Class: T2Flow::Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/t2flow/parser.rb

Instance Method Summary collapse

Instance Method Details

#add_annotation(dataflow, annotation) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 234

def add_annotation(dataflow, annotation) # :nodoc:
  node = LibXML::XML::Parser.string("#{annotation}").parse
  content_node = node.find_first("//annotationBean")

  case content_node["class"]
    when /freetextdescription/i
      dataflow.annotations.descriptions << content_node.find_first('./text').content
    when /descriptivetitle/i
      dataflow.annotations.titles << content_node.find_first('./text').content
    when /author/i
      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

#add_coordination(dataflow, condition) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 225

def add_coordination(dataflow, condition) # :nodoc:
  coordination = Coordination.new
  
  coordination.control = condition["control"]
  coordination.target = condition["target"]
  
  dataflow.coordinations << coordination
end

#add_link(dataflow, link) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 201

def add_link(dataflow, link) # :nodoc:
  datalink = Datalink.new
  
  if sink = link.find_first('./t2:sink')
    if processor = sink.find_first('./t2:processor')
      datalink.sink = "#{processor.content}:"
    else
      datalink.sink = ""
    end
    datalink.sink += "#{sink.find_first('./t2:port').content}"
  end

  if source = link.find_first('./t2:source')
    if processor = source.find_first('./t2:processor')
      datalink.source = "#{processor.content}:"
    else
      datalink.source = ""
    end
    datalink.source += "#{source.find_first('./t2:port').content}"
  end

  dataflow.datalinks << datalink
end

#add_processor(dataflow, element) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 110

def add_processor(dataflow, element) # :nodoc:
  processor = Processor.new
  
  temp_inputs = []
  temp_outputs = []
  
  element.each_element do |elt|
    case elt.name
      when "name"
        processor.name = elt.content
      when /inputports/i # ports from services
        elt.each_element { |port| port.each_element { |x| temp_inputs << x.content if x.name=="name" }}
      when /outputports/i # ports from services
        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.find_first('./t2:activity')
        activity.each_element do |node|
          if node.name == "configBean"
              activity_node = node.child

              if activity_node.name == "net.sf.taverna.t2.component.ComponentActivityConfigurationBean"
                processor.configuration[:component] = {}
                processor.configuration[:component][:registry] = activity_node.find_first('./registryBase').content
                processor.configuration[:component][:family_name] = activity_node.find_first('./familyName').content
                processor.configuration[:component][:name] = activity_node.find_first('./componentName').content
                processor.configuration[:component][:version] = activity_node.find_first('./componentVersion').content.to_i
              end
              
              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_element do |value_node|
                  case value_node.name
                    when "wsdl"
                      processor.configuration[:wsdl] = value_node.content
                    when "operation"
                      processor.configuration[:wsdl_operation] = value_node.content
                    when /endpoint/i
                      processor.configuration[:endpoint] = value_node.content
                    when /servicename/i
                      processor.configuration[:biomoby_service_name] = value_node.content
                    when /authorityname/i
                      processor.configuration[:biomoby_authority_name] = value_node.content
                    when "category"
                      processor.configuration[:biomoby_category] = value_node.content
                    when "script"
                      processor.configuration[:script] = value_node.content
                    when "value"
                      processor.configuration[:value] = value_node.content
                    when "presentationOrigin"
                      processor.configuration[:interaction_page] = value_node.content
                    when "connectionSettings"
                      if processor.type == 'rshell'
                        processor.configuration[:r_server] = value_node.find_first('./host').content + ":" +
                            value_node.find_first('./port').content
                      end
                    when "xpathExpression"
                      processor.configuration[:xpath_expression] = value_node.content
                    when "inputs" # ALL ports present in beanshell
                      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_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"
          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

#add_sink(dataflow, port) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 102

def add_sink(dataflow, port) # :nodoc:
  return if port.nil? || port.content.chomp.strip.empty?
  
  sink = Sink.new      
  extract_port_metadata(sink, port)      
  dataflow.sinks << sink
end

#add_source(dataflow, port) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 94

def add_source(dataflow, port) # :nodoc:
  return if port.nil? || port.content.chomp.strip.empty?

  source = Source.new
  extract_port_metadata(source, port)            
  dataflow.sources << source
end

#create_model(element, version) ⇒ Object

:nodoc:



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# File 'lib/t2flow/parser.rb', line 42

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_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_element do |elt|
      case elt.name
        when "name"
          dataflow_obj.annotations.name = elt.content
        when "inputPorts"
          elt.each_element { |port| add_source(dataflow_obj, port) }
        when "outputPorts"
          elt.each_element { |port| add_sink(dataflow_obj, port) }
        when "processors"
          elt.each_element { |proc| add_processor(dataflow_obj, proc) }
        when "datalinks"
          elt.each_element { |link| add_link(dataflow_obj, link) }
        when "conditions"
          elt.each_element { |coord| add_coordination(dataflow_obj, coord) }
        when "annotations"
          elt.each_element { |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

#parse(t2flow) ⇒ Object

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)



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# File 'lib/t2flow/parser.rb', line 22

def parse(t2flow)
  case t2flow.class.to_s
    when /^string$/i
      document = LibXML::XML::Parser.string(t2flow, :options => LibXML::XML::Parser::Options::NOBLANKS).parse
    when /^stringio|file$/i
      t2flow.rewind
      document = LibXML::XML::Parser.string(t2flow.read, :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"]
  
  create_model(root, version)
end