openehr 1.3.0 → 2.0.0

data/lib/openehr/serializer/xml_serializer.rb

@@ -0,0 +1,260 @@
+require 'rexml/document'
+require 'builder'
+require_relative 'base'
+
+module OpenEHR
+  module Serializer
+    class XMLSerializer < BaseSerializer
+      def header
+        header = ''
+        xml = Builder::XmlMarkup.new(:indent => 2, :target => header)
+        xml.archetype_id do
+          xml.value @archetype.archetype_id.value
+        end
+        xml.concept @archetype.concept
+        xml.original_language do
+          xml.terminology_id do
+            xml.value @archetype.original_language.terminology_id.value
+          end
+          xml.code_string @archetype.original_language.code_string
+        end
+        return header
+      end
+
+      def description
+        desc = ''
+        xml = Builder::XmlMarkup.new(:indent => 2, :target => desc)
+        ad = @archetype.description
+        if ad
+          xml.description do
+            ad.original_author.each do |key,value|
+              xml.original_author(value,"id"=>key)
+            end
+            if ad.other_contributors
+              ad.other_contributors.each do |co|
+                xml.other_contributors co
+              end
+            end
+            xml.lifecycle_state ad.lifecycle_state
+            xml.details do
+              ad.details.each do |lang, item|
+                xml.language do
+                  xml.terminology_id do
+                    xml.value item.language.terminology_id.value
+                  end
+                  xml.code_string lang
+                end
+                xml.purpose item.purpose
+                if item.keywords then
+                  item.keywords.each do |word|
+                    xml.keywords word
+                  end
+                end
+                xml.use item.use if item.use
+                xml.misuse item.misuse if item.misuse
+                xml.copyright item.copyright if item.copyright
+                if ad.other_details
+                  ad.other_details.each do |key,value|
+                    xml.other_details(value, "id"=>key)
+                  end
+                end
+              end
+            end
+          end
+        end
+        return desc
+      end
+
+      def definition
+        definition = ''
+        xml = Builder::XmlMarkup.new(:indent => 2, :target => definition)
+        xml.definition do
+          emit_c_object_body(xml, @archetype.definition)
+        end
+        return definition
+      end
+
+      def ontology
+        ontology = ''
+        ao = @archetype.ontology
+        xml = Builder::XmlMarkup.new(:indent => 2, :target => ontology)
+        xml.ontology do
+          xml.specialisation_depth ao.specialisation_depth
+          (ao.languages_available || []).each { |lang| xml.languages_available lang }
+          (ao.terminologies_available || []).each { |t| xml.terminologies_available t }
+          xml.term_definitions do
+            ao.term_definitions.each do |lang, terms|
+              xml.language lang
+              xml.terms do
+                terms.each do |code, term|
+                  xml.code code
+                  xml.items do
+                    term.items.each do |key, value|
+                      xml.item do
+                        xml.key key
+                        xml.value value
+                      end
+                    end
+                  end
+                end
+              end
+            end
+          end
+          emit_term_bindings(xml, ao.term_bindings)
+        end
+      end
+
+      def merge
+        archetype = "<?xml version='1.0' encoding='UTF-8'?>" + NL +
+          "<archetype xmlns=\"http://schemas.openehr.org/v1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">" + NL +
+          header + description + definition +
+          ontology + '</archetype>'
+        return archetype
+      end
+
+      include OpenEHR::AM::Archetype::ConstraintModel
+      Primitive = OpenEHR::AM::Archetype::ConstraintModel::Primitive
+      OpenEHRProfile = OpenEHR::AM::OpenEHRProfile
+
+      private
+
+      # Emits a C_OBJECT's own fields (rm_type_name/occurrence/node_id
+      # plus, unless any_allowed?, its attributes) directly into the
+      # current xml element - used both for the root <definition> and,
+      # via emit_child, for every nested C_COMPLEX_OBJECT.
+      def emit_c_object_body(xml, node)
+        xml.rm_type_name node.rm_type_name
+        xml.occurrence { emit_interval(xml, node.occurrences) }
+        xml.node_id node.node_id
+        return if node.any_allowed?
+
+        node.attributes.each { |a| emit_attribute(xml, a) }
+      end
+
+      def emit_interval(xml, interval)
+        xml.lower_included interval.lower_included? unless interval.lower_included?.nil?
