sequenceserver 2.0.0.beta3 → 2.0.0.beta4

data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb

@@ -32,9 +32,9 @@ module SequenceServer
     no_hits_report = BLAST::Report.new(no_hits)
 
     it 'will return queries with valid length' do
-      hits_report.queries.first.length.should be_a Fixnum
+      hits_report.queries.first.length.should be_a Integer
       hits_report.queries.first.length.should satisfy { |n| n > 0 }
-      no_hits_report.queries.first.length.should be_a Fixnum
+      no_hits_report.queries.first.length.should be_a Integer
       no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
     end
 
@@ -79,45 +79,45 @@ module SequenceServer
     # Test Random HSPs to ensure that all the values from HSP struct are valid.
     it 'have correct alignment values' do
       hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
-      hits_report.queries.last.hits.first.hsps.last.score.should be_a Fixnum
+      hits_report.queries.last.hits.first.hsps.last.score.should be_a Integer
 
       hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
       hits_report.queries.first.hits.first.hsps.first.evalue
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Fixnum
+      hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Integer
       hits_report.queries.first.hits.last.hsps.first.qstart
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.first.hits.last.hsps.first.qend.should be_a Fixnum
+      hits_report.queries.first.hits.last.hsps.first.qend.should be_a Integer
       hits_report.queries.first.hits.last.hsps.first.qend
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Fixnum
+      hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Integer
       hits_report.queries.last.hits.last.hsps.last.sstart
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.first.hits.first.hsps.last.send.should be_a Fixnum
+      hits_report.queries.first.hits.first.hsps.last.send.should be_a Integer
       hits_report.queries.first.hits.first.hsps.last.send
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Fixnum
-      hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Fixnum
+      hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Integer
+      hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Integer
 
-      hits_report.queries.first.hits.first.hsps.last.identity.should be_a Fixnum
+      hits_report.queries.first.hits.first.hsps.last.identity.should be_a Integer
       hits_report.queries.first.hits.first.hsps.last.identity
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Fixnum
+      hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Integer
       hits_report.queries.first.hits.first.hsps.last.gaps
         .should_not satisfy { |n| n < 0 }
 
       hits_report.queries.first.hits.first.hsps.last.positives
-        .should be_a Fixnum
+        .should be_a Integer
       hits_report.queries.first.hits.first.hsps.last.positives
         .should_not satisfy { |n| n < 0 }
 
-      hits_report.queries.first.hits.first.hsps.last.length.should be_a Fixnum
+      hits_report.queries.first.hits.first.hsps.last.length.should be_a Integer
       hits_report.queries.first.hits.first.hsps.last.length
         .should satisfy { |n| n > 0 }
 

data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb

@@ -1,53 +1,585 @@
-require 'spec_helper'
-require 'sauce_whisk'
-require 'capybara/rspec'
-require 'selenium-webdriver'
+describe 'report generated from imported XML',type: :feature, js: true do
 
-RSpec.configure do |config|
-  config.include Capybara::DSL
-end
+  # Test suite to test features of imported XML report. Fasta files used for
+  # testing consist of TP53 and COX41 protein/nucleotide sequences for
+  # reproducibility. Each query was limited to 20 hits to not to overload the
+  # test suite.
+
+  # BLASTP test scenarios
+  it 'loads BLASTP XML and tests hit alignment and sidebar Alignment download' do
+    access_by_uuid('blast_2.9.0/blastp')
+
+    # Click on the first hit Alignment download button on the page and wait for
+    # the download to finish.
+
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt"))
+
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-40_hits_blastp.txt"))
+
+    clear_downloads
+
+    # Check the cheboxes of indicted hits and click on the download of Alignment
+    # of selected hits and compare the downloaded content
+
+    page.check('Query_1_hit_1_checkbox')
+    page.check('Query_1_hit_2_checkbox')
+    page.check('Query_2_hit_1_checkbox')
+    page.check('Query_2_hit_2_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-4_hits_blastp.txt"))
+  end
+
+  it 'loads BLASTP XML and tests alignment overview and hit PNG/SVG download' do
+    access_by_uuid('blast_2.9.0/blastp')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
+
+    clear_downloads
+
+    # Click on the PNG/SVG download button of the first hit available and
+    # compare the downloaded content.
 
-describe 'report generated from imported XML', :js => true do
-  before do |scenario|
-    Capybara.app = SequenceServer.init
-    Capybara.server = :webrick
-    Capybara.javascript_driver = :selenium
-    Capybara.default_max_wait_time = 10
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.png')
 
-   Capybara.register_driver :selenium do |app|
-     options = ::Selenium::WebDriver::Firefox::Options.new
-     options.args << '--headless'
-    Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
-    end
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.svg')
+    page.should have_content('BLASTP')
   end
 
-  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
-  it 'loads BLASTP xml output' do
+  it 'loads BLASTP XML and tests Circos download' do
     access_by_uuid('blast_2.9.0/blastp')
+
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+  end
+
+  it 'loads BLASTP XML and tests Length distribution download' do
+    access_by_uuid('blast_2.9.0/blastp')
+
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
+  end
+
+  # BLASTX test scenarios
+
+  it 'loads BLASTX XML and tests hit alignment and sidebar Alignment download' do
+    access_by_uuid('blast_2.9.0/blastx')
+
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783307_gb_AYF55702_1.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt"))
+
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-40_hits_blastx.txt"))
+
+    clear_downloads
+
+    # Select four hit checkboxes and click on the Alignment of selected hits.
+    # Compare the downloaded content.
+
+    page.check('Query_1_hit_3_checkbox')
+    page.check('Query_1_hit_4_checkbox')
+    page.check('Query_2_hit_3_checkbox')
+    page.check('Query_2_hit_4_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-4_hits_blastx.txt"))
+
+    page.should have_content('BLASTX')
+  end
+
+  it 'loads BLASTX XML and tests hit PNG/SVG download' do
+    access_by_uuid('blast_2.9.0/blastx')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
+
+    clear_downloads
+
+    # Click on the PNG/SVG download button of the first hit available and
+    # compare the downloaded content.
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.svg')
+    page.should have_content('BLASTX')
+  end
+
+  it 'loads BLASTX XML and tests Circos download' do
+    access_by_uuid('blast_2.9.0/blastx')
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
   end
 
