sequenceserver 1.0.0.pre.2 → 1.0.0.pre.3

data/public/js/sequenceserver.js

@@ -1,59 +1,83 @@
-//helpers methods to disable, enable, and uncheck radio buttons and checkboxes
-(function( $ ){
-    //disable an element
-    $.fn.disable = function() {
+/**
+ * Load necessary polyfills.
+ */
+$.webshims.polyfill('forms');
+
+
+/**
+ * Simple, small jQuery extensions for convenience.
+ */
+(function ($) {
+    /**
+     * Disable an element.
+     *
+     * Sets `disabled` property to `true` and adds `disabled` class.
+     */
+    $.fn.disable = function () {
         return this.prop('disabled', true).addClass('disabled');
     };
-})( jQuery );
 
-(function( $ ){
-    //enable an element
-    $.fn.enable = function() {
+    /**
+     * Enable an element.
+     *
+     * Sets `disabled` property to `false` and removes `disabled` class
+     * if present.
+     */
+    $.fn.enable = function () {
         return this.prop('disabled', false).removeClass('disabled');
     };
-})( jQuery );
 
-(function( $ ){
-    //uncheck an element
-    $.fn.uncheck = function() {
+    /**
+     * Check an element.
+     *
+     * Sets `checked` property to `true`.
+     */
+    $.fn.check = function () {
+        return this.prop('checked', true);
+    };
+
+    /**
+     * Un-check an element.
+     *
+     * Sets `checked` property to `false`.
+     */
+    $.fn.uncheck = function () {
         return this.prop('checked', false);
     };
-})( jQuery );
 
-(function( $ ){
-    //check an element
-    $.fn.check = function() {
-        return this.prop('checked', true);
+
+    /**
+     * Initialise Bootstrap tooltip on an element with presets. Takes title.
+     */
+    $.fn._tooltip = $.fn.tooltip;
+    $.fn.tooltip  = function (options) {
+        this
+        ._tooltip('destroy')
+        ._tooltip($.extend({
+            container: 'body',
+            placement: 'left'
+        }, options));
     };
-})( jQuery );
 
-/**
- * Wiggle an element.
- *
- * Used for wiggling BLAST button.
- */
-(function ($) {
-    $.fn.wiggle = function() {
+
+    /**
+     * Wiggle an element.
+     *
+     * Used for wiggling BLAST button.
+     */
+    $.fn.wiggle = function () {
         this.finish().effect("bounce", {
             direction: 'left',
             distance: 24,
             times: 4,
         }, 250);
     };
-}(jQuery));
 
-(function( $ ){
-    //(pre-)check the only active database checkbox
-    $.onedb = function(selector) {
-        active_dbs = $(".databases input[type=checkbox]").not(":disabled")
-        if (active_dbs.length == 1){
-            active_dbs.check()
-        }
-        return active_dbs;
-    };
-})( jQuery );
 
-(function ($) {
+    /**
+     * Check's every 100 ms if an element's value has changed. Triggers
+     * `change` event on the element if it has.
+     */
     $.fn.poll = function () {
         var that = this;
         var val  = null;
@@ -109,6 +133,17 @@ if (!SS) {
       }).join('');
     };
 
+    /**
+     * Pre-check the only active database checkbox.
+     */
+    SS.onedb = function () {
+        var database_checkboxes = $(".databases input:checkbox");
+        if (database_checkboxes.length === 1) {
+            database_checkboxes.check();
+        }
+    };
+
+
     SS.generateGraphicalOverview = function () {
         $("[data-graphit='overview']").each(function () {
             var $this = $(this);
@@ -130,32 +165,27 @@ if (!SS) {
             $a
             .enable()
             .attr('href', SS.generateURI(sequence_ids, $a.data().databases))
-            .tooltip('destroy')
             .tooltip({
-                placement: 'left',
                 title: num_hits + " hit(s)."
             });
             return;
         }
 
-        if (num_hits == 0) {
-            $a
-            .tooltip('destroy')
-            .tooltip({
-                placement: 'left',
+        if (num_hits === 0) {
+            $a.tooltip({
                 title: "No hit to download."
             });
         }
 
         if (num_hits > 30) {
-            $a
-            .tooltip('destroy')
-            .tooltip({
-                placement: 'left',
+            $a.tooltip({
                 title: "Can't download more than 30 hits."
             });
         }
-        $a.disable();
+
+        $a
+        .disable()
+        .removeAttr('href');
     };
 
