inferno_core 0.1.3.pre → 0.1.4.pre

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e77fe0b6b1077a64dce0244964847c57ed6c57aa6a388bae212658f300563486
-  data.tar.gz: 52259f5560f7838e1d9c3763cff3a7686b0be12601e3e2cd5f5b7e9e380d6050
+  metadata.gz: 01e79c40f1051646f284439abdf537dfff524de78fee0837511b66681e997e16
+  data.tar.gz: '00759057270c563dc193cc76ecd869febfd767fa3ac4de51de0dc000f74103e5'
 SHA512:
-  metadata.gz: 38665e97697ea4bb570d7721197e05f16345e8e09b05fb2d573b10ed3b25cde28734433e9bf2be8cc874beaa9849c379e10acf70310e3aea7df00941fad8216f
-  data.tar.gz: fd44ae1fb46bac9358cc7b0b8a444bd1dcdf545fbd75588afc10d175f489601c6b2211d143f7387119bf6ac363644dfe9984b9e706efaf2fe4968b147ce479c2
+  metadata.gz: 89b46a4683518f552a13f62d6ef241af0feb31d93eefaa8553576ba0242fca2c85a316f81513034bcb48cf4a0644c3aabd1ab165e84b39faebb8f97913f487c7
+  data.tar.gz: 728d39ce5ef5c407d232912f9c09ab89b1b4bf7c33290fdc9200d4ccea3185b0a6ec7007c6ad6fd0e92c15ba80b94440658c26d57a0f36ba253e4566abd0bfc4

data/lib/inferno/apps/cli/main.rb

@@ -1,5 +1,7 @@
 require_relative 'console'
 require_relative 'migration'
+require_relative 'suite'
+require_relative 'suites'
 
 module Inferno
   module CLI
@@ -13,6 +15,14 @@ module Inferno
       def migrate
         Migration.new.run
       end
+
+      desc 'suites', 'List available test suites'
+      def suites
+        Suites.new.run
+      end
+
+      desc 'suite SUBCOMMAND ...ARGS', 'Perform suite-based operations'
+      subcommand 'suite', Suite
     end
   end
 end

data/lib/inferno/apps/cli/suite.rb

@@ -0,0 +1,19 @@
+require_relative 'suite_input_template'
+
+module Inferno
+  module CLI
+    class Suite < Thor
+      desc 'input_template SUITE_ID', 'Create a template for preset inputs'
+      long_desc <<~LONGDESC
+        Generates a template for creating an input preset for a Test Suite.
+
+        With -f option, the preset template is written to the specified
+        filename.
+      LONGDESC
+      option :filename, banner: '<filename>', aliases: [:f]
+      def input_template(suite_id)
+        SuiteInputTemplate.new.run(suite_id, options)
+      end
+    end
+  end
+end

data/lib/inferno/apps/cli/suite_input_template.rb

@@ -0,0 +1,30 @@
+require_relative '../../utils/preset_template_generator'
+
+module Inferno
+  module CLI
+    class SuiteInputTemplate
+      def run(suite_id, options)
+        require_relative '../../../inferno'
+
+        Inferno::Application.start(:suites)
+
+        suite = Inferno::Repositories::TestSuites.new.find(suite_id)
+        if suite.nil?
+          puts "No Test Suite found with id: #{suite_id}"
+          return 1
+        end
+
+        output = JSON.pretty_generate(Inferno::Utils::PresetTemplateGenerator.new(suite).generate)
+
+        if options[:filename].present?
+          path = File.join(Dir.pwd, 'config', 'presets', options[:filename])
+          FileUtils.mkdir_p(File.dirname(path))
+
+          File.open(path, 'w') { |f| f.puts(output) }
+        else
+          puts output
+        end
+      end
+    end
+  end
+end

data/lib/inferno/apps/cli/suites.rb

@@ -0,0 +1,23 @@
+module Inferno
+  module CLI
+    class Suites
+      def run
+        require_relative '../../../inferno'
+
+        Inferno::Application.start(:suites)
+
+        suites = Inferno::Repositories::TestSuites.new.all
+        suite_hash = suites.each_with_object({}) { |suite, hash| hash[suite.id] = suite.title }
+
+        id_column_length = suite_hash.keys.map(&:length).max + 1
+        title_column_length = suite_hash.values.map(&:length).max
+
+        puts "#{'ID'.ljust(id_column_length)}| Title"
+        puts "#{'-' * id_column_length}+-#{'-' * title_column_length}"
+        suite_hash.each do |id, title|
+          puts "#{id.ljust(id_column_length)}| #{title}"
+        end
+      end
+    end
+  end
+end

