inferno_core 0.6.0 → 0.6.2

data/lib/inferno/dsl/fhir_evaluation/rules/all_must_supports_present.rb

@@ -0,0 +1,379 @@
+require_relative '../../fhir_resource_navigation'
+require_relative '../../must_support_metadata_extractor'
+require_relative '../profile_conformance_helper'
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module Rules
+        # AllMustSupportsPresent checks that at least one instance of every MustSupport element
+        #  defined in the given profiles is populated in the given data.
+        # MustSupport elements include plain elements, extensions, and slices.
+        # The basis of the test is metadata generated in a first pass that processes the profile into a list of fields,
+        #  then the second pass check that all elements in the list are present.
+        # This metadata approach allows for customizing what is checked, for example elements may be added or removed,
+        #  or choices may be defined where only one choice of multiple must be populated to demonstrate support.
+        class AllMustSupportsPresent < Rule
+          include FHIRResourceNavigation
+          include ProfileConformanceHelper
+          attr_accessor :metadata
+
+          # check is invoked from the evaluator CLI and applies the logic for this Rule to the provided data.
+          # At least one instance of every MustSupport element defined in the profiles must be populated in the data.
+          # Findings from the rule will be added to context.results.
+          # The logic is configurable with a few options, but this method does not support customizing the metadata.
+          # @param context [Inferno::DSL::FHIREvaluation::EvaluationContext]
+          # @return [void]
+          def check(context)
+            missing_items_by_profile = {}
+            context.ig.profiles.each do |profile|
+              resources = pick_resources_for_profile(profile, context)
+              if resources.blank?
+                missing_items_by_profile[profile.url] = ['No matching resources were found to check']
+                next
+              end
+              requirement_extension = context.config.data['Rule']['AllMustSupportsPresent']['RequirementExtensionUrl']
+              debug_metadata = context.config.data['Rule']['AllMustSupportsPresent']['WriteMetadataForDebugging']
+              profile_metadata = extract_metadata(profile, context.ig, requirement_extension:)
+              missing_items = perform_must_support_test_with_metadata(resources, profile_metadata, debug_metadata:)
+
+              missing_items_by_profile[profile.url] = missing_items if missing_items.any?
+            end
+
+            if missing_items_by_profile.count.zero?
+              result = EvaluationResult.new('All MustSupports are present', severity: 'success', rule: self)
+            else
+              message = 'Found Profiles with not all MustSupports represented:'
+              missing_items_by_profile.each do |profile_url, missing_items|
+                message += "\n\t\t#{profile_url}: #{missing_items.join(', ')}"
+              end
+              result = EvaluationResult.new(message, rule: self)
+            end
+            context.add_result result
+          end
+
+          def pick_resources_for_profile(profile, context)
+            conformance_options = context.config.data['Rule']['AllMustSupportsPresent']['ConformanceOptions'].to_options
+
+            # Unless specifically looking for Bundles, break them out into the resources they include
+            all_resources =
+              if profile.type == 'Bundle'
+                context.data
+              else
+                flatten_bundles(context.data)
+              end
+
+            all_resources.filter do |r|
+              conforms_to_profile?(r, profile, conformance_options, context.validator)
+            end
+          end
+
+          # perform_must_support_test is invoked from DSL assertions, allows customizing the metadata with a block.
+          # Customizing the metadata may add, modify, or remove items.
+          # For instance, US Core 3.1.1 Patient "Previous Name" is defined as MS only in narrative.
+          # Choices are also defined only in narrative.
+          # @param profile [FHIR::StructureDefinition]
+          # @param resources [Array<FHIR::Model>]
+          # @param ig [Inferno::Entities::IG]
+          # @param debug_metadata [Boolean] if true, write out the final metadata used to a temporary file
+          # @param requirement_extension [String] Extension URL that implies "required" as an alternative to the MS flag
+          # @yield [Metadata] Customize the metadata before running the test
+          # @return [Array<String>] list of elements that were not found in the provided resources
+          def perform_must_support_test(profile, resources, ig, debug_metadata: false, requirement_extension: nil)
+            profile_metadata = extract_metadata(profile, ig, requirement_extension:)
+            yield profile_metadata if block_given?
+
+            perform_must_support_test_with_metadata(resources, profile_metadata, debug_metadata:)
+          end
+
+          # perform_must_support_test_with_metadata is invoked from check and perform_must_support_test,
+          # with the metadata to be used as the basis for the test.
+          # It may also be invoked directly from a test if you want to completely overwrite the metadata.
