us_core_test_kit 0.2.1 → 0.2.4

data/lib/us_core_test_kit/generator/validation_test_generator.rb

@@ -84,6 +84,12 @@ module USCoreTestKit
         read_interaction[:expectation]
       end
 
+      def skip_if_empty
+        # Return true if a system must demonstrate at least one example of the resource type.
+        # This drives omit vs. skip result statuses in this test.
+        resource_type != 'Medication'
+      end
+
       def generate
         FileUtils.mkdir_p(output_file_directory)
         File.open(output_file_name, 'w') { |f| f.write(output) }
@@ -121,6 +127,7 @@ module USCoreTestKit
           <<~GENERIC_INTRO
           This test verifies resources returned from the first search conform to
           the [#{profile_name}](#{profile_url}).
+          Systems must demonstrate at least one valid example in order to pass this test.
           GENERIC_INTRO
         end
       end

data/lib/us_core_test_kit/must_support_test.rb

@@ -36,8 +36,16 @@ module USCoreTestKit
       end
     end
 
+    def include_uscdi_only_test?
+      config.options[:include_uscdi_only_test] == true
+    end
+
     def must_support_extensions
-      metadata.must_supports[:extensions]
+      if include_uscdi_only_test?
+        metadata.must_supports[:extensions]
+      else
+        metadata.must_supports[:extensions].reject{ |extension| extension[:uscdi_only] }
+      end
     end
 
     def missing_extensions(resources = [])
@@ -50,7 +58,11 @@ module USCoreTestKit
     end
 
     def must_support_elements
-      metadata.must_supports[:elements]
+      if include_uscdi_only_test?
+        metadata.must_supports[:elements]
+      else
+        metadata.must_supports[:elements].reject{ |element| element[:uscdi_only] }
+      end
     end
 
     def missing_elements(resources = [])
@@ -85,7 +97,11 @@ module USCoreTestKit
     end
 
     def must_support_slices
-      metadata.must_supports[:slices]
+      if include_uscdi_only_test?
+        metadata.must_supports[:slices]
+      else
+        metadata.must_supports[:slices].reject{ |slice| slice[:uscdi_only] }
+      end
     end
 
     def missing_slices(resources = [])

data/lib/us_core_test_kit/search_test.rb

@@ -31,7 +31,7 @@ module USCoreTestKit
             if fixed_value_search?
               fixed_value_search_param_values.map { |value| fixed_value_search_params(value, patient_id) }
             else
-              [search_params_with_values(patient_id)]
+              [search_params_with_values(search_param_names, patient_id)]
             end
           new_params.reject! do |params|
             params.any? { |_key, value| value.blank? }
@@ -135,6 +135,9 @@ module USCoreTestKit
       check_search_response
 
       post_search_resources = fetch_all_bundled_resources.select { |resource| resource.resourceType == resource_type }
+
+      filter_devices(post_search_resources) if resource_type == 'Device'
+
       get_resource_count = get_search_resources.length
       post_resource_count = post_search_resources.length
 
@@ -240,10 +243,11 @@ module USCoreTestKit
       new_search_params = params.merge('patient' => "Patient/#{params['patient']}")
       search_and_check_response(new_search_params)
 
-      new_resource_count =
-        fetch_all_bundled_resources
-          .select { |resource| resource.resourceType == resource_type }
-          .count
+      reference_with_type_resources = fetch_all_bundled_resources.select { |resource| resource.resourceType == resource_type }
+
+      filter_devices(reference_with_type_resources) if resource_type == 'Device'
+
+      new_resource_count = reference_with_type_resources.count
 
       assert new_resource_count == resource_count,
              "Expected search by `#{params['patient']}` to to return the same results as searching " \
@@ -256,9 +260,7 @@ module USCoreTestKit
     def perform_search_with_system(params, patient_id)
       return if search_variant_test_records[:token_variants]
 
-      new_search_params = token_search_params.each_with_object({}) do |name, search_params|
-        search_params[name] = search_param_value(name, patient_id, include_system: true)
-      end
+      new_search_params = search_params_with_values(token_search_params, patient_id, include_system: true)
       return if new_search_params.any? { |_name, value| value.blank? }
 
       search_params = params.merge(new_search_params)
@@ -308,7 +310,7 @@ module USCoreTestKit
       definition = metadata.search_definitions[param_name]
       return [] if definition.blank?
 
