us_core_test_kit 0.6.0 → 0.6.2

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -36,7 +36,7 @@ module USCoreTestKit
       end
 
       def all_must_support_elements
-        profile_elements.select { |element| element.mustSupport || is_uscdi_requirement_element?(element) }
+        profile_elements.select { |element| (element.mustSupport || is_uscdi_requirement_element?(element))}
       end
 
       def must_support_extension_elements
@@ -77,7 +77,8 @@ module USCoreTestKit
       def pattern_slices
         must_support_pattern_slice_elements.map do |current_element|
           {
-            name: current_element.id,
+            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
@@ -89,7 +90,6 @@ module USCoreTestKit
               else
                 current_element
               end
-
             metadata[:discriminator] =
               if pattern_element.patternCodeableConcept.present?
                 {
@@ -156,7 +156,8 @@ module USCoreTestKit
           type_code = type_element.type.first.code
 
           {
-            name: current_element.id,
+            slice_id: current_element.id,
+            slice_name: current_element.sliceName,
             path: current_element.path.gsub("#{resource}.", ''),
             discriminator: {
               type: 'type',
@@ -179,7 +180,8 @@ module USCoreTestKit
       def value_slices
         must_support_value_slice_elements.map do |current_element|
           {
-            name: current_element.id,
+            slice_id: current_element.id,
+            slice_name: current_element.sliceName,
             path: current_element.path.gsub("#{resource}.", ''),
             discriminator: {
               type: 'value'
@@ -209,18 +211,23 @@ module USCoreTestKit
       end
 
       def plain_must_support_elements
-        all_must_support_elements - must_support_extension_elements - must_support_slice_elements
+        plain_must_supports = all_must_support_elements - must_support_extension_elements - must_support_slice_elements
+      end
+
+      def element_part_of_slice_discrimination?(element)
+        must_support_slice_elements.any? { |ms_slice| element.id.include?(ms_slice.id) }
       end
 
+
       def handle_fixed_values(metadata, element)
         if element.fixedUri.present?
           metadata[:fixed_value] = element.fixedUri
-        elsif element.patternCodeableConcept.present?
+        elsif element.patternCodeableConcept.present? && !element_part_of_slice_discrimination?(element)
           metadata[:fixed_value] = element.patternCodeableConcept.coding.first.code
           metadata[:path] += '.coding.code'
         elsif element.fixedCode.present?
           metadata[:fixed_value] = element.fixedCode
-        elsif element.patternIdentifier.present?
+        elsif element.patternIdentifier.present? && !element_part_of_slice_discrimination?(element)
           metadata[:fixed_value] = element.patternIdentifier.system
           metadata[:path] += '.system'
         end
@@ -254,17 +261,25 @@ module USCoreTestKit
       end
 
       def handle_type_must_support_target_profiles(type, metadata)
-        index = 0
+        # US Core 3.1.1 profiles do not have US Core target profiles.
+        # Vital Sign proifles from FHIR R4 (version 4.0.1) do not have US Core target profiles either.
+        return if ['3.1.1', '4.0.1'].include?(profile.version)
+
         target_profiles = []
 
-        type.source_hash['_targetProfile']&.each do |hash|
-          if hash.present?
-            element = FHIR::Element.new(hash)
-            target_profiles << type.targetProfile[index] if type_must_support_extension?(element.extension)
+        if type.targetProfile&.length == 1
+          target_profiles << type.targetProfile.first
+        else
+          type.source_hash['_targetProfile']&.each_with_index do |hash, index|
+            if hash.present?
+              element = FHIR::Element.new(hash)
+              target_profiles << type.targetProfile[index] if type_must_support_extension?(element.extension)
+            end
           end
-          index += 1
         end
 
+        # remove target_profile for FHIR Base resource type.
+        target_profiles.delete_if { |reference| reference.start_with?('http://hl7.org/fhir/StructureDefinition')}
         metadata[:target_profiles] = target_profiles if target_profiles.present?
       end
 
