Ditch Solr for pg_search

Gemfile

@@ -26,10 +26,7 @@ gem 'newrelic_rpm'
 gem 'pg'
 gem 'activerecord-import', '~> 0.2.11'
 gem 'composite_primary_keys'
-
-# for solr (indexing, searching)
-gem 'sunspot_rails'#, '2.0.0'
-gem 'sunspot_solr'#, '2.0.0'
+gem 'pg_search'
 
 # so we can create zip-files for genotypes
 gem 'rubyzip', :git => 'git://github.com/rubyzip/rubyzip.git'

Gemfile.lock

@@ -225,6 +225,10 @@ GEM
       cocaine (~> 0.5.3)
       mime-types
     pg (0.17.0)
+    pg_search (0.7.8)
+      activerecord (>= 3.1)
+      activesupport (>= 3.1)
+      arel
     plos (0.0.7)
       nokogiri
       rest-client
@@ -348,7 +352,6 @@ GEM
       nokogiri
       rails (>= 3)
       sunspot (= 2.1.1)
-    sunspot_solr (2.0.0)
     temple (0.6.7)
     therubyracer (0.12.0)
       libv8 (~> 3.16.14.0)
@@ -419,6 +422,7 @@ DEPENDENCIES
   newrelic_rpm
   paperclip (~> 4.0)
   pg
+  pg_search
   plos
   pry-rails
   rails (~> 3.2.18)
@@ -438,8 +442,6 @@ DEPENDENCIES
   slim (~> 1.3.8)
   spring
   spring-commands-rspec
-  sunspot_rails
-  sunspot_solr
   sunspot_test!
   therubyracer
   twitter-bootstrap-rails

app/controllers/search_results_controller.rb

@@ -1,24 +1,14 @@
 class SearchResultsController < ApplicationController
 
-  def search_type(type)
-	  return type.solr_search { |p| p.keywords params[:search] }
-  end
-
   def search
-	  @title = "Search results"
-	  @snps = search_type Snp
-	  @phenotypes = search_type Phenotype
-	  @users  = search_type User
-	  @user_phenotypes = search_type UserPhenotype
-	  @snp_comments  = search_type SnpComment
-	  @phenotype_comments  = search_type PhenotypeComment
-	  @mendeley_papers  = search_type MendeleyPaper
-	  @plos_papers  = search_type PlosPaper
-	  @snpedia_papers   = search_type SnpediaPaper
-      @all_len = @snps.results.length + @phenotypes.results.length + @users.results.length +
-          @user_phenotypes.results.length + @snp_comments.results.length + @phenotype_comments.results.length +
-          @mendeley_papers.results.length + @plos_papers.results.length + @snpedia_papers.results.length
+    @title = "Search results"
+    @all_len = 0
+    [
+      :snps, :phenotypes, :users, :user_phenotypes, :snp_comments,
+      :phenotype_comments, :mendeley_papers, :plos_papers, :snpedia_papers,
+    ].each do |type|
+      instance_variable_set(:"@#{type}", type.to_s.singularize.camelize.constantize.search(params[:search]))
+      @all_len += instance_variable_get(:"@#{type}").length
+    end
   end
- 
-
 end

app/models/achievement.rb

@@ -1,8 +1,8 @@
 class Achievement < ActiveRecord::Base
+  include PgSearch
+
   attr_accessible :award,:short_name
   has_many :user_achievements
 
-  searchable do
-    text :award
-  end
+  pg_search_scope :search, against: :award
 end

app/models/genome_gov_paper.rb

@@ -1,8 +1,8 @@
 class GenomeGovPaper < ActiveRecord::Base
+  include PgSearch
+
   has_many :snp_references, as: :paper
   has_many :snps, through: :snp_references
 
-  searchable do
-    text :title
-  end
+  pg_search_scope :search, against: :title
 end

app/models/mendeley_paper.rb

@@ -1,12 +1,12 @@
 class MendeleyPaper < ActiveRecord::Base
+  include PgSearch
+
   has_many :snp_references, as: :paper
   has_many :snps, through: :snp_references
   validates_presence_of :title, :uuid
   validates_uniqueness_of :uuid
 
-  searchable do
-    text :title
-  end
+  pg_search_scope :search, against: :title
 
   def first_author
     read_attribute(:first_author).presence || "Unknown"

app/models/pgp_annotation.rb

@@ -1,9 +1,7 @@
 class PgpAnnotation < ActiveRecord::Base
+  include PgSearch
+
    belongs_to :snp
 