+        xml.upper_included interval.upper_included? unless interval.upper_included?.nil?
+        xml.lower_unbounded interval.lower_unbounded?
+        xml.upper_unbounded interval.upper_unbounded?
+        xml.lower interval.lower
+        xml.upper interval.upper
+      end
+
+      def emit_attribute(xml, attribute)
+        xml.attributes do
+          xml.rm_attribute_name attribute.rm_attribute_name
+          xml.existence { emit_interval(xml, attribute.existence) } if attribute.existence
+          emit_cardinality(xml, attribute.cardinality) if attribute.is_a?(CMultipleAttribute)
+          (attribute.children || []).each { |c| emit_child(xml, c) }
+        end
+      end
+
+      def emit_cardinality(xml, cardinality)
+        xml.cardinality do
+          next if cardinality.nil?
+
+          xml.is_ordered cardinality.is_ordered?
+          xml.is_unique cardinality.is_unique?
+          xml.interval { emit_interval(xml, cardinality.interval) } if cardinality.interval
+        end
+      end
+
+      # Dispatches an attribute's child node, tagging each <children>
+      # element with an xsi:type discriminator (the AOM node's class,
+      # in openEHR's own naming) since the children of one attribute
+      # can be a mix of concrete constraint node types.
+      def emit_child(xml, node)
+        case node
+        when ArchetypeSlot
+          xml.children('xsi:type' => 'ARCHETYPE_SLOT') { emit_archetype_slot_body(xml, node) }
+        when ArchetypeInternalRef
+          xml.children('xsi:type' => 'ARCHETYPE_INTERNAL_REF') { xml.target_path node.target_path }
+        when ConstraintRef
+          xml.children('xsi:type' => 'CONSTRAINT_REF') { xml.reference node.reference }
+        when CPrimitiveObject
+          xml.children('xsi:type' => 'C_PRIMITIVE_OBJECT') { emit_primitive_body(xml, node.item) }
+        when OpenEHRProfile::DataTypes::Quantity::CDvOrdinal
+          xml.children('xsi:type' => 'C_DV_ORDINAL') { emit_ordinal_body(xml, node) }
+        when OpenEHRProfile::DataTypes::Text::CCodePhrase
+          xml.children('xsi:type' => 'C_CODE_PHRASE') { emit_code_phrase_body(xml, node) }
+        when CComplexObject
+          xml.children('xsi:type' => 'C_COMPLEX_OBJECT') { emit_c_object_body(xml, node) }
+        else
+          raise ArgumentError, "XMLSerializer cannot emit a #{node.class} node"
+        end
+      end
+
+      def emit_archetype_slot_body(xml, node)
+        xml.rm_type_name node.rm_type_name
+        xml.occurrence { emit_interval(xml, node.occurrences) }
+        xml.node_id node.node_id if node.node_id
+        emit_assertions(xml, 'includes', node.includes)
+        emit_assertions(xml, 'excludes', node.excludes)
+      end
+
+      def emit_assertions(xml, tag, assertions)
+        return if assertions.nil?
+
+        xml.tag!(tag) { assertions.each { |a| xml.assertion a.string_expression } }
+      end
+
+      def emit_primitive_body(xml, item)
+        xml.primitive_type item.type
+        if item.is_a?(Primitive::CBoolean)
+          xml.true_valid item.true_valid
+          xml.false_valid item.false_valid
+        elsif item.respond_to?(:pattern) && item.pattern
+          xml.pattern item.pattern
+        elsif item.list
+          item.list.each { |v| xml.item literal(v) }
+        elsif item.range
+          xml.range { emit_bound_interval(xml, item.range) }
+        end
+        xml.assumed_value literal(item.assumed_value) if item.has_assumed_value?
+      end
+
+      def emit_bound_interval(xml, range)
+        xml.lower literal(range.lower) unless range.lower_unbounded?
+        xml.upper literal(range.upper) unless range.upper_unbounded?
+      end
+
+      def literal(value)
+        value.respond_to?(:value) ? value.value.to_s : value.to_s
+      end
+
+      def emit_ordinal_body(xml, node)
+        return if node.any_allowed?
+
+        node.list.each do |o|
+          xml.item do
+            xml.value o.value
+            xml.symbol o.symbol.code_string
+          end
+        end
+        xml.assumed_value literal(node.assumed_value) if node.has_assumed_value?
+      end
+
+      def emit_code_phrase_body(xml, node)
+        return if node.any_allowed?
+
+        xml.terminology_id node.terminology_id.value
+        node.code_list.each { |c| xml.code c }
+      end
+
+      def emit_term_bindings(xml, term_bindings)
+        return if term_bindings.nil?
+
+        term_bindings.each do |terminology, codes|
+          codes.each do |code, bindings|
+            code_phrase = Array(bindings).first
+            xml.term_bindings do
+              xml.terminology terminology
+              xml.code code
+              xml.value "#{code_phrase.terminology_id.value}::#{code_phrase.code_string}"
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/openehr/serializer.rb

