taverna-t2flow 0.2.0 → 0.3.0

data/test/test_helper.rb

@@ -0,0 +1,50 @@
+module TestHelper
+  
+  def generic_model_test(model)
+    assert !model.nil?, "Model is nil!"
+
+    assert !(model.name.nil? || model.name.strip.empty?), "Model#name is empty/nil!"
+    
+    assert !(model.main.name.nil? || model.main.name.strip.empty?), "Model#main#name is empty/nil!"
+    assert_type(model.main, T2Flow::Dataflow, "Model#main")
+    
+    # Model
+    assert_type(model.dependencies, Array, "Model#dependencies")
+    assert_type(model.processors, Array, "Model#processors")
+    assert_type(model.sources, Array, "Model#sources")
+    assert_type(model.sinks, Array, "Model#sinks")
+    assert_type(model.coordinations, Array, "Model#coordinations")
+    assert_type(model.datalinks, Array, "Model#datalinks")
+
+    assert_type(model.all_processors, Array, "Model#all_processors")
+    assert_type(model.all_sources, Array, "Model#all_sources")
+    assert_type(model.all_sinks, Array, "Model#all_sinks")
+    assert_type(model.all_coordinations, Array, "Model#all_coordinations")
+    assert_type(model.all_datalinks, Array, "Model#all_datalinks")
+
+    assert_type(model.annotations, T2Flow::DataflowAnnotation, "Model#annotations")
+    assert_type(model.annotations.titles, Array, "Model#annotations#titles")
+    assert_type(model.annotations.authors, Array, "Model#annotations#authors")
+    assert_type(model.annotations.descriptions, Array, "Model#annotations#descriptions")
+    assert_type(model.annotations.name, String, "Model#annotations#name")
+
+    assert_type(model.beanshells, Array, "Model#beanshells")
+    assert_type(model.web_services, Array, "Model#web_services")
+    assert_type(model.local_workers, Array, "Model#local_workers")
+            
+    # ProcessorLinks
+    processor_links = model.get_processor_links(model.processors[0])
+    assert_type(processor_links, T2Flow::ProcessorLinks, "Model#get_processor_links")
+    assert_type(processor_links.sinks, Array, "ProcessorLinks#sinks")
+    assert_type(processor_links.sources, Array, "ProcessorLinks#sources")
+  end
+  
+  def assert_type(object, required_class, caption)
+    assert object.is_a?(required_class), "#{caption} has an incorrect type: #{object.class.name} -- #{required_class} expected"
+  end
+  
+  def assert_count(list, required_size, caption)
+    assert_equal required_size, list.size, "#{caption} has incorrect count: #{list.size} -- #{required_size} expected"
+  end
+  
+end

