Ran RuboCop Style over project.

.rubocop.yml

@@ -0,0 +1,2 @@
+Metrics/LineLength:
+  Max: 120

Capfile

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Load DSL and Setup Up Stages
 require 'capistrano/setup'
 require 'capistrano/deploy'
@@ -17,4 +19,4 @@ require 'capistrano/sidekiq/monit'
 require 'whenever/capistrano'
 
 # Loads custom tasks from `lib/capistrano/tasks' if you have any defined.
-Dir.glob('lib/capistrano/tasks/*.rake').each { |r| import r }
+Dir.glob('lib/capistrano/tasks/*.rake').each { |r| import r }

GBOLapp/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class BiorubyGenerator < Rails::Generator::Base
   def manifest
     record do |m|
@@ -26,4 +28,3 @@ def manifest
     end
   end
 end
-

GBOLapp/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb

@@ -1,9 +1,10 @@
-module BiorubyHelper
+# frozen_string_literal: true
 
+module BiorubyHelper
   include Bio::Shell
 
   def project_workdir
-    if Bio::Shell.cache[:savedir].match(/\.bioruby$/)
+    if Bio::Shell.cache[:savedir] =~ /\.bioruby$/
       Bio::Shell.cache[:workdir]
     else
       Bio::Shell.cache[:savedir]
@@ -15,13 +16,13 @@ def have_results
   end
 
   def local_variables
-    eval("local_variables", Bio::Shell.cache[:binding]) -
+    eval('local_variables', Bio::Shell.cache[:binding]) -
       BiorubyController::HIDE_VARIABLES
   end
 
   def render_log(page)
-    page.insert_html :top, :logs, :partial => "log"
-    page.replace_html "variables", :partial => "variables"
+    page.insert_html :top, :logs, partial: 'log'
+    page.replace_html 'variables', partial: 'variables'
     page.hide "methods_#{@number}"
     page.hide "classes_#{@number}"
     page.hide "modules_#{@number}"
@@ -31,17 +32,15 @@ def reference_link(class_or_module)
     name = class_or_module.to_s
     case name
     when /Bio::(.+)/
-      path = $1.split('::').join('/')
+      path = Regexp.last_match(1).split('::').join('/')
       url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html"
     when /Chem::(.+)/
-      path = $1.split('::').join('/')
+      path = Regexp.last_match(1).split('::').join('/')
       url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html"
     else
       path = name.split('::').join('/')
       url = "http://www.ruby-doc.org/core/classes/#{path}.html"
     end
-    return "<a href='#{url}'>#{name}</a>"
+    "<a href='#{url}'>#{name}</a>"
   end
-
 end
-

Gemfile

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 source 'https://rubygems.org'
 
 ruby '2.3.3'
@@ -12,9 +14,9 @@ gem 'pg_search'
 gem 'puma', '~> 3.0'
 gem 'redis', '~> 3.0' # Use Redis adapter to run Action Cable in production
 gem 'sidekiq'
-gem 'sidekiq-limit_fetch'
 gem 'sidekiq-client-cli'
-gem 'sinatra', :require => false # Needed to monitor sidekiq jobs
+gem 'sidekiq-limit_fetch'
+gem 'sinatra', require: false # Needed to monitor sidekiq jobs
 
 # Asset pipeline
 gem 'coffee-rails', '~> 4.2' # Use CoffeeScript for .coffee assets and views
@@ -32,12 +34,12 @@ gem 'aws-sdk'
 gem 'paperclip'
 
