taverna-player 0.6.0 → 0.7.0

checksums.yaml

@@ -0,0 +1,15 @@
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+  metadata.gz: !binary |-
+    NDIzMTk5MTVmNTA4MWMzNDUyYWExMjFjMThiZTcxY2IzNDdmNTM1NA==
+  data.tar.gz: !binary |-
+    YzNjZTVjNzBhN2JkYmQxNjBkZWM3NTAwMGU0NmViMDBhYjRiZjc4Ng==
+SHA512:
+  metadata.gz: !binary |-
+    MDNmNGNkMTI4MWI5NDJjYTQ5NGFlZWQ4NDYxMmQ2YjBkMjIwY2MyZDhmZGQw
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+  data.tar.gz: !binary |-
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+    Y2U3N2RkYWUzZWNiMjA5ZDhkNDI2ZWQ3M2VjYzM5NWI5ODg5OGQ=

data/.ruby-gemset

@@ -0,0 +1 @@
+taverna-player

data/.ruby-version

@@ -0,0 +1 @@
+ruby-1.9.3-p484

data/CHANGES.rdoc

@@ -1,5 +1,24 @@
 = Changes log for Taverna Player
 
+== Version 0.7.0
+
+* Refactor full run JSON output.
+* Improve the runs/new JSON output.
+* Add more interaction fields to the JSON output.
+* Fix non-ASCII character in gemspec info.
+* Fix non-ASCII character in README.
+* [TAV-508] Allow workers to run against different servers.
+* [TAV-511] Don't save run log if it's an empty file.
+* Add note about JSON interface to the Readme.
+* Add a note about the API Docs to the Readme.
+* Rework the testing of an empty log file for better testing.
+* Add tests for taverna credentials in env variable.
+* [TAV-512] Fix overzealous file extension restrictions for inputs.
+* Add an alert flash to the test layout.
+* Use flash[:alert] not flash[:error].
+* Recover from failed run creation more gracefully.
+* Bump version of t2-server gem we are using.
+
 == Version 0.6.0
 
 * [TAV-485] Set up separate worker integration test.

data/README.rdoc

@@ -6,9 +6,9 @@ URL::         http://www.taverna.org.uk
 Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
 Copyright::   (c) 2013, 2014 The University of Manchester, UK
 
-{<img src="https://badge.fury.io/rb/taverna-player.png" alt="Gem Version" />}[http://badge.fury.io/rb/taverna-player]
+{<img src="https://badge.fury.io/rb/taverna-player.svg" alt="Gem Version" />}[http://badge.fury.io/rb/taverna-player]
 {<img src="https://codeclimate.com/github/myGrid/taverna-player.png" />}[https://codeclimate.com/github/myGrid/taverna-player]
-{<img src="https://travis-ci.org/myGrid/taverna-player.png?branch=master" alt="Build Status" />}[https://travis-ci.org/myGrid/taverna-player]
+{<img src="https://travis-ci.org/myGrid/taverna-player.svg?branch=master" alt="Build Status" />}[https://travis-ci.org/myGrid/taverna-player]
 {<img src="https://coveralls.io/repos/myGrid/taverna-player/badge.png?branch=master" alt="Coverage Status" />}[https://coveralls.io/r/myGrid/taverna-player?branch=master]
 
 == Synopsis
@@ -154,8 +154,8 @@ And everything should be found by the asset pipeline automatically.
 Make sure you have flash messages in your main layout
 (usually <tt>app/views/layouts/application.html.erb</tt>). For example:
 
-  <p class="notice"><%= notice %></p>
-  <p class="alert"><%= alert %></p>
+  <p id="notice"><%= notice %></p>
+  <p id="alert"><%= alert %></p>
 
 Taverna Player uses delayed_job to run workflows on a Taverna Server. If your
 application is not already using delayed_job then you can install the
@@ -687,7 +687,7 @@ running:
   https://example.com:8443/
 
 The above example shows a https server running on port 8443. If the service is
-on port 80 for http or port 443 for https then you don’t need to specify the
+on port 80 for http or port 443 for https then you don't need to specify the
 port.
 
 If there are services on the same host that require different credentials then
@@ -712,6 +712,25 @@ it is rserve:
 
   rserve://example.com:6311
 
+== The Taverna Player API
+
+There is more information about how you can more closely integrate Taverna
+Player into your host application in the
+{API Documentation}[http://mygrid.github.io/taverna-player].
+
+== Embedding a workflow into another Web site
+
+Workflow runs handled by Taverna Player can be embedded in other Web sites in
+much the same way that media like YouTube videos can be. Documentation on how
+to achieve this
+{is available separately[https://github.com/myGrid/taverna-player/wiki/Embedding].
+
+== Using Taverna Player as a Web Service
+
+As well as providing HTML views to the host application, Taverna Player also
+provides a RESTful Web Service interface. Documentation for this interface
+{is available separately}[https://github.com/myGrid/taverna-player/wiki/JSON-API-Documentation].
+
 == Limitations and to-do list
 
 The most serious limitation is with the Service Credentials. Because Taverna
@@ -731,13 +750,10 @@ moment.
 
