From 4423d6c42a25275589350eb3b15ee4d8be2e140d Mon Sep 17 00:00:00 2001
From: Helge Rausch <helge@rausch.io>
Date: Thu, 7 Feb 2013 17:14:53 +0100
Subject: [PATCH] upgrading Rails to 3.1

---
 Gemfile                                       |   2 +-
 Gemfile.lock                                  | 146 ++++++++++--------
 app/controllers/genotypes_controller.rb       |   2 +-
 app/controllers/phenotypes_controller.rb      |  98 ++++--------
 app/models/genotype.rb                        |   5 +-
 .../genotypes/{rss.rxml => rss.xml.builder}   |   0
 .../{paper_rss.rxml => paper_rss.xml.builder} |   0
 .../phenotypes/{rss.rxml => rss.xml.builder}  |   0
 .../{rss.rxml => rss.xml.builder}             |   0
 config/environments/development.rb            |   1 -
 lib/phenotype_recommender.rb                  |   6 +
 lib/variation_recommender.rb                  |   6 +
 test/fixtures/.gitkeep                        |   0
 test/functional/genotypes_controller_test.rb  |  19 ++-
 test/functional/phentoypes_controller_test.rb |   6 +-
 test/test_helper.rb                           |   2 +
 test/unit/genotype_test.rb                    |  15 ++
 17 files changed, 160 insertions(+), 148 deletions(-)
 rename app/views/genotypes/{rss.rxml => rss.xml.builder} (100%)
 rename app/views/news/{paper_rss.rxml => paper_rss.xml.builder} (100%)
 rename app/views/phenotypes/{rss.rxml => rss.xml.builder} (100%)
 rename app/views/picture_phenotypes/{rss.rxml => rss.xml.builder} (100%)
 create mode 100644 lib/phenotype_recommender.rb
 create mode 100644 lib/variation_recommender.rb
 create mode 100644 test/fixtures/.gitkeep
 create mode 100644 test/unit/genotype_test.rb

diff --git a/Gemfile b/Gemfile
index 1d67af0..f71e9d4 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,6 +1,6 @@
 source 'http://rubygems.org'
 
-gem 'rails', '~> 3.0.20'
+gem 'rails', '~> 3.1.0'
 gem 'authlogic' # lots of user-related magic
 gem 'rails3-generators'
 gem "jquery-rails"
diff --git a/Gemfile.lock b/Gemfile.lock
index b93e6d1..27ad5f0 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -14,7 +14,7 @@ GIT
 
 GIT
   remote: git://github.com/ryanb/nested_form.git
-  revision: f6744578d25a73c23608668fde2a20f7ae9d7d77
+  revision: 8655e352c8f8dd26a6918e72f6d152954b65676a
   specs:
     nested_form (0.3.1)
 
