quorum 0.4.0 → 0.5.0

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.4.0)
+    quorum (0.5.0)
       bio-blastxmlparser (~> 1.1.0)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -46,7 +46,7 @@ GEM
       nokogiri (>= 1.5.0)
     bio-logger (1.0.1)
       log4r (>= 1.1.9)
-    builder (3.0.0)
+    builder (3.0.3)
     capybara (1.1.2)
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
@@ -61,18 +61,18 @@ GEM
     erubis (2.7.0)
     ffi (1.1.5)
     hike (1.2.1)
-    i18n (0.6.0)
-    jasmine (1.2.0)
+    i18n (0.6.1)
+    jasmine (1.2.1)
       jasmine-core (>= 1.2.0)
       rack (~> 1.0)
       rspec (>= 1.3.1)
       selenium-webdriver (>= 0.1.3)
     jasmine-core (1.2.0)
     journey (1.0.4)
-    jquery-rails (2.0.2)
-      railties (>= 3.2.0, < 5.0)
+    jquery-rails (2.1.2)
+      railties (>= 3.1.0, < 5.0)
       thor (~> 0.14)
-    json (1.7.4)
+    json (1.7.5)
     libwebsocket (0.1.5)
       addressable
     log4r (1.1.10)
@@ -134,9 +134,9 @@ GEM
       rspec-expectations (~> 2.11.0)
       rspec-mocks (~> 2.11.0)
     rspec-core (2.11.1)
-    rspec-expectations (2.11.2)
+    rspec-expectations (2.11.3)
       diff-lcs (~> 1.1.3)
-    rspec-mocks (2.11.1)
+    rspec-mocks (2.11.2)
     rspec-rails (2.11.0)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
@@ -148,7 +148,7 @@ GEM
       libwebsocket (~> 0.1.3)
       multi_json (~> 1.0)
       rubyzip
-    sinatra (1.3.2)
+    sinatra (1.3.3)
       rack (~> 1.3, >= 1.3.6)
       rack-protection (~> 1.2)
       tilt (~> 1.3, >= 1.3.3)
@@ -156,7 +156,7 @@ GEM
       hike (~> 1.2)
       rack (~> 1.0)
       tilt (~> 1.1, != 1.3.0)
-    thor (0.15.4)
+    thor (0.16.0)
     tilt (1.3.3)
     treetop (1.4.10)
       polyglot

data/HISTORY.md

@@ -1,3 +1,11 @@
+## 0.5.0 (2012-09-14)
+
+* Fixed partial data load bug. https://github.com/ncgr/quorum/issues/2
+  Requires running quorum:install and quorum:views generators.
+  See the Upgrading? section in the README for more information.
+* Added better support for jQuery ajax errors in quorum.js.
+* Added better support for URLs in quorum.js.
+
 ## 0.4.0 (2012-08-10)
 
 * Added Hsp gaps to Blast Job Reports.

data/README.rdoc

@@ -399,7 +399,7 @@ https://github.com/ncgr/quorum/issues
 === Contributors
 
 * John Crow (https://github.com/crowja)
-* Andrew Farmer
+* Andrew Farmer (https://github.com/adf-ncgr)
 
 == License
 

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

@@ -13,13 +13,16 @@ QUORUM.algorithms = ["blastn", "blastx", "tblastn", "blastp"];
 // Poll search results asynchronously.
 //
 // Allow user to define callback / callback_obj. If callback is
-// undefined, render buildTemplate.
+// undefined, render default view.
 //
-QUORUM.pollResults = function(id, callback, callback_obj, interval, algos) {
+QUORUM.pollResults = function(callback, callback_obj, interval, algos) {
 
   var self = this,
-    interval = interval || 5000,
-    algos = algos || self.algorithms;
+      url = document.URL + '/get_quorum_search_results.json',
+      interval = interval || 5000,
+      algos = algos || self.algorithms,
+      error = false,
+      timeoutIds = {};
 
