us_core_test_kit 0.6.5 → 0.7.1

data/lib/us_core_test_kit/generated/v7.0.0-ballot/us_core_test_suite.rb

@@ -5,6 +5,7 @@ require_relative '../../custom_groups/v4.0.0/clinical_notes_guidance_group'
 require_relative '../../custom_groups/data_absent_reason_group'
 require_relative '../../custom_groups/smart_app_launch_group'
 require_relative '../../custom_groups/v7.0.0-ballot/smart_granular_scopes_group'
+require_relative '../../custom_groups/v7.0.0-ballot/screening_assessment_group'
 require_relative '../../provenance_validator'
 require_relative '../../us_core_options'
 
@@ -87,6 +88,7 @@ module USCoreTestKit
         /Provenance.agent\[\d*\]: Rule provenance-1/, #Invalid invariant in US Core v5.0.1
         %r{Unknown Code System 'http://hl7.org/fhir/us/core/CodeSystem/us-core-tags'}, # Validator has an issue with this US Core 5 code system in US Core 6 resource
         %r{URL value 'http://hl7.org/fhir/us/core/CodeSystem/us-core-tags' does not resolve}, # Validator has an issue with this US Core 5 code system in US Core 6 resource
+        /\A\S+: \S+: URL value '.*' does not resolve/,
         %r{Observation.component\[\d+\].value.ofType\(Quantity\): The code provided \(http://unitsofmeasure.org#L/min\) was not found in the value set 'Vital Signs Units'} # Known issue with the Pulse Oximetry Profile
       ].freeze
 
@@ -98,8 +100,10 @@ module USCoreTestKit
           end
       end
 
-      validator do
-        url ENV.fetch('V700_BALLOT_VALIDATOR_URL', 'http://validator_service:4567')
+      id :us_core_v700_ballot
+
+      fhir_resource_validator do
+        igs 'hl7.fhir.us.core#7.0.0-ballot'
         message_filters = VALIDATION_MESSAGE_FILTERS + VERSION_SPECIFIC_MESSAGE_FILTERS
 
         exclude_message do |message|
@@ -112,8 +116,6 @@ module USCoreTestKit
         end
       end
 
-      id :us_core_v700_ballot
-
       input :url,
         title: 'FHIR Endpoint',
         description: 'URL of the FHIR endpoint'
@@ -206,10 +208,11 @@ module USCoreTestKit
         group from: :us_core_v700_ballot_related_person
         group from: :us_core_v700_ballot_specimen
         group from: :us_core_v400_clinical_notes_guidance
+        group from: :us_core_v700_ballot_screening_assessment
         group from: :us_core_311_data_absent_reason
       end
 
-      group from: :us_core_v700_ballot_smart_granular_scopes,
+      group from: :'us_core_v700_ballot_smart_granular_scopes',
             required_suite_options: USCoreOptions::SMART_2_REQUIREMENT
       
     end

data/lib/us_core_test_kit/generator/granular_scope_group_generator.rb

@@ -4,11 +4,18 @@ require_relative '../custom_groups/smart_scopes_constants'
 module USCoreTestKit
   class Generator
     class GranularScopeGroupGenerator
+      include SmartScopesConstants
+
       class << self
         def generate(ig_metadata, base_output_dir)
           return unless ['6', '7'].include? ig_metadata.ig_version[1]
 
           [1, 2].each do |group_number|
+            scopes =
+              SmartScopesConstants
+                .const_get("SMART_GRANULAR_SCOPES_GROUP#{group_number}")[ig_metadata.reformatted_version]
+            next if scopes.blank?
+
             new(ig_metadata, base_output_dir, group_number).generate
           end
         end

