Update Rails to 4.2.*

Gemfile

@@ -1,6 +1,6 @@
 source 'http://rubygems.org'
 
-gem 'rails', '~> 4.0.0'
+gem 'rails', '~> 4.1.0'
 gem 'authlogic' # lots of user-related magic
 gem 'i18n', '>= 0.6.6'
 gem 'rails3-generators'
@@ -26,7 +26,7 @@ gem 'newrelic_rpm'
 # DB
 gem 'pg'
 gem 'activerecord-import', '>= 0.4.0'
-gem 'composite_primary_keys', '~> 6.0'
+gem 'composite_primary_keys', '~> 7.0'
 gem 'pg_search'
 
 # so we can create zip-files for genotypes
@@ -67,8 +67,7 @@ group :test do
   gem 'test-unit' # TODO: Remove me
   gem 'minitest' # TODO: Remove me
   gem 'rspec-rails'
-  gem 'shoulda-context', require: false
-  gem 'factory_girl_rails'
+  gem 'shoulda-context'
   gem 'mocha', require: false
   gem 'simplecov', require: false
   gem 'webmock'
@@ -80,6 +79,7 @@ end
 group :development, :test do
   gem 'uuidtools'
   gem 'pry-rails', require: 'pry' unless ENV['CI']
+  gem 'factory_girl_rails'
 end
 