   // Render default view.
   function buildTemplate(data, a) {
@@ -33,24 +36,56 @@ QUORUM.pollResults = function(id, callback, callback_obj, interval, algos) {
     $('#' + 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 {
-            buildTemplate(data, a);
-          }
-        }
+  // Process returned data from ajax call. If data is present, render,
+  // otherwise call function via setTimeout().
+  function processData(data, a) {
+    if (data.length === 0) {
+      timeoutIds[a] = setTimeout(function() {
+        getData(a);
+      }, interval);
+    } else {
+      clearTimeout(timeoutIds[a]);
+      if (_.isFunction(callback)) {
+        callback.call(callback_obj, data, a);
+      } else {
+        buildTemplate(data, a);
       }
-    );
+    }
+  }
+
+  // Render jqXHR error message.
+  function renderError(jqXHR) {
+    var msg = "<div class='ui-state-error ui-corner-all' " +
+      "style='padding: 0 .7em;'><p class='text'>" +
+      "<span class='ui-icon ui-icon-alert' style='float: left; " +
+      "margin-right: .3em;';></span>Something went wrong. " +
+      "Error: " + jqXHR.status + " " + jqXHR.statusText + "</p></div>";
+    if (error === false) {
+      $('#show').append(msg);
+      error = true;
+    }
+  }
+
+  // Get Quorum results.
+  function getData(a) {
+    $.ajax({
+      url: url,
+      type: 'get',
+      dataType: 'json',
+      data: { 'algo': a },
+      cache: false,
+      timeout: 10000,
+      success: function(data) {
+        processData(data, a);
+      },
+      error: function(jqXHR) {
+        renderError(jqXHR);
+      }
+    });
+  }
+
+  _.each(algos, function(a) {
+    getData(a);
   });
 
 };
@@ -60,9 +95,10 @@ QUORUM.pollResults = function(id, callback, callback_obj, interval, algos) {
 // 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) {
+QUORUM.viewDetailedReport = function(focus_id, query, algo) {
 
-  var self = this;
+  var self = this,
+      url = document.URL + '/get_quorum_search_results.json';
 
   // Create the modal box.
   $('#detailed_report_dialog').html(
@@ -75,33 +111,50 @@ QUORUM.viewDetailedReport = function(id, focus_id, query, algo) {
     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 sequence data on mouse enter.
-      $('#detailed_report_dialog .sequence').mouseenter(function() {
-        $(this).find('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
-      });
-
-      // Highlight the selected id.
-      $('#' + focus_id).addClass("ui-state-highlight");
-
-      // Automatically scroll to the selected id.
-      self.autoScroll(focus_id, false);
+  function renderTemplate(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 sequence data on mouse enter.
+    $('#detailed_report_dialog .sequence').mouseenter(function() {
+      $(this).find('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
+    });
+    // Highlight the selected id.
+    $('#' + focus_id).addClass("ui-state-highlight");
+    // Automatically scroll to the selected id.
+    self.autoScroll(focus_id, false);
+  }
+
+  function renderError(jqXHR) {
+    $('#detailed_report_dialog').empty().html(
+      "<div class='ui-state-error ui-corner-all' " +
+      "style='padding: 0 .7em;'><p class='text'>" +
+      "<span class='ui-icon ui-icon-alert' style='float: left; " +
+      "margin-right: .3em;';></span>Something went wrong. " +
+      "Error: " + jqXHR.status + " " + jqXHR.statusText + "</p></div>"
+    );
+  }
+
+  $.ajax({
+    url: url,
+    type: 'get',
+    dataType: 'json',
+    data: { 'algo': algo, 'query': query },
+    timeout: 10000,
+    success: function(data) {
+      renderTemplate(data);
+    },
+    error: function(jqXHR) {
+      renderError(jqXHR);
     }
-  );
+  });
 
 };
 
@@ -273,51 +326,64 @@ QUORUM.displayHspLinks = function(focus, group, data) {
 //
 // Download Blast hit sequence.
 //
-QUORUM.downloadSequence = function(id, algo_id, algo, el) {
+QUORUM.downloadSequence = function(algo_id, algo, el) {
 
-  var self = this;
+  var self = this,
+      url = document.URL + '/get_quorum_blast_hit_sequence.json';
 
   $(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);
+  function renderError(jqXHR) {
+    $(el).addClass('ui-state-error').html(
+      "Error: " + jqXHR.status + " " + jqXHR.statusText
+    );
+  }
+
+  $.ajax({
+    url: url,
+    dataType: 'json',
+    data: { 'algo_id': algo_id, 'algo': algo },
+    timeout: 10000,
+    success: function(data) {
+      self.getSequenceFile(data[0].meta_id, el);
+    },
+    error: function(jqXHR) {
+      renderError(jqXHR);
     }
-  );
+  });
 
 };
 
 //
 // Poll application for Blast hit sequence.
 //
-QUORUM.getSequenceFile = function(id, meta_id, el) {
+QUORUM.getSequenceFile = function(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);
+      url = document.URL + '/send_quorum_blast_hit_sequence?meta_id=' + meta_id,
+      timeoutId = 0;
+
+  function downloadFile(data) {
+    if (data.length === 0) {
+      timeoutId = setTimeout(function() {
+        self.getSequenceFile(meta_id, el)
+      }, 2500);
+    } else {
+      clearTimeout(timeoutId);
+      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();
       }
     }
-  );
+  }
+
+  $.get(url, function(data) { downloadFile(data); });
 
