taverna-player 0.5.0 → 0.6.0
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- data/.gitignore +1 -0
- data/.travis.yml +8 -0
- data/CHANGES.rdoc +47 -0
- data/README.rdoc +43 -3
- data/Rakefile +1 -4
- data/app/assets/stylesheets/taverna_player/coderay.css +30 -20
- data/app/controllers/taverna_player/application_controller.rb +2 -2
- data/app/controllers/taverna_player/job_queue_controller.rb +18 -0
- data/app/models/taverna_player/run.rb +10 -3
- data/app/views/taverna_player/job_queue/index.html.erb +47 -0
- data/app/views/taverna_player/runs/_interaction.html.erb +7 -1
- data/app/views/taverna_player/runs/embedded/new.html.erb +1 -1
- data/config/locales/en.yml +36 -0
- data/config/routes.rb +4 -1
- data/db/migrate/20140226135723_change_taverna_player_runs_status_message_to_use_keys.rb +19 -0
- data/lib/generators/taverna_player/install_generator.rb +6 -1
- data/lib/generators/templates/ReadMe.txt +6 -0
- data/lib/generators/templates/controllers/job_queue_controller.rb +19 -0
- data/lib/generators/templates/player_initializer.rb +8 -0
- data/lib/tasks/delete-cancelled-runs.rake +1 -1
- data/lib/taverna-player.rb +9 -1
- data/lib/taverna_player/concerns/controllers/job_queue_controller.rb +38 -0
- data/lib/taverna_player/concerns/controllers/runs_controller.rb +2 -13
- data/lib/taverna_player/concerns/models/run.rb +22 -9
- data/lib/taverna_player/concerns/models/run_port.rb +5 -0
- data/lib/taverna_player/port_renderer.rb +1 -1
- data/lib/taverna_player/version.rb +1 -1
- data/lib/taverna_player/worker.rb +78 -51
- data/taverna_player.gemspec +7 -5
- data/test/dummy/app/views/home/index.html.erb +1 -1
- data/test/dummy/app/views/layouts/application.html.erb +2 -1
- data/test/dummy/config/application.rb +1 -0
- data/test/dummy/config/initializers/taverna_player.rb +8 -3
- data/test/dummy/config/locales/taverna_player.en.yml +36 -0
- data/test/dummy/db/migrate/20140226143013_change_taverna_player_runs_status_message_to_use_keys.taverna_player.rb +20 -0
- data/test/dummy/db/schema.rb +9 -9
- data/test/dummy/lib/callbacks.rb +1 -5
- data/test/fixtures/files/non-ascii.csv +30 -0
- data/test/fixtures/taverna_player/interactions.yml +4 -1
- data/test/fixtures/taverna_player/runs.yml +6 -1
- data/test/functional/taverna_player/job_queue_controller_test.rb +35 -0
- data/test/functional/taverna_player/runs_controller_test.rb +20 -0
- data/test/functional/taverna_player/service_credentials_controller_test.rb +3 -3
- data/test/test_helper.rb +4 -1
- data/test/unit/helpers/taverna_player/runs_helper_test.rb +20 -1
- data/test/unit/taverna_player/run_port_test.rb +41 -5
- data/test/unit/{utils_test.rb → taverna_player/utils_test.rb} +0 -0
- data/test/unit/taverna_player/worker_test.rb +201 -0
- metadata +67 -18
- data/test/fixtures/files/crassostrea_gigas.csv +0 -737
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#------------------------------------------------------------------------------
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# Copyright (c) 2014 The University of Manchester, UK.
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#
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# BSD Licenced. See LICENCE.rdoc for details.
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#
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# Taverna Player was developed in the BioVeL project, funded by the European
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# Commission 7th Framework Programme (FP7), through grant agreement
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# number 283359.
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#
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# Author: Robert Haines
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#------------------------------------------------------------------------------
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require 'flexmock'
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require 'test_helper'
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class WorkerTest < ActiveSupport::TestCase
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include FlexMock::TestCase
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setup do
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@noop_callback = Proc.new { }
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# Taverna Server config that we need to set here for Travis, etc.
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TavernaPlayer.setup do |config|
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config.server_address = "http://localhost:1111/taverna"
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config.server_username = "taverna"
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config.server_password = "taverna"
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config.server_poll_interval = 0
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config.server_retry_interval = 0
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config.pre_run_callback = @noop_callback
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config.post_run_callback = @noop_callback
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config.run_cancelled_callback = @noop_callback
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config.run_failed_callback = @noop_callback
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end
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# Stuff we can't test yet in TavernaPlayer::Worker.
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flexmock(TavernaPlayer::Worker).new_instances do |w|
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w.should_receive(:download_outputs).and_return_undefined
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w.should_receive(:download_log).and_return_undefined
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w.should_receive(:process_outputs).and_return([])
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end
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@run = taverna_player_runs(:seven)
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@worker = TavernaPlayer::Worker.new(@run)
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end
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test "max attempts should be 1" do
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assert_equal 1, @worker.max_attempts, "Max attempts was not 1."
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end
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test "run a workflow" do
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# Stub the creation of a run on a Taverna Server with a failure first.
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flexmock(T2Server::Server).new_instances do |s|
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s.should_receive(:initialize_run).twice.
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and_raise(T2Server::ServerAtCapacityError).
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and_return(URI.parse("http://localhost/run/01"))
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end
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# Stub the Taverna Server run calls.
