Changeset 411

Timestamp:

Apr 23, 2010, 12:00:31 AM (14 years ago)

Author:

KOBAYASHI, Shinji

Message:

fixed archetype ontology bugs

Location:

ruby/trunk

Files:

• lib/open_ehr/am/archetype/ontology.rb (modified) (1 diff)
• lib/open_ehr/serializer.rb (modified) (1 diff)
• spec/lib/open_ehr/am/archetype/ontology/archetype_ontology_spec.rb (modified) (2 diffs)
• spec/lib/open_ehr/am/archetype/ontology/archetype_term_spec.rb (modified) (2 diffs)
• spec/lib/open_ehr/serializer/adl_serializer_spec.rb (modified) (2 diffs)

ruby/trunk/lib/open_ehr/am/archetype/ontology.rb

@@ -4 +4 @@
       module Ontology
         class ArchetypeOntology
-          attr_accessor :constraint_codes, :specialisation_depth
-          attr_accessor :term_attribute_names, :term_codes
-          attr_reader :terminologies_available
+          attr_accessor :constraint_definitions, :specialisation_depth
+          attr_accessor :term_attribute_names, :term_bindings
+          attr_reader :terminologies_available, :term_definitions
 
           def initialize(args = { })
-            self.terminologies_available = args[:terminologies_available]
             self.specialisation_depth = args[:specialisation_depth]
-            self.term_codes = args[:term_codes]
-            self.constraint_codes = args[:constraint_codes]
-            self.term_attribute_names = args[:term_attribute_names]
+            self.term_definitions = args[:term_definitions]
+            self.constraint_definitions = args[:constraint_definitions]
+            self.term_bindings = args[:term_bindings]
           end
 
-          def terminologies_available=(terminologies_available)
-            if terminologies_available.nil?
-              raise ArgumentError, 'terminologies_available is mandatory'
+          # def terminologies_available=(terminologies_available)
+          #   if terminologies_available.nil?
+          #     raise ArgumentError, 'terminologies_available is mandatory'
+          #   end
+          #   @terminologies_available = terminologies_available
+          # end
+
+          def term_definitions=(term_definitions)
+            if term_definitions.nil?
+              raise ArgumentError, 'term_definitions is mandatory'
             end
-            @terminologies_available = terminologies_available
+            @term_definitions = term_definitions
+          end
+
+          def term_codes
+            return @term_definitions.values.collect {|value|
+              value.collect {|term| term.code}}.flatten.uniq
+          end
+
+          def constraint_codes
+            if @constraint_definitions.nil?
+              return nil
+            else
+              return @constraint_definitions.values.collect {|value|
+                value.collect {|term| term.code}}.flatten.uniq
+            end
           end
 

ruby/trunk/lib/open_ehr/serializer.rb

@@ -102 +102 @@
 
       def ontology
+        ao = @archetype.ontology
+        ontology = 'ontology'+NL
+        ontology << INDENT + 'term_definitions = <' + NL
+        ao.term_codes.each do |term, items|
+          ontology << INDENT*2 + "[\"#{term}\"] = <" + NL
+          ontology << INDENT*3 + 'items = <'  + NL
+          items.each do |code, attribute|
+            ontology << INDENT*4 + "[\"#{code}\] = <" + NL
+            terms.each do |name, description|
+              ontology << INDENT*5 + "#{name} = <\"#{description}\">" +NL
+            end
+            ontology << INDENT*4 + '>'+NL
+          end
+          ontogoly << INDENT*3 + '>' + NL
+          ontology << INDENT*2 + '>' + NL
+        end
+        ontology << INDENT + '>' + NL
       end
 

ruby/trunk/spec/lib/open_ehr/am/archetype/ontology/archetype_ontology_spec.rb

@@ -1 +1 @@
 require File.dirname(__FILE__) + '/../../../../../spec_helper'
 include OpenEHR::AM::Archetype::Ontology
+include OpenEHR::RM::DataTypes::Text
 
