fhir_models 1.6.4 → 1.6.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 348c0ac6566160061a8ecea33defd3485ea7ef6a
+  metadata.gz: d8d5ba026745d19e4eab57461d9df5dbf731b540
+  data.tar.gz: b5acd0da79199bb9ea202c56674b065f7ce94432
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+  data.tar.gz: 589812ea7e6f30e2136c4270a895cef564e7775e12d2d0bc51109f9c16c9a0da4f48a4eb3ece0958f9f5533289653891bd210dee85fab687e487d4ded6bd1162

data/.rubocop.yml

@@ -3,6 +3,8 @@ AllCops:
   Exclude:
     - 'test/**/*'
     - 'lib/fhir_models/fhir/**/*'
+    - 'lib/fhir_models/fluentpath/evaluate.rb'
+    - 'tmp/**/*'
 
 #################### Lint ################################
 

data/Rakefile

@@ -19,6 +19,8 @@ task :rubocop do
   RuboCop::RakeTask.new
 end
 
-task default: [:test, :rubocop] do
+task test: [:rubocop] do
   system('open coverage/index.html')
 end
+
+task default: [:test]

data/bin/console

@@ -7,8 +7,8 @@ require 'fhir_models'
 # with your gem easier. You can also use a different console, if you like.
 
 # (If you use this, don't forget to add pry to your Gemfile!)
-# require "pry"
-# Pry.start
+require 'pry'
+Pry.start
 
-require 'irb'
-IRB.start
+# require 'irb'
+# IRB.start

data/lib/fhir_models.rb

@@ -15,6 +15,7 @@ Dir.chdir('lib') do
 
   require_relative 'fhir_models/fhir'
 
+  require_relative 'fhir_models/fhir/metadata'
   # require generated models
   Dir['fhir_models/fhir/**/*.rb'].each do |file|
     require_relative file

data/lib/fhir_models/bootstrap/hashable.rb

@@ -50,27 +50,12 @@ module FHIR
               value.map! do |child|
                 obj = child
                 unless [FHIR::RESOURCES, FHIR::TYPES].flatten.include? child.class.name.gsub('FHIR::', '')
-                  if child['resourceType']
-                    klass = Module.const_get("FHIR::#{child['resourceType']}") rescue nil
-                  end
-                  begin
-                    obj = klass.new(child)
-                  rescue => e
-                    FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{e.backtrace}")
-                  end
+                  obj = make_child(child, klass)
                 end
                 obj
               end
             else # handle single object
-              if value['resourceType']
-                klass = Module.const_get("FHIR::#{value['resourceType']}") rescue nil
-              end
-              begin
-                obj = klass.new(value)
-                value = obj
-              rescue => e
-                FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{e.backtrace}")
-              end
+              value = make_child(value, klass)
               # if there is only one of these, but cardinality allows more, we need to wrap it in an array.
               value = [ value ] if(value && (meta['max'] > 1))
             end
@@ -96,6 +81,18 @@ module FHIR
       self
     end
 
+    def make_child(child, klass)
+      if child['resourceType']
+        klass = Module.const_get("FHIR::#{child['resourceType']}") rescue nil
+      end
+      begin
+        obj = klass.new(child)
+      rescue => e
+        FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{e.backtrace}")
+      end
+      obj
+    end
+
     def convert_primitive(value, meta)
       return value if !value.is_a?(String)
 
@@ -117,6 +114,6 @@ module FHIR
       rval
     end
 
-    private :convert_primitive
+    private :make_child, :convert_primitive
   end
 end

data/lib/fhir_models/bootstrap/model.rb

@@ -52,7 +52,7 @@ module FHIR
     end
 
     def to_reference
-      FHIR::Reference.new(reference: "#{self.class.name.demodulize}/#{self.id}")
+      FHIR::Reference.new(reference: "#{self.class.name.split('::').last}/#{self.id}")
     end
 
