taverna-player 0.4.0 → 0.5.0

data/CHANGES.rdoc

@@ -1,5 +1,23 @@
 = Changes log for Taverna Player
 
+== Version 0.5.0
+
+* [TAV-480] Refactor output port downloading.
+* [TAV-480] Add a method to download input ports.
+* [TAV-475] Add RunPort::value_size= setter.
+* [TAV-475] Add RunPort::value_type= setter.
+* Use the new metadata setters in the worker code.
+* Add some tests for internal list code.
+* [TAV-482] Refactor Zip operations into a concern.
+* Fix typo in RunPort#value_is_text? documentation.
+* Add RunPort#value_is_error? method.
+* [TAV-483] Fix getting error values from deep values.
+* Minor fix in RunPort#deep_value.
+* [TAV-484] RunPort#value returns zipped lists.
+* Add RunPort#filename.
+* Refactor RunsController.
+* [TAV-482] Refactor worker code to use Zip concern.
+
 == Version 0.4.0
 
 * [TAV-466] Add port metadata to JSON output.

data/LICENCE.rdoc

@@ -1,4 +1,4 @@
-Copyright (c) 2013 The University of Manchester, UK.
+Copyright (c) 2013, 2014 The University of Manchester, UK.
 
 All rights reserved.
 

data/README.rdoc

@@ -4,7 +4,7 @@ Authors::     Robert Haines
 Contact::     mailto:support@mygrid.org.uk
 URL::         http://www.taverna.org.uk
 Licence::     BSD (See LICENCE or http://www.opensource.org/licenses/bsd-license.php)
-Copyright::   (c) 2013 The University of Manchester, UK
+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://codeclimate.com/github/myGrid/taverna-player.png" />}[https://codeclimate.com/github/myGrid/taverna-player]

data/app/models/taverna_player/run_port.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.
 #
@@ -28,6 +28,15 @@ module TavernaPlayer
     # Convert this port's name to a more presentable form. In practice this
     # means converting underscores (_) to spaces, while preserving case.
 
+    ##
+    # :method: filename
+    # :call-seq:
+    #   filename -> string
+    #
+    # Return a suitable filename to be used when saving data from a port. This
+    # is generated by concatenating the port's name onto the end of the name
+    # of its parent run.
+
     ##
     # :method: value_preview
     # :call-seq:
@@ -39,13 +48,22 @@ module TavernaPlayer
     ##
     # :method: value_size
     # :call-seq:
-    #   value_size -> string
-    #   value_size(indices) -> string
+    #   value_size -> integer
+    #   value_size(indices) -> integer
     #
     # Get the size (in bytes) of the value held in this port. Pass in a list
     # of indices if it is a list port. Returns nil if there is no port
     # metadata.
 
+    ##
+    # :method: value_size=
+    # :call-seq:
+    #   value_size=
+    #
+    # Set the size (in bytes) of the value held in this port. Pass in a list
+    # of sizes if it is a list port. This method does nothing if the depth of
+    # the input list does not match that of the port itself.
+
     ##
     # :method: value_type
     # :call-seq:
@@ -57,16 +75,34 @@ module TavernaPlayer
     # metadata so if you create a port and put any other type of data in then
     # you should adjust the metadata to match.
 
+    ##
+    # :method: value_type=
+    # :call-seq:
+    #   value_type=
+    #
+    # Set the MIME type of the value held in this port. Pass in a list of
+    # types if it is a list port. This method does nothing if the depth of
+    # the input list does not match that of the port itself.
+
     ##
     # :method: value_is_text?
     # :call-seq:
-    #   value_is_text? -> string
-    #   value_is_text?(indices) -> string
+    #   value_is_text? -> boolean
+    #   value_is_text?(indices) -> boolean
     #
     # Is the type of the value held in this port some sort of text? This
     # returns true if the media type section of the MIME type is "text". Pass
     # in a list of indices if it is a list port.
 
