quorum 0.1.0

data/spec/requests/jobs_spec.rb

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+require 'spec_helper'
+
+describe "Jobs" do
+  describe "GET /" do
+    it "redirects to new" do
+      visit jobs_path
+      current_path.should eq(new_job_path)
+    end
+  end
+
+  describe "submit empty form" do
+    it "displays error and renders form" do
+      visit new_job_path
+      current_path.should eq(new_job_path)
+
+      fill_in "job_sequence", :with => ""
+      click_button "Submit"
+
+      page.should have_content("Please enter your sequence(s) in Plain Text " << 
+        "as FASTA.")
+    end
+  end
+
+  describe "submit sequences in Word file" do
+    it "displays error and renders form" do
+      visit new_job_path
+      current_path.should eq(new_job_path)
+
+      word_file = File.expand_path("../../data/seqs.docx", __FILE__)
+      attach_file "job_sequence_file", word_file
+      click_button "Submit"
+      page.should have_content("Please enter your sequence(s) in Plain Text " << 
+        "as FASTA.")
+    end
+  end
+
+  describe "submit sequences not in FASTA format" do
+    it "displays error and renders form" do
+      visit new_job_path
+      current_path.should eq(new_job_path)
+
+      file = File.expand_path("../../data/seqs_not_fa.txt", __FILE__)
+      attach_file "job_sequence_file", file
+      click_button "Submit"
+      page.should have_content("Please enter your sequence(s) in Plain Text " << 
+        "as FASTA.")
+    end
+  end
+
+  context "javascript", @javascript do
+    before(:all) do
+      Capybara.current_driver = :selenium
+    end
+    describe "submit sequences in attached file" do
+	    it "check Blast algorithms, fill in default values and view query results" do
+	      visit new_job_path
+	      current_path.should eq(new_job_path)
+	
+	      nucl_seqs = File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
+	      attach_file "job_sequence_file", nucl_seqs
+	
+        # Blastn
+	      check "job_blastn_job_attributes_queue"
+	      select "tmp", :from => "job_blastn_job_attributes_blast_dbs" 
+        check "job_blastn_job_attributes_filter"
+        fill_in "job_blastn_job_attributes_expectation", :with => "5e-20"
+        fill_in "job_blastn_job_attributes_min_bit_score", :with => "0"
+        fill_in "job_blastn_job_attributes_max_score", :with => "25"
+        select "Yes", :from => "job_blastn_job_attributes_gapped_alignments"
+        select "11, 2", :from => "job_blastn_job_attributes_gap_opening_extension"
+	
+        # Blastx
+	      check "job_blastx_job_attributes_queue"
+	      select "tmp", :from => "job_blastx_job_attributes_blast_dbs" 
+        check "job_blastx_job_attributes_filter"
+        fill_in "job_blastx_job_attributes_expectation", :with => "5e-20"
+        fill_in "job_blastx_job_attributes_min_bit_score", :with => "0"
+        fill_in "job_blastx_job_attributes_max_score", :with => "25"
+        select "Yes", :from => "job_blastx_job_attributes_gapped_alignments"
+        select "10, 2", :from => "job_blastx_job_attributes_gap_opening_extension"
+	
+	      # Tblastn
+	      check "job_tblastn_job_attributes_queue"
+	      select "tmp", :from => "job_tblastn_job_attributes_blast_dbs" 
+        check "job_tblastn_job_attributes_filter"
+        fill_in "job_tblastn_job_attributes_expectation", :with => "5e-20"
