inferno_core 0.0.8 → 0.1.1

data/lib/inferno/dsl/http_client.rb

@@ -103,6 +103,68 @@ module Inferno
         end
       end
 
+      # Perform an HTTP DELETE request
+      #
+      # @param url [String] if this request is using a defined client, this will
+      #   be appended to the client's url. Must be an absolute url for requests
+      #   made without a defined client
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @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'
+          end
+        end
+      end
+
+      # Perform an HTTP GET request and stream the response
+      #
+      # @param block [Proc] A Proc object whose input will be the string chunks
+      #   received while streaming response to the get request.
+      # @param url [String] If this request is using a defined client, this will
+      #   be appended to the client's url. Must be an absolute url for requests
+      #   made without a defined client
+      # @param limit [Integer] The number of streamed-in chunks to be stored in
+      #   the response body. This optional input defaults to 100.
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @option options [Hash] Input headers here - headers are optional and
+      #   must be entered as the last piece of input to this method
+      # @return [Inferno::Entities::Request]
+      def stream(block, url = '', limit = 100, client: :default, name: nil, **options)
+        streamed = []
+
+        collector = proc do |chunk, bytes|
+          streamed << chunk if limit.positive?
+          limit -= 1
+          block.call(chunk, bytes)
+        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'
+          end
+          response.env.body = streamed.join
+          response
+        end
+      end
+
       module ClassMethods
         # @private
         def http_client_definitions

data/lib/inferno/dsl/oauth_credentials.rb

@@ -0,0 +1,119 @@
+require_relative '../entities/attributes'
+
+module Inferno
+  module DSL
+    class OAuthCredentials
+      ATTRIBUTES = [
+        :access_token,
+        :refresh_token,
+        :token_url,
+        :client_id,
+        :client_secret,
+        :token_retrieval_time,
+        :expires_in,
+        :name
+      ].freeze
+
+      include Entities::Attributes
+
+      attr_accessor :client
+
+      def initialize(raw_attributes_hash)
+        attributes_hash = raw_attributes_hash.symbolize_keys
+
+        invalid_keys = attributes_hash.keys - ATTRIBUTES
+
+        raise Exceptions::UnknownAttributeException.new(invalid_keys, self.class) if invalid_keys.present?
+
+        attributes_hash.each do |name, value|
+          value = DateTime.parse(value) if name == :token_retrieval_time && value.is_a?(String)
+
+          instance_variable_set(:"@#{name}", value)
+        end
+
+        self.token_retrieval_time = DateTime.now if token_retrieval_time.blank?
+      end
+
+      # @api private
+      def to_hash
+        self.class::ATTRIBUTES.each_with_object({}) do |attribute, hash|
+          value = send(attribute)
+          next if value.nil?
+
+          value = token_retrieval_time.iso8601 if attribute == :token_retrieval_time
+
+          hash[attribute] = value
+        end
+      end
+
+      # @api private
+      def to_s
+        JSON.generate(to_hash)
+      end
+
+      # @api private
+      def add_to_client(client)
+        client.oauth_credentials = self
+        self.client = client
+
+        return unless access_token.present?
+
+        client.set_bearer_token(access_token)
+      end
+
+      # @api private
+      def need_to_refresh?
+        return false if access_token.blank? || refresh_token.blank?
+
+        return true if expires_in.blank?
+
+        token_retrieval_time.to_i + expires_in - DateTime.now.to_i < 60
+      end
+
+      # @api private
+      def able_to_refresh?
+        refresh_token.present? && token_url.present?
+      end
+
+      # @api private
+      def confidential_client?
+        client_id.present? && client_secret.present?
+      end
+
+      # @api private
+      def oauth2_refresh_params
+        {
+          'grant_type' => 'refresh_token',
+          'refresh_token' => refresh_token
+        }
+      end
+
+      # @api private
+      def oauth2_refresh_headers
+        base_headers = { 'Content-Type' => 'application/x-www-form-urlencoded' }
+
+        return base_headers unless confidential_client?
+
+        credentials = "#{client_id}:#{client_secret}"
+
+        base_headers.merge(
+          'Authorization' => "Basic #{Base64.strict_encode64(credentials)}"
+        )
+      end
+
+      def update_from_response_body(request)
+        token_response_body = JSON.parse(request.response_body)
+
+        expires_in = token_response_body['expires_in'].is_a?(Numeric) ? token_response_body['expires_in'] : nil
+
+        self.access_token = token_response_body['access_token']
+        self.refresh_token = token_response_body['refresh_token']
+        self.expires_in = expires_in
+        self.token_retrieval_time = DateTime.now
+
+        add_to_client(client)
+        self
+      end
+    end
+  end
+end

