quorum 0.3.1 → 0.3.2

data/.travis.yml

@@ -0,0 +1,21 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+gemfile:
+  - gemfiles/Gemfile.rails-3.1.x
+  - gemfiles/Gemfile.rails-3.2.x
+before_install:
+  - sudo apt-get update
+  - sudo apt-get install ncbi-blast+ emboss
+before_script:
+  - "export DISPLAY=:99.0"
+  - "sh -e /etc/init.d/xvfb start"
+  - bundle install
+  - mysql -e "create database quorum_test;"
+  - "rake travis:create_db_config"
+  - "rake app:db:schema:load"
+script: "rake travis:spec"
+notifications:
+  email:
+    - "kas@ncgr.org"

data/Gemfile

@@ -1,15 +1,7 @@
 source "http://rubygems.org"
 
-# Declare your gem's dependencies in quorum.gemspec.
-# Bundler will treat runtime dependencies like base dependencies, and
-# development dependencies will be added by default to the :development group.
 gemspec
 
-# Declare any dependencies that are still in development here instead of in
-# your gemspec. These might include edge Rails or gems from your path or
-# Git. Remember to move these dependencies to your gemspec before releasing
-# your gem to rubygems.org.
-
-# To use debugger
-# gem 'ruby-debug19', :require => 'ruby-debug'
-
+group :test do
+  gem 'rake', '~> 0.9.2'
+end