     def equals?(other, exclude=[])
@@ -185,32 +185,7 @@ module FHIR
           if klassname=='Reference'
             validation = v.validate(contained_here)
             errors[field] << validation if !validation.empty?
-            if v.reference && meta['type_profiles']
-              matches_one_profile = false
-              meta['type_profiles'].each do |p|
-                basetype = p.split('/').last
-                matches_one_profile = true if v.reference.include?(basetype)
-                # check profiled resources
-                profile_basetype = FHIR::Definitions.get_basetype(p)
-                matches_one_profile = true if profile_basetype && v.reference.include?(profile_basetype)
-              end
-              matches_one_profile = true if meta['type_profiles'].include?('http://hl7.org/fhir/StructureDefinition/Resource')
-              if !matches_one_profile && v.reference.start_with?('#')
-                # we need to look at the local contained resources
-                begin
-                  r = contained_here.select{|x|x.id==v.reference[1..-1]}.first
-                rescue
-                  FHIR.logger.warn "Unable to resolve reference #{v.reference}"
-                end
-                if !r.nil?
-                  meta['type_profiles'].each do |p|
-                    p = p.split('/').last
-                    matches_one_profile = true if r.resourceType==p
-                  end
-                end
-              end
-              errors[field] << "#{meta['path']}: incorrect Reference type, expected #{meta['type_profiles'].map{|x|x.split('/').last}.join('|')}" if !matches_one_profile
-            end
+            validate_reference_type(v, meta, contained_here, errors[field])
           else
             errors[field] << "#{meta['path']}: expected Reference, found #{klassname}"
           end
@@ -260,6 +235,33 @@ module FHIR
       errors.delete(field) if errors[field].empty?
     end
 
+    def validate_reference_type(ref, meta, contained_here, errors)
+      if ref.reference && meta['type_profiles']
+        matches_one_profile = false
+        meta['type_profiles'].each do |p|
+          basetype = p.split('/').last
+          matches_one_profile = true if ref.reference.include?(basetype)
+          # check profiled resources
+          profile_basetype = FHIR::Definitions.get_basetype(p)
+          matches_one_profile = true if profile_basetype && ref.reference.include?(profile_basetype)
+        end
+        matches_one_profile = true if meta['type_profiles'].include?('http://hl7.org/fhir/StructureDefinition/Resource')
+        if !matches_one_profile && ref.reference.start_with?('#')
+          # we need to look at the local contained resources
+          r = contained_here.find{|x|x.id==ref.reference[1..-1]}
+          if !r.nil?
+            meta['type_profiles'].each do |p|
+              p = p.split('/').last
+              matches_one_profile = true if r.resourceType==p
+            end
+          else
+            FHIR.logger.warn "Unable to resolve reference #{ref.reference}"
+          end
+        end
+        errors << "#{meta['path']}: incorrect Reference type, expected #{meta['type_profiles'].map{|x|x.split('/').last}.join('|')}" if !matches_one_profile
+      end
+    end
+
     def is_primitive?(datatype, value)
       # Remaining data types: handle special cases before checking type StructureDefinitions
       case datatype.downcase
@@ -299,16 +301,16 @@ module FHIR
         json_or_xml = value.downcase.include?('xml') || value.downcase.include?('json')
         known_weird = ['application/cql+text'].include?(value)
         valid = json_or_xml || known_weird || (!matches.nil? && !matches.empty?)
-      elsif uri=='http://tools.ietf.org/html/bcp47'
-        hasRegion = (!(value =~ /-/).nil?)
-        valid = !BCP47::Language.identify(value.downcase).nil? && (!hasRegion || !BCP47::Region.identify(value.upcase).nil?)
+      elsif uri=='http://hl7.org/fhir/ValueSet/languages' || uri=='http://tools.ietf.org/html/bcp47'
+        has_region = (!(value =~ /-/).nil?)
+        valid = !BCP47::Language.identify(value.downcase).nil? && (!has_region || !BCP47::Region.identify(value.upcase).nil?)
       else
         FHIR.logger.warn "Unable to check_binding on unknown ValueSet: #{uri}"
       end
       valid
     end
 
-    private :is_primitive?, :check_binding, :validate_field
+    private :validate_reference_type, :is_primitive?, :check_binding, :validate_field
 
   end
 end

data/lib/fhir_models/fhir_ext/{StructureDefinition.rb → structure_definition.rb}

@@ -412,10 +412,10 @@ module FHIR
       end
 
       resource_type = json['resourceType']
-      baseType = snapshot.element[0].path
+      base_type = snapshot.element[0].path
       snapshot.element.each do |element|
         path = element.path
-        path = path[(baseType.size+1)..-1] if path.start_with? baseType
+        path = path[(base_type.size+1)..-1] if path.start_with? base_type
 
         nodes = get_json_nodes(json, path)
 
