quorum 0.3.1 → 0.3.2

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

@@ -1,9 +1,9 @@
 <div id="show">
   <h1>Search Results</h1>
   <p class="small right"><%= link_to raw("Search Again &raquo;"), :jobs %></p>
-  <!-- Tabs -->
-  <!-- To remove an algorithm from the view, simply comment out the -->
-  <!-- div#tabs ul li and corresponding div#tabs-(tab number) -->
+  <%# Tabs %>
+  <%# To remove an algorithm from the view, simply comment out the %>
+  <%# div#tabs ul li and corresponding div#tabs-(tab number) %>
   <div id="tabs">
     <ul>
       <li><a href="#tabs-1">Blastn</a></li>
@@ -12,7 +12,7 @@
       <li><a href="#tabs-4">Blastp</a></li>
     </ul>
 
-    <!-- Search results per algorithm -->
+    <%# Search results per algorithm %>
     <div id="tabs-1">
       <h2>Blastn</h2>
       <div id="blastn-results">
@@ -41,10 +41,10 @@
       </div>
     </div>
   </div>
-  <!-- End Tabs -->
+  <%# End Tabs %>
   <p class="small right"><%= link_to raw("Search Again &raquo;"), :jobs %></p>
 
-  <!-- Detailed report element -->
+  <%# Detailed report element %>
   <div id="detailed_report_dialog" title="Quorum Report Details"></div>
 </div>
 <div id="quorum">
@@ -54,7 +54,7 @@
   </p>
 </div>
 
-<!-- Templates -->
+<%# Templates %>
 <%= render :partial => "quorum/jobs/templates/blast_template" %>
 <%= render :partial => "quorum/jobs/templates/blast_detailed_report_template" %>
 
@@ -63,10 +63,24 @@
     //
     // Asynchronously poll Quorum for search results.
     //
-    //  pollResults(id, interval)
+    //  QUORUM.pollResults(id, callback, callback_obj, interval)
     //    id: Job.id
+    //    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);
+    //
+    //  Example callback:
+    //    MYAPP.myCoolCallback = function(id, data, algo) {
+    //      // awesome logic
+    //    };
+    //
     QUORUM.pollResults(<%= @jobs.id %>);
   });
 </script>

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

@@ -1,4 +1,4 @@
-<!-- Detailed Report Template -->
+<%# Detailed Report Template %>
 <script type="text/template" id="detailed_report_template">
   <h3>Query Accession {{= query }}</h3>
   {{ _.each(data, function(v) { }}
@@ -19,7 +19,7 @@
       <p class="small">Hit Description: {{= v.hit_def }}</p>
       <table class="report_details">
         <tr>
-          <td>E-value: {{= v.evalue }}</td>
+          <td>E-value: {{= QUORUM.formatEvalue(v.evalue) }}</td>
           <td>Bit Score: {{= v.bit_score }}</td>
           <td></td>
         </tr>

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

@@ -1,4 +1,4 @@
-<!-- Blast Results Template -->
+<%# Blast Results Template %>
 <script type="text/template" id="blast_template">
   {{ if (data[0].results === false) { }}
     <p><strong>Your search returned 0 hits.</strong></p>
@@ -56,7 +56,7 @@
                 {{= v.id }},
                 '{{= v.query }}',
                 '{{= algo }}')">
-                {{= v.evalue }}
+                {{= QUORUM.formatEvalue(v.evalue) }}
             </a>
           </td>
         </tr>

data/lib/generators/templates/blast.rb

@@ -232,18 +232,6 @@ module Quorum
         end
       end
 
-      #
-      # Make the E-value look pretty.
-      #
-      def format_evalue(evalue)
-        evalue = evalue.to_s
-        e      = evalue.slice!(/e.*/)
-        unless e.nil?
-          e = " x 10<sup>" << e.sub(/e/, '') << "</sup>"
-        end
-        evalue.to_f.round(1).to_s << e.to_s
-      end
-
       #
       # Format Blast report hit_display_id and hit_def.
       #
@@ -295,7 +283,7 @@ module Quorum
                 @data[:hsp_num]     = hsp.hsp_num
                 @data[:bit_score]   = hsp.bit_score
                 @data[:score]       = hsp.score
-                @data[:evalue]      = format_evalue(hsp.evalue)
+                @data[:evalue]      = hsp.evalue
                 @data[:query_from]  = hsp.query_from
                 @data[:query_to]    = hsp.query_to
                 @data[:hit_from]    = hsp.hit_from

