quorum 0.2.1 → 0.3.0

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.2.0)
+    quorum (0.3.0)
       bio-blastxmlparser (~> 1.0.1)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -12,31 +12,31 @@ PATH
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (3.2.0)
-      actionpack (= 3.2.0)
+    actionmailer (3.2.1)
+      actionpack (= 3.2.1)
       mail (~> 2.4.0)
-    actionpack (3.2.0)
-      activemodel (= 3.2.0)
-      activesupport (= 3.2.0)
+    actionpack (3.2.1)
+      activemodel (= 3.2.1)
+      activesupport (= 3.2.1)
       builder (~> 3.0.0)
       erubis (~> 2.7.0)
-      journey (~> 1.0.0)
+      journey (~> 1.0.1)
       rack (~> 1.4.0)
       rack-cache (~> 1.1)
       rack-test (~> 0.6.1)
       sprockets (~> 2.1.2)
-    activemodel (3.2.0)
-      activesupport (= 3.2.0)
+    activemodel (3.2.1)
+      activesupport (= 3.2.1)
       builder (~> 3.0.0)
-    activerecord (3.2.0)
-      activemodel (= 3.2.0)
-      activesupport (= 3.2.0)
+    activerecord (3.2.1)
+      activemodel (= 3.2.1)
+      activesupport (= 3.2.1)
       arel (~> 3.0.0)
       tzinfo (~> 0.3.29)
-    activeresource (3.2.0)
-      activemodel (= 3.2.0)
-      activesupport (= 3.2.0)
-    activesupport (3.2.0)
+    activeresource (3.2.1)
+      activemodel (= 3.2.1)
+      activesupport (= 3.2.1)
+    activesupport (3.2.1)
       i18n (~> 0.6)
       multi_json (~> 1.0)
     arel (3.0.0)
@@ -66,7 +66,13 @@ GEM
     ffi (1.0.11)
     hike (1.2.1)
     i18n (0.6.0)
-    journey (1.0.0)
+    jasmine (1.1.2)
+      jasmine-core (>= 1.1.0)
+      rack (>= 1.1)
+      rspec (>= 1.3.1)
+      selenium-webdriver (>= 0.1.3)
+    jasmine-core (1.1.0)
+    journey (1.0.1)
     jquery-rails (2.0.0)
       railties (>= 3.2.0.beta, < 5.0)
       thor (~> 0.14)
@@ -91,17 +97,17 @@ GEM
       rack
     rack-test (0.6.1)
       rack (>= 1.0)
-    rails (3.2.0)
-      actionmailer (= 3.2.0)
-      actionpack (= 3.2.0)
-      activerecord (= 3.2.0)
-      activeresource (= 3.2.0)
-      activesupport (= 3.2.0)
+    rails (3.2.1)
+      actionmailer (= 3.2.1)
+      actionpack (= 3.2.1)
+      activerecord (= 3.2.1)
+      activeresource (= 3.2.1)
+      activesupport (= 3.2.1)
       bundler (~> 1.0)
-      railties (= 3.2.0)
-    railties (3.2.0)
-      actionpack (= 3.2.0)
-      activesupport (= 3.2.0)
+      railties (= 3.2.1)
+    railties (3.2.1)
+      actionpack (= 3.2.1)
+      activesupport (= 3.2.1)
       rack-ssl (~> 1.3.2)
       rake (>= 0.8.7)
       rdoc (~> 3.4)
@@ -139,7 +145,7 @@ GEM
       railties (>= 3.0)
       rspec (~> 2.8.0)
     rubyzip (0.9.5)
-    selenium-webdriver (2.17.0)
+    selenium-webdriver (2.18.0)
       childprocess (>= 0.2.5)
       ffi (~> 1.0.9)
       multi_json (~> 1.0.4)
@@ -170,6 +176,7 @@ DEPENDENCIES
   capybara (~> 1.1)
   database_cleaner (~> 0.6)
   factory_girl_rails (~> 1.2)
+  jasmine (~> 1.1)
   mysql2 (~> 0.3.11)
   quorum!
   resque_spec (~> 0.8)

data/HISTORY.md

@@ -1,3 +1,7 @@
+## 0.3.0 (2012-01-31)
+
+* Created QUORUM JS object and added properties.
+
 ## 0.2.1 (2012-01-24)
 
 * Rails 3.2 compatible.

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

@@ -9,5 +9,6 @@
 //= require jquery-ui
 //= require underscore-min
 //= require jquery.tipsy
+//= require jquery.autohint
 //= require_tree .
 

