davinci_us_drug_formulary_test_kit 0.9.0

data/lib/davinci_us_drug_formulary_test_kit/generator/suite_generator.rb

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+require_relative 'naming'
+
+module DaVinciUSDrugFormularyTestKit
+  class Generator
+    class SuiteGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          new(ig_metadata, base_output_dir).generate
+        end
+      end
+
+      attr_accessor :ig_metadata, :base_output_dir
+
+      def initialize(ig_metadata, base_output_dir)
+        self.ig_metadata = ig_metadata
+        self.base_output_dir = base_output_dir
+      end
+
+      def version_specific_message_filters
+        []
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'suite.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template).result(binding)
+      end
+
+      def base_output_file_name
+        'usdf_test_suite.rb'
+      end
+
+      def class_name
+        'USDFTestSuite'
+      end
+
+      def module_name
+        "USDF#{ig_metadata.reformatted_version.upcase}"
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def suite_id
+        "davinci_us_drug_formulary_#{ig_metadata.reformatted_version}"
+      end
+
+      def title
+        "Da Vinci US Drug Formulary #{ig_metadata.ig_version}"
+      end
+
+      def short_title
+        "US Drug Formulary #{ig_metadata.ig_version}"
+      end
+
+      def validator_env_name
+        "#{ig_metadata.reformatted_version.upcase}_VALIDATOR_URL"
+      end
+
+      def ig_link
+        'https://hl7.org/fhir/us/davinci-drug-formulary/STU2.0.1/'
+      end
+
+      def generate
+        File.write(output_file_name, output)
+      end
+
+      def groups
+        ig_metadata.ordered_groups
+      end
+
+      def group_id_list
+        @group_id_list ||=
+          groups.map(&:id)
+      end
+
+      def group_file_list
+        @group_file_list ||=
+          groups.map { |group| group.file_name.delete_suffix('.rb') }
+      end
+
+      def capability_statement_file_name
+        "../../custom_groups/#{ig_metadata.ig_version}/capability_statement_group"
+      end
+
+      def capability_statement_group_id
+        "usdf_#{ig_metadata.reformatted_version}_capability_statement"
+      end
+    end
+  end
+end

data/lib/davinci_us_drug_formulary_test_kit/generator/terminology_binding_metadata_extractor.rb

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+module DaVinciUSDrugFormularyTestKit
+  class Generator
+    class TerminologyBindingMetadataExtractor
+      attr_accessor :profile_elements, :ig_resources, :resource
+
+      def initialize(profile_elements, ig_resources, resource)
+        self.profile_elements = profile_elements
+        self.ig_resources = ig_resources
+        self.resource = resource
+      end
+
+      def terminology_bindings
+        (element_terminology_bindings + extension_terminology_bindings).compact
+        # add_terminology_bindings_from_extensions
+        # profile_elements.select { |element| element.type&.first&.code == 'Extension' }
+        #   .each { |extension| add_terminology_bindings_from_extension(extension) }
+      end
+
+      def element_has_fixed_value?(element)
+        case element.type.first.code
+        when 'Quantity'
+          code = profile_elements.find { |e| e.path == "#{element.path}.code" }
+          system = profile_elements.find { |e| e.path == "#{element.path}.system" }
+          code&.fixedCode || system&.fixedUri
+        when 'code'
+          element.fixedCode.present?
+        end
+      end
+
+      def element_has_optional_binding_slice?(element)
+        element.sliceName.present? && element.min.zero?
+      end
+
+      def profile_elements_with_bindings
+        profile_elements
+          .select { |element| element.binding.present? && element.binding.strength == 'required' }
+          .reject { |element| element_has_fixed_value?(element) || element_has_optional_binding_slice?(element) }
+      end
+
+      def element_terminology_bindings
+        profile_elements_with_bindings.map do |element|
+          binding = {
+            type: element.type.first.code,
+            strength: element.binding.strength,
+            # Goal.target.detail has an unbound binding
+            system: element.binding.valueSet&.split('|')&.first,
+            path: element.path.gsub('[x]', '').gsub("#{resource}.", '')
+          }
+
+          binding[:required_binding_slice] = true if element.sliceName.present? && element.min.positive?
+
+          binding
+        end
+      end
+
+      def extension_profile_elements
+        profile_elements
+          .select { |element| element.type&.first&.code == 'Extension' }
+          .select { |element| extension_profile_url(element).present? }
+      end
+
+      def extension_profile_url(extension)
+        extension.type.first.profile&.first
+      end
+
+      def extension_terminology_bindings
+        extension_profile_elements
+          .flat_map do |extension_profile_element|
+            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')
+            end
+
+            elements_with_bindings.map do |element|
+              {
+                type: element.type.first.code,
+                strength: element.binding.strength,
+                system: element.binding.valueSet&.split('|')&.first,
+                path: element.path.gsub('[x]', '').gsub('Extension.', ''),
+                extensions: [url]
+              }
+            end + nested_extension_terminology_bindings(elements, url)
+          end
+      end
+
+      def nested_extension_terminology_bindings(elements, extension_url)
+        nested_extensions = elements.select { |element| element.path == 'Extension.extension' }
+        nested_extensions.flat_map do |nested_extension|
+          nested_extension_element = elements.find { |element| element.id == "#{nested_extension.id}.url" }
+          next unless nested_extension_element.present?
+
+          nested_extension_url = nested_extension_element.fixedUri
+          nested_elements_with_bindings = elements.select do |element|
+            element.id.include?(nested_extension.id) && element.binding.present?
+          end
+
+          nested_elements_with_bindings.map do |element|
+            {
+              type: element.type.first.code,
+              strength: element.binding.strength,
+              system: element.binding.valueSet&.split('|')&.first,
+              path: element.path.gsub('[x]', '').gsub('Extension.extension.', ''),
+              extensions: [extension_url, nested_extension_url]
+            }
+          end
+        end
+      end
+    end
+  end
+end