data/lib/generators/templates/logger.rb

@@ -29,13 +29,13 @@ module Quorum
     # Removes instance files.
     #
     def remove_files(files)
-      unless Dir.glob(files).empty?
-        `rm #{files}`
-      else
-        log(
+      if Dir.glob(files).empty?
+         log(
           "remove_files",
           "Unable to remove #{files}"
         )
+      else
+       `rm #{files}`
       end
     end
 

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.3.1"
+  VERSION = "0.3.2"
 end

data/lib/workers/quorum.rb

@@ -24,9 +24,7 @@ module Workers
         Net::SSH.start(ssh_host, ssh_user, ssh_options) do |ssh|
           ssh.open_channel do |ch|
             ch.exec(cmd) do |ch, success|
-              unless success
-                Rails.logger.warn "Channel Net::SSH exec() failed. :'("
-              else
+              if success
                 # Capture STDOUT from ch.exec()
                 if stdout
                   ch.on_data do |ch, data|
@@ -37,6 +35,8 @@ module Workers
                 ch.on_request("exit-status") do |ch, data|
                   exit_status = data.read_long
                 end
+              else
+                Rails.logger.warn "Channel Net::SSH exec() failed. :'("
               end
             end
           end

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

@@ -13,9 +13,9 @@ module Quorum
       class QuorumJob < ActiveRecord::Base
         self.table_name = "quorum_jobs"
 
-        has_one :quorum_blastn_job, 
+        has_one :quorum_blastn_job,
           :foreign_key => "job_id"
-        has_many :quorum_blastn_job_reports, 
+        has_many :quorum_blastn_job_reports,
           :foreign_key => "blastn_job_id"
 
         has_one :quorum_blastx_job,
@@ -217,7 +217,7 @@ module Quorum
         File.open(@na_fasta, "w") { |f| f << @na_sequence }
         File.open(@aa_fasta, "w") { |f| f << @aa_sequence }
 
-        @out = File.join(@tmp, @hash + ".out.xml") 
+        @out = File.join(@tmp, @hash + ".out.xml")
         File.new(@out, "w")
 
         case @algorithm
@@ -232,18 +232,6 @@ module Quorum
         end
       end
 
-      #
-      # Make the E-value look pretty.
-      #
-      def format_evalue(evalue)
-        evalue = evalue.to_s
-        e      = evalue.slice!(/e.*/)
-        unless e.nil?
-          e = " x 10<sup>" << e.sub(/e/, '') << "</sup>"
-        end
-        evalue.to_f.round(1).to_s << e.to_s 
-      end
-
       #
       # Format Blast report hit_display_id and hit_def.
       #
@@ -269,7 +257,7 @@ module Quorum
 
       #
       # Parse and save Blast results using bio-blastxmlparser.
-      # Only save Blast results if results.bit_score > @min_score. 
+      # Only save Blast results if results.bit_score > @min_score.
       #
       def parse_and_save_results
         # Helper to avoid having to perform a query.
@@ -295,7 +283,7 @@ module Quorum
                 @data[:hsp_num]     = hsp.hsp_num
                 @data[:bit_score]   = hsp.bit_score
                 @data[:score]       = hsp.score
-                @data[:evalue]      = format_evalue(hsp.evalue)
+                @data[:evalue]      = hsp.evalue
                 @data[:query_from]  = hsp.query_from
                 @data[:query_to]    = hsp.query_to
                 @data[:hit_from]    = hsp.hit_from
@@ -311,7 +299,7 @@ module Quorum
 