data/lib/us_core_test_kit/generator/granular_scope_read_test_generator.rb

@@ -0,0 +1,102 @@
+require_relative 'naming'
+require_relative 'special_cases'
+require_relative '../custom_groups/smart_scopes_constants'
+
+module USCoreTestKit
+  class Generator
+    class GranularScopeReadTestGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          
+          return unless ['6', '7'].include? ig_metadata.ig_version[1]
+          
+          scopes =
+            SmartScopesConstants::SMART_GRANULAR_SCOPES_GROUP1[ig_metadata.reformatted_version] +
+            (SmartScopesConstants::SMART_GRANULAR_SCOPES_GROUP2[ig_metadata.reformatted_version] || [])
+
+          SmartScopesConstants::SMART_GRANULAR_SCOPE_RESOURCES.each do |resource_type|
+            group = ig_metadata.groups.find { |group| group.resource == resource_type }
+
+            next if scopes.none? { |scope| scope.start_with? "patient/#{group.resource}" }
+
+          new(group, base_output_dir).generate
+          end
+        end
+      end
+
+      attr_accessor :group_metadata, :base_output_dir, :group_number
+
+      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', 'granular_scope_read_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, 'granular_scope_tests', resource_type.underscore)
+      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}_#{resource_type}_granular_scope_read_test"
+      end
+
+      def class_name
+        "#{resource_type}GranularScopeReadTest"
+      end
+
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def path_for_value(path)
+        path == 'class' ? 'local_class' : path
+      end
+
+      def array_of_strings(array)
+        quoted_strings = array.map { |element| "'#{element}'" }
+        "[#{quoted_strings.join(', ')}]"
+      end
+
+      def generate
+        FileUtils.mkdir_p(output_file_directory)
+        File.open(output_file_name, 'w') { |f| f.write(output) }
+
+        group_metadata.add_granular_scope_test(
+          id: test_id,
+          file_name: base_output_file_name
+        )
+      end
+
+      def description
+        <<~DESCRIPTION.gsub(/\n{3,}/, "\n\n")
+          This test attempts #{resource_type} reads 
+          and verifies that the results have been
+          filtered based on the granted granular scopes.
+        DESCRIPTION
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator/granular_scope_resource_type_group_generator.rb

@@ -16,7 +16,7 @@ module USCoreTestKit
                 .const_get("SMART_GRANULAR_SCOPES_GROUP#{group_number}")[ig_metadata.reformatted_version]
 
             groups.each do |group_metadata|
-              next if scopes.none? { |scope| scope.start_with? "patient/#{group_metadata.resource}" }
+              next if scopes.blank? || scopes.none? { |scope| scope.start_with? "patient/#{group_metadata.resource}" }
 
               new(GroupMetadata.new(group_metadata.to_hash), ig_metadata, base_output_dir, group_number).generate
             end

data/lib/us_core_test_kit/generator/granular_scope_test_generator.rb

@@ -11,12 +11,12 @@ module USCoreTestKit
 
           scopes =
             SmartScopesConstants::SMART_GRANULAR_SCOPES_GROUP1[ig_metadata.reformatted_version] +
-            SmartScopesConstants::SMART_GRANULAR_SCOPES_GROUP2[ig_metadata.reformatted_version]
+            (SmartScopesConstants::SMART_GRANULAR_SCOPES_GROUP2[ig_metadata.reformatted_version] || [])
 
           SmartScopesConstants::SMART_GRANULAR_SCOPE_RESOURCES.each do |resource_type|
             group = ig_metadata.groups.find { |group| group.resource == resource_type }
 
-            next if scopes.none? { |scope| scope.start_with? "patient/#{group.resource}" }
+            next if scopes.blank? || scopes.none? { |scope| scope.start_with? "patient/#{group.resource}" }
 
             group.searches
               .each { |search| new(group, search, base_output_dir).generate }
@@ -57,7 +57,7 @@ module USCoreTestKit
       end
 
       def test_id
-        "us_core_#{group_metadata.reformatted_version}_#{resource_type}_#{search_identifier}_granular_scope_test"
+        "us_core_#{group_metadata.reformatted_version}_#{resource_type}_#{search_identifier}_granular_scope_search_test"
       end
 
       def search_identifier
@@ -69,7 +69,7 @@ module USCoreTestKit
       end
 
       def class_name
-        "#{resource_type}#{search_title}GranularScopeTest"
+        "#{resource_type}#{search_title}GranularScopeSearchTest"
       end
 
       def module_name

data/lib/us_core_test_kit/generator/group_metadata.rb

@@ -56,7 +56,7 @@ module USCoreTestKit
       end
 
       def no_patient_searches?
-        searches.none? { |search| search[:names].include? 'patient' }
+        searches.none? { |search| search[:names].include?('patient') && search[:expectation] == 'SHALL' }
       end
 
       def non_uscdi_resource?