 group :development do

Gemfile.lock

@@ -30,44 +30,46 @@ GIT
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (4.0.13)
-      actionpack (= 4.0.13)
+    actionmailer (4.1.9)
+      actionpack (= 4.1.9)
+      actionview (= 4.1.9)
       mail (~> 2.5, >= 2.5.4)
-    actionpack (4.0.13)
-      activesupport (= 4.0.13)
-      builder (~> 3.1.0)
-      erubis (~> 2.7.0)
+    actionpack (4.1.9)
+      actionview (= 4.1.9)
+      activesupport (= 4.1.9)
       rack (~> 1.5.2)
       rack-test (~> 0.6.2)
-    activemodel (4.0.13)
-      activesupport (= 4.0.13)
-      builder (~> 3.1.0)
-    activerecord (4.0.13)
-      activemodel (= 4.0.13)
-      activerecord-deprecated_finders (~> 1.0.2)
-      activesupport (= 4.0.13)
-      arel (~> 4.0.0)
-    activerecord-deprecated_finders (1.0.3)
+    actionview (4.1.9)
+      activesupport (= 4.1.9)
+      builder (~> 3.1)
+      erubis (~> 2.7.0)
+    activemodel (4.1.9)
+      activesupport (= 4.1.9)
+      builder (~> 3.1)
+    activerecord (4.1.9)
+      activemodel (= 4.1.9)
+      activesupport (= 4.1.9)
+      arel (~> 5.0.0)
     activerecord-import (0.7.0)
       activerecord (>= 3.0)
-    activesupport (4.0.13)
+    activesupport (4.1.9)
       i18n (~> 0.6, >= 0.6.9)
-      minitest (~> 4.2)
-      multi_json (~> 1.3)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
       thread_safe (~> 0.1)
-      tzinfo (~> 0.3.37)
+      tzinfo (~> 1.1)
     addressable (2.3.5)
     airbrake (4.0.0)
       builder
       multi_json
-    arel (4.0.2)
+    arel (5.0.1.20140414130214)
     authlogic (3.4.5)
       activerecord (>= 3.2)
       activesupport (>= 3.2)
       request_store (~> 1.0)
       scrypt (~> 1.2)
     bcrypt-ruby (3.1.2)
-    builder (3.1.4)
+    builder (3.2.2)
     capistrano (2.15.5)
       highline
       net-scp (>= 1.0.0)
@@ -88,8 +90,8 @@ GEM
     cocaine (0.5.4)
       climate_control (>= 0.0.3, < 1.0)
     coderay (1.1.0)
-    composite_primary_keys (6.0.8)
-      activerecord (~> 4.0.6)
+    composite_primary_keys (7.0.13)
+      activerecord (~> 4.1.7)
     connection_pool (1.1.0)
     crack (0.4.1)
       safe_yaml (~> 0.9.0)
@@ -98,10 +100,10 @@ GEM
     dynamic_form (1.1.4)
     erubis (2.7.0)
     execjs (2.0.2)
-    factory_girl (4.4.0)
+    factory_girl (4.5.0)
       activesupport (>= 3.0.0)
-    factory_girl_rails (4.4.1)
-      factory_girl (~> 4.4.0)
+    factory_girl_rails (4.5.0)
+      factory_girl (~> 4.5.0)
       railties (>= 3.0.0)
     ffi (1.9.3)
     ffi-compiler (0.1.3)
@@ -149,7 +151,7 @@ GEM
     method_source (0.8.2)
     mime-types (2.4.3)
     mini_portile (0.6.2)
-    minitest (4.7.5)
+    minitest (5.5.1)
     mocha (0.14.0)
       metaclass (~> 0.0.1)
     multi_json (1.11.0)
@@ -190,19 +192,21 @@ GEM
       rack
     rack-test (0.6.3)
       rack (>= 1.0)
-    rails (4.0.13)
-      actionmailer (= 4.0.13)
-      actionpack (= 4.0.13)
-      activerecord (= 4.0.13)
-      activesupport (= 4.0.13)
+    rails (4.1.9)
+      actionmailer (= 4.1.9)
+      actionpack (= 4.1.9)
+      actionview (= 4.1.9)
+      activemodel (= 4.1.9)
+      activerecord (= 4.1.9)
+      activesupport (= 4.1.9)
       bundler (>= 1.3.0, < 2.0)
-      railties (= 4.0.13)
+      railties (= 4.1.9)
       sprockets-rails (~> 2.0)
     rails3-generators (1.0.0)
       railties (>= 3.0.0)
-    railties (4.0.13)
-      actionpack (= 4.0.13)
-      activesupport (= 4.0.13)
+    railties (4.1.9)
+      actionpack (= 4.1.9)
+      activesupport (= 4.1.9)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
     rake (10.4.2)
@@ -247,7 +251,7 @@ GEM
     scrypt (1.2.1)
       ffi-compiler (>= 0.0.2)
       rake
-    shoulda-context (1.1.5)
+    shoulda-context (1.2.1)
     sidekiq (2.16.0)
       celluloid (>= 0.15.2)
       connection_pool (>= 1.0.0)
@@ -295,7 +299,8 @@ GEM
       execjs
       rails (>= 3.1)
       railties (>= 3.1)
-    tzinfo (0.3.43)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
     uglifier (2.3.0)
       execjs (>= 0.3.0)
       json (>= 1.8.0)
@@ -325,7 +330,7 @@ DEPENDENCIES
   bcrypt-ruby
   capistrano (~> 2.0)
   capybara
-  composite_primary_keys (~> 6.0)
+  composite_primary_keys (~> 7.0)
   database_cleaner
   dynamic_form
   execjs
@@ -349,7 +354,7 @@ DEPENDENCIES
   pg_search
   plos
   pry-rails
-  rails (~> 4.0.0)
+  rails (~> 4.1.0)
   rails3-generators
   recaptcha
   recommendify!

