pacio_inferno_core 0.1.0

data/lib/pacio_inferno_core/generator/search_definition_metadata_extractor.rb

@@ -0,0 +1,228 @@
+require_relative 'value_extractor'
+
+module PacioInfernoCore
+  class Generator
+    class SearchDefinitionMetadataExtractor
+      attr_accessor :ig_resources, :name, :profile_elements, :group_metadata
+
+      def initialize(name, ig_resources, profile_elements, group_metadata)
+        self.name = name
+        self.ig_resources = ig_resources
+        self.profile_elements = profile_elements
+        self.group_metadata = group_metadata
+      end
+
+      def search_definition
+        @search_definition ||=
+          {
+            paths: paths,
+            full_paths: full_paths,
+            comparators: comparators,
+            values: values,
+            type: type,
+            contains_multiple: contains_multiple?,
+            multiple_or: multiple_or_expectation,
+            chain: chain
+          }.compact
+      end
+
+      def resource
+        group_metadata[:resource]
+      end
+
+      def param
+        @param ||= ig_resources.search_param_by_resource_and_name(resource, name)
+      end
+
+      def param_hash
+        param.source_hash
+      end
+
+      def full_paths
+        @full_paths ||=
+          begin
+            path = param.expression.gsub(/.where\(resolve\((.*)/, '').gsub('url = \'', 'url=\'')
+            path = path[1..-2] if path.start_with?('(') && path.end_with?(')')
+            path.scan(/[. ]as[( ]([^)]*)[)]?/).flatten.map do |as_type|
+              path.gsub!(/[. ]as[( ](#{as_type}[^)]*)[)]?/, as_type.upcase_first) if as_type.present?
+            end
+
+            path.gsub!('Resource.', "#{resource}.") if path.start_with?('Resource.')
+
+            full_paths = path.split('|')
+
+            # There is a bug in US Core 5 asserted-date search parameter. See FHIR-40573
+            if param.respond_to?(:version) && param.version == '5.0.1' && name == 'asserted-date'
+              remove_additional_extension_from_asserted_date(full_paths)
+            end
+
+            full_paths
+          end
+      end
+
+      def remove_additional_extension_from_asserted_date(full_paths)
+        full_paths.each do |full_path|
+          next unless full_path.include?('http://hl7.org/fhir/StructureDefinition/condition-assertedDate')
+
+          full_path.gsub!(/\).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) } ||
+          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
+        @comparator_expectation_extensions ||= param_hash['_comparator'] || []
+      end
+
+      def support_expectation(extension)
+        extension['extension'].first['valueCode']
+      end
+
+      def comparator_expectation(extension)
+        if extension.nil?
+          'MAY'
+        else
+          support_expectation(extension)
+        end
+      end
+
+      def comparators
+        {}.tap do |comparators|
+          param.comparator&.each_with_index do |comparator, index|
+            comparators[comparator.to_sym] = comparator_expectation(comparator_expectation_extensions[index])
+          end
+        end
+      end
+
+      def type
+        if profile_element.present?
+          profile_element.type.first.code
+        else
+          # search is a variable type, eg. Condition.onsetDateTime - element
+          # in profile def is Condition.onset[x]
+          param.type
+        end
+      end
+
+      def contains_multiple?
+        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
+        param_hash['_chain']
+      end
+
+      def chain_expectations
+        chain_extensions.map { |extension| support_expectation(extension) }
+      end
+
+      def chain
+        return nil if param.chain.blank?
+
+        param.chain
+          .zip(chain_expectations)
+          .map { |chain, expectation| { chain: chain, expectation: expectation } }
+      end
+
+      def multiple_or_expectation
+        param_hash['_multipleOr'] ? param_hash['_multipleOr']['extension'].first['valueCode'] : 'MAY'
+      end
+
+      def values
+        values_from_must_supports(profile_element).presence ||
+          value_extractor.values_from_fixed_codes(profile_element, type).presence ||
+          value_extractor.codes_from_value_set_binding(profile_element).presence ||
+          values_from_resource_metadata(paths).presence ||
+          []
+      end
+
+      def values_from_must_supports(profile_element)
+        return if profile_element.nil?
