us_quality_core_test_kit 0.1.1 → 0.2.0

data/lib/us_quality_core_test_kit/generator/document_reference_custodian_test_generator.rb

@@ -0,0 +1,68 @@
+# frozen_string_literal: true
+
+module USQualityCoreTestKit
+  class Generator
+    class DocumentReferenceCustodianTestGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          ig_metadata.groups
+                     .select { |group| group.resource == 'DocumentReference' }
+                     .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', 'document_reference_custodian_test.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 profile_identifier
+        Naming.snake_case_for_profile(group_metadata)
+      end
+
+      def test_id
+        "us_quality_core_#{group_metadata.reformatted_version}_#{profile_identifier}_custodian_test"
+      end
+
+      def class_name
+        "#{Naming.upper_camel_case_for_profile(group_metadata)}DocumentReferenceCustodianTest"
+      end
+
+      def module_name
+        "USQualityCore#{group_metadata.reformatted_version.upcase}"
+      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
+    end
+  end
+end

data/lib/us_quality_core_test_kit/generator/group_generator.rb

@@ -1,13 +1,11 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/group_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class GroupGenerator < USCoreTestKit::Generator::GroupGenerator
+    class GroupGenerator
       class << self
         def generate(ig_metadata, base_output_dir)
           ig_metadata.ordered_groups
@@ -16,10 +14,29 @@ module USQualityCoreTestKit
         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', 'group.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 base_metadata_file_name
+        'metadata.yml'
+      end
+
       def class_name
         "#{Naming.upper_camel_case_for_profile(group_metadata)}Group"
       end
@@ -28,6 +45,22 @@ module USQualityCoreTestKit
         "USQualityCore#{group_metadata.reformatted_version.upcase}"
       end
 
+      def title
+        group_metadata.title
+      end
+
+      def short_description
+        group_metadata.short_description
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def metadata_file_name
+        File.join(base_output_dir, profile_identifier, base_metadata_file_name)
+      end
+
       def profile_identifier
         Naming.snake_case_for_profile(group_metadata)
       end
@@ -36,16 +69,49 @@ module USQualityCoreTestKit
         "us_quality_core_#{group_metadata.reformatted_version}_#{profile_identifier}"
       end
 
+      def resource_type
+        group_metadata.resource
+      end
+
       def search_validation_resource_type
         "#{resource_type} resources"
       end
 
+      def profile_name
+        group_metadata.profile_name
+      end
+
+      def profile_url
+        group_metadata.profile_url
+      end
+
       def optional?
         SpecialCases::OPTIONAL_RESOURCES.include?(resource_type) || group_metadata.optional_profile?
       end
 
+      def generate
+        add_special_tests
+        File.write(output_file_name, output)
+        group_metadata.id = group_id
+        group_metadata.file_name = base_output_file_name
+        File.write(metadata_file_name, YAML.dump(group_metadata.to_hash))
+      end
+
       def add_special_tests; end
 
+      def test_id_list
+        @test_id_list ||=
+          group_metadata.tests.map { |test| test[:id] }
+      end
+
+      def test_file_list
+        @test_file_list ||=
+          group_metadata.tests.map do |test|
+            name_without_suffix = test[:file_name].delete_suffix('.rb')
+            name_without_suffix.start_with?('..') ? name_without_suffix : "#{profile_identifier}/#{name_without_suffix}"
+          end
+      end
+
       def required_searches
         group_metadata.searches.select { |search| search[:expectation] == 'SHALL' }
       end
@@ -77,7 +143,7 @@ module USQualityCoreTestKit
 
           ## Profile Validation
           Each resource returned from the first search is expected to conform to
-          the [#{profile_name} Profile](#{profile_url}). Each element is checked against
+          the [#{profile_name}](#{profile_url}). Each element is checked against
           teminology binding and cardinality requirements.
 
           Elements with a required binding are validated against their bound

data/lib/us_quality_core_test_kit/generator/group_metadata.rb

@@ -2,14 +2,110 @@
 
 require_relative 'special_cases'
 
