taverna-player 0.1.0

data/test/functional/taverna_player/service_credentials_controller_test.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
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+module TavernaPlayer
+  class ServiceCredentialsControllerTest < ActionController::TestCase
+    setup do
+      @sc1 = taverna_player_service_credentials(:one)
+      @sc2 = taverna_player_service_credentials(:two)
+      @routes = TavernaPlayer::Engine.routes
+    end
+
+    test "should route to service credentials" do
+      assert_routing "/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",
+        { :controller => "taverna_player/service_credentials",
+          :action => "show", :id => "1" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should get index and be overridden" do
+      get :index
+      assert_response :success
+      assert_not_nil assigns(:service_credentials)
+      assert_not_nil assigns(:override)
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should get new" do
+      get :new
+      assert_response :success
+      assert_not_nil assigns(:service_credential)
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should create service_credential" do
+      assert_difference('ServiceCredential.count') do
+        post :create, :service_credential => {
+          :description => @sc1.description,
+          :login => @sc1.login,
+          :name => @sc1.name,
+          :password => @sc1.password,
+          :password_confirmation => @sc1.password,
+          :uri => @sc1.uri
+        }
+      end
+
+      assert_redirected_to service_credential_path(assigns(:service_credential))
+    end
+
+    test "should show service_credential and not be overridden" do
+      get :show, :id => @sc1
+      assert_response :success
+      refute assigns(:override)
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should get edit" do
+      get :edit, :id => @sc1
+      assert_response :success
+    end
+
+    test "should update service_credential" do
+      put :update, :id => @sc1, :service_credential => {
+        :description => @sc1.description,
+        :login => @sc1.login,
+        :name => @sc1.name,
+        :password => @sc1.password,
+        :password_confirmation => @sc1.password,
+        :uri => @sc1.uri
+      }
+
+      assert_redirected_to service_credential_path(assigns(:service_credential))
+    end
+
+    test "should destroy service_credential" do
+      assert_difference('ServiceCredential.count', -1) do
+        delete :destroy, :id => @sc1
+      end
+
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to service_credentials_path
+    end
+  end
+end

data/test/taverna_player_test.rb

@@ -0,0 +1,25 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+class TavernaPlayerTest < ActiveSupport::TestCase
+  test "truth" do
+    assert_kind_of Module, TavernaPlayer
+  end
+
+  test "extra mime types present" do
+    ["application/x-error", "application/x-empty", "inode/x-empty"].each do |type|
+      assert_not_empty MIME::Types[type], "MIME type '#{type}' missing"
+    end
+  end
+end

data/test/test_helper.rb

@@ -0,0 +1,33 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+# Configure Rails Environment
+ENV["RAILS_ENV"] = "test"
+
+require File.expand_path("../dummy/config/environment.rb",  __FILE__)
+require "rails/test_help"
+
+Rails.backtrace_cleaner.remove_silencers!
+
+# Load support files
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each { |f| require f }
+
+# Load fixtures from the engine
+if ActiveSupport::TestCase.method_defined?(:fixture_path=)
+  ActiveSupport::TestCase.fixture_path = File.expand_path("../fixtures", __FILE__)
+end
+
+class ActiveSupport::TestCase
+  include TavernaPlayer::Engine.routes.url_helpers
+  include ActionDispatch::TestProcess
+  fixtures :all
+end

data/test/unit/helpers/taverna_player/application_helper_test.rb

@@ -0,0 +1,70 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+module TavernaPlayer
+  class ApplicationHelperTest < ActionView::TestCase
+    setup do
+      @run = taverna_player_runs(:one)
+      @workflow = workflows(:one)
+    end
+
+    test "should output embedded run path from id" do
+      id = 2
+      path = new_embedded_run_path(id)
+      assert path.include?("embedded=true"), "Path missing 'embedded=true'"
+      assert path.include?("workflow_id=#{id}"), "Path missing workflow_id"
+      refute path.include?("http://"), "Path should not have a URI scheme"
+    end
+
+    test "should output embedded run path from run" do
+      id = @run.workflow_id
+      path = new_embedded_run_path(@run)
+      assert path.include?("embedded=true"), "Path missing 'embedded=true'"
+      assert path.include?("workflow_id=#{id}"), "Path missing workflow_id"
+      refute path.include?("http://"), "Path should not have a URI scheme"
+    end
+
+    test "should output embedded run path from workflow" do
+      id = @workflow.id
+      path = new_embedded_run_path(@workflow)
+      assert path.include?("embedded=true"), "Path missing 'embedded=true'"
+      assert path.include?("workflow_id=#{id}"), "Path missing workflow_id"
+      refute path.include?("http://"), "Path should not have a URI scheme"
+    end
+
+    test "should output embedded run url from id" do
+      id = 2
+      path = new_embedded_run_url(id)
+      assert path.include?("embedded=true"), "Path missing 'embedded=true'"
+      assert path.include?("workflow_id=#{id}"), "Path missing workflow_id"
+      assert path.include?("http://"), "Path missing a URI scheme"
+    end
+
+    test "should output embedded run url from run" do
+      id = @run.workflow_id
+      path = new_embedded_run_url(@run)
+      assert path.include?("embedded=true"), "Path missing 'embedded=true'"
+      assert path.include?("workflow_id=#{id}"), "Path missing workflow_id"
+      assert path.include?("http://"), "Path missing a URI scheme"
+    end
+
+    test "should output embedded run url from workflow" do
+      id = @workflow.id
+      path = new_embedded_run_url(@workflow)
+      assert path.include?("embedded=true"), "Path missing 'embedded=true'"
+      assert path.include?("workflow_id=#{id}"), "Path missing workflow_id"
+      assert path.include?("http://"), "Path missing a URI scheme"
+    end
+  end
+end