@@ -546,18 +546,18 @@ module FHIR
       if FHIR::RESOURCES.include?(data_type_code)
         definition = FHIR::Definitions.get_resource_definition(data_type_code)
         if !definition.nil?
-          retVal = false
+          ret_val = false
           begin
             klass = Module.const_get("FHIR::#{data_type_code}")
-            retVal = definition.validates_resource?(klass.new(deep_copy(value)))
-            if !retVal
+            ret_val = definition.validates_resource?(klass.new(deep_copy(value)))
+            if !ret_val
               @errors += definition.errors
               @warnings += definition.warnings
             end
           rescue
             @errors << "Unable to verify #{data_type_code} as a FHIR Resource."
           end
-          return retVal
+          return ret_val
         end
       end
 
@@ -615,18 +615,18 @@ module FHIR
         resource_type = value['resourceType']
         definition = FHIR::Definitions.get_resource_definition(resource_type)
         if !definition.nil?
-          retVal = false
+          ret_val = false
           begin
             klass = Module.const_get("FHIR::#{resource_type}")
-            retVal = definition.validates_resource?(klass.new(deep_copy(value)))
-            if !retVal
+            ret_val = definition.validates_resource?(klass.new(deep_copy(value)))
+            if !ret_val
               @errors += definition.errors
               @warnings += definition.warnings
             end
           rescue
             @errors << "Unable to verify #{resource_type} as a FHIR Resource."
           end
-          retVal
+          ret_val
         else
           @errors << "Unable to find base Resource definition: #{resource_type}"
           false
@@ -638,18 +638,18 @@ module FHIR
         definition = FHIR::Definitions.get_type_definition(data_type_code)
         definition = FHIR::Definitions.get_resource_definition(data_type_code) if definition.nil?
         if !definition.nil?
-          retVal = false
+          ret_val = false
           begin
             klass = Module.const_get("FHIR::#{data_type_code}")
-            retVal = definition.validates_resource?(klass.new(deep_copy(value)))
-            if !retVal
+            ret_val = definition.validates_resource?(klass.new(deep_copy(value)))
+            if !ret_val
               @errors += definition.errors
               @warnings += definition.warnings
             end
           rescue
             @errors << "Unable to verify #{data_type_code} as a FHIR type."
           end
-          retVal
+          ret_val
         else
           @errors << "Unable to find base type definition: #{data_type_code}"
           false
@@ -659,26 +659,26 @@ module FHIR
 
     def check_binding(element, value)
 
-      vsUri = element.binding.valueSetUri || element.binding.valueSetReference.reference
-      valueset = FHIR::Definitions.get_codes(vsUri)
+      vs_uri = element.binding.valueSetUri || element.binding.valueSetReference.reference
+      valueset = FHIR::Definitions.get_codes(vs_uri)
 
       matching_type = 0
 
-      if vsUri=='http://hl7.org/fhir/ValueSet/content-type' || vsUri=='http://www.rfc-editor.org/bcp/bcp13.txt'
+      if vs_uri=='http://hl7.org/fhir/ValueSet/content-type' || vs_uri=='http://www.rfc-editor.org/bcp/bcp13.txt'
         matches = MIME::Types[value]
         if (matches.nil? || matches.size==0) && !is_some_type_of_xml_or_json(value)
           @errors << "#{element.path} has invalid mime-type: '#{value}'"
           matching_type-=1 if element.binding.strength=='required'
         end
-      elsif vsUri=='http://tools.ietf.org/html/bcp47'
-        hasRegion = (!(value =~ /-/).nil?)
-        valid = !BCP47::Language.identify(value.downcase).nil? && (!hasRegion || !BCP47::Region.identify(value.upcase).nil?)
+      elsif vs_uri=='http://hl7.org/fhir/ValueSet/languages' || vs_uri=='http://tools.ietf.org/html/bcp47'
+        has_region = (!(value =~ /-/).nil?)
+        valid = !BCP47::Language.identify(value.downcase).nil? && (!has_region || !BCP47::Region.identify(value.upcase).nil?)
         if !valid
           @errors << "#{element.path} has unrecognized language: '#{value}'"
           matching_type-=1 if element.binding.strength=='required'
         end
       elsif valueset.nil?
-        @warnings << "#{element.path} has unknown ValueSet: '#{vsUri}'"
+        @warnings << "#{element.path} has unknown ValueSet: '#{vs_uri}'"
         matching_type-=1 if element.binding.strength=='required'
       elsif !valueset.values.flatten.include?(value)
         message = "#{element.path} has invalid code '#{value}' from #{valueset}"

