quorum 0.2.1 → 0.3.0

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 (38) hide show
  1. data/Gemfile.lock +35 -28
  2. data/HISTORY.md +4 -0
  3. data/app/assets/javascripts/quorum/application.js +1 -0
  4. data/app/assets/javascripts/quorum/jobs.js +5 -345
  5. data/app/assets/javascripts/quorum/quorum.js +275 -0
  6. data/app/assets/javascripts/quorum/template_settings.js +8 -0
  7. data/app/assets/javascripts/quorum/utilities.js +12 -0
  8. data/app/assets/stylesheets/quorum/application.css +0 -4
  9. data/app/assets/stylesheets/quorum/autohint.css +4 -0
  10. data/app/controllers/quorum/jobs_controller.rb +9 -9
  11. data/app/views/quorum/jobs/form/_blastn_form.html.erb +62 -62
  12. data/app/views/quorum/jobs/form/_blastp_form.html.erb +62 -62
  13. data/app/views/quorum/jobs/form/_blastx_form.html.erb +62 -62
  14. data/app/views/quorum/jobs/form/_tblastn_form.html.erb +62 -62
  15. data/app/views/quorum/jobs/show.html.erb +1 -1
  16. data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb +22 -22
  17. data/app/views/quorum/jobs/templates/_blast_template.html.erb +29 -29
  18. data/app/views/shared/_error_messages.html.erb +8 -8
  19. data/lib/quorum/version.rb +1 -1
  20. data/lib/tasks/jasmine.rake +8 -0
  21. data/quorum.gemspec +1 -0
  22. data/spec/data/seqs_not_fa.txt +16 -16
  23. data/spec/javascripts/fixtures/formatted_sequence.html +6 -0
  24. data/spec/javascripts/fixtures/quorum_search_form.html +461 -0
  25. data/spec/javascripts/fixtures/quorum_tabs.html +10 -0
  26. data/spec/javascripts/helpers/jasmine-jquery.js +288 -0
  27. data/spec/javascripts/jobs_spec.js +99 -0
  28. data/spec/javascripts/jquery/jquery-ui.min.js +791 -0
  29. data/spec/javascripts/jquery/jquery.min.js +4 -0
  30. data/spec/javascripts/jquery/jquery_ujs.js +373 -0
  31. data/spec/javascripts/quorum_spec.js +106 -0
  32. data/spec/javascripts/string_spec.js +18 -0
  33. data/spec/javascripts/support/jasmine.yml +84 -0
  34. data/spec/javascripts/support/jasmine_config.rb +23 -0
  35. data/spec/javascripts/support/jasmine_runner.rb +33 -0
  36. data/spec/requests/jobs_spec.rb +34 -33
  37. data/vendor/assets/javascripts/jquery.autohint.js +87 -0
  38. metadata +62 -26
@@ -0,0 +1,288 @@
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+ var readFixtures = function() {
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+ return jasmine.getFixtures().proxyCallTo_('read', arguments);
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+ };
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+
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+ var preloadFixtures = function() {
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+ jasmine.getFixtures().proxyCallTo_('preload', arguments);
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+ };
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+
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+ var loadFixtures = function() {
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+ jasmine.getFixtures().proxyCallTo_('load', arguments);
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+ };
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+
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+ var setFixtures = function(html) {
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+ jasmine.getFixtures().set(html);
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+ };
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+
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+ var sandbox = function(attributes) {
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+ return jasmine.getFixtures().sandbox(attributes);
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+ };
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+
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+ var spyOnEvent = function(selector, eventName) {
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+ jasmine.JQuery.events.spyOn(selector, eventName);
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+ }
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+
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+ jasmine.getFixtures = function() {
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+ return jasmine.currentFixtures_ = jasmine.currentFixtures_ || new jasmine.Fixtures();
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+ };
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+
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+ jasmine.Fixtures = function() {
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+ this.containerId = 'jasmine-fixtures';
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+ this.fixturesCache_ = {};
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+ this.fixturesPath = 'spec/javascripts/fixtures';
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+ };
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+
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+ jasmine.Fixtures.prototype.set = function(html) {
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+ this.cleanUp();
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+ this.createContainer_(html);
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+ };
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+
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+ jasmine.Fixtures.prototype.preload = function() {
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+ this.read.apply(this, arguments);
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+ };
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+
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+ jasmine.Fixtures.prototype.load = function() {
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+ this.cleanUp();
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+ this.createContainer_(this.read.apply(this, arguments));
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+ };
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+
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+ jasmine.Fixtures.prototype.read = function() {
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+ var htmlChunks = [];
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+
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+ var fixtureUrls = arguments;
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+ for(var urlCount = fixtureUrls.length, urlIndex = 0; urlIndex < urlCount; urlIndex++) {
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+ htmlChunks.push(this.getFixtureHtml_(fixtureUrls[urlIndex]));
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+ }
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+
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+ return htmlChunks.join('');
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+ };
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+
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+ jasmine.Fixtures.prototype.clearCache = function() {
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+ this.fixturesCache_ = {};
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+ };
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+
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+ jasmine.Fixtures.prototype.cleanUp = function() {
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+ jQuery('#' + this.containerId).remove();
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+ };
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+
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+ jasmine.Fixtures.prototype.sandbox = function(attributes) {
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+ var attributesToSet = attributes || {};
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+ return jQuery('<div id="sandbox" />').attr(attributesToSet);
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+ };
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+
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+ jasmine.Fixtures.prototype.createContainer_ = function(html) {
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+ var container;
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+ if(html instanceof jQuery) {
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+ container = jQuery('<div id="' + this.containerId + '" />');
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+ container.html(html);
