quorum 0.1.0 → 0.2.0

data/Gemfile.lock

@@ -1,116 +1,116 @@
 PATH
   remote: .
   specs:
-    quorum (0.1.0)
+    quorum (0.2.0)
       bio-blastxmlparser (~> 1.0.1)
       jquery-rails
       net-ssh (~> 2.2.1)
       rails (~> 3.1.0)
       resque (~> 1.19.0)
+      resque-result (~> 1.0.1)
 
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (3.1.0)
-      actionpack (= 3.1.0)
+    actionmailer (3.1.3)
+      actionpack (= 3.1.3)
       mail (~> 2.3.0)
-    actionpack (3.1.0)
-      activemodel (= 3.1.0)
-      activesupport (= 3.1.0)
+    actionpack (3.1.3)
+      activemodel (= 3.1.3)
+      activesupport (= 3.1.3)
       builder (~> 3.0.0)
       erubis (~> 2.7.0)
       i18n (~> 0.6)
-      rack (~> 1.3.2)
-      rack-cache (~> 1.0.3)
+      rack (~> 1.3.5)
+      rack-cache (~> 1.1)
       rack-mount (~> 0.8.2)
       rack-test (~> 0.6.1)
-      sprockets (~> 2.0.0)
-    activemodel (3.1.0)
-      activesupport (= 3.1.0)
-      bcrypt-ruby (~> 3.0.0)
+      sprockets (~> 2.0.3)
+    activemodel (3.1.3)
+      activesupport (= 3.1.3)
       builder (~> 3.0.0)
       i18n (~> 0.6)
-    activerecord (3.1.0)
-      activemodel (= 3.1.0)
-      activesupport (= 3.1.0)
+    activerecord (3.1.3)
+      activemodel (= 3.1.3)
+      activesupport (= 3.1.3)
       arel (~> 2.2.1)
       tzinfo (~> 0.3.29)
-    activeresource (3.1.0)
-      activemodel (= 3.1.0)
-      activesupport (= 3.1.0)
-    activesupport (3.1.0)
+    activeresource (3.1.3)
+      activemodel (= 3.1.3)
+      activesupport (= 3.1.3)
+    activesupport (3.1.3)
       multi_json (~> 1.0)
     arel (2.2.1)
-    bcrypt-ruby (3.0.0)
     bio-blastxmlparser (1.0.1)
       bio-logger (>= 1.0.0)
       nokogiri (>= 1.5.0)
     bio-logger (1.0.0)
       log4r (>= 1.1.9)
     builder (3.0.0)
-    capybara (1.1.1)
+    capybara (1.1.2)
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       selenium-webdriver (~> 2.0)
       xpath (~> 0.1.4)
-    childprocess (0.2.2)
+    childprocess (0.3.0)
       ffi (~> 1.0.6)
     database_cleaner (0.6.7)
     diff-lcs (1.1.3)
     erubis (2.7.0)
-    factory_girl (2.1.0)
+    factory_girl (2.1.2)
+      activesupport
     factory_girl_rails (1.2.0)
       factory_girl (~> 2.1.0)
       railties (>= 3.0.0)
-    ffi (1.0.9)
+    ffi (1.0.11)
     hike (1.2.1)
     i18n (0.6.0)
-    jquery-rails (1.0.16)
+    jquery-rails (1.0.19)
       railties (~> 3.0)
       thor (~> 0.14)
-    json_pure (1.5.4)
-      spruz (~> 0.2.8)
-    log4r (1.1.9)
+    json (1.6.5)
+    log4r (1.1.10)
     mail (2.3.0)
       i18n (>= 0.4.0)
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
-    mime-types (1.16)
-    multi_json (1.0.3)
-    mysql2 (0.3.7)
-    net-ssh (2.2.1)
+    mime-types (1.17.2)
+    multi_json (1.0.4)
+    mysql2 (0.3.11)
+    net-ssh (2.2.2)
     nokogiri (1.5.0)
-    polyglot (0.3.2)
-    rack (1.3.2)
-    rack-cache (1.0.3)
+    polyglot (0.3.3)
+    rack (1.3.6)
+    rack-cache (1.1)
       rack (>= 0.4)
     rack-mount (0.8.3)