@@ -38,43 +38,44 @@ GIT
 GEM
   remote: http://rubygems.org/
   specs:
-    abstract (1.0.0)
-    actionmailer (3.0.20)
-      actionpack (= 3.0.20)
-      mail (~> 2.2.19)
-    actionpack (3.0.20)
-      activemodel (= 3.0.20)
-      activesupport (= 3.0.20)
-      builder (~> 2.1.2)
-      erubis (~> 2.6.6)
-      i18n (~> 0.5.0)
-      rack (~> 1.2.5)
-      rack-mount (~> 0.6.14)
-      rack-test (~> 0.5.7)
-      tzinfo (~> 0.3.23)
-    activemodel (3.0.20)
-      activesupport (= 3.0.20)
-      builder (~> 2.1.2)
-      i18n (~> 0.5.0)
-    activerecord (3.0.20)
-      activemodel (= 3.0.20)
-      activesupport (= 3.0.20)
-      arel (~> 2.0.10)
-      tzinfo (~> 0.3.23)
+    actionmailer (3.1.10)
+      actionpack (= 3.1.10)
+      mail (~> 2.3.3)
+    actionpack (3.1.10)
+      activemodel (= 3.1.10)
+      activesupport (= 3.1.10)
+      builder (~> 3.0.0)
+      erubis (~> 2.7.0)
+      i18n (~> 0.6)
+      rack (~> 1.3.6)
+      rack-cache (~> 1.2)
+      rack-mount (~> 0.8.2)
+      rack-test (~> 0.6.1)
+      sprockets (~> 2.0.4)
+    activemodel (3.1.10)
+      activesupport (= 3.1.10)
+      builder (~> 3.0.0)
+      i18n (~> 0.6)
+    activerecord (3.1.10)
+      activemodel (= 3.1.10)
+      activesupport (= 3.1.10)
+      arel (~> 2.2.3)
+      tzinfo (~> 0.3.29)
     activerecord-import (0.2.11)
       activerecord (~> 3.0)
       activerecord (~> 3.0)
-    activeresource (3.0.20)
-      activemodel (= 3.0.20)
-      activesupport (= 3.0.20)
-    activesupport (3.0.20)
-    arel (2.0.10)
+    activeresource (3.1.10)
+      activemodel (= 3.1.10)
+      activesupport (= 3.1.10)
+    activesupport (3.1.10)
+      multi_json (>= 1.0, < 1.3)
+    arel (2.2.3)
     authlogic (3.2.0)
       activerecord (>= 3.0.0)
       activesupport (>= 3.0.0)
     bartt-ssl_requirement (1.4.2)
     bcrypt-ruby (3.0.1)
-    builder (2.1.2)
+    builder (3.0.4)
     capistrano (2.14.1)
       highline
       net-scp (>= 1.0.0)
@@ -83,27 +84,26 @@ GEM
       net-ssh-gateway (>= 1.1.0)
     cocaine (0.4.2)
     columnize (0.3.6)
-    debugger (1.3.0)
+    debugger (1.3.1)
       columnize (>= 0.3.1)
       debugger-linecache (~> 1.1.1)
-      debugger-ruby_core_source (~> 1.1.7)
+      debugger-ruby_core_source (~> 1.1.8)
     debugger-linecache (1.1.2)
       debugger-ruby_core_source (>= 1.1.1)
-    debugger-ruby_core_source (1.1.7)
-    erubis (2.6.6)
-      abstract (>= 1.0.0)
+    debugger-ruby_core_source (1.1.8)
+    erubis (2.7.0)
     factory_girl (4.2.0)
       activesupport (>= 3.0.0)
     fitgem (0.5.2)
       oauth
     highline (1.6.15)
-    i18n (0.5.0)
+    hike (1.2.1)
+    i18n (0.6.1)
     jquery-rails (2.2.0)
       railties (>= 3.0, < 5.0)
       thor (>= 0.14, < 2.0)
     json (1.7.6)
-    mail (2.2.19)
-      activesupport (>= 2.3.6)
+    mail (2.3.3)
       i18n (>= 0.4.0)
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
@@ -111,19 +111,19 @@ GEM
       activesupport
       rest-client (>= 1.3.0)
     metaclass (0.0.1)
-    mime-types (1.19)
+    mime-types (1.20.1)
     minitest (4.3.3)
     mocha (0.13.2)
       metaclass (~> 0.0.1)
-    multi_json (1.5.0)
-    net-scp (1.0.4)
-      net-ssh (>= 1.99.1)
-    net-sftp (2.0.5)
-      net-ssh (>= 2.0.9)
-    net-ssh (2.6.3)
-    net-ssh-gateway (1.1.0)
-      net-ssh (>= 1.99.1)
-    newrelic_rpm (3.5.5.38)
+    multi_json (1.2.0)
+    net-scp (1.1.0)
+      net-ssh (>= 2.6.5)
+    net-sftp (2.1.1)
+      net-ssh (>= 2.6.5)
+    net-ssh (2.6.5)
+    net-ssh-gateway (1.2.0)
+      net-ssh (>= 2.6.5)
