open_ehr 0.9.0 → 0.9.1

data/Gemfile.lock

@@ -9,12 +9,12 @@ GEM
     diff-lcs (1.1.3)
     ffi (1.0.9)
     git (1.2.5)
-    guard (0.7.0)
+    guard (0.8.4)
       thor (~> 0.14.6)
     guard-rspec (0.4.5)
       guard (>= 0.4.0)
-    guard-spork (0.2.1)
-      guard (>= 0.2.2)
+    guard-spork (0.3.0)
+      guard (>= 0.8.2)
       spork (>= 0.8.4)
     i18n (0.6.0)
     jeweler (1.6.4)
@@ -28,7 +28,7 @@ GEM
     multi_json (1.0.3)
     polyglot (0.3.2)
     rake (0.9.2)
-    rb-inotify (0.8.6)
+    rb-inotify (0.8.8)
       ffi (>= 0.5.0)
     rdoc (3.9.4)
     rspec (2.6.0)

data/History.txt

@@ -1,11 +1,15 @@
-=== 0.6.1 2011-05-09
-
-* First gem package release
+=== 0.9.1 2011-10-04
+Archetype instance generated from ADL file.
 
-=== 0.6.2 2011-05-09
-* Fixed some package hierachy
+=== 0.9.0 2011-09
+* Fixed ADL parser and AOM generation
 
 === 0.7.0 2011-05
 * Fixed ADL parser library
 
+=== 0.6.2 2011-05-09
+* Fixed some package hierachy
 
+=== 0.6.1 2011-05-09
+
+* First gem package release

data/VERSION

@@ -1 +1 @@
-0.9.0
+0.9.1

data/lib/open_ehr/parser/adl_grammar.tt

@@ -47,6 +47,10 @@ module OpenEHR
           def definition
             arch_definition.value
           end
+
+          def ontology
+            arch_ontology.value
+          end
         }
       end
 
@@ -148,7 +152,22 @@ module OpenEHR
       end
 
       rule arch_ontology
-        SYM_ONTOLOGY V_DADL_TEXT space
+        SYM_ONTOLOGY ontology:V_DADL_TEXT space {
+          def value
+            ao = ontology.value[:term_definitions]
+            term_definitions = {}
+            ao.map do |lang, term_defs|
+              items = term_defs[:items]
+              terms = items.map do |code, item|
+                OpenEHR::AM::Archetype::Ontology::ArchetypeTerm.new(
+                  :code => code.to_s, :items => item)
+              end
+              term_definitions[lang.to_s] = terms
+            end
+            OpenEHR::AM::Archetype::Ontology::ArchetypeOntology.new(
+              :term_definitions => term_definitions)
+          end
+        }
       end
     end
   end

data/lib/open_ehr/parser/adl_parser.rb

@@ -4,6 +4,9 @@ require 'polyglot'
 require 'treetop'
 
 include OpenEHR::Parser
+include OpenEHR::AM::Archetype
+include OpenEHR::RM::DataTypes::Text
+include OpenEHR::RM::Support::Identification
 
 module OpenEHR
   module Parser
@@ -22,13 +25,21 @@ module OpenEHR
       end
 
       def parse
-        archetype = ArchetypeMock.new(:archetype_id => @result.archetype_id,
-                                      :adl_version => @result.adl_version,
-                                      :concept => @result.concept,
-                                      :original_language => @result.original_language,
-                                      :translation => @result.translations,
-                                      :description => @result.description,
-                                      :definition => @result.definition)
+        terminology_id = TerminologyID.new(:value => 'ISO_639-1')
+        original_language = CodePhrase.new(
+          :terminology_id => terminology_id,
+          :code_string => @result.original_language)
+        archetype_id = ArchetypeID.new(:value => @result.archetype_id)
+        definition = @result.definition
+        ontology = @result.ontology
+        archetype = Archetype.new(:archetype_id => archetype_id,
+                                  :adl_version => @result.adl_version,
+                                  :concept => @result.concept,
+                                  :original_language => original_language,
+                                  :translation => @result.translations,
+                                  :description => @result.description,
+                                  :definition => @result.definition,
+                                  :ontology => @result.ontology)
         return archetype
       end
 

data/open_ehr.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{open_ehr}
-  s.version = "0.9.0"
+  s.version = "0.9.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Shinji KOBAYASHI}, %q{Akimichi Tatsukawa}]
-  s.date = %q{2011-09-25}
+  s.date = %q{2011-10-04}
   s.description = %q{This project is an implementation of the openEHR specification on Ruby.}
   s.email = %q{skoba@moss.gr.jp}
   s.executables = [%q{adl_validator.rb}]
@@ -22,7 +22,6 @@ Gem::Specification.new do |s|
     "Gemfile.lock",
     "Guardfile",
     "History.txt",
-    "Manifest.txt",
     "PostInstall.txt",
     "README.rdoc",
     "Rakefile",

data/spec/lib/open_ehr/parser/adl_parser_spec.rb

@@ -1,7 +1,9 @@
 require File.dirname(__FILE__) + '/../../../spec_helper'
 include OpenEHR::Parser
+include OpenEHR::AM::Archetype
 include OpenEHR::AM::Archetype::ConstraintModel
 include OpenEHR::AM::Archetype::Assertion
+include OpenEHR::AM::Archetype::Ontology
 
 describe ADLParser do
 
@@ -24,8 +26,13 @@ describe ADLParser do
           @archetype = @ap.parse
         end
 
