ols 0.0.1 → 0.1.0

data/lib/ols/version.rb

@@ -1,3 +1,6 @@
+# encoding: utf-8
+
 module OLS
-  VERSION = "0.0.1"
+  # OLS::VERSION - The OLS gem version
+  VERSION = "0.1.0"
 end

data/ols.gemspec

@@ -9,15 +9,10 @@ Gem::Specification.new do |s|
   s.authors     = ["Darren Oakley"]
   s.email       = ["daz.oakley@gmail.com"]
   s.homepage    = "https://github.com/dazoakley/ols"
-  s.summary     = %q{A simple wrapper around a local copy of the OLS database}
+  s.summary     = %q{A simple wrapper around the EBI's Ontology Lookup Service (OLS)}
   s.description = %q{
-    OLS provides a simple interface to the EBI's Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup/).  
-    It provides an easy lookup of ontology terms and automagically builds up ontology trees using RubyTree 
-    (http://rubytree.rubyforge.org/) as a base library.
-
-    PLEASE NOTE: The current version of this gem requires a local install of the OLS database running on MySQL.  
-    Please see http://www.ebi.ac.uk/ontology-lookup/databaseExport.do  I will update the code in the future 
-    to run off the soap service.
+    OLS provides a simple interface to the EBI's Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup/).
+    It provides an easy lookup of ontology terms and automagically builds up ontology trees for you.
   }
 
   s.rubyforge_project = "ols"
@@ -27,13 +22,13 @@ Gem::Specification.new do |s|
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
   
-  s.add_dependency "rubytree"
-  s.add_dependency "sequel"
-  s.add_dependency "mysql2"
-  s.add_dependency "json"
+  s.add_dependency "savon"
   
   s.add_development_dependency "rake"
   s.add_development_dependency "shoulda"
+  s.add_development_dependency "vcr"
+  s.add_development_dependency "webmock"
   s.add_development_dependency "simplecov"
   s.add_development_dependency "simplecov-rcov"
+  s.add_development_dependency "mocha"
 end

data/script/console

@@ -0,0 +1,9 @@
+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/ols.rb'}"
+
+puts "Loading ols gem"
+exec "#{irb} #{libs} --simple-prompt"

data/test/test_helper.rb

@@ -8,27 +8,42 @@ if /^1.9/ === RUBY_VERSION
   begin
     require 'simplecov'
     require 'simplecov-rcov'
-    
+
     class SimpleCov::Formatter::MergedFormatter
       def format(result)
          SimpleCov::Formatter::HTMLFormatter.new.format(result)
          SimpleCov::Formatter::RcovFormatter.new.format(result)
       end
     end
-    
+
     SimpleCov.formatter = SimpleCov::Formatter::MergedFormatter
-    SimpleCov.start
+    SimpleCov.start do
+      add_filter "/test/"
+    end
   rescue LoadError
     puts "[ERROR] Unable to load 'simplecov' - please run 'bundle install'"
   end
 end
 
 require 'shoulda'
+require 'vcr'
+require 'mocha'
 require 'ols'
 
-OLS.db_connection_details = {
-  :port     => 13306,
-  :database => 'htgt_ols',
-  :user     => 'htgt',
-  :password => 'htgt'
-}
+# Set-up VCR for mocking up web requests.
+VCR.config do |c|
+  if /^1\.8/ === RUBY_VERSION
+    c.cassette_library_dir = 'test/vcr_cassettes_ruby1.8'
+  elsif RUBY_VERSION == "1.9.1"
+    c.cassette_library_dir = 'test/vcr_cassettes_ruby1.9.1'
+  else
+    c.cassette_library_dir = 'test/vcr_cassettes_ruby1.9.2+'
+  end
+
+  c.stub_with                :webmock
+  c.ignore_localhost         = true
+  c.default_cassette_options = { 
+    :record            => :new_episodes, 
+    :match_requests_on => [:uri, :method, :body]
+  }
+end

data/test/test_ols.rb

@@ -1,124 +1,56 @@
 require 'test_helper'
 
