Add frozen string literal pragma to all files

.rubocop.yml

@@ -30,3 +30,6 @@ Style/TrailingCommaInLiteral:
 # Only relevant for Rails 5.
 Rails/HttpPositionalArguments:
   Enabled: false
+
+Style/FrozenStringLiteralComment:
+  EnforcedStyle: always

Capfile

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 load 'deploy'
 # Uncomment if you are using Rails' asset pipeline
     # load 'deploy/assets'

Gemfile

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 source 'https://rubygems.org'
 
 gem 'dotenv-rails'

Guardfile

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 # A sample Guardfile
 # More info at https://github.com/guard/guard#readme
 

Rakefile

@@ -1,3 +1,4 @@
+# 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.
 

TODO.md

@@ -0,0 +1,6 @@
+# TODO
+
+* fix postfix
+* trigger paper searches from parsing worker
+* unique/scheduled recommender jobs
+* persist `echo 1 > /proc/sys/vm/overcommit_memory` on redis machine

Vagrantfile

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 # -*- mode: ruby -*-
 # vi: set ft=ruby :
 

app/controllers/achievements_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class AchievementsController < ApplicationController
 
 def show

app/controllers/application_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class ApplicationController < ActionController::Base
   protect_from_forgery
   helper :all

app/controllers/beacon_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 # simple Beacon implementation according to the GA4GH v0.2 standard
 # see http://dnastack.com/ga4gh/bob/subscribe.html
 # chrom={chromosome}&

app/controllers/das_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class DasController < ApplicationController
 
     def show

app/controllers/fitbit_profiles_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class FitbitProfilesController < ApplicationController
   before_filter :require_user, except: [:new_notification, :show, :index]
   before_filter :require_user, only: [:update,:destroy,:init,:edit,:start_auth,:verify_auth,:dump]

app/controllers/genotypes_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class GenotypesController < ApplicationController
 
   before_filter :require_user, except: [ :show, :feed,:index,:dump_download ]

app/controllers/index_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class IndexController < ApplicationController
   def index
     if current_user

app/controllers/messages_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class MessagesController < ApplicationController
   before_filter :require_user
   before_filter :require_owner, only: [:show, :destroy]

app/controllers/news_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class NewsController < ApplicationController
 
   def index

app/controllers/password_resets_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PasswordResetsController < ApplicationController
 
 	before_filter :load_user_using_perishable_token, :only => [:edit, :update]

app/controllers/phenotype_comments_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PhenotypeCommentsController < ApplicationController
   before_filter :require_user
 

app/controllers/phenotype_sets_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PhenotypeSetsController < ApplicationController
   before_filter :require_user
 

app/controllers/phenotypes_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PhenotypesController < ApplicationController
   before_filter :require_user, only: %i(new create get_genotypes recommend_phenotype)
   helper_method :sort_column, :sort_direction

app/controllers/picture_phenotype_comments_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PicturePhenotypeCommentsController < ApplicationController
   before_filter :require_user
 

app/controllers/picture_phenotypes_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PicturePhenotypesController < ApplicationController
   before_filter :require_user, only: [ :new, :create, ]
   helper_method :sort_column, :sort_direction

app/controllers/search_results_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class SearchResultsController < ApplicationController
 
   def search

app/controllers/snp_comments_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class SnpCommentsController < ApplicationController
   before_filter :require_user
 

app/controllers/snps_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class SnpsController < ApplicationController
   helper_method :sort_column, :sort_direction
   before_filter :find_snp, except: [:index, :json,:json_annotation]

app/controllers/static_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class StaticController < ApplicationController
 	def index
 		@title = "Welcome"

app/controllers/user_phenotypes_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserPhenotypesController < ApplicationController
   before_filter :require_user
 

app/controllers/user_picture_phenotypes_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserPicturePhenotypesController < ApplicationController
   before_filter :require_user
 

app/controllers/user_sessions_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserSessionsController < ApplicationController
   before_filter :require_no_user, :only => [:new, :create]
   before_filter :require_user, :only => :destroy

app/controllers/user_snps_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserSnpsController < ApplicationController
   def show
     @user_snps = UserSnp.where(user_id: current_user.id).paginate(page: params[:page])

app/controllers/users_controller.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UsersController < ApplicationController
 
   helper_method :sort_column, :sort_direction

app/helpers/application_helper.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 module ApplicationHelper
   def sortable(column, title = nil)
     title ||= column.titleize

app/helpers/snpedia_papers_helper.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 module SnpediaPapersHelper
   def bold_if_matching_variation(snpedia_paper, user_snp, &block)
     if snpedia_paper && user_snp &&

app/mailers/user_mailer.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserMailer < ActionMailer::Base
 default :from => "donotreply@opensnp.org"
 

app/models/achievement.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Achievement < ActiveRecord::Base
   include PgSearchCommon
   has_many :user_achievements

app/models/concerns/pg_search_common.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 module PgSearchCommon
   extend ActiveSupport::Concern
   include PgSearch

app/models/fitbit_activity.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class FitbitActivity < ActiveRecord::Base
   belongs_to :fitbit_profile
 

app/models/fitbit_body.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class FitbitBody < ActiveRecord::Base
   belongs_to :fitbit_profile
 

app/models/fitbit_profile.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class FitbitProfile < ActiveRecord::Base
   belongs_to :user
   has_many :fitbit_bodies, dependent: :destroy

app/models/fitbit_sleep.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class FitbitSleep < ActiveRecord::Base
   belongs_to :fitbit_profile
 

