us_quality_core_test_kit 0.1.0 → 0.1.2

data/lib/us_quality_core_test_kit/generator/read_test_generator.rb

@@ -1,13 +1,64 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/read_test_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class ReadTestGenerator < USCoreTestKit::Generator::ReadTestGenerator
+    class ReadTestGenerator
+      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 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 resource_type
+        group_metadata.resource
+      end
+
+      def resource_collection_string
+        if group_metadata.delayed? && resource_type != 'Provenance'
+          "scratch.dig(:references, '#{resource_type}'), delayed_reference: true"
+        else
+          'all_scratch_resources'
+        end
+      end
+
+      def conformance_expectation
+        read_interaction[:expectation]
+      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
+
       class << self
         def generate(ig_metadata, base_output_dir)
           ig_metadata.groups

data/lib/us_quality_core_test_kit/generator/reference_resolution_test_generator.rb

@@ -1,13 +1,67 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/reference_resolution_test_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class ReferenceResolutionTestGenerator < USCoreTestKit::Generator::ReferenceResolutionTestGenerator
+    class ReferenceResolutionTestGenerator
+      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 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 resource_type
+        group_metadata.resource
+      end
+
+      def resource_collection_string
+        'scratch_resources[:all]'
+      end
+
+      def must_support_references
+        group_metadata.must_supports[:elements]
+                      .select { |element| element[:types]&.include?('Reference') }
+      end
+
+      def must_support_reference_list_string
+        must_support_references
+          .map { |element| "#{' ' * 8}* #{resource_type}.#{element[:path]}" }
+          .uniq
+          .sort
+          .join("\n")
+      end
+
+      def generate
+        return if must_support_references.empty?
+
+        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
+
       class << self
         def generate(ig_metadata, base_output_dir)
           ig_metadata.groups

data/lib/us_quality_core_test_kit/generator/search_definition_metadata_extractor.rb

@@ -1,13 +1,183 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/search_definition_metadata_extractor'
-
-require_relative 'special_cases'
 require_relative 'value_extractor'
+require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class SearchDefinitionMetadataExtractor < USCoreTestKit::Generator::SearchDefinitionMetadataExtractor
+    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\((.*)/, '').gsub('url = \'', 'url=\'')
+            path = path[1..-2] if path.start_with?('(') && path.end_with?(')')
+            path.scan(/[. ]as[( ]([^)]*)[)]?/).flatten.map do |as_type|
+              path.gsub!(/[. ]as[( ](#{as_type}[^)]*)[)]?/, as_type.upcase_first) if as_type.present?
+            end
+
+            path.gsub!('Resource.', "#{resource}.") if path.start_with?('Resource.')
+
+            full_paths = path.split('|')
+
+            full_paths
+          end
+      end
+
+      def remove_additional_extension_from_asserted_date(full_paths)
+        full_paths.each do |full_path|
+          next unless full_path.include?('http://hl7.org/fhir/StructureDefinition/condition-assertedDate')
+
+          full_path.gsub!(/\).extension./, ').')
+        end
+      end
+
+      def 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 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_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_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
+
       EXTENSION_URL_REGEX = /(?:modifierExtension|extension)\.where\(url='([^']+)'\)/
       EXTENSION_VALUE_PATH_REGEX = /\.(?:value(?:[A-Z]\w*|\[x\])?)\z/
 
@@ -71,10 +241,16 @@ module USQualityCoreTestKit
         category_search = paths.any? { |path| path.split('.').first == 'category' }
         fixed_boolean = profile_element.fixedBoolean if profile_element.respond_to?(:fixedBoolean)
         fixed_boolean_value = [fixed_boolean.to_s] unless fixed_boolean.nil?
+        base_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 ||
+          []
 
         fixed_boolean_value.presence ||
           (SpecialCases::PROFILE_CATEGORY_SEARCH_VALUES[group_metadata[:profile_url]] if category_search).presence ||
-          super.presence ||
+          base_values.presence ||
           (value_extractor.codes_from_system_code_pair(value_extractor.values_from_resource_metadata(paths)) if category_search).presence ||
           []
       end

data/lib/us_quality_core_test_kit/generator/search_metadata_extractor.rb

@@ -1,12 +1,70 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/search_metadata_extractor'
-
 require_relative 'search_definition_metadata_extractor'
 
 module USQualityCoreTestKit
   class Generator
-    class SearchMetadataExtractor < USCoreTestKit::Generator::SearchMetadataExtractor
+    class SearchMetadataExtractor
+      COMBO_EXTENSION_URL =
+        'http://hl7.org/fhir/StructureDefinition/capabilitystatement-search-parameter-combination'
+
+      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 { |search_param| %w[SHALL SHOULD].include? conformance_expectation(search_param) }
+                             .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] =

data/lib/us_quality_core_test_kit/generator/search_test_generator.rb

@@ -1,13 +1,196 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/search_test_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class SearchTestGenerator < USCoreTestKit::Generator::SearchTestGenerator
+    class SearchTestGenerator
+      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 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 search_identifier
+        search_metadata[:names].join('_').tr('-', '_')
+      end
+
+      def search_title
+        search_identifier.camelize
+      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_param_name
+        (search_metadata[:names] - [:patient]).first
+      end
+
+      def search_param_name_string
+        search_metadata[:names].join(' + ')
+      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
+        @required_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_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?
+          properties[:multiple_or_search_params] = required_multiple_or_search_params_string if required_multiple_or_search_params.present?
+          properties[:test_post_search] = 'true' if first_search?
+        end
+      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 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
+
       class << self
         def generate(ig_metadata, base_output_dir)
           ig_metadata.groups

data/lib/us_quality_core_test_kit/generator/suite_generator.rb

@@ -1,20 +1,47 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/suite_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class SuiteGenerator < USCoreTestKit::Generator::SuiteGenerator
+    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 output
+        @output ||= ERB.new(template, trim_mode: '-').result(binding)
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def generate
+        File.write(output_file_name, output)
+      end
+
+      def group_file_list
+        @group_file_list ||=
+          groups.map { |group| group.file_name.delete_suffix('.rb') }
+      end
+
       def version_specific_message_filters
         [
-          # Patient validation warnings suppressed for US Core extensions because
-          # validator tries to validate against different US Core version than we require
-          %r{Patient.*Patient\.extension\[\d+\]\[url='http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)\|\d+\.\d+(?:\.\d+)?'\]:\s*The extension URL must not contain a version\.},
-          %r{Patient.*Patient\.extension\[\d+\]\.url:\s*Value is 'http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)\|\d+\.\d+(?:\.\d+)?'\s*but is fixed to 'http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)'\s*in the profile http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)\|\d+\.\d+(?:\.\d+)?#Extension\.url},
-          # This extension is correct but is not yet correctly passing in the validator
+          # Patient extension messages are suppressed because the CQL package can load US Core 7 into
+          # the validator session while US Quality Core 0.5.0 uses US Core 6.1.0.
+          /\bPatient\.extension/,
+          # This extension is correct but is not yet correctly passing in the validator.
           %r{DeviceRequest.*DeviceRequest\.modifierExtension\[\d+\]:\s*Slicing cannot be evaluated:\s*Unable to resolve profile CanonicalType\[http://hl7\.org/fhir/5\.0/StructureDefinition/extension-DeviceRequest\.doNotPerform\]}
         ]
       end