quorum 0.3.3 → 0.4.0

data/Gemfile.lock

@@ -1,47 +1,47 @@
 PATH
   remote: .
   specs:
-    quorum (0.3.3)
-      bio-blastxmlparser (~> 1.0.1)
+    quorum (0.4.0)
+      bio-blastxmlparser (~> 1.1.0)
       jquery-rails
       net-ssh (~> 2.3.0)
       rails (~> 3.1)
-      resque (~> 1.19.0)
+      resque (~> 1.20.0)
       resque-result (~> 1.0.1)
 
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (3.2.6)
-      actionpack (= 3.2.6)
+    actionmailer (3.2.8)
+      actionpack (= 3.2.8)
       mail (~> 2.4.4)
-    actionpack (3.2.6)
-      activemodel (= 3.2.6)
-      activesupport (= 3.2.6)
+    actionpack (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
       builder (~> 3.0.0)
       erubis (~> 2.7.0)
-      journey (~> 1.0.1)
+      journey (~> 1.0.4)
       rack (~> 1.4.0)
       rack-cache (~> 1.2)
       rack-test (~> 0.6.1)
       sprockets (~> 2.1.3)
-    activemodel (3.2.6)
-      activesupport (= 3.2.6)
+    activemodel (3.2.8)
+      activesupport (= 3.2.8)
       builder (~> 3.0.0)
-    activerecord (3.2.6)
-      activemodel (= 3.2.6)
-      activesupport (= 3.2.6)
+    activerecord (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
       arel (~> 3.0.2)
       tzinfo (~> 0.3.29)
-    activeresource (3.2.6)
-      activemodel (= 3.2.6)
-      activesupport (= 3.2.6)
-    activesupport (3.2.6)
+    activeresource (3.2.8)
+      activemodel (= 3.2.8)
+      activesupport (= 3.2.8)
+    activesupport (3.2.8)
       i18n (~> 0.6)
       multi_json (~> 1.0)
-    addressable (2.2.8)
+    addressable (2.3.2)
     arel (3.0.2)
-    bio-blastxmlparser (1.0.1)
+    bio-blastxmlparser (1.1.0)
       bio-logger (>= 1.0.0)
       nokogiri (>= 1.5.0)
     bio-logger (1.0.1)
@@ -54,17 +54,12 @@ GEM
       rack-test (>= 0.5.4)
       selenium-webdriver (~> 2.0)
       xpath (~> 0.1.4)
-    childprocess (0.3.3)
-      ffi (~> 1.0.6)
+    childprocess (0.3.5)
+      ffi (~> 1.0, >= 1.0.6)
     database_cleaner (0.8.0)
     diff-lcs (1.1.3)
     erubis (2.7.0)
-    factory_girl (2.6.4)
-      activesupport (>= 2.3.9)
-    factory_girl_rails (1.7.0)
-      factory_girl (~> 2.6.0)
-      railties (>= 3.0.0)
-    ffi (1.0.11)
+    ffi (1.1.5)
     hike (1.2.1)
     i18n (0.6.0)
     jasmine (1.2.0)
@@ -77,8 +72,8 @@ GEM
     jquery-rails (2.0.2)
       railties (>= 3.2.0, < 5.0)
       thor (~> 0.14)
-    json (1.7.3)
-    libwebsocket (0.1.4)
+    json (1.7.4)
+    libwebsocket (0.1.5)
       addressable
     log4r (1.1.10)
     mail (2.4.4)
@@ -100,17 +95,17 @@ GEM
       rack
     rack-test (0.6.1)
       rack (>= 1.0)
-    rails (3.2.6)
-      actionmailer (= 3.2.6)
-      actionpack (= 3.2.6)
-      activerecord (= 3.2.6)
-      activeresource (= 3.2.6)
-      activesupport (= 3.2.6)
+    rails (3.2.8)
+      actionmailer (= 3.2.8)
+      actionpack (= 3.2.8)
+      activerecord (= 3.2.8)
+      activeresource (= 3.2.8)
+      activesupport (= 3.2.8)
       bundler (~> 1.0)
-      railties (= 3.2.6)
-    railties (3.2.6)
-      actionpack (= 3.2.6)
-      activesupport (= 3.2.6)
+      railties (= 3.2.8)
+    railties (3.2.8)
+      actionpack (= 3.2.8)
+      activesupport (= 3.2.8)
       rack-ssl (~> 1.3.2)
       rake (>= 0.8.7)
       rdoc (~> 3.4)
@@ -121,7 +116,7 @@ GEM
     redis (2.2.2)
     redis-namespace (1.0.3)
       redis (< 3.0.0)
-    resque (1.19.0)
+    resque (1.20.0)
       multi_json (~> 1.0)
       redis-namespace (~> 1.0.2)
       sinatra (>= 0.9.2)
@@ -131,7 +126,7 @@ GEM
     resque-result (1.0.1)
       resque (~> 1.9)
       resque-meta (~> 1.0)
-    resque_spec (0.12.2)
+    resque_spec (0.12.3)
       resque (>= 1.19.0)
       rspec (>= 2.5.0)
     rspec (2.11.0)
@@ -139,7 +134,7 @@ GEM
       rspec-expectations (~> 2.11.0)
       rspec-mocks (~> 2.11.0)
     rspec-core (2.11.1)
-    rspec-expectations (2.11.1)
+    rspec-expectations (2.11.2)
       diff-lcs (~> 1.1.3)
     rspec-mocks (2.11.1)
     rspec-rails (2.11.0)
@@ -177,11 +172,10 @@ PLATFORMS
 
