taverna-player 0.8.0 → 0.9.0

data/test/functional/taverna_player/workflows_controller_test.rb

@@ -0,0 +1,37 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2013, 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 WorkflowsControllerTest < ActionController::TestCase
+    setup do
+      @routes = TavernaPlayer::Engine.routes
+    end
+
+    test "should route to workflows" do
+      assert_routing "/workflows",
+        { :controller => "taverna_player/workflows", :action => "index" }, {},
+        {}, "Did not route correctly"
+    end
+
+    test "should get index html" do
+      get :index
+      assert_response :success
+    end
+
+    test "should get index json" do
+      get :index, :format => :json
+      assert_response :success
+    end
+  end
+end

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

@@ -16,7 +16,7 @@ module TavernaPlayer
   class ApplicationHelperTest < ActionView::TestCase
     setup do
       @run = taverna_player_runs(:one)
-      @workflow = workflows(:one)
+      @workflow = taverna_player_workflows(:one)
     end
 
     test "should output embedded run path from id" do

data/test/unit/taverna_player/interaction_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.
 #
@@ -22,7 +22,7 @@ module TavernaPlayer
     test "should not allow two identical serial numbers for the same run" do
       int = Interaction.new
       int.serial = "ask0"
-      int.run_id = 4
+      int.run = taverna_player_runs(:four)
       refute int.save, "Saved the interaction with a non-unique serial number"
     end
 

data/test/unit/taverna_player/model_proxy_test.rb

@@ -0,0 +1,58 @@
+#------------------------------------------------------------------------------
+# 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'
+
+class NameTest
+  def proxy_method
+    1
+  end
+end
+
+class ModelProxyTest < ActiveSupport::TestCase
+
+  setup do
+    @name = "NameTest"
+    @rooted_name = "::#{@name}"
+    @constant = ::NameTest
+    @methods = [ :test1, :test2 ]
+  end
+
+  test "name is rooted" do
+    mp = TavernaPlayer::ModelProxy.new(@name)
+
+    assert_equal @rooted_name, mp.class_name
+    assert_equal @constant, mp.class_const
+  end
+
+  test "already rooted name" do
+    mp = TavernaPlayer::ModelProxy.new(@rooted_name)
+
+    assert_equal @rooted_name, mp.class_name
+    assert_equal @constant, mp.class_const
+  end
+
+  test "proxy methods" do
+    mp = TavernaPlayer::ModelProxy.new(@name, @methods)
+
+    @methods.each do |method|
+      setter = "#{method}_method_name=".to_sym
+      assert mp.respond_to?(method)
+      assert mp.respond_to?(setter)
+
+      # Set the proxy method, then call it.
+      mp.send(setter, :proxy_method)
+      assert_equal 1, mp.send(method, NameTest.new)
+    end
+  end
+
+end

data/test/unit/taverna_player/run_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.
 #
@@ -14,9 +14,24 @@ require 'test_helper'
 
 module TavernaPlayer
   class RunTest < ActiveSupport::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)
+      @run6 = taverna_player_runs(:six)
+      @run8 = taverna_player_runs(:eight)
+      @run9 = taverna_player_runs(:nine)
+      @run10 = taverna_player_runs(:ten)
+      @run11 = taverna_player_runs(:eleven)
+      @workflow = taverna_player_workflows(:one)
+    end
+
     test "should not save run with an illegal state" do
       run = Run.new
-      run.workflow = workflows(:one)
+      run.workflow = @workflow
       run.state = :not_a_state
       assert !run.save, "Saved the run with an illegal state"
     end
@@ -37,7 +52,7 @@ module TavernaPlayer
 
     test "should not save run with cancelled state if not marked as stopped" do
       run = Run.new
-      run.workflow = workflows(:one)
+      run.workflow = @workflow
       run.saved_state = "cancelled"
       run.stop = false
       refute run.save, "Saved run with cancelled state when not stopped first"
@@ -45,7 +60,7 @@ module TavernaPlayer
 
     test "should cancel run if run set to stop first" do
       run = Run.new
-      run.workflow = workflows(:one)
+      run.workflow = @workflow
       refute run.stop, "Run's stop flag was set upon creation"
       run.cancel
       run.state = :cancelled
@@ -56,7 +71,7 @@ module TavernaPlayer
 
