sequenceserver 2.0.0.beta3 → 2.0.0.beta4
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- checksums.yaml +5 -5
- data/.eslintrc.json +36 -0
- data/.rubocop.yml +1 -1
- data/.travis.yml +53 -20
- data/AppImage/recipe.yml +15 -0
- data/AppImage/sequenceserver.desktop +8 -0
- data/AppImage/sequenceserver.png +0 -0
- data/AppImage/sequenceserver.sh +11 -0
- data/README.md +79 -46
- data/bin/sequenceserver +4 -4
- data/lib/sequenceserver/version.rb +1 -1
- data/package.json +2 -0
- data/public/css/grapher.css +3 -0
- data/public/css/sequenceserver.css +17 -6
- data/public/css/sequenceserver.min.css +3 -3
- data/public/js/circos.js +515 -491
- data/public/js/grapher.js +12 -6
- data/public/js/hits_overview.js +321 -308
- data/public/js/hsp.js +12 -7
- data/public/js/length_distribution.js +241 -234
- data/public/js/report.js +196 -174
- data/public/js/search.js +3 -3
- data/public/js/sequenceserver.js +9 -9
- data/public/js/utils.js +17 -10
- data/public/js/visualisation_helpers.js +77 -77
- data/public/sequenceserver-report.min.js +17 -17
- data/public/sequenceserver-search.min.js +1 -1
- data/public/vendor/github/nicgirault/circosJs@1.7.0/dist/circosJS.js +1 -5
- data/sequenceserver.gemspec +1 -2
- data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +13 -13
- data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +555 -25
- data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +13 -13
- data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +558 -24
- data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +13 -13
- data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +561 -26
- data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +13 -13
- data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +561 -25
- data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +13 -13
- data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +558 -24
- data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +13 -13
- data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +559 -24
- data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +13 -13
- data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +559 -28
- data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +13 -13
- data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +559 -27
- data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +13 -13
- data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +557 -25
- data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +13 -13
- data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +219 -21
- data/spec/capybara_spec.rb +25 -28
- data/spec/download_helper.rb +6 -3
- data/spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt +6 -0
- data/spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt +6 -0
- data/spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt +30 -0
- data/spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt +6 -0
- data/spec/sequences/alignment-35_hits_diamond_blastp.txt +210 -0
- data/spec/sequences/alignment-35_hits_diamond_blastx.txt +210 -0
- data/spec/sequences/alignment-3_hits.txt +18 -0
- data/spec/sequences/alignment-40_hits_blastn.txt +246 -0
- data/spec/sequences/alignment-40_hits_blastp.txt +240 -0
- data/spec/sequences/alignment-40_hits_blastp_2.2.30.txt +240 -0
- data/spec/sequences/alignment-40_hits_blastx.txt +240 -0
- data/spec/sequences/alignment-40_hits_tblastn.txt +240 -0
- data/spec/sequences/alignment-40_hits_tblastn_2.2.30.txt +240 -0
- data/spec/sequences/alignment-40_hits_tblastx.txt +2664 -0
- data/spec/sequences/alignment-4_hits.txt +24 -0
- data/spec/sequences/alignment-4_hits_blastn.txt +24 -0
- data/spec/sequences/alignment-4_hits_blastp.txt +24 -0
- data/spec/sequences/alignment-4_hits_blastp_2.2.30.txt +24 -0
- data/spec/sequences/alignment-4_hits_blastx.txt +24 -0
- data/spec/sequences/alignment-4_hits_diamond_blastp.txt +24 -0
- data/spec/sequences/alignment-4_hits_diamond_blastx.txt +24 -0
- data/spec/sequences/alignment-4_hits_tblastn.txt +24 -0
- data/spec/sequences/alignment-4_hits_tblastn_2.2.30.txt +24 -0
- data/spec/sequences/alignment-4_hits_tblastx.txt +318 -0
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt +6 -0
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt +6 -0
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt +6 -0
- data/spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt +6 -0
- data/spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt +6 -0
- data/spec/spec_helper.rb +3 -3
- metadata +67 -57
- data/.eslintrc +0 -213
- data/Rakefile +0 -8
- data/spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml +0 -1181
- data/spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml +0 -18813
- data/spec/import_spec_capybara_local.rb +0 -61
@@ -32,9 +32,9 @@ module SequenceServer
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no_hits_report = BLAST::Report.new(no_hits)
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it 'will return queries with valid length' do
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hits_report.queries.first.length.should be_a
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hits_report.queries.first.length.should be_a Integer
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hits_report.queries.first.length.should satisfy { |n| n > 0 }
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no_hits_report.queries.first.length.should be_a
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no_hits_report.queries.first.length.should be_a Integer
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no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
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end
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# Test Random HSPs to ensure that all the values from HSP struct are valid.
