quorum 0.3.0 → 0.3.1

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

@@ -1,6 +1,6 @@
 //
 // QUORUM
-//---------------------------------------------------------------------------// 
+//---------------------------------------------------------------------------//
 
 var QUORUM = {
 
@@ -8,31 +8,31 @@ var QUORUM = {
   // Supported algorithms.
   //
   algorithms: ["blastn", "blastx", "tblastn", "blastp"],
-  
-  // 
+
+  //
   // Poll quorum search results asynchronously and insert them into
   // the DOM via #blast_template.
   //
   pollResults: function(id, interval, algos) {
-  
+
     // Set the default poll interval to 5 seconds.
     interval = interval || 5000;
-  
+
     // Algorithms
     algos = algos || QUORUM.algorithms;
-  
+
     _.each(algos, function(a) {
       $.getJSON(
         '/quorum/jobs/' + id + '/get_quorum_search_results.json?algo=' + a,
         function(data) {
           if (data.length === 0) {
-            setTimeout(function() { 
-              QUORUM.pollResults(id, interval, [a]); 
+            setTimeout(function() {
+              QUORUM.pollResults(id, interval, [a]);
             }, interval);
           } else {
             $('#' + a + '-results').empty();
             var temp = _.template(
-              $('#blast_template').html(), { 
+              $('#blast_template').html(), {
                 data: data,
                 algo: a
               }
@@ -40,20 +40,20 @@ var QUORUM = {
             $('#' + a + '-results').html(temp);
             return;
           }
-        } 
+        }
       );
     });
   },
-  
+
   //
-  // Display jQuery UI modal box containing detailed report of all hits 
+  // Display jQuery UI modal box containing detailed report of all hits
   // to the same query. After the modal box is inserted into the DOM,
   // automatically scroll to the highlighted hit.
   //
   viewDetailedReport: function(id, focus_id, query, algo) {
     // Create the modal box.
     $('#detailed_report_dialog').html(
-      "<p class='center'>" + 
+      "<p class='center'>" +
       "Loading... <img src='/assets/quorum/loading.gif' alt='Loading'>" +
       "</p>"
     ).dialog({
@@ -61,9 +61,9 @@ var QUORUM = {
       width:    850,
       position: 'top'
     });
-  
+
     $.getJSON(
-      '/quorum/jobs/' + id + '/get_quorum_search_results.json?algo=' + algo + 
+      '/quorum/jobs/' + id + '/get_quorum_search_results.json?algo=' + algo +
       '&query=' + query,
       function(data) {
         var temp = _.template(
@@ -73,54 +73,54 @@ var QUORUM = {
             algo:  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' });
-        
+
         // Highlight the selected id.
         $('#' + focus_id).addClass("ui-state-highlight");
-        
+
         // Automatically scroll to the selected id.
         QUORUM.autoScroll(focus_id, false);
       }
-    );  
+    );
   },
-  
+
   //
   // Helper to add title sequence position attribute for tipsy.
   //
   // If from > to decrement index; otherwise increment.
-  // If the algo is tblastn and type is hit OR algo is blastx and type is query, 
+  // If the algo is tblastn and type is hit OR algo is blastx and type is query,
   // increment / decrement by 3; otherwise increment / decrement by 1.
   //
   addBaseTitleIndex: function(bases, from, to, algo, type) {
     var forward = true;
     var value   = 1;
     var index   = from;
-  
+
     if (from > to) {
       forward = false;
     }
-  
+
     // Set value to 3 for the below.
     if ((type === "hit" && algo === "tblastn") ||
         (type === "query" && algo === "blastx")) {
       value = 3;
     }
-  
+
     // Add tipsy to each base.
     return _.map(bases.split(''), function(c) {
       var str = "<a rel='quorum-tipsy' title=" + index + ">" + c + "</a>";
       forward ? index += value : index -= value;
       return str;
-    }).join(''); 
+    }).join('');
   },
-  
+
   //
-  // Format sequence data for detailed report. 
+  // Format sequence data for detailed report.
   //
   // If q_from > q_to or h_from > h_to, subtract by increment; otherwise add
   // by increment.
@@ -133,26 +133,26 @@ var QUORUM = {
     var s         = 0;           // start position
     var e         = increment;   // end position
     var seq       = "\n";        // seq string to return
-  
+
     while(true) {
       seq += "qseq " + QUORUM.addBaseTitleIndex(qseq.slice(s, e), q_from, q_to, algo, 'query') + "\n";
       seq += "     " + midline.slice(s, e) + "\n";