+
+        short_path = profile_element.path.split('.', 2)[1]
+
+        values_from_must_support_slices(profile_element, short_path, true).presence ||
+          values_from_must_support_slices(profile_element, short_path, false).presence ||
+          values_from_must_support_elements(short_path).presence ||
+          []
+      end
+
+      def values_from_must_support_slices(profile_element, short_path, mandatory_slice_only)
+        group_metadata[:must_supports][:slices]
+          .select { |slice| [short_path, "#{short_path}.coding"].include?(slice[:path]) }
+          .map do |slice|
+            slice_element = profile_elements.find { |element| slice[:slice_id] == element.id }
+            next if profile_element.min.positive? && slice_element.min.zero? && mandatory_slice_only
+
+            case slice[:discriminator][:type]
+            when 'patternCoding', 'patternCodeableConcept'
+              slice[:discriminator][:code]
+            when 'requiredBinding'
+              value_extractor.codes_from_system_code_pair(slice[:discriminator][:values])
+            when 'value'
+              slice[:discriminator][:values]
+                .select { |value| value[:path] == 'coding.code' }
+                .map { |value| value[:value] }
+            end
+          end
+          .compact.flatten
+      end
+
+      def values_from_must_support_elements(short_path)
+        group_metadata[:must_supports][:elements]
+          .select { |element| element[:path] == "#{short_path}.coding.code" }
+          .map { |element| element[:fixed_value] }
+      end
+
+      def values_from_resource_metadata(paths)
+        if multiple_or_expectation == 'SHALL' || paths.any? { |path| path.downcase.include?('status') }
+          value_extractor.codes_from_system_code_pair(value_extractor.values_from_resource_metadata(paths))
+        else
+          []
+        end
+      end
+
+      def value_extractor
+        @value_extractor ||= ValueExactor.new(ig_resources, resource, profile_elements)
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/search_metadata_extractor.rb

@@ -0,0 +1,78 @@
+require_relative 'search_definition_metadata_extractor'
+
+module PacioInfernoCore
+  class Generator
+    class SearchMetadataExtractor
+      COMBO_EXTENSION_URL =
+        'http://hl7.org/fhir/StructureDefinition/capabilitystatement-search-parameter-combination'.freeze
+
+      attr_accessor :resource_capabilities, :ig_resources, :profile_elements, :group_metadata
+
+      def initialize(resource_capabilities, ig_resources, profile_elements, group_metadata)
+        self.resource_capabilities = resource_capabilities
+        self.ig_resources = ig_resources
+        self.profile_elements = profile_elements
+        self.group_metadata = group_metadata
+      end
+
+      def searches
+        @searches ||= basic_searches + combo_searches
+      end
+
+      def conformance_expectation(search_param)
+        search_param.extension.first.valueCode # TODO: fix expectation extension finding
+      end
+
+      def no_search_params?
+        resource_capabilities.searchParam.blank?
+      end
+
+      def basic_searches
+        return [] if no_search_params?
+
+        resource_capabilities.searchParam
+          .select do |search_param|
+          %w[SHALL
+             SHOULD].include? conformance_expectation(search_param)
+        end
+          .map do |search_param|
+            {
+              names: [search_param.name],
+              expectation: conformance_expectation(search_param)
+            }
+          end
+      end
+
+      def search_extensions
+        resource_capabilities.extension
+      end
+
+      def combo_searches
+        return [] if search_extensions.blank?
+
+        search_extensions
+          .select { |extension| extension.url == COMBO_EXTENSION_URL }
+          .select { |extension| %w[SHALL SHOULD].include? conformance_expectation(extension) }
+          .map do |extension|
+            names = extension.extension.select { |param| param.valueString.present? }.map(&:valueString)
+            {
+              expectation: conformance_expectation(extension),
+              names: names
+            }
+          end
+      end
+
+      def search_param_names
+        searches.flat_map { |search| search[:names] }.uniq
+      end
+
+      def search_definitions
+        search_param_names.each_with_object({}) do |name, definitions|
+          definitions[name.to_sym] =
+            SearchDefinitionMetadataExtractor.new(name, ig_resources, profile_elements,
+                                                  group_metadata).search_definition
+        end
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/search_test_generator.rb

@@ -0,0 +1,298 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module PacioInfernoCore
+  class Generator
+    class SearchTestGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          ig_metadata.groups
+            .reject { |group| SpecialCases.exclude_group? group }
+            .select { |group| group.searches.present? }
+            .each do |group|
+              group.searches.each do |search|
+                new(group, search, base_output_dir).generate
+              end
+            end
+        end
+      end
+
+      attr_accessor :group_metadata, :search_metadata, :base_output_dir
+
+      def initialize(group_metadata, search_metadata, base_output_dir)
+        self.group_metadata = group_metadata
+        self.search_metadata = search_metadata
+        self.base_output_dir = base_output_dir
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'search.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template, trim_mode: '-').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 naming
+        self.class.module_parent::Naming
+      end
+
+      def profile_identifier
+        naming.snake_case_for_profile(group_metadata)
+      end
+
+      def test_id
+        "#{naming.prefix}_#{group_metadata.reformatted_version}_#{profile_identifier}_#{search_identifier}_search_test"
+      end
+
+      def search_identifier
+        search_metadata[:names].join('_').tr('-', '_')
+      end
+
+      def search_title
+        search_identifier.camelize
+      end
+
+      def class_name
+        "#{naming.upper_camel_case_for_profile(group_metadata)}#{search_title}SearchTest"
+      end
+
+      def module_name_with_version
+        "#{naming.module_name}#{group_metadata.reformatted_version.upcase}"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def conformance_expectation
+        search_metadata[:expectation]
+      end
+
+      def search_params
+        @search_params ||=
+          search_metadata[:names].map do |name|
+            {
+              name: name,
+              path: search_definition(name)[:path]
+            }
+          end
+      end
+
+      def first_search?
