Refactor ZipGenotypingFiles (#527)

.rubocop.yml

@@ -22,3 +22,7 @@ Style/FrozenStringLiteralComment:
 
 Metrics/LineLength:
   Max: 100
+
+Metrics/BlockLength:
+  Exclude:
+    - 'spec/**/*.rb'

app/controllers/phenotypes_controller.rb

@@ -123,8 +123,11 @@ def feed
   end
 
   def get_genotypes
-    Sidekiq::Client.enqueue(Zipgenotypingfiles, params[:id],
-                            params[:variation], current_user.email)
+    ZipGenotypingFiles.perform_async(
+      params[:id],
+      params[:variation],
+      current_user.email
+    )
     @phenotype = Phenotype.find(params[:id])
     @variation = params[:variation]
   end

app/workers/zip_genotyping_files.rb

@@ -0,0 +1,81 @@
+# frozen_string_literal: true
+
+class ZipGenotypingFiles
+  include Sidekiq::Worker
+  sidekiq_options queue: :zipgenotyping, retry: 5, unique: true
+
+  def perform(phenotype_id, variation, target_address)
+    @phenotype = Phenotype.find(phenotype_id)
+    @variation = variation
+    @target_address = target_address
+    @time = Time.current.to_s.tr(':', '_')
+
+    if genotypes.empty?
+      send_no_results
+    else
+      zip_genotypes
+      send_results
+    end
+  end
+
+  def zip_genotypes
+    return if File.exist?(zip_file_path)
+
+    Zip::File.open(zip_file_path, Zip::File::CREATE) do |zipfile|
+      genotypes.each do |genotype|
+        zipfile.add(
+          zipped_file_name(genotype),
+          Rails.root.join('public', 'data', genotype.fs_filename)
+        )
+      end
+    end
+    File.chmod(0o777, zip_file_path)
+  end
+
+  def send_results
+    UserMailer.genotyping_results(
+      target_address,
+      zip_file_path.to_s,
+      phenotype.characteristic,
+      variation
+    ).deliver_later
+  end
+
+  def zipped_file_name(genotype)
+    "user#{genotype.user_id}_file#{genotype.id}_yearofbirth" \
+      "#{genotype.user.yearofbirth}_sex#{genotype.user.sex}.#{genotype.filetype}.txt"
+  end
+
+  def send_no_results
+    UserMailer.no_genotyping_results(
+      target_address,
+      phenotype.characteristic,
+      variation
+    ).deliver_later
+  end
+
+  private
+
+  attr_reader :phenotype, :variation, :target_address, :time
+
+  def genotypes
+    @genotypes ||= user_phenotypes.includes(:user).flat_map do |user_phenotype|
+      user_phenotype.user.genotypes
+    end
+  end
+
+  def user_phenotypes
+    UserPhenotype
+      .where(phenotype_id: phenotype.id)
+      .search(variation)
+  end
+
+  def zip_file_path
+    @zip_file_path ||= Rails.root.join(
+      'public',
+      'data',
+      'zip',
+      "#{phenotype.id}.#{time.to_s.tr(' ', '_')}.zip"
+    )
+  end
+end

spec/factories/achievements.rb

@@ -2,6 +2,6 @@
 
 FactoryBot.define do
   factory :achievement do
-    award 'Foooooooo'
+    award { 'Foooooooo' }
   end
 end

spec/factories/fitbit_activities.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   factory :fitbit_activity do
-    steps 100
-    floors 1
+    steps { 100 }
+    floors { 1 }
   end
 end

spec/factories/fitbit_bodies.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   factory :fitbit_body do
-    weight '100'
-    bmi '200'
+    weight { '100' }
+    bmi { '200' }
   end
 end

spec/factories/fitbit_sleeps.rb

@@ -2,9 +2,9 @@
 
 FactoryBot.define do
   factory :fitbit_sleep do
-    minutes_asleep 480
-    minutes_awake 10
-    number_awakenings 1
-    minutes_to_sleep 10
+    minutes_asleep { 480 }
+    minutes_awake { 10 }
+    number_awakenings { 1 }
+    minutes_to_sleep { 10 }
   end
 end

spec/factories/genome_gov_papers.rb

@@ -2,6 +2,6 @@
 
 FactoryBot.define do
   factory :genome_gov_paper do
-    title 'A Genome.gov Paper'
+    title { 'A Genome.gov Paper' }
   end
 end

