us_core_test_kit 0.11.5 → 0.11.6

data/lib/us_core_test_kit/generator/group_generator.rb

@@ -32,7 +32,7 @@ module USCoreTestKit
       end
 
       def base_metadata_file_name
-        "metadata.yml"
+        'metadata.yml'
       end
 
       def class_name
@@ -93,23 +93,29 @@ module USCoreTestKit
         group_metadata.profile_url
       end
 
-
       def optional?
         SpecialCases::OPTIONAL_RESOURCES.include?(resource_type) || group_metadata.optional_profile?
       end
 
       def generate
         add_special_tests
-        File.open(output_file_name, 'w') { |f| f.write(output) }
+        File.write(output_file_name, output)
         group_metadata.id = group_id
         group_metadata.file_name = base_output_file_name
-        File.open(metadata_file_name, 'w') { |f| f.write(YAML.dump(group_metadata.to_hash)) }
+        File.write(metadata_file_name, YAML.dump(group_metadata.to_hash))
       end
 
       def add_special_tests
         return if group_metadata.reformatted_version == 'v311'
 
-        if group_metadata.resource == 'DocumentReference'
+        return unless group_metadata.resource == 'DocumentReference'
+
+        if group_metadata.profile_url.end_with?('us-core-adi-documentreference')
+          group_metadata.add_test(
+            id: 'us_core_v800_adi_document_reference_custodian_test',
+            file_name: '../../custom_groups/v8.0.0/adi_document_reference_custodian_test.rb'
+          )
+        else
           group_metadata.add_test(
             id: 'us_core_v400_document_reference_custodian_test',
             file_name: '../../custom_groups/v4.0.0/document_reference_custodian_test.rb'
@@ -145,65 +151,65 @@ module USCoreTestKit
         return '' if required_searches.blank?
 
         <<~SEARCH_DESCRIPTION
-        ## Searching
-        This test sequence will first perform each required search associated
-        with this resource. This sequence will perform searches with the
-        following parameters:
-
-        #{search_param_name_string}
-
-        ### Search Parameters
-        The first search uses the selected patient(s) from the prior launch
-        sequence. Any subsequent searches will look for its parameter values
-        from the results of the first search. For example, the `identifier`
-        search in the patient sequence is performed by looking for an existing
-        `Patient.identifier` from any of the resources returned in the `_id`
-        search. If a value cannot be found this way, the search is skipped.
-
-        ### Search Validation
-        Inferno will retrieve up to the first 20 bundle pages of the reply for
-        #{search_validation_resource_type} and save them for subsequent tests. Each of
-        these resources is then checked to see if it matches the searched
-        parameters in accordance with [FHIR search
-        guidelines](https://www.hl7.org/fhir/search.html). The test will fail,
-        for example, if a Patient search for `gender=male` returns a `female`
-        patient.
+          ## Searching
+          This test sequence will first perform each required search associated
+          with this resource. This sequence will perform searches with the
+          following parameters:
+
+          #{search_param_name_string}
+
+          ### Search Parameters
+          The first search uses the selected patient(s) from the prior launch
+          sequence. Any subsequent searches will look for its parameter values
+          from the results of the first search. For example, the `identifier`
+          search in the patient sequence is performed by looking for an existing
+          `Patient.identifier` from any of the resources returned in the `_id`
+          search. If a value cannot be found this way, the search is skipped.
+
+          ### Search Validation
+          Inferno will retrieve up to the first 20 bundle pages of the reply for
+          #{search_validation_resource_type} and save them for subsequent tests. Each of
+          these resources is then checked to see if it matches the searched
+          parameters in accordance with [FHIR search
+          guidelines](https://www.hl7.org/fhir/search.html). The test will fail,
+          for example, if a Patient search for `gender=male` returns a `female`
+          patient.
         SEARCH_DESCRIPTION
       end
 
