taverna-t2flow 0.3.0 → 0.4.0

data/.rvmrc

@@ -0,0 +1 @@
+rvm --create use 1.8.7@taverna2-gem

data/CHANGES.rdoc

@@ -1,5 +1,11 @@
 = Changes log for the T2Flow Ruby Gem
 
+== Version 0.4.0
+
+* Made parser more robust.
+* Processor annotations are now extracted properly.
+* Semantic annotations on ports, processors and dataflows are now extracted.
+
 == Version 0.3.0
 
 * Minor changes for ruby 1.9 compatibility.

data/Rakefile

@@ -14,13 +14,13 @@ require 'jeweler'
 
 task :default => [:test]
 
-T2FLOW_GEM_VERSION = "0.3.0"
+T2FLOW_GEM_VERSION = "0.4.0"
 
 Jeweler::Tasks.new do |s|
   s.name             = "taverna-t2flow"
   s.version          = T2FLOW_GEM_VERSION
-  s.authors          = ["Robert Haines", "David Withers", "Mannie Tagarira"]
-  s.email            = ["rhaines@manchester.ac.uk"]
+  s.authors          = ["Finn Bacall", "Robert Haines", "David Withers", "Mannie Tagarira"]
+  s.email            = ["finn.bacall@cs.man.ac.uk", "rhaines@manchester.ac.uk"]
   s.homepage         = "http://www.taverna.org.uk/"
   s.platform         = Gem::Platform::RUBY
   s.summary          = "Support for interacting with Taverna 2 workflows."

data/lib/t2flow/model.rb

@@ -231,7 +231,11 @@ module T2Flow # :nodoc:
     
     # A string containing the description of the processor if available.  
     # Returns nil otherwise.
-    attr_accessor :description
+    attr_accessor :descriptions
+
+    def description
+      @descriptions.first
+    end
     
     # A string for the type of processor, e.g. beanshell, workflow, webservice, etc...
     attr_accessor :type 
@@ -273,6 +277,12 @@ module T2Flow # :nodoc:
     # Value for string constants
     attr_accessor :value
 
+    attr_accessor :semantic_annotation
+
+    def initialize
+      @descriptions = []
+    end
+
   end
 
 
@@ -308,9 +318,11 @@ module T2Flow # :nodoc:
     
     # A list of authors of the dataflow
     attr_accessor :authors
+
+    attr_accessor :semantic_annotation
     
     def initialize
-      @authors, @descriptions, @titles = [], [], []
+      @authors, @descriptions, @titles  = [], [], []
     end
   end
   
@@ -347,7 +359,7 @@ module T2Flow # :nodoc:
   # A string that does not contain a colon can often be returned, signifiying
   # a workflow source as opposed to that of a processor.
   class Source
-  	attr_accessor :name, :descriptions, :example_values
+  	attr_accessor :name, :descriptions, :example_values, :semantic_annotation
   end
   
   
@@ -358,7 +370,27 @@ module T2Flow # :nodoc:
   # A string that does not contain a colon can often be returned, signifiying
   # a workflow sink as opposed to that of a processor.
   class Sink
-	  attr_accessor :name, :descriptions, :example_values
-  end  	
+	  attr_accessor :name, :descriptions, :example_values, :semantic_annotation
+  end
+
+
+  # A representation of a semantic annotation. It is linked to a +subject+,
+  # which can be a processor, port, or dataflow object. It has a +type+, which
+  # indicates the MIME type of it's +content+. By default, this will be text/rdf+n3.
+  # +Content+ is the content of the annotation, which in n3 form consists of one or more
+  # triples.
+  class SemanticAnnotation
+    attr_reader :subject, :type, :content
+
+    def initialize(subject, type, content)
+      @subject = subject
+      @type = type
+      @content = content
+    end
+
+    def to_s
+      @content
+    end
+  end
 
 end

data/lib/t2flow/parser.rb

@@ -1,4 +1,5 @@
 require "libxml"
+require "cgi"
 
 module T2Flow
   
@@ -11,15 +12,17 @@ module T2Flow
     def parse(t2flow)
       case t2flow.class.to_s
         when /^string$/i
-          document = LibXML::XML::Parser.string(t2flow).parse 
+          document = LibXML::XML::Parser.string(t2flow, :options => LibXML::XML::Parser::Options::NOBLANKS).parse
         when /^stringio|file$/i
           t2flow.rewind
-          document = LibXML::XML::Parser.string(t2flow.read).parse 
+          document = LibXML::XML::Parser.string(t2flow.read, :options => LibXML::XML::Parser::Options::NOBLANKS).parse
         else 
           raise "Error parsing file."
       end
 
       root = document.root
+      root.namespaces.default_prefix = "t2"
+
       raise "Doesn't appear to be a workflow!" if root.name != "workflow"
       version = root["version"]
       
