex,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,323586215,49.180744,-2.186292,1998-09-09,1998-09-09,70.7,,Anon @Conch Soc,,Ouaisne  Jersey,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,323566084,48.574139,-2.767877,1997-05-11,1997-05-11,70.7,,Ian Killeen;Jan Light,,Tournemine W Greve des Rosaires,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251613062,53.14742113099659,-4.302225486046831,2001-07-25,2001-07-25,70.7,GB,Tom Clifton,,"Menaifron, Menai Strait, Anglesey.",,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251609930,53.31752338375657,-4.641740177559318,1993-05-22,1993-05-22,70.7,GB,Tom Clifton,,"Holyhead Harbour, Anglesey.",,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251556416,50.57310347016449,-2.4943183095345627,1989-11-23,1989-11-23,7071,GB,Dennis Seaward,,Middle and East Fleet Dorset,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,323585993,49.151749,-2.042473,1998-09-08,1998-09-08,70.7,,Ian Killeen;Jan Light,,Le Hocq  St Crements Bay,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,323586310,49.251403,-2.115802,1998-09-10,1998-09-10,70.7,,Ian Killeen;Jan Light,,Bonne Nuit Bay  Jersey,,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,
+,,,,,Crassostrea gigas,,Crassostrea gigas,251613098,53.166018176771246,-4.270302423010207,1991-09-15,1991-09-15,70.7,GB,Tom Clifton,,"Barras, Menai Strait, Anglesey.",,,,,,UK National Biodiversity Network,Conchological Society of Great Britain & Ireland - Mollusc (marine) data for Great Britain and Ireland,Access Constraints: None Use Constraints: None,

data/test/fixtures/taverna_player/interactions.yml

@@ -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.
 #
@@ -15,15 +15,18 @@ one:
   replied: false
   displayed: false
   run_id: 4
+  page_uri: ""
 
 two:
   serial: Nested_workflow:Interaction0
   replied: true
   displayed: true
   run_id: 3
+  page_uri: "http://www.example.com/interactions/1.html"
 
 three:
   serial: Nested_workflow:Interaction0
   replied: false
   displayed: true
   run_id: 5
+  page_uri: "http://www.example.com/interactions/2.html"

data/test/fixtures/taverna_player/runs.yml

@@ -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.
 #
@@ -67,3 +67,8 @@ six:
   create_time: 2013-03-13 10:55:46
   start_time: 2013-03-13 10:55:48
   workflow_id: 1
+
+seven:
+  name: Test run 7
+  saved_state: pending
+  workflow_id: 1

data/test/functional/taverna_player/job_queue_controller_test.rb

@@ -0,0 +1,35 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+module TavernaPlayer
+  class JobQueueControllerTest < ActionController::TestCase
+    setup do
+      @routes = TavernaPlayer::Engine.routes
+    end
+
+    test "should route to the job queue" do
+      assert_routing "#{TavernaPlayer.admin_scope}/job_queue",
+        { :controller => "taverna_player/job_queue",
+          :action => "index" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should get index" do
+      get :index
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:jobs), "Jobs not assigned"
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+  end
+end

data/test/functional/taverna_player/runs_controller_test.rb

@@ -174,6 +174,26 @@ module TavernaPlayer
       refute assigns(:run).user_id.nil?, "Run should have a user_id"
     end
 
+    test "should create inputs along with run" do
+      assert_difference("Run.count") do
+        assert_difference("RunPort.count") do
+          post :create, :run => { :workflow_id => workflows(:three).id,
+                                  :inputs_attributes => [{:value => 'test', :name => 'IN'}]
+          }
+        end
+      end
+
+      assert_redirected_to run_path(assigns(:run)),
+        "Did not redirect correctly"
+      assert_equal "Run was successfully created.", flash[:notice],
+        "Incorrect or missing flash notice"
+      assert assigns(:run).valid?, "Created run was invalid"
+      refute assigns(:run).user_id.nil?, "Run should have a user_id"
+
+      assert_equal 1, assigns(:run).inputs.size
+      assert_equal 'test', assigns(:run).inputs.first.value
+    end
+
     test "should create embedded run via browser" do
       assert_difference("Run.count") do
         post :create,

data/test/functional/taverna_player/service_credentials_controller_test.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.
 #
@@ -21,13 +21,13 @@ module TavernaPlayer
     end
 
     test "should route to service credentials" do
-      assert_routing "/service_credentials",
+      assert_routing "#{TavernaPlayer.admin_scope}/service_credentials",
         { :controller => "taverna_player/service_credentials",
           :action => "index" }, {}, {}, "Did not route correctly"
     end
 
     test "should route to a service credential" do
-      assert_routing "/service_credentials/1",
+      assert_routing "#{TavernaPlayer.admin_scope}/service_credentials/1",
         { :controller => "taverna_player/service_credentials",
           :action => "show", :id => "1" }, {}, {}, "Did not route correctly"
     end

data/test/test_helper.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.
 #
@@ -10,6 +10,9 @@
 # Author: Robert Haines
 #------------------------------------------------------------------------------
 