app/views/phenotypes/index.html.erb

@@ -1,26 +1,27 @@
 <legend>Listing all phenotypes</legend>
 <%if current_user%>
-    <h4>
-        <%=link_to(image_tag("addphenotype_small.png",:style => "vertical-align:middle" ),:action =>"new")%> <%=link_to "The phenotype of your interest is missing? Add a new one!",:action => "new"%>
-    </h4>
+  <h4>
+    <%= link_to(image_tag("addphenotype_small.png", style: 'vertical-align: middle;' ), action: 'new')%>
+    <%= link_to "The phenotype of your interest is missing? Add a new one!", action: 'new' %>
+  </h4>
 <%end%>
 <br/>
 <table class="table table-striped" id="no_snp_overview">
-<tr>
- 	<th>#</th>
-	<th><%= sortable "id", "ID"%></th>
-	<th><%= sortable "characteristic","Phenotype"%></th>
-	<th><%= sortable "number_of_users","Number of users"%></th>
-	<th><%= sortable "created_at", "Created"%>
-</tr>
-<% @phenotypes_paginate.each do |s| %>
-	<tr>
-    <td><%= Phenotype.all.sort! { |a,b| a.id <=> b.id}.index(s) + 1%></td>
-    <td><%= s.id %></td>
-	<td><%= link_to(s.characteristic, s) %></td>
-	<td><%=s.number_of_users%></td>
-	<td><%=s.created_at%></td>
-</tr>
-<% end %>
+  <tr>
+    <th>#</th>
+    <th><%= sortable "id", "ID" %></th>
+    <th><%= sortable "characteristic", "Phenotype" %></th>
+    <th><%= sortable "number_of_users", "Number of users" %></th>
+    <th><%= sortable "created_at", "Created" %></th>
+  </tr>
+  <% @phenotypes_paginate.each_with_index do |phenotype, i| %>
+    <tr>
+      <td><%= i + 1 %></td>
+      <td><%= phenotype.id %></td>
+      <td><%= link_to(phenotype.characteristic, phenotype) %></td>
+      <td><%= phenotype.number_of_users %></td>
+      <td><%= phenotype.created_at %></td>
+    </tr>
+  <% end %>
 </table>
 <%= page_navigation_links @phenotypes_paginate %>

app/views/snp_comments/_show.html.erb

@@ -7,22 +7,17 @@ function sendCommentId(e, text)
 
 <% @comments.each do |c|%>
 
-  <div id="<%="comment"+c.id.to_s%>">
-    <b><%= c.subject %></b> by user <%if User.find_by_id(c.user_id) != nil%><%= link_to User.find_by_id(c.user_id).name, User.find_by_id(c.user_id)%><%else%>Deleted User<%end%> on <%= c.created_at %><br/>
-    <div class="well">
-      <a href="#" rel="comment_tooltip" title="<%if c.reply_to_id != -1 and c.reply_to_id != nil%><%if SnpComment.find_by_id(c.reply_to_id).user != nil%><b><%=SnpComment.find_by_id(c.reply_to_id).user.name%><%else%>Deleted User<%end%></b> wrote:"data-content="<%=SnpComment.find_by_id(c.reply_to_id).comment_text%><%end%>"><% if c.reply_to_id != -1 and c.reply_to_id != nil%><%if SnpComment.find_by_id(c.reply_to_id).user%>@<%=SnpComment.find_by_id(c.reply_to_id).user.name%><%else%>@Deleted User<%end%><% end %></a>
-      <% if User.where(id: c.user_id).count > 0 # TODO: Move to controller %>
-        <%=image_tag c.user.avatar.url(:head),:style => "vertical-align:middle;margin: 10px;float:left"%>
-      <% end %>
-      <%= simple_format(c.comment_text) %>
-      <br/>
-      <a onclick="sendCommentId(document.new_comment.snp_comment_comment_text,'@#<%= c.id.to_s %>: '); return false;" href="#">reply to</a>
-    </div>
-  </div>
+	<div id="<%="comment"+c.id.to_s%>">
+	<b><%= c.subject %></b> by user <%if User.find_by_id(c.user_id) != nil%><%= link_to User.find_by_id(c.user_id).name, User.find_by_id(c.user_id)%><%else%>Deleted User<%end%> on <%= c.created_at %><br/>
+	<div class="well">
+		<a href="#" rel="comment_tooltip" title="<%if c.reply_to_id != -1 and c.reply_to_id != nil%><%if SnpComment.find_by_id(c.reply_to_id).user != nil%><b><%=SnpComment.find_by_id(c.reply_to_id).user.name%><%else%>Deleted User<%end%></b> wrote:"data-content="<%=SnpComment.find_by_id(c.reply_to_id).comment_text%><%end%>"><% if c.reply_to_id != -1 and c.reply_to_id != nil%><%if SnpComment.find_by_id(c.reply_to_id).user%>@<%=SnpComment.find_by_id(c.reply_to_id).user.name%><%else%>@Deleted User<%end%><% end %></a>
+    <%if User.find_by_id(c.user_id) != nil%><%=image_tag c.user.avatar.url(:head),:style => "vertical-align:middle;margin: 10px;float:left"%><%end%>  <%= simple_format(c.comment_text) %><br/><a onclick="sendCommentId(document.new_comment.snp_comment_comment_text,'@#<%= c.id %>: '); return false;" href="#">reply to</a>
+	</div>
+</div>
 <% end %>
 
