inferno_core 0.0.7 → 0.1.0.pre

data/lib/inferno/dsl/fhir_validation.rb

@@ -1,38 +1,113 @@
 module Inferno
   module DSL
+    # This module contains the methods needed to configure a validator to
+    # perform validation of FHIR resources. The actual validation is performed
+    # by an external FHIR validation service. Tests will typically rely on
+    # `assert_valid_resource` for validation rather than directly calling
+    # methods on a validator.
+    #
+    # @example
+    #
+    #   validator do
+    #     url 'http://example.com/validator'
+    #     exclude_message { |message| message.type == 'info' }
+    #     perform_additional_validation do |resource, profile_url|
+    #       if something_is_wrong
+    #         { type: 'error', message: 'something is wrong' }
+    #       else
+    #         { type: 'info', message: 'everything is ok' }
+    #       end
+    #     end
+    #   end
     module FHIRValidation
       def self.included(klass)
         klass.extend ClassMethods
       end
 
+      # Perform validation, and add validation messages to the runnable
+      #
+      # @param resource [FHIR::Model]
+      # @param profile_url [String]
+      # @param validator [Symbol] the name of the validator to use
+      # @return [Boolean] whether the resource is valid
       def resource_is_valid?(resource: self.resource, profile_url: nil, validator: :default)
         find_validator(validator).resource_is_valid?(resource, profile_url, self)
       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)
         self.class.find_validator(validator_name)
       end
 
       class Validator
+        # @private
         def initialize(&block)
           instance_eval(&block)
         end
 
+        # @private
         def default_validator_url
           ENV.fetch('VALIDATOR_URL')
         end
 
+        # Set the url of the validator service
+        #
+        # @param url [String]
         def url(validator_url = nil)
           @url = validator_url if validator_url
 
           @url
         end
 
+        # @private
+        def additional_validations
+          @additional_validations ||= []
+        end
+
+        # Perform validation steps in addition to FHIR validation.
+        #
+        # @example
+        #   perform_additional_validation do |resource, profile_url|
+        #     if something_is_wrong
+        #       { type: 'error', message: 'something is wrong' }
+        #     else
+        #       { type: 'info', message: 'everything is ok' }
+        #     end
+        #   end
+        # @yieldparam resource [FHIR::Model] the resource being validated
+        # @yieldparam profile_url [String] the profile the resource is being
+        #   validated against
+        # @yieldreturn [Array<Hash<Symbol, String>>,Hash<Symbol, String>] The
+        #   block should return a Hash or an Array of Hashes if any validation
+        #   messages should be added. The Hash must contain two keys: `:type`
+        #   and `:message`. `:type` can have a value of `'info'`, `'warning'`,
+        #   or `'error'`. A type of `'error'` means the resource is invalid.
+        #   `:message` contains the message string itself.
+        def perform_additional_validation(&block)
+          additional_validations << block
+        end
+
+        # @private
+        def additional_validation_messages(resource, profile_url)
+          additional_validations
+            .flat_map { |step| step.call(resource, profile_url) }
+            .select { |message| message.is_a? Hash }
+        end
+
+        # Filter out unwanted validation messages
+        #
+        # @example
+        #   validator do
+        #     exclude_message { |message| message.type == 'info' }
+        #   end
+        # @yieldparam message [Inferno::Entities::Message]
         def exclude_message(&block)
           @exclude_message = block if block_given?
           @exclude_message
         end
 
+        # @see Inferno::DSL::FHIRValidation#resource_is_valid?
         def resource_is_valid?(resource, profile_url, runnable)
           profile_url ||= FHIR::Definitions.resource_definition(resource.resourceType).url
 
@@ -40,6 +115,8 @@ module Inferno
 
           message_hashes = outcome.issue&.map { |issue| message_hash_from_issue(issue) } || []
 
+          message_hashes.concat(additional_validation_messages(resource, profile_url))
+
           filter_messages(message_hashes)
 
           message_hashes
@@ -47,10 +124,12 @@ module Inferno
             .none? { |message_hash| message_hash[:type] == 'error' }
         end
 
+        # @private
         def filter_messages(message_hashes)
           message_hashes.reject! { |message| exclude_message.call(Entities::Message.new(message)) } if exclude_message
         end
 
+        # @private
         def message_hash_from_issue(issue)
           {
             type: issue_severity(issue),
@@ -58,6 +137,7 @@ module Inferno
           }
         end
 
+        # @private
         def issue_severity(issue)
           case issue.severity
           when 'warning'
@@ -69,6 +149,7 @@ module Inferno
           end
         end
 
+        # @private
         def issue_message(issue)
           location = if issue.respond_to?(:expression)
                        issue.expression&.join(', ')
@@ -79,6 +160,11 @@ module Inferno
           "#{location}: #{issue&.details&.text}"
         end
 
+        # Post a resource to the validation service for validating.
+        #
+        # @param resource [FHIR::Model]
+        # @param profile_url [String]
+        # @return [String] the body of the validation response
         def validate(resource, profile_url)
           RestClient.post(
             "#{url}/validate",
@@ -94,10 +180,28 @@ module Inferno
           @fhir_validators ||= {}
         end
 
+        # Define a validator
+        # @example
+        #   validator do
+        #     url 'http://example.com/validator'
+        #     exclude_message { |message| message.type == 'info' }
+        #     perform_additional_validation do |resource, profile_url|
+        #       if something_is_wrong
+        #         { type: 'error', message: 'something is wrong' }
+        #       else
+        #         { type: 'info', message: 'everything is ok' }
+        #       end
+        #     end
+        #   end
+        #
+        # @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)
         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)
 

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

@@ -229,12 +229,14 @@ 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
@@ -252,14 +254,24 @@ module Inferno
 
       # 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
 

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/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

data/lib/inferno/public/217.bundle.js

@@ -1 +1 @@
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