@@ -1,291 +1,5 @@
-require 'rexml/document'
-require 'builder'
-
-module OpenEHR
-  module Serializer
-    NL = "\r\n"
-    INDENT = '    '
-
-    class BaseSerializer
-      def initialize(archetype)
-        @archetype = archetype
-      end
-
-      def serialize
-        return self.merge
-      end
-
-      private
-      def merge
-      end
-    end
-
-    class ADLSerializer < BaseSerializer
-      def header
-        hd = 'archetype'
-        unless @archetype.adl_version.nil?
-          hd << " (adl_version = #{@archetype.adl_version})"
-        end
-        hd << NL+INDENT + "#{@archetype.archetype_id.value}"+NL*2
-        hd << 'concept'+NL+ INDENT+"[#{@archetype.concept}]"+NL
-        hd << NL+'language'+NL+INDENT+'original_language = <['+
-          @archetype.original_language.terminology_id.value+'::'+
-          @archetype.original_language.code_string+']>'+NL
-        return hd
-      end
-
-      def description
-        desc = ''
-        if @archetype.description
-          ad = @archetype.description
-          desc << 'description' + NL
-          desc << INDENT + 'original_author = <' + NL
-          ad.original_author.each do |k,v|
-            desc << INDENT+INDENT+'["'+k+'"] = <"'+v+'">'+NL
-          end
-          desc << INDENT+'>'+NL
-          desc << INDENT+'lifecycle_state = <"'+ad.lifecycle_state+'">'+NL
-          desc << INDENT+'details = <'+NL
-          ad.details.each do |lang,item|
-            desc << INDENT*2+'["'+lang+'"] = <'+NL
-            desc << INDENT*3+'language = <['+
-              item.language.terminology_id.value+'::'+
-              item.language.code_string+']>'+NL
-            desc << INDENT*3+'purpose = <"'+item.purpose+'">'+NL
-            if item.keywords then
-              desc << INDENT*3+'keywords = <'
-              item.keywords.each do |word|
-                desc << '"'+word+'",'
-              end
-              desc.chop! << '>'+NL
-            end
-            desc << INDENT*3+'use = <"'+item.use+'">'+NL if item.use
-            desc << INDENT*3+'misuse = <"'+item.misuse+'">'+NL if item.misuse
-            desc << INDENT*3+'copyright = <"'+item.copyright+'">'+NL if item.copyright
-            if item.original_resource_uri
-              desc << INDENT*3 + 'original_resource_uri = <'
-              item.original_resource_uri.each do |k,v|
-                desc << INDENT*4+'["'+k+'"] = <"'+v+'">'+NL
-              end
-              desc << INDENT*3+'>'+NL
-            end
-            if item.other_details
-              desc << INDENT*3 + 'other_details = <'
-              item.original_resource_uri.each do |k,v|
-                desc << INDENT*4+'["'+k+'"] = <"'+v+'">'+NL
-              end
-              desc << INDENT*3+'>'+NL
-            end
-            desc << INDENT*2+'>'+NL
-          end
-          desc << INDENT+'>'+NL
-        end
-        return desc
-      end
-
-      def definition
-        ad = @archetype.definition
-        definition = 'definition'+NL
-        definition << INDENT+ad.rm_type_name+"[#{ad.node_id}] matches {"
-        if ad.any_allowed?
-          definition << '*}'+NL
-        else
-          definition << NL
-          if ad.attributes
-            attributes = ad.attributes
-            indents = 2
-            while attributes
-              definition << INDENT*indents+attributes.rm_type_name
-              definition << "[#{attributes.node_id}] "
-              definition << existence(attributes.existence)
-              definition << " matches {"
-            end
-          end
-        end
-      end
-
-      def ontology
-        ao = @archetype.ontology
-        ontology = 'ontology'+NL
-        ontology << INDENT + 'term_definitions = <' + NL
-        ao.term_definitions.each do |lang, items|
-          ontology << INDENT*2 + "[\"#{lang}\"] = <" + NL
-          ontology << INDENT*3 + 'items = <'  + NL
-          items.each do |item|
-            ontology << INDENT*4 + "[\"#{item.code}\"] = <" + NL            
-            item.items.each do |name, desc|
-              ontology << INDENT*5 + "#{name} = <\"#{desc}\">" +NL
-            end
-            ontology << INDENT*4 + '>'+NL
-          end
-          ontology << INDENT*3 + '>' + NL
-          ontology << INDENT*2 + '>' + NL
-        end
-        ontology << INDENT + '>' + NL
-      end
-
-      def merge
-        return header + NL + description + NL + definition + NL + ontology
-      end
-
-      private
-      def c_object
-      end
-
-      def existence(existence)
-        "existence matches {#{existence.lower}..#{existence.upper}}"
-      end
-    end
-
-    class XMLSerializer < BaseSerializer
-      def header