+require 'coveralls'
+Coveralls.wear!('rails')
+
 # Configure Rails Environment
 ENV["RAILS_ENV"] = "test"
 

data/test/unit/helpers/taverna_player/runs_helper_test.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.
 #
@@ -14,6 +14,25 @@ require 'test_helper'
 
 module TavernaPlayer
   class RunsHelperTest < ActionView::TestCase
+    setup do
+      @int1 = taverna_player_interactions(:one)
+      @int2 = taverna_player_interactions(:two)
+    end
 
+    test "should redirect internally" do
+      redirect = interaction_redirect(@int1)
+      refute redirect.blank?, "Redirect was blank."
+      assert redirect.include?("/interaction/#{@int1.serial}"),
+        "Redirect did not include interaction serial number"
+    end
+
+    test "should redirect externally" do
+      redirect = interaction_redirect(@int2)
+      refute redirect.blank?, "Redirect was blank."
+      assert_equal redirect, @int2.page_uri,
+        "Redirect did not match the page URI."
+      refute redirect.include?("/interaction/#{@int2.serial}"),
+        "Redirect included interaction serial number"
+    end
   end
 end

data/test/unit/taverna_player/run_port_test.rb

@@ -117,6 +117,24 @@ module TavernaPlayer
       assert_nil port.file.path, "File present"
     end
 
+    test "should handle non ascii/utf-8 characters in small input values" do
+      test_value =
+        "\xC2"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "\xC2"
+
+      port = RunPort::Input.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_nil port.file.path, "File present"
+      assert_equal test_value, port.value, "Saved value does not match test"
+      assert_equal port.value_preview, port.value,
+        "Value and preview should be equal"
+    end
+
     test "should handle non ascii/utf-8 characters in large input values" do
       test_value =
         "\xC2"\
@@ -136,6 +154,24 @@ module TavernaPlayer
       assert_not_equal port.value_preview, port.value, "Value and preview same"
     end
 
+    test "should handle non ascii/utf-8 characters in small output values" do
+      test_value =
+        "\xC2"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "\xC2"
+
+      port = RunPort::Output.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_nil port.file.path, "File present"
+      assert_equal test_value, port.value, "Saved value does not match test"
+      assert_equal port.value_preview, port.value,
+        "Value and preview should be equal"
+    end
+
     test "should handle non ascii/utf-8 characters in large output values" do
       test_value =
         "\xC2"\
@@ -173,7 +209,7 @@ module TavernaPlayer
     end
 
     test "should not allow both file and value on create input" do
-      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      file = fixture_file_upload "/files/non-ascii.csv"
       port = RunPort::Input.create(:name => "test_port", :value => "test",
         :file => file)
 
@@ -182,7 +218,7 @@ module TavernaPlayer
     end
 
     test "should not allow both file and value on create output" do
-      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      file = fixture_file_upload "/files/non-ascii.csv"
       port = RunPort::Output.create(:name => "test_port", :value => "test",
         :file => file)
 
@@ -191,7 +227,7 @@ module TavernaPlayer
     end
 
     test "should not allow both file and value on update input" do
-      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      file = fixture_file_upload "/files/non-ascii.csv"
       port = RunPort::Input.create(:name => "test_port")
 
       port.file = file
@@ -203,7 +239,7 @@ module TavernaPlayer
     end
 
     test "should not allow both file and value on update output" do
-      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      file = fixture_file_upload "/files/non-ascii.csv"
       port = RunPort::Output.create(:name => "test_port")
 
       port.file = file
@@ -283,7 +319,7 @@ module TavernaPlayer
       refute port.value.blank?, "Value is empty"
       refute port.file.blank?, "File not present"
 
-      port.file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      port.file = fixture_file_upload "/files/non-ascii.csv"
       port.save
       assert_nil port[:value], "Port value not nil"
       refute port.file.blank?, "File not present"