 describe ArchetypeOntology do
   before(:each) do
-    terminologies_available = stub(Set, :size =>1)
-    term_codes = stub(Array, :size => 2)
-    constraint_codes = stub(Array, :size => 3)
-    term_attribute_names = stub(Array, :size => 4)
+    items = {'TEXT' => 'text', 'DESC' => 'description'}
+    term1 = ArchetypeTerm.new(:code => 'at0000', :items => items)
+    items = {'TEXT' => 'concept'}
+    term2 = ArchetypeTerm.new(:code => 'at0001', :items => items)
+    term_definitions = {'ja' => [term1, term2]}
+    items = {'text' => 'test', 'description' => 'test item'}
+    term3 = ArchetypeTerm.new(:code => 'ac0000', :items => items)
+    constraint_definitions = {'ja' => [term3]}
+    code_phrase = stub(CodePhrase, :code_string => '163020007')
+    bind = {'at0000' => code_phrase}
+    term_bindings = {'SNOMED-CT(2003)' => [bind]}
     @archetype_ontology =
-      ArchetypeOntology.new(:terminologies_available => terminologies_available,
-                            :specialisation_depth => 0,
-                            :term_codes => term_codes,
-                            :constraint_codes => constraint_codes,
-                            :term_attribute_names => term_attribute_names)
+      ArchetypeOntology.new(:term_definitions => term_definitions,
+                            :constraint_definitions => constraint_definitions,
+                            :term_bindings => term_bindings,
+                            :specialisation_depth => 0)
   end
 
@@ -20 +27 @@
   end
 
-  it 'terminologies_available should be assigned properly' do
-    @archetype_ontology.terminologies_available.size.should be_equal 1
-  end
-
-  it 'should raise ArgumentError if terminologies_available is nil' do
-    lambda {
-      @archetype_ontology.terminologies_available = nil
-    }.should raise_error ArgumentError
-  end
-
-  it 'term_codes should be assigned properly' do
-    @archetype_ontology.term_codes.size.should be_equal 2
-  end
-
   it 'specialisation depth should be assigned properly' do
     @archetype_ontology.specialisation_depth.should be_equal 0
   end
 
-  it 'constraint_codes should be assigned properly' do
-    @archetype_ontology.constraint_codes.size.should be_equal 3
+  it 'term_definitions should be assigned properly' do
+    @archetype_ontology.term_definitions['ja'][0].code.should == 'at0000'
   end
 
-  it 'term_attribute_names should be assigned properly' do
-    @archetype_ontology.term_attribute_names.size.should be_equal 4
+  it 'term_codes should returnd all at codes' do
+    @archetype_ontology.term_codes.should == ['at0000','at0001']
+  end
+
+  it 'constraint_definitions should be assigned properly' do
+    @archetype_ontology.constraint_definitions['ja'][0].items['text'].
+      should == 'test'
+  end
+
+  it 'constrant_codes should return all ac codes' do
+    @archetype_ontology.constraint_codes.should == ['ac0000']
+  end
+
+  it 'term_bindings should be assigned properly' do
+    @archetype_ontology.term_bindings['SNOMED-CT(2003)'][0]['at0000'].
+      code_string.should == '163020007'
   end
 end

ruby/trunk/spec/lib/open_ehr/am/archetype/ontology/archetype_term_spec.rb

@@ -4 +4 @@
 describe ArchetypeTerm do
   before(:each) do
-    items = Hash['TEXT', 'text']
+    items = {'TEXT' => 'text', 'DESC' => 'description'}
     @archetype_term = ArchetypeTerm.new(:code => 'at0001',
                                         :items => items)
@@ -34 +34 @@
 
   it 'keys should be a set of keys of item' do
-    @archetype_term.keys.should == Set.new('TEXT')
+    @archetype_term.keys.should == Set['TEXT', 'DESC']
   end
 

ruby/trunk/spec/lib/open_ehr/serializer/adl_serializer_spec.rb

@@ -15 +15 @@
     @sample_description = adl[9..22].join
     @sample_definition = adl[24..25].join
+    @sample_ontology = adl[27..37].join
     adl_file.close
   end
@@ -37 +38 @@
     @adl_serializer.definition.should == @sample_definition
   end
+
+  it 'ontology should return ADL formatted ontology' do
+    @adl_serializer.ontology.should == @sample_definition
+  end
 end