fhir_models 1.8.2 → 1.8.3

data/lib/fhir_models/bootstrap/field.rb

@@ -36,7 +36,7 @@ module FHIR
 
     def fix_name(name)
       fix = nil
-      fix = "local_#{name}" if %w(class method resourceType).include?(name)
+      fix = "local_#{name}" if %w[class method resourceType].include?(name)
       fix
     end
   end

data/lib/fhir_models/bootstrap/generator.rb

@@ -6,7 +6,7 @@ module FHIR
       # templates keeps track of all the templates in context within a given StructureDefinition
       attr_accessor :templates
 
-      def initialize(auto_setup = true)
+      def initialize(auto_setup: true)
         # load the valueset expansions
         @defn = FHIR::Definitions
         # templates is an array
@@ -29,7 +29,7 @@ module FHIR
       def generate_metadata
         template = FHIR::Boot::Template.new([], true)
 
-        primitives = @defn.get_primitive_types
+        primitives = @defn.primitive_types
         hash = {}
         primitives.each do |p|
           field = FHIR::Field.new
@@ -52,10 +52,10 @@ module FHIR
         end
         template.constants['PRIMITIVES'] = hash
 
-        template.constants['TYPES'] = @defn.get_complex_types.map { |t| t['id'] }
+        template.constants['TYPES'] = @defn.complex_types.map { |t| t['id'] }
 
         # resources
-        template.constants['RESOURCES'] = @defn.get_resource_definitions.map { |r| r['id'] }
+        template.constants['RESOURCES'] = @defn.resource_definitions.map { |r| r['id'] }
 
         filename = File.join(@lib, 'fhir', 'metadata.rb')
         file = File.open(filename, 'w:UTF-8')
@@ -67,13 +67,13 @@ module FHIR
         folder = File.join @lib, 'fhir', 'types'
         # complex data types start with an uppercase letter
         # and we'll filter out profiles on types (for example, Age is a profile on Quantity)
-        complex_types = @defn.get_complex_types
+        complex_types = @defn.complex_types
         generate_class_files(folder, complex_types)
       end
 
       def generate_resources
         folder = File.join @lib, 'fhir', 'resources'
-        generate_class_files(folder, @defn.get_resource_definitions)
+        generate_class_files(folder, @defn.resource_definitions)
       end
 
       def generate_class_files(folder = @lib, structure_defs = [])
@@ -81,7 +81,7 @@ module FHIR
           @templates.clear
           type_name = structure_def['id']
           template = generate_class([type_name], structure_def, true)
-          params = @defn.get_search_parameters(type_name)
+          params = @defn.search_parameters(type_name)
           template.constants['SEARCH_PARAMS'] = params unless params.nil?
           filename = File.join(folder, "#{type_name}.rb")
           file = File.open(filename, 'w:UTF-8')
@@ -98,7 +98,7 @@ module FHIR
 
       def generate_class(hierarchy, structure_def, top_level = false)
         type_name = structure_def['id']
-        constrained_type = structure_def['constrained_type']
+        constrained_type = structure_def['type']
         path_type = type_name
         path_type = constrained_type if constrained_type
 
@@ -162,7 +162,7 @@ module FHIR
             element['type'].select { |t| t['code'] == 'Reference' || t['code'] == 'Extension' }.each do |data_type|
               profiles << data_type['targetProfile']
             end
-            profiles.select! { |p| !p.nil? }
+            profiles.reject!(&:nil?)
             profiles.flatten!
 
             # Calculate fields that have multiple data types
@@ -186,7 +186,7 @@ module FHIR
               field.max = field.max.to_i
               field.max = '*' if element['max'] == '*'
 