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.3.1)
+    quorum (0.3.2)
       bio-blastxmlparser (~> 1.0.1)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -12,38 +12,39 @@ PATH
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (3.2.2)
-      actionpack (= 3.2.2)
-      mail (~> 2.4.0)
-    actionpack (3.2.2)
-      activemodel (= 3.2.2)
-      activesupport (= 3.2.2)
+    actionmailer (3.2.6)
+      actionpack (= 3.2.6)
+      mail (~> 2.4.4)
+    actionpack (3.2.6)
+      activemodel (= 3.2.6)
+      activesupport (= 3.2.6)
       builder (~> 3.0.0)
       erubis (~> 2.7.0)
       journey (~> 1.0.1)
       rack (~> 1.4.0)
-      rack-cache (~> 1.1)
+      rack-cache (~> 1.2)
       rack-test (~> 0.6.1)
-      sprockets (~> 2.1.2)
-    activemodel (3.2.2)
-      activesupport (= 3.2.2)
+      sprockets (~> 2.1.3)
+    activemodel (3.2.6)
+      activesupport (= 3.2.6)
       builder (~> 3.0.0)
-    activerecord (3.2.2)
-      activemodel (= 3.2.2)
-      activesupport (= 3.2.2)
+    activerecord (3.2.6)
+      activemodel (= 3.2.6)
+      activesupport (= 3.2.6)
       arel (~> 3.0.2)
       tzinfo (~> 0.3.29)
-    activeresource (3.2.2)
-      activemodel (= 3.2.2)
-      activesupport (= 3.2.2)
-    activesupport (3.2.2)
+    activeresource (3.2.6)
+      activemodel (= 3.2.6)
+      activesupport (= 3.2.6)
+    activesupport (3.2.6)
       i18n (~> 0.6)
       multi_json (~> 1.0)
+    addressable (2.2.8)
     arel (3.0.2)
     bio-blastxmlparser (1.0.1)
       bio-logger (>= 1.0.0)
       nokogiri (>= 1.5.0)
-    bio-logger (1.0.0)
+    bio-logger (1.0.1)
       log4r (>= 1.1.9)
     builder (3.0.0)
     capybara (1.1.2)
@@ -53,9 +54,9 @@ GEM
       rack-test (>= 0.5.4)
       selenium-webdriver (~> 2.0)
       xpath (~> 0.1.4)
-    childprocess (0.3.1)
+    childprocess (0.3.2)
       ffi (~> 1.0.6)
-    database_cleaner (0.7.2)
+    database_cleaner (0.8.0)
     diff-lcs (1.1.3)
     erubis (2.7.0)
     factory_girl (2.6.4)
@@ -66,27 +67,29 @@ GEM
     ffi (1.0.11)
     hike (1.2.1)
     i18n (0.6.0)
-    jasmine (1.1.2)
-      jasmine-core (>= 1.1.0)
-      rack (>= 1.1)
+    jasmine (1.2.0)
+      jasmine-core (>= 1.2.0)
+      rack (~> 1.0)
       rspec (>= 1.3.1)
       selenium-webdriver (>= 0.1.3)
-    jasmine-core (1.1.0)
-    journey (1.0.3)
-    jquery-rails (2.0.1)
+    jasmine-core (1.2.0)
+    journey (1.0.4)
+    jquery-rails (2.0.2)
       railties (>= 3.2.0, < 5.0)
       thor (~> 0.14)
-    json (1.6.6)
+    json (1.7.3)
+    libwebsocket (0.1.3)
+      addressable
     log4r (1.1.10)
     mail (2.4.4)
       i18n (>= 0.4.0)
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
-    mime-types (1.18)
-    multi_json (1.2.0)
+    mime-types (1.19)
+    multi_json (1.3.6)
     mysql2 (0.3.11)
     net-ssh (2.3.0)
-    nokogiri (1.5.2)
+    nokogiri (1.5.4)
     polyglot (0.3.3)
     rack (1.4.1)
     rack-cache (1.2)
@@ -97,21 +100,21 @@ GEM
       rack
     rack-test (0.6.1)
       rack (>= 1.0)
-    rails (3.2.2)
-      actionmailer (= 3.2.2)
-      actionpack (= 3.2.2)
-      activerecord (= 3.2.2)
-      activeresource (= 3.2.2)
-      activesupport (= 3.2.2)
+    rails (3.2.6)
+      actionmailer (= 3.2.6)
+      actionpack (= 3.2.6)
+      activerecord (= 3.2.6)
+      activeresource (= 3.2.6)
+      activesupport (= 3.2.6)
       bundler (~> 1.0)
-      railties (= 3.2.2)
-    railties (3.2.2)
-      actionpack (= 3.2.2)
-      activesupport (= 3.2.2)
+      railties (= 3.2.6)
+    railties (3.2.6)
+      actionpack (= 3.2.6)
+      activesupport (= 3.2.6)
       rack-ssl (~> 1.3.2)
       rake (>= 0.8.7)
       rdoc (~> 3.4)
-      thor (~> 0.14.6)
+      thor (>= 0.14.6, < 2.0)
     rake (0.9.2.2)
     rdoc (3.12)
       json (~> 1.4)
@@ -128,42 +131,42 @@ GEM
     resque-result (1.0.1)
       resque (~> 1.9)
       resque-meta (~> 1.0)
-    resque_spec (0.9.2)
+    resque_spec (0.12.2)
       resque (>= 1.19.0)
       rspec (>= 2.5.0)
-    rspec (2.9.0)
-      rspec-core (~> 2.9.0)
-      rspec-expectations (~> 2.9.0)
-      rspec-mocks (~> 2.9.0)
-    rspec-core (2.9.0)
-    rspec-expectations (2.9.0)
+    rspec (2.10.0)
+      rspec-core (~> 2.10.0)
+      rspec-expectations (~> 2.10.0)
+      rspec-mocks (~> 2.10.0)
+    rspec-core (2.10.1)
+    rspec-expectations (2.10.0)
       diff-lcs (~> 1.1.3)
-    rspec-mocks (2.9.0)
-    rspec-rails (2.9.0)
+    rspec-mocks (2.10.1)
+    rspec-rails (2.10.1)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       railties (>= 3.0)
-      rspec (~> 2.9.0)
-    rubyzip (0.9.6.1)
-    selenium-webdriver (2.20.0)
+      rspec (~> 2.10.0)
+    rubyzip (0.9.9)
+    selenium-webdriver (2.24.0)
       childprocess (>= 0.2.5)
-      ffi (~> 1.0)
+      libwebsocket (~> 0.1.3)
       multi_json (~> 1.0)
       rubyzip
     sinatra (1.3.2)
       rack (~> 1.3, >= 1.3.6)
       rack-protection (~> 1.2)
       tilt (~> 1.3, >= 1.3.3)
-    sprockets (2.1.2)
+    sprockets (2.1.3)
       hike (~> 1.2)
       rack (~> 1.0)
       tilt (~> 1.1, != 1.3.0)
-    thor (0.14.6)
+    thor (0.15.3)
     tilt (1.3.3)
     treetop (1.4.10)
       polyglot
       polyglot (>= 0.3.1)
-    tzinfo (0.3.32)
+    tzinfo (0.3.33)
     vegas (0.1.11)
       rack (>= 1.0.0)
     xpath (0.1.4)
@@ -179,5 +182,6 @@ DEPENDENCIES
   jasmine (~> 1.1)
   mysql2 (~> 0.3.11)
   quorum!
+  rake (~> 0.9.2)
   resque_spec (~> 0.8)
   rspec-rails (~> 2.6)