@@ -283,7 +298,7 @@ module USCoreTestKit
       def must_support_elements
         plain_must_support_elements.each_with_object([]) do |current_element, must_support_elements_metadata|
           {
-            path: current_element.path.gsub("#{resource}.", '')
+            path: current_element.id.gsub("#{resource}.", '')
           }.tap do |current_metadata|
             if is_uscdi_requirement_element?(current_element)
               current_metadata[:uscdi_only] = true
@@ -317,7 +332,7 @@ module USCoreTestKit
 
       def handle_special_cases
         remove_vital_sign_component
-        remove_blood_pressure_value
+        remove_blood_pressure_value_data_absent_reason
         remove_observation_data_absent_reason
 
         case profile.version
@@ -345,7 +360,9 @@ module USCoreTestKit
 
       # Exclude Observation.component from vital sign profiles except observation-bp and observation-pulse-ox
       def remove_vital_sign_component
-        if is_vital_sign? && !is_blood_pressure? && profile.name != 'USCorePulseOximetryProfile'
+        return if is_blood_pressure? || profile.name == 'USCorePulseOximetryProfile'
+
+        if is_vital_sign?
           @must_supports[:elements].delete_if do |element|
             element[:path].start_with?('component')
           end
@@ -353,14 +370,22 @@ module USCoreTestKit
       end
 
       # Exclude Observation.value[x] from observation-bp
-      def remove_blood_pressure_value
-        if is_blood_pressure?
-          @must_supports[:elements].delete_if do |element|
-            element[:path].start_with?('value[x]') || element[:original_path]&.start_with?('value[x]')
-          end
-          @must_supports[:slices].delete_if do |slice|
-            slice[:path].start_with?('value[x]')
-          end
+      def remove_blood_pressure_value_data_absent_reason
+        return unless is_blood_pressure?
+
+        pattern = /component(:[^.]+)?\.dataAbsentReason/
+
+        @must_supports[:elements].delete_if do |element|
+          element[:path].start_with?('value[x]') ||
+          element[:original_path]&.start_with?('value[x]') ||
+          element[:path] == ('dataAbsentReason') ||
+          (
+            pattern.match?(element[:path]) && ['3.1.1', '4.0.0'].include?(ig_resources.ig.version)
+          )
+        end
+
+        @must_supports[:slices].delete_if do |slice|
+          slice[:path].start_with?('value[x]')
         end
       end
 
@@ -368,10 +393,15 @@ module USCoreTestKit
       # are not required to demonstrate Health IT Module support for "dataAbsentReason" elements.
       # Remove MS check for dataAbsentReason and component.dataAbsentReason from vital sign profiles and observation lab profile
       # Smoking status profile does not have MS on dataAbsentReason. It is safe to use profile.type == 'Observation'
+      # Since US Core 5.0.1, Blood Pressure profile restores component.dataAbsentReason as MustSupport.
       def remove_observation_data_absent_reason
+        return if is_blood_pressure?
+
+        pattern = /(component(:[^.]+)?\.)?dataAbsentReason/
+
         if profile.type == 'Observation'
           @must_supports[:elements].delete_if do |element|
-            ['dataAbsentReason', 'component.dataAbsentReason'].include?(element[:path])
+            pattern.match?(element[:path])
           end
         end
       end

data/lib/us_core_test_kit/generator/must_support_test_generator.rb

@@ -78,7 +78,7 @@ module USCoreTestKit
       def build_must_support_list_string(uscdi_only)
         slice_names = group_metadata.must_supports[:slices]
           .select { |slice| slice[:uscdi_only].presence == uscdi_only.presence }
-          .map { |slice| slice[:name] }
+          .map { |slice| slice[:slice_id] }
 
         element_names = group_metadata.must_supports[:elements]
           .select { |element| element[:uscdi_only].presence == uscdi_only.presence }

data/lib/us_core_test_kit/generator/search_test_generator.rb

@@ -257,9 +257,9 @@ module USCoreTestKit
         return '' unless test_medication_inclusion?
 
