au_core_test_kit 1.4.5 → 1.4.7

data/lib/au_core_test_kit/generator/group_metadata_extractor.rb

@@ -1,334 +0,0 @@
-# frozen_string_literal: true
-
-require_relative 'group_metadata'
-require_relative 'ig_metadata'
-require_relative 'must_support_metadata_extractor'
-require_relative 'search_metadata_extractor'
-require_relative 'terminology_binding_metadata_extractor'
-
-module AUCoreTestKit
-  class Generator
-    class GroupMetadataExtractor
-      attr_accessor :resource_capabilities, :profile_url, :ig_metadata, :ig_resources
-
-      def initialize(resource_capabilities, profile_url, ig_metadata, ig_resources)
-        self.resource_capabilities = resource_capabilities
-        self.profile_url = profile_url
-        self.ig_metadata = ig_metadata
-        self.ig_resources = ig_resources
-      end
-
-      def group_metadata
-        @group_metadata ||=
-          GroupMetadata.new(group_metadata_hash)
-      end
-
-      def group_metadata_hash
-        @group_metadata_hash ||=
-          {
-            name:,
-            class_name:,
-            version:,
-            reformatted_version:,
-            # test_id_prefix: test_id_prefix,
-            resource:,
-            profile_url:,
-            profile_name:,
-            profile_version:,
-            title:,
-            short_description:,
-            interactions:,
-            operations:,
-            searches:,
-            search_definitions:,
-            include_params:,
-            revincludes:,
-            required_concepts:,
-            must_supports:,
-            mandatory_elements:,
-            bindings:,
-            references:
-            # tests: []
-          }
-
-        mark_mandatory_and_must_support_searches
-        handle_special_cases
-
-        @group_metadata_hash
-      end
-
-      def mark_mandatory_and_must_support_searches
-        searches.each do |search|
-          search[:names_not_must_support_or_mandatory] = search[:names].reject do |name|
-            full_paths = search_definitions[name.to_sym][:full_paths]
-            any_must_support_elements = must_supports[:elements].any? do |element|
-              full_must_support_paths = ["#{resource}.#{element[:original_path]}", "#{resource}.#{element[:path]}"]
-
-              full_paths.any? do |path|
-                # allow for non-choice, choice types, and _id
-                name == '_id' || full_must_support_paths.include?(path) || full_must_support_paths.include?("#{path}[x]")
-              end
-            end
-
-            any_must_support_slices = must_supports[:slices].any? do |slice|
-              # only handle type slices because that is all we need for now
-              # for a slice like Observation.effective[x]:effectiveDateTime, the search parameter's expression could be
-              # either Observation.effective or Observation.effectiveDateTime.
-              if slice[:discriminator] && slice[:discriminator][:type] == 'type'
-                full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
-                base_must_support_path = "#{resource}.#{slice[:path].sub('[x]', '')}"
-
-                full_paths.intersection([full_must_support_path, base_must_support_path]).present?
-              else
-                false
-              end
-            end
-
-            any_mandatory_elements = mandatory_elements.any? do |element|
-              full_paths.include?(element)
-            end
-
-            any_must_support_elements || any_must_support_slices || any_mandatory_elements
-          end
-
-          search[:must_support_or_mandatory] = search[:names_not_must_support_or_mandatory].empty?
-        end
-      end
-
-      ### BEGIN SPECIAL CASES ###
-
-      ALL_VERSION_CATEGORY_FIRST_PROFILES = [
-        'http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult-path',
-        'http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult-imag'
-      ].freeze
-
-      ALL_VERSION_PATIENT_FIRST_PROFILES = [
-        'http://hl7.org.au/fhir/core/StructureDefinition/au-core-observation',
-      ].freeze
-
-      ALL_VERSION_ID_FIRST_PROFILES = [
-        'http://hl7.org.au/fhir/core/StructureDefinition/au-core-organization',
-        'http://hl7.org.au/fhir/core/StructureDefinition/au-core-practitioner'
-      ].freeze
-
-      ALL_VERSION_NAME_FIRST_PROFILES = [
-        'http://hl7.org.au/fhir/core/StructureDefinition/au-core-healthcareservice'
-      ].freeze
-
-      # Usage example
-      VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES = {
-        # 'http://hl7.org.au/fhir/core/StructureDefinition/au-core-healthcareservice' => ['v030']
-      }.freeze
-
-      def name_first_profile?
-        ALL_VERSION_NAME_FIRST_PROFILES.include? profile_url
-      end
-
-      def id_first_profile?
-        ALL_VERSION_ID_FIRST_PROFILES.include? profile_url
-      end
-
-      def category_first_profile?
-        ALL_VERSION_CATEGORY_FIRST_PROFILES.include?(profile_url) ||
-          VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES[profile_url]&.include?(reformatted_version)
-      end
-
-      def patient_first_profile?
-        ALL_VERSION_PATIENT_FIRST_PROFILES.include?(profile_url)
-      end
-
-      def first_search_params
-        @first_search_params ||=
-          if category_first_profile?
-            %w[patient category]