-   searchable do
-	   text :gene
-	   text :summary
-	   text :trait
-   end
+  pg_search_scope :search, against: [:search, :summary, :trait]
 end

app/models/phenotype.rb

@@ -1,24 +1,21 @@
 class Phenotype < ActiveRecord::Base
+  include PgSearch
+
   has_many :user_phenotypes, dependent: :destroy
   has_many :phenotype_comments, dependent: :destroy
   has_and_belongs_to_many :phenotype_sets
 
   validates_presence_of :characteristic
 
-  searchable do
-    text :characteristic
-  end
-  
+  pg_search_scope :search, against: :characteristic
+
   def known_phenotypes
     if @known_phenotypes.nil?
-      @known_phenotypes =
-        user_phenotypes.select('variation').all.
-        map!(&:variation).
-        map!(&:capitalize)
+      @known_phenotypes = user_phenotypes.pluck(:variation).map(&:capitalize)
       @known_phenotypes.uniq!
       @known_phenotypes.compact
     end
     @known_phenotypes
   end
-  
+
 end

app/models/phenotype_comment.rb

@@ -1,8 +1,8 @@
 class PhenotypeComment < ActiveRecord::Base
-   belongs_to :phenotype
-   belongs_to :user
-   
-   searchable do
-      text :comment_text, :subject
-   end                     
+  include PgSearch
+
+  belongs_to :phenotype
+  belongs_to :user
+
+  pg_search_scope :search, against: [:comment_text, :subject]
 end

app/models/phenotype_set.rb

@@ -1,11 +1,9 @@
 class PhenotypeSet < ActiveRecord::Base
+  include PgSearch
+
   has_and_belongs_to_many :phenotypes
 
   validates_presence_of :title,:description
 
-  searchable do
-    text :title
-  end
-
-  
+  pg_search_scope :search, against: :title
 end

app/models/picture_phenotype.rb

@@ -1,12 +1,11 @@
 class PicturePhenotype < ActiveRecord::Base
+  include PgSearch
+
   has_many :user_picture_phenotypes, dependent: :destroy
   has_many :picture_phenotype_comments, dependent: :destroy
   #has_and_belongs_to_many :phenotype_sets
 
   validates_presence_of :characteristic
 
-  searchable do
-    text :characteristic
-  end
-    
-end
+  pg_search_scope :search, against: :characteristic
+end

app/models/picture_phenotype_comment.rb

@@ -1,8 +1,8 @@
 class PicturePhenotypeComment < ActiveRecord::Base
-   belongs_to :picture_phenotype
-   belongs_to :user
-   
-   searchable do
-      text :comment_text, :subject
-   end                     
+  include PgSearch
+
+  belongs_to :picture_phenotype
+  belongs_to :user
+
+  pg_search_scope :search, against: [:comment_text, :subject]
 end

app/models/plos_paper.rb

@@ -1,8 +1,8 @@
 class PlosPaper < ActiveRecord::Base
+  include PgSearch
+
   has_many :snp_references, as: :paper
   has_many :snps, through: :snp_references
 
-  searchable do
-    text :title
-  end
+  pg_search_scope :search, against: :title
 end

app/models/snp.rb

@@ -1,4 +1,6 @@
 class Snp < ActiveRecord::Base
+  include PgSearch
+
   has_many :user_snps, foreign_key: :snp_name, primary_key: :name
   has_many :users, through: :user_snps
   has_many :pgp_annotations
@@ -13,9 +15,7 @@ class Snp < ActiveRecord::Base
 
   validates_uniqueness_of :name
 
-  searchable :ignore_attribute_changes_of => [:genotype_frequency, :allele_frequency, :ranking, :number_of_users, :mendeley_updated, :plos_updated, :snpedia_updated, :user_snps_count, :updated_at] do
-    text :name
-  end
+  pg_search_scope :search, against: :name
 
   after_create :default_frequencies
 

app/models/snp_comment.rb

@@ -1,8 +1,8 @@
 class SnpComment < ActiveRecord::Base
-   belongs_to :snp
-   belongs_to :user
-   
-   searchable do
-      text :comment_text, :subject
-   end
+  include PgSearch
+
+  belongs_to :snp
+  belongs_to :user
+
+  pg_search_scope :search, against: :subject
 end

app/models/snpedia_paper.rb

@@ -1,10 +1,10 @@
 class SnpediaPaper < ActiveRecord::Base
+  include PgSearch
+
   has_many :snp_references, as: :paper
   has_many :snps, through: :snp_references
 
-  searchable do
-    text :summary
-  end
+  pg_search_scope :search, against: :summary
 
   def summary
     read_attribute(:summary).presence || "No summary provided."

app/models/user.rb

@@ -1,4 +1,6 @@
 class User < ActiveRecord::Base
+  include PgSearch
+
   has_attached_file :avatar,
     styles: { medium: "300x300>", thumb: "100x100>#", head: "32x32#" },
     default_url: 'standard_:style.png'
@@ -45,10 +47,7 @@ class User < ActiveRecord::Base
   accepts_nested_attributes_for :homepages, allow_destroy: true
   accepts_nested_attributes_for :user_phenotypes, allow_destroy: true
 
