inferno_core 0.3.3 → 0.3.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 884936b347ee4892198605b7ae408f3889e74bed0a4e33b6ec2a5ee7ed3adcd9
-  data.tar.gz: b0e30f11313a6a5b690e96a08fdb083ba9d85b94b512ec105fce75631802f0cb
+  metadata.gz: 5c905fd9a450198c42daa6a7f3119277d1eeb1e39acb788856d90c3817719d02
+  data.tar.gz: e11d6fcfa8acb3c487c62d512b9210db18f5d7bba5c9148063587de8a3e78420
 SHA512:
-  metadata.gz: 13b145c224d9b762b2ae8019048d6775dea2bd0ce47abcb3450959e3148224a523914eaf06b480a25d1a065c449e32b9c64ed83056118b611e8be2c4d9640755
-  data.tar.gz: 78a7bd5437739a2e1e7384dc500d46a99c8795f03638023839fdf4c24131fcc9a6ba8ca1ec507cd0b0bd559d8c9741e07ce2c6e3b04954b72bf6ba4ce7158805
+  metadata.gz: d62c7ebc7b9f9ac2024bfb933254cd54010b869fde72d15c77e935e7228096e2ba45844e3f8ba2f7b28f71315120d7a194b63d7e95675600e26efd1bbe822cc1
+  data.tar.gz: ed6b0d392219155cd2cd6865e01d9ba838c067f36bfdd86ac10e80e923b51ddf688cff4f8e8a67e62e53a1d28c151f1c76d5e791166e920ff9832676fa1239c0

data/lib/inferno/config/boot/db.rb

@@ -11,7 +11,7 @@ Inferno::Application.boot(:db) do
 
     config_path = File.expand_path('database.yml', File.join(Dir.pwd, 'config'))
     config_contents = ERB.new(File.read(config_path)).result
-    config = YAML.safe_load(config_contents)[ENV['APP_ENV']]
+    config = YAML.safe_load(config_contents)[ENV.fetch('APP_ENV', nil)]
       .merge(logger: Inferno::Application['logger'])
     connection_attempts_remaining = ENV.fetch('MAX_DB_CONNECTION_ATTEMPTS', '10').to_i
     connection_retry_delay = ENV.fetch('DB_CONNECTION_RETRY_DELAY', '5').to_i

data/lib/inferno/config/boot.rb

@@ -4,4 +4,4 @@ ENV['APP_ENV'] ||= 'development'
 
 root_path = Dir.pwd
 
-Dotenv.load(File.join(root_path, '.env'), File.join(root_path, ".env.#{ENV['APP_ENV']}"))
+Dotenv.load(File.join(root_path, '.env'), File.join(root_path, ".env.#{ENV.fetch('APP_ENV', nil)}"))

data/lib/inferno/dsl/configurable.rb

@@ -16,7 +16,7 @@ module Inferno
 
         @config.apply(new_configuration)
 
-        children.each { |child| child.config(new_configuration) }
+        all_children.each { |child| child.config(new_configuration) }
 
         @config
       end

data/lib/inferno/dsl/fhir_client.rb

@@ -1,4 +1,5 @@
 require_relative 'request_storage'
+require_relative 'tcp_exception_handler'
 
 module Inferno
   module DSL
@@ -40,6 +41,7 @@ module Inferno
         klass.extend ClassMethods
         klass.extend Forwardable
         klass.include RequestStorage
+        klass.include TCPExceptionHandler
 
         klass.def_delegators 'self.class', :profile_url, :validator_url
       end
@@ -73,11 +75,13 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def fhir_operation(path, body: nil, client: :default, name: nil, headers: {})
         store_request_and_refresh_token(fhir_client(client), name) do
-          operation_headers = fhir_client(client).fhir_headers
-          operation_headers.merge!('Content-Type' => 'application/fhir+json') if body.present?
-          operation_headers.merge!(headers) if headers.present?
+          tcp_exception_handler do
+            operation_headers = fhir_client(client).fhir_headers
+            operation_headers.merge!('Content-Type' => 'application/fhir+json') if body.present?
+            operation_headers.merge!(headers) if headers.present?
 