       def description
         <<~DESCRIPTION
-        # Background
-
-        The US Core #{title} sequence verifies that the system under test is
-        able to provide correct responses for #{resource_type} queries. These queries
-        must contain resources conforming to the #{profile_name} as
-        specified in the US Core #{group_metadata.version} Implementation Guide.
-
-        # Testing Methodology
-        #{search_description}
-
-        ## Must Support
-        Each profile contains elements marked as "must support". This test
-        sequence expects to see each of these elements at least once. If at
-        least one cannot be found, the test will fail. The test will look
-        through the #{resource_type} resources found in the first test for these
-        elements.
-
-        ## Profile Validation
-        Each resource returned from the first search is expected to conform to
-        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
-        ValueSet. If the code/system in the element is not part of the ValueSet,
-        then the test will fail.
-
-        ## Reference Validation
-        At least one instance of each external reference in elements marked as
-        "must support" within the resources provided by the system must resolve.
-        The test will attempt to read each reference found and will fail if no
-        read succeeds.
+          # Background
+
+          The US Core #{title} sequence verifies that the system under test is
+          able to provide correct responses for #{resource_type} queries. These queries
+          must contain resources conforming to the #{profile_name} as
+          specified in the US Core #{group_metadata.version} Implementation Guide.
+
+          # Testing Methodology
+          #{search_description}
+
+          ## Must Support
+          Each profile contains elements marked as "must support". This test
+          sequence expects to see each of these elements at least once. If at
+          least one cannot be found, the test will fail. The test will look
+          through the #{resource_type} resources found in the first test for these
+          elements.
+
+          ## Profile Validation
+          Each resource returned from the first search is expected to conform to
+          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
+          ValueSet. If the code/system in the element is not part of the ValueSet,
+          then the test will fail.
+
+          ## Reference Validation
+          At least one instance of each external reference in elements marked as
+          "must support" within the resources provided by the system must resolve.
+          The test will attempt to read each reference found and will fail if no
+          read succeeds.
         DESCRIPTION
       end
     end

data/lib/us_core_test_kit/generator/group_metadata_extractor.rb

@@ -61,7 +61,7 @@ module USCoreTestKit
         searches.each do |search|
           search[:names_not_must_support_or_mandatory] = search[:names].reject do |name|
             full_paths = search_definitions[name.to_sym][:full_paths]
-            any_must_support_elements = (must_supports[:elements]).any? do |element|
+            any_must_support_elements = must_supports[:elements].any? do |element|
               full_must_support_paths = ["#{resource}.#{element[:original_path]}", "#{resource}.#{element[:path]}"]
 
               full_paths.any? do |path|
@@ -78,7 +78,7 @@ module USCoreTestKit
                 full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
                 base_must_support_path = "#{resource}.#{slice[:path].sub('[x]', '')}"
 
-                full_paths.intersection([full_must_support_path,base_must_support_path]).present?
+                full_paths.intersection([full_must_support_path, base_must_support_path]).present?
               else
                 false
               end
@@ -98,22 +98,23 @@ module USCoreTestKit
       ### BEGIN SPECIAL CASES ###
       def category_first_profile?
         SpecialCases::ALL_VERSION_CATEGORY_FIRST_PROFILES.include?(profile_url) ||
-        SpecialCases::VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES[profile_url]&.include?(reformatted_version)
+          SpecialCases::VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES[profile_url]&.include?(reformatted_version)
       end
 
       def first_search_params
         @first_search_params ||=
-        if category_first_profile?
-          ['patient', 'category']
-        elsif resource == 'Observation'
-          ['patient', 'code']
-        elsif resource == 'MedicationRequest'
-          ['patient', 'intent']
-        elsif resource == 'CareTeam'
-          ['patient', 'status']
-        else
-          ['patient']
-        end
+          if category_first_profile? ||
+             (profile_url.end_with?('us-core-adi-documentreference') && profile_version.to_i > 7)
+            ['patient', 'category']
+          elsif resource == 'Observation'
+            ['patient', 'code']
+          elsif resource == 'MedicationRequest'
+            ['patient', 'intent']
+          elsif resource == 'CareTeam'
+            ['patient', 'status']
+          else
+            ['patient']
+          end
       end
 
       def handle_special_cases
@@ -178,7 +179,7 @@ module USCoreTestKit
       def title
         title = profile.title.gsub(/US\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
 
-        if (Naming.resources_with_multiple_profiles.include?(resource)) && !title.start_with?(resource) && version != 'v3.1.1'
+        if Naming.resources_with_multiple_profiles.include?(resource) && !title.start_with?(resource) && version != 'v3.1.1'
           title = resource + ' ' + title.split(resource).map(&:strip).join(' ')
         end
 