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

@@ -6,8 +6,11 @@ module Inferno
           PARAMS = [:test_suite_id].freeze
 
           def call(params)
-            result = repo.create(create_params(params))
-            self.body = serialize(result)
+            session = repo.create(create_params(params))
+
+            repo.apply_preset(session.id, params[:preset_id]) if params[:preset_id].present?
+
+            self.body = serialize(session)
           rescue Sequel::ValidationFailed, Sequel::ForeignKeyConstraintViolation => e
             self.body = { errors: e.message }.to_json
             self.status = 422

data/lib/inferno/apps/web/controllers/test_sessions/session_data/apply_preset.rb

@@ -0,0 +1,43 @@
+module Inferno
+  module Web
+    module Controllers
+      module TestSessions
+        module SessionData
+          class ApplyPreset < Controller
+            include Import[
+                      test_sessions_repo: 'repositories.test_sessions',
+                      presets_repo: 'repositories.presets'
+                    ]
+
+            def self.resource_class
+              'SessionData'
+            end
+
+            def call(params)
+              test_session_id = params[:test_session_id]
+              test_session = test_sessions_repo.find(test_session_id)
+
+              if test_session.nil?
+                Application[:logger].error("Unknown test session #{test_session_id}")
+                self.status = 404
+                return
+              end
+
+              preset_id = params[:preset_id]
+              preset = presets_repo.find(preset_id)
+
+              if preset.nil?
+                Application[:logger].error("Unknown preset #{preset_id}")
+                self.status = 404
+                return
+              end
+
+              test_sessions_repo.apply_preset(test_session_id, preset_id)
+              self.status = 200
+            end
+          end
+        end
+      end
+    end
+  end
+end

data/lib/inferno/apps/web/controllers/test_suites/check_configuration.rb

@@ -0,0 +1,17 @@
+module Inferno
+  module Web
+    module Controllers
+      module TestSuites
+        class CheckConfiguration < Controller
+          def call(params)
+            test_suite = repo.find(params[:id])
+            halt 404 if test_suite.nil?
+
+            self.body =
+              Inferno::Web::Serializers::Message.render(test_suite.configuration_messages(force_recheck: true))
+          end
+        end
+      end
+    end
+  end
+end

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

@@ -1,21 +1,21 @@
 <!DOCTYPE html>
 <html lang="en">
   <head>
-    <base href="/">
     <meta charset="utf-8" />
-    <link rel="icon" href="/public/favicon.ico" />
+    <link rel="icon" href="<%= Inferno::Application['public_path'] %>/favicon.ico" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="theme-color" content="#000000" />
+    <meta id="base-path" name="base-path" content="<%= Inferno::Application['base_path'] %>">
     <meta
       name="description"
       content="FHIR Testing"
     />
-    <link rel="apple-touch-icon" href="/public/logo192.png" />
+    <link rel="apple-touch-icon" href="<%= Inferno::Application['public_path'] %>/logo192.png" />
     <!--
       manifest.json provides metadata used when your web app is installed on a
       user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
     -->
-    <link rel="manifest" href="/public/manifest.json" />
+    <link rel="manifest" href="<%= Inferno::Application['public_path'] %>/manifest.json" />
     <!--
       Notice the use of %PUBLIC_URL% in the tags above.
       It will be replaced with the URL of the `public` folder during the build.
@@ -40,6 +40,6 @@
       To begin the development, run `npm start` or `yarn start`.
       To create a production bundle, use `npm run build` or `yarn build`.
     -->
-    <script src='<%= Inferno::Application['js_host'] %>/public/bundle.js'></script>
+    <script src='<%= Inferno::Application['js_host'] %>/bundle.js'></script>
   </body>
 </html>

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

@@ -6,35 +6,48 @@ module Inferno
                                               'index.html.erb'))).result
 
     Router = Hanami::Router.new(namespace: Inferno::Web::Controllers) do
-      namespace 'api' do
-        resources 'test_runs', only: [:create, :show, :destroy] do
-          resources 'results', only: [:index]
-        end
+      namespace Application['base_path'] do
+        namespace 'api' do
+          resources 'test_runs', only: [:create, :show, :destroy] do
+            resources 'results', only: [:index]
+          end
 