+        it 'archetype is an instance of Archetype' do
+          @archetype.should be_an_instance_of Archetype
+        end
+
         it 'archetype_id should be openEHR-EHR-SECTION-summary' do
-          @archetype.archetype_id.should == 'openEHR-EHR-SECTION.summary.v1'
+          @archetype.archetype_id.value.should == 
+            'openEHR-EHR-SECTION.summary.v1'
         end
 
         it 'adl_version should be 1.4' do
@@ -37,7 +44,8 @@ describe ADLParser do
         end
 
         it 'original language is ISO_639-1::en' do
-          @archetype.original_language.should == 'ISO_639-1::en'
+          @archetype.original_language.code_string.should ==
+            'ISO_639-1::en'
         end
 
         context 'description' do
@@ -188,7 +196,7 @@ describe ADLParser do
                     @assertion0 = @includes[0]
                   end
 
-                  it 'assertion0 should be an instance of assertion' do
+                  it 'assertion0 should be an instance of Assertion' do
                     @assertion0.should be_an_instance_of Assertion
                   end
 
@@ -200,10 +208,140 @@ describe ADLParser do
                     @assertion0.expression.item.pattern.should == '/clinical_synopsis\.v1/'
                   end
                 end
+
+                context '2nd assertion' do
+                  before(:all) do
+                    @assertion1 = @includes[1]
+                  end
+
+                  it 'assertion1 is an instanse of Assertion' do
+                    @assertion1.should be_an_instance_of Assertion
+                  end
+
+                  it 'Assertion1 type is Boolean' do
+                    @assertion1.expression.type.should == 'Boolean'
+                  end
+
+                  it 'expression value of assertion1 is /problem\.v1/' do
+                    @assertion1.expression.item.pattern.should ==
+                      '/problem\.v1/'
+                  end
+                end
+
+                context '3rd assertion' do
+                  before(:all) do
+                    @assertion2 = @includes[2]
+                  end
+
+                  it 'assertion2 is an instanse of Assertion' do
+                    @assertion2.should be_an_instance_of Assertion
+                  end
+
+                  it 'Assertion2 type is Boolean' do
+                    @assertion2.expression.type.should == 'Boolean'
+                  end
+
+                  it 'expression value of Assertion2 is /problem\.v1/' do
+                    @assertion2.expression.item.pattern.should ==
+                      '/problem-diagnosis\.v1/'
+                  end
+                end
+
+                context '4th assertion' do
+                  before(:all) do
+                    @assertion3 = @includes[3]
+                  end
+
+                  it 'assertion3 is an instanse of Assertion' do
+                    @assertion3.should be_an_instance_of Assertion
+                  end
+
+                  it 'Assertion3 type is Boolean' do
+                    @assertion3.expression.type.should == 'Boolean'
+                  end
+
+                  it 'expression value of assertion3 is /problem\.v1/' do
+                    @assertion3.expression.item.pattern.should ==
+                      '/problem-diagnosis-histological\.v1/'
+                  end
+                end
+
+                context '5th assertion' do
+                  before(:all) do
+                    @assertion4 = @includes[4]
+                  end
+
+                  it 'assertion4 is an instanse of Assertion' do
+                    @assertion4.should be_an_instance_of Assertion
+                  end
+
+                  it 'Assertion4 type is Boolean' do
+                    @assertion4.expression.type.should == 'Boolean'
+                  end
+
+                  it 'expression value of assertion4 is /problem\.v1/' do
+                    @assertion4.expression.item.pattern.should ==
+                      '/problem-genetic\.v1/'
+                  end
+                end
+
+                context '6th assertion' do
+                  before(:all) do
+                    @assertion5 = @includes[5]
+                  end
+
+                  it 'assertion5 is an instanse of Assertion' do
+                    @assertion5.should be_an_instance_of Assertion
+                  end
+
+                  it 'Assertion5 type is Boolean' do
+                    @assertion5.expression.type.should == 'Boolean'
+                  end
+
+                  it 'expression value of assertion5 is /problem\.v1/' do
+                    @assertion5.expression.item.pattern.should ==
+                      '/risk\.v1/'
+                  end
+                end
+
+                context '7th assertion(is null)' do
+                  it '7th assersion is nil' do
+                    @includes[6].should be_nil
+                  end
+                end
               end
             end
           end
         end #definition
+
+        context 'ontology section' do
+          before(:all) do
+            @archetype_ontology = @archetype.ontology
+          end
+
+          it 'is an ArchtypeOntology instance' do
+            @archetype_ontology.should be_an_instance_of ArchetypeOntology
+          end
+
+          it 'term_definitions parsed and assigned properly' do
+            @archetype_ontology.term_definition(:lang => 'en',
+               :code => 'at0000')[:text].should == 'Summary'
+          end
+
+          it 'description term_definitions parsed and assigned properly' do
+            @archetype_ontology.term_definition(:lang => 'en',
+               :code => 'at0000')[:description].should ==
+                 'A heading for conclusions and other evaluations'
