inferno_core 0.3.4 → 0.3.7

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: f606bb9364a4e08b29754706692fc1e525e3592c2c01490183574673201ee1be
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+  data.tar.gz: eca623df2965155c9b4867c426e75fba81758214495160afd8236ada7e6930fda72cab708561673c2daffd45045fb3fa8994e7d2b7194272eb543f9664cf6018

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

@@ -11,8 +11,8 @@ module Inferno
 
           PARAMS = [:test_session_id, :test_suite_id, :test_group_id, :test_id].freeze
 
-          def verify_runnable(runnable, inputs)
-            missing_inputs = runnable&.missing_inputs(inputs)
+          def verify_runnable(runnable, inputs, selected_suite_options)
+            missing_inputs = runnable&.missing_inputs(inputs, selected_suite_options)
             user_runnable = runnable&.user_runnable?
             raise Inferno::Exceptions::RequiredInputsNotFound, missing_inputs if missing_inputs&.any?
             raise Inferno::Exceptions::NotUserRunnableException unless user_runnable
@@ -26,7 +26,7 @@ module Inferno
                   &.last
 
               if input.nil?
-                Inferno::Application['logger'].warning(
+                Inferno::Application['logger'].warn(
                   "Unknown input `#{input_params[:name]}` for #{test_run.runnable.id}: #{test_run.runnable.title}"
                 )
                 next
@@ -51,7 +51,11 @@ module Inferno
               return
             end
 
-            verify_runnable(repo.build_entity(create_params(params)).runnable, params[:inputs])
+            verify_runnable(
+              repo.build_entity(create_params(params)).runnable,
+              params[:inputs],
+              test_session.suite_options
+            )
 
             test_run = repo.create(create_params(params).merge(status: 'queued'))
 

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

@@ -3,9 +3,12 @@ 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)
+            params = raw_params.to_h
+            params.merge!(JSON.parse(request.body.string).symbolize_keys) unless request.body.string.blank?
 
-          def call(params)
             session = repo.create(create_params(params))
 
             repo.apply_preset(session.id, params[:preset_id]) if params[:preset_id].present?
@@ -21,7 +24,7 @@ module Inferno
           end
 
           def create_params(params)
-            params.to_h.slice(*PARAMS)
+            params.slice(*PARAMS)
           end
         end
       end

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

@@ -51,6 +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/input.rb

@@ -6,9 +6,13 @@ module Inferno
       class Input < Serializer
         identifier :name
 
-        field :label, if: :field_present?
+        field :title, if: :field_present?
         field :description, if: :field_present?
-        field :required, if: :field_present?
+        field :type, if: :field_present?
+        field :default, if: :field_present?
+        field :optional, if: :field_present?
+        field :options, if: :field_present?
+        field :locked, if: :field_present?
         field :value, if: :field_present?
       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.rb

@@ -7,7 +7,10 @@ module Inferno
         field :short_id
         field :title
         field :short_title
-        field :available_inputs, name: :inputs, extractor: HashValueExtractor, blueprint: Input
+        field :inputs do |test, options|
+          suite_options = options[:suite_options]
+          Input.render_as_hash(test.available_inputs(suite_options).values)
+        end
         field :output_definitions, name: :outputs, extractor: HashValueExtractor
         field :description
         field :short_description

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

@@ -15,9 +15,18 @@ module Inferno
         field :user_runnable?, name: :user_runnable
         field :optional?, name: :optional
 
-        association :groups, name: :test_groups, blueprint: TestGroup
-        association :tests, blueprint: Test
-        field :available_inputs, name: :inputs, extractor: HashValueExtractor, blueprint: Input
+        field :test_groups do |group, options|
+          suite_options = options[:suite_options]
+          TestGroup.render_as_hash(group.groups(suite_options), suite_options: suite_options)
+        end
+        field :tests do |group, options|
+          suite_options = options[:suite_options]
+          Test.render_as_hash(group.tests(suite_options), suite_options: suite_options)
+        end
+        field :inputs do |group, options|
+          suite_options = options[:suite_options]
+          Input.render_as_hash(group.available_inputs(suite_options).values)
+        end
         field :output_definitions, name: :outputs, extractor: HashValueExtractor
       end
     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

