taverna-t2flow 0.4.5 → 0.5.0

data/CHANGES.rdoc

@@ -1,5 +1,10 @@
 = Changes log for the T2Flow Ruby Gem
 
+== Version 0.5.0
+
+* Split out model classes into different files.
+* Added +configuration+ hash to Processor model, where various type-specific attributes are stored.
+
 == Version 0.4.5
 
 * Add a top-level include file that matches the gem name.

data/Rakefile

@@ -17,7 +17,7 @@ require 'jeweler'
 
 task :default => [:test]
 
-T2FLOW_GEM_VERSION = "0.4.5"
+T2FLOW_GEM_VERSION = "0.5.0"
 
 Jeweler::Tasks.new do |s|
   s.name             = "taverna-t2flow"

data/lib/t2flow/model.rb

@@ -10,78 +10,85 @@
 # This is the module containing the T2Flow model implementation i.e. the
 # model structure/definition and all its internals.
 
+require 't2flow/model/coordination'
+require 't2flow/model/dataflow'
+require 't2flow/model/datalink'
+require 't2flow/model/port'
+require 't2flow/model/processor'
+require 't2flow/model/semantic_annotation'
+
 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 = []
       @dependencies = []
     end
-    
+
     # Retrieve the top level dataflow's name
     def name
       main.name
     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 =[]
@@ -94,43 +101,43 @@ module T2Flow # :nodoc:
     def coordinations
       self.main.coordinations
     end
-    
+
     # Retrieve ALL the coordinations found in a nested workflow
     def all_coordinations
       coordinations =[]
       @dataflows.each { |dataflow| coordinations << dataflow.coordinations }
       return coordinations.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.
@@ -143,7 +150,7 @@ module T2Flow # :nodoc:
     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 = []
@@ -153,254 +160,32 @@ module T2Flow # :nodoc:
       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
-    
-    # The role of the workflow
-    attr_accessor :role
 
-    # Creates a new Dataflow object.
-    def initialize
-      @annotations = DataflowAnnotation.new
-      @processors = []
-      @datalinks = []
-      @sources = []
-      @sinks = []
-      @coordinations = []
-    end
-    
-    def name
-      @annotations.name
-    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 :descriptions
-
-    def description
-      @descriptions.first
-    end
-    
-    # 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
-
-    # Value for string constants
-    attr_accessor :value
-
-    attr_accessor :semantic_annotation
-
-    def initialize
-      @descriptions = []
-    end
-
-  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
-
-    attr_accessor :semantic_annotation
-    
-    def initialize
-      @authors, @descriptions, @titles  = [], [], []
-    end
-  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, :semantic_annotation
-  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, :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
+      return proc_links
     end
   end
-
 end

data/lib/t2flow/model/coordination.rb

@@ -0,0 +1,11 @@
+# This is a representation of the 'Run after...' function in Taverna
+# where the selected processor or workflow is set to run after another.
+module T2Flow
+  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
+end

data/lib/t2flow/model/dataflow.rb

@@ -0,0 +1,72 @@
+# The entities within the Taverna 2 mdoel which contains the different
+# elements of the workflows; processors, sinks, sources, etc...
+module T2Flow
+  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
+
+    # The role of the workflow
+    attr_accessor :role
+
+    # Creates a new Dataflow object.
+    def initialize
+      @annotations = DataflowAnnotation.new
+      @processors = []
+      @datalinks = []
+      @sources = []
+      @sinks = []
+      @coordinations = []
+    end
+
+    def name
+      @annotations.name
+    end
+
+    # Retrieve beanshell processors specific to this dataflow.
+    def beanshells
+      @processors.select { |x| x.type == "beanshell" }
+    end
+  end
+
+
+# TODO: Remove this class. Not useful
+# 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
+
+    attr_accessor :semantic_annotation
+
+    def initialize
+      @authors, @descriptions, @titles  = [], [], []
+    end
+  end
+end

data/lib/t2flow/model/datalink.rb

@@ -0,0 +1,12 @@
+# This represents a connection between any of the following pair of entities:
+# {processor -> processor}, {workflow -> workflow}, {workflow -> processor},
+# and {processor -> workflow}.
+module T2Flow
+  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
+end

data/lib/t2flow/model/port.rb

@@ -0,0 +1,22 @@
+module T2Flow
+  class Port
+    attr_accessor :name, :descriptions, :example_values, :semantic_annotation
+  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 < Port
+  end
+
+
+# This is the end 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 < Port
+  end
+end

