RubyGems - myGrid-taverna-t2flow - Versions diffs - 0.0.0 - Mend

myGrid-taverna-t2flow 0.0.0

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data/LICENCE ADDED Viewed

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+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
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data/README ADDED Viewed

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+= Taverna[http://taverna.sourceforge.net] 2 Interaction Gem
+Author::        Emmanuel Tagarira
+Version::       0.0.0
+Contact::       mailto:emmanuel.tagarira@student.manchester.ac.uk
+URL::           http://taverna.sourceforge.net/
+Licence::       LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html)
+Copyright::     (c) 2008-2009 University of Manchester, UK
+== Synopsis
+This is a Ruby library to support the interaction with Taverna[http://taverna.sourceforge.net] version 2 workflows (T2Flows).  This relies on the functionality provided by the libxml library.  To be able to utilise this gem to its full potential, you will need to have the following installed on your system.
+- GraphViz[http://www.graphviz.org/Download.php] (a graph visualization package)
+- Rdoc gem
+- Darkfish-Rdoc gem
+== The T2Flow Model Implementation
+Much like the Taverna[http://taverna.sourceforge.net] 1 Scufl model, T2Flows contain Processors, Sinks, and Sources.  T2Flows however, encapsulate these elements within Dataflow objects.  A Dataflow objects is the container for all the different elements present within the Taverna[http://taverna.sourceforge.net] 2 workflows, hence a single T2Flow may have one or more dataflows.  WorkflowDescriptions and Links, from the original Taverna[http://taverna.sourceforge.net] 1 workflows (Scufl), have been renamed in T2Flows to DataflowAnnotations and Datalinks respectively.  DataflowAnnotations, however, allow for multiple titles, authors, and descriptions, as opposed to the single value attributes held for Scufls.
+== Installation
+To install the gems required by the Taverna 2 gem library, type into your command prompt:
+  [sudo] gem install libxml-ruby
+  [sudo] gem install rdoc
+  [sudo] gem install darkfish-rdoc
+When you have the required gems on your system, you may install this gem using the following commands:
+  gem sources -a http://gems.github.com
+  [sudo] gem install myGrid-taverna-t2flow
+== Usage
+To be able to generate at least a T2Flow model using the gem, you need to include in your ruby code the following lines:
+  require "t2flow/model.rb"
+  require "t2flow/parser.rb"
+To generate the model you can then use the gem as follows:
+  foo = File.new("path/to/workflow/file", "r")
+  bar = T2Flow::Parser.new.parse(foo)
+Alternatively:
+  foo = File.new("path/to/workflow/file", "r").read
+  bar = T2Flow::Parser.new.parse(foo)
+You will then be able to use your T2Flow model to retrieve information about the workflow by invoking the different methods and attributes.
+  bar.INVOKED
+... where INVOKED is the method or attribute required.
+You can also interact with remote workflows.
+  require "open-uri"
+  foo = Uri.parse("xxxx://uri_to_workflow").read
+  bar = T2Flow::Parser.new.parse(foo)
+To be enable you to draw images of the T2Flow, you need to include:
+  require "t2flow/dot.rb"
+To be able to use any functionality included in "t2flow/dot.rb", you need to have GraphViz[http://www.graphviz.org/Download.php] installed on your system.  Once this package has been installed, you may use the gem to draw an image showing the structure of the T2Flow as follows.
+  out_file = File.new("path/to/file/you/want/the/dot/script/to/be/written", "w+")
+  T2Flow::Dot.new.write_dot(out_file, bar)
+  `dot -Tpng -o"path/to/the/output/image" #{out_file.path}`
+The last line draws a PNG image using +out_file+.  To learn more about dot, try typing into your command prompt:
+  % man dot
+or
+  % dot -h
+== References
+[1] http://taverna.sourceforge.net
+[2] http://www.graphviz.org

data/lib/t2flow/dot.rb ADDED Viewed

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+module T2Flow
+  # This class enables you to write the script will will be used by dot
+  # (which is part of GraphViz[http://www.graphviz.org/Download.php])
+  # to generate the image showing the structure of a given model.
