pacio_inferno_core 0.1.0

data/lib/pacio_inferno_core/generator/suite_generator.rb

@@ -0,0 +1,105 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module PacioInfernoCore
+  class Generator
+    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 version_specific_message_filters
+        []
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'suite.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template, trim_mode: '-').result(binding)
+      end
+
+      def naming
+        self.class.module_parent::Naming
+      end
+
+      def base_output_file_name
+        "#{naming.prefix}_test_suite.rb"
+      end
+
+      def class_name
+        "#{naming.module_name}TestSuite"
+      end
+
+      def module_name
+        naming.module_name.to_s
+      end
+
+      def module_name_with_version
+        "#{naming.module_name}#{ig_metadata.reformatted_version.upcase}"
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def suite_id
+        "#{naming.prefix}_#{ig_metadata.reformatted_version}"
+      end
+
+      def fhir_api_group_id
+        "#{naming.prefix}_#{ig_metadata.reformatted_version}_fhir_api"
+      end
+
+      def title
+        "#{naming.long_name} #{ig_metadata.ig_version}"
+      end
+
+      def ig_identifier
+        version = ig_metadata.ig_version[1..] # Remove leading 'v'
+        "#{ig_metadata.ig_package_id}##{version}"
+      end
+
+      def ig_link
+        naming.ig_link(ig_metadata.ig_version)
+      end
+
+      def generate
+        File.write(output_file_name, output)
+      end
+
+      def groups
+        ig_metadata.ordered_groups
+          .reject { |group| SpecialCases.exclude_group? group }
+      end
+
+      def group_id_list
+        @group_id_list ||=
+          groups.map(&:id)
+      end
+
+      def group_file_list
+        @group_file_list ||=
+          groups.map { |group| group.file_name.delete_suffix('.rb') }
+      end
+
+      def capability_statement_file_name
+        "../../custom_groups/#{ig_metadata.ig_version}/capability_statement_group"
+      end
+
+      def capability_statement_group_id
+        "#{naming.prefix}_#{ig_metadata.reformatted_version}_capability_statement"
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/templates/group.rb.erb

@@ -0,0 +1,27 @@
+<% test_file_list.each do |file_name| %>require_relative '<%= file_name %>'
+<% end %>
+module <%= naming.module_name %>TestKit
+  module <%= module_name_with_version %>
+    class <%= class_name %> < Inferno::TestGroup
+      title '<%= title %> Tests'
+      short_description <<~DESC
+        '<%= short_description %>'
+      DESC
+      description %(
+<%= description %>
+      )
+
+      id :<%= group_id %>
+      run_as_group<% if optional? %>
+      optional<% end %>
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(
+          YAML.load_file(File.join(__dir__, '<%= profile_identifier %>', 'metadata.yml'), aliases: true)
+        )
+      end
+<% test_id_list.each do |id| %>
+      test from: :<%= id %><% end %>
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/templates/must_support.rb.erb

@@ -0,0 +1,36 @@
+require_relative '../../../must_support_test'
+
+module <%= naming.module_name %>TestKit
+  module <%= module_name_with_version %>
+    class <%= class_name %> < Inferno::Test
+      include PacioInfernoCore::MustSupportTest
+
+      title 'All must support elements are provided in the <%= resource_type %> resources returned'
+      
+      description %(
+        This test will look through the <%= resource_type %> resources
+        found previously for the following must support elements:
+
+<%= must_support_list_string %>
+      )
+
+      id :<%= test_id %>
+
+      def resource_type
+        '<%= resource_type %>'
+      end
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:<%= profile_identifier %>_resources] ||= {}
+      end
+
+      run do
+        perform_must_support_test(<%= resource_collection_string %>)
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/templates/read.rb.erb

@@ -0,0 +1,34 @@
+require_relative '../../../read_test'
+
+module <%= naming.module_name %>TestKit
+  module <%= module_name_with_version %>
+    class <%= class_name %> < Inferno::Test
+      include PacioInfernoCore::ReadTest
+
+      title 'Server returns correct <%= resource_type %> resource from <%= resource_type %> read interaction'
+      description 'A server <%= conformance_expectation %> support the <%= resource_type %> read interaction.'
+
+      id :<%= test_id %>
+<% if input_resource_id? %>
+      input :<%= resource_id_input_string %>,
+            title: 'ID(s) for <%= group_title %> resources present on the server.',
+            description: %(
+              Comma separated list of <%= group_title %> ids that in sum contain
+              all MUST SUPPORT elements
+            )<% if optional_profile? %>,
+            optional: true<% end %>
+<% end %>
+      def resource_type
+        '<%= resource_type %>'
+      end
+
+      def scratch_resources
+        scratch[:<%= profile_identifier %>_resources] ||= {}
+      end
+
+      run do
+        perform_read_test(<%= resource_collection_string %>)
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/templates/reference_resolution.rb.erb

@@ -0,0 +1,40 @@
+require_relative '../../../reference_resolution_test'
+
+module <%= naming.module_name %>TestKit
+  module <%= module_name_with_version %>
+    class <%= class_name %> < Inferno::Test
+      include PacioInfernoCore::ReferenceResolutionTest
+
+      title 'MustSupport references within <%= resource_type %> resources are valid'
+      description %(
+        This test will attempt to read external references provided within elements
+        marked as 'MustSupport', if any are available.
+
+        It verifies that at least one external reference for each MustSupport Reference element
+        can be accessed by the test client, and conforms to corresponding US Core profile.
+
+        Elements which may provide external references include:
+
+<%= must_support_reference_list_string %>
+      )
+
+      id :<%= test_id %>
+
+      def resource_type
+        '<%= resource_type %>'
+      end
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:<%= profile_identifier %>_resources] ||= {}
+      end
+
+      run do
+        perform_reference_resolution_test(<%= resource_collection_string %>)
+      end
+    end
+  end
+end

