quorum 0.3.1 → 0.3.2

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

@@ -2,274 +2,350 @@
 // 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);
+var QUORUM = QUORUM || {};
+
+//
+// Supported algorithms.
+//
+QUORUM.algorithms = ["blastn", "blastx", "tblastn", "blastp"];
+
+//
+// Poll search results asynchronously.
+//
+// Allow user to define callback / callback_obj. If callback is
+// undefined, render buildTemplate.
+//
+QUORUM.pollResults = function(id, callback, callback_obj, interval, algos) {
+
+  var self = this,
+    interval = interval || 5000,
+    algos = algos || self.algorithms;
+
+  // Render default view.
+  function buildTemplate(data, a) {
+    $('#' + a + '-results').empty();
+    var temp = _.template(
+      $('#blast_template').html(), {
+        data: data,
+        algo: a
+      }
+    );
+    $('#' + a + '-results').html(temp);
+  }
+
+  _.each(algos, function(a) {
+    $.getJSON(
+      '/quorum/jobs/' + id + '/get_quorum_search_results.json?algo=' + a,
+      function(data) {
+        if (data.length === 0) {
+          // Continue to check until results are returned.
+          setTimeout(function() {
+            self.pollResults(id, callback, callback_obj, interval, [a]);
+          }, interval);
+        } else {
+          if (typeof callback === "function") {
+            callback.call(callback_obj, id, data, a);
           } else {
-            $('#' + a + '-results').empty();
-            var temp = _.template(
-              $('#blast_template').html(), {
-                data: data,
-                algo: a
-              }
-            );
-            $('#' + a + '-results').html(temp);
-            return;
+            buildTemplate(data, a);
           }
         }
+      }
+    );
+  });
+
+};
+
+//
+// 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.
+//
+QUORUM.viewDetailedReport = function(id, focus_id, query, algo) {
+
+  var self = this;
+
+  // 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
+        }
       );
-    });
-  },
-
-  //
-  // 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);
 
-        // Insert the detailed report data.
-        $('#detailed_report_dialog').empty().html(temp);
+      // Add tipsy to the sequence data.
+      $('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
 
-        // Add tipsy to the sequence data.
-        $('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
+      // Highlight the selected id.
+      $('#' + focus_id).addClass("ui-state-highlight");
 
-        // Highlight the selected id.
-        $('#' + focus_id).addClass("ui-state-highlight");
+      // Automatically scroll to the selected id.
+      self.autoScroll(focus_id, false);
+    }
+  );
 
-        // 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;
+};
+
+//
+// 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.
+//
+QUORUM.addBaseTitleIndex = function(bases, from, to, algo, type) {
+
+  var self = this,
+      forward = true,
+      value = 1,
+      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.
+//
+QUORUM.formatSequenceReport = function(qseq, midline, hseq, q_from, q_to, h_from, h_to, algo) {
+
+  var self = this,
+      max = qseq.length, // max length
+      increment = 60,    // increment value
+      s = 0,             // start position
+      e = increment,     // end position
+      seq = "\n";        // seq string to return
+
+  while(true) {
+    seq += "qseq " + self.addBaseTitleIndex(qseq.slice(s, e), q_from, q_to, algo, 'query') + "\n";
+    seq += "     " + midline.slice(s, e) + "\n";
+    seq += "hseq " + self.addBaseTitleIndex(hseq.slice(s, e), h_from, h_to, algo, 'hit') + "\n\n";
+
+    if (e >= max) {
+      break;
     }
 
-    // Set value to 3 for the below.
-    if ((type === "hit" && algo === "tblastn") ||
-        (type === "query" && algo === "blastx")) {
-      value = 3;
+    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;
     }
 
-    // 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;
-      }
+    // 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>";
 
-      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;
-      }
+//
+// Format Query and Hit Strand.
+//
+// If query_frame or hit_frame < 0, print 'reverse'; print 'forward' otherwise.
+//
+QUORUM.formatStrand = function(qstrand, hstrand) {
+
+  var self = this,
+      q = "",
+      h = "";
+
+  qstrand < 0 ? q = "reverse" : q = "forward";
+  hstrand < 0 ? h = "reverse" : h = "forward";
+
+  return q + " / " + h;
 