       rack (>= 1.0.0)
-    rack-protection (1.1.4)
+    rack-protection (1.2.0)
       rack
     rack-ssl (1.3.2)
       rack
     rack-test (0.6.1)
       rack (>= 1.0)
-    rails (3.1.0)
-      actionmailer (= 3.1.0)
-      actionpack (= 3.1.0)
-      activerecord (= 3.1.0)
-      activeresource (= 3.1.0)
-      activesupport (= 3.1.0)
+    rails (3.1.3)
+      actionmailer (= 3.1.3)
+      actionpack (= 3.1.3)
+      activerecord (= 3.1.3)
+      activeresource (= 3.1.3)
+      activesupport (= 3.1.3)
       bundler (~> 1.0)
-      railties (= 3.1.0)
-    railties (3.1.0)
-      actionpack (= 3.1.0)
-      activesupport (= 3.1.0)
+      railties (= 3.1.3)
+    railties (3.1.3)
+      actionpack (= 3.1.3)
+      activesupport (= 3.1.3)
       rack-ssl (~> 1.3.2)
       rake (>= 0.8.7)
       rdoc (~> 3.4)
       thor (~> 0.14.6)
-    rake (0.9.2)
-    rdoc (3.9.4)
+    rake (0.9.2.2)
+    rdoc (3.12)
+      json (~> 1.4)
     redis (2.2.2)
     redis-namespace (1.0.3)
       redis (< 3.0.0)
@@ -119,40 +119,47 @@ GEM
       redis-namespace (~> 1.0.2)
       sinatra (>= 0.9.2)
       vegas (~> 0.1.2)
-    rspec (2.6.0)
-      rspec-core (~> 2.6.0)
-      rspec-expectations (~> 2.6.0)
-      rspec-mocks (~> 2.6.0)
-    rspec-core (2.6.4)
-    rspec-expectations (2.6.0)
+    resque-meta (1.0.3)
+      resque (~> 1.8)
+    resque-result (1.0.1)
+      resque (~> 1.9)
+      resque-meta (~> 1.0)
+    resque_spec (0.8.1)
+      resque (>= 1.19.0)
+      rspec (>= 2.5.0)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
       diff-lcs (~> 1.1.2)
-    rspec-mocks (2.6.0)
-    rspec-rails (2.6.1)
-      actionpack (~> 3.0)
-      activesupport (~> 3.0)
-      railties (~> 3.0)
-      rspec (~> 2.6.0)
-    rubyzip (0.9.4)
-    selenium-webdriver (2.5.0)
-      childprocess (>= 0.2.1)
-      ffi (>= 1.0.7)
-      json_pure
+    rspec-mocks (2.8.0)
+    rspec-rails (2.8.1)
+      actionpack (>= 3.0)
+      activesupport (>= 3.0)
+      railties (>= 3.0)
+      rspec (~> 2.8.0)
+    rubyzip (0.9.5)
+    selenium-webdriver (2.17.0)
+      childprocess (>= 0.2.5)
+      ffi (~> 1.0.9)
+      multi_json (~> 1.0.4)
       rubyzip
-    sinatra (1.3.0)
-      rack (~> 1.3)
-      rack-protection (~> 1.1)
-      tilt (~> 1.3)
-    sprockets (2.0.0)
+    sinatra (1.3.2)
+      rack (~> 1.3, >= 1.3.6)
+      rack-protection (~> 1.2)
+      tilt (~> 1.3, >= 1.3.3)
+    sprockets (2.0.3)
       hike (~> 1.2)
       rack (~> 1.0)
       tilt (~> 1.1, != 1.3.0)
-    spruz (0.2.13)
     thor (0.14.6)
     tilt (1.3.3)
     treetop (1.4.10)
       polyglot
       polyglot (>= 0.3.1)
-    tzinfo (0.3.30)
+    tzinfo (0.3.31)
     vegas (0.1.8)
       rack (>= 1.0.0)
     xpath (0.1.4)
@@ -162,9 +169,10 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  capybara
-  database_cleaner
+  capybara (~> 1.1.1)
+  database_cleaner (~> 0.6.7)
   factory_girl_rails (~> 1.2.0)
   mysql2
   quorum!
+  resque_spec (~> 0.8.1)
   rspec-rails (~> 2.6)