     test "should not be able to set state to cancelling directly" do
       run = Run.new
-      run.workflow = workflows(:one)
+      run.workflow = @workflow
       assert run.save, "Could not save run initially"
 
       run.state = :cancelling
@@ -65,7 +80,7 @@ module TavernaPlayer
 
     test "should be in cancelling state after being cancelled" do
       run = Run.new
-      run.workflow = workflows(:one)
+      run.workflow = @workflow
       run.state = :running
       assert run.save, "Could not save run initially."
       run.delayed_job_id = nil # Remove delayed job to pretend it is running.
@@ -96,35 +111,39 @@ module TavernaPlayer
     end
 
     test "complete run states" do
-      refute taverna_player_runs(:one).complete?, "Run not complete"
-      refute taverna_player_runs(:two).complete?, "Run not complete"
-      assert taverna_player_runs(:three).complete?, "Run is complete"
-      refute taverna_player_runs(:four).complete?, "Run not complete"
-      refute taverna_player_runs(:five).complete?, "Run not complete"
-      assert taverna_player_runs(:six).complete?, "Run is complete"
+      refute @run1.complete?, "Run not complete"
+      refute @run2.complete?, "Run not complete"
+      assert @run3.complete?, "Run is complete"
+      refute @run4.complete?, "Run not complete"
+      refute @run5.complete?, "Run not complete"
+      assert @run6.complete?, "Run is complete"
+      refute @run8.complete?, "Run not complete"
+      assert @run9.complete?, "Run is complete"
+      assert @run10.complete?, "Run is complete"
+      refute @run11.complete?, "Run not complete"
     end
 
     test "a parent cannot be younger than its child" do
-      older = Run.create(:workflow_id => 1)
-      young = Run.create(:workflow_id => 1)
+      older = Run.create(:workflow_id => @workflow.id)
+      young = Run.create(:workflow_id => @workflow.id)
       older.parent = young
       refute older.save, "Run saved with a younger parent"
     end
 
     test "parent/child graph should be acyclic" do
-      parent = Run.create(:workflow_id => 1)
-      child = Run.create(:workflow_id => 1)
+      parent = Run.create(:workflow_id => @workflow.id)
+      child = Run.create(:workflow_id => @workflow.id)
       parent.children << child
       parent.parent = child
       refute parent.save, "Run saved with child as its parent"
     end
 
     test "finding root ancestor of a run" do
-      one = Run.create(:workflow_id => 1)
+      one = Run.create(:workflow_id => @workflow.id)
       assert_same one, one.root_ancestor, "Single run is not its own root"
       assert_equal 0, one.children.count, "Not a parent, should not have children"
 
-      two = Run.create(:workflow_id => 1)
+      two = Run.create(:workflow_id => @workflow.id)
       assert_same two, two.root_ancestor, "Single run is not its own root"
 
       two.parent = one
@@ -133,7 +152,7 @@ module TavernaPlayer
       assert_same one, two.root_ancestor, "Child run does not have parent as its root"
       assert_equal 1, one.children.count, "Parent should have one child"
 
-      three = Run.create(:workflow_id => 1)
+      three = Run.create(:workflow_id => @workflow.id)
       assert_same three, three.root_ancestor, "Single run is not its own root"
 
       three.parent = two
@@ -144,7 +163,7 @@ module TavernaPlayer
       assert_equal 1, two.children.count, "Parent should have one child"
       assert_equal 1, one.children.count, "Grandparent should have one child"
 
