open_ehr 0.9.5 → 1.0.0

data/History.txt

@@ -1,3 +1,6 @@
+=== 1.0.0 2011-12-24
+First stable release
+
 === 0.9.5 2011-12-02
 Bug fix around ADL parser, data types, constranit
 

data/README.rdoc

@@ -5,7 +5,7 @@ Ruby openEHR implementation project.
 
 = Version
 
-Release-0.9.5
+Release-1.0.0
 
 = Requirements
 
@@ -18,15 +18,24 @@ Release-0.9.5
 
 == DESCRIPTION:
 
-This is the beta version 0.9.4 release of Ruby openEHR implementation
-project. This release is still experimental preview of our work based
-on openEHR specification release 1.0.2. We implemented almost of the
-specifications of the openEHR.  The work is still in progress. The
-intention is to have a sample EHR to utilize all over the world
-quickly with Ruby on Rails.
-
-Parser is nearly performing completely. We now consider to descrive
-archetype as another formalism such as YAML, instead of ADL.
+This is the fist stable branch version 1.0.0 release of Ruby openEHR
+implementation project. This release is based on openEHR specification
+release 1.0.2. We implemented almost of the specifications of the openEHR.
+The work is still in progress to implement related tools, such as
+archetype validator or serializer.
+The intention is to have a sample EHR to utilize all over the world
+quickly with Ruby on Rails for many other porject.
+From this release we changed license from MPL 1.1 to Apache 2.0 license,
+as regards to the other openEHR aretefact license.
+
+This package includes:
+* ADL 1.4 parser
+* AM/RM packages based on the openEHR specification 1.0.2
+
+This package excludes:
+* ADL serializer(in progress)
+* ADL validator(in progress)
+* Data store/retrieve would be separate to the other project.
 
 Almost all classes passed the test constructed by RSpec2 (formaly used
 test/unit). These spec files are under /spec.
@@ -35,7 +44,7 @@ Some specifications are not well determined yet, such as rm/security
 and so on. We postponed to implement such classes.
 
 Terminology and Demographic server will be implemented in other
-project.
+project. 
 
 = Authors
 * Main codes
@@ -54,17 +63,18 @@ All Rights Reserved.
 
 = License
 
-This product is under openEHR Open Source Software License
-
-The openEHR Foundation has used the Mozilla Tri-license 1.1 on all
-software copyrighted to the Foundation. Therefore, we release this
-product under Mozilla Tri-license at now, but the openEHR foundation
-is discussing about lincense for the resouces. We would change our
-license for this package after the decision. The Mozilla tri-licence
-essentially provides the user a choice of licence conditionsunder
-which to operate with any given piece of software, being: the Mozilla
-Public licence (MPL), and the Free Software Foundation GNU General
-Public Licence (GPL) and Lesser GNU General Public Licence (LGPL). See
-the Mozilla relicensing FAQ for details of this license. This in no
-way constrains the way in which software created by other
-organisations is licenced.
+This product is under Apache 2.0 license
+
+   Copyright [2011] Shinji Kobayashi, Akimichi Tatsukawa, openEHR.jp
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

data/VERSION

@@ -1 +1 @@
-0.9.5
+1.0.0

data/lib/open_ehr.rb

@@ -1,8 +1,7 @@
-$:.unshift(File.dirname(__FILE__)) unless
-  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+$:.unshift(File.dirname(__FILE__))
 
 module OpenEHR
-  VERSION = '0.9.5'
+  VERSION = '1.0.0'
   autoload :AssumedLibraryTypes, 'open_ehr/assumed_library_types'
   autoload :RM, 'open_ehr/rm'
   autoload :AM, 'open_ehr/am'

data/lib/open_ehr/am.rb

@@ -1,5 +1,4 @@
-$:.unshift(File.dirname(__FILE__)) unless
-  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+$:.unshift(File.dirname(__FILE__))
 
 module OpenEHR
   module AM

data/lib/open_ehr/am/openehr_profile.rb

@@ -4,7 +4,6 @@ module OpenEHR
   module AM
     module OpenEHRProfile
       autoload :DataTypes, 'openehr_profile/data_types'
-
     end
   end
 end

data/lib/open_ehr/am/openehr_profile/data_types.rb

@@ -5,7 +5,8 @@ module OpenEHR
     module OpenEHRProfile
       module DataTypes
         autoload :Text, 'data_types/text'
-
+        autoload :Quantity, 'data_types/quantity'
+        autoload :Basic, 'data_types/basic'
       end
     end
   end

data/lib/open_ehr/am/openehr_profile/data_types/basic.rb

@@ -3,22 +3,109 @@ module OpenEHR
     module OpenEHRProfile
       module DataTypes
         module Basic
-          class CDvState
+          include OpenEHR::AM::Archetype::ConstraintModel
+
+          class CDvState < CDomainType
+            attr_reader :value
+
+            def initialize(args = { })
+              args[:rm_type_name] = 'DvState'
+              super
+              self.value = args[:value]
+            end
+
+            def value=(value)
+              raise ArgumentError, 'value is mandatory' if value.nil?
+              @value = value
+            end
           end
 