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+ } else {
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+ container = '<div id="' + this.containerId + '">' + html + '</div>'
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+ }
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+ jQuery('body').append(container);
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+ };
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+
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+ jasmine.Fixtures.prototype.getFixtureHtml_ = function(url) {
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+ if (typeof this.fixturesCache_[url] == 'undefined') {
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+ this.loadFixtureIntoCache_(url);
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+ }
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+ return this.fixturesCache_[url];
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+ };
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+
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+ jasmine.Fixtures.prototype.loadFixtureIntoCache_ = function(relativeUrl) {
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+ var self = this;
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+ var url = this.fixturesPath.match('/$') ? this.fixturesPath + relativeUrl : this.fixturesPath + '/' + relativeUrl;
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+ jQuery.ajax({
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+ async: false, // must be synchronous to guarantee that no tests are run before fixture is loaded
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+ cache: false,
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+ dataType: 'html',
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+ url: url,
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+ success: function(data) {
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+ self.fixturesCache_[relativeUrl] = data;
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+ },
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+ error: function(jqXHR, status, errorThrown) {
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+ throw Error('Fixture could not be loaded: ' + url + ' (status: ' + status + ', message: ' + errorThrown.message + ')');
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+ }
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+ });
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+ };
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+
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+ jasmine.Fixtures.prototype.proxyCallTo_ = function(methodName, passedArguments) {
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+ return this[methodName].apply(this, passedArguments);
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+ };
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+
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+
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+ jasmine.JQuery = function() {};
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+
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+ jasmine.JQuery.browserTagCaseIndependentHtml = function(html) {
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+ return jQuery('<div/>').append(html).html();
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+ };
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+
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+ jasmine.JQuery.elementToString = function(element) {
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+ return jQuery('<div />').append(element.clone()).html();
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+ };
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+
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+ jasmine.JQuery.matchersClass = {};
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+
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+ (function(namespace) {
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+ var data = {
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+ spiedEvents: {},
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+ handlers: []
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+ };
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+
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+ namespace.events = {
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+ spyOn: function(selector, eventName) {
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+ var handler = function(e) {
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+ data.spiedEvents[[selector, eventName]] = e;
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+ };
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+ jQuery(selector).bind(eventName, handler);
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+ data.handlers.push(handler);
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+ },
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+
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+ wasTriggered: function(selector, eventName) {
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+ return !!(data.spiedEvents[[selector, eventName]]);
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+ },
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+
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+ cleanUp: function() {
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+ data.spiedEvents = {};
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+ data.handlers = [];
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+ }
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+ }
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+ })(jasmine.JQuery);
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+
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+ (function(){
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+ var jQueryMatchers = {
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+ toHaveClass: function(className) {
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+ return this.actual.hasClass(className);
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+ },
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+
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+ toBeVisible: function() {
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+ return this.actual.is(':visible');
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+ },
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+
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+ toBeHidden: function() {
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+ return this.actual.is(':hidden');
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+ },
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+
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+ toBeSelected: function() {
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+ return this.actual.is(':selected');
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+ },
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+
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+ toBeChecked: function() {
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+ return this.actual.is(':checked');
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+ },
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+
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+ toBeEmpty: function() {
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+ return this.actual.is(':empty');
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+ },
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+
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+ toExist: function() {
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+ return this.actual.size() > 0;
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+ },
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+
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+ toHaveAttr: function(attributeName, expectedAttributeValue) {
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+ return hasProperty(this.actual.attr(attributeName), expectedAttributeValue);
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+ },
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+
