sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb

@@ -0,0 +1,55 @@
+require 'spec_helper'
+require 'sauce_whisk'
+require 'capybara/rspec'
+require 'selenium-webdriver'
+
+RSpec.configure do |config|
+  config.include Capybara::DSL
+end
+
+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 = 45
+
+   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
+  end
+
+  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
+  it 'loads BLASTP xml output' do
+    access_by_uuid('blast_2.8.1/blastp')
+    page.save_screenshot('abc.png')
+  end
+
+  it 'loads BLASTX xml output' do
+    access_by_uuid('blast_2.8.1/blastx')
+  end
+
+  it 'loads BLASTN xml output' do
+    access_by_uuid('blast_2.8.1/blastn')
+  end
+
+  it 'loads TBLASTN xml output' do
+    access_by_uuid('blast_2.8.1/tblastn')
+  end
+
+  it 'loads TBLASTX xml output' do
+    access_by_uuid('blast_2.8.1/tblastx')
+    page.save_screenshot('screen.png')
+  end
+
+  ## Helpers ##
+
+  def access_by_uuid(id)
+    url = url_encode(id)
+    visit "/#{url}"
+    page.should have_content('Query')
+    page.execute_script("return $('.view-sequence').is(':disabled')").should eq(false)
+  end
+end

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

@@ -0,0 +1,228 @@
+require 'spec_helper'
+
+# Test BLAST module.
+module SequenceServer
+ with_hits = Job.fetch('blast_2.9.0/blastn')
+  no_hits = Job.fetch('blast_2.9.0/blastn_nohits')
+
+  init
+
+  describe 'Report' do
+    hits_report = BLAST::Report.new(with_hits)
+    no_hits_report = BLAST::Report.new(no_hits)
+
+    it 'will return an Array of queries' do
+      hits_report.queries.should be_a Array
+      no_hits_report.queries.should be_a Array
+    end
+
+    it 'will return a Hash of stats' do
+      hits_report.stats.should be_a Hash
+      no_hits_report.stats.should be_a Hash
+    end
+
+    it 'contains all the necessary stats' do
+      hits_report.stats.length.should eql(7)
+      no_hits_report.stats.length.should eql(7)
+    end
+  end
+
+  describe 'Query' do
+    hits_report = BLAST::Report.new(with_hits)
+    no_hits_report = BLAST::Report.new(no_hits)
+
+    it 'will return queries with valid length' do
+      hits_report.queries.first.length.should be_a Fixnum
+      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 satisfy { |n| n > 0 }
+    end
+
+    it 'will return an Array of hits' do
+      hits_report.queries.first.hits.should be_a Array
+      no_hits_report.queries.first.hits.should be_a Array
+    end
+  end
+
+  describe 'Hits' do
+    hits_report = BLAST::Report.new(with_hits)
+    no_hits_report = BLAST::Report.new(no_hits)
+
+    it 'will have non zero length' do
+      hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
+    end
+
+    it 'will return an Array of HSPs' do
+      hits_report.queries.first.hits.first.hsps.should be_a Array
+    end
+
+    it 'will return an Array with atleast one HSP' do
+      hits_report.queries.first.hits.first.hsps.length.should be >= 1
+    end
+
+    it 'will contain no element if no hits were obtained' do
+      no_hits_report.queries.first.hits.length.should eql(0)
+    end
+  end
+
+  # Test general features of HSPs. Algorithm specific customizations are
+  # tested separetly.
+  describe 'HSPs' do
+    hits_report = BLAST::Report.new(with_hits)
+
+    # Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
+    # hit object it belongs to.
+    it 'have all the necessary values' do