app/models/genome_gov_paper.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class GenomeGovPaper < ActiveRecord::Base
   include PgSearchCommon
 

app/models/genotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 require 'fileutils'
 
 class Genotype < ActiveRecord::Base

app/models/homepage.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Homepage < ActiveRecord::Base
    belongs_to :user
    after_save :destroy_if_blank

app/models/mendeley_paper.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class MendeleyPaper < ActiveRecord::Base
   include PgSearchCommon
 

app/models/message.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Message < ActiveRecord::Base
   # from http://stackoverflow.com/questions/5141564/model-users-message-in-rails-3
   belongs_to :user

app/models/pgp_annotation.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PgpAnnotation < ActiveRecord::Base
   include PgSearchCommon
 

app/models/phenotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Phenotype < ActiveRecord::Base
   include PgSearchCommon
 

app/models/phenotype_comment.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PhenotypeComment < ActiveRecord::Base
   include PgSearchCommon
 

app/models/phenotype_set.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PhenotypeSet < ActiveRecord::Base
   include PgSearchCommon
 

app/models/picture_phenotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PicturePhenotype < ActiveRecord::Base
   include PgSearchCommon
 

app/models/picture_phenotype_comment.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PicturePhenotypeComment < ActiveRecord::Base
   include PgSearchCommon
 

app/models/plos_paper.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PlosPaper < ActiveRecord::Base
   include PgSearchCommon
 

app/models/search_result.rb

@@ -1,2 +1,3 @@
+# frozen_string_literal: true
 class SearchResult < ActiveRecord::Base
 end

app/models/snp.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Snp < ActiveRecord::Base
   include PgSearchCommon
 

app/models/snp_comment.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class SnpComment < ActiveRecord::Base
   include PgSearchCommon
 

app/models/snp_reference.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class SnpReference < ActiveRecord::Base
   self.primary_keys = :snp_id, :paper_id, :paper_type
   belongs_to :snp

app/models/snpedia_paper.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class SnpediaPaper < ActiveRecord::Base
   include PgSearchCommon
 

app/models/user.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class User < ActiveRecord::Base
   include PgSearchCommon
 

app/models/user_achievement.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserAchievement < ActiveRecord::Base
    belongs_to :achievement
    belongs_to :user

app/models/user_phenotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserPhenotype < ActiveRecord::Base
   include PgSearchCommon
 

app/models/user_picture_phenotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserPicturePhenotype < ActiveRecord::Base
   include PgSearchCommon
 

app/models/user_session.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserSession < Authlogic::Session::Base
 
 	# rails 3 broke something, this is for fix

app/models/user_snp.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class UserSnp < ActiveRecord::Base
   self.primary_keys = [:genotype_id, :snp_name]
   belongs_to :snp, foreign_key: :snp_name, primary_key: :name, counter_cache: true

app/recommenders/concerns/recommender_delete_items.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 module RecommenderDeleteItems
   def delete_items
     all_items.each do |i|

app/recommenders/phenotype_recommender.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class PhenotypeRecommender < Recommendify::Base
   include RecommenderDeleteItems
 

app/recommenders/variation_recommender.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class VariationRecommender < Recommendify::Base
   include RecommenderDeleteItems
 

app/workers/delete_genotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class DeleteGenotype
   include Sidekiq::Worker
   sidekiq_options queue: :user_snps, retry: 5, unique: true

app/workers/fitbit_dump.rb

@@ -1,5 +1,6 @@
 
 
+# frozen_string_literal: true
 class FitbitDump
    include Sidekiq::Worker
    sidekiq_options :queue => :fitbit, :retry => 5, :unique => true

app/workers/fitbit_edit.rb

@@ -1,5 +1,6 @@
 
 
+# frozen_string_literal: true
 class FitbitEdit
    include Sidekiq::Worker
    sidekiq_options :queue => :fitbit, :retry => 5, :unique => true

app/workers/fitbit_endsubscription.rb

@@ -1,5 +1,6 @@
 
 
+# frozen_string_literal: true
 class FitbitEndSubscription
    include Sidekiq::Worker
    sidekiq_options :queue => :fitbit, :retry => 5, :unique => true

app/workers/fitbit_init.rb

@@ -1,5 +1,6 @@
 
 
+# frozen_string_literal: true
 class FitbitInit
    include Sidekiq::Worker
    sidekiq_options :queue => :fitbit, :retry => 5, :unique => true

app/workers/fitbit_notification.rb

@@ -1,5 +1,6 @@
 
 
+# frozen_string_literal: true
 class FitbitNotification
    include Sidekiq::Worker
    sidekiq_options :queue => :fitbit, :retry => 5, :unique => true

app/workers/fixphenotypes.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Fixphenotypes
   include Sidekiq::Worker
   sidekiq_options :queue => :fixphenotypes, :retry => 5, :unique => true

app/workers/frequency.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Frequency
   include Sidekiq::Worker
   sidekiq_options queue: :frequency, retry: 5, unique: true

app/workers/genome_gov.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 require 'set'
 require 'open-uri'
 

app/workers/mailnewphenotype.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 class Mailnewphenotype
   include Sidekiq::Worker
   sidekiq_options queue: :mailnewgenotype, unique: true, retry: false # avoid spam on breakage

app/workers/mendeley_details.rb

@@ -1,3 +1,4 @@
+# frozen_string_literal: true
 require "rubygems"
 require "net/http"
 require "json"