quorum 0.3.0 → 0.3.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (56) hide show
  1. data/Gemfile.lock +58 -58
  2. data/HISTORY.md +4 -0
  3. data/README.rdoc +31 -31
  4. data/app/assets/javascripts/quorum/jobs.js +2 -2
  5. data/app/assets/javascripts/quorum/quorum.js +55 -55
  6. data/app/assets/stylesheets/quorum/application.css +23 -23
  7. data/app/assets/stylesheets/quorum/jquery-ui-1.8.16.custom.css +5 -5
  8. data/app/controllers/quorum/jobs_controller.rb +7 -7
  9. data/app/models/quorum/blastn_job.rb +1 -1
  10. data/app/models/quorum/blastp_job.rb +1 -1
  11. data/app/models/quorum/blastx_job.rb +1 -1
  12. data/app/models/quorum/job.rb +19 -19
  13. data/app/models/quorum/tblastn_job.rb +1 -1
  14. data/app/views/quorum/jobs/form/_blastn_form.html.erb +7 -7
  15. data/app/views/quorum/jobs/form/_blastp_form.html.erb +7 -7
  16. data/app/views/quorum/jobs/form/_blastx_form.html.erb +7 -7
  17. data/app/views/quorum/jobs/form/_tblastn_form.html.erb +7 -7
  18. data/app/views/quorum/jobs/new.html.erb +9 -9
  19. data/app/views/quorum/jobs/show.html.erb +7 -7
  20. data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb +3 -3
  21. data/app/views/quorum/jobs/templates/_blast_template.html.erb +4 -4
  22. data/lib/generators/quorum/install_generator.rb +3 -3
  23. data/lib/generators/quorum/views_generator.rb +7 -6
  24. data/lib/generators/templates/README +3 -3
  25. data/lib/generators/templates/blast.rb +7 -7
  26. data/lib/generators/templates/blast_db.rb +6 -6
  27. data/lib/generators/templates/fetch +3 -3
  28. data/lib/generators/templates/quorum_initializer.rb +1 -1
  29. data/lib/generators/templates/quorum_settings.yml +1 -1
  30. data/lib/generators/templates/search +8 -8
  31. data/lib/generators/templates/trollop.rb +4 -4
  32. data/lib/quorum/sequence.rb +6 -6
  33. data/lib/quorum/version.rb +1 -1
  34. data/lib/quorum.rb +1 -1
  35. data/lib/tasks/blastdb/build_blast_db.rb +7 -7
  36. data/lib/tasks/quorum_tasks.rake +6 -6
  37. data/lib/workers/quorum.rb +2 -2
  38. data/quorum.gemspec +1 -1
  39. data/spec/dummy/quorum/blastdb/test.nin +0 -0
  40. data/spec/dummy/quorum/blastdb/test.pin +0 -0
  41. data/spec/javascripts/fixtures/quorum_search_form.html +8 -8
  42. data/spec/javascripts/quorum_spec.js +12 -12
  43. data/spec/javascripts/string_spec.js +2 -2
  44. data/spec/models/blastn_job_report_spec.rb +3 -3
  45. data/spec/models/blastp_job_report_spec.rb +3 -3
  46. data/spec/models/blastx_job_report_spec.rb +3 -3
  47. data/spec/models/job_spec.rb +1 -1
  48. data/spec/models/tblastn_job_report_spec.rb +3 -3
  49. data/spec/quorum/quorum_sequence_spec.rb +1 -1
  50. data/spec/requests/jobs_spec.rb +12 -11
  51. data/spec/spec_helper.rb +1 -1
  52. data/spec/tasks/blastdb_rake_spec.rb +5 -5
  53. data/spec/templates/blast_spec.rb +5 -5
  54. data/vendor/assets/javascripts/jquery.autohint.js +16 -16
  55. data/vendor/assets/javascripts/jquery.tipsy.js +33 -33
  56. metadata +96 -31
@@ -8,7 +8,7 @@
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  (function($) {
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  var methods = {
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-
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+
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  init: function() {
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  return this.each(function() {
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  var $this = $(this);
@@ -22,20 +22,20 @@
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  addHints: function() {
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  return this.each(function() {
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  var $this = $(this);
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- if ($this.attr('title') === '') {
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- return;
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+ if ($this.attr('title') === '') {
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+ return;
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  }
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- if ($this.val() === '') {
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- $this.val($this.attr('title'));
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+ if ($this.val() === '') {
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+ $this.val($this.attr('title'));
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  if (!$this.hasClass('auto-hint')) {
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  $this.addClass('auto-hint');
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  }
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- } else {
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- $this.removeClass('auto-hint');
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+ } else {
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+ $this.removeClass('auto-hint');
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  }
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- });
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+ });
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  },
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  // Remove hint and class on focus.
