inferno_core 0.4.7 → 0.4.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 465037be8e153e91216eb5318e39a92176efe14c868a7aa0f16c76b61d39dbd8
-  data.tar.gz: 338f10609d31827ffd211968a4a5a95c759ee4e4ac381c92fd5a495a9124669b
+  metadata.gz: 470abbacaa895d2d3451f130734c0e34eec9303ec19858976f79b0456c0d619b
+  data.tar.gz: c60351312c3116c39260332b88675f2d8e2b0a3732be2dbf68c2a41c63cd62ab
 SHA512:
-  metadata.gz: fa86e30c72fd8a8ad5fa4ebdf9deb8f04298a16f6601e9bb1128126a105573b681ce40f7a0941e967e78c86fd035e6dcc7f3c5cb232d02005793dbc272eb2e54
-  data.tar.gz: 353befc4c0be11354e2caafab74c39503fc81eb17123a0bfa2bb8d3cca4c424506edfbac9977c35df4c4992170cded60b53b07d2887e63a6419766ad813a5e56
+  metadata.gz: 1ff98dd5180315c77a4627710a7bb9c5eaf82d87f81a173f849e24aadf6cad908feb71ac3d92b6a9ca14b38163cf9a821ce236c407e5eb688467e36295fd148e
+  data.tar.gz: 324efe61696b3e86b061adede76bd6c3a1d997f15e2c2e1225dc5edb3bc1f24f3ca7ec21b6363c060ed68eb1d66306baa247d34df8cb465a82c7d70b239a1bec

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

@@ -1,3 +1,5 @@
+require 'tty-markdown'
+
 require_relative 'suite_input_template'
 
 module Inferno
@@ -12,8 +14,44 @@ module Inferno
       LONGDESC
       option :filename, banner: '<filename>', aliases: [:f]
       def input_template(suite_id)
+        ENV['NO_DB'] = 'true'
         SuiteInputTemplate.new.run(suite_id, options)
       end
+
+      desc 'describe SUITE_ID', 'Show information about a suite'
+      long_desc <<~LONGDESC
+        Display a suite's description and available options.
+      LONGDESC
+      def describe(suite_id)
+        ENV['NO_DB'] = 'true'
+        Inferno::Application.start(:suites)
+
+        suite = Inferno::Repositories::TestSuites.new.find(suite_id)
+
+        if suite.blank?
+          message = "No suite found with id `#{suite_id}`. Run `inferno suites` to see a list of available suites"
+
+          puts TTY::Markdown.parse(message)
+          return
+        end
+
+        description = ''
+        description += "# #{suite.title}\n"
+        description += "#{suite.description}\n" if suite.description
+
+        if suite.suite_options.present?
+          description += "***\n\n"
+          description += "# Suite Options\n\n"
+          suite.suite_options.each do |option|
+            description += "* `#{option.id}`: #{option.title}\n"
+            option.list_options.each do |list_option|
+              description += "  * `#{list_option[:value]}`: #{list_option[:label]}\n"
+            end
+          end
+        end
+
+        puts TTY::Markdown.parse(description)
+      end
     end
   end
 end

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

@@ -1,7 +1,11 @@
+require 'tty-markdown'
+
 module Inferno
   module CLI
     class Suites
       def run
+        ENV['NO_DB'] = 'true'
+
         require_relative '../../../inferno'
 
         Inferno::Application.start(:suites)
@@ -9,14 +13,18 @@ module Inferno
         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
+        id_column_length = suite_hash.keys.map(&:length).max + 2
+        title_column_length = suite_hash.values.map(&:length).max + 1
+
+        output = ''
+        output += "| #{'Title'.ljust(title_column_length)}| #{'ID'.ljust(id_column_length)}|\n"
+        output += "|-#{'-' * title_column_length}|-#{'-' * id_column_length}|\n"
 
-        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}"
+          output += "| #{title.ljust(title_column_length)}| #{id.ljust(id_column_length)}|\n"
         end
+
+        puts TTY::Markdown.parse(output)
       end
     end
   end