data/lib/t2flow/model/processor.rb

@@ -0,0 +1,97 @@
+# This is the (shim) object within the workflow.  This can be a beanshell,
+# a webservice, a workflow, etc...
+module T2Flow
+  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 :descriptions
+
+    def description
+      @descriptions.first
+    end
+
+    # 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.
+    def wsdl
+      @configuration[:wsdl]
+    end
+
+    # For processors of type "arbitrarywsdl", this is the operation invoked.
+    def wsdl_operation
+      @configuration[:wsdl_operation]
+    end
+
+    # For soaplab and biomoby services, this is the endpoint URI.
+    def endpoint
+      @configuration[:endpoint]
+    end
+
+    # Authority name for the biomoby service.
+    def biomoby_authority_name
+      @configuration[:biomoby_authority_name]
+    end
+
+    # Service name for the biomoby service. This is not necessarily the same
+    # as the processors name.
+    def biomoby_service_name
+      @configuration[:biomoby_service_name]
+    end
+
+    # Category for the biomoby service.
+    def biomoby_category
+      @configuration[:biomoby_category]
+    end
+
+    # Value for string constants
+    def value
+      @configuration[:value]
+    end
+
+    attr_accessor :semantic_annotation
+
+    # Hash containing details of the processors configuration.
+    attr_accessor :configuration
+
+    def initialize
+      @descriptions = []
+      @configuration = {}
+    end
+
+  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
+end

data/lib/t2flow/model/semantic_annotation.rb

@@ -0,0 +1,20 @@
+# 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.
+module T2Flow
+  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

@@ -128,6 +128,14 @@ module T2Flow
             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"]
@@ -139,21 +147,30 @@ module T2Flow
                     activity_node.each_element do |value_node|
                       case value_node.name
                         when "wsdl"
-                          processor.wsdl = value_node.content
+                          processor.configuration[:wsdl] = value_node.content
                         when "operation"
-                          processor.wsdl_operation = value_node.content
+                          processor.configuration[:wsdl_operation] = value_node.content
                         when /endpoint/i
-                          processor.endpoint = value_node.content
+                          processor.configuration[:endpoint] = value_node.content
                         when /servicename/i
-                          processor.biomoby_service_name = value_node.content
+                          processor.configuration[:biomoby_service_name] = value_node.content
                         when /authorityname/i
-                          processor.biomoby_authority_name = value_node.content
+                          processor.configuration[:biomoby_authority_name] = value_node.content
                         when "category"
-                          processor.biomoby_category = value_node.content
+                          processor.configuration[:biomoby_category] = value_node.content
                         when "script"
-                          processor.script = value_node.content
+                          processor.configuration[:script] = value_node.content
                         when "value"
-                          processor.value = value_node.content
+                          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|

data/taverna-t2flow.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "taverna-t2flow"
-  s.version = "0.4.5"
+  s.version = "0.5.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Finn Bacall", "Robert Haines", "David Withers", "Mannie Tagarira"]
-  s.date = "2013-03-14"
+  s.date = "2014-03-11"
   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 = ["support@mygrid.org.uk"]
   s.extra_rdoc_files = [
@@ -18,13 +18,18 @@ Gem::Specification.new do |s|
     "README.rdoc"
   ]
   s.files = [
-    ".rvmrc",
     "CHANGES.rdoc",
     "LICENCE",
     "README.rdoc",
     "Rakefile",
     "lib/t2flow/dot.rb",
     "lib/t2flow/model.rb",
+    "lib/t2flow/model/coordination.rb",
+    "lib/t2flow/model/dataflow.rb",
+    "lib/t2flow/model/datalink.rb",
+    "lib/t2flow/model/port.rb",
+    "lib/t2flow/model/processor.rb",
+    "lib/t2flow/model/semantic_annotation.rb",
     "lib/t2flow/parser.rb",
     "lib/taverna-t2flow.rb",
     "taverna-t2flow.gemspec",
@@ -38,6 +43,7 @@ Gem::Specification.new do |s|
     "test/fixtures/998.t2flow",
     "test/fixtures/999.t2flow",
     "test/fixtures/basic.t2flow",
+    "test/fixtures/component_using_workflow.t2flow",
     "test/fixtures/coordinated.t2flow",
     "test/fixtures/image_to_tiff_migration_action.t2flow",
     "test/fixtures/linked.t2flow",
@@ -52,7 +58,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://www.taverna.org.uk/"
   s.rdoc_options = ["-N", "--tab-width=2", "--main=README.rdoc"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.21"
+  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/component_using_workflow.t2flow

