us_core_test_kit 0.1.1 → 0.2.2

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -10,40 +10,19 @@ module USCoreTestKit
       end
 
       def must_supports
-        {
+        @must_supports = {
           extensions: must_support_extensions,
           slices: must_support_slices,
           elements: must_support_elements
         }
-      end
-
-      # exclude component from vital sign profiles except observation-bp and observation-pulse-ox
-      # observation-bp is excluded by profile.name != 'observation-bp'
-      # observation-plux-ox is excluded by profile.baseDefinition == 'http://hl7.org/fhir/StructureDefinition/vitalsigns'
-      def vital_signs_component?(element)
-        profile.baseDefinition == 'http://hl7.org/fhir/StructureDefinition/vitalsigns' &&
-          profile.name != 'observation-bp' &&
-          element.path.include?('component')
-      end
 
-      def blood_pressure_value?(element)
-        profile.name == 'observation-bp' && element.path.include?('Observation.value[x]')
-      end
+        handle_special_cases
 
-      # ONC clarified that health IT developers that always provide HL7 FHIR "observation" values
-      # are not required to demonstrate Health IT Module support for "dataAbsentReason" elements.
-      # Remove MS check for dataAbsentReason and component.dataAbsentReason from vital sign profiles      
-      def data_absent_reason?(element)
-        profile.type == 'Observation' && ['Observation.dataAbsentReason', 'Observation.component.dataAbsentReason'].include?(element.path)
+        @must_supports
       end
 
       def all_must_support_elements
-        profile_elements
-          .select { |element| element.mustSupport }
-          .reject do |element|
-            # TODO: Can special cases be moved out of here?
-            vital_signs_component?(element) || blood_pressure_value?(element) || data_absent_reason?(element)
-          end
+        profile_elements.select { |element| element.mustSupport }
       end
 
       def must_support_extension_elements
@@ -101,6 +80,13 @@ module USCoreTestKit
                   code: pattern_element.patternCodeableConcept.coding.first.code,
                   system: pattern_element.patternCodeableConcept.coding.first.system
                 }
+              elsif pattern_element.patternCoding.present?
+                {
+                  type: 'patternCoding',
+                  path: discriminator_path,
+                  code: pattern_element.patternCoding.code,
+                  system: pattern_element.patternCoding.system
+                }
               elsif pattern_element.patternIdentifier.present?
                 {
                   type: 'patternIdentifier',
@@ -198,24 +184,230 @@ module USCoreTestKit
         end
       end
 
+      def type_must_support_extension?(extensions)
+        extensions&.any? do |extension|
+          extension.url == 'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support' &&
+          extension.valueBoolean
+        end
+      end
+
+      def save_type_code?(type)
+        'Reference' == type.code
+      end
+
+      def get_type_must_support_metadata(current_metadata, current_element)
+        current_element.type.map do |type|
+          if type_must_support_extension?(type.extension)
+            metadata =
+            {
+              path: "#{current_metadata[:path].delete_suffix('[x]')}#{type.code.upcase_first}",
+              original_path: current_metadata[:path]
+            }
+            metadata[:type] = [type.code] if save_type_code?(type)
+            handle_type_must_support_target_profiles(type, metadata) if type.code == 'Reference'
+
+            metadata
+          end
+        end.compact
+      end
+
+      def handle_type_must_support_target_profiles(type, metadata)
+        index = 0
+        target_profiles = []
+
+        type.source_hash['_targetProfile']&.each do |hash|
+          element = FHIR::Element.new(hash)
+          target_profiles << type.targetProfile[index] if type_must_support_extension?(element.extension)
+          index += 1
+        end
+
+        metadata[:target_profiles] = target_profiles if target_profiles.present?
+      end
+
+      def handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata)
+        choice_element_metadata = must_support_elements_metadata.find do |metadata|
+          metadata[:original_path].present? &&
+          current_metadata[:path].include?( metadata[:original_path] )
+        end
+
+        if choice_element_metadata.present?
+          current_metadata[:original_path] = current_metadata[:path]
+          current_metadata[:path] = current_metadata[:path].sub(choice_element_metadata[:original_path], choice_element_metadata[:path])
+        end
+      end
+
       def must_support_elements
         plain_must_support_elements.each_with_object([]) do |current_element, must_support_elements_metadata|
           {
             path: current_element.path.gsub("#{resource}.", '')
           }.tap do |current_metadata|
-            path = current_element.path.gsub("#{resource}.", '')
-            current_metadata[:path] = path
+            type_must_support_metadata = get_type_must_support_metadata(current_metadata, current_element)
 