 In no particular order:
 
-* Taverna Player as a service. Allow usage of Taverna Player via a fully
-  RESTful interface with JSON and XML support (in progress).
 * User specific (and therefore private) credentials wallet for secure services.
 * Comprehensive Taverna Server administration panel. This would allow admin
   users to view and manage runs directly on the Taverna Server along with
   other such admin tasks.
-* I18n support.
 * oEmbed support (see http://oembed.com/ for more details).
 
 == Support

data/app/views/taverna_player/runs/_info.json.jbuilder

@@ -1,2 +1 @@
-json.extract! run, :id, :name, :workflow_id, :saved_state, :status_message,
-  :start_time, :finish_time
+json.extract! run, :id, :name, :workflow_id, :state, :start_time, :finish_time

data/app/views/taverna_player/runs/_port.json.jbuilder

@@ -0,0 +1 @@
+json.extract! port, :name, :depth, :value_type, :value_size, :path

data/app/views/taverna_player/runs/create.json.jbuilder

@@ -1,3 +1,5 @@
 json.partial! "info", :run => @run
 
-json.partial! "inputs", :inputs => @run.inputs
+json.inputs @run.inputs do |input|
+  json.partial! "port", :port => input
+end

data/app/views/taverna_player/runs/new.json.jbuilder

@@ -1 +1,15 @@
-json.partial! "info", :run => @run
+workflow_title = TavernaPlayer.workflow_proxy.title(@workflow) || "None"
+workflow_inputs = TavernaPlayer.workflow_proxy.inputs(@workflow)
+
+json.run do
+  json.workflow_id @run.workflow_id
+  json.name workflow_title
+  unless workflow_inputs.empty?
+    json.inputs_attributes do
+      json.array! workflow_inputs do |input|
+        json.name input[:name]
+        json.value input[:example]
+      end
+    end
+  end
+end

data/app/views/taverna_player/runs/show.json.jbuilder

@@ -1,16 +1,16 @@
 json.partial! "info", :run => @run
 
-json.partial! "inputs", :inputs => @run.inputs
+json.status_message @run.status_message
 
-if @run.outputs.size > 0
-  json.outputs @run.outputs do |output|
-    json.name output.name
-    json.depth output.depth
-    json.type output.metadata[:type]
-    json.size output.metadata[:size]
-    json.uri run_path(@run) + "/output/#{output.name}"
-  end
+json.inputs @run.inputs do |input|
+  json.partial! "port", :port => input
+end
 
+json.outputs @run.outputs do |output|
+  json.partial! "port", :port => output
+end
+
+if @run.outputs.size > 0
   json.outputs_zip @run.results.url
 end
 
@@ -22,5 +22,7 @@ unless @interaction.nil?
   json.interaction do
     json.serial @interaction.serial
     json.uri interaction_redirect(@interaction)
+    json.data @interaction.data
+    json.reply_uri "#{run_url(@run)}/interaction/#{@interaction.serial}"
   end
 end

data/lib/taverna_player/concerns/controllers/runs_controller.rb

@@ -126,11 +126,18 @@ module TavernaPlayer
         # POST /runs
         def create
           @run = Run.new(params[:run])
+
+          # Set workflow, just in case the create fails and needs to redirect
+          # back to the form
+          @workflow = @run.workflow
+
           if @run.save
             flash[:notice] = "Run was successfully created."
+            respond_with(@run, :status => :created, :location => @run)
+          else
+            flash[:alert] = "Run was not successfully created."
+            respond_with(@run)
           end
-
-          respond_with(@run, :status => :created, :location => @run)
         end
 