 class OLSTest < Test::Unit::TestCase
-  include OLS
-  
-  context "An OntologyTerm object" do
+  context 'The OLS module' do
     setup do
-      @emap_id   = "EMAP:3018"
-      @emap_name = "TS18,nose"
-      @ont = OntologyTerm.new(@emap_id)
+      VCR.insert_cassette('test_ols')
     end
-    
-    should "have basic attributes" do
-      assert_equal( @emap_id, @ont.name, "OntologyTerm.name does not equal '#{@emap_id}'." )
-      assert_equal( @emap_id, @ont.term, "OntologyTerm.term does not equal '#{@emap_id}'." )
-      
-      assert_equal( @emap_name, @ont.content, "OntologyTerm.content does not equal '#{@emap_name}'." )
-      assert_equal( @emap_name, @ont.term_name, "OntologyTerm.term_name does not equal '#{@emap_name}'." )
-      
-      assert_equal( false, @ont.term_name.nil?, "The OntologyTerm.term_name is nil." )
-      assert_equal( false, @ont.content.nil?, "The OntologyTerm.term_name is nil." )
-    end
-    
-    should "raise appropriate errors" do
-      assert_raise(OntologyTermNotFoundError) { OntologyTerm.new("FLIBBLE:5") }
-    end
-    
-    should "be able to represent itself as a String" do
-      string = @ont.to_s
-      
-      assert( string.include?('Term Name'), "OntologyTerm.to_s does not include 'Term Name'." )
-      assert( string.include?(@ont.content), "OntologyTerm.to_s does not include '@content'." )
-      assert( string.include?('Root Term?'), "OntologyTerm.to_s does not include 'Root Term?'." )
-      assert( string.include?('Leaf Node?'), "OntologyTerm.to_s does not include 'Leaf Node?'." )
-    end
-    
-    should "respond correctly to the .parentage method" do
-      assert( @ont.parentage.is_a?(Array), "OntologyTerm.parentage is not an Array when we have parents." )
-      assert( @ont.parentage[0].is_a?(OntologyTerm), "OntologyTerm.parentage[0] does not return an OntologyTerm tree." )
-      assert_equal( 4, @ont.parentage.size, "OntologyTerm.parentage is not returning the correct number of entries (we expect 4 for #{@emap_id})." )
-    end
-    
-    should "be able to generate its child tree" do
-      assert( @ont.child_tree.is_a?(OntologyTerm), "OntologyTerm.child_tree does not return an OntologyTerm tree." )
-      assert_equal( @ont.term, @ont.child_tree.term, "OntologyTerm.child_tree.root is equal to self." )
-    end
-        
-    should "respond correctly to the .children method" do
-      assert( @ont.children.is_a?(Array), "OntologyTerm.children is not an Array when we have children." )
-      assert( @ont.children[0].is_a?(OntologyTerm), "OntologyTerm.children[0] does not return an OntologyTerm tree." )
-      assert_equal( 3, @ont.children.size, "OntologyTerm.children is not returning the correct number of entries (we expect 3 direct children for #{@emap_id})." )
+
+    teardown do
+      VCR.eject_cassette
     end
-    
-    should "be able to generate a flat list of all child terms/names" do
-      assert( @ont.all_child_terms.is_a?(Array), "OntologyTerm.all_child_terms is not an Array." )
-      assert( @ont.all_child_terms[0].is_a?(String), "OntologyTerm.all_child_terms[0] is not an String." )
-      assert_equal( 14, @ont.all_child_terms.size, "OntologyTerm.all_child_terms is not returning the correct number of entries (we expect 14 children for #{@emap_id})." )
-      
-      assert( @ont.all_child_names.is_a?(Array), "OntologyTerm.all_child_names is not an Array." )
-      assert( @ont.all_child_names[0].is_a?(String), "OntologyTerm.all_child_names[0] is not an String." )
-      assert_equal( 14, @ont.all_child_names.size, "OntologyTerm.all_child_names is not returning the correct number of entries (we expect 14 children for #{@emap_id})." )
-      
-      assert_equal( @ont.all_child_terms.size, @ont.all_child_names.size, "OntologyTerm.all_child_terms and OntologyTerm.all_child_names do not produce an array of the same size." )