-          fhir_client(client).send(:post, path, body, operation_headers)
+            fhir_client(client).send(:post, path, body, operation_headers)
+          end
         end
       end
 
@@ -89,8 +93,10 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def fhir_get_capability_statement(client: :default, name: nil)
         store_request_and_refresh_token(fhir_client(client), name) do
-          fhir_client(client).conformance_statement
-          fhir_client(client).reply
+          tcp_exception_handler do
+            fhir_client(client).conformance_statement
+            fhir_client(client).reply
+          end
         end
       end
 
@@ -104,7 +110,9 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def fhir_read(resource_type, id, client: :default, name: nil)
         store_request_and_refresh_token(fhir_client(client), name) do
-          fhir_client(client).read(fhir_class_from_resource_type(resource_type), id)
+          tcp_exception_handler do
+            fhir_client(client).read(fhir_class_from_resource_type(resource_type), id)
+          end
         end
       end
 
@@ -126,8 +134,10 @@ module Inferno
           end
 
         store_request_and_refresh_token(fhir_client(client), name) do
-          fhir_client(client)
-            .search(fhir_class_from_resource_type(resource_type), { search: search })
+          tcp_exception_handler do
+            fhir_client(client)
+              .search(fhir_class_from_resource_type(resource_type), { search: search })
+          end
         end
       end
 
@@ -141,7 +151,9 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def fhir_delete(resource_type, id, client: :default, name: nil)
         store_request('outgoing', name) do
-          fhir_client(client).destroy(fhir_class_from_resource_type(resource_type), id)
+          tcp_exception_handler do
+            fhir_client(client).destroy(fhir_class_from_resource_type(resource_type), id)
+          end
         end
       end
 

data/lib/inferno/dsl/fhir_validation.rb

@@ -1,5 +1,4 @@
 require_relative '../ext/fhir_models'
-
 module Inferno
   module DSL
     # This module contains the methods needed to configure a validator to
@@ -39,13 +38,16 @@ module Inferno
       # Find a particular validator. Looks through a runnable's parents up to
       # the suite to find a validator with a particular name
       def find_validator(validator_name)
-        self.class.find_validator(validator_name)
+        self.class.find_validator(validator_name, suite_options)
       end
 
       class Validator
+        attr_reader :requirements
+
         # @private
-        def initialize(&block)
+        def initialize(requirements = nil, &block)
           instance_eval(&block)
+          @requirements = requirements
         end
 
         # @private
@@ -115,7 +117,7 @@ module Inferno
 
           outcome = FHIR::OperationOutcome.new(JSON.parse(validate(resource, profile_url)))
 
-          message_hashes = outcome.issue&.map { |issue| message_hash_from_issue(issue) } || []
+          message_hashes = outcome.issue&.map { |issue| message_hash_from_issue(issue, resource) } || []
 
           message_hashes.concat(additional_validation_messages(resource, profile_url))
 
@@ -132,10 +134,10 @@ module Inferno
         end
 
         # @private
-        def message_hash_from_issue(issue)
+        def message_hash_from_issue(issue, resource)
           {
             type: issue_severity(issue),
-            message: issue_message(issue)
+            message: issue_message(issue, resource)
           }
         end
 
@@ -152,14 +154,16 @@ module Inferno
         end
 
         # @private
-        def issue_message(issue)
+        def issue_message(issue, resource)
           location = if issue.respond_to?(:expression)
                        issue.expression&.join(', ')
                      else
                        issue.location&.join(', ')
                      end
 
-          "#{location}: #{issue&.details&.text}"
+          location_prefix = resource.id ? "#{resource.resourceType}/#{resource.id}" : resource.resourceType
+
+          "#{location_prefix}: #{location}: #{issue&.details&.text}"
         end
 
         # Post a resource to the validation service for validating.
@@ -198,14 +202,33 @@ module Inferno
         #
         # @param name [Symbol] the name of the validator, only needed if you are
         #   using multiple validators
-        def validator(name = :default, &block)
-          fhir_validators[name] = Inferno::DSL::FHIRValidation::Validator.new(&block)
+        # @param required_suite_options [Hash] suite options that must be
+        #   selected in order to use this validator
+        def validator(name = :default, required_suite_options: nil, &block)
+          current_validators = fhir_validators[name] || []
+
+          new_validator = Inferno::DSL::FHIRValidation::Validator.new(required_suite_options, &block)
+
+          current_validators.reject! { |validator| validator.requirements == required_suite_options }
+          current_validators << new_validator
+
+          fhir_validators[name] = current_validators
         end
 