-      four = Run.create(:workflow_id => 1)
+      four = Run.create(:workflow_id => @workflow.id)
       assert_same four, four.root_ancestor, "Single run is not its own root"
 
       four.parent = one
@@ -155,7 +174,7 @@ module TavernaPlayer
 
     test "create run from another run" do
       assert_difference(["Run.count", "RunPort::Input.count"]) do
-        parent = taverna_player_runs(:three)
+        parent = @run3
         run = Run.create(:parent_id => parent.id)
         assert run.valid?, "Run is invalid"
         refute run.new_record?, "Run was not saved"
@@ -167,7 +186,7 @@ module TavernaPlayer
 
     test "new run from another run" do
       assert_difference(["Run.count", "RunPort::Input.count"]) do
-        parent = taverna_player_runs(:three)
+        parent = @run3
         run = Run.new(:parent_id => parent.id)
         assert run.save, "Run was not saved"
         assert run.has_parent?, "Run should have a parent"
@@ -177,7 +196,7 @@ module TavernaPlayer
     end
 
     test "killing parent should orphan child" do
-      parent = taverna_player_runs(:three)
+      parent = @run3
       run = Run.create(:parent_id => parent.id)
       assert run.valid?, "Child run is invalid"
       assert_not_nil run.parent_id, "Child run has no parent"
@@ -192,5 +211,66 @@ module TavernaPlayer
       run.reload
       assert_nil run.parent_id, "Child run still has a parent"
     end
+
+    test "delayed job state affects run state" do
+      assert @run8.initialized?, "Run should be initialized"
+      assert @run9.pending?, "Run should be pending"
+
+      assert @run10.running?, "Run should be running"
+      assert @run11.running?, "Run should be running"
+
+      refute @run8.job_failed?, "Job has not failed"
+      assert @run9.job_failed?, "Job has failed"
+      assert @run10.job_failed?, "Job has failed"
+      refute @run11.job_failed?, "Job has not failed"
+    end
+
+    test "can delete running run with failed delayed job" do
+      assert_difference(["Run.count", "Delayed::Job.count"], -1) do
+        @run9.destroy
+      end
+    end
+
+    test "cannot delete running run with running delayed job" do
+      assert_no_difference(["Run.count", "Delayed::Job.count"]) do
+        @run8.destroy
+      end
+    end
+
+    test "cancelling run where delayed job not locked" do
+      assert_no_difference("Run.count") do
+        assert_difference("Delayed::Job.count", -1) do
+          @run8.cancel
+        end
+      end
+
+      assert @run8.cancelled?, "Run should be cancelled"
+    end
+
+    test "cancelling run where delayed job has failed" do
+      assert_no_difference("Run.count") do
+        assert_difference("Delayed::Job.count", -1) do
+          @run9.cancel
+        end
+      end
+
+      assert @run9.cancelled?, "Run should be cancelled"
+
+      assert_no_difference("Run.count") do
+        assert_difference("Delayed::Job.count", -1) do
+          @run10.cancel
+        end
+      end
+
+      assert @run10.cancelled?, "Run should be cancelled"
+    end
+
+    test "do not destroy running delayed job upon cancel" do
+      assert_no_difference(["Run.count", "Delayed::Job.count"]) do
+        @run11.cancel
+      end
+
+      assert @run11.cancelling?, "Run should be cancelling"
+    end
   end
 end

data/test/unit/taverna_player/worker_test.rb

@@ -32,6 +32,8 @@ class WorkerTest < ActiveSupport::TestCase
       config.post_run_callback = @noop_callback
       config.run_cancelled_callback = @noop_callback
       config.run_failed_callback = @noop_callback
+      config.current_user_callback =
+        Proc.new { User.find(ActiveRecord::Fixtures.identify(:test_user)) }
     end
 