@@ -32,7 +35,7 @@ module T2Flow
       local_depends = element.find("//localDependencies")
       if local_depends
         local_depends.each do |dependency|
-          dependency.each do |dep| 
+          dependency.each do |dep|
             model.dependencies = [] if model.dependencies.nil?
             model.dependencies << dep.content unless dep.content =~ /^\s*$/
           end
@@ -40,29 +43,29 @@ module T2Flow
         model.dependencies.uniq! if model.dependencies
       end
     
-      element.each do |dataflow|
+      element.each_element do |dataflow|
         next if dataflow["id"].nil? || dataflow["id"].chomp.strip.empty?
 
         dataflow_obj = Dataflow.new
         dataflow_obj.dataflow_id = dataflow["id"]
         dataflow_obj.role = dataflow["role"]
         
-        dataflow.each do |elt|
+        dataflow.each_element do |elt|
           case elt.name
             when "name"
               dataflow_obj.annotations.name = elt.content
             when "inputPorts"
-              elt.each { |port| add_source(dataflow_obj, port) }
+              elt.each_element { |port| add_source(dataflow_obj, port) }
             when "outputPorts"
-              elt.each { |port| add_sink(dataflow_obj, port) }
+              elt.each_element { |port| add_sink(dataflow_obj, port) }
             when "processors"
-              elt.each { |proc| add_processor(dataflow_obj, proc) }
+              elt.each_element { |proc| add_processor(dataflow_obj, proc) }
             when "datalinks"
-              elt.each { |link| add_link(dataflow_obj, link) }
+              elt.each_element { |link| add_link(dataflow_obj, link) }
             when "conditions"
-              elt.each { |coord| add_coordination(dataflow_obj, coord) }
+              elt.each_element { |coord| add_coordination(dataflow_obj, coord) }
             when "annotations"
-              elt.each { |ann| add_annotation(dataflow_obj, ann) }
+              elt.each_element { |ann| add_annotation(dataflow_obj, ann) }
           end # case elt.name
         end # dataflow.each
         
@@ -82,89 +85,37 @@ module T2Flow
       return if port.nil? || port.content.chomp.strip.empty?
 
       source = Source.new
-
-      port.each do |elt|
-        case elt.name
-          when "name"
-            source.name = elt.content
-          when "annotations"
-            elt.each do |ann|
-              next if ann.nil? || ann.content.chomp.strip.empty?
-              
-              node = LibXML::XML::Parser.string("#{ann}").parse
-              content_node = node.find_first("//annotationBean")
-              content = content_node.child.next.content
-      
-              case content_node["class"]
-                when /freetextdescription/i
-                  source.descriptions = [] unless source.descriptions
-                  source.descriptions << content
-                when /examplevalue/i
-                  source.example_values = [] unless source.example_values
-                  source.example_values << content
-              end # case
-            end # elt.each
-        end # case
-      end # port.each
-      
+      extract_port_metadata(source, port)            
       dataflow.sources << source
     end
     
     def add_sink(dataflow, port) # :nodoc:
       return if port.nil? || port.content.chomp.strip.empty?
       
-      sink = Sink.new
-      
-      port.each do |elt|
-        case elt.name
-          when "name"
-            sink.name = elt.content
-          when "annotations"
-            elt.each do |ann|
-              next if ann.nil? || ann.content.chomp.strip.empty?
-              
-              node = LibXML::XML::Parser.string("#{ann}").parse
-              content_node = node.find_first("//annotationBean")
-              content = content_node.child.next.content
-      
-              case content_node["class"]
-                when /freetextdescription/i
-                  sink.descriptions = [] unless sink.descriptions
-                  sink.descriptions << content
-                when /examplevalue/i
-                  sink.example_values = [] unless sink.example_values
-                  sink.example_values << content
-              end # case
-            end # elt.each
-        end # case
-      end # port.each
-      
+      sink = Sink.new      
+      extract_port_metadata(sink, port)      
       dataflow.sinks << sink
     end
     
     def add_processor(dataflow, element) # :nodoc:
-      return if element.nil? || element.content.chomp.strip.empty?
-
       processor = Processor.new
       
       temp_inputs = []
       temp_outputs = []
       
