quorum 0.2.1 → 0.3.0

data/spec/javascripts/quorum_spec.js

@@ -0,0 +1,106 @@
+//
+// Test the methods not covered in RSpec request specs.
+//
+
+describe("QUORUM", function() {
+
+  // 
+  // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
+  //
+  // Blastn should increment qseq's title by 1 and hseq's title by 1.
+  //
+  it("formats blastn sequence report for Blast detailed report", function() {
+    var report = QUORUM.formatSequenceReport(
+      "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastn"  
+    );
+    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=7>C</a><a rel='quorum-tipsy' title=8>G</a><a rel='quorum-tipsy' title=9>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
+  });
+
+  // 
+  // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
+  //
+  // Blastx should increment qseq's title by 3 and hseq's title by 1.
+  //
+  it("formats blastx sequence report for Blast detailed report", function() {
+    var report = QUORUM.formatSequenceReport(
+      "ACGT", "|| |", "ACCT", 6, 9, 2, 8, "blastx"  
+    );
+    expect(report).toEqual("<p class='small'>Alignment (Mouse over for positions):</p><span class='small'><pre>\nqseq <a rel='quorum-tipsy' title=6>A</a><a rel='quorum-tipsy' title=9>C</a><a rel='quorum-tipsy' title=12>G</a><a rel='quorum-tipsy' title=15>T</a>\n     || |\nhseq <a rel='quorum-tipsy' title=2>A</a><a rel='quorum-tipsy' title=3>C</a><a rel='quorum-tipsy' title=4>C</a><a rel='quorum-tipsy' title=5>T</a>\n\n</pre></span>");
+  });
+
+  // 
+  // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
+  //
+  // Tblastn should increment qseq's title by 1 and hseq's title by 3.
+  //
+  it("formats tblastn sequence report for Blast detailed report", function() {
+    var report = QUORUM.formatSequenceReport(
+      "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 136, "tblastn"  
+    );
+    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=124>L</a><a rel='quorum-tipsy' title=127>V</a><a rel='quorum-tipsy' title=130>I</a><a rel='quorum-tipsy' title=133>S</a>\n\n</pre></span>");
+  });
+
+  // 
+  // Spec covers QUORUM.formatSequenceReport & QUORUM.addBaseTitleIndex.
+  //
+  // Blastp should increment qseq's title by 1 and hseq's title by 1.
+  //
+  it("formats blastx sequence report for Blast detailed report", function() {
+    var report = QUORUM.formatSequenceReport(
+      "ELVIS", "ELVIS", "ELVIS", 10, 14, 121, 125, "blastp"  
+    );
+    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>");
+  });
+
+  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' });
+
+    $('a[rel=quorum-tipsy]').trigger('mouseover');
+    expect($('.tipsy')).toBeVisible();
+
+    $('a[rel=quorum-tipsy]').trigger('mouseout');
+    expect($('.tipsy')).not.toBeVisible();
+  });
+
+  it("prints hit strand as forward / forward for + / + intergers", function() {
+    expect(QUORUM.formatStrand(1, 1)).toEqual("forward / forward");
+  }); 
+
+  it("prints hit strand as forward / reverse for + / - integers", function() {
+    expect(QUORUM.formatStrand(1, -1)).toEqual("forward / reverse");
+  }); 
+
+  it("prints hit strand as reverse / forward for - / + integers", function() {
+    expect(QUORUM.formatStrand(-1, 1)).toEqual("reverse / forward");
+  }); 
+
+  it("prints hit strand as reverse / reverse for - / - integers", function() {
+    expect(QUORUM.formatStrand(-1, -1)).toEqual("reverse / reverse");
+  }); 
+
+  //
+  // 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);
+    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> ");
+  });
+
+  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;
+    QUORUM.openWindow(url, name, width, height);
+    expect(window.open).toHaveBeenCalledWith(url, name, "width=" + width + ",height=" + height + ",scrollbars=yes");
+  });
+
+});

data/spec/javascripts/string_spec.js

@@ -0,0 +1,18 @@
+describe("String", function() {
+
+  it("truncates a string to length n", function() {
+    var str = "this is a long string.";
+    expect(str.trunc(5)).toEqual("this...");    
+  });
+
+  it("truncates a string to length n", function() {
+    var str = "this is a long string.";
+    expect(str.trunc(15)).toEqual("this is a long...");    
+  });
+
+  it("doesn't truncate string when length is less than n", function() {
+    var str = "this is a long string.";
+    expect(str.trunc(50)).toEqual(str);
+  });
+
+});