+    ##
+    # :method: value_is_error?
+    # :call-seq:
+    #   value_is_error? -> boolean
+    #   value_is_error?(indices) -> boolean
+    #
+    # Is the type of the value held in this port an error? Pass in a list of
+    # indices if it is a list port.
+
     ##
     # :method: value
     # :call-seq:
@@ -119,9 +155,12 @@ module TavernaPlayer
     #    :type => ["text/plain", "image/png"]
     #  }
     #
-    # <b>Note:</b> By default Taverna Player only uses this field on outputs.
+    # <b>Note 1:</b> By default Taverna Player only uses this field on outputs.
     # It is provided as a field for inputs too as a convenience for
     # implementors and for possible future use.
+    #
+    # <b>Note 2:</b> It is preferable to use the #value_size= and #value_type=
+    # methods to set this information most of the time.
 
   end
 

data/config/routes.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.
 #
@@ -20,6 +20,7 @@ TavernaPlayer::Engine.routes.draw do
       scope "download" do
         get "log", :action => "download_log"
         get "results", :action => "download_results"
+        get "input/:port", :action => "download_input"
         get "output/:port", :action => "download_output"
       end
 

data/lib/taverna_player/concerns/controllers/runs_controller.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.
 #
@@ -26,6 +26,7 @@ module TavernaPlayer
           before_filter :find_runs, :only => [ :index ]
           before_filter :find_run, :except => [ :index, :new, :create ]
           before_filter :find_workflow, :only => [ :new ]
+          before_filter :find_port, :only => [ :download_input, :download_output, :input, :output ]
           before_filter :setup_new_run, :only => :new
           before_filter :set_run_user, :only => :create
           before_filter :filter_update_parameters, :only => :update
@@ -49,6 +50,10 @@ module TavernaPlayer
             @workflow = TavernaPlayer.workflow_proxy.class_name.find(params[:workflow_id])
           end
 
+          def find_port
+            @port = RunPort.find_by_run_id_and_name(@run.id, params[:port])
+          end
+
           def setup_new_run
             @run = Run.new(:workflow_id => @workflow.id)
             @run.embedded = true if params[:embedded] == "true"
@@ -72,11 +77,14 @@ module TavernaPlayer
             @interaction = Interaction.find_by_run_id_and_serial(@run.id, params[:serial])
           end
 
-          # Read the data from the results zip file.
-          def read_from_zip(file)
-            Zip::ZipFile.open(@run.results.path) do |zip|
-              zip.read(file)
-            end
+          # Download an input or output port as an "attachment" (i.e. not
+          # "inline").
+          def download_port
+            # If there is no such port then return a 404.
+            raise ActionController::RoutingError.new('Not Found') if @port.nil?
+
+            type = @port.depth == 0 ? @port.value_type : "application/zip"
+            send_data @port.value, :type => type, :filename => @port.filename
           end
 
           # Choose a layout for the page depending on action and embedded status.
@@ -183,34 +191,23 @@ module TavernaPlayer
             :filename => "#{@run.name}-all-results.zip"
         end
 
+        # GET /runs/1/download/input/:port
+        def download_input
+          download_port
+        end
+
         # GET /runs/1/download/output/:port
         def download_output
-          output = RunPort::Output.find_by_run_id_and_name(@run.id, params[:port])
-
-          # If there is no such output port then return a 404.
-          raise ActionController::RoutingError.new('Not Found') if output.nil?
-
-          if output.file.blank?
-            send_data output.value, :type => "text/plain",
-              :filename => "#{@run.name}-#{output.name}.txt"
-          else
-            send_file output.file.path, :type => output.file.content_type,
-              :filename => "#{@run.name}-#{output.file_file_name}"
-          end
+          download_port
         end
 
         # GET /runs/1/input/*
         def input
-          input = RunPort::Input.find_by_run_id_and_name(@run.id, params[:port])
-
           # If there is no such input port then return a 404.
-          raise ActionController::RoutingError.new('Not Found') if input.nil?
+          raise ActionController::RoutingError.new('Not Found') if @port.nil?
 
