us_core_test_kit 0.4.5 → 0.4.7

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -1,4 +1,7 @@
 require_relative 'value_extractor'
+require_relative 'must_support_metadata_extractor_us_core_3'
+require_relative 'must_support_metadata_extractor_us_core_4'
+require_relative 'must_support_metadata_extractor_us_core_5'
 
 module USCoreTestKit
   class Generator
@@ -218,7 +221,7 @@ module USCoreTestKit
               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)
+            metadata[:types] = [type.code] if save_type_code?(type)
             handle_type_must_support_target_profiles(type, metadata) if type.code == 'Reference'
 
             metadata
@@ -288,18 +291,14 @@ module USCoreTestKit
         remove_vital_sign_component
         remove_blood_pressure_value
         remove_observation_data_absent_reason
-        add_must_support_choices
 
         case profile.version
         when '3.1.1'
-          remove_document_reference_custodian
+          MustSupportMetadataExtractorUsCore3.new(profile, @must_supports).handle_special_cases
         when '4.0.0'
-          add_device_distinct_identifier
-          add_patient_uscdi_elements
+          MustSupportMetadataExtractorUsCore4.new(profile, @must_supports).handle_special_cases
         when '5.0.1'
-          add_patient_uscdi_elements
-          add_document_reference_category_values
-          remove_survey_questionnaire_response
+          MustSupportMetadataExtractorUsCore5.new(profile, @must_supports).handle_special_cases
         end
       end
 
@@ -346,165 +345,6 @@ module USCoreTestKit
           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
-
-      # US Core clarified that server implmentation is not required to support DocumentReference.custodian (FHIR-28393)
-      def remove_document_reference_custodian
-        if profile.type == 'DocumentReference'
-          @must_supports[:elements].delete_if do |element|
-            element[:path] == 'custodian'
-          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
-        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'] }
-          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
-        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.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:genderIdentity',
-            url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-genderIdentity',
-            uscdi_only: true
-          }
-          @must_supports[:elements] << {
-            path: 'address.use',
-            fixed_value: 'old',
-            uscdi_only: true
-          }
-          @must_supports[:elements] << {
-            path: 'name.use',
-            fixed_value: 'old',
-            uscdi_only: true
-          }
-        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
   end
 end

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_3.rb

@@ -0,0 +1,62 @@
+module USCoreTestKit
+  class Generator
+    class MustSupportMetadataExtractorUsCore3
+      attr_accessor :profile, :must_supports
+
+      def initialize(profile, must_supports)
+        self.profile = profile
+        self.must_supports = must_supports
+      end
+
+      def handle_special_cases
+        add_must_support_choices
+        remove_patient_address_period
+        remove_document_reference_custodian
+      end
+
+      def add_must_support_choices
+        choices = []
+
+        case profile.type
+        when 'Device'
+          choices << { paths: ['udiCarrier.carrierAIDC', 'udiCarrier.carrierHRF'] }
+        when 'DocumentReference'
+          choices << { paths: ['content.attachment.data', 'content.attachment.url'] }
+        when 'Patient'
+          # FHIR-40299 adds USCDI MustSupport choices for:
+          # * address.period.end and address.use,
+          # * name.period.end and name.use
+          choices << {
+            paths: ['address.period.end', 'address.use'],
+            uscdi_only: true
+          }
+
+          choices << {
+            paths: ['name.period.end', 'name.use'],
+            uscdi_only: true
+          }
+        end
+
+        must_supports[:choices] = choices if choices.present?
+      end
+
+      # FHIR-40299 removes Patient.address.period from MustSupport,
+      def remove_patient_address_period
+        return unless profile.type == 'Patient'
+
+        must_supports[:elements].delete_if do |element|
+          element[:path] == 'address.period'
+        end
+      end
+
+      # US Core clarified that server implmentation is not required to support DocumentReference.custodian (FHIR-28393)
+      def remove_document_reference_custodian
+        return unless profile.type == 'DocumentReference'
+
+        must_supports[:elements].delete_if do |element|
+          element[:path] == 'custodian'
+        end
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_4.rb

@@ -0,0 +1,110 @@
+require_relative 'must_support_metadata_extractor_us_core_3'
+
+module USCoreTestKit
+  class Generator
+    class MustSupportMetadataExtractorUsCore4
+      attr_accessor :profile, :must_supports
+
+      def initialize(profile, must_supports)
+        self.profile = profile
+        self.must_supports = must_supports
+      end
+
+      def us_core_3_extractor
+        @us_core_3_extractor ||= MustSupportMetadataExtractorUsCore3.new(profile, must_supports)
+      end
+
+      def handle_special_cases
+        add_must_support_choices
+        remove_patient_address_period
+        add_device_distinct_identifier
+        add_patient_uscdi_elements
+      end
+
+      def add_must_support_choices
+        choices = []
+
+        case profile.type
+        when 'DocumentReference'
+          choices << { paths: ['content.attachment.data', 'content.attachment.url'] }
+        when 'Encounter'
+          choices << { paths: ['reasonCode', 'reasonReference'] }
+          choices << { paths: ['location.location', 'serviceProvider'] }
+        when 'MedicationRequest'
+          choices << { paths: ['reportedBoolean', 'reportedReference'] }
+        when 'Patient'
+          # FHIR-40299 adds USCDI MustSupport choices for:
+          # * address.period.end and address.use,
+          # * name.period.end and name.use
+          choices << {
+            paths: ['address.period.end', 'address.use'],
+            uscdi_only: true
+          }
+
+          choices << {
+            paths: ['name.period.end', 'name.use'],
+            uscdi_only: true
+          }
+        end
+
+        must_supports[:choices] = choices if choices.present?
+      end
+
+      def remove_patient_address_period
+        us_core_3_extractor.remove_patient_address_period
+      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
+        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: '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
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_5.rb