@@ -46,7 +46,7 @@
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  $this.val('');
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  $this.removeClass('auto-hint');
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  }
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- });
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+ });
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  },
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  // Retain value or add hint.
@@ -57,17 +57,17 @@
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  $this.val($this.attr('title'));
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  $this.addClass('auto-hint');
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  }
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- });
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+ });
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  },
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-
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+
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  // Remove hints.
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  removeHints: function() {
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  return this.each(function() {
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  var $this = $(this);
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- if ($this.val() === $this.attr('title')) {
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- $this.val('');
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- }
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- });
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+ if ($this.val() === $this.attr('title')) {
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+ $this.val('');
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+ }
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+ });
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  }
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  };
@@ -80,7 +80,7 @@
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  return methods.init.apply(this, arguments);
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  } else {
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  $.error('Method ' + method + ' does not exist for jQuery autoHint.');
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- }
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+ }
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  };
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@@ -4,37 +4,37 @@
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  // released under the MIT license
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  (function($) {
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-
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+
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  function maybeCall(thing, ctx) {
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  return (typeof thing == 'function') ? (thing.call(ctx)) : thing;
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  };
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-
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+
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  function Tipsy(element, options) {
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  this.$element = $(element);
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  this.options = options;
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  this.enabled = true;
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  this.fixTitle();
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  };
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-
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+
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  Tipsy.prototype = {
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  show: function() {
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  var title = this.getTitle();
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  if (title && this.enabled) {
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  var $tip = this.tip();
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-
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+
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  $tip.find('.tipsy-inner')[this.options.html ? 'html' : 'text'](title);
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  $tip[0].className = 'tipsy'; // reset classname in case of dynamic gravity
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  $tip.remove().css({top: 0, left: 0, visibility: 'hidden', display: 'block'}).prependTo(document.body);
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-
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+
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  var pos = $.extend({}, this.$element.offset(), {
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  width: this.$element[0].offsetWidth,
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  height: this.$element[0].offsetHeight
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  });
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-
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+
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  var actualWidth = $tip[0].offsetWidth,
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  actualHeight = $tip[0].offsetHeight,
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  gravity = maybeCall(this.options.gravity, this.$element[0]);
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-
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+
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  var tp;
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  switch (gravity.charAt(0)) {
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  case 'n':
@@ -50,7 +50,7 @@
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  tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width + this.options.offset};
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  break;
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  }
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-
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+
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  if (gravity.length == 2) {
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  if (gravity.charAt(1) == 'w') {
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  tp.left = pos.left + pos.width / 2 - 15;
@@ -58,13 +58,13 @@
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  tp.left = pos.left + pos.width / 2 - actualWidth + 15;
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  }
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  }
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-
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+
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  $tip.css(tp).addClass('tipsy-' + gravity);
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  $tip.find('.tipsy-arrow')[0].className = 'tipsy-arrow tipsy-arrow-' + gravity.charAt(0);
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  if (this.options.className) {
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  $tip.addClass(maybeCall(this.options.className, this.$element[0]));
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  }
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-
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+
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  if (this.options.fade) {
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  $tip.stop().css({opacity: 0, display: 'block', visibility: 'visible'}).animate({opacity: this.options.opacity});
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  } else {
@@ -72,7 +72,7 @@
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  }
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  }
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  },
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-
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  hide: function() {
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  if (this.options.fade) {
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  this.tip().stop().fadeOut(function() { $(this).remove(); });
@@ -80,14 +80,14 @@
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  this.tip().remove();
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  }
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  },
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-
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+
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  fixTitle: function() {