data/lib/inferno/dsl/runnable.rb

@@ -85,7 +85,6 @@ module Inferno
 
         klass.parent = self
 
-        child_metadata[:collection] << klass
         children << klass
 
         configure_child_class(klass, hash_args)
@@ -164,6 +163,8 @@ module Inferno
 
         klass.config(config)
 
+        klass.children.select!(&:required?) if hash_args.delete(:exclude_optional)
+
         hash_args.each do |key, value|
           if value.is_a? Array
             klass.send(key, *value)
@@ -212,6 +213,16 @@ module Inferno
         @title = new_title
       end
 
+      # Set/Get a runnable's short title
+      #
+      # @param new_short_title [String]
+      # @return [String] the short title
+      def short_title(new_short_title = nil)
+        return @short_title if new_short_title.nil?
+
+        @short_title = new_short_title
+      end
+
       # Set/Get a runnable's description
       #
       # @param new_description [String]
@@ -222,6 +233,26 @@ module Inferno
         @description = format_markdown(new_description)
       end
 
+      # Set/Get a runnable's short one-sentence description
+      #
+      # @param new_short_description [String]
+      # @return [String] the one-sentence description
+      def short_description(new_short_description = nil)
+        return @short_description if new_short_description.nil?
+
+        @short_description = format_markdown(new_short_description)
+      end
+
+      # Set/Get a runnable's input instructions
+      #
+      # @param new_input_instructions [String]
+      # @return [String] the input instructions
+      def input_instructions(new_input_instructions = nil)
+        return @input_instructions if new_input_instructions.nil?
+
+        @input_instructions = format_markdown(new_input_instructions)
+      end
+
       # Define inputs
       #
       # @param identifier [Symbol] identifier for the input
@@ -229,12 +260,14 @@ module Inferno
       # @param input_definition [Hash] options for input such as type, description, or title
       # @option input_definition [String] :title Human readable title for input
       # @option input_definition [String] :description Description for the input
-      # @option input_definition [String] :type text | textarea
+      # @option input_definition [String] :type text | textarea | radio
       # @option input_definition [String] :default The default value for the input
       # @option input_definition [Boolean] :optional Set to true to not require input for test execution
+      # @option input_definition [Hash] :options Possible input option formats based on input type
+      # @option options [Array] :list_options Array of options for input formats that require a list of possible values
       # @return [void]
       # @example
-      #   input :patientid, title: 'Patient ID', description: 'The ID of the patient being searched for',
+      #   input :patient_id, title: 'Patient ID', description: 'The ID of the patient being searched for',
       #                     default: 'default_patient_id'
       # @example
       #   input :textarea, title: 'Textarea Input Example', type: 'textarea', optional: true
@@ -250,16 +283,60 @@ module Inferno
         end
       end
 