+  # To get started quickly, you could try:
+  #   out_file = File.new("path/to/file/you/want/the/dot/script/to/be/written", "w+")
+  #   workflow = File.new("path/to/workflow/file", "r").read
+  #   model = T2Flow::Parser.new.parse(workflow)
+  #   T2Flow::Dot.new.write_dot(out_file, model)
+  #   `dot -Tpng -o"path/to/the/output/image" #{out_file.path}`
+  class Dot
+    @@processor_colours = {
+      'apiconsumer' => 'palegreen',
+      'beanshell' => 'burlywood2',
+      'biomart' => 'lightcyan2',
+      'local' => 'mediumorchid2',
+      'biomobywsdl' => 'darkgoldenrod1',
+      'biomobyobject' => 'gold',
+      'biomobyparser' => 'white',
+      'inferno' => 'violetred1',
+      'notification' => 'mediumorchid2',
+      'rdfgenerator' => 'purple',
+      'rserv' => 'lightgoldenrodyellow',
+      'seqhound' => '#836fff',
+      'soaplabwsdl' => 'lightgoldenrodyellow',
+      'stringconstant' => 'lightsteelblue',
+      'talisman' => 'plum2',
+      'bsf' => 'burlywood2',
+      'abstractprocessor' => 'lightgoldenrodyellow',
+      'rshell' => 'lightgoldenrodyellow',
+      'arbitrarywsdl' => 'darkolivegreen3',
+      'workflow' => 'crimson'}
+    @@fill_colours = %w{white aliceblue antiquewhite beige}
+    @@ranksep = '0.22'
+    @@nodesep = '0.05'
+    # Creates a new dot object for interaction.
+    def initialize
+      # @port_style IS CURRENTLY UNUSED. IGNORE!!!
+      @port_style = 'none' # 'all', 'bound' or 'none'
+    end
+    # Writes to the given stream (File, StringIO, etc) the script to generate
+    # the image showing the internals of the given workflow model.
+    # === Usage
+    #   stream = File.new("path/to/file/you/want/the/dot/script/to/be/written", "w+")
+    #   workflow = .......
+    #   model = T2Flow::Parser.new.parse(workflow)
+    #   T2Flow::Dot.new.write_dot(stream, model)
+    def write_dot(stream, model)
+      @t2flow_model = model
+      stream.puts 'digraph t2flow_graph {'
+      stream.puts ' graph ['
+      stream.puts '  style=""'
+      stream.puts '  labeljust="left"'
+      stream.puts '  clusterrank="local"'
+      stream.puts "  ranksep=\"#@@ranksep\""
+      stream.puts "  nodesep=\"#@@nodesep\""
+      stream.puts ' ]'
+      stream.puts
+      stream.puts ' node ['
+      stream.puts '  fontname="Helvetica",'
+      stream.puts '  fontsize="10",'
+      stream.puts '  fontcolor="black", '
+      stream.puts '  shape="box",'
+      stream.puts '  height="0",'
+      stream.puts '  width="0",'
+      stream.puts '  color="black",'
+      stream.puts '  fillcolor="lightgoldenrodyellow",'
+      stream.puts '  style="filled"'
+      stream.puts ' ];'
+      stream.puts
+      stream.puts ' edge ['
+      stream.puts '  fontname="Helvetica",'
+      stream.puts '  fontsize="8",'
+      stream.puts '  fontcolor="black",'
+      stream.puts '  color="black"'
+      stream.puts ' ];'
+      write_dataflow(stream, model.top_level)
+      stream.puts '}'
+      stream.flush
+    end
+    def write_dataflow(stream, dataflow, prefix="", name="", depth=0) # :nodoc:
+      if name != ""
+        stream.puts "subgraph cluster_#{prefix}#{name} {"
+        stream.puts " label=\"#{name}\""
+        stream.puts ' fontname="Helvetica"'
+        stream.puts ' fontsize="10"'
+        stream.puts ' fontcolor="black"'
+        stream.puts ' clusterrank="local"'
+        stream.puts " fillcolor=\"#{@@fill_colours[depth % @@fill_colours.length]}\""
+        stream.puts ' style="filled"'
+      end
+      dataflow.processors.each {|processor| write_processor(stream, processor, prefix, depth)}
+      write_source_cluster(stream, dataflow.sources, prefix)