       seq += "hseq " + QUORUM.addBaseTitleIndex(hseq.slice(s, e), h_from, h_to, algo, 'hit') + "\n\n";
-  
+
       if (e >= max) {
         break;
       }
-  
+
       s += increment;
       e += increment;
-  
+
       // If the algorithm is blastx, increment * 3 only for qseq.
       if (algo === "blastx") {
         q_from < q_to ? q_from += (increment * 3) : q_from -= (increment * 3);
       } else {
         q_from < q_to ? q_from += increment : q_from -= increment;
       }
-  
+
       // If the algorithm is tblastn, increment * 3 only for hseq.
       if (algo === "tblastn") {
         h_from < h_to ? h_from += (increment * 3) : h_from -= (increment * 3);
@@ -160,10 +160,10 @@ var QUORUM = {
         h_from < h_to ? h_from += increment : h_from -= increment;
       }
     }
-    return "<p class='small'>Alignment (Mouse over for positions):</p>" + 
+    return "<p class='small'>Alignment (Mouse over for positions):</p>" +
       "<span class='small'><pre>" + seq + "</pre></span>";
   },
-  
+
   //
   // Format Query and Hit Strand.
   //
@@ -172,29 +172,29 @@ var QUORUM = {
   formatStrand: function(qstrand, hstrand) {
     var q = "";
     var h = "";
-  
+
     qstrand < 0 ? q = "reverse" : q = "forward";
     hstrand < 0 ? h = "reverse" : h = "forward";
-  
+
     return q + " / " + h;
   },
-  
+
   //
   // Display links to Hsps in the same group.
   //
   displayHspLinks: function(focus, group, data) {
     if (group !== null) {
-      var str = "Related <a onclick=\"(QUORUM.openWindow(" + 
-        "'http://www.ncbi.nlm.nih.gov/books/NBK62051/def-item/blast_glossary.HSP'," + 
+      var str = "Related <a onclick=\"(QUORUM.openWindow(" +
+        "'http://www.ncbi.nlm.nih.gov/books/NBK62051/def-item/blast_glossary.HSP'," +
         "'HSP', 800, 300))\">HSPs</a>: ";
-  
+
       var ids = _.map(group.split(","), function(i) { return parseInt(i, 10); });
-    
+
       var selected = _(data).chain()
         .reject(function(d) { return !_.include(ids, d.id); })
         .sortBy(function(d) { return d.id; })
         .value();
-  
+
       _.each(selected, function(e) {
         if (e.id !== focus) {
           str += "<a onclick='(QUORUM.autoScroll(" + e.id + ", true))'>" + e.hsp_num + "</a> ";
@@ -205,13 +205,13 @@ var QUORUM = {
       return str;
     }
   },
-  
+
   //
   // Download Blast hit sequence.
   //
   downloadSequence: function(id, algo_id, algo, el) {
     $(el).html('Fetching sequence...');
-  
+
     $.getJSON(
       "/quorum/jobs/" + id + "/get_quorum_blast_hit_sequence.json?algo_id=" +
       algo_id + "&algo=" + algo,
@@ -220,12 +220,12 @@ var QUORUM = {
       }
     );
   },
-  
+
   //
   // Poll application for Blast hit sequence.
   //
   getSequenceFile: function(id, meta_id, el) {
-    var url = "/quorum/jobs/" + id + 
+    var url = "/quorum/jobs/" + id +
       "/send_quorum_blast_hit_sequence?meta_id=" + meta_id;
     $.get(
       url,
@@ -235,19 +235,19 @@ var QUORUM = {
         } else {
           if (data.indexOf("error") !== -1) {
             // Print error message.
-            $(el).addClass('ui-state-error').html(data);  
+            $(el).addClass('ui-state-error').html(data);
           } else {
             // Force browser to download file via iframe.
-            $(el).addClass('ui-state-highlight').html('Sequence Downloaded Successfully');  
+            $(el).addClass('ui-state-highlight').html('Sequence Downloaded Successfully');
             $('.quorum_sequence_download').remove();
             $('body').append('<iframe class="quorum_sequence_download"></iframe>');
             $('.quorum_sequence_download').attr('src', url).hide();
           }
         }
-      } 
+      }
     );
   },
-  
+
   //
   // Autoscroll to given div id.
   //
@@ -255,19 +255,19 @@ var QUORUM = {
     $('html, body').animate({
       scrollTop: $('#' + id).offset().top
     }, 1000);
-  
+
     if (highlight) {
       $('#' + id).effect("highlight", {}, 4000);
     }
   },
-  
+
   //
   // Open URL in new window.
   //
   openWindow: function(url, name, width, height) {
-  
+
     var windowSize = "width=" + width + ",height=" + height + ",scrollbars=yes";
-  
+
     window.open(url, name, windowSize);
   }
 

data/app/assets/stylesheets/quorum/application.css

@@ -3,14 +3,14 @@
  * and any sub-directories. You're free to add application-wide styles to this file and they'll appear at
  * the top of the compiled file, but it's generally better to create a new file per style scope.
  *= require_self
- *= require_tree . 
+ *= require_tree .
 */
 
