inferno_core 0.3.2 → 0.3.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d44d2d4f0afb51b463a128ce7725183159791fe21464c2fa28b10b3b919c37ab
-  data.tar.gz: b62acf63e2bb524bcb22048e4e4d5b433a727c6a7a8201ae8161237fc4dbcfb3
+  metadata.gz: 40fa8983d93a7fc191a7d03bdb78c0bd80e138cfe5245d377c15f28360fb6b03
+  data.tar.gz: 4aa592411c216c13bc55ebcef30ce2019522cc3575edc184fcb10593eb28239a
 SHA512:
-  metadata.gz: 7658c22a6d5595f39a36589a853992420b31717c6002ce0262eabcfcabe4def7c97de8f8fa5a52ad785a7e4c6b25fb471282584bdbfde266ed6388ee8dfc7b8b
-  data.tar.gz: 9972288e75af701edc3f70457835384f6f51ad5e64d14bfaf4b5ec0855786ca51455e79067de007f44964bbecfc9b84b1a862b6468a72464026152c41acb5536
+  metadata.gz: bb0f7e9aafced3a1181cd40d8638f4ac07fefc0239ab771b85ce22aaec3785b7328ca82969cd83b1617051201fa149272ba80a53a05789129e6ee35302cf3a1b
+  data.tar.gz: 5f14e0db2c0a2d3238198600a736790ea549ea11c91bb84578dda2e3de2270c31cb314b44972ec2fbc6635aa77b93f0ce4df2926d45c072745b19a1d6371b34f

data/lib/inferno/apps/web/controllers/test_sessions/create.rb

@@ -3,9 +3,13 @@ module Inferno
     module Controllers
       module TestSessions
         class Create < Controller
-          PARAMS = [:test_suite_id].freeze
+          PARAMS = [:test_suite_id, :suite_options].freeze
+
+          def call(raw_params)
+            query_params = raw_params.to_h
+            body_params = JSON.parse(request.body.string).symbolize_keys
+            params = query_params.merge(body_params)
 
-          def call(params)
             session = repo.create(create_params(params))
 
             repo.apply_preset(session.id, params[:preset_id]) if params[:preset_id].present?
@@ -21,7 +25,7 @@ module Inferno
           end
 
           def create_params(params)
-            params.to_h.slice(*PARAMS)
+            params.slice(*PARAMS)
           end
         end
       end

data/lib/inferno/apps/web/index.html.erb

@@ -29,6 +29,11 @@
       Learn how to configure a non-root public URL by running `npm run build`.
     -->
     <style>
+      @media print {
+        .no-print {
+          display: none;
+        }
+      }
       .wrapper {
         height: 100%;
         display: flex;
@@ -49,7 +54,7 @@
     <noscript>You need to enable JavaScript to run this app.</noscript>
     <div class='wrapper'>
       <% if File.exist? (File.join(Dir.pwd, 'config', 'banner.html.erb')) %>
-        <div class='banner'><%= ERB.new(File.read(File.join(Dir.pwd, 'config', 'banner.html.erb'))).result %></div>
+        <div class='banner no-print'><%= ERB.new(File.read(File.join(Dir.pwd, 'config', 'banner.html.erb'))).result %></div>
       <% end %>
       <div class='app' id="root"></div>
     </div>

data/lib/inferno/apps/web/router.rb

@@ -36,8 +36,10 @@ module Inferno
           get '/version', to: ->(_env) { [200, {}, [{ 'version' => Inferno::VERSION.to_s }.to_json]] }, as: :api_version
         end
 
-        get '/', to: ->(_env) { [200, {}, [client_page]] }
-        get '/test_sessions/:id', to: ->(_env) { [200, {}, [client_page]] }
+        # Should not need Content-Type header but GitHub Codespaces will not work without them.
+        # This could be investigated and likely removed if addressed properly elsewhere.
+        get '/', to: ->(_env) { [200, { 'Content-Type' => 'text/html' }, [client_page]] }
+        get '/test_sessions/:id', to: ->(_env) { [200, { 'Content-Type' => 'text/html' }, [client_page]] }
 
