inferno_core 0.0.6 → 0.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 8bbf5aaa2b09d7d5ff54e56a3ed33ce4e1f4df29fc53e3737f18e9972dc34f1e
+  metadata.gz: 86c8b0374d22ea35f07944360943d2a1240f8ef7365b97d625b32facde4a2eaa
+  data.tar.gz: '0258752a8738b7e9c1da7d9112d0ee4f15bac0a8c7b2acac5f9973bb35d8146c'
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+  metadata.gz: 76cd8133722b109ed66f9b79eea46279c177fdac68cfe9abea4d0e9caaa76b861e533909923a94121d17e15483be5254f8e36e67cf6abb6121bc12f1e37f5fd7
+  data.tar.gz: 9be9f363e78e653b33818a8e8eee7fc74474ec2ca019b715054b7926d7e5675c46b290e138c0ee020e586d91eecef2759ead3272b6087461af89afeb8fdd7e94

data/bin/inferno

@@ -0,0 +1,7 @@
+#!/usr/bin/env ruby
+
+require 'pry'
+require_relative '../lib/inferno/config/application'
+require_relative '../lib/inferno/apps/cli'
+
+Inferno::CLI::Main.start

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

@@ -0,0 +1,12 @@
+module Inferno
+  module CLI
+    class Console
+      def run
+        require_relative '../../../inferno'
+
+        Inferno::Application.finalize!
+        Pry.start
+      end
+    end
+  end
+end

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

@@ -0,0 +1,18 @@
+require_relative 'console'
+require_relative 'migration'
+
+module Inferno
+  module CLI
+    class Main < Thor
+      desc 'console', 'Start an interactive console session with Inferno'
+      def console
+        Console.new.run
+      end
+
+      desc 'migrate', 'Run database migrations'
+      def migrate
+        Migration.new.run
+      end
+    end
+  end
+end

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

@@ -0,0 +1,14 @@
+require_relative '../../utils/migration'
+
+module Inferno
+  module CLI
+    class Migration
+      def run
+        Inferno::Application.start(:logging)
+        Inferno::Application['logger'].level = Logger::DEBUG
+
+        Utils::Migration.new.run
+      end
+    end
+  end
+end

data/lib/inferno/apps/cli.rb

@@ -0,0 +1,8 @@
+require 'thor'
+
+require_relative 'cli/main'
+
+module Inferno
+  module CLI
+  end
+end

data/lib/inferno/config/application.rb

@@ -1,4 +1,7 @@
+require 'active_support/all'
+require 'dotenv'
 require 'dry/system/container'
+require 'sequel'
 require_relative 'boot'
 
 module Inferno

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

@@ -12,6 +12,7 @@ Inferno::Application.boot(:db) do
     config = YAML.load_file(config_path)[ENV['APP_ENV']]
       .merge(logger: Inferno::Application['logger'])
     connection = Sequel.connect(config)
+    connection.sql_log_level = :debug
 
     register('db.config', config)
     register('db.connection', connection)
@@ -19,14 +20,5 @@ Inferno::Application.boot(:db) do
 
   start do
     Sequel.extension :migration
-    db = Inferno::Application['db.connection']
-    migration_path = File.join(Inferno::Application.root, 'lib', 'inferno', 'db', 'migrations')
-    Sequel::Migrator.run(db, migration_path)
-
-    if ENV['APP_ENV'] == 'development'
-      schema_path = File.join(Inferno::Application.root, 'lib', 'inferno', 'db', 'schema.rb')
-      db.extension :schema_dumper
-      File.open(schema_path, 'w') { |f| f.print(db.dump_schema_migration) }
-    end
   end
 end

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

@@ -11,6 +11,8 @@ Inferno::Application.boot(:logging) do
         Logger.new($stdout)
       end
 
+    logger.level = Logger::INFO
+
     register('logger', logger)
   end
 end

data/lib/inferno/dsl/assertions.rb

@@ -3,22 +3,43 @@ require_relative '../exceptions'
 module Inferno
   module DSL
     module Assertions
+      # Make an assertion
+      #
+      # @param test a value whose truthiness will determine whether the
+      #   assertion passes or fails
+      # @param message [String] failure message
       def assert(test, message = '')
         raise Exceptions::AssertionException, message unless test
       end
 