+        group_metadata.searches.first == search_metadata
+      end
+
+      def fixed_value_search?
+        first_search? && search_metadata[:names] != ['patient'] &&
+          !group_metadata.delayed? && resource_type != 'Patient'
+      end
+
+      def fixed_value_search_param_name
+        (search_metadata[:names] - [:patient]).first
+      end
+
+      def search_param_name_string
+        search_metadata[:names].join(' + ')
+      end
+
+      def needs_patient_id?
+        search_metadata[:names].include?('patient') ||
+          (resource_type == 'Patient' && search_metadata[:names].include?('_id'))
+      end
+
+      def search_param_names
+        search_params.map { |param| param[:name] }
+      end
+
+      def search_param_names_array
+        array_of_strings(search_param_names)
+      end
+
+      def path_for_value(path)
+        path == 'class' ? 'local_class' : path
+      end
+
+      def required_comparators_for_param(name)
+        search_definition(name)[:comparators].select { |_comparator, expectation| expectation == 'SHALL' }
+      end
+
+      def required_comparators
+        @required_comparators ||=
+          search_param_names.each_with_object({}) do |name, comparators|
+            required_comparators = required_comparators_for_param(name)
+            comparators[name] = required_comparators if required_comparators.present?
+          end
+      end
+
+      def optional?
+        conformance_expectation != 'SHALL' || !search_metadata[:must_support_or_mandatory]
+      end
+
+      def search_definition(name)
+        group_metadata.search_definitions[name.to_sym]
+      end
+
+      def saves_delayed_references?
+        first_search? && group_metadata.delayed_references.present?
+      end
+
+      def possible_status_search?
+        search_metadata[:names].none? { |name| name.include? 'status' } &&
+          group_metadata.search_definitions.keys.any? { |key| key.to_s.include? 'status' }
+      end
+
+      def token_search_params
+        @token_search_params ||=
+          search_param_names.select do |name|
+            %w[Identifier CodeableConcept Coding].include? group_metadata.search_definitions[name.to_sym][:type]
+          end
+      end
+
+      def token_search_params_string
+        array_of_strings(token_search_params)
+      end
+
+      def required_multiple_or_search_params
+        @multiple_or_search_params ||=
+          search_param_names.select do |name|
+            search_definition(name)[:multiple_or] == 'SHALL'
+          end
+      end
+
+      def required_multiple_or_search_params_string
+        array_of_strings(required_multiple_or_search_params)
+      end
+
+      def required_comparators_string
+        array_of_strings(required_comparators.keys)
+      end
+
+      def array_of_strings(array)
+        quoted_strings = array.map { |element| "'#{element}'" }
+        "[#{quoted_strings.join(', ')}]"
+      end
+
+      def test_reference_variants?
+        first_search? && search_param_names.include?('patient')
+      end
+
+      def test_medication_inclusion?
+        %w[MedicationRequest MedicationDispense].include?(resource_type)
+      end
+
+      def test_post_search?
+        first_search?
+      end
+
+      def search_properties
+        {}.tap do |properties|
+          properties[:first_search] = 'true' if first_search?
+          properties[:fixed_value_search] = 'true' if fixed_value_search?
+          properties[:resource_type] = "'#{resource_type}'"
+          properties[:search_param_names] = search_param_names_array
+          properties[:saves_delayed_references] = 'true' if saves_delayed_references?
+          properties[:possible_status_search] = 'true' if possible_status_search?
+          properties[:test_medication_inclusion] = 'true' if test_medication_inclusion?
+          properties[:token_search_params] = token_search_params_string if token_search_params.present?