-  # The following should turn off auto-reindex of user on login
-  searchable :ignore_attribute_changes_of => [:persistence_token, :perishable_token, :updated_at] do
-    text :description, :name
-  end
+  pg_search_scope :search, against: [:description, :name]
 
   def deliver_password_reset_instructions!
     reset_perishable_token!

app/models/user_phenotype.rb

@@ -1,14 +1,13 @@
 class UserPhenotype < ActiveRecord::Base
+  include PgSearch
+
   belongs_to :phenotype
   belongs_to :user
   validates_presence_of :variation
 
   attr_accessible :variation,:phenotype_id,:js_modal
 
-  searchable do
-    text :variation
-    integer :phenotype_id
-  end
+  pg_search_scope :search, against: [:variation, :phenotype_id]
 
   def give_me_user_phenotype(phenotype_id, user_id)
       # needed for the phenotype_set_forms

app/models/user_picture_phenotype.rb

@@ -1,4 +1,6 @@
 class UserPicturePhenotype < ActiveRecord::Base
+  include PgSearch
+
   belongs_to :picture_phenotype
   belongs_to :user
 
@@ -11,9 +13,7 @@ class UserPicturePhenotype < ActiveRecord::Base
   validates_attachment_content_type :phenotype_picture ,
     :content_type => ['image/jpeg', 'image/png', 'image/gif']
 
-  searchable do
-    integer :picture_phenotype_id
-  end
+  pg_search_scope :search, against: :picture_phenotype_id
 
   def give_me_user_phenotype(phenotype_id, user_id)
     # needed for the phenotype_set_forms

app/views/search_results/search.html.erb

@@ -2,24 +2,24 @@
 <%if @all_len != 0 %>
 <div id="tab-container">
   <ul class="nav nav-tabs">
-	<%if not @users.results == [] %>
-	<li><a href="#users">Users (<%=@users.results.length%>)</a></li>
+	<%if not @users == [] %>
+	<li><a href="#users">Users (<%=@users.length%>)</a></li>
 	<%end%>
-	<%if not @phenotypes.results == []%>
-	<li><a href="#phenotypes">Phenotypes (<%=@phenotypes.results.length%>)</a></li>
+	<%if not @phenotypes == []%>
+	<li><a href="#phenotypes">Phenotypes (<%=@phenotypes.length%>)</a></li>
 	<%end%>
-	<%if not @snps.results == []%>
-	<li><a href="#snps">SNPs (<%=@snps.results.length%>)</a></li>
+	<%if not @snps == []%>
+	<li><a href="#snps">SNPs (<%=@snps.length%>)</a></li>
 	<%end%>
-	<% if not (@mendeley_papers.results == [] and @plos_papers.results == [])%>
-    <li><a href="#papers">Papers (<%=@plos_papers.results.length + @mendeley_papers.results.length%>)</a></li>
+	<% if not (@mendeley_papers == [] and @plos_papers == [])%>
+    <li><a href="#papers">Papers (<%=@plos_papers.length + @mendeley_papers.length%>)</a></li>
 	<%end%>
-    <%if not (@snp_comments.results == [] and @phenotype_comments.results == [])%>
-    <li><a href="#comments">Comments (<%=@snp_comments.results.length + @phenotype_comments.results.length%>)</a></li>
+    <%if not (@snp_comments == [] and @phenotype_comments == [])%>
+    <li><a href="#comments">Comments (<%=@snp_comments.length + @phenotype_comments.length%>)</a></li>
 	<%end%>	
   </ul>
 <% end %>
-<% if not @phenotypes.results == [] %>
+<% if not @phenotypes == [] %>
 <div id="phenotypes">
 	<table class="table table-striped">
 			<tr>
@@ -27,7 +27,7 @@
 				<th># of Users</th>
 				<th>Known Variation</th>
 			</tr>
-<% for p in @phenotypes.results %>
+<% for p in @phenotypes %>
 		<tr>
 			<td><%= link_to p.characteristic, p %></td>
 			<td><%= p.number_of_users%></td>
@@ -42,7 +42,7 @@
 </table>
 </div>
 <% end %>
-<% if not @snps.results == [] %>
+<% if not @snps == [] %>
 <div id="snps">
 	<h5>SNPs</h5>
     <table class="table table-striped">
@@ -51,7 +51,7 @@
             <th>Chromosome</th>
             <th>Position</th>
         </tr>
-        <% for p in @snps.results %>
+        <% for p in @snps %>
         <tr>
             <td><%= link_to p.name, p %></td>
             <td><%= p.chromosome %></td>
@@ -62,7 +62,7 @@
 </div>
 <% end %>
 