-require 'us_core_test_kit/generator/group_metadata'
-
 module USQualityCoreTestKit
   class Generator
-    class GroupMetadata < USCoreTestKit::Generator::GroupMetadata
+    class GroupMetadata
+      ATTRIBUTES = %i[
+        name
+        class_name
+        version
+        reformatted_version
+        resource
+        profile_url
+        profile_name
+        profile_version
+        title
+        short_description
+        is_delayed
+        interactions
+        operations
+        searches
+        search_definitions
+        include_params
+        revincludes
+        required_concepts
+        must_supports
+        mandatory_elements
+        bindings
+        references
+        tests
+        granular_scope_tests
+        id
+        file_name
+        delayed_references
+        resource_conformance_expectation
+      ].freeze
+
+      ATTRIBUTES.each { |name| attr_accessor name }
+
+      def initialize(metadata)
+        metadata.each do |key, value|
+          raise "Unknown attribute #{key}" unless ATTRIBUTES.include? key
+
+          instance_variable_set(:"@#{key}", value)
+        end
+      end
+
+      def exclude_search_tests?
+        delayed? && !searchable_delayed_resource?
+      end
+
+      def non_uscdi_resource?
+        SpecialCases::NON_USCDI_RESOURCES.key?(resource) && SpecialCases::NON_USCDI_RESOURCES[resource].include?(reformatted_version)
+      end
+
+      def optional_profile?
+        SpecialCases::OPTIONAL_PROFILES.key?(profile_url) && SpecialCases::OPTIONAL_PROFILES[profile_url].include?(reformatted_version)
+      end
+
+      def searchable_delayed_resource?
+        SpecialCases::SEARCHABLE_DELAYED_RESOURCES.key?(resource) && SpecialCases::SEARCHABLE_DELAYED_RESOURCES[resource].include?(reformatted_version)
+      end
+
+      def add_test(id:, file_name:)
+        self.tests ||= []
+
+        test_metadata = {
+          id: id,
+          file_name: file_name
+        }
+
+        if delayed? && id.include?('read')
+          self.tests.unshift(test_metadata)
+        else
+          self.tests << test_metadata
+        end
+      end
+
+      def add_granular_scope_test(id:, file_name:)
+        self.granular_scope_tests ||= []
+
+        self.granular_scope_tests << {
+          id:,
+          file_name:
+        }
+      end
+
+      def to_hash
+        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) unless send(key).nil? }
+      end
+
+      def add_delayed_references(delayed_profiles, ig_resources)
+        self.delayed_references =
+          references
+          .select { |reference| (reference[:profiles] & delayed_profiles).present? }
+          .map do |reference|
+            profile_urls = (reference[:profiles] & delayed_profiles)
+            delayed_resources = profile_urls.map { |url| ig_resources.resource_for_profile(url) }
+            {
+              path: reference[:path].gsub("#{resource}.", ''),
+              resources: delayed_resources
+            }
+          end
+      end
+
       def delayed?
         # rubocop:disable Naming/MemoizedInstanceVariableName
-        # @is_delayed is used in USCoreTestKit::Generator::GroupMetadata
         @is_delayed ||= if resource == 'Patient'
                           false
                         else

data/lib/us_quality_core_test_kit/generator/group_metadata_extractor.rb

@@ -1,19 +1,198 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/group_metadata_extractor'
-
 require_relative 'group_metadata'
-require_relative 'special_cases'
-require_relative 'naming'
+require_relative 'ig_metadata'
+require_relative 'must_support_metadata_extractor'
 require_relative 'search_metadata_extractor'
 require_relative 'terminology_binding_metadata_extractor'
-require_relative 'must_support_metadata_extractor'
-
-require_relative 'ig_metadata'
+require_relative 'naming'
+require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class GroupMetadataExtractor < USCoreTestKit::Generator::GroupMetadataExtractor
+    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_hash
+        @group_metadata_hash ||=
+          {
+            name: name,
+            class_name: class_name,
+            version: version,
+            reformatted_version: reformatted_version,
+            resource: resource,
+            profile_url: profile_url,
+            profile_name: profile_name,
+            profile_version: profile_version,
+            title: title,
+            short_description: short_description,
+            interactions: interactions,
+            operations: operations,
+            searches: searches,
+            search_definitions: search_definitions,
+            include_params: include_params,
+            revincludes: revincludes,
+            required_concepts: required_concepts,
+            must_supports: must_supports,
+            mandatory_elements: mandatory_elements,
+            bindings: bindings,
+            references: references,
+            resource_conformance_expectation: resource_conformance_expectation
+          }
+
+        mark_mandatory_and_must_support_searches
+        handle_special_cases
+
+        @group_metadata_hash
+      end
+
+      ### BEGIN SPECIAL CASES ###
+
+      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 version
+        ig_metadata.ig_version
+      end
+
+      def reformatted_version
+        ig_metadata.reformatted_version
+      end
+
+      def resource
+        resource_capabilities.type
+      end
+
+      def profile_name
+        profile_name = profile.title.gsub('  ', ' ')
+        # This covers both US Core title style: "US Core Patient Profile" and
+        # US Quality Core title style: "US Quality Core Patient"
+        profile_name.end_with?(' Profile') ? profile_name : "#{profile_name} Profile"
+      end
+
+      def profile_version
+        profile.version
+      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 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 bindings
+        @bindings ||=
+          terminology_binding_metadata_extractor.terminology_bindings
+      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
+
+      def resource_conformance_expectation
+        @resource_conformance_expectation ||=
+          resource_capabilities.extension.find do |extension|
+            extension.url == 'http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation'
+          end&.valueCode
+      end
+
       def group_metadata
         @group_metadata ||=
           GroupMetadata.new(group_metadata_hash)
@@ -24,6 +203,10 @@ module USQualityCoreTestKit
           SpecialCases::VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES[profile_url]&.include?(reformatted_version)
       end
 