+        fill_in "job_tblastn_job_attributes_min_bit_score", :with => "0"
+        fill_in "job_tblastn_job_attributes_max_score", :with => "25"
+        select "Yes", :from => "job_tblastn_job_attributes_gapped_alignments"
+        select "9, 2", :from => "job_tblastn_job_attributes_gap_opening_extension"
+	
+	      # Blastp
+	      check "job_blastp_job_attributes_queue"
+	      select "tmp", :from => "job_blastp_job_attributes_blast_dbs" 
+        check "job_blastp_job_attributes_filter"
+        fill_in "job_blastp_job_attributes_expectation", :with => "5e-20"
+        fill_in "job_blastp_job_attributes_min_bit_score", :with => "0"
+        fill_in "job_blastp_job_attributes_max_score", :with => "25"
+        select "Yes", :from => "job_blastp_job_attributes_gapped_alignments"
+        select "13, 1", :from => "job_blastp_job_attributes_gap_opening_extension"
+	
+	      click_button "Submit"
+	
+	      page.should have_content("Search Results") 
+        
+        click_link "Blastx"
+	      page.should have_content("Your search returned 0 hits.") 
+
+        click_link "Tblastn"
+	      page.should have_content("Your search returned 0 hits.") 
+
+        click_link "Blastn"
+	      find("#blastn-results").find("td a").click
+        page.should have_content("Quorum Report Details")
+        page.should have_content("qseq")
+        page.should have_content("hseq")
+
+        click_link "Blastp"
+	      find("#blastp-results").find("td a").click
+        page.should have_content("Quorum Report Details")
+        page.should have_content("qseq")
+        page.should have_content("hseq")
+	    end
+    end
+    after(:all) do
+      Capybara.use_default_driver
+    end
+  end
+
+  describe "GET /quorum/jobs/unknown_id" do
+    it "displays notice and renders form" 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
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,45 @@
+# This file is copied to spec/ when you run 'rails generate rspec:install'
+ENV["RAILS_ENV"] ||= 'test'
+require File.expand_path("../dummy/config/environment.rb", __FILE__)
+require 'rspec/rails'
+require 'capybara/rspec'
+require 'factory_girl'
+require 'database_cleaner'
+
+FactoryGirl.definition_file_paths << File.join(File.dirname(__FILE__), 'factories')
+FactoryGirl.find_definitions
+
+ENGINE_RAILS_ROOT = File.expand_path("../../", __FILE__)
+
+# Requires supporting ruby files with custom matchers and macros, etc,
+# in spec/support/ and its subdirectories.
+Dir[Rails.root.join("spec/support/**/*.rb")].each {|f| require f}
+
+RSpec.configure do |config|
+  config.mock_with :rspec
+  config.use_transactional_fixtures = false
+  config.include Capybara::DSL, :example_group => { :file_path => /\bspec\/requests\// }
+
+  # This will include the routing helpers in the specs so that we can use
+  # quorum_path, etc., to get to the routes.
+  config.include Quorum::Engine.routes.url_helpers
+
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.filter_run :focus => true
+  config.run_all_when_everything_filtered = true
+
+  ## DatabaseCleaner ##
+  DatabaseCleaner.logger = Rails.logger
+  config.before(:suite) do
+    DatabaseCleaner.strategy = :truncation
+    DatabaseCleaner.clean_with(:truncation)
+  end
+
+  config.before(:each) do
+    DatabaseCleaner.start
+  end
+
+  config.after(:each) do
+    DatabaseCleaner.clean
+  end
+end

