us_core_test_kit 0.4.0 → 0.4.2

data/lib/us_core_test_kit/generated/v5.0.1/smokingstatus/metadata.yml

@@ -168,66 +168,10 @@
 - Observation.value[x]
 - Observation.component.code
 :bindings:
-- :type: code
-  :strength: preferred
-  :system: http://hl7.org/fhir/ValueSet/languages
-  :path: language
 - :type: code
   :strength: required
   :system: http://hl7.org/fhir/us/core/ValueSet/us-core-observation-smoking-status-status
   :path: status
-- :type: CodeableConcept
-  :strength: preferred
-  :system: http://hl7.org/fhir/ValueSet/observation-category
-  :path: category
-- :type: CodeableConcept
-  :strength: preferred
-  :system: http://hl7.org/fhir/ValueSet/observation-category
-  :path: category
-- :type: CodeableConcept
-  :strength: extensible
-  :system: http://hl7.org/fhir/us/core/ValueSet/us-core-smoking-status-observation-codes
-  :path: code
-- :type: CodeableConcept
-  :strength: preferred
-  :system: http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.11.20.9.38
-  :path: value
-- :type: CodeableConcept
-  :strength: extensible
-  :system: http://hl7.org/fhir/ValueSet/data-absent-reason
-  :path: dataAbsentReason
-- :type: CodeableConcept
-  :strength: extensible
-  :system: http://hl7.org/fhir/ValueSet/observation-interpretation
-  :path: interpretation
-- :type: CodeableConcept
-  :strength: example
-  :system: http://hl7.org/fhir/ValueSet/body-site
-  :path: bodySite
-- :type: CodeableConcept
-  :strength: example
-  :system: http://hl7.org/fhir/ValueSet/observation-methods
-  :path: method
-- :type: CodeableConcept
-  :strength: preferred
-  :system: http://hl7.org/fhir/ValueSet/referencerange-meaning
-  :path: referenceRange.type
-- :type: CodeableConcept
-  :strength: example
-  :system: http://hl7.org/fhir/ValueSet/referencerange-appliesto
-  :path: referenceRange.appliesTo
-- :type: CodeableConcept
-  :strength: example
-  :system: http://hl7.org/fhir/ValueSet/observation-codes
-  :path: component.code
-- :type: CodeableConcept
-  :strength: extensible
-  :system: http://hl7.org/fhir/ValueSet/data-absent-reason
-  :path: component.dataAbsentReason
-- :type: CodeableConcept
-  :strength: extensible
-  :system: http://hl7.org/fhir/ValueSet/observation-interpretation
-  :path: component.interpretation
 :references:
 - :path: Observation.basedOn
   :profiles:

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

@@ -3,6 +3,7 @@ require_relative '../../version'
 require_relative '../../custom_groups/v5.0.1/capability_statement_group'
 require_relative '../../custom_groups/v4.0.0/clinical_notes_guidance_group'
 require_relative '../../custom_groups/data_absent_reason_group'
+require_relative '../../provenance_validator'
 require_relative 'patient_group'
 require_relative 'allergy_intolerance_group'
 require_relative 'care_plan_group'
@@ -48,13 +49,27 @@ module USCoreTestKit
   module USCoreV501
     class USCoreTestSuite < Inferno::TestSuite
       title 'US Core v5.0.1'
+      description %(
+        The US Core Test Kit tests systems for their conformance to the [US Core
+        Implementation Guide](http://hl7.org/fhir/us/core/STU5.0.1).
+
+        Resources are validated with the FHIR Java validator using `tx.fhir.org`
+        as the terminology server. Users should note that the although the ONC
+        Certification (g)(10) Standardized API Test Suite includes tests from
+        this suite, [it uses a different method to perform terminology
+        validation](https://github.com/onc-healthit/onc-certification-g10-test-kit/wiki/FAQ#q-why-do-some-resources-fail-in-us-core-test-kit-with-terminology-validation-errors).
+        As a result, resource validation results may not be consistent between
+        the US Core Test Suite and the ONC Certification (g)(10) Standardized
+        API Test Suite.
+      )
       version VERSION
 
