quorum 0.5.2 → 0.6.0

data/lib/generators/templates/blast.rb

@@ -105,7 +105,7 @@ module Quorum
 
         @filter                = @job.method(@job_association).call.filter
         @expectation           = @job.method(@job_association).call.expectation
-        @max_score             = @job.method(@job_association).call.max_score
+        @max_target_seqs       = @job.method(@job_association).call.max_target_seqs
         @min_score             = @job.method(@job_association).call.min_bit_score
         @gapped_alignments     = @job.method(@job_association).call.gapped_alignments
         @gap_opening_penalty   = @job.method(@job_association).call.gap_opening_penalty
@@ -136,15 +136,17 @@ module Quorum
         "-outfmt 5 " <<
         "-num_threads #{@threads} " <<
         "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
+        "-max_target_seqs #{@max_target_seqs} " <<
         "-out #{@out} "
         if @gapped_alignments
-          blastn << "-gapopen #{@gap_opening_penalty} "
-          blastn << "-gapextend #{@gap_extension_penalty} "
+          if @gap_opening_penalty && @gap_extension_penalty
+            blastn << "-gapopen #{@gap_opening_penalty} "
+            blastn << "-gapextend #{@gap_extension_penalty} "
+          end
         else
           blastn << "-ungapped "
         end
-        blastn << "-dust yes " if @filter
+        blastn << "-dust #{@filter ? 'yes' : 'no'} "
         blastn
       end
 
@@ -158,15 +160,17 @@ module Quorum
         "-outfmt 5 " <<
         "-num_threads #{@threads} " <<
         "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
+        "-max_target_seqs #{@max_target_seqs} " <<
         "-out #{@out} "
         if @gapped_alignments
-          blastx << "-gapopen #{@gap_opening_penalty} "
-          blastx << "-gapextend #{@gap_extension_penalty} "
+          if @gap_opening_penalty && @gap_extension_penalty
+            blastx << "-gapopen #{@gap_opening_penalty} "
+            blastx << "-gapextend #{@gap_extension_penalty} "
+          end
         else
           blastx << "-ungapped "
         end
-        blastx << "-seg yes " if @filter
+        blastx << "-seg #{@filter ? 'yes' : 'no'} "
         blastx
       end
 
@@ -180,17 +184,19 @@ module Quorum
         "-outfmt 5 " <<
         "-num_threads #{@threads} " <<
         "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
+        "-max_target_seqs #{@max_target_seqs} " <<
         "-out #{@out} "
         if @gapped_alignments
-          tblastn << "-gapopen #{@gap_opening_penalty} "
-          tblastn << "-gapextend #{@gap_extension_penalty} "
+          if @gap_opening_penalty && @gap_extension_penalty
+            tblastn << "-gapopen #{@gap_opening_penalty} "
+            tblastn << "-gapextend #{@gap_extension_penalty} "
+          end
           tblastn << "-comp_based_stats D "
         else
           tblastn << "-ungapped "
           tblastn << "-comp_based_stats F "
         end
-        tblastn << "-seg yes " if @filter
+        tblastn << "-seg #{@filter ? 'yes' : 'no'} "
         tblastn
       end
 
@@ -204,17 +210,19 @@ module Quorum
         "-outfmt 5 " <<
         "-num_threads #{@threads} " <<
         "-evalue #{@expectation} " <<
-        "-max_target_seqs #{@max_score} " <<
+        "-max_target_seqs #{@max_target_seqs} " <<
         "-out #{@out} "
         if @gapped_alignments
-          blastp << "-gapopen #{@gap_opening_penalty} "
-          blastp << "-gapextend #{@gap_extension_penalty} "
+          if @gap_opening_penalty && @gap_extension_penalty
+            blastp << "-gapopen #{@gap_opening_penalty} "
+            blastp << "-gapextend #{@gap_extension_penalty} "
+          end
           blastp << "-comp_based_stats D "
         else
           blastp << "-ungapped "
           blastp << "-comp_based_stats F "
         end
-        blastp << "-seg yes " if @filter
+        blastp << "-seg #{@filter ? 'yes' : 'no'} "
         blastp
       end
 
@@ -277,20 +285,18 @@ module Quorum
       # 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
+        @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
 