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

@@ -1,72 +1,9 @@
-//
-// Mustache style Underscore.js templating.
-//
-_.templateSettings = {
-  evaluate: /\{\{(.+?)\}\}/g,
-  interpolate: /\{\{\=(.+?)\}\}/g
-};
-
 //
 // jQuery
 //---------------------------------------------------------------------------//
 
 $(function() {
 
-  // jQuery Functions //
-
-  $.fn.extend({
-    // Add hints to the form elements.
-    addHints: function() {
-      $(this).each(function() {
-        if ($(this).attr('title') === '') { 
-          return; 
-        }
-
-        if ($(this).val() === '') { 
-          $(this).val($(this).attr('title')); 
-
-          if (!$(this).hasClass('auto-hint')) {
-            $(this).addClass('auto-hint');
-          }
-        } else { 
-          $(this).removeClass('auto-hint'); 
-        }
-      });          
-    },
-
-    // Remove hints on submit.
-    removeHintsOnSubmit: function() {
-      $(this).each(function() {
-        if ($(this).val() === $(this).attr('title')) { 
-          $(this).val(''); 
-        }     
-      });                      
-    },
-
-    // Remove hint and class on focus.
-    focusHint: function() {
-      $(this).focus(function() {
-        if ($(this).val() === $(this).attr('title')) {
-          $(this).val('');
-          $(this).removeClass('auto-hint');
-        }
-      });               
-    },
-
-    // Retain value or add hint.
-    blurHint: function() {
-      $(this).blur(function() {
-        if ($(this).val() === '' && $(this).attr('title') !== '') {
-          $(this).val($(this).attr('title'));
-          $(this).addClass('auto-hint');
-        }
-      });     
-    }
-  });
-
-  // End jQuery Functions //
-
-
   // Hide Elements //
 
   if (!$('#job_blastn_job_attributes_queue').is(':checked')) {
@@ -91,9 +28,7 @@ $(function() {
   // Form //
 
   var form = $('form :input.auto-hint');
-  form.focusHint();
-  form.blurHint();
-  form.addHints();
+  form.autoHint();
 
   // Toggle Algorithms //
 
@@ -121,21 +56,22 @@ $(function() {
       'disabled', 'disabled'
     );
 
-    form.removeHintsOnSubmit();
+    form.autoHint('removeHints');
   });
 
   // Reset form.
   $('#quorum_job_reset').click(function() {
+    $('textarea').val('');
     $('input:text').val('');
     $('input:file').val('');
-    $('input:checkbox').attr('checked', false);
+    $('input:checkbox').prop('checked', false);
     $('select').val('');
 
     $('.toggle').each(function() {
       $(this).hide();
     });
 
-    form.addHints();
+    form.autoHint('addHints');
   });
 
   // End Form //
@@ -150,279 +86,3 @@ $(function() {
 
 });
 
-
-//
-// JavaScript Functions
-//---------------------------------------------------------------------------// 
-
-// 
-// Poll quorum search results asynchronously and insert them into
-// the DOM via #blast_template.
-//
-var pollResults = function(id, interval, algos) {
-
-  // Set the default poll interval to 5 seconds.
-  interval = interval || 5000;
-
-  // Algorithms
-  algos = algos || ["blastn", "blastx", "tblastn", "blastp"];
-
-  _.each(algos, function(a) {
-    $.getJSON(
-      '/quorum/jobs/' + id + '/get_quorum_search_results.json?algo=' + a,
-      function(data) {
-        if (data.length === 0) {
-          setTimeout(function() { 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.
-//
-var 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.
-      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.
-//
-var 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.
-//
-var 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 " + addBaseTitleIndex(qseq.slice(s, e), q_from, q_to, algo, 'query') + "\n";
-    seq += "     " + midline.slice(s, e) + "\n";
-    seq += "hseq " + 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.
-//
-var 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.
-//
-var displayHspLinks = function(focus, group, data) {
-  if (group !== null) {
-    var str = "Related <a onclick=\"(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); });
-  
-    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='(autoScroll(" + e.id + ", true))'>" + e.hsp_num + "</a> ";
-      } else {
-        str += e.hsp_num + " ";
-      }
-    });
-    return str;
-  }
-}
-
-//
-// Download Blast hit sequence.
-//
-var 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) {
-      getSequenceFile(id, data[0].meta_id, el);
-    }
-  );
-}
-
-//
-// Poll application for Blast hit sequence.
-//
-var 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() { 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.
-//
-var autoScroll = function(id, highlight) {
-  $('html, body').animate({
-    scrollTop: $('#' + id).offset().top
-  }, 1000);
-
-  if (highlight) {
-    $('#' + id).effect("highlight", {}, 4000);
-  }
-}
-
-//
-// Truncate string to length n using word boundary.
-//
-String.prototype.trunc = function(n) {
-  var longStr = this.length > n;
-  var str     = longStr ? this.substr(0, n-1) : this;
-
-  longStr ? str.substr(0, str.lastIndexOf(' ')) : str;
-  return longStr ? str + '...' : str;
-}
-
-//
-// Open URL in new window.
-//
-var openWindow = function(url, name, width, height) {
-
-  var windowSize = "width=" + width + ",height=" + height + ",scrollbars=yes";
-
-  window.open(url, name, windowSize);
-}
-