+
+    should 'make a connection to the OLS SOAP service' do
+      assert OLS.client
+      assert OLS.client.is_a? Savon::Client
     end
-    
-    should "be able to locate ontology terms via synonyms" do
-      go_id = 'GO:0007242'
-      ont   = OntologyTerm.new(go_id)
-      
-      assert_equal( 'GO:0023034', ont.term, "A synonym search for GO:0007242 has not found GO:0023034." )
-      assert_equal( 'intracellular signaling pathway', ont.term_name, "A synonym search for GO:0007242 has not found 'intracellular signaling pathway'." )
+
+    should 'give access to version metadata' do
+      assert OLS.version
+      assert OLS.version.is_a? String
     end
-    
-    should "be able to serialize/deserialize itself as a JSON string" do
-      @ont.build_tree()
-      
-      json_string = nil
-      assert_nothing_raised(Exception) { json_string = @ont.to_json }
-      assert( json_string.is_a?(String) )
-      
-      duplicate = nil
-      assert_nothing_raised(Exception) { duplicate = JSON.parse(json_string) }
-      assert( duplicate.is_a?(OntologyTerm) )
-      assert_equal( @ont.term, duplicate.term )
-      assert_equal( @ont.term_name, duplicate.term_name )
-      assert_equal( @ont.is_root?, duplicate.is_root? )
-      assert_equal( @ont.is_leaf?, duplicate.is_leaf? )
+
+    should 'list the available ontologies' do
+      assert OLS.ontologies
+      assert OLS.ontologies.is_a? Hash
+      assert OLS.ontologies.include?('EMAP')
     end
-    
-    should "be able to produce a detached copy of itself" do
-      @ont.build_tree()
-      duplicate = @ont.detached_copy
-      
-      assert_equal( @ont.term, duplicate.term )
-      assert_equal( @ont.term_name, duplicate.term_name )
-      assert_equal( @ont.is_root?, duplicate.is_root? )
-      assert_equal( @ont.is_leaf?, duplicate.is_leaf? )
-      
-      assert_equal( false, duplicate.send(:already_fetched_parents) )
-      assert_equal( false, duplicate.send(:already_fetched_children) )
+
+    should 'provide easy access to the root terms of ontologies' do
+      emap_roots = OLS.root_terms('EMAP')
+      emap_root  = emap_roots.first
+
+      assert emap_roots.is_a? Array
+      assert emap_root.is_a? OLS::Term
+      assert_equal 'EMAP:0', emap_root.term_id
+      assert_equal 'Mouse_anatomy_by_time_xproduct', emap_root.term_name
+      assert emap_root.parents.empty?
+      assert_equal 3, OLS.root_terms('GO').size
     end
-    
-    should "be able to merge two ontology trees" do
-      @ont2 = OntologyTerm.new('EMAP:3003')
-      
-      @ont.build_tree
-      @ont2.build_tree
-      
-      merged_tree = @ont.merge(@ont2)
-      
-      assert( merged_tree['EMAP:2636']['EMAP:2822']['EMAP:2987'].is_a?(OntologyTerm) )
-      assert_equal( 2, merged_tree['EMAP:2636']['EMAP:2822']['EMAP:2987'].children.size )
-      assert_equal( 34, merged_tree.size )
-      
-      another_ont     = OntologyTerm.new('GO:0023034')
-      yet_another_ont = OntologyTerm.new('EMAP:3003')
-      another_ont.build_tree
-      yet_another_ont.build_tree
-      
-      assert_raise(ArgumentError) { foo = another_ont.merge(yet_another_ont) }
-      assert_raise(TypeError) { bar = another_ont.merge('EMAP:3003') }
+
+    should 'find terms by id' do
+      emap_0 = OLS.find_by_id('EMAP:0')
+      assert emap_0.is_a? OLS::Term
+      assert_equal 'Mouse_anatomy_by_time_xproduct', emap_0.term_name
+      assert_raise(OLS::TermNotFoundError) { OLS.find_by_id('MP:WIBBLE') }
     end
+
+    # should 'be able to find terms by name' do
+    #   terms = OLS.find_by_name('mitochondrion','GO')
+    #   assert terms.first.is_a? OLS::Term
+    #   assert terms.size > 2
+    #   assert terms.delete_if { |elm| elm.term_name =~ /mitochondrion/ }.size == 0
+    # end
   end
-end
+end
+