data/HISTORY.md

@@ -0,0 +1,9 @@
+## 0.2.0 (2012-01-20)
+
+* Added link to Download Sequence in detailed report view.
+* Added `rails g quorum:images` to override images.
+* Deprecated Quorum initializer method `blast_script`.
+
+## 0.1.0 (2012-01-06)
+
+* Initial release.

data/README.rdoc

@@ -11,8 +11,8 @@ Dependencies:
 
 * Rails >= 3.1.0
 * Redis >= 0.900 for Resque (https://github.com/defunkt/resque)
-* NCBI Blast+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
-* Emboss (http://emboss.sourceforge.net/)
+* NCBI Blast+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST)
+* Emboss (http://emboss.sourceforge.net)
 
 See the gem in action.
 
@@ -41,6 +41,36 @@ Migrate the database.
   rake quorum:install:migrations
   rake db:migrate
 
+== Upgrading?
+
+Follow these steps to safely upgrade Quorum.
+
+* Make a copy of "config/quorum_settings.yml".
+
+  <tt>cp config/quorum_settings.yml config/quorum_settings.yml.old</tt>
+
+* If you overrode Quorum's styles and / or views, make a copy of the 
+  existing directories before upgrading.
+
+  <tt>cp -R app/assets/stylesheets/quorum app/assets/stylesheets/quorum_old</tt>
+  <tt>cp -R app/views/quorum/jobs app/views/quorum/jobs_old</tt>
+
+* Run the install generator and answer "Yes" to all conflicts.
+
+  <tt>rails generate quorum:install</tt>
+
+* Copy the old Search Database(s) to the newly generated
+  "config/quorum_settings.yml" file.
+
+* Update the database migrations.
+
+  <tt>rake quorum:install:migrations
+  rake db:migrate</tt>
+
+* If applicable, override Quorum's views, styles and images.
+
+* Update the remote machine(s).
+
 == Getting Started
 
 === NCBI Blast+ Setup
@@ -88,6 +118,38 @@ For a full list of supported arguments.
 Don't forget to update "config/quorum_settings.yml" with your newly created 
 database(s).
 
+==== Download Blast Hit Sequence
+
+Quorum provides a link to download a Blast hit sequence in the detailed report.
+For this process to work smoothly, the sequence identifier MUST be unique 
+across ALL Blast databases.
+
+Example:
+"example_blast_database/contigs.fa"
+
+  >my_unique_sequence_identifier_201201201327077953
+  ATGC...
+
+"another_example_blast_database/contigs.fa"
+
+  >my_unique_sequence_identifier_201201201327078017
+  CGTA...
+
+If the sequence identifiers are not unique across all Blast databases and
+you wish to remove the link to download a Blast hit sequence, follow the
+steps below.
+
+* Override Quorum's views (see Customize Quorum below)
+* Comment out or remove the lines below in 
+  "app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb" 
+
+  \<p class="small">
+    <a id="download_sequence_{{= id }}" 
+     onclick="downloadSequence(<%= @jobs.id %>, {{= id }}, '{{= algo }}', this)">
+     Download Sequence
+    </a>
+  \</p>
+
 === Remote Machine Setup -- Recommended for Production Use
 
 Follow the steps below to execute Quorum remotely via Net::SSH.
@@ -100,9 +162,9 @@ Follow the steps below to execute Quorum remotely via Net::SSH.
 * Ensure you have supplied the necessary information in 
   "config/quorum_settings.yml" to execute Quorum remotely.
 