           class StateMachine
+            attr_reader :states
+
+            def initialize(args = { })
+              self.states = args[:states]
+            end
+
+            def states=(states)
+              if states.nil? or states.empty?
+                raise ArgumentError, 'states are mandatory'
+              end
+              @states = states
+            end
           end
 
           class State
+            attr_reader :name
+
+            def initialize(args = { })
+              self.name = args[:name]
+            end
+
+            def name=(name)
+              if name.nil? or name.empty?
+                raise ArgumentError, 'Invalid name'
+              end
+              @name = name
+            end
           end
 
           class TerminalState < State
+
           end
 
           class NonTerminalState < State
+            attr_reader :transitions
+            def initialize(args = { })
+              super
+              self.transitions = args[:transitions]
+            end
+
+            def transitions=(transitions)
+              if transitions.nil? or transitions.empty?
+                raise ArgumentError, 'transition should not be empty'
+              end
+              @transitions = transitions
+            end
           end
 
           class Transition
+            attr_reader :event, :action, :guard, :next_state
+
+            def initialize(args = { })
+              self.event = args[:event]
+              self.guard = args[:guard]
+              self.action = args[:action]
+              self.next_state = args[:next_state]
+            end
+
+            def event=(event)
+              if event.nil? or event.empty?
+                raise ArgumentError, 'event is mandatory'
+              end
+              @event = event
+            end
+
+            def guard=(guard)
+              if !guard.nil? && guard.empty?
+                raise ArgumentError, 'guard should not be empty'
+              end
+              @guard = guard
+            end
+
+            def action=(action)
+              if !action.nil? && action.empty?
+                raise ArgumentError, 'action should not be empty'
+              end
+              @action = action
+            end
+
+            def next_state=(next_state)
+              if next_state.nil?
+                raise ArgumentError, 'next state is mandatory'
+              end
+              @next_state = next_state
+            end
           end
         end
       end # of DataTypes

data/lib/open_ehr/am/openehr_profile/data_types/quantity.rb

@@ -3,13 +3,62 @@ module OpenEHR
     module OpenEHRProfile
       module DataTypes
         module Quantity
-          class CDvQuantity < OpenEHR::AM::Archetype::ConstraintModel::CDomainType
+          include OpenEHR::AM::Archetype::ConstraintModel
+
+          class CDvQuantity < CDomainType
+            attr_accessor :property, :list
+
+            def initialize(args = { })
+              super
+              self.property = args[:property]
+              self.list = args[:list]
+            end
+
+            def any_allowed?
+              if @property.nil? && @list.nil?
+                return true
+              else
+                return false
+              end
+            end
           end
           
-          class CDvOrdinal < OpenEHR::AM::Archetype::ConstraintModel::CDomainType
+          class CDvOrdinal < CDomainType
+            attr_accessor :list
+            def initialize(args = { })
+              super
+              self.list = args[:list]
+            end
+
+            def any_allowed?
+              @list.nil?
+            end
           end
 
           class CQuantityItem
+            attr_accessor :magnitude, :precision
+            attr_reader :units
+
+            def initialize(args = { })
+              self.magnitude = args[:magnitude]
+              self.precision = args[:precision]
+              self.units = args[:units]
+            end
+
+            def units=(units)
+              if units.nil? or units.empty?
+                raise ArgumentError, 'units are mandatory'
+              end
+              @units = units
+            end
+
+            def precision_unconstrained?
+              if @precision.upper == -1 && @precision.lower == -1
+                return true
+              else
+                return false
+              end
+            end
           end
         end
       end # of DataTypes

data/lib/open_ehr/am/openehr_profile/data_types/text.rb

@@ -1,10 +1,10 @@
-include OpenEHR::AM::Archetype::ConstraintModel
-
+$:.unshift(File.dirname(__FILE__))
 module OpenEHR
   module AM
     module OpenEHRProfile
       module DataTypes
         module Text
+          include OpenEHR::AM::Archetype::ConstraintModel
           class CCodePhrase < CDomainType
             attr_accessor :terminology_id, :code_list
 

data/lib/open_ehr/assumed_library_types.rb

@@ -64,6 +64,11 @@ module OpenEHR
         end
       end
 
+      def ==(value)
+        return (@lower == value.lower) && (@upper == value.upper) &&
+          (@lower_included == value.lower_included?) &&
+            (@upper_included == value.upper_included?)
+      end
       private
 
       def check_lower_upper(lower, upper)

data/lib/open_ehr/parser/adl.rb

@@ -1,6 +1,6 @@
+require 'open_ehr/rm/data_types/text'
 include OpenEHR::RM::Support::Identification
 include OpenEHR::RM::Common::Resource
-include OpenEHR::RM::DataTypes::Text
 
 module OpenEHR
   module Parser
@@ -11,12 +11,12 @@ module OpenEHR
 
       class ArchLanguage < Base
         def value
-          Language.new(lang.value)
+          return Language.new(lang.value)
         end
       end
 