data/test/test_starter_pack_workflows.rb

@@ -0,0 +1,132 @@
+require 'rubygems'
+require 'test/unit'
+
+require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "model.rb"))
+require File.expand_path(File.join(__FILE__, "..", "..", "lib", "t2flow", "parser.rb"))
+
+require File.expand_path(File.join(__FILE__, "..", "test_helper.rb"))
+
+class StarterPackWorkflowsTest < Test::Unit::TestCase
+    
+  include TestHelper
+
+  def setup
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "996.t2flow"))
+    @emboss_tutorial_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "997.t2flow"))
+    @biomart_emboss_analysis_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "998.t2flow"))
+    @iteration_demo_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "999.t2flow"))
+    @interproscan_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "1000.t2flow"))
+    @pdb_fetch_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "1001.t2flow"))
+    @comic_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "1002.t2flow"))
+    @gbseq_wf = T2Flow::Parser.new.parse(File.new(path))
+    
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "1003.t2flow"))
+    @pipeline_list_wf = T2Flow::Parser.new.parse(File.new(path))
+
+    path = File.expand_path(File.join(__FILE__, "..", "fixtures", "1004.t2flow"))
+    @retrieve_seq_wf = T2Flow::Parser.new.parse(File.new(path))
+  end
+
+  def test_emboss_tutorial_wf
+    generic_model_test(@emboss_tutorial_wf)
+
+    assert_count(@emboss_tutorial_wf.processors, 15, "@emboss_tutorial_wf.processors")
+    assert_count(@emboss_tutorial_wf.sources, 0, "@emboss_tutorial_wf.sources")
+    assert_count(@emboss_tutorial_wf.sinks, 3, "@emboss_tutorial_wf.sinks")
+    assert_count(@emboss_tutorial_wf.datalinks, 17, "@emboss_tutorial_wf.datalinks")
+    assert_count(@emboss_tutorial_wf.coordinations, 0, "@emboss_tutorial_wf.coordinations")
+  end
+
+  def test_biomart_emboss_analysis_wf
+    generic_model_test(@biomart_emboss_analysis_wf)
+
+    assert_count(@biomart_emboss_analysis_wf.processors, 10, "@biomart_emboss_analysis_wf.processors")
+    assert_count(@biomart_emboss_analysis_wf.sources, 0, "@biomart_emboss_analysis_wf.sources")
+    assert_count(@biomart_emboss_analysis_wf.sinks, 4, "@biomart_emboss_analysis_wf.sinks")
+    assert_count(@biomart_emboss_analysis_wf.datalinks, 17, "@biomart_emboss_analysis_wf.datalinks")
+    assert_count(@biomart_emboss_analysis_wf.coordinations, 0, "@biomart_emboss_analysis_wf.coordinations")
+  end
+  
+  def test_iteration_demo_wf
+    generic_model_test(@iteration_demo_wf)
+
+    assert_count(@iteration_demo_wf.processors, 8, "@iteration_demo_wf.processors")
+    assert_count(@iteration_demo_wf.sources, 0, "@iteration_demo_wf.sources")
+    assert_count(@iteration_demo_wf.sinks, 1, "@iteration_demo_wf.sinks")
+    assert_count(@iteration_demo_wf.datalinks, 8, "@iteration_demo_wf.datalinks")
+    assert_count(@iteration_demo_wf.coordinations, 0, "@iteration_demo_wf.coordinations")
+  end
+
+  def test_interproscan_wf
+    generic_model_test(@interproscan_wf)
+
+    assert_count(@interproscan_wf.processors, 17, "@interproscan_wf.processors")
+    assert_count(@interproscan_wf.sources, 2, "@interproscan_wf.sources")
+    assert_count(@interproscan_wf.sinks, 5, "@interproscan_wf.sinks")
+    assert_count(@interproscan_wf.datalinks, 23, "@interproscan_wf.datalinks")
+    assert_count(@interproscan_wf.coordinations, 2, "@interproscan_wf.coordinations")
+  end
+
+  def test_pdb_fetch_wf
+    generic_model_test(@pdb_fetch_wf)
+
+    assert_count(@pdb_fetch_wf.processors, 5, "@pdb_fetch_wf.processors")
+    assert_count(@pdb_fetch_wf.sources, 1, "@pdb_fetch_wf.sources")
+    assert_count(@pdb_fetch_wf.sinks, 1, "@pdb_fetch_wf.sinks")
+    assert_count(@pdb_fetch_wf.datalinks, 6, "@pdb_fetch_wf.datalinks")
+    assert_count(@pdb_fetch_wf.coordinations, 0, "@pdb_fetch_wf.coordinations")
+  end
+  
+  def test_comic_wf
+    generic_model_test(@comic_wf)
+
+    assert_count(@comic_wf.processors, 6, "@comic_wf.processors")
+    assert_count(@comic_wf.sources, 0, "@comic_wf.sources")
+    assert_count(@comic_wf.sinks, 1, "@comic_wf.sinks")
+    assert_count(@comic_wf.datalinks, 7, "@comic_wf.datalinks")
+    assert_count(@comic_wf.coordinations, 0, "@comic_wf.coordinations")
+  end
+
+  def test_gbseq_wf
+    generic_model_test(@gbseq_wf)
+
+    assert_count(@gbseq_wf.processors, 10, "@gbseq_wf.processors")
+    assert_count(@gbseq_wf.sources, 0, "@gbseq_wf.sources")
+    assert_count(@gbseq_wf.sinks, 8, "@gbseq_wf.sinks")
+    assert_count(@gbseq_wf.datalinks, 16, "@gbseq_wf.datalinks")
+    assert_count(@gbseq_wf.coordinations, 0, "@gbseq_wf.coordinations")
+  end
+
+  def test_pipeline_list_wf
+    generic_model_test(@pipeline_list_wf)
+
+    assert_count(@pipeline_list_wf.processors, 8, "@pipeline_list_wf.processors")
+    assert_count(@pipeline_list_wf.sources,1, "@pipeline_list_wf.sources")
+    assert_count(@pipeline_list_wf.sinks, 1, "@pipeline_list_wf.sinks")
+    assert_count(@pipeline_list_wf.datalinks, 9, "@pipeline_list_wf.datalinks")
+    assert_count(@pipeline_list_wf.coordinations, 0, "@pipeline_list_wf.coordinations")
+  end
+  
+  def test_retrieve_seq_wf
+    generic_model_test(@retrieve_seq_wf)
+
+    assert_count(@retrieve_seq_wf.processors, 4, "@retrieve_seq_wf.processors")
+    assert_count(@retrieve_seq_wf.sources, 0, "@retrieve_seq_wf.sources")
+    assert_count(@retrieve_seq_wf.sinks, 1, "@retrieve_seq_wf.sinks")
+    assert_count(@retrieve_seq_wf.datalinks, 4, "@retrieve_seq_wf.datalinks")
+    assert_count(@retrieve_seq_wf.coordinations, 0, "@retrieve_seq_wf.coordinations")
+  end
+
+end