+          properties[:test_reference_variants] = 'true' if test_reference_variants?
+          properties[:params_with_comparators] = required_comparators_string if required_comparators.present?
+          if required_multiple_or_search_params.present?
+            properties[:multiple_or_search_params] =
+              required_multiple_or_search_params_string
+          end
+          properties[:test_post_search] = 'true' if first_search?
+        end
+      end
+
+      def ig_link
+        Naming.ig_link(group_metadata.version)
+      end
+
+      def search_test_properties_string
+        search_properties
+          .map { |key, value| "#{' ' * 8}#{key}: #{value}" }
+          .join(",\n")
+      end
+
+      def generate
+        FileUtils.mkdir_p(output_file_directory)
+        File.write(output_file_name, output)
+
+        group_metadata.add_test(
+          id: test_id,
+          file_name: base_output_file_name
+        )
+      end
+
+      def reference_search_description
+        return '' unless test_reference_variants?
+
+        <<~REFERENCE_SEARCH_DESCRIPTION
+          This test verifies that the server supports searching by reference using
+          the form `patient=[id]` as well as `patient=Patient/[id]`. The two
+          different forms are expected to return the same number of results. US
+          Core requires that both forms are supported by US Core responders.
+        REFERENCE_SEARCH_DESCRIPTION
+      end
+
+      def first_search_description
+        return '' unless first_search?
+
+        <<~FIRST_SEARCH_DESCRIPTION
+          Because this is the first search of the sequence, resources in the
+          response will be used for subsequent tests.
+        FIRST_SEARCH_DESCRIPTION
+      end
+
+      def medication_inclusion_description
+        return '' unless test_medication_inclusion?
+
+        <<~MEDICATION_INCLUSION_DESCRIPTION
+          If any #{resource_type} resources use external references to
+          Medications, the search will be repeated with
+          `_include=#{resource_type}:medication`.
+        MEDICATION_INCLUSION_DESCRIPTION
+      end
+
+      def post_search_description
+        return '' unless test_post_search?
+
+        <<~POST_SEARCH_DESCRIPTION
+          Additionally, this test will check that GET and POST search methods
+          return the same number of results. Search by POST is required by the
+          FHIR R4 specification, and these tests interpret search by GET as a
+          requirement of US Core #{group_metadata.version}.
+        POST_SEARCH_DESCRIPTION
+      end
+
+      def description
+        <<~DESCRIPTION.gsub(/\n{3,}/, "\n\n")
+          A server #{conformance_expectation} support searching by
+          #{search_param_name_string} on the #{resource_type} resource. This test
+          will pass if resources are returned and match the search criteria. If
+          none are returned, the test is skipped.
+
+          #{medication_inclusion_description}
+          #{reference_search_description}
+          #{first_search_description}
+          #{post_search_description}
+
+          [US Core Server CapabilityStatement](#{ig_link}/CapabilityStatement-us-core-server.html)
+        DESCRIPTION
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/special_cases.rb

@@ -0,0 +1,61 @@
+module PacioInfernoCore
+  class Generator
+    module SpecialCases
+      # These resources are excluded from US Core Test Suite
+      RESOURCES_TO_EXCLUDE = {
+        'Location' => %w[v311 v400 v501 v610],
+        'Medication' => %w[v311 v400 v501 v610 v700 v800],
+        'PractitionerRole' => %w[v311 v400]
+      }.freeze
+
+      # These profiles are excluded from US Core Test Suite
+      PROFILES_TO_EXCLUDE = [
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs'
+      ].freeze
+
+      OPTIONAL_RESOURCES = %w[
+        PractitionerRole
+        QuestionnaireResponse
+      ].freeze
+
+      OPTIONAL_PROFILES = {
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation' => %w[v610 v700]
+      }.freeze
+
+      # These resources relies on references from other resources but they also have mandatory search tests.
+      SEARCHABLE_DELAYED_RESOURCES = {
+        'Location' => %w[v700 v800]
+      }.freeze
+
+      ALL_VERSION_CATEGORY_FIRST_PROFILES = [
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-screening-assessment',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-sdoh-assessment',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation'
+      ].freeze
+
+      VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES = {
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis' => %w[v610 v700
+                                                                                                      v800],
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-problems-health-concerns' => %w[v610
+                                                                                                           v700 v800]
+      }.freeze
+
+      class << self
+        def exclude_group?(group)
+          RESOURCES_TO_EXCLUDE.key?(group.resource) &&
+            RESOURCES_TO_EXCLUDE[group.resource].include?(group.reformatted_version)
+        end
+      end
+    end
+  end
+end