         <<~MEDICATION_INCLUSION_DESCRIPTION
-        If any MedicationRequest resources use external references to
+        If any #{resource_type} resources use external references to
         Medications, the search will be repeated with
-        `_include=MedicationRequest:medication`.
+        `_include=#{resource_type}:medication`.
         MEDICATION_INCLUSION_DESCRIPTION
       end
 

data/lib/us_core_test_kit/generator.rb

@@ -8,7 +8,6 @@ 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'
@@ -33,7 +32,6 @@ module USCoreTestKit
       puts "Generating tests for IG #{File.basename(ig_file_name)}"
       load_ig_package
       extract_metadata
-      generate_resource_list
       generate_search_tests
       generate_read_tests
       # TODO: generate_vread_tests
@@ -66,10 +64,6 @@ module USCoreTestKit
       self.ig_resources = IGLoader.new(ig_file_name).load
     end
 
-    def generate_resource_list
-      ResourceListGenerator.generate(ig_metadata, base_output_dir)
-    end
-
     def generate_reference_resolution_tests
       ReferenceResolutionTestGenerator.generate(ig_metadata, base_output_dir)
     end

data/lib/us_core_test_kit/must_support_test.rb

@@ -23,7 +23,6 @@ module USCoreTestKit
       if (missing_elements + missing_slices + missing_extensions).length.zero?
         pass
       end
-
       skip "Could not find #{missing_must_support_strings.join(', ')} in the #{resources.length} " \
            "provided #{resource_type} resource(s)"
     end
@@ -56,8 +55,8 @@ module USCoreTestKit
 
     def missing_must_support_strings
       missing_elements.map { |element_definition| missing_element_string(element_definition) } +
-        missing_slices.map { |slice_definition| slice_definition[:name] } +
-        missing_extensions.map { |extension_definition| extension_definition[:id] }
+      missing_slices.map { |slice_definition| slice_definition[:slice_id] } +
+      missing_extensions.map { |extension_definition| extension_definition[:id] }
     end
 
     def missing_element_string(element_definition)
@@ -110,12 +109,10 @@ module USCoreTestKit
                 (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
           end
         end
-
       @missing_elements
     end
 

data/lib/us_core_test_kit/reference_resolution_test.rb

@@ -12,7 +12,7 @@ module USCoreTestKit
 
       pass if unresolved_references(resources).length.zero?
 
-      skip "Could not resolve Must Support references #{unresolved_references_strings.join(', ')}"
+      skip "Could not resolve and validate any Must Support references for #{unresolved_references_strings.join(', ')}"
     end
 
     def unresolved_references_strings
@@ -20,7 +20,7 @@ module USCoreTestKit
         unresolved_references.each_with_object(Hash.new { |hash, key| hash[key] = [] }) do |missing, hash|
           hash[missing[:path]] << missing[:target_profile]
         end
-      unresolved_reference_hash.map { |path, profiles| "#{path}#{"(#{profiles.join('|')})" unless profiles.first.empty?}" }
+      unresolved_reference_hash.map { |path, profiles| "#{path} element: Reference#{"(#{profiles.join('|')})" unless profiles.first.empty?}" }
     end
 
     def record_resolved_reference(reference, target_profile)

data/lib/us_core_test_kit/search_test.rb

@@ -373,7 +373,7 @@ module USCoreTestKit
       end
     end
 
-    def test_medication_inclusion(medication_requests, params, patient_id)
+    def test_medication_inclusion(base_resources, params, patient_id)
       return if search_variant_test_records[:medication_inclusion]
 
       scratch[:medication_resources] ||= {}
@@ -381,13 +381,13 @@ module USCoreTestKit
       scratch[:medication_resources][patient_id] ||= []
       scratch[:medication_resources][:contained] ||= []
 
-      requests_with_external_references =
-        medication_requests
+      base_resources_with_external_reference =
+        base_resources
           .select { |request| request&.medicationReference&.present? }
           .reject { |request| request&.medicationReference&.reference&.start_with? '#' }
 
       contained_medications =
-        medication_requests
+        base_resources
           .select { |request| request&.medicationReference&.reference&.start_with? '#' }
           .flat_map(&:contained)
           .select { |resource| resource.resourceType == 'Medication' }
@@ -396,15 +396,32 @@ module USCoreTestKit
       scratch[:medication_resources][patient_id] += contained_medications
       scratch[:medication_resources][:contained] += contained_medications
 
-      return if requests_with_external_references.blank?
+      return if base_resources_with_external_reference.blank?
 
