ipa_test_kit 0.2.0 → 0.3.1

data/lib/ipa_test_kit/generator/group_generator.rb

@@ -5,17 +5,19 @@ module IpaTestKit
   class Generator
     class GroupGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           ig_metadata.ordered_groups
-            .reject { |group| SpecialCases.exclude_resource? group.resource }
-            .each { |group| new(group).generate }
+            .reject { |group| group.nil?}
+            .reject { |group| SpecialCases.exclude_group? group }
+            .each { |group| new(group, base_output_dir).generate }
         end
       end
 
-      attr_accessor :group_metadata
+      attr_accessor :group_metadata, :base_output_dir
 
-      def initialize(group_metadata)
+      def initialize(group_metadata, base_output_dir)
         self.group_metadata = group_metadata
+        self.base_output_dir = base_output_dir
       end
 
       def template
@@ -38,6 +40,10 @@ module IpaTestKit
         "#{Naming.upper_camel_case_for_profile(group_metadata)}Group"
       end
 
+      def module_name
+        "Ipa#{group_metadata.reformatted_version.upcase}"
+      end
+
       def title
         group_metadata.title
       end
@@ -47,11 +53,11 @@ module IpaTestKit
       end
 
       def output_file_name
-        File.join(__dir__, '..', 'generated', base_output_file_name)
+        File.join(base_output_dir, base_output_file_name)
       end
 
       def metadata_file_name
-        File.join(__dir__, '..', 'generated', profile_identifier, base_metadata_file_name)
+        File.join(base_output_dir, profile_identifier, base_metadata_file_name)
       end
 
       def profile_identifier
@@ -59,13 +65,27 @@ module IpaTestKit
       end
 
       def group_id
-        "ipa_010_#{profile_identifier}"
+        "ipa_#{group_metadata.reformatted_version}_#{profile_identifier}"
       end
 
       def resource_type
         group_metadata.resource
       end
 
+      def search_validation_resource_type
+        text = "#{resource_type} resources"
+        if resource_type == 'Condition' && group_metadata.reformatted_version == 'v501'
+          case profile_url
+          when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis'
+            text.concat(' with category `encounter-diagnosis`')
+          when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-problems-health-concerns'
+            text.concat(' with category `problem-list-item | health-concern`')
+          end
+        end
+
+        text
+      end
+
       def profile_name
         group_metadata.profile_name
       end
@@ -74,13 +94,31 @@ module IpaTestKit
         group_metadata.profile_url
       end
 
+      def base_observation_group?
+        profile_url == 'http://hl7.org/fhir/uv/ipa/StructureDefinition/ipa-observation'
+      end
+
+      def optional?
+        resource_type == 'QuestionnaireResponse'
+      end
+
+      def read_all_resources?(id)
+        ['Medication', 'Practitioner', 'PractitionerRole'].include?(resource_type) &&
+          id.end_with?('read_test')
+      end
+
       def generate
+        add_special_tests
         File.open(output_file_name, 'w') { |f| f.write(output) }
         group_metadata.id = group_id
         group_metadata.file_name = base_output_file_name
         File.open(metadata_file_name, 'w') { |f| f.write(YAML.dump(group_metadata.to_hash)) }
       end
 
+      def add_special_tests
+
+      end
+
       def test_id_list
         @test_id_list ||=
           group_metadata.tests.map { |test| test[:id] }
@@ -88,7 +126,10 @@ module IpaTestKit
 
       def test_file_list
         @test_file_list ||=
-          group_metadata.tests.map { |test| test[:file_name].delete_suffix('.rb') }
+          group_metadata.tests.map do |test|
+            name_without_suffix = test[:file_name].delete_suffix('.rb')
+            name_without_suffix.start_with?('..') ? name_without_suffix : "#{profile_identifier}/#{name_without_suffix}"
+          end
       end
 