-      element.each do |elt|
+      element.each_element do |elt|
         case elt.name
           when "name"
             processor.name = elt.content
           when /inputports/i # ports from services
-            elt.each { |port| 
-              port.each { |x| temp_inputs << x.content if x.name=="name" }
-            }
+            elt.each_element { |port| port.each_element { |x| temp_inputs << x.content if x.name=="name" }}
           when /outputports/i # ports from services
-            elt.each { |port| 
-              port.each { |x| temp_outputs << x.content if x.name=="name" }
-            }
+            elt.each_element { |port| port.each_element { |x| temp_outputs << x.content if x.name=="name" }}
+          when "annotations"
+            extract_annotations(processor, elt)
           when "activities" # a processor can only have one kind of activity
-            activity = elt.child
-            activity.each do |node|
+            activity = elt.find_first('./t2:activity')
+            activity.each_element do |node|
               if node.name == "configBean"
                   activity_node = node.child
                   
@@ -175,7 +126,7 @@ module T2Flow
                     processor.type = (activity_node.name =~ /martquery/i ?
                         "biomart" : activity_node.name.split(".")[-2])
                     
-                    activity_node.each do |value_node|
+                    activity_node.each_element do |value_node|
                       case value_node.name
                         when "wsdl"
                           processor.wsdl = value_node.content
@@ -194,19 +145,19 @@ module T2Flow
                         when "value"
                           processor.value = value_node.content
                         when "inputs" # ALL ports present in beanshell
-                          value_node.each { |input| 
-                            input.each { |x| 
+                          value_node.each_element do |input|
+                            input.each_element do |x|
                               processor.inputs = [] if processor.inputs.nil?
                               processor.inputs << x.content if x.name == "name" 
-                            }
-                          }
+                            end
+                          end
                         when "outputs" # ALL ports present in beanshell
-                          value_node.each { |output| 
-                            output.each { |x| 
+                          value_node.each_element do |output|
+                            output.each_element do |x|
                               processor.outputs = [] if processor.outputs.nil?
                               processor.outputs << x.content if x.name == "name" 
-                            }
-                          }
+                            end
+                          end
                       end # case value_node.name
                     end # activity_node.each
                   end # if else node["encoding"] == "dataflow"
@@ -221,27 +172,22 @@ module T2Flow
     end
     
     def add_link(dataflow, link) # :nodoc:
-      return if link.nil? || link.content.chomp.strip.empty?
-
       datalink = Datalink.new
       
-      link.each do |sink_source|
-        case sink_source.name
-          when "sink"
-            datalink.sink = sink_source.child.content
-            datalink.sink += ":" + sink_source.last.content if sink_source["type"] == "processor"
-          when "source"
-            datalink.source = sink_source.child.content
-            datalink.source += ":" + sink_source.last.content if sink_source["type"] == "processor"
-        end
+      if sink = link.find_first('./t2:sink')
+        datalink.sink = (sink["type"] == "processor" ? "#{sink.find_first('./t2:processor').content}:" : "") +
+                        "#{sink.find_first('./t2:port').content}"
       end
-      
+
+      if source = link.find_first('./t2:source')
+        datalink.source = (source["type"] == "processor" ? "#{source.find_first('./t2:processor').content}:" : "") +
+                          "#{source.find_first('./t2:port').content}"
+      end
+
       dataflow.datalinks << datalink
     end
     
     def add_coordination(dataflow, condition) # :nodoc:
-      return if condition.nil?
-
       coordination = Coordination.new
       
       coordination.control = condition["control"]
@@ -251,22 +197,60 @@ module T2Flow
     end
     
     def add_annotation(dataflow, annotation) # :nodoc:
-      return if annotation.nil? || annotation.empty?
-      
       node = LibXML::XML::Parser.string("#{annotation}").parse
       content_node = node.find_first("//annotationBean")
-      content = content_node.child.next.content if content_node.child.next
 
       case content_node["class"]
         when /freetextdescription/i
-          dataflow.annotations.descriptions << content
+          dataflow.annotations.descriptions << content_node.find_first('./text').content
         when /descriptivetitle/i
-          dataflow.annotations.titles << content
+          dataflow.annotations.titles << content_node.find_first('./text').content
         when /author/i
-          dataflow.annotations.authors << content
+          dataflow.annotations.authors << content_node.find_first('./text').content
+        when /semanticannotation/i
+          dataflow.annotations.semantic_annotation = parse_semantic_annotation(dataflow, content_node)
         end # case
     end
     
