au_core_test_kit 1.4.5 → 1.4.7

data/lib/au_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -1,472 +0,0 @@
-# frozen_string_literal: true
-
-require_relative 'value_extractor'
-require_relative 'must_support_metadata_extractor_au_core_3'
-
-module AUCoreTestKit
-  class Generator
-    class MustSupportMetadataExtractor
-      attr_accessor :profile_elements, :profile, :resource, :ig_resources
-
-      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
-        @must_supports = {
-          extensions: must_support_extensions,
-          slices: must_support_slices,
-          elements: must_support_elements
-        }
-
-        handle_special_cases
-
-        @must_supports
-      end
-
-      def is_uscdi_requirement_element?(_element)
-        # TODO: Temporary fix
-        false
-      end
-
-      def all_must_support_elements
-        profile_elements.select { |element| element.mustSupport || is_uscdi_requirement_element?(element) }
-      end
-
-      def must_support_extension_elements
-        all_must_support_elements.select { |element| element.path.end_with? 'extension' }
-      end
-
-      def must_support_extensions
-        must_support_extension_elements.map do |element|
-          {
-            id: element.id,
-            url: element.type.first.profile.first
-          }.tap do |metadata|
-            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(element)
-          end
-        end
-      end
-
-      def must_support_slice_elements
-        all_must_support_elements.select do |element|
-          !element.path.end_with?('extension') && element.sliceName.present?
-        end
-      end
-
-      def sliced_element(slice)
-        profile_elements.find do |element|
-          element.id == slice.path || element.id == slice.id.sub(":#{slice.sliceName}", '')
-        end
-      end
-
-      def discriminators(slice)
-        slice.slicing.discriminator
-      end
-
-      def must_support_pattern_slice_elements
-        must_support_slice_elements.select do |element|
-          discriminators(sliced_element(element)).first.type == 'pattern'
-        end
-      end
-
-      def pattern_slices
-        must_support_pattern_slice_elements.map do |current_element|
-          next if current_element.id.include? ':'
-
-          {
-            slice_id: current_element.id,
-            slice_name: current_element.sliceName,
-            path: current_element.path.gsub("#{resource}.", '')
-          }.tap do |metadata|
-            discriminator = discriminators(sliced_element(current_element)).first
-            discriminator_path = discriminator.path
-            discriminator_path = '' if discriminator_path == '$this'
-            pattern_element =
-              if discriminator_path.present?
-                profile_elements.find { |element| element.id == "#{current_element.id}.#{discriminator_path}" }
-              else
-                current_element
-              end
-            metadata[:discriminator] =
-              if pattern_element.patternCodeableConcept.present?
-                {
-                  type: 'patternCodeableConcept',
-                  path: discriminator_path,
-                  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',
-                  path: discriminator_path,
-                  system: pattern_element.patternIdentifier.system
-                }
-              elsif pattern_element.binding&.strength == 'required' &&
-                    pattern_element.binding&.valueSet.present?
-
-                value_extractor = ValueExactor.new(ig_resources, resource, profile_elements)
-
-                values = value_extractor.values_from_value_set_binding(pattern_element).presence ||
-                         value_extractor.values_from_resource_metadata([metadata[:path]]).presence || []
-
-                {
-                  type: 'requiredBinding',
-                  path: discriminator_path,
-                  values:
-                }
-              else
-                raise StandardError, 'Unsupported discriminator pattern type'
-              end
-
-            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
-          end
-        end.compact
-      end
-
-      def must_support_type_slice_elements
-        must_support_slice_elements.select do |element|
-          discriminators(sliced_element(element)).first.type == 'type'
-        end
-      end
-
-      def type_slices
-        must_support_type_slice_elements.map do |current_element|
-          discriminator = discriminators(sliced_element(current_element)).first
-          type_path = discriminator.path
-          type_path = '' if type_path == '$this'
-          type_element =
-            if type_path.present?
