us_core_test_kit 0.2.4 → 0.3.1

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -1,12 +1,13 @@
 module USCoreTestKit
   class Generator
     class MustSupportMetadataExtractor
-      attr_accessor :profile_elements, :profile, :resource
+      attr_accessor :profile_elements, :profile, :resource, :ig_resources
 
-      def initialize(profile_elements, profile, resource)
+      def initialize(profile_elements, profile, resource, ig_resources)
         self.profile_elements = profile_elements
         self.profile = profile
         self.resource = resource
+        self.ig_resources = ig_resources
       end
 
       def must_supports
@@ -93,6 +94,22 @@ module USCoreTestKit
                   path: discriminator_path,
                   system: pattern_element.patternIdentifier.system
                 }
+              elsif pattern_element.binding&.strength == 'required' &&
+                    pattern_element.binding&.valueSet.present?
+
+                value_set = ig_resources.value_set_by_url(pattern_element.binding.valueSet)
+                bound_systems = value_set&.compose&.include&.reject { |code| code.concept.blank? }
+                values = []
+
+                if bound_systems.present?
+                  values = bound_systems&.flat_map { |system| system.concept.map { |code| code.code } }.uniq
+                end
+
+                {
+                  type: 'requiredBinding',
+                  path: discriminator_path,
+                  values: values
+                }
               else
                 raise StandardError, 'Unsupported discriminator pattern type'
               end
@@ -152,7 +169,6 @@ module USCoreTestKit
                   element.path == "#{current_element.path}.#{discriminator.path}"
               end
 
-              binding.pry if fixed_element.nil?
               {
                 path: discriminator.path,
                 value: fixed_element.fixedUri || fixed_element.fixedCode
@@ -251,7 +267,7 @@ module USCoreTestKit
               supported_types = current_element.type.select { |type| save_type_code?(type) }.map { |type| type.code }
               current_metadata[:types] = supported_types if supported_types.present?
 
-              handle_type_must_support_target_profiles(current_element.type.first, current_metadata) if current_element.type.first.code == 'Reference'
+              handle_type_must_support_target_profiles(current_element.type.first, current_metadata) if current_element.type.first&.code == 'Reference'
 
               handle_fixed_values(current_metadata, current_element)
 
@@ -277,6 +293,10 @@ module USCoreTestKit
         when '4.0.0'
           add_device_distinct_identifier
           add_patient_uscdi_elements
+        when '5.0.1'
+          add_patient_uscdi_elements
+          add_document_reference_category_values
+          remove_survey_questionnaire_response
         end
       end
 
@@ -361,6 +381,32 @@ module USCoreTestKit
               uscdi_only: true
             }
           end
+        when '5.0.1'
+          case profile.type
+          when 'CareTeam'
+            choices << {
+              target_profiles: [
+                'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner',
+                'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole'
+              ]
+            }
+          when 'Condition'
+            choices << {
+              paths: ['onsetDateTime'],
+              extension_ids: ['Condition.extension:assertedDate']
+            }
+          when 'Encounter'
+            choices << { paths: ['reasonCode', 'reasonReference'] }
+            choices << { paths: ['location.location', 'serviceProvider'] }
+          when 'MedicationRequest'
+            choices << { paths: ['reportedBoolean', 'reportedReference'] }
+          when 'Patient'
+            choices << {
+              paths: ['name.period.end', 'name.use'],
+              uscdi_only: true
+            }
+          end
+
         end
 
         @must_supports[:choices] = choices if choices.present?
@@ -377,48 +423,85 @@ module USCoreTestKit
       end
 
