mannie-taverna-t2flow 0.0.4 → 0.0.5

data/{README → README.rdoc}

@@ -1,7 +1,7 @@
 = Taverna[http://taverna.sourceforge.net] 2 Interaction Gem
 
-Author::        Emmanuel Tagarira
-Version::       0.0.4
+Authors::       Emmanuel Tagarira, David Withers
+Version::       0.0.5
 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

@@ -0,0 +1,7 @@
+= Version 0.0.5
+
+== Bug fixes
+- BioMart services now return a type value instead of nil when processor.type is invoked.
+
+== Added Functionality
+- Extraction of *some* inputs and outputs for service type processors.

data/lib/t2flow/parser.rb

@@ -132,10 +132,21 @@ module T2Flow
     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|
@@ -146,20 +157,21 @@ module T2Flow
                     processor.dataflow_id = activity_node["ref"]
                     processor.type = "workflow"
                   else
-                    processor.type = activity_node.name.split(".")[-2]
-
+                    processor.type = (activity_node.name =~ /martquery/i ?
+                        "biomart" : activity_node.name.split(".")[-2])
+                    
                     activity_node.each do |value_node|
                       case value_node.name
                         when "script"
                           processor.script = value_node.content
-                        when "inputs"
+                        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"
+                        when "outputs" # ALL ports present in beanshell
                           value_node.each { |output| 
                             output.each { |x| 
                               processor.outputs = [] if processor.outputs.nil?
@@ -174,6 +186,8 @@ module T2Flow
         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
     

metadata

@@ -1,14 +1,15 @@
 --- !ruby/object:Gem::Specification 
 name: mannie-taverna-t2flow
 version: !ruby/object:Gem::Version 
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors: 
 - Emmanuel Tagarira
+- David Withers
 autorequire: t2flow
 bindir: bin
 cert_chain: 
-date: 2009-08-21 00:00:00 -07:00
+date: 2009-09-10 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -48,23 +49,24 @@ executables: []
 extensions: []
 
 extra_rdoc_files: 
-- README
+- README.rdoc
 - LICENCE
+- Release_Notes.rdoc
 files: 
 - lib/t2flow
 - lib/t2flow/dot.rb
 - lib/t2flow/model.rb
 - lib/t2flow/parser.rb
-- README
+- README.rdoc
 - LICENCE
+- Release_Notes.rdoc
 has_rdoc: true
 homepage: http://www.mygrid.org.uk/
-licenses: 
 post_install_message: 
 rdoc_options: 
 - -N
 - --tab-width=2
-- --main=README
+- --main=README.rdoc
 - --exclude='scufl.gemspec|test'
 require_paths: 
 - lib
@@ -83,7 +85,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.5
+rubygems_version: 1.2.0
 signing_key: 
 specification_version: 1
 summary: Support for interacting with the Taverna 2 workflow system (T2Flow).