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.5.2"
+  VERSION = "0.6.0"
 end

data/spec/config/quorum_settings.yml

@@ -0,0 +1,55 @@
+development:
+  blast:
+    remote: false
+    ssh_host:
+    ssh_user:
+    ssh_options:
+    bin: "%{RAILS_ROOT}/quorum/bin"
+    log_dir: "%{RAILS_ROOT}/quorum/log"
+    tmp_dir: "%{RAILS_ROOT}/quorum/tmp"
+    blast_db: "%{RAILS_ROOT}/quorum/blastdb"
+    blastn:
+      "tmp": test
+    blastx:
+      "tmp": test
+    tblastn:
+      "tmp": test
+    blastp:
+      "tmp": test
+    blast_threads: 4
+
+test:
+  blast:
+    remote: false
+    ssh_host:
+    ssh_user:
+    ssh_options:
+    bin: "%{RAILS_ROOT}/quorum/bin"
+    log_dir: "%{RAILS_ROOT}/quorum/log"
+    tmp_dir: "%{RAILS_ROOT}/quorum/tmp"
+    blast_db: "%{RAILS_ROOT}/quorum/blastdb"
+    blastn:
+      "tmp": test
+    blastx:
+      "tmp": test
+    tblastn:
+      "tmp": test
+    blastp:
+      "tmp": test
+    blast_threads:
+
+production:
+  blast:
+    remote: true
+    ssh_host:
+    ssh_user:
+    ssh_options:
+    bin:
+    log_dir:
+    tmp_dir:
+    blast_db:
+    blastn:
+    blastx:
+    tblastn:
+    blastp:
+    blast_threads:

data/spec/javascripts/fixtures/quorum_search_form.html

@@ -82,10 +82,10 @@
             </tr>
             <tr>
                 <td>
-                    <label for="job_blastn_job_attributes_max_score">Max score</label>
+                    <label for="job_blastn_job_attributes_max_target_seqs">Max score</label>
                 </td>
                 <td>
-                    <input class="auto-hint" id="job_blastn_job_attributes_max_score" name="job[blastn_job_attributes][max_score]" size="15" title="25" type="text" />
+                    <input class="auto-hint" id="job_blastn_job_attributes_max_target_seqs" name="job[blastn_job_attributes][max_target_seqs]" size="15" title="25" type="text" />
                 </td>
                 <td>
                     <label for="job_blastn_job_attributes_gapped_alignments">Gapped alignments</label>
@@ -192,10 +192,10 @@
             </tr>
             <tr>
                 <td>
-                    <label for="job_blastx_job_attributes_max_score">Max score</label>
+                    <label for="job_blastx_job_attributes_max_target_seqs">Max score</label>
                 </td>
                 <td>
-                    <input class="auto-hint" id="job_blastx_job_attributes_max_score" name="job[blastx_job_attributes][max_score]" size="15" title="25" type="text" />
+                    <input class="auto-hint" id="job_blastx_job_attributes_max_target_seqs" name="job[blastx_job_attributes][max_target_seqs]" size="15" title="25" type="text" />
                 </td>
                 <td>
                     <label for="job_blastx_job_attributes_gapped_alignments">Gapped alignments</label>
@@ -304,10 +304,10 @@
             </tr>
             <tr>
                 <td>
-                    <label for="job_tblastn_job_attributes_max_score">Max score</label>
+                    <label for="job_tblastn_job_attributes_max_target_seqs">Max score</label>
                 </td>
                 <td>
-                    <input class="auto-hint" id="job_tblastn_job_attributes_max_score" name="job[tblastn_job_attributes][max_score]" size="15" title="25" type="text" />
+                    <input class="auto-hint" id="job_tblastn_job_attributes_max_target_seqs" name="job[tblastn_job_attributes][max_target_seqs]" size="15" title="25" type="text" />
                 </td>
                 <td>
                     <label for="job_tblastn_job_attributes_gapped_alignments">Gapped alignments</label>
@@ -414,10 +414,10 @@
             </tr>
             <tr>
                 <td>
-                    <label for="job_blastp_job_attributes_max_score">Max score</label>
+                    <label for="job_blastp_job_attributes_max_target_seqs">Max score</label>
                 </td>
                 <td>
-                    <input class="auto-hint" id="job_blastp_job_attributes_max_score" name="job[blastp_job_attributes][max_score]" size="15" title="25" type="text" />
+                    <input class="auto-hint" id="job_blastp_job_attributes_max_target_seqs" name="job[blastp_job_attributes][max_target_seqs]" size="15" title="25" type="text" />
                 </td>
                 <td>
                     <label for="job_blastp_job_attributes_gapped_alignments">Gapped alignments</label>

data/spec/javascripts/jobs_spec.js

@@ -67,17 +67,17 @@ describe("Quorum Search Form", function() {
       $('#job_blastp_job_attributes_min_bit_score').attr('title')
     );
 