-        resources 'test_sessions', only: [:create, :show] do
-          resources 'results', only: [:index]
-          resources 'session_data', only: [:index]
-        end
-        get 'test_sessions/:test_session_id/last_test_run',
-            to: Inferno::Web::Controllers::TestSessions::LastTestRun,
-            as: :last_test_run
+          resources 'test_sessions', only: [:create, :show] do
+            resources 'results', only: [:index]
+            resources 'session_data', only: [:index] do
+              collection do
+                put '/apply_preset',
+                    to: Inferno::Web::Controllers::TestSessions::SessionData::ApplyPreset,
+                    as: :apply_preset
+              end
+            end
+          end
+          get 'test_sessions/:test_session_id/last_test_run',
+              to: Inferno::Web::Controllers::TestSessions::LastTestRun,
+              as: :last_test_run
 
-        resources 'test_suites', only: [:index, :show]
+          resources 'test_suites', only: [:index, :show]
+          put 'test_suites/:id/check_configuration',
+              to: Inferno::Web::Controllers::TestSuites::CheckConfiguration,
+              as: :check_configuration
 
-        resources 'requests', only: [:show]
-      end
+          resources 'requests', only: [:show]
+
+          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]] }
 
-      get '/', to: ->(_env) { [200, {}, [client_page]] }
-      get '/test_sessions/:id', to: ->(_env) { [200, {}, [client_page]] }
-
-      Inferno.routes.each do |route|
-        cleaned_id = route[:suite].id.gsub(/[^a-zA-Z\d\-._~]/, '_')
-        path = "/custom/#{cleaned_id}#{route[:path]}"
-        Application['logger'].info("Registering custom route: #{path}")
-        if route[:method] == :all
-          mount route[:handler], at: path
-        else
-          send(route[:method], path, to: route[:handler])
+        Inferno.routes.each do |route|
+          cleaned_id = route[:suite].id.gsub(/[^a-zA-Z\d\-._~]/, '_')
+          path = "/custom/#{cleaned_id}#{route[:path]}"
+          Application['logger'].info("Registering custom route: #{path}")
+          if route[:method] == :all
+            mount route[:handler], at: path
+          else
+            send(route[:method], path, to: route[:handler])
+          end
         end
       end
     end

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

@@ -0,0 +1,17 @@
+module Inferno
+  module Web
+    module Serializers
+      class Preset < Serializer
+        view :summary do
+          identifier :id
+          field :title
+        end
+
+        # view :full do
+        #   include_view :summary
+        #   field :inputs, blueprint: Input
+        # end
+      end
+    end
+  end
+end

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

@@ -3,6 +3,8 @@ module Inferno
     module Serializers
       class Test < Serializer
         identifier :id
+
+        field :short_id
         field :title
         field :short_title
         field :input_definitions, name: :inputs, extractor: HashValueExtractor, blueprint: Input

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

@@ -4,6 +4,7 @@ module Inferno
       class TestGroup < Serializer
         identifier :id
 
+        field :short_id
         field :title
         field :short_title
         field :description

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

@@ -10,11 +10,14 @@ module Inferno
           field :short_description
           field :input_instructions
           field :test_count
+          field :version
+          association :presets, view: :summary, blueprint: Preset
         end
 
         view :full do
           include_view :summary
           association :groups, name: :test_groups, blueprint: TestGroup
+          field :configuration_messages
         end
       end
     end

data/lib/inferno/config/application.rb

@@ -10,9 +10,17 @@ module Inferno
 
     use :env, inferrer: -> { ENV.fetch('APP_ENV', :development).to_sym }
 
-    Application.register('js_host', ENV.fetch('JS_HOST', ''))
+    raw_js_host = ENV.fetch('JS_HOST', '')
+    base_path = ENV.fetch('BASE_PATH', '')
+    public_path = base_path.blank? ? '/public' : "/#{base_path}/public"
+    js_host = raw_js_host.present? ? "#{raw_js_host}/public" : public_path
+
+    Application.register('js_host', js_host)
+    Application.register('base_path', base_path)
+    Application.register('public_path', public_path)
     Application.register('async_jobs', ENV['ASYNC_JOBS'] != 'false')
     Application.register('inferno_host', ENV.fetch('INFERNO_HOST', 'http://localhost:4567'))
+    Application.register('base_url', URI.join(Application['inferno_host'], base_path).to_s)
 
     configure do |config|
       config.root = File.expand_path('../../..', __dir__)