@@ -291,8 +292,8 @@ module USCoreTestKit
       end
 
       def resource_conformance_expectation
-        @resource_conformance_expectation ||= 
-          resource_capabilities.extension.find do |extension| 
+        @resource_conformance_expectation ||=
+          resource_capabilities.extension.find do |extension|
             extension.url == 'http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation'
           end&.valueCode
       end

data/lib/us_core_test_kit/generator/ig_metadata_extractor.rb

@@ -21,7 +21,7 @@ module USCoreTestKit
       end
 
       def add_metadata_from_ig
-        metadata.ig_version = "v#{ig_resources.ig.version}"
+        metadata.ig_version = "v#{ig_resources.ig.version}".delete('-ballot')
       end
 
       def resources_in_capability_statement
@@ -29,8 +29,10 @@ module USCoreTestKit
       end
 
       def add_missing_supported_profiles
-        case ig_resources.ig.version
+        case ig_resources.ig.version.delete('-ballot')
         when '3.1.1'
+          # TODO: Remove these after v8.0.0 IG is fixed
+
           # The US Core v3.1.1 Server Capability Statement does not list support for the
           # required vital signs profiles, so they need to be added
           ig_resources.capability_statement.rest.first.resource
@@ -61,17 +63,17 @@ module USCoreTestKit
 
       def remove_extra_supported_profiles
         ig_resources.capability_statement.rest.first.resource
-            .find { |resource| resource.type == 'Observation' }
-            .supportedProfile.delete_if do |profile_url|
-              SpecialCases::PROFILES_TO_EXCLUDE.include?(profile_url)
-            end
+          .find { |resource| resource.type == 'Observation' }
+          .supportedProfile.delete_if do |profile_url|
+          SpecialCases::PROFILES_TO_EXCLUDE.include?(profile_url)
+        end
       end
 
       def add_metadata_from_resources
         metadata.groups =
           resources_in_capability_statement.flat_map do |resource|
             resource.supportedProfile&.map do |supported_profile|
-              #supported_profile = supported_profile.split('|').first
+              # supported_profile = supported_profile.split('|').first
               next if supported_profile == 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire'
 
               GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources).group_metadata

data/lib/us_core_test_kit/generator/interpreter_required_extension_test_generator.rb

@@ -0,0 +1,68 @@
+module USCoreTestKit
+  class Generator
+    class InterpreterRequiredExtensionTestGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          ig_metadata.groups
+            .reject { |group| SpecialCases.exclude_group? group }
+            .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', 'interpreter_required_extension_test.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(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_core_#{group_metadata.reformatted_version}_interpreter_required_extension_test"
+      end
+
+      def class_name
+        'InterpreterRequiredExtensionTest'
+      end
+
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
+      def generate
+        return unless group_metadata.resource == 'Encounter' && group_metadata.version[1].to_i > 7
+
+        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_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -4,6 +4,7 @@ require_relative 'must_support_metadata_extractor_us_core_4'
 require_relative 'must_support_metadata_extractor_us_core_5'
 require_relative 'must_support_metadata_extractor_us_core_6'
 require_relative 'must_support_metadata_extractor_us_core_7'
+require_relative 'must_support_metadata_extractor_us_core_8'
 
 module USCoreTestKit
   class Generator
@@ -70,73 +71,6 @@ module USCoreTestKit
         slice.slicing.discriminator
       end
 
-      def must_support_pattern_slice_elements
-        must_support_slice_elements.select do |element|
-          discriminators(sliced_element(element)).first.type == 'pattern'
-        end
-      end
-
-      def pattern_slices
-        must_support_pattern_slice_elements.map do |current_element|
-          {
-            slice_id: current_element.id,
-            slice_name: current_element.sliceName,
-            path: current_element.path.gsub("#{resource}.", '')
-          }.tap do |metadata|
-            discriminator = discriminators(sliced_element(current_element)).first
-            discriminator_path = discriminator.path
-            discriminator_path = '' if discriminator_path == '$this'
-            pattern_element =
-              if discriminator_path.present?
-                profile_elements.find { |element| element.id == "#{current_element.id}.#{discriminator_path}" }
-              else
-                current_element
-              end
-            metadata[:discriminator] =
-              if pattern_element.patternCodeableConcept.present?
-                {
-                  type: 'patternCodeableConcept',
-                  path: discriminator_path,
-                  code: pattern_element.patternCodeableConcept.coding.first.code,
-                  system: pattern_element.patternCodeableConcept.coding.first.system
-                }
-              elsif pattern_element.patternCoding.present?
-                {
-                  type: 'patternCoding',
-                  path: discriminator_path,
-                  code: pattern_element.patternCoding.code,
-                  system: pattern_element.patternCoding.system
-                }
-              elsif pattern_element.patternIdentifier.present?
-                {
-                  type: 'patternIdentifier',
-                  path: discriminator_path,
-                  system: pattern_element.patternIdentifier.system
-                }
-              elsif pattern_element.binding&.strength == 'required' &&
-                    pattern_element.binding&.valueSet.present?
-
-                value_extractor = ValueExactor.new(ig_resources, resource, profile_elements)
-
-                values = value_extractor.codings_from_value_set_binding(pattern_element).presence ||
-                         value_extractor.values_from_resource_metadata([metadata[:path]]).presence || []
-
-                {
-                  type: 'requiredBinding',
-                  path: discriminator_path,
-                  values: values
-                }
-              else
-                raise StandardError, 'Unsupported discriminator pattern type'
-              end
-
-            if is_uscdi_requirement_element?(current_element)
-              metadata[:uscdi_only] = true
-            end
-          end
-        end
-      end
-
       def must_support_type_slice_elements
         must_support_slice_elements.select do |element|
           discriminators(sliced_element(element)).first.type == 'type'
@@ -175,7 +109,10 @@ module USCoreTestKit
 
