sequenceserver 2.0.0.rc7 → 2.0.0.rc8

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

@@ -1,228 +0,0 @@
-require 'spec_helper'
-
-# Test BLAST module.
-module SequenceServer
- with_hits = Job.fetch('blast_2.9.0/blastn')
-  no_hits = Job.fetch('blast_2.9.0/blastn_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 BLAST+ algorithms
-  #
-  describe 'BLASTN' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.9.0/blastn'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      [1, -1].should include(hsp.qframe)
-      [1, -1].should include(hsp.sframe)
-    end
-
-    it 'have correct qstart, qend, sstart, send' do
-      if hsp.sframe > 0
-        hsp.sstart.should be <= hsp.send
-      else
-        hsp.sstart.should be >= hsp.send
-      end
-    end
-  end
-
-  describe 'BLASTP' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.9.0/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 'BLASTX' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.9.0/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
-
-  describe 'TBLASTX' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.9.0/tblastx'))
-      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_not 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
-
-  describe 'TBLASTN' do
-    let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blast_2.9.0/tblastn'))
-      report.queries.first.hits.last.hsps.first
-    end
-
-    it 'have correct query and subject frame' do
-      hsp.qframe.should eql(0)
-      hsp.sframe.should_not 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/blast_2.9.0/import_spec_capybara_local_2.9.0.rb

@@ -1,585 +0,0 @@
-describe 'report generated from imported XML',type: :feature, js: true do
-
-  # 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("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
-
-    clear_downloads
-
-    # Click on the PNG/SVG download button of the first hit available and
-    # compare the downloaded content.
-
-    page.execute_script("$('.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')
-
-    clear_downloads
-
-    page.execute_script("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.svg')
-    page.should have_content('BLASTP')
-  end
-
-  it 'loads BLASTP XML and tests Circos download' do
-    access_by_uuid('blast_2.9.0/blastp')
-
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').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("$('.length-distribution > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.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('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.export-to-png:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
-    clear_downloads
-
-    page.execute_script("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
-  end
-
-  it 'loads BLASTX XML and tests Length distribution download' do
-    access_by_uuid('blast_2.9.0/blastx')
-    # Click on the Length distribution expanding button, wait for animation,
-    # click on the download of PNG/SVG file and test that it initiated a file
-    # download in a right format.
-
-    page.should have_content('Length distribution of hits')
-    page.execute_script("$('.length-distribution > .grapher-header > h4').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
-
-  # 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("$('.download-aln:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt"))
-
-    clear_downloads
-
-    # Click on the Alignment of all hits download and compare the downloaded
-    # content
-
-    page.click_link('Alignment of all hits')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-40_hits_blastn.txt"))
-
-    clear_downloads
-
-    # Select four hit checkboxes and click on the Alignment of selected hits.
-    # Compare the downloaded content.
-    page.check('Query_1_hit_5_checkbox')
-    page.check('Query_1_hit_6_checkbox')
-    page.check('Query_2_hit_5_checkbox')
-    page.check('Query_2_hit_6_checkbox')
-    page.click_link('Alignment of 4 selected hit(s)')
-    wait_for_download
-
-    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-4_hits_blastn.txt"))
-    page.should have_content('BLASTN')
-  end
-
-  it 'loads BLASTN XML and tests hit PNG/SVG download' do
-    access_by_uuid('blast_2.9.0/blastn')
-
-    # Click on the PNG/SVG download button of the alignment overview and compare
-    # the downloaded content.
-    page.execute_script("$('.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("$('.export-to-svg:eq(2)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
-    page.should have_content('BLASTN')
-  end
-
-  it 'loads BLASTN XML and tests Circos download' do
-    access_by_uuid('blast_2.9.0/blastn')
-
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').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("$('.length-distribution > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.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 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('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.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 > h4').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("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
-    page.should have_content('TBLASTX')
-  end
-
-  it 'loads TBLASTX XML and tests Circos download' do
-    access_by_uuid('blast_2.9.0/tblastx')
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > h4').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("$('.length-distribution > .grapher-header > h4').click()")
-    sleep 1
-
-    page.execute_script("$('.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')
-  end
-end