     /* Update the FASTA downloader button's state appropriately.
@@ -177,30 +207,22 @@ if (!SS) {
             $a
             .enable()
             .attr('href', SS.generateURI(sequence_ids, $a.data().databases))
-            .tooltip('destroy')
             .tooltip({
-                placement: 'left',
                 title: num_checked + " hit(s) selected."
             })
             .find('span').html(num_checked);
             return;
         }
 
-        if (num_checked == 0) {
+        if (num_checked === 0) {
             $n.empty();
-            $a
-            .tooltip('destroy')
-            .tooltip({
-                placement: 'left',
+            $a.tooltip({
                 title: "No hit selected."
             });
         }
 
         if (num_checked > 30) {
-            $a
-            .tooltip('destroy')
-            .tooltip({
-                placement: 'left',
+            $a.tooltip({
                 title: "Can't download more than 30 hits."
             });
         }
@@ -228,11 +250,32 @@ if (!SS) {
         });
     };
 
-    SS.setupTooltipsForPosLabels = function () {
+    SS.setupTooltips = function () {
         $('.pos-label').each(function () {
             $(this).tooltip({
-                container: 'body',
-                placement: 'right',
+                placement: 'right'
+            });
+        });
+
+        $('.downloads a').each(function () {
+            $(this).tooltip();
+        });
+    };
+
+    SS.setupDownloadLinks = function () {
+        $('.download').on('click', function (event) {
+            event.preventDefault();
+            event.stopPropagation();
+
+            if (event.target.disabled) return;
+
+            var url = this.href;
+            $.get(url)
+            .done(function (data) {
+                window.location.href = url;
+            })
+            .fail(function (jqXHR, status, error) {
+                SS.showErrorModal(jqXHR, function () {});
             });
         });
     };
@@ -246,7 +289,7 @@ if (!SS) {
             "&database_ids=" + database_ids + '&download=fasta';
 
         return url;
-    },
+    };
 
     SS.showErrorModal = function (jqXHR, beforeShow) {
         setTimeout(function () {
@@ -258,7 +301,7 @@ if (!SS) {
                 $("#error-no-response").modal();
             }
         }, 500);
-    },
+    };
 
     SS.init = function () {
         this.$sequence = $('#sequence');
@@ -267,7 +310,6 @@ if (!SS) {
 
         SS.blast.init();
     };
-
 }()); //end SS module
 
 /**
@@ -498,7 +540,7 @@ $(document).ready(function(){
         reader.onerror = function (e) {
             // Couldn't read. Means dropped stuff wasn't FASTA file.
             dndError('dnd-format');
-        }
+        };
         reader.readAsText(file);
     });
     // end drag-and-drop
@@ -522,10 +564,10 @@ $(document).ready(function(){
     // Handle clearing query sequences(s) when x button is pressed.
     $('#btn-sequence-clear').click(function (e) {
         $('#sequence').val("").focus();
-    })
+    });
 
-    // pre-select if only on db
-    $.onedb();
+    // Pre-select if only one database available.
+    SS.onedb();
 
     // Handles the form submission when Ctrl+Enter is pressed anywhere on page
     $(document).bind("keydown", function (e) {
@@ -559,11 +601,11 @@ $(document).ready(function(){
     $('.databases').on('database_type_changed', function (event, type) {
         switch (type) {
             case 'protein':
-                $('.databases.nucleotide input:checkbox').uncheck().disable();
+                $('.databases.nucleotide input:checkbox').disable();
                 $('.databases.nucleotide .checkbox').addClass('disabled');
                 break;
             case 'nucleotide':
-                $('.databases.protein input:checkbox').uncheck().disable();
+                $('.databases.protein input:checkbox').disable();
                 $('.databases.protein .checkbox').addClass('disabled');
                 break;
             default:
@@ -666,7 +708,6 @@ $(document).ready(function(){
         SS.selectHit(this);
     });
 
-
     $('#blast').submit(function(){
         //parse AJAX URL
         var action = $(this).attr('action');
@@ -708,7 +749,8 @@ $(document).ready(function(){
             SS.updateDownloadFastaOfAllLink();
             SS.updateDownloadFastaOfSelectedLink();
             SS.updateSequenceViewerLinks();
-            SS.setupTooltipsForPosLabels();
+            SS.setupTooltips();
+            SS.setupDownloadLinks();
 