       def add_patient_uscdi_elements
-        if profile.type == 'Patient'
-          #US Core 4.0.0 Section 10.112.1.1 Additional USCDI v1 Requirement:
-          @must_supports[:extensions] << {
-            id: 'Patient.extension:race',
-            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race',
-            uscdi_only: true
-          }
-          @must_supports[:extensions] << {
-            id: 'Patient.extension:ethnicity',
-            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity',
-            uscdi_only: true
-          }
+        return unless profile.type == 'Patient'
+
+        #US Core 4.0.0 Section 10.112.1.1 Additional USCDI v1 Requirement:
+        @must_supports[:extensions] << {
+          id: 'Patient.extension:race',
+          url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race',
+          uscdi_only: true
+        }
+        @must_supports[:extensions] << {
+          id: 'Patient.extension:ethnicity',
+          url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity',
+          uscdi_only: true
+        }
+        @must_supports[:extensions] << {
+          id: 'Patient.extension:birthsex',
+          url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex',
+          uscdi_only: true
+        }
+        @must_supports[:elements] << {
+          path: 'name.suffix',
+          uscdi_only: true
+        }
+        @must_supports[:elements] << {
+          path: 'name.use',
+          fixed_value: 'old',
+          uscdi_only: true
+        }
+        @must_supports[:elements] << {
+          path: 'name.period.end',
+          uscdi_only: true
+        }
+        @must_supports[:elements] << {
+          path: 'telecom',
+          uscdi_only: true
+        }
+        @must_supports[:elements] << {
+          path: 'communication',
+          uscdi_only: true
+        }
+        # Though telecom.system, telecom.value, telecom.use, and communication.language are marked as MustSupport since US Core v4.0.0,
+        # their parent elements telecom, and communication are not MustSupport but listed under "Additional USCDI requirements"
+        # According to the updated FHIR spec that "When a child element is defined as Must Support and the parent element isn't,
+        # a system must support the child if it support the parent, but there's no expectation that the system must support the parent.",
+        # We add uscdi_only tag to these elements
+        @must_supports[:elements].each do |element|
+          path = element[:path]
+          element[:uscdi_only] = true if path.include?('telecom.') || path.include?('communication.')
+        end
+
+        if profile.version == '5.0.1'
           @must_supports[:extensions] << {
-            id: 'Patient.extension:birthsex',
-            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex',
-            uscdi_only: true
-          }
-          @must_supports[:elements] << {
-            path: 'name.suffix',
+            id: 'Patient.extension:genderIdentity',
+            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-genderIdentity',
             uscdi_only: true
           }
           @must_supports[:elements] << {
-            path: 'name.use',
+            path: 'address.use',
             fixed_value: 'old',
             uscdi_only: true
           }
-          @must_supports[:elements] << {
-            path: 'name.period.end',
-            uscdi_only: true
-          }
-          @must_supports[:elements] << {
-            path: 'telecom',
-            uscdi_only: true
-          }
-          @must_supports[:elements] << {
-            path: 'communication',
-            uscdi_only: true
-          }
-          @must_supports[:elements].each do |element|
-            path = element[:path]
-            element[:uscdi_only] = true if path.include?('telecom.') || path.include?('communication.')
-          end
+        end
+      end
+
+      def add_document_reference_category_values
+        return unless profile.type == 'DocumentReference'
+
+        slice = @must_supports[:slices].find{|slice| slice[:path] == 'category'}
+
+        slice[:discriminator][:values] << 'clinical-note' if slice.present?
+      end
+
+      # FHIR-37794 Server systems are not required to support US Core QuestionnaireResponse
+      def remove_survey_questionnaire_response
+        return unless profile.type == 'Observation' &&
+          ['us-core-observation-survey', 'us-core-observation-sdoh-assessment'].include?(profile.id)
+
+        element = @must_supports[:elements].find { |element| element[:path] == 'derivedFrom' }
+        element[:target_profiles].delete_if do |url|
+          url == 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-questionnaireresponse'
         end
       end
     end

data/lib/us_core_test_kit/generator/must_support_test_generator.rb

@@ -89,7 +89,8 @@ module USCoreTestKit
           .map { |extension| extension[:id] }
 
         group_metadata.must_supports[:choices]&.each do |choice|
-          next unless choice[:uscdi_only].presence == uscdi_only.presence
+          next unless choice[:uscdi_only].presence == uscdi_only.presence && choice.key?(:paths)
+
           choice[:paths].each { |path| element_names.delete("#{resource_type}.#{path}") }
           element_names << choice[:paths].map { |path| "#{resource_type}.#{path}" }.join(' or ')
         end