data/HISTORY.md

@@ -1,3 +1,12 @@
+## 0.3.2 (2012-06--22)
+
+* Added support for user defined callback in QUORUM.pollResults().
+  Useful if user chooses to define their own view template(s).
+  See app/assets/javascripts/quorum/quorum.js and
+  app/views/quorum/jobs/show.html.erb for more information.
+* JS bug fixes.
+* Added specs and updated gems.
+
 ## 0.3.1 (2012-04-02)
 
 * Added quorum layouts to quorum:views generator.

data/README.rdoc

@@ -1,4 +1,4 @@
-= Quorum
+= Quorum {<img src="https://secure.travis-ci.org/ncgr/quorum.png?branch=master"alt="Build Status" />}[http://travis-ci.org/ncgr/quorum]
 
 A flexible bioinformatics search tool.
 
@@ -9,6 +9,7 @@ bioinformatics search tools.
 
 Dependencies:
 
+* Ruby >= 1.9.2
 * 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)
@@ -162,9 +163,10 @@ 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.
 
-  <tt>remote: true</tt>
-  <tt>ssh_host: remote.machine.org</tt>
-  <tt>ssh_user: remote_user</tt>
+  blast:
+    remote: true
+    ssh_host: remote.machine.org
+    ssh_user: remote_user
 
 Net::SSH.start() optional params (http://net-ssh.github.com/ssh/v2/api/index.html)
 
@@ -224,7 +226,7 @@ To override Quorum's default images, run the generator.
 A copy of Quorum's images can be found in your application under
 "app/assets/images/quorum/".
 
-<b>jQuery UI</b>
+==== jQuery UI
 
 Don't like Quorum's jQuery UI theme? Override it!
 
@@ -233,34 +235,36 @@ Don't like Quorum's jQuery UI theme? Override it!
 * 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".
+==== 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".
 
 For example:
 
 Remove Blastp in "app/views/quorum/jobs/new.html.erb"
 
-  <!-- Search Algorithms -->
-  <!-- Comment out an algorithm below to remove it from the form. -->
+  <%# Search Algorithms %>
+  <%# Comment out an algorithm below to remove it from the form. %>
 
-  <!-- blastn -->
+  <%# blastn %>
   <%= render :partial => "quorum/jobs/form/blastn_form", :locals => {
     :f => f, :blast_dbs => @blast_dbs } %>
 
-  <!-- blastx -->
+  <%# blastx %>
   <%= render :partial => "quorum/jobs/form/blastx_form", :locals => {
     :f => f, :blast_dbs => @blast_dbs } %>
 
-  <!-- tblastn -->
+  <%# tblastn %>
   <%= render :partial => "quorum/jobs/form/tblastn_form", :locals => {
     :f => f, :blast_dbs => @blast_dbs } %>
 
