quorum 0.3.0 → 0.3.1

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

@@ -1,6 +1,6 @@
 <%= f.fields_for :blastn_job do |n| %>
   <p>
-    <strong>blastn</strong> 
+    <strong>blastn</strong>
     <%= n.check_box :queue %>
   </p>
   <div id="blastn" class="toggle">
@@ -10,7 +10,7 @@
           <label>Database(s)</label>
         </td>
         <td>
-          <%= n.select :blast_dbs, @blast_dbs[:blastn], {}, { :multiple => true } %> 
+          <%= n.select :blast_dbs, @blast_dbs[:blastn], {}, { :multiple => true } %>
         </td>
         <td>
           <%= n.label :filter, "DUST" %>
@@ -24,14 +24,14 @@
           <%= n.label :expectation %>
         </td>
         <td>
-          <%= n.text_field :expectation, :size => 15, :title => "5e-20", 
+          <%= n.text_field :expectation, :size => 15, :title => "5e-20",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :min_bit_score %>
         </td>
         <td>
-          <%= n.text_field :min_bit_score, :size => 15, :title => "0", 
+          <%= n.text_field :min_bit_score, :size => 15, :title => "0",
             :class => "auto-hint" %>
         </td>
       </tr>
@@ -40,7 +40,7 @@
           <%= n.label :max_score %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25", 
+          <%= n.text_field :max_score, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
@@ -55,8 +55,8 @@
           <%= n.label :gap_opening_extension %>
         </td>
         <td>
-          <%= 
-            n.select :gap_opening_extension, 
+          <%=
+            n.select :gap_opening_extension,
               options_for_select(
                 @job.blastn_job.gap_opening_extension_values,
                 @job.blastn_job.gap_opening_extension

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

@@ -1,6 +1,6 @@
 <%= f.fields_for :blastp_job do |n| %>
   <p>
-    <strong>blastp</strong> 
+    <strong>blastp</strong>
     <%= n.check_box :queue %>
   </p>
   <div id="blastp" class="toggle">
@@ -10,7 +10,7 @@
           <label>Database(s)</label>
         </td>
         <td>
-          <%= n.select :blast_dbs, @blast_dbs[:blastp], {}, { :multiple => true } %> 
+          <%= n.select :blast_dbs, @blast_dbs[:blastp], {}, { :multiple => true } %>
         </td>
         <td>
           <%= n.label :filter, "SEG" %>
@@ -24,14 +24,14 @@
           <%= n.label :expectation %>
         </td>
         <td>
-          <%= n.text_field :expectation, :size => 15, :title => "5e-20", 
+          <%= n.text_field :expectation, :size => 15, :title => "5e-20",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :min_bit_score %>
         </td>
         <td>
-          <%= n.text_field :min_bit_score, :size => 15, :title => "0", 
+          <%= n.text_field :min_bit_score, :size => 15, :title => "0",
             :class => "auto-hint" %>
         </td>
       </tr>
@@ -40,7 +40,7 @@
           <%= n.label :max_score %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25", 
+          <%= n.text_field :max_score, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
@@ -55,8 +55,8 @@
           <%= n.label :gap_opening_extension %>
         </td>
         <td>
-          <%= 
-            n.select :gap_opening_extension, 
+          <%=
+            n.select :gap_opening_extension,
               options_for_select(
                 @job.blastn_job.gap_opening_extension_values,
                 @job.blastn_job.gap_opening_extension