 };
 

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

@@ -41,6 +41,6 @@
 <div id="quorum">
   <hr class="big" />
   <p>
-    Powered by <%= link_to "Quorum", "https://github.com/ncgr/quorum" %>
+    Powered by <%= link_to "Quorum v#{Quorum::VERSION}", "https://github.com/ncgr/quorum" %>
   </p>
 </div>

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

@@ -50,7 +50,7 @@
 <div id="quorum">
   <hr class="big" />
   <p>
-    Powered by <%= link_to "Quorum", "https://github.com/ncgr/quorum" %>
+    Powered by <%= link_to "Quorum v#{Quorum::VERSION}", "https://github.com/ncgr/quorum" %>
   </p>
 </div>
 
@@ -63,24 +63,22 @@
     //
     // Asynchronously poll Quorum for search results.
     //
-    //  QUORUM.pollResults(id, callback, callback_obj, interval)
-    //    id: Job.id
+    //  QUORUM.pollResults(callback, callback_obj, interval)
     //    callback: Define your own callback function to override the default.
     //      callback should expect the following params.
-    //        id: Job.id (Int),
     //        data: JSON data (JSON),
     //        algorithm: Supported algorithm (String).
     //    callback_obj: Callback object.
     //    interval: poll interval in milliseconds. 5000 default.
     //
     //  Example:
-    //    QUORUM.pollResults(<%= @jobs.id %>, MYAPP.myCoolCallback, MYAPP, 5000);
+    //    QUORUM.pollResults(MYAPP.myCoolCallback, MYAPP, 5000);
     //
     //  Example callback:
-    //    MYAPP.myCoolCallback = function(id, data, algo) {
+    //    MYAPP.myCoolCallback = function(data, algo) {
     //      // awesome logic
     //    };
     //
-    QUORUM.pollResults(<%= @jobs.id %>);
+    QUORUM.pollResults();
   });
 </script>

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

@@ -41,7 +41,7 @@
       </table>
       <p class="small">
         <a id="download_sequence_{{= id }}"
-          onclick="QUORUM.downloadSequence(<%= @jobs.id %>, {{= id }}, '{{= algo }}', this)">
+          onclick="QUORUM.downloadSequence({{= id }}, '{{= algo }}', this)">
           Download Sequence
         </a>
       </p>

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

@@ -52,7 +52,6 @@
           <td class="right">
             <a class="detailed_report"
               onclick="QUORUM.viewDetailedReport(
-                <%= @jobs.id %>,
                 {{= v.id }},
                 '{{= v.query }}',
                 '{{= algo }}')">

data/db/migrate/20120910175911_change_hsp_group_column_type.rb

@@ -0,0 +1,15 @@
+class ChangeHspGroupColumnType < ActiveRecord::Migration
+  def up
+    change_column :quorum_blastn_job_reports, :hsp_group, :text
+    change_column :quorum_blastx_job_reports, :hsp_group, :text
+    change_column :quorum_tblastn_job_reports, :hsp_group, :text
+    change_column :quorum_blastp_job_reports, :hsp_group, :text
+  end
+
+  def down
+    change_column :quorum_blastn_job_reports, :hsp_group, :string
+    change_column :quorum_blastx_job_reports, :hsp_group, :string
+    change_column :quorum_tblastn_job_reports, :hsp_group, :string
+    change_column :quorum_blastp_job_reports, :hsp_group, :string
+  end
+end

data/lib/generators/templates/blast.rb

@@ -437,8 +437,13 @@ module Quorum
         generate_blast_cmd
         @logger.log("NCBI Blast", @cmd)
         system(@cmd)
-        parse_and_save_results
-        add_hps_groups_to_reports
+
+        # Wrap these methods in a transaction to prevent premature return.
+        @job.method(@job_report_association).call.transaction do
+          parse_and_save_results
+          add_hps_groups_to_reports
+        end
+
         remove_tmp_files
       end
 

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.4.0"
+  VERSION = "0.5.0"
 end

data/spec/dummy/db/schema.rb

@@ -11,7 +11,7 @@
 #
 # It's strongly recommended to check this file into your version control system.
 
