@@ -118,14 +187,7 @@
-
Deleting
-
Genotypes
- <% if not @user.genotypes.empty? %>
- <% @user.genotypes.each do |ug| %>
-
<%= link_to "Genotype #{ug.genotype_file_name}", ug, method: "delete", confirm: "Are you sure you want to delete genotype #{ug.genotype_file_name.to_s}?", class: "btn btn-default settings__deleting-button" %>
- <% end %>
- <% end %>
-
Account
+
Delete account
<%= link_to "Delete this account", @user, method: "delete", class: "btn btn-default settings__deleting-button", data: { confirm: 'Are you sure you want to delete your account?' } %>
diff --git a/app/workers/parsing.rb b/app/workers/parsing.rb
index 11617d3f..bbf5c877 100644
--- a/app/workers/parsing.rb
+++ b/app/workers/parsing.rb
@@ -1,7 +1,7 @@
# frozen_string_literal: true
class Parsing
include Sidekiq::Worker
- sidekiq_options queue: :user_snps, retry: 5, unique: true
+ sidekiq_options queue: :user_snps, retry: false, unique: true
attr_reader :genotype, :temp_table_name, :normalized_csv, :stats, :start_time
@@ -21,11 +21,13 @@ def perform(genotype_id)
send_logged(:insert_into_snps)
send_logged(:insert_into_user_snps)
end
+ genotype.update!(parse_status: 'done')
send_logged(:notify_user)
stats[:duration] = "#{(Time.current - start_time).round(3)}s"
logger.info("Finished parsing: #{stats.to_a.map { |s| s.join('=') }.join(', ')}")
rescue => e
+ genotype.update!(parse_status: 'error') unless genotype.parse_status == 'done'
logger.error("Failed with #{e.class}: #{e.message}")
raise
end
@@ -58,6 +60,7 @@ def normalize_csv
row[3].is_a?(String) && (1..2).include?(row[3].length)
end
@normalized_csv = csv.map { |row| row.join(',') }.join("\n")
+ raise(ParseError, 'No data found in file') if @normalized_csv.empty?
stats[:rows_after_parsing] = csv.length
end
@@ -234,4 +237,6 @@ def send_logged(method)
logger.info("calling of method `#{method}` took #{took} s")
ret
end
+
+ ParseError = Class.new(RuntimeError)
end
diff --git a/app/workers/preparsing.rb b/app/workers/preparsing.rb
index 0f4e2d16..2eee513a 100644
--- a/app/workers/preparsing.rb
+++ b/app/workers/preparsing.rb
@@ -4,11 +4,11 @@
class Preparsing
include Sidekiq::Worker
- # only retry 10 times - after that, the genotyping probably has already been deleted
- sidekiq_options queue: :preparse, retry: 10, unique: true
+ sidekiq_options queue: :preparse, retry: false, unique: true
def perform(genotype_id)
genotype = Genotype.find(genotype_id)
+ genotype.update!(parse_status: 'parsing')
logger.info "Starting preparse"
biggest = ''
@@ -28,8 +28,8 @@ def perform(genotype_id)
logger.info "copied file"
end
- rescue
- logger.info "nothing to unzip, seems to be a text-file in the first place"
+ rescue Zip::Error
+ logger.info 'nothing to unzip, seems to be a text-file in the first place'
end
# now that they are unzipped, check if they're actually proper files
@@ -112,19 +112,14 @@ def perform(genotype_id)
# not proper file!
if not file_is_ok
+ genotype.update!(parse_status: 'error')
if file_is_duplicate
UserMailer.duplicate_file(genotype.user_id).deliver_later
- system("rm #{Rails.root}/public/data/#{genotype.fs_filename}")
- Genotype.find_by_id(genotype.id).delete
elsif file_has_mails
UserMailer.file_has_mails(genotype.user_id).deliver
- system("rm #{Rails.root}/public/data/#{genotype.fs_filename}")
- Genotype.find_by_id(genotype.id).delete
else
UserMailer.parsing_error(genotype.user_id).deliver_later
logger.info "file is not ok, sending email"
- system("rm #{Rails.root}/public/data/#{genotype.fs_filename}")
- Genotype.find_by_id(genotype.id).delete
end
else
logger.info "Updating genotype with md5sum #{md5}"
@@ -134,5 +129,8 @@ def perform(genotype_id)
Parsing.perform_async(genotype.id)
end
+ rescue StandardError
+ genotype.update!(parse_status: 'error')
+ raise
end
end
diff --git a/config/locales/en.genotypes.yml b/config/locales/en.genotypes.yml
new file mode 100644
index 00000000..41e748de
--- /dev/null
+++ b/config/locales/en.genotypes.yml
@@ -0,0 +1,4 @@
+en:
+ genotypes:
+ create:
+ uploaded_successfully: 'Genotype was successfully uploaded! Parsing and annotating might take a couple of minutes.'