-  remote: true
-  ssh_host: remote.machine.org
-  ssh_user: remote_user
+  <tt>remote: true</tt>
+  <tt>ssh_host: remote.machine.org</tt>
+  <tt>ssh_user: remote_user</tt>
   
 Net::SSH.start() optional params (http://net-ssh.github.com/ssh/v2/api/index.html)
 
@@ -112,28 +174,28 @@ Net::SSH.start() optional params (http://net-ssh.github.com/ssh/v2/api/index.htm
 
 * Tar and compress quorum.
 
-  tar -czvf quorum.tar.gz quorum/
+  <tt>tar -czvf quorum.tar.gz quorum/</tt>
 
 * Copy the newly created tarball to the remote machine.
 
-  scp quorum.tar.gz <username>@<host>:/path/to/install
+  <tt>scp quorum.tar.gz <username>@<host>:/path/to/install</tt>
 
 * Expand the tarball on the remote machine.
 
-  ssh <username>@<host>        
+  <tt>ssh <username>@<host></tt>
 
-  tar -xzvf quorum.tar.gz
+  <tt>tar -xzvf quorum.tar.gz</tt>
 
 * Ensure Quorum script dependencies are added to the remote machine's PATH. 
   If the remote machine doesn't have a .bashrc file, create one.
 
-  touch /path/to/.bashrc
+  <tt>touch /path/to/.bashrc</tt>
 
 and add script dependencies to PATH.
 
   echo "export PATH=/path/to/dependencies:$PATH" >> /path/to/.bashrc
 
-=== Customize Quorum's Views and Styles
+=== Customize Quorum's Views, Styles and Images
 
 To override Quorum's default views, run the generator.
 
@@ -155,6 +217,22 @@ it's a good idea to remove
 in "app/assets/stylesheets/application.css" and require your stylesheets 
 individually.
 
+To override Quorum's default images, run the generator.
+
+  rails generate quorum:images
+
+A copy of Quorum's images can be found in your application under
+"app/assets/images/quorum/".
+
+<b>jQuery UI</b>
+
+Don't like Quorum's jQuery UI theme? Override it!
+
+* Override Quorum's styles and images.
+* Roll your own jQuery UI theme. http://jqueryui.com/themeroller
+* Replace Quorum's theme in "app/assets/{stylesheets:images}/quorum" with
+  your own.
+
 Don't plan on supporting all of Quorum's alogrithms? Override Quorum's views 
 and comment out any unwanted algorithms in "app/views/quorum/jobs/new.html.erb" 
 and "app/views/quorum/jobs/show.html.erb".
@@ -164,22 +242,22 @@ For example:
 Remove Blastp in "app/views/quorum/jobs/new.html.erb"
 
   <!-- Search Algorithms -->
-  <!-- Comment out an alorithm below to remove it from the form. -->
+  <!-- Comment out an algorithm below to remove it from the form. -->
 
   <!-- blastn -->
-  <%= render :partial => "blastn_form", :locals => { 
+  <%= render :partial => "quorum/jobs/form/blastn_form", :locals => { 
     :f => f, :blast_dbs => @blast_dbs } %>
 
   <!-- blastx -->
-  <%= render :partial => "blastx_form", :locals => { 
+  <%= render :partial => "quorum/jobs/form/blastx_form", :locals => { 
     :f => f, :blast_dbs => @blast_dbs } %>
 
   <!-- tblastn -->
-  <%= render :partial => "tblastn_form", :locals => { 
+  <%= render :partial => "quorum/jobs/form/tblastn_form", :locals => { 
     :f => f, :blast_dbs => @blast_dbs } %>
 
   <!-- blastp -->
-  <% render :partial => "blastp_form", :locals => { 
+  <% render :partial => "quorum/jobs/form/blastp_form", :locals => { 
     :f => f, :blast_dbs => @blast_dbs } %>
 
   <!-- End Search Algorithms -->
@@ -200,21 +278,21 @@ Remove Blastp in "app/views/quorum/jobs/show.html.erb"
     <div id="tabs-1">
       <h2>Blastn</h2>
       <div id="blastn-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
 
     <div id="tabs-2">
       <h2>Blastx</h2>
       <div id="blastx-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
 
     <div id="tabs-3">
       <h2>Tblastn</h2>
       <div id="tblastn-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
 
@@ -222,7 +300,7 @@ Remove Blastp in "app/views/quorum/jobs/show.html.erb"
     <div id="tabs-4">
       <h2>Blastp</h2>
       <div id="blastp-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
     -->
@@ -232,7 +310,7 @@ Remove Blastp in "app/views/quorum/jobs/show.html.erb"
 
 For detailed Redis installation instructions, follow the links below.
 