data/test/test_ols_graph.rb

@@ -0,0 +1,36 @@
+require 'test_helper'
+
+class OLSGraphTest < Test::Unit::TestCase
+  context 'An OLS::Graph object' do
+    setup do
+      VCR.insert_cassette('test_ols_term')
+    end
+
+    teardown do
+      VCR.eject_cassette
+    end
+
+    context 'once created' do
+      setup do
+        @graph = OLS::Graph.new
+      end
+
+      should 'initialize correctly' do
+        assert @graph.instance_variable_get(:@graph).is_a? Hash
+        assert @graph.instance_variable_get(:@graph).empty?
+      end
+
+      should 'only allow OLS::Term objects to be addded to the graph' do
+        assert_raises (TypeError) { @graph.add_to_graph('foo') }
+        @graph.add_to_graph( OLS.find_by_id('EMAP:3018') )
+      end
+
+      should 'allow access to the nodes of the graph' do
+        assert_nil @graph['EMAP:3018']
+        @graph.add_to_graph( OLS.find_by_id('EMAP:3018') )
+        assert @graph['EMAP:3018'].is_a? Hash
+        assert @graph.find('EMAP:3018').is_a? OLS::Term
+      end
+    end
+  end
+end

data/test/test_ols_term.rb

@@ -0,0 +1,484 @@
+require 'test_helper'
+
+class OLSTermTest < Test::Unit::TestCase
+  context 'An OLS::Term object' do
+    setup do
+      VCR.insert_cassette('test_ols_term')
+    end
+
+    teardown do
+      VCR.eject_cassette
+    end
+
+    context 'once created' do
+      setup do
+        @emap_term = OLS.find_by_id('EMAP:3018')
+        @mp_term   = OLS.find_by_id('MP:0002115')
+      end
+
+      should 'have an id/term and a name' do
+        assert_equal 'EMAP:3018', @emap_term.term_id
+        assert_equal 'TS18,nose', @emap_term.term_name
+        assert_equal 'MP:0002115', @mp_term.term_id
+        assert_equal 'abnormal skeleton extremities morphology', @mp_term.term_name
+      end
+
+      should 'be able to represent itself as a string' do
+        assert_equal 'EMAP:3018 - TS18,nose', @emap_term.to_s
+      end
+
+      should 'be able to say if it is an obsolete term' do
+        assert_equal false, @emap_term.is_obsolete?
+        assert_equal false, OLS.find_by_id('GO:0007242').is_obsolete?
+        assert OLS.find_by_id('GO:0008945').is_obsolete?
+      end
+
+      should 'be able to give its definition' do
+        assert_nil @emap_term.definition
+        assert_equal 'any structural anomaly of the limb, autopod or tail bones', @mp_term.definition
+
+        go_term = OLS.find_by_id('GO:0007242')
+        assert_equal 'intracellular signal transduction', go_term.term_name
+        assert_equal(
+          'The process in which a signal is passed on to downstream components within '+\
+          'the cell, which become activated themselves to further propagate the signal '+\
+          'and finally trigger a change in the function or state of the cell.',
+          go_term.definition
+        )
+      end
+
+      should 'be able to give a terms synonyms' do
+        go_term = OLS.find_by_id('GO:0007242')
+
+        assert_equal 'intracellular signal transduction', go_term.term_name
+
+        assert go_term.synonyms.keys.include? :exact
+        assert go_term.synonyms[:exact].include? 'intracellular signaling chain'
+
+        assert go_term.synonyms.keys.include? :related
+        assert go_term.synonyms[:related].include? 'intracellular signaling pathway'
+
+        assert go_term.synonyms.keys.include? :narrow
+        assert go_term.synonyms[:narrow].include? 'signal transmission via intracellular cascade'
+
+        assert go_term.synonyms.keys.include? :alt_id
+        assert go_term.synonyms[:alt_id].include? 'GO:0023013'
+
+        assert_equal Hash, @emap_term.synonyms.class
+        assert @emap_term.synonyms.empty?
+      end
+
+      should 'be able to report its parents' do
+        assert_equal 1, @emap_term.parents.size
+        assert_equal 'EMAP:2987', @emap_term.parents.first.term_id
+
+        assert_equal 2, @mp_term.parents.size
+
+        mp_term_parent_term_ids = @mp_term.parent_ids
+        assert mp_term_parent_term_ids.include?('MP:0000545')
+        assert mp_term_parent_term_ids.include?('MP:0009250')
+
+        mp_term_parent_term_names = @mp_term.parent_names
