quorum 0.3.3 → 0.4.0

data/spec/dummy/quorum/bin/search

@@ -33,8 +33,8 @@ Options:
         HEAD
 
         # Search tool
-        opt :search_tool, "Search tool to execute. Available tools: " << 
-        "#{SEARCH_TOOLS.keys.join(', ')}", :type => :string, 
+        opt :search_tool, "Search tool to execute. Available tools: " <<
+        "#{SEARCH_TOOLS.keys.join(', ')}", :type => :string,
           :required => true, :short => "-s"
 
         # General settings
@@ -48,19 +48,19 @@ Options:
           :short => "-i"
         opt :database, "Database name", :type => :string, :required => true,
           :short => "-d"
-        opt :database_adapter, "ActiveRecord database adapter", 
+        opt :database_adapter, "ActiveRecord database adapter",
           :type => :string, :required => true, :short => "-a"
-        opt :database_host, "Database host", :type => :string, 
+        opt :database_host, "Database host", :type => :string,
           :required => true, :short => "-k"
-        opt :database_user, "Database username", :type => :string, 
+        opt :database_user, "Database username", :type => :string,
           :required => true, :short => "-u"
         opt :database_password, "Database password", :type => :string,
           :required => true, :short => "-p"
-       
+
         # Global settings
         opt :search_database, "Path to search tool database", :type => :string,
           :short => "-b"
-        opt :threads, "Number of threads to spawn for search tool", 
+        opt :threads, "Number of threads to spawn for search tool",
           :type => :int, :short => "-t"
       end
 
@@ -136,6 +136,6 @@ Options:
 end
 
 if __FILE__ == $0
-  Quorum::Search.new  
+  Quorum::Search.new
 end
 

data/spec/dummy/quorum/blastdb/test/contigs.fa

@@ -1,2 +1,15 @@
 >TOG900080
 TGATAGGATAATTCTAGACAAAACATTAGCCGATCAAGTGTCATCATGGAAAAGCAGCAGGGGCCTTAGTGATACAGTGGTGACTGATCATGCTTGTTCTGGGGAAACATGCTCGTACTACGCAATTGGAGATGTATTTATTTGTGAAAAGACTGGACAAGTTCATGTTTGTGACGAAACATGTAGGGAAGTAGTAATGGATCCCACCAACGAGCTTTTGGTCTGTACAATATCTGGCCACTGTTTTGACAGATTGCTATCACCTGCTGAAATGGAGCCTGATGCTGAGCAGCAGCAAGGTGGTGCGGCAGATGAGGCAGAACCGTTTATGGGATCTGGCCGTTTTGCACGGGCTTATTTGCTGGGATACAATTGTGCTGATGAAAAGGAGCTTGAAGCTACTTTGAGGTTTTGCTGATCCCTATTGGCCCTTCTGGAGTGGATGATCTCATGTCTCAGCATTTACCTATTTAAGATCAAATAAATCGGGTTTCCTTTTCGTGTTTCTCTTGGCATAAGAATGTTTGATTAGATCTAGATTATGAAACTCTAATCGTCTTCTATATTAATAATTGTATGCTTAAATTTATAGTTGAAATTCCATTGATGAATTTTTCTT
+>reverse translation of ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum] to a 687 base sequence of most likely codons.
+atggaacagtattggagcggcagcgcgattaacgaaaacaaaggcatggtggaaaacctg
+cagcgctatggcattattaaaagcagcaaagtggcggaaaccatggaaaaaattgatcgc
+ggcctgtttgtgccgaacggcgtgcagccgtatattgatagcccgatgagcattggctat
+aacgcgaccattagcgcgccgcatatgcatgcgacctgcctgcagctgctggaaaactat
+ctgcagccgggcatgcatgcgctggatgtgggcagcggcaccggctatctgaccgcgtgc
+tttgcgatgatggtgggcccgaacggccgcgcggtgggcgtggaacatattccggaactg
+gtgagctttagcattaacaacattgaaaaaagcgcggcggcgccgcagctgaaagatggc
+agcctgagcgtgcatgaaggcgatggccgccagggctggccggaatttgcgacctatgat
+gcgattcatgtgggcgcggcggcgccggaaattccgcagccgctgattgatcagctgaaa
+accggcggccgcatgattattccggtgggcaacgtgtttcaggatctgaaagtggtggat
+aaaaacagcgatggcagcattagcattcgcaccgaaaccagcgtgcgctatgtgccgctg
+accagcaaagaagcgcagctgaaagaa