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

@@ -11,7 +11,22 @@ Inferno::Application.boot(:db) do
     config_path = File.expand_path('database.yml', File.join(Dir.pwd, 'config'))
     config = YAML.load_file(config_path)[ENV['APP_ENV']]
       .merge(logger: Inferno::Application['logger'])
-    connection = Sequel.connect(config)
+    connection_attempts_remaining = ENV.fetch('MAX_DB_CONNECTION_ATTEMPTS', '10').to_i
+    connection_retry_delay = ENV.fetch('DB_CONNECTION_RETRY_DELAY', '5').to_i
+    connection = nil
+    loop do
+      connection = Sequel.connect(config)
+      break
+    rescue StandardError => e
+      connection_attempts_remaining -= 1
+      if connection_attempts_remaining.positive?
+        Inferno::Application['logger'].error("Unable to connect to database: #{e.message}")
+        Inferno::Application['logger'].error("#{connection_attempts_remaining} connection attempts remaining.")
+        sleep connection_retry_delay
+        next
+      end
+      raise
+    end
     connection.sql_log_level = :debug
 
     register('db.config', config)

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

@@ -0,0 +1,15 @@
+require_relative '../../repositories/presets'
+
+Inferno::Application.boot(:presets) do
+  init do
+    use :suites
+
+    files_to_load = Dir.glob(File.join(Dir.pwd, 'config', 'presets', '*.json'))
+    files_to_load.map! { |path| File.realpath(path) }
+    presets_repo = Inferno::Repositories::Presets.new
+
+    files_to_load.each do |path|
+      presets_repo.insert_from_file(path)
+    end
+  end
+end

data/lib/inferno/db/schema.rb

@@ -5,7 +5,7 @@ Sequel.migration do
     end
     
     create_table(:test_sessions) do
-      String :id, :size=>255, :null=>false
+      String :id, :size=>36, :null=>false
       String :test_suite_id, :size=>255, :null=>false
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
@@ -15,7 +15,7 @@ Sequel.migration do
     
     create_table(:session_data, :ignore_index_errors=>true) do
       String :id, :size=>255, :null=>false
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255, :null=>false
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>36, :null=>false, :key=>[:id]
       String :name, :size=>255, :null=>false
       String :value, :text=>true
       
@@ -25,9 +25,9 @@ Sequel.migration do
     end
     
     create_table(:test_runs, :ignore_index_errors=>true) do
-      String :id, :size=>255, :null=>false
+      String :id, :size=>36, :null=>false
       String :status, :size=>255
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>36, :key=>[:id]
       String :test_suite_id, :size=>255
       String :test_group_id, :size=>255
       String :test_id, :size=>255
@@ -47,11 +47,11 @@ Sequel.migration do
     end
     
     create_table(:results, :ignore_index_errors=>true) do
-      String :id, :size=>255, :null=>false
-      foreign_key :test_run_id, :test_runs, :type=>String, :size=>255, :null=>false
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255, :null=>false
+      String :id, :size=>36, :null=>false
+      foreign_key :test_run_id, :test_runs, :type=>String, :size=>36, :null=>false, :key=>[:id]
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>36, :null=>false, :key=>[:id]
       String :result, :size=>255
-      String :result_message, :size=>255
+      String :result_message, :text=>true
       String :test_suite_id, :size=>255
       String :test_group_id, :size=>255
       String :test_id, :size=>255
@@ -72,10 +72,10 @@ Sequel.migration do
     
     create_table(:messages, :ignore_index_errors=>true) do
       primary_key :index
-      String :id, :size=>255, :null=>false
-      foreign_key :result_id, :results, :type=>String, :size=>255, :null=>false
+      String :id, :size=>36, :null=>false
+      foreign_key :result_id, :results, :type=>String, :size=>36, :null=>false, :key=>[:id]
       String :type, :size=>255, :null=>false
-      String :message, :size=>255, :null=>false
+      String :message, :text=>true, :null=>false
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
       
@@ -85,31 +85,31 @@ Sequel.migration do
     
     create_table(:requests, :ignore_index_errors=>true) do
       primary_key :index
-      String :id, :size=>255, :null=>false
+      String :id, :size=>36, :null=>false
       String :verb, :size=>255, :null=>false
-      String :url, :size=>255, :null=>false
+      String :url, :text=>true, :null=>false
       String :direction, :size=>255, :null=>false
       Integer :status
       String :name, :size=>255
       String :request_body, :text=>true
       String :response_body, :text=>true
-      foreign_key :result_id, :results, :type=>String, :size=>255, :null=>false
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255, :null=>false
-      String :"[:test_session_id, :name]"
+      foreign_key :result_id, :results, :type=>String, :size=>36, :null=>false, :key=>[:id]
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>36, :null=>false, :key=>[:id]
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
       