+    newrelic_rpm (3.5.6.46)
     nokogiri (1.5.6)
     oauth (0.4.7)
     paperclip (3.4.0)
@@ -135,29 +135,36 @@ GEM
     pg (0.14.1)
     polyglot (0.3.3)
     pr_geohash (1.0.0)
-    rack (1.2.7)
-    rack-mount (0.6.14)
+    rack (1.3.9)
+    rack-cache (1.2)
+      rack (>= 0.4)
+    rack-mount (0.8.3)
       rack (>= 1.0.0)
-    rack-test (0.5.7)
+    rack-protection (1.3.2)
+      rack
+    rack-ssl (1.3.3)
+      rack
+    rack-test (0.6.2)
       rack (>= 1.0)
-    rails (3.0.20)
-      actionmailer (= 3.0.20)
-      actionpack (= 3.0.20)
-      activerecord (= 3.0.20)
-      activeresource (= 3.0.20)
-      activesupport (= 3.0.20)
+    rails (3.1.10)
+      actionmailer (= 3.1.10)
+      actionpack (= 3.1.10)
+      activerecord (= 3.1.10)
+      activeresource (= 3.1.10)
+      activesupport (= 3.1.10)
       bundler (~> 1.0)
-      railties (= 3.0.20)
+      railties (= 3.1.10)
     rails3-generators (1.0.0)
       railties (>= 3.0.0)
-    railties (3.0.20)
-      actionpack (= 3.0.20)
-      activesupport (= 3.0.20)
+    railties (3.1.10)
+      actionpack (= 3.1.10)
+      activesupport (= 3.1.10)
+      rack-ssl (~> 1.3.2)
       rake (>= 0.8.7)
       rdoc (~> 3.4)
-      thor (~> 0.14.4)
+      thor (~> 0.14.6)
     rake (10.0.3)
-    rdoc (3.12)
+    rdoc (3.12.1)
       json (~> 1.4)
     recaptcha (0.3.4)
     redis (3.0.2)
@@ -184,9 +191,14 @@ GEM
       multi_json (~> 1.0)
       simplecov-html (~> 0.7.1)
     simplecov-html (0.7.1)
-    sinatra (1.2.8)
-      rack (~> 1.1)
-      tilt (>= 1.2.2, < 2.0)
+    sinatra (1.3.3)
+      rack (~> 1.3, >= 1.3.6)
+      rack-protection (~> 1.2)
+      tilt (~> 1.3, >= 1.3.3)
+    sprockets (2.0.4)
+      hike (~> 1.2)
+      rack (~> 1.0)
+      tilt (~> 1.1, != 1.3.0)
     sunspot (1.3.3)
       pr_geohash (~> 1.0)
       rsolr (~> 1.0.7)
@@ -227,7 +239,7 @@ DEPENDENCIES
   newrelic_rpm
   paperclip (~> 3.0)
   pg
-  rails (~> 3.0.20)
+  rails (~> 3.1.0)
   rails3-generators
   recaptcha
   recommendify!
diff --git a/app/controllers/genotypes_controller.rb b/app/controllers/genotypes_controller.rb
index fb4657c..5bc8681 100644
--- a/app/controllers/genotypes_controller.rb
+++ b/app/controllers/genotypes_controller.rb
@@ -34,7 +34,7 @@ class GenotypesController < ApplicationController
       @award = Achievement.find_by_award("Published genotyping")
       user_achievement_attrs = { achievement_id: @award.id,
                                  user_id: current_user.id }
-      if UserAchievement.where(user_achievement_attrs).count == 0
+      if UserAchievement.where(user_achievement_attrs).count.zero?
         UserAchievement.create(user_achievement_attrs)
 			  flash[:achievement] = "Congratulations! You've unlocked an achievement:" +
           " <a href=\"#{url_for(@award)}\">#{@award.award}</a>"
diff --git a/app/controllers/phenotypes_controller.rb b/app/controllers/phenotypes_controller.rb
index cb918fc..668af9b 100644
--- a/app/controllers/phenotypes_controller.rb
+++ b/app/controllers/phenotypes_controller.rb
@@ -74,9 +74,9 @@ class PhenotypesController < ApplicationController
           check_and_award_additional_phenotypes(20, "Entered 20 additional phenotypes")
           check_and_award_additional_phenotypes(50, "Entered 50 additional phenotypes")
           check_and_award_additional_phenotypes(100, "Entered 100 additional phenotypes")
-          
+
           Resque.enqueue(Recommendvariations)
-      	  Resque.enqueue(Recommendphenotypes)
+          Resque.enqueue(Recommendphenotypes)
 