 # Javascript
+gem 'bootstrap-multiselect_rails' # multi select boxes using bootstrap
 gem 'chosen-rails' # Javascript select boxes
 gem 'jquery-datatables-rails', github: 'rweng/jquery-datatables-rails'
 gem 'jquery-fileupload-rails'
 gem 'jquery-turbolinks'
 gem 'select2-rails' # Integrate Select2 Javascript library
-gem 'bootstrap-multiselect_rails' # multi select boxes using bootstrap
 
 gem 'bcrypt', '~> 3.1.7', platforms: :ruby
 gem 'bio' # BioRuby
@@ -51,14 +53,14 @@ gem 'roo-xls' # Handle excel files
 gem 'rubyzip' # Handle zip files
 gem 'simple_form'
 gem 'slim' # TODO: Used anywhere?
-gem 'sprockets-rails', :require => 'sprockets/railtie'
+gem 'sprockets-rails', require: 'sprockets/railtie'
 # gem 'turbolinks' # Turbolinks makes navigating your web application faster TODO: Does not work unless first changes to js code, in particular data-tables (see http://guides.rubyonrails.org/working_with_javascript_in_rails.html#turbolinks)
 gem 'whenever', require: false # Runs scheduled jobs via cron
 gem 'will_paginate', '> 3.0' # TODO: Really needed?
 gem 'will_paginate-bootstrap' # TODO: Really needed?
 
 # Windows does not include zoneinfo files, so bundle the tzinfo-data gem
-gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+gem 'tzinfo-data', platforms: %i[mingw mswin x64_mingw jruby]
 
 group :development do
   gem 'capistrano',         require: false

Rakefile

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 # Add your own tasks in files placed in lib/tasks ending in .rake,
 # for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
 

app/controllers/application_controller.rb

@@ -1,11 +1,13 @@
+# frozen_string_literal: true
+
 class ApplicationController < ActionController::Base
-  check_authorization :unless => :devise_controller?
+  check_authorization unless: :devise_controller?
 
   # Prevent CSRF attacks by raising an exception.
   # For APIs, you may want to use :null_session instead.
   protect_from_forgery with: :exception
 
-  rescue_from CanCan::AccessDenied do |exception|
+  rescue_from CanCan::AccessDenied do |_exception|
     redirect_back(fallback_location: root_url, alert: 'You are not authorized to access this page or perform this action.')
   end
 end

app/controllers/concerns/project_concern.rb

@@ -1,7 +1,9 @@
+# frozen_string_literal: true
+
 module ProjectConcern
   extend ActiveSupport::Concern
 
   def current_project_id
-    user_signed_in? ? current_user.default_project_id : Project.where('name like ?', "All%").first.id
+    user_signed_in? ? current_user.default_project_id : Project.where('name like ?', 'All%').first.id
   end
-end
+end

app/controllers/contig_searches_controller.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 class ContigSearchesController < ApplicationController
   load_and_authorize_resource
 
@@ -15,8 +17,8 @@ def new
   def create
     @contig_search = ContigSearch.create!(contig_search_params)
 
-    @contig_search.update(:user_id => current_user.id)
-    @contig_search.update(:project_id => current_user.default_project_id)
+    @contig_search.update(user_id: current_user.id)
+    @contig_search.update(project_id: current_user.default_project_id)
 
     redirect_to @contig_search
   end
@@ -51,7 +53,7 @@ def delete_all
   def export_as_pde
     @contig_search = ContigSearch.find(params[:contig_search_id])
     file_name = @contig_search.title.empty? ? "contig_search_#{@contig_search.created_at}" : @contig_search.title
-    send_data(ContigSearch.pde(@contig_search.contigs.includes(:partial_cons, isolate: [individual: :species]), add_reads: false), :filename => "#{file_name}.pde", :type => "application/txt")
+    send_data(ContigSearch.pde(@contig_search.contigs.includes(:partial_cons, isolate: [individual: :species]), add_reads: false), filename: "#{file_name}.pde", type: 'application/txt')
   end
 
   # TODO: Unfinished feature
@@ -68,6 +70,7 @@ def export_as_pde
   # end
 
   private
+
   # Never trust parameters from the scary internet, only allow the white list through.
   def contig_search_params
     params.require(:contig_search).permit(:title, :assembled, :has_warnings, :family, :marker, :max_age, :max_update, :min_age, :min_update, :name, :order, :species, :specimen, :verified, :verified_by, :project_id, :search_result_archive)