                 # Hsps are only reported if a query hit against the Blast db.
                 # Only save the @data if bit_score exists.
-                if @data[:bit_score] && 
+                if @data[:bit_score] &&
                   (@data[:bit_score].to_i > @min_score.to_i)
                   @data[:results] = true
                   @data["#{@algorithm}_job_id".to_sym] = @job.method(@job_association).call.job_id
@@ -410,7 +398,7 @@ module Quorum
       # Execute Blast on a given dataset.
       #
       def execute_blast
-        generate_blast_cmd 
+        generate_blast_cmd
         @logger.log("NCBI Blast", @cmd)
         system(@cmd)
         parse_and_save_results

data/spec/javascripts/fixtures/quorum_tabs.html

@@ -8,3 +8,8 @@
     <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>

data/spec/javascripts/quorum_spec.js

@@ -1,9 +1,73 @@
 //
-// Test the methods not covered in RSpec request specs.
+// QUORUM Specs
 //
 
 describe("QUORUM", function() {
 
+  //
+  // Spec covers QUORUM.algorithms.
+  //
+  // QUORUM.algorithms should be an array of strings.
+  //
+  it("contains an array of strings", function() {
+    expect(QUORUM.algorithms.join('')).toMatch(/[a-zA-Z]/g);
+  });
+
+  //
+  // Spec covers QUORUM.pollResults.
+  //
+  // QUORUM.pollResults calls itself via setTimeout() if the returned JSON
+  // dataset is empty.
+  //
+  // If callback is defined, call callback function. Otherwise call default
+  // anonymous function buildTemplate().
+  //
+  it("fetches JSON and calls user defined callback function", function() {
+    spyOn($, 'getJSON');
+    spyOn(window, 'setTimeout');
+    var id = 1,
+        callback = jasmine.createSpy(),
+        data = 'foo';
+
+    QUORUM.pollResults(id, callback, null, 5000, ['a']);
+
+    // setTimeout()
+    $.getJSON.mostRecentCall.args[1]('');
+    expect(window.setTimeout).toHaveBeenCalled();
+
+    // callback()
+    $.getJSON.mostRecentCall.args[1](data);
+    expect(callback).toHaveBeenCalledWith(id, data, 'a');
+  });
+
+  //
+  // Spec covers QUORUM.viewDetailedReport.
+  //
+  // Open detailed report dialog modal box and load template.
+  //
+  it("renders modal box containing detailed report", function() {
+    loadFixtures('quorum_tabs.html');
+
+    spyOn($, 'getJSON');
+    spyOn(QUORUM, 'autoScroll');
+    var id = 1,
+        focus_id = 1,
+        query = 'foo',
+        algo = 'a',
+        data = 'bar';
+
+    QUORUM.viewDetailedReport(id, focus_id, query, algo);
+
+    expect($("#detailed_report_dialog")).toBeVisible();
+
+    // Fetch JSON to build the template and scroll to focus_id.
+    $.getJSON.mostRecentCall.args[1](data);
+    expect(QUORUM.autoScroll).toHaveBeenCalledWith(focus_id, false);
+
+    // Close the dialog box.
+    $("#detailed_report_dialog").dialog('close');
+  });
+
   //
   // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
   //
@@ -52,6 +116,10 @@ describe("QUORUM", function() {
     expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=10>E</a><a rel='quorum-tipsy' title=11>L</a><a rel='quorum-tipsy' title=12>V</a><a rel='quorum-tipsy' title=13>I</a><a rel='quorum-tipsy' title=14>S</a>\n     ELVIS\nhseq <a rel='quorum-tipsy' title=121>E</a><a rel='quorum-tipsy' title=122>L</a><a rel='quorum-tipsy' title=123>V</a><a rel='quorum-tipsy' title=124>I</a><a rel='quorum-tipsy' title=125>S</a>\n\n</pre></span>");
   });
 
+  //
+  // jQuery tipsy plugin should display anchor's title attribute on mouseover
+  // and hide on mouseout.
+  //
   it("should display title via jquery.tipsy on mouse over hide on mouse out", function() {
     loadFixtures('formatted_sequence.html');
     $('a[rel=quorum-tipsy]').tipsy({ gravity: 's' });
@@ -63,6 +131,12 @@ describe("QUORUM", function() {
     expect($('.tipsy')).not.toBeVisible();
   });
 