-              if %w(code Coding CodeableConcept).include?(data_type) && element['binding']
+              if %w[code Coding CodeableConcept].include?(data_type) && element['binding']
                 field.binding = element['binding']
                 field.binding['uri'] = field.binding['valueSetUri']
                 field.binding['uri'] = field.binding['valueSetReference'] if field.binding['uri'].nil?
@@ -199,7 +199,7 @@ module FHIR
                 codes = @defn.get_codes(field.binding['uri'])
                 field.valid_codes = codes unless codes.nil?
                 FHIR.logger.warn "  MISSING EXPANSION -- #{field.path} #{field.min}..#{field.max}: #{field.binding['uri']} (#{field.binding['strength']})" if field.valid_codes.empty? && field.binding['uri'] && !field.binding['uri'].end_with?('bcp47') && !field.binding['uri'].end_with?('bcp13.txt')
-              elsif %w(Element BackboneElement).include?(data_type)
+              elsif %w[Element BackboneElement].include?(data_type)
                 # This is a nested structure or class
                 field.type = "#{hierarchy.join('::')}::#{cap_first(field.name)}"
               end

data/lib/fhir_models/bootstrap/hashable.rb

@@ -40,9 +40,14 @@ module FHIR
         next if meta.nil?
         local_name = key
         local_name = meta['local_name'] if meta['local_name']
-        instance_variable_set("@#{local_name}", value) rescue nil
+        begin
+          instance_variable_set("@#{local_name}", value)
+        rescue
+          # TODO: this appears to be a dead code branch
+          nil
+        end
         # inflate the value if it isn't a primitive
-        klass = Module.const_get("FHIR::#{meta['type']}") rescue nil
+        klass = FHIR::PRIMITIVES.key?(meta['type']) ? nil : FHIR.const_get(meta['type'])
         if !klass.nil? && !value.nil?
           # handle array of objects
           if value.is_a?(Array)
@@ -78,12 +83,20 @@ module FHIR
 
     def make_child(child, klass)
       if child['resourceType']
-        klass = Module.const_get("FHIR::#{child['resourceType']}") rescue nil
+        klass = begin
+          FHIR.const_get(child['resourceType'])
+        rescue => _exception
+          # TODO: this appears to be a dead code branch
+          # TODO: should this log / re-raise the exception if encountered instead of silently swallowing it?
+          nil
+        end
       end
       begin
         obj = klass.new(child)
-      rescue => e
-        FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{e.backtrace}")
+      rescue => exception
+        # TODO: this appears to be a dead code branch
+        # TODO: should this re-raise the exception if encountered instead of silently swallowing it?
+        FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{exception.backtrace}")
       end
       obj
     end

data/lib/fhir_models/bootstrap/json.rb

@@ -16,7 +16,8 @@ module FHIR
         klass = Module.const_get("FHIR::#{resource_type}")
         resource = klass.new(hash)
       rescue => e
-        FHIR.logger.error("Failed to deserialize JSON:\n#{json}\n#{e.backtrace}")
+        FHIR.logger.error("Failed to deserialize JSON:\n#{e.backtrace}")
+        FHIR.logger.debug("JSON:\n#{json}")
         resource = nil
       end
       resource

data/lib/fhir_models/bootstrap/model.rb

@@ -5,6 +5,7 @@ require 'bcp47'
 
 module FHIR
   class Model
+    extend FHIR::Deprecate
     def initialize(hash = {})
       from_hash(hash)
       self.class::METADATA.each do |key, value|
@@ -14,11 +15,11 @@ module FHIR
       end
     end
 
-    def method_missing(method, *args, &block)
+    def method_missing(method, *_args, &_block)
       if defined?(self.class::MULTIPLE_TYPES) && self.class::MULTIPLE_TYPES[method.to_s]
         self.class::MULTIPLE_TYPES[method.to_s].each do |type|
           type[0] = type[0].upcase
-          value = self.method("#{method}#{type}").call
+          value = send("#{method}#{type}".to_sym)
           return value unless value.nil?
         end
         return nil
@@ -41,7 +42,7 @@ module FHIR
           return ext.first.value.nil? ? ext.first : ext.first.value
         end
       end
-      super(method, *args, &block)
+      raise NoMethodError.new("undefined method `#{method}' for #{inspect}", method)
     end
 
     def to_reference
@@ -87,9 +88,10 @@ module FHIR
       end
     end
 
-    def is_valid?
+    def valid?
       validate.empty?
     end
+    deprecate :is_valid?, :valid?
 
