sequenceserver 2.0.0.rc3 → 2.0.0.rc8

data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb

@@ -1,176 +0,0 @@
-require 'spec_helper'
-
-# Test BLAST module.
-module SequenceServer
-
-  with_hits = Job.fetch('diamond_0.9.24/blastx')
-  no_hits = Job.fetch('diamond_0.9.24/blastx_nohits')
-
-  init
-
-  describe 'Report' do
-    hits_report = BLAST::Report.new(with_hits)
-    no_hits_report = BLAST::Report.new(no_hits)
-
-    it 'will return an Array of queries' do
-      hits_report.queries.should be_a Array
-      no_hits_report.queries.should be_a Array
-    end
-
-    it 'will return a Hash of stats' do
-      hits_report.stats.should be_a Hash
-      no_hits_report.stats.should be_a Hash
-    end
-
-    it 'contains all the necessary stats' do
-      hits_report.stats.length.should eql(7)
-      no_hits_report.stats.length.should eql(7)
-    end
-  end
-
-  describe 'Query' do
-    hits_report = BLAST::Report.new(with_hits)
-    no_hits_report = BLAST::Report.new(no_hits)
-
-    it 'will return queries with valid length' do
-      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 Integer
-      no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
-    end
-
-    it 'will return an Array of hits' do
-      hits_report.queries.first.hits.should be_a Array
-      no_hits_report.queries.first.hits.should be_a Array
-    end
-  end
-
-  describe 'Hits' do
-    hits_report = BLAST::Report.new(with_hits)
-    no_hits_report = BLAST::Report.new(no_hits)
-
-    it 'will have non zero length' do
-      hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
-    end
-
-    it 'will return an Array of HSPs' do
-      hits_report.queries.first.hits.first.hsps.should be_a Array
-    end
-
-    it 'will return an Array with atleast one HSP' do
-      hits_report.queries.first.hits.first.hsps.length.should be >= 1
-    end
-
-    it 'will contain no element if no hits were obtained' do
-      no_hits_report.queries.first.hits.length.should eql(0)
-    end
-  end
-
-  # Test general features of HSPs. Algorithm specific customizations are
-  # tested separetly.
-  describe 'HSPs' do
-    hits_report = BLAST::Report.new(with_hits)
-
-    # Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
-    # hit object it belongs to.
-    it 'have all the necessary values' do
-      hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
-    end
-
-    # 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 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 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 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 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 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 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 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 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 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 Integer
-      hits_report.queries.first.hits.first.hsps.last.length
-        .should satisfy { |n| n > 0 }
-
-      hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
-      hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
-      hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
-    end
-
-    it 'have correctly matched query, hit and midline alignments' do
-      hsp = hits_report.queries.last.hits.last.hsps.first
-      hsp.qseq.length.should eql(hsp.sseq.length)
-      hsp.sseq.length.should eql(hsp.midline.length)
-      hsp.midline.length.should eql(hsp.qseq.length)
-    end
-  end
-
-  # Individually test different DIAMOND BLASTP/BLASTX algorithms
-  #
-
-  describe 'diamond BLASTP' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('diamond_0.9.24/blastp'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should eql(0)
-      hsp.sframe.should eql(0)
-    end
-
-    it 'have correct qstart, qend, sstart, send values' do
-      hsp.qstart.should be <= hsp.qend
-      hsp.sstart.should be <= hsp.send
-    end
-
-  end
-
-  describe 'diamond BLASTX' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('diamond_0.9.24/blastx'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should_not eql(0)
-      hsp.sframe.should eql(0)
-    end
-
-    it 'have correct qstart, qend, sstart, send' do
-      hsp.qstart.should be <= hsp.qend
-      hsp.sstart.should be <= hsp.send
-    end
-  end
-end
-