data/spec/dummy/quorum/blastdb/test/peptides.fa

@@ -1,2 +1,4 @@
 >ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
 MEQYWSGSAINENKGMVENLQRYGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETSVRYVPLTSKEAQLKE
+>VIRT10447
+TVLPHLPHHLAAAQHQAPFQQVIAICQNSGQILYRPKARWWDPLLLPYMFRHKHELVQSFHK

data/spec/dummy/quorum/blastdb/test.nhd

@@ -1 +1,2 @@
+34432766131
 8824380950

data/spec/dummy/quorum/blastdb/test.nsd

@@ -1 +1,2 @@
 gnl|bl_ord_id|00
+gnl|bl_ord_id|11

data/spec/dummy/quorum/blastdb/test.phd

@@ -1 +1,2 @@
+24330897691
 28413460680

data/spec/dummy/quorum/blastdb/test.psd

@@ -1 +1,2 @@
 gnl|bl_ord_id|00
+gnl|bl_ord_id|11

data/spec/dummy/quorum/lib/fetch_tools/blast_db.rb

@@ -77,10 +77,10 @@ module Quorum
       #
       # Execute the blastdbcmd(s) and return the matching sequence.
       #
-      # To make Blast execute as quickly as possible, each selected 
-      # algorithm blasts against all supplied databases at once. 
-      # 
-      # See quorum/lib/search_tools/blast.rb for more information. 
+      # To make Blast execute as quickly as possible, each selected
+      # algorithm blasts against all supplied databases at once.
+      #
+      # See quorum/lib/search_tools/blast.rb for more information.
       #
       # One consequence of this is not knowing which Blast database to use
       # when retrieving a hit sequence via blastdbcmd.
@@ -93,10 +93,10 @@ module Quorum
       def execute_blast_db_cmd
         generate_blast_db_cmds
         @logger.log("NCBI Blast", @cmds.join('; '))
-        
+
         @seqs = ""
         @cmds.each { |c| @seqs << `#{c} 2> /dev/null` }
-        
+
         seq = parse_and_send_results
         $stdout.print seq
       end

data/spec/dummy/quorum/lib/logger.rb

@@ -29,13 +29,13 @@ module Quorum
     # Removes instance files.
     #
     def remove_files(files)
-      unless Dir.glob(files).empty?
-        `rm #{files}`
-      else
-        log(
+      if Dir.glob(files).empty?
+         log(
           "remove_files",
           "Unable to remove #{files}"
         )
+      else
+       `rm #{files}`
       end
     end
 

data/spec/dummy/quorum/lib/search_tools/blast.rb

@@ -126,6 +126,9 @@ module Quorum
         Digest::MD5.hexdigest(sequence).to_s + "-" + Time.now.to_f.to_s
       end
 
+      #
+      # Blastn command
+      #
       def generate_blastn_cmd
         blastn = "blastn " <<
         "-db \"#{@db}\" " <<
@@ -145,6 +148,9 @@ module Quorum
         blastn
       end
 
+      #
+      # Blastx command
+      #
       def generate_blastx_cmd
         blastx = "blastx " <<
         "-db \"#{@db}\" " <<
@@ -164,6 +170,9 @@ module Quorum
         blastx
       end
 
+      #
+      # Tblastn command
+      #
       def generate_tblastn_cmd
         tblastn = "tblastn " <<
         "-db \"#{@db}\" " <<
@@ -185,6 +194,9 @@ module Quorum
         tblastn
       end
 
+      #
+      # Blastp command
+      #
       def generate_blastp_cmd
         blastp = "blastp " <<
         "-db \"#{@db}\" " <<
@@ -256,12 +268,65 @@ module Quorum
       end
 
