sequenceserver 2.0.0.beta3 → 2.0.0.beta4

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

@@ -33,9 +33,9 @@ module SequenceServer
     no_hits_report = BLAST::Report.new(no_hits)
 
     it 'will return queries with valid length' do
-      hits_report.queries.first.length.should be_a Fixnum
+      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 Fixnum
+      no_hits_report.queries.first.length.should be_a Integer
       no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
     end
 
@@ -80,45 +80,45 @@ module SequenceServer
     # 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 Fixnum
+      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 Fixnum
+      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 Fixnum
+      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 Fixnum
+      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 Fixnum
+      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 Fixnum
-      hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Fixnum
+      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 Fixnum
+      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 Fixnum
+      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 Fixnum
+        .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 Fixnum
+      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 }
 

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

@@ -1,34 +1,232 @@
-require 'spec_helper'
-require 'sauce_whisk'
-require 'capybara/rspec'
-require 'selenium-webdriver'
+describe 'report generated from imported XML', type: :feature, js: true do
+  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide
+  # sequences for reproducibility.
+  it 'loads diamond BLASTP xml and tests hit alignment and sidebar Alignment download' do
+    access_by_uuid('diamond_0.9.24/blastp')
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt')
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt'))
 
-RSpec.configure do |config|
-  config.include Capybara::DSL
-end
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-35_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-35_hits_diamond_blastp.txt'))
+    clear_downloads
+
+    # Check the cheboxes of indicted hits and click on the download of Alignment
+    # of selected hits and compare the downloaded content
+
+    page.check('Query_1_hit_1_checkbox')
+    page.check('Query_1_hit_2_checkbox')
+    page.check('Query_2_hit_1_checkbox')
+    page.check('Query_2_hit_2_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_diamond_blastp.txt'))
+    page.should have_content('BLASTP')
+  end
+
+  it 'loads diamond BLASTP XML and tests alignment overview and hit PNG/SVG download' do
+    access_by_uuid('diamond_0.9.24/blastp')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
+
+    clear_downloads
+
+    # Click on the PNG/SVG download button of the first hit available and
+    # compare the downloaded content.
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-sp_P04637_P53_HUMAN.png')
 
-describe 'report generated from imported XML', :js => true do
-  before do |scenario|
-    Capybara.app = SequenceServer.init
-    Capybara.server = :webrick
-    Capybara.javascript_driver = :selenium
-    Capybara.default_max_wait_time = 60
+    clear_downloads
 
-   Capybara.register_driver :selenium do |app|
-     options = ::Selenium::WebDriver::Firefox::Options.new
-     options.args << '--headless'
-          Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
-    end
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-sp_P04637_P53_HUMAN.svg')
+    page.should have_content('BLASTP')
   end
 
-  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
-  it 'loads Diamond blastp xml report' do
+  it 'loads diamond BLASTP XML and tests Circos download' do
     access_by_uuid('diamond_0.9.24/blastp')
+
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+  end
+
+  it 'loads BLASTP XML and tests Length distribution download' do
+    access_by_uuid('diamond_0.9.24/blastp')
+
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
+  end
+
+  # BLASTX test scenarios
+
+  it 'loads diamond BLASTX XML and tests hit alignment and sidebar Alignment download' do
+    access_by_uuid('diamond_0.9.24/blastx')
+
+    # Click on the first Alignment download button on the page and wait for the
+    # download to finish.
+    page.execute_script("$('.download-aln:eq(0)').click()")
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('MH011443_1_sp_P04637_P53_HUMAN.txt')
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt'))
+
+    clear_downloads
+
+    # Click on the Alignment of all hits download and compare the downloaded
+    # content
+
+    page.click_link('Alignment of all hits')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-35_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-35_hits_diamond_blastx.txt'))
+    clear_downloads
+
+    # Select four hit checkboxes and click on the Alignment of selected hits.
+    # Compare the downloaded content.
+    page.check('Query_1_hit_3_checkbox')
+    page.check('Query_1_hit_4_checkbox')
+    page.check('Query_2_hit_3_checkbox')
+    page.check('Query_2_hit_4_checkbox')
+    page.click_link('Alignment of 4 selected hit(s)')
+    wait_for_download
+
+    expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_diamond_blastx.txt'))
+
+    page.should have_content('BLASTX')
   end
 
-  it 'loads Diamond blastx xml report' do
+  it 'loads diamond BLASTX XML and tests alignment overview and hit PNG/SVG download' do
     access_by_uuid('diamond_0.9.24/blastx')
+
+    # Click on the PNG/SVG download button of the alignment overview and compare
+    # the downloaded content.
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
+
+    clear_downloads
+    # Click on the PNG/SVG download button of the first hit available and
+    # compare the downloaded content.
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-sp_P04637_P53_HUMAN.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-sp_P04637_P53_HUMAN.svg')
+    page.should have_content('BLASTX')
   end
+
+  it 'loads diamond BLASTX XML and tests Circos download' do
+    access_by_uuid('diamond_0.9.24/blastx')
+    # Click on the Circos expanding button, wait for animation, click on the
+    # download of PNG/SVG file and test that it initiated a file download in a
+    # right format.
+
+    page.should have_content('Chord diagram: queries and their top hits')
+    page.execute_script("$('.circos > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(0)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
+  end
+
+  it 'loads diamond BLASTX XML and tests Length distribution download' do
+    access_by_uuid('diamond_0.9.24/blastx')
+
+    # Click on the Length distribution expanding button, wait for animation,
+    # click on the download of PNG/SVG file and test that it initiated a file
+    # download in a right format.
+
+    page.should have_content('Length distribution of hits')
+    page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
+    sleep 1
+
+    page.execute_script("$('.export-to-png:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
+
+    clear_downloads
+
+    page.execute_script("$('.export-to-svg:eq(1)').click()")
+    wait_for_download
+    expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
+  end
+
   ## Helpers ##
 
