ipa_test_kit 0.2.0

data/lib/ipa_test_kit/generator/group_metadata.rb

@@ -0,0 +1,98 @@
+module IpaTestKit
+  class Generator
+    class GroupMetadata
+      ATTRIBUTES = [
+        :name,
+        :class_name,
+        :version,
+        :reformatted_version,
+        :resource,
+        :profile_url,
+        :profile_name,
+        :title,
+        :short_description,
+        :interactions,
+        :operations,
+        :searches,
+        :search_definitions,
+        :include_params,
+        :revincludes,
+        :required_concepts,
+        :must_supports,
+        :mandatory_elements,
+        :bindings,
+        :references,
+        :tests,
+        :id,
+        :file_name,
+        :delayed_references
+      ].freeze
+
+      NON_USCDI_RESOURCES = [
+        'Encounter',
+        'Location',
+        'Organization',
+        'Practitioner',
+        'PractitionerRole',
+        'Provenance'
+      ].freeze
+
+      ATTRIBUTES.each { |name| attr_accessor name }
+
+      def initialize(params)
+        params.each do |key, value|
+          raise "Unknown attribute #{key}" unless ATTRIBUTES.include? key
+
+          instance_variable_set(:"@#{key}", value)
+        end
+      end
+
+      def delayed?
+        return false if resource == 'Patient'
+
+        no_patient_searches? || non_uscdi_resource?
+      end
+
+      def no_patient_searches?
+        searches.none? { |search| search[:names].include? 'patient' }
+      end
+
+      def non_uscdi_resource?
+        NON_USCDI_RESOURCES.include? resource
+      end
+
+      def add_test(id:, file_name:)
+        self.tests ||= []
+
+        test_metadata = {
+          id: id,
+          file_name: file_name
+        }
+
+        if delayed? && id.include?('read')
+          self.tests.unshift(test_metadata)
+        else
+          self.tests << test_metadata
+        end
+      end
+
+      def to_hash
+        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) }
+      end
+
+      def add_delayed_references(delayed_profiles, ig_resources)
+        self.delayed_references =
+          references
+            .select { |reference| (reference[:profiles] & delayed_profiles).present? }
+            .map do |reference|
+              profile_urls = (reference[:profiles] & delayed_profiles)
+              delayed_resources = profile_urls.map { |url| ig_resources.resource_for_profile(url) }
+              {
+                path: reference[:path].gsub("#{resource}.", ''),
+                resources: delayed_resources
+              }
+            end
+      end
+    end
+  end
+end