-      search_params = params.merge(_include: 'MedicationRequest:medication')
+      search_params = params.merge(_include: "#{resource_type}:medication")
 
       search_and_check_response(search_params)
 
       medications = fetch_all_bundled_resources.select { |resource| resource.resourceType == 'Medication' }
       assert medications.present?, 'No Medications were included in the search results'
 
+      included_medications = medications.map { |medication| "#{medication.resourceType}/#{medication.id}" }
+
+      matched_base_resources = base_resources_with_external_reference.select do |base_resource|
+        included_medications.any? do |medication_reference|
+          is_reference_match?(base_resource.medicationReference.reference, medication_reference)
+        end
+      end
+
+      not_matched_included_medications = included_medications.select do |medication_reference|
+        matched_base_resources.none? do |base_resource|
+          is_reference_match?(base_resource.medicationReference.reference, medication_reference)
+        end
+      end
+
+      not_matched_included_medications_string = not_matched_included_medications.join(',')
+      assert not_matched_included_medications.empty?, "No #{resource_type} references #{not_matched_included_medications_string} in the search result."
+
       medications.uniq!(&:id)
 
       scratch[:medication_resources][:all] += medications
@@ -413,6 +430,11 @@ module USCoreTestKit
       search_variant_test_records[:medication_inclusion] = true
     end
 
+    def is_reference_match? (reference, local_reference)
+      regex_pattern = /^(#{Regexp.escape(local_reference)}|\S+\/#{Regexp.escape(local_reference)}(?:[\/|]\S+)*)$/
+      reference.match?(regex_pattern)
+    end
+
     def all_scratch_resources
       scratch_resources[:all] ||= []
     end
@@ -547,7 +569,7 @@ module USCoreTestKit
       end
 
       valid_resource_types = [resource_type, 'OperationOutcome'].concat(additional_resource_types)
-      valid_resource_types << 'Medication' if resource_type == 'MedicationRequest'
+      valid_resource_types << 'Medication' if ['MedicationRequest', 'MedicationDispense'].include?(resource_type)
 
       invalid_resource_types =
         resources.reject { |entry| valid_resource_types.include? entry.resourceType }

