quorum 0.2.1 → 0.3.0

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

@@ -0,0 +1,275 @@
+//
+// QUORUM
+//---------------------------------------------------------------------------// 
+
+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]); 
+            }, interval);
+          } else {
+            $('#' + a + '-results').empty();
+            var temp = _.template(
+              $('#blast_template').html(), { 
+                data: data,
+                algo: a
+              }
+            );
+            $('#' + a + '-results').html(temp);
+            return;
+          }
+        } 
+      );
+    });
+  },
+  
+  //
+  // 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'>" + 
+      "Loading... <img src='/assets/quorum/loading.gif' alt='Loading'>" +
+      "</p>"
+    ).dialog({
+      modal:    true,
+      width:    850,
+      position: 'top'
+    });
+  
+    $.getJSON(
+      '/quorum/jobs/' + id + '/get_quorum_search_results.json?algo=' + algo + 
+      '&query=' + query,
+      function(data) {
+        var temp = _.template(
+          $('#detailed_report_template').html(), {
+            data:  data,
+            query: query,
+            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, 
+  // 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(''); 
+  },
+  
+  //
+  // Format sequence data for detailed report. 
+  //
+  // If q_from > q_to or h_from > h_to, subtract by increment; otherwise add
+  // by increment.
+  //
+  // If algo is tblastn or blastx, multiple increment by 3.
+  //
+  formatSequenceReport: function(qseq, midline, hseq, q_from, q_to, h_from, h_to, algo) {
+    var max       = qseq.length; // max length
+    var increment = 60;          // increment value
+    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);
+      } else {
+        h_from < h_to ? h_from += increment : h_from -= increment;
+      }
+    }
+    return "<p class='small'>Alignment (Mouse over for positions):</p>" + 
+      "<span class='small'><pre>" + seq + "</pre></span>";
+  },
+  
+  //
+  // Format Query and Hit Strand.
+  //
+  // If query_frame or hit_frame < 0, print 'reverse'; print 'forward' otherwise.
+  //
+  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'," + 
+        "'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> ";
+        } else {
+          str += e.hsp_num + " ";
+        }
+      });
+      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,
+      function(data) {
+        QUORUM.getSequenceFile(id, data[0].meta_id, el);
+      }
+    );
+  },
+  
+  //
+  // Poll application for Blast hit sequence.
+  //
+  getSequenceFile: function(id, meta_id, el) {
+    var url = "/quorum/jobs/" + id + 
+      "/send_quorum_blast_hit_sequence?meta_id=" + meta_id;
+    $.get(
+      url,
+      function(data) {
+        if (data.length === 0) {
+          setTimeout(function() { QUORUM.getSequenceFile(id, meta_id, el) }, 2500);
+        } else {
+          if (data.indexOf("error") !== -1) {
+            // Print error message.
+            $(el).addClass('ui-state-error').html(data);  
+          } else {
+            // Force browser to download file via iframe.
+            $(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.
+  //
+  autoScroll: function(id, highlight) {
+    $('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/javascripts/quorum/template_settings.js

@@ -0,0 +1,8 @@
+//
+// Mustache style Underscore.js templating.
+//---------------------------------------------------------------------------//
+_.templateSettings = {
+  evaluate: /\{\{(.+?)\}\}/g,
+  interpolate: /\{\{\=(.+?)\}\}/g
+};
+

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

@@ -0,0 +1,12 @@
+//
+// Truncate string to length n using word boundary.
+//
+String.prototype.trunc = function(n) {
+  var longStr = this.length > n;
+  var str     = longStr ? this.slice(0, n) : this;
+
+  longStr ? str = str.slice(0, str.lastIndexOf(' ')) : str;
+
+  return longStr ? str + '...' : str;
+}
+

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

@@ -194,10 +194,6 @@ form label {
 	font-size: 12px;
 }
 
-.auto-hint {
-    color: #aaa;
-}
-
 #loading {
     padding: 5px;
 }

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

@@ -0,0 +1,4 @@
+.auto-hint {
+    color: #aaa;
+}
+

data/app/controllers/quorum/jobs_controller.rb

@@ -61,13 +61,13 @@ module Quorum
         queued = "#{params[:algo]}_job".to_sym
         report = "#{params[:algo]}_job_reports".to_sym
 
-	      begin
-	        job = Job.find(params[:id])
-	      rescue ActiveRecord::RecordNotFound => e
-	        json = empty
-	      else
-	        if job.method(queued).call.present?
-	          if job.method(report).call.present?
+        begin
+          job = Job.find(params[:id])
+        rescue ActiveRecord::RecordNotFound => e
+          json = empty
+        else
+          if job.method(queued).call.present?
+            if job.method(report).call.present?
               if params[:query]
                 json = job.method(report).call.by_query(params[:query]).default_order
               else
@@ -76,8 +76,8 @@ module Quorum
             else
               json = []
             end
-	        end
-	      end
+          end
+        end
       end
 