+    private 
+    
+    def extract_port_metadata(port, element)
+      element.each_element do |elt|
+        case elt.name
+          when "name"
+            port.name = elt.content
+          when "annotations"
+            extract_annotations(port, elt)
+        end # case
+      end # port.each
+    end
+
+    def extract_annotations(object, element)
+      element.each_element do |ann|
+        next if ann.nil? || ann.content.chomp.strip.empty?
+
+        node = LibXML::XML::Parser.string("#{ann}").parse
+        content_node = node.find_first("//annotationBean")
+
+        case content_node["class"]
+          when /freetextdescription/i
+            object.descriptions ||= []
+            object.descriptions << content_node.find_first('./text').content
+          when /examplevalue/i
+            object.example_values ||= []
+            object.example_values << content_node.find_first('./text').content
+          when /semanticannotation/i
+            object.semantic_annotation = parse_semantic_annotation(object, content_node)
+        end # case
+      end # element.each
+    end
+
+    def parse_semantic_annotation(object, content_node)
+      type = content_node.find_first('./mimeType').content
+      content = CGI.unescapeHTML(content_node.find_first('./content').content)
+      SemanticAnnotation.new(object, type, content)
+    end
+    
   end
   
 end

data/taverna-t2flow.gemspec

@@ -5,19 +5,20 @@
 
 Gem::Specification.new do |s|
   s.name = "taverna-t2flow"
-  s.version = "0.3.0"
+  s.version = "0.4.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Robert Haines", "David Withers", "Mannie Tagarira"]
-  s.date = "2012-05-02"
+  s.authors = ["Finn Bacall", "Robert Haines", "David Withers", "Mannie Tagarira"]
+  s.date = "2012-12-03"
   s.description = "This a gem developed by myGrid for the purpose of interacting with Taverna 2 workflows. An example use would be the image genaration for the model representing Taverna 2 workflows as used in myExperiment."
-  s.email = ["rhaines@manchester.ac.uk"]
+  s.email = ["finn.bacall@cs.man.ac.uk", "rhaines@manchester.ac.uk"]
   s.extra_rdoc_files = [
     "CHANGES.rdoc",
     "LICENCE",
     "README.rdoc"
   ]
   s.files = [
+    ".rvmrc",
     "CHANGES.rdoc",
     "LICENCE",
     "README.rdoc",
@@ -37,18 +38,20 @@ Gem::Specification.new do |s|
     "test/fixtures/999.t2flow",
     "test/fixtures/basic.t2flow",
     "test/fixtures/coordinated.t2flow",
+    "test/fixtures/image_to_tiff_migration_action.t2flow",
     "test/fixtures/linked.t2flow",
     "test/fixtures/nested.t2flow",
     "test/fixtures/processors.t2flow",
     "test/run_tests.rb",
     "test/test_bogus_workflows.rb",
+    "test/test_component_workflows.rb",
     "test/test_helper.rb",
     "test/test_starter_pack_workflows.rb"
   ]
   s.homepage = "http://www.taverna.org.uk/"
   s.rdoc_options = ["-N", "--tab-width=2", "--main=README.rdoc"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.10"
+  s.rubygems_version = "1.8.24"
   s.summary = "Support for interacting with Taverna 2 workflows."
   s.test_files = ["test/run_tests.rb"]
 