         # Find a particular validator. Looks through a runnable's parents up to
         # the suite to find a validator with a particular name
-        def find_validator(validator_name)
-          validator = fhir_validators[validator_name] || parent&.find_validator(validator_name)
+        def find_validator(validator_name, selected_suite_options = nil)
+          validators = fhir_validators[validator_name] ||
+                       Array.wrap(parent&.find_validator(validator_name, selected_suite_options))
+
+          validator =
+            if selected_suite_options.present?
+              validators.find do |possible_validator|
+                possible_validator.requirements.nil? || selected_suite_options >= possible_validator.requirements
+              end
+            else
+              validators.first
+            end
 
           raise Exceptions::ValidatorNotFoundException, validator_name if validator.nil?
 

data/lib/inferno/dsl/http_client.rb

@@ -1,4 +1,5 @@
 require_relative 'request_storage'
+require_relative 'tcp_exception_handler'
 
 module Inferno
   module DSL
@@ -31,6 +32,7 @@ module Inferno
       def self.included(klass)
         klass.extend ClassMethods
         klass.include RequestStorage
+        klass.include TCPExceptionHandler
       end
 
       # Return a previously defined HTTP client
@@ -44,7 +46,9 @@ module Inferno
         definition = self.class.http_client_definitions[client]
         return nil if definition.nil?
 
-        http_clients[client] = HTTPClientBuilder.new.build(self, definition)
+        tcp_exception_handler do
+          http_clients[client] = HTTPClientBuilder.new.build(self, definition)
+        end
       end
 
       # @private
@@ -65,14 +69,16 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def get(url = '', client: :default, name: nil, **options)
         store_request('outgoing', name) do
-          client = http_client(client)
-
-          if client
-            client.get(url, nil, options[:headers])
-          elsif url.match?(%r{\Ahttps?://})
-            Faraday.get(url, nil, options[:headers])
-          else
-            raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+          tcp_exception_handler do
+            client = http_client(client)
+
+            if client
+              client.get(url, nil, options[:headers])
+            elsif url.match?(%r{\Ahttps?://})
+              Faraday.get(url, nil, options[:headers])
+            else
+              raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+            end
           end
         end
       end
@@ -91,14 +97,16 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def post(url = '', body: nil, client: :default, name: nil, **options)
         store_request('outgoing', name) do
-          client = http_client(client)
-
-          if client
-            client.post(url, body, options[:headers])
-          elsif url.match?(%r{\Ahttps?://})
-            Faraday.post(url, body, options[:headers])
-          else
-            raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+          tcp_exception_handler do
+            client = http_client(client)
+
+            if client
+              client.post(url, body, options[:headers])
+            elsif url.match?(%r{\Ahttps?://})
+              Faraday.post(url, body, options[:headers])
+            else
+              raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+            end
           end
         end
       end
@@ -114,14 +122,16 @@ module Inferno
       # @return [Inferno::Entities::Request]
       def delete(url = '', client: :default, name: :nil, **options)
         store_request('outgoing', name) do
-          client = http_client(client)
-
-          if client
-            client.delete(url, nil, options[:headers])
-          elsif url.match?(%r{\Ahttps?://})
-            Faraday.delete(url, nil, options[:headers])
-          else
-            raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+          tcp_exception_handler do
+            client = http_client(client)
+
+            if client
+              client.delete(url, nil, options[:headers])
+            elsif url.match?(%r{\Ahttps?://})
+              Faraday.delete(url, nil, options[:headers])
+            else
+              raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+            end
           end
         end
       end
@@ -151,17 +161,19 @@ module Inferno
         end
 