-          if input.file.blank?
-            send_data input.value, :disposition => "inline"
-          else
-            send_file input.file.path, :disposition => "inline"
-          end
+          send_data @port.value, :type => @port.value_type,
+            :disposition => "inline"
         end
 
         # GET /runs/1/output/*
@@ -222,38 +219,15 @@ module TavernaPlayer
             path = params[:path].split("/").map { |p| p.to_i }
           end
 
-          output = RunPort::Output.find_by_run_id_and_name(@run.id, params[:port])
-
           # If there is no such output port or the path is the wrong depth then
           # return a 404.
-          if output.nil? || path.length != output.depth
+          if @port.nil? || path.length != @port.depth
             raise ActionController::RoutingError.new('Not Found')
           end
 
-          # A singleton should just return the value (if it's small enough) or the
-          # file if it's bigger. If it's a value in the database then it'll always
-          # be a text value, although not necessarily "plain".
-          if output.depth == 0 && !output.value.blank?
-            send_data output.value, :disposition => "inline",
-              :type => output.metadata[:type]
-          else
-          # We need to rebuild the path indices into a string here (and can't
-          # re-use the params[:path] variable directly) because files are
-          # indexed from one in the zip we get back from Server, not zero.
-            path_s = path.map { |p| p += 1 }.join("/")
-            file = path_s.blank? ? "#{output.name}" : "#{output.name}/#{path_s}"
-            type = recurse_into_lists(output.metadata[:type], path)
-
-            # If it's an error, then we need to further hack the file path and
-            # content type.
-            if type == "application/x-error"
-              file += ".error"
-              type = "text/plain"
-            end
-
-            send_data read_from_zip(file), :type => type,
-              :disposition => "inline"
-          end
+          # Just need to mangle the MIME type when sending error messages.
+          type = @port.value_is_error?(path) ? "text/plain" : @port.value_type(path)
+          send_data @port.value(path), :type => type, :disposition => "inline"
         end
 
         # GET /runs/1/interaction/:int_id

data/lib/taverna_player/concerns/models/run_port.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.
 #
@@ -18,6 +18,7 @@ module TavernaPlayer
         extend ActiveSupport::Concern
 
         include TavernaPlayer::Concerns::Utils
+        include TavernaPlayer::Concerns::Zip
 
         included do
 
@@ -80,14 +81,13 @@ module TavernaPlayer
           end
 
           def deep_value(index)
-            path = index.map { |j| j += 1 }.join("/")
+            # Need to mangle the path here in two ways:
+            # * Files are indexed from 1 (not zero) in the output zip files.
+            # * Errors are saved to a file with a '.error' suffix.
+            path = index.map { |i| i + 1 }.join("/")
+            path += ".error" if value_is_error?(index)
 
-            data = String.new
-            Zip::ZipFile.open(file.path) do |zip|
-              data = zip.read("#{path}")
-            end
-
-            data
+            read_file_from_zip(file.path, path)
           end
 
           def value_metadata(field, *indices)
@@ -96,38 +96,66 @@ module TavernaPlayer
             recurse_into_lists(metadata[field], index)
           end
 
+          def set_value_metadata(field, value)
+            return unless depth == list_depth(value)
+
+            md = metadata
+            md = Hash.new if md.nil?
+            md[field] = value
+            update_attribute(:metadata, md)
+          end
+
         end # included
 
         def display_name
           name.gsub('_', ' ')
         end
 
+        def filename
+          port_file = depth == 0 ? name : "#{name}.zip"
+          "#{run.name}-#{port_file}"
+        end
+
         def value_type(*indices)
           value_metadata(:type, *indices) || "text/plain"
         end
 
+        def value_type=(type)
+          set_value_metadata(:type, type)
+        end
+
         def value_is_text?(*indices)
           type = value_type(*indices)
           type.starts_with?("text")
         end
 