+  //
+  // Spec covers QUORUM.formatStrand.
+  //
+  // If number is > 0 print forward.
+  // If number is < 0 print reverse.
+  //
   it("prints hit strand as forward / forward for + / + intergers", function() {
     expect(QUORUM.formatStrand(1, 1)).toEqual("forward / forward");
   });
@@ -79,26 +153,127 @@ describe("QUORUM", function() {
     expect(QUORUM.formatStrand(-1, -1)).toEqual("reverse / reverse");
   });
 
+  //
+  // Spec covers QUORUM.formatEvalue
+  //
+  // Format Blast Evalues for HTML.
+  //
+  it("returns empty string if evalue is not set", function() {
+    expect(QUORUM.formatEvalue("")).toEqual("");
+    expect(QUORUM.formatEvalue(null)).toEqual("");
+    expect(QUORUM.formatEvalue(undefined)).toEqual("");
+  });
+
+  it("formats blast evalue", function() {
+    expect(QUORUM.formatEvalue("0")).toEqual("0.0");
+    expect(QUORUM.formatEvalue("0.0")).toEqual("0.0");
+    expect(QUORUM.formatEvalue("1.23966346466766e-65")).toEqual("1.2 x 10<sup>-65</sup>");
+    expect(QUORUM.formatEvalue("1.2966346466766e-165")).toEqual("1.3 x 10<sup>-165</sup>");
+    expect(QUORUM.formatEvalue("1.23456789")).toEqual("1.2");
+  });
+
+  //
+  // Spec covers QUORUM.displayHspLinks.
   //
   // Only print links to HSPs whers data id != focus.
   //
   it("prints HSP links", function() {
-    var focus = 1;
-    var group = "1,2";
-    var data  = [
-      {"id":1,"hsp_group":"1,2","hsp_num":1},
-      {"id":2,"hsp_group":"1,2","hsp_num":2}
-    ];
-    var hsps  = QUORUM.displayHspLinks(focus, group, data);
+    var focus = 1,
+        group = "1,2",
+        data = [
+          {"id":1,"hsp_group":"1,2","hsp_num":1},
+          {"id":2,"hsp_group":"1,2","hsp_num":2}
+        ];
+
+    var hsps = QUORUM.displayHspLinks(focus, group, data);
     expect(hsps).toEqual("Related <a onclick=\"(QUORUM.openWindow('http://www.ncbi.nlm.nih.gov/books/NBK62051/def-item/blast_glossary.HSP','HSP', 800, 300))\">HSPs</a>: 1 <a onclick='(QUORUM.autoScroll(2, true))'>2</a> ");
   });
 