+      # @private
       def bad_response_status_message(expected, received)
         "Bad response status: expected #{Array.wrap(expected).join(', ')}, but received #{received}"
       end
 
+      # Check an response's status
+      #
+      # @param status [Integer, Array<Integer>] a single integer or an array of
+      #   integer status codes
+      # @param response [Hash]
       def assert_response_status(status, response: self.response)
         assert Array.wrap(status).include?(response[:status]), bad_response_status_message(status, response[:status])
       end
 
+      # @private
       def bad_resource_type_message(expected, received)
         "Bad resource type received: expected #{expected}, but received #{received}"
       end
 
+      # Check a FHIR resource's type
+      #
+      # @param resource_type [String, Symbol, Class]
+      # @param resource [FHIR::Model]
+      # @example
+      #   # The resource type can be a symbol, String, or FHIR::Model class
+      #   assert_resource_type(:capability_statement)
+      #   assert_resource_type('CapabilityStatement')
+      #   assert_resource_type(FHIR::CapabilityStatement)
       def assert_resource_type(resource_type, resource: self.resource)
         resource_type_name = normalize_resource_type(resource_type)
 
@@ -26,15 +47,48 @@ module Inferno
                bad_resource_type_message(resource_type_name, resource&.resourceType)
       end
 
+      # @private
       def invalid_resource_message(profile_url)
         "Resource does not conform to the profile: #{profile_url}"
       end
 
+      # Validate a FHIR resource
+      #
+      # @param resource [FHIR::Model]
+      # @param profile_url [String] url of the profile to validate against,
+      #   defaults to validating against the base FHIR resource
       def assert_valid_resource(resource: self.resource, profile_url: nil)
         assert resource_is_valid?(resource: resource, profile_url: profile_url),
                invalid_resource_message(profile_url)
       end
 
+      # Validate each entry of a Bundle
+      #
+      # @param bundle [FHIR::Bundle]
+      # @param resource_types
+      # [String,Symbol,FHIR::Model,Array<String,Symbol,FHIR::Model>,Hash] If a
+      #   string, symbol, or FHIR::Model is provided, only that resource type
+      #   will be validated. If an array of strings is provided, only those
+      #   resource types will be validated. If a hash is provided with resource
+      #   types as keys and profile urls (or nil) as values, only those resource
+      #   types will be validated against the provided profile url or the base
+      #   resource if nil.
+      # @example
+      #   # Only validate Patient bundle entries
+      #   assert_valid_bundle_entries(resource_types: 'Patient')
+      #
+      #   # Only valiadte Patient and Condition bundle entries
+      #   assert_valid_bundle_entries(resource_types: ['Patient', 'Condition'])
+      #
+      #   # Only validate Patient and Condition bundle entries. Validate Patient
+      #   # resources against the given profile, and Codition resources against the
+      #   # base FHIR Condition resource.
+      #   assert_valid_bundle_entries(
+      #     resource_types: {
+      #       'Patient': 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient',
+      #       'Condition': nil
+      #     }
+      #   )
       def assert_valid_bundle_entries(bundle: resource, resource_types: {})
         assert_resource_type('Bundle', resource: bundle)
 
@@ -56,6 +110,7 @@ module Inferno
         assert invalid_resources.empty?, invalid_bundle_entries_message(invalid_resources)
       end
 
+      # @private
       def invalid_bundle_entries_message(invalid_resources)
         identifier_strings =
           invalid_resources
@@ -64,6 +119,7 @@ module Inferno
         "The following bundle entries are invalid: #{identifier_strings}"
       end
 
+      # @private
       def normalize_resource_type(resource_type)
         if resource_type.is_a? Class
           resource_type.name.demodulize
@@ -72,6 +128,7 @@ module Inferno
         end
       end
 
+      # @private
       def normalize_types_to_check(resource_types)
         case resource_types
         when Hash
@@ -83,14 +140,22 @@ module Inferno
         end
       end
 