-  <!-- blastp -->
+  <%# blastp %>
   <% render :partial => "quorum/jobs/form/blastp_form", :locals => {
     :f => f, :blast_dbs => @blast_dbs } %>
 
-  <!-- End Search Algorithms -->
+  <%# End Search Algorithms %>
 
 Remove Blastp in "app/views/quorum/jobs/show.html.erb"
 
@@ -269,12 +273,12 @@ Remove Blastp in "app/views/quorum/jobs/show.html.erb"
       <li><a href="#tabs-1">Blastn</a></li>
       <li><a href="#tabs-2">Blastx</a></li>
       <li><a href="#tabs-3">Tblastn</a></li>
-      <!--
+      <%#
       <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">
@@ -306,6 +310,12 @@ Remove Blastp in "app/views/quorum/jobs/show.html.erb"
     -->
   </div>
 
+==== Don't like Quorum's default show template?
+
+Override Quorum's views and specify your own JavaScript callback function!
+
+See "app/views/quorum/show.html.erb" for more details.
+
 === Redis
 
 For detailed Redis installation instructions, follow the links below.
@@ -321,7 +331,7 @@ the link below.
 
 * Resque (https://github.com/defunkt/resque)
 
-<b>Resque Web Interface</b>
+==== Resque Web Interface
 
 Quorum mounts Resque's web interface by default via
 

data/Rakefile

@@ -29,3 +29,54 @@ task :default => :spec
 
 Bundler::GemHelper.install_tasks
 
+# Travis Tasks
+namespace :travis do
+  # Specs
+  task :spec do
+    Rake::Task["travis:create_dirs"].execute
+    ["rake spec", "rake app:jasmine:ci JASMINE_PORT=53331"].each do |cmd|
+      puts "Starting to run #{cmd}..."
+      system("export DISPLAY=:99.0 && bundle exec #{cmd}")
+      raise "#{cmd} failed!" unless $?.exitstatus == 0
+    end
+    Rake::Task["travis:remove_db_config"].execute
+  end
+
+  # Create spec/dummy/config/database.yml for Travis.
+  task :create_db_config do
+    config = File.expand_path("../spec/dummy/config", __FILE__)
+    File.open(File.join(config, "database.yml"), "w+") do |file|
+      file.puts "test:\n  adapter: mysql2\n  database: quorum_test\n" <<
+      "  username: root\n  password:\n  host: localhost\n  encoding: utf8"
+    end
+  end
+
+  # Remove spec/dummy/config/database.yml after Travis.
+  task :remove_db_config do
+    config = File.expand_path("../spec/dummy/config", __FILE__)
+    File.delete(File.join(config, "database.yml"))
+  end
+
+  # Create necessary directories for test. Mimic a real app install
+  # via rails g quorum:install.
+  #
+  # The directories below are not in the git repo.
+  task :create_dirs do
+    app    = File.expand_path("../spec/dummy", __FILE__)
+    quorum = File.expand_path("../spec/dummy/quorum", __FILE__)
+
+    app_tmp   = File.join(app, "tmp")
+    app_pids  = File.join(app_tmp, "pids")
+    app_cache = File.join(app_tmp, "cache")
+
+    Dir.mkdir(app_tmp) unless File.directory?(app_tmp)
+    Dir.mkdir(app_pids) unless File.directory?(app_pids)
+    Dir.mkdir(app_cache) unless File.directory?(app_cache)
+
+    quorum_log = File.join(quorum, "log")
+    quorum_tmp = File.join(quorum, "tmp")
+
+    Dir.mkdir(quorum_log) unless File.directory?(quorum_log)
+    Dir.mkdir(quorum_tmp) unless File.directory?(quorum_tmp)
+  end
+end

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

@@ -59,6 +59,10 @@ $(function() {
     form.autoHint('removeHints');
   });
 
+  $(window).unload(function() {
+    $('input[type=submit]', 'form').val('Submit').removeAttr('disabled');
+  });
+
   // Reset form.
   $('#quorum_job_reset').click(function() {
     $('textarea').val('');