+        assert mp_term_parent_term_names.include? OLS.find_by_id('MP:0000545').term_name
+        assert mp_term_parent_term_names.include? OLS.find_by_id('MP:0009250').term_name
+      end
+
+      should 'be able to generate a flat list of ALL parents (up the ontology)' do
+        assert @emap_term.all_parents.is_a? Array
+        assert @emap_term.all_parents.first.is_a? OLS::Term
+        assert_equal 4, @emap_term.all_parents.size
+        assert_equal 'EMAP:0', @emap_term.all_parents.first.term_id
+
+        assert @mp_term.all_parents.is_a? Array
+        assert @mp_term.all_parents.first.is_a? OLS::Term
+        assert_equal 7, @mp_term.all_parents.size
+        assert_equal 'MP:0000001', @mp_term.all_parents.first.term_id
+        assert_equal 'MP:0000001', @mp_term.all_parents[2].term_id
+        assert @mp_term.all_parents.last.term_id =~ /MP:0000545|MP:0009250/
+      end
+
+      should 'be able to generate a flat list of ALL parent terms/names' do
+        assert @emap_term.all_parent_ids.is_a? Array
+        assert_equal 4, @emap_term.all_parent_ids.size
+        assert_equal 'EMAP:0', @emap_term.all_parent_ids.first
+
+        assert @emap_term.all_parent_names.is_a? Array
+        assert_equal 4, @emap_term.all_parent_names.size
+        assert_equal 'Mouse_anatomy_by_time_xproduct', @emap_term.all_parent_names.first
+
+        assert @mp_term.all_parent_ids.is_a? Array
+        assert_equal 6, @mp_term.all_parent_ids.size
+        assert_equal 'MP:0000001', @mp_term.all_parent_ids.first
+
+        assert @mp_term.all_parent_names.is_a? Array
+        assert_equal 6, @mp_term.all_parent_names.size
+        assert_equal 'mammalian phenotype', @mp_term.all_parent_names.first
+      end
+
+      should 'be able to report its children' do
+        assert @emap_term.has_children?
+        assert_equal 3, @emap_term.children.size
+        assert @emap_term['EMAP:3022'].is_a? OLS::Term
+        assert @emap_term.children_ids.include? 'EMAP:3022'
+        assert @emap_term.children_names.include? OLS.find_by_id('EMAP:3022').term_name
+      end
+
+      should 'be able to generate a flat list of ALL children (down the ontology)' do
+        assert @emap_term.all_children.is_a? Array
+        assert @emap_term.all_children.first.is_a? OLS::Term
+        assert_equal 14, @emap_term.all_children.size
+        emap3032_included = false
+        @emap_term.all_children.each do |child|
+          emap3032_included = true if child.term_id.eql?('EMAP:3032')
+        end
+      end
+
+      should 'be able to generate a flat list of ALL child terms/names' do
+        assert @emap_term.all_child_ids.is_a? Array
+        assert_equal 14, @emap_term.all_child_ids.size
+        assert @emap_term.all_child_ids.include?('EMAP:3032')
+
+        assert @emap_term.all_child_names.is_a? Array
+        assert_equal 14, @emap_term.all_child_names.size
+        assert @emap_term.all_child_names.include?('TS18,mesenchyme,medial-nasal process')
+      end
+
+      should 'allow easy access to child terms using the [] helper' do
+        emap = OLS.find_by_id('EMAP:0')
+        assert emap['EMAP:2636'].is_a? OLS::Term
+        assert emap['EMAP:2636']['EMAP:2822'].is_a? OLS::Term
+        assert_equal 'EMAP:2636', emap['EMAP:2636'].term_id
+        assert_equal 'TS18,embryo', emap['EMAP:2636'].term_name
+      end
+
+      should "be able to say if it's a root/leaf node" do
+        assert_equal false, @emap_term.is_root?
+        assert_equal false, @emap_term.is_leaf?
+
+        emap3032 = OLS.find_by_id('EMAP:3032')
+        assert_equal false, emap3032.is_root?
+        assert emap3032.is_leaf?
+
+        emap0 = OLS.find_by_id('EMAP:0')
+        assert emap0.is_root?
+        assert_equal false, emap0.is_leaf?
+      end
+
+      should 'be able to give its depth level' do
+        assert_equal 0, OLS.find_by_id('EMAP:0').level
+        assert_equal 4, @emap_term.level
+        assert_equal 4, @mp_term.level
+      end
+
+      should 'be able to "focus" a empty ontology graph around a given term' do
+        # First, test the following EMAP graph...