     def validate(contained = nil)
       validate_profile(self.class::METADATA, contained)
@@ -125,7 +127,11 @@ module FHIR
         end
       end # metadata.each
       # check multiple types
-      multiple_types = self.class::MULTIPLE_TYPES rescue {}
+      multiple_types = begin
+                         self.class::MULTIPLE_TYPES
+                       rescue
+                         {}
+                       end
       multiple_types.each do |prefix, suffixes|
         present = []
         suffixes.each do |suffix|
@@ -137,10 +143,11 @@ module FHIR
         end
         errors[prefix] = ["#{prefix}[x]: more than one type present."] if present.length > 1
         # remove errors for suffixes that are not present
+        next unless present.length == 1
         suffixes.each do |suffix|
           typename = "#{prefix}#{suffix[0].upcase}#{suffix[1..-1]}"
           errors.delete(typename) unless present.include?(typename)
-        end if present.length==1
+        end
       end
       errors.keep_if { |_k, v| (v && !v.empty?) }
     end
@@ -195,7 +202,7 @@ module FHIR
             match = (v =~ Regexp.new(primitive_meta['regex']))
             errors[field] << "#{meta['path']}: #{v} does not match #{datatype} regex" if match.nil?
           else
-            errors[field] << "#{meta['path']}: #{v} is not a valid #{datatype}" unless is_primitive?(datatype, v)
+            errors[field] << "#{meta['path']}: #{v} is not a valid #{datatype}" unless FHIR.primitive?(datatype: datatype, value: v)
           end
         end
         # check binding
@@ -226,12 +233,13 @@ module FHIR
 
     def validate_reference_type(ref, meta, contained_here, errors)
       return unless ref.reference && meta['type_profiles']
+      return if ref.reference.start_with?('urn:uuid:', 'urn:oid:')
       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)
+        profile_basetype = FHIR::Definitions.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')
@@ -250,37 +258,11 @@ module FHIR
       errors << "#{meta['path']}: incorrect Reference type, expected #{meta['type_profiles'].map { |x| x.split('/').last }.join('|')}" unless matches_one_profile
     end
 
-    def is_primitive?(datatype, value)
-      # Remaining data types: handle special cases before checking type StructureDefinitions
-      case datatype.downcase
-      when 'boolean'
-        value == true || value == false || value.downcase == 'true' || value.downcase == 'false'
-      when 'code'
-        value.is_a?(String) && value.size >= 1 && value.size == value.rstrip.size
-      when 'string', 'markdown'
-        value.is_a?(String)
-      when 'xhtml'
-        fragment = Nokogiri::HTML::DocumentFragment.parse(value)
-        value.is_a?(String) && fragment.errors.size.zero?
-      when 'base64binary'
-        regex = /[^0-9\+\/\=A-Za-z\r\n ]/
-        value.is_a?(String) && (regex =~ value).nil?
-      when 'uri'
-        !URI.parse(value).nil? rescue false
-      when 'instant'
-        regex = /\A[0-9]{4}(-(0[1-9]|1[0-2])(-(0[0-9]|[1-2][0-9]|3[0-1])(T([01][0-9]|2[0-3]):[0-5][0-9]:[0-5][0-9](\.[0-9]+)?(Z|(\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00)))))\Z/
-        value.is_a?(String) && !(regex =~ value).nil?
-      when 'integer', 'unsignedint'
-        (!Integer(value).nil? rescue false)
-      when 'positiveint'
-        (!Integer(value).nil? rescue false) && (Integer(value) >= 0)
-      when 'decimal'
-        (!Float(value).nil? rescue false)
-      else
-        FHIR.logger.warn "Unable to check #{value} for datatype #{datatype}"
-        false
-      end
+    def primitive?(datatype, value)
+      FHIR.logger.warn("prefer using FHIR.primitive? Called from #{caller.first}")
+      FHIR.primitive?(datatype: datatype, value: value)
     end
+    deprecate :is_primitive?, :primitive?
 
     def check_binding(uri, value)
       valid = false
@@ -298,6 +280,6 @@ module FHIR
       valid
     end
 