data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb

@@ -1,237 +0,0 @@
-describe 'report generated from imported XML', type: :feature, js: true do
-  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide
-  # sequences for reproducibility.
-  it 'loads diamond BLASTP xml and tests hit alignment and sidebar Alignment download' do
-    access_by_uuid('diamond_0.9.24/blastp')
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt'))
-
-    clear_downloads
-
-    # Click on the Alignment of all hits download and compare the downloaded
-    # content
-
-    page.click_link('Alignment of all hits')
-    wait_for_download
-
-    expect(File.basename(downloaded_file)).to eq('alignment-35_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-35_hits_diamond_blastp.txt'))
-    clear_downloads
-
-    # Check the cheboxes of indicted hits and click on the download of Alignment
-    # of selected hits and compare the downloaded content
-
-    page.check('Query_1_hit_1_checkbox')
-    page.check('Query_1_hit_2_checkbox')
-    page.check('Query_2_hit_1_checkbox')
-    page.check('Query_2_hit_2_checkbox')
-    page.click_link('Alignment of 4 selected hit(s)')
-    wait_for_download
-
-    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_diamond_blastp.txt'))
-    page.should have_content('BLASTP')
-  end
-
-  it 'loads diamond BLASTP XML and tests alignment overview and hit PNG/SVG download' do
-    access_by_uuid('diamond_0.9.24/blastp')
-
-    # Click on the PNG/SVG download button of the alignment overview and compare
-    # the downloaded content.
-
-    page.execute_script("$('.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("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
-
-    clear_downloads
-
-    # Click on the PNG/SVG download button of the first hit available and
-    # compare the downloaded content.
-    page.execute_script("$('.export-to-png:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-sp_P04637_P53_HUMAN.png')
-
-    clear_downloads
-
-    page.execute_script("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-sp_P04637_P53_HUMAN.svg')
-    page.should have_content('BLASTP')
-  end
-
-  it 'loads diamond BLASTP XML and tests Circos download' do
-    access_by_uuid('diamond_0.9.24/blastp')
-
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.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('diamond_0.9.24/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("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
-  end
-
-  # BLASTX test scenarios
-
-  it 'loads diamond BLASTX XML and tests hit alignment and sidebar Alignment download' do
-    access_by_uuid('diamond_0.9.24/blastx')
-
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
-    wait_for_download
-
-    expect(File.basename(downloaded_file)).to eq('MH011443_1_sp_P04637_P53_HUMAN.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.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-35_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-35_hits_diamond_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_diamond_blastx.txt'))
-
-    page.should have_content('BLASTX')
-  end
-
-  it 'loads diamond BLASTX XML and tests alignment overview and hit PNG/SVG download' do
-    access_by_uuid('diamond_0.9.24/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("$('.export-to-png:eq(1)').click()")
-
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-sp_P04637_P53_HUMAN.png')
-
-    clear_downloads
-
-    page.execute_script("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-sp_P04637_P53_HUMAN.svg')
-    page.should have_content('BLASTX')
-  end
-
-  it 'loads diamond BLASTX XML and tests Circos download' do
-    access_by_uuid('diamond_0.9.24/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('Queries and their top hits: chord diagram')
-    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("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
-  end
-
-  it 'loads diamond BLASTX XML and tests Length distribution download' do
-    access_by_uuid('diamond_0.9.24/blastx')
-
-    # Click on the Length distribution expanding button, wait for animation,
-    # click on the download of PNG/SVG file and test that it initiated a file
-    # download in a right format.
-
-    page.should have_content('Length distribution of hits')
-    page.execute_script("$('.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
-
-  ## Helpers ##
-
-  def access_by_uuid(id)
-    url = url_encode(id)
-    visit "/#{url}"
-    page.should have_content('Query')
-  end
-end

data/spec/capybara_spec.rb

@@ -1,334 +0,0 @@
-describe 'a browser', type: :feature, js: true do
-  it 'properly controls blast button' do
-    visit '/'
-
-    fill_in('sequence', with: nucleotide_query)
-    page.evaluate_script("$('#method').is(':disabled')").should eq(true)
-
-    check(nucleotide_databases.first)
-    page.evaluate_script("$('#method').is(':disabled')").should eq(false)
-  end
-
-  it 'properly controls interaction with database listing' do
-    visit '/'
-    fill_in('sequence', with: nucleotide_query)
-    check(nucleotide_databases.first)
-    page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
-        .should eq(true)
-  end
-
-  it 'shows a dropdown menu when other blast methods are available' do
-    visit '/'
-    fill_in('sequence', with: nucleotide_query)
-    check(nucleotide_databases.first)
-    page.has_css?('button.dropdown-toggle').should eq(true)
-  end
-
-  it 'can run a simple blastn search' do
-    perform_search query: nucleotide_query,
-                   databases: nucleotide_databases
-    page.should have_content('BLASTN')
-  end
-
-  it 'can run a simple blastp search' do
-    perform_search query: protein_query,
-                   databases: protein_databases
-    page.should have_content('BLASTP')
-  end
-
-  it 'can run a simple blastx search' do
-    perform_search query: nucleotide_query,
-                   databases: protein_databases
-    page.should have_content('BLASTX')
-  end
-
-  it 'can run a simple tblastx search' do
-    perform_search query: nucleotide_query,
-                   databases: nucleotide_databases,
-                   method: 'tblastx'
-    page.should have_content('TBLASTX')
-  end
-
-  it 'can run a simple tblastn search' do
-    perform_search query: protein_query,
-                   databases: nucleotide_databases
-    page.should have_content('TBLASTN')
-  end
-
-  ### Test aspects of the generated report.
-
-  it 'can download FASTA of each hit' do
-    # Do a BLASTP search. protein_query refers to the first two sequence in
-    # protein_databases[0], so the top hits are the query sequences themselves.
-    perform_search(query: protein_query,
-                   databases: protein_databases.values_at(0))
-
-    # Click on the first FASTA download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.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("$('.view-sequence').is(':disabled')").should eq(true)
-  end
-
-  it 'can download visualisations in svg and png format' do
-    # Do a BLASTP search. protein_query refers to the first two sequence in
-    # protein_databases[0], so the top hits are the query sequences themselves.
-    perform_search(query: protein_query,
-                   databases: protein_databases.values_at(0))
-
-    ## Check that there is a circos vis and unfold it.
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').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("$('.length-distribution > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.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 '/'
-
-    # Fill in query, select databases, submit form.
-    fill_in('sequence', with: query)
-    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)
-
-    # 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__, 'sequences', 'nucleotide_query.fa')
-  end
-
-  def protein_query
-    File.read File.join(__dir__, 'sequences', '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