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

@@ -0,0 +1,40 @@
+require_relative '../../../search_test'
+require_relative '../../../generator/group_metadata'
+
+module <%= naming.module_name %>TestKit
+  module <%= module_name_with_version %>
+    class <%= class_name %> < Inferno::Test
+      include PacioInfernoCore::SearchTest
+
+      title 'Server returns valid results for <%= resource_type %> search by <%= search_param_name_string %>'
+      description %(
+<%= description %>
+      )
+
+      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 %>
+      def self.properties
+        @properties ||= SearchTestProperties.new(
+  <%= search_test_properties_string %>
+        )
+      end
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:<%= profile_identifier %>_resources] ||= {}
+      end
+
+      run do
+        run_search_test
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/templates/validation.rb.erb

@@ -0,0 +1,36 @@
+require_relative '../../../validation_test'
+
+module <%= naming.module_name %>TestKit
+  module <%= module_name_with_version %>
+    class <%= class_name %> < Inferno::Test
+      include PacioInfernoCore::ValidationTest
+
+      id :<%= test_id %>
+
+      title <<~DESC
+        <%= resource_type %> resources returned during previous tests conform to the <%= profile_name %>
+      DESC
+
+      description %(
+<%= description %>
+      )
+
+      output :dar_code_found, :dar_extension_found
+
+      def resource_type
+        '<%= resource_type %>'
+      end
+
+      def scratch_resources
+        scratch[:<%= profile_identifier %>_resources] ||= {}
+      end
+
+      run do
+        perform_validation_test(scratch_resources[:all] || [],
+                                '<%= profile_url %>',
+                                '<%= profile_version %>',
+                                skip_if_empty: <%= skip_if_empty %>)
+      end
+    end
+  end
+end

data/lib/pacio_inferno_core/generator/terminology_binding_metadata_extractor.rb

@@ -0,0 +1,116 @@
+module PacioInfernoCore
+  class Generator
+    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
+        # add_terminology_bindings_from_extensions
+        # profile_elements.select { |element| element.type&.first&.code == 'Extension' }
+        #   .each { |extension| add_terminology_bindings_from_extension(extension) }
+      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,
+            # Goal.target.detail has an unbound binding
+            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

data/lib/pacio_inferno_core/generator/validation_test_generator.rb

@@ -0,0 +1,146 @@
+require_relative 'naming'
+require_relative 'special_cases'
+
+module PacioInfernoCore
+  class Generator
+    class ValidationTestGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          ig_metadata.groups
+            .reject { |group| SpecialCases.exclude_group? group }
+            .each do |group|
+              new(group, base_output_dir: base_output_dir).generate
+              next unless group.resource == 'MedicationRequest'
+
+              # The Medication validation test lives in the MedicationRequest
+              # group, so we need to pass in that group's metadata
+              medication_group_metadata = ig_metadata.groups.find do |group|
+                group.resource == 'Medication'
+              end
+              new(medication_group_metadata, group, base_output_dir: base_output_dir).generate
+            end
+        end
+      end
+
+      attr_accessor :group_metadata, :medication_request_metadata, :base_output_dir
+
+      def initialize(group_metadata, medication_request_metadata = nil, base_output_dir:)
+        self.group_metadata = group_metadata
+        self.medication_request_metadata = medication_request_metadata
+        self.base_output_dir = base_output_dir
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'validation.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template, trim_mode: '-').result(binding)
+      end
+
+      def naming
+        self.class.module_parent::Naming
+      end
+
+      def base_output_file_name
+        "#{class_name.underscore}.rb"
+      end
+
+      def output_file_directory
+        File.join(base_output_dir, directory_name)
+      end
+
+      def output_file_name
+        File.join(output_file_directory, base_output_file_name)
+      end
+
+      def directory_name
+        naming.snake_case_for_profile(medication_request_metadata || group_metadata)
+      end
+
+      def profile_identifier
+        naming.snake_case_for_profile(group_metadata)
+      end
+
+      def profile_url
+        group_metadata.profile_url
+      end
+
+      def profile_name
+        group_metadata.profile_name
+      end
+
+      def profile_version
+        group_metadata.profile_version
+      end
+
+      def test_id
+        "#{naming.prefix}_#{group_metadata.reformatted_version}_#{profile_identifier}_validation_test"
+      end
+
+      def class_name
+        "#{naming.upper_camel_case_for_profile(group_metadata)}ValidationTest"
+      end
+
+      def module_name_with_version
+        "#{naming.module_name}#{group_metadata.reformatted_version.upcase}"
+      end
+
+      def resource_type
+        group_metadata.resource
+      end
+
+      def conformance_expectation
+        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.write(output_file_name, output)
+
+        test_metadata = {
+          id: test_id,
+          file_name: base_output_file_name
+        }
+
+        if resource_type == 'Medication'
+          medication_request_metadata.add_test(**test_metadata)
+        else
+          group_metadata.add_test(**test_metadata)
+        end
+      end
+
+      def description
+        <<~DESCRIPTION
+          #{description_intro}
+          It verifies the presence of mandatory elements and that elements with
+          required bindings contain appropriate values. CodeableConcept element
+          bindings will fail if none of their codings have a code/system belonging
+          to the bound ValueSet. Quantity, Coding, and code element bindings will
+          fail if their code/system are not found in the valueset.
+        DESCRIPTION
+      end
+
+      def description_intro
+        if resource_type == 'Medication'
+          <<~MEDICATION_INTRO
+            This test verifies resources returned from previous tests conform to
+            the [#{profile_name}](#{profile_url}).
+          MEDICATION_INTRO
+        else
+          <<~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
+    end
+  end
+end