RubyGems - sequenceserver - Versions diffs - 2.0.0.rc3 → 2.0.0.rc8 - Mend

sequenceserver 2.0.0.rc3 → 2.0.0.rc8

Files changed (473) hide show

data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb DELETED

@@ -1,583 +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. BLAST 2.2.30 displays hits in a different order than versions
-  # 2.2.31 upwards for protein queries (BLASTP, TBLASTN), hence the test takes
-  # different files for comparison.
-  # BLASTP test scenarios
-  it 'loads BLASTP XML and tests hit alignment and sidebar Alignment download' do
-    access_by_uuid('blast_2.2.30/blastp')
-    # Click on the first hit Alignment download button on the page and wait for
-    # the download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt'))
-    clear_downloads
-    # Click on the Alignment of all hits download and compare the downloaded
-    # content
-    page.click_link('Alignment of all hits')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastp_2.2.30.txt'))
-    clear_downloads
-    # Check the cheboxes of indicted hits and click on the download of Alignment
-    # of selected hits and compare the downloaded content
-    page.check('Query_1_hit_1_checkbox')
-    page.check('Query_1_hit_2_checkbox')
-    page.check('Query_2_hit_1_checkbox')
-    page.check('Query_2_hit_2_checkbox')
-    page.click_link('Alignment of 4 selected hit(s)')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastp_2.2.30.txt'))
-  end
-  it 'loads BLASTP XML and tests alignment overiview and hit PNG/SVG download' do
-    access_by_uuid('blast_2.2.30/blastp')
-    # Click on the PNG/SVG download button of the alignment overview and compare
-    # the downloaded content.
-    page.execute_script("$('.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_120407068_ref_NP_000537_3.png')
-    clear_downloads
-    page.execute_script("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_120407068_ref_NP_000537_3.svg')
-    page.should have_content('BLASTP')
-  end
-  it 'loads BLASTP XML and tests Circos download' do
-    access_by_uuid('blast_2.2.30/blastp')
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.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('blast_2.2.30/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("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
-  end
-  # BLASTX test scenarios
-  it 'loads BLASTX XML and tests hit alignment and sidebar Alignment download' do
-    access_by_uuid('blast_2.2.30/blastx')
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.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_2.2.30/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_2.2.30/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("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
-  end
-  it 'loads BLASTX XML and tests Length distribution download' do
-    access_by_uuid('blast_2.2.30/blastx')
-    # Click on the Length distribution expanding button, wait for animation,
-    # click on the download of PNG/SVG file and test that it initiated a file
-    # download in a right format.
-    page.should have_content('Length distribution of hits')
-    page.execute_script("$('.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
-  # BLASTN Test scenarios
-  it 'loads BLASTN XML and tests hit alignment and sidebar Alignment download' do
-    access_by_uuid('blast_2.2.30/blastn')
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt'))
-    clear_downloads
-    # Click on the Alignment of all hits download and compare the downloaded
-    # content
-    page.click_link('Alignment of all hits')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastn.txt'))
-    clear_downloads
-    # Select four hit checkboxes and click on the Alignment of selected hits.
-    # Compare the downloaded content.
-    page.check('Query_1_hit_5_checkbox')
-    page.check('Query_1_hit_6_checkbox')
-    page.check('Query_2_hit_5_checkbox')
-    page.check('Query_2_hit_6_checkbox')
-    page.click_link('Alignment of 4 selected hit(s)')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastn.txt'))
-    page.should have_content('BLASTN')
-  end
-  it 'loads BLASTN XML and tests alignment overview and hit PNG/SVG download' do
-    access_by_uuid('blast_2.2.30/blastn')
-    # Click on the PNG/SVG download button of the alignment overview and compare
-    # the downloaded content.
-    page.execute_script("$('.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("$('.export-to-svg:eq(2)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
-    page.should have_content('BLASTN')
-  end
-  it 'loads BLASTN XML and tests Circos download' do
-    access_by_uuid('blast_2.2.30/blastn')
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > 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_2.2.30/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("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
-  end
-  # TBLASTN Test scenarios
-  it 'loads TBLASTN XML and tests hit alignment and sidebar Alignment download' do
-    access_by_uuid('blast_2.2.30/tblastn')
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-aln:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_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_2.2.30.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_2.2.30.txt'))
-    page.should have_content('TBLASTN')
-  end
-  it 'loads TBLASTN XML and tests alignment overview and hit PNG/SVG download' do
-    access_by_uuid('blast_2.2.30/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("$('.export-to-png:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1484127324_gb_MG595988_1.png')
-    clear_downloads
-    # Click on the SVG download button of the first hit available and compare
-    # the downloaded content.
-    page.execute_script("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1484127324_gb_MG595988_1.svg')
-    page.should have_content('TBLASTN')
-  end
-  it 'loads TBLASTN XML and tests Circos download' do
-    access_by_uuid('blast_2.2.30/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("$('.circos > .grapher-header > h5').click()")
-    sleep 1
-    page.execute_script("$('.export-to-png:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
-    clear_downloads
-    page.execute_script("$('.export-to-svg:eq(0)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
-  end
-  it 'loads TBLASTN XML and tests Length distribution download' do
-    access_by_uuid('blast_2.2.30/tblastn')
-    # Click on the Length distribution expanding button, wait for animation,
-    # click on the download of PNG/SVG file and test that it initiated a file
-    # download in a right format.
-    page.should have_content('Length distribution of hits')
-    page.execute_script("$('.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_2.2.30/tblastx')
-    # Click on the first Alignment download button on the page and wait for the
-    # download to finish.
-    page.execute_script("$('.download-aln:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1528997474_gb_MH447967_1.txt')
-    expect(File.read(downloaded_file)). to eq(File.read('spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt'))
-    clear_downloads
-    # Click on the Alignment of all hits download and compare the downloaded
-    # content
-    page.click_link('Alignment of all hits')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastx.txt'))
-    clear_downloads
-    # Select four hit checkboxes and click on the Alignment of selected hits.
-    # Compare the downloaded content.
-    page.check('Query_1_hit_9_checkbox')
-    page.check('Query_1_hit_10_checkbox')
-    page.check('Query_2_hit_9_checkbox')
-    page.check('Query_2_hit_10_checkbox')
-    page.click_link('Alignment of 4 selected hit(s)')
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastx.txt'))
-    page.should have_content('TBLASTX')
-  end
-  it 'loads TBLASTX XML and tests hit PNG/SVG download' do
-    access_by_uuid('blast_2.2.30/tblastx')
-    # Click on the PNG/SVG download button of the alignment overview and compare
-    # the downloaded content.
-    page.execute_script("$('.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("$('.export-to-svg:eq(1)').click()")
-    wait_for_download
-    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
-    page.should have_content('TBLASTX')
-  end
-  it 'loads TBLASTX XML and tests Circos download' do
-    access_by_uuid('blast_2.2.30/tblastx')
-    # Click on the Circos expanding button, wait for animation, click on the
-    # download of PNG/SVG file and test that it initiated a file download in a
-    # right format.
-    page.should have_content('Queries and their top hits: chord diagram')
-    page.execute_script("$('.circos > .grapher-header > 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_2.2.30/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')
-  end
-end