metadata

@@ -1,94 +1,146 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: taverna-t2flow
-version: !ruby/object:Gem::Version 
-  hash: 23
-  prerelease: false
-  segments: 
-  - 0
-  - 2
-  - 0
-  version: 0.2.0
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+  prerelease: 
 platform: ruby
-authors: 
-- Mannie Tagarira
+authors:
+- Robert Haines
 - David Withers
-autorequire: t2flow
+- Mannie Tagarira
+autorequire: 
 bindir: bin
-cert_chain: 
-date: 2010-07-27 00:00:00 +01:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: libxml-ruby
+cert_chain: []
+date: 2012-05-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.2
+  type: :development
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 21
-        segments: 
-        - 1
-        - 1
-        - 3
-        version: 1.1.3
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.9.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.9.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 3.9.4
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+- !ruby/object:Gem::Dependency
+  name: libxml-ruby
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.4
   type: :runtime
-  version_requirements: *id001
-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
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.4
+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:
+- rhaines@manchester.ac.uk
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
+- CHANGES.rdoc
+- LICENCE
 - README.rdoc
+files:
+- CHANGES.rdoc
 - LICENCE
-- ChangeLog.rdoc
-files: 
+- README.rdoc
+- Rakefile
 - 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/
+- taverna-t2flow.gemspec
+- test/fixtures/1000.t2flow
+- test/fixtures/1001.t2flow
+- test/fixtures/1002.t2flow
+- test/fixtures/1003.t2flow
+- test/fixtures/1004.t2flow
+- test/fixtures/996.t2flow
+- test/fixtures/997.t2flow
+- test/fixtures/998.t2flow
+- test/fixtures/999.t2flow
+- test/fixtures/basic.t2flow
+- test/fixtures/coordinated.t2flow
+- test/fixtures/linked.t2flow
+- test/fixtures/nested.t2flow
+- test/fixtures/processors.t2flow
+- test/run_tests.rb
+- test/test_bogus_workflows.rb
+- test/test_helper.rb
+- test/test_starter_pack_workflows.rb
+homepage: http://www.taverna.org.uk/
 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - -N
 - --tab-width=2
 - --main=README.rdoc
-- --exclude='t2flow.gemspec|test'
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+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 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.8.21
 signing_key: 
-specification_version: 1
-summary: Support for interacting with the Taverna 2 workflow system (T2Flow).
-test_files: []
-
+specification_version: 3
+summary: Support for interacting with Taverna 2 workflows.
+test_files:
+- test/run_tests.rb

data/ChangeLog.rdoc

@@ -1,7 +0,0 @@
-= Version 0.2.0
-Released:: Tuesday, July 27, 2010
-
-== Changes
-- Updated the unit tests which can now be run by entering "ruby tests/run_tests.rb"
-- Misc. bug fixes.
-- Added the following methods to the T2Flow::Model class: coordinates, all_coordinates, name