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

@@ -1,6 +1,6 @@
 <%= f.fields_for :blastx_job do |n| %>
   <p>
-    <strong>blastx</strong> 
+    <strong>blastx</strong>
     <%= n.check_box :queue %>
   </p>
   <div id="blastx" class="toggle">
@@ -10,7 +10,7 @@
           <label>Database(s)</label>
         </td>
         <td>
-          <%= n.select :blast_dbs, @blast_dbs[:blastx], {}, { :multiple => true } %> 
+          <%= n.select :blast_dbs, @blast_dbs[:blastx], {}, { :multiple => true } %>
         </td>
         <td>
           <%= n.label :filter, "SEG" %>
@@ -24,14 +24,14 @@
           <%= n.label :expectation %>
         </td>
         <td>
-          <%= n.text_field :expectation, :size => 15, :title => "5e-20", 
+          <%= n.text_field :expectation, :size => 15, :title => "5e-20",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :min_bit_score %>
         </td>
         <td>
-          <%= n.text_field :min_bit_score, :size => 15, :title => "0", 
+          <%= n.text_field :min_bit_score, :size => 15, :title => "0",
             :class => "auto-hint" %>
         </td>
       </tr>
@@ -40,7 +40,7 @@
           <%= n.label :max_score %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25", 
+          <%= n.text_field :max_score, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
@@ -55,8 +55,8 @@
           <%= n.label :gap_opening_extension %>
         </td>
         <td>
-          <%= 
-            n.select :gap_opening_extension, 
+          <%=
+            n.select :gap_opening_extension,
               options_for_select(
                 @job.blastn_job.gap_opening_extension_values,
                 @job.blastn_job.gap_opening_extension

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

@@ -1,6 +1,6 @@
 <%= f.fields_for :tblastn_job do |n| %>
   <p>
-    <strong>tblastn</strong> 
+    <strong>tblastn</strong>
     <%= n.check_box :queue %>
   </p>
   <div id="tblastn" class="toggle">
@@ -10,7 +10,7 @@
           <label>Database(s)</label>
         </td>
         <td>
-          <%= n.select :blast_dbs, @blast_dbs[:tblastn], {}, { :multiple => true } %> 
+          <%= n.select :blast_dbs, @blast_dbs[:tblastn], {}, { :multiple => true } %>
         </td>
         <td>
           <%= n.label :filter, "SEG" %>
@@ -24,14 +24,14 @@
           <%= n.label :expectation %>
         </td>
         <td>
-          <%= n.text_field :expectation, :size => 15, :title => "5e-20", 
+          <%= n.text_field :expectation, :size => 15, :title => "5e-20",
             :class => "auto-hint" %>
         </td>
         <td>
           <%= n.label :min_bit_score %>
         </td>
         <td>
-          <%= n.text_field :min_bit_score, :size => 15, :title => "0", 
+          <%= n.text_field :min_bit_score, :size => 15, :title => "0",
             :class => "auto-hint" %>
         </td>
       </tr>
@@ -40,7 +40,7 @@
            <%= n.label :max_score %>
         </td>
         <td>
-          <%= n.text_field :max_score, :size => 15, :title => "25", 
+          <%= n.text_field :max_score, :size => 15, :title => "25",
             :class => "auto-hint" %>
         </td>
         <td>
@@ -55,8 +55,8 @@
           <%= n.label :gap_opening_extension %>
         </td>
         <td>
-          <%= 
-            n.select :gap_opening_extension, 
+          <%=
+            n.select :gap_opening_extension,
               options_for_select(
                 @job.blastn_job.gap_opening_extension_values,
                 @job.blastn_job.gap_opening_extension

data/app/views/quorum/jobs/new.html.erb

@@ -3,8 +3,8 @@
   <%= form_for @job, :html => {:id => "quorum_job"} do |f| %>
     <%= render "shared/error_messages", :target => @job %>
     <div>
-      <%= f.text_area :sequence, 
-        :title => "Paste nucleic and amino acid FASTA sequence(s) here " << 
+      <%= f.text_area :sequence,
+        :title => "Paste nucleic and amino acid FASTA sequence(s) here " <<
           "or upload a file below.",
         :class => "auto-hint" %>
     </div>
@@ -15,32 +15,32 @@
     <!-- Comment out an algorithm below to remove it from the form. -->
 