@@ -11,14 +11,22 @@ module Inferno
           field :input_instructions
           field :test_count
           field :version
+          field :links
+          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|
+            suite_options = options[:suite_options]
+            TestGroup.render_as_hash(suite.groups(suite_options), suite_options: suite_options)
+          end
           field :configuration_messages
-          field :available_inputs, name: :inputs, extractor: HashValueExtractor, blueprint: Input
+          field :inputs do |suite, options|
+            suite_options = options[:suite_options]
+            Input.render_as_hash(suite.available_inputs(suite_options).values)
+          end
         end
       end
     end

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

@@ -4,7 +4,7 @@ Inferno::Application.boot(:presets) do
   init do
     use :suites
 
-    files_to_load = Dir.glob(File.join(Dir.pwd, 'config', 'presets', '*.json'))
+    files_to_load = Dir.glob(['config/presets/*.json', 'config/presets/*.json.erb'])
     files_to_load.map! { |path| File.realpath(path) }
     presets_repo = Inferno::Repositories::Presets.new
 

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/http_client.rb

@@ -1,3 +1,5 @@
+require 'faraday_middleware'
+
 require_relative 'request_storage'
 require_relative 'tcp_exception_handler'
 
@@ -75,7 +77,7 @@ module Inferno
             if client
               client.get(url, nil, options[:headers])
             elsif url.match?(%r{\Ahttps?://})
-              Faraday.get(url, nil, options[:headers])
+              connection.get(url, nil, options[:headers])
             else
               raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
             end
@@ -83,6 +85,14 @@ module Inferno
         end
       end
 
+      # @private
+      def connection
+        Faraday.new do |f|
+          f.request :url_encoded
+          f.use FaradayMiddleware::FollowRedirects
+        end
+      end
+
       # Perform an HTTP POST request
       #
       # @param url [String] if this request is using a defined client, this will
@@ -103,7 +113,7 @@ module Inferno
             if client
               client.post(url, body, options[:headers])
             elsif url.match?(%r{\Ahttps?://})
-              Faraday.post(url, body, options[:headers])
+              connection.post(url, body, options[:headers])
             else
               raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
             end
@@ -128,7 +138,7 @@ module Inferno
             if client
               client.delete(url, nil, options[:headers])
             elsif url.match?(%r{\Ahttps?://})
-              Faraday.delete(url, nil, options[:headers])
+              connection.delete(url, nil, options[:headers])
             else
               raise StandardError, 'Must use an absolute url or define an HTTP client with a base url'
             end
@@ -167,7 +177,7 @@ module Inferno
             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 }
+              response = connection.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

data/lib/inferno/dsl/http_client_builder.rb

@@ -1,3 +1,5 @@
+require 'faraday_middleware'
+
 module Inferno
   module DSL
     # This module contains the HTTP DSL available to test writers.
@@ -12,7 +14,10 @@ module Inferno
         params = { url: url }
         params.merge!(headers: headers) if headers
 
-        Faraday.new(params)
+        Faraday.new(params) do |f|
+          f.request :url_encoded
+          f.use FaradayMiddleware::FollowRedirects
+        end
       end
 
       # Define the base url for an HTTP client. A string or symbol can be

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
 
@@ -70,17 +90,17 @@ module Inferno
       end
 
       # @private
-      def required_inputs
-        available_inputs
+      def required_inputs(selected_suite_options)
+        available_inputs(selected_suite_options)
           .reject { |_, input| input.optional }
           .map { |_, input| input.name }
       end
 
       # @private
-      def missing_inputs(submitted_inputs)
+      def missing_inputs(submitted_inputs, selected_suite_options)
         submitted_inputs = [] if submitted_inputs.nil?
 