     # Stuff we can't test yet in TavernaPlayer::Worker.

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: taverna-player
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.9.0
 platform: ruby
 authors:
 - Robert Haines
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-25 00:00:00.000000000 Z
+date: 2014-09-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -52,6 +52,20 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: '4.1'
+- !ruby/object:Gem::Dependency
+  name: taverna-t2flow
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.5.1
 - !ruby/object:Gem::Dependency
   name: t2-server
   requirement: !ruby/object:Gem::Requirement
@@ -237,6 +251,7 @@ files:
 - .ruby-version
 - .travis.yml
 - CHANGES.rdoc
+- CITATION
 - Gemfile
 - LICENCE.rdoc
 - README.rdoc
@@ -250,12 +265,14 @@ files:
 - app/controllers/taverna_player/job_queue_controller.rb
 - app/controllers/taverna_player/runs_controller.rb
 - app/controllers/taverna_player/service_credentials_controller.rb
+- app/controllers/taverna_player/workflows_controller.rb
 - app/helpers/taverna_player/application_helper.rb
 - app/helpers/taverna_player/runs_helper.rb
 - app/models/taverna_player/interaction.rb
 - app/models/taverna_player/run.rb
 - app/models/taverna_player/run_port.rb
 - app/models/taverna_player/service_credential.rb
+- app/models/taverna_player/workflow.rb
 - app/views/layouts/taverna_player/embedded.html.erb
 - app/views/taverna_player/job_queue/index.html.erb
 - app/views/taverna_player/runs/_button.html.erb
@@ -286,6 +303,9 @@ files:
 - app/views/taverna_player/service_credentials/index.html.erb
 - app/views/taverna_player/service_credentials/new.html.erb
 - app/views/taverna_player/service_credentials/show.html.erb
+- app/views/taverna_player/workflows/_info.json.jbuilder
+- app/views/taverna_player/workflows/index.html.erb
+- app/views/taverna_player/workflows/index.json.jbuilder
 - config/locales/en.yml
 - config/routes.rb
 - db/migrate/20130313105546_create_taverna_player_runs.rb
@@ -318,6 +338,7 @@ files:
 - db/migrate/20131127163438_remove_run_id_index_from_taverna_player_runs.rb
 - db/migrate/20131127171823_remove_unused_paperclip_columns.rb
 - db/migrate/20140226135723_change_taverna_player_runs_status_message_to_use_keys.rb
+- db/migrate/20140917165505_create_taverna_player_workflows.rb
 - lib/generators/taverna_player/callbacks_generator.rb
 - lib/generators/taverna_player/controllers_generator.rb
 - lib/generators/taverna_player/install_generator.rb
@@ -331,8 +352,10 @@ files:
 - lib/generators/templates/controllers/job_queue_controller.rb
 - lib/generators/templates/controllers/runs_controller.rb
 - lib/generators/templates/controllers/service_credentials_controller.rb
+- lib/generators/templates/controllers/workflows_controller.rb
 - lib/generators/templates/models/run.rb
 - lib/generators/templates/models/run_port.rb
+- lib/generators/templates/models/workflow.rb
 - lib/generators/templates/player_initializer.rb
 - lib/generators/templates/server_initializer.rb
 - lib/tasks/delete-cancelled-runs.rake
@@ -342,10 +365,12 @@ files:
 - lib/taverna_player/concerns/controllers/job_queue_controller.rb
 - lib/taverna_player/concerns/controllers/runs_controller.rb
 - lib/taverna_player/concerns/controllers/service_credentials_controller.rb
+- lib/taverna_player/concerns/controllers/workflows_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/concerns/models/workflow.rb
 - lib/taverna_player/concerns/utils.rb
 - lib/taverna_player/concerns/zip.rb
 - lib/taverna_player/engine.rb
@@ -365,12 +390,9 @@ files:
 - test/dummy/app/controllers/home_controller.rb
 - test/dummy/app/controllers/taverna_player/runs_controller.rb
 - test/dummy/app/controllers/taverna_player/service_credentials_controller.rb
-- test/dummy/app/controllers/workflows_controller.rb
 - test/dummy/app/models/user.rb
-- test/dummy/app/models/workflow.rb
 - test/dummy/app/views/home/index.html.erb
 - test/dummy/app/views/layouts/application.html.erb
-- test/dummy/app/views/workflows/index.html.erb
 - test/dummy/config.ru
 - test/dummy/config/application.rb