+      write_sink_cluster(stream, dataflow.sinks, prefix)
+      dataflow.datalinks.each {|link| write_link(stream, link, dataflow, prefix)}
+      dataflow.coordinations.each {|coordination| write_coordination(stream, coordination, dataflow, prefix)}
+      if name != ""
+        stream.puts '}'
+      end
+    end
+    def write_processor(stream, processor, prefix, depth) # :nodoc:
+      # nested workflows
+      if "#{processor.type}" == "workflow"
+        dataflow = @t2flow_model.dataflow(processor.dataflow_id)
+        write_dataflow(stream, dataflow, prefix + dataflow.annotations.name, dataflow.annotations.name, depth.next)
+      else
+        stream.puts " \"#{prefix}#{processor.name}\" ["
+        stream.puts "  fillcolor=\"#{get_colour processor.type}\","
+        stream.puts '  shape="box",'
+        stream.puts '  style="filled",'
+        stream.puts '  height="0",'
+        stream.puts '  width="0",'
+        stream.puts "  label=\"#{processor.name}\""
+        stream.puts ' ];'
+      end
+    end
+    def write_source_cluster(stream, sources, prefix) # :nodoc:
+      if sources.length > 0
+        stream.puts " subgraph cluster_#{prefix}sources {"
+        stream.puts '  style="dotted"'
+        stream.puts '  label="Workflow Inputs"'
+        stream.puts '  fontname="Helvetica"'
+        stream.puts '  fontsize="10"'
+        stream.puts '  fontcolor="black"'
+        stream.puts '  rank="same"'
+        stream.puts " \"#{prefix}WORKFLOWINTERNALSOURCECONTROL\" ["
+        stream.puts '  shape="triangle",'
+        stream.puts '  width="0.2",'
+        stream.puts '  height="0.2",'
+        stream.puts '  fillcolor="brown1"'
+        stream.puts '  label=""'
+        stream.puts ' ]'
+        sources.each {|source| write_source(stream, source, prefix)}
+        stream.puts ' }'
+      end
+    end
+    def write_source(stream, source, prefix) # :nodoc:
+      stream.puts " \"#{prefix}WORKFLOWINTERNALSOURCE_#{source.name}\" ["
+      stream.puts '   shape="box",'
+      stream.puts "   label=\"#{source.name}\""
+      stream.puts '   width="0",'
+      stream.puts '   height="0",'
+      stream.puts '   fillcolor="skyblue"'
+      stream.puts ' ]'
+    end
+    def write_sink_cluster(stream, sinks, prefix) # :nodoc:
+      if sinks.length > 0
+        stream.puts " subgraph cluster_#{prefix}sinks {"
+        stream.puts '  style="dotted"'
+        stream.puts '  label="Workflow Outputs"'
+        stream.puts '  fontname="Helvetica"'
+        stream.puts '  fontsize="10"'
+        stream.puts '  fontcolor="black"'
+        stream.puts '  rank="same"'
+        stream.puts " \"#{prefix}WORKFLOWINTERNALSINKCONTROL\" ["
+        stream.puts '  shape="invtriangle",'
+        stream.puts '  width="0.2",'
+        stream.puts '  height="0.2",'
+        stream.puts '  fillcolor="chartreuse3"'
+        stream.puts '  label=""'
+        stream.puts ' ]'
+        sinks.each {|sink| write_sink(stream, sink, prefix)}
+        stream.puts ' }'
+      end
+    end
+    def write_sink(stream, sink, prefix) # :nodoc:
+      stream.puts " \"#{prefix}WORKFLOWINTERNALSINK_#{sink.name}\" ["
+      stream.puts '   shape="box",'
+      stream.puts "   label=\"#{sink.name}\""
+      stream.puts '   width="0",'
+      stream.puts '   height="0",'
+      stream.puts '   fillcolor="lightsteelblue2"'
+      stream.puts ' ]'
+    end
+    def write_link(stream, link, dataflow, prefix) # :nodoc:
+      if dataflow.sources.select{|s| s.name == link.source} != []
+        stream.write " \"#{prefix}WORKFLOWINTERNALSOURCE_#{link.source}\""
+      else