-      index [:id]
+      index [:id], :unique=>true
       index [:result_id]
       index [:test_session_id]
+      index [:test_session_id, :name]
     end
     
     create_table(:headers, :ignore_index_errors=>true) do
-      String :id, :size=>255, :null=>false
-      foreign_key :request_id, :requests, :type=>String, :size=>255, :null=>false
+      String :id, :size=>36, :null=>false
+      foreign_key :request_id, :requests, :null=>false, :key=>[:index]
       String :type, :size=>255, :null=>false
       String :name, :size=>255, :null=>false
-      String :value, :size=>255
+      String :value, :text=>true
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
       
@@ -118,8 +118,8 @@ Sequel.migration do
     end
     
     create_table(:requests_results, :ignore_index_errors=>true) do
-      foreign_key :results_id, :results, :type=>String, :size=>255, :null=>false
-      foreign_key :requests_id, :requests, :type=>String, :size=>255, :null=>false
+      foreign_key :results_id, :results, :type=>String, :size=>36, :null=>false, :key=>[:id]
+      foreign_key :requests_id, :requests, :null=>false, :key=>[:index]
       
       index [:requests_id]
       index [:results_id]

data/lib/inferno/dsl/oauth_credentials.rb

@@ -31,7 +31,7 @@ module Inferno
           instance_variable_set(:"@#{name}", value)
         end
 
-        self.token_retrieval_time = DateTime.now if token_retrieval_time.blank?
+        self.token_retrieval_time = DateTime.now if access_token.present? && token_retrieval_time.blank?
       end
 
       # @api private

data/lib/inferno/dsl/resume_test_route.rb

@@ -55,7 +55,7 @@ module Inferno
 
       # @private
       def redirect_route
-        "/test_sessions/#{test_run.test_session_id}##{waiting_group_id}"
+        "#{Application['base_url']}/test_sessions/#{test_run.test_session_id}##{waiting_group_id}"
       end
 
       # @private

data/lib/inferno/dsl/runnable.rb

@@ -479,6 +479,24 @@ module Inferno
                            !parent.respond_to?(:run_as_group?) ||
                            (parent.user_runnable? && !parent.run_as_group?)
       end
+
+      # @private
+      def available_input_definitions(prior_outputs = [])
+        available_input_definitions =
+          inputs
+            .each_with_object({}) do |input, definitions|
+              definitions[config.input_name(input)] =
+                config.input_config(input)
+            end
+        available_input_definitions.reject! { |input, _| prior_outputs.include? input }
+
+        children_available_input_definitions =
+          children.each_with_object({}) do |child, definitions|
+            definitions.merge!(child.available_input_definitions(prior_outputs))
+          end
+        prior_outputs.concat(outputs.map { |output| config.output_name(output) })
+        children_available_input_definitions.merge(available_input_definitions)
+      end
     end
   end
 end

data/lib/inferno/entities/preset.rb

@@ -0,0 +1,24 @@
+require_relative 'attributes'
+require_relative 'entity'
+require_relative 'has_runnable'
+
+module Inferno
+  module Entities
+    # A `Preset` represents a set of input values for a runnable.
+    class Preset < Entity
+      ATTRIBUTES = [
+        :id,
+        :test_suite_id,
+        :inputs,
+        :title
+      ].freeze
+
+      include Inferno::Entities::Attributes
+      include Inferno::Entities::HasRunnable
+
+      def initialize(params)
+        super(params, ATTRIBUTES)
+      end
+    end
+  end
+end

data/lib/inferno/entities/test.rb

@@ -171,6 +171,14 @@ module Inferno
 
         alias run block
 
+        def short_id
+          @short_id ||= begin
+            prefix = parent.respond_to?(:short_id) ? "#{parent.short_id}." : ''
+            suffix = parent ? (parent.tests.find_index(self) + 1).to_s.rjust(2, '0') : 'x'
+            "#{prefix}#{suffix}"
+          end
+        end
+
         # @private
         def default_id
           return name if name.present?

data/lib/inferno/entities/test_group.rb

@@ -65,6 +65,14 @@ module Inferno
           }
         end
 
+        def short_id
+          @short_id ||= begin
+            prefix = parent.respond_to?(:short_id) ? "#{parent.short_id}." : ''
+            suffix = parent ? (parent.groups.find_index(self) + 1).to_s : 'X'
+            "#{prefix}#{suffix}"
+          end
+        end
+
         def default_id
           return name if name.present?