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it 'have correct alignment values' do
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hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
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hits_report.queries.last.hits.first.hsps.last.score.should be_a
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hits_report.queries.last.hits.first.hsps.last.score.should be_a Integer
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hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
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hits_report.queries.first.hits.first.hsps.first.evalue
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.last.hsps.first.qstart.should be_a
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hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Integer
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hits_report.queries.first.hits.last.hsps.first.qstart
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.last.hsps.first.qend.should be_a
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hits_report.queries.first.hits.last.hsps.first.qend.should be_a Integer
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hits_report.queries.first.hits.last.hsps.first.qend
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.last.hits.last.hsps.last.sstart.should be_a
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hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Integer
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hits_report.queries.last.hits.last.hsps.last.sstart
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.send.should be_a
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hits_report.queries.first.hits.first.hsps.last.send.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.send
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.qframe.should be_a
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hits_report.queries.first.hits.first.hsps.last.sframe.should be_a
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hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.identity.should be_a
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hits_report.queries.first.hits.first.hsps.last.identity.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.identity
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.gaps.should be_a
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hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.gaps
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.positives
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.should be_a
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.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.positives
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.should_not satisfy { |n| n < 0 }
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hits_report.queries.first.hits.first.hsps.last.length.should be_a
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hits_report.queries.first.hits.first.hsps.last.length.should be_a Integer
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hits_report.queries.first.hits.first.hsps.last.length
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.should satisfy { |n| n > 0 }
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@@ -1,51 +1,587 @@
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describe 'report generated from imported XML', type: :feature, js: true do
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# Test suite to test features of imported XML report. Fasta files used for
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# testing consist of TP53 and COX41 protein/nucleotide sequences for
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# reproducibility. Each query was limited to 20 hits to not to overload the
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# test suite.
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# BLASTP test scenarios
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it 'loads BLASTP XML and tests hit alignment and sidebar Alignment download' do
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access_by_uuid('blast_2.4.0/blastp')
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# Click on the first hit Alignment download button on the page and wait for
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# the download to finish.
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page.execute_script("$('.download-aln:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt'))
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clear_downloads
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# Click on the Alignment of all hits download and compare the downloaded
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# content
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page.click_link('Alignment of all hits')
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastp.txt'))
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clear_downloads
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# Check the cheboxes of indicted hits and click on the download of Alignment
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# of selected hits and compare the downloaded content
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page.check('Query_1_hit_1_checkbox')
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page.check('Query_1_hit_2_checkbox')
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page.check('Query_2_hit_1_checkbox')
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page.check('Query_2_hit_2_checkbox')
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page.click_link('Alignment of 4 selected hit(s)')
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastp.txt'))
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end
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it 'loads BLASTP XML and tests alignment overview and hit PNG/SVG download' do
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access_by_uuid('blast_2.4.0/blastp')
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# Click on the PNG/SVG download button of the alignment overview and compare
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# the downloaded content.
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page.execute_script("$('.export-to-png:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
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clear_downloads
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Capybara.server = :webrick
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Capybara.javascript_driver = :selenium
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Capybara.default_max_wait_time = 220
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page.execute_script("$('.export-to-svg:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
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clear_downloads
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# Click on the PNG/SVG download button of the first hit available and
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# compare the downloaded content.