-            handle_fixed_values(current_metadata, current_element)
+            if type_must_support_metadata.any?
+              must_support_elements_metadata.concat(type_must_support_metadata)
+            else
+              handle_choice_type_in_sliced_element(current_metadata, must_support_elements_metadata)
 
-            must_support_elements_metadata.delete_if do |metadata|
-              metadata[:path] == current_metadata[:path] && metadata[:fixed_value].blank?
-            end
+              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_fixed_values(current_metadata, current_element)
+
+              must_support_elements_metadata.delete_if do |metadata|
+                metadata[:path] == current_metadata[:path] && metadata[:fixed_value].blank?
+              end
 
-            must_support_elements_metadata << current_metadata
+              must_support_elements_metadata << current_metadata
+            end
           end
         end.uniq
       end
+
+      #### SPECIAL CASE ####
+
+      def handle_special_cases
+        remove_vital_sign_component
+        remove_blood_pressure_value
+        remove_observation_data_absent_reason
+        add_must_support_choices
+
+        case profile.version
+        when '4.0.0'
+          add_device_distinct_identifier
+          add_patient_uscdi_elements
+          add_provenance_agent_who
+        end
+      end
+
+      def is_vital_sign?
+        [
+          'http://hl7.org/fhir/StructureDefinition/vitalsigns',
+          'http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs'
+        ].include?(profile.baseDefinition)
+      end
+
+      def is_blood_pressure?
+        ['observation-bp', 'USCoreBloodPressureProfile'].include?(profile.name)
+      end
+
+      # Exclude Observation.component from vital sign profiles except observation-bp and observation-pulse-ox
+      def remove_vital_sign_component
+        if is_vital_sign? && !is_blood_pressure? && profile.name != 'USCorePulseOximetryProfile'
+          @must_supports[:elements].delete_if do |element|
+            element[:path].start_with?('component')
+          end
+        end
+      end
+
+      # Exclude Observation.value[x] from observation-bp
+      def remove_blood_pressure_value
+        if is_blood_pressure?
+          @must_supports[:elements].delete_if do |element|
+            element[:path].start_with?('value[x]') || element[:original_path]&.start_with?('value[x]')
+          end
+          @must_supports[:slices].delete_if do |slice|
+            slice[:path].start_with?('value[x]')
+          end
+        end
+      end
+
+      # ONC and US Core 4.0.0 both clarified that health IT developers that always provide HL7 FHIR "observation" values
+      # are not required to demonstrate Health IT Module support for "dataAbsentReason" elements.
+      # Remove MS check for dataAbsentReason and component.dataAbsentReason from vital sign profiles and observation lab profile
+      # Smoking status profile does not have MS on dataAbsentReason. It is safe to use profile.type == 'Observation'
+      def remove_observation_data_absent_reason
+        if profile.type == 'Observation'
+          @must_supports[:elements].delete_if do |element|
+            ['dataAbsentReason', 'component.dataAbsentReason'].include?(element[:path])
+          end
+        end
+      end
+
+      def remove_device_carrier
+        if profile.type == 'Device'
+          @must_supports[:elements].delete_if do |element|
+            ['udiCarrier.carrierAIDC', 'udiCarrier.carrierHRF'].include?(element[:path])
+          end
+        end
+      end
+
+      def remove_document_reference_attachment_data_url
+        if profile.type == 'DocumentReference'
+          @must_supports[:elements].delete_if do |element|
+            ['content.attachment.data', 'content.attachment.url'].include?(element[:path])
+          end
+        end
+      end
+
+      def add_must_support_choices
+        choices = []
+
+        choices << {paths: ['content.attachment.data', 'content.attachment.url']} if profile.type == 'DocumentReference'
+
+        case profile.version
+        when '3.1.1'
+          choices << {paths: ['udiCarrier.carrierAIDC', 'udiCarrier.carrierHRF']} if profile.type == 'Device'
+        when '4.0.0'
+          case profile.type
+          when 'Encounter'
+            choices << {paths: ['reasonCode', 'reasonReference']}
+            choices << {paths: ['location.location', 'serviceProvider']}
+          when 'MedicationRequest'
+            choices << {paths: ['reportedBoolean', 'reportedReference']}
+          end
+        end
+
+        @must_supports[:choices] = choices if choices.present?
+      end
+
+      def add_device_distinct_identifier
+        if profile.type == 'Device'
+          # FHIR-36303 US Core 4.0.0 mistakenly removed MS from Device.distinctIdentifier
+          # This will be fixed in US Core 5.0.0
+          @must_supports[:elements] << {
+            path: 'distinctIdentifier'
+          }
+        end
+      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'
+          }
+          @must_supports[:extensions] << {
+            id: 'Patient.extension:ethnicity',
+            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'
+          }
+          @must_supports[:extensions] << {
+            id: 'Patient.extension:birthsex',
+            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex'
+          }
+          @must_supports[:elements] << {
+            path: 'telecom'
+          }
+          @must_supports[:elements] << {
+            path: 'name.suffix'
+          }
+          @must_supports[:elements] << {
+            path: 'name.use',
+            fixed_value: 'old'
+          }
+        end
+      end
+
+      def add_provenance_agent_who
+        # FHIR-36344 US Core 4.0.0 mistakenly not lable us-core-organization as MS for Provenance.agent.who
+        # This will be fixed in US Core 5.0.0
+        if profile.type == 'Provenance'
+          target_element = @must_supports[:elements].find { |element| element[:path] == 'agent.who'}
+          target_element[:target_profiles] << 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization'
+        end
+      end
     end
   end
 end