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  var $e = this.$element;
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  if ($e.attr('title') || typeof($e.attr('original-title')) != 'string') {
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  $e.attr('original-title', $e.attr('title') || '').removeAttr('title');
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  }
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  },
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-
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+
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  getTitle: function() {
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  var title, $e = this.$element, o = this.options;
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  this.fixTitle();
@@ -100,14 +100,14 @@
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  title = ('' + title).replace(/(^\s*|\s*$)/, "");
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  return title || o.fallback;
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  },
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-
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+
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  tip: function() {
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  if (!this.$tip) {
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  this.$tip = $('<div class="tipsy"></div>').html('<div class="tipsy-arrow"></div><div class="tipsy-inner"></div>');
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  }
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  return this.$tip;
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  },
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  validate: function() {
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  if (!this.$element[0].parentNode) {
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  this.hide();
@@ -115,14 +115,14 @@
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  this.options = null;
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  }
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  },
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-
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  enable: function() { this.enabled = true; },
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  disable: function() { this.enabled = false; },
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  toggleEnabled: function() { this.enabled = !this.enabled; }
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  };
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  $.fn.tipsy = function(options) {
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  if (options === true) {
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  return this.data('tipsy');
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  } else if (typeof options == 'string') {
@@ -130,9 +130,9 @@
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  if (tipsy) tipsy[options]();
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  return this;
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  }
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  options = $.extend({}, $.fn.tipsy.defaults, options);
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  function get(ele) {
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  var tipsy = $.data(ele, 'tipsy');
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  if (!tipsy) {
@@ -141,7 +141,7 @@
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  }
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  return tipsy;
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  }
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  function enter() {
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  var tipsy = get(this);
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  tipsy.hoverState = 'in';
@@ -152,7 +152,7 @@
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  setTimeout(function() { if (tipsy.hoverState == 'in') tipsy.show(); }, options.delayIn);
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  }
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  };
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  function leave() {
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  var tipsy = get(this);
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  tipsy.hoverState = 'out';
@@ -162,20 +162,20 @@
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  setTimeout(function() { if (tipsy.hoverState == 'out') tipsy.hide(); }, options.delayOut);
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  }
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  };
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  if (!options.live) this.each(function() { get(this); });
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  if (options.trigger != 'manual') {
169
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  var binder = options.live ? 'live' : 'bind',
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  eventIn = options.trigger == 'hover' ? 'mouseenter' : 'focus',
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  eventOut = options.trigger == 'hover' ? 'mouseleave' : 'blur';
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  this[binder](eventIn, enter)[binder](eventOut, leave);
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  }
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  return this;
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-
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+
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  };
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  $.fn.tipsy.defaults = {
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  className: null,
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  delayIn: 0,
@@ -190,7 +190,7 @@
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  title: 'title',
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  trigger: 'hover'
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  };
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  // Overwrite this method to provide options on a per-element basis.
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  // For example, you could store the gravity in a 'tipsy-gravity' attribute:
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  // return $.extend({}, options, {gravity: $(ele).attr('tipsy-gravity') || 'n' });
@@ -198,15 +198,15 @@
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  $.fn.tipsy.elementOptions = function(ele, options) {
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  return $.metadata ? $.extend({}, options, $(ele).metadata()) : options;
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  };
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-
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  $.fn.tipsy.autoNS = function() {
203
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  return $(this).offset().top > ($(document).scrollTop() + $(window).height() / 2) ? 's' : 'n';
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  };
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-
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  $.fn.tipsy.autoWE = function() {
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  return $(this).offset().left > ($(document).scrollLeft() + $(window).width() / 2) ? 'e' : 'w';
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  };
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  /**
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  * yields a closure of the supplied parameters, producing a function that takes
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  * no arguments and is suitable for use as an autogravity function like so:
@@ -217,7 +217,7 @@
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  * @param prefer (string, e.g. 'n', 'sw', 'w') - the direction to prefer
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  * if there are no viewable region edges effecting the tooltip's
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  * gravity. It will try to vary from this minimally, for example,
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- * if 'sw' is preferred and an element is near the right viewable
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+ * if 'sw' is preferred and an element is near the right viewable
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  * region edge, but not the top edge, it will set the gravity for
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  * that element's tooltip to be 'se', preserving the southern
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  * component.