diff --git a/config/locales/en.users.yml b/config/locales/en.users.yml
new file mode 100644
index 00000000..1bc56797
--- /dev/null
+++ b/config/locales/en.users.yml
@@ -0,0 +1,12 @@
+en:
+ users:
+ edit:
+ genotypes:
+ confirm_delete: 'Are you sure you want to delete genotype %{file_name}?'
+ imported_snps: 'Imported SNPs'
+ upload_new: 'Upload new genotype'
+ parse_error_info: >
+ If the parse status shows %{error_label}, check if your uploaded file
+ looks alright and try again. Note: While zipped files (.zip) work,
+ gzipped ones (.gz) do not for now. If it still does not work,
+
contact us.
diff --git a/config/locales/en.yml b/config/locales/en.yml
index 250291ba..df82fae9 100644
--- a/config/locales/en.yml
+++ b/config/locales/en.yml
@@ -4,9 +4,15 @@
en:
hello: "Hello world"
activerecord:
+ attributes:
+ genotype:
+ created_at: 'Uploaded at'
errors:
models:
user_phenotype:
attributes:
phenotype:
taken: 'has already been entered.'
+ confirm_delete: 'Are you sure?'
+ delete: 'delete'
+ download: 'download'
diff --git a/config/routes.rb b/config/routes.rb
index ed8bfb48..c56ff998 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -18,7 +18,9 @@
end
end
resources :user_picture_phenotypes
- resources :genotypes
+ resources :genotypes do
+ get 'download', on: :member
+ end
resources :user_phenotypes
resources :snps
resources :users
diff --git a/db/migrate/20171231121548_add_parse_status_to_genotypes.rb b/db/migrate/20171231121548_add_parse_status_to_genotypes.rb
new file mode 100644
index 00000000..c7503042
--- /dev/null
+++ b/db/migrate/20171231121548_add_parse_status_to_genotypes.rb
@@ -0,0 +1,7 @@
+# frozen_string_literal: true
+
+class AddParseStatusToGenotypes < ActiveRecord::Migration
+ def change
+ add_column :genotypes, :parse_status, :string
+ end
+end
diff --git a/db/structure.sql b/db/structure.sql
index 23081466..57c6d620 100644
--- a/db/structure.sql
+++ b/db/structure.sql
@@ -501,7 +501,8 @@ CREATE TABLE genotypes (
genotype_file_name character varying(255),
genotype_content_type character varying(255),
genotype_file_size integer,
- genotype_updated_at timestamp without time zone
+ genotype_updated_at timestamp without time zone,
+ parse_status character varying
);
@@ -2169,3 +2170,5 @@ INSERT INTO schema_migrations (version) VALUES ('20161226175703');
INSERT INTO schema_migrations (version) VALUES ('20171113104813');
+INSERT INTO schema_migrations (version) VALUES ('20171231121548');
+
diff --git a/spec/features/delete_genotype_spec.rb b/spec/features/delete_genotype_spec.rb
index 0a153fd1..833a2152 100644
--- a/spec/features/delete_genotype_spec.rb
+++ b/spec/features/delete_genotype_spec.rb
@@ -1,5 +1,6 @@
# frozen_string_literal: true
-RSpec.feature 'Delete a genotype', sidekiq: :inline do
+
+RSpec.feature 'Delete a genotype', :js, sidekiq: :inline do
let(:user) { create(:user, name: 'Gregor Mendel') }
let!(:genotype) { create(:genotype, user: user, genotype_file_name: 'test.txt') }
let(:award) { Achievement.find_by(award: 'Published genotyping') }
@@ -16,8 +17,12 @@
click_on('Gregor Mendel')
click_on('Settings')
- click_on('Deleting')
- click_on('Genotype test.txt')
+ click_on('Your genotypes')
+ within('#genotypes') do
+ page.accept_confirm(
+ "Are you sure you want to delete genotype #{genotype.genotype_file_name}"
+ ) { find('[title="delete"]').click }
+ end
expect(page).to have_content('Your Genotyping will be deleted. ' \
'This may take a few minutes.')