             $('body').scrollspy({target: '.sidebar'});
 

data/sequenceserver.gemspec

@@ -1,33 +1,37 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '1.0.0-2'
-  s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Vivek Rai', 'Yannick Wurm']
+  s.version     = '1.0.0-3'
+  s.authors     = ['Anurag Priyam', 'Ben J Woodcroft',
+                   'Vivek Rai', 'Yannick Wurm']
   s.email       = ['anurag08priyam@gmail.com', 'b.woodcroft@uq.edu.au']
   s.homepage    = 'http://sequenceserver.com'
   s.license     = 'SequenceServer (custom)'
 
   s.summary     = 'BLAST search made easy!'
   s.description = <<DESC
-SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
+SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user
+interface for use locally or over the web.
 DESC
 
   # dependencies
-  s.add_dependency('thin',    '~> 1.6.2')
-  s.add_dependency('sinatra', '~> 1.4.5')
-  s.add_dependency('ox',      '~> 2.1.1')
-  s.add_dependency('slop',    '~> 3.6.0')
-
-  s.add_development_dependency('rack-test', '~> 0.6.2')
-  s.add_development_dependency('rspec',     '~> 2.8.0')
-  s.add_development_dependency('rake',      '~> 10.3.2')
-  s.add_development_dependency('rubocop',   '~> 0.26.1')
-  s.add_development_dependency('capybara',   '~> 2.4.4')
-  s.add_development_dependency('capybara-webkit',   '~> 1.3.0')
+  s.add_dependency('thin',    '~> 1.6',  '>= 1.6.2')
+  s.add_dependency('sinatra', '~> 1.4',  '>= 1.4.5')
+  s.add_dependency('ox',      '~> 2.1',  '>= 2.1.1')
+  s.add_dependency('slop',    '~> 3.6',  '>= 3.6.0')
+
+  s.add_development_dependency('rack-test',       '~> 0.6',  '>= 0.6.2')
+  s.add_development_dependency('rspec',           '~> 2.8',  '>= 2.8.0')
+  s.add_development_dependency('rake',            '~> 10.3', '>= 10.3.2')
+  s.add_development_dependency('rubocop',         '~> 0.28', '>= 0.28.0')
+  s.add_development_dependency('capybara',        '~> 2.4',  '>= 2.4.4')
+  s.add_development_dependency('capybara-webkit', '~> 1.3',  '>= 1.3.0')
+  s.add_development_dependency('codeclimate-test-reporter')
 
   # gem
-  s.files         = Dir['lib/**/*'] + Dir['views/**/*'] + Dir['public/**/*'] + Dir['tests/**/*']
-  s.files         = s.files + ['config.ru', 'Gemfile', 'sequenceserver.gemspec']
+  s.files         = Dir['lib/**/*'] + Dir['views/**/*'] + Dir['public/**/*']
+  s.files         = s.files + ['config.ru'] + Dir['tests/**/*']
+  s.files         = s.files + ['Gemfile', 'sequenceserver.gemspec']
   s.files         = s.files + ['LICENSE.txt', 'LICENSE.Apache.txt', 'README.md']
   s.executables   = ['sequenceserver']
   s.require_paths = ['lib']

data/views/400.erb

@@ -5,7 +5,7 @@
     <div
       class="modal-header">
       <h3>
-        Oops! BLAST Failed
+        Oops! Request Failed
       </h3>
     </div>
 
@@ -19,6 +19,7 @@
     <div
       class="modal-footer">
       <button
+        type="button"
         class="btn btn-default btn-danger"
         data-dismiss="modal">
         Close

data/views/500.erb

@@ -32,7 +32,12 @@
 
     <div
       class="modal-footer">
-      <button class="btn btn-danger" data-dismiss="modal">Done</button>
+      <button
+        type="button"
+        class="btn btn-danger"
+        data-dismiss="modal">
+        Done
+      </button>
     </div>
   </div>
 </div>