data/test/unit/helpers/taverna_player/runs_helper_test.rb

@@ -0,0 +1,45 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+module TavernaPlayer
+  class RunsHelperTest < ActionView::TestCase
+    setup do
+      @run1 = taverna_player_runs(:one)
+      @port1 = taverna_player_run_ports(:one)
+
+      @run2 = taverna_player_runs(:three)
+      @port2 = taverna_player_run_ports(:four)
+
+      @run3 = taverna_player_runs(:four)
+      @port3 = taverna_player_run_ports(:five)
+    end
+
+    test "should show text outputs" do
+      assert_equal "Hello, World!", @port1.value, "Unexpected workflow output"
+      assert show_output(@run1, @port1).include?("<pre>Hello, World!</pre>"),
+        "Workflow output not formatted correctly"
+
+      assert_equal "Rob", @port2.value, "Unexpected workflow output"
+      assert show_output(@run2, @port2).include?("<pre>Rob</pre>"),
+        "Workflow output not formatted correctly"
+    end
+
+    test "should autolink text output" do
+      assert_equal "(http://example.com/path?query=1)", @port3.value,
+        "Unexpected workflow output"
+      assert show_output(@run3, @port3).include?("(<a href=\"http://example.com/path?query=1\" target=\"_blank\">http://example.com/path?query=1</a>)"),
+        "Workflow output not formatted correctly"
+    end
+  end
+end

data/test/unit/taverna_player/interaction_test.rb

@@ -0,0 +1,47 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+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"
+    end
+
+    test "replied defaults to false" do
+      int = Interaction.new
+      refute int.replied, "Interaction#replied did not default to false"
+    end
+
+    test "displayed defaults to false" do
+      int = Interaction.new
+      refute int.displayed, "Interaction#displayed did not default to false"
+    end
+  end
+end