-              elements.find { |element| element.id == "#{current_element.id}.#{type_path}" }
-            else
-              current_element
-            end
-
-          type_code = type_element.type.first.code
-
-          {
-            slice_id: current_element.id,
-            slice_name: current_element.sliceName,
-            path: current_element.path.gsub("#{resource}.", ''),
-            discriminator: {
-              type: 'type',
-              code: type_code.upcase_first
-            }
-          }.tap do |metadata|
-            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
-          end
-        end
-      end
-
-      def must_support_value_slice_elements
-        must_support_slice_elements.select do |element|
-          discriminators(sliced_element(element)).first.type == 'value'
-        end
-      end
-
-      def value_slices
-        must_support_value_slice_elements.map do |current_element|
-          {
-            slice_id: current_element.id,
-            slice_name: current_element.sliceName,
-            path: current_element.path.gsub("#{resource}.", ''),
-            discriminator: {
-              type: 'value'
-            }
-          }.tap do |metadata|
-            metadata[:discriminator][:values] = discriminators(sliced_element(current_element)).map do |discriminator|
-              fixed_element = profile_elements.find do |element|
-                element.id.starts_with?(current_element.id) &&
-                  element.path == "#{current_element.path}.#{discriminator.path}"
-              end
-
-              {
-                path: discriminator.path,
-                value: fixed_element.fixedUri || fixed_element.fixedCode
-              }
-            end
-
-            metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
-          end
-        end
-      end
-
-      def must_support_slices
-        pattern_slices + type_slices + value_slices
-      end
-
-      def plain_must_support_elements
-        all_must_support_elements - must_support_extension_elements - must_support_slice_elements
-      end
-
-      def element_part_of_slice_discrimination?(element)
-        must_support_slice_elements.any? { |ms_slice| element.id.include?(ms_slice.id) }
-      end
-
-      def handle_fixed_values(metadata, element)
-        if element.fixedUri.present?
-          metadata[:fixed_value] = element.fixedUri
-        elsif element.patternCodeableConcept.present? && !element_part_of_slice_discrimination?(element)
-          metadata[:fixed_value] = element.patternCodeableConcept.coding.first.code
-          metadata[:path] += '.coding.code'
-        elsif element.fixedCode.present?
-          metadata[:fixed_value] = element.fixedCode
-        elsif element.patternIdentifier.present? && !element_part_of_slice_discrimination?(element)
-          metadata[:fixed_value] = element.patternIdentifier.system
-          metadata[:path] += '.system'
-        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)
-        type.code == 'Reference'
-      end
-
-      def get_type_must_support_metadata(current_metadata, current_element)
-        current_element.type.map do |type|
-          next unless type_must_support_extension?(type.extension)
-
-          metadata =
-            {
-              path: "#{current_metadata[:path].delete_suffix('[x]')}#{type.code.upcase_first}",
-              original_path: current_metadata[:path]
-            }
-          metadata[:types] = [type.code] if save_type_code?(type)
-          handle_type_must_support_target_profiles(type, metadata) if type.code == 'Reference'
-
-          metadata
-        end.compact
-      end
-
-      def handle_type_must_support_target_profiles(type, metadata)
-        # AU Core 3.1.1 profiles do not have AU Core target profiles.
-        # Vital Sign proifles from FHIR R4 (version 4.0.1) do not have AU Core target profiles either.
-        return if ['3.1.1', '4.0.1'].include?(profile.version)
-
-        target_profiles = []
-
-        if type.targetProfile&.length == 1
-          target_profiles << type.targetProfile.first
-        else
-          type.source_hash['_targetProfile']&.each_with_index do |hash, index|
-            if hash.present?
-              element = FHIR::Element.new(hash)
-              target_profiles << type.targetProfile[index] if type_must_support_extension?(element.extension)
-            end
-          end
-        end
-
-        # remove target_profile for FHIR Base resource type.
-        target_profiles.delete_if { |reference| reference.start_with?('http://hl7.org/fhir/StructureDefinition') }
-        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
-
-        return unless 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
-
-      def must_support_elements
-        plain_must_support_elements.each_with_object([]) do |current_element, must_support_elements_metadata|
-          {
-            path: current_element.id.gsub("#{resource}.", '')
-          }.tap do |current_metadata|
-            current_metadata[:uscdi_only] = true if is_uscdi_requirement_element?(current_element)
-
-            type_must_support_metadata = get_type_must_support_metadata(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)
-
-              supported_types = current_element.type.select { |type| save_type_code?(type) }.map(&:code)
-              current_metadata[:types] = supported_types if supported_types.present?