 /*** Content Styles ***/
 
 html {
     color: #222222;
-    font-family: Lucida Grande, Helvetica, Arial, sans-serif;	
+    font-family: Lucida Grande, Helvetica, Arial, sans-serif;
     background: #b8b8b8 url("bg.png") repeat-x top;
 }
 
@@ -30,18 +30,18 @@ img {
 }
 
 hr.big {
-    height: 3px; 
-    border: 0; 
-    background-color: #8C8C8C; 
-    margin: 5px 0 5px 0; 
+    height: 3px;
+    border: 0;
+    background-color: #8C8C8C;
+    margin: 5px 0 5px 0;
 	width: 100%;
 	overflow: hidden;
 }
 
 hr {
-    height: 1px; 
-    border: 0; 
-    background-color: #8C8C8C; 
+    height: 1px;
+    border: 0;
+    background-color: #8C8C8C;
     margin: 5px 0 5px 0;
     width: 100%;
 }
@@ -77,22 +77,22 @@ hr {
 }
 
 .right {
-    text-align: right;	
+    text-align: right;
     font-style: italic;
 }
 
 .left {
-    text-align: left;	
+    text-align: left;
 }
 
 .center {
-    margin-left: auto;   
-    margin-right: auto;   
-    text-align: center;	
+    margin-left: auto;
+    margin-right: auto;
+    text-align: center;
 }
 
 .indent {
-    margin: 0 0 0 5px;   
+    margin: 0 0 0 5px;
     padding: 0;
 }
 
@@ -104,17 +104,17 @@ hr {
 }
 
 div.center {
-    margin-left: auto;   
-    margin-right: auto;   
-    text-align: center;	
+    margin-left: auto;
+    margin-right: auto;
+    text-align: center;
 }
 
 img.right {
 	float: right;
 }
 
-img.center {   
-    text-align: center;	
+img.center {
+    text-align: center;
 }
 
 img.left {
@@ -151,14 +151,14 @@ img.left {
 #error_explanation ul li {
 	margin: 0;
     padding: 0 0 0 5px;
-    font-size: 14px;	
+    font-size: 14px;
     line-height: 18px;
 }
 
 #notice, #alert, #error {
 	margin: 10px 0 15px 0;
 	padding: 0;
-	
+
 	color: #0065de;
 	font-size: 18px;
 	font-weight: bold;
@@ -207,7 +207,7 @@ form label {
   font-size: 12px;
 }
 
-#quorum p, #quorum p a { 
+#quorum p, #quorum p a {
   text-decoration: none;
   color: #f8f8ff;
 }

data/app/assets/stylesheets/quorum/jquery-ui-1.8.16.custom.css

@@ -344,7 +344,7 @@
  *
  * http://docs.jquery.com/UI/Autocomplete#theming
  */
-.ui-autocomplete { position: absolute; cursor: default; }	
+.ui-autocomplete { position: absolute; cursor: default; }
 
 /* workarounds */
 * html .ui-autocomplete { width:1px; } /* without this, the menu expands to 100% in IE6 */
@@ -400,8 +400,8 @@
 .ui-button { display: inline-block; position: relative; padding: 0; margin-right: .1em; text-decoration: none !important; cursor: pointer; text-align: center; zoom: 1; overflow: visible; } /* the overflow property removes extra width in IE */
 .ui-button-icon-only { width: 2.2em; } /* to make room for the icon, a width needs to be set here */
 button.ui-button-icon-only { width: 2.4em; } /* button elements seem to need a little more width */
-.ui-button-icons-only { width: 3.4em; } 
-button.ui-button-icons-only { width: 3.7em; } 
+.ui-button-icons-only { width: 3.4em; }
+button.ui-button-icons-only { width: 3.7em; }
 