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+ toHaveId: function(id) {
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+ return this.actual.attr('id') == id;
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+ },
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+
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+ toHaveHtml: function(html) {
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+ return this.actual.html() == jasmine.JQuery.browserTagCaseIndependentHtml(html);
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+ },
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+
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+ toHaveText: function(text) {
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+ if (text && jQuery.isFunction(text.test)) {
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+ return text.test(this.actual.text());
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+ } else {
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+ return this.actual.text() == text;
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+ }
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+ },
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+
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+ toHaveValue: function(value) {
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+ return this.actual.val() == value;
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+ },
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+
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+ toHaveData: function(key, expectedValue) {
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+ return hasProperty(this.actual.data(key), expectedValue);
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+ },
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+
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+ toBe: function(selector) {
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+ return this.actual.is(selector);
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+ },
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+
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+ toContain: function(selector) {
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+ return this.actual.find(selector).size() > 0;
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+ },
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+
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+ toBeDisabled: function(selector){
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+ return this.actual.is(':disabled');
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+ },
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+
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+ // tests the existence of a specific event binding
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+ toHandle: function(eventName) {
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+ var events = this.actual.data("events");
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+ return events && events[eventName].length > 0;
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+ },
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+
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+ // tests the existence of a specific event binding + handler
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+ toHandleWith: function(eventName, eventHandler) {
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+ var stack = this.actual.data("events")[eventName];
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+ var i;
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+ for (i = 0; i < stack.length; i++) {
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+ if (stack[i].handler == eventHandler) {
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+ return true;
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+ }
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+ }
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+ return false;
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+ }
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+ };
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+
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+ var hasProperty = function(actualValue, expectedValue) {
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+ if (expectedValue === undefined) {
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+ return actualValue !== undefined;
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+ }
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+ return actualValue == expectedValue;
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+ };
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+
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+ var bindMatcher = function(methodName) {
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+ var builtInMatcher = jasmine.Matchers.prototype[methodName];
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+
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+ jasmine.JQuery.matchersClass[methodName] = function() {
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+ if (this.actual instanceof jQuery) {
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+ var result = jQueryMatchers[methodName].apply(this, arguments);
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+ this.actual = jasmine.JQuery.elementToString(this.actual);
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+ return result;
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+ }
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+
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+ if (builtInMatcher) {
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+ return builtInMatcher.apply(this, arguments);
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+ }
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+
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+ return false;
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+ };
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+ };
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+
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+ for(var methodName in jQueryMatchers) {
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+ bindMatcher(methodName);
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+ }
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+ })();
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+
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+ beforeEach(function() {
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+ this.addMatchers(jasmine.JQuery.matchersClass);
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+ this.addMatchers({
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+ toHaveBeenTriggeredOn: function(selector) {
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+ this.message = function() {
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+ return [
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+ "Expected event " + this.actual + " to have been triggered on" + selector,
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+ "Expected event " + this.actual + " not to have been triggered on" + selector
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+ ];
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+ };
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+ return jasmine.JQuery.events.wasTriggered(selector, this.actual);
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+ }
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+ })
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+ });
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+
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+ afterEach(function() {
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+ jasmine.getFixtures().cleanUp();
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+ jasmine.JQuery.events.cleanUp();
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+ });
@@ -0,0 +1,99 @@
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+ //
2
+ // Quorum Job Views
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+ //
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+
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+ describe("Quorum Search Form", function() {