       def required_searches
@@ -123,7 +164,7 @@ module IpaTestKit
 
         ### Search Validation
         Inferno will retrieve up to the first 20 bundle pages of the reply for
-        #{resource_type} resources and save them for subsequent tests. Each of
+        #{search_validation_resource_type} and save them for subsequent tests. Each of
         these resources is then checked to see if it matches the searched
         parameters in accordance with [FHIR search
         guidelines](https://www.hl7.org/fhir/search.html). The test will fail,
@@ -139,7 +180,7 @@ module IpaTestKit
         The IPA #{title} sequence verifies that the system under test is
         able to provide correct responses for #{resource_type} queries. These queries
         must contain resources conforming to the #{profile_name} as
-        specified in the IPA v0.1.0 Implementation Guide.
+        specified in the IPA #{group_metadata.version} Implementation Guide.
 
         # Testing Methodology
         #{search_description}
@@ -161,9 +202,10 @@ module IpaTestKit
         then the test will fail.
 
         ## Reference Validation
-        Each reference within the resources found from the previous tests must
-        resolve. The test will attempt to read each reference found and will
-        fail if any attempted read fails.
+        At least one instance of each external reference in elements marked as
+        "must support" within the resources provided by the system must resolve.
+        The test will attempt to read each reference found and will fail if no
+        read succeeds.
         DESCRIPTION
       end
     end

data/lib/ipa_test_kit/generator/group_metadata.rb

@@ -9,6 +9,7 @@ module IpaTestKit
         :resource,
         :profile_url,
         :profile_name,
+        :profile_version,
         :title,
         :short_description,
         :interactions,
@@ -28,19 +29,10 @@ module IpaTestKit
         :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|
+      def initialize(metadata)
+        metadata.each do |key, value|
           raise "Unknown attribute #{key}" unless ATTRIBUTES.include? key
 
           instance_variable_set(:"@#{key}", value)
@@ -50,17 +42,13 @@ module IpaTestKit
       def delayed?
         return false if resource == 'Patient'
 
-        no_patient_searches? || non_uscdi_resource?
+        no_patient_searches?
       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 ||= []
 
@@ -77,7 +65,7 @@ module IpaTestKit
       end
 
       def to_hash
-        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) }
+        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) unless send(key).nil? }
       end
 
       def add_delayed_references(delayed_profiles, ig_resources)

data/lib/ipa_test_kit/generator/group_metadata_extractor.rb

@@ -7,13 +7,14 @@ require_relative 'terminology_binding_metadata_extractor'
 module IpaTestKit
   class Generator
     class GroupMetadataExtractor
-      attr_accessor :resource_capabilities, :profile_url, :ig_metadata, :ig_resources
+      attr_accessor :resource_capabilities, :profile_url, :ig_metadata, :ig_resources, :base_search_params
 
-      def initialize(resource_capabilities, profile_url, ig_metadata, ig_resources)
+      def initialize(resource_capabilities, profile_url, ig_metadata, ig_resources, base_search_params)
         self.resource_capabilities = resource_capabilities
         self.profile_url = profile_url
         self.ig_metadata = ig_metadata
         self.ig_resources = ig_resources
+        self.base_search_params = base_search_params
       end
 
       def group_metadata
@@ -32,6 +33,7 @@ module IpaTestKit
             resource: resource,
             profile_url: profile_url,
             profile_name: profile_name,
+            profile_version: profile_version,
             title: title,
             short_description: short_description,
             interactions: interactions,
@@ -57,26 +59,32 @@ module IpaTestKit
       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]
+            full_paths = search_definitions[name.to_sym][:full_paths]
             any_must_support_elements = (must_supports[:elements]).any? do |element|
-              full_must_support_path = "#{resource}.#{element[:path]}"
+              full_must_support_paths = ["#{resource}.#{element[:original_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]"
+              full_paths.any? do |path|
+                # allow for non-choice, choice types, and _id
+                name == '_id' || full_must_support_paths.include?(path) || full_must_support_paths.include?("#{path}[x]")
+              end
             end
 