data/lib/davinci_us_drug_formulary_test_kit/generator/validation_test_generator.rb

@@ -0,0 +1,102 @@
+require_relative 'naming'
+module DaVinciUSDrugFormularyTestKit
+  class Generator
+    class ValidationTestGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          ig_metadata.groups
+            .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', 'validation.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, directory_name)
+      end
+
+      def output_file_name
+        File.join(output_file_directory, base_output_file_name)
+      end
+
+      def directory_name
+        Naming.snake_case_for_profile(group_metadata)
+      end
+
+      def profile_identifier
+        Naming.snake_case_for_profile(group_metadata)
+      end
+
+      def profile_url
+        group_metadata.profile_url
+      end
+
+      def profile_name
+        group_metadata.profile_name
+      end
+
+      def profile_version
+        group_metadata.profile_version
+      end
+
+      def test_id
+        "usdf_#{group_metadata.reformatted_version}_#{profile_identifier}_validation_test"
+      end
+
+      def class_name
+        "#{Naming.upper_camel_case_for_profile(group_metadata)}ValidationTest"
+      end
+
+      def module_name
+        "DaVinciUSDrugFormulary#{group_metadata.reformatted_version.upcase}"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def description
+        <<~DESCRIPTION
+          This test verifies resources returned from the first search conform to
+          the [#{profile_name} profile](#{profile_url}).
+
+          Systems must demonstrate at least one valid example in order to pass this test.
+          It verifies the presence of mandatory elements and that elements with
+          required bindings contain appropriate values. CodeableConcept element
+          bindings will fail if none of their codings have a code/system belonging
+          to the bound ValueSet. Quantity, Coding, and code element bindings will
+          fail if their code/system are not found in the valueset.
+        DESCRIPTION
+      end
+
+      def generate
+        FileUtils.mkdir_p(output_file_directory)
+        File.write(output_file_name, output)
+
+        test_metadata = {
+          id: test_id,
+          file_name: base_output_file_name
+        }
+
+        group_metadata.add_test(**test_metadata)
+      end
+    end
+  end
+end