-      definition[:multiple_or] == 'SHALL' ? [definition[:values].join(',')] : [definition[:values]]
+      definition[:multiple_or] == 'SHALL' ? [definition[:values].join(',')] : Array.wrap(definition[:values])
     end
 
 
@@ -317,7 +319,7 @@ module USCoreTestKit
 
       all_search_params.each do |patient_id, params_list|
         next unless params_list.present?
-        
+
         search_params = params_list.first
         existing_values = {}
         missing_values = {}
@@ -423,11 +425,29 @@ module USCoreTestKit
       end
     end
 
-    def search_params_with_values(patient_id)
-      search_param_names.each_with_object({}) do |name, params|
-        value = patient_id_param?(name) ? patient_id : search_param_value(name, patient_id)
-        params[name] = value
+    def search_params_with_values(search_param_names, patient_id, include_system: false)
+      resources = scratch_resources_for_patient(patient_id)
+
+      if resources.empty?
+        return search_param_names.each_with_object({}) do |name, params|
+          value = patient_id_param?(name) ? patient_id : nil
+          params[name] = value
+        end
+      end
+
+      params_with_partial_value = resources.each_with_object({}) do |resource, outer_params|
+        results_from_one_resource = search_param_names.each_with_object({}) do |name, params|
+          value = patient_id_param?(name) ? patient_id : search_param_value(name, resource, include_system: include_system)
+          params[name] = value
+        end
+
+        outer_params.merge!(results_from_one_resource)
+
+        # stop if all parameter values are found
+        return outer_params if outer_params.all? { |_key, value| value.present? }
       end
+
+      params_with_partial_value
     end
 
     def patient_id_list
@@ -446,10 +466,10 @@ module USCoreTestKit
 
     def search_param_paths(name)
       paths = metadata.search_definitions[name.to_sym][:paths]
-      if paths.first =='class' 
+      if paths.first =='class'
         paths[0] = 'local_class'
       end
-      
+
       paths
     end
 
@@ -470,8 +490,13 @@ module USCoreTestKit
     end
 
     def no_resources_skip_message(resource_type = self.resource_type)
-      "No #{resource_type} resources appear to be available. " \
-      "Please use patients with more information"
+      msg = "No #{resource_type} resources appear to be available"
+
+      if (resource_type == 'Device' && implantable_device_codes.present?)
+        msg.concat(" with the following Device Type Code filter: #{implantable_device_codes}")
+      end
+
+      msg + ". Please use patients with more information"
     end
 
     def fetch_all_bundled_resources(
@@ -507,11 +532,16 @@ module USCoreTestKit
       valid_resource_types = [resource_type, 'OperationOutcome'].concat(additional_resource_types)
       valid_resource_types << 'Medication' if resource_type == 'MedicationRequest'
 
-      all_valid_resource_types =
-        resources.all? { |entry| valid_resource_types.include? entry.resourceType }
+      invalid_resource_types =
+        resources.reject { |entry| valid_resource_types.include? entry.resourceType }
+                 .map(&:resourceType)
+                 .uniq
 
-      assert all_valid_resource_types,
-             "All resources returned must be of the type: #{valid_resource_types.join(', ')}"
+      if invalid_resource_types.any?
+        info "Received resource type(s) #{invalid_resource_types.join(', ')} in search bundle, " \
+             "but only expected resource types #{valid_resource_types.join(', ')}. " + \
+             "This is unusual but allowed if the server believes additional resource types are relevant."
+      end
 
       resources
     end
@@ -520,11 +550,11 @@ module USCoreTestKit
       "Could not resolve next bundle: #{link}"
     end
 
-    def search_param_value(name, patient_id, include_system: false)
+    def search_param_value(name, resource, include_system: false)
       paths = search_param_paths(name)
       search_value = nil
       paths.each do |path|
-        element = find_a_value_at(scratch_resources_for_patient(patient_id), path)
+        element = find_a_value_at(resource, path) { |element| element_has_valid_value?(element, include_system) }
 
