taverna-player 0.7.0 → 0.8.0

checksums.yaml

@@ -1,15 +1,15 @@
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data/.travis.yml

@@ -2,7 +2,7 @@ language: ruby
 rvm:
   - 1.9.3
   - 2.0.0
-  - 2.1.0
+  - 2.1.2
 script:
   - RAILS_ENV=test bundle exec rake db:schema:load
   - bundle exec rake test

data/CHANGES.rdoc

@@ -1,5 +1,12 @@
 = Changes log for Taverna Player
 
+== Version 0.8.0
+
+* Add a note about Taverna Server compatibility to the ReadMe.
+* [SERVINF-457] Clear "waiting for user input" message.
+* Remove odd save! in worker code.
+* Move to use the rubyzip 1.0 API.
+
 == Version 0.7.0
 
 * Refactor full run JSON output.

data/README.rdoc

@@ -26,6 +26,20 @@ It, purposefully, does not:
 * Manage workflows
 * Manage users
 
+== Prerequisites
+
+Taverna Player requires access to a
+{Taverna Server}[http://www.taverna.org.uk/download/server/2-5/] version 2.5
+or later.
+
+== A note about rubyzip
+
+This library uses the new {rubyzip}[https://rubygems.org/gems/rubyzip] API. If
+your code, or any of its dependencies, need the old API then please read the
+<em>Important note</em> in the
+{rubyzip ReadMe}[https://github.com/rubyzip/rubyzip/blob/master/README.md] for
+details of how to get everything working together.
+
 == Getting started
 
 These instructions assume that you are familiar with Rails and its concepts.

data/lib/taverna-player.rb

@@ -21,7 +21,7 @@ require "rails_autolink"
 require "t2-server"
 require "taverna-t2flow"
 require "tmpdir"
-require "zip/zip"
+require "zip"
 
 # Grab everything in the taverna_player directory using the require_all gem.
 require_rel "taverna_player"

data/lib/taverna_player/concerns/zip.rb

@@ -17,7 +17,7 @@ module TavernaPlayer
       extend ActiveSupport::Concern
 
       def read_file_from_zip(zip, file)
-        ::Zip::ZipFile.open(zip) do |z|
+        ::Zip::File.open(zip) do |z|
           z.read(file)
         end
       end

data/lib/taverna_player/version.rb

@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.7.0"
+  VERSION = "0.8.0"
 end

data/lib/taverna_player/worker.rb

@@ -135,7 +135,6 @@ module TavernaPlayer
                 new_int.save
               end
             else
-              waiting = true unless note.has_reply?
               int = Interaction.find_or_initialize_by_run_id_and_serial(@run.id, note.serial)
 
               # Need to catch this here in case some other process has replied.
@@ -177,6 +176,8 @@ module TavernaPlayer
 
                 int.save
               end
+
+              waiting = true unless int.replied?
             end
           end
 
@@ -306,7 +307,7 @@ module TavernaPlayer
 
     def status_message(key)
       @run.status_message_key = key
-      @run.save!
+      @run.save
     end
 
     def cancelled?

data/taverna_player.gemspec

@@ -39,7 +39,7 @@ Gem::Specification.new do |s|
   s.add_dependency "t2-server", "~> 1.1"
   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 "rubyzip", "~> 1.1.4"
   s.add_dependency "coderay", "~> 1.1"
   s.add_dependency "rails_autolink", "~> 1.1.0"
   s.add_dependency "require_all", "~> 1.3.1"

data/test/unit/taverna_player/worker_test.rb

@@ -158,7 +158,7 @@ class WorkerTest < ActiveSupport::TestCase
     assert_not_nil @run.failure_message, "Run's failure message is nil"
   end
 
-  test "cancelled run" do
+  test "immediately cancelled run" do
     # Stub the creation of a run on a Taverna Server with a failure.
     flexmock(T2Server::Server).new_instances do |s|
       s.should_receive(:initialize_run).once.
@@ -176,6 +176,71 @@ class WorkerTest < ActiveSupport::TestCase
     assert_equal :cancelled, @run.state, "Final run state not ':cancelled'"
   end
 
+  test "run cancelled while waiting to start" do
+    # Stub the creation of a run on a Taverna Server.
+    flexmock(T2Server::Server).new_instances do |s|
+      s.should_receive(:initialize_run).once.
+        and_return(URI.parse("http://localhost/run/02"))
+    end
+
+    # Stub the Taverna Server run calls.
+    flexmock(T2Server::Run).new_instances do |r|
+      r.should_receive(:status).and_return(:initialized)
+      r.should_receive(:create_time).and_return(Time.now)
+      r.should_receive(:add_password_credential).and_return(true)
+      r.should_receive(:name=).once.and_return(true)
+      r.should_receive(:start).and_return(false)
+      r.should_receive(:log).once.and_return(0)
+      r.should_receive(:delete).and_return_undefined
+    end
+
+    # Stub the TavernaPlayer::Worker.cancelled? method and set the internal
+    # run model state stop to true.
+    worker = TavernaPlayer::Worker.new(@run)
+    flexmock(worker).should_receive(:cancelled?).once.and_return(true)
+    @run.stop = true
+    @run.save
+
+    assert_equal :pending, @run.state, "Initial run state not ':pending'"
+
+    worker.perform
+
+    assert_equal :cancelled, @run.state, "Final run state not ':cancelled'"
+  end
+
+  test "run cancelled while running" do
+    # Stub the creation of a run on a Taverna Server.
+    flexmock(T2Server::Server).new_instances do |s|
+      s.should_receive(:initialize_run).once.
+        and_return(URI.parse("http://localhost/run/03"))
+    end
+
+    # Stub the Taverna Server run calls.
+    flexmock(T2Server::Run).new_instances do |r|
+      r.should_receive(:status).times(3).and_return(:initialized, :running, :running)
+      r.should_receive(:create_time).and_return(Time.now)
+      r.should_receive(:add_password_credential).and_return(true)
+      r.should_receive(:name=).once.and_return(true)
+      r.should_receive(:start).and_return(true)
+      r.should_receive(:start_time).and_return(Time.now)
+      r.should_receive(:log).once.and_return(0)
+      r.should_receive(:delete).and_return_undefined
+    end
+
+    # Stub the TavernaPlayer::Worker.cancelled? method and set the internal
+    # run model state stop to true.
+    worker = TavernaPlayer::Worker.new(@run)
+    flexmock(worker).should_receive(:cancelled?).once.and_return(true)
+    @run.stop = true
+    @run.save
+
+    assert_equal :pending, @run.state, "Initial run state not ':pending'"
+
+    worker.perform
+
+    assert_equal :cancelled, @run.state, "Final run state not ':cancelled'"
+  end
+
   test "fail in cancelled callback" do
     # Stub the creation of a run on a Taverna Server with a failure.
     flexmock(T2Server::Server).new_instances do |s|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: taverna-player
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.8.0
 platform: ruby
 authors:
 - Robert Haines
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-28 00:00:00.000000000 Z
+date: 2014-06-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -100,14 +100,14 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.9
+        version: 1.1.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.9.9
+        version: 1.1.4
 - !ruby/object:Gem::Dependency
   name: coderay
   requirement: !ruby/object:Gem::Requirement