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
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require 'spec_helper'
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require 'sauce_whisk'
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require 'capybara/rspec'
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require 'selenium-webdriver'
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RSpec.configure do |config|
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config.include Capybara::DSL
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end
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SequenceServer::DOTDIR = File.join(__dir__, 'imported_xml_reports')
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describe 'report generated from imported XML', :js => true do
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before do |scenario|
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Capybara.app = SequenceServer.init
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Capybara.server = :webrick
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Capybara.javascript_driver = :selenium
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Capybara.default_max_wait_time = 10
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options = ::Selenium::WebDriver::Firefox::Options.new
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options.args << '--headless'
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Capybara.register_driver :selenium do |app|
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Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
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end
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end
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# Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
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it 'loads BLASTP xml output' do
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access_by_uuid('ea347d79-6397-44e5-9048-c90e58c56200')
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end
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it 'loads BLASTX xml output' do
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access_by_uuid('e39d30a2-304f-4b85-ad1c-a114cc0b383f')
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end
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it 'loads BLASTN xml output' do
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access_by_uuid('85ca3be1-b495-43d3-b267-2e50aced9cc7')
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end
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it 'loads TBLASTN xml output' do
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access_by_uuid('148e0664-4ab8-41af-86cb-127ff19f2d33')
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end
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it 'loads TBLASTX xml output' do
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access_by_uuid('752b6b87-2670-47a0-aa57-d0dc8cdd7667')
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end
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it 'loads diamond_BLASTP xml output' do
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access_by_uuid('043110ae-faf9-4258-8098-3384fb16fbb1')
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end
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it 'loads diamond_BLASTX xml output' do
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access_by_uuid('8e400eed-4ef2-48e6-aee8-a55a45606e77')
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end
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## Helpers ##
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def access_by_uuid(id)
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visit "/#{id}"
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page.should have_content('Query')
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end
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end
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