 DEPENDENCIES
   capybara (~> 1.1)
-  database_cleaner (~> 0.6)
-  factory_girl_rails (~> 1.2)
-  jasmine (~> 1.1)
+  database_cleaner (~> 0.8)
+  jasmine (~> 1.2)
   mysql2 (~> 0.3.11)
   quorum!
   rake (~> 0.9.2)
-  resque_spec (~> 0.8)
-  rspec-rails (~> 2.6)
+  resque_spec (~> 0.12)
+  rspec-rails (~> 2.11)

data/HISTORY.md

@@ -1,3 +1,14 @@
+## 0.4.0 (2012-08-10)
+
+* Added Hsp gaps to Blast Job Reports.
+  To add gaps: `rake quorum:install:migrations` `rake db:migrate`
+* Upgraded bio-blastxmlparser to v1.1.0.
+  See https://github.com/pjotrp/blastxmlparser/pull/1
+* Fixed JavaScript RangeError: Max call stack size exceeded bug in views.
+  Bug was present in large datasets.
+* General refactoring.
+* Updated dependencies.
+
 ## 0.3.3 (2012-07-19)
 
 * Fixed discover input sequence type bug. Upper and lowercase

data/app/assets/javascripts/quorum/quorum.js

@@ -90,8 +90,10 @@ QUORUM.viewDetailedReport = function(id, focus_id, query, algo) {
       // Insert the detailed report data.
       $('#detailed_report_dialog').empty().html(temp);
 
-      // Add tipsy to the sequence data.
-      $('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
+      // Add tipsy to sequence data on mouse enter.
+      $('#detailed_report_dialog .sequence').mouseenter(function() {
+        $(this).find('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
+      });
 
       // Highlight the selected id.
       $('#' + focus_id).addClass("ui-state-highlight");
@@ -115,7 +117,8 @@ QUORUM.addBaseTitleIndex = function(bases, from, to, algo, type) {
   var self = this,
       forward = true,
       value = 1,
-      index = from;
+      index = from,
+      str;
 
   if (from > to) {
     forward = false;
@@ -129,7 +132,7 @@ QUORUM.addBaseTitleIndex = function(bases, from, to, algo, type) {
 
   // Add tipsy to each base.
   return _.map(bases.split(''), function(c) {
-    var str = "<a rel='quorum-tipsy' title=" + index + ">" + c + "</a>";
+    str = "<a rel='quorum-tipsy' title=" + index + ">" + c + "</a>";
     forward ? index += value : index -= value;
     return str;
   }).join('');
@@ -180,7 +183,7 @@ QUORUM.formatSequenceReport = function(qseq, midline, hseq, q_from, q_to, h_from
     }
   }
   return "<p class='small'>Alignment (Mouse over for positions):</p>" +
-    "<span class='small'><pre>" + seq + "</pre></span>";
+    "<span class='small sequence'><pre>" + seq + "</pre></span>";
 