+        def value_is_error?(*indices)
+          value_type(*indices) == "application/x-error"
+        end
+
         def value_size(*indices)
           value_metadata(:size, *indices)
         end
 
+        def value_size=(size)
+          set_value_metadata(:size, size)
+        end
+
         def value_preview
           self[:value]
         end
 
         def value(*indices)
+          file_path = file.path
           if depth == 0
-            if file.path.blank?
+            if file_path.blank?
               self[:value]
             else
-              value_is_text? ? File.read(file.path) : File.binread(file.path)
+              value_is_text? ? File.read(file_path) : File.binread(file_path)
             end
           else
-            deep_value([*indices].flatten)
+            index = [*indices].flatten
+            index.empty? ? File.binread(file_path) : deep_value(index)
           end
         end
 

data/lib/taverna_player/concerns/utils.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.
 #
@@ -25,6 +25,13 @@ module TavernaPlayer
         recurse_into_lists(list[i], indexes)
       end
 
+      # Sometimes we need to test an array's depth to check that it matches a
+      # port's depth. An empty list has depth 1, because it is a list.
+      def list_depth(list, depth = 0)
+        return depth if !list.is_a?(Array)
+        list.empty? ? depth + 1 : list.map { |l| list_depth(l, depth + 1) }.max
+      end
+
     end
   end
 end

data/lib/taverna_player/concerns/zip.rb

@@ -0,0 +1,27 @@
+#------------------------------------------------------------------------------
+# 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
+#------------------------------------------------------------------------------
+
+module TavernaPlayer
+  module Concerns
+    module Zip
+
+      extend ActiveSupport::Concern
+
+      def read_file_from_zip(zip, file)
+        ::Zip::ZipFile.open(zip) do |z|
+          z.read(file)
+        end
+      end
+
+    end
+  end
+end

data/lib/taverna_player/version.rb

@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.4.0"
+  VERSION = "0.5.0"
 end

data/lib/taverna_player/worker.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.
 #
@@ -13,6 +13,7 @@
 module TavernaPlayer
   class Worker
     include TavernaPlayer::Concerns::Callback
+    include TavernaPlayer::Concerns::Zip
 
     # How to get the interaction presentation frame out of the interaction page.
     INTERACTION_REGEX = /document\.getElementById\(\'presentationFrame\'\)\.src = \"(.+)\";/
@@ -249,13 +250,11 @@ module TavernaPlayer
           tmp_file_name = File.join(tmp_dir, port.name)
 
           if port.depth == 0
-            Zip::ZipFile.open(@run.results.path) do |zip|
-             if port.type =~ /text/
-                output.value = zip.read(port.name)
-              else
-                port_name = port.error? ? "#{port.name}.error" : port.name
-                output.file = singleton_output(port_name, tmp_file_name, zip)
-              end
+            if port.type =~ /text/
+              output.value = read_file_from_zip(@run.results.path, port.name)
+            else
+              port_name = port.error? ? "#{port.name}.error" : port.name
+              output.file = singleton_output(port_name, tmp_file_name)
             end
           else
             # TODO: Need to rework this so it's not just re-downloading the
@@ -264,10 +263,9 @@ module TavernaPlayer
             output.file = File.new("#{tmp_file_name}.zip")
           end
 
-          output.metadata = {
-            :size => port.size,
-            :type => port.type
-          }
+          # Set the output port size and type metadata.
+          output.value_type = port.type
+          output.value_size = port.size
 
           outputs << output
         end
@@ -276,9 +274,9 @@ module TavernaPlayer
       outputs
     end
 
-    def singleton_output(name, tmp_file, zip)
+    def singleton_output(name, tmp_file)
       File.open(tmp_file, "wb") do |file|
-        file.write zip.read(name)
+        file.write read_file_from_zip(@run.results.path, name)
       end
 