data/spec/javascripts/support/jasmine.yml

@@ -0,0 +1,84 @@
+# src_files
+#
+# Return an array of filepaths relative to src_dir to include before jasmine specs.
+# Default: []
+#
+# EXAMPLE:
+#
+# src_files:
+#   - lib/source1.js
+#   - lib/source2.js
+#   - dist/**/*.js
+#
+src_files:
+  - spec/javascripts/jquery/jquery.min.js
+  - spec/javascripts/jquery/jquery-ui.min.js
+  - spec/javascripts/jquery/jquery_ujs.js
+  - vendor/assets/javascripts/underscore-min.js
+  - app/assets/javascripts/quorum/jobs.js
+  - app/assets/javascripts/quorum/quorum.js
+  - app/assets/javascripts/quorum/utilities.js
+  - app/assets/javascripts/quorum/template_settings.js
+  - vendor/assets/javascripts/jquery.autohint.js
+  - vendor/assets/javascripts/jquery.tipsy.js
+
+# stylesheets
+#
+# Return an array of stylesheet filepaths relative to src_dir to include before jasmine specs.
+# Default: []
+#
+# EXAMPLE:
+#
+# stylesheets:
+#   - css/style.css
+#   - stylesheets/*.css
+#
+stylesheets:
+
+# helpers
+#
+# Return an array of filepaths relative to spec_dir to include before jasmine specs.
+# Default: ["helpers/**/*.js"]
+#
+# EXAMPLE:
+#
+# helpers:
+#   - helpers/**/*.js
+#
+helpers:
+  - helpers/**/*.js
+
+# spec_files
+#
+# Return an array of filepaths relative to spec_dir to include.
+# Default: ["**/*[sS]pec.js"]
+#
+# EXAMPLE:
+#
+# spec_files:
+#   - **/*[sS]pec.js
+#
+spec_files:
+  - '**/*[sS]pec.js'
+
+# src_dir
+#
+# Source directory path. Your src_files must be returned relative to this path. Will use root if left blank.
+# Default: project root
+#
+# EXAMPLE:
+#
+# src_dir: public
+#
+src_dir:
+
+# spec_dir
+#
+# Spec directory path. Your spec_files must be returned relative to this path.
+# Default: spec/javascripts
+#
+# EXAMPLE:
+#
+# spec_dir: spec/javascripts
+#
+spec_dir: spec/javascripts

data/spec/javascripts/support/jasmine_config.rb

@@ -0,0 +1,23 @@
+module Jasmine
+  class Config
+
+    # Add your overrides or custom config code here
+
+  end
+end
+
+
+# Note - this is necessary for rspec2, which has removed the backtrace
+module Jasmine
+  class SpecBuilder
+    def declare_spec(parent, spec)
+      me = self
+      example_name = spec["name"]
+      @spec_ids << spec["id"]
+      backtrace = @example_locations[parent.description + " " + example_name]
+      parent.it example_name, {} do
+        me.report_spec(spec["id"])
+      end
+    end
+  end
+end

data/spec/javascripts/support/jasmine_runner.rb

@@ -0,0 +1,33 @@
+$:.unshift(ENV['JASMINE_GEM_PATH']) if ENV['JASMINE_GEM_PATH'] # for gem testing purposes
+
+require 'rubygems'
+require File.expand_path("../../../dummy/config/environment", __FILE__)
+require 'jasmine'
+jasmine_config_overrides = File.expand_path(File.join(File.dirname(__FILE__), 'jasmine_config.rb'))
+require jasmine_config_overrides if File.exist?(jasmine_config_overrides)
+if Jasmine::Dependencies.rspec2?
+  require 'rspec'
+else
+  require 'spec'
+end
+
+jasmine_config = Jasmine::Config.new
+spec_builder = Jasmine::SpecBuilder.new(jasmine_config)
+
+should_stop = false
+
+if Jasmine::Dependencies.rspec2?
+  RSpec.configuration.after(:suite) do
+    spec_builder.stop if should_stop
+  end
+else
+  Spec::Runner.configure do |config|
+    config.after(:suite) do
+      spec_builder.stop if should_stop
+    end
+  end
+end
+
+spec_builder.start
+should_stop = true
+spec_builder.declare_suites

data/spec/requests/jobs_spec.rb

@@ -17,7 +17,7 @@ describe "Jobs" do
       click_button "Submit"
 
       page.should have_content("Please enter your sequence(s) in Plain Text " << 
-        "as FASTA.")
+                               "as FASTA.")
     end
   end
 