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page.execute_script("$('.export-to-png:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.png')
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clear_downloads
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page.execute_script("$('.export-to-svg:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1099170394_ref_XP_018868681_1.svg')
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page.should have_content('BLASTP')
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end
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it 'loads BLASTP xml output' do
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it 'loads BLASTP XML and tests Circos download' do
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access_by_uuid('blast_2.4.0/blastp')
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# Click on the Circos expanding button, wait for animation, click on the
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# download of PNG/SVG file and test that it initiated a file download in a
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# right format.
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page.should have_content('Chord diagram: queries and their top hits')
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page.execute_script("$('.circos > .grapher-header > h5').click()")
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sleep 1
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page.execute_script("$('.export-to-png:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
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clear_downloads
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page.execute_script("$('.export-to-svg:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
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end
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it 'loads BLASTP XML and tests Length distribution download' do
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access_by_uuid('blast_2.4.0/blastp')
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# Click on the Length distribution expanding button, wait for animation,
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# click on the download of PNG/SVG file and test that it initiated a file
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# download in a right format.
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page.should have_content('Length distribution of hits')
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page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
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sleep 1
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page.execute_script("$('.export-to-png:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
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clear_downloads
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page.execute_script("$('.export-to-svg:eq(1)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
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end
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# BLASTX test scenarios
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it 'loads BLASTX XML and tests hit alignment and sidebar Alignment download' do
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access_by_uuid('blast_2.4.0/blastx')
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# Click on the first Alignment download button on the page and wait for the
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# download to finish.
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page.execute_script("$('.download-aln:eq(0)').click()")
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783307_gb_AYF55702_1.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt'))
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clear_downloads
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# Click on the Alignment of all hits download and compare the downloaded
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# content
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page.click_link('Alignment of all hits')
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wait_for_download
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expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
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expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastx.txt'))
|
141
|
+
clear_downloads
|
142
|
+
|
143
|
+
# Select four hit checkboxes and click on the Alignment of selected hits.
|
144
|
+
# Compare the downloaded content.
|
145
|
+
page.check('Query_1_hit_3_checkbox')
|
146
|
+
page.check('Query_1_hit_4_checkbox')
|
147
|
+
page.check('Query_2_hit_3_checkbox')
|
148
|
+
page.check('Query_2_hit_4_checkbox')
|
149
|
+
page.click_link('Alignment of 4 selected hit(s)')
|
150
|
+
wait_for_download
|
151
|
+
|
152
|
+
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
153
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastx.txt'))
|
154
|
+
|
155
|
+
page.should have_content('BLASTX')
|
27
156
|
end
|
28
157
|
|
29
|
-
it 'loads BLASTX
|
158
|
+
it 'loads BLASTX XML and tests hit PNG/SVG download' do
|
30
159
|
access_by_uuid('blast_2.4.0/blastx')
|
160
|
+
|
161
|
+
# Click on the PNG/SVG download button of the alignment overview and compare
|
162
|
+
# the downloaded content.
|
163
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
164
|
+
wait_for_download
|
165
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
166
|
+
|
167
|
+
clear_downloads
|
168
|
+
|
169
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
170
|
+
wait_for_download
|
171
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
172
|
+
|
173
|
+
clear_downloads
|
174
|
+
# Click on the PNG/SVG download button of the first hit available and
|
175
|
+
# compare the downloaded content.
|
176
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
177
|
+
|
178
|
+
wait_for_download
|
179
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.png')
|
180
|
+
clear_downloads
|
181
|
+
|
182
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
183
|
+
wait_for_download
|
184
|
+
|
185
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.svg')
|
186
|
+
page.should have_content('BLASTX')
|
187
|
+
end
|
188
|
+
|
189
|
+
it 'loads BLASTX XML and tests Circos download' do
|
190
|
+
access_by_uuid('blast_2.4.0/blastx')