+        processor = dataflow.processors.select{|p| p.name == link.source.split(':')[0]}[0]
+        if "#{processor.type}" == "workflow"
+          df = @t2flow_model.dataflow(processor.dataflow_id)
+          stream.write " \"#{prefix}#{df.annotations.name}WORKFLOWINTERNALSINK_#{link.source.split(':')[1]}\""
+        else
+          stream.write " \"#{prefix}#{processor.name}\""
+        end
+      end
+      stream.write '->'
+      if dataflow.sinks.select{|s| s.name == link.sink} != []
+        stream.write "\"#{prefix}WORKFLOWINTERNALSINK_#{link.sink}\""
+      else
+        processor = dataflow.processors.select{|p| p.name == link.sink.split(':')[0]}[0]
+        if "#{processor.type}" == "workflow"
+          df = @t2flow_model.dataflow(processor.dataflow_id)
+          stream.write "\"#{prefix}#{df.annotations.name}WORKFLOWINTERNALSOURCE_#{link.sink.split(':')[1]}\""
+        else
+          stream.write "\"#{prefix}#{processor.name}\""
+        end
+      end
+      stream.puts ' ['
+      stream.puts ' ];'
+    end
+    def write_coordination(stream, coordination, dataflow, prefix) # :nodoc:
+      stream.write " \"#{prefix}#{coordination.control}"
+      processor = dataflow.processors.select{|p| p.name == coordination.control}[0]
+      stream.write 'WORKFLOWINTERNALSINKCONTROL' if "#{processor.type}" == "workflow"
+      stream.write '"->"'
+      stream.write "#{prefix}#{coordination.target}"
+      processor = dataflow.processors.select{|p| p.name == coordination.target}[0]
+      stream.write 'WORKFLOWINTERNALSOURCECONTROL' if "#{processor.type}" == "workflow"
+      stream.write "\""
+      stream.puts ' ['
+      stream.puts '  color="gray",'
+      stream.puts '  arrowhead="odot",'
+      stream.puts '  arrowtail="none"'
+      stream.puts ' ];'
+    end
+    def get_colour(processor_name) # :nodoc:
+      colour = @@processor_colours[processor_name]
+      if colour
+        colour
+      else
+        'white'
+      end
+    end
+    # Returns true if the given name is a processor; false otherwise
+    def Dot.is_processor?(processor_name)
+      true if @@processor_colours[processor_name]
+    end
+  end
+end

data/lib/t2flow/model.rb ADDED Viewed

@@ -0,0 +1,245 @@
+# This is the module containing the T2Flow model implementation i.e. the model structure/definition and all its internals.
+module T2Flow # :nodoc:
+  # The model for a given Taverna 2 workflow.
+  class Model
+    # The list of all the dataflows that make up the workflow.
+    attr_accessor :dataflows
+    # The list of any dependencies that have been found inside the workflow.
+    attr_accessor :dependencies
+    # Creates an empty model for a Taverna 2 workflow.
+    def initialize
+      @dataflows = []
+    end
+    # Retrieve the top-level dataflow ie the MAIN (containing) dataflow
+    def top_level
+      @dataflows[0]
+    end
+    # Retrieve the dataflow with the given ID
+    def dataflow(df_id)
+      df = @dataflows.select { |x| x.dataflow_id == df_id }
+      return df[0]
+    end
+    # Retrieve ALL the processors containing beanshells within the workflow.
+    def beanshells
+      beanshells = []
+      @dataflows.each { |dataflow|
+        dataflow.beanshells.each { |bean|
+          beanshells << bean
+        }
+      }
+      return beanshells
+    end
+    # Retrieve ALL the datalinks within the workflow
+    def datalinks
+      links = []
+      @dataflows.each { |dataflow|
+        dataflow.datalinks.each { |link|
+          links << link
+        }
+      }
+      return links
+    end
+    # Retrieve the annotations within the workflow.
