taverna-player 0.1.0

data/test/fixtures/taverna_player/interactions.yml

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+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
+  run_id: 5

data/test/fixtures/taverna_player/run_ports.yml

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+one:
+  id: 1
+  name: Message
+  value: Hello, World!
+  port_type: TavernaPlayer::RunPort::Output
+  run_id: 1
+  depth: 0
+  metadata: "---\n:size: 13\n:type: text/plain"
+
+two:
+  id: 2
+  name: OUT
+  port_type: TavernaPlayer::RunPort::Output
+  run_id: 2
+  depth: 1
+  metadata: "---\n:size:\n- 7\n- 7\n- 974\n- 974\n- 7\n:type:\n- text/plain\n- text/plain\n- application/x-error\n- application/x-error\n- text/plain"
+
+three:
+  id: 3
+  name: IN_Value
+  value: Rob
+  port_type: TavernaPlayer::RunPort::Input
+  run_id: 3
+  depth: 0
+
+four:
+  id: 4
+  name: OUT
+  value: Rob
+  port_type: TavernaPlayer::RunPort::Output
+  run_id: 3
+  depth: 0
+  metadata: "---\n:size: 3\n:type: text/plain"
+
+five:
+  id: 5
+  name: Long_N_unnecessary_Name_OUT
+  value: (http://example.com/path?query=1)
+  port_type: TavernaPlayer::RunPort::Output
+  run_id: 4
+  depth: 0
+  metadata: "---\n:size: 33\n:type: text/plain"

data/test/fixtures/taverna_player/runs.yml

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+one:
+  id: 1
+  run_id: 9dcfbaf1-4c55-40f0-9853-baa7f8410879
+  name: Test run 1
+  saved_state: pending
+  create_time: 2013-03-13 10:55:46
+  start_time: 2013-03-13 10:56:00
+  finish_time: 2013-03-13 10:56:32
+  workflow_id: 1
+
+two:
+  id: 2
+  run_id: 13246c77-ffa3-449f-9b18-0f085717f8eb
+  name: Test run 2
+  saved_state: running
+  create_time: 2013-03-13 10:55:46
+  start_time: 2013-03-13 10:55:55
+  finish_time: 2013-03-13 10:57:07
+  workflow_id: 2
+
+three:
+  id: 3
+  run_id: f8250afc-09c1-4129-ab28-e889a284594f
+  name: Test run 3
+  saved_state: finished
+  create_time: 2013-03-13 10:55:46
+  start_time: 2013-03-13 10:55:48
+  finish_time: 2013-03-13 10:58:22
+  workflow_id: 3
+  embedded: true
+
+four:
+  id: 4
+  run_id: f8250afc-09c1-4129-ab28-e889a284594f
+  name: Test run 4
+  saved_state: running
+  create_time: 2013-03-13 10:55:46
+  start_time: 2013-03-13 10:55:48
+  workflow_id: 1
+
+five:
+  id: 5
+  run_id: f8250afc-09c1-4129-ab28-e889a284594f
+  name: Test run 5
+  saved_state: running
+  create_time: 2013-03-13 10:55:46
+  start_time: 2013-03-13 10:55:48
+  workflow_id: 1
+
+six:
+  id: 6
+  run_id: f8250afc-09c1-4129-ab28-e889a284594f
+  name: Test run 6
+  saved_state: failed
+  create_time: 2013-03-13 10:55:46
+  start_time: 2013-03-13 10:55:48
+  workflow_id: 1

data/test/fixtures/taverna_player/service_credentials.yml

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+one:
+  uri: rserve://example.com:6311
+  name: My R Server
+  description: R Server
+  login: myname
+  password: insecure!
+
+two:
+  uri: http://example.org/my_service
+  name: My Web Service
+  description: Web Service
+  login: aname
+  password: bad-password!

data/test/fixtures/users.yml

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+one:
+  id: 1
+  name: Rob
+  email: rob@example.com

data/test/fixtures/workflows.yml

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+one:
+  id: 1
+  title: Hello, World!
+  author: Robert Haines
+  description: Say "Hello, World!"
+  file: test/workflows/hello.t2flow
+
+two:
+  id: 2
+  title: List of Fail
+  author: Robert Haines
+  description: Produce a list littered with errors
+  file: test/workflows/list_with_errors.t2flow
+
+three:
+  id: 3
+  title: Pass Through
+  author: Robert Haines
+  description: Pass the input straight through to the output
+  file: test/workflows/pass_through.t2flow