data/lib/davinci_us_drug_formulary_test_kit/generator/value_extractor.rb

@@ -0,0 +1,113 @@
+module DaVinciUSDrugFormularyTestKit
+  class Generator
+    class ValueExactor
+      attr_accessor :ig_resources, :resource, :profile_elements
+
+      def initialize(ig_resources, resource, profile_elements)
+        self.ig_resources = ig_resources
+        self.resource = resource
+        self.profile_elements = profile_elements
+      end
+
+      def values_from_slicing(profile_element, type)
+        (
+          values_from_fixed_codes(profile_element, type) +
+          values_from_pattern_coding(profile_element, type) +
+          values_from_pattern_codeable_concept(profile_element, type)
+        ).uniq
+      end
+
+      def values_from_required_binding(profile_element)
+        return [] unless profile_element&.max == '*'
+
+        profile_elements
+          .select do |element|
+            element.path == profile_element.path && element.binding&.strength == 'required'
+          end
+          .map { |element| values_from_value_set_binding(element) }
+          .flatten.compact
+      end
+
+      def values_from_fixed_codes(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        profile_elements
+          .select do |element|
+            element.path == "#{profile_element.path}.coding.code" && element.fixedCode.present?
+          end
+          .map(&:fixedCode)
+      end
+
+      def values_from_pattern_coding(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        profile_elements
+          .select do |element|
+            element.path == "#{profile_element.path}.coding" && element.patternCoding.present?
+          end
+          .map { |element| element.patternCoding.code }
+      end
+
+      def values_from_pattern_codeable_concept(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        profile_elements
+          .select do |element|
+            element.path == profile_element.path && element.patternCodeableConcept.present? && element.min.positive?
+          end
+          .map { |element| element.patternCodeableConcept.coding.first.code }
+      end
+
+      def value_set_binding(the_element)
+        the_element&.binding
+      end
+
+      def value_set(the_element)
+        ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
+      end
+
+      def bound_systems(the_element)
+        bound_systems_from_valueset(value_set(the_element))
+      end
+
+      def bound_systems_from_valueset(value_set)
+        value_set&.compose&.include&.map do |include|
+          if include.concept.present?
+            include
+          elsif include.system.present? && include.filter&.empty? # Cannot process intensional value set with filters
+            ig_resources.code_system_by_url(include.system)
+          elsif include.valueSet.present?
+            include.valueSet.map do |vs|
+              a_value_set = ig_resources.value_set_by_url(vs)
+              bound_systems_from_valueset(a_value_set)
+            end
+          end
+        end&.flatten&.compact
+      end
+
+      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) }.uniq
+      end
+
+      def fhir_metadata(current_path)
+        FHIR.const_get(resource)::METADATA[current_path]
+      end
+
+      def values_from_resource_metadata(paths)
+        values = []
+
+        paths.each do |current_path|
+          current_metadata = fhir_metadata(current_path)
+
+          values += current_metadata['valid_codes'].values.flatten if current_metadata&.dig('valid_codes').present?
+        end
+
+        values
+      end
+    end
+  end
+end

data/lib/davinci_us_drug_formulary_test_kit/generator.rb

@@ -0,0 +1,94 @@
+require 'fhir_models'
+require 'inferno/ext/fhir_models'
+
+require_relative 'generator/ig_loader'
+require_relative 'generator/ig_metadata_extractor'
+require_relative 'generator/group_generator'
+require_relative 'generator/must_support_test_generator'
+require_relative 'generator/read_test_generator'
+require_relative 'generator/reference_resolution_test_generator'
+require_relative 'generator/search_test_generator'
+require_relative 'generator/suite_generator'
+require_relative 'generator/validation_test_generator'
+require_relative 'generator/include_search_test_generator'
+
+module DaVinciUSDrugFormularyTestKit
+  class Generator
+    def self.generate
+      ig_packages = Dir.glob(File.join(Dir.pwd, 'lib', 'davinci_us_drug_formulary_test_kit', 'igs', '*.tgz'))
+
+      ig_packages.each do |ig_package|
+        new(ig_package).generate
+      end
+    end
+
+    attr_accessor :ig_resources, :ig_metadata, :ig_file_name
+
+    def initialize(ig_file_name)
+      self.ig_file_name = ig_file_name
+    end
+
+    def generate
+      load_ig_package
+      extract_metadata
+      generate_search_tests
+      generate_read_tests
+      generate_include_search_tests
+      generate_validation_tests
+      generate_must_support_tests
+      generate_reference_resolution_tests
+
+      generate_groups
+
+      generate_suites
+    end
+
+    def extract_metadata
+      self.ig_metadata = IGMetadataExtractor.new(ig_resources).extract
+
+      FileUtils.mkdir_p(base_output_dir)
+      File.write(File.join(base_output_dir, 'metadata.yml'), YAML.dump(ig_metadata.to_hash))
+    end
+
+    def base_output_dir
+      File.join(__dir__, 'generated', ig_metadata.ig_version)
+    end
+
+    def load_ig_package
+      FHIR.logger = Logger.new('/dev/null')
+      self.ig_resources = IGLoader.new(ig_file_name).load
+    end
+
+    def generate_reference_resolution_tests
+      ReferenceResolutionTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_must_support_tests
+      MustSupportTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_validation_tests
+      ValidationTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_read_tests
+      ReadTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_search_tests
+      SearchTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_include_search_tests
+      IncludeSearchTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_groups
+      GroupGenerator.generate(ig_metadata, base_output_dir)
+    end
+
+    def generate_suites
+      SuiteGenerator.generate(ig_metadata, base_output_dir)
+    end
+  end
+end