ols 0.2.1 → 0.3.0

data/History.txt

@@ -1,3 +1,9 @@
+=== 0.3.0 2011-11-08
+
+* Addition of new functions to deatch graphs from parents/children.
+* Small code clean and refactor of utility functions.
+* The OLS::Term.size method has been altered to return a count of unique nodes.
+
 === 0.2.1 2011-11-07
 
 * Cache bugfix.  Removed the use of 'Dir.chdir' as it was firing warnings.
@@ -9,12 +15,13 @@
 === 0.1.0 2011-11-04
 
 * Total rewrite (as a result please note API changes)...
-  * Switch to using the OLS SOAP service instead of local MySQL instance
-  * Remove the use of RubyTree as ontologies are Directed Acyclic Graphs (DAGs), not trees
+  * Switch to using the OLS SOAP service instead of local MySQL instance.
+  * Remove the use of RubyTree as ontologies are Directed Acyclic Graphs (DAGs), not trees.
 
 === 0.0.1 2011-04-15
 
 * Initial release:
-  * Basic wrapper around OLS database
-  * Builds tree objects automagically
-  * User configurable connection details
+  * Basic wrapper around OLS database.
+  * Builds tree objects automagically.
+  * User configurable connection details.
+

data/lib/ols/graph.rb

@@ -81,10 +81,10 @@ module OLS
     def add_relationship(parent,child)
       raise TypeError, "You must pass an OLS::Term object" unless parent.is_a? OLS::Term
       raise TypeError, "You must pass an OLS::Term object" unless child.is_a? OLS::Term
-      
+
       add_to_graph(parent) if self.find(parent.term_id).nil?
       add_to_graph(child) if self.find(child.term_id).nil?
-      
+
       @graph[parent.term_id][:children].push(child.term_id) unless @graph[parent.term_id][:children].include?(child.term_id)
       @graph[child.term_id][:parents].push(parent.term_id) unless @graph[child.term_id][:parents].include?(parent.term_id)
     end

data/lib/ols/term.rb

@@ -82,11 +82,11 @@ module OLS
       "#{@term_id} - #{@term_name}"
     end
 
-    # Returns the size of the full ontology graph.
+    # Returns the size of the full ontology graph (unique nodes).
     #
-    # @return [Integer] The size of the full ontology graph
+    # @return [Integer] The size of the full ontology graph (unique nodes)
     def size
-      self.root.all_children.size + 1
+      self.root.all_children.uniq.size + 1
     end
 
     # Returns depth of this term in its ontology graph.  Depth of a node is defined as:
@@ -351,7 +351,7 @@ module OLS
     #
     # @see #focus_graph
     def focus_graph!
-      really_focus_graph_around_term(self)
+      self.really_focus_graph_around_term!
     end
 
     # Flesh out and/or focus the ontology graph around this term.
@@ -395,36 +395,47 @@ module OLS
     # @see #focus_graph!
     def focus_graph
       copy = self.dup
-      really_focus_graph_around_term(copy)
+      copy.really_focus_graph_around_term!
       copy
     end
 
-    # Utility function for the #focus_graph and #focus_graph! methods.  This does the 
-    # real work of editing the OLS::Graph.
+    # Remove the children from this ontology graph.
     #
-    # @param [OLS::Term] term The term (and graph) to focus around
-    def really_focus_graph_around_term(term)
-      term.all_parents.each { |parent| parent.lock }
-      term.all_children.each { |child| child.lock }
+    # @see #detach_parents
+    # @since 0.3.0
+    def detach_parents!
+      self.really_detach_parents!
+    end
 
-      focus_terms = [term.term_id] + term.all_parent_ids + term.all_child_ids
-      graph = term.graph.raw_graph
+    # Returns a copy of this ontology term object with the children removed.
+    #
+    # @return [OLS::Term] A copy of this term with the children removed
+    #
+    # @see #detach_parents!
+    # @since 0.3.0
+    def detach_parents
+      copy = self.dup
+      copy.really_detach_parents!
+      copy
+    end
 
