Merge pull request #167 from samvera/bixby

Address dependency vulnerability for rubocop by updating to use bixby

Author: elrayle

.rubocop.yml

@@ -1,122 +1,26 @@
-inherit_from: .rubocop_todo.yml
-
-AllCops:
-  DisplayCopNames: true
-  Include:
-    - '**/Rakefile'
-
-Metrics/LineLength:
-  Enabled: false
-
-Metrics/AbcSize:
-  Enabled: false
-
-Metrics/MethodLength:
-  Enabled: false
-
-Style/BlockDelimiters:
-  Exclude:
-    - 'spec/**/*'
-
-Style/BlockEndNewline:
-  Exclude:
-    - 'spec/**/*'
-
-Style/MultilineBlockLayout:
-  Exclude:
-    - 'spec/**/*'
-
-Style/IndentationConsistency:
-  EnforcedStyle: rails
-
-Style/CollectionMethods:
-  PreferredMethods:
-    collect: 'map'
-    collect!: 'map!'
-    inject: 'reduce'
-    detect: 'find'
-    find_all: 'select'
-
-Style/WordArray:
-  Enabled: false
-
-Style/RegexpLiteral:
-  Enabled: false
-
-Style/StringLiterals:
-  Enabled: false
-
-Style/ClassAndModuleChildren:
-  Enabled: false
-
-Style/Documentation:
-  Enabled: false
-
-Style/HashSyntax:
-  Exclude:
-
-Style/LineEndConcatenation:
-  Exclude:
+inherit_gem:
+  bixby: bixby_default.yml
 
-Style/PredicateName:
-  Exclude:
-
-Style/GlobalVars:
-  Exclude:
-    - 'spec/**/*'
-
-Style/SingleLineBlockParams:
-  Enabled: false
-
-Style/ClassVars:
-  Exclude:
+inherit_from: .rubocop_todo.yml
 
-Style/SignalException:
+# By default RSpec/MessageSpies has the following:
+#   Prefer have_received for setting message expectations. Setup form as a spy using allow or instance_spy.
+# The default assumes EnforcedStyle is 'have_received'. Most of our specs are 'receive'
+RSpec/MessageSpies:
   Enabled: false
 
-Style/FileName:
+Metrics/BlockLength:
+  ExcludedMethods: ['included']
   Exclude:
+    - 'qa.gemspec'
+    - 'spec/**/*.rb'
 
-Style/VariableName:
-  Exclude:
-    - 'lib/share_notify/push_document.rb'
-
-Style/FrozenStringLiteralComment:
-  Enabled: false
-
-RSpec/ExampleWording:
-  CustomTransform:
-    be: is
-    have: has
-    not: does not
-    NOT: does NOT
-  IgnoredWords:
-    - only
-
-RSpec/ExpectActual:
-  Enabled: false
-
-RSpec/FilePath:
-  Enabled: false
-
-RSpec/InstanceVariable:
-  Enabled: false
-
-RSpec/DescribeClass:
+AllCops:
+  TargetRubyVersion: 2.1
+  DisplayCopNames: true
   Exclude:
-    - 'spec/lib/tasks/mesh.rake_spec.rb'
-
-RSpec/LetSetup:
-  Enabled: false
-
-RSpec/MessageExpectation:
-  Enabled: false
-
-RSpec/MultipleExpectations:
-  Enabled: false
-
-RSpec/NestedGroups:
-  Enabled: false
-
-RSpec/LeadingSubject:
-  Enabled: false
+    - 'db/**/*'
+    - 'script/**/*'
+    - 'vendor/**/*'
+  Include:
+    - '**/Rakefile'

.rubocop_todo.yml

@@ -1,8 +1,12 @@
 require: rubocop-rspec
 
-Metrics/CyclomaticComplexity:
+RSpec/NamedSubject:
+  Enabled: false
+
+RSpec/ExampleLength:
+  Max: 9
   Exclude:
-    - 'lib/qa/authorities/mesh_tools/mesh_data_parser.rb'
+    - 'spec/**/*.rb'
 
 Metrics/ClassLength:
   Exclude:
@@ -11,11 +15,6 @@ Metrics/ClassLength:
     - 'lib/qa/authorities/linked_data/search_query.rb'
     - 'lib/qa/authorities/linked_data/config/term_config.rb'
 
-RSpec/ExampleLength:
-  Max: 7
+Metrics/CyclomaticComplexity:
   Exclude:
-    - 'spec/lib/mesh_data_parser_spec.rb'
-    - 'spec/lib/authorities/mesh_spec.rb'
-
-RSpec/NamedSubject:
-  Enabled: false
+    - 'lib/qa/authorities/mesh_tools/mesh_data_parser.rb'