data/lib/us_core_test_kit/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module USCoreTestKit
-  VERSION = '0.6.0'
+  VERSION = '0.6.2'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: us_core_test_kit
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.6.2
 platform: ruby
 authors:
 - Stephen MacVicar
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-08-29 00:00:00.000000000 Z
+date: 2023-12-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: inferno_core
@@ -113,6 +113,7 @@ files:
 - lib/us_core_test_kit/custom_groups/data_absent_reason_group.rb
 - lib/us_core_test_kit/custom_groups/v3.1.1/capability_statement_group.rb
 - lib/us_core_test_kit/custom_groups/v3.1.1/clinical_notes_guidance_group.rb
+- lib/us_core_test_kit/custom_groups/v3.1.1/profile_support_test.rb
 - lib/us_core_test_kit/custom_groups/v4.0.0/capability_statement_group.rb
 - lib/us_core_test_kit/custom_groups/v4.0.0/clinical_notes_guidance_group.rb
 - lib/us_core_test_kit/custom_groups/v4.0.0/document_reference_custodian_test.rb
@@ -420,7 +421,6 @@ files:
 - lib/us_core_test_kit/generated/v3.1.1/pulse_oximetry/pulse_oximetry_reference_resolution_test.rb
 - lib/us_core_test_kit/generated/v3.1.1/pulse_oximetry/pulse_oximetry_validation_test.rb
 - lib/us_core_test_kit/generated/v3.1.1/pulse_oximetry_group.rb
-- lib/us_core_test_kit/generated/v3.1.1/resource_list.rb
 - lib/us_core_test_kit/generated/v3.1.1/resprate/metadata.yml
 - lib/us_core_test_kit/generated/v3.1.1/resprate/resprate_must_support_test.rb
 - lib/us_core_test_kit/generated/v3.1.1/resprate/resprate_patient_category_date_search_test.rb
@@ -770,7 +770,6 @@ files:
 - lib/us_core_test_kit/generated/v4.0.0/pulse_oximetry/pulse_oximetry_reference_resolution_test.rb
 - lib/us_core_test_kit/generated/v4.0.0/pulse_oximetry/pulse_oximetry_validation_test.rb
 - lib/us_core_test_kit/generated/v4.0.0/pulse_oximetry_group.rb
-- lib/us_core_test_kit/generated/v4.0.0/resource_list.rb
 - lib/us_core_test_kit/generated/v4.0.0/respiratory_rate/metadata.yml
 - lib/us_core_test_kit/generated/v4.0.0/respiratory_rate/respiratory_rate_must_support_test.rb
 - lib/us_core_test_kit/generated/v4.0.0/respiratory_rate/respiratory_rate_patient_category_date_search_test.rb
@@ -1229,7 +1228,6 @@ files:
 - lib/us_core_test_kit/generated/v5.0.1/related_person/related_person_reference_resolution_test.rb
 - lib/us_core_test_kit/generated/v5.0.1/related_person/related_person_validation_test.rb
 - lib/us_core_test_kit/generated/v5.0.1/related_person_group.rb
-- lib/us_core_test_kit/generated/v5.0.1/resource_list.rb
 - lib/us_core_test_kit/generated/v5.0.1/respiratory_rate/metadata.yml
 - lib/us_core_test_kit/generated/v5.0.1/respiratory_rate/respiratory_rate_must_support_test.rb
 - lib/us_core_test_kit/generated/v5.0.1/respiratory_rate/respiratory_rate_patient_category_date_search_test.rb
@@ -1736,7 +1734,6 @@ files:
 - lib/us_core_test_kit/generated/v6.1.0/related_person/related_person_reference_resolution_test.rb
 - lib/us_core_test_kit/generated/v6.1.0/related_person/related_person_validation_test.rb
 - lib/us_core_test_kit/generated/v6.1.0/related_person_group.rb
-- lib/us_core_test_kit/generated/v6.1.0/resource_list.rb
 - lib/us_core_test_kit/generated/v6.1.0/respiratory_rate/metadata.yml
 - lib/us_core_test_kit/generated/v6.1.0/respiratory_rate/respiratory_rate_must_support_test.rb
 - lib/us_core_test_kit/generated/v6.1.0/respiratory_rate/respiratory_rate_patient_category_date_search_test.rb
@@ -1814,7 +1811,6 @@ files:
 - lib/us_core_test_kit/generator/provenance_revinclude_search_test_generator.rb
 - lib/us_core_test_kit/generator/read_test_generator.rb
 - lib/us_core_test_kit/generator/reference_resolution_test_generator.rb
-- lib/us_core_test_kit/generator/resource_list_generator.rb
 - lib/us_core_test_kit/generator/search_definition_metadata_extractor.rb
 - lib/us_core_test_kit/generator/search_metadata_extractor.rb
 - lib/us_core_test_kit/generator/search_test_generator.rb

data/lib/us_core_test_kit/generated/v3.1.1/resource_list.rb

@@ -1,28 +0,0 @@
-module USCoreTestKit
-  module USCoreV311
-    module ResourceList
-      RESOURCE_LIST = [
-        'AllergyIntolerance',
-      'CarePlan',
-      'CareTeam',
-      'Condition',
-      'Device',
-      'DiagnosticReport',
-      'DocumentReference',
-      'Encounter',
-      'Goal',
-      'Immunization',
-      'Location',
-      'Medication',
-      'MedicationRequest',
-      'Observation',
-      'Organization',
-      'Patient',
-      'Practitioner',
-      'PractitionerRole',
-      'Procedure',
-      'Provenance'
-      ].freeze
-    end
-  end
-end