-  it 'loads BLASTX xml output' do
+  it 'loads BLASTX XML and tests Length distribution download' do
     access_by_uuid('blast_2.9.0/blastx')
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
   end
 
-  it 'loads BLASTN xml output' do
+  # BLASTN Test scenarios
+
+  it 'loads BLASTN XML and tests hit alignment and sidebar Alignment download' do
     access_by_uuid('blast_2.9.0/blastn')
+    # 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
+    expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt"))
+
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-40_hits_blastn.txt"))
+
+    clear_downloads
+
+    # Select four hit checkboxes and click on the Alignment of selected hits.
+    # Compare the downloaded content.
+    page.check('Query_1_hit_5_checkbox')
+    page.check('Query_1_hit_6_checkbox')
+    page.check('Query_2_hit_5_checkbox')
+    page.check('Query_2_hit_6_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-4_hits_blastn.txt"))
+    page.should have_content('BLASTN')
   end
 
-  it 'loads TBLASTN xml output' do
+  it 'loads BLASTN XML and tests hit PNG/SVG download' do
+    access_by_uuid('blast_2.9.0/blastn')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
+
+    clear_downloads
+    # Click on the PNG download button of the first hit available and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-png:eq(2)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.png')
+
+    clear_downloads
+
+    # Click on the SVG download button of the first hit available and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-svg:eq(2)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
+    page.should have_content('BLASTN')
+  end
+
+  it 'loads BLASTN XML and tests Circos download' do
+    access_by_uuid('blast_2.9.0/blastn')
+
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+  end
+
+  it 'loads BLASTN XML and tests Length distribution download' do
+    access_by_uuid('blast_2.9.0/blastn')
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
+  end
+
+  #TBLASTN Test scenarios
+
+  it 'loads TBLASTN XML and tests hit alignment and sidebar Alignment download' do
+    access_by_uuid('blast_2.9.0/tblastn')
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt"))
+
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-40_hits_tblastn.txt"))
+
+    clear_downloads
+
+    # Select four hit checkboxes and click on the Alignment of selected hits.
+    # Compare the downloaded content.
+    page.check('Query_1_hit_7_checkbox')
+    page.check('Query_1_hit_8_checkbox')
+    page.check('Query_2_hit_7_checkbox')
+    page.check('Query_2_hit_8_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-4_hits_tblastn.txt"))
+    page.should have_content('TBLASTN')
+  end
+
+  it 'loads TBLASTN XML and tests hit PNG/SVG download' do
     access_by_uuid('blast_2.9.0/tblastn')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
+    clear_downloads
+    # Click on the PNG download button of the first hit available and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_395440626_gb_JQ694049_1.png')
+
+    clear_downloads
+
+    # Click on the SVG download button of the first hit available and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_395440626_gb_JQ694049_1.svg')
+    page.should have_content('TBLASTN')
   end
 
-  it 'loads TBLASTX xml output' do
+  it 'loads TBLASTN XML and tests Circos download' do
+    access_by_uuid('blast_2.9.0/tblastn')
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+  end
+
+  it 'loads TBLASTN XML and tests Length distribution download' do
+    access_by_uuid('blast_2.9.0/tblastn')
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
+  end
+
+  #TBLASTX Test scenarios
+
+  it 'loads TBLASTX XML and tests hit alignment and sidebar Alignment download' do
     access_by_uuid('blast_2.9.0/tblastx')
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+
+    page.execute_script("$('.download-aln:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1528997474_gb_MH447967_1.txt')
+    expect(File.read(downloaded_file)). to eq(File.read("spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt"))
+
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-40_hits_tblastx.txt"))
+
+    clear_downloads
+
+    # Select four hit checkboxes and click on the Alignment of selected hits.
+    # Compare the downloaded content.
+    page.check('Query_1_hit_9_checkbox')
+    page.check('Query_1_hit_10_checkbox')
+    page.check('Query_2_hit_9_checkbox')
+    page.check('Query_2_hit_10_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-4_hits_tblastx.txt"))
+    page.should have_content('TBLASTX')
+  end
+
+  it 'loads TBLASTX XML and tests hit PNG/SVG download' do
+    access_by_uuid('blast_2.9.0/tblastx')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
+
+    clear_downloads
+    # Click on the PNG download button of the first hit available and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.png')
+
+    clear_downloads
+
+    # Click on the SVG download button of the first hit available and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
+    page.should have_content('TBLASTX')
+  end
+
+  it 'loads TBLASTX XML and tests Circos download' do
+    access_by_uuid('blast_2.9.0/tblastx')
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+  end
+
+  it 'loads TBLASTX XML and tests Length distribution download' do
+    access_by_uuid('blast_2.9.0/tblastx')
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
   end
 
   ## Helpers ##
 
   def access_by_uuid(id)
+    # Method to access the XML report in the browser
     url = url_encode(id)
     visit "/#{url}"
     page.should have_content('Query')
-    page.execute_script("return $('.view-sequence').is(':disabled')").should eq(false)
   end
 end