all tests clean

app/controllers/genotypes_controller.rb

@@ -35,7 +35,7 @@ def create
         end
 
         @genotype.move_file
-        Resque.enqueue(Preparsing, @genotype)
+        Resque.enqueue(Preparsing, @genotype.id)
         format.html { redirect_to(current_user, :notice => 'Genotype was successfully uploaded! Parsing and stuff might take a couple of hours.') }
         format.xml { render :xml => current_user, :status => :created, :location => @user }
       else

app/jobs/parsing.rb

@@ -3,13 +3,14 @@
 class Parsing
   @queue = :parse
 
-  def self.perform(genotyp,temp_file)
+  def self.perform(genotype_id, temp_file)
     Rails.logger.level = 0
     Rails.logger = Logger.new("#{Rails.root}/log/parsing_#{Rails.env}.log")
-    @genotype = Genotype.find_by_id(genotyp["genotype"]["id"].to_i)
+    genotype_id = genotype_id["genotype"]["id"].to_i if genotype_id.is_a?(Hash)
+    @genotype = Genotype.find(genotype_id)
 
     if @genotype.filetype != "other"
-      
+
       genotype_file = File.open(temp_file, "r")
       log "Loading known Snps."
       known_snps = {}

app/jobs/preparsing.rb

@@ -3,16 +3,17 @@
 class Preparsing
   @queue = :preparse
 
-  def self.perform(genotyp)
-    @genotype = Genotype.find_by_id(genotyp["genotype"]["id"].to_i)
+  def self.perform(genotype_id)
+    genotype_id = genotype_id["genotype"]["id"].to_i if genotype_id.is_a?(Hash)
+    @genotype = Genotype.find(genotype_id)
     filename = "#{Rails.root}/public/data/#{@genotype.fs_filename}"
 
     system("csplit -k -f #{@genotype.id}_tmpfile -n 4 #{filename} 20000 {2000}")
     system("mv #{@genotype.id}_tmpfile* tmp/")
 
     temp_files = Dir.glob("tmp/#{@genotype.id}_tmpfile*")
     temp_files.each do |single_temp_file|
-      Resque.enqueue(Parsing,@genotype,single_temp_file)
+      Resque.enqueue(Parsing, @genotype.id, single_temp_file)
     end
   end
-end
+end

test/data/23andMe_test.csv

@@ -0,0 +1,5 @@
+rs4477212	1	72017	AA
+rs3094315	1	742429	AA
+rs3131972	1	742584	GG
+rs12124819	1	766409	AG
+rs11240777	1	788822	AG

test/data/deCODEme_test.csv

@@ -1,4 +1,3 @@
-Name,Variation,Chromosome,Position,Strand,YourCode
 rs4477212,A/G,1,72017,+,AA
 rs2185539,C/T,1,556738,+,CC
 rs6681105,C/T,1,581938,+,TT

test/functional/genotypes_controller_test.rb

@@ -5,6 +5,7 @@ class GenotypesControllerTest < ActionController::TestCase
     setup do
       Sunspot.stubs(:index)
       @genotype = Factory :genotype
+      UserAchievement.delete_all
     end
 
     context "unauthenticated users" do
@@ -53,11 +54,11 @@ class GenotypesControllerTest < ActionController::TestCase
         Resque.expects(:enqueue).with do |*args|
           assert_equal 2, args.size
           assert_equal Preparsing, args[0]
-          assert args[1].is_a?(Genotype)
+          assert args[1].is_a?(Fixnum)
         end
         genotype_file_upload = ActionDispatch::Http::UploadedFile.new(
           filename: '23andme.txt', content_type: 'text/plain',
-          tempfile: File.new("#{Rails.root}/test/data/23andMe_test.txt"))
+          tempfile: File.new("#{Rails.root}/test/data/23andMe_test.csv"))
         assert_difference 'UserAchievement.count' do
           put :create, commit: "Upload", genotype:
             { filename: genotype_file_upload, filetype: "23andme"}

test/unit/parsing_test.rb

@@ -3,38 +3,38 @@
 class ParsingTest < ActiveSupport::TestCase
   context "parser" do
     setup do
+
       Sunspot.stubs(:index)
       Snp.delete_all
       UserSnp.delete_all
 
-      @file_23andMe = "#{Rails.root}/test/data/23andMe_test.txt"
+      @file_23andMe = "#{Rails.root}/test/data/23andMe_test.csv"
       @genotype_23andme = Factory :genotype,
         originalfilename: @file_23andMe.split('/').last, filetype: '23andme'
-      FileUtils.cp @file_23andMe, 
-        "#{Rails.root}/public/data/#{@genotype_23andme.user.id}.#{@genotype_23andme.filetype}.#{@genotype_23andme.id}"
 