-        required_inputs.map(&:to_s) - submitted_inputs.map { |input| input[:name] }
+        required_inputs(selected_suite_options).map(&:to_s) - submitted_inputs.map { |input| input[:name] }
       end
 
       # Define a particular order for inputs to be presented in the API/UI
@@ -133,52 +153,46 @@ module Inferno
       # Inputs available for this runnable's children. A running list of outputs
       # created by the children is used to exclude any inputs which are provided
       # by an earlier child's output.
-      def children_available_inputs
-        @children_available_inputs ||=
-          begin
-            child_outputs = []
-            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]
-
-                updated_definition =
-                  if existing_definition.present?
-                    existing_definition.merge_with_child(new_definition)
-                  else
-                    new_definition
-                  end
-
-                next if child_outputs.include?(updated_definition.name.to_sym)
-
-                definitions[updated_definition.name.to_sym] = updated_definition
+      def children_available_inputs(selected_suite_options = nil)
+        child_outputs = []
+        children(selected_suite_options).each_with_object({}) do |child, definitions|
+          new_definitions = child.available_inputs(selected_suite_options).map(&:dup)
+          new_definitions.each do |input, new_definition|
+            existing_definition = definitions[input]
+
+            updated_definition =
+              if existing_definition.present?
+                existing_definition.merge_with_child(new_definition)
+              else
+                new_definition
               end
 
-              child_outputs.concat(child.all_outputs).uniq!
-            end
+            next if child_outputs.include?(updated_definition.name.to_sym)
+
+            definitions[updated_definition.name.to_sym] = updated_definition
           end
+
+          child_outputs.concat(child.all_outputs).uniq!
+        end
       end
 
       # @private
       # Inputs available for the user for this runnable and all its children.
-      def available_inputs
-        @available_inputs ||=
-          begin
-            available_inputs =
-              config.inputs
-                .slice(*inputs)
-                .each_with_object({}) do |(_, input), inputs|
-                  inputs[input.name.to_sym] = input
-                end
-
-            available_inputs.each do |input, current_definition|
-              child_definition = children_available_inputs[input]
-              current_definition.merge_with_child(child_definition)
+      def available_inputs(selected_suite_options = nil)
+        available_inputs =
+          config.inputs
+            .slice(*inputs)
+            .each_with_object({}) do |(_, input), inputs|
+              inputs[input.name.to_sym] = Entities::Input.new(input.to_hash)
             end
 
-            available_inputs = children_available_inputs.merge(available_inputs)
-            order_available_inputs(available_inputs)
-          end
+        available_inputs.each do |input, current_definition|
+          child_definition = children_available_inputs(selected_suite_options)[input]
+          current_definition.merge_with_child(child_definition)
+        end
+
+        available_inputs = children_available_inputs(selected_suite_options).merge(available_inputs)
+        order_available_inputs(available_inputs)
       end
     end
   end

data/lib/inferno/dsl/runnable.rb

@@ -379,7 +379,7 @@ module Inferno
       end
 
       # @private
-      def test_count(selected_suite_options = {})
+      def test_count(selected_suite_options = [])
         @test_counts ||= {}
 
         @test_counts[selected_suite_options] ||=
@@ -395,17 +395,23 @@ module Inferno
       end
 
       def required_suite_options(suite_option_requirements)
-        @suite_option_requirements = suite_option_requirements
+        @suite_option_requirements =
+          suite_option_requirements.map do |key, value|
+            DSL::SuiteOption.new(id: key, value: value)
+          end
       end
 
-      def children(selected_suite_options = nil)
+      def children(selected_suite_options = [])
         return all_children if selected_suite_options.blank?
 
         all_children.select do |child|
-          requirements = child.suite_option_requirements || {}
+          requirements = child.suite_option_requirements
 
-          # requirements are a subset of selected options or equal to selected options
-          selected_suite_options >= requirements
+          if requirements.blank?
+            true
+          else
+            requirements.all? { |requirement| selected_suite_options.include? requirement }
+          end
         end
       end
     end