         # PUT /runs/1
@@ -146,7 +153,7 @@ module TavernaPlayer
             flash[:notice] = "Run was deleted."
             respond_with(@run)
           else
-            flash[:error] = "Run must be cancelled before deletion."
+            flash[:alert] = "Run must be cancelled before deletion."
             respond_with(@run, :nothing => true, :status => :forbidden) do |format|
               format.html { redirect_to :back }
             end

data/lib/taverna_player/extras/paperclip-spoofing-fix.rb

@@ -0,0 +1,25 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+# We need to override the default Paperclip spoofing detector because it does
+# not allow us to have arbitrary file extensions on files.
+#
+# See https://github.com/thoughtbot/paperclip/issues/1470 and many others.
+module Paperclip
+  class MediaTypeSpoofDetector
+    alias :original_spoofed? :spoofed?
+
+    def spoofed?
+      original_spoofed? ? !(calculated_content_type == "text/plain") : false
+    end
+  end
+end

data/lib/taverna_player/version.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.
 #
@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.6.0"
+  VERSION = "0.7.0"
 end

data/lib/taverna_player/worker.rb

@@ -25,6 +25,13 @@ module TavernaPlayer
     def initialize(run, workflow_file = nil)
       @run = run
       @workflow = workflow_file || TavernaPlayer.workflow_proxy.file(@run.workflow)
+      @server = "Run not yet initialized"
+    end
+
+    # Return the server address that this worker is using. Used mainly for
+    # testing.
+    def server
+      @server.to_s
     end
 
     # This tells delayed_job to only try and complete each run once.
@@ -37,13 +44,12 @@ module TavernaPlayer
 
       status_message("connect")
 
-      server_uri = URI.parse(TavernaPlayer.server_address)
-      credentials = T2Server::HttpBasic.new(TavernaPlayer.server_username,
-        TavernaPlayer.server_password)
+      @server = URI.parse(ENV["TAVERNA_URI"] || TavernaPlayer.server_address)
+      credentials = server_credentials
       conn_params = TavernaPlayer.server_connection
 
       begin
-        server = T2Server::Server.new(server_uri, conn_params)
+        server = T2Server::Server.new(@server, conn_params)
         wkf = File.read(@workflow)
 
         # Try and create the run bearing in mind that the server might be at
@@ -199,6 +205,20 @@ module TavernaPlayer
 
     private
 
+    # Get the credentials for the server
+    def server_credentials
+      creds = ENV["TAVERNA_CREDENTIALS"]
+
+      if creds.nil?
+        user = TavernaPlayer.server_username
+        pass = TavernaPlayer.server_password
+      else
+        user, pass = creds.split(':')
+      end
+
+      T2Server::HttpBasic.new(user, pass)
+    end
+
     # Run the specified callback and return false on error so that we know to
     # return out of the worker code completely.
     def run_callback(cb, message)
@@ -220,9 +240,12 @@ module TavernaPlayer
       Dir.mktmpdir(run.id, Rails.root.join("tmp")) do |tmp_dir|
         tmp_file_name = File.join(tmp_dir, "log.txt")
         begin
-          run.log(tmp_file_name)
-          @run.log = File.new(tmp_file_name)
-          @run.save
+          # Only save the log file if it's not empty so as not to confuse
+          # Paperclip
+          unless run.log(tmp_file_name) == 0
+            @run.log = File.new(tmp_file_name)
+            @run.save
+          end
         rescue T2Server::AttributeNotFoundError
           # We don't care if there's no log but we do want to catch the error!
         end

data/taverna_player.gemspec

@@ -25,7 +25,7 @@ Gem::Specification.new do |s|
     "Workflows using Taverna Server. Taverna Player surfaces a workflow in "\
     "three ways: As a Web interface in the browser; As an embeddable widget "\
     "to be included in any other Web page; As a REST-based Web Service. All "\
-    "three modes provide functionality to fully configure a workflow’s "\
+    "three modes provide functionality to fully configure a workflow's "\
     "inputs; run the workflow on a Taverna Server; collect workflow outputs, "\
     "logs and messages; and present the results in an appropriate manner."
   s.license     = "BSD"
@@ -36,7 +36,7 @@ Gem::Specification.new do |s|
   s.add_dependency "rails", "~> 3.2.12"
   s.add_dependency "jquery-rails", "~> 3.0"
   s.add_dependency "paperclip", "~> 4.1"
-  s.add_dependency "t2-server", "~> 1.0.0"
+  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"

data/test/dummy/app/views/layouts/application.html.erb

@@ -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.
   #
@@ -33,6 +33,7 @@
 	</p>
 
 	<p id="notice"><%= notice %></p>
+	<p id="alert"><%= alert %></p>
 
 	<%= yield %>
 

data/test/fixtures/files/plain-text.bad-extension

@@ -0,0 +1 @@
+This is a plain text file with a non-standard extension!

data/test/functional/taverna_player/runs_controller_test.rb

@@ -161,6 +161,15 @@ module TavernaPlayer
         "Did not render with the correct layout"
     end
 