     <!-- blastn -->
-    <%= render :partial => "quorum/jobs/form/blastn_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/blastn_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- blastx -->
-    <%= render :partial => "quorum/jobs/form/blastx_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/blastx_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- tblastn -->
-    <%= render :partial => "quorum/jobs/form/tblastn_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/tblastn_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- blastp -->
-    <%= render :partial => "quorum/jobs/form/blastp_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/blastp_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- End Search Algorithms -->
     <div>
       <%= f.submit "Submit" %>&nbsp;&nbsp;
-      <%= submit_tag "Reset", :name => "reset", 
+      <%= submit_tag "Reset", :name => "reset",
         :type => "button", :id => "quorum_job_reset" %>
     </div>
   <% end %>
 </div>
-<div id="quorum">              
+<div id="quorum">
   <hr class="big" />
-  <p> 
+  <p>
     Powered by <%= link_to "Quorum", "https://github.com/ncgr/quorum" %>
   </p>
 </div>

data/app/views/quorum/jobs/show.html.erb

@@ -16,28 +16,28 @@
     <div id="tabs-1">
       <h2>Blastn</h2>
       <div id="blastn-results">
-        Searching... <%= image_tag "quorum/loading.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %>
       </div>
     </div>
 
     <div id="tabs-2">
       <h2>Blastx</h2>
       <div id="blastx-results">
-        Searching... <%= image_tag "quorum/loading.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %>
       </div>
     </div>
 
     <div id="tabs-3">
       <h2>Tblastn</h2>
       <div id="tblastn-results">
-        Searching... <%= image_tag "quorum/loading.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %>
       </div>
     </div>
 
     <div id="tabs-4">
       <h2>Blastp</h2>
       <div id="blastp-results">
-        Searching... <%= image_tag "quorum/loading.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %>
       </div>
     </div>
   </div>
@@ -47,9 +47,9 @@
   <!-- Detailed report element -->
   <div id="detailed_report_dialog" title="Quorum Report Details"></div>
 </div>
-<div id="quorum">              
+<div id="quorum">
   <hr class="big" />
-  <p> 
+  <p>
     Powered by <%= link_to "Quorum", "https://github.com/ncgr/quorum" %>
   </p>
 </div>
@@ -63,7 +63,7 @@
     //
     // Asynchronously poll Quorum for search results.
     //
-    //  pollResults(id, interval) 
+    //  pollResults(id, interval)
     //    id: Job.id
     //    interval: poll interval in milliseconds. 5000 default.
     //

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

@@ -8,8 +8,8 @@
     {{ 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 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 }}
@@ -40,7 +40,7 @@
         </tr>
       </table>
       <p class="small">
-        <a id="download_sequence_{{= id }}" 
+        <a id="download_sequence_{{= id }}"
           onclick="QUORUM.downloadSequence(<%= @jobs.id %>, {{= id }}, '{{= algo }}', this)">
           Download Sequence
         </a>

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

@@ -50,11 +50,11 @@
           <td class="right">{{= v.align_len }}</td>
           <td class="right">{{= v.bit_score }}</td>
           <td class="right">
-            <a class="detailed_report" 
+            <a class="detailed_report"
               onclick="QUORUM.viewDetailedReport(
-                <%= @jobs.id %>, 
-                {{= v.id }}, 
-                '{{= v.query }}', 
+                <%= @jobs.id %>,
+                {{= v.id }},
+                '{{= v.query }}',
                 '{{= algo }}')">
                 {{= v.evalue }}
             </a>

data/lib/generators/quorum/install_generator.rb

@@ -12,7 +12,7 @@ module Quorum
       DEPENDENCIES = ["makeblastdb", "seqret"]
 
       def copy_quorum
-        template "quorum_initializer.rb", 
+        template "quorum_initializer.rb",
           "config/initializers/quorum_initializer.rb"
         template "quorum_settings.yml", "config/quorum_settings.yml"
         template "search", "quorum/bin/search"
@@ -45,7 +45,7 @@ module Quorum
         @quorum = %Q(mount Quorum::Engine => "/quorum")
         @resque = %Q(mount Resque::Server.new, :at => "/quorum/resque")
       end
-      
+
       def read_routes_file
         @routes = File.open(File.join("config", "routes.rb"), "r")
         @routes = @routes.read
@@ -56,7 +56,7 @@ module Quorum
       end
 
       def add_mount_engine
-        route @quorum unless mount_engine_exists? 
+        route @quorum unless mount_engine_exists?
       end
 
       def resque_mount_engine_exists?