-          elsif patient_first_profile?
-            ['patient']
-          elsif id_first_profile?
-            ['_id']
-          elsif name_first_profile?
-            ['name']
-          elsif resource == 'Observation'
-            %w[patient code]
-          elsif resource == 'MedicationRequest'
-            ['patient']
-          elsif resource == 'CareTeam'
-            %w[patient status]
-          else
-            ['patient']
-          end
-      end
-
-      def handle_special_cases
-        set_first_search
-      end
-
-      def set_first_search
-        search = searches.find { |param| param[:names] == first_search_params }
-        return if search.nil?
-
-        searches.delete(search)
-        searches.unshift(search)
-      end
-
-      ### END SPECIAL CASES ###
-
-      def profile
-        @profile ||= ig_resources.profile_by_url(profile_url)
-      end
-
-      def profile_elements
-        @profile_elements ||= profile.snapshot.element
-      end
-
-      def base_name
-        profile_url.split('StructureDefinition/').last
-      end
-
-      def name
-        base_name.tr('-', '_')
-      end
-
-      def class_name
-        base_name
-          .split('-')
-          .map(&:capitalize)
-          .join
-          .gsub('AUCore', "AUCore#{ig_metadata.reformatted_version}")
-          .concat('Sequence')
-      end
-
-      def version
-        ig_metadata.ig_version
-      end
-
-      def reformatted_version
-        ig_metadata.reformatted_version
-      end
-
-      def resource
-        resource_capabilities.type
-      end
-
-      def profile_name
-        profile.title.gsub('  ', ' ')
-      end
-
-      def profile_version
-        profile.version
-      end
-
-      def title
-        title = profile.title.gsub(/AU\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
-
-        title = "#{resource} #{title.split(resource).map(&:strip).join(' ')}" if Naming.resources_with_multiple_profiles.include?(resource) && !title.start_with?(resource) && version != 'v3.1.1'
-
-        title
-      end
-
-      def short_description
-        "Verify support for the server capabilities required by the #{profile_name}."
-      end
-
-      def interactions
-        @interactions ||=
-          resource_capabilities.interaction.map do |interaction|
-            {
-              code: interaction.code,
-              expectation: interaction.extension.first.valueCode # TODO: fix expectation extension finding
-            }
-          end
-      end
-
-      def operations
-        @operations ||=
-          resource_capabilities.operation.map do |operation|
-            {
-              code: operation.name,
-              expectation: operation.extension.first.valueCode # TODO: fix expectation extension finding
-            }
-          end
-      end
-
-      def search_metadata_extractor
-        @search_metadata_extractor ||= SearchMetadataExtractor.new(
-          resource_capabilities,
-          ig_resources,
-          profile_elements,
-          {
-            resource:,
-            profile_url:,
-            must_supports:
-          }
-        )
-      end
-
-      def searches
-        @searches ||= search_metadata_extractor.searches
-      end
-
-      def search_definitions
-        @search_definitions ||= search_metadata_extractor.search_definitions
-      end
-
-      def include_params
-        resource_capabilities.searchInclude || []
-      end
-
-      def revincludes
-        resource_capabilities.searchRevInclude || []
-      end
-
-      def required_concepts
-        # The base FHIR vital signs profile has a required binding that isn't
-        # relevant for any of its child profiles
-        return [] if resource == 'Observation'
-
-        profile_elements
-          .select { |element| element.type&.any? { |type| type.code == 'CodeableConcept' } }
-          .select { |element| element.binding&.strength == 'required' }
-          .map { |element| element.path.gsub("#{resource}.", '').gsub('[x]', 'CodeableConcept') }
-          .uniq
-      end
-
-      def terminology_binding_metadata_extractor
-        @terminology_binding_metadata_extractor ||=
-          TerminologyBindingMetadataExtractor.new(profile_elements, ig_resources, resource)
-      end
-
-      def bindings
-        @bindings ||=
-          terminology_binding_metadata_extractor.terminology_bindings
-      end
-
-      def must_support_metadata_extractor
-        @must_support_metadata_extractor ||=
-          MustSupportMetadataExtractor.new(profile_elements, profile, resource, ig_resources)
-      end
-
-      def must_supports
-        @must_supports ||=
-          must_support_metadata_extractor.must_supports
-      end
-
-      def mandatory_elements
-        @mandatory_elements ||=
-          profile_elements
-          .select { |element| element.min.positive? }
-          .map(&:path)
-          .uniq
-      end
-
-      def references
-        @references ||=
-          profile_elements
-          .select { |element| element.type&.first&.code == 'Reference' }
-          .map do |reference_definition|
-            {
-              path: reference_definition.path,
-              profiles: reference_definition.type.first.targetProfile,
-            }
-          end
-      end
-    end
-  end
-end

