ols 0.3.1 → 0.3.2

data/History.txt

@@ -1,3 +1,8 @@
+=== 0.3.2 2011-11-09
+
+* Bugfix - the term_name was getting lost off of the new nodes when we merged two graphs.
+* Small feature enhancement - when printing the graph to stdout, add an option to print out the term_name too.
+
 === 0.3.1 2011-11-08
 
 * Renamed the OLS::Term.detach_* methods to much more sensible names.

data/lib/ols/graph.rb

@@ -21,7 +21,7 @@ module OLS
       source.raw_graph.each do |term_id,term_details|
         old_term = term_details[:object]
 
-        new_term = OLS::Term.new( old_term.term_id, old_term.term_id, self )
+        new_term = OLS::Term.new( old_term.term_id, old_term.term_name, self )
         [
           :@already_fetched_parents,
           :@already_fetched_children,

data/lib/ols/term.rb

@@ -447,8 +447,9 @@ module OLS
 
     # Pretty prints the (sub)graph rooted at this ontology term.
     #
+    # @param [Boolean] show_term_name Show the term name?
     # @param [Number] level The indentation level (4 spaces) to start with.
-    def print_graph(level=1)
+    def print_graph(show_term_name=false,level=1)
       if is_root?
         print "*"
       else
@@ -457,9 +458,11 @@ module OLS
         print( self.has_children? ? "+" : ">" )
       end
 
-      puts " #{self.term_id}"
+      print_str = " #{self.term_id}"
+      print_str << " - #{self.term_name}" if show_term_name
+      puts print_str
 
-      self.children.each { |child| child.print_graph(level + 1)}
+      self.children.each { |child| child.print_graph(show_term_name,level + 1)}
     end
 
     # Save an image file showing graph structure of all children from the current term.

data/lib/ols/version.rb

@@ -2,5 +2,5 @@
 
 module OLS
   # OLS::VERSION - The OLS gem version
-  VERSION = "0.3.1"
+  VERSION = "0.3.2"
 end

data/test/test_ols_term.rb

@@ -435,6 +435,9 @@ class OLSTermTest < Test::Unit::TestCase
         assert main_merge_node.children.map(&:term_id).include? 'EMAP:3003'
         assert main_merge_node.children.map(&:term_id).include? 'EMAP:3018'
 
+        assert_equal 'TS18,perioptic mesenchyme', @emap_term.root['EMAP:2636']['EMAP:2822']['EMAP:2987']['EMAP:3003']['EMAP:3012'].term_name
+        assert_equal 'TS18,retina', @emap_term.root['EMAP:2636']['EMAP:2822']['EMAP:2987']['EMAP:3003']['EMAP:3013'].term_name
+
         # 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
@@ -517,29 +520,29 @@ class OLSTermTest < Test::Unit::TestCase
       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:0 - Mouse_anatomy_by_time_xproduct
+    |---+ EMAP:2636 - TS18,embryo
+        |---+ EMAP:2822 - TS18,organ system
+            |---+ EMAP:2987 - TS18,sensory organ
+                |---+ EMAP:3018 - TS18,nose
+                    |---+ EMAP:3022 - TS18,process,nose
+                        |---+ EMAP:3023 - TS18,fronto-nasal process
+                            |---+ EMAP:3024 - TS18,frontal process
+                                |---> EMAP:3025 - TS18,ectoderm,frontal process
+                                |---> EMAP:3026 - TS18,mesenchyme,frontal process
+                            |---+ EMAP:3027 - TS18,latero-nasal process
+                                |---> EMAP:3029 - TS18,mesenchyme,latero-nasal process
+                                |---> EMAP:3028 - TS18,ectoderm,latero-nasal process
+                            |---+ EMAP:3030 - TS18,medial-nasal process
+                                |---> EMAP:3031 - TS18,ectoderm,medial-nasal process
+                                |---> EMAP:3032 - TS18,mesenchyme,medial-nasal process
+                    |---> EMAP:3019 - TS18,naso-lacrimal groove
+                    |---+ EMAP:3020 - TS18,olfactory pit
+                        |---> EMAP:3021 - TS18,nasal epithelium
 EMAP
 
         assert_output(emap_graph.lstrip,nil) do
-          @emap_term.root.print_graph
+          @emap_term.root.print_graph(true)
         end
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ols
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-08 00:00:00.000000000 Z
+date: 2011-11-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: savon
-  requirement: &2157249240 !ruby/object:Gem::Requirement
+  requirement: &2156771440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2157249240
+  version_requirements: *2156771440
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2157248800 !ruby/object:Gem::Requirement
+  requirement: &2156771000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157248800
+  version_requirements: *2156771000
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2157248380 !ruby/object:Gem::Requirement
+  requirement: &2156770580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157248380
+  version_requirements: *2156770580
 - !ruby/object:Gem::Dependency
   name: vcr
-  requirement: &2157247960 !ruby/object:Gem::Requirement
+  requirement: &2156770160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157247960
+  version_requirements: *2156770160
 - !ruby/object:Gem::Dependency
   name: webmock
-  requirement: &2157247540 !ruby/object:Gem::Requirement
+  requirement: &2156769740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157247540
+  version_requirements: *2156769740
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &2157247120 !ruby/object:Gem::Requirement
+  requirement: &2156769320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157247120
+  version_requirements: *2156769320
 - !ruby/object:Gem::Dependency
   name: simplecov-rcov
-  requirement: &2157246700 !ruby/object:Gem::Requirement
+  requirement: &2156768900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157246700
+  version_requirements: *2156768900
 - !ruby/object:Gem::Dependency
   name: mocha
-  requirement: &2157246280 !ruby/object:Gem::Requirement
+  requirement: &2156768480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2157246280
+  version_requirements: *2156768480
 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  "