data/lib/fhir_models/fhir_ext/{StructureDefinitionFinding.rb → structure_definition_finding.rb}

@@ -42,25 +42,25 @@ module FHIR
       from_json(to_json)
     end
 
-    def warning(path, attribute, message, valueA, valueB)
+    def warning(path, attribute, message, value_a, value_b)
       obj = clone
       obj.status = 'WARNING'
       obj.path = path
       obj.attribute = attribute
       obj.message = message
-      obj.valueA = valueA
-      obj.valueB = valueB
+      obj.valueA = value_a
+      obj.valueB = value_b
       obj
     end
 
-    def error(path, attribute, message, valueA, valueB)
+    def error(path, attribute, message, value_a, value_b)
       obj = clone
       obj.status = 'ERROR'
       obj.path = path
       obj.attribute = attribute
       obj.message = message
-      obj.valueA = valueA
-      obj.valueB = valueB
+      obj.valueA = value_a
+      obj.valueB = value_b
       obj
     end
 

data/lib/fhir_models/fluentpath/evaluate.rb

@@ -64,6 +64,10 @@ module FluentPath
     return true
   end
 
+  def self.clean_index(tree, index)
+    tree[index] = nil if !index.nil?
+  end
+
   # evaluate a parsed expression given some context data
   def self.compute(tree, data)
     tree = tree.tree if tree.is_a?(FluentPath::Expression)
@@ -104,7 +108,7 @@ module FluentPath
           end
           if previous_node.is_a?(Hash) || previous_node.is_a?(Array)
             tree[index] = get(node, previous_node)
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
           elsif !previous_node.is_a?(FluentPath::Expression)
             tree[index] = get(node, data)
           end
@@ -131,16 +135,15 @@ module FluentPath
                 convert_to_boolean(sub)
               end
               tree[index] = previous_node
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             elsif previous_node.is_a?(Hash)
               sub = compute(block, previous_node)
               if convert_to_boolean(sub)
                 tree[index] = previous_node
-                tree[previous_index] = nil if !previous_index.nil?
+                clean_index(tree, previous_index)
               else
                 tree[index] = {}
-                tree[previous_index] = nil if !previous_index.nil?
-
+                clean_index(tree, previous_index)
               end
             else
               raise "Where function not applicable to #{previous_node.class}: #{previous_node}"
@@ -162,10 +165,10 @@ module FluentPath
                 compute(block.clone, item)
               end
               tree[index] = previous_node
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             elsif previous_node.is_a?(Hash)
               tree[index] = compute(block, previous_node)
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "Select function not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -191,7 +194,7 @@ module FluentPath
                 end
                 ext = exts.select{|x|x['url']==url}.first
                 tree[index] = ext
-                tree[previous_index] = nil if !previous_index.nil?
+                clean_index(tree, previous_index)
               else
                 raise "Extension function not applicable to #{exts.class}: #{exts}"
               end
@@ -204,7 +207,7 @@ module FluentPath
             # otherwise, use the context as data
             if previous_node.is_a?(Hash)
               tree[index] = previous_node.values
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
               substitutions+=1
             elsif data.is_a?(Hash)
               tree[index] = data.values
@@ -217,7 +220,7 @@ module FluentPath
             # the previous node should be an Array of length > 1
             if previous_node.is_a?(Array)
               tree[index] = previous_node.first
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "First function is not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -225,7 +228,7 @@ module FluentPath
             # the previous node should be an Array of length > 1
             if previous_node.is_a?(Array)
               tree[index] = previous_node.last
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "Last function is not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -233,7 +236,7 @@ module FluentPath
             # the previous node should be an Array of length > 1
             if previous_node.is_a?(Array)
               tree[index] = previous_node.last(previous_node.length-1)
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "Tail function is not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -268,28 +271,28 @@ module FluentPath
               result = true