data/lib/au_core_test_kit/generator/ig_download.rb

@@ -1,77 +0,0 @@
-# frozen_string_literal: true
-
-require 'nokogiri'
-require 'json'
-require 'net/http'
-
-url = 'http://hl7.org.au/fhir/core/history.html'
-
-begin
-  uri = URI.parse(url)
-  response = Net::HTTP.get_response(uri)
-
-  unless response.is_a?(Net::HTTPSuccess)
-    puts "Failed to fetch HTML content from #{url}. HTTP Status: #{response.code} #{response.message}"
-    exit
-  end
-
-  html_content = response.body
-
-  doc = Nokogiri::HTML(html_content)
-
-  script_tag = doc.at('script:contains("var pageJSON")')
-
-  ig_versions_to_skip = [
-    # R1 sequence:
-    '0.1.0-draft',
-    '0.2.0-preview',
-    '0.2.1-preview',
-    '0.2.2-preview',
-    '0.3.0-ballot',
-    '0.4.1-preview',
-    '1.0.0-ballot',
-    '1.0.0-preview',
-
-    # R2 sequence:
-    '1.1.0-preview',
-    '2.0.0-draft',
-    '2.0.0-ballot',
-    '2.0.0-preview',
-
-    'current'
-  ]
-
-  if script_tag&.content
-    json_data = script_tag.content[/\{.*\}/m]
-    if json_data
-      data_hash = JSON.parse(json_data)
-      data_hash['list'].each do |item|
-        version = item['version']
-        next if ig_versions_to_skip.include? version
-
-        package_url = "#{item['path']}/package.tgz"
-        file_name = "#{version}.tgz"
-        output_directory = 'lib/au_core_test_kit/igs'
-
-        Dir.mkdir(output_directory) unless File.directory?(output_directory)
-
-        File.open(File.join(output_directory, file_name), 'wb') do |file|
-          uri = URI.parse(package_url)
-          response = Net::HTTP.get_response(uri)
-          if response.is_a?(Net::HTTPSuccess)
-            file.write(response.body)
-            puts "Successfully downloaded #{file_name}"
-          else
-            puts "Failed to download #{file_name}. HTTP Status: #{response.code} #{response.message}"
-          end
-        end
-      end
-    else
-      puts 'Error: Unable to extract JSON data from script tag.'
-    end
-  else
-    puts 'Error: Script tag containing pageJSON variable not found.'
-  end
-rescue StandardError => e
-  puts "An error occurred: #{e.message}"
-end