-
       class Language
+        include OpenEHR::RM::DataTypes::Text
         attr_reader :original_language, :translations
         
         def initialize(value)
@@ -25,7 +25,7 @@ module OpenEHR
         end
         
         def original_language=(original_language)
-          @original_language = code2lang original_language
+          @original_language = original_language
         end
         
         def translations=(translations)
@@ -35,7 +35,7 @@ module OpenEHR
             tr = translations.inject({ }) do |trans, lang|
               code, details  = lang
               td = TranslationDetails.new(
-                     :language => code2lang(details['language']),
+                     :language => details['language'],
                      :author => details['author'],
                      :accreditation => details['accreditation'],
                      :other_details => details['other_details'])

data/lib/open_ehr/parser/adl_grammar.tt

@@ -33,11 +33,11 @@ module OpenEHR
 	  end
 
 	  def original_language
-            lang.value.original_language
+            lang.value.original_language unless lang.empty?
           end
 
           def translations
-            lang.value.translations
+            lang.value.translations unless lang.empty?
           end
 
           def description
@@ -144,18 +144,13 @@ module OpenEHR
             params = desc.value
             details = { }
             params['details'].each do |lang, attrs|
-              term_id, la = attrs['language'].split('::')
-              terminology_id = 
-                OpenEHR::RM::Support::Identification::TerminologyID.new(
-                  :value => term_id)
               misuse = attrs['misuse']
               misuse = nil if misuse.nil? or misuse.empty?
+              purpose = attrs['purpose'] || '__unknown__' # for backward compat.
               item =
                 OpenEHR::RM::Common::Resource::ResourceDescriptionItem.new(
-                  :language => OpenEHR::RM::DataTypes::Text::CodePhrase.new(
-                                :terminology_id => terminology_id,
-                                :code_string => la),
-                  :purpose => attrs["purpose"],
+                  :language => attrs['language'],
+                  :purpose => purpose,
                   :keywords => attrs["keywords"],
                   :use => attrs["use"],
                   :misuse => misuse,
@@ -201,19 +196,21 @@ module OpenEHR
             if cd
               cd = itemizer(cd , arc_term)
             end
-            tb = ao['term_bindings']
+            tb = ao['term_bindings'] || ao['term_binding']
             term_bind = Proc.new do |code, item|
-              term_id, code_string = item.split '::'
-              term_id = OpenEHR::RM::Support::Identification::TerminologyID.new(:value => term_id)
-              OpenEHR::RM::DataTypes::Text::CodePhrase.new(:terminology_id => term_id, :code_string => code_string)
+              unless item.class == Array
+                [item]
+              else
+                item
+              end
             end
             if tb
               tb = itemizer(tb, term_bind)
             end
             cons_bind = Proc.new do |code, item|
-              item
+	      OpenEHR::RM::DataTypes::URI::DvUri.new(:value => item)
             end
-            cb = ao['constraint_bindings']
+            cb = ao['constraint_bindings'] || ao['constraint_binding']
             if cb
               cb = itemizer(cb, cons_bind)
             end

data/lib/open_ehr/parser/adl_parser.rb

@@ -2,22 +2,23 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 require 'polyglot'
 require 'treetop'
-
 include OpenEHR::Parser
 include OpenEHR::AM::Archetype
-include OpenEHR::RM::DataTypes::Text
 include OpenEHR::RM::Support::Identification
+include OpenEHR::RM::DataTypes::Text
 
 module OpenEHR
   module Parser
     class ADLParser < Base
       def initialize(filename)
         super(filename)
-        data = File.read(filename)
+        file = File.open(filename, 'r:bom|utf-8')
+        data = file.read
         Treetop.load(File.dirname(__FILE__)+'/adl_grammar.tt')
         ap = ADLGrammarParser.new
         @result = ap.parse(data)
-        if @result.nil?
+        file.close
+        unless @result
           puts ap.failure_reason
           puts ap.failure_line
           puts ap.failure_column
@@ -25,10 +26,17 @@ module OpenEHR
       end
 
       def parse
-        original_language = @result.original_language
         archetype_id = ArchetypeID.new(:value => @result.archetype_id)
         definition = @result.definition
         ontology = @result.ontology
+        original_language = nil
+        if @result.original_language
+          original_language = @result.original_language
+        else
+          terminology_id = TerminologyID.new(:value => 'ISO639-1')
+          original_language = CodePhrase.new(:terminology_id => terminology_id,
+                                      :code_string =>ontology.primary_language)
+        end
         archetype = Archetype.new(:archetype_id => archetype_id,
                                   :adl_version => @result.adl_version,
                                   :concept => @result.concept,