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -48,6 +48,7 @@ module USCoreTestKit
         must_support_extension_elements.map do |element|
           {
             id: element.id,
+            path: element.path.gsub("#{resource}.", ''),
             url: element.type.first.profile.first
           }.tap do |metadata|
             if is_uscdi_requirement_element?(element)

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_4.rb

@@ -52,16 +52,19 @@ module USCoreTestKit
         #US Core 4.0.0 Section 10.112.1.1 Additional USCDI v1 Requirement:
         must_supports[:extensions] << {
           id: 'Patient.extension:race',
+          path: 'extension',
           url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race',
           uscdi_only: true
         }
         must_supports[:extensions] << {
           id: 'Patient.extension:ethnicity',
+          path: 'extension',
           url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity',
           uscdi_only: true
         }
         must_supports[:extensions] << {
           id: 'Patient.extension:birthsex',
+          path: 'extension',
           url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex',
           uscdi_only: true
         }

data/lib/us_core_test_kit/generator/must_support_metadata_extractor_us_core_5.rb

@@ -54,6 +54,7 @@ module USCoreTestKit
 
         must_supports[:extensions] << {
           id: 'Patient.extension:genderIdentity',
+          path: 'extension',
           url: 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-genderIdentity',
           uscdi_only: true
         }

data/lib/us_core_test_kit/generator/special_cases.rb

@@ -25,16 +25,14 @@ module USCoreTestKit
         'Encounter' => ['v311', 'v400'],
         'Location' => ['v311', 'v400', 'v501', 'v610'],
         'Organization' => ['v311', 'v400', 'v501', 'v610', 'v700_ballot'],
-        'Practitioner' => ['v311', 'v400'],
+        'Practitioner' => ['v311', 'v400', 'v501', 'v610', 'v700_ballot'],
         'PractitionerRole' => ['v311', 'v400', 'v501', 'v610', 'v700_ballot'],
         'Provenance' => ['v311', 'v400', 'v501', 'v610', 'v700_ballot'],
-        'RelatedPerson' => ['v501', 'v610', 'v700_ballot'],
-        'Specimen' => ['v610', 'v700_ballot']
+        'RelatedPerson' => ['v501', 'v610', 'v700_ballot']
       }.freeze
 
       SEARCHABLE_DELAYED_RESOURCES = {
-        'Location' => ['v700_ballot'],
-        'Practitioner' => ['v501', 'v610', 'v700_ballot']
+        'Location' => ['v700_ballot']
       }.freeze
 
       ALL_VERSION_CATEGORY_FIRST_PROFILES = [

data/lib/us_core_test_kit/generator/suite_generator.rb

@@ -57,12 +57,15 @@ module USCoreTestKit
         "US Core #{ig_metadata.ig_version}"
       end
 
-      def validator_env_name
-        "#{ig_metadata.reformatted_version.upcase}_VALIDATOR_URL"
+      def ig_identifier
+        version = ig_metadata.ig_version[1..] # Remove leading 'v'
+        "hl7.fhir.us.core##{version}"
       end
 
       def ig_link
         case ig_metadata.ig_version
+        when 'v6.1.0'
+          'http://hl7.org/fhir/us/core/STU6'
         when 'v5.0.1'
           'http://hl7.org/fhir/us/core/STU5.0.1'
         when 'v4.0.0'
@@ -72,7 +75,7 @@ module USCoreTestKit
         end
       end
 