 /*button text element */
 .ui-button .ui-button-text { display: block; line-height: 1.4;  }
@@ -437,7 +437,7 @@ button.ui-button::-moz-focus-inner { border: 0; padding: 0; } /* reset extra pad
  */
 .ui-dialog { position: absolute; padding: .2em; width: 300px; overflow: hidden; }
 .ui-dialog .ui-dialog-titlebar { padding: .4em 1em; position: relative;  }
-.ui-dialog .ui-dialog-title { float: left; margin: .1em 16px .1em 0; } 
+.ui-dialog .ui-dialog-title { float: left; margin: .1em 16px .1em 0; }
 .ui-dialog .ui-dialog-titlebar-close { position: absolute; right: .3em; top: 50%; width: 19px; margin: -10px 0 0 0; padding: 1px; height: 18px; }
 .ui-dialog .ui-dialog-titlebar-close span { display: block; margin: 1px; }
 .ui-dialog .ui-dialog-titlebar-close:hover, .ui-dialog .ui-dialog-titlebar-close:focus { padding: 0; }
@@ -509,7 +509,7 @@ button.ui-button::-moz-focus-inner { border: 0; padding: 0; } /* reset extra pad
 .ui-datepicker .ui-datepicker-title { margin: 0 2.3em; line-height: 1.8em; text-align: center; }
 .ui-datepicker .ui-datepicker-title select { font-size:1em; margin:1px 0; }
 .ui-datepicker select.ui-datepicker-month-year {width: 100%;}
-.ui-datepicker select.ui-datepicker-month, 
+.ui-datepicker select.ui-datepicker-month,
 .ui-datepicker select.ui-datepicker-year { width: 49%;}
 .ui-datepicker table {width: 100%; font-size: .9em; border-collapse: collapse; margin:0 0 .4em; }
 .ui-datepicker th { padding: .7em .3em; text-align: center; font-weight: bold; border: 0;  }

data/app/controllers/quorum/jobs_controller.rb

@@ -35,7 +35,7 @@ module Quorum
         @job.build_tblastn_job if @job.tblastn_job.nil?
         @job.build_blastp_job  if @job.blastp_job.nil?
         render :action => "new"
-        return 
+        return
       end
       redirect_to job_path(@job.id)
     end
@@ -46,7 +46,7 @@ module Quorum
       rescue ActiveRecord::RecordNotFound => e
         set_flash_message(:notice, :data_not_found)
         redirect_to :action => "new"
-      end        
+      end
     end
 
     #
@@ -101,7 +101,7 @@ module Quorum
           )
           json = [{ :meta_id => data.meta_id }]
         end
-      end   
+      end
 
       respond_with json
     end
@@ -116,8 +116,8 @@ module Quorum
       data = Workers::System.get_meta(params[:meta_id])
       if data.succeeded?
         unless data.result.downcase.include?("error")
-          send_data data.result, 
-            :filename    => "#{params[:meta_id]}.fa", 
+          send_data data.result,
+            :filename    => "#{params[:meta_id]}.fa",
             :type        => "text/plain",
             :disposition => "attachment"
           return
@@ -137,8 +137,8 @@ module Quorum
     def set_blast_dbs
       @blast_dbs = {
         :blastn  => Quorum.blastn,
-        :blastx  => Quorum.blastx, 
-        :tblastn => Quorum.tblastn, 
+        :blastx  => Quorum.blastx,
+        :tblastn => Quorum.tblastn,
         :blastp  => Quorum.blastp
       }
     end

data/app/models/quorum/blastn_job.rb

@@ -4,7 +4,7 @@ module Quorum
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
-    has_many :blastn_job_reports, 
+    has_many :blastn_job_reports,
       :dependent   => :destroy,
       :foreign_key => :blastn_job_id,
       :primary_key => :job_id

data/app/models/quorum/blastp_job.rb

@@ -4,7 +4,7 @@ module Quorum
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
-    has_many :blastp_job_reports, 
+    has_many :blastp_job_reports,
       :dependent   => :destroy,
       :foreign_key => :blastp_job_id,
       :primary_key => :job_id

data/app/models/quorum/blastx_job.rb

@@ -4,7 +4,7 @@ module Quorum
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
-    has_many :blastx_job_reports, 
+    has_many :blastx_job_reports,
       :dependent   => :destroy,
       :foreign_key => :blastx_job_id,
       :primary_key => :job_id

data/app/models/quorum/job.rb

@@ -1,31 +1,31 @@
 module Quorum
   class Job < ActiveRecord::Base
-  
+
     include Quorum::Sequence
 
     after_save :queue_workers
 
     has_one :blastn_job, :dependent => :destroy
-    has_many :blastn_job_reports, :through => :blastn_job, 
+    has_many :blastn_job_reports, :through => :blastn_job,
       :dependent => :destroy
 