diff --git a/spec/features/upload_genotype_spec.rb b/spec/features/upload_genotype_spec.rb
index a76f4c3e..1d16082d 100644
--- a/spec/features/upload_genotype_spec.rb
+++ b/spec/features/upload_genotype_spec.rb
@@ -7,12 +7,49 @@
sign_in(user)
end
+ let(:genotype) { Genotype.last }
+
scenario 'uploads first genotype' do
visit '/genotypes/new'
+
attach_file('genotype[genotype]', File.absolute_path('test/data/23andMe_test.csv'))
choose '23andme-format'
- click_on 'Upload'
- expect(page).to have_content('Genotype was successfully uploaded!')
- expect(page).to have_content("You've unlocked an achievement:")
+ Sidekiq::Testing.disable! do
+ click_on 'Upload'
+ expect(page).to have_content('Genotype was successfully uploaded!')
+ expect(page).to have_content("You've unlocked an achievement:")
+ end
+
+ expect(page).to have_content('Your genotypes')
+
+ within('#genotypes') do
+ expect(find_all('table tbody tr td').map(&:text)).to eq(
+ [
+ '23andme',
+ genotype.genotype_file_name,
+ genotype.created_at.to_s,
+ 'queued',
+ '0',
+ ''
+ ]
+ )
+ end
+
+ Preparsing.perform_async(genotype.id)
+
+ visit current_url
+
+ within('#genotypes') do
+ expect(find_all('table tbody tr td').map(&:text)).to eq(
+ [
+ '23andme',
+ genotype.genotype_file_name,
+ genotype.created_at.to_s,
+ 'done',
+ '5',
+ ''
+ ]
+ )
+ end
end
end
diff --git a/spec/spec_helper.rb b/spec/spec_helper.rb
index 3f086cbf..33dd7344 100644
--- a/spec/spec_helper.rb
+++ b/spec/spec_helper.rb
@@ -10,9 +10,8 @@
require 'factory_girl_rails'
require 'pry-rails' unless ENV['CI']
require 'authlogic/test_case'
-require 'capybara/poltergeist'
-Capybara.javascript_driver = :poltergeist
+Capybara.javascript_driver = :chrome_headless
# Requires supporting ruby files with custom matchers and macros, etc,
# in spec/support/ and its subdirectories.
diff --git a/spec/support/chrome_webdriver.rb b/spec/support/chrome_webdriver.rb
new file mode 100644
index 00000000..64978e74
--- /dev/null
+++ b/spec/support/chrome_webdriver.rb
@@ -0,0 +1,19 @@
+# frozen_string_literal: true
+
+require 'selenium/webdriver'
+
+Capybara.register_driver :chrome do |app|
+ Capybara::Selenium::Driver.new(app, browser: :chrome)
+end
+
+Capybara.register_driver :chrome_headless do |app|
+ capabilities = Selenium::WebDriver::Remote::Capabilities.chrome(
+ chromeOptions: { args: %w[headless disable-gpu] }
+ )
+
+ Capybara::Selenium::Driver.new(
+ app,
+ browser: :chrome,
+ desired_capabilities: capabilities
+ )
+end
diff --git a/spec/workers/parsing_spec.rb b/spec/workers/parsing_spec.rb
index 43e50a7b..673be66f 100644
--- a/spec/workers/parsing_spec.rb
+++ b/spec/workers/parsing_spec.rb
@@ -1,18 +1,53 @@
# frozen_string_literal: true
+
+# TODO: Add test cases for different filetypes.