         store_request('outgoing', name) do
-          client = http_client(client)
-
-          if client
-            response = client.get(url, nil, options[:headers]) { |req| req.options.on_data = collector }
-          elsif url.match?(%r{\Ahttps?://})
-            response = Faraday.get(url, nil, options[:headers]) { |req| req.options.on_data = collector }
-          else
-            raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+          tcp_exception_handler do
+            client = http_client(client)
+
+            if client
+              response = client.get(url, nil, options[:headers]) { |req| req.options.on_data = collector }
+            elsif url.match?(%r{\Ahttps?://})
+              response = Faraday.get(url, nil, options[:headers]) { |req| req.options.on_data = collector }
+            else
+              raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
+            end
+            response.env.body = streamed.join
+            response
           end
-          response.env.body = streamed.join
-          response
         end
       end
 

data/lib/inferno/dsl/input_output_handling.rb

@@ -125,7 +125,7 @@ module Inferno
       def all_outputs
         outputs
           .map { |output_identifier| config.output_name(output_identifier) }
-          .concat(children.flat_map(&:all_outputs))
+          .concat(all_children.flat_map(&:all_outputs))
           .uniq
       end
 
@@ -137,7 +137,7 @@ module Inferno
         @children_available_inputs ||=
           begin
             child_outputs = []
-            children.each_with_object({}) do |child, definitions|
+            all_children.each_with_object({}) do |child, definitions|
               new_definitions = child.available_inputs.map(&:dup)
               new_definitions.each do |input, new_definition|
                 existing_definition = definitions[input]

data/lib/inferno/dsl/runnable.rb

@@ -9,6 +9,7 @@ module Inferno
     # definition framework.
     module Runnable
       attr_accessor :parent
+      attr_reader :suite_option_requirements
 
       include Inferno::Utils::MarkdownFormatter
 
@@ -48,7 +49,7 @@ module Inferno
       VARIABLES_NOT_TO_COPY = [
         :@id, # New runnable will have a different id
         :@parent, # New runnable unlikely to have the same parent
-        :@children, # New subclasses have to be made for each child
+        :@all_children, # New subclasses have to be made for each child
         :@test_count, # Needs to be recalculated
         :@config, # Needs to be set by calling .config, which does extra work
         :@available_inputs, # Needs to be recalculated
@@ -63,13 +64,13 @@ module Inferno
 
         subclass.config(config)
 
-        new_children = children.map do |child|
+        new_children = all_children.map do |child|
           Class.new(child).tap do |subclass_child|
             subclass_child.parent = subclass
           end
         end
 
-        subclass.instance_variable_set(:@children, new_children)
+        subclass.instance_variable_set(:@all_children, new_children)
       end
 
       # @private
@@ -94,7 +95,7 @@ module Inferno
 
         klass.parent = self
 
-        children << klass
+        all_children << klass
 
         configure_child_class(klass, hash_args)
 
@@ -172,7 +173,7 @@ module Inferno
 
         klass.config(config)
 
-        klass.children.select!(&:required?) if hash_args.delete(:exclude_optional)
+        klass.all_children.select!(&:required?) if hash_args.delete(:exclude_optional)
 
         hash_args.each do |key, value|
           if value.is_a? Array
@@ -182,7 +183,7 @@ module Inferno
           end
         end
 
-        klass.children.each do |child_class|
+        klass.all_children.each do |child_class|
           klass.configure_child_class(child_class, {})
           child_class.add_self_to_repository
         end
@@ -302,8 +303,8 @@ module Inferno
       end
 
       # @private
-      def children
-        @children ||= []
+      def all_children
+        @all_children ||= []
       end
 
       def validator_url(url = nil)
@@ -378,8 +379,12 @@ module Inferno
       end
 
       # @private
-      def test_count
-        @test_count ||= children&.reduce(0) { |sum, child| sum + child.test_count } || 0
+      def test_count(selected_suite_options = {})
+        @test_counts ||= {}
+
+        @test_counts[selected_suite_options] ||=
+          children(selected_suite_options)
+            &.reduce(0) { |sum, child| sum + child.test_count(selected_suite_options) } || 0
       end
 