data/lib/us_core_test_kit/generator/naming.rb

@@ -30,7 +30,7 @@ module USCoreTestKit
 
       class << self
         def resources_with_multiple_profiles
-          ['Observation', 'DiagnosticReport']
+          ['Condition', 'DiagnosticReport', 'Observation']
         end
 
         def resource_has_multiple_profiles?(resource)

data/lib/us_core_test_kit/generator/search_definition_metadata_extractor.rb

@@ -114,11 +114,12 @@ module USCoreTestKit
       def values
         values = (
           (
-          values_from_slices +
-          values_from_fixed_codes +
-          values_from_pattern_coding +
-          values_from_pattern_codeable_concept          
-          ).uniq.presence || values_from_value_set_binding
+            values_from_pattern_codeable_concept_slices +
+            values_from_required_binding_slices +
+            values_from_fixed_codes +
+            values_from_pattern_coding +
+            values_from_pattern_codeable_concept
+          ).uniq.presence || values_from_value_set_binding(profile_element)
         ).presence || values_from_resource_metadata
         values
       end
@@ -129,14 +130,25 @@ module USCoreTestKit
         profile_elements.select do |element|
           full_paths.include?(element.path) &&
             element.sliceName.present? &&
-            element.patternCodeableConcept.present?
+            (
+              element.patternCodeableConcept.present? ||
+              element.binding.present? && element.binding.strength == 'required'
+            )
         end
       end
 
-      def values_from_slices
+      def values_from_pattern_codeable_concept_slices
         slices.map do |slice|
-          slice.patternCodeableConcept.coding.first.code
-        end
+          slice.patternCodeableConcept.coding.first.code if slice.patternCodeableConcept.present?
+        end.compact
+      end
+
+      def values_from_required_binding_slices
+        slices.map do |slice|
+          if slice.binding.present? && slice.binding.strength == 'required'
+            values_from_value_set_binding(slice)
+          end
+        end.flatten.compact
       end
 
       def values_from_fixed_codes
@@ -152,7 +164,7 @@ module USCoreTestKit
 
         profile_elements
           .select { |element| element.path == "#{profile_element.path}.coding" && element.patternCoding.present? }
-          .map { |element| element.patternCoding.code }        
+          .map { |element| element.patternCoding.code }
       end
 
       def values_from_pattern_codeable_concept
@@ -161,19 +173,21 @@ module USCoreTestKit
         [profile_element.patternCodeableConcept.coding.first.code]
       end
 
-      def value_set_binding
-        profile_element&.binding
+      def value_set_binding(the_element)
+        the_element&.binding
       end
 
-      def value_set
-        ig_resources.value_set_by_url(value_set_binding&.valueSet)
+      def value_set(the_element)
+        ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
       end
 
-      def bound_systems
-        value_set&.compose&.include&.reject { |code| code.concept.nil? }
+      def bound_systems(the_element)
+        value_set(the_element)&.compose&.include&.reject { |code| code.concept.nil? }
       end
 
-      def values_from_value_set_binding
+      def values_from_value_set_binding(the_element)
+        bound_systems = bound_systems(the_element)
+
         return [] if bound_systems.blank?
 
         bound_systems.flat_map { |system| system.concept.map { |code| code.code } }.uniq
@@ -190,7 +204,7 @@ module USCoreTestKit
           current_metadata = fhir_metadata(current_path)
 
           if current_metadata&.dig('valid_codes').present?
-            values = values + current_metadata['valid_codes'].values.flatten 
+            values = values + current_metadata['valid_codes'].values.flatten
           end
         end
 

data/lib/us_core_test_kit/generator/special_cases.rb

@@ -8,17 +8,13 @@ module USCoreTestKit
       ].freeze
 
       PROFILES_TO_EXCLUDE = [
-        'us_core_vital_signs'
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs'
       ].freeze
 
       class << self
-        def exclude_resource?(resource)
-          RESOURCES_TO_EXCLUDE.include? resource
-        end
-
         def exclude_group?(group)
-          RESOURCES_TO_EXCLUDE.include?(group.resource) ||
-          PROFILES_TO_EXCLUDE.include?(group.name)
+          RESOURCES_TO_EXCLUDE.include?(group.resource)
         end
       end
     end

