inferno_core 0.5.4 → 0.6.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e11d6b274778016418f7189d8ec9e724cf20861c6e03385dc9c302299f198d18
-  data.tar.gz: '09c65484d51b2f7be0a3985b374d51593d59c432ba11c21bd10d54c798ccafa4'
+  metadata.gz: 511a1a15fdcb49bcf9a58821b087d8a42394085f6c735971857a2e45710b7269
+  data.tar.gz: 2635bf69d9662b8afbaea341348d8dbc446707c6804be1f491c555376b8e31a6
 SHA512:
-  metadata.gz: 0daf93ce97d8a5a8e9b409200d7c001e4ac49107887db05073399a74795a94b449d3c1eb1d139214c1402e1ea10a954ee1271b80c642909c379cd7bb0ba7a1f0
-  data.tar.gz: 3a70bb18128af1494e0fcd1a023d8e18e8043dd535ae9c00f8471c8eb85e23678fa7c8bcb19591852c3593c6588ba92af206a90644cf6288659179fef98c1a41
+  metadata.gz: 3a31b3fe1f72ff67cc2be3c8ff11d7dfd7f6c7c203e84c55b2072f205343c6c522686accc2b927088d31ade270fa127d8ad741fbced1827497f4a3d8102d9df3
+  data.tar.gz: 1bc84724a28ae55cecc8550b51143f3c2f4ff414891c8241012ca1f94e7ea20915a801d3c3616b4ab5a4667caf12f42a273f589ad2537ab13faec9aa36144c7e

data/lib/inferno/apps/cli/execute/console_outputter.rb

@@ -51,8 +51,8 @@ module Inferno
 
         # private
 
-        def verbose_print(options, *args)
-          print(color.dim(*args)) if options[:verbose]
+        def verbose_print(options, *)
+          print(color.dim(*)) if options[:verbose]
         end
 
         def color

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

@@ -71,6 +71,7 @@ module Inferno
         inside(root_name) do
           bundle_install
           inferno_migrate
+          initialize_git_repo
           load_igs
         end
 
@@ -85,7 +86,7 @@ module Inferno
       private
 
       def authors
-        options['author'].presence || [default_author]
+        (options['author'].presence || [default_author]).to_json.gsub('"', "'")
       end
 
       def default_author
@@ -106,6 +107,10 @@ module Inferno
         run 'bundle exec inferno migrate', verbose: !options['quiet'], capture: options['quiet']
       end
 
+      def initialize_git_repo
+        run 'git init -q && git add . && git commit -aqm "initial commit"'
+      end
+
       def load_igs
         config = { verbose: !options['quiet'] }
         options['implementation_guide']&.each_with_index do |ig, idx|
@@ -119,8 +124,8 @@ module Inferno
         end
       end
 
-      def say_unless_quiet(*args)
-        say(*args) unless options['quiet']
+      def say_unless_quiet(*)
+        say(*) unless options['quiet']
       end
     end
   end

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

@@ -6,8 +6,6 @@ module Inferno
       def run
         ENV['NO_DB'] = 'true'
 
-        require_relative '../../../inferno'
-
         Inferno::Application.start(:suites)
 
         suites = Inferno::Repositories::TestSuites.new.all

data/lib/inferno/apps/cli/templates/%library_name%.gemspec.tt

@@ -5,29 +5,18 @@ Gem::Specification.new do |spec|
   spec.version       = <%= module_name %>::VERSION
   spec.authors       = <%= authors %>
   # spec.email         = ['TODO']
-  spec.date          = Time.now.utc.strftime('%Y-%m-%d')
   spec.summary       = '<%= title_name %>'
   # spec.description   = <<~DESCRIPTION
   #   This is a big markdown description of the test kit.
   # DESCRIPTION
   # spec.homepage      = 'TODO'
   spec.license       = 'Apache-2.0'
-  spec.add_runtime_dependency 'inferno_core', '~> <%= Inferno::VERSION %>'
-  spec.add_development_dependency 'database_cleaner-sequel', '~> 1.8'
-  spec.add_development_dependency 'factory_bot', '~> 6.1'
-  spec.add_development_dependency 'rspec', '~> 3.10'
-  spec.add_development_dependency 'webmock', '~> 3.11'
-  spec.required_ruby_version = Gem::Requirement.new('>= 3.1.2')
+  spec.add_dependency 'inferno_core', '~> <%= Inferno::VERSION %>'
+  spec.required_ruby_version = Gem::Requirement.new('>= 3.3.6')
   spec.metadata['inferno_test_kit'] = 'true'
   # spec.metadata['homepage_uri'] = spec.homepage
   # spec.metadata['source_code_uri'] = 'TODO'
-  spec.files = [
-    Dir['lib/**/*.rb'],
-    Dir['lib/**/*.json'],
-    Dir['config/presets/*.json'],
-    Dir['config/presets/*.json.erb'],
-    'LICENSE'
-  ].flatten
+  spec.files         = `[ -d .git ] && git ls-files -z lib config/presets LICENSE`.split("\x0")
 
