sequenceserver 1.1.0.beta12 → 2.0.0.beta1

data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.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 = 20
+
+   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_2.2.31/blastp')
+  end
+
+  it 'loads BLASTX xml output' do
+    access_by_uuid('blast_2.2.31/blastx')
+  end
+
+  it 'loads BLASTN xml output' do
+    access_by_uuid('blast_2.2.31/blastn')
+  end
+
+  it 'loads TBLASTN xml output' do
+    access_by_uuid('blast_2.2.31/tblastn')
+  end
+
+  it 'loads TBLASTX xml output' do
+    access_by_uuid('blast_2.2.31/tblastx')
+  end
+
+
+  ## Helpers ##
+
+  def access_by_uuid(id)
+    url = url_encode(id)
+    visit "/#{url}"
+    page.should have_content('Query')
+  end
+end

data/spec/{blast_spec.rb → blast_versions/blast_2.3.0/blast_2.3.0_spec.rb}

@@ -2,9 +2,9 @@ require 'spec_helper'
 
 # Test BLAST module.
 module SequenceServer
-  SequenceServer::DOTDIR = File.join(__dir__, 'sample_reports')
-  with_hits = Job.fetch('with_hits_sample')
-  no_hits = Job.fetch('no_hits_sample')
+
+  with_hits = Job.fetch('blast_2.3.0/blastn')
+  no_hits = Job.fetch('blast_2.3.0/blastn_nohits')
 
   init
 
@@ -133,35 +133,19 @@ module SequenceServer
       hsp.sseq.length.should eql(hsp.midline.length)
       hsp.midline.length.should eql(hsp.qseq.length)
     end
-
-    it 'have correct pretty printing' do
-      hsp = hits_report.queries.last.hits.last.hsps.first
-      pp  = hsp.pp
-
-      pp.should_not be_empty
-      pp.should be_a_kind_of(String)
-      (pp.lines.count % 3).should eql(0)
-
-      pp.should match(/^Query/)
-      pp.should match(/Subject/)
-    end
-
   end
 
   # Individually test different BLAST+ algorithms
   #
   describe 'BLASTN' do
     let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blastn_sample'))
+      report = BLAST::Report.new(Job.fetch('blast_2.3.0/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)
-
-      hsp.qframe_unit.should eq(1)
-      hsp.sframe_unit.should eq(1)
     end
 
     it 'have correct qstart, qend, sstart, send' do
@@ -175,16 +159,13 @@ module SequenceServer
 
   describe 'BLASTP' do
     let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blastp_sample'))
+      report = BLAST::Report.new(Job.fetch('blast_2.3.0/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)
-
-      hsp.qframe_unit.should eq(1)
-      hsp.sframe_unit.should eq(1)
     end
 
     it 'have correct qstart, qend, sstart, send values' do
@@ -196,7 +177,7 @@ module SequenceServer
 
   describe 'BLASTX' do
     let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('blastx_sample'))
+      report = BLAST::Report.new(Job.fetch('blast_2.3.0/blastx'))
 
       report.queries.first.hits.last.hsps.first
     end
@@ -204,9 +185,6 @@ module SequenceServer
     it 'have correct query and subject frame' do
       hsp.qframe.should_not eql(0)
       hsp.sframe.should eql(0)
-
-      hsp.qframe_unit.should eq(3)
-      hsp.sframe_unit.should eq(1)
     end
 
     it 'have correct qstart, qend, sstart, send' do
@@ -217,16 +195,13 @@ module SequenceServer
 
   describe 'TBLASTX' do
     let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('tblastx_sample'))
+      report = BLAST::Report.new(Job.fetch('blast_2.3.0/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)
-
-      hsp.qframe_unit.should eq(3)
-      hsp.sframe_unit.should eq(3)
     end
 
     it 'have correct qstart, qend, sstart, send' do
@@ -237,22 +212,18 @@ module SequenceServer
 
   describe 'TBLASTN' do
     let 'hsp' do
-      report = BLAST::Report.new(Job.fetch('tblastn_sample'))
+      report = BLAST::Report.new(Job.fetch('blast_2.3.0/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)
-
-      hsp.qframe_unit.should eq(1)
-      hsp.sframe_unit.should eq(3)
     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_2.3.0/import_spec_capybara_local_2.3.0.rb

@@ -0,0 +1,52 @@
+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 = 20
+
+   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_2.3.0/blastp')
+  end
+
+  it 'loads BLASTX xml output' do
+    access_by_uuid('blast_2.3.0/blastx')
+  end
+
+  it 'loads BLASTN xml output' do
+    access_by_uuid('blast_2.3.0/blastn')
+  end
+
+  it 'loads TBLASTN xml output' do
+    access_by_uuid('blast_2.3.0/tblastn')
+  end
+
+  it 'loads TBLASTX xml output' do
+    access_by_uuid('blast_2.3.0/tblastx')
+  end
+
+ ## Helpers ##
+
+  def access_by_uuid(id)
+    url= url_encode(id)
+    visit "/#{url}"
+    page.should have_content('Query')
+  end
+end

data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb

@@ -0,0 +1,228 @@
+require 'spec_helper'
+
+# Test BLAST module.
+module SequenceServer
+ with_hits = Job.fetch('blast_2.4.0/blastn')
+  no_hits = Job.fetch('blast_2.4.0/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_2.4.0/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_2.4.0/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_2.4.0/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_2.4.0/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_2.4.0/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