           redirect_to current_user
         else
@@ -90,68 +90,28 @@ class PhenotypesController < ApplicationController
     end
   end
 
-  class PhenotypeRecommender < Recommendify::Base
-
-    max_neighbors 50
-
-    input_matrix :users_to_phenotypes, 
-      :similarity_func => :jaccard,
-      :weight => 5.0
-
-  end
-  
-  class VariationRecommender < Recommendify::Base
-    
-    max_neighbors 50
-    
-    input_matrix :users_to_variations,
-      :similarity_func => :jaccard,
-      :weight => 5.0
-  
-  end
-
   def show
-    #@phenotypes = Phenotype.where(:user_id => current_user.id).all
-    #@title = "Phenotypes"
     @phenotype = Phenotype.find(params[:id]) || not_found
     @comments = PhenotypeComment.where(:phenotype_id => params[:id]).all(:order => "created_at ASC")
     @phenotype_comment = PhenotypeComment.new
     @user_phenotype = UserPhenotype.new
 
-
-
-    @recommender = PhenotypeRecommender.new
-    
-    @similar_ids = @recommender.for(params[:id])
-    @similar_phenotypes = []
-    @it_counter = 0
-    
-    @similar_ids.each do |s|
-      if @it_counter < 6
-        @similar_phenotypes << Phenotype.find(s.item_id)
-        @it_counter += 1
-      else
-        break
-      end
-    end
-
-    respond_to do |format|
-      format.html
-      format.xml
-    end
+    recommender = PhenotypeRecommender.new
+    similar_ids = recommender.for(params[:id])
+    @similar_phenotypes = Phenotype.where(['id in (?)', similar_ids]).limit(6)
   end
 
   def recommend_phenotype
     # init the recommendation-engines
     @phenotype_recommender = PhenotypeRecommender.new
     @variation_recommender = VariationRecommender.new
-  
+
     # get up to three similar phenotypes regardless of variation
-    
+
     @similar_ids = @phenotype_recommender.for(params[:id])
     @similar_phenotypes = []
     @item_counter = 0
-    
+
     @similar_ids.each do |s|
       if @item_counter < 3
         @phenotype = Phenotype.find(s.item_id)
@@ -163,7 +123,7 @@ class PhenotypesController < ApplicationController
         break
       end
     end
-    
+
     # get up to three similar combinations of phenotype and variation
     @user_phenotype = UserPhenotype.find_by_phenotype_id_and_user_id(params[:id],current_user.id)
     if @user_phenotype != nil
@@ -172,11 +132,11 @@ class PhenotypesController < ApplicationController
     else
       @variation_recommend_request = ""
     end
-   
+
     @similar_combinations = @phenotype_recommender.for(@variation_recommend_request)
     @similar_variations = []
     @combination_counter = 0
-    
+
     @similar_combinations.each do |s|
       if @combination_counter < 3
         @phenotype = Phenotype.find_by_id(s.item_id.split("=>")[0])
@@ -188,9 +148,9 @@ class PhenotypesController < ApplicationController
         break
       end
     end
-    
+
     @phenotype = Phenotype.find_by_id(params[:id])
-    
+
     if @similar_phenotypes == [] and @similar_variations == []
       redirect_to :action => "index"
     else  
@@ -242,37 +202,37 @@ class PhenotypesController < ApplicationController
     rescue
       @result["error"] = "Sorry, this phenotype doesn't exist"
     end
-    
+
     respond_to do |format|
       format.json { render :json => @result } 
     end    
-    
+
   end
 