data/lib/us_core_test_kit/generator/suite_generator.rb

@@ -81,11 +81,19 @@ module USCoreTestKit
       end
 
       def clinical_notes_guidance_file_name
-        "../../custom_groups/#{ig_metadata.ig_version}/clinical_notes_guidance_group"
+        if ig_metadata.ig_version == 'v3.1.1'
+          "../../custom_groups/#{ig_metadata.ig_version}/clinical_notes_guidance_group"
+        else
+          '../../custom_groups/v4.0.0/clinical_notes_guidance_group'
+        end
       end
 
       def clinical_notes_guidance_group_id
-        "us_core_#{ig_metadata.reformatted_version}_clinical_notes_guidance"
+        if ig_metadata.reformatted_version == 'v311'
+          "us_core_#{ig_metadata.reformatted_version}_clinical_notes_guidance"
+        else
+          'us_core_v400_clinical_notes_guidance'
+        end
       end
     end
   end

data/lib/us_core_test_kit/generator/terminology_binding_metadata_extractor.rb

@@ -61,6 +61,9 @@ module USCoreTestKit
             url = extension_profile_url(extension_profile_element)
             extension = ig_resources.profile_by_url(url)
 
+            # TODO: Temporaray fix for extension defined out of US Core. FI-1623
+            next if extension.nil?
+
             elements = extension.snapshot.element
             elements_with_bindings = elements.select do |element|
               element.binding.present? && !element.id.include?('Extension.extension')

data/lib/us_core_test_kit/generator/validation_test_generator.rb

@@ -64,6 +64,10 @@ module USCoreTestKit
         group_metadata.profile_name
       end
 
+      def profile_version
+        group_metadata.profile_version
+      end
+
       def test_id
         "us_core_#{group_metadata.reformatted_version}_#{profile_identifier}_validation_test"
       end

data/lib/us_core_test_kit/generator.rb

@@ -16,26 +16,21 @@ require_relative 'generator/validation_test_generator'
 module USCoreTestKit
   class Generator
     def self.generate
-      base_ig_directory = File.join(Dir.pwd, 'lib', 'us_core_test_kit', 'igs')
-      ig_directories =
-        Dir.entries(base_ig_directory)
-          .reject { |path| path.start_with? '.' }
-          .map { |path| File.join(base_ig_directory, path) }
-          .select { |path| File.directory? path }
-
-      ig_directories.each do |ig_directory|
-        new(ig_directory).generate
+      ig_packages = Dir.glob(File.join(Dir.pwd, 'lib', 'us_core_test_kit', 'igs', '*.tgz'))
+
+      ig_packages.each do |ig_package|
+        new(ig_package).generate
       end
     end
 
-    attr_accessor :ig_resources, :ig_metadata, :ig_directory
+    attr_accessor :ig_resources, :ig_metadata, :ig_file_name
 
-    def initialize(ig_directory)
-      self.ig_directory = ig_directory
+    def initialize(ig_file_name)
+      self.ig_file_name = ig_file_name
     end
 
     def generate
-      puts "Generating tests for IG in #{ig_directory}"
+      puts "Generating tests for IG #{File.basename(ig_file_name)}"
       load_ig_package
       extract_metadata
       generate_resource_list
@@ -68,7 +63,7 @@ module USCoreTestKit
 
     def load_ig_package
       FHIR.logger = Logger.new('/dev/null')
-      self.ig_resources = IGLoader.new(ig_directory).load
+      self.ig_resources = IGLoader.new(ig_file_name).load
     end
 
     def generate_resource_list

data/lib/us_core_test_kit/must_support_test.rb

@@ -14,7 +14,13 @@ module USCoreTestKit
     def perform_must_support_test(resources)
       skip_if resources.blank?, "No #{resource_type} resources were found"
 
-      if (missing_elements(resources) + missing_slices(resources) + missing_extensions(resources)).length.zero?
+      missing_elements(resources)
+      missing_slices(resources)
+      missing_extensions(resources)
+
+      handle_must_support_choices if metadata.must_supports[:choices].present?
+
+      if (missing_elements + missing_slices + missing_extensions).length.zero?
         pass
       end
 