         search_value =
           case element
@@ -541,34 +571,37 @@ module USCoreTestKit
             if include_system
               coding =
                 find_a_value_at(element, 'coding') { |coding| coding.code.present? && coding.system.present? }
-              coding.present? ? "#{coding.system}|#{coding.code}" : nil
+              "#{coding.system}|#{coding.code}"
             else
               find_a_value_at(element, 'coding.code')
             end
           when FHIR::Identifier
-            if include_system
-              identifier = find_a_value_at(scratch_resources_for_patient(patient_id), path) do |identifier|
-                identifier.value.present? && identifier.system.present?
-              end
-              identifier.present? ? "#{identifier.system}|#{identifier.value}" : nil
-            else
-              element.value
-            end
+            include_system ? "#{element.system}|#{element.value}" : element.value
           when FHIR::Coding
-            if include_system
-              coding = find_a_value_at(scratch_resources_for_patient(patient_id), path) do |coding|
-                coding.code.present? && coding.system.present?
-              end
-              coding.present? ? "#{coding.system}|#{coding.code}" : nil
-            else
-              element.code
-            end
+            include_system ? "#{element.system}|#{element.code}" : element.code
           when FHIR::HumanName
             element.family || element.given&.first || element.text
           when FHIR::Address
             element.text || element.city || element.state || element.postalCode || element.country
           else
-            element
+            if metadata.version != 'v3.1.1' &&
+               metadata.search_definitions[name.to_sym][:type] == 'date' &&
+               params_with_comparators&.include?(name)
+              # convert date search to greath-than comparator search with correct precision
+              # For all date search parameters:
+              #   Patient.birthDate does not mandate comparators so cannot be converted
+              #   Goal.target-date has day precision
+              #   All others have second + time offset precision
+              if /^\d{4}$/.match?(element) || # YYYY
+                 /^\d{4}-\d{2}$/.match?(element) || # YYYY-MM
+                (/^\d{4}-\d{2}-\d{2}$/.match?(element) && resource_type != "Goal") # YYYY-MM-DD AND Resource is NOT Goal
+                "gt#{(DateTime.xmlschema(element)-1).xmlschema}"
+              else
+                element
+              end
+            else
+              element
+            end
           end
 
           break if search_value.present?
@@ -578,6 +611,31 @@ module USCoreTestKit
       escaped_value
     end
 
+    def element_has_valid_value?(element, include_system)
+      case element
+      when FHIR::Reference
+        element.reference.present?
+      when FHIR::CodeableConcept
+        if include_system
+          coding =
+            find_a_value_at(element, 'coding') { |coding| coding.code.present? && coding.system.present? }
+          coding.present?
+        else
+          find_a_value_at(element, 'coding.code').present?
+        end
+      when FHIR::Identifier
+        include_system ? element.value.present? && element.system.present? : element.value.present?
+      when FHIR::Coding
+        include_system ? element.code.present? && element.system.present? : element.code.present?
+      when FHIR::HumanName
+        (element.family || element.given&.first || element.text).present?
+      when FHIR::Address
+        (element.text || element.city || element.state || element.postalCode || element.country).present?
+      else
+        true
+      end
+    end
+
     def save_resource_reference(resource_type, reference)
       scratch[:references] ||= {}
       scratch[:references][resource_type] ||= Set.new
@@ -647,9 +705,9 @@ module USCoreTestKit
                 address&.country&.downcase&.start_with?(search_value_downcase)
               end
             when 'CodeableConcept'
-              # FHIR token search (https://www.hl7.org/fhir/search.html#token): "When in doubt, servers SHOULD 
-              # treat tokens in a case-insensitive manner, on the grounds that including undesired data has 
-              # less safety implications than excluding desired behavior". 
+              # FHIR token search (https://www.hl7.org/fhir/search.html#token): "When in doubt, servers SHOULD
+              # treat tokens in a case-insensitive manner, on the grounds that including undesired data has
+              # less safety implications than excluding desired behavior".
               codings = values_found.flat_map(&:coding)
               if search_value.include? '|'
                 system = search_value.split('|').first
@@ -691,7 +749,7 @@ module USCoreTestKit
                 values_found.any? { |value_found| search_values.include? value_found }
               end
             end
-          
+
           break if match_found
         end
 

data/lib/us_core_test_kit/validation_test.rb

@@ -3,9 +3,15 @@ module USCoreTestKit
     DAR_CODE_SYSTEM_URL = 'http://terminology.hl7.org/CodeSystem/data-absent-reason'.freeze
     DAR_EXTENSION_URL = 'http://hl7.org/fhir/StructureDefinition/data-absent-reason'.freeze
 
-    def perform_validation_test(resources, profile_url)
-      skip_if resources.blank?,
-              "No #{resource_type} resources conforming to the #{profile_url} profile were returned."
+    def perform_validation_test(resources,
+                                profile_url,
+                                skip_if_empty: true)
+
+      skip_if skip_if_empty && resources.blank?,
+              "No #{resource_type} resources conforming to the #{profile_url} profile were returned"
+
+      omit_if resources.blank?,
+              "No #{resource_type} resources provided so the #{profile_url} profile does not apply"
 
       resources.each do |resource|
         resource_is_valid?(resource: resource, profile_url: profile_url)

data/lib/us_core_test_kit/version.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module USCoreTestKit
-  VERSION = '0.2.1'
+  VERSION = '0.2.4'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: us_core_test_kit
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.4
 platform: ruby
 authors:
 - Stephen MacVicar
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-04-11 00:00:00.000000000 Z
+date: 2022-07-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: inferno_core