inferno_core 0.1.0 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9b9bcb584c21004b00bc1ebb9fa2cce3b89f55bd7cb8f1565a9a29242e293e2b
-  data.tar.gz: b8a2e7ad09a42bb802289859ca6d48ba1c5473cd0553230a53563063b44c2194
+  metadata.gz: b15a9d2a0905bfb338974e70ceb0045a096b76dcc1cf795490f2f8b90231016b
+  data.tar.gz: 86d7bb32e8ca9a5e56983be39f3e4d7b177237b59624d2c7ac2e45d7cc7f0725
 SHA512:
-  metadata.gz: 51d1cfeeed361f0b1647568ed179b9f45eeadb26b635d21fbd59a8d314f9a85141fd8e64d4dce5453fde0d61866b0c55fb6dcac9529caf379af507f7cefaa20c
-  data.tar.gz: a9479200fa536bf1031d03f47dfda90885caa4135a5aa195de74d9302b2dd8a3ebfefa3ad6b0a265fa24d29bc3ac40fde3ec0e32089cd085a8648dc6ce73274c
+  metadata.gz: '090c15c98e9d555cf8ca4c17d7ac246d74effed1463f87ffe6ff3aa1f9f415798a7758b9d8df45713f46bfb586e81c78e87fa32535426372c3a4ee952c5fb353'
+  data.tar.gz: b76a85e0633115721f1033724c62e6910a6666bd5f47510f454666da7aff744970b871ea25f7fa216837d14c42fdc94c563cd22a4a6e9d151a36d92af7211bee

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

@@ -0,0 +1,39 @@
+module Inferno
+  module Web
+    module Controllers
+      module TestRuns
+        class Destroy < Controller
+          include Import[
+                    test_runs_repo: 'repositories.test_runs',
+                    results_repo: 'repositories.results'
+                  ]
+
+          def call(params)
+            test_run = test_runs_repo.find(params[:id])
+
+            if test_run.nil? || ['done', 'cancelling'].include?(test_run.status)
+              # If it doesn't exist, already finished, or currently being cancelled
+              self.status = 204
+              return
+            end
+
+            test_run_is_waiting = (test_run.status == 'waiting')
+            test_runs_repo.mark_as_cancelling(params[:id])
+
+            if test_run_is_waiting
+              waiting_result = results_repo.find_waiting_result(test_run_id: test_run.id)
+              results_repo.cancel_waiting_result(waiting_result.id, 'Test cancelled by user')
+              Jobs.perform(Jobs::ResumeTestRun, test_run.id)
+            end
+
+            self.status = 204
+          rescue StandardError => e
+            Application['logger'].error(e.full_message)
+            self.body = { errors: e.message }.to_json
+            self.status = 500
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -7,7 +7,7 @@ module Inferno
 
     Router = Hanami::Router.new(namespace: Inferno::Web::Controllers) do
       namespace 'api' do
-        resources 'test_runs', only: [:create, :show] do
+        resources 'test_runs', only: [:create, :show, :destroy] do
           resources 'results', only: [:index]
         end
 

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

@@ -16,6 +16,7 @@ module Inferno
         field :result_message, if: :field_present?
         field :created_at
         field :updated_at
+        field :optional?, name: :optional
 
         field :outputs do |result, _options|
           result.output_json.present? ? JSON.parse(result.output_json) : []

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

@@ -4,10 +4,14 @@ module Inferno
       class Test < Serializer
         identifier :id
         field :title
+        field :short_title
         field :input_definitions, name: :inputs, extractor: HashValueExtractor, blueprint: Input
         field :output_definitions, name: :outputs, extractor: HashValueExtractor
         field :description
+        field :short_description
+        field :input_instructions
         field :user_runnable?, name: :user_runnable
+        field :optional?, name: :optional
       end
     end
   end

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

@@ -5,10 +5,14 @@ module Inferno
         identifier :id
 
         field :title
+        field :short_title
         field :description
+        field :short_description
+        field :input_instructions
         field :test_count
         field :run_as_group?, name: :run_as_group
         field :user_runnable?, name: :user_runnable
+        field :optional?, name: :optional
 
         association :groups, name: :test_groups, blueprint: TestGroup
         association :tests, blueprint: Test

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

@@ -5,7 +5,10 @@ module Inferno
         view :summary do
           identifier :id
           field :title
+          field :short_title
           field :description
+          field :short_description
+          field :input_instructions
           field :test_count
         end
 

data/lib/inferno/dsl/configurable.rb

@@ -13,6 +13,10 @@ module Inferno
         return @config if new_configuration.blank?
 
         @config.apply(new_configuration)
+
+        children.each { |child| child.config(new_configuration) }
+
+        @config
       end
 
       # @private

data/lib/inferno/dsl/fhir_client.rb

@@ -131,6 +131,20 @@ module Inferno
         end
       end
 
+      # Perform a FHIR delete interaction.
+      #
+      # @param resource_type [String, Symbol, Class]
+      # @param id [String]
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @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)
+        end
+      end
+
       # @todo Make this a FHIR class method? Something like
       #   FHIR.class_for(resource_type)
       # @api private

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/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
@@ -252,6 +283,40 @@ 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 identifier [Symbol] identifier for the output
@@ -407,6 +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/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

@@ -32,7 +32,7 @@ module Inferno
     #   @return [String, nil] identfier for a waiting `TestRun`
     # @!attribute wait_timeout
     class TestRun < Entity
-      STATUS_OPTIONS = ['queued', 'running', 'waiting', 'done'].freeze
+      STATUS_OPTIONS = ['queued', 'running', 'waiting', 'cancelling', 'done'].freeze
       ATTRIBUTES = [
         :id,
         :test_session_id,
@@ -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'