quorum 0.5.2 → 0.6.0

data/.gitignore

@@ -1,10 +1,8 @@
 .bundle/
 log/*.log
 pkg/
-spec/dummy/db/*.sqlite3
-spec/dummy/db/migrate/
+spec/dummy/db/*
 spec/dummy/log/*.log
-spec/dummy/tmp/
+spec/dummy/tmp/*
 spec/dummy/config/database.yml
-spec/dummy/quorum/log/*
-spec/dummy/quorum/tmp/*
+spec/dummy/quorum/

data/.travis.yml

@@ -13,8 +13,6 @@ before_script:
   - "sh -e /etc/init.d/xvfb start"
   - bundle install
   - mysql -e "create database quorum_test;"
-  - "rake travis:create_db_config"
-  - "rake app:db:schema:load"
 script: "rake travis:spec"
 notifications:
   email:

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.5.2)
+    quorum (0.6.0)
       bio-blastxmlparser (~> 1.1.0)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -136,7 +136,7 @@ GEM
     rspec-core (2.11.1)
     rspec-expectations (2.11.3)
       diff-lcs (~> 1.1.3)
-    rspec-mocks (2.11.2)
+    rspec-mocks (2.11.3)
     rspec-rails (2.11.0)
       actionpack (>= 3.0)
       activesupport (>= 3.0)

data/HISTORY.md

@@ -1,3 +1,15 @@
+## 0.6.0 (2012-09-21)
+
+* Renamed blast report max_score to max_target_seqs to match NCBI Blast
+  reports. Updated search interface. NOTE: requires migration install.
+* Updated the default search interface:
+* Enabled gapped alignments by default.
+* Improved existing filter options (NCBI Blast DUST and SEG) to use NCBI Blast
+  default values.
+* Fixed Rails 3.2 multiple select validation error.
+* Refactored travis-ci rake tasks.
+* Added default spec runner task.
+
 ## 0.5.2 (2012-09-14)
 
 * Removed jQuery ajax timeout for long lasting blast jobs.

data/Rakefile

@@ -25,58 +25,23 @@ load 'rails/tasks/engine.rake'
 
 require 'rspec/core/rake_task'
 RSpec::Core::RakeTask.new(:spec)
-task :default => :spec
 
 Bundler::GemHelper.install_tasks
 
-# Travis Tasks
-namespace :travis do
-  # Specs
-  task :spec do
-    Rake::Task["travis:create_dirs"].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_db_config"].execute
-  end
+# Travis tasks
+load 'spec/lib/tasks/travis.rake'
 
-  # Create spec/dummy/config/database.yml for Travis.
-  task :create_db_config do
-    config = File.expand_path("../spec/dummy/config", __FILE__)
-    File.open(File.join(config, "database.yml"), "w+") do |file|
-      file.puts "test:\n  adapter: mysql2\n  database: quorum_test\n" <<
-      "  username: root\n  password:\n  host: localhost\n  encoding: utf8"
-    end
+# Spec runner
+task :spec_runner do
+  unless File.exists?(File.expand_path("../spec/dummy/quorum", __FILE__))
+    Rake::Task["travis:quorum_install"].execute
+    Rake::Task["travis:copy_quorum_settings"].execute
   end
-
-  # Remove spec/dummy/config/database.yml after Travis.
-  task :remove_db_config do
-    config = File.expand_path("../spec/dummy/config", __FILE__)
-    File.delete(File.join(config, "database.yml"))
-  end
-
-  # Create necessary directories for test. Mimic a real app install
-  # via rails g quorum:install.
-  #
-  # The directories below are not in the git repo.
-  task :create_dirs do
-    app    = File.expand_path("../spec/dummy", __FILE__)
-    quorum = File.expand_path("../spec/dummy/quorum", __FILE__)
-
-    app_tmp   = File.join(app, "tmp")
-    app_pids  = File.join(app_tmp, "pids")
-    app_cache = File.join(app_tmp, "cache")
-
-    Dir.mkdir(app_tmp) unless File.directory?(app_tmp)
-    Dir.mkdir(app_pids) unless File.directory?(app_pids)
-    Dir.mkdir(app_cache) unless File.directory?(app_cache)
-
-    quorum_log = File.join(quorum, "log")
-    quorum_tmp = File.join(quorum, "tmp")
-
-    Dir.mkdir(quorum_log) unless File.directory?(quorum_log)
-    Dir.mkdir(quorum_tmp) unless File.directory?(quorum_tmp)
+  unless File.exists?(File.expand_path("../spec/dummy/tmp", __FILE__))
+    Rake::Task["travis:create_dummy_tmp"].execute
   end
+  Rake::Task["spec"].execute
+  Rake::Task["app:jasmine:ci"].execute
 end
+
+task :default => :spec_runner