|
191
|
+
# Click on the Circos expanding button, wait for animation, click on the
|
192
|
+
# download of PNG/SVG file and test that it initiated a file download in a
|
193
|
+
# right format.
|
194
|
+
|
195
|
+
page.should have_content('Chord diagram: queries and their top hits')
|
196
|
+
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
197
|
+
sleep 1
|
198
|
+
|
199
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
200
|
+
wait_for_download
|
201
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
202
|
+
clear_downloads
|
203
|
+
|
204
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
205
|
+
wait_for_download
|
206
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
207
|
+
end
|
208
|
+
|
209
|
+
it 'loads BLASTX XML and tests Length distribution download' do
|
210
|
+
access_by_uuid('blast_2.4.0/blastx')
|
211
|
+
# Click on the Length distribution expanding button, wait for animation,
|
212
|
+
# click on the download of PNG/SVG file and test that it initiated a file
|
213
|
+
# download in a right format.
|
214
|
+
|
215
|
+
page.should have_content('Length distribution of hits')
|
216
|
+
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
217
|
+
sleep 1
|
218
|
+
|
219
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
220
|
+
wait_for_download
|
221
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
222
|
+
|
223
|
+
clear_downloads
|
224
|
+
|
225
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
226
|
+
wait_for_download
|
227
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
228
|
+
end
|
229
|
+
|
230
|
+
# BLASTN Test scenarios
|
231
|
+
|
232
|
+
it 'loads BLASTN XML and tests hit alignment and sidebar Alignment download' do
|
233
|
+
access_by_uuid('blast_2.4.0/blastn')
|
234
|
+
# Click on the first Alignment download button on the page and wait for the
|
235
|
+
# download to finish.
|
236
|
+
|
237
|
+
page.execute_script("$('.download-aln:eq(0)').click()")
|
238
|
+
wait_for_download
|
239
|
+
|
240
|
+
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
|
241
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt'))
|
242
|
+
|
243
|
+
clear_downloads
|
244
|
+
|
245
|
+
# Click on the Alignment of all hits download and compare the downloaded
|
246
|
+
# content
|
247
|
+
|
248
|
+
page.click_link('Alignment of all hits')
|
249
|
+
wait_for_download
|
250
|
+
|
251
|
+
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
252
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastn.txt'))
|
253
|
+
|
254
|
+
clear_downloads
|
255
|
+
|
256
|
+
# Select four hit checkboxes and click on the Alignment of selected hits.
|
257
|
+
# Compare the downloaded content.
|
258
|
+
page.check('Query_1_hit_5_checkbox')
|
259
|
+
page.check('Query_1_hit_6_checkbox')
|
260
|
+
page.check('Query_2_hit_5_checkbox')
|
261
|
+
page.check('Query_2_hit_6_checkbox')
|
262
|
+
page.click_link('Alignment of 4 selected hit(s)')
|
263
|
+
wait_for_download
|
264
|
+
|
265
|
+
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
266
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastn.txt'))
|
267
|
+
page.should have_content('BLASTN')
|
268
|
+
end
|
269
|
+
|
270
|
+
it 'loads BLASTN XML and tests hit PNG/SVG download' do
|
271
|
+
access_by_uuid('blast_2.4.0/blastn')
|
272
|
+
|
273
|
+
# Click on the PNG/SVG download button of the alignment overview and compare
|
274
|
+
# the downloaded content.
|
275
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
276
|
+
wait_for_download
|
277
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
278
|
+
|
279
|
+
clear_downloads
|
280
|
+
|
281
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
282
|
+
wait_for_download
|
283
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
284
|
+
|
285
|
+
clear_downloads
|
286
|
+
# Click on the PNG download button of the first hit available and compare
|
287
|
+
# the downloaded content.
|
288
|
+
|
289
|
+
page.execute_script("$('.export-to-png:eq(2)').click()")
|
290
|
+
|
291
|
+
wait_for_download
|
292
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.png')