       def must_support_value_slice_elements
         must_support_slice_elements.select do |element|
-          discriminators(sliced_element(element)).first.type == 'value'
+          # 'pattern' is deparected in FHIR R5
+          # 'pattern' type is used in US Core v7 and all earlier versions.
+          # Since US Core v8, all 'patten' types are moved to 'value' type
+          ['value','pattern'].include?(discriminators(sliced_element(element)).first.type)
         end
       end
 
@@ -184,21 +121,45 @@ module USCoreTestKit
           {
             slice_id: current_element.id,
             slice_name: current_element.sliceName,
-            path: current_element.path.gsub("#{resource}.", ''),
-            discriminator: {
-              type: 'value'
-            }
+            path: current_element.path.gsub("#{resource}.", '')
           }.tap do |metadata|
-            metadata[:discriminator][:values] = discriminators(sliced_element(current_element)).map do |discriminator|
-              fixed_element = profile_elements.find do |element|
-                element.id.starts_with?(current_element.id) &&
-                  element.path == "#{current_element.path}.#{discriminator.path}"
+            fixed_values = []
+            pattern_value = {}
+
+            discriminators(sliced_element(current_element)).each do |discriminator|
+              discriminator_path = discriminator.path
+              discriminator_path = '' if discriminator_path == '$this'
+              pattern_element =
+                if discriminator_path.present?
+                  sliced_target_path = "#{current_element.path}.#{discriminator_path}"
+
+                  profile_elements.find do |element|
+                    element.id.starts_with?(current_element.id) &&
+                      element.path == sliced_target_path
+                  end
+                else
+                  current_element
+                end
+
+              if pattern_element.fixedCode.present? || pattern_element.fixedUri.present?
+                fixed_values << {
+                  path: discriminator.path,
+                  value: pattern_element.fixedUri || pattern_element.fixedCode
+                }
+              elsif pattern_value.present?
+                raise StandardError, "Found more than one pattern slices for the same element #{pattern_element}."
+              else
+                pattern_value = save_pattern_slice(pattern_element, discriminator_path, metadata)
               end
+            end
 
-              {
-                path: discriminator.path,
-                value: fixed_element.fixedUri || fixed_element.fixedCode
+            if !fixed_values.empty?
+              metadata[:discriminator] = {
+                type: 'value',
+                values: fixed_values
               }
+            elsif pattern_value.present?
+              metadata[:discriminator] = pattern_value
             end
 
             if is_uscdi_requirement_element?(current_element)
@@ -208,8 +169,47 @@ module USCoreTestKit
         end
       end
 
+      def save_pattern_slice(pattern_element, discriminator_path, metadata)
+        if pattern_element.patternCodeableConcept.present?
+          {
+            type: 'patternCodeableConcept',
+            path: discriminator_path,
+            code: pattern_element.patternCodeableConcept.coding.first.code,
+            system: pattern_element.patternCodeableConcept.coding.first.system
+          }
+        elsif pattern_element.patternCoding.present?
+          {
+            type: 'patternCoding',
+            path: discriminator_path,
+            code: pattern_element.patternCoding.code,
+            system: pattern_element.patternCoding.system
+          }
+        elsif pattern_element.patternIdentifier.present?
+          {
+            type: 'patternIdentifier',
+            path: discriminator_path,
+            system: pattern_element.patternIdentifier.system
+          }
+        elsif pattern_element.binding&.strength == 'required' &&
+              pattern_element.binding&.valueSet.present?
+
+          value_extractor = ValueExactor.new(ig_resources, resource, profile_elements)
+
+          values = value_extractor.codings_from_value_set_binding(pattern_element).presence ||
+                  value_extractor.values_from_resource_metadata([metadata[:path]]).presence || []
+
+          {
+            type: 'requiredBinding',
+            path: discriminator_path,
+            values: values
+          }
+        else
+          raise StandardError, 'Unsupported discriminator pattern type'
+        end
+      end
+
       def must_support_slices
-        pattern_slices + type_slices + value_slices
+        type_slices + value_slices
       end
 