data/app/models/quorum/blastn_job.rb

@@ -1,6 +1,8 @@
 module Quorum
   class BlastnJob < ActiveRecord::Base
 
+    before_validation :check_blast_dbs, :if => :queue
+
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
@@ -9,7 +11,7 @@ module Quorum
       :foreign_key => :blastn_job_id,
       :primary_key => :job_id
 
-    attr_accessible :expectation, :max_score, :min_bit_score,
+    attr_accessible :expectation, :max_target_seqs, :min_bit_score,
       :filter,  :gapped_alignments, :gap_opening_penalty,
       :gap_extension_penalty, :gap_opening_extension, :queue,
       :blast_dbs
@@ -18,7 +20,7 @@ module Quorum
       :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
-    validates_numericality_of :max_score,
+    validates_numericality_of :max_target_seqs,
       :only_integer => true,
       :allow_blank  => true
     validates_numericality_of :min_bit_score,
@@ -31,7 +33,6 @@ module Quorum
       :only_integer => true,
       :allow_blank  => true
     validates_presence_of :blast_dbs, :if => :queue
-    validate :gap_opening_extension_exists
 
     #
     # Gapped alignment helper.
@@ -79,32 +80,24 @@ module Quorum
 
     private
 
-    def set_blast_dbs
+    def check_blast_dbs
       if self.blast_dbs.present?
-        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }.join(';')
+        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }
       end
     end
 
-    def set_optional_params
-      self.expectation   = "5e-20" if self.expectation.blank?
-      self.max_score     ||= 25
-      self.min_bit_score ||= 0
-      unless self.gapped_alignments
-        self.gap_opening_penalty   = 0
-        self.gap_extension_penalty = 0
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
       end
     end
 
-    #
-    # Add error if gapped_alignment? without gap_opening_extension.
-    #
-    def gap_opening_extension_exists
-      if gap_opening_extension.split(',').blank? && gapped_alignment?
-        errors.add(
-          :gap_opening_extension,
-          " - Please select a value."
-        )
-      end
+    def set_optional_params
+      self.expectation = "5e-20" if self.expectation.blank?
+      self.max_target_seqs ||= 25
+      self.min_bit_score ||= 0
+      self.gap_opening_penalty ||= nil
+      self.gap_extension_penalty ||= nil
     end
 
   end

data/app/models/quorum/blastp_job.rb

@@ -1,6 +1,8 @@
 module Quorum
   class BlastpJob < ActiveRecord::Base
 
+    before_validation :check_blast_dbs, :if => :queue
+
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
@@ -9,7 +11,7 @@ module Quorum
       :foreign_key => :blastp_job_id,
       :primary_key => :job_id
 
-    attr_accessible :expectation, :max_score, :min_bit_score,
+    attr_accessible :expectation, :max_target_seqs, :min_bit_score,
       :filter,  :gapped_alignments, :gap_opening_penalty,
       :gap_extension_penalty, :gap_opening_extension, :queue,
       :blast_dbs
@@ -18,7 +20,7 @@ module Quorum
       :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
-    validates_numericality_of :max_score,
+    validates_numericality_of :max_target_seqs,
       :only_integer => true,
       :allow_blank  => true
     validates_numericality_of :min_bit_score,
@@ -31,7 +33,6 @@ module Quorum
       :only_integer => true,
       :allow_blank  => true
     validates_presence_of :blast_dbs, :if => :queue
-    validate :gap_opening_extension_exists
 