-      def test_granular_scopes?
+      def us_core_6_and_above?
         ig_metadata.ig_version[1].to_i > 5
       end
 
@@ -126,6 +129,14 @@ module USCoreTestKit
       def granular_scopes_id
         "us_core_#{ig_metadata.reformatted_version}_smart_granular_scopes"
       end
+
+      def screening_assessment_file_name
+        "../../custom_groups/#{ig_metadata.ig_version}/screening_assessment_group"
+      end
+
+      def screening_assessment_id
+        "us_core_#{ig_metadata.reformatted_version}_screening_assessment"
+      end
     end
   end
 end

data/lib/us_core_test_kit/generator.rb

@@ -6,6 +6,7 @@ require_relative 'generator/ig_metadata_extractor'
 require_relative 'generator/granular_scope_group_generator'
 require_relative 'generator/granular_scope_resource_type_group_generator'
 require_relative 'generator/granular_scope_test_generator'
+require_relative 'generator/granular_scope_read_test_generator'
 require_relative 'generator/group_generator'
 require_relative 'generator/must_support_test_generator'
 require_relative 'generator/provenance_revinclude_search_test_generator'
@@ -104,6 +105,7 @@ module USCoreTestKit
 
     def generate_granular_scope_tests
       GranularScopeTestGenerator.generate(ig_metadata, base_output_dir)
+      GranularScopeReadTestGenerator.generate(ig_metadata, base_output_dir)
     end
 
     def generate_groups

data/lib/us_core_test_kit/granular_scope.rb

@@ -0,0 +1,63 @@
+module USCoreTestKit
+  module GranularScope
+
+    def granular_scopes
+      @granular_scopes ||=
+        received_scopes
+          .split(' ')
+          .select do |scope|
+            (scope.start_with?("patient/#{resource_type}") || scope.start_with?("user/#{resource_type}")) &&
+              scope.include?('?')
+          end
+    end
+
+    def granular_scope_search_params
+      @granular_scope_search_params ||=
+        granular_scopes.map do |scope|
+          _, granular_scope = scope.split('?')
+          name, value = granular_scope.split('=')
+
+          {
+            name:,
+            value:
+          }
+        end
+    end
+
+    def resource_specific_granular_scope_search_params
+      @resource_specific_granular_scope_search_params ||=
+        granular_scopes.select {|scope| scope.include?(resource_type)}.map do |scope|
+          _, granular_scope = scope.split('?')
+          name, value = granular_scope.split('=')
+          _, value = value.split('|')
+          {
+            name:,
+            value:
+          }
+      end
+    end
+
+    def previous_request_resources
+      first_request = previous_requests.first
+      next_page_url = nil
+      hash = Hash.new { |hash, key| hash[key] = [] }
+      previous_requests.each_with_object(hash) do |request, request_resource_hash|
+        request_resources =
+          if request.status == 200
+            request.resource.entry.map(&:resource).select { |resource| resource.resourceType == resource_type }
+          else
+            []
+          end
+
+        first_request = request if request.url != next_page_url
+
+        request_resource_hash[first_request].concat(request_resources)
+
+        next if request.resource&.resourceType != 'Bundle'
+
+        next_page_url = request.resource&.link&.find { |link| link.relation == 'next' }&.url
+      end
+    end
+
+  end
+end