|
293
|
+
|
294
|
+
clear_downloads
|
295
|
+
|
296
|
+
# Click on the SVG download button of the first hit available and compare
|
297
|
+
# the downloaded content.
|
298
|
+
|
299
|
+
page.execute_script("$('.export-to-svg:eq(2)').click()")
|
300
|
+
wait_for_download
|
301
|
+
|
302
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
|
303
|
+
page.should have_content('BLASTN')
|
31
304
|
end
|
32
305
|
|
33
|
-
it 'loads BLASTN
|
306
|
+
it 'loads BLASTN XML and tests Circos download' do
|
34
307
|
access_by_uuid('blast_2.4.0/blastn')
|
308
|
+
# Click on the Circos expanding button, wait for animation, click on the
|
309
|
+
# download of PNG/SVG file and test that it initiated a file download in a
|
310
|
+
# right format.
|
311
|
+
|
312
|
+
page.should have_content('Chord diagram: queries and their top hits')
|
313
|
+
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
314
|
+
sleep 1
|
315
|
+
|
316
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
317
|
+
wait_for_download
|
318
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
319
|
+
clear_downloads
|
320
|
+
|
321
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
322
|
+
wait_for_download
|
323
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
324
|
+
end
|
325
|
+
|
326
|
+
it 'loads BLASTN XML and tests Length distribution download' do
|
327
|
+
access_by_uuid('blast_2.4.0/blastn')
|
328
|
+
# Click on the Length distribution expanding button, wait for animation,
|
329
|
+
# click on the download of PNG/SVG file and test that it initiated a file
|
330
|
+
# download in a right format.
|
331
|
+
|
332
|
+
page.should have_content('Length distribution of hits')
|
333
|
+
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
334
|
+
sleep 1
|
335
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
336
|
+
wait_for_download
|
337
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
338
|
+
clear_downloads
|
339
|
+
|
340
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
341
|
+
wait_for_download
|
342
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
35
343
|
end
|
36
344
|
|
37
|
-
|
345
|
+
# TBLASTN Test scenarios
|
346
|
+
|
347
|
+
it 'loads TBLASTN XML and tests hit alignment and sidebar Alignment download' do
|
38
348
|
access_by_uuid('blast_2.4.0/tblastn')
|
349
|
+
# Click on the first Alignment download button on the page and wait for the
|
350
|
+
# download to finish.
|
351
|
+
|
352
|
+
page.execute_script("$('.download-aln:eq(0)').click()")
|
353
|
+
wait_for_download
|
354
|
+
|
355
|
+
expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt')
|
356
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt'))
|
357
|
+
|
358
|
+
clear_downloads
|
359
|
+
|
360
|
+
# Click on the Alignment of all hits download and compare the downloaded
|
361
|
+
# content
|
362
|
+
|
363
|
+
page.click_link('Alignment of all hits')
|
364
|
+
wait_for_download
|
365
|
+
|
366
|
+
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
367
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastn.txt'))
|
368
|
+
|
369
|
+
clear_downloads
|
370
|
+
|
371
|
+
# Select four hit checkboxes and click on the Alignment of selected hits.
|
372
|
+
# Compare the downloaded content.
|
373
|
+
page.check('Query_1_hit_7_checkbox')
|
374
|
+
page.check('Query_1_hit_8_checkbox')
|
375
|
+
page.check('Query_2_hit_7_checkbox')
|
376
|
+
page.check('Query_2_hit_8_checkbox')
|
377
|
+
page.click_link('Alignment of 4 selected hit(s)')
|
378
|
+
wait_for_download
|
379
|
+
|
380
|
+
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
381
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastn.txt'))
|
382
|
+
page.should have_content('TBLASTN')
|
39
383
|
end
|
40
384
|
|
41
|
-
it 'loads
|
385
|
+
it 'loads TBLASTN XML and tests hit PNG/SVG download' do
|
386
|
+
access_by_uuid('blast_2.4.0/tblastn')
