capybara_spec.rb in sequenceserver-2.0.0.beta3

- old
+ new

@@ -1,51 +1,6 @@
-require 'spec_helper'
-require 'sauce_whisk'
-require 'capybara/rspec'
-require 'selenium-webdriver'
-
-RSpec.configure do |config|
-  config.include Capybara::DSL
-end
-
-describe 'a browser', :js => true do
-  before do |scenario|
-    Capybara.app = SequenceServer.init
-    Capybara.server = :webrick
-    Capybara.javascript_driver = :selenium
-    Capybara.default_max_wait_time = 30
-
-    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
-
-  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
-
+describe 'a browser', type: :feature, js: true do
   it 'properly controls blast button' do
     visit '/'
 
     fill_in('sequence', with: nucleotide_query)
     page.evaluate_script("$('#method').is(':disabled')").should eq(true)
@@ -71,43 +26,272 @@
   end
 
   it 'can run a simple blastn search' do
     perform_search query: nucleotide_query,
       databases: nucleotide_databases
+    page.should have_content('BLASTN')
   end
 
   it 'can run a simple blastp search' do
     perform_search query: protein_query,
       databases: protein_databases
+    page.should have_content('BLASTP')
   end
 
   it 'can run a simple blastx search' do
     perform_search query: nucleotide_query,
       databases: protein_databases
+    page.should have_content('BLASTX')
   end
 
   it 'can run a simple tblastx search' do
     perform_search query: nucleotide_query,
       databases: nucleotide_databases,
       method: 'tblastx'
+    page.should have_content('TBLASTX')
   end
 
   it 'can run a simple tblastn search' do
     perform_search query: protein_query,
       databases: nucleotide_databases
+    page.should have_content('TBLASTN')
   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
+  ### Test aspects of the generated report.
+
+  it "can download FASTA of each hit" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click on the first FASTA download button on the page and wait for the
+    # download to finish.
+    page.execute_script("$('.download-fa:eq(0)').click()")
+    wait_for_download
+
+    # Test name and content of the downloaded file.
+    expect(File.basename(downloaded_file)).
+      to eq('sequenceserver-SI2.2.0_06267.fa')
+    expect(File.read(downloaded_file)).
+      to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
+  end
+
+  it "can download FASTA of selected hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Select first hit for each query and click 'FASTA of 2 selected hits'.
+    page.check('Query_1_hit_1_checkbox')
+    page.check('Query_2_hit_1_checkbox')
+    page.click_link('FASTA of 2 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+  end
+
+  it "can download FASTA of all hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click 'FASTA of all hits'.
+    page.click_link('FASTA of all hits')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+  end
+
+  it "can download alignment for each hit" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+
+    # Test name and content of the downloaded file.
+    expect(File.basename(downloaded_file)).to eq('Query_1_SI2_2_0_06267.txt')
+    expect(File.read(downloaded_file)).
+      to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
+  end
+
+  it "can download Alignment of selected hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Select first hit for each query and click 'Alignment of 2 selected hits'.
+    page.check('Query_1_hit_1_checkbox')
+    page.check('Query_2_hit_1_checkbox')
+    page.click_link('Alignment of 2 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+  end
+
+  it "can download Alignment of all hits" do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click 'Alignment of all hits'.
+    page.click_link('Alignment of all hits')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+  end
+
+  it 'can download BLAST results in XML and tabular formats' do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    page.click_link('Standard tabular report')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-std_tsv_report.tsv')
+    clear_downloads
+
+    page.click_link('Full tabular report')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-full_tsv_report.tsv')
+    clear_downloads
+
+    page.click_link('Full XML report')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sequenceserver-xml_report.xml')
+    clear_downloads
+  end
+
+  it 'can show hit sequences in a modal' do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    # Click on the first sequence viewer link in the report.
+    page.execute_script("$('.view-sequence:eq(0)').click()")
+
+    within('.sequence-viewer') do
+      page.should have_content('SI2.2.0_06267')
+      page.should have_content(<<~SEQ.chomp)
+        MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIP
+        LAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPIS
+        CRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITD
+        ITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPL
+        YMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+      SEQ
     end
+
+    # Dismiss the first modal.
+    page.execute_script("$('.sequence-viewer').modal('hide')")
+
+    # Click on the second sequence viewer link in the report.
+    page.execute_script("$('.view-sequence:eq(1)').click()")
+
+    within('.sequence-viewer') do
+      page.should have_content('SI2.2.0_13722')
+      page.should have_content(<<~SEQ.chomp)
+        MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSA
+        VSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNK
+        RHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVS
+        EMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYR
+        RESRGIHEECCINGCTINELTSYCGP
+      SEQ
+    end
   end
 
+  it 'disables sequence viewer links if hits are longer than 10kb' do
+    # BLASTN transcripts against genome. nucleotide_query refers to two fire
+    # ant transcripts and nucleotide_databases[0] is subset of the fire ant
+    # genome (few longest scaffolds). We expect sequence viewer links to be
+    # disabled for all hits of this search.
+    perform_search(query: nucleotide_query,
+                   databases: nucleotide_databases.values_at(0))
+
+    # Check that the sequence viewer links are disabled.
+    page.evaluate_script("$('.view-sequence').is(':disabled')").should eq(true)
+  end
+
+  it 'can download visualisations in svg and png format' do
+    # Do a BLASTP search. protein_query refers to the first two sequence in
+    # protein_databases[0], so the top hits are the query sequences themselves.
+    perform_search(query: protein_query,
+                   databases: protein_databases.values_at(0))
+
+    ## Check that there is a circos vis and unfold it.
+    page.should have_content('Circos')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+    clear_downloads
+
+
+    ## Check that there is a graphical overview of hits.
+    page.should have_content('Graphical overview of hits')
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
+    clear_downloads
+
+
+    ## Check that there is a length distribution of hits.
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-svg:eq(2)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(2)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-Query_1.png')
+    clear_downloads
+
+    ## Check that there is a kablammo vis of query vs hit.
+    page.should have_content('Graphical overview of aligning region(s)')
+
+    page.execute_script("$('.export-to-svg:eq(3)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.svg')
+    clear_downloads
+
+    page.execute_script("$('.export-to-png:eq(3)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-Query_1-SI2_2_0_06267.png')
+    clear_downloads
+  end
+
   ## Helpers ##
 
   def perform_search(query: , databases: , method: nil)
     # Load search form.
     visit '/'
@@ -119,22 +303,23 @@
       find('.dropdown-toggle').click
       find('.dropdown-menu li').click
     end
     click_button('method')
 
-    # switch to new window because link opens in new window
+    # 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.
+    # It is important to have this line or the examples end prematurely with a
+    # failure.
     page.should have_content('Query')
   end
 
   def nucleotide_query
-    File.read File.join __dir__, 'nucleotide_query.fa'
+    File.read File.join(__dir__, 'sequences', 'nucleotide_query.fa')
   end
 
   def protein_query
-    File.read File.join __dir__, 'protein_query.fa'
+    File.read File.join(__dir__, 'sequences', 'protein_query.fa')
   end
 
   def nucleotide_databases
     [
       'Solenopsis invicta gnG subset',