       VALIDATION_MESSAGE_FILTERS = [
         %r{Sub-extension url 'introspect' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris$},
         %r{Sub-extension url 'revoke' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris$},
         /Observation\.effective\.ofType\(Period\): .*vs-1:/, # Invalid invariant in FHIR v4.0.1
-        /Observation\.effective\.ofType\(Period\): .*us-core-1:/ # Invalid invariant in US Core v3.1.1
+        /Observation\.effective\.ofType\(Period\): .*us-core-1:/, # Invalid invariant in US Core v3.1.1
+        /Provenance.agent\[\d*\]: Rule provenance-1/ #Invalid invariant in US Core v5.0.1
       ].freeze
 
       def self.metadata
@@ -68,6 +83,10 @@ module USCoreTestKit
         exclude_message do |message|
           VALIDATION_MESSAGE_FILTERS.any? { |filter| filter.match? message.message }
         end
+
+        perform_additional_validation do |resource, profile_url|
+          ProvenanceValidator.validate(resource) if resource.instance_of?(FHIR::Provenance)
+        end
       end
 
       id :us_core_v501

data/lib/us_core_test_kit/generator/must_support_metadata_extractor.rb

@@ -1,3 +1,5 @@
+require_relative 'value_extractor'
+
 module USCoreTestKit
   class Generator
     class MustSupportMetadataExtractor
@@ -97,13 +99,10 @@ module USCoreTestKit
               elsif pattern_element.binding&.strength == 'required' &&
                     pattern_element.binding&.valueSet.present?
 
-                value_set = ig_resources.value_set_by_url(pattern_element.binding.valueSet)
-                bound_systems = value_set&.compose&.include&.reject { |code| code.concept.blank? }
-                values = []
+                value_extractor = ValueExactor.new(ig_resources, resource, profile_elements)
 
-                if bound_systems.present?
-                  values = bound_systems&.flat_map { |system| system.concept.map { |code| code.code } }.uniq
-                end
+                values = value_extractor.values_from_value_set_binding(pattern_element).presence ||
+                         value_extractor.values_from_resource_metadata([metadata[:path]]).presence || []
 
                 {
                   type: 'requiredBinding',
@@ -292,6 +291,8 @@ module USCoreTestKit
         add_must_support_choices
 
         case profile.version
+        when '3.1.1'
+          remove_document_reference_custodian
         when '4.0.0'
           add_device_distinct_identifier
           add_patient_uscdi_elements
@@ -354,6 +355,15 @@ module USCoreTestKit
         end
       end
 
+      # US Core clarified that server implmentation is not required to support DocumentReference.custodian (FHIR-28393)
+      def remove_document_reference_custodian
+        if profile.type == 'DocumentReference'
+          @must_supports[:elements].delete_if do |element|
+            element[:path] == 'custodian'
+          end
+        end
+      end
+
       def remove_document_reference_attachment_data_url
         if profile.type == 'DocumentReference'
           @must_supports[:elements].delete_if do |element|
@@ -482,7 +492,7 @@ module USCoreTestKit
 
         slice = @must_supports[:slices].find{|slice| slice[:path] == 'category'}
 
-        slice[:discriminator][:values] << 'clinical-note' if slice.present?
+        slice[:discriminator][:values] = ['clinical-note'] if slice.present?
       end
 
       # FHIR-37794 Server systems are not required to support US Core QuestionnaireResponse

data/lib/us_core_test_kit/generator/search_definition_metadata_extractor.rb

@@ -1,3 +1,5 @@
+require_relative 'value_extractor'
+
 module USCoreTestKit
   class Generator
     class SearchDefinitionMetadataExtractor
@@ -112,103 +114,21 @@ module USCoreTestKit
       end
 
       def values
-        values = (
-          (
-            values_from_pattern_codeable_concept_slices +
-            values_from_required_binding_slices +
-            values_from_fixed_codes +
-            values_from_pattern_coding +
-            values_from_pattern_codeable_concept
-          ).uniq.presence || values_from_value_set_binding(profile_element)
-        ).presence || values_from_resource_metadata
-        values
-      end
-
-      def slices
-        return [] unless contains_multiple?
-
-        profile_elements.select do |element|
-          full_paths.include?(element.path) &&
-            element.sliceName.present? &&
-            (
-              element.patternCodeableConcept.present? ||
-              element.binding.present? && element.binding.strength == 'required'
-            )
-        end
+          value_extractor.values_from_slicing(profile_element, type).presence ||
+          value_extractor.values_from_value_set_binding(profile_element).presence ||
+          values_from_resource_metadata(paths).presence || []
       end
 