+    test "should fail to create run via browser" do
+      assert_no_difference("Run.count") do
+        post :create, :run => { :workflow_id => @workflow.id, :name => nil }
+      end
+
+      assert_equal "Run was not successfully created.", flash[:alert],
+        "Incorrect or missing flash notice"
+    end
+
     test "should create run via browser" do
       assert_difference("Run.count") do
         post :create, :run => { :workflow_id => @workflow.id }
@@ -244,7 +253,7 @@ module TavernaPlayer
           delete :destroy, :id => @run1, :use_route => :taverna_player
       end
 
-      assert_equal "Run must be cancelled before deletion.", flash[:error],
+      assert_equal "Run must be cancelled before deletion.", flash[:alert],
         "Incorrect or missing flash notice"
       assert_response :redirect, "Response was not a redirect"
       assert_redirected_to runs_path, "Did not redirect correctly"
@@ -256,7 +265,7 @@ module TavernaPlayer
           delete :destroy, :id => @run1, :format => :json
       end
 
-      assert_equal "Run must be cancelled before deletion.", flash[:error],
+      assert_equal "Run must be cancelled before deletion.", flash[:alert],
         "Incorrect or missing flash notice"
       assert_response :forbidden, "Response was not forbidden"
     end

data/test/unit/taverna_player/run_port_test.rb

@@ -478,5 +478,23 @@ module TavernaPlayer
         "Incorrect filename generated"
       refute @port7.filename.ends_with?(".zip"), "Filename has 'zip' suffix"
     end
+
+    test "non-standard extensions for plain text files on input ports" do
+      file = fixture_file_upload "/files/plain-text.bad-extension"
+      assert_difference("RunPort::Input.count", 1, "Port was not created") do
+        port = RunPort::Input.create(:name => "test_port", :file => file)
+        assert port.valid?, "Port is invalid"
+        refute port.file.blank?, "File should be present"
+      end
+    end
+
+    test "non-standard extensions for plain text files on output ports" do
+      file = fixture_file_upload "/files/plain-text.bad-extension"
+      assert_difference("RunPort::Output.count", 1, "Port was not created") do
+        port = RunPort::Output.create(:name => "test_port", :file => file)
+        assert port.valid?, "Port is invalid"
+        refute port.file.blank?, "File should be present"
+      end
+    end
   end
 end

data/test/unit/taverna_player/worker_test.rb

@@ -16,12 +16,14 @@ require 'test_helper'
 class WorkerTest < ActiveSupport::TestCase
   include FlexMock::TestCase
 
+  SERVER_ADDRESS = "http://localhost:1111/taverna"
+
   setup do
     @noop_callback = Proc.new { }
 
     # Taverna Server config that we need to set here for Travis, etc.
     TavernaPlayer.setup do |config|
-      config.server_address = "http://localhost:1111/taverna"
+      config.server_address = SERVER_ADDRESS
       config.server_username = "taverna"
       config.server_password = "taverna"
       config.server_poll_interval = 0
@@ -35,7 +37,6 @@ class WorkerTest < ActiveSupport::TestCase
     # Stuff we can't test yet in TavernaPlayer::Worker.
     flexmock(TavernaPlayer::Worker).new_instances do |w|
       w.should_receive(:download_outputs).and_return_undefined
-      w.should_receive(:download_log).and_return_undefined
       w.should_receive(:process_outputs).and_return([])
     end
 
@@ -47,6 +48,41 @@ class WorkerTest < ActiveSupport::TestCase
     assert_equal 1, @worker.max_attempts, "Max attempts was not 1."
   end
 
+  test "server address not set to a uri initially" do
+    assert_raise(URI::InvalidURIError) do
+      URI.parse(@worker.server)
+    end
+  end
+
+  test "server address and creds from config" do
+    # Stub the creation of a run on a Taverna Server so it fails.
+    flexmock(T2Server::Server).new_instances do |s|
+      s.should_receive(:initialize_run).once.
+        and_raise(RuntimeError)
+    end
+
+    @worker.perform
+
+    assert_equal SERVER_ADDRESS, @worker.server.to_s,
+      "Server address not read from config."
+  end
+
+  test "server address and creds from env" do
+    ENV["TAVERNA_URI"] = "https://localhost:8080/taverna"
+    ENV["TAVERNA_CREDENTIALS"] = "taverna:taverna"
+
+    # Stub the creation of a run on a Taverna Server so it fails.
+    flexmock(T2Server::Server).new_instances do |s|
+      s.should_receive(:initialize_run).once.
+        and_raise(RuntimeError)
+    end
+
+    @worker.perform
+
+    assert_equal ENV["TAVERNA_URI"], @worker.server.to_s,
+      "Server address not read from env."
+  end
+
   test "run a workflow" do
     # Stub the creation of a run on a Taverna Server with a failure first.
     flexmock(T2Server::Server).new_instances do |s|
@@ -65,6 +101,7 @@ class WorkerTest < ActiveSupport::TestCase
       r.should_receive(:start_time).and_return(Time.now)
       r.should_receive(:notifications).and_return([])
       r.should_receive(:finish_time).and_return(Time.now)
+      r.should_receive(:log).once.and_return(0)
       r.should_receive(:delete).and_return_undefined
     end
 