data/lib/inferno/dsl/suite_option.rb

@@ -0,0 +1,40 @@
+require_relative '../entities/attributes'
+
+module Inferno
+  module DSL
+    class SuiteOption
+      ATTRIBUTES = [
+        :id,
+        :title,
+        :description,
+        :list_options,
+        :value
+      ].freeze
+
+      include Entities::Attributes
+
+      def initialize(raw_params)
+        params = raw_params.deep_symbolize_keys
+        bad_params = params.keys - ATTRIBUTES
+
+        raise Exceptions::UnknownAttributeException.new(bad_params, self.class) if bad_params.present?
+
+        params
+          .compact
+          .each { |key, value| send("#{key}=", value) }
+
+        self.id = id.to_sym if id.is_a? String
+      end
+
+      def ==(other)
+        id == other.id && value == other.value
+      end
+
+      def to_hash
+        self.class::ATTRIBUTES.each_with_object({}) do |attribute, hash|
+          hash[attribute] = send(attribute)
+        end.compact
+      end
+    end
+  end
+end

data/lib/inferno/entities/input.rb

@@ -13,7 +13,8 @@ module Inferno
         :default,
         :optional,
         :options,
-        :locked
+        :locked,
+        :value
       ].freeze
       include Entities::Attributes
 

data/lib/inferno/entities/test.rb

@@ -145,10 +145,12 @@ module Inferno
         # Define outputs for this Test
         #
         # @param output_definitions [Symbol]
+        # @param _output_params [Hash] Unused parameter. Just makes method
+        #   signature compatible with `Inferno::DSL::InputOutputHandling.output`
         # @return [void]
         # @example
         #   output :patient_id, :bearer_token
-        def output(*output_definitions)
+        def output(*output_definitions, **_output_params)
           super
 
           output_definitions.each do |output|

data/lib/inferno/entities/test_group.rb

@@ -31,12 +31,12 @@ module Inferno
           Inferno::Repositories::TestGroups.new
         end
 
-        def groups
-          all_children.select { |child| child < Inferno::Entities::TestGroup }
+        def groups(options = nil)
+          children(options).select { |child| child < Inferno::Entities::TestGroup }
         end
 
-        def tests
-          all_children.select { |child| child < Inferno::Entities::Test }
+        def tests(options = nil)
+          children(options).select { |child| child < Inferno::Entities::Test }
         end
 
         # Methods to configure Inferno::DSL::Runnable

data/lib/inferno/entities/test_session.rb

@@ -37,6 +37,34 @@ module Inferno
 
       def initialize(params)
         super(params, ATTRIBUTES)
+
+        self.suite_options ||= []
+
+        test_suite.suite_options&.each do |option|
+          if suite_options.none? { |selected_option| selected_option.id == option.id }
+            suite_options << DSL::SuiteOption.new(id: option.id, value: option.list_options.first[:value])
+          end
+        end
+      end
+
+      def test_suite
+        @test_suite ||= Repositories::TestSuites.new.find(test_suite_id)
+      end
+
+      def to_hash
+        session_hash = (self.class::ATTRIBUTES - [:suite_options]).each_with_object({}) do |attribute, hash|
+          hash[attribute] = send(attribute)
+        end
+
+        session_hash[:suite_options] = suite_options&.map(&:to_hash) || []
+
+        session_hash.compact
+      end
+
+      def suite_options_hash
+        (suite_options || []).each_with_object({}) do |option, hash|
+          hash[option.id] = option.value
+        end
       end
     end
   end

data/lib/inferno/entities/test_suite.rb

@@ -1,5 +1,6 @@
 require_relative 'test_group'
 require_relative '../dsl/runnable'
+require_relative '../dsl/suite_option'
 require_relative '../repositories/test_groups'
 require_relative '../repositories/test_suites'
 
@@ -30,8 +31,8 @@ module Inferno
           Inferno::Repositories::TestSuites.new
         end
 
-        def groups
-          all_children.select { |child| child < Inferno::Entities::TestGroup }
+        def groups(options = nil)
+          children(options).select { |child| child < Inferno::Entities::TestGroup }
         end
 
         # Methods to configure Inferno::DSL::Runnable
@@ -86,11 +87,17 @@ module Inferno
         end
 
         def suite_option(identifier, **input_params)
-          suite_options[identifier] = input_params
+          suite_options << DSL::SuiteOption.new(input_params.merge(id: identifier))
         end
 
         def suite_options
-          @suite_options ||= {}
+          @suite_options ||= []
+        end
+
+        def links(links = nil)
+          return @links if links.nil?
+
+          @links = links
         end
       end
     end