   def access_by_uuid(id)

data/spec/capybara_spec.rb

@@ -14,51 +14,50 @@ describe 'a browser', type: :feature, js: true do
     fill_in('sequence', with: nucleotide_query)
     check(nucleotide_databases.first)
     page.evaluate_script("$('.protein .database').first().hasClass('disabled')")
-      .should eq(true)
+        .should eq(true)
   end
 
   it 'shows a dropdown menu when other blast methods are available' do
     visit '/'
     fill_in('sequence', with: nucleotide_query)
     check(nucleotide_databases.first)
-    page.save_screenshot('screenshot.png')
     page.has_css?('button.dropdown-toggle').should eq(true)
   end
 
   it 'can run a simple blastn search' do
     perform_search query: nucleotide_query,
-      databases: nucleotide_databases
+                   databases: nucleotide_databases
     page.should have_content('BLASTN')
   end
 
   it 'can run a simple blastp search' do
     perform_search query: protein_query,
-      databases: protein_databases
+                   databases: protein_databases
     page.should have_content('BLASTP')
   end
 
   it 'can run a simple blastx search' do
     perform_search query: nucleotide_query,
-      databases: protein_databases
+                   databases: protein_databases
     page.should have_content('BLASTX')
   end
 
   it 'can run a simple tblastx search' do
     perform_search query: nucleotide_query,
-      databases: nucleotide_databases,
-      method: 'tblastx'
+                   databases: nucleotide_databases,
+                   method: 'tblastx'
     page.should have_content('TBLASTX')
   end
 
   it 'can run a simple tblastn search' do
     perform_search query: protein_query,
-      databases: nucleotide_databases
+                   databases: nucleotide_databases
     page.should have_content('TBLASTN')
   end
 
   ### Test aspects of the generated report.
 
-  it "can download FASTA of each hit" do
+  it 'can download FASTA of each hit' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
@@ -70,13 +69,13 @@ describe 'a browser', type: :feature, js: true do
     wait_for_download
 
     # Test name and content of the downloaded file.
-    expect(File.basename(downloaded_file)).
-      to eq('sequenceserver-SI2.2.0_06267.fa')
-    expect(File.read(downloaded_file)).
-      to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
+    expect(File.basename(downloaded_file))
+      .to eq('sequenceserver-SI2.2.0_06267.fa')
+    expect(File.read(downloaded_file))
+      .to eq(File.read("#{__dir__}/sequences/sequenceserver-SI2.2.0_06267.fa"))
   end
 
-  it "can download FASTA of selected hits" do
+  it 'can download FASTA of selected hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
@@ -89,10 +88,10 @@ describe 'a browser', type: :feature, js: true do
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sequenceserver-2_hits.fa'))
   end
 
-  it "can download FASTA of all hits" do
+  it 'can download FASTA of all hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
@@ -103,10 +102,10 @@ describe 'a browser', type: :feature, js: true do
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('sequenceserver-2_hits.fa')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/sequenceserver-2_hits.fa"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sequenceserver-2_hits.fa'))
   end
 
-  it "can download alignment for each hit" do
+  it 'can download alignment for each hit' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
@@ -119,11 +118,11 @@ describe 'a browser', type: :feature, js: true do
 
     # Test name and content of the downloaded file.
     expect(File.basename(downloaded_file)).to eq('Query_1_SI2_2_0_06267.txt')
-    expect(File.read(downloaded_file)).
-      to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
+    expect(File.read(downloaded_file))
+      .to eq(File.read("#{__dir__}/sequences/Query_1_SI2_2_0_06267.txt"))
   end
 
-  it "can download Alignment of selected hits" do
+  it 'can download Alignment of selected hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
@@ -136,10 +135,10 @@ describe 'a browser', type: :feature, js: true do
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-2_hits.txt'))
   end
 
-  it "can download Alignment of all hits" do
+  it 'can download Alignment of all hits' do
     # Do a BLASTP search. protein_query refers to the first two sequence in
     # protein_databases[0], so the top hits are the query sequences themselves.
     perform_search(query: protein_query,
@@ -150,7 +149,7 @@ describe 'a browser', type: :feature, js: true do
     wait_for_download
 
     expect(File.basename(downloaded_file)).to eq('alignment-2_hits.txt')
-    expect(File.read(downloaded_file)).to eq(File.read("spec/sequences/alignment-2_hits.txt"))
+    expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-2_hits.txt'))
   end
 
   it 'can download BLAST results in XML and tabular formats' do
@@ -232,7 +231,7 @@ describe 'a browser', type: :feature, js: true do
                    databases: protein_databases.values_at(0))
 
     ## Check that there is a circos vis and unfold it.
-    page.should have_content('Circos')
+    page.should have_content('Chord diagram: queries and their top hits')
     page.execute_script("$('.circos > .grapher-header > h5').click()")
     sleep 1
 
@@ -246,7 +245,6 @@ describe 'a browser', type: :feature, js: true do
     expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
     clear_downloads
 
-
     ## Check that there is a graphical overview of hits.
     page.should have_content('Graphical overview of hits')
 
@@ -260,7 +258,6 @@ describe 'a browser', type: :feature, js: true do
     expect(File.basename(downloaded_file)).to eq('Alignment-Overview-Query_1.png')
     clear_downloads
 
-
     ## Check that there is a length distribution of hits.
     page.should have_content('Length distribution of hits')
     page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
@@ -292,7 +289,7 @@ describe 'a browser', type: :feature, js: true do
 
   ## Helpers ##
 
-  def perform_search(query: , databases: , method: nil)
+  def perform_search(query:, databases:, method: nil)
     # Load search form.
     visit '/'