       #
-      # Parse and save Blast results using bio-blastxmlparser.
-      # Only save Blast results if results.bit_score > @min_score.
+      # Save Blast Job Report
+      #
+      # Hsps are only reported if a query hit against the Blast db.
+      # Only save the @data if bit_score exists and it's > the user
+      # defined minimum score.
+      #
+      # Set the attribute results to true for downstream processes.
+      #
+      def save_hsp_results
+        if @data[:bit_score] && (@data[:bit_score].to_i > @min_score.to_i)
+          @data[:results] = true
+          @data["#{@algorithm}_job_id".to_sym] = @job.method(@job_association).call.job_id
+
+          job_report = @job.method(@job_report_association).call.build(@data)
+
+          unless job_report.save!
+            @logger.log(
+              "ActiveRecord",
+              "Unable to save #{@algorithm} results to database.",
+              1,
+              @tmp_files
+            )
+          end
+        end
+      end
+
+      #
+      # Save empty Blast Job Report
+      #
+      # Set the attribute results to false for downstream processes.
+      #
+      def save_empty_results
+        job_report = @job.method(@job_report_association).call.build(
+          "#{@algorithm}_job_id" => @job.method(@job_association).call.job_id,
+          "results"              => false
+        )
+        unless job_report.save!
+          @logger.log(
+            "ActiveRecord",
+            "Unable to save #{@algorithm} results to database.",
+            1,
+            @tmp_files
+          )
+        end
+        @logger.log(
+          "NCBI Blast",
+          "#{@algorithm} report empty.",
+          0,
+          @tmp_files
+        )
+      end
+
+      #
+      # Parse and save Blast results.
+      #
+      # Parse the Blast XML output and save results.
       #
       def parse_and_save_results
-        # Helper to avoid having to perform a query.
-        saved = false
+        @results = false # Did the xml contain results?
 
         if File.size(@out) > 0
           report = Bio::Blast::XmlIterator.new(@out)
@@ -292,28 +357,16 @@ module Quorum
                 @data[:hit_frame]   = hsp.hit_frame
                 @data[:identity]    = hsp.identity
                 @data[:positive]    = hsp.positive
+                @data[:gaps]        = hsp.gaps
                 @data[:align_len]   = hsp.align_len
                 @data[:qseq]        = hsp.qseq
                 @data[:hseq]        = hsp.hseq
                 @data[:midline]     = hsp.midline
 
-                # Hsps are only reported if a query hit against the Blast db.
-                # Only save the @data if bit_score exists.
                 if @data[:bit_score] &&
                   (@data[:bit_score].to_i > @min_score.to_i)
-                  @data[:results] = true
-                  @data["#{@algorithm}_job_id".to_sym] = @job.method(@job_association).call.job_id
-                  saved = true
-                  # Build a new report for each Hsp.
-                  job_report = @job.method(@job_report_association).call.build(@data)
-                  unless job_report.save!
-                    @logger.log(
-                      "ActiveRecord",
-                      "Unable to save #{@algorithm} results to database.",
-                      1,
-                      @tmp_files
-                    )
-                  end
+                  @results = true
+                  save_hsp_results
                 end
 
               end
@@ -321,27 +374,7 @@ module Quorum
           end
         end
 
-        # Save the record and set results to false.
-        unless saved
-          job_report = @job.method(@job_report_association).call.build(
-            "#{@algorithm}_job_id" => @job.method(@job_association).call.job_id,
-            "results"              => false
-          )
-          unless job_report.save!
-            @logger.log(
-              "ActiveRecord",
-              "Unable to save #{@algorithm} results to database.",
-              1,
-              @tmp_files
-            )
-          end
-          @logger.log(
-            "NCBI Blast",
-            "#{@algorithm} report empty.",
-            0,
-            @tmp_files
-          )
-        end
+        save_empty_results unless @results
       end
 
       #
@@ -388,6 +421,9 @@ module Quorum
         end
       end
 
+      #
+      # Remove tmp files.
+      #
       def remove_tmp_files
         `rm #{@tmp_files}` if @tmp_files
       end

data/spec/dummy/quorum/lib/trollop.rb

@@ -12,7 +12,7 @@ VERSION = "1.16.2"
 ## Thrown by Parser in the event of a commandline error. Not needed if
 ## you're using the Trollop::options entry.
 class CommandlineError < StandardError; end
-  
+
 ## Thrown by Parser if the user passes in '-h' or '--help'. Handled
 ## automatically by Trollop#options.
 class HelpNeeded < StandardError; end
@@ -250,7 +250,7 @@ class Parser
     syms.each { |sym| raise ArgumentError, "unknown option '#{sym}'" unless @specs[sym] }
     @constraints << [:depends, syms]
   end
-  
+
   ## Marks two (or more!) options as conflicting.
   def conflicts *syms
     syms.each { |sym| raise ArgumentError, "unknown option '#{sym}'" unless @specs[sym] }
@@ -426,7 +426,7 @@ class Parser
           # call this unless the cursor's at the beginning of a line.
 