@@ -237,5 +237,5 @@
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  return dir.ns + (dir.ew ? dir.ew : '');
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  }
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  };
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-
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  })(jQuery);
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: quorum
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.3.0
4
+ version: 0.3.1
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -9,11 +9,11 @@ authors:
9
9
  autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
- date: 2012-01-31 00:00:00.000000000Z
12
+ date: 2012-04-02 00:00:00.000000000 Z
13
13
  dependencies:
14
14
  - !ruby/object:Gem::Dependency
15
15
  name: rails
16
- requirement: &16508360 !ruby/object:Gem::Requirement
16
+ requirement: !ruby/object:Gem::Requirement
17
17
  none: false
18
18
  requirements:
19
19
  - - ~>
@@ -21,10 +21,15 @@ dependencies:
21
21
  version: '3.1'
22
22
  type: :runtime
23
23
  prerelease: false
24
- version_requirements: *16508360
24
+ version_requirements: !ruby/object:Gem::Requirement
25
+ none: false
26
+ requirements:
27
+ - - ~>
28
+ - !ruby/object:Gem::Version
29
+ version: '3.1'
25
30
  - !ruby/object:Gem::Dependency
26
31
  name: jquery-rails
27
- requirement: &16507560 !ruby/object:Gem::Requirement
32
+ requirement: !ruby/object:Gem::Requirement
28
33
  none: false
29
34
  requirements:
30
35
  - - ! '>='
@@ -32,10 +37,15 @@ dependencies:
32
37
  version: '0'
33
38
  type: :runtime
34
39
  prerelease: false
35
- version_requirements: *16507560
40
+ version_requirements: !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ! '>='
44
+ - !ruby/object:Gem::Version
45
+ version: '0'
36
46
  - !ruby/object:Gem::Dependency
37
47
  name: net-ssh
38
- requirement: &16506660 !ruby/object:Gem::Requirement
48
+ requirement: !ruby/object:Gem::Requirement
39
49
  none: false
40
50
  requirements:
41
51
  - - ~>
@@ -43,10 +53,15 @@ dependencies:
43
53
  version: 2.3.0
44
54
  type: :runtime
45
55
  prerelease: false
46
- version_requirements: *16506660
56
+ version_requirements: !ruby/object:Gem::Requirement
57
+ none: false
58
+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
61
+ version: 2.3.0
47
62
  - !ruby/object:Gem::Dependency
48
63
  name: resque
49
- requirement: &16506000 !ruby/object:Gem::Requirement
64
+ requirement: !ruby/object:Gem::Requirement
50
65
  none: false
51
66
  requirements:
52
67
  - - ~>
@@ -54,10 +69,15 @@ dependencies:
54
69
  version: 1.19.0
55
70
  type: :runtime
56
71
  prerelease: false
57
- version_requirements: *16506000
72
+ version_requirements: !ruby/object:Gem::Requirement
73
+ none: false
74
+ requirements:
75
+ - - ~>
76
+ - !ruby/object:Gem::Version
77
+ version: 1.19.0
58
78
  - !ruby/object:Gem::Dependency
59
79
  name: resque-result
60
- requirement: &16505320 !ruby/object:Gem::Requirement
80
+ requirement: !ruby/object:Gem::Requirement
61
81
  none: false
62
82
  requirements:
63
83
  - - ~>
@@ -65,10 +85,15 @@ dependencies:
65
85
  version: 1.0.1
66
86
  type: :runtime
67
87
  prerelease: false
68
- version_requirements: *16505320
88
+ version_requirements: !ruby/object:Gem::Requirement
89
+ none: false
90
+ requirements:
91
+ - - ~>
92
+ - !ruby/object:Gem::Version
93
+ version: 1.0.1
69
94
  - !ruby/object:Gem::Dependency
70
95
  name: bio-blastxmlparser
71
- requirement: &16504660 !ruby/object:Gem::Requirement
96
+ requirement: !ruby/object:Gem::Requirement
72
97
  none: false
73
98
  requirements:
74
99
  - - ~>
@@ -76,10 +101,15 @@ dependencies:
76
101
  version: 1.0.1
77
102
  type: :runtime
78
103
  prerelease: false
79
- version_requirements: *16504660
104
+ version_requirements: !ruby/object:Gem::Requirement
105
+ none: false
106
+ requirements:
107
+ - - ~>
108
+ - !ruby/object:Gem::Version
109
+ version: 1.0.1
80
110
  - !ruby/object:Gem::Dependency
81
111
  name: mysql2
82
- requirement: &16500480 !ruby/object:Gem::Requirement
112
+ requirement: !ruby/object:Gem::Requirement
83
113
  none: false
84
114
  requirements:
85
115
  - - ~>
@@ -87,10 +117,15 @@ dependencies:
87
117
  version: 0.3.11
88
118
  type: :development
89
119
  prerelease: false
90
- version_requirements: *16500480