-      graph.delete_if { |key,val| !focus_terms.include?(key) }
-      graph.each do |key,val|
-        val[:parents].delete_if { |elm| !focus_terms.include?(elm) }
-        val[:children].delete_if { |elm| !focus_terms.include?(elm) }
-      end
+    # Removes the parents from this ontology graph.
+    #
+    # @see #detach_children
+    # @since 0.3.0
+    def detach_children!
+      self.really_detach_children!
     end
-    private(:really_focus_graph_around_term)
 
     # Returns a copy of this ontology term object with the parents removed.
     #
-    # @return [OLS::Term] A copy of this ontology term object with the parents removed
-    def detached_subgraph_copy
+    # @return [OLS::Term] A copy of this term with the parents removed
+    #
+    # @see #detach_children!
+    # @since 0.3.0
+    def detach_children
       copy = self.dup
-      copy.parents = []
-      copy.lock_parents
+      copy.really_detach_children!
       copy
     end
 
@@ -551,6 +562,12 @@ module OLS
       @graph[self.term_id][:parents] = parents.map(&:term_id)
     end
 
+    def children=(children)
+      raise ArgumentError, "You must pass an array" unless children.is_a?(Array)
+      children.each { |p| raise TypeError, "You must pass an array of OLS::Term objects" unless p.is_a?(OLS::Term) }
+      @graph[self.term_id][:children] = children.map(&:term_id)
+    end
+
     # Graph access function. Adds a parent relationship (for this term) to the graph.
     #
     # @param [OLS::Term] parent The OLS::Term to add as a parent
@@ -576,6 +593,53 @@ module OLS
       @graph.find(term_id)
     end
 
+    # Graph utility function.  Removes terms from the ontology graph
+    # that are not in the list passed to it.
+    #
+    # @param [Array] ids_to_retain The list of term_ids to keep in the graph
+    def flush_graph( ids_to_retain )
+      graph = @graph.raw_graph
+
+      graph.delete_if { |key,val| !ids_to_retain.include?(key) }
+      graph.each do |key,val|
+        val[:parents].delete_if { |elm| !ids_to_retain.include?(elm) }
+        val[:children].delete_if { |elm| !ids_to_retain.include?(elm) }
+      end
+    end
+
+    # Utility function for the #focus_graph and #focus_graph! methods.  This does the
+    # real work of editing the OLS::Graph.
+    #
+    # @see #focus_graph
+    # @see #focus_graph!
+    def really_focus_graph_around_term!
+      self.all_parents.each { |parent| parent.lock }
+      self.all_children.each { |child| child.lock }
+      self.flush_graph( [self.term_id] + self.all_parent_ids + self.all_child_ids )
+    end
+
+    # Utility function for #detach_parents and #detach_parents! that
+    # actually does the work of removing children.
+    #
+    # @see #detach_parents
+    # @see #detach_parents!
+    def really_detach_parents!
+      self.children = []
+      self.lock_children
+      self.flush_graph( [self.term_id] + self.all_parent_ids )
+    end
+
+    # Utility function for #detach_children and #detach_children! that
+    # actually does the work of removing parents.
+    #
+    # @see #detach_children
+    # @see #detach_children!
+    def really_detach_children!
+      self.parents = []
+      self.lock_parents
+      self.flush_graph( [self.term_id] + self.all_child_ids )
+    end
+
     private
 
     # Utility function to hit the :get_term_metadata soap endpoint and extract the
@@ -611,7 +675,7 @@ module OLS
       names_to_merge = names2 - names1
       names_to_merge.each do |name|
         # puts "--- MERGING #{name} INTO #{graph1.term_id} ---"
-        new_child = graph2[name].detached_subgraph_copy
+        new_child = graph2[name].detach_children
 
         # replace the new_child's graph
         graph1_graph             = graph1.graph

data/lib/ols/version.rb

@@ -2,5 +2,5 @@
 
 module OLS
   # OLS::VERSION - The OLS gem version
-  VERSION = "0.2.1"
+  VERSION = "0.3.0"
 end

data/test/test_helper.rb

@@ -42,8 +42,8 @@ VCR.config do |c|
 
   c.stub_with                :webmock
   c.ignore_localhost         = true
-  c.default_cassette_options = { 
-    :record            => :new_episodes, 
+  c.default_cassette_options = {
+    :record            => :new_episodes,
     :match_requests_on => [:uri, :method, :body]
   }
 end

data/test/test_ols_term.rb

@@ -240,7 +240,7 @@ class OLSTermTest < Test::Unit::TestCase
         # 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')
@@ -260,17 +260,85 @@ class OLSTermTest < Test::Unit::TestCase
 