     left = {}
-    @specs.each do |name, spec| 
+    @specs.each do |name, spec|
       left[name] = "--#{spec[:long]}" +
         (spec[:short] && spec[:short] != :none ? ", -#{spec[:short]}" : "") +
         case spec[:type]
@@ -647,7 +647,7 @@ private
     start = 0
     ret = []
     until start > str.length
-      nextt = 
+      nextt =
         if start + width >= str.length
           str.length
         else

data/spec/javascripts/fixtures/formatted_sequence.html

@@ -1,4 +1,4 @@
-<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>
+<p class='small'>Alignment (Mouse over for positions):</p><span class='small sequence'><pre>
 qseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>
      ELVIS
 hseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=122>L</a><a rel='quorum-tipsy' title=123>V</a><a rel='quorum-tipsy' title=124>I</a><a rel='quorum-tipsy' title=125>S</a>

data/spec/javascripts/quorum_spec.js

@@ -77,7 +77,7 @@ describe("QUORUM", function() {
     var report = QUORUM.formatSequenceReport(
       "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastn"
     );
-    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=7>C</a><a rel='quorum-tipsy' title=8>G</a><a rel='quorum-tipsy' title=9>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
+    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small sequence'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=7>C</a><a rel='quorum-tipsy' title=8>G</a><a rel='quorum-tipsy' title=9>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
   });
 
   //
@@ -89,7 +89,7 @@ describe("QUORUM", function() {
     var report = QUORUM.formatSequenceReport(
       "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastx"
     );
-    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=9>C</a><a rel='quorum-tipsy' title=12>G</a><a rel='quorum-tipsy' title=15>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
+    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small sequence'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=9>C</a><a rel='quorum-tipsy' title=12>G</a><a rel='quorum-tipsy' title=15>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
   });
 
   //
@@ -101,7 +101,7 @@ describe("QUORUM", function() {
     var report = QUORUM.formatSequenceReport(
       "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 136, "tblastn"
     );
-    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=124>L</a><a rel='quorum-tipsy' title=127>V</a><a rel='quorum-tipsy' title=130>I</a><a rel='quorum-tipsy' title=133>S</a>\n\n</pre></span>");
+    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small sequence'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=124>L</a><a rel='quorum-tipsy' title=127>V</a><a rel='quorum-tipsy' title=130>I</a><a rel='quorum-tipsy' title=133>S</a>\n\n</pre></span>");
   });
 
   //
@@ -113,16 +113,18 @@ describe("QUORUM", function() {
     var report = QUORUM.formatSequenceReport(
       "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 125, "blastp"
     );
-    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=122>L</a><a rel='quorum-tipsy' title=123>V</a><a rel='quorum-tipsy' title=124>I</a><a rel='quorum-tipsy' title=125>S</a>\n\n</pre></span>");
+    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small sequence'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=122>L</a><a rel='quorum-tipsy' title=123>V</a><a rel='quorum-tipsy' title=124>I</a><a rel='quorum-tipsy' title=125>S</a>\n\n</pre></span>");
   });
 
   //
   // jQuery tipsy plugin should display anchor's title attribute on mouseover
   // and hide on mouseout.
   //
-  it("should display title via jquery.tipsy on mouse over hide on mouse out", function() {
+  it("should display title via jquery.tipsy on mouse over and hide on mouse out", function() {
     loadFixtures('formatted_sequence.html');
-    $('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
+    $('.sequence').mouseenter(function() {
+      $(this).find('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
+    });
 