   def json
     if params[:user_id].index(",")
       @user_ids = params[:user_id].split(",")
-	    @results = []
-	    @user_ids.each do |id|
-	      @new_param = {}
-	      @new_param[:user_id] = id
+      @results = []
+      @user_ids.each do |id|
+        @new_param = {}
+        @new_param[:user_id] = id
         @results << json_element(@new_param)
       end
-      
+
     elsif params[:user_id].index("-")
       @results = []
       @id_array = params[:user_id].split("-")
       @user_ids = (@id_array[0].to_i..@id_array[1].to_i).to_a
       @user_ids.each do |id|
         @new_param = {}
-	      @new_param[:user_id] = id
-	      @results << json_element(@new_param)
+        @new_param[:user_id] = id
+        @results << json_element(@new_param)
       end
-      
-	  else 
+
+    else 
       @results = json_element(params)	  
     end   
-    
+
     respond_to do |format|
       format.json { render :json => @results } 
     end
@@ -283,19 +243,19 @@ class PhenotypesController < ApplicationController
       @user = User.find_by_id(params[:user_id])
       @result = {}
       @user_phenotypes = UserPhenotype.find_all_by_user_id(@user.id)
-   
+
       @result["user"] = {}
       @result["user"]["name"] = @user.name
       @result["user"]["id"] = @user.id
-   
+
       @phenotype_hash = {}
-   
+
       @user_phenotypes.each do |up|
         @phenotype_hash[up.phenotype.characteristic] = {}
         @phenotype_hash[up.phenotype.characteristic]["phenotype_id"] = up.phenotype.id
         @phenotype_hash[up.phenotype.characteristic]["variation"] = up.variation
       end
-   
+
       @result["phenotypes"] = @phenotype_hash
     rescue
       @result = {}
diff --git a/app/models/genotype.rb b/app/models/genotype.rb
index ef35226..cce88f6 100644
--- a/app/models/genotype.rb
+++ b/app/models/genotype.rb
@@ -8,7 +8,10 @@ class Genotype < ActiveRecord::Base
   has_attached_file :genotype, url: '/data/:fs_filename',
                                path: "#{Rails.root}/public/data/:fs_filename"
   before_post_process :is_image?
-  validates_attachment_presence :genotype
+  validates_attachment :genotype,
+    presence: true,
+    content_type: { content_type: 'text/plain' },
+    size: { in: 0..100.megabytes }
 
   attr_accessible :genotype, :filetype, :user_id
   after_create :parse_genotype
diff --git a/app/views/genotypes/rss.rxml b/app/views/genotypes/rss.xml.builder
similarity index 100%
rename from app/views/genotypes/rss.rxml
rename to app/views/genotypes/rss.xml.builder
diff --git a/app/views/news/paper_rss.rxml b/app/views/news/paper_rss.xml.builder
similarity index 100%
rename from app/views/news/paper_rss.rxml
rename to app/views/news/paper_rss.xml.builder
diff --git a/app/views/phenotypes/rss.rxml b/app/views/phenotypes/rss.xml.builder
similarity index 100%
rename from app/views/phenotypes/rss.rxml
rename to app/views/phenotypes/rss.xml.builder
diff --git a/app/views/picture_phenotypes/rss.rxml b/app/views/picture_phenotypes/rss.xml.builder
similarity index 100%
rename from app/views/picture_phenotypes/rss.rxml
rename to app/views/picture_phenotypes/rss.xml.builder
diff --git a/config/environments/development.rb b/config/environments/development.rb
index e1d0b13..6415280 100644
--- a/config/environments/development.rb
+++ b/config/environments/development.rb
@@ -12,7 +12,6 @@ Snpr::Application.configure do
 
   # Show full error reports and disable caching
   config.consider_all_requests_local       = true
-  config.action_view.debug_rjs             = true
   config.action_controller.perform_caching = false
 
   # Don't care if the mailer can't send
diff --git a/lib/phenotype_recommender.rb b/lib/phenotype_recommender.rb
new file mode 100644
index 0000000..5004918
--- /dev/null
+++ b/lib/phenotype_recommender.rb
@@ -0,0 +1,6 @@
+class PhenotypeRecommender < Recommendify::Base
+  max_neighbors 50
+  input_matrix :users_to_phenotypes, 
+    :similarity_func => :jaccard,
+    :weight => 5.0
+end
diff --git a/lib/variation_recommender.rb b/lib/variation_recommender.rb
new file mode 100644
index 0000000..0860adb
--- /dev/null
+++ b/lib/variation_recommender.rb
@@ -0,0 +1,6 @@
+class VariationRecommender < Recommendify::Base
+  max_neighbors 50
+  input_matrix :users_to_variations,
+    :similarity_func => :jaccard,
+    :weight => 5.0
+end
diff --git a/test/fixtures/.gitkeep b/test/fixtures/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/test/functional/genotypes_controller_test.rb b/test/functional/genotypes_controller_test.rb
index 1f43691..0be8181 100644
--- a/test/functional/genotypes_controller_test.rb
+++ b/test/functional/genotypes_controller_test.rb
@@ -25,7 +25,7 @@ class GenotypesControllerTest < ActionController::TestCase
       end
 