@@ -0,0 +1,24 @@
+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="fa8eeaf3-5816-4e19-afb4-468c318c9832" role="top"><name>Workflow1</name><inputPorts><port><name>in</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>out</name><annotations /></port></outputPorts><processors><processor><name>Extract_PNG_dimensions</name><inputPorts><port><name>fromFilename</name><depth>0</depth></port></inputPorts><outputPorts><port><name>dimensions</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.component</group><artifact>component-activity</artifact><version>1.1.2</version></raven><class>net.sf.taverna.t2.component.ComponentActivity</class><inputMap><map from="fromFilename" to="fromFilename" /></inputMap><outputMap><map from="dimensions" to="dimensions" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.component.ComponentActivityConfigurationBean xmlns="">
+  <registryBase>http://www.myexperiment.org</registryBase>
+  <familyName>SCAPE Image Characterisation Component</familyName>
+  <componentName>Extract PNG dimensions</componentName>
+  <componentVersion>2</componentVersion>
+</net.sf.taverna.t2.component.ComponentActivityConfigurationBean></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="fromFilename" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Extract_PNG_dimensions</processor><port>fromFilename</port></sink><source type="dataflow"><port>in</port></source></datalink><datalink><sink type="dataflow"><port>out</port></sink><source type="processor"><processor>Extract_PNG_dimensions</processor><port>dimensions</port></source></datalink></datalinks><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.IdentificationAssertion">
+        <identification>fa8eeaf3-5816-4e19-afb4-468c318c9832</identification>
+      </annotationBean>
+      <date>2014-03-11 09:20:07.794 UTC</date>
+      <creators />
+      <curationEventList />
+    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
+  </annotationAssertions>
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>

data/test/test_component_workflows.rb

@@ -48,4 +48,17 @@ class ComponentWorkflowTest < Test::Unit::TestCase
                  @image_migration_wf.processors[0].semantic_annotation.content.gsub(/\s+/, ""),
                  "@image_migration_wf.processors[0].semantic_annotation")
   end
+
+  def test_parses_component_information
+    p = File.expand_path(File.join(__FILE__, "..", "fixtures", "component_using_workflow.t2flow"))
+    wf = T2Flow::Parser.new.parse(File.new(p))
+
+    proc = wf.processors[0]
+    assert_not_nil(proc)
+    assert_not_nil(proc.configuration[:component])
+    assert_equal('http://www.myexperiment.org', proc.configuration[:component][:registry])
+    assert_equal('SCAPE Image Characterisation Component', proc.configuration[:component][:family_name])
+    assert_equal('Extract PNG dimensions', proc.configuration[:component][:name])
+    assert_equal(2, proc.configuration[:component][:version])
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taverna-t2flow
 version: !ruby/object:Gem::Version
-  version: 0.4.5
+  version: 0.5.0
   prerelease: 
 platform: ruby
 authors:
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-14 00:00:00.000000000 Z
+date: 2014-03-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -90,13 +90,18 @@ extra_rdoc_files:
 - LICENCE
 - README.rdoc
 files:
-- .rvmrc
 - CHANGES.rdoc
 - LICENCE
 - README.rdoc
 - Rakefile
 - lib/t2flow/dot.rb
 - lib/t2flow/model.rb
+- lib/t2flow/model/coordination.rb
+- lib/t2flow/model/dataflow.rb
+- lib/t2flow/model/datalink.rb
+- lib/t2flow/model/port.rb
+- lib/t2flow/model/processor.rb
+- lib/t2flow/model/semantic_annotation.rb
 - lib/t2flow/parser.rb
 - lib/taverna-t2flow.rb
 - taverna-t2flow.gemspec
@@ -110,6 +115,7 @@ files:
 - test/fixtures/998.t2flow
 - test/fixtures/999.t2flow
 - test/fixtures/basic.t2flow
+- test/fixtures/component_using_workflow.t2flow
 - test/fixtures/coordinated.t2flow
 - test/fixtures/image_to_tiff_migration_action.t2flow
 - test/fixtures/linked.t2flow
@@ -143,7 +149,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       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.

data/.rvmrc

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