-ActiveRecord::Schema.define(:version => 20120807211452) do
+ActiveRecord::Schema.define(:version => 20120910180642) do
 
   create_table "quorum_blastn_job_reports", :force => true do |t|
     t.string   "query"
@@ -21,7 +21,7 @@ ActiveRecord::Schema.define(:version => 20120807211452) do
     t.string   "hit_accession"
     t.integer  "hit_len"
     t.integer  "hsp_num"
-    t.string   "hsp_group"
+    t.text     "hsp_group"
     t.integer  "bit_score"
     t.integer  "score"
     t.string   "evalue"
@@ -68,7 +68,7 @@ ActiveRecord::Schema.define(:version => 20120807211452) do
     t.string   "hit_accession"
     t.integer  "hit_len"
     t.integer  "hsp_num"
-    t.string   "hsp_group"
+    t.text     "hsp_group"
     t.integer  "bit_score"
     t.integer  "score"
     t.string   "evalue"
@@ -115,7 +115,7 @@ ActiveRecord::Schema.define(:version => 20120807211452) do
     t.string   "hit_accession"
     t.integer  "hit_len"
     t.integer  "hsp_num"
-    t.string   "hsp_group"
+    t.text     "hsp_group"
     t.integer  "bit_score"
     t.integer  "score"
     t.string   "evalue"
@@ -171,7 +171,7 @@ ActiveRecord::Schema.define(:version => 20120807211452) do
     t.string   "hit_accession"
     t.integer  "hit_len"
     t.integer  "hsp_num"
-    t.string   "hsp_group"
+    t.text     "hsp_group"
     t.integer  "bit_score"
     t.integer  "score"
     t.string   "evalue"

data/spec/dummy/quorum/lib/search_tools/blast.rb

@@ -437,8 +437,13 @@ module Quorum
         generate_blast_cmd
         @logger.log("NCBI Blast", @cmd)
         system(@cmd)
-        parse_and_save_results
-        add_hps_groups_to_reports
+
+        # Wrap these methods in a transaction to prevent premature return.
+        @job.method(@job_report_association).call.transaction do
+          parse_and_save_results
+          add_hps_groups_to_reports
+        end
+
         remove_tmp_files
       end
 

data/spec/javascripts/fixtures/quorum_tabs.html

@@ -1,15 +1,17 @@
-<div id="tabs">
-    <ul>
-        <li><a href="#tabs-1">Tab 1</a></li>
-        <li><a href="#tabs-2">Tab 2</a></li>
-        <li><a href="#tabs-3">Tab 3</a></li>
-    </ul>
-    <div id="tabs-1">Tab 1</div>
-    <div id="tabs-2">Tab 2</div>
-    <div id="tabs-3">Tab 3</div>
-</div>
+<div id="show">
+    <div id="tabs">
+        <ul>
+            <li><a href="#tabs-1">Tab 1</a></li>
+            <li><a href="#tabs-2">Tab 2</a></li>
+            <li><a href="#tabs-3">Tab 3</a></li>
+        </ul>
+        <div id="tabs-1">Tab 1</div>
+        <div id="tabs-2">Tab 2</div>
+        <div id="tabs-3">Tab 3</div>
+    </div>
 
-<div id="detailed_report_dialog" title="Quorum Report Details"></div>
-<script type="text/template" id="blast_template"></script>
-<script type="text/template" id="detailed_report_template"></script>
-<a id="download_sequence">Download Sequence</a>
+    <div id="detailed_report_dialog" title="Quorum Report Details"></div>
+    <script type="text/template" id="blast_template"></script>
+    <script type="text/template" id="detailed_report_template"></script>
+    <a id="download_sequence">Download Sequence</a>
+</div>

data/spec/javascripts/quorum_spec.js

@@ -23,21 +23,32 @@ describe("QUORUM", function() {
   // anonymous function buildTemplate().
   //
   it("fetches JSON and calls user defined callback function", function() {
-    spyOn($, 'getJSON');
+    loadFixtures('quorum_tabs.html');
+
+    spyOn($, 'ajax');
     spyOn(window, 'setTimeout');
-    var id = 1,
-        callback = jasmine.createSpy(),
-        data = 'foo';
+    var callback = jasmine.createSpy(),
+        data = 'foo',
+        error = {
+          status: 400,
+          statusText: 'bad news'
+        };
 
-    QUORUM.pollResults(id, callback, null, 5000, ['a']);
+    QUORUM.pollResults(callback, null, 5000, ['a']);
 
     // setTimeout()
-    $.getJSON.mostRecentCall.args[1]('');
+    $.ajax.mostRecentCall.args[0].success([]);
     expect(window.setTimeout).toHaveBeenCalled();
 