data/views/result.erb

@@ -16,8 +16,9 @@
             </small>
           </h3>
           <span
-            class="label label-reset cursor-pointer pos-label"
-            title="<%= "Query #{query.number}." %>">
+            class="label label-reset pos-label"
+            title="<%= "Query #{query.number}." %>"
+            data-toggle="tooltip">
             <%= "#{query.number} / #{report.queries.length}"%>
           </span>
         </div>
@@ -47,8 +48,8 @@
                 <tr>
                   <td class="text-left"><%= h + 1 %>.</td>
                   <td> <a href="<%="#Query_#{query.number}_hit_#{hit.number}"%>"><%= "#{hit.id}" %></a> </td>
-                  <td class="text-right"><%= prettify_score hit.score %></td>
-                  <td class="text-right"><%= prettify_evalue hit.evalue %></td>
+                  <td class="text-right"><%= prettify_float hit.score  %></td>
+                  <td class="text-right"><%= prettify_float hit.evalue %></td>
                 </tr>
               <% end %>
               </tbody>
@@ -71,8 +72,9 @@
                     </span>
                   </h4>
                   <span
-                    class="label label-reset cursor-pointer pos-label"
-                    title="<%= "Query #{query.number}. Hit #{hit.number}/#{query.hits.length}." %>">
+                    class="label label-reset pos-label"
+                    title="<%= "Query #{query.number}. Hit #{hit.number} of #{query.hits.length}." %>"
+                    data-toggle="tooltip">
                     <%= "#{hit.number} / #{query.hits.length}"%>
                   </span>
                 </div>
@@ -91,19 +93,19 @@
                       <table
                         class="table table-condensed hsp-stats">
                         <thead>
-                          <% report.filter_hsp_stats(hsp).each do |key, value| %>
+                          <% hsp.stats.keys.each do |key| %>
                             <th> <%= key %> </th>
                           <% end %>
                         </thead>
                         <tbody>
                           <tr>
-                            <% report.filter_hsp_stats(hsp).each do |key, value| %>
-                              <td> <%= value %> </th>
+                            <% hsp.stats.values.each do |value| %>
+                              <td> <%= prettify value %> </th>
                             <% end %>
                           </tr>
                         </tbody>
                       </table>
-                      <div class="alignment"><%= report.pp_hsp hsp%></div>
+                      <div class="alignment"><%= hsp.pp %></div>
                     </div>
                   <% end %>
                   <div class="hit-links text-right">
@@ -177,32 +179,50 @@ Total letters in queried databases: <%= report.stats[1] %>
           </h4>
         </div>
         <ul
-          class="list-unstyled list-padded">
+          class="downloads list-unstyled list-padded">
           <li>
             <a
-              href="#"
-              class="download-fasta-of-all"
+              class="download download-fasta-of-all disabled"
               data-databases="<%= report.querydb.map(&:id).join(' ') %>">
               FASTA of all hits
             </a>
           </li>
           <li>
             <a
-              class="download-fasta-of-selected disabled"
+              class="download download-fasta-of-selected disabled"
               data-databases="<%= report.querydb.map(&:id).join(' ') %>">
               FASTA of <span class="text-bold"></span> selected hit(s)
             </a>
           </li>
           <li>
             <a
-              class="disabled">
-              XML report (coming soon)
+              class="download"
+              title="12 columns: query and subject ID; alignment length,
+              mismatches, gaps, identity, start and end coordinates,
+              e value and bitscore."
+              data-toggle="tooltip"
+              href="get_report/?report=<%= File.basename(report.archive_file) %>&format=tsv_commented&type=std">
+              Standard tabular report
             </a>
           </li>
           <li>
             <a
-              class="disabled">
-              TSV report (coming soon)
+              class="download"
+              title="44 columns: query and subject ID, GI, accessions,
+              and length; alignment details; taxonomy details of subject
+              sequence(s) and query coverage per subject and per HSP."
+              data-toggle="tooltip"
+              href="get_report/?report=<%= File.basename(report.archive_file) %>&format=tsv_commented&download=true&specifiers=qseqid qgi qacc sseqid sallseqid sgi sallgi sacc sallacc qstart qend sstart send qseq sseq evalue bitscore score length length pident nident mismatch positive gapopen gaps ppos frames qframe hframe btop staxids sscinames scomnames sblastnames sskingdoms stitle salltitles sstrand qcovs qcovhsp&type=full">
+              Full tabular report
+            </a>
+          </li>
+          <li>
+            <a
+              class="download"
+              title="Results in XML format."
+              data-toggle="tooltip"
+              href="get_report/?report=<%= File.basename(report.archive_file) %>&format=xml&type=full">
+              Full XML report
             </a>
           </li>
         </ul>