data/lib/us_core_test_kit/granular_scope_read_test.rb

@@ -0,0 +1,71 @@
+require_relative 'resource_search_param_checker'
+require_relative 'granular_scope'
+
+module USCoreTestKit
+  module GranularScopeReadTest
+    extend Forwardable
+    include ResourceSearchParamChecker
+    include GranularScope
+
+    def_delegators 'self.class', :metadata
+    def self.included(klass)
+      klass.input(:received_scopes)
+      klass.attr_accessor :previous_requests
+    end
+
+    def run_scope_read_test
+      assert granular_scopes.present?, "No granular scopes were received for #{resource_type} resources"
+      resource_scopes = granular_scopes.select {|scope| scope.include?(resource_type)}
+
+      load_previous_requests
+      skip_if previous_requests.blank?,
+              "No #{resource_type} reads found"
+      previous_resources_for_reads = previous_request_resources.values.flatten
+
+      resource_specific_granular_scope_search_params.each do |scope| 
+        current_scope = granular_scopes.find {|granular| granular.include?(scope[:name]) && granular.include?(scope[:value])}
+
+        resource_matching_scope = previous_resources_for_reads.find do |prev_resource| 
+          resource_matches_param?(prev_resource, scope[:name], scope[:value])
+        end
+        skip_if resource_matching_scope.nil?, "Unable to find any resources to match scope #{current_scope}"
+
+        fhir_read resource_type, resource_matching_scope.id
+
+        assert_response_status(200)
+        assert_resource_type(resource_type)
+      end
+
+      nonmatching_resource = previous_resources_for_reads.find do |prev_resource|
+        resource_specific_granular_scope_search_params.none? do |scope| 
+          resource_matches_param?(prev_resource, scope[:name], scope[:value])
+        end
+      end
+      if nonmatching_resource
+        fhir_read resource_type, nonmatching_resource.id
+        assert (response && response[:status]) != 200, "Server incorrectly responded with a successful status, read should fail due to scopes."
+        assert (resource && resource.resourceType != resource_type), "Server incorrectly returned a #{resource_type}, read should fail due to scopes"
+      else
+        info "Unable to find a resource that does not match scopes."
+      end
+    end
+    
+    def load_previous_requests
+      params = metadata.searches.first[:names]
+      search_params_as_hash = params.each_with_object({}) do |name, hash|
+        hash[name] = nil
+      end
+      @previous_requests ||=
+        load_tagged_requests(search_params_tag(search_params_as_hash))
+          .sort_by { |request| request.index }
+    end
+
+    def unescape_search_value(value)
+      value&.gsub('\\,', ',')
+    end
+
+    def search_params_tag(params)
+      "#{resource_type}?#{params.keys.join('&')}"
+    end
+  end
+end

data/lib/us_core_test_kit/{granular_scope_checker.rb → granular_scope_search_test.rb}

@@ -1,11 +1,17 @@
+require_relative 'resource_search_param_checker'
+require_relative 'granular_scope'
+
 module USCoreTestKit
-  module GranularScopeChecker
+  module GranularScopeSearchTest
+    include ResourceSearchParamChecker
+    include GranularScope
+
     def self.included(klass)
       klass.input(:received_scopes)
       klass.attr_accessor :previous_requests
     end
 
-    def run_scope_check_test
+    def run_scope_search_test
       assert granular_scopes.present?, "No granular scopes were received for #{resource_type} resources"
 
       load_previous_requests
@@ -47,51 +53,6 @@ module USCoreTestKit
       end
     end
 
-    def previous_request_resources
-      first_request = previous_requests.first
-      next_page_url = nil
-      hash = Hash.new { |hash, key| hash[key] = [] }
-      previous_requests.each_with_object(hash) do |request, request_resource_hash|
-        request_resources =
-          if request.status == 200
-            request.resource.entry.map(&:resource).select { |resource| resource.resourceType == resource_type }
-          else
-            []
-          end
-
-        first_request = request if request.url != next_page_url
-
-        request_resource_hash[first_request].concat(request_resources)
-
-        next if request.resource&.resourceType != 'Bundle'
-
-        next_page_url = request.resource&.link&.find { |link| link.relation == 'next' }&.url
-      end
-    end
-
-    def granular_scopes
-      @granular_scopes ||=
-        received_scopes
-          .split(' ')
-          .select do |scope|
-            (scope.start_with?("patient/#{resource_type}") || scope.start_with?("user/#{resource_type}")) &&
-              scope.include?('?')
-          end
-    end
-
-    def granular_scope_search_params
-      @granular_scope_search_params ||=
-        granular_scopes.map do |scope|
-          _, granular_scope = scope.split('?')
-          name, value = granular_scope.split('=')
-
-          {
-            name:,
-            value:
-          }
-        end
-    end
-
     def load_previous_requests
       search_params_as_hash = search_param_names.each_with_object({}) do |name, hash|
         hash[name] = nil