+    # In the event that the workflow is nested,
+    # retrieve the top-level annotations.
+    def annotations
+      @dataflows[0].annotations
+    end
+    # Retrieve ALL the processors within the workflow
+    def processors
+      procs =[]
+      @dataflows.each { |dataflow|
+        dataflow.processors.each { |proc|
+          procs << proc
+        }
+      }
+      return procs
+    end
+    # Retrieve ALL the sources within the workflow
+    def sources
+      sources =[]
+      @dataflows.each { |dataflow|
+        dataflow.sources.each { |source|
+          sources << source
+        }
+      }
+      return sources
+    end
+    # Retrieve ALL the sinks within the workflow
+    def sinks
+      sinks =[]
+      @dataflows.each { |dataflow|
+        dataflow.sinks.each { |sink|
+          sinks << sink
+        }
+      }
+      return sinks
+    end
+    # Retrieve ALL the coordinations within the workflow
+    def coordinations
+      coordinations =[]
+      @dataflows.each { |dataflow|
+        dataflow.coordinations.each { |coordination|
+          coordinations << coordination
+        }
+      }
+      return coordinations
+    end
+    # Retrieve the unique dataflow ID for the top level dataflow.
+    def dataflow_id
+      @dataflows[0].dataflow_id
+    end
+  end
+  # The entities within the Taverna 2 mdoel which contains the different
+  # elements of the workflows; processors, sinks, sources, etc...
+  class Dataflow
+    # This returns a DataflowAnnotation object.
+    attr_reader :annotations
+    # Retrieve the list of processors specific to the dataflow.
+    attr_reader :processors
+    # Retrieve the list of datalinks specific to the dataflow.
+    attr_reader :datalinks
+    # Retrieve the list of sources specific to the dataflow.
+    attr_reader :sources
+    # Retrieve the list of sinks specific to the dataflow.
+    attr_reader :sinks
+    # Retrieve the list of coordinations specific to the dataflow.
+    attr_reader :coordinations
+    # The unique identifier of the dataflow.
+    attr_accessor :dataflow_id
+    # Creates a new Dataflow object.
+    def initialize
+      @annotations = DataflowAnnotation.new
+      @processors = []
+      @datalinks = []
+      @sources = []
+      @sinks = []
+      @coordinations = []
+    end
+    # Retrieve beanshell processors specific to this dataflow.
+    def beanshells
+      @processors.select { |x| x.type == "beanshell" }
+    end
+  end
+  # This is the (shim) object within the workflow.  This can be a beanshell,
+  # a webservice, a workflow, etc...
+  class Processor
+    # A string containing name of the processor.
+    attr_accessor :name
+    # A string containing the description of the processor if available.
+    # Returns nil otherwise.
+    attr_accessor :description
+    # A string for the type of processor, e.g. beanshell, workflow, webservice, etc...
+    attr_accessor :type
+    # For processors that have type == "dataflow", this is the the reference
+    # to the dataflow.  For all other processor types, this is nil.
+    attr_accessor :dataflow_id
+    # This only has a value in beanshell processors.  This is the actual script
+    # embedded with the processor which does all the "work"
+    attr_accessor :script
+    # This is a list of inputs that the processor can take in.
+    attr_accessor :inputs
+    # This is a list of outputs that the processor can produce.
+    attr_accessor :outputs
+  end
+  # This is the annotation object specific to the dataflow it belongs to.
+  # A DataflowAnnotation contains metadata about a given dataflow element.
+  class DataflowAnnotation
+    # The name used of the dataflow
+    attr_accessor :name
+    # A list of titles that have been assigned to the dataflow.
+    attr_accessor :titles
+    # A list ot descriptive strings about the dataflow.
+    attr_accessor :descriptions
+    # A list of authors of the dataflow
+    attr_accessor :authors
+  end
+  # This represents a connection between any of the following pair of entities:
+  # {processor -> processor}, {workflow -> workflow}, {workflow -> processor},
+  # and {processor -> workflow}.
