mannie-taverna-t2flow 0.0.5 → 0.1.0

data/README.rdoc

@@ -1,7 +1,7 @@
 = Taverna[http://taverna.sourceforge.net] 2 Interaction Gem
 
 Authors::       Emmanuel Tagarira, David Withers
-Version::       0.0.5
+Version::       0.1.0
 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)

data/Release_Notes.rdoc

@@ -1,7 +1,8 @@
-= Version 0.0.5
-
-== Bug fixes
-- BioMart services now return a type value instead of nil when processor.type is invoked.
+= Version 0.1.0
+Released:: Monday, September 14, 2009
 
 == Added Functionality
-- Extraction of *some* inputs and outputs for service type processors.
+- Retrieval of processors directly connected/linked to the given processor.
+=== New instance method in T2Flow::Model
+      get_processor_links(processor)
+=== New supporting object T2Flow::ProcessorLinks

data/lib/t2flow/model.rb

@@ -28,13 +28,12 @@ module T2Flow # :nodoc:
     
     # Retrieve ALL the processors containing beanshells within the workflow.
     def beanshells
-      beanshells = []
-      @dataflows.each { |dataflow| 
-        dataflow.beanshells.each { |bean|
-          beanshells << bean
-        }
-      }
-      return 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 the datalinks from the top level of a nested workflow.
@@ -46,12 +45,8 @@ module T2Flow # :nodoc:
     # Retrieve ALL the datalinks within a nested workflow
     def all_datalinks
       links = []
-      @dataflows.each { |dataflow|
-        dataflow.datalinks.each { |link|
-          links << link
-        }
-      }
-      return links
+      @dataflows.each { |dataflow| links << dataflow.datalinks }
+      return links.flatten
     end
     
     # Retrieve the annotations specific to the workflow.  This does not return 
@@ -69,12 +64,8 @@ module T2Flow # :nodoc:
     # Retrieve ALL the processors found in a nested workflow
     def all_processors
       procs =[]
-      @dataflows.each { |dataflow|
-        dataflow.processors.each { |proc|
-          procs << proc
-        }
-      }
-      return procs
+      @dataflows.each { |dataflow| procs << dataflow.processors }
+      return procs.flatten
     end
     
     # Retrieve the sources(inputs) to the workflow
@@ -85,12 +76,8 @@ module T2Flow # :nodoc:
     # Retrieve ALL the sources(inputs) within the workflow
     def all_sources
       sources =[]
-      @dataflows.each { |dataflow|
-        dataflow.sources.each { |source|
-          sources << source
-        }
-      }
-      return sources
+      @dataflows.each { |dataflow| sources << dataflow.sources }
+      return sources.flatten
     end
     
     # Retrieve the sinks(outputs) to the workflow
@@ -101,18 +88,64 @@ module T2Flow # :nodoc:
     # Retrieve ALL the sinks(outputs) within the workflow
     def all_sinks
       sinks =[]
-      @dataflows.each { |dataflow|
-        dataflow.sinks.each { |sink|
-          sinks << sink
-        }
-      }
-      return 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
   
   
@@ -121,22 +154,22 @@ module T2Flow # :nodoc:
   # elements of the workflows; processors, sinks, sources, etc...
   class Dataflow
     # This returns a DataflowAnnotation object.
-    attr_reader :annotations
+    attr_accessor :annotations
     
     # Retrieve the list of processors specific to the dataflow.
-    attr_reader :processors
+    attr_accessor :processors
     
     # Retrieve the list of datalinks specific to the dataflow.
-    attr_reader :datalinks
+    attr_accessor :datalinks
     
     # Retrieve the list of sources specific to the dataflow.
-    attr_reader :sources
+    attr_accessor :sources
     
     # Retrieve the list of sinks specific to the dataflow.
-    attr_reader :sinks
+    attr_accessor :sinks
     
     # Retrieve the list of coordinations specific to the dataflow.
-    attr_reader :coordinations
+    attr_accessor :coordinations
     
     # The unique identifier of the dataflow.
     attr_accessor :dataflow_id
@@ -156,8 +189,8 @@ module T2Flow # :nodoc:
       @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...
@@ -172,7 +205,7 @@ module T2Flow # :nodoc:
     # 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 
+    # 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
     
@@ -185,9 +218,46 @@ module T2Flow # :nodoc:
     
     # 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.

data/lib/t2flow/parser.rb

@@ -162,6 +162,18 @@ module T2Flow
                     
                     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

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: mannie-taverna-t2flow
 version: !ruby/object:Gem::Version 
-  version: 0.0.5
+  version: 0.1.0
 platform: ruby
 authors: 
 - Emmanuel Tagarira
@@ -9,7 +9,7 @@ authors:
 autorequire: t2flow
 bindir: bin
 cert_chain: 
-date: 2009-09-10 00:00:00 -07:00
+date: 2009-09-14 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency