us_quality_core_test_kit 0.1.1 → 0.2.0

data/lib/us_quality_core_test_kit/generator/search_test_generator.rb

@@ -1,13 +1,196 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/search_test_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class SearchTestGenerator < USCoreTestKit::Generator::SearchTestGenerator
+    class SearchTestGenerator
+      attr_accessor :group_metadata, :search_metadata, :base_output_dir
+
+      def initialize(group_metadata, search_metadata, base_output_dir)
+        self.group_metadata = group_metadata
+        self.search_metadata = search_metadata
+        self.base_output_dir = base_output_dir
+      end
+
+      def output
+        @output ||= ERB.new(template, trim_mode: '-').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 search_identifier
+        search_metadata[:names].join('_').tr('-', '_')
+      end
+
+      def search_title
+        search_identifier.camelize
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def conformance_expectation
+        search_metadata[:expectation]
+      end
+
+      def search_params
+        @search_params ||=
+          search_metadata[:names].map do |name|
+            {
+              name: name,
+              path: search_definition(name)[:path]
+            }
+          end
+      end
+
+      def first_search?
+        group_metadata.searches.first == search_metadata
+      end
+
+      def fixed_value_search_param_name
+        (search_metadata[:names] - [:patient]).first
+      end
+
+      def search_param_name_string
+        search_metadata[:names].join(' + ')
+      end
+
+      def search_param_names
+        search_params.map { |param| param[:name] }
+      end
+
+      def search_param_names_array
+        array_of_strings(search_param_names)
+      end
+
+      def path_for_value(path)
+        path == 'class' ? 'local_class' : path
+      end
+
+      def required_comparators_for_param(name)
+        search_definition(name)[:comparators].select { |_comparator, expectation| expectation == 'SHALL' }
+      end
+
+      def required_comparators
+        @required_comparators ||=
+          search_param_names.each_with_object({}) do |name, comparators|
+            required_comparators = required_comparators_for_param(name)
+            comparators[name] = required_comparators if required_comparators.present?
+          end
+      end
+
+      def optional?
+        conformance_expectation != 'SHALL' || !search_metadata[:must_support_or_mandatory]
+      end
+
+      def search_definition(name)
+        group_metadata.search_definitions[name.to_sym]
+      end
+
+      def saves_delayed_references?
+        first_search? && group_metadata.delayed_references.present?
+      end
+
+      def possible_status_search?
+        search_metadata[:names].none? { |name| name.include? 'status' } &&
+          group_metadata.search_definitions.keys.any? { |key| key.to_s.include? 'status' }
+      end
+
+      def token_search_params
+        @token_search_params ||=
+          search_param_names.select do |name|
+            %w[Identifier CodeableConcept Coding].include? group_metadata.search_definitions[name.to_sym][:type]
+          end
+      end
+
+      def token_search_params_string
+        array_of_strings(token_search_params)
+      end
+
+      def required_multiple_or_search_params
+        @required_multiple_or_search_params ||=
+          search_param_names.select do |name|
+            search_definition(name)[:multiple_or] == 'SHALL'
+          end
+      end
+
+      def required_multiple_or_search_params_string
+        array_of_strings(required_multiple_or_search_params)
+      end
+
+      def required_comparators_string
+        array_of_strings(required_comparators.keys)
+      end
+
+      def array_of_strings(array)
+        quoted_strings = array.map { |element| "'#{element}'" }
+        "[#{quoted_strings.join(', ')}]"
+      end
+
+      def test_reference_variants?
+        first_search? && search_param_names.include?('patient')
+      end
+
+      def test_post_search?
+        first_search?
+      end
+
+      def search_properties
+        {}.tap do |properties|
+          properties[:first_search] = 'true' if first_search?
+          properties[:fixed_value_search] = 'true' if fixed_value_search?
+          properties[:resource_type] = "'#{resource_type}'"
+          properties[:search_param_names] = search_param_names_array
+          properties[:saves_delayed_references] = 'true' if saves_delayed_references?
+          properties[:possible_status_search] = 'true' if possible_status_search?
+          properties[:test_medication_inclusion] = 'true' if test_medication_inclusion?
+          properties[:token_search_params] = token_search_params_string if token_search_params.present?
+          properties[:test_reference_variants] = 'true' if test_reference_variants?
+          properties[:params_with_comparators] = required_comparators_string if required_comparators.present?
+          properties[:multiple_or_search_params] = required_multiple_or_search_params_string if required_multiple_or_search_params.present?
+          properties[:test_post_search] = 'true' if first_search?
+        end
+      end
+
+      def search_test_properties_string
+        search_properties
+          .map { |key, value| "#{' ' * 8}#{key}: #{value}" }
+          .join(",\n")
+      end
+
+      def generate
+        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
+
+      def medication_inclusion_description
+        return '' unless test_medication_inclusion?
+
+        <<~MEDICATION_INCLUSION_DESCRIPTION
+          If any #{resource_type} resources use external references to
+          Medications, the search will be repeated with
+          `_include=#{resource_type}:medication`.
+        MEDICATION_INCLUSION_DESCRIPTION
+      end
+
       class << self
         def generate(ig_metadata, base_output_dir)
           ig_metadata.groups
@@ -33,6 +216,12 @@ module USQualityCoreTestKit
           (resource_type == 'Patient' && search_metadata[:names].include?('_id'))
       end
 
+      def needs_care_plan_category_code?
+        group_metadata.version == 'v1.0.0-ballot' &&
+          resource_type == 'CarePlan' &&
+          search_param_names.include?('category')
+      end
+
       def fixed_value_search?
         first_search? && search_metadata[:names] != ['patient'] &&
           search_metadata[:names] != ['subject'] &&

data/lib/us_quality_core_test_kit/generator/special_cases.rb

@@ -10,7 +10,7 @@ module USQualityCoreTestKit
       # The generator will not create tests for resources found in this list
       # for the specified IG versions.
       RESOURCES_TO_EXCLUDE = {
-        'Medication' => %w[v050]
+        'Medication' => %w[v050 v100_ballot]
       }.freeze
 
       # This list is meant to capture "abstract" profiles that do not themselves
@@ -33,27 +33,50 @@ module USQualityCoreTestKit
       # These resources will be gathered for testing via references from other
       # resources.
       DELAYED = {
-        'Encounter' => %w[v050],
-        'Location' => %w[v050]
+        'Encounter' => %w[v050 v100_ballot],
+        'Location' => %w[v050 v100_ballot]
       }.freeze
 
       # Category should be included in the initial search for these profiles.
       ALL_VERSION_CATEGORY_FIRST_PROFILES = [
         CARE_PLAN,
+        CONDITION_ENCOUNTER_DIAGNOSIS,
+        CONDITION_PROBLEMS_HEALTH_CONCERNS,
         DIAGNOSTIC_REPORT_LAB,
         DIAGNOSTIC_REPORT_NOTE,
-        CONDITION_ENCOUNTER_DIAGNOSIS,
-        CONDITION_PROBLEMS_HEALTH_CONCERNS
+        DOCUMENT_REFERENCE,
+        ADI_DOCUMENT_REFERENCE
       ].freeze
 
-      VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES = {}.freeze
+      VERSION_SPECIFIC_CATEGORY_FIRST_PROFILES = {
+        'http://fhir.org/guides/onc/us-quality-core/StructureDefinition/us-quality-core-careplan' => ['v050'],
+        'http://fhir.org/guides/onc/us-quality-core/StructureDefinition/us-quality-core-condition-encounter-diagnosis' => ['v050'],
+        'http://fhir.org/guides/onc/us-quality-core/StructureDefinition/us-quality-core-condition-problems-health-concerns' => ['v050'],
+        'http://fhir.org/guides/onc/us-quality-core/StructureDefinition/us-quality-core-diagnosticreport-lab' => ['v050'],
+        'http://fhir.org/guides/onc/us-quality-core/StructureDefinition/us-quality-core-diagnosticreport-note' => ['v050']
+
+      }.freeze
 
       PROFILE_CATEGORY_SEARCH_VALUES = {
         OBSERVATION_CLINICAL_RESULT => ['exam'],
-        SIMPLE_OBSERVATION => ['activity'],
         OBSERVATION_CANCELLED => ['activity']
       }.freeze
 
+      DO_NOT_PERFORM_PROFILES = [
+        DEVICE_NOT_REQUESTED, # v0.5.0
+        DEVICE_REQUEST_V050, # v0.5.0
+        MEDICATION_REQUEST_NOT_REQUESTED, # v0.5.0
+        MEDICATION_REQUEST_V050, # v0.5.0
+        SERVICE_NOT_REQUESTED, # v0.5.0
+        SERVICE_REQUEST_V050, # v0.5.0
+        DEVICE_REQUESTED,
+        DEVICE_PROHIBITED,
+        MEDICATION_REQUEST_REQUESTED,
+        MEDICATION_REQUEST_PROHIBITED,
+        SERVICE_REQUESTED,
+        SERVICE_PROHIBITED
+      ].freeze
+
       class << self
         def exclude_group?(group)
           RESOURCES_TO_EXCLUDE.key?(group.resource) &&

data/lib/us_quality_core_test_kit/generator/suite_generator.rb

@@ -1,20 +1,47 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/suite_generator'
-
 require_relative 'naming'
 require_relative 'special_cases'
 
 module USQualityCoreTestKit
   class Generator
-    class SuiteGenerator < USCoreTestKit::Generator::SuiteGenerator
+    class SuiteGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          new(ig_metadata, base_output_dir).generate
+        end
+      end
+
+      attr_accessor :ig_metadata, :base_output_dir
+
+      def initialize(ig_metadata, base_output_dir)
+        self.ig_metadata = ig_metadata
+        self.base_output_dir = base_output_dir
+      end
+
+      def output
+        @output ||= ERB.new(template, trim_mode: '-').result(binding)
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def generate
+        File.write(output_file_name, output)
+      end
+
+      def group_file_list
+        @group_file_list ||=
+          groups.map { |group| group.file_name.delete_suffix('.rb') }
+      end
+
       def version_specific_message_filters
         [
-          # Patient validation warnings suppressed for US Core extensions because
-          # validator tries to validate against different US Core version than we require
-          %r{Patient.*Patient\.extension\[\d+\]\[url='http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)\|\d+\.\d+(?:\.\d+)?'\]:\s*The extension URL must not contain a version\.},
-          %r{Patient.*Patient\.extension\[\d+\]\.url:\s*Value is 'http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)\|\d+\.\d+(?:\.\d+)?'\s*but is fixed to 'http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)'\s*in the profile http://hl7\.org/fhir/us/core/StructureDefinition/us-core-(race|ethnicity|tribal-affiliation)\|\d+\.\d+(?:\.\d+)?#Extension\.url},
-          # This extension is correct but is not yet correctly passing in the validator
+          # Patient extension messages are suppressed because the CQL package can load US Core 7 into
+          # the validator session while US Quality Core 0.5.0 uses US Core 6.1.0.
+          /\bPatient\.extension/,
+          # This extension is correct but is not yet correctly passing in the validator.
           %r{DeviceRequest.*DeviceRequest\.modifierExtension\[\d+\]:\s*Slicing cannot be evaluated:\s*Unable to resolve profile CanonicalType\[http://hl7\.org/fhir/5\.0/StructureDefinition/extension-DeviceRequest\.doNotPerform\]}
         ]
       end
@@ -49,7 +76,11 @@ module USQualityCoreTestKit
 
       def ig_identifier
         version = ig_metadata.ig_version[1..] # Remove leading 'v'
-        "fhir.onc.us-quality-core##{version}"
+        if version == '0.5.0'
+          "fhir.onc.us-quality-core##{version}"
+        else
+          "hl7.fhir.us.quality-core##{version}"
+        end
       end
 
       def ig_link

data/lib/us_quality_core_test_kit/generator/templates/document_reference_custodian_test.rb.erb

@@ -0,0 +1,56 @@
+module USQualityCoreTestKit
+  module <%= module_name %>
+    class <%= class_name %> < Inferno::Test
+      id :<%= test_id %>
+
+      title 'DocumentReference resources returned during previous tests have custodian'
+      description %(
+        This test verifies the organization responsible for the DocumentReference is present either in DocumentReference.custodian
+        or accessible in the Provenance resource targeting the DocumentReference using Provenance.agent.who or Provenance.agent.onBehalfOf.
+      )
+
+      def scratch_resources
+        scratch[:<%= profile_identifier %>_resources] ||= {}
+      end
+
+      def scratch_provenance_resources
+        scratch[:provenance_resources] ||= {}
+      end
+
+      run do
+        resources = scratch_resources[:all] || []
+        provenances = scratch_provenance_resources[:all] || []
+
+        skip_if resources.blank?,
+                'No DocumentReference resources appear to be available. ' \
+                'Please use patients with more information.'
+
+        resources.each do |docref|
+          has_custodian = docref.custodian.present?
+
+          if provenances.present?
+            has_agent = provenances.any? do |provenance|
+              has_target = provenance.target.any? do |target|
+                target.reference&.end_with?("DocumentReference/#{docref.id}")
+              end
+              has_agent = provenance.agent.any? { |agent| agent.who.present? || agent.onBehalfOf.present? }
+
+              has_target && has_agent
+            end
+          end
+
+          unless has_custodian || has_agent
+            add_message(
+              'error',
+              "DocumentReference/#{docref.id} does not have DocumentReference.custodian, " \
+                'Provenance.agent.who, nor Provenance.agent.onBehalfOf'
+            )
+          end
+        end
+
+        assert messages.blank?,
+               'Resource does not have DocumentReference.custodian, Provenance.agent.who, nor Provenance.agent.onBehalfOf'
+      end
+    end
+  end
+end

data/lib/us_quality_core_test_kit/generator/templates/interpreter_required_extension_test.rb.erb

@@ -0,0 +1,25 @@
+require_relative '../../../interpreter_required_extension_test'
+
+module USQualityCoreTestKit
+  module <%= module_name %>
+    class <%= class_name %> < Inferno::Test
+      include USQualityCoreTestKit::InterpreterRequiredExtensionTest
+
+      title 'Certifying server system supports the US Core Interpreter Needed Extension on either the US Core Patient or US Core Encounter Profiles'
+      description %(
+        Servers can use the US Core Interpreter Needed Extension on the US Quality Core Patient
+        or US Quality Core Encounter Profiles to communicate whether a patient needs an interpreter.
+        Although the extension is marked as an Additional USCDI Requirements on both US Quality Core
+        Patient and US Quality Core Encounter Profiles, the certifying Server system is not required
+        to support the extension on both profiles, but SHALL support the extension on at least
+        one.
+      )
+
+      id :<%= test_id %>
+
+      run do
+        verify_interpreter_required_extension_exists
+      end
+    end
+  end
+end

data/lib/us_quality_core_test_kit/generator/templates/practitioner_address_test.rb.erb

@@ -0,0 +1,32 @@
+require_relative '../../../practitioner_address_test'
+
+module USQualityCoreTestKit
+  module <%= module_name %>
+    class <%= class_name %> < Inferno::Test
+      include USQualityCoreTestKit::PractitionerAddressTest
+
+      title 'Server support either Practitioner.address or PractitionerRole'
+      description %(
+        US Quality Core Responders SHALL support either US Quality Core PractitionerRole Profile or
+        these data elements in US Quality Core Practitioner Profile
+
+        * Practitioner.address
+        * Practitioner.address.city
+        * Practitioner.address.country
+        * Practitioner.address.line
+        * Practitioner.address.postalCode
+        * Practitioner.address.state
+      )
+
+      id :<%= test_id %>
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      run do
+        verify_practitioner_address
+      end
+    end
+  end
+end

data/lib/us_quality_core_test_kit/generator/templates/provenance_revinclude_search.rb.erb

@@ -21,6 +21,16 @@ module USQualityCoreTestKit
         title: 'Patient IDs',
         description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
   
+      <%- end -%>
+      <%- if needs_care_plan_category_code? -%>
+      input :care_plan_category_code,
+        title: 'CarePlan Category Code',
+        description: 'Code used for the CarePlan category search parameter'
+
+      def fixed_value_search_param_values
+        [care_plan_category_code]
+      end
+
       <%- end -%>
       def properties
         @properties ||= SearchTestProperties.new(

data/lib/us_quality_core_test_kit/generator/templates/search.rb.erb

@@ -13,16 +13,21 @@ module USQualityCoreTestKit
 <%= description %>
       )
 
-      id :<%= test_id %>
-
-  <% if optional? %>optional<% end %>
-
-  <% if needs_patient_id? %>
+      id :<%= test_id %><% if optional? %>
+      optional
+  <% end %><% if needs_patient_id? %>
       input :patient_ids,
         title: 'Patient IDs',
         description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
-  <% end %>
+  <% end %><% if needs_care_plan_category_code? %>
+      input :care_plan_category_code,
+        title: 'CarePlan Category Code',
+        description: 'Code used for the CarePlan category search parameter'
 
+      def fixed_value_search_param_values
+        [care_plan_category_code]
+      end
+<% end %>
       def self.properties
         @properties ||= SearchTestProperties.new(
   <%= search_test_properties_string %>

data/lib/us_quality_core_test_kit/generator/terminology_binding_metadata_extractor.rb

@@ -1,10 +1,114 @@
 # frozen_string_literal: true
 
-require 'us_core_test_kit/generator/terminology_binding_metadata_extractor'
-
 module USQualityCoreTestKit
   class Generator
-    class TerminologyBindingMetadataExtractor < USCoreTestKit::Generator::TerminologyBindingMetadataExtractor
+    class TerminologyBindingMetadataExtractor
+      attr_accessor :profile_elements, :ig_resources, :resource
+
+      def initialize(profile_elements, ig_resources, resource)
+        self.profile_elements = profile_elements
+        self.ig_resources = ig_resources
+        self.resource = resource
+      end
+
+      def terminology_bindings
+        (element_terminology_bindings + extension_terminology_bindings).compact
+      end
+
+      def element_has_fixed_value?(element)
+        case element.type.first.code
+        when 'Quantity'
+          code = profile_elements.find { |e| e.path == "#{element.path}.code" }
+          system = profile_elements.find { |e| e.path == "#{element.path}.system" }
+          code&.fixedCode || system&.fixedUri
+        when 'code'
+          element.fixedCode.present?
+        end
+      end
+
+      def element_has_optional_binding_slice?(element)
+        element.sliceName.present? && element.min.zero?
+      end
+
+      def profile_elements_with_bindings
+        profile_elements
+          .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,
+            system: element.binding.valueSet&.split('|')&.first,
+            path: element.path.gsub('[x]', '').gsub("#{resource}.", '')
+          }
+
+          binding[:required_binding_slice] = true if element.sliceName.present? && element.min.positive?
+
+          binding
+        end
+      end
+
+      def extension_profile_elements
+        profile_elements
+          .select { |element| element.type&.first&.code == 'Extension' }
+          .select { |element| extension_profile_url(element).present? }
+      end
+
+      def extension_profile_url(extension)
+        extension.type.first.profile&.first
+      end
+
+      def extension_terminology_bindings
+        extension_profile_elements
+          .flat_map do |extension_profile_element|
+            url = extension_profile_url(extension_profile_element)
+            extension = ig_resources.profile_by_url(url)
+
+            # TODO: Temporaray fix for extension defined out of US Core. FI-1623
+            next if extension.nil?
+
+            elements = extension.snapshot.element
+            elements_with_bindings = elements.select do |element|
+              element.binding.present? && !element.id.include?('Extension.extension')
+            end
+
+            elements_with_bindings.map do |element|
+              {
+                type: element.type.first.code,
+                strength: element.binding.strength,
+                system: element.binding.valueSet&.split('|')&.first,
+                path: element.path.gsub('[x]', '').gsub('Extension.', ''),
+                extensions: [url]
+              }
+            end + nested_extension_terminology_bindings(elements, url)
+          end
+      end
+
+      def nested_extension_terminology_bindings(elements, extension_url)
+        nested_extensions = elements.select { |element| element.path == 'Extension.extension' }
+        nested_extensions.flat_map do |nested_extension|
+          nested_extension_element = elements.find { |element| element.id == "#{nested_extension.id}.url" }
+          next unless nested_extension_element.present?
+
+          nested_extension_url = nested_extension_element.fixedUri
+          nested_elements_with_bindings = elements.select do |element|
+            element.id.include?(nested_extension.id) && element.binding.present?
+          end
+
+          nested_elements_with_bindings.map do |element|
+            {
+              type: element.type.first.code,
+              strength: element.binding.strength,
+              system: element.binding.valueSet&.split('|')&.first,
+              path: element.path.gsub('[x]', '').gsub('Extension.extension.', ''),
+              extensions: [extension_url, nested_extension_url]
+            }
+          end
+        end
+      end
     end
   end
 end