@@ -22,6 +28,32 @@ module USCoreTestKit
            "provided #{resource_type} resource(s)"
     end
 
+    def handle_must_support_choices
+      missing_elements.delete_if do |element|
+        choices = metadata.must_supports[:choices].find { |choice| choice[:paths]&.include?(element[:path]) }
+        is_any_choice_supported?(choices)
+      end
+
+      missing_extensions.delete_if do |extension|
+        choices = metadata.must_supports[:choices].find { |choice| choice[:extension_ids]&.include?(extension[:id]) }
+        is_any_choice_supported?(choices)
+      end
+
+      missing_slices.delete_if do |slice|
+        choices = metadata.must_supports[:choices].find { |choice| choice[:slice_names]&.include?(slice[:name]) }
+        is_any_choice_supported?(choices)
+      end
+    end
+
+    def is_any_choice_supported? (choices)
+      choices.present? &&
+      (
+        choices[:paths]&.any? { |path| missing_elements.none? { |element| element[:path] == path } } ||
+        choices[:extension_ids]&.any? { |extension_id| missing_extensions.none? { |extension| extension[:id] == extension_id} } ||
+        choices[:slice_names]&.any? { |slice_name| missing_slices.none? { |slice| slice[:name] == slice_name} }
+      )
+    end
+
     def missing_must_support_strings
       missing_elements.map { |element_definition| missing_element_string(element_definition) } +
         missing_slices.map { |slice_definition| slice_definition[:name] } +
@@ -36,15 +68,15 @@ module USCoreTestKit
       end
     end
 
-    def include_uscdi_only_test?
-      config.options[:include_uscdi_only_test] == true
+    def exclude_uscdi_only_test?
+      config.options[:exclude_uscdi_only_test] == true
     end
 
     def must_support_extensions
-      if include_uscdi_only_test?
-        metadata.must_supports[:extensions]
-      else
+      if exclude_uscdi_only_test?
         metadata.must_supports[:extensions].reject{ |extension| extension[:uscdi_only] }
+      else
+        metadata.must_supports[:extensions]
       end
     end
 
@@ -58,10 +90,10 @@ module USCoreTestKit
     end
 
     def must_support_elements
-      if include_uscdi_only_test?
-        metadata.must_supports[:elements]
-      else
+      if exclude_uscdi_only_test?
         metadata.must_supports[:elements].reject{ |element| element[:uscdi_only] }
+      else
+        metadata.must_supports[:elements]
       end
     end
 
@@ -84,23 +116,14 @@ module USCoreTestKit
           end
         end
 
-      if metadata.must_supports[:choices].present?
-        @missing_elements.delete_if do |element|
-          choice_paths = metadata.must_supports[:choices].find { |choice| choice[:paths].include?(element[:path]) }
-
-          choice_paths.present? &&
-            choice_paths[:paths].any? { |path| @missing_elements.none? { |element| element[:path] == path } }
-        end
-      end
-
       @missing_elements
     end
 
     def must_support_slices
-      if include_uscdi_only_test?
-        metadata.must_supports[:slices]
-      else
+      if exclude_uscdi_only_test?
         metadata.must_supports[:slices].reject{ |slice| slice[:uscdi_only] }
+      else
+        metadata.must_supports[:slices]
       end
     end
 
@@ -140,11 +163,20 @@ module USCoreTestKit
             rescue ArgumentError
               false
             end
+          when 'DateTime'
+            begin
+              DateTime.parse(element)
+            rescue ArgumentError
+              false
+            end
           when 'String'
             element.is_a? String
           else
             element.is_a? FHIR.const_get(discriminator[:code])
           end
+        when 'requiredBinding'
+          coding_path = discriminator[:path].present? ? "#{discriminator[:path]}.coding" : 'coding'
+          find_a_value_at(element, coding_path) {|coding| discriminator[:values].include?(coding.code) }
         end
       end
     end

data/lib/us_core_test_kit/read_test.rb

@@ -47,7 +47,7 @@ module USCoreTestKit
     end
 
     def no_resources_skip_message
-      "No #{resource_type} resources appeart to be available. " \
+      "No #{resource_type} resources appear to be available. " \
       'Please use patients with more information.'
     end