data/lib/us_core_test_kit/generator/must_support_test_generator.rb

@@ -5,17 +5,18 @@ module USCoreTestKit
   class Generator
     class MustSupportTestGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           ig_metadata.groups
-            .reject { |group| SpecialCases.exclude_resource? group.resource }
-            .each { |group| new(group).generate }
+            .reject { |group| SpecialCases.exclude_group? group }
+            .each { |group| new(group, base_output_dir).generate }
         end
       end
 
-      attr_accessor :group_metadata
+      attr_accessor :group_metadata, :base_output_dir
 
-      def initialize(group_metadata)
+      def initialize(group_metadata, base_output_dir)
         self.group_metadata = group_metadata
+        self.base_output_dir = base_output_dir
       end
 
       def template
@@ -31,7 +32,7 @@ module USCoreTestKit
       end
 
       def output_file_directory
-        File.join(__dir__, '..', 'generated', profile_identifier)
+        File.join(base_output_dir, profile_identifier)
       end
 
       def output_file_name
@@ -47,13 +48,17 @@ module USCoreTestKit
       end
 
       def test_id
-        "us_core_311_#{profile_identifier}_must_support_test"
+        "us_core_#{group_metadata.reformatted_version}_#{profile_identifier}_must_support_test"
       end
 
       def class_name
         "#{Naming.upper_camel_case_for_profile(group_metadata)}MustSupportTest"
       end
 