+    // Print jqXHR error message.
+    $.ajax.mostRecentCall.args[0].error(error);
+    expect($(".ui-state-error")).toHaveText(
+      'Something went wrong. Error: 400 bad news'
+    );
+
     // callback()
-    $.getJSON.mostRecentCall.args[1](data);
-    expect(callback).toHaveBeenCalledWith(id, data, 'a');
+    $.ajax.mostRecentCall.args[0].success(data);
+    expect(callback).toHaveBeenCalledWith(data, 'a');
   });
 
   //
@@ -48,20 +59,29 @@ describe("QUORUM", function() {
   it("renders modal box containing detailed report", function() {
     loadFixtures('quorum_tabs.html');
 
-    spyOn($, 'getJSON');
+    spyOn($, 'ajax');
     spyOn(QUORUM, 'autoScroll');
-    var id = 1,
-        focus_id = 1,
+    var focus_id = 1,
         query = 'foo',
         algo = 'a',
-        data = 'bar';
+        data = 'bar',
+        error = {
+          status: 500,
+          statusText: 'bad news'
+        };
 
-    QUORUM.viewDetailedReport(id, focus_id, query, algo);
+    QUORUM.viewDetailedReport(focus_id, query, algo);
 
     expect($("#detailed_report_dialog")).toBeVisible();
 
+    // Print jqXHR error message.
+    $.ajax.mostRecentCall.args[0].error(error);
+    expect($("#detailed_report_dialog")).toHaveText(
+      'Something went wrong. Error: 500 bad news'
+    );
+
     // Fetch JSON to build the template and scroll to focus_id.
-    $.getJSON.mostRecentCall.args[1](data);
+    $.ajax.mostRecentCall.args[0].success(data);
     expect(QUORUM.autoScroll).toHaveBeenCalledWith(focus_id, false);
 
     // Close the dialog box.
@@ -214,20 +234,27 @@ describe("QUORUM", function() {
   it("sends request to server to extract Blast hit sequence", function() {
     loadFixtures("quorum_tabs.html");
 
-    spyOn($, 'getJSON');
+    spyOn($, 'ajax');
     spyOn(QUORUM, 'getSequenceFile');
-    var id = 1,
-        algo_id = 1,
+    var algo_id = 1,
         algo = 'a',
         el = $("#download_sequence"),
-        data = [{meta_id:"foo"}];
+        data = [{meta_id:"foo"}],
+        error = {
+          status: 505,
+          statusText: 'wut?'
+        };
 
-    QUORUM.downloadSequence(id, algo_id, algo, el);
+    QUORUM.downloadSequence(algo_id, algo, el);
 
     expect(el.html()).toEqual('Fetching sequence...');
 
-    $.getJSON.mostRecentCall.args[1](data);
-    expect(QUORUM.getSequenceFile).toHaveBeenCalledWith(id, data[0].meta_id, el);
+    // Print jqXHR error message.
+    $.ajax.mostRecentCall.args[0].error(error);
+    expect(el).toHaveText("Error: 505 wut?");
+
+    $.ajax.mostRecentCall.args[0].success(data);
+    expect(QUORUM.getSequenceFile).toHaveBeenCalledWith(data[0].meta_id, el);
   });
 
   //
@@ -241,19 +268,18 @@ describe("QUORUM", function() {
 
     spyOn($, 'get');
     spyOn(window, 'setTimeout');
-    var id = 1,
-        meta_id = 'foo',
+    var meta_id = 'foo',
         el = $("#download_sequence"),
         data = 'bar',
         error = 'error';
 
-    QUORUM.getSequenceFile(id, meta_id, el);
+    QUORUM.getSequenceFile(meta_id, el);
 
     // setTimeout()
-    $.get.mostRecentCall.args[1]('');
+    $.get.mostRecentCall.args[1]([]);
     expect(window.setTimeout).toHaveBeenCalled();
 
-    // Print error message
+    // Print error message.
     $.get.mostRecentCall.args[1](error);
     expect(el.html()).toEqual(error);
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.5.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-10 00:00:00.000000000 Z
+date: 2012-09-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -280,6 +280,7 @@ files:
 - db/migrate/20111031204941_create_tblastn_job_reports.rb
 - db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb
 - db/migrate/20120807202555_add_gaps_to_blast_reports.rb
+- db/migrate/20120910175911_change_hsp_group_column_type.rb
 - lib/generators/quorum/images_generator.rb
 - lib/generators/quorum/install_generator.rb
 - lib/generators/quorum/styles_generator.rb
@@ -426,7 +427,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3860118891920834630
+      hash: -220393998352510462
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -435,7 +436,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3860118891920834630
+      hash: -220393998352510462
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24