         Inferno.routes.each do |route|
           cleaned_id = route[:suite].id.gsub(/[^a-zA-Z\d\-._~]/, '_')
@@ -49,6 +51,11 @@ module Inferno
             send(route[:method], path, to: route[:handler])
           end
         end
+
+        Inferno::Repositories::TestSuites.all.map { |suite| "/#{suite.id}" }.each do |suite_path|
+          Application['logger'].info("Registering suite route: #{suite_path}")
+          get suite_path, to: ->(_env) { [200, {}, [client_page]] }
+        end
       end
     end
   end

data/lib/inferno/apps/web/serializers/suite_option.rb

@@ -0,0 +1,13 @@
+module Inferno
+  module Web
+    module Serializers
+      class SuiteOption < Serializer
+        identifier :id
+        field :title, if: :field_present?
+        field :description, if: :field_present?
+        field :list_options, if: :field_present?
+        field :value, if: :field_present?
+      end
+    end
+  end
+end

data/lib/inferno/apps/web/serializers/test_group.rb

@@ -15,8 +15,12 @@ module Inferno
         field :user_runnable?, name: :user_runnable
         field :optional?, name: :optional
 
-        association :groups, name: :test_groups, blueprint: TestGroup
-        association :tests, blueprint: Test
+        field :test_groups do |group, options|
+          TestGroup.render_as_hash(group.groups(options[:suite_options]))
+        end
+        field :tests do |group, options|
+          Test.render_as_hash(group.tests(options[:suite_options]))
+        end
         field :available_inputs, name: :inputs, extractor: HashValueExtractor, blueprint: Input
         field :output_definitions, name: :outputs, extractor: HashValueExtractor
       end

data/lib/inferno/apps/web/serializers/test_session.rb

@@ -1,3 +1,4 @@
+require_relative 'suite_option'
 require_relative 'test_suite'
 
 module Inferno
@@ -7,10 +8,11 @@ module Inferno
         identifier :id
 
         field :test_suite_id
+        association :suite_options, blueprint: SuiteOption
 
-        association :test_suite, blueprint: TestSuite, view: :full
-        # association :test_runs, blueprint: TestRun
-        # association :results, blueprint: Result
+        field :test_suite do |session, _options|
+          TestSuite.render_as_hash(session.test_suite, view: :full, suite_options: session.suite_options)
+        end
       end
     end
   end

data/lib/inferno/apps/web/serializers/test_suite.rb

@@ -11,12 +11,15 @@ module Inferno
           field :input_instructions
           field :test_count
           field :version
+          association :suite_options, blueprint: SuiteOption
           association :presets, view: :summary, blueprint: Preset
         end
 
         view :full do
           include_view :summary
-          association :groups, name: :test_groups, blueprint: TestGroup
+          field :test_groups do |suite, options|
+            TestGroup.render_as_hash(suite.groups(options[:suite_options]))
+          end
           field :configuration_messages
           field :available_inputs, name: :inputs, extractor: HashValueExtractor, blueprint: Input
         end

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/db/migrations/007_add_suite_options.rb

@@ -0,0 +1,5 @@
+Sequel.migration do
+  change do
+    add_column :test_sessions, :suite_options, String, text: true, size: 255
+  end
+end

data/lib/inferno/db/schema.rb

@@ -9,6 +9,7 @@ Sequel.migration do
       String :test_suite_id, :size=>255, :null=>false
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
+      String :suite_options, :text=>true
       
       primary_key [:id]
     end

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

@@ -24,10 +24,20 @@ module Inferno
           [identifier, *other_identifiers].compact.each do |input_identifier|
             inputs << input_identifier
             config.add_input(input_identifier)
+            children
+              .reject { |child| child.inputs.include? input_identifier }
+              .each do |child|
+                child.input(input_identifier)
+              end
           end
         else
           inputs << identifier
           config.add_input(identifier, input_params)
+          children
+            .reject { |child| child.inputs.include? identifier }
+            .each do |child|
+              child.input(identifier, **input_params)
+            end
         end
       end
 
@@ -47,10 +57,20 @@ module Inferno
           [identifier, *other_identifiers].compact.each do |output_identifier|
             outputs << output_identifier
             config.add_output(output_identifier)
+            children
+              .reject { |child| child.outputs.include? output_identifier }
+              .each do |child|
+                child.output(output_identifier)
+              end
           end
         else
           outputs << identifier
           config.add_output(identifier, output_definition)
+          children
+            .reject { |child| child.outputs.include? identifier }
+            .each do |child|
+              child.output(identifier, **output_definition)
+            end
         end
       end
 
@@ -125,7 +145,7 @@ 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 +157,7 @@ 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]