data/lib/generators/quorum/views_generator.rb

@@ -1,16 +1,17 @@
 module Quorum
   module Generators
     class ViewsGenerator < Rails::Generators::Base
-      source_root File.expand_path("../../../../app/views/quorum", __FILE__)
+      source_root File.expand_path("../../../../app/views", __FILE__)
       desc "Copy quorum views to your application."
 
-      VIEW_DIRECTORIES = [
-        "jobs"
+      DIRECTORIES = [
+        "quorum/jobs",
+        "layouts/quorum"
       ]
 
-      def copy_views
-        VIEW_DIRECTORIES.each do |d|
-          directory d.to_s, "app/views/quorum/#{d.to_s}"
+      def copy_directories
+        DIRECTORIES.each do |d|
+          directory d.to_s, "app/views/#{d.to_s}"
         end
       end
     end

data/lib/generators/templates/README

@@ -6,8 +6,8 @@ Thanks for installing Quorum!!
 Quorum Manual Setup:
 
 1. Ensure you have defined root_url in your config/routes.rb.
-   If you are deploying Quorum as a standalone application, 
-   add the below after the engine is mounted. 
+   If you are deploying Quorum as a standalone application,
+   add the below after the engine is mounted.
 
      mount Quorum::Engine => "/quorum"
 
@@ -19,7 +19,7 @@ Quorum Manual Setup:
 
    For all available quorum:blastdb:build options
 
-     rake -D 
+     rake -D
 
 ==============================================================================
 

data/lib/generators/templates/blast.rb

@@ -13,9 +13,9 @@ module Quorum
       class QuorumJob < ActiveRecord::Base
         self.table_name = "quorum_jobs"
 
-        has_one :quorum_blastn_job, 
+        has_one :quorum_blastn_job,
           :foreign_key => "job_id"
-        has_many :quorum_blastn_job_reports, 
+        has_many :quorum_blastn_job_reports,
           :foreign_key => "blastn_job_id"
 
         has_one :quorum_blastx_job,
@@ -217,7 +217,7 @@ module Quorum
         File.open(@na_fasta, "w") { |f| f << @na_sequence }
         File.open(@aa_fasta, "w") { |f| f << @aa_sequence }
 
-        @out = File.join(@tmp, @hash + ".out.xml") 
+        @out = File.join(@tmp, @hash + ".out.xml")
         File.new(@out, "w")
 
         case @algorithm
@@ -241,7 +241,7 @@ module Quorum
         unless e.nil?
           e = " x 10<sup>" << e.sub(/e/, '') << "</sup>"
         end
-        evalue.to_f.round(1).to_s << e.to_s 
+        evalue.to_f.round(1).to_s << e.to_s
       end
 
       #
@@ -269,7 +269,7 @@ module Quorum
 
       #
       # Parse and save Blast results using bio-blastxmlparser.
-      # Only save Blast results if results.bit_score > @min_score. 
+      # Only save Blast results if results.bit_score > @min_score.
       #
       def parse_and_save_results
         # Helper to avoid having to perform a query.
@@ -311,7 +311,7 @@ module Quorum
 
                 # Hsps are only reported if a query hit against the Blast db.
                 # Only save the @data if bit_score exists.
-                if @data[:bit_score] && 
+                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
@@ -410,7 +410,7 @@ module Quorum
       # Execute Blast on a given dataset.
       #
       def execute_blast
-        generate_blast_cmd 
+        generate_blast_cmd
         @logger.log("NCBI Blast", @cmd)
         system(@cmd)
         parse_and_save_results

data/lib/generators/templates/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/lib/generators/templates/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
 

data/lib/generators/templates/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/lib/generators/templates/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

data/lib/generators/templates/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/lib/generators/templates/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