-    private :validate_reference_type, :is_primitive?, :check_binding, :validate_field
+    private :validate_reference_type, :check_binding, :validate_field
   end
 end

data/lib/fhir_models/bootstrap/preprocess.rb

@@ -11,7 +11,7 @@ module FHIR
 
         # Remove entries that do not interest us: CompartmentDefinitions, OperationDefinitions, Conformance statements
         hash['entry'].select! do |entry|
-          %w(StructureDefinition ValueSet CodeSystem SearchParameter).include? entry['resource']['resourceType']
+          %w[StructureDefinition ValueSet CodeSystem SearchParameter].include? entry['resource']['resourceType']
         end
 
         # Remove unnecessary elements from the hash
@@ -34,37 +34,25 @@ module FHIR
 
       def self.pre_process_structuredefinition(hash)
         # Remove large HTML narratives and unused content
-        %w(text publisher contact description requirements mapping).each { |key| hash.delete(key) }
+        %w[text publisher contact description requirements mapping].each { |key| hash.delete(key) }
 
-        # Remove unused descriptions within the snapshot elements
-        if hash['snapshot']
-          hash['snapshot']['element'].each do |element|
-            %w(short definition comments requirements alias mapping).each { |key| element.delete(key) }
-          end
-        end
-        # Remove unused descriptions within the differential elements
-        if hash['differential']
-          hash['differential']['element'].each do |element|
-            %w(short definition comments requirements alias mapping).each { |key| element.delete(key) }
+        # Remove unused descriptions within the snapshot and differential elements
+        %w[snapshot differential].each do |key|
+          next unless hash[key]
+          hash[key]['element'].each do |element|
+            %w[short definition comments requirements alias mapping].each { |subkey| element.delete(subkey) }
           end
         end
       end
 
       def self.pre_process_valueset(hash)
         # Remove large HTML narratives and unused content
-        %w(meta text publisher contact description requirements).each { |key| hash.delete(key) }
-
-        if hash['compose'] && hash['compose']['include']
-          hash['compose']['include'].each do |element|
-            next unless element['concept']
-            element['concept'].each do |concept|
-              concept.delete('designation')
-            end
-          end
-        end
+        %w[meta text publisher contact description requirements].each { |key| hash.delete(key) }
 
-        if hash['compose'] && hash['compose']['exclude']
-          hash['compose']['exclude'].each do |element|
+        return unless hash['compose']
+        %w[include exclude].each do |key|
+          next unless hash['compose'][key]
+          hash['compose'][key].each do |element|
             next unless element['concept']
             element['concept'].each do |concept|
               concept.delete('designation')
@@ -75,27 +63,24 @@ module FHIR
 
       def self.pre_process_codesystem(hash)
         # Remove large HTML narratives and unused content
-        %w(meta text publisher contact description requirements).each { |key| hash.delete(key) }
-
-        if hash['concept']
-          hash['concept'].each do |concept|
-            pre_process_codesystem_concept(concept)
-          end
+        %w[meta text publisher contact description requirements].each { |key| hash.delete(key) }
+        return unless hash['concept']
+        hash['concept'].each do |concept|
+          pre_process_codesystem_concept(concept)
         end
       end
 
       def self.pre_process_codesystem_concept(hash)
-        %w(extension definition designation).each { |key| hash.delete(key) }
-        if hash['concept']
-          hash['concept'].each do |concept|
-            pre_process_codesystem_concept(concept)
-          end
+        %w[extension definition designation].each { |key| hash.delete(key) }
+        return unless hash['concept']
+        hash['concept'].each do |concept|
+          pre_process_codesystem_concept(concept)
         end
       end
 
       def self.pre_process_searchparam(hash)
         # Remove large HTML narratives and unused content
-        %w(id url name date publisher contact description xpathUsage).each { |key| hash.delete(key) }
+        %w[id url name date publisher contact description xpathUsage].each { |key| hash.delete(key) }
       end
 
       def self.remove_fhir_comments(hash)

data/lib/fhir_models/bootstrap/template.rb

@@ -2,6 +2,7 @@ module FHIR
   module Boot
     class Template
       include FHIR::Hashable
+      extend FHIR::Deprecate
 
       attr_accessor :name
       attr_accessor :hierarchy
@@ -21,7 +22,7 @@ module FHIR
         @top_level = top_level
       end
 