-    expect($('#job_blastn_job_attributes_max_score')).toHaveValue(
-      $('#job_blastn_job_attributes_max_score').attr('title')
+    expect($('#job_blastn_job_attributes_max_target_seqs')).toHaveValue(
+      $('#job_blastn_job_attributes_max_target_seqs').attr('title')
     );
-    expect($('#job_blastx_job_attributes_max_score')).toHaveValue(
-      $('#job_blastx_job_attributes_max_score').attr('title')
+    expect($('#job_blastx_job_attributes_max_target_seqs')).toHaveValue(
+      $('#job_blastx_job_attributes_max_target_seqs').attr('title')
     );
-    expect($('#job_tblastn_job_attributes_max_score')).toHaveValue(
-      $('#job_tblastn_job_attributes_max_score').attr('title')
+    expect($('#job_tblastn_job_attributes_max_target_seqs')).toHaveValue(
+      $('#job_tblastn_job_attributes_max_target_seqs').attr('title')
     );
-    expect($('#job_blastp_job_attributes_max_score')).toHaveValue(
-      $('#job_blastp_job_attributes_max_score').attr('title')
+    expect($('#job_blastp_job_attributes_max_target_seqs')).toHaveValue(
+      $('#job_blastp_job_attributes_max_target_seqs').attr('title')
     );
   });
 

data/spec/lib/tasks/travis.rake

@@ -0,0 +1,120 @@
+# Travis Tasks
+namespace :travis do
+  # Install
+  task :install do
+    Rake::Task["travis:create_db_config"].execute
+    Rake::Task["travis:quorum_install"].execute
+    Rake::Task["travis:copy_quorum_settings"].execute
+    Rake::Task["travis:create_dummy_tmp"].execute
+  end
+
+  # Remove
+  task :remove do
+    Rake::Task["travis:remove_db_config"].execute
+    Rake::Task["travis:remove_quorum"].execute
+  end
+
+  # Specs
+  task :spec do
+    Rake::Task["travis:install"].execute
+    ["rake spec", "rake app:jasmine:ci JASMINE_PORT=53331"].each do |cmd|
+      puts "Starting to run #{cmd}..."
+      system("export DISPLAY=:99.0 && bundle exec #{cmd}")
+      raise "#{cmd} failed!" unless $?.exitstatus == 0
+    end
+    Rake::Task["travis:remove"].execute
+  end
+
+  # Install quorum, run migrations and prepare database.
+  task :quorum_install => :environment do
+    puts "Installing Quorum..."
+
+    app_dir = Dir.getwd
+    Dir.chdir(File.expand_path("../../../dummy", __FILE__))
+
+    blastdb_dir = File.expand_path("../../../../../data/tmp", __FILE__)
+
+    cmds = [
+      "rails g quorum:install",
+      "rails g quorum:views",
+      "rails g quorum:styles",
+      "rails g quorum:images",
+      "rake quorum:install:migrations",
+      "rake db:migrate",
+      "rake db:test:prepare",
+      "rake quorum:blastdb:build DIR=#{blastdb_dir}"
+    ]
+    cmds.each do |cmd|
+      system("bundle exec #{cmd}")
+      raise "#{cmd} failed!" unless $?.exitstatus == 0
+    end
+
+    Dir.chdir(app_dir)
+  end
+
+  # Copy quorum_settings.yml for specs.
+  task :copy_quorum_settings do
+    settings = File.expand_path("../../../config/quorum_settings.yml", __FILE__)
+    config = File.expand_path("../../../dummy/config/quorum_settings.yml", __FILE__)
+    FileUtils.copy_file(settings, config)
+  end
+
+  # Remove quorum.
+  task :remove_quorum do
+    dummy = File.expand_path("../../../dummy", __FILE__)
+    if File.exists?(File.join(dummy, "quorum"))
+      FileUtils.rm_rf File.join(dummy, "quorum")
+    end
+    if File.exists?(File.join(dummy, "app", "assets", "images", "quorum"))
+      FileUtils.rm_rf File.join(dummy, "app", "assets", "images", "quorum")
+    end
+    if File.exists?(File.join(dummy, "app", "assets", "stylesheets", "quorum"))
+      FileUtils.rm_rf File.join(dummy, "app", "assets", "stylesheets", "quorum")
+    end
+    if File.exists?(File.join(dummy, "app", "views", "layouts", "quorum"))
+      FileUtils.rm_rf File.join(dummy, "app", "views", "layouts", "quorum")
+    end
+    if File.exists?(File.join(dummy, "app", "views", "quorum"))
+      FileUtils.rm_rf File.join(dummy, "app", "views", "quorum")
+    end
+    if File.exists?(File.join(dummy, "quorum"))
+      FileUtils.rm_rf File.join(dummy, "quorum")
+    end
+    if File.exists?(File.join(dummy, "config", "quorum_settings.yml"))
+      FileUtils.rm File.join(dummy, "config", "quorum_settings.yml")
+    end
+    if File.exists?(File.join(dummy, "config", "initializers", "quorum_initializer.rb"))
+      FileUtils.rm File.join(dummy, "config", "initializers", "quorum_initializer.rb")
+    end
+    if File.exists?(File.join(dummy, "config", "locales", "quorum.en.yml"))
+      FileUtils.rm File.join(dummy, "config", "locales", "quorum.en.yml")
+    end
+  end
+
+  # Create spec/dummy/config/database.yml for Travis.
+  task :create_db_config do
+    config = File.expand_path("../../../dummy/config", __FILE__)
+    File.open(File.join(config, "database.yml"), "w+") do |file|
+      file.puts "\ntest:\n  adapter: mysql2\n  encoding: utf8\n" <<
+      "  reconnect: false\n  database: quorum_test\n" <<
+      "  pool: 5\n  username: root\n  password:\n" <<
+      "  host: localhost\n"
+    end
+  end
+
+  # Remove spec/dummy/config/database.yml after Travis.
+  task :remove_db_config do
+    config = File.expand_path("../../../dummy/config", __FILE__)
+    if File.exists?(File.join(config, "database.yml"))
+      FileUtils.rm File.join(config, "database.yml")
+    end
+  end
+
+  # Create tmp directory for dummy app.
+  task :create_dummy_tmp do
+    FileUtils.mkdir_p File.expand_path("../../../dummy", __FILE__) +
+      "/tmp/" + "pids"
+    FileUtils.mkdir_p File.expand_path("../../../dummy", __FILE__) +
+      "/tmp/" + "cache"
+  end
+end