+      # Mark as optional. Tests are required by default.
+      #
+      # @param optional [Boolean]
+      # @return [void]
+      #
+      def optional(optional = true) # rubocop:disable Style/OptionalBooleanParameter
+        @optional = optional
+      end
+
+      # Mark as required
+      #
+      # Tests are required by default. This method is provided to make an
+      # existing optional test required.
+      #
+      # @param required[Boolean]
+      # @return [void]
+      def required(required = true) # rubocop:disable Style/OptionalBooleanParameter
+        @optional = !required
+      end
+
+      # The test or group is optional if true
+      #
+      # @return [Boolean]
+      def optional?
+        !!@optional
+      end
+
+      # The test or group is required if true
+      #
+      # @return [Boolean]
+      def required?
+        !optional?
+      end
+
       # Define outputs
       #
-      # @param output_list [Symbol]
+      # @param identifier [Symbol] identifier for the output
+      # @param other_identifiers [Symbol] array of symbols if specifying multiple outputs
+      # @param output_definition [Hash] options for output
+      # @option output_definition [String] :type text | textarea | oauth_credentials
       # @return [void]
       # @example
-      #   output :patient_id, :bearer_token
-      def output(*output_list)
-        output_list.each do |output_identifier|
-          outputs << output_identifier
-          config.add_output(output_identifier)
+      #   output :patient_id, :condition_id, :observation_id
+      # @example
+      #   output :oauth_credentials, type: 'oauth_credentials'
+      def output(identifier, *other_identifiers, **output_definition)
+        if other_identifiers.present?
+          [identifier, *other_identifiers].compact.each do |output_identifier|
+            outputs << output_identifier
+            config.add_output(output_identifier)
+          end
+        else
+          outputs << identifier
+          config.add_output(identifier, output_definition)
         end
       end
 
@@ -395,6 +472,7 @@ module Inferno
         required_inputs.map(&:to_s) - submitted_inputs.map { |input| input[:name] }
       end
 
+      # @private
       def user_runnable?
         @user_runnable ||= parent.nil? ||
                            !parent.respond_to?(:run_as_group?) ||

data/lib/inferno/entities/has_runnable.rb

@@ -0,0 +1,26 @@
+module Inferno
+  module Entities
+    module HasRunnable
+      # Returns the Test, TestGroup, or TestSuite associated with this entity
+      #
+      # @return [Inferno::Entities::Test, Inferno::Entities::TestGroup, Inferno::Entities::TestSuite]
+      def runnable
+        return @runnable if @runnable
+
+        @runnable = (test || test_group || test_suite || load_runnable)
+      end
+
+      private
+
+      def load_runnable
+        if test_id.present?
+          @test = Inferno::Repositories::Tests.new.find(test_id)
+        elsif test_group_id.present?
+          @test_group = Inferno::Repositories::TestGroups.new.find(test_group_id)
+        elsif test_suite_id.present?
+          @test_suite = Inferno::Repositories::TestSuites.new.find(test_suite_id)
+        end
+      end
+    end
+  end
+end

data/lib/inferno/entities/request.rb

@@ -186,6 +186,12 @@ module Inferno
             .map { |header_name, value| Header.new(name: header_name.downcase, value: value, type: 'request') }
           response_headers = response[:headers]
             .map { |header_name, value| Header.new(name: header_name.downcase, value: value, type: 'response') }
+          request_body =
+            if request.dig(:headers, 'Content-Type')&.include?('application/x-www-form-urlencoded')
+              URI.encode_www_form(request[:payload])
+            else
+              request[:payload]
+            end
 
           new(
             verb: request[:method],
@@ -193,7 +199,7 @@ module Inferno
             direction: direction,
             name: name,
             status: response[:code].to_i,
-            request_body: request[:payload],
+            request_body: request_body,
             response_body: response[:body],
             test_session_id: test_session_id,
             headers: request_headers + response_headers

data/lib/inferno/entities/result.rb

@@ -47,9 +47,10 @@ module Inferno
         :test_session_id, :result, :result_message, :messages, :requests,
         :input_json, :output_json
       ].freeze
-      RESULT_OPTIONS = ['cancel', 'wait', 'running', 'error', 'fail', 'skip', 'omit', 'pass'].freeze
+      RESULT_OPTIONS = ['cancel', 'wait', 'running', 'error', 'fail', 'skip', 'pass', 'omit'].freeze
 
       include Inferno::Entities::Attributes
+      include Inferno::Entities::HasRunnable
 
       def initialize(params)
         super(params, ATTRIBUTES - [:messages, :requests])
@@ -58,9 +59,12 @@ module Inferno
         @requests = (params[:requests] || []).map { |request| Request.new(request) }
       end
 
-      # @return [Inferno::Entities::Test, Inferno::Entities::TestGroup, Inferno::Entities::TestSuite]
-      def runnable
-        test || test_group || test_suite
+      def optional?
+        runnable.optional?
+      end
+
+      def required?
+        !optional?
       end
 