+        #
+        # * EMAP:0
+        #     |---+ EMAP:2636
+        #         |---+ EMAP:2822
+        #             |---+ EMAP:2987
+        #                 |---+ EMAP:3018
+        #                     |---+ EMAP:3022
+        #                         |---+ EMAP:3023
+        #                             |---+ EMAP:3024
+        #                                 |---> EMAP:3025
+        #                                 |---> EMAP:3026
+        #                             |---+ EMAP:3027
+        #                                 |---> EMAP:3029
+        #                                 |---> EMAP:3028
+        #                             |---+ EMAP:3030
+        #                                 |---> EMAP:3031
+        #                                 |---> EMAP:3032
+        #                     |---> EMAP:3019
+        #                     |---+ EMAP:3020
+        #                         |---> EMAP:3021
+
+        @emap_term.focus_graph!
+
+        assert_equal 'EMAP:0', @emap_term.root.term_id
+        assert_equal 1, @emap_term.root.children.size
+        assert_equal 3, @emap_term.children.size
+        assert_equal 4, @emap_term.level
+
+        assert @emap_term.instance_variable_get :@already_fetched_parents
+        assert @emap_term.instance_variable_get :@already_fetched_children
+
+        assert @emap_term.root.instance_variable_get :@already_fetched_parents
+        assert @emap_term.root.instance_variable_get :@already_fetched_children
+
+        # Now test the following MP graph...
+        #
+        # * MP:0000001
+        #     |---+ MP:0005371
+        #         |---+ MP:0000545
+        #                 |---+ MP:0002115
+        #                     ...
+        #     |---+ MP:0005390
+        #         |---+ MP:0005508
+        #             |---+ MP:0009250
+        #                 |---+ MP:0002115
+        #                     ...
+        #
+
+        @mp_term.focus_graph!
+
+        assert_equal 'MP:0000001', @mp_term.root.term_id
+        assert_equal 2, @mp_term.root.children.size
+        assert @mp_term.root.children.map(&:term_id).include? 'MP:0005371'
+        assert @mp_term.root.children.map(&:term_id).include? 'MP:0005390'
+      end
+
+      should 'be able to "focus" a large pre-populated graph around a single term' do
+        # bulk out the target graph
+        @emap_term.focus_graph!
+        assert_equal 19, @emap_term.size
+
+        # make it a touch larger
+        @emap_term.merge!( OLS.find_by_id('EMAP:3003') )
+        assert_equal 34, @emap_term.size
+
+        # cut it back to the origninal focused graph
+        @emap_term.focus_graph!
+        raw_graph = @emap_term.instance_variable_get(:@graph).raw_graph
+        
+        assert_equal 19, @emap_term.size
+        assert_equal 19, raw_graph.keys.size
+        assert_equal false, raw_graph.keys.include?('EMAP:3003')
+      end
+
+      should 'be able to "focus" a large pre-populated graph around a single term without clobbering the existing graph' do
+        # bulk out the target graph
+        @emap_term.focus_graph!
+        assert_equal 19, @emap_term.size
+
+        # make it a touch larger
+        @emap_term.merge!( OLS.find_by_id('EMAP:3003') )
+        assert_equal 34, @emap_term.size
+
+        # cut it back to the origninal focused graph
+        new_graph = @emap_term.focus_graph
+
+        orig_raw_graph = @emap_term.instance_variable_get(:@graph).raw_graph
+        new_raw_graph  = new_graph.instance_variable_get(:@graph).raw_graph
+        
+        assert_equal 34, @emap_term.size
+        assert_equal 19, new_graph.size
+        
+        assert_equal 34, orig_raw_graph.keys.size
+        assert_equal 19, new_raw_graph.keys.size
+        
+        assert orig_raw_graph.keys.include?('EMAP:3003')
+        assert_equal false, new_raw_graph.keys.include?('EMAP:3003')
+      end
+
+      should 'be able to merge in another ontology graph that shares a common root term' do
+        # We're going to try and merge this subgraph (for EMAP:3018)
+        #
+        # * EMAP:0
+        #     |---+ EMAP:2636
