sequenceserver 1.1.0.beta2 → 1.1.0.beta3

data/sequenceserver.gemspec

@@ -28,8 +28,9 @@ DESC
   s.add_development_dependency('rspec', '~> 3.7',  '>= 3.7.0')
   s.add_development_dependency('capybara', '~> 2.18',  '>= 2.18.0')
   s.add_development_dependency('rack-test', '~> 1.0',  '>= 1.0.0')
+  s.add_development_dependency('sauce_whisk', '~> 0.0', '>= 0.0.19')
   s.add_development_dependency('selenium-webdriver', '~> 3.11', '>= 3.11.0')
-  s.add_development_dependency('codeclimate-test-reporter', '~> 0.6', '>= 0.6.0')
+  s.add_development_dependency('codeclimate-test-reporter', '~> 1.0', '>= 1.0.8')
 
   # gem
   s.files         = `git ls-files`.split("\n") - ['Gemfile', 'Gemfile.lock']

data/spec/capybara_spec.rb

@@ -1,51 +1,150 @@
 require 'spec_helper'
+require 'sauce_whisk'
+require 'capybara/rspec'
+require 'selenium-webdriver'
 
-# Cause the test to fail if Capybara is not available
-exit! unless $capybara_available
+RSpec.configure do |config|
+  config.include Capybara::DSL
+end
 
 describe 'a browser', :js => true do
-  sequence = 'ATCGATCAGCTACGATCAGCATCGACTAGCATCGACTACGA'
-  sample_nucl_db = 'Sinvicta 2-2-3 cdna subset'
-  # sample_prot_db = 'Sinvicta2-2-3.prot'
-
-  before do
+  before do |scenario|
     Capybara.app = SequenceServer.init
     Capybara.javascript_driver = :selenium
+
+    Capybara.register_driver :selenium do |app|
+      capabilities = {
+        name: scenario.full_description,
+        platform: ENV['platform'],
+        browserName: ENV['browserName'],
+        browserVersion: ENV['browserVersion'],
+        build: ENV['TRAVIS_BUILD_NUMBER'],
+        'tunnel-identifier': ENV['TRAVIS_JOB_NUMBER']
+      }
+      url = "https://#{ENV['SAUCE_USERNAME']}:#{ENV['SAUCE_ACCESS_KEY']}" \
+        "@ondemand.saucelabs.com:443/wd/hub".strip
+
+      Capybara::Selenium::Driver.new(app, browser: :remote, url: url,
+                                     desired_capabilities: capabilities)
+    end
   end
 
-  it 'runs a simple blastn search' do
-    visit '/'
-    fill_in('sequence', with: sequence, wait: 5)
-    check(sample_nucl_db)
-    click_button('method')
-    # switch to new window because link opens in new window
-    page.driver.browser.switch_to.window(page.driver.browser.window_handles.last)
-    page.should have_content('Query', wait: 5)
+  before :each do |scenario|
+    jobname = scenario.full_description
+    Capybara.session_name = "#{jobname} - #{ENV['platform']} - " +
+      "#{ENV['browserName']} - #{ENV['browserVersion']}"
+
+      @driver = Capybara.current_session.driver
+
+      # Output sessionId and jobname to std out for Sauce OnDemand Plugin to
+      # display embeded results
+      @session_id = @driver.browser.session_id
+      puts "SauceOnDemandSessionID=#{@session_id} job-name=#{jobname}"
   end
 
   it 'properly controls blast button' do
     visit '/'
 
-    fill_in('sequence', :with => sequence)
+    fill_in('sequence', with: nucleotide_query, wait: 5)
     page.evaluate_script("$('#method').is(':disabled')").should eq(true)
 
-    check(sample_nucl_db)
+    check(nucleotide_databases.first)
     page.evaluate_script("$('#method').is(':disabled')").should eq(false)
   end
 
   it 'properly controls interaction with database listing' do
     visit '/'
-    fill_in('sequence', :with => sequence)
-    check(sample_nucl_db)
+    fill_in('sequence', with: nucleotide_query, wait: 5)
+    check(nucleotide_databases.first)
     page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
       .should eq(true)
   end
 
   it 'shows a dropdown menu when other blast methods are available' do
     visit '/'
-    fill_in('sequence', :with => sequence)
-    check(sample_nucl_db)
+    fill_in('sequence', with: nucleotide_query, wait: 5)
+    check(nucleotide_databases.first)
     page.save_screenshot('screenshot.png')
     page.has_css?('button.dropdown-toggle').should eq(true)
   end
+
+  it 'can run a simple blastn search' do
+    perform_search query: nucleotide_query,
+      databases: nucleotide_databases
+  end
+
+  it 'can run a simple blastp search' do
+    perform_search query: protein_query,
+      databases: protein_databases
+  end
+
+  it 'can run a simple blastx search' do
+    perform_search query: nucleotide_query,
+      databases: protein_databases
+  end
+
+  it 'can run a simple tblastx search' do
+    perform_search query: nucleotide_query,
+      databases: nucleotide_databases,
+      method: 'tblastx'
+  end
+
+  it 'can run a simple tblastn search' do
+    perform_search query: protein_query,
+      databases: nucleotide_databases
+  end
+
+  after :each do |scenario|
+    @driver.quit
+    Capybara.use_default_driver
+    if scenario.exception
+      SauceWhisk::Jobs.fail_job @session_id
+    else
+      SauceWhisk::Jobs.pass_job @session_id
+    end
+  end
+
+  ## Helpers ##
+
+  def perform_search(query: , databases: , method: nil)
+    # Load search form.
+    visit '/'
+
+    # Fill in query, select databases, submit form.
+    fill_in('sequence', with: query, wait: 5)
+    databases.each { |db| check db }
+    if method == 'tblastx'
+      find('.dropdown-toggle').click
+      find('.dropdown-menu li').click
+    end
+    click_button('method')
+
+    # switch to new window because link opens in new window
+    page.driver.browser.switch_to.window(page.driver.browser.window_handles.last)
+
+    # Check that results loaded.
+    page.should have_content('Query', wait: 10)
+  end
+
+  def nucleotide_query
+    File.read File.join __dir__, 'nucleotide_query.fa'
+  end
+
+  def protein_query
+    File.read File.join __dir__, 'protein_query.fa'
+  end
+
+  def nucleotide_databases
+    [
+      'Solenopsis invicta gnG subset',
+      'Sinvicta 2-2-3 cdna subset'
+    ]
+  end
+
+  def protein_databases
+    [
+      'Sinvicta 2-2-3 prot subset',
+      '2018-04 Swiss-Prot insecta'
+    ]
+  end
 end

data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd

@@ -0,0 +1,8 @@
+20800950682
+27659162461
+32306292125
+32590696114
+36652027840
+36720233313
+5917078937
+7230465466

data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd

@@ -0,0 +1,16 @@
+nw_0117949335
+nw_011794933.15
+nw_0117952763
+nw_011795276.13
+nw_0117968480
+nw_011796848.10
+nw_0117969511
+nw_011796951.11
+nw_0117981057
+nw_011798105.17
+nw_0117982564
+nw_011798256.14
+nw_0118003602
+nw_011800360.12
+nw_0118046886
+nw_011804688.16

data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt

@@ -0,0 +1,8 @@
+NW_011796848.1	6355204
+NW_011796951.1	6173698
+NW_011800360.1	5918258
+NW_011795276.1	5092386
+NW_011798256.1	4342353
+NW_011794933.1	4234449
+NW_011804688.1	3708818
+NW_011798105.1	3360376