 - test/dummy/config/boot.rb
@@ -422,6 +444,8 @@ files:
 - 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/migrate/20140226143013_change_taverna_player_runs_status_message_to_use_keys.taverna_player.rb
+- test/dummy/db/migrate/20140917165846_drop_workflows.rb
+- test/dummy/db/migrate/20140917170017_create_taverna_player_workflows.taverna_player.rb
 - test/dummy/db/schema.rb
 - test/dummy/lib/callbacks.rb
 - test/dummy/log/.gitkeep
@@ -432,24 +456,26 @@ files:
 - test/dummy/script/delayed_job
 - test/dummy/script/rails
 - test/dummy/test/functional/home_controller_test.rb
-- test/dummy/test/functional/workflows_controller_test.rb
 - test/dummy/tmp/.gitkeep
+- test/fixtures/delayed_jobs.yml
 - test/fixtures/files/non-ascii.csv
 - test/fixtures/files/plain-text.bad-extension
 - test/fixtures/taverna_player/interactions.yml
 - test/fixtures/taverna_player/run_ports.yml
 - test/fixtures/taverna_player/runs.yml
 - test/fixtures/taverna_player/service_credentials.yml
+- test/fixtures/taverna_player/workflows.yml
 - test/fixtures/users.yml
-- test/fixtures/workflows.yml
 - test/functional/taverna_player/job_queue_controller_test.rb
 - test/functional/taverna_player/runs_controller_test.rb
 - test/functional/taverna_player/service_credentials_controller_test.rb
+- test/functional/taverna_player/workflows_controller_test.rb
 - test/taverna_player_test.rb
 - test/test_helper.rb
 - test/unit/helpers/taverna_player/application_helper_test.rb
 - test/unit/helpers/taverna_player/runs_helper_test.rb
 - test/unit/taverna_player/interaction_test.rb
+- test/unit/taverna_player/model_proxy_test.rb
 - test/unit/taverna_player/run_port_test.rb
 - test/unit/taverna_player/run_test.rb
 - test/unit/taverna_player/service_credential_test.rb
@@ -490,12 +516,9 @@ test_files:
 - test/dummy/app/controllers/home_controller.rb
 - test/dummy/app/controllers/taverna_player/runs_controller.rb
 - test/dummy/app/controllers/taverna_player/service_credentials_controller.rb
-- test/dummy/app/controllers/workflows_controller.rb
 - test/dummy/app/models/user.rb
-- test/dummy/app/models/workflow.rb
 - test/dummy/app/views/home/index.html.erb
 - test/dummy/app/views/layouts/application.html.erb
-- test/dummy/app/views/workflows/index.html.erb
 - test/dummy/config.ru
 - test/dummy/config/application.rb
 - test/dummy/config/boot.rb
@@ -547,6 +570,8 @@ test_files:
 - 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/migrate/20140226143013_change_taverna_player_runs_status_message_to_use_keys.taverna_player.rb
+- test/dummy/db/migrate/20140917165846_drop_workflows.rb
+- test/dummy/db/migrate/20140917170017_create_taverna_player_workflows.taverna_player.rb
 - test/dummy/db/schema.rb
 - test/dummy/lib/callbacks.rb
 - test/dummy/log/.gitkeep
@@ -557,24 +582,26 @@ test_files:
 - test/dummy/script/delayed_job
 - test/dummy/script/rails
 - test/dummy/test/functional/home_controller_test.rb
-- test/dummy/test/functional/workflows_controller_test.rb
 - test/dummy/tmp/.gitkeep
+- test/fixtures/delayed_jobs.yml
 - test/fixtures/files/non-ascii.csv
 - test/fixtures/files/plain-text.bad-extension
 - test/fixtures/taverna_player/interactions.yml
 - test/fixtures/taverna_player/run_ports.yml
 - test/fixtures/taverna_player/runs.yml
 - test/fixtures/taverna_player/service_credentials.yml
+- test/fixtures/taverna_player/workflows.yml
 - test/fixtures/users.yml
-- test/fixtures/workflows.yml
 - test/functional/taverna_player/job_queue_controller_test.rb
 - test/functional/taverna_player/runs_controller_test.rb
 - test/functional/taverna_player/service_credentials_controller_test.rb
+- test/functional/taverna_player/workflows_controller_test.rb
 - test/taverna_player_test.rb
 - test/test_helper.rb
 - test/unit/helpers/taverna_player/application_helper_test.rb
 - test/unit/helpers/taverna_player/runs_helper_test.rb
 - test/unit/taverna_player/interaction_test.rb
+- test/unit/taverna_player/model_proxy_test.rb
 - test/unit/taverna_player/run_port_test.rb
 - test/unit/taverna_player/run_test.rb
 - test/unit/taverna_player/service_credential_test.rb