+        #         |---+ EMAP:2822
+        #             |---+ EMAP:2987
+        #                 |---+ EMAP:3018
+        #                     |---+ EMAP:3022
+        #                         |---+ EMAP:3023
+        #                             |---+ EMAP:3024
+        #                                 |---> EMAP:3025
+        #                                 |---> EMAP:3026
+        #                             |---+ EMAP:3027
+        #                                 |---> EMAP:3029
+        #                                 |---> EMAP:3028
+        #                             |---+ EMAP:3030
+        #                                 |---> EMAP:3031
+        #                                 |---> EMAP:3032
+        #                     |---> EMAP:3019
+        #                     |---+ EMAP:3020
+        #                         |---> EMAP:3021
+        #
+        # With this one (for EMAP:3003)
+        #
+        # * EMAP:0
+        #     |---+ EMAP:2636
+        #         |---+ EMAP:2822
+        #             |---+ EMAP:2987
+        #                 |---+ EMAP:3003
+        #                     |---> EMAP:3012
+        #                     |---+ EMAP:3013
+        #                         |---> EMAP:3014
+        #                         |---> EMAP:3016
+        #                         |---> EMAP:3015
+        #                         |---> EMAP:3017
+        #                     |---+ EMAP:3004
+        #                         |---> EMAP:3005
+        #                     |---> EMAP:3006
+        #                     |---+ EMAP:3007
+        #                         |---> EMAP:3008
+        #                         |---> EMAP:3009
+        #                     |---+ EMAP:3010
+        #                         |---> EMAP:3011
+        #
+        # To give us...
+        #
+        # * EMAP:0
+        #     |---+ EMAP:2636
+        #         |---+ EMAP:2822
+        #             |---+ EMAP:2987
+        #                 |---+ EMAP:3018
+        #                     |---+ EMAP:3022
+        #                         |---+ EMAP:3023
+        #                             |---+ EMAP:3024
+        #                                 |---> EMAP:3025
+        #                                 |---> EMAP:3026
+        #                             |---+ EMAP:3027
+        #                                 |---> EMAP:3029
+        #                                 |---> EMAP:3028
+        #                             |---+ EMAP:3030
+        #                                 |---> EMAP:3031
+        #                                 |---> EMAP:3032
+        #                     |---> EMAP:3019
+        #                     |---+ EMAP:3020
+        #                         |---> EMAP:3021
+        #                 |---+ EMAP:3003
+        #                     |---> EMAP:3012
+        #                     |---+ EMAP:3013
+        #                         |---> EMAP:3014
+        #                         |---> EMAP:3016
+        #                         |---> EMAP:3015
+        #                         |---> EMAP:3017
+        #                     |---+ EMAP:3004
+        #                         |---> EMAP:3005
+        #                     |---> EMAP:3006
+        #                     |---+ EMAP:3007
+        #                         |---> EMAP:3008
+        #                         |---> EMAP:3009
+        #                     |---+ EMAP:3010
+        #                         |---> EMAP:3011
+        #
+
+        @emap_term.focus_graph!
+        assert_equal 19, @emap_term.size
+
+        @emap_term.merge!( OLS.find_by_id('EMAP:3003') )
+        assert_equal 34, @emap_term.size
+
+        main_merge_node = @emap_term.root['EMAP:2636']['EMAP:2822']['EMAP:2987']
+
+        assert main_merge_node.is_a?(OLS::Term)
+        assert_equal 2, main_merge_node.children.size
+        assert main_merge_node.children.map(&:term_id).include? 'EMAP:3003'
+        assert main_merge_node.children.map(&:term_id).include? 'EMAP:3018'
+
+        # Also check that the internal graph has been merged accordingly