+  //
+  // QUORUM.displayHspLinks should return an empty string if group is not set.
+  //
+  it("prints HSP links", function() {
+    var focus = 1,
+        group = null,
+        data = [
+          {"id":1,"hsp_group":"1,2","hsp_num":1},
+          {"id":2,"hsp_group":"1,2","hsp_num":2}
+        ];
+
+    var hsps = QUORUM.displayHspLinks(focus, group, data);
+    expect(hsps).toEqual("");
+  });
+
+  //
+  // Spec covers QUORUM.downloadSequence.
+  //
+  // Download a Blast hit sequence file.
+  //
+  it("sends request to server to extract Blast hit sequence", function() {
+    loadFixtures("quorum_tabs.html");
+
+    spyOn($, 'getJSON');
+    spyOn(QUORUM, 'getSequenceFile');
+    var id = 1,
+        algo_id = 1,
+        algo = 'a',
+        el = $("#download_sequence"),
+        data = [{meta_id:"foo"}];
+
+    QUORUM.downloadSequence(id, algo_id, algo, el);
+
+    expect(el.html()).toEqual('Fetching sequence...');
+
+    $.getJSON.mostRecentCall.args[1](data);
+    expect(QUORUM.getSequenceFile).toHaveBeenCalledWith(id, data[0].meta_id, el);
+  });
+
+  //
+  // Spec covers QUORUM.getSequenceFile.
+  //
+  // Poll application for Blast hit sequence file and force browser to
+  // download via iframe.
+  //
+  it("polls server to extract Blast hit sequence, once found, force browser to download via iframe", function() {
+    loadFixtures("quorum_tabs.html");
+
+    spyOn($, 'get');
+    spyOn(window, 'setTimeout');
+    var id = 1,
+        meta_id = 'foo',
+        el = $("#download_sequence"),
+        data = 'bar',
+        error = 'error';
+
+    QUORUM.getSequenceFile(id, meta_id, el);
+
+    // setTimeout()
+    $.get.mostRecentCall.args[1]('');
+    expect(window.setTimeout).toHaveBeenCalled();
+
+    // Print error message
+    $.get.mostRecentCall.args[1](error);
+    expect(el.html()).toEqual(error);
+
+    // Force browser to download file.
+    $.get.mostRecentCall.args[1](data);
+    expect(el.html()).toEqual('Sequence Downloaded Successfully');
+    expect($('iframe.quorum_sequence_download')).toBeDefined();
+    $('.quorum_sequence_download').remove();
+  });
+
+  //
+  // Spec covers QUORUM.openWindow.
+  //
+  // Open a URL in a new window.
+  //
   it("opens url in a new window", function() {
     spyOn(window, 'open');
-    var url    = "http://google.com";
-    var name   = "Google";
-    var width  = 300;
-    var height = 300;
+    var url = "http://google.com",
+        name = "Google",
+        width = 300,
+        height = 300;
+
     QUORUM.openWindow(url, name, width, height);
     expect(window.open).toHaveBeenCalledWith(url, name, "width=" + width + ",height=" + height + ",scrollbars=yes");
   });

data/spec/requests/jobs_spec.rb

@@ -49,8 +49,9 @@ describe "Jobs" do
 
   context "javascript", @javascript do
     before(:all) do
-      Capybara.current_driver    = :selenium
       Capybara.default_wait_time = 5
+      Capybara.server_port       = 53331
+      Capybara.current_driver    = :selenium
     end
     before(:each) do
       ResqueSpec.reset!
@@ -142,12 +143,30 @@ describe "Jobs" do
     end
   end
 
-  describe "GET /quorum/jobs/unknown_id" do
-    it "displays notice and renders form" do
+  describe "GET /quorum/jobs/id" do
+    it "displays notice and renders form with invalid id" do
       visit job_path('12893479812347912')
       page.should have_content("The data you requested is unavailable. Please check your URL and try again.")
       current_path.should eq(new_job_path)
     end
   end
 
+  describe "GET /quorum/jobs/id/get_quorum_search_results" do
+    it "renders JSON results => false with invalid id" do
+      visit "/quorum/jobs/23542352345/get_quorum_search_results.json"
+      page.should have_content("[{\"results\":false}]")
+    end
+  end
+
+  describe "GET /quorum/jobs/id/get_quorum_blast_hit_sequence" do
+    it "renders empty JSON with invalid id" do
+      visit "/quorum/jobs/23542352345/get_quorum_blast_hit_sequence.json"
+      page.should have_content("[]")
+    end
+
+    it "renders empty JSON with invalid id and valid params" do
+      visit "/quorum/jobs/23542352345/get_quorum_blast_hit_sequence.json?algo=blastn"
+      page.should have_content("[]")
+    end
+  end
 end

data/spec/templates/logger_spec.rb

@@ -4,7 +4,7 @@ require 'generators/templates/logger'
 describe "Quorum::Logger" do
   describe "#log" do
     before(:all) do
-      @args   = File.join(::Rails.root.to_s, "log") 
+      @args   = File.join(::Rails.root.to_s, "log")
       @logger = Quorum::Logger.new(@args)
     end
 
@@ -21,7 +21,7 @@ describe "Quorum::Logger" do
     it "records program, message, exits and removes files" do
       lambda {
         @logger.log(
-          "RSpec", "This is a test.", 1, 
+          "RSpec", "This is a test.", 1,
           File.join(@args, "quorum.log")
         )
       }.should raise_error(SystemExit)
@@ -31,5 +31,5 @@ describe "Quorum::Logger" do
       ).should be_false
 
     end
-  end  
+  end
 end