-* Redis (http://redis.io/)
+* Redis (http://redis.io)
 * Resque (https://github.com/defunkt/resque)
 
 === Resque
@@ -301,7 +379,7 @@ https://github.com/ncgr/quorum/issues
 === TODO
 
 * Add GFF3 annotations to detailed Blast reports
-* Add link to download Blast hit sequence in detailed report
+* Add link to download multiple Blast hit sequences in detailed report
 * Support Hmmer3
 
 === Maintained By
@@ -315,4 +393,4 @@ https://github.com/ncgr/quorum/issues
 
 == License
 
-MIT License. Copyright NCGR http://ncgr.org/
+MIT License. Copyright NCGR http://ncgr.org

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

@@ -180,7 +180,7 @@ var pollResults = function(id, interval, algos) {
               data: data,
               algo: a
             }
-            );
+          );
           $('#' + a + '-results').html(temp);
           return;
         }
@@ -198,7 +198,7 @@ var viewDetailedReport = function(id, focus_id, query, algo) {
   // Create the modal box.
   $('#detailed_report_dialog').html(
     "<p class='center'>" + 
-    "Loading... <img src='/assets/quorum/knight_rider.gif' alt='Loading'>" +
+    "Loading... <img src='/assets/quorum/loading.gif' alt='Loading'>" +
     "</p>"
   ).dialog({
     modal:    true,
@@ -249,7 +249,7 @@ var addBaseTitleIndex = function(bases, from, to, algo, type) {
     forward = false;
   }
 
-  // Only set value to 3 if hseq is true and algo is tblastn.
+  // Set value to 3 for the below.
   if ((type === "hit" && algo === "tblastn") ||
       (type === "query" && algo === "blastx")) {
     value = 3;
@@ -350,6 +350,48 @@ var displayHspLinks = function(focus, group, data) {
   }
 }
 
+//
+// 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.
 //

data/app/controllers/quorum/jobs_controller.rb

@@ -53,12 +53,11 @@ module Quorum
     # Returns Resque worker results.
     #
     def get_quorum_search_results
-      valid = ["blastn", "blastx", "tblastn", "blastp"]
       empty = [{ :results => false }].to_json
 
       json = empty
 
-      if valid.include? params[:algo]
+      if Quorum::BLAST_ALGORITHMS.include?(params[:algo])
         queued = "#{params[:algo]}_job".to_sym
         report = "#{params[:algo]}_job_reports".to_sym
 
@@ -84,6 +83,52 @@ module Quorum
       respond_with json
     end
 
+    #
+    # Find hit sequence, queue worker and return worker meta_id
+    # for lookup.
+    #
+    def get_quorum_blast_hit_sequence
+      json = []
+
+      if Quorum::BLAST_ALGORITHMS.include?(params[:algo])
+        begin
+          job = Job.find(params[:id])
+        rescue ActiveRecord::RecordNotFound => e
+          logger.error e.message
+        else
+          data = job.fetch_quorum_blast_sequence(
+            params[:algo], params[:algo_id]
+          )
+          json = [{ :meta_id => data.meta_id }]
+        end
+      end   
+
+      respond_with json
+    end
+
+    #
+    # Send Blast hit sequence as attached file or render
+    # error message as text.
+    #
+    # See lib/generators/templates/blast_db.rb for more info.
+    #
+    def send_quorum_blast_hit_sequence
+      data = Workers::System.get_meta(params[:meta_id])
+      if data.succeeded?
+        unless data.result.downcase.include?("error")
+          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 => ""
+    end
+
     private
 
     #