data/lib/au_core_test_kit/generator/ig_loader.rb

@@ -1,88 +0,0 @@
-# frozen_string_literal: true
-
-require 'active_support/all'
-require 'fhir_models'
-require 'pathname'
-require 'rubygems/package'
-require 'zlib'
-require 'json'
-require_relative 'ig_resources'
-
-module AUCoreTestKit
-  class Generator
-    class IGLoader
-      attr_accessor :ig_file_name
-
-      def initialize(ig_file_name)
-        self.ig_file_name = ig_file_name
-      end
-
-      def ig_resources
-        @ig_resources ||= IGResources.new
-      end
-
-      def load
-        load_ig
-        load_standalone_resources
-      end
-
-      def load_ig
-        tar = Gem::Package::TarReader.new(
-          Zlib::GzipReader.open(ig_file_name)
-        )
-
-        tar.each do |entry|
-          next if entry.directory?
-
-          file_name = entry.full_name.split('/').last
-
-          next if file_name.end_with? 'openapi.json'
-
-          next unless file_name.end_with? '.json'
-
-          next unless entry.full_name.start_with? 'package/'
-
-          begin
-            resource = FHIR.from_contents(entry.read)
-            next if resource.nil?
-          rescue StandardError
-            puts "#{file_name} does not appear to be a FHIR resource."
-            next
-          end
-
-          ig_resources.add(resource)
-        end
-        json_files = Dir.glob(File.join(Dir.pwd, 'lib', 'au_core_test_kit', 'igs', '*.json'))
-        json_files.each do |file_path|
-          file_content = File.read(file_path)
-          bundle = FHIR.from_contents(file_content)
-          bundle.entry.each do |entry|
-            ig_resources.add(entry.resource)
-          end
-        end
-        ig_resources
-      end
-
-      def load_standalone_resources
-        ig_directory = ig_file_name.chomp('.tgz')
-
-        return ig_resources unless File.exist? ig_directory
-
-        Dir.glob(File.join(ig_directory, '*.json')).each do |file_path|
-          begin
-            resource = FHIR.from_contents(File.read(file_path))
-            next if resource.nil?
-          rescue StandardError
-            file_name = file_path.split('/').last
-            puts "#{file_name} does not appear to be a FHIR resource."
-            next
-          end
-
-          ig_resources.add(resource)
-        end
-
-        ig_resources
-      end
-    end
-  end
-end

data/lib/au_core_test_kit/generator/ig_metadata.rb

@@ -1,51 +0,0 @@
-# frozen_string_literal: true
-
-module AUCoreTestKit
-  class Generator
-    class IGMetadata
-      attr_accessor :ig_version, :groups
-
-      def reformatted_version
-        @reformatted_version ||= ig_version.delete('.').gsub('-', '_')
-      end
-
-      def ordered_groups
-        @ordered_groups ||=
-          [patient_group] + non_delayed_groups + delayed_groups
-      end
-
-      def patient_group
-        @patient_group ||=
-          groups.find { |group| group.resource == 'Patient' }
-      end
-
-      def delayed_groups
-        @delayed_groups ||=
-          groups.select(&:delayed?)
-      end
-
-      def non_delayed_groups
-        @non_delayed_groups ||=
-          groups.reject(&:delayed?) - [patient_group]
-      end
-
-      def delayed_profiles
-        @delayed_profiles ||=
-          delayed_groups.map(&:profile_url)
-      end
-
-      def postprocess_groups(ig_resources)
-        groups.each do |group|
-          group.add_delayed_references(delayed_profiles, ig_resources)
-        end
-      end
-
-      def to_hash
-        {
-          ig_version:,
-          groups: groups.map(&:to_hash)
-        }
-      end
-    end
-  end
-end