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
       def resource_type
         group_metadata.resource
       end
@@ -67,8 +72,9 @@ module USCoreTestKit
         element_names = group_metadata.must_supports[:elements].map { |slice| "#{resource_type}.#{slice[:path]}" }
         extension_names = group_metadata.must_supports[:extensions].map { |slice| slice[:id] }
         (slice_names + element_names + extension_names)
+          .uniq
           .sort
-          .map { |name| "      * #{name}" }
+          .map { |name| "#{' ' * 8}* #{name}" }
           .join("\n")
       end
 

data/lib/us_core_test_kit/generator/naming.rb

@@ -41,7 +41,9 @@ module USCoreTestKit
           resource = group_metadata.resource
           return resource.underscore unless resource_has_multiple_profiles?(resource)
 
-          return 'head_circumference' if group_metadata.profile_url == HEAD_CIRCUMFERENCE
+          if group_metadata.profile_url == HEAD_CIRCUMFERENCE
+            return group_metadata.reformatted_version == 'v311' ? 'head_circumference' : 'head_circumference_percentile'
+          end
 
           group_metadata.name
             .delete_prefix('us_core_')

data/lib/us_core_test_kit/generator/provenance_revinclude_search_test_generator.rb

@@ -5,19 +5,20 @@ module USCoreTestKit
   class Generator
     class ProvenanceRevincludeSearchTestGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           ig_metadata.groups
-            .reject { |group| SpecialCases.exclude_resource? group.resource }
+            .reject { |group| SpecialCases.exclude_group? group }
             .select { |group| group.revincludes.include? 'Provenance:target' }
-            .each { |group| new(group, group.searches.first).generate }
+            .each { |group| new(group, group.searches.first, base_output_dir).generate }
         end
       end
 
-      attr_accessor :group_metadata, :search_metadata
+      attr_accessor :group_metadata, :search_metadata, :base_output_dir
 
-      def initialize(group_metadata, search_metadata)
+      def initialize(group_metadata, search_metadata, base_output_dir)
         self.group_metadata = group_metadata
         self.search_metadata = search_metadata
+        self.base_output_dir = base_output_dir
       end
 
       def template
@@ -33,7 +34,7 @@ module USCoreTestKit
       end
 
       def output_file_directory
-        File.join(__dir__, '..', 'generated', profile_identifier)
+        File.join(base_output_dir, profile_identifier)
       end
 
       def output_file_name
@@ -45,7 +46,7 @@ module USCoreTestKit
       end
 
       def test_id
-        "us_core_311_#{profile_identifier}_#{search_identifier}_search_test"
+        "us_core_#{group_metadata.reformatted_version}_#{profile_identifier}_#{search_identifier}_search_test"
       end
 
       def search_identifier
@@ -60,6 +61,10 @@ module USCoreTestKit
         "#{Naming.upper_camel_case_for_profile(group_metadata)}#{search_title}SearchTest"
       end
 
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
       def resource_type
         group_metadata.resource
       end

data/lib/us_core_test_kit/generator/read_test_generator.rb

@@ -5,11 +5,11 @@ module USCoreTestKit
   class Generator
     class ReadTestGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           ig_metadata.groups
-            .reject { |group| SpecialCases.exclude_resource? group.resource }
+            .reject { |group| SpecialCases.exclude_group? group }
             .select { |group| read_interaction(group).present? }
-            .each { |group| new(group).generate }
+            .each { |group| new(group, base_output_dir).generate }
         end
 
         def read_interaction(group_metadata)
@@ -17,10 +17,11 @@ module USCoreTestKit
         end
       end
 
-      attr_accessor :group_metadata
+      attr_accessor :group_metadata, :base_output_dir
 
-      def initialize(group_metadata)
+      def initialize(group_metadata, base_output_dir)
         self.group_metadata = group_metadata
+        self.base_output_dir = base_output_dir
       end
 
       def template
@@ -36,7 +37,7 @@ module USCoreTestKit
       end
 
       def output_file_directory
-        File.join(__dir__, '..', 'generated', profile_identifier)
+        File.join(base_output_dir, profile_identifier)
       end
 
       def output_file_name
@@ -52,13 +53,17 @@ module USCoreTestKit
       end
 
       def test_id
-        "us_core_311_#{profile_identifier}_read_test"
+        "us_core_#{group_metadata.reformatted_version}_#{profile_identifier}_read_test"
       end
 
       def class_name
         "#{Naming.upper_camel_case_for_profile(group_metadata)}ReadTest"
       end
 