     #
     # Gapped alignment helper.
@@ -79,32 +80,24 @@ module Quorum
 
     private
 
-    def set_blast_dbs
+    def check_blast_dbs
       if self.blast_dbs.present?
-        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }.join(';')
+        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }
       end
     end
 
-    def set_optional_params
-      self.expectation   = "5e-20" if self.expectation.blank?
-      self.max_score     ||= 25
-      self.min_bit_score ||= 0
-      unless self.gapped_alignments
-        self.gap_opening_penalty   = 0
-        self.gap_extension_penalty = 0
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
       end
     end
 
-    #
-    # Add error if gapped_alignment? without gap_opening_extension.
-    #
-    def gap_opening_extension_exists
-      if gap_opening_extension.split(',').blank? && gapped_alignment?
-        errors.add(
-          :gap_opening_extension,
-          " - Please select a value."
-        )
-      end
+    def set_optional_params
+      self.expectation = "5e-20" if self.expectation.blank?
+      self.max_target_seqs ||= 25
+      self.min_bit_score ||= 0
+      self.gap_opening_penalty ||= nil
+      self.gap_extension_penalty ||= nil
     end
 
   end

data/app/models/quorum/blastx_job.rb

@@ -1,6 +1,8 @@
 module Quorum
   class BlastxJob < ActiveRecord::Base
 
+    before_validation :check_blast_dbs, :if => :queue
+
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
@@ -9,7 +11,7 @@ module Quorum
       :foreign_key => :blastx_job_id,
       :primary_key => :job_id
 
-    attr_accessible :expectation, :max_score, :min_bit_score,
+    attr_accessible :expectation, :max_target_seqs, :min_bit_score,
       :filter,  :gapped_alignments, :gap_opening_penalty,
       :gap_extension_penalty, :gap_opening_extension, :queue,
       :blast_dbs
@@ -18,7 +20,7 @@ module Quorum
       :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
-    validates_numericality_of :max_score,
+    validates_numericality_of :max_target_seqs,
       :only_integer => true,
       :allow_blank  => true
     validates_numericality_of :min_bit_score,
@@ -31,7 +33,6 @@ module Quorum
       :only_integer => true,
       :allow_blank  => true
     validates_presence_of :blast_dbs, :if => :queue
-    validate :gap_opening_extension_exists
 
     #
     # Gapped alignment helper.
@@ -79,32 +80,24 @@ module Quorum
 
     private
 
-    def set_blast_dbs
+    def check_blast_dbs
       if self.blast_dbs.present?
-        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }.join(';')
+        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }
       end
     end
 
-    def set_optional_params
-      self.expectation   = "5e-20" if self.expectation.blank?
-      self.max_score     ||= 25
-      self.min_bit_score ||= 0
-      unless self.gapped_alignments
-        self.gap_opening_penalty   = 0
-        self.gap_extension_penalty = 0
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
       end
     end
 
-    #
-    # Add error if gapped_alignment? without gap_opening_extension.
-    #
-    def gap_opening_extension_exists
-      if gap_opening_extension.split(',').blank? && gapped_alignment?
-        errors.add(
-          :gap_opening_extension,
-          " - Please select a value."
-        )
-      end
+    def set_optional_params
+      self.expectation = "5e-20" if self.expectation.blank?
+      self.max_target_seqs ||= 25
+      self.min_bit_score ||= 0
+      self.gap_opening_penalty ||= nil
+      self.gap_extension_penalty ||= nil
     end
 
   end

data/app/models/quorum/tblastn_job.rb

@@ -1,6 +1,8 @@
 module Quorum
   class TblastnJob < ActiveRecord::Base
 
+    before_validation :check_blast_dbs, :if => :queue
+
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
@@ -9,7 +11,7 @@ module Quorum
       :foreign_key => :tblastn_job_id,
       :primary_key => :job_id
 