data/test/functional/taverna_player/runs_controller_test.rb

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+#------------------------------------------------------------------------------
+# Copyright (c) 2013 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Taverna Player was developed in the BioVeL project, funded by the European
+# Commission 7th Framework Programme (FP7), through grant agreement
+# number 283359.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'test_helper'
+
+module TavernaPlayer
+  class RunsControllerTest < ActionController::TestCase
+    setup do
+      @run1 = taverna_player_runs(:one)
+      @run2 = taverna_player_runs(:two)
+      @run3 = taverna_player_runs(:three)
+      @run4 = taverna_player_runs(:four)
+      @run5 = taverna_player_runs(:five)
+      @int = taverna_player_interactions(:one)
+      @workflow = workflows(:one)
+      @routes = TavernaPlayer::Engine.routes
+    end
+
+    test "should route to runs" do
+      assert_routing "/runs",
+        { :controller => "taverna_player/runs", :action => "index" }, {}, {},
+        "Did not route correctly"
+    end
+
+    test "should route to a run" do
+      assert_routing "/runs/1",
+        { :controller => "taverna_player/runs", :action => "show",
+          :id => "1" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should route to a run output" do
+      assert_routing "/runs/1/output/OUT",
+        { :controller => "taverna_player/runs", :action => "output",
+          :id => "1", :port => "OUT" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should route to a deep run output" do
+      assert_routing "/runs/1/output/OUT/0/0",
+        { :controller => "taverna_player/runs", :action => "output",
+          :id => "1", :port => "OUT", :path => "0/0" }, {}, {},
+        "Did not route correctly"
+    end
+
+    test "should route to a run input" do
+      assert_routing "/runs/1/input/IN",
+        { :controller => "taverna_player/runs", :action => "input",
+          :id => "1", :port => "IN" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should route to cancel on a run" do
+      assert_routing({ :method => "put", :path => "/runs/1/cancel" },
+        { :controller => "taverna_player/runs", :action => "cancel",
+          :id => "1" }, {}, {}, "Did not route correctly")
+    end
+
+    test "should route to interaction write proxy" do
+      assert_routing({ :method => "post",
+        :path => "/runs/1/interaction/#{@int.unique_id}" },
+        { :controller => "taverna_player/runs", :action => "write_interaction",
+          :id => "1", :int_id => @int.unique_id }, {}, {},
+        "Did not route correctly")
+    end
+
+    test "should route to interaction read proxy" do
+      assert_routing "/runs/1/interaction/#{@int.unique_id}",
+        { :controller => "taverna_player/runs", :action => "read_interaction",
+          :id => "1", :int_id => @int.unique_id, }, {}, {},
+        "Did not route correctly"
+    end
+
+    test "should route to results download" do
+      assert_routing "/runs/1/download/results",
+        { :controller => "taverna_player/runs", :action => "download_results",
+          :id => "1" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should route to log download" do
+      assert_routing "/runs/1/download/log",
+        { :controller => "taverna_player/runs", :action => "download_log",
+          :id => "1" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should route to output port download" do
+      assert_routing "/runs/1/download/output/Message",
+        { :controller => "taverna_player/runs", :action => "download_output",
+          :id => "1", :port => "Message" }, {}, {}, "Did not route correctly"
+    end
+
+    test "should get index and be overridden" do
+      get :index, :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:runs), "Did not assign a valid runs instance"
+      assert_not_nil assigns(:override)
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should get new and not be overridden" do
+      get :new, :workflow_id => 1, :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      refute assigns(:override)
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should get new embedded" do
+      get :new, :workflow_id => 1, :embedded => "true",
+        :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      assert_template "taverna_player/embedded",
+        "Did not render with the correct layout"
+    end
+
+    test "should show run with no interactions" do
+      get :show, :id => @run1, :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      refute assigns(:interaction), "No interactions for this run"
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should show run with an undisplayed interaction" do
+      get :show, :id => @run4, :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      assert assigns(:interaction), "Should have an interaction for this run"
+      assert assigns(:new_interaction), "Should have new interaction flag"
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should show run with a displayed interaction" do
+      get :show, :id => @run5, :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      assert assigns(:interaction), "Should have an interaction for this run"
+      refute assigns(:new_interaction), "Should not have new interaction flag"
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should show run embedded ignoring replied interaction" do
+      get :show, :id => @run3, :use_route => :taverna_player
+      assert_response :success, "Response was not success"
+      refute assigns(:interaction), "Should not show replied interaction"
+      refute assigns(:new_interaction), "Should not have new interaction flag"
+      assert_template "taverna_player/embedded",
+        "Did not render with the correct layout"
+    end
+
+    test "should create run via browser" do