 };
 

data/db/migrate/20120807202555_add_gaps_to_blast_reports.rb

@@ -0,0 +1,8 @@
+class AddGapsToBlastReports < ActiveRecord::Migration
+  def change
+    add_column :quorum_blastn_job_reports, :gaps, :integer
+    add_column :quorum_blastx_job_reports, :gaps, :integer
+    add_column :quorum_tblastn_job_reports, :gaps, :integer
+    add_column :quorum_blastp_job_reports, :gaps, :integer
+  end
+end

data/lib/generators/templates/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/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.3.3"
+  VERSION = "0.4.0"
 end

data/quorum.gemspec

@@ -18,15 +18,14 @@ Gem::Specification.new do |s|
   s.add_dependency "rails", "~> 3.1"
   s.add_dependency "jquery-rails"
   s.add_dependency "net-ssh", "~> 2.3.0"
-  s.add_dependency "resque", "~> 1.19.0"
+  s.add_dependency "resque", "~> 1.20.0"
   s.add_dependency "resque-result", "~> 1.0.1"
-  s.add_dependency "bio-blastxmlparser", "~> 1.0.1"
+  s.add_dependency "bio-blastxmlparser", "~> 1.1.0"
 
   s.add_development_dependency "mysql2", "~> 0.3.11"
-  s.add_development_dependency "rspec-rails", "~> 2.6"
-  s.add_development_dependency "resque_spec", "~> 0.8"
+  s.add_development_dependency "rspec-rails", "~> 2.11"
+  s.add_development_dependency "resque_spec", "~> 0.12"
   s.add_development_dependency "capybara", "~> 1.1"
-  s.add_development_dependency "database_cleaner", "~> 0.6"
-  s.add_development_dependency "factory_girl_rails", "~> 1.2"
-  s.add_development_dependency "jasmine", "~> 1.1"
+  s.add_development_dependency "database_cleaner", "~> 0.8"
+  s.add_development_dependency "jasmine", "~> 1.2"
 end