data/test/fixtures/image_to_tiff_migration_action.t2flow

@@ -0,0 +1,278 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="16841f82-e1fe-4527-b7ef-411c4c59493b" role="top"><name>Image_to_tiff_migrat</name><inputPorts><port><name>from_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+        <text>description</text>
+      </annotationBean>
+      <date>2012-11-16 16:22:56.977 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
+        <text>example</text>
+      </annotationBean>
+      <date>2012-11-16 16:22:43.712 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
+        <mimeType>text/rdf+n3</mimeType>
+        <content>[]    &lt;http://scape-project.eu/pc/vocab/profiles#hasPortType&gt;
+              &lt;http://scape-project.eu/pc/vocab/profiles#FromURIPort&gt; .
+</content>
+      </annotationBean>
+      <date>2012-11-19 15:53:49.250 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port><port><name>to_uri</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
+        <mimeType>text/rdf+n3</mimeType>
+        <content>[]    &lt;http://scape-project.eu/pc/vocab/profiles#hasPortType&gt;
+              &lt;http://scape-project.eu/pc/vocab/profiles#ToURIPort&gt; .
+</content>
+      </annotationBean>
+      <date>2012-11-20 12:09:41.928 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></port></inputPorts><outputPorts /><processors><processor><name>Tool</name><inputPorts><port><name>to_uri</name><depth>0</depth></port><port><name>from_uri</name><depth>0</depth></port></inputPorts><outputPorts /><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
+        <mimeType>text/rdf+n3</mimeType>
+        <content>[]    &lt;http://scape-project.eu/pc/vocab/profiles#hasDependency&gt;
+              &lt;http://scape-project.eu/pc/vocab/profiles#imagemagick-image2tiff&gt; .
+</content>
+      </annotationBean>
+      <date>2012-11-20 12:17:37.420 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="to_uri" to="to_uri" /><map from="from_uri" to="from_uri" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
+  <mechanismType>789663B8-DA91-428A-9F7D-B3F3DA185FD4</mechanismType>
+  <mechanismName>default local</mechanismName>
+  <mechanismXML>&lt;?xml version="1.0" encoding="UTF-8"?&gt;&#xD;
+&lt;localInvocation&gt;&lt;shellPrefix&gt;/bin/sh -c&lt;/shellPrefix&gt;&lt;linkCommand&gt;/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%&lt;/linkCommand&gt;&lt;/localInvocation&gt;&#xD;
+</mechanismXML>
+  <externaltoolid>1c6b3cec-667d-4364-8a77-315a3b3c71f8</externaltoolid>
+  <useCaseDescription>
+    <usecaseid />
+    <description />
+    <command>convert %%from_uri%% tiff:%%to_uri%%</command>
+    <preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
+    <executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
+    <tags>
+      <string>from_uri</string>
+      <string>to_uri</string>
+    </tags>
+    <REs />
+    <queue__preferred />
+    <queue__deny />
+    <static__inputs />
+    <inputs>
+      <entry>
+        <string>to_uri</string>
+        <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+          <tag>to_uri</tag>
+          <file>false</file>
+          <tempFile>false</tempFile>
+          <binary>false</binary>
+          <charsetName>MacRoman</charsetName>
+          <forceCopy>false</forceCopy>
+          <list>false</list>
+          <concatenate>false</concatenate>
+          <mime />
+        </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+      </entry>
+      <entry>
+        <string>from_uri</string>
+        <de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+          <tag>from_uri</tag>
+          <file>false</file>
+          <tempFile>false</tempFile>
+          <binary>false</binary>
+          <charsetName>MacRoman</charsetName>
+          <forceCopy>false</forceCopy>
+          <list>false</list>
+          <concatenate>false</concatenate>
+          <mime />
+        </de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
+      </entry>
+    </inputs>
+    <outputs />
+    <includeStdIn>false</includeStdIn>
+    <includeStdOut>true</includeStdOut>
+    <includeStdErr>true</includeStdErr>
+    <validReturnCodes>
+      <int>0</int>
+    </validReturnCodes>
+  </useCaseDescription>
+  <edited>false</edited>
+</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
+  <maxJobs>1</maxJobs>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
+  <backoffFactor>1.0</backoffFactor>
+  <initialDelay>1000</initialDelay>
+  <maxDelay>5000</maxDelay>
+  <maxRetries>0</maxRetries>
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="to_uri" depth="0" /><port name="from_uri" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Tool</processor><port>to_uri</port></sink><source type="dataflow"><port>to_uri</port></source></datalink><datalink><sink type="processor"><processor>Tool</processor><port>from_uri</port></sink><source type="dataflow"><port>from_uri</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
+        <text>SCAPE Migration Components that converts any ImageMagick supported image format to TIFF</text>
+      </annotationBean>
+      <date>2012-11-15 13:07:59.763 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>fd401dac-c521-4d94-8014-8efeba355d7a</identification>
+      </annotationBean>
+      <date>2012-11-19 15:55:14.145 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>22bc577f-9a74-4981-8725-c3b4ac28d88b</identification>
+      </annotationBean>
+      <date>2012-11-20 12:10:07.110 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>052219d1-09ed-4c6b-a5a4-2bad004a10ed</identification>
+      </annotationBean>
+      <date>2012-11-19 16:17:25.295 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>5abab48b-a3f0-4f14-9894-e824a2fa5966</identification>
+      </annotationBean>
+      <date>2012-11-16 16:39:00.691 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
+        <text>David Withers</text>
+      </annotationBean>
+      <date>2012-11-15 12:25:42.359 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>b5361a0e-6abd-4070-8655-5dd7b4237576</identification>
+      </annotationBean>
+      <date>2012-11-15 13:36:38.115 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>2bec9695-c132-4728-988c-c3a03ddcc78d</identification>
+      </annotationBean>
+      <date>2012-11-15 13:08:31.374 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>0d60174b-0d75-481d-8b4d-194c6109bc96</identification>
+      </annotationBean>
+      <date>2012-11-20 12:17:54.280 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.SemanticAnnotation">
+        <mimeType>text/rdf+n3</mimeType>
+        <content>[]    &lt;http://scape-project.eu/pc/vocab/profiles#hasMigrationPath&gt;
+              &lt;http://scape-project.eu/pc/vocab/profiles#jpegToTiff&gt; .
+</content>
+      </annotationBean>
+      <date>2012-11-20 12:17:49.904 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>16841f82-e1fe-4527-b7ef-411c4c59493b</identification>
+      </annotationBean>
+      <date>2012-11-21 11:00:56.248 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
+        <identification>a5aee4f0-01d8-4ae3-96f0-c992b8d40af2</identification>
+      </annotationBean>
+      <date>2012-11-15 13:14:14.243 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
+  <annotationAssertions>
+    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+      <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
+        <text>Image to tiff migration action</text>
+      </annotationBean>
+      <date>2012-11-21 11:00:54.84 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>