   spec.require_paths = ['lib']
 end

data/lib/inferno/apps/cli/templates/.rubocop.yml

@@ -0,0 +1,77 @@
+require:
+  - rubocop-rspec
+
+AllCops:
+  NewCops: enable
+  SuggestExtensions: false
+  TargetRubyVersion: 3.3
+  Exclude:
+    - 'Gemfile'
+    - 'vendor/**/*'
+
+Layout/LineLength:
+  Max: 120
+
+Layout/MultilineMethodCallIndentation:
+  EnforcedStyle: 'indented'
+
+Style/Documentation:
+  Enabled: false
+
+Style/FrozenStringLiteralComment:
+  Enabled: false
+
+Style/NumericLiterals:
+  Enabled: false
+
+Style/OpenStructUse:
+  Exclude:
+    - 'spec/**/*'
+
+Style/SymbolArray:
+  Enabled: false
+
+Style/WordArray:
+  Enabled: false
+
+Metrics/AbcSize:
+  Enabled: false
+
+Metrics/BlockLength:
+  Enabled: false
+
+Metrics/ClassLength:
+  Enabled: false
+
+Metrics/MethodLength:
+  Enabled: false
+
+Metrics/ModuleLength:
+  Enabled: false
+
+Metrics/PerceivedComplexity:
+  Enabled: false
+
+Metrics/ParameterLists:
+  Enabled: false
+
+RSpec/AnyInstance:
+  Enabled: false
+
+RSpec/ExampleLength:
+  Enabled: false
+
+RSpec/MultipleExpectations:
+  Enabled: false
+
+RSpec/MultipleMemoizedHelpers:
+  Enabled: false
+
+RSpec/NestedGroups:
+  Enabled: false
+
+RSpec/NotToNot:
+  EnforcedStyle: to_not
+
+Gemspec/RequireMFA:
+  Enabled: false

data/lib/inferno/apps/cli/templates/.ruby-version

@@ -1 +1 @@
-3.1.2
+3.3.6

data/lib/inferno/apps/cli/templates/.tool-versions

@@ -1 +1 @@
-ruby 3.1.2
+ruby 3.3.6

data/lib/inferno/apps/cli/templates/Dockerfile.tt

@@ -1,4 +1,4 @@
-FROM ruby:3.1.2
+FROM ruby:3.3.6
 
 ENV INSTALL_PATH=/opt/inferno/
 ENV APP_ENV=production
@@ -7,6 +7,7 @@ RUN mkdir -p $INSTALL_PATH
 WORKDIR $INSTALL_PATH
 
 ADD lib/<%= library_name %>/metadata.rb $INSTALL_PATH/lib/<%= library_name %>/metadata.rb
+ADD lib/<%= library_name %>/version.rb $INSTALL_PATH/lib/<%= library_name %>/version.rb
 ADD *.gemspec $INSTALL_PATH
 ADD Gemfile* $INSTALL_PATH
 RUN gem install bundler

data/lib/inferno/apps/cli/templates/Gemfile.tt

@@ -6,8 +6,15 @@ gemspec
 
 group :development, :test do
   gem 'debug'
+  gem 'rubocop', '~> 1.9'
+  gem 'rubocop-rspec', require: false
 end
 
 group :test do
+  gem 'database_cleaner-sequel', '~> 1.8'
+  gem 'factory_bot', '~> 6.1'
   gem 'rack-test'
+  gem 'rspec', '~> 3.10'
+  gem 'simplecov', '0.21.2', require: false
+  gem 'webmock', '~> 3.11'
 end

data/lib/inferno/apps/cli/templates/lib/%library_name%/suite.rb.tt

@@ -56,4 +56,4 @@ module <%= module_name %>
     # using their id
     group from: :patient_group
   end
-end
+end