-      def values_from_pattern_codeable_concept_slices
-        slices.map do |slice|
-          slice.patternCodeableConcept.coding.first.code if slice.patternCodeableConcept.present?
-        end.compact
-      end
-
-      def values_from_required_binding_slices
-        slices.map do |slice|
-          if slice.binding.present? && slice.binding.strength == 'required'
-            values_from_value_set_binding(slice)
-          end
-        end.flatten.compact
-      end
-
-      def values_from_fixed_codes
-        return [] unless type == 'CodeableConcept'
-
-        profile_elements
-          .select { |element| element.path == "#{profile_element.path}.coding.code" && element.fixedCode.present? }
-          .map { |element| element.fixedCode }
-      end
-
-      def values_from_pattern_coding
-        return [] unless type == 'CodeableConcept'
-
-        profile_elements
-          .select { |element| element.path == "#{profile_element.path}.coding" && element.patternCoding.present? }
-          .map { |element| element.patternCoding.code }
-      end
-
-      def values_from_pattern_codeable_concept
-        return [] if type != 'CodeableConcept' || profile_element.patternCodeableConcept.blank?
-
-        [profile_element.patternCodeableConcept.coding.first.code]
-      end
-
-      def value_set_binding(the_element)
-        the_element&.binding
-      end
-
-      def value_set(the_element)
-        ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
-      end
-
-      def bound_systems(the_element)
-        value_set(the_element)&.compose&.include&.reject { |code| code.concept.nil? }
-      end
-
-      def values_from_value_set_binding(the_element)
-        bound_systems = bound_systems(the_element)
-
-        return [] if bound_systems.blank?
-
-        bound_systems.flat_map { |system| system.concept.map { |code| code.code } }.uniq
-      end
-
-      def fhir_metadata(current_path)
-        FHIR.const_get(resource)::METADATA[current_path]
-      end
-
-      def values_from_resource_metadata
-        values = []
-
-        paths.each do |current_path|
-          current_metadata = fhir_metadata(current_path)
-
-          if current_metadata&.dig('valid_codes').present?
-            values = values + current_metadata['valid_codes'].values.flatten
-          end
+      def values_from_resource_metadata(paths)
+        if multiple_or_expectation == 'SHALL' || paths.include?('status')
+          value_extractor.values_from_resource_metadata(paths)
+        else
+          []
         end
+      end
 
-        values
+      def value_extractor
+        @value_extractor ||= ValueExactor.new(ig_resources, resource, profile_elements)
       end
     end
   end

data/lib/us_core_test_kit/generator/suite_generator.rb

@@ -53,6 +53,17 @@ module USCoreTestKit
         "#{ig_metadata.reformatted_version.upcase}_VALIDATOR_URL"
       end
 
+      def ig_link
+        case ig_metadata.ig_version
+        when 'v5.0.1'
+          'http://hl7.org/fhir/us/core/STU5.0.1'
+        when 'v4.0.0'
+          'http://hl7.org/fhir/us/core/STU4'
+        when 'v3.1.1'
+          'http://hl7.org/fhir/us/core/STU3.1.1'
+        end
+      end
+
       def generate
         File.open(output_file_name, 'w') { |f| f.write(output) }
       end

data/lib/us_core_test_kit/generator/terminology_binding_metadata_extractor.rb

@@ -27,21 +27,33 @@ module USCoreTestKit
         end
       end
 
+      def element_has_optional_binding_slice?(element)
+        element.sliceName.present? && element.min == 0
+      end
+
       def profile_elements_with_bindings
         profile_elements
-          .select { |element| element.binding.present? }
-          .reject { |element| element_has_fixed_value? element }
+          .select { |element| element.binding.present? && element.binding.strength == 'required'}
+          .reject { |element| element_has_fixed_value?(element) || element_has_optional_binding_slice?(element) }
       end
 
+
+
       def element_terminology_bindings
         profile_elements_with_bindings.map do |element|
-          {
+          binding = {
             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}.", '')
           }
+
+          if element.sliceName.present? && element.min > 0
+            binding[:required_binding_slice] = true
+          end
+
+          binding
         end
       end
 