data/spec/tasks/blastdb_rake_spec.rb

@@ -0,0 +1,119 @@
+require 'spec_helper'
+require 'tasks/blastdb/build_blast_db'
+
+describe "blastdb rake tasks" do
+  describe "rake quorum:blastdb:build" do
+    before(:each) do
+      # Set args as though we executed the rake task.
+      @args = {
+        :dir         => File.expand_path("../../data/tmp",  __FILE__),
+        :empty       => false,
+        :type        => "both",
+        :prot_file   => "peptides.fa",
+        :nucl_file   => "contigs.fa",
+        :rebuild_db  => true,
+        :blastdb_dir => File.expand_path(
+          "../../dummy/quorum/blastdb", __FILE__
+        ),
+        :gff_dir     => File.expand_path(
+          "../../dummy/quorum/gff3", __FILE__
+        ),
+        :log_dir     => File.expand_path(
+          "../../dummy/quorum/log", __FILE__
+        )
+      }
+    end
+    
+    it "raises exception without DIR argument" do
+      expect {
+        Quorum::BuildBlastDB.new({}).build_blast_db_data
+      }.to raise_error(
+        RuntimeError, 
+        'DIR must be set to continue. Execute `rake -D` for more information.'
+      )
+    end
+
+    it "raises exception with unknown TYPE" do
+      @args[:type] = "unknown"
+      expect {
+        Quorum::BuildBlastDB.new(@args).build_blast_db_data
+      }.to raise_error(
+        RuntimeError, 
+        "Unknown type: #{@args[:type]}. Please provide one: both, nucl or prot."
+      )
+    end
+
+    it "raise exception with unknown directory" do
+      @args[:dir] = "foo_bar_baz"
+      @build = Quorum::BuildBlastDB.new(@args)
+      expect {
+        @build.build_blast_db_data
+        @build.stub(:check_dependencies)
+        @build.stub(:make_directories)
+      }.to raise_error(
+        RuntimeError,
+        "Directory not found: foo_bar_baz"
+      )
+    end
+
+    it "raise exception without correct data directory" do
+      @args[:dir] = File.dirname( __FILE__)
+      @build = Quorum::BuildBlastDB.new(@args)
+      expect {
+        @build.build_blast_db_data
+        @build.stub(:check_dependencies)
+        @build.stub(:make_directories)
+      }.to raise_error(
+        RuntimeError,
+        "Data not found. Please check your directory and try again.\n" <<
+        "Directory Entered: #{File.dirname(__FILE__)}"
+      )
+    end
+
+    it "creates directories and ignores makeblastdb if empty is true" do
+      # Suppress printing to STDOUT.
+      output = double("IO")
+      output.stub(:puts)
+      output.stub(:print)
+
+      @args[:empty] = true
+      @build = Quorum::BuildBlastDB.new(@args, output)
+
+      expect {
+        @build.build_blast_db_data 
+      }.to_not raise_error
+
+      File.directory?(@args[:blastdb_dir]).should be_true
+      File.directory?(@args[:gff_dir]).should be_true
+    end
+
+    it "builds Blast database with valid arguments" do
+      # Suppress printing to STDOUT.
+      output = double("IO")
+      output.stub(:puts)
+      output.stub(:print)
+
+      @args[:empty] = false
+      @build = Quorum::BuildBlastDB.new(@args, output)
+      
+      expect {
+        @build.build_blast_db_data
+      }.to_not raise_error
+
+      ## Make sure build_blast_db_data created files and directories ##
+
+      Dir.glob(@args[:blastdb_dir]).length.should be > 0
+
+      File.exists?(
+        File.join(@args[:blastdb_dir], "test", "contigs.fa")
+      ).should be_true
+
+      File.exists?(
+        File.join(@args[:blastdb_dir], "test", "peptides.fa")
+      ).should be_true
+
+      File.directory?(@args[:gff_dir]).should be_true
+    end
+  end
+end
+

data/spec/templates/blast_spec.rb

@@ -0,0 +1,8 @@
+require 'spec_helper'
+require 'generators/templates/blast'
+
+# Let the request specs handle Quorum::SearchTools
+describe "Quorum::SearchTools::Blast" do
+  describe "#execute_blast" do
+  end
+end

data/spec/templates/logger_spec.rb

@@ -0,0 +1,35 @@
+require 'spec_helper'
+require 'generators/templates/logger'
+
+describe "Quorum::Logger" do
+  describe "#log" do
+    before(:all) do
+      @args   = File.join(::Rails.root.to_s, "log") 
+      @logger = Quorum::Logger.new(@args)
+    end
+
+    it "records program and message in a log file" do
+      @logger.log("RSpec", "This is a test.")
+
+      File.size(
+        File.join(@args, "quorum.log")
+      ).should be > 0
+
+      `rm #{File.join(@args, "quorum.log")}`
+    end
+
+    it "records program, message, exits and removes files" do
+      lambda {
+        @logger.log(
+          "RSpec", "This is a test.", 1, 
+          File.join(@args, "quorum.log")
+        )
+      }.should raise_error(SystemExit)
+
+      File.exists?(
+        File.join(@args, "quorum.log")
+      ).should be_false
+
+    end
+  end  
+end