+  class Datalink
+    # The name of the source (the starting point of the connection).
+    attr_accessor :source
+    # The name of the sink (the endpoint of the connection).
+    attr_accessor :sink
+  end
+  # This is a representation of the 'Run after...' function in Taverna
+  # where the selected processor or workflow is set to run after another.
+  class Coordination
+    # The name of the processor/workflow which is to run first.
+    attr_accessor :control
+    # The name of the processor/workflow which is to run after the control.
+    attr_accessor :target
+  end
+  # This is the start node of a Datalink.  Each source has a name and a port
+  # which is seperated by a colon; ":".
+  # This is represented as "source of a processor:port_name".
+  # 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
+  end
+  # This is the start node of a Datalink.  Each sink has a name and a port
+  # which is seperated by a colon; ":".
+  # This is represented as "sink of a processor:port_name".
+  # 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
+  end
+end

data/lib/t2flow/parser.rb ADDED Viewed

@@ -0,0 +1,192 @@
+require "libxml"
+module T2Flow
+  class Parser
+    # Returns the model for the given t2flow_file.
+    # The method accepts objects of classes File and String only.
+    # ===Usage
+    #   foo = ... # stuff to initialize foo here
+    #   bar = T2Flow::Parser.new.parse(foo)
+    def parse(t2flow)
+      case t2flow.class.to_s
+        when /string/i: document = LibXML::XML::Parser.string(t2flow).parse
+        when /file/i: document = LibXML::XML::Parser.string(t2flow.read).parse
+        else raise "Error parsing file."
+      end
+      root = document.root
+      raise "Doesn't appear to be a workflow!" if root.name != "workflow"
+      version = root["version"]
+      create_model(root, version)
+    end
+    def create_model(element, version) # :nodoc:
+      model = Model.new
+      local_depends = element.find("//localDependencies")
+      if local_depends
+        local_depends.each do |dependency|
+          dependency.each do |dep|
+            model.dependencies = [] if model.dependencies.nil?
+            model.dependencies << dep.content unless dep.content =~ /^\s*$/
+          end
+        end
+        model.dependencies.uniq! if model.dependencies
+      end
+      element.each do |dataflow|
+        dataflow_obj = Dataflow.new
+        dataflow_obj.dataflow_id = dataflow["id"]
+        dataflow.each do |elt|
+          case elt.name
+            when "name"
+              dataflow_obj.annotations.name = elt.content
+            when "inputPorts"
+              elt.each { |port| add_source(dataflow_obj, port) }
+            when "outputPorts"
+              elt.each { |port| add_sink(dataflow_obj, port) }
+            when "processors"
+              elt.each { |proc| add_processor(dataflow_obj, proc) }
+            when "datalinks"
+              elt.each { |link| add_link(dataflow_obj, link) }
+            when "conditions"
+              elt.each { |coord| add_coordination(dataflow_obj, coord) }
+            when "annotations"
+              elt.each { |ann| add_annotation(dataflow_obj, ann) }
+          end # case elt.name
+        end # dataflow.each
+        model.dataflows << dataflow_obj
+      end # element.each
+      temp = model.processors.select { |x| x.type == "workflow" }
+      temp.each do |proc|
+        df = model.dataflow(proc.dataflow_id)
+        df.annotations.name = proc.name
+      end
+      return model
+    end
+    def add_source(dataflow, port) # :nodoc:
+      source = Source.new
+      port.each do |elt|
+        case elt.name
+          when "name": source.name = elt.content
+        end
+      end
+      dataflow.sources << source
+    end
+    def add_sink(dataflow, port) # :nodoc:
+      sink = Sink.new
+      port.each do |elt|
+        case elt.name
+          when "name": sink.name = elt.content
+        end
+      end
+      dataflow.sinks << sink
+    end
+    def add_processor(dataflow, element) # :nodoc:
+      processor = Processor.new
+      element.each do |elt|
+        case elt.name
+          when "name"
+            processor.name = elt.content
+          when "activities" # a processor can only have one kind of activity
+            activity = elt.child
+            activity.each do |node|
+              if node.name == "configBean"
+                  activity_node = node.child
+                  if node["encoding"] == "dataflow"
+                    processor.dataflow_id = activity_node["ref"]
+                    processor.type = "workflow"
+                  else
+                    processor.type = activity_node.name.split(".")[-2]
+                    activity_node.each do |value_node|
+                      case value_node.name
+                        when "script"
+                          processor.script = value_node.content
+                        when "inputs"
+                          value_node.each { |input|
+                            input.each { |x|
+                              processor.inputs = [] if processor.inputs.nil?