data/test/run_tests.rb

@@ -5,3 +5,4 @@ require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
 
 require File.expand_path(File.join(__FILE__, "..", "test_bogus_workflows.rb"))
 require File.expand_path(File.join(__FILE__, "..", "test_starter_pack_workflows.rb"))
+require File.expand_path(File.join(__FILE__, "..", "test_component_workflows.rb"))

data/test/test_component_workflows.rb

@@ -0,0 +1,50 @@
+require 'rubygems'
+require 'test/unit'
+
+require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "model.rb"))
+require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "parser.rb"))
+
+require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
+
+class ComponentWorkflowTest < Test::Unit::TestCase
+  
+  include TestHelper
+  
+  def setup
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "image_to_tiff_migration_action.t2flow"))
+    @image_migration_wf = T2Flow::Parser.new.parse(File.new(path))
+  end
+  
+  def test_image_migration_workflow
+    generic_model_test(@image_migration_wf)
+    
+    assert_count(@image_migration_wf.processors, 1, "@image_migration_wf.processors")
+    assert_count(@image_migration_wf.sources, 2, "@image_migration_wf.sources")
+    assert_count(@image_migration_wf.sinks, 0, "@image_migration_wf.sinks")
+    assert_count(@image_migration_wf.datalinks, 2, "@image_migration_wf.datalinks")
+    assert_count(@image_migration_wf.coordinations, 0, "@image_migration_wf.coordinations")
+  end
+
+  def test_semantic_annotations
+    assert_not_nil(@image_migration_wf.sources[0].semantic_annotation)
+    assert_equal(@image_migration_wf.sources[0], @image_migration_wf.sources[0].semantic_annotation.subject)
+    assert_equal("text/rdf+n3", @image_migration_wf.sources[0].semantic_annotation.type)
+    assert_equal("[]<http://scape-project.eu/pc/vocab/profiles#hasPortType><http://scape-project.eu/pc/vocab/profiles#FromURIPort>.",
+                 @image_migration_wf.sources[0].semantic_annotation.content.gsub(/\s+/, ""),
+                 "@image_migration_wf.sources[0].semantic_annotation")
+
+    assert_not_nil(@image_migration_wf.sources[1].semantic_annotation)
+    assert_equal(@image_migration_wf.sources[1], @image_migration_wf.sources[1].semantic_annotation.subject)
+    assert_equal("text/rdf+n3", @image_migration_wf.sources[1].semantic_annotation.type)
+    assert_equal("[]<http://scape-project.eu/pc/vocab/profiles#hasPortType><http://scape-project.eu/pc/vocab/profiles#ToURIPort>.",
+                 @image_migration_wf.sources[1].semantic_annotation.content.gsub(/\s+/, ""),
+                 "@image_migration_wf.sources[1].semantic_annotation")
+
+    assert_not_nil(@image_migration_wf.processors[0].semantic_annotation)
+    assert_equal(@image_migration_wf.processors[0], @image_migration_wf.processors[0].semantic_annotation.subject)
+    assert_equal("text/rdf+n3", @image_migration_wf.processors[0].semantic_annotation.type)
+    assert_equal("[]<http://scape-project.eu/pc/vocab/profiles#hasDependency><http://scape-project.eu/pc/vocab/profiles#imagemagick-image2tiff>.",
+                 @image_migration_wf.processors[0].semantic_annotation.content.gsub(/\s+/, ""),
+                 "@image_migration_wf.processors[0].semantic_annotation")
+  end
+end