data/lib/ipa_test_kit/generator/group_metadata_extractor.rb

@@ -0,0 +1,278 @@
+require_relative 'group_metadata'
+require_relative 'ig_metadata'
+require_relative 'must_support_metadata_extractor'
+require_relative 'search_metadata_extractor'
+require_relative 'terminology_binding_metadata_extractor'
+
+module IpaTestKit
+  class Generator
+    class GroupMetadataExtractor
+      attr_accessor :resource_capabilities, :profile_url, :ig_metadata, :ig_resources
+
+      def initialize(resource_capabilities, profile_url, ig_metadata, ig_resources)
+        self.resource_capabilities = resource_capabilities
+        self.profile_url = profile_url
+        self.ig_metadata = ig_metadata
+        self.ig_resources = ig_resources
+      end
+
+      def group_metadata
+        @group_metadata ||=
+          GroupMetadata.new(group_metadata_hash)
+      end
+
+      def group_metadata_hash
+        @group_metadata_hash ||=
+          {
+            name: name,
+            class_name: class_name,
+            version: version,
+            reformatted_version: reformatted_version,
+            # test_id_prefix: test_id_prefix,
+            resource: resource,
+            profile_url: profile_url,
+            profile_name: profile_name,
+            title: title,
+            short_description: short_description,
+            interactions: interactions,
+            operations: operations,
+            searches: searches,
+            search_definitions: search_definitions,
+            include_params: include_params,
+            revincludes: revincludes,
+            required_concepts: required_concepts,
+            must_supports: must_supports,
+            mandatory_elements: mandatory_elements,
+            bindings: bindings,
+            references: references
+            # tests: []
+          }
+
+        mark_mandatory_and_must_support_searches
+        handle_special_cases
+
+        @group_metadata_hash
+      end
+
+      def mark_mandatory_and_must_support_searches
+        searches.each do |search|
+          search[:names_not_must_support_or_mandatory] = search[:names].reject do |name|
+            path = search_definitions[name.to_sym][:full_path]
+            any_must_support_elements = (must_supports[:elements]).any? do |element|
+              full_must_support_path = "#{resource}.#{element[:path]}"
+
+              # allow for non-choice, choice types, and _id
+              name == '_id' || full_must_support_path == path || full_must_support_path == "#{path}[x]"
+            end
+
+            any_must_support_slices = must_supports[:slices].any? do |slice|
+              # only handle type slices because that is all we need for now
+              if slice[:discriminator] && slice[:discriminator][:type] == 'type'
+                full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
+                full_must_support_path == path
+              else
+                false
+              end
+            end
+
+            any_mandatory_elements = mandatory_elements.any? do |element|
+              element == path
+            end
+
+            any_must_support_elements || any_must_support_slices || any_mandatory_elements
+          end
+
+          search[:must_support_or_mandatory] = search[:names_not_must_support_or_mandatory].empty?
+        end
+      end
+
+      ### BEGIN SPECIAL CASES ###
+
+      CATEGORY_FIRST_PROFILES = [
+        'http://hl7.org/fhir/uv/ipa/StructureDefinition/ipa-observation',
+      ]
+
+      def category_first_profile?
+        CATEGORY_FIRST_PROFILES.include?(profile_url)
+      end
+
+      def first_search_params
+        @first_search_params ||=
+        if category_first_profile?
+          ['patient', 'category']
+        elsif resource == 'Observation'
+          ['patient', 'code']
+        elsif resource == 'MedicationRequest'
+          ['patient', 'intent']
+        else
+          ['patient']
+        end
+      end
+
+      def handle_special_cases
+        set_first_search
+
+        case profile_url
+        when 'http://hl7.org/fhir/uv/ipa/StructureDefinition/ipa-implantable-device'
+          must_supports[:elements].delete_if do |element|
+            ['udiCarrier.carrierAIDC', 'udiCarrier.carrierHRF'].include? element[:path]
+          end
+        when 'http://hl7.org/fhir/uv/ipa/StructureDefinition/ipa-documentreference'
+          must_supports[:elements].delete_if do |element|
+            ['content.attachment.data', 'content.attachment.url'].include? element[:path]
+          end
+        end
+      end
+
+      def set_first_search
+        search = searches.find { |param| param[:names] == first_search_params }
+        return if search.nil?
+
+        searches.delete(search)
+        searches.unshift(search)
+      end
+
+      ### END SPECIAL CASES ###
+
+      def profile
+        @profile ||= ig_resources.profile_by_url(profile_url)
+      end
+
+      def profile_elements
+        @profile_elements ||= profile.snapshot.element
+      end
+
+      def base_name
+        profile_url.split('StructureDefinition/').last
+      end
+
+      def name
+        base_name.tr('-', '_')
+      end
+
+      def class_name
+        base_name
+          .split('-')
+          .map(&:capitalize)
+          .join
+          .gsub('Ipa', "Ipa#{ig_metadata.reformatted_version}")
+          .concat('Sequence')
+      end
+
+      def version
+        ig_metadata.ig_version
+      end
+
+      def reformatted_version
+        ig_metadata.reformatted_version
+      end
+
+      def resource
+        resource_capabilities.type
+      end
+
+      def profile_name
+        profile.title.gsub('  ', ' ')
+      end
+
+      def title
+        profile.title.gsub(/IPA\s*/, '').gsub(/\s*Profile/, '').strip
+      end
+
+      def short_description
+        "Verify support for the server capabilities required by the #{profile_name}."
+      end
+
+      def interactions
+        @interactions ||=
+          resource_capabilities.interaction.map do |interaction|
+            {
+              code: interaction.code,
+              expectation: interaction.extension.first.valueCode # TODO: fix expectation extension finding
+            }
+          end
+      end
+
+      def operations
+        @operations ||=
+          resource_capabilities.operation.map do |operation|
+            {
+              code: operation.name,
+              expectation: operation.extension.first.valueCode # TODO: fix expectation extension finding
+            }
+          end
+      end
+
+      def search_metadata_extractor
+        @search_metadata_extractor ||=
+          SearchMetadataExtractor.new(resource_capabilities, ig_resources, resource, profile_elements)
+      end
+
+      def searches
+        @searches ||= search_metadata_extractor.searches
+      end
+
+      def search_definitions
+        @search_definitions ||= search_metadata_extractor.search_definitions
+      end
+
+      def include_params
+        resource_capabilities.searchInclude || []
+      end
+
+      def revincludes
+        resource_capabilities.searchRevInclude || []
+      end
+
+      def required_concepts
+        # The base FHIR vital signs profile has a required binding that isn't
+        # relevant for any of its child profiles
+        return if resource == 'Observation'
+
+        profile_elements
+          .select { |element| element.type&.any? { |type| type.code == 'CodeableConcept' } }
+          .select { |element| element.binding&.strength == 'required' }
+          .map { |element| element.path.gsub("#{resource}.", '').gsub('[x]', 'CodeableConcept') }
+      end
+
+      def terminology_binding_metadata_extractor
+        @terminology_binding_metadata_extractor ||=
+          TerminologyBindingMetadataExtractor.new(profile_elements, ig_resources, resource)
+      end
+
+      def bindings
+        @bindings ||=
+          terminology_binding_metadata_extractor.terminology_bindings
+      end
+
+      def must_support_metadata_extractor
+        @must_support_metadata_extractor ||=
+          MustSupportMetadataExtractor.new(profile_elements, profile, resource)
+      end
+
+      def must_supports
+        @must_supports ||=
+          must_support_metadata_extractor.must_supports
+      end
+
+      def mandatory_elements
+        @mandatory_elements ||=
+          profile_elements
+            .select { |element| element.min.positive? }
+            .map { |element| element.path }
+      end
+
+      def references
+        @references ||=
+          profile_elements
+            .select { |element| element.type&.first&.code == 'Reference' }
+            .map do |reference_definition|
+              {
+                path: reference_definition.path,
+                profiles: reference_definition.type.first.targetProfile
+              }
+            end
+      end
+    end
+  end
+end