-      // 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);
+};
+
+//
+// Format Blast E-value.
+//
+QUORUM.formatEvalue = function(evalue) {
+
+  var self = this,
+      index,
+      f,
+      e,
+      formatted;
+
+  if (_.isUndefined(evalue) || _.isNull(evalue) || evalue === "") {
+    return "";
+  }
+
+  index = evalue.indexOf('e');
+
+  if (index > -1) {
+    f = parseFloat(evalue.slice(0, index)).toPrecision(2);
+    e = evalue.slice(index).replace('e', '');
+
+    formatted = f + " x 10<sup>" + e + "</sup>";
+  } else {
+    formatted = parseFloat(evalue).toPrecision(2);
+  }
+
+  return formatted;
+
+};
+
+//
+// Display links to Hsps in the same group.
+//
+QUORUM.displayHspLinks = function(focus, group, data) {
+
+  var self = this,
+      str = "",
+      ids,
+      selected;
+
+  if (!_.isNull(group)) {
+    str = "Related <a onclick=\"(QUORUM.openWindow(" +
+      "'http://www.ncbi.nlm.nih.gov/books/NBK62051/def-item/blast_glossary.HSP'," +
+      "'HSP', 800, 300))\">HSPs</a>: ";
+
+    ids = _.map(group.split(","), function(i) { return parseInt(i, 10); });
+
+    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 {
-        h_from < h_to ? h_from += increment : h_from -= increment;
+        str += e.hsp_num + " ";
       }
+    });
+  }
+
+  return str;
+
+};
+
+//
+// Download Blast hit sequence.
+//
+QUORUM.downloadSequence = function(id, algo_id, algo, el) {
+
+  var self = this;
+
+  $(el).html('Fetching sequence...');
+
+  $.getJSON(
+    "/quorum/jobs/" + id + "/get_quorum_blast_hit_sequence.json?algo_id=" +
+    algo_id + "&algo=" + algo,
+    function(data) {
+      self.getSequenceFile(id, data[0].meta_id, el);
     }
-    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);
+//
+// Poll application for Blast hit sequence.
+//
+QUORUM.getSequenceFile = function(id, meta_id, el) {
+
+  var self = this,
+      url;
+
+  url = "/quorum/jobs/" + id +
+    "/send_quorum_blast_hit_sequence?meta_id=" + meta_id;
+  $.get(
+    url,
+    function(data) {
+      if (data.length === 0) {
+        setTimeout(function() { self.getSequenceFile(id, meta_id, el) }, 2500);
+      } else {
+        if (data.indexOf("error") !== -1) {
+          // Print error message.
+          $(el).addClass('ui-state-error').html(data);
         } 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();
-          }
+          // 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) {
+//
+// Autoscroll to given div id.
+//
+QUORUM.autoScroll = function(id, highlight) {
 
-    var windowSize = "width=" + width + ",height=" + height + ",scrollbars=yes";
+  var self = this;
 
-    window.open(url, name, windowSize);
+  $('html, body').animate({
+    scrollTop: $('#' + id).offset().top
+  }, 1000);
+
+  if (highlight) {
+    $('#' + id).effect("highlight", {}, 4000);
   }
 
 };
 
+//
+// Open URL in new window.
+//
+QUORUM.openWindow = function(url, name, width, height) {
+
+  var self = this,
+      windowSize;
+
+  windowSize = "width=" + width + ",height=" + height + ",scrollbars=yes";
+
+  window.open(url, name, windowSize);
+
+};
+

data/app/controllers/quorum/jobs_controller.rb

@@ -115,15 +115,15 @@ module Quorum
     def send_quorum_blast_hit_sequence
       data = Workers::System.get_meta(params[:meta_id])
       if data.succeeded?
-        unless data.result.downcase.include?("error")
+        if data.result.downcase.include?("error")
+          render :text => data.result
+          return
+        else
           send_data data.result,
             :filename    => "#{params[:meta_id]}.fa",
             :type        => "text/plain",
             :disposition => "attachment"
           return
-        else
-          render :text => data.result
-          return
         end
       end
       render :text => ""

data/app/models/quorum/job.rb

@@ -200,7 +200,7 @@ module Quorum
         "-a #{ActiveRecord::Base.configurations[::Rails.env.to_s]['adapter']} " <<
         "-k #{ActiveRecord::Base.configurations[::Rails.env.to_s]['host']} " <<
         "-u #{ActiveRecord::Base.configurations[::Rails.env.to_s]['username']} " <<
-        "-p #{ActiveRecord::Base.configurations[::Rails.env.to_s]['password']} "
+        "-p '#{ActiveRecord::Base.configurations[::Rails.env.to_s]['password']}' "
     end
 
   end

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

@@ -11,26 +11,26 @@
     <div>
       <%= f.file_field :sequence_file %>
     </div>
-    <!-- Search Algorithms -->
-    <!-- Comment out an algorithm below to remove it from the form. -->
+    <%# Search Algorithms %>
+    <%# Comment out an algorithm below to remove it from the form. %>
 
-    <!-- blastn -->
+    <%# blastn %>
     <%= render :partial => "quorum/jobs/form/blastn_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
-    <!-- blastx -->
+    <%# blastx %>
     <%= render :partial => "quorum/jobs/form/blastx_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
-    <!-- tblastn -->
+    <%# tblastn %>
     <%= render :partial => "quorum/jobs/form/tblastn_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
-    <!-- blastp -->
+    <%# blastp %>
     <%= render :partial => "quorum/jobs/form/blastp_form", :locals => {
       :f => f, :blast_dbs => @blast_dbs } %>
 
-    <!-- End Search Algorithms -->
+    <%# End Search Algorithms %>
     <div>
       <%= f.submit "Submit" %>&nbsp;&nbsp;
       <%= submit_tag "Reset", :name => "reset",