       # @private
@@ -388,6 +393,21 @@ module Inferno
                            !parent.respond_to?(:run_as_group?) ||
                            (parent.user_runnable? && !parent.run_as_group?)
       end
+
+      def required_suite_options(suite_option_requirements)
+        @suite_option_requirements = suite_option_requirements
+      end
+
+      def children(selected_suite_options = nil)
+        return all_children if selected_suite_options.blank?
+
+        all_children.select do |child|
+          requirements = child.suite_option_requirements || {}
+
+          # requirements are a subset of selected options or equal to selected options
+          selected_suite_options >= requirements
+        end
+      end
     end
   end
 end

data/lib/inferno/dsl/tcp_exception_handler.rb

@@ -0,0 +1,11 @@
+module Inferno
+  module DSL
+    module TCPExceptionHandler
+      def tcp_exception_handler(&block)
+        block.call
+      rescue Faraday::ConnectionFailed, SocketError => e
+        e.message.include?('Failed to open TCP') ? raise(Exceptions::AssertionException, e.message) : raise(e)
+      end
+    end
+  end
+end

data/lib/inferno/entities/test.rb

@@ -13,13 +13,14 @@ module Inferno
       def_delegators 'self.class', :title, :id, :block, :inputs, :outputs
 
       attr_accessor :result_message
-      attr_reader :test_session_id, :scratch
+      attr_reader :test_session_id, :scratch, :suite_options
 
       # @private
       def initialize(**params)
         params[:inputs]&.each { |key, value| instance_variable_set("@#{key}", value) }
         @scratch = params[:scratch]
         @test_session_id = params[:test_session_id]
+        @suite_options = params[:suite_options].presence || {}
       end
 
       # @private
@@ -195,7 +196,8 @@ module Inferno
         end
 
         # @private
-        def test_count
+        # Has an unused argument to match the method signature of Runnable#test_count
+        def test_count(_ = nil)
           1
         end
 

data/lib/inferno/entities/test_group.rb

@@ -32,11 +32,11 @@ module Inferno
         end
 
         def groups
-          children.select { |child| child < Inferno::Entities::TestGroup }
+          all_children.select { |child| child < Inferno::Entities::TestGroup }
         end
 
         def tests
-          children.select { |child| child < Inferno::Entities::Test }
+          all_children.select { |child| child < Inferno::Entities::Test }
         end
 
         # Methods to configure Inferno::DSL::Runnable

data/lib/inferno/entities/test_session.rb

@@ -19,8 +19,19 @@ module Inferno
     # @!attribute results
     #   @return [Array<Inferno::Entities::TestResult>] the `TestResults`
     #   associated with this session
+    # @!attribute suite_options
+    #   @return [Hash] the suite options associated with this session
     class TestSession < Entity
-      ATTRIBUTES = [:id, :created_at, :updated_at, :test_suite_id, :test_suite, :test_runs, :results].freeze
+      ATTRIBUTES = [
+        :id,
+        :created_at,
+        :updated_at,
+        :test_suite_id,
+        :test_suite,
+        :test_runs,
+        :results,
+        :suite_options
+      ].freeze
 
       include Inferno::Entities::Attributes
 

data/lib/inferno/entities/test_suite.rb

@@ -22,7 +22,7 @@ module Inferno
           return @default_group if @default_group
 
           @default_group = Class.new(TestGroup)
-          children << @default_group
+          all_children << @default_group
           @default_group
         end
 
@@ -31,7 +31,7 @@ module Inferno
         end
 
         def groups
-          children.select { |child| child < Inferno::Entities::TestGroup }
+          all_children.select { |child| child < Inferno::Entities::TestGroup }
         end
 
         # Methods to configure Inferno::DSL::Runnable
@@ -60,17 +60,6 @@ module Inferno
           @version = version
         end
 
-        def find_validator(validator_name)
-          validator = fhir_validators[validator_name]
-
-          return validator if validator
-
-          raise Exceptions::ValidatorNotFoundException, validator_name unless validator_name == :default
-
-          fhir_validators[:default] =
-            Inferno::DSL::FHIRValidation::Validator.new { |v| v.url default_validator_url }
-        end
-
         def configuration_messages(new_messages = nil, force_recheck: false)
           return @configuration_messages = new_messages unless new_messages.nil?
 
@@ -95,6 +84,14 @@ module Inferno
         def presets
           @presets ||= Repositories::Presets.new.presets_for_suite(id)
         end
+
+        def suite_option(identifier, **input_params)
+          suite_options[identifier] = input_params
+        end
+
+        def suite_options
+          @suite_options ||= {}
+        end
       end
     end
   end