taverna-player 0.3.0 → 0.4.0

data/CHANGES.rdoc

@@ -1,5 +1,16 @@
 = Changes log for Taverna Player
 
+== Version 0.4.0
+
+* [TAV-466] Add port metadata to JSON output.
+* [TAV-472] Fix port model overriding stubs.
+* Add methods to query a port value's type.
+* Add a method to get a port value's size.
+* Add protection for value size and type methods.
+* Check that index lists are not altered.
+* Use the new port value methods in the port renderer.
+* [TAV-473] Get all values types directly from a port.
+
 == Version 0.3.0
 
 * Refactor callback code out into its own module.

data/README.rdoc

@@ -372,6 +372,11 @@ clashes.
 If you wanted to add a before filter to authenticate your users you would add
 that line before the +include+ statement, for example.
 
+<b>Important note!</b> If you override the RunPort model then you _must_
+override the RunPort::Input and RunPort::Output models too (even if you just
+leave the generated stubs unedited). This is because they are subclasses of
+RunPort and the inheritances must be re-established with the overridden model.
+
 == Run callbacks
 
 Taverna Player provides four points around a workflow run for you to specify

data/app/models/taverna_player/run_port.rb

@@ -36,6 +36,37 @@ module TavernaPlayer
     # Show up to the first 256 characters of the port's value. This returns
     # nil if the port has a file instead of a value.
 
+    ##
+    # :method: value_size
+    # :call-seq:
+    #   value_size -> string
+    #   value_size(indices) -> string
+    #
+    # 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_type
+    # :call-seq:
+    #   value_type -> string
+    #   value_type(indices) -> string
+    #
+    # Get the MIME type of the value held in this port. Pass in a list of
+    # indices if it is a list port. Returns "text/plain" if there is no port
+    # 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_is_text?
+    # :call-seq:
+    #   value_is_text? -> string
+    #   value_is_text?(indices) -> string
+    #
+    # 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
     # :call-seq:

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

@@ -6,6 +6,8 @@ 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
 

data/lib/generators/taverna_player/models_generator.rb

@@ -19,7 +19,7 @@ module TavernaPlayer
         "customization."
 
       def copy_models
-        ["run.rb", "run_port.rb", "input.rb", "output.rb"].each do |file|
+        ["run.rb", "run_port.rb"].each do |file|
           copy_file file, "app/models/taverna_player/#{file}"
         end
       end

data/lib/generators/templates/models/run_port.rb

@@ -17,4 +17,18 @@ module TavernaPlayer
 
     # Extend the RunPort model here.
   end
+
+  class RunPort::Input < RunPort
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Models::Input
+
+    # Extend the RunPort::Input model here.
+  end
+
+  class RunPort::Output < RunPort
+    # Do not remove the next line.
+    include TavernaPlayer::Concerns::Models::Output
+
+    # Extend the RunPort::Output model here.
+  end
 end

data/lib/taverna_player/concerns/models/run_port.rb

@@ -17,6 +17,8 @@ module TavernaPlayer
 
         extend ActiveSupport::Concern
 
+        include TavernaPlayer::Concerns::Utils
+
         included do
 
           MAXIMUM_DATABASE_VALUE_SIZE = 255
@@ -88,21 +90,42 @@ module TavernaPlayer
             data
           end
 
+          def value_metadata(field, *indices)
+            return if metadata.nil?
+            index = [*indices].flatten
+            recurse_into_lists(metadata[field], index)
+          end
+
         end # included
 
         def display_name
           name.gsub('_', ' ')
         end
 
+        def value_type(*indices)
+          value_metadata(:type, *indices) || "text/plain"
+        end
+
+        def value_is_text?(*indices)
+          type = value_type(*indices)
+          type.starts_with?("text")
+        end
+
+        def value_size(*indices)
+          value_metadata(:size, *indices)
+        end
+
         def value_preview
           self[:value]
         end
 
         def value(*indices)
           if depth == 0
-            v = self[:value]
-
-            (!v.blank? && !file.path.blank?) ? File.read(file.path) : v
+            if file.path.blank?
+              self[:value]
+            else
+              value_is_text? ? File.read(file.path) : File.binread(file.path)
+            end
           else
             deep_value([*indices].flatten)
           end

data/lib/taverna_player/port_renderer.rb

@@ -21,7 +21,6 @@ module TavernaPlayer
   # etc) available to them.
   class PortRenderer
     include TavernaPlayer::Concerns::Callback
-    include TavernaPlayer::Concerns::Utils
 
     # The renderers are all called in the scope of this class so we include
     # ActionView::Helpers here so that they are all available to them.
@@ -96,7 +95,7 @@ module TavernaPlayer
       if port.depth > 0 && index.empty?
         renderer = @hash[:list]
       else
-        type = MIME::Types[recurse_into_lists(port.metadata[:type], index.dup)].first
+        type = MIME::Types[port.value_type(index)].first
         renderer = @hash[type.media_type][type.sub_type] ||
           @hash[type.media_type][:default] || @hash[:default]
       end

data/lib/taverna_player/version.rb

@@ -11,5 +11,5 @@
 #------------------------------------------------------------------------------
 
 module TavernaPlayer
-  VERSION = "0.3.0"
+  VERSION = "0.4.0"
 end

data/test/fixtures/taverna_player/run_ports.yml

@@ -53,3 +53,10 @@ five:
   run_id: 4
   depth: 0
   metadata: "---\n:size: 33\n:type: text/plain"
+
+six:
+  name: Output
+  port_type: TavernaPlayer::RunPort::Output
+  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"

data/test/unit/taverna_player/run_port_test.rb

@@ -19,6 +19,7 @@ module TavernaPlayer
       @port2 = taverna_player_run_ports(:two)
       @port3 = taverna_player_run_ports(:three)
       @port5 = taverna_player_run_ports(:five)
+      @port6 = taverna_player_run_ports(:six)
     end
 
     test "run port inheritance types" do
@@ -175,7 +176,7 @@ module TavernaPlayer
       port = RunPort::Input.create(:name => "test_port", :value => "test",
         :file => file)
 