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+
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+ beforeEach(function() {
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+ loadFixtures('quorum_search_form.html');
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+ });
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+
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+ it("toggles algorithm queues on change", function() {
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+ spyOnEvent($("#job_blastn_job_attributes_queue"), 'change');
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+ spyOnEvent($("#job_blastx_job_attributes_queue"), 'change');
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+ spyOnEvent($("#job_tblastn_job_attributes_queue"), 'change');
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+ spyOnEvent($("#job_blastp_job_attributes_queue"), 'change');
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+
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+ $('#job_blastn_job_attributes_queue').change();
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+ expect('change').toHaveBeenTriggeredOn($('#blastn'));
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+
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+ $('#job_blastx_job_attributes_queue').change();
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+ expect('change').toHaveBeenTriggeredOn($('#blastx'));
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+
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+ $('#job_tblastn_job_attributes_queue').change();
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+ expect('change').toHaveBeenTriggeredOn($('#tblastn'));
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+
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+ $('#job_blastp_job_attributes_queue').change();
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+ expect('change').toHaveBeenTriggeredOn($('#blastp'));
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+ });
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+
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+ it("resets form", function() {
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+ spyOnEvent($('#quorum_job_reset'), 'click');
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+ $('#quorum_job_reset').click();
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+ expect('click').toHaveBeenTriggeredOn($('textarea'));
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+ expect('click').toHaveBeenTriggeredOn($('input:text'));
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+ expect('click').toHaveBeenTriggeredOn($('input:file'));
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+ expect('click').toHaveBeenTriggeredOn($('input:checkbox'));
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+ expect('click').toHaveBeenTriggeredOn($('select'));
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+ });
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+
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+ it("inserts form hints", function() {
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+ $('form :input.auto-hint').autoHint();
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+ expect($('#job_sequence')).toHaveValue($('#job_sequence').attr('title'));
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+
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+ expect($('#job_blastn_job_attributes_expectation')).toHaveValue(
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+ $('#job_blastn_job_attributes_expectation').attr('title')
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+ );
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+ expect($('#job_blastx_job_attributes_expectation')).toHaveValue(
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+ $('#job_blastx_job_attributes_expectation').attr('title')
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+ );
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+ expect($('#job_tblastn_job_attributes_expectation')).toHaveValue(
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+ $('#job_tblastn_job_attributes_expectation').attr('title')
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+ );
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+ expect($('#job_blastp_job_attributes_expectation')).toHaveValue(
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+ $('#job_blastp_job_attributes_expectation').attr('title')
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+ );
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+
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+ expect($('#job_blastn_job_attributes_min_bit_score')).toHaveValue(
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+ $('#job_blastn_job_attributes_min_bit_score').attr('title')
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+ );
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+ expect($('#job_blastx_job_attributes_min_bit_score')).toHaveValue(
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+ $('#job_blastx_job_attributes_min_bit_score').attr('title')
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+ );
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+ expect($('#job_tblastn_job_attributes_min_bit_score')).toHaveValue(
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+ $('#job_tblastn_job_attributes_min_bit_score').attr('title')
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+ );
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+ expect($('#job_blastp_job_attributes_min_bit_score')).toHaveValue(
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+ $('#job_blastp_job_attributes_min_bit_score').attr('title')
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+ );
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+
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+ expect($('#job_blastn_job_attributes_max_score')).toHaveValue(
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+ $('#job_blastn_job_attributes_max_score').attr('title')
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+ );
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+ expect($('#job_blastx_job_attributes_max_score')).toHaveValue(
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+ $('#job_blastx_job_attributes_max_score').attr('title')
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+ );
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+ expect($('#job_tblastn_job_attributes_max_score')).toHaveValue(
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+ $('#job_tblastn_job_attributes_max_score').attr('title')
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+ );
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+ expect($('#job_blastp_job_attributes_max_score')).toHaveValue(
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+ $('#job_blastp_job_attributes_max_score').attr('title')
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+ );
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+ });
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+
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+ });
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+
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+ describe("Quorum Search Results", function() {
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+
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+ beforeEach(function() {
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+ loadFixtures('quorum_tabs.html');
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+ });
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+
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+ it("displays results in tabs", function() {
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+ $('#tabs').tabs();
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+ expect($('#tabs-1')).not.toHaveClass('ui-tabs-hide');
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+ expect($('#tabs-2')).toHaveClass('ui-tabs-hide');
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+ expect($('#tabs-3')).toHaveClass('ui-tabs-hide');
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+ });
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+
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+ });