data/lib/us_core_test_kit/generated/v4.0.0/resource_list.rb

@@ -1,28 +0,0 @@
-module USCoreTestKit
-  module USCoreV400
-    module ResourceList
-      RESOURCE_LIST = [
-        'AllergyIntolerance',
-      'CarePlan',
-      'CareTeam',
-      'Condition',
-      'Device',
-      'DiagnosticReport',
-      'DocumentReference',
-      'Encounter',
-      'Goal',
-      'Immunization',
-      'Location',
-      'Medication',
-      'MedicationRequest',
-      'Observation',
-      'Organization',
-      'Patient',
-      'Practitioner',
-      'PractitionerRole',
-      'Procedure',
-      'Provenance'
-      ].freeze
-    end
-  end
-end

data/lib/us_core_test_kit/generated/v5.0.1/resource_list.rb

@@ -1,31 +0,0 @@
-module USCoreTestKit
-  module USCoreV501
-    module ResourceList
-      RESOURCE_LIST = [
-        'AllergyIntolerance',
-      'CarePlan',
-      'CareTeam',
-      'Condition',
-      'Device',
-      'DiagnosticReport',
-      'DocumentReference',
-      'Encounter',
-      'Goal',
-      'Immunization',
-      'Location',
-      'Medication',
-      'MedicationRequest',
-      'Observation',
-      'Organization',
-      'Patient',
-      'Practitioner',
-      'PractitionerRole',
-      'Procedure',
-      'Provenance',
-      'QuestionnaireResponse',
-      'RelatedPerson',
-      'ServiceRequest'
-      ].freeze
-    end
-  end
-end

data/lib/us_core_test_kit/generated/v6.1.0/resource_list.rb

@@ -1,34 +0,0 @@
-module USCoreTestKit
-  module USCoreV610
-    module ResourceList
-      RESOURCE_LIST = [
-        'AllergyIntolerance',
-      'CarePlan',
-      'CareTeam',
-      'Condition',
-      'Coverage',
-      'Device',
-      'DiagnosticReport',
-      'DocumentReference',
-      'Encounter',
-      'Goal',
-      'Immunization',
-      'Location',
-      'Medication',
-      'MedicationDispense',
-      'MedicationRequest',
-      'Observation',
-      'Organization',
-      'Patient',
-      'Practitioner',
-      'PractitionerRole',
-      'Procedure',
-      'Provenance',
-      'QuestionnaireResponse',
-      'RelatedPerson',
-      'ServiceRequest',
-      'Specimen'
-      ].freeze
-    end
-  end
-end

data/lib/us_core_test_kit/generator/resource_list_generator.rb

@@ -1,42 +0,0 @@
-module USCoreTestKit
-  class Generator
-    class ResourceListGenerator
-      class << self
-        def generate(ig_metadata, base_output_dir)
-          @ig_metadata = ig_metadata
-
-          FileUtils.mkdir_p(base_output_dir)
-          File.open(File.join(base_output_dir, base_output_file_name), 'w') { |f| f.write(output) }
-        end
-
-        def resource_list          
-          @ig_metadata.groups.map(&:resource).uniq
-        end
-
-        def resource_list_string
-          resource_list.map { |resource| "      '#{resource}'" }.join(",\n")
-        end
-
-        def module_name
-          "USCore#{@ig_metadata.reformatted_version.upcase}"
-        end
-
-        def read_interaction(group_metadata)
-          group_metadata.interactions.find { |interaction| interaction[:code] == 'read' }
-        end
-
-        def template
-          @template ||= File.read(File.join(__dir__, 'templates', 'resource_list.rb.erb'))
-        end
-
-        def output
-          ERB.new(template).result(binding)
-        end
-
-        def base_output_file_name
-          "resource_list.rb"
-        end
-      end
-    end
-  end
-end