       File.new(tmp_file)

data/taverna_player.gemspec

@@ -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.
 #

data/test/fixtures/taverna_player/run_ports.yml

@@ -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.
 #
@@ -60,3 +60,10 @@ six:
   run_id: 2
   depth: 2
   metadata: "---\n:size:\n- - 15\n  - 20\n- - 17\n  - 22\n- - 19\n  - 24\n:type:\n- - text/plain\n  - text/plain\n- - text/plain\n  - text/plain\n- - text/plain\n  - text/plain\n"
+
+seven:
+  name: OUT_Error
+  port_type: TavernaPlayer::RunPort::Output
+  run_id: 2
+  depth: 0
+  metadata: "---\n:size: 718\n:type: application/x-error"

data/test/functional/taverna_player/runs_controller_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.
 #
@@ -94,6 +94,12 @@ module TavernaPlayer
           :id => "1" }, {}, {}, "Did not route correctly"
     end
 
+    test "should route to input port download" do
+      assert_routing "/runs/3/download/input/IN_Value",
+        { :controller => "taverna_player/runs", :action => "download_input",
+          :id => "3", :port => "IN_Value" }, {}, {}, "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",
@@ -317,5 +323,61 @@ module TavernaPlayer
       assert_equal "New name", assigns(:run).name, "Run name not updated"
       assert_response :success, "Response was not success"
     end
+
+    test "should get run input" do
+      get :input, :id => @run3, :port => "IN_Value"
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:port), "Did not assign a valid port instance"
+      assert_not_nil response.headers["Content-Disposition"],
+        "Content-Disposition header not set in response"
+      assert_equal response.headers["Content-Disposition"], "inline",
+        "Content-Disposition should be set to 'inline'"
+      assert_not_nil response.headers["Content-Type"],
+        "Content-Type header not set in response"
+    end
+
+    test "should download run input" do
+      get :download_input, :id => @run3, :port => "IN_Value"
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:port), "Did not assign a valid port instance"
+      assert_not_nil response.headers["Content-Disposition"],
+        "Content-Disposition header not set in response"
+      assert response.headers["Content-Disposition"].include?("attachment"),
+        "Content-Disposition should be set to 'attachment'"
+      assert response.headers["Content-Disposition"].include?("filename="),
+        "Content-Disposition should provide a filename"
+      assert_not_nil response.headers["Content-Type"],
+        "Content-Type header not set in response"
+    end
+
+    test "should get run output" do
+      get :output, :id => @run1, :port => "Message"
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:port), "Did not assign a valid port instance"
+      assert_not_nil response.headers["Content-Disposition"],
+        "Content-Disposition header not set in response"
+      assert_equal response.headers["Content-Disposition"], "inline",
+        "Content-Disposition should be set to 'inline'"
+      assert_not_nil response.headers["Content-Type"],
+        "Content-Type header not set in response"
+    end
+
+    test "should download run output" do
+      get :download_output, :id => @run1, :port => "Message"
+      assert_response :success, "Response was not success"
+      assert_not_nil assigns(:run), "Did not assign a valid run instance"
+      assert_not_nil assigns(:port), "Did not assign a valid port instance"
+      assert_not_nil response.headers["Content-Disposition"],
+        "Content-Disposition header not set in response"
+      assert response.headers["Content-Disposition"].include?("attachment"),
+        "Content-Disposition should be set to 'attachment'"
+      assert response.headers["Content-Disposition"].include?("filename="),
+        "Content-Disposition should provide a filename"
+      assert_not_nil response.headers["Content-Type"],
+        "Content-Type header not set in response"
+    end
   end
 end

data/test/unit/taverna_player/run_port_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.
 #
@@ -20,6 +20,7 @@ module TavernaPlayer
       @port3 = taverna_player_run_ports(:three)
       @port5 = taverna_player_run_ports(:five)
       @port6 = taverna_player_run_ports(:six)
+      @port7 = taverna_player_run_ports(:seven)
     end
 
     test "run port inheritance types" do
@@ -326,6 +327,34 @@ module TavernaPlayer
       assert_nil port.value_size, "Unspecified size should return nil"
     end
 