metadata

@@ -1,94 +1,103 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: taverna-t2flow
-version: !ruby/object:Gem::Version
-  version: 0.3.0
+version: !ruby/object:Gem::Version 
+  hash: 15
   prerelease: 
+  segments: 
+  - 0
+  - 4
+  - 0
+  version: 0.4.0
 platform: ruby
-authors:
+authors: 
+- Finn Bacall
 - Robert Haines
 - David Withers
 - Mannie Tagarira
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-02 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
+
+date: 2012-12-03 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
+      - !ruby/object:Gem::Version 
+        hash: 63
+        segments: 
+        - 0
+        - 9
+        - 2
         version: 0.9.2
   type: :development
+  name: rake
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 0.9.2
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 43
+        segments: 
+        - 3
+        - 9
+        - 4
         version: 3.9.4
   type: :development
+  name: rdoc
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 3.9.4
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
+      - !ruby/object:Gem::Version 
+        hash: 49
+        segments: 
+        - 1
+        - 8
+        - 3
         version: 1.8.3
   type: :development
+  name: jeweler
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.8.3
-- !ruby/object:Gem::Dependency
-  name: libxml-ruby
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 27
+        segments: 
+        - 1
+        - 1
+        - 4
         version: 1.1.4
   type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.1.4
-description: This a gem developed by myGrid for the purpose of interacting with Taverna
-  2 workflows. An example use would be the image genaration for the model representing
-  Taverna 2 workflows as used in myExperiment.
-email:
+  name: libxml-ruby
+  version_requirements: *id004
+description: This a gem developed by myGrid for the purpose of interacting with Taverna 2 workflows. An example use would be the image genaration for the model representing Taverna 2 workflows as used in myExperiment.
+email: 
+- finn.bacall@cs.man.ac.uk
 - rhaines@manchester.ac.uk
 executables: []
+
 extensions: []
-extra_rdoc_files:
+
+extra_rdoc_files: 
 - CHANGES.rdoc
 - LICENCE
 - README.rdoc
-files:
+files: 
+- .rvmrc
 - CHANGES.rdoc
 - LICENCE
 - README.rdoc
@@ -108,39 +117,49 @@ files:
 - test/fixtures/999.t2flow
 - test/fixtures/basic.t2flow
 - test/fixtures/coordinated.t2flow
+- test/fixtures/image_to_tiff_migration_action.t2flow
 - test/fixtures/linked.t2flow
 - test/fixtures/nested.t2flow
 - test/fixtures/processors.t2flow
 - test/run_tests.rb
 - test/test_bogus_workflows.rb
+- test/test_component_workflows.rb
 - test/test_helper.rb
 - test/test_starter_pack_workflows.rb
 homepage: http://www.taverna.org.uk/
 licenses: []
+
 post_install_message: 
-rdoc_options:
+rdoc_options: 
 - -N
 - --tab-width=2
 - --main=README.rdoc
-require_paths:
+require_paths: 
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
 requirements: []
+
 rubyforge_project: 
-rubygems_version: 1.8.21
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Support for interacting with Taverna 2 workflows.
-test_files:
+test_files: 
 - test/run_tests.rb