data/vendor/assets/javascripts/jquery.tipsy.js

@@ -0,0 +1,241 @@
+// tipsy, facebook style tooltips for jquery
+// version 1.0.0a
+// (c) 2008-2010 jason frame [jason@onehackoranother.com]
+// released under the MIT license
+
+(function($) {
+    
+    function maybeCall(thing, ctx) {
+        return (typeof thing == 'function') ? (thing.call(ctx)) : thing;
+    };
+    
+    function Tipsy(element, options) {
+        this.$element = $(element);
+        this.options = options;
+        this.enabled = true;
+        this.fixTitle();
+    };
+    
+    Tipsy.prototype = {
+        show: function() {
+            var title = this.getTitle();
+            if (title && this.enabled) {
+                var $tip = this.tip();
+                
+                $tip.find('.tipsy-inner')[this.options.html ? 'html' : 'text'](title);
+                $tip[0].className = 'tipsy'; // reset classname in case of dynamic gravity
+                $tip.remove().css({top: 0, left: 0, visibility: 'hidden', display: 'block'}).prependTo(document.body);
+                
+                var pos = $.extend({}, this.$element.offset(), {
+                    width: this.$element[0].offsetWidth,
+                    height: this.$element[0].offsetHeight
+                });
+                
+                var actualWidth = $tip[0].offsetWidth,
+                    actualHeight = $tip[0].offsetHeight,
+                    gravity = maybeCall(this.options.gravity, this.$element[0]);
+                
+                var tp;
+                switch (gravity.charAt(0)) {
+                    case 'n':
+                        tp = {top: pos.top + pos.height + this.options.offset, left: pos.left + pos.width / 2 - actualWidth / 2};
+                        break;
+                    case 's':
+                        tp = {top: pos.top - actualHeight - this.options.offset, left: pos.left + pos.width / 2 - actualWidth / 2};
+                        break;
+                    case 'e':
+                        tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth - this.options.offset};
+                        break;
+                    case 'w':
+                        tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width + this.options.offset};
+                        break;
+                }
+                
+                if (gravity.length == 2) {
+                    if (gravity.charAt(1) == 'w') {
+                        tp.left = pos.left + pos.width / 2 - 15;
+                    } else {
+                        tp.left = pos.left + pos.width / 2 - actualWidth + 15;
+                    }
+                }
+                
+                $tip.css(tp).addClass('tipsy-' + gravity);
+                $tip.find('.tipsy-arrow')[0].className = 'tipsy-arrow tipsy-arrow-' + gravity.charAt(0);
+                if (this.options.className) {
+                    $tip.addClass(maybeCall(this.options.className, this.$element[0]));
+                }
+                
+                if (this.options.fade) {
+                    $tip.stop().css({opacity: 0, display: 'block', visibility: 'visible'}).animate({opacity: this.options.opacity});
+                } else {
+                    $tip.css({visibility: 'visible', opacity: this.options.opacity});
+                }
+            }
+        },
+        
+        hide: function() {
+            if (this.options.fade) {
+                this.tip().stop().fadeOut(function() { $(this).remove(); });
+            } else {
+                this.tip().remove();
+            }
+        },
+        
+        fixTitle: function() {
+            var $e = this.$element;
+            if ($e.attr('title') || typeof($e.attr('original-title')) != 'string') {
+                $e.attr('original-title', $e.attr('title') || '').removeAttr('title');
+            }
+        },
+        
+        getTitle: function() {
+            var title, $e = this.$element, o = this.options;
+            this.fixTitle();
+            var title, o = this.options;
+            if (typeof o.title == 'string') {
+                title = $e.attr(o.title == 'title' ? 'original-title' : o.title);
+            } else if (typeof o.title == 'function') {
+                title = o.title.call($e[0]);
+            }
+            title = ('' + title).replace(/(^\s*|\s*$)/, "");
+            return title || o.fallback;
+        },
+        
+        tip: function() {
+            if (!this.$tip) {
+                this.$tip = $('<div class="tipsy"></div>').html('<div class="tipsy-arrow"></div><div class="tipsy-inner"></div>');
+            }
+            return this.$tip;
+        },
+        
+        validate: function() {
+            if (!this.$element[0].parentNode) {
+                this.hide();
+                this.$element = null;
+                this.options = null;
+            }
+        },
+        