             any_must_support_slices = must_supports[:slices].any? do |slice|
               # only handle type slices because that is all we need for now
+              # for a slice like Observation.effective[x]:effectiveDateTime, the search parameter's expression could be
+              # either Observation.effective or Observation.effectiveDateTime.
               if slice[:discriminator] && slice[:discriminator][:type] == 'type'
                 full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
-                full_must_support_path == path
+                base_must_support_path = "#{resource}.#{slice[:path].sub('[x]', '')}"
+
+                full_paths.intersection([full_must_support_path,base_must_support_path]).present?
               else
                 false
               end
             end
 
             any_mandatory_elements = mandatory_elements.any? do |element|
-              element == path
+              full_paths.include?(element)
             end
 
             any_must_support_elements || any_must_support_slices || any_mandatory_elements
@@ -89,7 +97,15 @@ module IpaTestKit
       ### BEGIN SPECIAL CASES ###
 
       CATEGORY_FIRST_PROFILES = [
-        'http://hl7.org/fhir/uv/ipa/StructureDefinition/ipa-observation',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-sdoh-assessment',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history',
+        # 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey'
       ]
 
       def category_first_profile?
@@ -100,10 +116,6 @@ module IpaTestKit
         @first_search_params ||=
         if category_first_profile?
           ['patient', 'category']
-        elsif resource == 'Observation'
-          ['patient', 'code']
-        elsif resource == 'MedicationRequest'
-          ['patient', 'intent']
         else
           ['patient']
         end
@@ -111,17 +123,6 @@ module IpaTestKit
 
       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
@@ -172,11 +173,22 @@ module IpaTestKit
       end
 
       def profile_name
+        binding.pry if profile.nil?
         profile.title.gsub('  ', ' ')
       end
 
+      def profile_version
+        profile.version
+      end
+
       def title
-        profile.title.gsub(/IPA\s*/, '').gsub(/\s*Profile/, '').strip
+        title = profile.title.gsub(/IPA\-/, ' ').strip
+
+        if (Naming.resources_with_multiple_profiles.include?(resource)) && !title.start_with?(resource) && version != 'v3.1.1'
+          title = "#{resource} (#{title.split(resource).map(&:strip).join(' ').gsub(/\-/, ' ')})".titleize
+        end
+
+        title
       end
 
       def short_description
@@ -205,7 +217,7 @@ module IpaTestKit
 
       def search_metadata_extractor
         @search_metadata_extractor ||=
-          SearchMetadataExtractor.new(resource_capabilities, ig_resources, resource, profile_elements)
+          SearchMetadataExtractor.new(resource_capabilities, ig_resources, resource, profile_elements, base_search_params)
       end
 
       def searches
@@ -227,7 +239,7 @@ module IpaTestKit
       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'
+        return [] if resource == 'Observation'
 
         profile_elements
           .select { |element| element.type&.any? { |type| type.code == 'CodeableConcept' } }
@@ -247,7 +259,7 @@ module IpaTestKit
 
       def must_support_metadata_extractor
         @must_support_metadata_extractor ||=
-          MustSupportMetadataExtractor.new(profile_elements, profile, resource)
+          MustSupportMetadataExtractor.new(profile_elements, profile, resource, ig_resources)
       end
 
       def must_supports
@@ -260,16 +272,18 @@ module IpaTestKit
           profile_elements
             .select { |element| element.min.positive? }
             .map { |element| element.path }
+            .uniq
       end
 
       def references
         @references ||=
           profile_elements
-            .select { |element| element.type&.first&.code == 'Reference' }
+            .select { |element| element.type&.any? { |type| type&.code == 'Reference' } }
             .map do |reference_definition|
+              reference_type = reference_definition.type.find { |type| type.code == 'Reference' }
               {
-                path: reference_definition.path,
-                profiles: reference_definition.type.first.targetProfile
+                path: reference_definition.path.gsub('[x]', 'Reference'),
+                profiles: reference_type.targetProfile
               }
             end
       end