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

@@ -14,7 +14,7 @@ module Inferno
 
             session = repo.create(create_params(params))
 
-            repo.apply_preset(session.id, params[:preset_id]) if params[:preset_id].present?
+            repo.apply_preset(session, params[:preset_id]) if params[:preset_id].present?
 
             res.body = serialize(session)
           rescue Sequel::ValidationFailed, Sequel::ForeignKeyConstraintViolation => e

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

@@ -32,7 +32,7 @@ module Inferno
                 halt 404
               end
 
-              test_sessions_repo.apply_preset(test_session_id, preset_id)
+              test_sessions_repo.apply_preset(test_session, preset_id)
               res.status = 200
             end
           end

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

@@ -2,6 +2,10 @@ Inferno::Application.boot(:suites) do
   init do
     use :logging
 
+    require 'inferno/entities/test'
+    require 'inferno/entities/test_group'
+    require 'inferno/entities/test_suite'
+
     files_to_load = Dir.glob(File.join(Dir.pwd, 'lib', '*.rb'))
 
     if ENV['LOAD_DEV_SUITES'].present?

data/lib/inferno/dsl/assertions.rb

@@ -12,6 +12,7 @@ module Inferno
       # @param test a value whose truthiness will determine whether the
       #   assertion passes or fails
       # @param message [String] failure message
+      # @return [void]
       def assert(test, message = '')
         raise Exceptions::AssertionException, message unless test
       end
@@ -26,6 +27,7 @@ module Inferno
       # @param status [Integer, Array<Integer>] a single integer or an array of
       #   integer status codes
       # @param response [Hash]
+      # @return [void]
       def assert_response_status(status, response: self.response)
         assert Array.wrap(status).include?(response[:status]), bad_response_status_message(status, response[:status])
       end
@@ -44,6 +46,7 @@ module Inferno
       #   assert_resource_type(:capability_statement)
       #   assert_resource_type('CapabilityStatement')
       #   assert_resource_type(FHIR::CapabilityStatement)
+      # @return [void]
       def assert_resource_type(resource_type, resource: self.resource)
         resource_type_name = normalize_resource_type(resource_type)
 
@@ -61,8 +64,10 @@ module Inferno
       # @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:, profile_url:),
+      # @param validator [Symbol] the name of the validator to use
+      # @return [void]
+      def assert_valid_resource(resource: self.resource, profile_url: nil, validator: :default)
+        assert resource_is_valid?(resource:, profile_url:, validator:),
                invalid_resource_message(profile_url)
       end
 
@@ -93,6 +98,7 @@ module Inferno
       #       'Condition': nil
       #     }
       #   )
+      # @return [void]
       def assert_valid_bundle_entries(bundle: resource, resource_types: {})
         assert_resource_type('Bundle', resource: bundle)
 
@@ -148,6 +154,7 @@ module Inferno
       #
       # @param maybe_json_string [String]
       # @param message [String] extra failure message
+      # @return [void]
       def assert_valid_json(maybe_json_string, message = '')
         assert JSON.parse(maybe_json_string)
       rescue JSON::ParserError
@@ -158,6 +165,7 @@ module Inferno
       #
       # @param uri [String]
       # @param message [String] custom failure message
+      # @return [void]
       def assert_valid_http_uri(uri, message = '')
         error_message = message.presence || "\"#{uri}\" is not a valid URI"
         assert uri =~ /\A#{URI::DEFAULT_PARSER.make_regexp(['http', 'https'])}\z/, error_message
@@ -167,6 +175,7 @@ module Inferno
       #
       # @param type [String]
       # @param request [Inferno::Entities::Request]
+      # @return [void]
       def assert_response_content_type(type, request: self.request)
         header = request.response_header('Content-Type')
         assert header.present?, no_content_type_message