-    attr_accessible :expectation, :max_score, :min_bit_score,
+    attr_accessible :expectation, :max_target_seqs, :min_bit_score,
       :filter,  :gapped_alignments, :gap_opening_penalty,
       :gap_extension_penalty, :gap_opening_extension, :queue,
       :blast_dbs
@@ -18,7 +20,7 @@ module Quorum
       :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
-    validates_numericality_of :max_score,
+    validates_numericality_of :max_target_seqs,
       :only_integer => true,
       :allow_blank  => true
     validates_numericality_of :min_bit_score,
@@ -31,7 +33,6 @@ module Quorum
       :only_integer => true,
       :allow_blank  => true
     validates_presence_of :blast_dbs, :if => :queue
-    validate :gap_opening_extension_exists
 
     #
     # Gapped alignment helper.
@@ -79,32 +80,24 @@ module Quorum
 
     private
 
-    def set_blast_dbs
+    def check_blast_dbs
       if self.blast_dbs.present?
-        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }.join(';')
+        self.blast_dbs = self.blast_dbs.delete_if { |b| b.empty? }
       end
     end
 
-    def set_optional_params
-      self.expectation   = "5e-20" if self.expectation.blank?
-      self.max_score     ||= 25
-      self.min_bit_score ||= 0
-      unless self.gapped_alignments
-        self.gap_opening_penalty   = 0
-        self.gap_extension_penalty = 0
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
       end
     end
 
-    #
-    # Add error if gapped_alignment? without gap_opening_extension.
-    #
-    def gap_opening_extension_exists
-      if gap_opening_extension.split(',').blank? && gapped_alignment?
-        errors.add(
-          :gap_opening_extension,
-          " - Please select a value."
-        )
-      end
+    def set_optional_params
+      self.expectation = "5e-20" if self.expectation.blank?
+      self.max_target_seqs ||= 25
+      self.min_bit_score ||= 0
+      self.gap_opening_penalty ||= nil
+      self.gap_extension_penalty ||= nil
     end
 
   end

data/app/views/quorum/jobs/form/_blastn_form.html.erb

@@ -16,7 +16,7 @@
           <%= n.label :filter, "DUST" %>
         </td>
         <td>
-          <%= n.check_box :filter %>
+          <%= n.select :filter, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>
@@ -37,17 +37,17 @@
       </tr>
       <tr>
         <td>
-          <%= n.label :max_score %>
+          <%= n.label :max_target_seqs, "Max target sequences" %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25",
+          <%= n.text_field :max_target_seqs, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :gapped_alignments %>
         </td>
         <td>
-          <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
+          <%= n.select :gapped_alignments, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>

data/app/views/quorum/jobs/form/_blastp_form.html.erb

@@ -16,7 +16,7 @@
           <%= n.label :filter, "SEG" %>
         </td>
         <td>
-          <%= n.check_box :filter %>
+          <%= n.select :filter, [['No', false], ['Yes', true]] %>
         </td>
       </tr>
       <tr>
@@ -37,17 +37,17 @@
       </tr>
       <tr>
         <td>
-          <%= n.label :max_score %>
+          <%= n.label :max_target_seqs, "Max target sequences" %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25",
+          <%= n.text_field :max_target_seqs, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :gapped_alignments %>
         </td>
         <td>
-          <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
+          <%= n.select :gapped_alignments, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>

data/app/views/quorum/jobs/form/_blastx_form.html.erb

@@ -16,7 +16,7 @@
           <%= n.label :filter, "SEG" %>
         </td>
         <td>
-          <%= n.check_box :filter %>
+          <%= n.select :filter, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>
@@ -37,17 +37,17 @@
       </tr>
       <tr>
         <td>
-          <%= n.label :max_score %>
+          <%= n.label :max_target_seqs, "Max target sequences" %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25",
+          <%= n.text_field :max_target_seqs, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :gapped_alignments %>
         </td>
         <td>
-          <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
+          <%= n.select :gapped_alignments, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>