data/lib/ipa_test_kit/generator/ig_loader.rb

@@ -0,0 +1,63 @@
+require 'active_support/all'
+require 'fhir_models'
+require 'rubygems/package'
+require 'zlib'
+require_relative 'ig_resources'
+
+module IpaTestKit
+  class Generator
+    class IGLoader
+      def ig_resources
+        @ig_resources ||= IGResources.new
+      end
+
+      def load
+        load_ig
+        load_standalone_resources
+      end
+
+      def load_ig
+        tar = Gem::Package::TarReader.new(Zlib::GzipReader.open(File.join(__dir__, '..', 'igs', 'package.tgz')))
+
+        tar.each do |entry|
+          next if entry.directory?
+
+          file_name = entry.full_name.split('/').last
+
+          next unless file_name.end_with? '.json'
+
+          next unless entry.full_name.start_with? 'package/'
+
+          begin
+            resource = FHIR.from_contents(entry.read)
+            next if resource.nil?
+          rescue StandardError
+            puts "#{file_name} does not appear to be a FHIR resource."
+            next
+          end
+
+          ig_resources.add(resource)
+        end
+
+        ig_resources
+      end
+
+      def load_standalone_resources
+        Dir.glob(File.join(__dir__, '..', 'igs', '*.json')).each do |file_path|
+          begin
+            resource = FHIR.from_contents(File.read(file_path))
+            next if resource.nil?
+          rescue StandardError
+            file_name = file_path.split('/').last
+            puts "#{file_name} does not appear to be a FHIR resource."
+            next
+          end
+
+          ig_resources.add(resource)
+        end
+
+        ig_resources
+      end
+    end
+  end
+end