data/spec/models/blastn_job_spec.rb

@@ -6,12 +6,12 @@ describe Quorum::BlastnJob do
     @blastn_job = Quorum::BlastnJob.new()
   end
 
-  it "fails validation with poorly formatted expectation (using error_on)" do
+  it "fails validation with poorly formatted expectation" do
     @blastn_job.expectation = "this is bad"
     @blastn_job.should have(1).error_on(:expectation)
   end
 
-  it "passes validation with valid expectation values (using error_on)" do
+  it "passes validation with valid expectation values" do
     @blastn_job.expectation = 12
     @blastn_job.should have(0).errors_on(:expectation)
     @blastn_job.expectation = 12.1201
@@ -22,49 +22,49 @@ describe Quorum::BlastnJob do
     @blastn_job.should have(0).errors_on(:expectation)
   end
 
-  it "fails validation with poorly formatted max_score (using error_on)" do
-    @blastn_job.max_score = 12.34
-    @blastn_job.should have(1).error_on(:max_score)
-    @blastn_job.max_score = "not a number"
-    @blastn_job.should have(1).error_on(:max_score)
+  it "fails validation with poorly formatted max_target_seqs" do
+    @blastn_job.max_target_seqs = 12.34
+    @blastn_job.should have(1).error_on(:max_target_seqs)
+    @blastn_job.max_target_seqs = "not a number"
+    @blastn_job.should have(1).error_on(:max_target_seqs)
   end
 
-  it "passed validation with valid max_score (using error_on)" do
-    @blastn_job.max_score = 1235
-    @blastn_job.should have(0).errors_on(:max_score)
+  it "passed validation with valid max_target_seqs" do
+    @blastn_job.max_target_seqs = 1235
+    @blastn_job.should have(0).errors_on(:max_target_seqs)
   end
 