data/lib/us_core_test_kit/must_support_test.rb

@@ -83,7 +83,17 @@ module USCoreTestKit
       @missing_extensions ||=
         must_support_extensions.select do |extension_definition|
           resources.none? do |resource|
-            resource.extension.any? { |extension| extension.url == extension_definition[:url] }
+            path = extension_definition[:path]
+
+            if path == 'extension'
+              resource.extension.any? { |extension| extension.url == extension_definition[:url] }
+            else
+              extension = find_a_value_at(resource, path) do |el|
+                el.url == extension_definition[:url]
+              end
+
+              extension.present?
+            end
           end
         end
     end
@@ -100,14 +110,24 @@ module USCoreTestKit
       @missing_elements ||=
         must_support_elements.select do |element_definition|
           resources.none? do |resource|
-            path = element_definition[:path] #.delete_suffix('[x]')
-            value_found = find_a_value_at(resource, path) do |value|
-              value_without_extensions =
-                value.respond_to?(:to_hash) ? value.to_hash.reject { |key, _| key == 'extension' } : value
+            path = element_definition[:path]
+            ms_extension_urls = must_support_extensions.select { |ex| ex[:path] == "#{path}.extension" }
+              .map { |ex| ex[:url] }
 
-              (value_without_extensions.present? || value_without_extensions == false) &&
+            value_found = find_a_value_at(resource, path) do |value|
+              if value.instance_of?(USCoreTestKit::PrimitiveType) && ms_extension_urls.present?
+                urls = value.extension&.map(&:url)
+                has_ms_extension = (urls & ms_extension_urls).present?
+              end
+
+              unless has_ms_extension
+                value = value.value if value.instance_of?(USCoreTestKit::PrimitiveType)
+                value_without_extensions =
+                  value.respond_to?(:to_hash) ? value.to_hash.reject { |key, _| key == 'extension' } : value
+              end
+
+              (has_ms_extension || value_without_extensions.present? || value_without_extensions == false) &&
                 (element_definition[:fixed_value].blank? || value == element_definition[:fixed_value])
-
             end
             # Note that false.present? => false, which is why we need to add this extra check
             value_found.present? || value_found == false

data/lib/us_core_test_kit/primitive_type.rb

@@ -0,0 +1,5 @@
+module USCoreTestKit
+  class PrimitiveType < FHIR::Element
+    attr_accessor :value
+  end
+end

data/lib/us_core_test_kit/provenance_validator.rb

@@ -19,11 +19,10 @@ module USCoreTestKit
 
       failed_provenance =
         find_a_value_at(resource, 'agent') do |agent|
-          ['Practitioner', 'Device'].any? { |resource_type| agent.who.reference&.include?(resource_type) } &&
-          agent.onBehalfOf.nil?
+          ['Practitioner', 'Device'].any? { |resource_type| agent.who&.reference&.include?(resource_type) } &&
+            agent.onBehalfOf.nil?
         end
 
-
       if failed_provenance.present?
         validation_messages << {
           type: 'error',
@@ -34,4 +33,4 @@ module USCoreTestKit
       validation_messages
     end
   end
-end
+end

data/lib/us_core_test_kit/reference_resolution_test.rb

@@ -165,7 +165,8 @@ module USCoreTestKit
 
       target_profile_with_version =  target_profile.include?('|') ? target_profile : "#{target_profile}|#{metadata.profile_version}"
 
-      outcome = FHIR::OperationOutcome.new(JSON.parse(validator.validate(resource, target_profile_with_version)))
+      validator_response = validator.validate(resource, target_profile_with_version)
+      outcome = validator.operation_outcome_from_hl7_wrapped_response(validator_response)
 
       message_hashes = outcome.issue&.map { |issue| validator.message_hash_from_issue(issue, resource) } || []