fhir_models 3.0.1 → 3.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 58bb4aa2afa1f20df0bd5c24d309088208635f5c
+  metadata.gz: ecf5c1936f2720e5d6bd078a8f90f04f1c893b92
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data/.rubocop_todo.yml

@@ -6,6 +6,15 @@
 # Note that changes in the inspected code, or installation of new
 # versions of RuboCop, may require this file to be generated again.
 
+Performance/Caller:
+  Enabled: false
+
+Style/MultipleComparison:
+  Enabled: false
+
+Style/YodaCondition:
+  Enabled: false
+
 # Offense count: 37
 Metrics/AbcSize:
   Max: 423
@@ -13,7 +22,7 @@ Metrics/AbcSize:
 # Offense count: 10
 # Configuration parameters: CountComments, ExcludedMethods.
 Metrics/BlockLength:
-  Max: 101
+  Max: 120
 
 # Offense count: 1
 # Configuration parameters: CountBlocks.

data/fhir_models.gemspec

@@ -23,7 +23,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency 'nokogiri', '>= 1.6'
   spec.add_dependency 'date_time_precision', '>= 0.8'
   spec.add_dependency 'bcp47', '>= 0.3'
-  spec.add_dependency 'mime-types', '>= 1.16', '< 3'
+  spec.add_dependency 'mime-types', '>= 1.16'
 
   spec.add_development_dependency 'bundler'
   spec.add_development_dependency 'rake'

data/lib/fhir_models/bootstrap/definitions.rb

@@ -197,7 +197,7 @@ module FHIR
     def self.get_codes(uri)
       return nil if uri.nil?
       return @@cache[uri] if @@cache[uri]
-      valueset = expansions.select { |x| x['url'] == uri }.first
+      valueset = expansions.find { |x| x['url'] == uri } || valuesets.find { |x| x['url'] == uri && x['resourceType'] == 'ValueSet' }
       unless valueset.nil?
         @@cache[uri] = {}
         if !valueset['expansion'].nil? && !valueset['expansion']['contains'].nil?
@@ -206,11 +206,18 @@ module FHIR
           valueset['expansion']['contains'].each { |x| @@cache[uri][x['system']] << x['code'] }
         end
         if !valueset['compose'].nil? && !valueset['compose']['include'].nil?
-          included_systems = valueset['compose']['include'].map { |x| x['system'] }.uniq
-          included_systems.each { |x| @@cache[uri][x] = [] unless @@cache[uri].keys.include?(x) }
+          # for each system, if codes are included add those, otherwise lookup the codesystem in the list
+          included_systems = []
+          valueset['compose']['include'].each do |code_group|
+            system_url = code_group['system']
+            @@cache[uri][system_url] ||= []
+            code_group['concept'].each { |y| @@cache[uri][system_url] << y['code'] } if code_group['concept']
+            included_systems << system_url
+          end
+          included_systems.each { |x| @@cache[uri][x] ||= [] }
           systems = valuesets.select { |x| x['resourceType'] == 'CodeSystem' && included_systems.include?(x['url']) }
-          systems.each do |x|
-            x['concept'].each { |y| @@cache[uri][x['url']] << y['code'] } if x['concept']
+          systems.each do |included_system|
+            included_system['concept'].each { |y| @@cache[uri][included_system['url']] << y['code'] } if included_system['concept']
           end
         end
         @@cache[uri].each { |_system, codes| codes.uniq! }

data/lib/fhir_models/bootstrap/model.rb

@@ -235,7 +235,7 @@ module FHIR
           end
         else
           the_codes.each do |code|
-            has_valid_code = true if check_binding(meta['binding']['uri'], code)
+            has_valid_code = true if check_binding_uri(meta['binding']['uri'], code)
             break if has_valid_code
           end
         end
@@ -277,7 +277,7 @@ module FHIR
     end
     deprecate :is_primitive?, :primitive?
 
-    def check_binding(uri, value)
+    def check_binding_uri(uri, value)
       valid = false
       if uri == 'http://hl7.org/fhir/ValueSet/content-type' || uri == 'http://www.rfc-editor.org/bcp/bcp13.txt'
         matches = MIME::Types[value]
@@ -288,11 +288,11 @@ module FHIR
         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}"
+        FHIR.logger.warn "Unable to check_binding_uri on unknown ValueSet: #{uri}"
       end
       valid
     end
 
-    private :validate_reference_type, :check_binding, :validate_field
+    private :validate_reference_type, :check_binding_uri, :validate_field
   end
 end

data/lib/fhir_models/fhir_ext/structure_definition.rb

@@ -113,9 +113,10 @@ module FHIR
       path = element.local_name || element.path
       path = path[(@hierarchy.path.size + 1)..-1] if path.start_with? @hierarchy.path
 
-      begin
+      if element.type && !element.type.empty?
         data_type_found = element.type.first.code
-      rescue
+      else
+        @warnings << "Unable to guess data type for #{describe_element(element)}"
         data_type_found = nil
       end
 
@@ -139,16 +140,12 @@ module FHIR
         nodes = nodes.select { |x| extension_profile.profile == x['url'] }
       end
 