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

@@ -6,6 +6,7 @@ Inferno::Application.register_provider(:suites) do
     require 'inferno/entities/test_group'
     require 'inferno/entities/test_suite'
     require 'inferno/entities/test_kit'
+    require 'inferno/route_storage'
 
     files_to_load = Dir.glob(File.join(Dir.pwd, 'lib', '*.rb'))
 

data/lib/inferno/dsl/fhir_resource_validation.rb

@@ -157,7 +157,7 @@ module Inferno
         end
 
         # @see Inferno::DSL::FHIRResourceValidation#resource_is_valid?
-        def resource_is_valid?(resource, profile_url, runnable)
+        def resource_is_valid?(resource, profile_url, runnable, add_messages_to_runnable: true) # rubocop:disable Metrics/CyclomaticComplexity
           profile_url ||= FHIR::Definitions.resource_definition(resource.resourceType).url
 
           begin
@@ -173,8 +173,10 @@ module Inferno
 
           message_hashes = message_hashes_from_outcome(outcome, resource, profile_url)
 
-          message_hashes
-            .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
+          if add_messages_to_runnable
+            message_hashes
+              .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
+          end
 
           unless response.status == 200
             raise Inferno::Exceptions::ErrorInValidatorException,
@@ -380,10 +382,10 @@ module Inferno
         #   using multiple validators
         # @param required_suite_options [Hash] suite options that must be
         #   selected in order to use this validator
-        def fhir_resource_validator(name = :default, required_suite_options: nil, &block)
+        def fhir_resource_validator(name = :default, required_suite_options: nil, &)
           current_validators = fhir_validators[name] || []
 
-          new_validator = Inferno::DSL::FHIRResourceValidation::Validator.new(name, id, required_suite_options, &block)
+          new_validator = Inferno::DSL::FHIRResourceValidation::Validator.new(name, id, required_suite_options, &)
 
           current_validators.reject! { |validator| validator.requirements == required_suite_options }
           current_validators << new_validator

data/lib/inferno/dsl/fhir_validation.rb

@@ -30,9 +30,13 @@ module Inferno
       # @param resource [FHIR::Model]
       # @param profile_url [String]
       # @param validator [Symbol] the name of the validator to use
+      # @param add_messages_to_runnable [Boolean] whether to add validation messages to runnable or not
       # @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)
+      def resource_is_valid?(
+        resource: self.resource, profile_url: nil,
+        validator: :default, add_messages_to_runnable: true
+      )
+        find_validator(validator).resource_is_valid?(resource, profile_url, self, add_messages_to_runnable:)
       end
 
       # Find a particular validator. Looks through a runnable's parents up to
@@ -113,7 +117,7 @@ module Inferno
         end
 
         # @see Inferno::DSL::FHIRValidation#resource_is_valid?
-        def resource_is_valid?(resource, profile_url, runnable)
+        def resource_is_valid?(resource, profile_url, runnable, add_messages_to_runnable: true) # rubocop:disable Metrics/CyclomaticComplexity
           profile_url ||= FHIR::Definitions.resource_definition(resource.resourceType).url
 
           begin
@@ -128,8 +132,10 @@ module Inferno
 
           message_hashes = message_hashes_from_outcome(outcome, resource, profile_url)
 
-          message_hashes
-            .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
+          if add_messages_to_runnable
+            message_hashes
+              .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
+          end
 
           unless response.status == 200
             raise Inferno::Exceptions::ErrorInValidatorException,
@@ -254,10 +260,10 @@ module Inferno
         #   using multiple validators
         # @param required_suite_options [Hash] suite options that must be
         #   selected in order to use this validator
-        def validator(name = :default, required_suite_options: nil, &block)
+        def validator(name = :default, required_suite_options: nil, &)
           current_validators = fhir_validators[name] || []
 
-          new_validator = Inferno::DSL::FHIRValidation::Validator.new(required_suite_options, &block)
+          new_validator = Inferno::DSL::FHIRValidation::Validator.new(required_suite_options, &)
 
           current_validators.reject! { |validator| validator.requirements == required_suite_options }
           current_validators << new_validator

data/lib/inferno/dsl/suite_endpoint.rb

@@ -12,7 +12,7 @@ module Inferno
     #     class AuthorizedEndpoint < Inferno::DSL::SuiteEndpoint
     #       # Identify the incoming request based on a bearer token
     #       def test_run_identifier
-    #         request.header['authorization']&.delete_prefix('Bearer ')
+    #         request.headers['authorization']&.delete_prefix('Bearer ')
     #       end
     #
     #       # Return a json FHIR Patient resource