|
387
|
+
|
388
|
+
# Click on the PNG/SVG download button of the alignment overview and compare
|
389
|
+
# the downloaded content.
|
390
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
391
|
+
wait_for_download
|
392
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
|
393
|
+
|
394
|
+
clear_downloads
|
395
|
+
|
396
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
397
|
+
wait_for_download
|
398
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
|
399
|
+
|
400
|
+
clear_downloads
|
401
|
+
# Click on the PNG download button of the first hit available and compare
|
402
|
+
# the downloaded content.
|
403
|
+
|
404
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
405
|
+
|
406
|
+
wait_for_download
|
407
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_395440626_gb_JQ694049_1.png')
|
408
|
+
clear_downloads
|
409
|
+
|
410
|
+
# Click on the SVG download button of the first hit available and compare
|
411
|
+
# the downloaded content.
|
412
|
+
|
413
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
414
|
+
wait_for_download
|
415
|
+
|
416
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_395440626_gb_JQ694049_1.svg')
|
417
|
+
page.should have_content('TBLASTN')
|
418
|
+
end
|
419
|
+
|
420
|
+
it 'loads TBLASTN XML and tests Circos download' do
|
421
|
+
access_by_uuid('blast_2.4.0/tblastn')
|
422
|
+
# Click on the Circos expanding button, wait for animation, click on the
|
423
|
+
# download of PNG/SVG file and test that it initiated a file download in a
|
424
|
+
# right format.
|
425
|
+
|
426
|
+
page.should have_content('Chord diagram: queries and their top hits')
|
427
|
+
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
428
|
+
sleep 1
|
429
|
+
|
430
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
431
|
+
wait_for_download
|
432
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
433
|
+
|
434
|
+
clear_downloads
|
435
|
+
|
436
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
437
|
+
wait_for_download
|
438
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
439
|
+
end
|
440
|
+
|
441
|
+
it 'loads TBLASTN XML and tests Length distribution download' do
|
442
|
+
access_by_uuid('blast_2.4.0/tblastn')
|
443
|
+
# Click on the Length distribution expanding button, wait for animation,
|
444
|
+
# click on the download of PNG/SVG file and test that it initiated a file
|
445
|
+
# download in a right format.
|
446
|
+
|
447
|
+
page.should have_content('Length distribution of hits')
|
448
|
+
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
449
|
+
sleep 1
|
450
|
+
|
451
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
452
|
+
wait_for_download
|
453
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
|
454
|
+
|
455
|
+
clear_downloads
|
456
|
+
|
457
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
458
|
+
wait_for_download
|
459
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
|
460
|
+
end
|
461
|
+
|
462
|
+
# TBLASTX Test scenarios
|
463
|
+
|
464
|
+
it 'loads TBLASTX XML and tests hit alignment and sidebar Alignment download' do
|
465
|
+
access_by_uuid('blast_2.4.0/tblastx')
|
466
|
+
# Click on the first Alignment download button on the page and wait for the
|
467
|
+
# download to finish.
|
468
|
+
|
469
|
+
page.execute_script("$('.download-aln:eq(1)').click()")
|
470
|
+
wait_for_download
|
471
|
+
|
472
|
+
expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1528997474_gb_MH447967_1.txt')
|
473
|
+
expect(File.read(downloaded_file)). to eq(File.read('spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt'))
|
474
|
+
|
475
|
+
clear_downloads
|
476
|
+
|
477
|
+
# Click on the Alignment of all hits download and compare the downloaded
|
478
|
+
# content
|
479
|
+
|
480
|
+
page.click_link('Alignment of all hits')
|
481
|
+
wait_for_download
|
482
|
+
|
483
|
+
expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
|
484
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastx.txt'))