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
       def resource_type
         group_metadata.resource
       end

data/lib/us_core_test_kit/generator/reference_resolution_test_generator.rb

@@ -5,17 +5,18 @@ module USCoreTestKit
   class Generator
     class ReferenceResolutionTestGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           ig_metadata.groups
-            .reject { |group| SpecialCases.exclude_resource? group.resource }
-            .each { |group| new(group).generate }
+            .reject { |group| SpecialCases.exclude_group? group }
+            .each { |group| new(group, base_output_dir).generate }
         end
       end
 
-      attr_accessor :group_metadata
+      attr_accessor :group_metadata, :base_output_dir
 
-      def initialize(group_metadata)
+      def initialize(group_metadata, base_output_dir)
         self.group_metadata = group_metadata
+        self.base_output_dir = base_output_dir
       end
 
       def template
@@ -31,7 +32,7 @@ module USCoreTestKit
       end
 
       def output_file_directory
-        File.join(__dir__, '..', 'generated', profile_identifier)
+        File.join(base_output_dir, profile_identifier)
       end
 
       def output_file_name
@@ -43,13 +44,17 @@ module USCoreTestKit
       end
 
       def test_id
-        "us_core_311_#{profile_identifier}_reference_resolution_test"
+        "us_core_#{group_metadata.reformatted_version}_#{profile_identifier}_reference_resolution_test"
       end
 
       def class_name
         "#{Naming.upper_camel_case_for_profile(group_metadata)}ReferenceResolutionTest"
       end
 
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
       def resource_type
         group_metadata.resource
       end
@@ -58,7 +63,22 @@ module USCoreTestKit
         'scratch_resources[:all]'
       end
 
+      def must_support_references
+        group_metadata.must_supports[:elements]
+          .select { |element| element[:types]&.include?('Reference') }
+      end
+      
+      def must_support_reference_list_string
+        must_support_references
+          .map { |element| "#{' ' * 8}* #{resource_type}.#{element[:path]}" }
+          .uniq
+          .sort
+          .join("\n")
+      end
+
       def generate
+        return if must_support_references.empty?
+
         FileUtils.mkdir_p(output_file_directory)
         File.open(output_file_name, 'w') { |f| f.write(output) }
 

data/lib/us_core_test_kit/generator/resource_list_generator.rb

@@ -2,14 +2,14 @@ module USCoreTestKit
   class Generator
     class ResourceListGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           @ig_metadata = ig_metadata
 
-          FileUtils.mkdir_p(output_file_directory)
-          File.open(output_file_name, 'w') { |f| f.write(output) }
+          FileUtils.mkdir_p(base_output_dir)
+          File.open(File.join(base_output_dir, base_output_file_name), 'w') { |f| f.write(output) }
         end
 
-        def resource_list
+        def resource_list          
           @ig_metadata.groups.map(&:resource).uniq
         end
 
@@ -17,6 +17,10 @@ module USCoreTestKit
           resource_list.map { |resource| "      '#{resource}'" }.join(",\n")
         end
 
+        def module_name
+          "USCore#{@ig_metadata.reformatted_version.upcase}"
+        end
+
         def read_interaction(group_metadata)
           group_metadata.interactions.find { |interaction| interaction[:code] == 'read' }
         end
@@ -26,20 +30,12 @@ module USCoreTestKit
         end
 
         def output
-          @output ||= ERB.new(template).result(binding)
+          ERB.new(template).result(binding)
         end
 
         def base_output_file_name
           "resource_list.rb"
         end
-
-        def output_file_directory
-          File.join(__dir__, '..', 'generated')
-        end
-
-        def output_file_name
-          File.join(output_file_directory, base_output_file_name)
-        end
       end
     end
   end