data/lib/inferno/dsl/configurable.rb

@@ -6,6 +6,7 @@ module Inferno
     # configuration provides a way to modify test behavior at boot time.
     #
     # The main features enabled by configuration are:
+    #
     # - Modifying the properties of a runnable's inputs. This could include
     #   locking a particular input, making a particular input optional/required,
     #   or changing an input's value.
@@ -81,6 +82,7 @@ module Inferno
       # will be applied to the runnable and all of its children.
       #
       # @param new_configuration [Hash]
+      # @return [Inferno::DSL::Configurable::Configuration]
       def config(new_configuration = {})
         @config ||= Configuration.new
 

data/lib/inferno/dsl/fhir_client.rb

@@ -243,6 +243,7 @@ module Inferno
         # @param block a block to configure the client
         # @see Inferno::FHIRClientBuilder Documentation for the client
         #   configuration DSL
+        # @return [void]
         def fhir_client(name = :default, &block)
           fhir_client_definitions[name] = block
         end

data/lib/inferno/dsl/fhir_validation.rb

@@ -99,7 +99,8 @@ module Inferno
             .select { |message| message.is_a? Hash }
         end
 
-        # Filter out unwanted validation messages
+        # Filter out unwanted validation messages. Any messages for which the
+        # block evalutates to a truthy value will be excluded.
         #
         # @example
         #   validator do

data/lib/inferno/dsl/http_client.rb

@@ -198,6 +198,7 @@ module Inferno
         # @param block a block to configure the client
         # @see Inferno::HTTPClientBuilder Documentation for the client
         #   configuration DSL
+        # @return [void]
         def http_client(name = :default, &block)
           http_client_definitions[name] = block
         end

data/lib/inferno/dsl/input_output_handling.rb

@@ -8,9 +8,10 @@ module Inferno
       # @param input_params [Hash] options for input such as type, description, or title
       # @option input_params [String] :title Human readable title for input
       # @option input_params [String] :description Description for the input
-      # @option input_params [String] :type text | textarea | radio
+      # @option input_params [String] :type text | textarea | radio | oauth_credentials
       # @option input_params [String] :default The default value for the input
       # @option input_params [Boolean] :optional Set to true to not require input for test execution
+      # @option input_params [Boolean] :locked If true, the user can not alter the value
       # @option input_params [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]
@@ -46,7 +47,7 @@ module Inferno
       # @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
+      # @option output_definition [String] :type text, textarea, or oauth_credentials
       # @return [void]
       # @example
       #   output :patient_id, :condition_id, :observation_id

data/lib/inferno/dsl/oauth_credentials.rb

@@ -121,7 +121,7 @@ module Inferno
         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.refresh_token = token_response_body['refresh_token'] if token_response_body['refresh_token'].present?
         self.expires_in = expires_in
         self.token_retrieval_time = DateTime.now
 

data/lib/inferno/dsl/request_storage.rb

@@ -89,6 +89,7 @@ module Inferno
         # Specify the named requests made by a test
         #
         # @param identifiers [Symbol] one or more request identifiers
+        # @return [void]
         def makes_request(*identifiers)
           named_requests_made.concat(identifiers).uniq!
           identifiers.each do |identifier|
@@ -99,6 +100,7 @@ module Inferno
         # Specify the name for a request received by a test
         #
         # @param identifier [Symbol]
+        # @return [void]
         def receives_request(identifier)
           config.add_request(identifier)
           @incoming_request_name = identifier
@@ -112,6 +114,7 @@ module Inferno
         # Specify the named requests used by a test
         #
         # @param identifiers [Symbol] one or more request identifiers
+        # @return [void]
         def uses_request(*identifiers)
           named_requests_used.concat(identifiers).uniq!
           identifiers.each do |identifier|