|
485
|
+
|
486
|
+
clear_downloads
|
487
|
+
|
488
|
+
# Select four hit checkboxes and click on the Alignment of selected hits.
|
489
|
+
# Compare the downloaded content.
|
490
|
+
page.check('Query_1_hit_9_checkbox')
|
491
|
+
page.check('Query_1_hit_10_checkbox')
|
492
|
+
page.check('Query_2_hit_9_checkbox')
|
493
|
+
page.check('Query_2_hit_10_checkbox')
|
494
|
+
page.click_link('Alignment of 4 selected hit(s)')
|
495
|
+
wait_for_download
|
496
|
+
|
497
|
+
expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
|
498
|
+
expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastx.txt'))
|
499
|
+
page.should have_content('TBLASTX')
|
500
|
+
end
|
501
|
+
|
502
|
+
it 'loads TBLASTX XML and tests hit PNG/SVG download' do
|
503
|
+
access_by_uuid('blast_2.4.0/tblastx')
|
504
|
+
|
505
|
+
# Click on the PNG/SVG download button of the alignment overview and compare
|
506
|
+
# the downloaded content.
|
507
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
508
|
+
wait_for_download
|
509
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
|
510
|
+
|
511
|
+
clear_downloads
|
512
|
+
|
513
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
514
|
+
wait_for_download
|
515
|
+
expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
|
516
|
+
|
517
|
+
clear_downloads
|
518
|
+
# Click on the PNG download button of the first hit available and compare
|
519
|
+
# the downloaded content.
|
520
|
+
|
521
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
522
|
+
|
523
|
+
wait_for_download
|
524
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.png')
|
525
|
+
|
526
|
+
clear_downloads
|
527
|
+
|
528
|
+
# Click on the SVG download button of the first hit available and compare
|
529
|
+
# the downloaded content.
|
530
|
+
|
531
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
532
|
+
wait_for_download
|
533
|
+
|
534
|
+
expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
|
535
|
+
page.should have_content('TBLASTX')
|
536
|
+
end
|
537
|
+
|
538
|
+
it 'loads TBLASTX XML and tests Circos download' do
|
42
539
|
access_by_uuid('blast_2.4.0/tblastx')
|
540
|
+
# Click on the Circos expanding button, wait for animation, click on the
|
541
|
+
# download of PNG/SVG file and test that it initiated a file download in a
|
542
|
+
# right format.
|
543
|
+
|
544
|
+
page.should have_content('Chord diagram: queries and their top hits')
|
545
|
+
page.execute_script("$('.circos > .grapher-header > h5').click()")
|
546
|
+
sleep 1
|
547
|
+
|
548
|
+
page.execute_script("$('.export-to-png:eq(0)').click()")
|
549
|
+
wait_for_download
|
550
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
|
551
|
+
|
552
|
+
clear_downloads
|
553
|
+
|
554
|
+
page.execute_script("$('.export-to-svg:eq(0)').click()")
|
555
|
+
wait_for_download
|
556
|
+
expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
|
557
|
+
end
|
558
|
+
|
559
|
+
it 'loads TBLASTX XML and tests Length distribution download' do
|
560
|
+
access_by_uuid('blast_2.4.0/tblastx')
|
561
|
+
# Click on the Length distribution expanding button, wait for animation,
|
562
|
+
# click on the download of PNG/SVG file and test that it initiated a file
|
563
|
+
# download in a right format.
|
564
|
+
|
565
|
+
page.should have_content('Length distribution of hits')
|
566
|
+
page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
|
567
|
+
sleep 1
|
568
|
+
|
569
|
+
page.execute_script("$('.export-to-png:eq(1)').click()")
|
570
|
+
wait_for_download
|
571
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
|
572
|
+
|
573
|
+
clear_downloads
|
574
|
+
|
575
|
+
page.execute_script("$('.export-to-svg:eq(1)').click()")
|
576
|
+
wait_for_download
|
577
|
+
expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
|
43
578
|
end
|
44
579
|
|
45
580
|
## Helpers ##
|
46
581
|
|
47
582
|
def access_by_uuid(id)
|
48
|
-
|
583
|
+
# Method to access the XML report in the browser
|
584
|
+
url = url_encode(id)
|
49
585
|
visit "/#{url}"
|
50
586
|
page.should have_content('Query')
|
51
587
|
end
|