+          # @param resources [Array<FHIR::Model>]
+          # @param profile_metadata [Metadata] Metadata object with must_supports field
+          # @param debug_metadata [Boolean] if true, write out the final metadata used to a temporary file
+          # @return [Array<String>] list of elements that were not found in the provided resources
+          def perform_must_support_test_with_metadata(resources, profile_metadata, debug_metadata: false)
+            return if resources.blank?
+
+            @metadata = profile_metadata
+
+            write_metadata_for_debugging if debug_metadata
+
+            missing_elements(resources)
+            missing_slices(resources)
+            missing_extensions(resources)
+
+            handle_must_support_choices if metadata.must_supports[:choices].present?
+
+            missing_must_support_strings
+          end
+
+          def extract_metadata(profile, ig, requirement_extension: nil)
+            MustSupportMetadataExtractor.new(profile.snapshot.element, profile, profile.type, ig, requirement_extension)
+          end
+
+          def write_metadata_for_debugging
+            outfile = "#{metadata.profile&.id}-#{SecureRandom.uuid}.yml"
+
+            File.open(File.join(Dir.tmpdir, outfile), 'w') do |f|
+              writable_metadata = { must_supports: @metadata.must_supports.to_hash }
+              f.write(YAML.dump(writable_metadata))
+              puts "Wrote MustSupport metadata to #{f.path}"
+            end
+          end
+
+          def handle_must_support_choices
+            handle_must_support_element_choices
+            handle_must_support_extension_choices
+            handle_must_support_slice_choices
+          end
+
+          def handle_must_support_element_choices
+            missing_elements.delete_if do |element|
+              choices = metadata.must_supports[:choices].find do |choice|
+                choice[:paths]&.include?(element[:path]) ||
+                  choice[:elements]&.any? { |ms_element| ms_element[:path] == element[:path] }
+              end
+              any_choice_supported?(choices)
+            end
+          end
+
+          def handle_must_support_extension_choices
+            missing_extensions.delete_if do |extension|
+              choices = metadata.must_supports[:choices].find do |choice|
+                choice[:extension_ids]&.include?(extension[:id])
+              end
+              any_choice_supported?(choices)
+            end
+          end
+
+          def handle_must_support_slice_choices
+            missing_slices.delete_if do |slice|
+              choices = metadata.must_supports[:choices].find { |choice| choice[:slice_names]&.include?(slice[:name]) }
+              any_choice_supported?(choices)
+            end
+          end
+
+          def any_choice_supported?(choices)
+            return false unless choices.present?
+
+            any_path_choice_supported?(choices) ||
+              any_extension_ids_choice_supported?(choices) ||
+              any_slice_names_choice_supported?(choices) ||
+              any_elements_choice_supported?(choices)
+          end
+
+          def any_path_choice_supported?(choices)
+            return false unless choices[:paths].present?
+
+            choices[:paths].any? { |path| missing_elements.none? { |element| element[:path] == path } }
+          end
+
+          def any_extension_ids_choice_supported?(choices)
+            return false unless choices[:extension_ids].present?
+
+            choices[:extension_ids].any? do |extension_id|
+              missing_extensions.none? { |extension| extension[:id] == extension_id }
+            end
+          end
+
+          def any_slice_names_choice_supported?(choices)
+            return false unless choices[:slice_names].present?
+
+            choices[:slice_names].any? { |slice_name| missing_slices.none? { |slice| slice[:name] == slice_name } }
+          end
+
+          def any_elements_choice_supported?(choices)
+            return false unless choices[:elements].present?
+
+            choices[:elements].any? do |choice|
+              missing_elements.none? do |element|
+                element[:path] == choice[:path] && element[:fixed_value] == choice[:fixed_value]
+              end
+            end
+          end
+
+          def missing_must_support_strings
+            missing_elements.map { |element_definition| missing_element_string(element_definition) } +
+              missing_slices.map { |slice_definition| slice_definition[:slice_id] } +
+              missing_extensions.map { |extension_definition| extension_definition[:id] }
+          end
+
+          def missing_element_string(element_definition)
+            if element_definition[:fixed_value].present?
+              "#{element_definition[:path]}:#{element_definition[:fixed_value]}"
+            else
+              element_definition[:path]
+            end
+          end
+
+          def must_support_extensions
+            metadata.must_supports[:extensions]
+          end
+
+          def missing_extensions(resources = [])
+            @missing_extensions ||=
+              must_support_extensions.select do |extension_definition|
+                resources.none? do |resource|
+                  path = extension_definition[:path]
+
+                  if path == 'extension'
+                    resource.extension.any? { |extension| extension.url == extension_definition[:url] }
+                  else
+                    extension = find_a_value_at(resource, path) do |el|
+                      el.url == extension_definition[:url]
+                    end
+
+                    extension.present?