+      # Check for valid JSON
+      #
+      # @param maybe_json_string [String]
+      # @param message [String] extra failure message
       def assert_valid_json(maybe_json_string, message = '')
         assert JSON.parse(maybe_json_string)
       rescue JSON::ParserError
         assert false, "Invalid JSON. #{message}"
       end
 
+      # Check for a valid http/https uri
+      #
+      # @param uri [String]
+      # @param message [String] custom failure message
       def assert_valid_http_uri(uri, message = '')
-        error_message = message || "\"#{uri}\" is not a valid URI"
+        error_message = message.presence || "\"#{uri}\" is not a valid URI"
         assert uri =~ /\A#{URI::DEFAULT_PARSER.make_regexp(['http', 'https'])}\z/, error_message
       end
 

data/lib/inferno/dsl/configurable.rb

@@ -15,7 +15,7 @@ module Inferno
         @config.apply(new_configuration)
       end
 
-      # @api private
+      # @private
       class Configuration
         attr_accessor :configuration
 

data/lib/inferno/dsl/fhir_client.rb

@@ -35,7 +35,7 @@ module Inferno
     # @see Inferno::FHIRClientBuilder Documentation for the client
     #   configuration DSL
     module FHIRClient
-      # @api private
+      # @private
       def self.included(klass)
         klass.extend ClassMethods
         klass.extend Forwardable
@@ -54,7 +54,7 @@ module Inferno
           FHIRClientBuilder.new.build(self, self.class.fhir_client_definitions[client])
       end
 
-      # @api private
+      # @private
       def fhir_clients
         @fhir_clients ||= {}
       end
@@ -128,13 +128,13 @@ module Inferno
 
       # @todo Make this a FHIR class method? Something like
       #   FHIR.class_for(resource_type)
-      # @api private
+      # @private
       def fhir_class_from_resource_type(resource_type)
         FHIR.const_get(resource_type.to_s.camelize)
       end
 
       module ClassMethods
-        # @api private
+        # @private
         def fhir_client_definitions
           @fhir_client_definitions ||= {}
         end

data/lib/inferno/dsl/fhir_client_builder.rb

@@ -6,7 +6,7 @@ module Inferno
     class FHIRClientBuilder
       attr_accessor :runnable
 
-      # @api private
+      # @private
       def build(runnable, block)
         self.runnable = runnable
         instance_exec(self, &block)
@@ -56,14 +56,14 @@ module Inferno
         @headers ||= headers
       end
 
-      # @api private
+      # @private
       def method_missing(name, *args, &block)
         return runnable.call(name, *args, &block) if runnable.respond_to? name
 
         super
       end
 
-      # @api private
+      # @private
       def respond_to_missing?(name)
         runnable.respond_to?(name) || super
       end

data/lib/inferno/dsl/fhir_validation.rb

@@ -89,7 +89,7 @@ module Inferno
       end
 
       module ClassMethods
-        # @api private
+        # @private
         def fhir_validators
           @fhir_validators ||= {}
         end

data/lib/inferno/dsl/http_client.rb

@@ -16,7 +16,7 @@ module Inferno
     #         # performs a GET to https://example.com
     #         get
     #         # performs a GET to https://example.com/abc
-    #          get('abc')
+    #         get('abc')
     #
     #         request  # the most recent request
     #         response # the most recent response
@@ -27,7 +27,7 @@ module Inferno
     # @see Inferno::FHIRClientBuilder Documentation for the client
     #   configuration DSL
     module HTTPClient
-      # @api private
+      # @private
       def self.included(klass)
         klass.extend ClassMethods
         klass.include RequestStorage
@@ -47,7 +47,7 @@ module Inferno
         http_clients[client] = HTTPClientBuilder.new.build(self, definition)
       end
 
-      # @api private
+      # @private
       def http_clients
         @http_clients ||= {}
       end
@@ -104,7 +104,7 @@ module Inferno
       end
 
       module ClassMethods
-        # @api private
+        # @private
         def http_client_definitions
           @http_client_definitions ||= {}
         end

data/lib/inferno/dsl/http_client_builder.rb

@@ -4,7 +4,7 @@ module Inferno
     class HTTPClientBuilder
       attr_accessor :runnable
 