+    test "set singleton value types" do
+      port = RunPort::Input.create(:depth => 0, :name => "test_port")
+
+      port.value_type = "text/html"
+      port.save
+      assert_equal "text/html", port.value_type,
+        "Value type was not set correctly"
+
+      port.value_type = ["text/plain", "text/plain"]
+      port.save
+      assert_equal "text/html", port.value_type,
+        "Value type was changed incorrectly"
+    end
+
+    test "set deep value types" do
+      port = RunPort::Input.create(:depth => 1, :name => "test_port")
+
+      port.value_type = ["text/plain", "text/plain"]
+      port.save
+      assert_equal ["text/plain", "text/plain"], port.value_type,
+        "Value type was not set correctly"
+
+      port.value_type = "text/html"
+      port.save
+      assert_equal ["text/plain", "text/plain"], port.value_type,
+        "Value type was changed incorrectly"
+    end
+
     test "detecting text values" do
       assert @port1.value_is_text?, "Value not detected as text"
       assert @port2.value_is_text?(0), "Value not detected as text"
@@ -335,6 +364,14 @@ module TavernaPlayer
       refute @port2.value_is_text?(2), "Value detected as text"
     end
 
+    test "detecting error values" do
+      refute @port1.value_is_error?, "Value detected as an error"
+      refute @port2.value_is_error?(0), "Value detected as an error"
+      assert @port2.value_is_error?(2), "Value not detected as an error"
+      refute @port6.value_is_error?(0, 1), "Value detected as an error"
+      assert @port7.value_is_error?, "Value not detected as an error"
+    end
+
     test "get value sizes" do
       assert_equal 13, @port1.value_size, "Value size not 13"
       assert_equal 974, @port2.value_size(2), "Value size not 974"
@@ -343,6 +380,32 @@ module TavernaPlayer
       assert_equal 24, @port6.value_size([2, 1]), "Value size not 24"
     end
 
+    test "set singleton value sizes" do
+      port = RunPort::Input.create(:depth => 0, :name => "test_port")
+      assert_nil port.value_size, "Unspecified size should return nil"
+
+      port.value_size = 12
+      port.save
+      assert_equal 12, port.value_size, "Value size was not set correctly"
+
+      port.value_size = [1, 2]
+      port.save
+      assert_equal 12, port.value_size, "Value size was changed incorrectly"
+    end
+
+    test "set deep value sizes" do
+      port = RunPort::Input.create(:depth => 1, :name => "test_port")
+      assert_nil port.value_size, "Unspecified size should return nil"
+
+      port.value_size = [1, 2]
+      port.save
+      assert_equal [1, 2], port.value_size, "Value size was not set correctly"
+
+      port.value_size = 12
+      port.save
+      assert_equal [1, 2], port.value_size, "Value size was changed incorrectly"
+    end
+
     test "value methods should not alter input parameters" do
       index = [1, 1]
       index_saved = index.dup
@@ -356,5 +419,28 @@ module TavernaPlayer
       @port6.value_size(index)
       assert_equal index_saved, index, "Parameter index was altered"
     end
+
+    test "port filenames" do
+      assert_equal "Test run 1-Message", @port1.filename,
+        "Incorrect filename generated"
+      refute @port1.filename.ends_with?(".zip"), "Filename has 'zip' suffix"
+      assert_equal "Test run 2-OUT.zip", @port2.filename,
+        "Incorrect filename generated"
+      assert @port2.filename.ends_with?(".zip"),
+        "Filename missing 'zip' suffix"
+      assert_equal "Test run 3-IN_Value", @port3.filename,
+        "Incorrect filename generated"
+      refute @port3.filename.ends_with?(".zip"), "Filename has 'zip' suffix"
+      assert_equal "Test run 4-Long_N_unnecessary_Name_OUT", @port5.filename,
+        "Incorrect filename generated"
+      refute @port5.filename.ends_with?(".zip"), "Filename has 'zip' suffix"
+      assert_equal "Test run 2-Output.zip", @port6.filename,
+        "Incorrect filename generated"
+      assert @port6.filename.ends_with?(".zip"),
+        "Filename missing 'zip' suffix"
+      assert_equal "Test run 2-OUT_Error", @port7.filename,
+        "Incorrect filename generated"
+      refute @port7.filename.ends_with?(".zip"), "Filename has 'zip' suffix"
+    end
   end
 end