+                  end
+                end
+              end
+          end
+
+          def must_support_elements
+            metadata.must_supports[:elements]
+          end
+
+          def missing_elements(resources = [])
+            @missing_elements ||= find_missing_elements(resources, must_support_elements)
+          end
+
+          def find_missing_elements(resources, must_support_elements)
+            must_support_elements.select do |element_definition|
+              resources.none? { |resource| resource_populates_element?(resource, element_definition) }
+            end
+          end
+
+          def resource_populates_element?(resource, element_definition)
+            path = element_definition[:path]
+            ms_extension_urls = must_support_extensions.select { |ex| ex[:path] == "#{path}.extension" }
+              .map { |ex| ex[:url] }
+
+            value_found = find_a_value_at(resource, path) do |potential_value|
+              matching_without_extensions?(potential_value, ms_extension_urls, element_definition[:fixed_value])
+            end
+
+            # Note that false.present? => false, which is why we need to add this extra check
+            value_found.present? || value_found == false
+          end
+
+          def matching_without_extensions?(value, ms_extension_urls, fixed_value)
+            if value.instance_of?(Inferno::DSL::PrimitiveType)
+              urls = value.extension&.map(&:url)
+              has_ms_extension = (urls & ms_extension_urls).present?
+              value = value.value
+            end
+
+            return false unless has_ms_extension || value_without_extensions?(value)
+
+            matches_fixed_value?(value, fixed_value)
+          end
+
+          def matches_fixed_value?(value, fixed_value)
+            fixed_value.blank? || value == fixed_value
+          end
+
+          def value_without_extensions?(value)
+            value_without_extensions = value.respond_to?(:to_hash) ? value.to_hash.except('extension') : value
+            value_without_extensions.present? || value_without_extensions == false
+          end
+
+          def must_support_slices
+            metadata.must_supports[:slices]
+          end
+
+          def missing_slices(resources = [])
+            @missing_slices ||=
+              must_support_slices.select do |slice|
+                resources.none? do |resource|
+                  path = slice[:path]
+                  find_slice(resource, path, slice[:discriminator]).present?
+                end
+              end
+          end
+
+          def find_slice(resource, path, discriminator)
+            # TODO: there is a lot of similarity
+            # between this and FHIRResourceNavigation.matching_slice?
+            # Can these be combined?
+            find_a_value_at(resource, path) do |element|
+              case discriminator[:type]
+              when 'patternCodeableConcept'
+                find_pattern_codeable_concept_slice(element, discriminator)
+              when 'patternCoding'
+                find_pattern_coding_slice(element, discriminator)
+              when 'patternIdentifier'
+                find_pattern_identifier_slice(element, discriminator)
+              when 'value'
+                find_value_slice(element, discriminator)
+              when 'type'
+                find_type_slice(element, discriminator)
+              when 'requiredBinding'
+                find_required_binding_slice(element, discriminator)
+              end
+            end
+          end
+
+          def find_pattern_codeable_concept_slice(element, discriminator)
+            coding_path = discriminator[:path].present? ? "#{discriminator[:path]}.coding" : 'coding'
+            find_a_value_at(element, coding_path) do |coding|
+              coding.code == discriminator[:code] && coding.system == discriminator[:system]
+            end
+          end
+
+          def find_pattern_coding_slice(element, discriminator)
+            coding_path = discriminator[:path].present? ? discriminator[:path] : ''
+            find_a_value_at(element, coding_path) do |coding|
+              coding.code == discriminator[:code] && coding.system == discriminator[:system]
+            end
+          end
+
+          def find_pattern_identifier_slice(element, discriminator)
+            find_a_value_at(element, discriminator[:path]) do |identifier|
+              identifier.system == discriminator[:system]
+            end
+          end
+
+          def find_value_slice(element, discriminator)
+            values = discriminator[:values].map { |value| value.merge(path: value[:path].split('.')) }
+            find_slice_by_values(element, values)
+          end
+
+          def find_type_slice(element, discriminator)
+            case discriminator[:code]
+            when 'Date'
+              begin
+                Date.parse(element)
+              rescue ArgumentError
+                false
+              end
+            when 'DateTime'
+              begin
+                DateTime.parse(element)
+              rescue ArgumentError
+                false
+              end
+            when 'String'
+              element.is_a? String
+            else