-
-              if current_element.type.first&.code == 'Reference'
-                handle_type_must_support_target_profiles(current_element.type.first,
-                                                         current_metadata)
-              end
-
-              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
-            end
-          end
-        end.uniq
-      end
-
-      #### SPECIAL CASE ####
-
-      def handle_special_cases
-        remove_vital_sign_component
-        remove_blood_pressure_value_data_absent_reason
-        remove_observation_data_absent_reason
-        remove_observation_method_attribute
-        remove_observation_value_attribute
-        remove_lipid_result_attributes
-        # remove_specimen_attribute
-
-        case profile.version
-        when '3.1.1'
-          MustSupportMetadataExtractorAUCore3.new(profile, @must_supports).handle_special_cases
-        when '4.0.0'
-          MustSupportMetadataExtractorAUCore4.new(profile, @must_supports).handle_special_cases
-        when '5.0.1'
-          MustSupportMetadataExtractorAUCore5.new(profile, @must_supports).handle_special_cases
-        when '6.1.0'
-          MustSupportMetadataExtractorAUCore6.new(profile, @must_supports).handle_special_cases
-        when '7.0.0-ballot'
-          MustSupportMetadataExtractorAUCore7.new(profile, @must_supports).handle_special_cases
-        end
-      end
-
-      def remove_specimen_attribute
-        # TODO: Temporary solution https://github.com/hl7au/au-fhir-core-inferno/issues/18
-        return unless profile.id == 'au-core-diagnosticresult-path'
-
-        @must_supports[:elements].delete_if do |element|
-          ['specimen'].include? element[:path]
-        end
-      end
-
-      def remove_lipid_result_attributes
-        # TODO: This code block should be discussed.
-        # We need to understand why there are a lot of extra attributes
-        # for the current Observation resource profile.
-        return unless profile.id == 'au-core-lipid-result'
-
-        @must_supports[:elements].delete_if do |element|
-          ['identifier', 'performer', 'note',
-           'specimen', 'referenceRange.type',
-           'referenceRange.text', 'hasMember'].include? element[:path]
-        end
-      end
-
-      def remove_observation_value_attribute
-        return unless is_observation_without_value?
-
-        @must_supports[:elements].delete_if do |element|
-          element[:path] == 'value[x]'
-        end
-      end
-
-      def remove_observation_method_attribute
-        # TODO: Discuss with the team the problem related to the method attribute.
-        if %w[AUCorePathologyResult AUCoreLipidResult AUCoreDiagnosticImagingResult
-              AUCoreDiagnosticResult].include? profile.name
-          @must_supports[:elements].delete_if do |element|
-            element[:path] == 'method'
-          end
-        end
-      end
-
-      def is_vital_sign?
-        [
-          'http://hl7.org/fhir/StructureDefinition/vitalsigns'
-        ].include?(profile.baseDefinition)
-      end
-
-      def is_observation_without_component?
-        %w[
-          au-core-bmi
-          au-core-bodyweight
-          au-core-oxygensat
-          au-core-bodyheight
-          au-core-headcircum
-          au-core-bodytemp
-          au-core-heartrate
-          au-core-resprate
-          au-core-vitalspanel
-          au-core-lipid-result
-        ].include?(profile.id)
-      end
-
-      def is_observation_without_value?
-        [
-          'au-core-vitalspanel'
-        ].include?(profile.id)
-      end
-
-      def is_blood_pressure?
-        ['au-core-bloodpressure'].include?(profile.id)
-      end
-
-      # Exclude Observation.component from vital sign profiles except observation-bp and observation-pulse-ox
-      def remove_vital_sign_component
-        return if is_blood_pressure? || profile.name == 'AUCorePulseOximetryProfile'
-
-        return unless is_vital_sign? || is_observation_without_component?
-
-        @must_supports[:elements].delete_if do |element|
-          element[:path].start_with?('component')
-        end
-      end
-
-      # Exclude Observation.value[x] from observation-bp
-      def remove_blood_pressure_value_data_absent_reason
-        return unless is_blood_pressure?