-<% if not @users.results == [] %>
+<% if not @users == [] %>
 <div id="users">
 	<table class="table table-striped">
 			<tr>
@@ -71,7 +71,7 @@
 				<th># of Phenotypes</th>
 				<th># of Achievements</th>
 			</tr>
-<% for u in @users.results %>
+<% for u in @users %>
 			<tr>
 				<td><%= image_tag u.avatar.url(:head),:style => "vertical-align:middle"%> <%= link_to u.name, u %></td>
 				<%if u.has_sequence%>
@@ -86,9 +86,9 @@
 </table>
 </div>
 <% end %>
-<%if not (@snp_comments.results == [] and @phenotype_comments.results == [])%>
+<%if not (@snp_comments == [] and @phenotype_comments == [])%>
 <div id="comments">
-<% if not @snp_comments.results == [] %>
+<% if not @snp_comments == [] %>
 	<h5>On SNPs</h5>
 	<table class="table table-striped">
 			<tr>
@@ -97,7 +97,7 @@
 				<th>Subject</th>
 				<th>Text</th>
 			</tr>
-<% for p in @snp_comments.results %>
+<% for p in @snp_comments %>
 	<tr>
 		<td><%if p.snp != nil%><%=link_to(p.snp.name,"/snps/"+p.snp.id.to_s+"#comments")%><%else%>SNP was deleted<%end%></td>
         <% if p.user %>
@@ -111,7 +111,7 @@
 <% end %>
 </table>
 <% end %>
-<% if not @phenotype_comments.results == [] %>
+<% if not @phenotype_comments == [] %>
 	<h5>On Phenotypes</h5>
 	<table class="table table-striped">
 			<tr>
@@ -120,7 +120,7 @@
 				<th>Subject</th>
 				<th>Text</th>
 			</tr>
-<% for p in @phenotype_comments.results %>
+<% for p in @phenotype_comments %>
 	<tr>
 		<td><%if p.phenotype != nil%><%=link_to(p.phenotype.characteristic,"/snps/"+p.phenotype.id.to_s+"#comments")%><%else%>Phenotype was deleted<%end%></td>
         <% if p.user %>
@@ -136,9 +136,9 @@
 <% end %>
 </div>
 <% end %>
-<% if not (@mendeley_papers.results == [] and @plos_papers.results == [] and @snpedia_papers.results == [])%>
+<% if not (@mendeley_papers == [] and @plos_papers == [] and @snpedia_papers == [])%>
 <div id="papers">                  
-<% if not @mendeley_papers.results == [] %>
+<% if not @mendeley_papers == [] %>
 	<h5>Papers on Mendeley</h5>
 	<table class="table table-striped">
 		<tr>
@@ -149,7 +149,7 @@
 			<th># of Readers</th>
 			<th>DOI</th>
 		</tr>
-<% for p in @mendeley_papers.results %>
+<% for p in @mendeley_papers %>
 		<tr>
 			<td><%= p.first_author%></td>
 			<td><%=link_to( p.title, p.mendeley_url)%></td>
@@ -169,7 +169,7 @@
 <% end %>
 </table>
 <% end %>
-<% if not @plos_papers.results == [] %>
+<% if not @plos_papers == [] %>
 	<h5>Papers at the Public Library of Science</h5>
 	<table class="table table-striped">
 			<tr>
@@ -179,7 +179,7 @@
 				<th>Year of Publication</th>
 				<th># of Readers</th>
 			</tr>
-<% for p in @plos_papers.results %>
+<% for p in @plos_papers %>
 			<tr>
 				<td><%= p.first_author%></td>
 				<td><%= link_to( p.title.html_safe, "http://dx.doi.org/"+p.doi)%></td>
@@ -190,14 +190,14 @@
 <% end %>
 	</table>
 <% end %>        
-<% if not @snpedia_papers.results == [] %>
+<% if not @snpedia_papers == [] %>
 	<h5>Entries in the SNPedia</h5>
 	<table class="table table-striped">
 			<tr>
 				<th>Title</th>
 				<th>Summary</th>
 			</tr>
-<% for p in @snpedia_papers.results %>
+<% for p in @snpedia_papers %>
 			<tr>
                 <td><% p.snps.each do |m| %> <%=link_to m.name+" "+p.url[-4]+"/"+p.url[-2], p.url%> <% end %></td>
 				<td><%=p.summary%></td>

spec/features/search_spec.rb

@@ -0,0 +1,10 @@
+require 'spec_helper'
+
+feature 'search' do
+  let!(:snp) { create(:snp, name: 'rs123') }
+
+  scenario 'searching' do
+    visit '/search?search=rs123'
+    expect(page).to have_content('rs123')
+  end
+end