+      assert_difference("Run.count") do
+        post :create, :run => { :workflow_id => @workflow.id }
+      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"
+    end
+
+    test "should create embedded run via browser" do
+      assert_difference("Run.count") do
+        post :create,
+          :run => { :workflow_id => @workflow.id, :embedded => "true" }
+      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"
+      assert assigns(:run).embedded?, "Run not marked as embedded"
+      assert assigns(:run).user_id.nil?, "Run should not have a user_id"
+    end
+
+    test "should create run via json" do
+      assert_difference("Run.count") do
+        post :create, :run => { :workflow_id => @workflow.id },
+          :format => :json
+      end
+
+      assert_response :created, "Response was not created"
+      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"
+    end
+
+    test "should create embedded run via json" do
+      assert_difference("Run.count") do
+        post :create,
+          :run => { :workflow_id => @workflow.id, :embedded => "true" },
+          :format => :json
+      end
+
+      assert_response :created, "Response was not created"
+      assert_equal "Run was successfully created.", flash[:notice],
+        "Incorrect or missing flash notice"
+      assert assigns(:run).valid?, "Created run was invalid"
+      assert assigns(:run).embedded?, "Run not marked as embedded"
+      assert assigns(:run).user_id.nil?, "Run should not have a user_id"
+    end
+
+    test "should not destroy running run via browser" do
+      @request.env["HTTP_REFERER"] = "/runs"
+      assert_no_difference(["Run.count", "RunPort::Output.count"],
+        "Run count and output port count changed") do
+          delete :destroy, :id => @run1, :use_route => :taverna_player
+      end
+
+      assert_equal "Run must be cancelled before deletion.", flash[:error],
+        "Incorrect or missing flash notice"
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to runs_path, "Did not redirect correctly"
+    end
+
+    test "should not destroy running run via json" do
+      assert_no_difference(["Run.count", "RunPort::Output.count"],
+        "Run count and output port count changed") do
+          delete :destroy, :id => @run1, :format => :json
+      end
+
+      assert_equal "Run must be cancelled before deletion.", flash[:error],
+        "Incorrect or missing flash notice"
+      assert_response :forbidden, "Response was not forbidden"
+    end
+
+    test "should cancel run and redirect to index via browser" do
+      @request.env["HTTP_REFERER"] = "/runs"
+      put :cancel, :id => @run1, :use_route => :taverna_player
+
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to runs_path, "Did not redirect correctly"
+    end
+
+    test "should cancel run and redirect to show via browser" do
+      @request.env["HTTP_REFERER"] = "/runs/1"
+      put :cancel, :id => @run1, :use_route => :taverna_player
+
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to run_path(@run1), "Did not redirect correctly"
+    end
+
+    test "should cancel run via json" do
+      put :cancel, :id => @run1, :format => :json
+
+      assert_response :success, "Response was not success"
+    end
+
+    test "should destroy run and all associated ports and interactions" do
+      assert_difference(["Run.count", "RunPort::Input.count",
+        "RunPort::Output.count", "Interaction.count"], -1,
+        "Counts of objects did not reduce by 1") do
+          delete :destroy, :id => @run3, :use_route => :taverna_player
+      end
+
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to runs_path, "Did not redirect correctly"
+    end
+
+    test "should only return runs from workflow id 1" do
+      get :index, :workflow_id => @workflow
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:runs), "Did not assign a valid runs instance"
+      assert_not_nil assigns(:override)
+      assert_not_equal Run.count, assigns(:runs).count, "Returned all runs"
+      assert_template "application", "Did not render with the correct layout"
+    end
+
+    test "should update run name via browser" do
+      put :update, :id => @run1, :run => { :name => "New name" }
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:update_parameters), "Did not filter params"
+      assert_equal "New name", assigns(:run).name, "Run name not updated"
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to run_path(assigns(:run)),
+        "Did not redirect correctly"
+    end
+
+    test "should only update run name via browser" do
+      put :update, :id => @run1,
+        :run => { :name => "New name", :run_id => "New id" }
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:update_parameters), "Did not filter params"
+      assert_equal "New name", assigns(:run).name, "Run name not updated"
+      assert_not_equal "New id", assigns(:run).run_id, "Run ID updated"
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to run_path(assigns(:run)),
+        "Did not redirect correctly"
+    end
+
+    test "should filter update parameters correctly" do
+      put :update, :id => @run1, :run => { :run_id => "New id" }
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_nil assigns(:update_parameters), "Did not filter params"
+      assert_not_equal "New id", assigns(:run).run_id, "Run ID updated"
+      assert_response :redirect, "Response was not a redirect"
+      assert_redirected_to run_path(assigns(:run)),
+        "Did not redirect correctly"
+    end
+
+    test "should update run name via json" do
+      put :update, :id => @run1, :run => { :name => "New name" },
+        :format => :json
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:update_parameters), "Did not filter params"
+      assert_equal "New name", assigns(:run).name, "Run name not updated"
+      assert_response :success, "Response was not success"
+    end
+  end
+end