data/test/unit/taverna_player/run_port_test.rb

@@ -0,0 +1,309 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+module TavernaPlayer
+  class RunIoTest < ActiveSupport::TestCase
+    setup do
+      @port1 = taverna_player_run_ports(:one)
+      @port2 = taverna_player_run_ports(:two)
+      @port3 = taverna_player_run_ports(:three)
+      @port5 = taverna_player_run_ports(:five)
+    end
+
+    test "run port inheritance types" do
+      in_port = RunPort::Input.new
+      assert_equal "TavernaPlayer::RunPort::Input", in_port.port_type,
+        "Input does not inherit as TavernaPlayer::RunPort::Input"
+
+      out_port = RunPort::Output.new
+      assert_equal "TavernaPlayer::RunPort::Output", out_port.port_type,
+        "Output does not inherit as TavernaPlayer::RunPort::Output"
+    end
+
+    test "should not save run ports without name" do
+      in_port = RunPort::Input.new
+      assert !in_port.save, "Saved the run input port without a name"
+
+      out_port = RunPort::Output.new
+      assert !out_port.save, "Saved the run output port without a name"
+    end
+
+    test "should not save small input values in a file" do
+      test_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      port = RunPort::Input.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_equal port.value_preview, port.value, "Value and preview differ"
+      assert_nil port.file.path, "File present"
+      assert_equal test_value, port.value, "Saved value does not match test"
+    end
+
+    test "should not save small output values in a file" do
+      test_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      port = RunPort::Output.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_equal port.value_preview, port.value, "Value and preview differ"
+      assert_nil port.file.path, "File present"
+      assert_equal test_value, port.value, "Saved value does not match test"
+    end
+
+    test "should save large input values in a file" do
+      test_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      port = RunPort::Input.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_not_nil port.file.path, "File not present"
+      assert port.read_attribute(:value).size == 255, "Port value size != 255"
+      assert_equal test_value, port.value, "Saved value does not match test"
+      assert_not_equal port.value_preview, port.value, "Value and preview same"
+
+      port.value = "small"
+      assert port.save, "Port did not save"
+      assert_nil port.file.path, "File present"
+    end
+
+    test "should save large output values in a file" do
+      test_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      port = RunPort::Output.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_not_nil port.file.path, "File not present"
+      assert port.read_attribute(:value).size == 255, "Port value size != 255"
+      assert_equal test_value, port.value, "Saved value does not match test"
+      assert_not_equal port.value_preview, port.value, "Value and preview same"
+
+      port.value = "small"
+      assert port.save, "Port did not save"
+      assert_nil port.file.path, "File present"
+    end
+
+    test "should handle non ascii/utf-8 characters in large input values" do
+      test_value =
+        "\xC2"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "\xC2"
+
+      port = RunPort::Input.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_not_nil port.file.path, "File not present"
+      assert_equal test_value, port.value, "Saved value does not match test"
+      assert_not_equal port.value_preview, port.value, "Value and preview same"
+    end
+
+    test "should handle non ascii/utf-8 characters in large output values" do
+      test_value =
+        "\xC2"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "\xC2"
+
+      port = RunPort::Output.create(:name => "test_port")
+      port.value = test_value
+      assert port.save, "Port did not save"
+      assert_not_nil port.file.path, "File not present"
+      assert_equal test_value, port.value, "Saved value does not match test"
+      assert_not_equal port.value_preview, port.value, "Value and preview same"
+    end
+
+    test "should display port names correctly" do
+      assert_equal @port1.name, @port1.display_name,
+        "Name with no spaces should not be changed"
+      assert_equal @port2.name, @port2.display_name,
+        "Name with no spaces should not be changed"
+      assert_not_equal @port3.name, @port3.display_name,
+        "Name with spaces should not be unchanged"
+      refute @port3.display_name.include?('_'),
+        "Display name should not have any underscores"
+      refute @port5.display_name.include?('_'),
+        "Display name should not have any underscores"
+      assert_equal @port3.name.gsub('_', ' '), @port3.display_name,
+        "Only underscores should be changed"
+      assert_equal @port5.name.gsub('_', ' '), @port5.display_name,
+        "Only underscores should be changed"
+    end
+
+    test "should not allow both file and value on create input" do
+      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      port = RunPort::Input.create(:name => "test_port", :value => "test",
+        :file => file)
+
+      assert port.value.blank?, "Value should be blank"
+      refute port.file.blank?, "File should be present"
+    end
+
+    test "should not allow both file and value on create output" do
+      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      port = RunPort::Output.create(:name => "test_port", :value => "test",
+        :file => file)
+
+      assert port.value.blank?, "Value should be blank"
+      refute port.file.blank?, "File should be present"
+    end
+
+    test "should not allow both file and value on update input" do
+      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      port = RunPort::Input.create(:name => "test_port")
+
+      port.file = file
+      port.value = "test"
+      port.save
+
+      assert port.value.blank?, "Value should be blank"
+      refute port.file.blank?, "File should be present"
+    end
+
+    test "should not allow both file and value on update output" do
+      file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      port = RunPort::Output.create(:name => "test_port")
+
+      port.file = file
+      port.value = "test"
+      port.save
+
+      assert port.value.blank?, "Value should be blank"
+      refute port.file.blank?, "File should be present"
+    end
+
+    test "should change large input value correctly" do
+      orig_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      new_value =
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
+
+      port = RunPort::Input.create(:name => "test_port", :value => orig_value)
+      refute port.value.blank?, "Value is empty"
+      refute port.file.blank?, "File not present"
+
+      port.value = new_value
+      port.save
+      refute port.value.blank?, "Value is empty"
+      refute port.file.blank?, "File not present"
+      assert_not_equal orig_value, port.value, "Port still has old value"
+    end
+
+    test "should change large output value correctly" do
+      orig_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      new_value =
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"\
+        "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ"
+
+      port = RunPort::Output.create(:name => "test_port", :value => orig_value)
+      refute port.value.blank?, "Value is empty"
+      refute port.file.blank?, "File not present"
+
+      port.value = new_value
+      port.save
+      refute port.value.blank?, "Value is empty"
+      refute port.file.blank?, "File not present"
+      assert_not_equal orig_value, port.value, "Port still has old value"
+    end
+
+    test "should blank out large value if file changed" do
+      orig_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      port = RunPort::Input.create(:name => "test_port", :value => orig_value)
+      refute port.value.blank?, "Value is empty"
+      refute port.file.blank?, "File not present"
+
+      port.file = fixture_file_upload "/files/crassostrea_gigas.csv"
+      port.save
+      assert_nil port.value, "Port value not nil"
+      refute port.file.blank?, "File not present"
+    end
+
+    test "should blank out large value if file removed" do
+      orig_value =
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"\
+        "01234567890123456789012345678901234567890123456789"
+
+      port = RunPort::Input.create(:name => "test_port", :value => orig_value)
+      refute port.value.blank?, "Value is empty"
+      refute port.file.blank?, "File not present"
+
+      port.file = nil
+      port.save
+      assert_nil port.value, "Port value not nil"
+      assert port.file.blank?, "File not present"
+    end
+  end
+end