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flexmock(T2Server::Run).new_instances do |r|
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r.should_receive(:status).times(4).and_return(:initialized, :running, :running, :finished)
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r.should_receive(:create_time).and_return(Time.now)
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r.should_receive(:add_password_credential).and_return(true)
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r.should_receive(:name=).once.and_return(true)
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r.should_receive(:start).twice.and_return(false, true)
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r.should_receive(:start_time).and_return(Time.now)
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r.should_receive(:notifications).and_return([])
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r.should_receive(:finish_time).and_return(Time.now)
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r.should_receive(:delete).and_return_undefined
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end
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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assert_nil @run.run_id, "Server run ID not nil before creation"
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assert_nil @run.create_time, "Create time not nil before creation"
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assert_nil @run.start_time, "Start time not nil before starting"
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assert_nil @run.finish_time, "Finish time not nil before run"
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@worker.perform
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assert_equal :finished, @run.state, "Final run state not ':finished'"
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assert_equal "01", @run.run_id, "Server run ID not set correctly"
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assert_not_nil @run.create_time, "Create time nil after creation"
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assert_not_nil @run.start_time, "Start time nil after starting"
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assert_not_nil @run.finish_time, "Finish time nil after finishing"
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end
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test "workflow failure" do
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# Stub the creation of a run on a Taverna Server.
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flexmock(T2Server::Server).new_instances do |s|
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s.should_receive(:initialize_run).
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and_return(URI.parse("http://localhost/run/01"))
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end
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# Stub a Taverna Server run calls so it fails.
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flexmock(T2Server::Run).new_instances do |r|
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r.should_receive(:status).and_raise(RuntimeError)
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end
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :failed, @run.state, "Final run state not ':failed'"
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assert_not_nil @run.failure_message, "Run's failure message is nil"
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end
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test "fail in failure handler" do
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# Stub the creation of a run on a Taverna Server with complete failure.
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flexmock(T2Server::Server).new_instances do |s|
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s.should_receive(:initialize_run).once.
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and_raise(RuntimeError)
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end
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# Set a failing failure callback
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TavernaPlayer.run_failed_callback = Proc.new { raise RuntimeError }
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :failed, @run.state, "Final run state not ':failed'"
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assert_not_nil @run.failure_message, "Run's failure message is nil"
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end
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test "cancelled run" do
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# Stub the creation of a run on a Taverna Server with a failure.
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flexmock(T2Server::Server).new_instances do |s|
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s.should_receive(:initialize_run).once.
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and_raise(T2Server::ServerAtCapacityError)
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end
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# Cancel the run.
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@run.stop = true
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@run.save
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :cancelled, @run.state, "Final run state not ':cancelled'"
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end
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test "fail in cancelled callback" do
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# Stub the creation of a run on a Taverna Server with a failure.
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flexmock(T2Server::Server).new_instances do |s|
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s.should_receive(:initialize_run).once.
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and_raise(T2Server::ServerAtCapacityError)
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end
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# Set a failing cancelled callback
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TavernaPlayer.run_cancelled_callback = Proc.new { raise RuntimeError }
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# Cancel the run.
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@run.stop = true
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@run.save
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :failed, @run.state, "Final run state not ':failed'"
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assert_not_nil @run.failure_message, "Run's failure message is nil"
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end
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test "fail in pre run callback" do
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# Set a failing pre_run callback
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TavernaPlayer.pre_run_callback = Proc.new { raise RuntimeError }
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :failed, @run.state, "Final run state not ':failed'"
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assert_not_nil @run.failure_message, "Run's failure message is nil"
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end
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test "fail in post run callback" do
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# Set a failing post_run callback
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TavernaPlayer.post_run_callback = Proc.new { raise RuntimeError }
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :failed, @run.state, "Final run state not ':failed'"
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assert_not_nil @run.failure_message, "Run's failure message is nil"
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end
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test "timed out run" do
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# Stub the creation of a run on a Taverna Server with a timeout.
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flexmock(T2Server::Server).new_instances do |s|
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s.should_receive(:initialize_run).once.
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and_raise(Delayed::WorkerTimeout)
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end
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assert_equal :pending, @run.state, "Initial run state not ':pending'"
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@worker.perform
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assert_equal :timeout, @run.state, "Final run state not ':timeout'"
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end
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end
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: taverna-player
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version: !ruby/object:Gem::Version
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version: 0.
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version: 0.6.0
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prerelease:
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platform: ruby
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authors:
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-
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date: 2014-03-06 00:00:00.000000000 Z
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dependencies:
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name: rails
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 3.0
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version: '3.0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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@@ -42,7 +42,7 @@ dependencies:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 3.0
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version: '3.0'
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- !ruby/object:Gem::Dependency
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name: paperclip
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requirement: !ruby/object:Gem::Requirement
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@@ -50,7 +50,7 @@ dependencies:
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requirements:
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version:
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version: '4.1'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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@@ -58,7 +58,7 @@ dependencies:
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requirements:
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version:
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version: '4.1'
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- !ruby/object:Gem::Dependency
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name: t2-server
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requirement: !ruby/object:Gem::Requirement
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@@ -82,7 +82,7 @@ dependencies:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version:
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version: '4.0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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@@ -90,7 +90,7 @@ dependencies:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version:
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version: '4.0'
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- !ruby/object:Gem::Dependency
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name: daemons
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requirement: !ruby/object:Gem::Requirement
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@@ -130,7 +130,7 @@ dependencies:
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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