+              element.is_a? FHIR.const_get(discriminator[:code])
+            end
+          end
+
+          def find_required_binding_slice(element, discriminator)
+            coding_path = discriminator[:path].present? ? "#{discriminator[:path]}.coding" : 'coding'
+
+            find_a_value_at(element, coding_path) do |coding|
+              discriminator[:values].any? { |value| value[:system] == coding.system && value[:code] == coding.code }
+            end
+          end
+
+          def find_slice_by_values(element, value_definitions)
+            Array.wrap(element).find { |el| verify_slice_by_values(el, value_definitions) }
+          end
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/rules/all_references_resolve.rb

@@ -0,0 +1,53 @@
+# frozen_string_literal: true
+
+require_relative '../reference_extractor'
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module Rules
+        class AllReferencesResolve < Rule
+          def check(context)
+            extractor = Inferno::DSL::FHIREvaluation::ReferenceExtractor.new
+            resource_type_ids = extractor.extract_resource_type_ids(context.data)
+            resource_ids = Set.new(resource_type_ids.values.flatten.uniq)
+            reference_map = extractor.extract_references(context.data)
+
+            unresolved_references = Hash.new { |reference, id| reference[id] = [] }
+
+            reference_map.each do |resource_id, references|
+              references.each do |reference|
+                if reference[:type] == ''
+                  unresolved_references[resource_id] << reference unless resource_ids.include?(reference[:id])
+                elsif !resource_type_ids[reference[:type]].include?(reference[:id])
+                  unresolved_references[resource_id] << reference
+                end
+              end
+            end
+
+            if unresolved_references.any?
+              message = gen_reference_fail_message(unresolved_references)
+              result = EvaluationResult.new(message, rule: self)
+            else
+              message = 'All references resolve'
+              result = EvaluationResult.new(message, severity: 'success', rule: self)
+            end
+
+            context.add_result result
+          end
+
+          def gen_reference_fail_message(unresolved_references)
+            result_message = unresolved_references.map do |resource_id, references|
+              reference_detail = references.map do |reference|
+                " \n\tpath: #{reference[:path]}, type: #{reference[:type]}, id: #{reference[:id]}"
+              end.join(',')
+              "\n Resource (id): #{resource_id} #{reference_detail}"
+            end.join(',')
+
+            "Found unresolved references: #{result_message}"
+          end
+        end
+      end
+    end
+  end
+end

data/lib/inferno/dsl/fhir_evaluation/rules/all_resources_reachable.rb

@@ -0,0 +1,63 @@
+# frozen_string_literal: true
+
+require_relative '../reference_extractor'
+
+module Inferno
+  module DSL
+    module FHIREvaluation
+      module Rules
+        class AllResourcesReachable < Rule
+          attr_accessor :config, :referenced_resources, :referencing_resources, :resource_ids, :resource_type_ids
+
+          def check(context)
+            @config = context.config
+            @referenced_resources = Set.new
+            @referencing_resources = Set.new
+
+            extractor = Inferno::DSL::FHIREvaluation::ReferenceExtractor.new
+            @resource_type_ids = extractor.extract_resource_type_ids(context.data)
+            @resource_ids = Set.new(resource_type_ids.values.flatten.uniq)
+            reference_map = extractor.extract_references(context.data)
+
+            reference_map.each do |resource_id, references|
+              assess_reachability(resource_id, references)
+            end
+
+            island_resources = resource_ids - referenced_resources - referencing_resources
+            island_resources.to_a.sort!
+
+            if island_resources.any?
+              message = "Found resources that have no resolved references and are not referenced: #{
+                island_resources.join(', ')}"
+              result = EvaluationResult.new(message, rule: self)
+            else
+              message = 'All resources are reachable'
+              result = EvaluationResult.new(message, severity: 'success', rule: self)
+            end
+
+            context.add_result result
+          end
+
+          def assess_reachability(resource_id, references)
+            makes_resolvable_reference = false
+            references.each do |reference|
+              type = reference[:type]
+              referenced_id = reference[:id]
+
+              if type == ''
+                if resource_ids.include?(referenced_id)
+                  makes_resolvable_reference = true
+                  referenced_resources.add(referenced_id)
+                end
+              elsif resource_type_ids[type].include?(referenced_id)
+                makes_resolvable_reference = true
+                referenced_resources.add(referenced_id)
+              end
+            end
+            referencing_resources.add(resource_id) if makes_resolvable_reference
+          end
+        end
+      end
+    end
+  end
+end