+        enable: function() { this.enabled = true; },
+        disable: function() { this.enabled = false; },
+        toggleEnabled: function() { this.enabled = !this.enabled; }
+    };
+    
+    $.fn.tipsy = function(options) {
+        
+        if (options === true) {
+            return this.data('tipsy');
+        } else if (typeof options == 'string') {
+            var tipsy = this.data('tipsy');
+            if (tipsy) tipsy[options]();
+            return this;
+        }
+        
+        options = $.extend({}, $.fn.tipsy.defaults, options);
+        
+        function get(ele) {
+            var tipsy = $.data(ele, 'tipsy');
+            if (!tipsy) {
+                tipsy = new Tipsy(ele, $.fn.tipsy.elementOptions(ele, options));
+                $.data(ele, 'tipsy', tipsy);
+            }
+            return tipsy;
+        }
+        
+        function enter() {
+            var tipsy = get(this);
+            tipsy.hoverState = 'in';
+            if (options.delayIn == 0) {
+                tipsy.show();
+            } else {
+                tipsy.fixTitle();
+                setTimeout(function() { if (tipsy.hoverState == 'in') tipsy.show(); }, options.delayIn);
+            }
+        };
+        
+        function leave() {
+            var tipsy = get(this);
+            tipsy.hoverState = 'out';
+            if (options.delayOut == 0) {
+                tipsy.hide();
+            } else {
+                setTimeout(function() { if (tipsy.hoverState == 'out') tipsy.hide(); }, options.delayOut);
+            }
+        };
+        
+        if (!options.live) this.each(function() { get(this); });
+        
+        if (options.trigger != 'manual') {
+            var binder   = options.live ? 'live' : 'bind',
+                eventIn  = options.trigger == 'hover' ? 'mouseenter' : 'focus',
+                eventOut = options.trigger == 'hover' ? 'mouseleave' : 'blur';
+            this[binder](eventIn, enter)[binder](eventOut, leave);
+        }
+        
+        return this;
+        
+    };
+    
+    $.fn.tipsy.defaults = {
+        className: null,
+        delayIn: 0,
+        delayOut: 0,
+        fade: false,
+        fallback: '',
+        gravity: 'n',
+        html: false,
+        live: false,
+        offset: 0,
+        opacity: 0.8,
+        title: 'title',
+        trigger: 'hover'
+    };
+    
+    // Overwrite this method to provide options on a per-element basis.
+    // For example, you could store the gravity in a 'tipsy-gravity' attribute:
+    // return $.extend({}, options, {gravity: $(ele).attr('tipsy-gravity') || 'n' });
+    // (remember - do not modify 'options' in place!)
+    $.fn.tipsy.elementOptions = function(ele, options) {
+        return $.metadata ? $.extend({}, options, $(ele).metadata()) : options;
+    };
+    
+    $.fn.tipsy.autoNS = function() {
+        return $(this).offset().top > ($(document).scrollTop() + $(window).height() / 2) ? 's' : 'n';
+    };
+    
+    $.fn.tipsy.autoWE = function() {
+        return $(this).offset().left > ($(document).scrollLeft() + $(window).width() / 2) ? 'e' : 'w';
+    };
+    
+    /**
+     * yields a closure of the supplied parameters, producing a function that takes
+     * no arguments and is suitable for use as an autogravity function like so:
+     *
+     * @param margin (int) - distance from the viewable region edge that an
+     *        element should be before setting its tooltip's gravity to be away
+     *        from that edge.
+     * @param prefer (string, e.g. 'n', 'sw', 'w') - the direction to prefer
+     *        if there are no viewable region edges effecting the tooltip's
+     *        gravity. It will try to vary from this minimally, for example,
+     *        if 'sw' is preferred and an element is near the right viewable 
+     *        region edge, but not the top edge, it will set the gravity for
+     *        that element's tooltip to be 'se', preserving the southern
+     *        component.
+     */
+     $.fn.tipsy.autoBounds = function(margin, prefer) {
+    return function() {
+      var dir = {ns: prefer[0], ew: (prefer.length > 1 ? prefer[1] : false)},
+          boundTop = $(document).scrollTop() + margin,
+          boundLeft = $(document).scrollLeft() + margin,
+          $this = $(this);
+
+      if ($this.offset().top < boundTop) dir.ns = 'n';
+      if ($this.offset().left < boundLeft) dir.ew = 'w';
+      if ($(window).width() + $(document).scrollLeft() - $this.offset().left < margin) dir.ew = 'e';
+      if ($(window).height() + $(document).scrollTop() - $this.offset().top < margin) dir.ns = 's';
+
+      return dir.ns + (dir.ew ? dir.ew : '');
+    }
+  };
+    
+})(jQuery);

data/vendor/assets/javascripts/underscore-min.js

@@ -0,0 +1,30 @@
+// Underscore.js 1.2.2
+// (c) 2011 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
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