data/lib/ipa_test_kit/generator/ig_loader.rb

@@ -1,5 +1,6 @@
 require 'active_support/all'
 require 'fhir_models'
+require 'pathname'
 require 'rubygems/package'
 require 'zlib'
 require_relative 'ig_resources'
@@ -7,6 +8,12 @@ require_relative 'ig_resources'
 module IpaTestKit
   class Generator
     class IGLoader
+      attr_accessor :ig_file_name
+
+      def initialize(ig_file_name)
+        self.ig_file_name = ig_file_name
+      end
+
       def ig_resources
         @ig_resources ||= IGResources.new
       end
@@ -17,7 +24,9 @@ module IpaTestKit
       end
 
       def load_ig
-        tar = Gem::Package::TarReader.new(Zlib::GzipReader.open(File.join(__dir__, '..', 'igs', 'package.tgz')))
+        tar = Gem::Package::TarReader.new(
+          Zlib::GzipReader.open(ig_file_name)
+        )
 
         tar.each do |entry|
           next if entry.directory?
@@ -43,7 +52,11 @@ module IpaTestKit
       end
 
       def load_standalone_resources
-        Dir.glob(File.join(__dir__, '..', 'igs', '*.json')).each do |file_path|
+        ig_directory = ig_file_name.chomp('.tgz')
+
+        return ig_resources unless File.exist? ig_directory
+
+        Dir.glob(File.join(ig_directory, '*.json')).each do |file_path|
           begin
             resource = FHIR.from_contents(File.read(file_path))
             next if resource.nil?

data/lib/ipa_test_kit/generator/ig_metadata.rb

@@ -4,12 +4,12 @@ module IpaTestKit
       attr_accessor :ig_version, :groups
 
       def reformatted_version
-        @reformatted_version ||= ig_version.delete('.')
+        @reformatted_version ||= ig_version.delete('.').delete('-')
       end
 
       def ordered_groups
         @ordered_groups ||=
-          [patient_group] + non_delayed_groups + delayed_groups
+          ([patient_group] + non_delayed_groups + delayed_groups).reject{|group| group.nil?}
       end
 
       def patient_group

data/lib/ipa_test_kit/generator/ig_metadata_extractor.rb

@@ -4,11 +4,13 @@ require_relative 'group_metadata_extractor'
 module IpaTestKit
   class Generator
     class IGMetadataExtractor
-      attr_accessor :ig_resources, :metadata
+      attr_accessor :ig_resources, :metadata, :base_search_params
 
-      def initialize(ig_resources)
+      def initialize(ig_resources, base_search_params)
         self.ig_resources = ig_resources
-        add_vital_signs_profiles
+        self.base_search_params = base_search_params
+        add_missing_supported_profiles
+        remove_extra_supported_profiles
         self.metadata = IGMetadata.new
       end
 
@@ -26,27 +28,28 @@ module IpaTestKit
         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
+      def add_missing_supported_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'
+            'http://hl7.org/fhir/StructureDefinition/vitalsigns'
           ]
       end
 
+      def remove_extra_supported_profiles
+        ig_resources.capability_statement.rest.first.resource
+            .find { |resource| resource.type == 'Observation' }
+            .supportedProfile.delete_if do |profile_url|
+              SpecialCases::PROFILES_TO_EXCLUDE.include?(profile_url)
+            end
+      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
+            ([resource.profile] + resource.supportedProfile).uniq&.map do |supported_profile|
+              GroupMetadataExtractor.new(resource, supported_profile, metadata, ig_resources, base_search_params).group_metadata
+            end.compact
           end
 
         metadata.postprocess_groups(ig_resources)

data/lib/ipa_test_kit/generator/ig_resources.rb

@@ -32,10 +32,11 @@ module IpaTestKit
       end
 
       def search_param_by_resource_and_name(resource, name)
-        normalized_name = name.to_s == '_id' ? 'id' : name.to_s
+        # remove '_' from search parameter name, such as _id or _tag
+        normalized_name = normalized_name = name.to_s.delete_prefix('_')
 
         resources_by_type['SearchParameter']
-          .find { |param| param.id == "ipa-#{resource.downcase}-#{normalized_name}" }
+          .find { |param| param.id == "us-core-#{resource.downcase}-#{normalized_name}" }
       end
 
       private