     $('a[rel=quorum-tipsy]').trigger('mouseover');
     expect($('.tipsy')).toBeVisible();

data/spec/requests/jobs_spec.rb

@@ -110,10 +110,20 @@ describe "Jobs" do
         page.should have_content("Search Results")
 
         click_link "Blastx"
-        page.should have_content("Your search returned 0 hits.")
+
+        # Render modal box.
+        find("#blastx-results").find("td a").click
+        page.should have_content("Quorum Report Details")
+        page.should have_content("qseq")
+        page.should have_content("hseq")
 
         click_link "Tblastn"
-        page.should have_content("Your search returned 0 hits.")
+
+        # Render modal box.
+        find("#tblastn-results").find("td a").click
+        page.should have_content("Quorum Report Details")
+        page.should have_content("qseq")
+        page.should have_content("hseq")
 
         ## Interact with the Blast results. ##
         click_link "Blastn"
@@ -125,7 +135,7 @@ describe "Jobs" do
         page.should have_content("hseq")
 
         # Download sequence
-        find("p.small a#download_sequence_1").click
+        find("p.small a#download_sequence_2").click
         page.should have_content("Fetching sequence...")
         page.should have_content("Sequence Downloaded Successfully")
 

data/spec/spec_helper.rb

@@ -3,13 +3,9 @@ ENV["RAILS_ENV"] ||= 'test'
 require File.expand_path("../dummy/config/environment.rb", __FILE__)
 require 'rspec/rails'
 require 'capybara/rspec'
-require 'factory_girl'
 require 'database_cleaner'
 require 'resque_spec'
 
-FactoryGirl.definition_file_paths << File.join(File.dirname(__FILE__), 'factories')
-FactoryGirl.find_definitions
-
 ENGINE_RAILS_ROOT = File.expand_path("../../", __FILE__)
 
 # Requires supporting ruby files with custom matchers and macros, etc,

data/spec/templates/blast_spec.rb

@@ -2,7 +2,7 @@ require 'spec_helper'
 require File.expand_path("../../dummy/quorum/lib/search_tools/blast", __FILE__)
 
 describe "Quorum::SearchTools::Blast" do
-  describe "#execute_blast" do
+  describe "#execute_blast non empty report" do
     before(:each) do
       # Set args as though we executed bin/search.
       @args = {
@@ -69,7 +69,7 @@ describe "Quorum::SearchTools::Blast" do
       blast = Quorum::SearchTools::Blast.new(@args)
       expect {
         blast.execute_blast
-      }.to raise_error(SystemExit)
+      }.to_not raise_error
 
       Dir.glob(
         File.join(@args[:tmp_directory], "*")
@@ -86,7 +86,7 @@ describe "Quorum::SearchTools::Blast" do
       blast = Quorum::SearchTools::Blast.new(@args)
       expect {
         blast.execute_blast
-      }.to raise_error(SystemExit)
+      }.to_not raise_error
 
       Dir.glob(
         File.join(@args[:tmp_directory], "*")
@@ -109,6 +109,56 @@ describe "Quorum::SearchTools::Blast" do
         File.join(@args[:tmp_directory], "*")
       ).length.should be == 0
     end
+  end
+
+  describe "#execute_blast empty report" do
+    before(:each) do
+      # Set args as though we executed bin/search.
+      @args = {
+        :search_tool     => "blastn",
+        :id              => nil,
+        :log_directory   => File.expand_path(
+          "../../dummy/quorum/log", __FILE__
+        ),
+        :tmp_directory   => File.expand_path(
+          "../../dummy/quorum/tmp", __FILE__
+        ),
+        :search_database => File.expand_path(
+          "../../dummy/quorum/blastdb", __FILE__
+        ),
+        :threads         => 1
+      }
+
+      @job = Quorum::Job.new()
+
+      @job.sequence = File.open(
+        File.expand_path("../../data/fake_seq.txt", __FILE__)
+      ).read
+
+      @job.build_blastn_job
+      @job.blastn_job.queue     = true
+      @job.blastn_job.blast_dbs = ["test"]
+    end
+
+    it "executes blastn on a given dataset and returns an empty report" do
+      @job.stub(:queue_workers)
+      @job.save!
+
+      @args[:id] = @job.id
+
+      blast = Quorum::SearchTools::Blast.new(@args)
+      expect {
+        blast.execute_blast
+      }.to raise_error
+
+      Dir.glob(
+        File.join(@args[:tmp_directory], "*")
+      ).length.should be == 0
+
+      log_file = File.join(@args[:log_directory], "quorum.log")
+
+      `tail -n 3 #{log_file}`.to_s.include?("blastn report empty").should be_true
+    end
 
   end
 end