data/lib/inferno/dsl/results.rb

@@ -5,6 +5,7 @@ module Inferno
       # Halt execution of the current test and mark it as passed.
       #
       # @param message [String]
+      # @return [void]
       def pass(message = '')
         raise Exceptions::PassException, message
       end
@@ -14,6 +15,7 @@ module Inferno
       #
       # @param test [Boolean]
       # @param message [String]
+      # @return [void]
       def pass_if(test, message = '')
         raise Exceptions::PassException, message if test
       end
@@ -21,6 +23,7 @@ module Inferno
       # Halt execution of the current test and mark it as skipped.
       #
       # @param message [String]
+      # @return [void]
       def skip(message = '')
         raise Exceptions::SkipException, message
       end
@@ -30,6 +33,7 @@ module Inferno
       #
       # @param test [Boolean]
       # @param message [String]
+      # @return [void]
       def skip_if(test, message = '')
         raise Exceptions::SkipException, message if test
       end
@@ -37,6 +41,7 @@ module Inferno
       # Halt execution of the current test and mark it as omitted.
       #
       # @param message [String]
+      # @return [void]
       def omit(message = '')
         raise Exceptions::OmitException, message
       end
@@ -46,6 +51,7 @@ module Inferno
       #
       # @param test [Boolean]
       # @param message [String]
+      # @return [void]
       def omit_if(test, message = '')
         raise Exceptions::OmitException, message if test
       end
@@ -75,6 +81,7 @@ module Inferno
       # @param message [String]
       # @param timeout [Integer] Number of seconds to wait for an incoming
       #   request
+      # @return [void]
       def wait(identifier:, message: '', timeout: 300)
         identifier(identifier)
         wait_timeout(timeout)

data/lib/inferno/dsl/runnable.rb

@@ -268,7 +268,6 @@ module Inferno
       #
       # @param optional [Boolean]
       # @return [void]
-      #
       def optional(optional = true) # rubocop:disable Style/OptionalBooleanParameter
         @optional = optional
       end
@@ -347,6 +346,7 @@ module Inferno
       #   route. The block has access to the `request` method which returns a
       #   {Inferno::Entities::Request} object with the information for the
       #   incoming request.
+      # @return [void]
       def resume_test_route(method, path, &block)
         route_class = Class.new(ResumeTestRoute) do |klass|
           klass.singleton_class.instance_variable_set(:@test_run_identifier_block, block)
@@ -368,6 +368,7 @@ module Inferno
       #   compatible object (e.g. a `Proc` object, a [Sinatra
       #   app](http://sinatrarb.com/)) as described in the [Hanami Router
       #   documentation.](https://github.com/hanami/router/tree/f41001d4c3ee9e2d2c7bb142f74b43f8e1d3a265#mount-rack-applications)
+      # @return [void]
       def route(method, path, handler)
         Inferno.routes << { method:, path:, handler:, suite: }
       end
@@ -414,6 +415,7 @@ module Inferno
       #   group from: :ig_v2_group do
       #     required_suite_options ig_version: 'ig_v2'
       #   end
+      # @return [void]
       def required_suite_options(suite_option_requirements)
         @suite_option_requirements =
           suite_option_requirements.map do |key, value|
@@ -436,6 +438,7 @@ module Inferno
         end
       end
 
+      # @private
       def inspect
         non_dynamic_ancestor = ancestors.find { |ancestor| !ancestor.to_s.start_with? '#' }
         "#<#{non_dynamic_ancestor}".tap do |inspect_string|

data/lib/inferno/entities/request.rb

@@ -58,29 +58,29 @@ module Inferno
       # Find a response header
       #
       # @param name [String] the header name
-      # @return [Inferno::Entities::RequestHeader, nil]
+      # @return [Inferno::Entities::Header, nil]
       def response_header(name)
         response_headers.find { |header| header.name.casecmp(name).zero? }
       end
 
       # Find a request header
       #
-      # @param name [String] the header name
-      # @return [Inferno::Entities::RequestHeader, nil]
+      # @param name [String] the header name.
+      # @return [Inferno::Entities::Header, nil]
       def request_header(name)
         request_headers.find { |header| header.name.casecmp(name).zero? }
       end
 
       # All of the request headers
       #
-      # @return [Array<Inferno::Entities::RequestHeader>]
+      # @return [Array<Inferno::Entities::Header>]
       def request_headers
         headers.select(&:request?)
       end
 