Gemfile

@@ -3,16 +3,15 @@ source "https://rubygems.org"
 gemspec path: File.expand_path('..', __FILE__)
 
 group :development, :test do
-  gem 'simplecov', require: false
   gem 'coveralls', require: false
+  gem 'simplecov', require: false
 end
 
 # BEGIN ENGINE_CART BLOCK
 # engine_cart: 0.10.0
 # engine_cart stanza: 0.10.0
 # the below comes from engine_cart, a gem used to test this Rails engine gem in the context of a Rails app.
-file = File.expand_path('Gemfile', ENV['ENGINE_CART_DESTINATION'] || ENV['RAILS_ROOT'] || File.expand_path('.internal_test_app', File.dirname(__FILE__
-)))
+file = File.expand_path('Gemfile', ENV['ENGINE_CART_DESTINATION'] || ENV['RAILS_ROOT'] || File.expand_path('.internal_test_app', File.dirname(__FILE__)))
 if File.exist?(file)
   begin
     eval_gemfile file
@@ -23,6 +22,7 @@ if File.exist?(file)
 else
   Bundler.ui.warn "[EngineCart] Unable to find test application dependencies in #{file}, using placeholder dependencies"
 
+  # rubocop:disable Bundler/DuplicatedGem
   if ENV['RAILS_VERSION']
     if ENV['RAILS_VERSION'] == 'edge'
       gem 'rails', github: 'rails/rails'
@@ -34,11 +34,12 @@ else
 
   case ENV['RAILS_VERSION']
   when /^4.2/
+    gem 'coffee-rails', '~> 4.1.0'
     gem 'responders', '~> 2.0'
     gem 'sass-rails', '>= 5.0'
-    gem 'coffee-rails', '~> 4.1.0'
   when /^4.[01]/
     gem 'sass-rails', '< 5.0'
   end
+  # rubocop:enable Bundler/DuplicatedGem
 end
 # END ENGINE_CART BLOCK

app/controllers/qa/linked_data_terms_controller.rb

@@ -14,7 +14,7 @@ def index
 
   # Return a list of terms based on a query
   # @see Qa::Authorities::LinkedData::SearchQuery#search
-  def search
+  def search # rubocop:disable Metrics/MethodLength
     begin
       terms = @authority.search(query, subauth: subauthority, language: language, replacements: replacement_params)
     rescue Qa::ServiceUnavailable
@@ -26,7 +26,8 @@ def search
       head :internal_server_error
       return
     rescue RDF::FormatError
-      logger.warn "RDF Format Error - Results from search query #{query} for#{subauth_warn_msg} authority #{vocab_param} was not identified as a valid RDF format.  You may need to include the linkeddata gem."
+      logger.warn "RDF Format Error - Results from search query #{query} for#{subauth_warn_msg} authority #{vocab_param} " \
+                  "was not identified as a valid RDF format.  You may need to include the linkeddata gem."
       head :internal_server_error
       return
     end
@@ -35,7 +36,7 @@ def search
 
   # Return all the information for a given term
   # @see Qa::Authorities::LinkedData::FindTerm#find
-  def show
+  def show # rubocop:disable Metrics/MethodLength, Metrics/AbcSize
     begin
       term = @authority.find(id, subauth: subauthority, language: language, replacements: replacement_params)
     rescue Qa::TermNotFound
@@ -51,7 +52,8 @@ def show
       head :internal_server_error
       return
     rescue RDF::FormatError
-      logger.warn "RDF Format Error - Results from fetch term #{id} for#{subauth_warn_msg} authority #{vocab_param} was not identified as a valid RDF format.  You may need to include the linkeddata gem."
+      logger.warn "RDF Format Error - Results from fetch term #{id} for#{subauth_warn_msg} authority #{vocab_param} " \
+                  "was not identified as a valid RDF format.  You may need to include the linkeddata gem."
       head :internal_server_error
       return
     end
@@ -61,23 +63,23 @@ def show
   private
 
     def check_authority
-      if params[:vocab].nil? || !params[:vocab].size.positive?
+      if params[:vocab].nil? || !params[:vocab].size.positive? # rubocop:disable Style/GuardClause
         logger.warn "Required param 'vocab' is missing or empty"
         head :bad_request
       end
     end
 
     def check_search_subauthority
       return if subauthority.nil?
-      unless @authority.search_subauthority?(subauthority)
+      unless @authority.search_subauthority?(subauthority) # rubocop:disable Style/GuardClause
         logger.warn "Unable to initialize linked data search sub-authority '#{subauthority}' for authority '#{vocab_param}'"
         head :bad_request
       end
     end
 