data/spec/data/fake_seq.txt

@@ -0,0 +1,2 @@
+>fakeseq
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

data/spec/data/nucl_prot_seqs.txt

@@ -30,7 +30,22 @@ GGCACCAGGGATCTTACAAGGCTGGATCTCCATAATAACAAGTTGACAGGGCCTATTCCTCCTCAAATTGGACGGTTGAA
 GGAAATGAGCACAATGTTAAGCAGATCAAGAATTACCGCCAAAAGGTTGAGGAGGAACTCTCCAAAATTTGTGGTGACATCCTGACTATTATAGACCAGCATCTAATTCCTTCTTCCGCCTCAGCAGAAGCTAGTGTTTTCTACTATAAGATGAAAGGTGATTATTATCGGTATCTTGCTGAGTTCAAGACCGACCAAGAAAGGAAAGAGGCAGCCGAGCAGTCACTCAAGGGATATGAGGCTGCTTCAGCCACTGCCAACACCGATCTTCCATCAACACATCCAATCCGTCTTGGACTTGCTCTCAACTTCTCTGTCTTTTATTACGAGATCATGAACTCTCCTGAAAGGGCCTGCCATTTGGCTAAACAAGCTTTTGATGAGGCAATTGCAGAGTTGGACACCTTGAGTGAAGAGTCATACAAGGACAGTACTTTGATCATGCAGTTGTTGAGAGACAACCTGACTCTCTGGACATCCGATTTGCCAGAAGATGGAGGCGAGGAGAACATAAAAGCTGAAGAAGCCAAACCTACTGAGCCTGAGAATTAACTAGGTTCTTTTGGATCTTTGGCCCTGATTCAATAGTCAGATTTTTGTGGTGCTCTGCAAAGAGGGCATTTTTCAGCTTTTCTTGCAATGGATTTGGAATGGACAATATGAGCTGTCGCCACTTCATAATTACCAACCAAAGCCAAAAGATCTGAGCCTGCCTTTTCTTTATTTCTTTAAATTGTTTTTCTTTCTTACTGCCTTTATCTATTTTAAGCAAAGTGGTCGGTTGAAACAATGGATAATTCACATTTAAATCATAAGAATCTTTTTCAAGTGTTCATTACATCCGTTTTGGTTCGTTTAAAATATTGTTTCCTATGCGCTCCTAGATGGGATACAGTACAAGTATTCAACTGTTGAGCAGAGATTTTTACCTCAAAAAATTAGT
 >TOG895871
 AGACACAACATCATAGAAACAGATCAACAACACATTAAAATTAGCATGGATCATAGCTTACGTTGTTTTGGGTCGACACTACCCAAAACTCTTCTTCAGTTTCTGTTATCACCTTCACTCCTTCTCTTCATCTCCTTCTTCAGTTTCTCCAACGCAGCCTTCGACCTCGCCACCATACCCTTCAACGATGCCTATTCACCCCTCTTTGGGGATGGCAACCTTGTCCGCTCCGCCGATGGCAACGGTGTTCAACTCCTCCTCGATCGCTTCACCGGTTCTGGTTTCGTTTCTTCCAATATGTACCAGCATGGATTCTTCAGCGCCAATATCAAGCTACCATCGAATTACAGCGCTGGTATTTGCGTGGCCTTTTATACATCAAACAATGAGATGTTTGAGAAGACACACGATGAGTTAGACTTTGAATTCTTAGGTAATATAGCCGGAAAGCCTTGGAGGTTTCAGACAAACTTGTACGGCAATGGCAGCACCAACCGTGGCCGTGAGGAGCGGTACCGCCTCTGGTTTGATCCAACCAAGGGATTCCATAGATACAGCATTCTATGGACAGCTAAGAACATCATATTTTACATAGATGAGGTTCCAATTAGAGAAATTATAAGAAGTGAAGAAATGGGAGCTGATTACCCAGCAAAGCCAATGGCATTATACGCCACAATATGGGATGCATCAAATTGGGCCACATCGGGTGGAAA
+>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
 >ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
 MEQYWSGSAINENKGMVENLQRYGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETSVRYVPLTSKEAQLKE
 >ADA84676.2 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
 MEQYWSGSAGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQINENKGMVENLQRYPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQSVRYVPLTSKEAQLKE
+>VIRT10447
+TVLPHLPHHLAAAQHQAPFQQVIAICQNSGQILYRPKARWWDPLLLPYMFRHKHELVQSFHK

data/spec/dummy/config/initializers/quorum_initializer.rb

@@ -10,7 +10,7 @@ settings = YAML.load_file(
 
 ## Sub %{RAILS_ROOT} ##
 settings.keys.each do |k|
-  settings[k.to_s].each_value do |v| 
+  settings[k.to_s].each_value do |v|
     if v.kind_of?(String)
       v.to_s.gsub!('%{RAILS_ROOT}', ::Rails.root.to_s)
     end

data/spec/dummy/config/quorum_settings.yml

@@ -2,7 +2,7 @@
 #
 # ==> General
 # Quorum initializer safely substitutes %{RAILS_ROOT} with ::Rails.root.to_s.
-# 
+#
 # ==> NCBI BLAST+ Settings
 # blast:
 #   remote: true to execute script on remote machine via
@@ -77,17 +77,13 @@ development:
     tmp_dir: "%{RAILS_ROOT}/quorum/tmp"
     blast_db: "%{RAILS_ROOT}/quorum/blastdb"
     blastn:
-      "camptotheca_acuminata-20101112": camptotheca_acuminata-20101112
-      "colchicum_autumnale-20101112": colchicum_autumnale-20101112
+      "tmp": test
     blastx:
-      "camptotheca_acuminata-20101112": camptotheca_acuminata-20101112
-      "colchicum_autumnale-20101112": colchicum_autumnale-20101112
+      "tmp": test
     tblastn:
-      "camptotheca_acuminata-20101112": camptotheca_acuminata-20101112
-      "colchicum_autumnale-20101112": colchicum_autumnale-20101112
+      "tmp": test
     blastp:
-      "camptotheca_acuminata-20101112": camptotheca_acuminata-20101112
-      "colchicum_autumnale-20101112": colchicum_autumnale-20101112
+      "tmp": test
     blast_threads: 4
 
 test:

data/spec/dummy/db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended to check this file into your version control system.
 