       should "get the rss feed" do
-        get :feed
+        get :feed, format: 'xml'
         assert_response :success
         assert_equal [@genotype], assigns(:genotypes)
       end
@@ -41,7 +41,8 @@ class GenotypesControllerTest < ActionController::TestCase
         activate_authlogic
         @user = FactoryGirl.create(:user)
         UserSession.create(@user)
-        @publishing_award = FactoryGirl.create(:achievement, award: "Published genotyping")
+        @publishing_award = FactoryGirl.
+          create(:achievement, award: "Published genotyping")
       end
 
       should "see the upload form" do
@@ -50,16 +51,20 @@ class GenotypesControllerTest < ActionController::TestCase
       end
 
       should "be able to upload genotypes" do
+        FileUtils.cp("#{Rails.root}/testdata/testdatensatz1_23andme.txt",
+                     "#{Rails.root}/test/fixtures")
+        genotype_file = fixture_file_upload('testdatensatz1_23andme.txt')
+        genotype_file.content_type = 'text/plain'
         Resque.expects(:enqueue).with(Preparsing, is_a(Fixnum))
-        genotype_file_upload = ActionDispatch::Http::UploadedFile.new(
-          filename: '23andme.txt', content_type: 'text/plain',
-          tempfile: File.new("#{Rails.root}/test/data/23andMe_test.csv"))
         assert_difference 'UserAchievement.count' do
-          put :create, commit: "Upload", genotype:
-            { genotype: genotype_file_upload, filetype: "23andme"}
+          assert_difference 'Genotype.count' do
+            put :create, commit: "Upload", genotype:
+              { genotype: genotype_file, filetype: "23andme"}
+          end
         end
         assert_redirected_to user_path(@user)
         assert_equal @publishing_award.id, UserAchievement.last.achievement_id
+        FileUtils.rm("#{Rails.root}/test/fixtures/testdatensatz1_23andme.txt")
       end
     end
   end
diff --git a/test/functional/phentoypes_controller_test.rb b/test/functional/phentoypes_controller_test.rb
index 51ab344..4637f7b 100644
--- a/test/functional/phentoypes_controller_test.rb
+++ b/test/functional/phentoypes_controller_test.rb
@@ -39,13 +39,17 @@ class PhenotypesControllerTest < ActionController::TestCase
       end
 
       should "see them" do
+        similar_phenotype = FactoryGirl.create(:phenotype)
+        PhenotypeRecommender.any_instance.expects(:for).
+          with(@phenotype.id.to_s).returns([similar_phenotype.id])
         get :show, id: @phenotype.id
         assert_response :success
         assert_equal @phenotype, assigns(:phenotype)
+        assert_equal [similar_phenotype], assigns(:similar_phenotypes)
       end
 
       should "get the feed" do
-        get :feed, id: @phenotype.id
+        get :feed, id: @phenotype.id, format: 'xml'
         assert_response :success
       end
 
diff --git a/test/test_helper.rb b/test/test_helper.rb
index 65d8fa0..d568970 100644
--- a/test/test_helper.rb
+++ b/test/test_helper.rb
@@ -11,6 +11,8 @@ SunspotTest.solr_startup_timeout = 30
 require 'sunspot_test/test_unit'
 require 'factory_girl'
 FactoryGirl.find_definitions
+require 'paperclip/matchers'
 
 class ActiveSupport::TestCase
+  extend Paperclip::Shoulda::Matchers
 end
diff --git a/test/unit/genotype_test.rb b/test/unit/genotype_test.rb
new file mode 100644
index 0000000..03d7cce
--- /dev/null
+++ b/test/unit/genotype_test.rb
@@ -0,0 +1,15 @@
+require_relative '../test_helper'
+
+class GenotypeTest < ActiveSupport::TestCase
+  context "Genotype" do
+    setup do
+      Genotype.any_instance.stubs(:fs_filename).returns("1.23andme.1")
+    end
+
+    should have_attached_file(:genotype)
+    should validate_attachment_presence(:genotype)
+    should validate_attachment_content_type(:genotype).
+      allowing('text/plain').rejecting('image/png', 'image/gif', 'text/xml')
+    should validate_attachment_size(:genotype).less_than(100.megabytes)
+  end
+end