+      hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
+    end
+
+    # Test Random HSPs to ensure that all the values from HSP struct are valid.
+    it 'have correct alignment values' do
+      hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
+      hits_report.queries.last.hits.first.hsps.last.score.should be_a Fixnum
+
+      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_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_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_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_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.identity.should be_a Fixnum
+      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_not satisfy { |n| n < 0 }
+
+      hits_report.queries.first.hits.first.hsps.last.positives
+        .should be_a Fixnum
+      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 satisfy { |n| n > 0 }
+
+      hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
+      hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
+      hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
+    end
+
+    it 'have correctly matched query, hit and midline alignments' do
+      hsp = hits_report.queries.last.hits.last.hsps.first
+      hsp.qseq.length.should eql(hsp.sseq.length)
+      hsp.sseq.length.should eql(hsp.midline.length)
+      hsp.midline.length.should eql(hsp.qseq.length)
+    end
+  end
+
+  # Individually test different BLAST+ algorithms
+  #
+  describe 'BLASTN' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('blast_2.9.0/blastn'))
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      [1, -1].should include(hsp.qframe)
+      [1, -1].should include(hsp.sframe)
+    end
+
+    it 'have correct qstart, qend, sstart, send' do
+      if hsp.sframe > 0
+        hsp.sstart.should be <= hsp.send
+      else
+        hsp.sstart.should be >= hsp.send
+      end
+    end
+  end
+
+  describe 'BLASTP' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('blast_2.9.0/blastp'))
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      hsp.qframe.should eql(0)
+      hsp.sframe.should eql(0)
+    end
+
+    it 'have correct qstart, qend, sstart, send values' do
+      hsp.qstart.should be <= hsp.qend
+      hsp.sstart.should be <= hsp.send
+    end
+
+  end
+
+  describe 'BLASTX' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('blast_2.9.0/blastx'))
+
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      hsp.qframe.should_not eql(0)
+      hsp.sframe.should eql(0)
+    end
+
+    it 'have correct qstart, qend, sstart, send' do
+      hsp.qstart.should be <= hsp.qend
+      hsp.sstart.should be <= hsp.send
+    end
+  end
+
+  describe 'TBLASTX' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('blast_2.9.0/tblastx'))
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      hsp.qframe.should_not eql(0)
+      hsp.sframe.should_not eql(0)
+    end
+
+    it 'have correct qstart, qend, sstart, send' do
+      hsp.qstart.should be <= hsp.qend
+      hsp.sstart.should be <= hsp.send
+    end
+  end
+
+  describe 'TBLASTN' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('blast_2.9.0/tblastn'))
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      hsp.qframe.should eql(0)
+      hsp.sframe.should_not eql(0)
+    end
+
+    it 'have correct qstart, qend, sstart, send' do
+      hsp.qstart.should be <= hsp.qend
+      hsp.sstart.should be <= hsp.send
+    end
+  end
+end