               previous_node.each{|item| result = (result && convert_to_boolean(item))}
               tree[index] = result
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               tree[index] = convert_to_boolean(previous_node)
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             end
           when :not
             tree[index] = !convert_to_boolean(previous_node)
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
           when :count
             tree[index] = 0
             tree[index] = 1 if !previous_node.nil?
             tree[index] = previous_node.length if previous_node.is_a?(Array)
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
           when :empty
             tree[index] = (previous_node==:null || previous_node.empty? rescue previous_node.nil?)
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
           when :exists
             tree[index] = !previous_node.nil? && previous_node!=:null
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
           when :distinct
             tree[index] = (previous_node.uniq rescue previous_node)
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
           when :startsWith
             # the previous node should be a data (as String)
             # the next node should be a block or subexpression (as FluentPath::Expression)
@@ -303,7 +306,7 @@ module FluentPath
               FHIR.logger.debug 'Evaling StartsWith Block....'
               prefix = compute(block, data)
               tree[index] = previous_node.start_with?(prefix) rescue false
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "StartsWith function not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -331,7 +334,7 @@ module FluentPath
                 length = previous_node.length - start
               end
               tree[index] = previous_node[start..(start+length)]
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "Substring function not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -349,7 +352,7 @@ module FluentPath
               FHIR.logger.debug 'Evaling Contains Block....'
               substring = compute(block, data)
               tree[index] = previous_node.include?(substring) rescue false
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "Contains function not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -370,7 +373,7 @@ module FluentPath
             end
             if previous_node.is_a?(String) || previous_node==true || previous_node==false || previous_node.is_a?(Numeric)
               tree[index] = array.include?(previous_node) rescue false
-              tree[previous_index] = nil if !previous_index.nil?
+              clean_index(tree, previous_index)
             else
               raise "In function not applicable to #{previous_node.class}: #{previous_node}"
             end
@@ -385,7 +388,7 @@ module FluentPath
               tree[index] = 0
               tree[index] = 1 if convert_to_boolean(previous_node)
             end
-            tree[previous_index] = nil if !previous_index.nil?
+            clean_index(tree, previous_index)
             break
           else
             raise "Function not implemented: #{node}"

data/lib/fhir_models/tasks/tasks.rake

@@ -100,8 +100,8 @@ namespace :fhir do
     d = FHIR::Definitions
     defs =  d.get_complex_types + d.get_resource_definitions
     invariants = {}
-    defs.each do |structureDef|
-      structureDef['snapshot']['element'].each do |element|
+    defs.each do |structure_definition|
+      structure_definition['snapshot']['element'].each do |element|
         if element['constraint']
           element['constraint'].each do |constraint|
             if constraint['expression']

data/lib/fhir_models/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   module Models
-    VERSION = '1.6.4'.freeze
+    VERSION = '1.6.6'.freeze
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_models
 version: !ruby/object:Gem::Version
-  version: 1.6.4
+  version: 1.6.6
 platform: ruby
 authors:
 - Jason Walonoski
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-10-10 00:00:00.000000000 Z
+date: 2016-10-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -1293,8 +1293,8 @@ files:
 - lib/fhir_models/fhir/types/Timing.rb
 - lib/fhir_models/fhir/types/TriggerDefinition.rb
 - lib/fhir_models/fhir/types/UsageContext.rb
-- lib/fhir_models/fhir_ext/StructureDefinition.rb
-- lib/fhir_models/fhir_ext/StructureDefinitionFinding.rb
+- lib/fhir_models/fhir_ext/structure_definition.rb
+- lib/fhir_models/fhir_ext/structure_definition_finding.rb
 - lib/fhir_models/fluentpath/evaluate.rb
 - lib/fhir_models/fluentpath/expression.rb
 - lib/fhir_models/fluentpath/parse.rb