       # All of the response headers
       #
-      # @return [Array<Inferno::Entities::RequestHeader>]
+      # @return [Array<Inferno::Entities::Header>]
       def response_headers
         headers.select(&:response?)
       end
@@ -131,7 +131,7 @@ module Inferno
 
       # Return the FHIR resource from the response body.
       #
-      # @return [FHIR::Model]
+      # @return [FHIR::Model, nil]
       def resource
         FHIR.from_contents(response_body)
       end

data/lib/inferno/entities/test.rb

@@ -28,6 +28,11 @@ module Inferno
         @messages ||= []
       end
 
+      # Add a message to the result.
+      #
+      # @param type [String] error, warning, or info
+      # @param message [String]
+      # @return [void]
       def add_message(type, message)
         messages << { type: type.to_s, message: format_markdown(message) }
       end
@@ -40,7 +45,6 @@ module Inferno
       # @example
       #   output(patient_id: '5', bearer_token: 'ABC')
       def output(outputs)
-        # TODO: update to track outputs that need to be updated
         outputs.each do |key, value|
           send("#{key}=", value)
           outputs_to_persist[key] = value
@@ -158,6 +162,7 @@ module Inferno
           end
         end
 
+        # @private
         def repository
           Inferno::Repositories::Tests.new
         end

data/lib/inferno/entities/test_group.rb

@@ -1,6 +1,5 @@
 require_relative '../dsl'
 require_relative '../repositories/test_groups'
-require_relative '../repositories/test_sessions'
 
 module Inferno
   module Entities
@@ -29,6 +28,7 @@ module Inferno
       end
 
       class << self
+        # @private
         def repository
           Inferno::Repositories::TestGroups.new
         end
@@ -54,12 +54,14 @@ module Inferno
         # Methods to configure Inferno::DSL::Runnable
 
         # Add a child group
+        # @return [void]
         def group(...)
           child_metadata(group_metadata)
           define_child(...)
         end
 
         # Add a test
+        # @return [void]
         def test(...)
           child_metadata(test_metadata)
           define_child(...)
@@ -109,6 +111,7 @@ module Inferno
         # UI, and this group must be run as a group.
         #
         # @param value [Boolean]
+        # @return [void]
         def run_as_group(value = true) # rubocop:disable Style/OptionalBooleanParameter
           @run_as_group = value
         end

data/lib/inferno/entities/test_suite.rb

@@ -28,6 +28,7 @@ module Inferno
           @default_group
         end
 
+        # @private
         def repository
           Inferno::Repositories::TestSuites.new
         end
@@ -44,6 +45,7 @@ module Inferno
         # Methods to configure Inferno::DSL::Runnable
 
         # Add a child group
+        # @return [void]
         def group(...)
           child_metadata(group_metadata)
           define_child(...)
@@ -93,6 +95,7 @@ module Inferno
         # @yieldreturn [Array<Hash>] An array of message hashes containing the
         #   keys `:type` and `:message`. Type options are `info`, `warning`, and
         #   `error`.
+        # @return [void]
         def check_configuration(&block)
           @check_configuration_block = block
         end
@@ -134,6 +137,7 @@ module Inferno
         #   group from: :ig_v2_group do
         #     required_suite_options ig_version: 'ig_v2'
         #   end
+        # @return [void]
         def suite_option(identifier, **option_params)
           suite_options << DSL::SuiteOption.new(option_params.merge(id: identifier))
         end

data/lib/inferno/ext/fhir_models.rb

@@ -27,7 +27,7 @@ end
 module InfernoJson
   def from_json(json)
     resource = super(json)
-    resource.source_text = json
+    resource&.source_text = json
     resource
   end
 end
@@ -37,7 +37,7 @@ end
 module InfernoXml
   def from_xml(xml)
     resource = super(xml)
-    resource.source_text = xml
+    resource&.source_text = xml
     resource
   end
 end