Merge pull request openSNP#20 from tsujigiri/known_phenotypes

Known phenotypes

.gitignore

@@ -20,3 +20,4 @@ vendor/bundle
 public/data
 coverage*
 hiredis/
+log/

.travis.yml

@@ -4,6 +4,7 @@ env: DB=postgres
 before_install: 
   - git clone https://github.com/antirez/hiredis.git && cd hiredis && make && sudo make install && sudo ldconfig && cd ..
 before_script:
+  - bash -c "find /home/vagrant/.rvm/gems -name sunspot_test.rb -exec sed -i 's/at_exit/#at_exit/' {} \;"
   - cp config/database.yml.ci config/database.yml
   - echo "foo" > mail_username.txt
   - echo "bar" > mail_password.txt

Gemfile

@@ -47,6 +47,7 @@ group :test do
   gem 'factory_girl'
   gem 'mocha'
   gem 'ruby-debug19'
+  gem 'sunspot_test'
 end
 
 # gem 'email_veracity' # to check whether user-mails are OK

Gemfile.ci

@@ -32,38 +32,8 @@ gem 'paperclip', '~> 2.4'
 gem 'friendly_id', :git => 'https://github.com/norman/friendly_id.git'
 gem 'recommendify', :git => 'https://github.com/paulasmuth/recommendify.git'
 
-#group :production do
-#	gem 'rpm_contrib'
-#	gem 'newrelic_rpm'
-#end
-
-group :test do
-  gem 'shoulda-context'
-  gem 'shoulda-matchers'
-  gem 'factory_girl'
-  gem 'mocha'
-  gem 'ruby-debug19'
-end
-
-
-# gem 'email_veracity' # to check whether user-mails are OK
-# authlogic does that anyway
-
-# Use unicorn as the web server
-# gem 'unicorn'
-
-# Deploy with Capistrano
-# gem 'capistrano'
-
-# Bundle the extra gems:
-# gem 'bj'
-# gem 'nokogiri'
-# gem 'sqlite3-ruby', :require => 'sqlite3'
-# gem 'aws-s3', :require => 'aws/s3'
-
-# Bundle gems for the local environment. Make sure to
-# put test-only gems in this group so their generators
-# and rake tasks are available in development mode:
-# group :development, :test do
-# gem 'webrat'
-# end
+gem 'shoulda-context'
+gem 'shoulda-matchers'
+gem 'factory_girl'
+gem 'mocha'
+gem 'sunspot_test'

Gemfile.lock

@@ -157,6 +157,8 @@ GEM
     sunspot_rails (1.2.1)
       nokogiri
       sunspot (= 1.2.1)
+    sunspot_test (0.4.0)
+      sunspot_rails (>= 1.2.1)
     thor (0.14.6)
     tilt (1.3.3)
     treetop (1.4.10)
@@ -194,4 +196,5 @@ DEPENDENCIES
   shoulda-context
   shoulda-matchers
   sunspot_rails (~> 1.2.1)
+  sunspot_test
   will_paginate (= 3.0.pre2)

app/jobs/zipgenotypingfiles.rb

@@ -3,8 +3,11 @@
 class Zipgenotypingfiles
   @queue = :zipgenotyping
 
-  def self.perform(phenotype_id,variation,target_address)
-    @user_phenotypes = UserPhenotype.find_all_by_phenotype_id_and_variation(phenotype_id,variation)
+  def self.perform(phenotype_id, variation, target_address)
+    @user_phenotypes = UserPhenotype.search do
+      with :phenotype_id, phenotype_id
+      fulltext variation
+    end.results
     @genotyping_files = []
     @user_phenotypes.each do |up|
       @user = User.find_by_id(up.user_id)

app/models/user_phenotype.rb

@@ -1,11 +1,12 @@
 class UserPhenotype < ActiveRecord::Base
-   belongs_to :phenotype, dependent: :destroy
-   belongs_to :user
-   validates_presence_of :variation
+  belongs_to :phenotype, dependent: :destroy
+  belongs_to :user
+  validates_presence_of :variation
 
-   attr_accessible :variation,:phenotype_id,:js_modal
+  attr_accessible :variation,:phenotype_id,:js_modal
 
-   searchable do
-     text :variation
-   end
+  searchable do
+    text :variation
+    integer :phenotype_id
+  end
 end

test/test_helper.rb

@@ -2,6 +2,8 @@
 require File.expand_path('../../config/environment', __FILE__)
 require 'rails/test_help'
 require "authlogic/test_case"
+SunspotTest.solr_startup_timeout = 30
+require 'sunspot_test/test_unit'
 
 class ActiveSupport::TestCase
   FactoryGirl.find_definitions

test/unit/user_phenotype_test.rb

@@ -0,0 +1,25 @@
+require_relative '../test_helper'
+
+class UserPhenotypeTest < ActiveSupport::TestCase
+  context "UserPhenotype" do
+    setup do
+      @phenotype = Factory :phenotype
+      @user_phenotype_0 = Factory :user_phenotype,
+        phenotype_id: @phenotype.id, variation: 'male'
+      @user_phenotype_1 = Factory :user_phenotype,
+        phenotype_id: @phenotype.id, variation: 'female'
+      @user_phenotype_2 = Factory :user_phenotype,
+        phenotype_id: @phenotype.id + 1, variation: 'male'
+      Sunspot.commit
+    end
+
+    should "find similar user phenotypes" do
+      phenotype = @phenotype
+      results = UserPhenotype.search do
+        with(:phenotype_id, phenotype.id)
+        fulltext 'male'
+      end.results
+      assert_equal [@user_phenotype_0], results.sort_by(&:id)
+    end
+  end
+end