       # @return [Boolean]

data/lib/inferno/entities/test_group.rb

@@ -32,11 +32,11 @@ module Inferno
         end
 
         def groups
-          @groups ||= []
+          children.select { |child| child < Inferno::Entities::TestGroup }
         end
 
         def tests
-          @tests ||= []
+          children.select { |child| child < Inferno::Entities::Test }
         end
 
         # Methods to configure Inferno::DSL::Runnable
@@ -54,16 +54,14 @@ module Inferno
         def group_metadata
           {
             class: TestGroup,
-            repo: repository,
-            collection: groups
+            repo: repository
           }
         end
 
         def test_metadata
           {
             class: Test,
-            repo: Inferno::Repositories::Tests.new,
-            collection: tests
+            repo: Inferno::Repositories::Tests.new
           }
         end
 

data/lib/inferno/entities/test_run.rb

@@ -52,6 +52,7 @@ module Inferno
       ].freeze
 
       include Inferno::Entities::Attributes
+      include Inferno::Entities::HasRunnable
 
       attr_accessor :test_session
 
@@ -63,12 +64,6 @@ module Inferno
         @test_session = params[:test_session]
       end
 
-      def runnable
-        return @runnable if @runnable
-
-        @runnable = (test || test_group || test_suite || load_runnable)
-      end
-
       def to_hash
         super.merge(test_session: test_session).compact
       end
@@ -76,18 +71,6 @@ module Inferno
       def test_count
         @test_count ||= runnable.test_count
       end
-
-      private
-
-      def load_runnable
-        if test_id.present?
-          @test = Inferno::Repositories::Tests.new.find(test_id)
-        elsif test_group_id.present?
-          @test_group = Inferno::Repositories::TestGroups.new.find(test_group_id)
-        elsif test_suite_id.present?
-          @test_suite = Inferno::Repositories::TestSuites.new.find(test_suite_id)
-        end
-      end
     end
   end
 end

data/lib/inferno/entities/test_suite.rb

@@ -22,7 +22,7 @@ module Inferno
           return @default_group if @default_group
 
           @default_group = Class.new(TestGroup)
-          groups << @default_group
+          children << @default_group
           @default_group
         end
 
@@ -31,7 +31,7 @@ module Inferno
         end
 
         def groups
-          @groups ||= []
+          children.select { |child| child < Inferno::Entities::TestGroup }
         end
 
         # Methods to configure Inferno::DSL::Runnable
@@ -44,8 +44,7 @@ module Inferno
         def group_metadata
           {
             class: TestGroup,
-            repo: Inferno::Repositories::TestGroups.new,
-            collection: groups
+            repo: Inferno::Repositories::TestGroups.new
           }
         end
 

data/lib/inferno/entities.rb

@@ -1,4 +1,5 @@
 require_relative 'entities/attributes'
+require_relative 'entities/has_runnable'
 require_relative 'entities/entity'
 require_relative 'entities/header'
 require_relative 'entities/message'

data/lib/inferno/exceptions.rb

@@ -62,5 +62,24 @@ module Inferno
         super('The chosen runnable must be run as part of a group')
       end
     end
+
+    class UnknownAttributeException < RuntimeError
+      def initialize(attributes, klass)
+        attributes_string = attributes.map { |attribute| "'#{attribute}'" }.join(', ')
+        super("Unknown attributes for #{klass.name}: #{attributes_string}")
+      end
+    end
+
+    class UnknownSessionDataType < RuntimeError
+      def initialize(output)
+        super("Unknown type '#{output[:type]}' for '#{output[:name]}'.")
+      end
+    end
+
+    class BadSessionDataType < RuntimeError
+      def initialize(name, expected_class, actual_class)
+        super("Expected '#{name}' to be a #{expected_class.name}, but found a #{actual_class.name}.")
+      end
+    end
   end
 end

data/lib/inferno/ext/fhir_client.rb

@@ -0,0 +1,13 @@
+module FHIR
+  class Client
+    attr_accessor :oauth_credentials
+
+    def need_to_refresh?
+      oauth_credentials&.need_to_refresh?
+    end
+
+    def able_to_refresh?
+      oauth_credentials&.able_to_refresh?
+    end
+  end
+end