       @file_deCODEme = "#{Rails.root}/test/data/deCODEme_test.csv"
-
       @genotype_decodeme = Factory :genotype,
         originalfilename: @file_deCODEme.split('/').last, filetype: 'decodeme'
-      FileUtils.cp @file_deCODEme, 
-        "#{Rails.root}/public/data/#{@genotype_decodeme.user.id}.#{@genotype_decodeme.filetype}.#{@genotype_decodeme.id}"
+
+      @temp_file = "#{Rails.root}/tmp/snp_file.txt"
+      FileUtils.rm(@temp_file) if File.exist?(@temp_file)
     end
 
     should "parse 23andMe data" do
-      Parsing.perform('genotype' => @genotype_23andme.attributes)
+      FileUtils.cp @file_23andMe, @temp_file
+      Parsing.perform(@genotype_23andme.id, @temp_file)
 
       # Snp
       snp_data = Snp.all.map do |s|
         [ s.name, s.position, s.chromosome, s.genotype_frequency, s.allele_frequency, s.ranking ]
       end.sort_by { |s| s[0] }
 
       expected =
-        [ [ "rs11240777", "788822", "1", {"AG"=>1}, {"A"=>1, "T"=>0, "G"=>1, "C"=>0}, 0 ],
-          [ "rs12124819", "766409", "1", {"AG"=>1}, {"A"=>1, "T"=>0, "G"=>1, "C"=>0}, 0 ],
-          [ "rs3094315",  "742429", "1", {"AA"=>1}, {"A"=>2, "T"=>0, "G"=>0, "C"=>0}, 0 ],
-          [ "rs3131972",  "742584", "1", {"GG"=>1}, {"A"=>0, "T"=>0, "G"=>2, "C"=>0}, 0 ],
-          [ "rs4477212",  "72017",  "1", {"AA"=>1}, {"A"=>2, "T"=>0, "G"=>0, "C"=>0}, 0 ]]
+        [ [ "rs11240777", "788822", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0 ],
+          [ "rs12124819", "766409", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0 ],
+          [ "rs3094315",  "742429", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0 ],
+          [ "rs3131972",  "742584", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0 ],
+          [ "rs4477212",  "72017",  "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0 ]]
 
       assert_equal expected, snp_data
 
@@ -52,19 +52,20 @@ class ParsingTest < ActiveSupport::TestCase
     end
 
     should "parse deCODEme data" do
-      Parsing.perform('genotype' => @genotype_decodeme.attributes)
+      FileUtils.cp @file_deCODEme, @temp_file
+      Parsing.perform(@genotype_decodeme.id, @temp_file)
 
       # Snp
       snp_data = Snp.all.map do |s|
         [ s.name, s.position, s.chromosome, s.genotype_frequency, s.allele_frequency, s.ranking ]
       end.sort_by { |s| s[0] }
 
       expected =
-        [ [ "rs11240767", "718814", "1", {"CC"=>1}, {"A"=>0, "T"=>0, "G"=>0, "C"=>2}, 0 ],
-          [ "rs2185539",  "556738", "1", {"CC"=>1}, {"A"=>0, "T"=>0, "G"=>0, "C"=>2}, 0 ],
-          [ "rs3094315",  "742429", "1", {"TT"=>1}, {"A"=>0, "T"=>2, "G"=>0, "C"=>0}, 0 ],
-          [ "rs4477212",  "72017",  "1", {"AA"=>1}, {"A"=>2, "T"=>0, "G"=>0, "C"=>0}, 0 ],
-          [ "rs6681105",  "581938", "1", {"TT"=>1}, {"A"=>0, "T"=>2, "G"=>0, "C"=>0}, 0 ]]
+        [ [ "rs11240767", "718814", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0],
+          [ "rs2185539",  "556738", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0],
+          [ "rs3094315",  "742429", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0],
+          [ "rs4477212",  "72017",  "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0],
+          [ "rs6681105",  "581938", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0] ]
 
       assert_equal expected, snp_data
 
@@ -80,31 +81,5 @@ class ParsingTest < ActiveSupport::TestCase
         assert snp_names.include?(s.snp_name)
       end
     end
-
-    context "existing Snps" do
-      setup do
-        [ "rs11240777", "rs12124819", "rs3094315", "rs3131972", "rs4477212" ].each_with_index do |snp_name|
-          Factory(:snp, name: snp_name)
-        end
-      end
-
-      should "be updated" do
-        Parsing.perform('genotype' => @genotype_23andme.attributes)
-        snps = Snp.all
-        assert_equal 5, snps.size
-        expected =
-          [ [ "rs11240777", {"AA"=>1, "AG"=>1}, {"A"=>1, "T"=>0, "G"=>1, "C"=>0} ],
-            [ "rs12124819", {"AA"=>1, "AG"=>1}, {"A"=>1, "T"=>0, "G"=>1, "C"=>0} ],
-            [ "rs3094315",  {"AA"=>2},          {"A"=>2, "T"=>0, "G"=>0, "C"=>0} ],
-            [ "rs3131972",  {"AA"=>1, "GG"=>1}, {"A"=>0, "T"=>0, "G"=>2, "C"=>0} ],
-            [ "rs4477212",  {"AA"=>2},          {"A"=>2, "T"=>0, "G"=>0, "C"=>0} ]]
-
-        # Snp
-        snp_data = snps.map do |s|
-          [ s.name, s.genotype_frequency, s.allele_frequency ]
-        end.sort_by { |s| s[0] }
-        assert_equal expected, snp_data
-      end
-    end
   end
 end