       respond_with json

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

@@ -4,68 +4,68 @@
     <%= n.check_box :queue %>
   </p>
   <div id="blastn" class="toggle">
-	  <table class="options">
-	    <tr>
-	      <td>
-	        <label>Database(s)</label>
-	      </td>
-	      <td>
+    <table class="options">
+      <tr>
+        <td>
+          <label>Database(s)</label>
+        </td>
+        <td>
           <%= n.select :blast_dbs, @blast_dbs[:blastn], {}, { :multiple => true } %> 
-	      </td>
-	      <td>
-	        <%= n.label :filter, "DUST" %>
-	      </td>
-	      <td>
-	        <%= n.check_box :filter %>
-	      </td>
-	    </tr>
-	    <tr>
-	      <td>
-	        <%= n.label :expectation %>
-	      </td>
-	      <td>
-	        <%= 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", 
-	          :class => "auto-hint" %>
-	      </td>
-	    </tr>
-	    <tr>
-	      <td>
-	        <%= n.label :max_score %>
-	      </td>
-	      <td>
-	        <%= n.text_field :max_score, :size => 15, :title => "25", 
-	          :class => "auto-hint" %>
-	      </td>
-	      <td>
-	        <%= n.label :gapped_alignments %>
-	      </td>
-	      <td>
-	        <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
-	      </td>
-	    </tr>
-	    <tr>
-	      <td>
-	        <%= n.label :gap_opening_extension %>
-	      </td>
-	      <td>
-	        <%= 
-	          n.select :gap_opening_extension, 
-	            options_for_select(
-	              @job.blastn_job.gap_opening_extension_values,
-	              @job.blastn_job.gap_opening_extension
-	            )
-	        %>
-	      </td>
-	      <td></td>
-	      <td></td>
-	    </tr>
-	  </table>
+        </td>
+        <td>
+          <%= n.label :filter, "DUST" %>
+        </td>
+        <td>
+          <%= n.check_box :filter %>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <%= n.label :expectation %>
+        </td>
+        <td>
+          <%= 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", 
+            :class => "auto-hint" %>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <%= n.label :max_score %>
+        </td>
+        <td>
+          <%= n.text_field :max_score, :size => 15, :title => "25", 
+            :class => "auto-hint" %>
+        </td>
+        <td>
+          <%= n.label :gapped_alignments %>
+        </td>
+        <td>
+          <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <%= n.label :gap_opening_extension %>
+        </td>
+        <td>
+          <%= 
+            n.select :gap_opening_extension, 
+              options_for_select(
+                @job.blastn_job.gap_opening_extension_values,
+                @job.blastn_job.gap_opening_extension
+              )
+          %>
+        </td>
+        <td></td>
+        <td></td>
+      </tr>
+    </table>
   </div>
 <% end %>

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

@@ -4,68 +4,68 @@
     <%= n.check_box :queue %>
   </p>
   <div id="blastp" class="toggle">
-	  <table class="options">
-	    <tr>
-	      <td>
-	        <label>Database(s)</label>
-	      </td>
-	      <td>
+    <table class="options">
+      <tr>
+        <td>
+          <label>Database(s)</label>
+        </td>
+        <td>
           <%= n.select :blast_dbs, @blast_dbs[:blastp], {}, { :multiple => true } %> 
-	      </td>
-	      <td>
-	        <%= n.label :filter, "SEG" %>
-	      </td>
-	      <td>
-	        <%= n.check_box :filter %>
-	      </td>
-	    </tr>
-	    <tr>
-	      <td>
-	        <%= n.label :expectation %>
-	      </td>
-	      <td>
-	        <%= 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", 
-	          :class => "auto-hint" %>
-	      </td>
-	    </tr>
-	    <tr>
-	      <td>
-	        <%= n.label :max_score %>
-	      </td>
-	      <td>
-	        <%= n.text_field :max_score, :size => 15, :title => "25", 
-	          :class => "auto-hint" %>
-	      </td>
-	      <td>
-	        <%= n.label :gapped_alignments %>
-	      </td>
-	      <td>
-	        <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
-	      </td>
-	    </tr>
-	    <tr>
-	      <td>
-	        <%= n.label :gap_opening_extension %>
-	      </td>
-	      <td>
-	        <%= 
-	          n.select :gap_opening_extension, 
-	            options_for_select(
-	              @job.blastn_job.gap_opening_extension_values,
-	              @job.blastn_job.gap_opening_extension
-	            )
-	        %>
-	      </td>
-	      <td></td>
-	      <td></td>
-	    </tr>
-	  </table>
+        </td>
+        <td>
+          <%= n.label :filter, "SEG" %>
+        </td>
+        <td>
+          <%= n.check_box :filter %>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <%= n.label :expectation %>
+        </td>
+        <td>
+          <%= 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", 
+            :class => "auto-hint" %>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <%= n.label :max_score %>
+        </td>
+        <td>
+          <%= n.text_field :max_score, :size => 15, :title => "25", 
+            :class => "auto-hint" %>
+        </td>
+        <td>
+          <%= n.label :gapped_alignments %>
+        </td>
+        <td>
+          <%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
+        </td>
+      </tr>
+      <tr>
+        <td>
+          <%= n.label :gap_opening_extension %>
+        </td>
+        <td>
+          <%= 
+            n.select :gap_opening_extension, 
+              options_for_select(
+                @job.blastn_job.gap_opening_extension_values,
+                @job.blastn_job.gap_opening_extension
+            )
+          %>
+        </td>
+        <td></td>
+        <td></td>
+      </tr>
+    </table>
   </div>
 <% end %>