taverna-t2flow 0.1.1

data/ChangeLog.rdoc

@@ -0,0 +1,8 @@
+= Version 0.1.1
+Released:: Wednesday, September 16, 2009
+
+== Added Functionality
+- Retrieval of Taverna local workers.
+
+=== New instance method in T2Flow::Model
+      local_workers

data/LICENCE

@@ -0,0 +1,165 @@
+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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+
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data/README.rdoc

@@ -0,0 +1,80 @@
+= Taverna[http://taverna.sourceforge.net] 2 Interaction Gem
+
+Authors::       Emmanuel Tagarira, David Withers
+Version::       0.1.1
+Contact::       mailto:mannie@mygrid.org.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 mannie-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

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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.main)
+      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

@@ -0,0 +1,330 @@
+# 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 main
+      @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
+      self.all_processors.select { |x| x.type == "beanshell" }
+    end
+    
+    # Retrieve ALL processors of that are webservices WITHIN the model.
+    def web_services
+      self.all_processors.select { |x| x.type =~ /wsdl|soaplab|biomoby/i }
+    end
+    
+    # Retrieve ALL local workers WITHIN the workflow
+    def local_workers
+      self.all_processors.select { |x| x.type =~ /local/i }
+    end
+    
+    # Retrieve the datalinks from the top level of a nested workflow.
+    # If the workflow is not nested, retrieve all datalinks.
+    def datalinks
+      self.main.datalinks
+    end
+    
+    # Retrieve ALL the datalinks within a nested workflow
+    def all_datalinks
+      links = []
+      @dataflows.each { |dataflow| links << dataflow.datalinks }
+      return links.flatten
+    end
+    
+    # Retrieve the annotations specific to the workflow.  This does not return 
+    # any annotations from workflows encapsulated within the main workflow.
+    def annotations
+      self.main.annotations
+    end
+    
+    # Retrieve processors from the top level of a nested workflow.
+    # If the workflow is not nested, retrieve all processors.
+    def processors
+      self.main.processors
+    end
+    
+    # Retrieve ALL the processors found in a nested workflow
+    def all_processors
+      procs =[]
+      @dataflows.each { |dataflow| procs << dataflow.processors }
+      return procs.flatten
+    end
+    
+    # Retrieve the sources(inputs) to the workflow
+    def sources
+      self.main.sources
+    end
+    
+    # Retrieve ALL the sources(inputs) within the workflow
+    def all_sources
+      sources =[]
+      @dataflows.each { |dataflow| sources << dataflow.sources }
+      return sources.flatten
+    end
+    
+    # Retrieve the sinks(outputs) to the workflow
+    def sinks
+      self.main.sinks
+    end
+    
+    # Retrieve ALL the sinks(outputs) within the workflow
+    def all_sinks
+      sinks =[]
+      @dataflows.each { |dataflow| sinks << dataflow.sinks }
+      return sinks.flatten
+    end
+    
+    # Retrieve the unique dataflow ID for the top level dataflow.
+    def model_id
+      self.main.dataflow_id
+    end
+    
+    # For the given dataflow, return the beanshells and/or services which 
+    # have direct links to or from the given processor.
+    # If no dataflow is specified, the top-level dataflow is used.
+    # This does a recursive search in nested workflows.
+    # == Usage
+    #   my_processor = model.processor[0]
+    #   linked_processors = model.get_processors_linked_to(my_processor)
+    #   processors_feeding_into_my_processor = linked_processors.sources
+    #   processors_feeding_from_my_processor = linked_processors.sinks
+    def get_processor_links(processor)
+      return nil unless processor
+      proc_links = ProcessorLinks.new
+      
+      # SOURCES
+      sources = self.all_datalinks.select { |x| x.sink =~ /#{processor.name}:.+/ }
+      proc_links.sources = []
+
+      # SINKS
+      sinks = self.all_datalinks.select { |x| x.source =~ /#{processor.name}:.+/ }
+      proc_links.sinks = []
+      temp_sinks = []
+      sinks.each { |x| temp_sinks << x.sink }
+      
+      # Match links by port into format
+      # my_port:name_of_link_im_linked_to:its_port
+      sources.each do |connection|
+        link = connection.sink
+        connected_proc_name = link.split(":")[0]
+        my_connection_port = link.split(":")[1]
+        
+        if my_connection_port
+          source = my_connection_port << ":" << connection.source
+          proc_links.sources << source if source.split(":").size == 3
+        end
+      end
+      
+      sinks.each do |connection|
+        link = connection.source
+        connected_proc_name = link.split(":")[0]
+        my_connection_port = link.split(":")[1]
+        
+        if my_connection_port
+          sink = my_connection_port << ":" << connection.sink
+          proc_links.sinks << sink if sink.split(":").size == 3
+        end
+      end
+      
+      return proc_links
+    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_accessor :annotations
+    
+    # Retrieve the list of processors specific to the dataflow.
+    attr_accessor :processors
+    
+    # Retrieve the list of datalinks specific to the dataflow.
+    attr_accessor :datalinks
+    
+    # Retrieve the list of sources specific to the dataflow.
+    attr_accessor :sources
+    
+    # Retrieve the list of sinks specific to the dataflow.
+    attr_accessor :sinks
+    
+    # Retrieve the list of coordinations specific to the dataflow.
+    attr_accessor :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
+    
+    # For processors of type "arbitrarywsdl", this is the URI to the location
+    # of the wsdl file.
+    attr_accessor :wsdl
+    
+    # For processors of type "arbitrarywsdl", this is the operation invoked.
+    attr_accessor :wsdl_operation
+    
+    # For soaplab and biomoby services, this is the endpoint URI.
+    attr_accessor :endpoint
+    
+    # Authority name for the biomoby service.
+    attr_accessor :biomoby_authority_name
+
+    # Service name for the biomoby service. This is not necessarily the same 
+    # as the processors name.
+    attr_accessor :biomoby_service_name
+    
+    # Category for the biomoby service.
+    attr_accessor :biomoby_category
+  end
+
+
+  # This object is returned after invoking model.get_processor_links(processor)
+  # .  The object contains two lists of processors.  Each element consists of: 
+  # the input or output port the processor uses as a link, the name of the
+  # processor being linked, and the port of the processor used for the linking,
+  # all seperated by a colon (:) i.e. 
+  #   my_port:name_of_processor:processor_port
+  class ProcessorLinks
+    # The processors whose output is fed as input into the processor used in
+    # model.get_processors_linked_to(processor).
+    attr_accessor :sources
+    
+    # A list of processors that are fed the output from the processor (used in
+    # model.get_processors_linked_to(processor) ) as input.
+    attr_accessor :sinks
+  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, :descriptions, :example_values
+  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, :descriptions, :example_values
+  end  	
+
+end