data/lib/ipa_test_kit/generator/ig_metadata.rb

@@ -0,0 +1,49 @@
+module IpaTestKit
+  class Generator
+    class IGMetadata
+      attr_accessor :ig_version, :groups
+
+      def reformatted_version
+        @reformatted_version ||= ig_version.delete('.')
+      end
+
+      def ordered_groups
+        @ordered_groups ||=
+          [patient_group] + non_delayed_groups + delayed_groups
+      end
+
+      def patient_group
+        @patient_group ||=
+          groups.find { |group| group.resource == 'Patient' }
+      end
+
+      def delayed_groups
+        @delayed_groups ||=
+          groups.select { |group| group.delayed? }
+      end
+
+      def non_delayed_groups
+        @non_delayed_groups ||=
+          groups.reject { |group| group.delayed? } - [patient_group]
+      end
+
+      def delayed_profiles
+        @delayed_profiles ||=
+          delayed_groups.map(&:profile_url)
+      end
+
+      def postprocess_groups(ig_resources)
+        groups.each do |group|
+          group.add_delayed_references(delayed_profiles, ig_resources)
+        end
+      end
+
+      def to_hash
+        {
+          ig_version: ig_version,
+          groups: groups.map(&:to_hash)
+        }
+      end
+    end
+  end
+end

data/lib/ipa_test_kit/generator/ig_metadata_extractor.rb

@@ -0,0 +1,56 @@
+require_relative 'ig_metadata'
+require_relative 'group_metadata_extractor'
+
+module IpaTestKit
+  class Generator
+    class IGMetadataExtractor
+      attr_accessor :ig_resources, :metadata
+
+      def initialize(ig_resources)
+        self.ig_resources = ig_resources
+        add_vital_signs_profiles
+        self.metadata = IGMetadata.new
+      end
+
+      def extract
+        add_metadata_from_ig
+        add_metadata_from_resources
+        metadata
+      end
+
+      def add_metadata_from_ig
+        metadata.ig_version = "v#{ig_resources.ig.version}"
+      end
+
+      def resources_in_capability_statement
+        ig_resources.capability_statement.rest.first.resource
+      end
+
+      # The IPA Server Capability Statement does not list support for the
+      # required vital signs profiles, so they need to be added
+      def add_vital_signs_profiles
+        ig_resources.capability_statement.rest.first.resource
+          .find { |resource| resource.type == 'Observation' }
+          .supportedProfile.concat [
+            'http://hl7.org/fhir/StructureDefinition/bodyheight',
+            'http://hl7.org/fhir/StructureDefinition/bodytemp',
+            'http://hl7.org/fhir/StructureDefinition/bp',
+            'http://hl7.org/fhir/StructureDefinition/bodyweight',
+            'http://hl7.org/fhir/StructureDefinition/heartrate',
+            'http://hl7.org/fhir/StructureDefinition/resprate'
+          ]
+      end
+
+      def add_metadata_from_resources
+        metadata.groups =
+          resources_in_capability_statement.flat_map do |resource|
+            resource.supportedProfile&.map do |supported_profile|
+              GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources).group_metadata
+            end
+          end
+
+        metadata.postprocess_groups(ig_resources)
+      end
+    end
+  end
+end

data/lib/ipa_test_kit/generator/ig_resources.rb

@@ -0,0 +1,48 @@
+module IpaTestKit
+  class Generator
+    class IGResources
+      def add(resource)
+        resources_by_type[resource.resourceType] << resource
+      end
+
+      def capability_statement(mode = 'server')
+        resources_by_type['CapabilityStatement'].find do |capability_statement_resource|
+          capability_statement_resource.rest.any? { |r| r.mode == mode }
+        end
+      end
+
+      def ig
+        resources_by_type['ImplementationGuide'].first
+      end
+
+      def inspect
+        'IGResources'
+      end
+
+      def profile_by_url(url)
+        resources_by_type['StructureDefinition'].find { |profile| profile.url == url }
+      end
+
+      def resource_for_profile(url)
+        resources_by_type['StructureDefinition'].find { |profile| profile.url == url }.type
+      end
+
+      def value_set_by_url(url)
+        resources_by_type['ValueSet'].find { |profile| profile.url == url }
+      end
+
+      def search_param_by_resource_and_name(resource, name)
+        normalized_name = name.to_s == '_id' ? 'id' : name.to_s
+
+        resources_by_type['SearchParameter']
+          .find { |param| param.id == "ipa-#{resource.downcase}-#{normalized_name}" }
+      end
+
+      private
+
+      def resources_by_type
+        @resources_by_type ||= Hash.new { |hash, key| hash[key] = [] }
+      end
+    end
+  end
+end