data/app/views/quorum/jobs/form/_tblastn_form.html.erb

@@ -16,7 +16,7 @@
           <%= n.label :filter, "SEG" %>
         </td>
         <td>
-          <%= n.check_box :filter %>
+          <%= n.select :filter, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>
@@ -37,17 +37,17 @@
       </tr>
       <tr>
         <td>
-           <%= n.label :max_score %>
+           <%= n.label :max_target_seqs, "Max target sequences" %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25",
+          <%= n.text_field :max_target_seqs, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :gapped_alignments %>
         </td>
         <td>
-          <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
+          <%= n.select :gapped_alignments, [['Yes', true],['No', false]] %>
         </td>
       </tr>
       <tr>

data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb

@@ -2,19 +2,8 @@
 <script type="text/template" id="detailed_report_template">
   <h3>Query Accession {{= query }}</h3>
   {{ _.each(data, function(v) { }}
-    {{ var id        = v.id }}
-    {{ var qseq      = v.qseq }}
-    {{ var midline   = v.midline }}
-    {{ var hseq      = v.hseq }}
-    {{ var q_from    = v.query_from }}
-    {{ var q_to      = v.query_to }}
-    {{ var h_from    = v.hit_from }}
-    {{ var h_to      = v.hit_to }}
-    {{ var qstrand   = v.query_frame }}
-    {{ var hstrand   = v.hit_frame }}
-    {{ var hsp_group = v.hsp_group }}
-    <div id="{{= id }}">
-      <p class="small">{{= QUORUM.displayHspLinks(id, hsp_group, data) }}</p>
+    <div id="{{= v.id }}">
+      <p class="small">{{= QUORUM.displayHspLinks(v.id, v.hsp_group, data) }}</p>
       <p class="small">Hit Accession: {{= v.hit_display_id }}</p>
       <p class="small">Hit Description: {{= v.hit_def }}</p>
       <table class="report_details">
@@ -25,7 +14,7 @@
         </tr>
         <tr>
           <td>Alignment Length: {{= v.align_len }}</td>
-          <td>Qstrand / Hstrand: {{= QUORUM.formatStrand(qstrand, hstrand) }}</td>
+          <td>Qstrand / Hstrand: {{= QUORUM.formatStrand(v.query_frame, v.hit_frame) }}</td>
           <td></td>
         </tr>
         <tr>
@@ -40,12 +29,12 @@
         </tr>
       </table>
       <p class="small">
-        <a id="download_sequence_{{= id }}"
-          onclick="QUORUM.downloadSequence({{= id }}, '{{= algo }}', this)">
+        <a id="download_sequence_{{= v.id }}"
+          onclick="QUORUM.downloadSequence({{= v.id }}, '{{= algo }}', this)">
           Download Sequence
         </a>
       </p>
-      {{= QUORUM.formatSequenceReport(qseq, midline, hseq, q_from, q_to, h_from, h_to, algo) }}
+      {{= QUORUM.formatSequenceReport(v.qseq, v.midline, v.hseq, v.query_from, v.query_to, v.hit_from, v.hit_to, algo) }}
     </div>
     <hr />
     {{ }); }}

data/db/migrate/20120918205556_rename_max_score_column.rb

@@ -0,0 +1,15 @@
+class RenameMaxScoreColumn < ActiveRecord::Migration
+  def up
+    rename_column :quorum_blastn_jobs, :max_score, :max_target_seqs
+    rename_column :quorum_blastp_jobs, :max_score, :max_target_seqs
+    rename_column :quorum_blastx_jobs, :max_score, :max_target_seqs
+    rename_column :quorum_tblastn_jobs, :max_score, :max_target_seqs
+  end
+
+  def down
+    rename_column :quorum_blastn_jobs, :max_target_seqs, :max_score
+    rename_column :quorum_blastp_jobs, :max_target_seqs, :max_score
+    rename_column :quorum_blastx_jobs, :max_target_seqs, :max_score
+    rename_column :quorum_tblastn_jobs, :max_target_seqs, :max_score
+  end
+end