Fix tests

.rspec

@@ -1 +1,2 @@
 --color
+--require spec_helper

Gemfile

@@ -64,6 +64,9 @@ gem "sass"
 #end
 
 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 'mocha', require: false
@@ -76,7 +79,6 @@ end
 
 group :development, :test do
   gem 'uuidtools'
-  gem 'rspec-rails'
   gem 'pry-rails', require: 'pry' unless ENV['CI']
 end
 
@@ -85,5 +87,5 @@ group :development do
   gem 'spring'
   gem 'spring-commands-rspec'
   gem 'capistrano', '~> 2.0'
-  gem 'rvm-capistrano', '1.4.4'
+  gem 'rvm-capistrano', '1.4.4', require: false
 end

Gemfile.lock

@@ -61,9 +61,11 @@ GEM
       builder
       multi_json
     arel (4.0.2)
-    authlogic (3.3.0)
+    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)
     capistrano (2.15.5)
@@ -72,7 +74,7 @@ GEM
       net-sftp (>= 2.0.0)
       net-ssh (>= 2.0.14)
       net-ssh-gateway (>= 1.1.0)
-    capybara (2.3.0)
+    capybara (2.4.4)
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
@@ -102,6 +104,9 @@ GEM
       factory_girl (~> 4.4.0)
       railties (>= 3.0.0)
     ffi (1.9.3)
+    ffi-compiler (0.1.3)
+      ffi (>= 1.0.0)
+      rake
     fitgem (0.10.0)
       oauth
     formatador (0.2.5)
@@ -143,7 +148,7 @@ GEM
     metaclass (0.0.1)
     method_source (0.8.2)
     mime-types (2.4.3)
-    mini_portile (0.6.0)
+    mini_portile (0.6.2)
     minitest (4.7.5)
     mocha (0.14.0)
       metaclass (~> 0.0.1)
@@ -157,8 +162,8 @@ GEM
       net-ssh (>= 2.6.5)
     netrc (0.7.7)
     newrelic_rpm (3.6.8.168)
-    nokogiri (1.6.2.1)
-      mini_portile (= 0.6.0)
+    nokogiri (1.6.6.2)
+      mini_portile (~> 0.6.0)
     oauth (0.4.7)
     paperclip (4.1.1)
       activemodel (>= 3.0.0)
@@ -173,11 +178,12 @@ GEM
     plos (0.0.7)
       nokogiri
       rest-client
-    pry (0.9.12.6)
-      coderay (~> 1.0)
-      method_source (~> 0.8)
+    power_assert (0.2.3)
+    pry (0.10.1)
+      coderay (~> 1.1.0)
+      method_source (~> 0.8.1)
       slop (~> 3.4)
-    pry-rails (0.3.2)
+    pry-rails (0.3.3)
       pry (>= 0.9.10)
     rack (1.5.2)
     rack-protection (1.5.1)
@@ -208,35 +214,39 @@ GEM
     redis-namespace (1.3.1)
       redis (~> 3.0.0)
     ref (1.0.5)
+    request_store (1.1.0)
     rest-client (1.7.2)
       mime-types (>= 1.16, < 3.0)
       netrc (~> 0.7)
     rspec (3.0.0)
       rspec-core (~> 3.0.0)
       rspec-expectations (~> 3.0.0)
       rspec-mocks (~> 3.0.0)
-    rspec-core (3.0.0)
+    rspec-core (3.0.4)
       rspec-support (~> 3.0.0)
-    rspec-expectations (3.0.0)
+    rspec-expectations (3.0.4)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.0.0)
-    rspec-mocks (3.0.1)
+    rspec-mocks (3.0.4)
       rspec-support (~> 3.0.0)
-    rspec-rails (3.0.1)
+    rspec-rails (3.0.2)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       railties (>= 3.0)
       rspec-core (~> 3.0.0)
       rspec-expectations (~> 3.0.0)
       rspec-mocks (~> 3.0.0)
       rspec-support (~> 3.0.0)
-    rspec-support (3.0.0)
+    rspec-support (3.0.4)
     rvm-capistrano (1.4.4)
       capistrano (>= 2.15.4)
     safe_yaml (0.9.7)
     sanitize (2.0.6)
       nokogiri (>= 1.4.4)
     sass (3.2.12)
+    scrypt (1.2.1)
+      ffi-compiler (>= 0.0.2)
+      rake
     shoulda-context (1.1.5)
     sidekiq (2.16.0)
       celluloid (>= 0.15.2)
@@ -257,7 +267,7 @@ GEM
     slim (1.3.9)
       temple (~> 0.6.3)
       tilt (~> 1.3, >= 1.3.3)
-    slop (3.5.0)
+    slop (3.6.0)
     spring (1.1.3)
     spring-commands-rspec (1.0.2)
       spring (>= 0.9.1)
@@ -271,6 +281,8 @@ GEM
       activesupport (>= 3.0)
       sprockets (>= 2.8, < 4.0)
     temple (0.6.7)
+    test-unit (3.0.9)
+      power_assert
     therubyracer (0.12.0)
       libv8 (~> 3.16.14.0)
       ref
@@ -328,6 +340,7 @@ DEPENDENCIES
   lograge
   mediawiki-gateway
   mendeley!
+  minitest
   mocha
   nested_form!
   newrelic_rpm
@@ -353,6 +366,7 @@ DEPENDENCIES
   slim (~> 1.3.8)
   spring
   spring-commands-rspec
+  test-unit
   therubyracer
   twitter-bootstrap-rails
   uglifier