-      # Check the cardinality
-      min = element.min
-      max = element.max == '*' ? Float::INFINITY : element.max.to_i
-      if (nodes.size < min) || (nodes.size > max)
-        @errors << "#{describe_element(element)} failed cardinality test (#{min}..#{max}) -- found #{nodes.size}"
-      end
+      verify_cardinality(element, nodes)
 
       return if nodes.empty?
       # Check the datatype for each node, only if the element has one declared, and it isn't the root element
       if !element.type.empty? && element.path != id
+        # element.type not being empty implies data_type_found != nil, for valid profiles
         codeable_concept_pattern = element.pattern && element.pattern.is_a?(FHIR::CodeableConcept)
         matching_pattern = false
         nodes.each do |value|
@@ -165,18 +162,18 @@ module FHIR
             # if extension_def
             #   verified_extension = extension_def.validates_resource?(FHIR::Extension.new(deep_copy(value)))
             # end
-          elsif data_type_found
+          else
             temp = @errors
             @errors = []
             verified_data_type = data_type?(data_type_found, value)
-            temp_messages << @errors
+            temp_messages += @errors
             @errors = temp
           end
-          if data_type_found && (verified_extension || verified_data_type)
+          if verified_extension || verified_data_type
             matching_type += 1
             if data_type_found == 'code' # then check the binding
               unless element.binding.nil?
-                matching_type += check_binding(element, value)
+                matching_type += check_binding_element(element, value)
               end
             elsif data_type_found == 'CodeableConcept' && codeable_concept_pattern
               vcc = FHIR::CodeableConcept.new(value)
@@ -189,12 +186,8 @@ module FHIR
             elsif data_type_found == 'String' && !element.maxLength.nil? && (value.size > element.maxLength)
               @errors << "#{describe_element(element)} exceed maximum length of #{element.maxLength}: #{value}"
             end
-          elsif data_type_found
-            temp_messages << "#{describe_element(element)} is not a valid #{data_type_found}: '#{value}'"
           else
-            # we don't know the data type... so we say "OK"
-            matching_type += 1
-            @warnings >> "Unable to guess data type for #{describe_element(element)}"
+            temp_messages << "#{describe_element(element)} is not a valid #{data_type_found}: '#{value}'"
           end
 
           if matching_type <= 0
@@ -203,9 +196,7 @@ module FHIR
           else
             @warnings += temp_messages
           end
-          if !element.fixed.nil? && element.fixed != value
-            @errors << "#{describe_element(element)} value of '#{value}' did not match fixed value: #{element.fixed}"
-          end
+          verify_fixed_value(element, value)
         end
         if codeable_concept_pattern && matching_pattern == false
           @errors << "#{describe_element(element)} CodeableConcept did not match defined pattern: #{element.pattern.to_hash}"
@@ -244,6 +235,17 @@ module FHIR
       end
     end
 
+    def verify_cardinality(element, nodes)
+      # Check the cardinality
+      min = element.min
+      max = element.max == '*' ? Float::INFINITY : element.max.to_i
+      @errors << "#{describe_element(element)} failed cardinality test (#{min}..#{max}) -- found #{nodes.size}" if (nodes.size < min) || (nodes.size > max)
+    end
+
+    def verify_fixed_value(element, value)
+      @errors << "#{describe_element(element)} value of '#{value}' did not match fixed value: #{element.fixed}" if !element.fixed.nil? && element.fixed != value
+    end
+
     # data_type_code == a FHIR DataType code (see http://hl7.org/fhir/2015May/datatypes.html)
     # value == the representation of the value
     def data_type?(data_type_code, value)
@@ -322,7 +324,7 @@ module FHIR
     end
     deprecate :is_data_type?, :data_type?
 
-    def check_binding(element, value)
+    def check_binding_element(element, value)
       vs_uri = element.binding.valueSetUri || element.binding.valueSetReference.reference
       valueset = FHIR::Definitions.get_codes(vs_uri)
 
@@ -353,7 +355,7 @@ module FHIR
           end
         end
       elsif !valueset.values.flatten.include?(value)
-        message = "#{element.path} has invalid code '#{value}' from #{valueset}"
+        message = "#{element.path} has invalid code '#{value}' from #{vs_uri}"
         if element.binding.strength == 'required'
           @errors << message
           matching_type -= 1
@@ -368,13 +370,12 @@ module FHIR
     def some_type_of_xml_or_json?(code)
       m = code.downcase
       return true if m == 'xml' || m == 'json'
-      return true if (m.starts_with?('application/') || m.starts_with?('text/')) && (m.ends_with?('json') || m.ends_with?('xml'))
-      return true if m.starts_with?('application/xml') || m.starts_with?('text/xml')
-      return true if m.starts_with?('application/json') || m.starts_with?('text/json')
+      return true if m.start_with?('application/', 'text/') && m.end_with?('json', 'xml')
+      return true if m.start_with?('application/xml', 'text/xml', 'application/json', 'text/json')
       false
     end
     deprecate :is_some_type_of_xml_or_json, :some_type_of_xml_or_json?
 
-    private :valid_json?, :get_json_nodes, :build_hierarchy, :verify_element, :check_binding
+    private :valid_json?, :get_json_nodes, :build_hierarchy, :verify_element, :check_binding_element
   end
 end

data/lib/fhir_models/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   module Models
-    VERSION = '3.0.1'.freeze
+    VERSION = '3.0.2'.freeze
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_models
 version: !ruby/object:Gem::Version
-  version: 3.0.1
+  version: 3.0.2
 platform: ruby
 authors:
 - Jason Walonoski
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-05-02 00:00:00.000000000 Z
+date: 2017-08-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -61,9 +61,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '1.16'
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -71,9 +68,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '1.16'
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '3'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -1633,7 +1627,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.7
+rubygems_version: 2.6.12
 signing_key: 
 specification_version: 4
 summary: A Gem for handling FHIR models in ruby