data/lib/t2flow/parser.rb

@@ -0,0 +1,252 @@
+require "libxml"
+
+module T2Flow
+  
+  class Parser
+    # Returns the model for the given t2flow_file.
+    # The method accepts objects of classes File, StringIO 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$/i
+          document = LibXML::XML::Parser.string(t2flow).parse 
+        when /^stringio|file$/i
+          t2flow.rewind
+          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
+          when "annotations"
+            elt.each do |ann|
+              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
+      
+      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
+          when "annotations"
+            elt.each do |ann|
+              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
+      
+      dataflow.sinks << sink
+    end
+    
+    def add_processor(dataflow, element) # :nodoc:
+      processor = Processor.new
+      
+      temp_inputs = []
+      temp_outputs = []
+      
+      element.each 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" }
+            }
+          when /outputports/i # ports from services
+            elt.each { |port| 
+              port.each { |x| temp_outputs << x.content if x.name=="name" }
+            }
+          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 =~ /martquery/i ?
+                        "biomart" : activity_node.name.split(".")[-2])
+                    
+                    activity_node.each do |value_node|
+                      case value_node.name
+                        when "wsdl"
+                          processor.wsdl = value_node.content
+                        when "operation"
+                          processor.wsdl_operation = value_node.content
+                        when /endpoint/i
+                          processor.endpoint = value_node.content
+                        when /servicename/i
+                          processor.biomoby_service_name = value_node.content
+                        when /authorityname/i
+                          processor.biomoby_authority_name = value_node.content
+                        when "category"
+                          processor.biomoby_category = value_node.content
+                        when "script"
+                          processor.script = value_node.content
+                        when "inputs" # ALL ports present in beanshell
+                          value_node.each { |input| 
+                            input.each { |x| 
+                              processor.inputs = [] if processor.inputs.nil?
+                              processor.inputs << x.content if x.name == "name" 
+                            }
+                          }
+                        when "outputs" # ALL ports present in beanshell
+                          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
+      
+      processor.inputs = temp_inputs if processor.inputs.nil? && !temp_inputs.empty?
+      processor.outputs = temp_outputs if processor.outputs.nil? && !temp_outputs.empty?
+      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

@@ -0,0 +1,126 @@
+--- !ruby/object:Gem::Specification 
+name: taverna-t2flow
+version: !ruby/object:Gem::Version 
+  hash: 25
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 1
+  version: 0.1.1
+platform: ruby
+authors: 
+- Emmanuel Tagarira
+- David Withers
+autorequire: t2flow
+bindir: bin
+cert_chain: 
+date: 2009-09-16 00:00:00 +01:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: libxml-ruby
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 21
+        segments: 
+        - 1
+        - 1
+        - 3
+        version: 1.1.3
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: rdoc
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 25
+        segments: 
+        - 2
+        - 4
+        - 3
+        version: 2.4.3
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: darkfish-rdoc
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 25
+        segments: 
+        - 1
+        - 1
+        - 5
+        version: 1.1.5
+  type: :runtime
+  version_requirements: *id003
+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: mannie@mygrid.org.uk
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+- LICENCE
+- ChangeLog.rdoc
+files: 
+- lib/t2flow/dot.rb
+- lib/t2flow/model.rb
+- lib/t2flow/parser.rb
+- README.rdoc
+- LICENCE
+- ChangeLog.rdoc
+has_rdoc: true
+homepage: http://www.mygrid.org.uk/
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- -N
+- --tab-width=2
+- --main=README.rdoc
+- --exclude='t2flow.gemspec|test'
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 21
+      segments: 
+      - 1
+      - 0
+      - 1
+      version: 1.0.1
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 1
+summary: Support for interacting with the Taverna 2 workflow system (T2Flow).
+test_files: []
+