+          end
+
+          it 'term_codes should be assigned properly' do
+            @archetype_ontology.term_codes.should == ['at0000']
+          end
+
+          it 'ArchetypeOntology has en lang' do
+            @archetype_ontology.should have_language 'en'
+          end
+        end
       end
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: open_ehr
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.9.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-09-25 00:00:00.000000000Z
+date: 2011-10-04 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: xml-simple
-  requirement: &17196536560 !ruby/object:Gem::Requirement
+  requirement: &17200461040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196536560
+  version_requirements: *17200461040
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &17196534820 !ruby/object:Gem::Requirement
+  requirement: &17200458540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196534820
+  version_requirements: *17200458540
 - !ruby/object:Gem::Dependency
   name: locale
-  requirement: &17196534160 !ruby/object:Gem::Requirement
+  requirement: &17200455940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196534160
+  version_requirements: *17200455940
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: &17196533300 !ruby/object:Gem::Requirement
+  requirement: &17200455020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196533300
+  version_requirements: *17200455020
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &17196532200 !ruby/object:Gem::Requirement
+  requirement: &17200453940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196532200
+  version_requirements: *17200453940
 - !ruby/object:Gem::Dependency
   name: i18n
-  requirement: &17196531600 !ruby/object:Gem::Requirement
+  requirement: &17200452240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196531600
+  version_requirements: *17200452240
 - !ruby/object:Gem::Dependency
   name: treetop
-  requirement: &17196530920 !ruby/object:Gem::Requirement
+  requirement: &17200451120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196530920
+  version_requirements: *17200451120
 - !ruby/object:Gem::Dependency
   name: polyglot
-  requirement: &17196530100 !ruby/object:Gem::Requirement
+  requirement: &17200448980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196530100
+  version_requirements: *17200448980
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &17196529060 !ruby/object:Gem::Requirement
+  requirement: &17200447680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *17196529060
+  version_requirements: *17200447680
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &17196526440 !ruby/object:Gem::Requirement
+  requirement: &17200446420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196526440
+  version_requirements: *17200446420
 - !ruby/object:Gem::Dependency
   name: guard-rspec
-  requirement: &17196525420 !ruby/object:Gem::Requirement
+  requirement: &17200445360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -132,10 +132,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196525420
+  version_requirements: *17200445360
 - !ruby/object:Gem::Dependency
   name: ruby-debug19
-  requirement: &17196524100 !ruby/object:Gem::Requirement
+  requirement: &17200443980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -143,10 +143,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196524100
+  version_requirements: *17200443980
 - !ruby/object:Gem::Dependency
   name: spork
-  requirement: &17196522540 !ruby/object:Gem::Requirement
+  requirement: &17200442260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -154,10 +154,10 @@ dependencies:
         version: 0.9.0.rc2
   type: :development
   prerelease: false
-  version_requirements: *17196522540
+  version_requirements: *17200442260
 - !ruby/object:Gem::Dependency
   name: guard-spork
-  requirement: &17196521000 !ruby/object:Gem::Requirement
+  requirement: &17200441080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -165,10 +165,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196521000
+  version_requirements: *17200441080
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &17196520360 !ruby/object:Gem::Requirement
+  requirement: &17200405560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -176,10 +176,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196520360
+  version_requirements: *17200405560
 - !ruby/object:Gem::Dependency
   name: rb-inotify
-  requirement: &17196519580 !ruby/object:Gem::Requirement
+  requirement: &17200402760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -187,10 +187,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196519580
+  version_requirements: *17200402760
 - !ruby/object:Gem::Dependency
   name: libnotify
-  requirement: &17196518140 !ruby/object:Gem::Requirement
+  requirement: &17200401640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -198,7 +198,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17196518140
+  version_requirements: *17200401640
 description: This project is an implementation of the openEHR specification on Ruby.
 email: skoba@moss.gr.jp
 executables:
@@ -212,7 +212,6 @@ files:
 - Gemfile.lock
 - Guardfile
 - History.txt
-- Manifest.txt
 - PostInstall.txt
 - README.rdoc
 - Rakefile
@@ -499,7 +498,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2975758498502846331
+      hash: -4104105171065841354
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/Manifest.txt

@@ -1,14 +0,0 @@
-Gemfile
-Guardfile
-History.txt
-Manifest.txt
-PostInstall.txt
-README.rdoc
-Rakefile
-VERSION
-lib/open_ehr.rb
-lib/open_ehr/cli.rb
-spec/open_ehr_cli_spec.rb
-spec/open_ehr_spec.rb
-spec/spec.opts
-spec/spec_helper.rb