data/lib/us_core_test_kit/generator/value_extractor.rb

@@ -0,0 +1,101 @@
+module USCoreTestKit
+  class Generator
+    class ValueExactor
+      attr_accessor :ig_resources, :resource, :profile_elements
+
+      def initialize(ig_resources, resource, profile_elements)
+        self.ig_resources = ig_resources
+        self.resource = resource
+        self.profile_elements = profile_elements
+      end
+
+      def values_from_slicing(profile_element, type)
+        (
+          values_from_required_binding(profile_element) +
+          values_from_fixed_codes(profile_element, type) +
+          values_from_pattern_coding(profile_element, type) +
+          values_from_pattern_codeable_concept(profile_element, type)
+        ).uniq
+      end
+
+      def values_from_required_binding(profile_element)
+        return [] unless profile_element&.max == '*'
+
+        profile_elements
+          .select do |element|
+            element.path == profile_element.path && element.binding&.strength == 'required'
+          end
+          .map { |element| values_from_value_set_binding(element) }
+          .flatten.compact
+      end
+
+      def values_from_fixed_codes(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        profile_elements
+          .select do
+            |element| element.path == "#{profile_element.path}.coding.code" && element.fixedCode.present?
+          end
+          .map { |element| element.fixedCode }
+      end
+
+      def values_from_pattern_coding(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        profile_elements
+          .select do |element|
+            element.path == "#{profile_element.path}.coding" && element.patternCoding.present?
+          end
+          .map { |element| element.patternCoding.code }
+      end
+
+      def values_from_pattern_codeable_concept(profile_element, type)
+        return [] unless type == 'CodeableConcept'
+
+        profile_elements
+          .select do |element|
+            element.path == profile_element.path && element.patternCodeableConcept.present? && element.min > 0
+          end
+          .map { |element| element.patternCodeableConcept.coding.first.code }
+      end
+
+      def value_set_binding(the_element)
+        the_element&.binding
+      end
+
+      def value_set(the_element)
+        ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
+      end
+
+      def bound_systems(the_element)
+        value_set(the_element)&.compose&.include&.reject { |code| code.concept.nil? }
+      end
+
+      def values_from_value_set_binding(the_element)
+        bound_systems = bound_systems(the_element)
+
+        return [] if bound_systems.blank?
+
+        bound_systems.flat_map { |system| system.concept.map { |code| code.code } }.uniq
+      end
+
+      def fhir_metadata(current_path)
+        FHIR.const_get(resource)::METADATA[current_path]
+      end
+
+      def values_from_resource_metadata(paths)
+        values = []
+
+        paths.each do |current_path|
+          current_metadata = fhir_metadata(current_path)
+
+          if current_metadata&.dig('valid_codes').present?
+            values = values + current_metadata['valid_codes'].values.flatten
+          end
+        end
+
+        values
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/provenance_validator.rb

@@ -0,0 +1,37 @@
+module USCoreTestKit
+  class ProvenanceValidator
+    include FHIRResourceNavigation
+
+    def self.validate(...)
+      new(...).validate
+    end
+
+    attr_reader :resource, :validation_messages
+
+    def initialize(resource)
+      @resource = resource
+      @validation_messages = []
+    end
+
+    def validate
+      # Invariant provenance-1 in US Core 5 causes validation error. See FHIR-39518
+      return validation_messages unless resource.instance_of?(FHIR::Provenance)
+
+      failed_provenance =
+        find_a_value_at(resource, 'agent') do |agent|
+          ['Practitioner', 'Device'].any? { |resource_type| agent.who.reference&.include?(resource_type) } &&
+          agent.onBehalfOf.nil?
+        end
+
+
+      if failed_provenance.present?
+        validation_messages << {
+          type: 'error',
+          message: "#{resource.resourceType}/#{resource.id}: Rule provenance-1: 'onBehalfOf SHALL be present when Provenance.agent.who is a Practitioner or Device' Failed"
+        }
+      end
+
+      validation_messages
+    end
+  end
+end

data/lib/us_core_test_kit/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module USCoreTestKit
-  VERSION = '0.4.0'
+  VERSION = '0.4.2'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: us_core_test_kit
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.2
 platform: ruby
 authors:
 - Stephen MacVicar
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-10-31 00:00:00.000000000 Z
+date: 2022-12-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: inferno_core
@@ -1292,6 +1292,7 @@ files:
 - lib/us_core_test_kit/generator/suite_generator.rb
 - lib/us_core_test_kit/generator/terminology_binding_metadata_extractor.rb
 - lib/us_core_test_kit/generator/validation_test_generator.rb
+- lib/us_core_test_kit/generator/value_extractor.rb
 - lib/us_core_test_kit/igs/us_core_311.tgz
 - lib/us_core_test_kit/igs/us_core_311/StructureDefinition-bodyheight.json
 - lib/us_core_test_kit/igs/us_core_311/StructureDefinition-bodytemp.json
@@ -1302,6 +1303,7 @@ files:
 - lib/us_core_test_kit/igs/us_core_400.tgz
 - lib/us_core_test_kit/igs/us_core_501.tgz
 - lib/us_core_test_kit/must_support_test.rb
+- lib/us_core_test_kit/provenance_validator.rb
 - lib/us_core_test_kit/read_test.rb
 - lib/us_core_test_kit/reference_resolution_test.rb
 - lib/us_core_test_kit/request_logger.rb