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ none: false
122
+ requirements:
123
+ - - ~>
124
+ - !ruby/object:Gem::Version
125
+ version: 0.3.11
91
126
  - !ruby/object:Gem::Dependency
92
127
  name: rspec-rails
93
- requirement: &16499900 !ruby/object:Gem::Requirement
128
+ requirement: !ruby/object:Gem::Requirement
94
129
  none: false
95
130
  requirements:
96
131
  - - ~>
@@ -98,10 +133,15 @@ dependencies:
98
133
  version: '2.6'
99
134
  type: :development
100
135
  prerelease: false
101
- version_requirements: *16499900
136
+ version_requirements: !ruby/object:Gem::Requirement
137
+ none: false
138
+ requirements:
139
+ - - ~>
140
+ - !ruby/object:Gem::Version
141
+ version: '2.6'
102
142
  - !ruby/object:Gem::Dependency
103
143
  name: resque_spec
104
- requirement: &16499360 !ruby/object:Gem::Requirement
144
+ requirement: !ruby/object:Gem::Requirement
105
145
  none: false
106
146
  requirements:
107
147
  - - ~>
@@ -109,10 +149,15 @@ dependencies:
109
149
  version: '0.8'
110
150
  type: :development
111
151
  prerelease: false
112
- version_requirements: *16499360
152
+ version_requirements: !ruby/object:Gem::Requirement
153
+ none: false
154
+ requirements:
155
+ - - ~>
156
+ - !ruby/object:Gem::Version
157
+ version: '0.8'
113
158
  - !ruby/object:Gem::Dependency
114
159
  name: capybara
115
- requirement: &16498840 !ruby/object:Gem::Requirement
160
+ requirement: !ruby/object:Gem::Requirement
116
161
  none: false
117
162
  requirements:
118
163
  - - ~>
@@ -120,10 +165,15 @@ dependencies:
120
165
  version: '1.1'
121
166
  type: :development
122
167
  prerelease: false
123
- version_requirements: *16498840
168
+ version_requirements: !ruby/object:Gem::Requirement
169
+ none: false
170
+ requirements:
171
+ - - ~>
172
+ - !ruby/object:Gem::Version
173
+ version: '1.1'
124
174
  - !ruby/object:Gem::Dependency
125
175
  name: database_cleaner
126
- requirement: &16498280 !ruby/object:Gem::Requirement
176
+ requirement: !ruby/object:Gem::Requirement
127
177
  none: false
128
178
  requirements:
129
179
  - - ~>
@@ -131,10 +181,15 @@ dependencies:
131
181
  version: '0.6'
132
182
  type: :development
133
183
  prerelease: false
134
- version_requirements: *16498280
184
+ version_requirements: !ruby/object:Gem::Requirement
185
+ none: false
186
+ requirements:
187
+ - - ~>
188
+ - !ruby/object:Gem::Version
189
+ version: '0.6'
135
190
  - !ruby/object:Gem::Dependency
136
191
  name: factory_girl_rails
137
- requirement: &16497740 !ruby/object:Gem::Requirement
192
+ requirement: !ruby/object:Gem::Requirement
138
193
  none: false
139
194
  requirements:
140
195
  - - ~>
@@ -142,10 +197,15 @@ dependencies:
142
197
  version: '1.2'
143
198
  type: :development
144
199
  prerelease: false
145
- version_requirements: *16497740
200
+ version_requirements: !ruby/object:Gem::Requirement
201
+ none: false
202
+ requirements:
203
+ - - ~>
204
+ - !ruby/object:Gem::Version
205
+ version: '1.2'
146
206
  - !ruby/object:Gem::Dependency
147
207
  name: jasmine
148
- requirement: &16497200 !ruby/object:Gem::Requirement
208
+ requirement: !ruby/object:Gem::Requirement
149
209
  none: false
150
210
  requirements:
151
211
  - - ~>
@@ -153,7 +213,12 @@ dependencies:
153
213
  version: '1.1'
154
214
  type: :development
155
215
  prerelease: false
156
- version_requirements: *16497200
216
+ version_requirements: !ruby/object:Gem::Requirement
217
+ none: false
218
+ requirements:
219
+ - - ~>
220
+ - !ruby/object:Gem::Version
221
+ version: '1.1'
157
222
  description: Flexible bioinformatics search tool.
158
223
  email:
159
224
  - kas@ncgr.org
@@ -369,7 +434,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
369
434
  version: '0'
370
435
  segments:
371
436
  - 0
372
- hash: 2758324715515745186
437
+ hash: -2365568155334163580
373
438
  required_rubygems_version: !ruby/object:Gem::Requirement
374
439
  none: false
375
440
  requirements:
@@ -378,10 +443,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
378
443
  version: '0'
379
444
  segments:
380
445
  - 0
381
- hash: 2758324715515745186
446
+ hash: -2365568155334163580
382
447
  requirements: []
383
448
  rubyforge_project:
384
- rubygems_version: 1.8.15
449
+ rubygems_version: 1.8.21
385
450
  signing_key:
386
451
  specification_version: 3
387
452
  summary: Flexible bioinformatics search tool.