-ActiveRecord::Schema.define(:version => 20120119000561) do
+ActiveRecord::Schema.define(:version => 20120807211452) do
 
   create_table "quorum_blastn_job_reports", :force => true do |t|
     t.string   "query"
@@ -39,9 +39,10 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "midline"
     t.boolean  "results"
     t.integer  "blastn_job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",     :null => false
+    t.datetime "updated_at",     :null => false
     t.string   "hit_display_id"
+    t.integer  "gaps"
   end
 
   create_table "quorum_blastn_jobs", :force => true do |t|
@@ -55,8 +56,8 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "blast_dbs"
     t.boolean  "queue"
     t.integer  "job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",            :null => false
+    t.datetime "updated_at",            :null => false
   end
 
   create_table "quorum_blastp_job_reports", :force => true do |t|
@@ -85,9 +86,10 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "midline"
     t.boolean  "results"
     t.integer  "blastp_job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",     :null => false
+    t.datetime "updated_at",     :null => false
     t.string   "hit_display_id"
+    t.integer  "gaps"
   end
 
   create_table "quorum_blastp_jobs", :force => true do |t|
@@ -101,8 +103,8 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "blast_dbs"
     t.boolean  "queue"
     t.integer  "job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",            :null => false
+    t.datetime "updated_at",            :null => false
   end
 
   create_table "quorum_blastx_job_reports", :force => true do |t|
@@ -131,9 +133,10 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "midline"
     t.boolean  "results"
     t.integer  "blastx_job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",     :null => false
+    t.datetime "updated_at",     :null => false
     t.string   "hit_display_id"
+    t.integer  "gaps"
   end
 
   create_table "quorum_blastx_jobs", :force => true do |t|
@@ -147,8 +150,8 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "blast_dbs"
     t.boolean  "queue"
     t.integer  "job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",            :null => false
+    t.datetime "updated_at",            :null => false
   end
 
   create_table "quorum_jobs", :force => true do |t|
@@ -156,8 +159,8 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "na_sequence"
     t.text     "aa_sequence"
     t.string   "sequence_hash"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",    :null => false
+    t.datetime "updated_at",    :null => false
   end
 
   create_table "quorum_tblastn_job_reports", :force => true do |t|
@@ -186,9 +189,10 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "midline"
     t.boolean  "results"
     t.integer  "tblastn_job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",     :null => false
+    t.datetime "updated_at",     :null => false
     t.string   "hit_display_id"
+    t.integer  "gaps"
   end
 
   create_table "quorum_tblastn_jobs", :force => true do |t|
@@ -202,8 +206,8 @@ ActiveRecord::Schema.define(:version => 20120119000561) do
     t.text     "blast_dbs"
     t.boolean  "queue"
     t.integer  "job_id"
-    t.datetime "created_at"
-    t.datetime "updated_at"
+    t.datetime "created_at",            :null => false
+    t.datetime "updated_at",            :null => false
   end
 
 end

data/spec/dummy/quorum/bin/fetch

@@ -37,7 +37,7 @@ Options:
           :required => true, :short => "-l"
         opt :tmp_directory, "Path to tmp directory", :type => :string,
           :required => true, :short => "-m"
-        
+
         # Global settings
         opt :fetch_database, "Path to fetch tool database", :type => :string,
           :short => "-d"
@@ -46,7 +46,7 @@ Options:
 
         # Algorithm specific opts
         opt :blast_hit_id, "Blast hit id", :type => :string, :short => "-b"
-        opt :blast_hit_display_id, "Blast hit display id", :type => :string, 
+        opt :blast_hit_display_id, "Blast hit display id", :type => :string,
           :short => "-s"
         opt :blast_algo, "Blast algorithm", :type => :string, :short => "-a"
       end
@@ -110,6 +110,6 @@ Options:
 end
 
 if __FILE__ == $0
-  Quorum::Fetch.new  
+  Quorum::Fetch.new
 end