-      assert port.value.blank?, "Value should be blank"
+      assert port[:value].blank?, "Value should be blank"
       refute port.file.blank?, "File should be present"
     end
 
@@ -184,7 +185,7 @@ module TavernaPlayer
       port = RunPort::Output.create(:name => "test_port", :value => "test",
         :file => file)
 
-      assert port.value.blank?, "Value should be blank"
+      assert port[:value].blank?, "Value should be blank"
       refute port.file.blank?, "File should be present"
     end
 
@@ -196,7 +197,7 @@ module TavernaPlayer
       port.value = "test"
       port.save
 
-      assert port.value.blank?, "Value should be blank"
+      assert port[:value].blank?, "Value should be blank"
       refute port.file.blank?, "File should be present"
     end
 
@@ -208,7 +209,7 @@ module TavernaPlayer
       port.value = "test"
       port.save
 
-      assert port.value.blank?, "Value should be blank"
+      assert port[:value].blank?, "Value should be blank"
       refute port.file.blank?, "File should be present"
     end
 
@@ -283,7 +284,7 @@ module TavernaPlayer
 
       port.file = fixture_file_upload "/files/crassostrea_gigas.csv"
       port.save
-      assert_nil port.value, "Port value not nil"
+      assert_nil port[:value], "Port value not nil"
       refute port.file.blank?, "File not present"
     end
 
@@ -305,5 +306,55 @@ module TavernaPlayer
       assert_nil port.value, "Port value not nil"
       assert port.file.blank?, "File not present"
     end
+
+    test "get value types" do
+      assert_equal "text/plain", @port1.value_type, "Type not text/plain"
+      assert_equal "text/plain", @port2.value_type(1), "Type not text/plain"
+      assert_equal "application/x-error", @port2.value_type(2),
+        "Type not application/x-error"
+      assert_equal "text/plain", @port3.value_type, "Type not text/plain"
+      assert_equal "text/plain", @port6.value_type(0, 0),
+        "Type not text/plain"
+      assert_equal "text/plain", @port6.value_type([2, 1]),
+        "Type not text/plain"
+
+      # Test when there is no metadata
+      port = RunPort::Input.create(:name => "test_port", :value => "Test")
+      assert_equal "text/plain", port.value_type,
+        "Unspecified type should return \"text/plain\""
+      assert port.value_is_text?, "Unspecified type should be text"
+      assert_nil port.value_size, "Unspecified size should return nil"
+    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"
+      assert @port3.value_is_text?, "Value not detected as text"
+      assert @port6.value_is_text?(0, 0), "Value not detected as text"
+      assert @port6.value_is_text?([1, 1]), "Value not detected as text"
+      refute @port2.value_is_text?(2), "Value detected as text"
+    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"
+      assert_equal 3, @port3.value_size, "Value size not 3"
+      assert_equal 15, @port6.value_size([0, 0]), "Value size not 15"
+      assert_equal 24, @port6.value_size([2, 1]), "Value size not 24"
+    end
+
+    test "value methods should not alter input parameters" do
+      index = [1, 1]
+      index_saved = index.dup
+
+      @port6.value_type(index)
+      assert_equal index_saved, index, "Parameter index was altered"
+
+      @port6.value_is_text?(index)
+      assert_equal index_saved, index, "Parameter index was altered"
+
+      @port6.value_size(index)
+      assert_equal index_saved, index, "Parameter index was altered"
+    end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taverna-player
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-10 00:00:00.000000000 Z
+date: 2013-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -322,8 +322,6 @@ files:
 - lib/generators/templates/callbacks/worker_callbacks.rb
 - lib/generators/templates/controllers/runs_controller.rb
 - lib/generators/templates/controllers/service_credentials_controller.rb
-- lib/generators/templates/models/input.rb
-- lib/generators/templates/models/output.rb
 - lib/generators/templates/models/run.rb
 - lib/generators/templates/models/run_port.rb
 - lib/generators/templates/player_initializer.rb
@@ -456,7 +454,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1554949292676939893
+      hash: -1589530692801981432
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -465,7 +463,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1554949292676939893
+      hash: -1589530692801981432
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.21

data/lib/generators/templates/models/input.rb

@@ -1,20 +0,0 @@
-#------------------------------------------------------------------------------
-# Copyright (c) 2013 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
-  class RunPort::Input < ActiveRecord::Base
-    # Do not remove the next line.
-    include TavernaPlayer::Concerns::Models::Input
-
-    # Extend the RunPort::Input model here.
-  end
-end

data/lib/generators/templates/models/output.rb

@@ -1,20 +0,0 @@
-#------------------------------------------------------------------------------
-# Copyright (c) 2013 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
-  class RunPort::Output < ActiveRecord::Base
-    # Do not remove the next line.
-    include TavernaPlayer::Concerns::Models::Output
-
-    # Extend the RunPort::Output model here.
-  end
-end