-        header = ''
-        xml = Builder::XmlMarkup.new(:indent => 2, :target => header)
-        xml.archetype_id do 
-          xml.value @archetype.archetype_id.value
-        end
-        xml.concept @archetype.concept
-        xml.original_language do
-          xml.terminology_id do
-            xml.value @archetype.original_language.terminology_id.value
-          end
-          xml.code_string @archetype.original_language.code_string
-        end
-        return header
-      end
-
-      def description
-        desc = ''
-        xml = Builder::XmlMarkup.new(:indent => 2, :target => desc)
-        ad = @archetype.description
-        if ad
-          xml.description do
-            ad.original_author.each do |key,value|
-              xml.original_author(value,"id"=>key)
-            end
-            if ad.other_contributors
-              ad.other_contributors.each do |co|
-                xml.other_contributors co
-              end
-            end
-            xml.lifecycle_state ad.lifecycle_state
-            xml.details do
-              ad.details.each do |lang, item|
-                xml.language do
-                  xml.terminology_id do
-                    xml.value item.language.terminology_id.value
-                  end
-                  xml.code_string lang
-                end
-                xml.purpose item.purpose
-                if item.keywords then
-                  item.keywords.each do |word|
-                    xml.keywords word
-                  end
-                end
-                xml.use item.use if item.use
-                xml.misuse item.misuse if item.misuse
-                xml.copyright item.copyright if item.copyright
-                if ad.other_details
-                  ad.other_details.each do |key,value|
-                    xml.other_details(value, "id"=>key)
-                  end
-                end
-              end
-            end
-          end
-        end
-        return desc
-      end
-
-      def definition
-        definition = ''
-        ad = @archetype.definition
-        xml = Builder::XmlMarkup.new(:indent => 2, :target => definition)
-        xml.definition do
-          xml.rm_type_name ad.rm_type_name
-          xml.occurrence do
-            oc = ad.occurrences
-            xml.lower_included oc.lower_included? unless oc.lower_included?.nil?
-            xml.upper_included oc.upper_included? unless oc.upper_included?.nil?
-            xml.lower_unbounded oc.lower_unbounded?
-            xml.upper_unbounded oc.upper_unbounded?
-            xml.lower oc.lower
-            xml.upper oc.lower
-          end
-          xml.node_id ad.node_id
-        end
-        return definition
-      end
-
-      def ontology
-        ontology = ''
-        ao = @archetype.ontology
-        xml = Builder::XmlMarkup.new(:indent => 2, :target => ontology)
-        xml.ontology do
-          xml.specialisation_depth ao.specialisation_depth
-          xml.term_definitions do
-            ao.term_definitions.each do |lang, terms|
-              xml.language lang
-              xml.terms do
-                terms.each do |term|
-                  xml.code term.code
-                  xml.items do
-                    term.items.each do |key, value|
-                      xml.item do
-                        xml.key key
-                        xml.value value
-                      end
-                    end
-                  end
-                end
-              end
-            end
-          end
-        end
-      end
-
-      def merge
-        archetype = "<?xml version='1.0' encoding='UTF-8'?>" + NL +
-          "<archetype xmlns=\"http://schemas.openehr.org/v1\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">" + NL +
-          header + description + definition +
-          ontology + '</archetype>'
-        return archetype
-      end
-    end
-
-    class OPTSerializer < BaseSerializer
-      def initialize(opt, format:)
-        @opt = OpenEHR::Parser::OPTParser.new(opt).parse
-      end
-
-      def name
-        @opt.definition.archetype_id.concept_name
-      end
-
-      def header
-
-      end
-
-
-    end
-  end
-end
-
-class Publisher
-  def initialize(serializer)
-    @serializer = serializer
-  end
-
-  def publish(writer)
-    writer.out(@serializer.serialize)
-  end
-end
-
-class Writer
-  def initialize(target)
-    @target = target
-  end
-  def out
-  end
-end
+require_relative 'serializer/base'
+require_relative 'serializer/adl_serializer'
+require_relative 'serializer/xml_serializer'
+require_relative 'serializer/opt_serializer'
+require_relative 'serializer/rm_json_serializer'