     def check_show_subauthority
       return if subauthority.nil?
-      unless @authority.term_subauthority?(subauthority)
+      unless @authority.term_subauthority?(subauthority) # rubocop:disable Style/GuardClause
         logger.warn "Unable to initialize linked data term sub-authority '#{subauthority}' for authority '#{vocab_param}'"
         head :bad_request
       end
@@ -95,7 +97,7 @@ def vocab_param
     end
 
     def check_query_param
-      if params[:q].nil? || !params[:q].size.positive?
+      if params[:q].nil? || !params[:q].size.positive? # rubocop:disable Style/GuardClause
         logger.warn "Required search param 'q' is missing or empty"
         head :bad_request
       end
@@ -107,7 +109,7 @@ def query
     end
 
     def check_id_param
-      if params[:id].nil? || !params[:id].size.positive?
+      if params[:id].nil? || !params[:id].size.positive? # rubocop:disable Style/GuardClause
         logger.warn "Required show param 'id' is missing or empty"
         head :bad_request
       end

app/controllers/qa/terms_controller.rb

@@ -32,7 +32,7 @@ def check_vocab_param
     head :not_found unless params[:vocab].present?
   end
 
-  def init_authority
+  def init_authority # rubocop:disable Metrics/MethodLength
     begin
       mod = authority_class.camelize.constantize
     rescue NameError

app/models/qa/mesh_tree.rb

@@ -6,12 +6,8 @@ def self.classify_all_trees
   end
 
   def eval_tree_path
-    trees = read_attribute(:eval_tree_path) || write_attribute(:eval_tree_path, "")
-    if trees
-      trees.split("|")
-    else
-      []
-    end
+    trees = self[:eval_tree_path] || (self[:eval_tree_path] = "")
+    trees ? trees.split("|") : []
   end
 
   def classify_tree
@@ -20,10 +16,10 @@ def classify_tree
   end
 
   def classify_tree!
-    unless classify_tree.empty?
+    unless classify_tree.empty? # rubocop:disable Style/GuardClause
       tree_path = classify_tree.join('|')
-      puts "After Join #{tree_path.inspect}"
-      update_attribute(:eval_tree_path, tree_path)
+      Rails.logger.info "After Join #{tree_path.inspect}"
+      update_attribute(:eval_tree_path, tree_path) # rubocop:disable Rails/SkipsModelValidations # TODO: Explore how to avoid use of update_attribute.
     end
   end
 

app/models/qa/subject_mesh_term.rb

@@ -10,17 +10,12 @@ def trees
   end
 
   def synonyms
-    s = read_attribute(:synonyms)
+    s = self[:synonyms]
     s.nil? ? [] : s.split("|")
   end
 
   def synonyms=(syn_list)
-    write_attribute(:synonyms,
-                    if syn_list.respond_to?(:join)
-                      syn_list.join('|')
-                    else
-                      syn_list
-                    end)
+    self[:synonyms] = syn_list.respond_to?(:join) ? syn_list.join('|') : syn_list
   end
 
   def parents

config/initializers/linked_data_authorities.rb

@@ -8,7 +8,7 @@
 end
 
 # load app configured linked data authorities and overrides
-Dir[File.join(Rails.root, 'config', 'authorities', 'linked_data', '*.json')].each do |fn|
+Dir[Rails.root.join('config', 'authorities', 'linked_data', '*.json')].each do |fn|
   auth = File.basename(fn, '.json').upcase.to_sym
   json = File.read(File.expand_path(fn, __FILE__))
   cfg = JSON.parse(json).deep_symbolize_keys

lib/generators/qa/local/tables/mysql/mysql_generator.rb

@@ -5,7 +5,7 @@ class MysqlGenerator < Rails::Generators::Base
       source_root File.expand_path('../templates', __FILE__)
       include ActiveRecord::Generators::Migration
 
-      def migrations
+      def migrations # rubocop:disable Metrics/MethodLength
         unless defined?(ActiveRecord::ConnectionAdapters::Mysql2Adapter) && ActiveRecord::Base.connection.instance_of?(ActiveRecord::ConnectionAdapters::Mysql2Adapter)
           message = "Use the table based generator if you are not using mysql 'rails generate qa:local:tables'"
           say_status("error", message, :red)

lib/generators/qa/local/tables/tables_generator.rb

@@ -4,7 +4,7 @@ class TablesGenerator < Rails::Generators::Base
     source_root File.expand_path('../templates', __FILE__)
     include ActiveRecord::Generators::Migration
 
-    def migrations
+    def migrations # rubocop:disable Metrics/MethodLength
       if defined?(ActiveRecord::ConnectionAdapters::Mysql2Adapter) && ActiveRecord::Base.connection.instance_of?(ActiveRecord::ConnectionAdapters::Mysql2Adapter)
         message = "Use the mysql table based generator if you are using mysql 'rails generate qa:local:tables:mysql'"
         say_status("error", message, :red)