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: taverna-player
 version: !ruby/object:Gem::Version
-  version: 0.6.0
-  prerelease: 
+  version: 0.7.0
 platform: ruby
 authors:
 - Robert Haines
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-06 00:00:00.000000000 Z
+date: 2014-04-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -30,7 +27,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: jquery-rails
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -38,7 +34,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -46,7 +41,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: paperclip
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -54,7 +48,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -62,23 +55,20 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: t2-server
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '1.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '1.1'
 - !ruby/object:Gem::Dependency
   name: delayed_job_active_record
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -86,7 +76,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -94,7 +83,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -102,7 +90,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -110,7 +97,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -118,7 +104,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -126,7 +111,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: coderay
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -134,7 +118,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -142,7 +125,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rails_autolink
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -150,7 +132,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -158,7 +139,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: require_all
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -166,7 +146,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -174,7 +153,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: jbuilder
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -182,7 +160,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -190,7 +167,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: pmrpc-rails
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -198,7 +174,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -206,7 +181,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: sqlite3
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -214,7 +188,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -222,7 +195,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -230,7 +202,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -238,7 +209,6 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: flexmock
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -246,7 +216,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
@@ -255,7 +224,7 @@ description: ! 'Taverna Player is a Ruby on Rails plugin to run Taverna Workflow
   using Taverna Server. Taverna Player surfaces a workflow in three ways: As a Web
   interface in the browser; As an embeddable widget to be included in any other Web
   page; As a REST-based Web Service. All three modes provide functionality to fully
-  configure a workflow’s inputs; run the workflow on a Taverna Server; collect workflow
+  configure a workflow''s inputs; run the workflow on a Taverna Server; collect workflow
   outputs, logs and messages; and present the results in an appropriate manner.'
 email:
 - support@mygrid.org.uk
@@ -264,6 +233,8 @@ extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- .ruby-gemset
+- .ruby-version
 - .travis.yml
 - CHANGES.rdoc
 - Gemfile
@@ -291,10 +262,10 @@ files:
 - app/views/taverna_player/runs/_info.html.erb
 - app/views/taverna_player/runs/_info.json.jbuilder
 - app/views/taverna_player/runs/_inputs.html.erb
-- app/views/taverna_player/runs/_inputs.json.jbuilder
 - app/views/taverna_player/runs/_interaction.html.erb
 - app/views/taverna_player/runs/_outputs.html.erb
 - app/views/taverna_player/runs/_poll.html.erb
+- app/views/taverna_player/runs/_port.json.jbuilder
 - app/views/taverna_player/runs/create.json.jbuilder
 - app/views/taverna_player/runs/embedded/_button.html.erb
 - app/views/taverna_player/runs/embedded/_info.html.erb
@@ -378,6 +349,7 @@ files:
 - lib/taverna_player/concerns/utils.rb
 - lib/taverna_player/concerns/zip.rb
 - lib/taverna_player/engine.rb
+- lib/taverna_player/extras/paperclip-spoofing-fix.rb
 - lib/taverna_player/model_proxy.rb
 - lib/taverna_player/port_renderer.rb
 - lib/taverna_player/render_callbacks.rb
@@ -463,6 +435,7 @@ files:
 - test/dummy/test/functional/workflows_controller_test.rb
 - test/dummy/tmp/.gitkeep
 - 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
@@ -488,33 +461,26 @@ files:
 homepage: http://www.taverna.org.uk
 licenses:
 - BSD
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 94152040374779137
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 94152040374779137
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.21
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Taverna Player is a rails plugin to run Taverna Workflows.
 test_files:
 - test/dummy/Rakefile
@@ -594,6 +560,7 @@ test_files:
 - test/dummy/test/functional/workflows_controller_test.rb
 - test/dummy/tmp/.gitkeep
 - 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

data/app/views/taverna_player/runs/_inputs.json.jbuilder

@@ -1,8 +0,0 @@
-json.inputs inputs do |input|
-  json.name input.name
-  if input.file.blank?
-    json.value input.value
-  else
-    json.file_uri input.file.url
-  end
-end