-      def get_metadata
+      def metadata
         metadata = {}
         @fields.each do |field|
           if metadata.keys.include?(field.name)
@@ -41,6 +42,7 @@ module FHIR
         end
         metadata
       end
+      deprecate :get_metadata, :metadata
 
       def to_s(offset = 0)
         # create an array of Strings, one per line
@@ -66,7 +68,6 @@ module FHIR
         s << ''
 
         # add mandatory METADATA constant
-        metadata = get_metadata
         @constants['METADATA'] = metadata unless metadata.empty?
 
         # add constants
@@ -94,18 +95,13 @@ module FHIR
         end
 
         # calculate the longest field name for whitespace layout
-        max_name_size = 0
-        @fields.each do |f|
-          name = f.local_name || f.name
-          max_name_size = name.length if name.length > max_name_size
-        end
-        max_name_size += 1
+        max_name_size = (@fields.map { |field| field.local_name || field.name }.map(&:length).max || 0) + 1
 
         # declare attributes
         @fields.each do |field|
           s << "#{space}attr_accessor :"
           local_name = field.local_name || field.name
-          s[-1] << ("%-#{max_name_size}s" % local_name.to_s)
+          s[-1] << format("%-#{max_name_size}s", local_name)
           # add comment after field declaration
           s[-1] << "# #{field.min}-#{field.max} "
           s[-1] << '[ ' if field.max.to_i > 1 || field.max == '*'

data/lib/fhir_models/bootstrap/xml.rb

@@ -1,6 +1,7 @@
 require 'nokogiri'
 module FHIR
   module Xml
+    extend FHIR::Deprecate
     #
     #  This module includes methods to serialize or deserialize FHIR resources to and from XML.
     #
@@ -32,7 +33,7 @@ module FHIR
       end
 
       hash.each do |key, value|
-        next if %w(extension modifierExtension).include?(name) && key == 'url'
+        next if %w[extension modifierExtension].include?(name) && key == 'url'
         next if key == 'id' && !FHIR::RESOURCES.include?(name)
         if value.is_a?(Hash)
           node.add_child(hash_to_xml_node(key, value, doc))
@@ -61,7 +62,7 @@ module FHIR
           node.add_child(child)
         end
       end
-      node.set_attribute('url', hash['url']) if %w(extension modifierExtension).include?(name)
+      node.set_attribute('url', hash['url']) if %w[extension modifierExtension].include?(name)
       node.set_attribute('id', hash['id']) if hash['id'] && !FHIR::RESOURCES.include?(name)
       node
     end
@@ -78,7 +79,8 @@ module FHIR
         klass = Module.const_get("FHIR::#{resource_type}")
         resource = klass.new(hash)
       rescue => e
-        FHIR.logger.error("Failed to deserialize XML:\n#{xml}\n#{e.backtrace}")
+        FHIR.logger.error("Failed to deserialize XML:\n#{e.backtrace}")
+        FHIR.logger.debug("XML:\n#{xml}")
         resource = nil
       end
       resource
@@ -106,7 +108,7 @@ module FHIR
           end
         end
       end
-      hash['url'] = node.get_attribute('url') if %w(extension modifierExtension).include?(node.name)
+      hash['url'] = node.get_attribute('url') if %w[extension modifierExtension].include?(node.name)
       hash['id'] = node.get_attribute('id') if node.get_attribute('id') # Testscript fixture ids (applies to any BackboneElement)
       hash['resourceType'] = node.name if FHIR::RESOURCES.include?(node.name)
 
@@ -122,9 +124,10 @@ module FHIR
       end
     end
 
-    def self.is_valid?(xml)
+    def self.valid?(xml)
       validate(xml).empty?
     end
+    deprecate :is_valid?, :valid?
 
     def self.validate(xml)
       defns = File.expand_path '../definitions/schema', File.dirname(File.absolute_path(__FILE__))