Formatting

spec/integration/genotype_parsing_spec.rb

@@ -14,39 +14,42 @@ describe 'genotype parsing' do
       create(:genotype, genotype_file_name: file.basename, filetype: '23andme')
     end
 
-    it "parse 23andMe data", truncate: true do
+    it 'parse 23andMe data', truncate: true do
       FileUtils.cp(file, temp_file)
       Parsing.new.perform(genotype.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] }
+        [s.name, s.position, s.chromosome, s.genotype_frequency,
+         s.allele_frequency, s.ranking]
+      end
+      snp_data = snp_data.sort_by { |s| s[0] }
 
-      expected =
-        [ [ "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 ]]
+      expected = [
+        ['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]
+      ]
 
-        expect(snp_data).to eq(expected)
+      expect(snp_data).to eq(expected)
 
-        # UserSnp
-        user_snps = UserSnp.all
-        user_snp_genotypes = user_snps.map(&:local_genotype)
-        expected_genotypes = %w[ AA AA GG AG AG ]
-        expect(user_snp_genotypes).to eq(expected_genotypes)
-        user_snps.each do |s|
-          expect(s.genotype_id).to eq(genotype.id)
-          expect(Snp.pluck(:name)).to include(s.snp_name)
-        end
+      # UserSnp
+      user_snps = UserSnp.all
+      user_snp_genotypes = user_snps.map(&:local_genotype)
+      expected_genotypes = %w(AA AA GG AG AG)
+      expect(user_snp_genotypes).to eq(expected_genotypes)
+      user_snps.each do |s|
+        expect(s.genotype_id).to eq(genotype.id)
+        expect(Snp.pluck(:name)).to include(s.snp_name)
+      end
     end
 
     # could put these deleting tests into their own file;
     # however, the genotyping exists at this point in time and we don't have to do any extra work
     # to pull it from the test DB
-    it "delete data" do
+    it 'delete data' do
       DeleteGenotype.new.perform(genotype)
       expect(Snp.count).to eq(0)
     end
@@ -58,36 +61,38 @@ describe 'genotype parsing' do
       create(:genotype, genotype_file_name: file.basename, filetype: 'decodeme')
     end
 
-    it "parse deCODEme data", truncate: true do
+    it 'parse deCODEme data', truncate: true do
       FileUtils.cp file, temp_file
       Parsing.new.perform(genotype.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, s.user_snps_count ]
+        [s.name, s.position, s.chromosome, s.genotype_frequency,
+         s.allele_frequency, s.ranking, s.user_snps_count]
       end.sort_by { |s| s[0] }
 
-      expected =
-        [ [ "rs11240767", "718814", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0, 1],
-          [ "rs2185539",  "556738", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0, 1],
-          [ "rs3094315",  "742429", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0, 1],
-          [ "rs4477212",  "72017",  "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0, 1],
-          [ "rs6681105",  "581938", "1", {}, {"A"=>0, "T"=>0, "G"=>0, "C"=>0}, 0, 1] ]
+      expected = [
+        ['rs11240767', '718814', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs2185539',  '556738', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs3094315',  '742429', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs4477212',  '72017',  '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1],
+        ['rs6681105',  '581938', '1', {}, { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 }, 0, 1]
+      ]
 
-        expect(snp_data).to eq(expected)
+      expect(snp_data).to eq(expected)
 
-        # UserSnp
-        user_snps = UserSnp.all
-        user_snp_genotypes = user_snps.map(&:local_genotype)
-        expected_genotypes = %w[ AA CC TT CC TT ]
-        expect(user_snp_genotypes).to eq(expected_genotypes)
-        user_snps.each do |s|
-          expect(s.genotype_id).to eq(genotype.id)
-          expect(Snp.pluck(:name)).to include(s.snp_name)
-        end
+      # UserSnp
+      user_snps = UserSnp.all
+      user_snp_genotypes = user_snps.map(&:local_genotype)
+      expected_genotypes = %w(AA CC TT CC TT)
+      expect(user_snp_genotypes).to eq(expected_genotypes)
+      user_snps.each do |s|
+        expect(s.genotype_id).to eq(genotype.id)
+        expect(Snp.pluck(:name)).to include(s.snp_name)
+      end
     end
 
-    it "delete deCODEme data" do
+    it 'delete deCODEme data' do
       DeleteGenotype.new.perform(genotype)
       expect(Snp.count).to eq(0)
     end