spec/factories/genotypes.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   factory :genotype do
-    genotype_file_name 'foo.txt'
+    genotype_file_name { 'foo.txt' }
     user
   end
 end

spec/factories/mendeley_papers.rb

@@ -2,11 +2,11 @@
 
 FactoryBot.define do
   factory :mendeley_paper do
-    title 'Musterstudie'
+    title { 'Musterstudie' }
     uuid { UUIDTools::UUID.random_create.to_s }
-    first_author 'Max Mustermann'
-    mendeley_url 'http://example.com'
-    doi '10.1000/182'
-    pub_year 2013
+    first_author { 'Max Mustermann' }
+    mendeley_url { 'http://example.com' }
+    doi { '10.1000/182' }
+    pub_year { 2013 }
   end
 end

spec/factories/messages.rb

@@ -3,8 +3,8 @@
 FactoryBot.define do
   factory :message do
     user
-    sent false
-    subject 'HELLO WORLD'
-    body 'THIS IS AN AWESOME MESSAGE'
+    sent { false }
+    subject { 'HELLO WORLD' }
+    body { 'THIS IS AN AWESOME MESSAGE' }
   end
 end

spec/factories/phenotypes.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   factory :phenotype do
-    characteristic 'Penis length'
+    characteristic { 'Penis length' }
 
     factory :phenotype_with_users do
       after :create do |t|

spec/factories/picture_phenotypes.rb

@@ -2,6 +2,6 @@
 
 FactoryBot.define do
   factory :picture_phenotype do
-    characteristic 'Eye color'
+    characteristic { 'Eye color' }
   end
 end

spec/factories/plos_papers.rb

@@ -2,6 +2,6 @@
 
 FactoryBot.define do
   factory :plos_paper do
-    title 'A PLOS Paper'
+    title { 'A PLOS Paper' }
   end
 end

spec/factories/snp_comments.rb

@@ -2,9 +2,9 @@
 
 FactoryBot.define do
   factory :snp_comment do
-    comment_text 'This is a great SNP!'
-    subject 'Great!'
-    user_id 1
-    snp_id 1
+    comment_text { 'This is a great SNP!' }
+    subject { 'Great!' }
+    user_id { 1 }
+    snp_id { 1 }
   end
 end

spec/factories/snpedia_papers.rb

@@ -2,6 +2,6 @@
 
 FactoryBot.define do
   factory :snpedia_paper do
-    url 'http://www.snpedia.com/index.php/Rs1234(A;C)'
+    url { 'http://www.snpedia.com/index.php/Rs1234(A;C)' }
   end
 end

spec/factories/snps.rb

@@ -5,8 +5,8 @@
     sequence(:name) { |i| "rs#{i}" }
     sequence(:position) { |i| i }
     sequence(:chromosome) { |i| i }
-    genotype_frequency('AA' => 1)
-    allele_frequency('A' => 0, 'T' => 0, 'G' => 0, 'C' => 0)
-    ranking 0
+    genotype_frequency { { 'AA' => 1 } }
+    allele_frequency { { 'A' => 0, 'T' => 0, 'G' => 0, 'C' => 0 } }
+    ranking { 0 }
   end
 end

spec/factories/user_phenotypes.rb

@@ -4,6 +4,6 @@
   factory :user_phenotype do
     association :user
     association :phenotype
-    variation 'pink'
+    variation { 'pink' }
   end
 end

spec/factories/user_picture_phenotypes.rb

@@ -2,6 +2,6 @@
 
 FactoryBot.define do
   factory :user_picture_phenotype do
-    variation 'pink'
+    variation { 'pink' }
   end
 end

spec/factories/user_snps.rb

@@ -2,7 +2,7 @@
 
 FactoryBot.define do
   factory :user_snp do
-    local_genotype 'AG'
+    local_genotype { 'AG' }
     genotype
     user
     snp

spec/factories/users.rb

@@ -2,11 +2,11 @@
 
 FactoryBot.define do
   factory :user do
-    name 'Dogbert'
+    name { 'Dogbert' }
     sequence(:email) { |i| "fubert#{i}@example.org" }
-    password 'strengjeheim'
-    password_confirmation 'strengjeheim'
-    sex 'yes please'
-    yearofbirth '1970'
+    password { 'strengjeheim' }
+    password_confirmation { 'strengjeheim' }
+    sex { 'yes please' }
+    yearofbirth { '1970' }
   end
 end