@@ -0,0 +1,113 @@
+require_relative 'must_support_metadata_extractor_us_core_4'
+
+module USCoreTestKit
+  class Generator
+    class MustSupportMetadataExtractorUsCore5
+      attr_accessor :profile, :must_supports
+
+      def initialize(profile, must_supports)
+        self.profile = profile
+        self.must_supports = must_supports
+      end
+
+
+      def us_core_4_extractor
+        @us_core_4_extractor ||= MustSupportMetadataExtractorUsCore4.new(profile, must_supports)
+      end
+
+      def handle_special_cases
+        add_must_support_choices
+        remove_patient_address_period
+        add_patient_uscdi_elements
+        add_value_set_expansion
+        remove_survey_questionnaire_response
+      end
+
+      def add_must_support_choices
+        us_core_4_extractor.add_must_support_choices
+
+        more_choices = []
+
+        case profile.type
+        when 'CareTeam'
+          more_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'
+          more_choices << {
+            paths: ['onsetDateTime'],
+            extension_ids: ['Condition.extension:assertedDate']
+          }
+        end
+
+        if more_choices.present?
+          must_supports[:choices] ||= []
+          must_supports[:choices].concat(more_choices)
+        end
+      end
+
+      def remove_patient_address_period
+        us_core_4_extractor.remove_patient_address_period
+      end
+
+      def add_patient_uscdi_elements
+        return unless profile.type == 'Patient'
+
+        us_core_4_extractor.add_patient_uscdi_elements
+
+        must_supports[:extensions] << {
+          id: 'Patient.extension:genderIdentity',
+          url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-genderIdentity',
+          uscdi_only: true
+        }
+        must_supports[:elements] << {
+          path: 'address.use',
+          fixed_value: 'old',
+          uscdi_only: true
+        }
+        must_supports[:elements] << {
+          path: 'name.use',
+          fixed_value: 'old',
+          uscdi_only: true
+        }
+      end
+
+      def add_value_set_expansion
+        add_document_reference_category_values
+        add_service_request_category_values
+      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
+
+      def add_service_request_category_values
+        return unless profile.type == 'ServiceRequest'
+
+        slice = must_supports[:slices].find{|slice| slice[:path] == 'category'}
+
+        if slice.present?
+          slice[:discriminator][:values].concat(['108252007', '363679005', '409063005', '409073007', '387713003'])
+        end
+      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
+  end
+end

data/lib/us_core_test_kit/generator/search_definition_metadata_extractor.rb

@@ -37,22 +37,58 @@ module USCoreTestKit
       def full_paths
         @full_paths ||=
           begin
-            path = param.expression.gsub(/.where\((.*)/, '')
+            path = param.expression.gsub(/.where\(resolve\((.*)/, '').gsub(/url = '/, 'url=\'')
             path = path[1..-2] if path.start_with?('(') && path.end_with?(')')
             path.scan(/[. ]as[( ]([^)]*)[)]?/).flatten.map do |as_type|
               path.gsub!(/[. ]as[( ](#{as_type}[^)]*)[)]?/, as_type.upcase_first) if as_type.present?
             end
-            path.split('|')
+
+            full_paths = path.split('|')
+
+            # There is a bug in US Core 5 asserted-date search parameter. See FHIR-40573
+            if param.respond_to?(:version) && param.version == '5.0.1' && name == 'asserted-date'
+              remove_additional_extension_from_asserted_date(full_paths)
+            end
+
+            full_paths
           end
       end
 
+      def remove_additional_extension_from_asserted_date(full_paths)
+        full_paths.each do |full_path|
+          next unless full_path.include?('http://hl7.org/fhir/StructureDefinition/condition-assertedDate')
+          full_path.gsub!(/\).extension./, ').')
+        end
+      end
+
       def paths
         @paths ||= full_paths.map { |a_path| a_path.gsub("#{resource}.", '') }
       end
 
+      def extensions
+        @extensions ||= full_paths.select { |a_path| a_path.include?('extension.where') }
+                                  .map { |a_path| { url: a_path[/(?<=extension.where\(url=').*(?='\))/] }}
+                                  .presence
+      end
+
       def profile_element
         @profile_element ||=
-          profile_elements.find { |element| full_paths.include?(element.id) }
+          (
+            profile_elements.find { |element| full_paths.include?(element.id) } ||
+            extension_definition&.differential&.element&.find { |element| element.id == 'Extension.value[x]'}
+          )
+      end
+
+      def extension_definition
+         @extension_definition ||=
+            begin
+              ext_definition = nil
+              extensions&.each do |ext_metadata|
+                ext_definition = ig_resources.profile_by_url(ext_metadata[:url])
+                break if ext_definition.present?
+              end
+              ext_definition
+            end
       end
 
       def comparator_expectation_extensions
@@ -90,7 +126,19 @@ module USCoreTestKit
       end
 
       def contains_multiple?
-        profile_element&.max == '*'
+        if profile_element.present?
+          if profile_element.id.start_with?('Extension') && extension_definition.present?
+            # Find the extension instance in a US Core profile
+            target_element = profile_elements.find do |element|
+              element.type.any? { |type| type.code == "Extension" && type.profile.include?(extension_definition.url) }
+            end
+            target_element&.max == '*'
+          else
+            profile_element.max == '*'
+          end
+        else
+          false
+        end
       end
 
       def chain_extensions

data/lib/us_core_test_kit/generator.rb

@@ -1,6 +1,6 @@
 require 'fhir_models'
+require 'inferno/ext/fhir_models'
 
-require_relative 'ext/fhir_models'
 require_relative 'generator/ig_loader'
 require_relative 'generator/ig_metadata_extractor'
 require_relative 'generator/group_generator'