+                              processor.inputs << x.content if x.name == "name"
+                            }
+                          }
+                        when "outputs"
+                          value_node.each { |output|
+                            output.each { |x|
+                              processor.outputs = [] if processor.outputs.nil?
+                              processor.outputs << x.content if x.name == "name"
+                            }
+                          }
+                      end # case value_node.name
+                    end # activity_node.each
+                  end # if else node["encoding"] == "dataflow"
+              end # if node.name == "configBean"
+            end # activity.each
+        end # case elt.name
+      end # element.each
+      dataflow.processors << processor
+    end
+    def add_link(dataflow, link) # :nodoc:
+      datalink = Datalink.new
+      link.each do |sink_source|
+        case sink_source.name
+          when "sink"
+            datalink.sink = sink_source.first.content
+            datalink.sink += ":" + sink_source.last.content if sink_source["type"] == "processor"
+          when "source"
+            datalink.source = sink_source.first.content
+            datalink.source += ":" + sink_source.last.content if sink_source["type"] == "processor"
+        end
+      end
+      dataflow.datalinks << datalink
+    end
+    def add_coordination(dataflow, condition) # :nodoc:
+      coordination = Coordination.new
+      coordination.control = condition["control"]
+      coordination.target = condition["target"]
+      dataflow.coordinations << coordination
+    end
+    def add_annotation(dataflow, annotation) # :nodoc:
+      node = LibXML::XML::Parser.string("#{annotation}").parse
+      content_node = node.find_first("//annotationBean")
+      content = content_node.child.next.content
+      case content_node["class"]
+        when /freetextdescription/i
+          dataflow.annotations.descriptions = [] unless dataflow.annotations.descriptions
+          dataflow.annotations.descriptions << content
+        when /descriptivetitle/i
+          dataflow.annotations.titles = [] unless dataflow.annotations.titles
+          dataflow.annotations.titles << content
+        when /author/i
+          dataflow.annotations.authors = [] unless dataflow.annotations.authors
+          dataflow.annotations.authors << content
+        end # case
+    end
+  end
+end

metadata ADDED Viewed

@@ -0,0 +1,91 @@
+--- !ruby/object:Gem::Specification
+name: myGrid-taverna-t2flow
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- Emmanuel Tagarira
+autorequire: t2flow
+bindir: bin
+cert_chain:
+date: 2009-08-18 00:00:00 -07:00
+default_executable:
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: libxml-ruby
+  type: :runtime
+  version_requirement:
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+    version:
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  type: :runtime
+  version_requirement:
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 2.4.3
+    version:
+- !ruby/object:Gem::Dependency
+  name: darkfish-rdoc
+  type: :runtime
+  version_requirement:
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.1.5
+    version:
+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: emmanuel.tagarira@student.manchester.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files:
+- README
+- LICENCE
+files:
+- lib/t2flow
+- lib/t2flow/dot.rb
+- lib/t2flow/model.rb
+- lib/t2flow/parser.rb
+- README
+- LICENCE
+has_rdoc: true
+homepage: http://www.mygrid.org.uk/
+licenses:
+post_install_message:
+rdoc_options:
+- -N
+- --tab-width=2
+- --main=README
+- --exclude='scufl.gemspec|test'
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 1.0.1
+  version:
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: "0"
+  version:
+requirements: []
+rubyforge_project:
+rubygems_version: 1.3.5
+signing_key:
+specification_version: 1
+summary: Support for interacting with the Taverna 2 workflow system (T2Flow).
+test_files: []