@@ -30,7 +30,7 @@ describe "Jobs" do
       attach_file "job_sequence_file", word_file
       click_button "Submit"
       page.should have_content("Please enter your sequence(s) in Plain Text " << 
-        "as FASTA.")
+                               "as FASTA.")
     end
   end
 
@@ -43,7 +43,7 @@ describe "Jobs" do
       attach_file "job_sequence_file", file
       click_button "Submit"
       page.should have_content("Please enter your sequence(s) in Plain Text " << 
-        "as FASTA.")
+                               "as FASTA.")
     end
   end
 
@@ -56,71 +56,72 @@ describe "Jobs" do
       ResqueSpec.inline = true
     end
     describe "submit sequences in attached file" do
-	    it "check algorithms, fill in values, view results and download hit sequence" 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
-	
+      it "check algorithms, fill in values, view results and download hit sequence" 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_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_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" 
+
+        # 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" 
+
+        # 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_button "Submit"
+
+        page.should have_content("Search Results") 
+
         click_link "Blastx"
-	      page.should have_content("Your search returned 0 hits.") 
+        page.should have_content("Your search returned 0 hits.") 
 
         click_link "Tblastn"
-	      page.should have_content("Your search returned 0 hits.") 
+        page.should have_content("Your search returned 0 hits.") 
 
         ## Interact with the Blast results. ##
         click_link "Blastn"
 
         # Render modal box.
-	      find("#blastn-results").find("td a").click
+        find("#blastn-results").find("td a").click
         page.should have_content("Quorum Report Details")
         page.should have_content("qseq")
         page.should have_content("hseq")
+
         # Download sequence
         find("p.small a#download_sequence_1").click
         page.should have_content("Fetching sequence...")
@@ -129,11 +130,11 @@ describe "Jobs" do
         click_link "Blastp"
 
         # Render modal box.
-	      find("#blastp-results").find("td a").click
+        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
     end
     after(:all) do
       Capybara.use_default_driver

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

@@ -0,0 +1,87 @@
+//
+// jQuery autoHint
+//
+// v0.2.0
+// Ken Seal hunzinker@gmail.com
+// License: MIT
+
+(function($) {
+
+  var methods = {
+  
+    init: function() {
+      return this.each(function() {
+        var $this = $(this);
+        $this.autoHint('addHints');
+        $this.autoHint('focusHint');
+        $this.autoHint('blurHint');
+      });
+    },
+
+    // Add hints to the form elements.
+    addHints: function() {
+      return this.each(function() {
+        var $this = $(this);
+        if ($this.attr('title') === '') { 
+          return; 
+        }
+
+        if ($this.val() === '') { 
+          $this.val($this.attr('title')); 
+
+          if (!$this.hasClass('auto-hint')) {
+            $this.addClass('auto-hint');
+          }
+        } else { 
+          $this.removeClass('auto-hint'); 
+        }
+      });          
+    },
+
+    // Remove hint and class on focus.
+    focusHint: function() {
+      return this.focus(function() {
+        var $this = $(this);
+        if ($this.val() === $this.attr('title')) {
+          $this.val('');
+          $this.removeClass('auto-hint');
+        }
+      });               
+    },
+
+    // Retain value or add hint.
+    blurHint: function() {
+      return this.blur(function() {
+        var $this = $(this);
+        if ($this.val() === '' && $this.attr('title') !== '') {
+          $this.val($this.attr('title'));
+          $this.addClass('auto-hint');
+        }
+      });     
+    },
+    
+    // Remove hints.
+    removeHints: function() {
+      return this.each(function() {
+        var $this = $(this);
+        if ($this.val() === $this.attr('title')) { 
+          $this.val(''); 
+        }     
+      });                      
+    }
+
+  };
+
+  $.fn.autoHint = function(method) {
+
+    if (methods[method]) {
+      return methods[method].apply(this, Array.prototype.slice.call(arguments, 1));
+    } else if (typeof method === 'object' || !method) {
+      return methods.init.apply(this, arguments);
+    } else {
+      $.error('Method ' +  method + ' does not exist for jQuery autoHint.');
+    }      
+
+  };
+
+})(jQuery);