 <script type="text/javascript">
   $(document).ready(function () {
-    $("[rel=comment_tooltip]").popover({ placement:'right' });
+    $("[rel=comment_tooltip]").popover({placement:'right'});
   });
 </script>

bin/rails

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+begin
+  load File.expand_path("../spring", __FILE__)
+rescue LoadError
+end
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+APP_PATH = File.expand_path('../../config/application',  __FILE__)
+require File.expand_path('../../config/boot',  __FILE__)
+require 'rails/commands'

bin/rake

@@ -0,0 +1,7 @@
+#!/usr/bin/env ruby
+begin
+  load File.expand_path("../spring", __FILE__)
+rescue LoadError
+end
+require 'bundler/setup'
+load Gem.bin_path('rake', 'rake')

bin/rspec

@@ -0,0 +1,7 @@
+#!/usr/bin/env ruby
+begin
+  load File.expand_path("../spring", __FILE__)
+rescue LoadError
+end
+require 'bundler/setup'
+load Gem.bin_path('rspec-core', 'rspec')

bin/spring

@@ -0,0 +1,18 @@
+#!/usr/bin/env ruby
+
+# This file loads spring without using Bundler, in order to be fast
+# It gets overwritten when you run the `spring binstub` command
+
+unless defined?(Spring)
+  require "rubygems"
+  require "bundler"
+
+  if match = Bundler.default_lockfile.read.match(/^GEM$.*?^    spring \((.*?)\)$.*?^$/m)
+    ENV["GEM_PATH"] = ([Bundler.bundle_path.to_s] + Gem.path).join(File::PATH_SEPARATOR)
+    ENV["GEM_HOME"] = ""
+    Gem.paths = ENV
+
+    gem "spring", match[1]
+    require "spring/binstub"
+  end
+end

config/application.rb

@@ -51,5 +51,10 @@ class Application < Rails::Application
 
     # Version of your assets, change this if you want to expire all your assets
     config.assets.version = '1.0'
+
+    config.generators do |g|
+      g.test_framework :rspec
+      g.factory_girl dir: 'test/factories'
+    end
   end
 end

config/environments/development.rb

@@ -20,10 +20,6 @@
   # Only use best-standards-support built into browsers
   config.action_dispatch.best_standards_support = :builtin
 
-  # Log the query plan for queries taking more than this (works
-  # with SQLite, MySQL, and PostgreSQL)
-  config.active_record.auto_explain_threshold_in_seconds = 0.1
-
   # Do not compress assets
   config.assets.compress = false
 

test/factories.rb → test/factories/factories.rb

@@ -1,6 +1,6 @@
+# TODO: One file per model.
+
 # Needed (?) when test/unit and Rspec tests are run
-unless $factories_already_read
-  $factories_already_read = true
 
   FactoryGirl.define do
     factory :user do
@@ -111,4 +111,3 @@
     factory :phenotype_comment do
     end
   end
-end

test/test_helper.rb

@@ -11,8 +11,7 @@
 require "authlogic/test_case"
 require 'webmock'
 WebMock.disable_net_connect!(:allow_localhost => true)
-require 'factory_girl'
-FactoryGirl.find_definitions
+require 'factory_girl_rails'
 require 'paperclip/matchers'
 require 'plos'