app/controllers/phenotypes_controller.rb

@@ -35,7 +35,7 @@ def new
 
   def create
     unless @phenotype = Phenotype.find_by_characteristic(params[:phenotype][:characteristic])
-      @phenotype = Phenotype.create(params[:phenotype])
+      @phenotype = Phenotype.create(phenotype_params)
 
       # award: created one (or more) phenotypes
       current_user.update_attributes(:phenotype_creation_counter => (current_user.phenotype_creation_counter + 1)  )
@@ -45,14 +45,14 @@ def create
       check_and_award_new_phenotypes(10, "Created 10 new phenotypes")
     end
 
-    if params[:phenotype][:characteristic] == ""
+    if params[:phenotype][:characteristic].blank?
       flash[:warning] = "Phenotype characteristic may not be empty"
       redirect_to :action => "new"
     else
 
       @phenotype.save
-      @phenotype = Phenotype.find_by_characteristic(params[:phenotype][:characteristic])
-      Sidekiq::Client.enqueue(Mailnewphenotype, @phenotype.id,current_user.id)
+      @phenotype = Phenotype.find_by(characteristic: params[:phenotype][:characteristic])
+      Sidekiq::Client.enqueue(Mailnewphenotype, @phenotype.id, current_user.id)
 
       if UserPhenotype.find_by_phenotype_id_and_user_id(@phenotype.id,current_user.id).nil?
 
@@ -182,7 +182,7 @@ def feed
 
   def get_genotypes
     Sidekiq::Client.enqueue(Zipgenotypingfiles, params[:id],
-                   params[:variation], current_user.email)
+                            params[:variation], current_user.email)
     @phenotype = Phenotype.find(params[:id])
     @variation = params[:variation]
     respond_to do |format|
@@ -301,4 +301,8 @@ def check_and_award_additional_phenotypes(amount, achievement_string)
       flash[:achievement] = %(Congratulations! You've unlocked an achievement: <a href="#{url_for(@achievement)}">#{@achievement.award}</a>).html_safe
     end
   end
+
+  def phenotype_params
+    params.require(:phenotype).permit(:description, :characteristic)
+  end
 end

app/controllers/snps_controller.rb

@@ -228,7 +228,8 @@ def json_element(params)
   end
 
   def find_snp
-    @snp = Snp.find(params[:id].downcase) || not_found
+    @snp = Snp.friendly.find(params[:id].downcase)
+    @snp ||= Snp.find(params[:id])
 
     # If an old id or a numeric id was used to find the record, then
     # the request path will not match the post_path, and we should do

app/models/snp_reference.rb

@@ -1,5 +1,6 @@
 class SnpReference < ActiveRecord::Base
+  self.primary_keys = :snp_id, :paper_id, :paper_type
   belongs_to :snp
   belongs_to :paper, polymorphic: true
-  validates_presence_of :snp, :paper
+  #validates_presence_of :snp, :paper
 end

app/models/user.rb

@@ -4,17 +4,17 @@ class User < ActiveRecord::Base
   has_attached_file :avatar,
     styles: { medium: "300x300>", thumb: "100x100>#", head: "32x32#" },
     default_url: 'standard_:style.png'
- 
+
   before_validation :clear_avatar
-  
+
   validates_attachment_size :avatar, less_than: 1.megabyte
   validates_attachment_content_type :avatar,
     content_type: ['image/jpeg', 'image/png', 'image/gif']
   # call on authlogic
   acts_as_authentic do |c| 
-      # replace SHA512 by bcrypt
-      c.transition_from_crypto_providers = Authlogic::CryptoProviders::Sha512
-      c.crypto_provider = Authlogic::CryptoProviders::BCrypt
+    # replace SHA512 by bcrypt
+    c.transition_from_crypto_providers = Authlogic::CryptoProviders::Sha512
+    c.crypto_provider = Authlogic::CryptoProviders::BCrypt
   end
   #after_create :make_standard_phenotypes
 