data/lib/au_core_test_kit/generator/ig_metadata_extractor.rb

@@ -1,94 +0,0 @@
-# frozen_string_literal: true
-
-require_relative 'ig_metadata'
-require_relative 'group_metadata_extractor'
-
-module AUCoreTestKit
-  class Generator
-    class IGMetadataExtractor
-      attr_accessor :ig_resources, :metadata
-
-      def initialize(ig_resources)
-        self.ig_resources = ig_resources
-        add_missing_supported_profiles
-        remove_extra_supported_profiles
-        self.metadata = IGMetadata.new
-      end
-
-      def extract
-        add_metadata_from_ig
-        add_metadata_from_resources
-        metadata
-      end
-
-      def add_metadata_from_ig
-        metadata.ig_version = "v#{ig_resources.ig.version}"
-      end
-
-      def resources_in_capability_statement
-        ig_resources.capability_statement.rest.first.resource
-      end
-
-      def add_missing_supported_profiles
-        case ig_resources.ig.version
-        when '3.1.1'
-          # The AU Core v3.1.1 Server Capability Statement does not list support for the
-          # required vital signs profiles, so they need to be added
-          ig_resources.capability_statement.rest.first.resource
-                      .find { |resource| resource.type == 'Observation' }
-                      .supportedProfile.concat [
-                        'http://hl7.org/fhir/StructureDefinition/bodyheight',
-                        'http://hl7.org/fhir/StructureDefinition/bodytemp',
-                        'http://hl7.org/fhir/StructureDefinition/bp',
-                        'http://hl7.org/fhir/StructureDefinition/bodyweight',
-                        'http://hl7.org/fhir/StructureDefinition/heartrate',
-                        'http://hl7.org/fhir/StructureDefinition/resprate'
-                      ]
-        end
-      end
-
-      def remove_extra_supported_profiles
-        ig_resources.capability_statement.rest.first.resource
-                    .find { |resource| resource.type == 'Observation' }
-                    .supportedProfile.delete_if do |profile_url|
-          SpecialCases::PROFILES_TO_EXCLUDE.include?(profile_url)
-        end
-      end
-
-      def add_metadata_from_resources
-        profile_arr_to_skip = [
-          'http://hl7.org.au/fhir/StructureDefinition/au-imagingresult',
-          'http://hl7.org.au/fhir/StructureDefinition/au-specimen', # https://github.com/hl7au/au-fhir-core-inferno/issues/244
-          'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire',
-          'http://hl7.org.au/fhir/core/StructureDefinition/au-core-norelevantfinding',
-          'http://hl7.org/fhir/StructureDefinition/DocumentReference' # https://github.com/hl7au/au-fhir-core-inferno/issues/216
-        ]
-
-        # NOTE: We use two different groups because of CapabilityStatement.rest.resource
-        # in AU Core IG supports two ways to describe the profile:
-        # 1. "profile" element which is a string
-        # 2. "supportedProfile" element which is an array of strings
-
-        supported_profile_groups = resources_in_capability_statement.flat_map do |resource|
-          resource.supportedProfile&.map do |supported_profile|
-            supported_profile = supported_profile.split('|').first
-            next if profile_arr_to_skip.include?(supported_profile)
-
-            GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources).group_metadata
-          end
-        end.compact
-
-        profile_groups = resources_in_capability_statement.flat_map do |resource|
-          next unless resource.profile.present?
-          next if profile_arr_to_skip.include?(resource.profile)
-
-          GroupMetadataExtractor.new(resource, resource.profile, metadata, ig_resources).group_metadata
-        end.compact
-
-        metadata.groups = supported_profile_groups + profile_groups
-
-        metadata.postprocess_groups(ig_resources)
-      end
-    end
-  end
-end