     has_one :blastx_job, :dependent => :destroy
-    has_many :blastx_job_reports, :through => :blastx_job, 
+    has_many :blastx_job_reports, :through => :blastx_job,
       :dependent => :destroy
 
     has_one :tblastn_job, :dependent => :destroy
-    has_many :tblastn_job_reports, :through => :tblastn_job, 
+    has_many :tblastn_job_reports, :through => :tblastn_job,
       :dependent => :destroy
 
     has_one :blastp_job, :dependent => :destroy
-    has_many :blastp_job_reports, :through => :blastp_job, 
+    has_many :blastp_job_reports, :through => :blastp_job,
       :dependent => :destroy
 
     accepts_nested_attributes_for :blastn_job, :blastx_job, :tblastn_job,
       :blastp_job,
       :reject_if => proc { |attributes| attributes['queue'] == '0' }
 
-    attr_accessible :sequence, :na_sequence, :aa_sequence, 
+    attr_accessible :sequence, :na_sequence, :aa_sequence,
       :blastn_job_attributes, :blastx_job_attributes, :tblastn_job_attributes,
       :blastp_job_attributes
 
@@ -34,7 +34,7 @@ module Quorum
     validate :filter_input_sequences, :algorithm_selected
 
     #
-    # Fetch Blast hit_id, hit_display_id, queue Resque worker and 
+    # Fetch Blast hit_id, hit_display_id, queue Resque worker and
     # return worker's meta_id.
     #
     def fetch_quorum_blast_sequence(algo, algo_id)
@@ -53,8 +53,8 @@ module Quorum
       cmd = create_blast_fetch_command(blast_dbs, hit_id, hit_display_id, algo)
 
       data = Workers::System.enqueue(
-        cmd, Quorum.blast_remote, 
-        Quorum.blast_ssh_host, Quorum.blast_ssh_user, 
+        cmd, Quorum.blast_remote,
+        Quorum.blast_ssh_host, Quorum.blast_ssh_user,
         Quorum.blast_ssh_options, true
       )
 
@@ -74,7 +74,7 @@ module Quorum
       rescue ActiveSupport::Multibyte::EncodingError => e
         logger.error e.message
         errors.add(
-          :sequence, 
+          :sequence,
           "Please enter your sequence(s) in Plain Text as FASTA."
         )
         self.sequence = ""
@@ -100,7 +100,7 @@ module Quorum
       self.na_sequence = ""
       self.aa_sequence = ""
 
-      # Split the sequences on >, check the type (AA or NA) and separate. 
+      # Split the sequences on >, check the type (AA or NA) and separate.
       seqs = fasta.split('>')
       seqs.delete_if { |s| s.empty? }
       seqs.each do |s|
@@ -110,8 +110,8 @@ module Quorum
         end
         if type == "amino_acid"
           self.aa_sequence << ">" << s
-        end 
-      end   
+        end
+      end
 
       self.na_sequence = nil if self.na_sequence.empty?
       self.aa_sequence = nil if self.aa_sequence.empty?
@@ -122,15 +122,15 @@ module Quorum
     #
     def algorithm_selected
       in_queue = false
-      if (self.blastn_job && self.blastn_job.queue) || 
+      if (self.blastn_job && self.blastn_job.queue) ||
         (self.blastx_job && self.blastx_job.queue) ||
-        (self.tblastn_job && self.tblastn_job.queue) || 
+        (self.tblastn_job && self.tblastn_job.queue) ||
         (self.blastp_job && self.blastp_job.queue)
         in_queue = true
       end
       unless in_queue
         errors.add(
-          :algorithm, 
+          :algorithm,
           " - Please select at least one algorithm to continue."
         )
       end
@@ -153,12 +153,12 @@ module Quorum
       if self.blastp_job && self.blastp_job.queue
         jobs << create_search_command("blastp")
       end
-     
+
       unless jobs.blank?
         jobs.each do |j|
           Workers::System.enqueue(
-            j, Quorum.blast_remote, 
-            Quorum.blast_ssh_host, Quorum.blast_ssh_user, 
+            j, Quorum.blast_remote,
+            Quorum.blast_ssh_host, Quorum.blast_ssh_user,
             Quorum.blast_ssh_options
           )
         end

data/app/models/quorum/tblastn_job.rb

@@ -4,7 +4,7 @@ module Quorum
     before_save :set_optional_params, :set_blast_dbs
 
     belongs_to :job
-    has_many :tblastn_job_reports, 
+    has_many :tblastn_job_reports,
       :dependent   => :destroy,
       :foreign_key => :tblastn_job_id,
       :primary_key => :job_id