@@ -47,17 +47,17 @@ def deliver_password_reset_instructions!
   end
 
   def phenotype_length
-     # tiny workaround for user-index
-     phenotypes.length
+    # tiny workaround for user-index
+    phenotypes.length
   end
 
   def user_has_sequence_string
-     # used in the user-index-page instead of ugly true/false
-     if has_sequence
-         "Yes"
-     else
-         "No"
-     end
+    # used in the user-index-page instead of ugly true/false
+    if has_sequence
+      "Yes"
+    else
+      "No"
+    end
   end
 
   def check_if_phenotype_exists(charact)
@@ -80,7 +80,7 @@ def check_and_make_standard_phenotypes(charact)
       UserPhenotype.create(phenotype_id: @phen_id, variation: '', user_id: id)
     end
   end
-   
+
   def make_standard_phenotypes
     check_and_make_standard_phenotypes('Hair color')
     check_and_make_standard_phenotypes('Eye color')
@@ -96,7 +96,7 @@ def delete_avatar
     !!@delete_avatar
   end
   alias_method :delete_avatar?, :delete_avatar
-  
+
   def clear_avatar
     self.avatar = nil if delete_avatar?
   end

config/boot.rb

@@ -3,4 +3,4 @@
 # Set up gems listed in the Gemfile.
 ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
 
-require 'bundler/setup' if File.exists?(ENV['BUNDLE_GEMFILE'])
+require 'bundler/setup' if File.exist?(ENV['BUNDLE_GEMFILE'])

config/environments/development.rb

@@ -7,9 +7,6 @@
   # since you don't have to restart the webserver when you make code changes.
   config.cache_classes = false
 
-  # Log error messages when you accidentally call methods on nil.
-  config.whiny_nils = true
-
   # Show full error reports and disable caching
   config.consider_all_requests_local       = true
   config.action_controller.perform_caching = false
@@ -23,9 +20,6 @@
   # Only use best-standards-support built into browsers
   config.action_dispatch.best_standards_support = :builtin
 
-  # Raise exception on mass assignment protection for Active Record models
-  config.active_record.mass_assignment_sanitizer = :strict
-
   # 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
@@ -35,5 +29,8 @@
 
   # Expands the lines which load the assets
   config.assets.debug = true
+
+  # Do not eager load code on boot.
+  config.eager_load = false
 end
 

config/environments/production.rb

@@ -60,4 +60,7 @@
   config.assets.digest = true
 
   config.lograge.enabled = true
+
+  # Eager load code on boot.
+  config.eager_load = true
 end

config/environments/staging.rb

@@ -46,4 +46,7 @@
 
   # Send deprecation notices to registered listeners
   config.active_support.deprecation = :notify
+
+  # Eager load code on boot.
+  config.eager_load = true
 end

config/environments/test.rb

@@ -7,9 +7,6 @@
   # and recreated between test runs.  Don't rely on the data there!
   config.cache_classes = true
 
-  # Log error messages when you accidentally call methods on nil.
-  config.whiny_nils = true
-
   # Show full error reports and disable caching
   config.consider_all_requests_local       = true
   config.action_controller.perform_caching = false
@@ -33,13 +30,13 @@
   # Print deprecation notices to the stderr
   config.active_support.deprecation = :stderr
 
-  # Raise exception on mass assignment protection for Active Record models
-  config.active_record.mass_assignment_sanitizer = :strict
-
   # Configure static asset server for tests with Cache-Control for performance
   config.serve_static_assets = true
   config.static_cache_control = "public, max-age=3600"
 
   # Allow pass debug_assets=true as a query parameter to load pages with unpackaged assets
   config.assets.allow_debugging = true
+
+  # Do not eager load code on boot.
+  config.eager_load = false
 end

config/initializers/0_load_app_config.rb

@@ -1,6 +1,2 @@
 raw_config = File.read("#{Rails.root}/config/app_config.yml")
 APP_CONFIG = YAML.load(raw_config)[Rails.env].symbolize_keys
-
-
-Rails.logger.instance_variable_get(:@logger).instance_variable_get(:@log_dest).sync = true if Rails.logger
-