-  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_opening_penalty" do
     @blastn_job.gap_opening_penalty = "not a number"
     @blastn_job.should have(1).error_on(:gap_opening_penalty)
     @blastn_job.gap_opening_penalty = 100.10
     @blastn_job.should have(1).error_on(:gap_opening_penalty)
   end
 
-  it "passed validation with valid gap_opening_penalty (using error_on)" do
-    @blastn_job.max_score = 13
+  it "passed validation with valid gap_opening_penalty" do
+    @blastn_job.max_target_seqs = 13
     @blastn_job.should have(0).errors_on(:gap_opening_penalty)
   end
 
-  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_extension_penalty" do
     @blastn_job.gap_extension_penalty = "who are you?"
     @blastn_job.should have(1).error_on(:gap_extension_penalty)
     @blastn_job.gap_extension_penalty = 0.3
     @blastn_job.should have(1).error_on(:gap_extension_penalty)
   end
 
-  it "passed validation with valid gap_extension_penalty (using error_on)" do
-    @blastn_job.max_score = 456
+  it "passed validation with valid gap_extension_penalty" do
+    @blastn_job.max_target_seqs = 456
     @blastn_job.should have(0).errors_on(:gap_extension_penalty)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "passes validation without selecting gap_opening_extension with gapped_alignment" do
     @blastn_job.gapped_alignments = true
     @blastn_job.gap_opening_extension = ""
-    @blastn_job.should have(1).error_on(:gap_opening_extension)
+    @blastn_job.should have(0).error_on(:gap_opening_extension)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "fails validation without selecting gap_opening_extension with gapped_alignment" do
     @blastn_job.gapped_alignments = true
     @blastn_job.gap_opening_extension = "11, 2"
     @blastn_job.should have(0).errors_on(:gap_opening_extension)
@@ -100,6 +100,25 @@ describe Quorum::BlastnJob do
     )
   end
 
+  it "passes validation if not enqueued and blast_dbs is empty" do
+    @blastn_job.queue = false
+    @blastn_job.blast_dbs = []
+    @blastn_job.should have(0).errors_on(:blast_dbs)
+  end
+
+  it "fails validation if blast_dbs is empty" do
+    @blastn_job.queue = true
+    @blastn_job.blast_dbs = []
+    @blastn_job.should have(1).errors_on(:blast_dbs)
+  end
+
+  # Test for removal of multiple select hidden field value.
+  it "fails validation if blast_dbs contains an empty string" do
+    @blastn_job.queue = true
+    @blastn_job.blast_dbs = ["", "", ""]
+    @blastn_job.should have(1).errors_on(:blast_dbs)
+  end
+
   it "joins blast_dbs on semicolon after save" do
     @blastn_job.blast_dbs = ["test_1", "test_2"]
     @blastn_job.save
@@ -109,10 +128,10 @@ describe Quorum::BlastnJob do
   it "sets optional params to default values if empty after save" do
     @blastn_job.save
     @blastn_job.expectation.should eq("5e-20")
-    @blastn_job.max_score.should eq(25)
+    @blastn_job.max_target_seqs.should eq(25)
     @blastn_job.min_bit_score.should eq(0)
-    @blastn_job.gap_opening_penalty.should eq(0)
-    @blastn_job.gap_extension_penalty.should eq(0)
+    @blastn_job.gap_opening_penalty.should be_nil
+    @blastn_job.gap_extension_penalty.should be_nil
   end
 
 end

data/spec/models/blastp_job_spec.rb

@@ -6,12 +6,12 @@ describe Quorum::BlastpJob do
     @blastp_job = Quorum::BlastpJob.new()
   end
 
-  it "fails validation with poorly formatted expectation (using error_on)" do
+  it "fails validation with poorly formatted expectation" do
     @blastp_job.expectation = "this is bad"
     @blastp_job.should have(1).error_on(:expectation)
   end
 
-  it "passes validation with valid expectation values (using error_on)" do
+  it "passes validation with valid expectation values" do
     @blastp_job.expectation = 12
     @blastp_job.should have(0).errors_on(:expectation)
     @blastp_job.expectation = 12.1201
@@ -22,49 +22,49 @@ describe Quorum::BlastpJob do
     @blastp_job.should have(0).errors_on(:expectation)
   end
 
