us_core_test_kit 0.1.0

data/lib/us_core_test_kit/generator/search_test_generator.rb

@@ -0,0 +1,280 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module USCoreTestKit
+  class Generator
+    class SearchTestGenerator
+      class << self
+        def generate(ig_metadata)
+          ig_metadata.groups
+            .reject { |group| SpecialCases.exclude_resource? group.resource }
+            .select { |group| group.searches.present? }
+            .each do |group|
+              group.searches.each { |search| new(group, search).generate }
+            end
+        end
+      end
+
+      attr_accessor :group_metadata, :search_metadata
+
+      def initialize(group_metadata, search_metadata)
+        self.group_metadata = group_metadata
+        self.search_metadata = search_metadata
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'search.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(__dir__, '..', 'generated', 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_core_311_#{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 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].any? { |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|
+            ['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?
+        resource_type == 'MedicationRequest'
+      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.open(output_file_name, 'w') { |f| f.write(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 MedicationRequest resources use external references to
+        Medications, the search will be repeated with
+        `_include=MedicationRequest: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 v3.1.1.
+        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](http://hl7.org/fhir/us/core/STU3.1.1/CapabilityStatement-us-core-server.html)
+        DESCRIPTION
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/special_cases.rb

@@ -0,0 +1,17 @@
+module USCoreTestKit
+  class Generator
+    module SpecialCases
+      RESOURCES_TO_EXCLUDE = [
+        'Location',
+        'Medication',
+        'PractitionerRole'
+      ].freeze
+
+      class << self
+        def exclude_resource?(resource)
+          RESOURCES_TO_EXCLUDE.include? resource
+        end
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/suite_generator.rb

@@ -0,0 +1,67 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module USCoreTestKit
+  class Generator
+    class SuiteGenerator
+      class << self
+        def generate(ig_metadata)
+          new(ig_metadata).generate
+        end
+      end
+
+      attr_accessor :ig_metadata
+
+      def initialize(ig_metadata)
+        self.ig_metadata = ig_metadata
+      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
+        "us_core_test_suite.rb"
+      end
+
+      def class_name
+        "USCoreTestSuite"
+      end
+
+      def output_file_name
+        File.join(__dir__, '..', 'generated', base_output_file_name)
+      end
+
+      def suite_id
+        'us_core_311'
+      end
+
+      def title
+        'US Core 3.1.1'
+      end
+
+      def generate
+        File.open(output_file_name, 'w') { |f| f.write(output) }
+      end
+
+      def groups
+        ig_metadata.ordered_groups
+          .reject { |group| SpecialCases.exclude_resource? group.resource }
+      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
+    end
+  end
+end

data/lib/us_core_test_kit/generator/terminology_binding_metadata_extractor.rb

@@ -0,0 +1,105 @@
+module USCoreTestKit
+  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 profile_elements_with_bindings
+        profile_elements
+          .select { |element| element.binding.present? }
+          .reject { |element| element_has_fixed_value? element }
+      end
+
+      def element_terminology_bindings
+        profile_elements_with_bindings.map do |element|
+          {
+            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}.", '')
+          }
+        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)
+
+            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/us_core_test_kit/generator/validation_test_generator.rb

@@ -0,0 +1,124 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module USCoreTestKit
+  class Generator
+    class ValidationTestGenerator
+      class << self
+        def generate(ig_metadata)
+          ig_metadata.groups
+            .reject { |group| SpecialCases.exclude_resource? group.resource }
+            .each do |group|
+              new(group).generate
+              next unless group.resource == 'MedicationRequest'
+
+              # The Medication validation test lives in the MedicationRequest
+              # group, so we need to pass in that group's metadata
+              medication_group_metadata = ig_metadata.groups.find { |group| group.resource == 'Medication' }
+              new(medication_group_metadata, group).generate
+            end
+        end
+      end
+
+      attr_accessor :group_metadata, :medication_request_metadata
+
+      def initialize(group_metadata, medication_request_metadata = nil)
+        self.group_metadata = group_metadata
+        self.medication_request_metadata = medication_request_metadata
+      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(__dir__, '..', 'generated', 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(medication_request_metadata || 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 test_id
+        "us_core_311_#{profile_identifier}_validation_test"
+      end
+
+      def class_name
+        "#{Naming.upper_camel_case_for_profile(group_metadata)}ValidationTest"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def conformance_expectation
+        read_interaction[:expectation]
+      end
+
+      def generate
+        FileUtils.mkdir_p(output_file_directory)
+        File.open(output_file_name, 'w') { |f| f.write(output) }
+
+        test_metadata = {
+          id: test_id,
+          file_name: base_output_file_name
+        }
+
+        if resource_type == 'Medication'
+          medication_request_metadata.add_test(test_metadata)
+        else
+          group_metadata.add_test(test_metadata)
+        end
+      end
+
+      def description
+        <<~DESCRIPTION
+        #{description_intro}
+        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 description_intro
+        if resource_type == 'Medication'
+          <<~MEDICATION_INTRO
+          This test verifies resources returned from previous tests conform to
+          the [#{profile_name}](#{profile_url}).
+          MEDICATION_INTRO
+        else
+          <<~GENERIC_INTRO
+          This test verifies resources returned from the first search conform to
+          the [#{profile_name}](#{profile_url}).
+          GENERIC_INTRO
+        end
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator.rb

@@ -0,0 +1,86 @@
+require 'fhir_models'
+
+require_relative '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/provenance_revinclude_search_test_generator'
+require_relative 'generator/read_test_generator'
+require_relative 'generator/reference_resolution_test_generator'
+require_relative 'generator/resource_list_generator'
+require_relative 'generator/search_test_generator'
+require_relative 'generator/suite_generator'
+require_relative 'generator/validation_test_generator'
+
+module USCoreTestKit
+  class Generator
+    attr_accessor :ig_resources, :ig_metadata
+
+    def generate
+      load_ig_package
+      extract_metadata
+      generate_resource_list
+      generate_search_tests
+      generate_read_tests
+      # TODO: generate_vread_tests
+      # TODO: generate_history_tests
+      generate_provenance_revinclude_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
+      File.open(File.join(__dir__, 'generated', 'metadata.yml'), 'w') do |file|
+        file.write(YAML.dump(ig_metadata.to_hash))
+      end
+    end
+
+    def load_ig_package
+      FHIR.logger = Logger.new('/dev/null')
+      self.ig_resources = IGLoader.new.load
+    end
+
+    def generate_resource_list
+      ResourceListGenerator.generate(ig_metadata)
+    end
+
+    def generate_reference_resolution_tests
+      ReferenceResolutionTestGenerator.generate(ig_metadata)
+    end
+
+    def generate_must_support_tests
+      MustSupportTestGenerator.generate(ig_metadata)
+    end
+
+    def generate_validation_tests
+      ValidationTestGenerator.generate(ig_metadata)
+    end
+
+    def generate_read_tests
+      ReadTestGenerator.generate(ig_metadata)
+    end
+
+    def generate_search_tests
+      SearchTestGenerator.generate(ig_metadata)
+    end
+
+    def generate_provenance_revinclude_search_tests
+      ProvenanceRevincludeSearchTestGenerator.generate(ig_metadata)
+    end
+
+    def generate_groups
+      GroupGenerator.generate(ig_metadata)
+    end
+
+    def generate_suites
+      SuiteGenerator.generate(ig_metadata)
+    end
+  end
+end