data/test/unit/utils_test.rb

@@ -0,0 +1,46 @@
+#------------------------------------------------------------------------------
+# 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 UtilsTest < ActiveSupport::TestCase
+
+  include TavernaPlayer::Concerns::Utils
+
+  test "recurse into list" do
+    test_list1 = [0, 1, 2, 3, 4]
+    test_list2 = [[0, 1], [2, 3], [4, 5]]
+
+    assert_equal 0, recurse_into_lists(0, [0, 0]),
+      "A non-list should just be returned unchanged."
+    assert_equal test_list1, recurse_into_lists(test_list1, []),
+      "With no indices the original list should be returned unchanged."
+    assert_equal 0, recurse_into_lists(test_list1, [0]), "Should return 0."
+    assert_equal 4, recurse_into_lists(test_list1, [4]), "Should return 4."
+    assert_equal 0, recurse_into_lists(test_list2, [0, 0]), "Should return 0."
+    assert_equal [0, 1], recurse_into_lists(test_list2, [0]),
+      "Should return [0, 1]."
+    assert_equal 5, recurse_into_lists(test_list2, [2, 1]), "Should return 5."
+  end
+
+  test "list depth" do
+    assert_equal 0, list_depth(1), "Non-list should have depth 0."
+    assert_equal 1, list_depth([]), "Empty list should have depth 1."
+    assert_equal 1, list_depth([0]), "Should have depth 1."
+    assert_equal 1, list_depth([0, 1, 2, 3]), "Should have depth 1."
+    assert_equal 2, list_depth([[]]), "Should have depth 2."
+    assert_equal 2, list_depth([0, []]), "Should have depth 2."
+    assert_equal 2, list_depth([[0], [1], [2]]), "Should have depth 2."
+    assert_equal 2, list_depth([0, [1], [2]]), "Should have depth 2."
+    assert_equal 10, list_depth([[[[[[[[[[]]]]]]]]]]), "Should have depth 10."
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taverna-player
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-12 00:00:00.000000000 Z
+date: 2014-01-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -337,6 +337,7 @@ files:
 - lib/taverna_player/concerns/models/run.rb
 - lib/taverna_player/concerns/models/run_port.rb
 - lib/taverna_player/concerns/utils.rb
+- lib/taverna_player/concerns/zip.rb
 - lib/taverna_player/engine.rb
 - lib/taverna_player/model_proxy.rb
 - lib/taverna_player/port_renderer.rb
@@ -436,6 +437,7 @@ files:
 - test/unit/taverna_player/run_port_test.rb
 - test/unit/taverna_player/run_test.rb
 - test/unit/taverna_player/service_credential_test.rb
+- test/unit/utils_test.rb
 - test/workflows/hello.t2flow
 - test/workflows/list_with_errors.t2flow
 - test/workflows/pass_through.t2flow
@@ -454,7 +456,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1589530692801981432
+      hash: -672196183231170536
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -463,7 +465,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1589530692801981432
+      hash: -672196183231170536
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.21
@@ -561,6 +563,7 @@ test_files:
 - test/unit/taverna_player/run_port_test.rb
 - test/unit/taverna_player/run_test.rb
 - test/unit/taverna_player/service_credential_test.rb
+- test/unit/utils_test.rb
 - test/workflows/hello.t2flow
 - test/workflows/list_with_errors.t2flow
 - test/workflows/pass_through.t2flow