data/lib/openehr/terminology_service.rb

@@ -0,0 +1,44 @@
+# OpenEHR::TerminologyService is the seam RM classes call through to
+# validate codes against openEHR/external terminologies (e.g.
+# COMPOSITION.language against ISO_639-1, COMPOSITION.category against
+# the openEHR "composition category" group). This gem carries no
+# terminology data of its own - that lives in the separate
+# openehr-terminology gem - so the default provider is fully
+# permissive: every code is accepted.
+#
+# To get real validation, plug in an adapter:
+#   OpenEHR::TerminologyService.provider = MyTerminologyAdapter.new
+# where the adapter responds to:
+#   #valid_code?(terminology_id, code)      -> Boolean
+#   #has_code_for_group?(group_id, code)    -> Boolean
+module OpenEHR
+  module TerminologyService
+    class NullProvider
+      def valid_code?(_terminology_id, _code)
+        true
+      end
+
+      def has_code_for_group?(_group_id, _code)
+        true
+      end
+    end
+
+    class << self
+      def provider
+        @provider ||= NullProvider.new
+      end
+
+      def provider=(provider)
+        @provider = provider || NullProvider.new
+      end
+
+      def valid_code?(terminology_id, code)
+        provider.valid_code?(terminology_id, code)
+      end
+
+      def has_code_for_group?(group_id, code)
+        provider.has_code_for_group?(group_id, code)
+      end
+    end
+  end
+end

data/lib/openehr/version.rb

@@ -1,3 +1,3 @@
 module OpenEHR
-  VERSION = "1.3.0"
+  VERSION = "2.0.0"
 end

data/lib/openehr.rb

@@ -1,4 +1,6 @@
 require_relative 'openehr/version'
+require_relative 'openehr/path'
+require_relative 'openehr/terminology_service'
 require_relative 'openehr/assumed_library_types'
 
 #Reference model
@@ -9,6 +11,7 @@ require_relative 'openehr/am'
 
 #Adl/xml parser/serializer
 require_relative 'openehr/parser'
-# require_relative 'openehr/parser/adl_parser'
-# require_relative 'openehr/parser/xml_parser'
 require_relative 'openehr/serializer'
+
+#Archetype Query Language
+require_relative 'openehr/aql'