-  it "fails validation with poorly formatted max_score (using error_on)" do
-    @blastp_job.max_score = 12.34
-    @blastp_job.should have(1).error_on(:max_score)
-    @blastp_job.max_score = "not a number"
-    @blastp_job.should have(1).error_on(:max_score)
+  it "fails validation with poorly formatted max_target_seqs" do
+    @blastp_job.max_target_seqs = 12.34
+    @blastp_job.should have(1).error_on(:max_target_seqs)
+    @blastp_job.max_target_seqs = "not a number"
+    @blastp_job.should have(1).error_on(:max_target_seqs)
   end
 
-  it "passed validation with valid max_score (using error_on)" do
-    @blastp_job.max_score = 1235
-    @blastp_job.should have(0).errors_on(:max_score)
+  it "passed validation with valid max_target_seqs" do
+    @blastp_job.max_target_seqs = 1235
+    @blastp_job.should have(0).errors_on(:max_target_seqs)
   end
 
-  it "fails validation with poorly formatted gap_opening_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_opening_penalty" do
     @blastp_job.gap_opening_penalty = "not a number"
     @blastp_job.should have(1).error_on(:gap_opening_penalty)
     @blastp_job.gap_opening_penalty = 100.10
     @blastp_job.should have(1).error_on(:gap_opening_penalty)
   end
 
-  it "passed validation with valid gap_opening_penalty (using error_on)" do
-    @blastp_job.max_score = 13
+  it "passed validation with valid gap_opening_penalty" do
+    @blastp_job.max_target_seqs = 13
     @blastp_job.should have(0).errors_on(:gap_opening_penalty)
   end
 
-  it "fails validation with poorly formatted gap_extension_penalty (using error_on)" do
+  it "fails validation with poorly formatted gap_extension_penalty" do
     @blastp_job.gap_extension_penalty = "who are you?"
     @blastp_job.should have(1).error_on(:gap_extension_penalty)
     @blastp_job.gap_extension_penalty = 0.3
     @blastp_job.should have(1).error_on(:gap_extension_penalty)
   end
 
-  it "passed validation with valid gap_extension_penalty (using error_on)" do
-    @blastp_job.max_score = 456
+  it "passed validation with valid gap_extension_penalty" do
+    @blastp_job.max_target_seqs = 456
     @blastp_job.should have(0).errors_on(:gap_extension_penalty)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it " sssesvalidation without selecting gap_opening_extension with gapped_alignment" do
     @blastp_job.gapped_alignments = true
     @blastp_job.gap_opening_extension = ""
-    @blastp_job.should have(1).error_on(:gap_opening_extension)
+    @blastp_job.should have(0).error_on(:gap_opening_extension)
   end
 
-  it "fails validation without selecting gap_opening_extension with gapped_alignment (using error_on)" do
+  it "fails validation without selecting gap_opening_extension with gapped_alignment" do
     @blastp_job.gapped_alignments = true
     @blastp_job.gap_opening_extension = "11, 2"
     @blastp_job.should have(0).errors_on(:gap_opening_extension)
@@ -100,6 +100,25 @@ describe Quorum::BlastpJob do
     )
   end
 
+  it "passes validation if not enqueued and blast_dbs is empty" do
+    @blastp_job.queue = false
+    @blastp_job.blast_dbs = []
+    @blastp_job.should have(0).errors_on(:blast_dbs)
+  end
+
+  it "fails validation if blast_dbs is empty" do
+    @blastp_job.queue = true
+    @blastp_job.blast_dbs = []
+    @blastp_job.should have(1).errors_on(:blast_dbs)
+  end
+
+  # Test for removal of multiple select hidden field value.
+  it "fails validation if blast_dbs contains an empty string" do
+    @blastp_job.queue = true
+    @blastp_job.blast_dbs = ["", "", ""]
+    @blastp_job.should have(1).errors_on(:blast_dbs)
+  end
+
   it "joins blast_dbs on semicolon after save" do
     @blastp_job.blast_dbs = ["test_1", "test_2"]
     @blastp_job.save
@@ -109,10 +128,10 @@ describe Quorum::BlastpJob do
   it "sets optional params to default values if empty after save" do
     @blastp_job.save
     @blastp_job.expectation.should eq("5e-20")
-    @blastp_job.max_score.should eq(25)
+    @blastp_job.max_target_seqs.should eq(25)
     @blastp_job.min_bit_score.should eq(0)
-    @blastp_job.gap_opening_penalty.should eq(0)
-    @blastp_job.gap_extension_penalty.should eq(0)
+    @blastp_job.gap_opening_penalty.should be_nil
+    @blastp_job.gap_extension_penalty.should be_nil
   end
 
 end