+      def do_not_perform_profile?
+        SpecialCases::DO_NOT_PERFORM_PROFILES.include?(profile_url)
+      end
+
       def first_search_params
         @first_search_params ||=
           if category_first_profile?
@@ -35,11 +218,13 @@ module USQualityCoreTestKit
               %w[patient code]
             end
           elsif resource == 'MedicationRequest'
-            %w[patient intent do-not-perform]
-          elsif %w[DeviceRequest ServiceRequest].include?(resource)
+            do_not_perform_profile? ? %w[patient intent do-not-perform] : %w[patient intent]
+          elsif do_not_perform_profile?
             %w[patient do-not-perform]
           elsif %w[CareTeam Immunization MedicationAdministration MedicationDispense Procedure Task].include?(resource)
             %w[patient status]
+          elsif resource == 'Communication'
+            %w[subject status]
           else
             ['patient']
           end
@@ -69,6 +254,10 @@ module USQualityCoreTestKit
       def mark_mandatory_and_must_support_searches
         searches.each do |search|
           search[:names_not_must_support_or_mandatory] = search[:names].reject do |name|
+            # Treat the ServiceRequest do-not-perform search parameter as required. See:
+            # https://github.com/onc-healthit/us-quality-core/issues/39
+            next true if resource == 'ServiceRequest' && name == 'do-not-perform'
+
             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]}"]
@@ -96,7 +285,9 @@ module USQualityCoreTestKit
             end
 
             any_mandatory_elements = mandatory_elements.any? do |element|
-              full_paths.include?(element)
+              full_paths.any? do |path|
+                mandatory_element_matches_search_path?(element, path)
+              end
             end
 
             any_must_support_elements || any_must_support_slices || any_mandatory_elements
@@ -106,6 +297,19 @@ module USQualityCoreTestKit
         end
       end
 
+      def mandatory_element_matches_search_path?(element, path)
+        # Extension search parameters identify an extension with a FHIRPath
+        # filter (for example, `modifierExtension.where(url='...').value`),
+        # while the snapshot records the mandatory value as
+        # `modifierExtension.value[x]`. Remove the filter and normalize choice
+        # elements before comparing the paths.
+        normalized_path = path.gsub(/\.where\(url\s*=\s*'[^']+'\)/, '').gsub('[x]', '')
+        normalized_element = element.gsub('[x]', '')
+
+        normalized_path == normalized_element ||
+          (element.end_with?('[x]') && normalized_path.start_with?(normalized_element))
+      end
+
       def search_metadata_extractor
         @search_metadata_extractor ||= SearchMetadataExtractor.new(
           resource_capabilities,

data/lib/us_quality_core_test_kit/generator/ig_loader.rb

@@ -1,12 +1,56 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/ig_loader'
-
+require 'active_support/all'
+require 'fhir_models'
+require 'pathname'
+require 'rubygems/package'
+require 'zlib'
 require_relative 'ig_resources'
 
 module USQualityCoreTestKit
   class Generator
-    class IGLoader < USCoreTestKit::Generator::IGLoader
+    class IGLoader
+      attr_accessor :ig_file_name
+
+      def initialize(ig_file_name)
+        self.ig_file_name = ig_file_name
+      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
+
+        ig_resources
+      end
+
       def ig_resources
         @ig_resources ||= IGResources.new
       end

data/lib/us_quality_core_test_kit/generator/ig_metadata.rb

@@ -1,11 +1,60 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/ig_metadata'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class IGMetadata < USCoreTestKit::Generator::IGMetadata
+    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 postprocess_groups(ig_resources)
+        groups.each do |group|
+          group.add_delayed_references(delayed_profiles, ig_resources)
+        end
+      end
+
+      def granular_scope_resource_type_groups
+        @granular_scope_resource_type_groups ||=
+          Hash.new { |hash, key| hash[key] = [] }
+      end
+
+      def granular_scope_groups
+        @granular_scope_groups ||= []
+      end
+
+      def to_hash
+        {
+          ig_version:,
+          groups: groups.map(&:to_hash),
+          granular_scope_resource_type_groups:,
+          granular_scope_groups:
+        }
+      end
+
       def delayed_profiles
         @delayed_profiles ||=
           delayed_groups.reject { |group| SpecialCases.exclude_group?(group) }.map(&:profile_url)