-
-        pattern = /component(:[^.]+)?\.dataAbsentReason/
-
-        @must_supports[:elements].delete_if do |element|
-          element[:path].start_with?('value[x]') ||
-            element[:original_path]&.start_with?('value[x]') ||
-            element[:path] == ('dataAbsentReason') ||
-            (
-              pattern.match?(element[:path]) && ['3.1.1', '4.0.0'].include?(ig_resources.ig.version)
-            )
-        end
-
-        @must_supports[:slices].delete_if do |slice|
-          slice[:path].start_with?('value[x]')
-        end
-      end
-
-      # ONC and AU 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'
-      # Since AU Core 5.0.1, Blood Pressure profile restores component.dataAbsentReason as MustSupport.
-      def remove_observation_data_absent_reason
-        return if is_blood_pressure?
-
-        pattern = /(component(:[^.]+)?\.)?dataAbsentReason/
-
-        return unless profile.type == 'Observation'
-
-        @must_supports[:elements].delete_if do |element|
-          pattern.match?(element[:path])
-        end
-      end
-    end
-  end
-end

data/lib/au_core_test_kit/generator/must_support_metadata_extractor_au_core_3.rb

@@ -1,64 +0,0 @@
-# frozen_string_literal: true
-
-module AUCoreTestKit
-  class Generator
-    class MustSupportMetadataExtractorAUCore3
-      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
-
-      # AU 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/au_core_test_kit/generator/must_support_test_generator.rb

@@ -1,118 +0,0 @@
-# frozen_string_literal: true
-
-require_relative 'naming'
-require_relative 'special_cases'
-
-module AUCoreTestKit
-  class Generator
-    class MustSupportTestGenerator
-      class << self
-        def generate(ig_metadata, base_output_dir)
-          ig_metadata.groups
-                     .reject { |group| SpecialCases.exclude_group? group }
-                     .each { |group| new(group, base_output_dir).generate }
-        end
-      end
-
-      attr_accessor :group_metadata, :base_output_dir
-
-      def initialize(group_metadata, base_output_dir)
-        self.group_metadata = group_metadata
-        self.base_output_dir = base_output_dir
-      end
-
-      def template
-        @template ||= File.read(File.join(__dir__, 'templates', 'must_support.rb.erb'))
-      end
-
-      def output
-        @output ||= ERB.new(template).result(binding)
-      end
-
-      def base_output_file_name
-        "#{class_name.underscore}.rb"
-      end
-
-      def output_file_directory
-        File.join(base_output_dir, profile_identifier)
-      end
-
-      def output_file_name
-        File.join(output_file_directory, base_output_file_name)
-      end
-
-      def read_interaction
-        self.class.read_interaction(group_metadata)
-      end
-
-      def profile_identifier
-        Naming.snake_case_for_profile(group_metadata)
-      end
-
-      def test_id
-        "au_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
-        "AUCore#{group_metadata.reformatted_version.upcase}"
-      end
-
-      def resource_type
-        group_metadata.resource
-      end
-
-      def resource_collection_string
-        'all_scratch_resources'
-      end
-
-      def must_support_list_string
-        build_must_support_list_string(false)
-      end
-
-      def uscdi_list_string
-        build_must_support_list_string(true)
-      end
-
-      def build_must_support_list_string(uscdi_only)
-        slice_names = group_metadata.must_supports[:slices]
-                                    .select { |slice| slice[:uscdi_only].presence == uscdi_only.presence }
-                                    .map { |slice| slice[:slice_id] }
-
-        element_names = group_metadata.must_supports[:elements]
-                                      .select { |element| element[:uscdi_only].presence == uscdi_only.presence }
-                                      .map { |element| "#{resource_type}.#{element[:path]}" }
-
-        extension_names = group_metadata.must_supports[:extensions]
-                                        .select { |extension| extension[:uscdi_only].presence == uscdi_only.presence }
-                                        .map { |extension| extension[:id] }
-
-        group_metadata.must_supports[:choices]&.each do |choice|
-          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
-
-        (slice_names + element_names + extension_names)
-          .uniq
-          .sort
-          .map { |name| "#{' ' * 8}* #{name}" }
-          .join("\n")
-      end
-
-      def generate
-        FileUtils.mkdir_p(output_file_directory)
-        File.open(output_file_name, 'w') { |f| f.write(output) }
-
-        group_metadata.add_test(
-          id: test_id,
-          file_name: base_output_file_name
-        )
-      end
-    end
-  end
-end