-      # @api private
+      # @private
       def build(runnable, block)
         self.runnable = runnable
         instance_exec(self, &block)
@@ -38,14 +38,14 @@ module Inferno
         @headers ||= headers
       end
 
-      # @api private
+      # @private
       def method_missing(name, *args, &block)
         return runnable.call(name, *args, &block) if runnable.respond_to? name
 
         super
       end
 
-      # @api private
+      # @private
       def respond_to_missing?(name)
         runnable.respond_to?(name) || super
       end

data/lib/inferno/dsl/request_storage.rb

@@ -41,7 +41,7 @@ module Inferno
         requests.find { |request| request.name == self.class.config.request_name(name.to_sym) }
       end
 
-      # @api private
+      # @private
       def store_request(direction, name = nil, &block)
         response = block.call
 
@@ -61,7 +61,7 @@ module Inferno
         request
       end
 
-      # @api private
+      # @private
       def load_named_requests
         requests_repo = Inferno::Repositories::Requests.new
         self.class.named_requests_used.map do |request_name|
@@ -74,19 +74,19 @@ module Inferno
       end
 
       module ClassMethods
-        # @api private
+        # @private
         def named_requests_made
           @named_requests_made ||= []
         end
 
-        # @api private
+        # @private
         def named_requests_used
           @named_requests_used ||= []
         end
 
         # Specify the named requests made by a test
         #
-        # @param *identifiers [Symbol] one or more Symbols
+        # @param identifiers [Symbol] one or more request identifiers
         def makes_request(*identifiers)
           named_requests_made.concat(identifiers).uniq!
           identifiers.each do |identifier|
@@ -96,20 +96,20 @@ module Inferno
 
         # Specify the name for a request received by a test
         #
-        # @param *identifiers [Symbol] one or more Symbols
+        # @param identifier [Symbol]
         def receives_request(identifier)
           config.add_request(identifier)
           @incoming_request_name = identifier
         end
 
-        # @api private
+        # @private
         def incoming_request_name
           @incoming_request_name
         end
 
         # Specify the named requests used by a test
         #
-        # @param *identifiers [Symbol] one or more Symbols
+        # @param identifiers [Symbol] one or more request identifiers
         def uses_request(*identifiers)
           named_requests_used.concat(identifiers).uniq!
           identifiers.each do |identifier|

data/lib/inferno/dsl/results.rb

@@ -94,7 +94,7 @@ module Inferno
       # and should not be used in real tests.
       #
       # @param message [String]
-      # @api private
+      # @private
       def cancel(message = '')
         raise Exceptions::CancelException, message
       end

data/lib/inferno/dsl/resume_test_route.rb

@@ -4,7 +4,7 @@ module Inferno
   module DSL
     # A base class for creating routes to resume test execution upon receiving
     # an incoming request.
-    # @api private
+    # @private
     # @see Inferno::DSL::Runnable#resume_test_route
     class ResumeTestRoute
       include Hanami::Action
@@ -26,23 +26,23 @@ module Inferno
         @request ||= Inferno::Entities::Request.from_rack_env(@params.env)
       end
 
-      # @api private
+      # @private
       def test_run
         @test_run ||=
           test_runs_repo.find_latest_waiting_by_identifier(test_run_identifier)
       end
 
-      # @api private
+      # @private
       def waiting_result
         @waiting_result ||= results_repo.find_waiting_result(test_run_id: test_run.id)
       end
 
-      # @api private
+      # @private
       def update_result
         results_repo.pass_waiting_result(waiting_result.id)
       end
 
-      # @api private
+      # @private
       def persist_request
         requests_repo.create(
           request.to_hash.merge(
@@ -53,22 +53,22 @@ module Inferno
         )
       end
 
-      # @api private
+      # @private
       def redirect_route
         "/test_sessions/#{test_run.test_session_id}##{waiting_group_id}"
       end
 
-      # @api private
+      # @private
       def test
         @test ||= tests_repo.find(waiting_result.test_id)
       end
 
-      # @api private
+      # @private
       def waiting_group_id
         test.parent.id
       end
 
-      # @api private
+      # @private
       def call(_params)
         if test_run.nil?
           status(500, "Unable to find test run with identifier '#{test_run_identifier}'.")