         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 "detach" the graph to be able to retain just parents' do
+        # We expect the following here...
+        #
+        # * EMAP:0
+        #     |---+ EMAP:2636
+        #         |---+ EMAP:2822
+        #             |---+ EMAP:2987
+        #                 |---+ EMAP:3018
+
+        @emap_term.focus_graph!
+        @emap_term.detach_parents!
+
+        assert_equal 'EMAP:3018', @emap_term.term_id
+        assert_equal 'EMAP:0', @emap_term.root.term_id
+        assert_equal 5, @emap_term.size
+        assert_equal 5, @emap_term.instance_variable_get(:@graph).raw_graph.size
+
+        # Test the copy variant of this function
+        @mp_term.focus_graph!
+        new_term = @mp_term.detach_parents
+
+        assert new_term.object_id != @mp_term.object_id
+        assert new_term.is_leaf?
+        assert_equal 'MP:0000001', new_term.root.term_id
+        assert_equal 7, new_term.size
+        assert_equal 7, new_term.instance_variable_get(:@graph).raw_graph.size
+        assert_equal 102, @mp_term.size
+        assert_equal 102, @mp_term.instance_variable_get(:@graph).raw_graph.size
+      end
+
+      should 'be able to "detach" the graph to be able to retain just children' do
+        # We expect the following here...
+        #
+        # |---+ 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!
+        @emap_term.detach_children!
+
+        assert_equal 'EMAP:3018', @emap_term.term_id
+        assert @emap_term.is_root?
+        assert_equal 15, @emap_term.size
+        assert_equal 15, @emap_term.instance_variable_get(:@graph).raw_graph.size
+
+        # Test the copy variant of this function
+        @mp_term.focus_graph!
+        new_term = @mp_term.detach_children
+
+        assert new_term.object_id != @mp_term.object_id
+        assert_equal 96, new_term.size
+        assert_equal 96, new_term.instance_variable_get(:@graph).raw_graph.size
+        assert_equal 102, @mp_term.size
+        assert_equal 102, @mp_term.instance_variable_get(:@graph).raw_graph.size
+      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)
         #

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ols
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-07 00:00:00.000000000 Z
+date: 2011-11-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: savon
-  requirement: &2156971680 !ruby/object:Gem::Requirement
+  requirement: &2157089040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2156971680
+  version_requirements: *2157089040
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2156971240 !ruby/object:Gem::Requirement
+  requirement: &2157088600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156971240
+  version_requirements: *2157088600
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2156970820 !ruby/object:Gem::Requirement
+  requirement: &2157088180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156970820
+  version_requirements: *2157088180
 - !ruby/object:Gem::Dependency
   name: vcr
-  requirement: &2156970400 !ruby/object:Gem::Requirement
+  requirement: &2157087760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156970400
+  version_requirements: *2157087760
 - !ruby/object:Gem::Dependency
   name: webmock
-  requirement: &2156969980 !ruby/object:Gem::Requirement
+  requirement: &2157087340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156969980
+  version_requirements: *2157087340
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &2156969560 !ruby/object:Gem::Requirement
+  requirement: &2157086920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156969560
+  version_requirements: *2157086920
 - !ruby/object:Gem::Dependency
   name: simplecov-rcov
-  requirement: &2156969140 !ruby/object:Gem::Requirement
+  requirement: &2157086500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156969140
+  version_requirements: *2157086500
 - !ruby/object:Gem::Dependency
   name: mocha
-  requirement: &2156968720 !ruby/object:Gem::Requirement
+  requirement: &2157086080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156968720
+  version_requirements: *2157086080
 description: ! "\n    OLS provides a simple interface to the EBI's Ontology Lookup
   Service (http://www.ebi.ac.uk/ontology-lookup/).\n    It provides an easy lookup
   of ontology terms and automagically builds up ontology trees for you.\n  "