describe Parsing do
- describe '#notify_user' do
- let(:mail) { double('mail') }
- let(:genotype) { double('genotype', id: 1) }
- let(:stats) { { foos: 7 } }
-
- it 'sends an email to the user' do
- subject.instance_variable_set(:@stats, stats)
- subject.instance_variable_set(:@genotype, genotype)
- expect(UserMailer).to receive(:finished_parsing).with(genotype.id, stats)
- .and_return(mail)
- expect(mail).to receive(:deliver_later)
-
- subject.notify_user
- end
+ let(:genotype) do
+ create(
+ :genotype,
+ genotype: File.open(File.absolute_path('test/data/23andMe_test.csv')),
+ filetype: '23andme',
+ parse_status: 'parsing'
+ )
+ end
+
+ let(:emails) do
+ ActionMailer::Base.deliveries
+ end
+
+ it 'parses a 23andme file' do
+ described_class.new.perform(genotype.id)
+
+ genotype.reload
+
+ expect(genotype.user_snps.count).to eq(5)
+ expect(
+ genotype
+ .user_snps
+ .order(:snp_name)
+ .pluck(:genotype_id, :snp_name, :local_genotype)
+ ).to eq(
+ [
+ [genotype.id, 'rs11240777', 'AG'],
+ [genotype.id, 'rs12124819', 'AG'],
+ [genotype.id, 'rs3094315', 'AA'],
+ [genotype.id, 'rs3131972', 'GG'],
+ [genotype.id, 'rs4477212', 'AA']
+ ]
+ )
+ expect(genotype.parse_status).to eq('done')
+
+ expect(emails.count).to eq(1)
+ expect(emails.first.subject).to eq('Finished parsing your genotyping')
+ end
+
+ it 'sets the parse status to "error" if parsing failed' do
+ genotype.update!(genotype: StringIO.new('💥'))
+
+ expect do
+ described_class.new.perform(genotype.id)
+ end.to raise_error(Parsing::ParseError, 'No data found in file')
+
+ expect(genotype.reload.parse_status).to eq('error')
end
end
diff --git a/spec/workers/preparsing_spec.rb b/spec/workers/preparsing_spec.rb
new file mode 100644
index 00000000..4d91cddc
--- /dev/null
+++ b/spec/workers/preparsing_spec.rb
@@ -0,0 +1,50 @@
+# frozen_string_literal: true
+
+RSpec.describe Preparsing do
+ context 'when the genotype is valid' do
+ let(:genotype) do
+ create(
+ :genotype,
+ genotype: File.open(File.absolute_path('test/data/23andMe_test.csv')),
+ filetype: '23andme',
+ parse_status: 'queued'
+ )
+ end
+
+ it "updates the genotype's parse status" do
+ described_class.new.perform(genotype.id)
+
+ expect(genotype.reload.parse_status).to eq('parsing')
+ end
+ end
+
+ context 'when the genotype file is faulty' do
+ let(:genotype) do
+ create(:genotype, genotype: StringIO.new('XXX'))
+ end
+
+ it "updates the genotype's parse status" do
+ described_class.new.perform(genotype.id)
+
+ expect(genotype.reload.parse_status).to eq('error')
+ end
+ end
+
+ context 'when the worker raises an error' do
+ let(:genotype) do
+ create(:genotype)
+ end
+
+ before do
+ expect(File).to receive(:open).and_raise('Meh.')
+ end
+
+ it "updates the genotype's parse status" do
+ expect do
+ described_class.new.perform(genotype.id)
+ end.to raise_error('Meh.')
+
+ expect(genotype.reload.parse_status).to eq('error')
+ end
+ end
+end
diff --git a/test/functional/genotypes_controller_test.rb b/test/functional/genotypes_controller_test.rb
index 01d1fd59..f92d52d6 100644
--- a/test/functional/genotypes_controller_test.rb
+++ b/test/functional/genotypes_controller_test.rb
@@ -62,7 +62,7 @@ class GenotypesControllerTest < ActionController::TestCase
{ genotype: genotype_file, filetype: "23andme"}
end
end
- assert_redirected_to user_path(@user)
+ assert_redirected_to edit_user_path(@user, anchor: 'genotypes')
assert_equal @publishing_award.id, UserAchievement.last.achievement_id
FileUtils.rm("#{Rails.root}/test/fixtures/testdatensatz1_23andme.txt")
end