data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb

@@ -0,0 +1,53 @@
+require 'spec_helper'
+require 'sauce_whisk'
+require 'capybara/rspec'
+require 'selenium-webdriver'
+
+RSpec.configure do |config|
+  config.include Capybara::DSL
+end
+
+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 = 10
+
+   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
+  end
+
+  # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
+  it 'loads BLASTP xml output' do
+    access_by_uuid('blast_2.9.0/blastp')
+  end
+
+  it 'loads BLASTX xml output' do
+    access_by_uuid('blast_2.9.0/blastx')
+  end
+
+  it 'loads BLASTN xml output' do
+    access_by_uuid('blast_2.9.0/blastn')
+  end
+
+  it 'loads TBLASTN xml output' do
+    access_by_uuid('blast_2.9.0/tblastn')
+  end
+
+  it 'loads TBLASTX xml output' do
+    access_by_uuid('blast_2.9.0/tblastx')
+  end
+
+  ## Helpers ##
+
+  def access_by_uuid(id)
+    url = url_encode(id)
+    visit "/#{url}"
+    page.should have_content('Query')
+    page.execute_script("return $('.view-sequence').is(':disabled')").should eq(false)
+  end
+end

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

@@ -0,0 +1,176 @@
+require 'spec_helper'
+
+# Test BLAST module.
+module SequenceServer
+
+  with_hits = Job.fetch('diamond_0.9.24/blastx')
+  no_hits = Job.fetch('diamond_0.9.24/blastx_nohits')
+
+  init
+
+  describe 'Report' do
+    hits_report = BLAST::Report.new(with_hits)
+    no_hits_report = BLAST::Report.new(no_hits)
+
+    it 'will return an Array of queries' do
+      hits_report.queries.should be_a Array
+      no_hits_report.queries.should be_a Array
+    end
+
+    it 'will return a Hash of stats' do
+      hits_report.stats.should be_a Hash
+      no_hits_report.stats.should be_a Hash
+    end
+
+    it 'contains all the necessary stats' do
+      hits_report.stats.length.should eql(7)
+      no_hits_report.stats.length.should eql(7)
+    end
+  end
+
+  describe 'Query' do
+    hits_report = BLAST::Report.new(with_hits)
+    no_hits_report = BLAST::Report.new(no_hits)
+
+    it 'will return queries with valid length' do
+      hits_report.queries.first.length.should be_a Fixnum
+      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 satisfy { |n| n > 0 }
+    end
+
+    it 'will return an Array of hits' do
+      hits_report.queries.first.hits.should be_a Array
+      no_hits_report.queries.first.hits.should be_a Array
+    end
+  end
+
+  describe 'Hits' do
+    hits_report = BLAST::Report.new(with_hits)
+    no_hits_report = BLAST::Report.new(no_hits)
+
+    it 'will have non zero length' do
+      hits_report.queries.last.hits.first.length.should satisfy { |n| n > 0 }
+    end
+
+    it 'will return an Array of HSPs' do
+      hits_report.queries.first.hits.first.hsps.should be_a Array
+    end
+
+    it 'will return an Array with atleast one HSP' do
+      hits_report.queries.first.hits.first.hsps.length.should be >= 1
+    end
+
+    it 'will contain no element if no hits were obtained' do
+      no_hits_report.queries.first.hits.length.should eql(0)
+    end
+  end
+
+  # Test general features of HSPs. Algorithm specific customizations are
+  # tested separetly.
+  describe 'HSPs' do
+    hits_report = BLAST::Report.new(with_hits)
+
+    # Currently using all 17 HSP parameters in BLAST Report + 1 to refer to the
+    # hit object it belongs to.
+    it 'have all the necessary values' do
+      hits_report.queries.last.hits.first.hsps.last.count.should eql(19)
+    end
+
+    # Test Random HSPs to ensure that all the values from HSP struct are valid.
+    it 'have correct alignment values' do
+      hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
+      hits_report.queries.last.hits.first.hsps.last.score.should be_a Fixnum
+
+      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_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_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_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_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.identity.should be_a Fixnum
+      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_not satisfy { |n| n < 0 }
+
+      hits_report.queries.first.hits.first.hsps.last.positives
+        .should be_a Fixnum
+      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 satisfy { |n| n > 0 }
+
+      hits_report.queries.last.hits.last.hsps.first.qseq.should be_a String
+      hits_report.queries.last.hits.last.hsps.first.sseq.should be_a String
+      hits_report.queries.last.hits.last.hsps.first.midline.should be_a String
+    end
+
+    it 'have correctly matched query, hit and midline alignments' do
+      hsp = hits_report.queries.last.hits.last.hsps.first
+      hsp.qseq.length.should eql(hsp.sseq.length)
+      hsp.sseq.length.should eql(hsp.midline.length)
+      hsp.midline.length.should eql(hsp.qseq.length)
+    end
+  end
+
+  # Individually test different DIAMOND BLASTP/BLASTX algorithms
+  #
+
+  describe 'diamond BLASTP' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('diamond_0.9.24/blastp'))
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      hsp.qframe.should eql(0)
+      hsp.sframe.should eql(0)
+    end
+
+    it 'have correct qstart, qend, sstart, send values' do
+      hsp.qstart.should be <= hsp.qend
+      hsp.sstart.should be <= hsp.send
+    end
+
+  end
+
+  describe 'diamond BLASTX' do
+    let 'hsp' do
+      report = BLAST::Report.new(Job.fetch('diamond_0.9.24/blastx'))
+      report.queries.first.hits.last.hsps.first
+    end
+
+    it 'have correct query and subject frame' do
+      hsp.qframe.should_not eql(0)
+      hsp.sframe.should eql(0)
+    end
+
+    it 'have correct qstart, qend, sstart, send' do
+      hsp.qstart.should be <= hsp.qend
+      hsp.sstart.should be <= hsp.send
+    end
+  end
+end
+