+        raw_graph      = @emap_term.instance_variable_get(:@graph).raw_graph
+        emap3003_graph = raw_graph['EMAP:3003'][:object].instance_variable_get(:@graph).raw_graph
+        assert_equal 34, raw_graph.size
+        assert_equal raw_graph.object_id, emap3003_graph.object_id
+
+        another_ont     = OLS.find_by_id('GO:0023034')
+        yet_another_ont = OLS.find_by_id('EMAP:3003')
+
+        assert_raise(ArgumentError) { another_ont.merge!(yet_another_ont) }
+        assert_raise(TypeError) { another_ont.merge!('EMAP:3003') }
+      end
+
+      should 'allow deep copying of objects' do
+        @emap_term.focus_graph!
+        copy = @emap_term.dup
+
+        assert @emap_term.object_id != copy.object_id
+        assert @emap_term.instance_variable_get(:@graph).object_id != copy.instance_variable_get(:@graph).object_id
+        assert @emap_term.instance_variable_get(:@graph).raw_graph.object_id != copy.instance_variable_get(:@graph).raw_graph.object_id
+        assert_equal @emap_term.size, copy.size
+        assert_equal @emap_term.root.term_id, copy.root.term_id
+      end
+
+      should 'allow serialization using Marshal' do
+        @emap_term.focus_graph!
+
+        OLS.stubs(:request).returns(nil)
+
+        # check the stubbing is okay...
+        foo = OLS.find_by_id('EMAP:3003')
+        foo.focus_graph!
+        assert_equal 1, foo.size
+
+        # now get on with testing marshal...
+        data = Marshal.dump(@emap_term)
+        copy = Marshal.load(data)
+
+        assert_equal @emap_term.term_id, copy.term_id
+        assert_equal @emap_term.term_name, copy.term_name
+        assert_equal @emap_term.size, copy.size
+        assert_equal @emap_term.root.term_id, copy.root.term_id
+        assert_equal @emap_term.all_parent_ids, copy.all_parent_ids
+        assert_equal @emap_term.all_parent_names, copy.all_parent_names
+
+        OLS.unstub(:request)
+      end
+
+      should 'allow serialization using YAML' do
+        @emap_term.focus_graph!
+
+        OLS.stubs(:request).returns(nil)
+
+        require 'yaml'
+
+        # check the stubbing is okay...
+        foo = OLS.find_by_id('EMAP:3003')
+        foo.focus_graph!
+        assert_equal 1, foo.size
+
+        # now get on with testing yaml...
+        data = @emap_term.to_yaml
+        copy = YAML.load(data)
+
+        assert_equal @emap_term.term_id, copy.term_id
+        assert_equal @emap_term.term_name, copy.term_name
+        assert_equal @emap_term.size, copy.size
+        assert_equal @emap_term.root.term_id, copy.root.term_id
+        assert_equal @emap_term.all_parent_ids, copy.all_parent_ids
+        assert_equal @emap_term.all_parent_names, copy.all_parent_names
+
+        OLS.unstub(:request)
+      end
+
+      should 'allow users to write image files showing the graph structure' do
+        @mp_term.focus_graph!
+        assert_silent do
+          @mp_term.write_children_to_graphic_file('children')
+          @mp_term.write_parentage_to_graphic_file('parentage')
+        end
+        system("rm children.dot children.png parentage.dot parentage.png")
+      end
+
+      should 'allow users to print a graph representation of the graph to STDOUT' do
+        @emap_term.focus_graph!
+        emap_graph = <<-EMAP
+* EMAP:0
+    |---+ EMAP:2636
+        |---+ EMAP:2822
+            |---+ EMAP:2987
+                |---+ EMAP:3018
+                    |---+ EMAP:3022
+                        |---+ EMAP:3023
+                            |---+ EMAP:3024
+                                |---> EMAP:3025
+                                |---> EMAP:3026
+                            |---+ EMAP:3027
+                                |---> EMAP:3029
+                                |---> EMAP:3028
+                            |---+ EMAP:3030
+                                |---> EMAP:3031
+                                |---> EMAP:3032
+                    |---> EMAP:3019
+                    |---+ EMAP:3020
+                        |---> EMAP:3021
+EMAP
+
+        assert_output(emap_graph.lstrip,nil) do
+          @emap_term.root.print_graph
+        end
+      end
+    end
+  end
+end
+