       def plain_must_support_elements
@@ -302,6 +302,14 @@ module USCoreTestKit
           {
             path: current_element.id.gsub("#{resource}.", '')
           }.tap do |current_metadata|
+
+            #binding.pry if current_element.id == 'Organization.identifier:NPI.system'
+            if current_element.id.include?(':') && !current_element.id.include?('extension')
+              slice_name = current_element.id.match(/:(\w+)/)[1]
+
+              next if must_support_slice_elements.none? { |slice| slice.sliceName == slice_name }
+            end
+
             if is_uscdi_requirement_element?(current_element)
               current_metadata[:uscdi_only] = true
             end
@@ -320,10 +328,6 @@ module USCoreTestKit
 
               handle_fixed_values(current_metadata, current_element)
 
-              must_support_elements_metadata.delete_if do |metadata|
-                metadata[:path] == current_metadata[:path] && metadata[:fixed_value].blank?
-              end
-
               must_support_elements_metadata << current_metadata
             end
           end
@@ -348,6 +352,8 @@ module USCoreTestKit
           MustSupportMetadataExtractorUsCore6.new(profile, @must_supports).handle_special_cases
         when '7.0.0'
           MustSupportMetadataExtractorUsCore7.new(profile, @must_supports).handle_special_cases
+        when '8.0.0', '8.0.0-ballot'
+          MustSupportMetadataExtractorUsCore8.new(profile, @must_supports).handle_special_cases
         end
       end
 

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_6.rb

@@ -1,12 +1,8 @@
-require_relative 'must_support_metadata_extractor_us_core_5'
-
 module USCoreTestKit
   class Generator
     class MustSupportMetadataExtractorUsCore6
       attr_accessor :profile, :must_supports
 
-      US_CORE_CATEGORY = ['sdoh', 'functional-status', 'disability-status', 'cognitive-status']
-
       def initialize(profile, must_supports)
         self.profile = profile
         self.must_supports = must_supports

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_7.rb

@@ -1,12 +1,8 @@
-require_relative 'must_support_metadata_extractor_us_core_6'
-
 module USCoreTestKit
   class Generator
     class MustSupportMetadataExtractorUsCore7
       attr_accessor :profile, :must_supports
 
-      US_CORE_CATEGORY = ['sdoh', 'functional-status', 'disability-status', 'cognitive-status'].freeze
-
       def initialize(profile, must_supports)
         self.profile = profile
         self.must_supports = must_supports

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_8.rb

@@ -0,0 +1,56 @@
+module USCoreTestKit
+  class Generator
+    class MustSupportMetadataExtractorUsCore8
+      attr_accessor :profile, :must_supports
+
+      def initialize(profile, must_supports)
+        self.profile = profile
+        self.must_supports = must_supports
+      end
+
+      def us_core_6_extractor
+        @us_core_6_extractor ||= MustSupportMetadataExtractorUsCore6.new(profile, must_supports)
+      end
+
+      def us_core_7_extractor
+        @us_core_7_extractor ||= MustSupportMetadataExtractorUsCore7.new(profile, must_supports)
+      end
+
+      def remove_patient_and_encounter_interpreter_extension
+        return unless ['Patient', 'Encounter'].include?(profile.type)
+
+        must_supports[:extensions].delete_if { |extension| extension[:url].end_with?('us-core-interpreter-needed') }
+      end
+
+      def handle_special_cases
+        us_core_6_extractor.add_patient_uscdi_elements
+        add_must_support_choices
+        us_core_6_extractor.remove_practitioner_address
+        remove_patient_and_encounter_interpreter_extension
+      end
+
+      def add_must_support_choices
+        us_core_7_extractor.add_must_support_choices
+
+        more_choices = []
+
+        case profile.id
+        when 'us-core-observation-screening-assessment', 'us-core-simple-observation'
+          more_choices << {
+            target_profiles: [
+              'http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient',
+              'http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner'
+            ]
+          }
+        when 'us-core-specimen'
+          more_choices << { paths: ['identifier', 'accessionIdentifier'] }
+        end
+
+        if more_choices.any?
+          must_supports[:choices] ||= []
+          must_supports[:choices].concat(more_choices)
+        end
+      end
+    end
+  end
+end